From 86732ecadb58865aa8d2b2efcd00924b2616fc6b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 12:41:31 +0300
Subject: [PATCH 01/75] initial try

---
 platforms/cuda/sharedTarget/CMakeLists.txt    |   1 +
 .../prepare_build_environment_linux_cpu.sh    |  38 ++++++
 .../prepare_build_environment_linux_cu118.sh  | 124 ++++++++++++++++++
 .../prepare_build_environment_linux_cu124.sh  |  31 +++++
 .../prepare_build_environment_osx.sh          |   0
 .../prepare_build_environment_windows_cpu.sh  |   8 ++
 ...prepare_build_environment_windows_cu118.sh |  19 +++
 ...prepare_build_environment_windows_cu124.sh |  19 +++
 wrappers/python/pyproject.toml                |  47 +++++++
 wrappers/python/setup.py                      |  31 +----
 10 files changed, 291 insertions(+), 27 deletions(-)
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh
 create mode 100644 wrappers/python/pyproject.toml

diff --git a/platforms/cuda/sharedTarget/CMakeLists.txt b/platforms/cuda/sharedTarget/CMakeLists.txt
index cdc0336ae8..8248a532de 100644
--- a/platforms/cuda/sharedTarget/CMakeLists.txt
+++ b/platforms/cuda/sharedTarget/CMakeLists.txt
@@ -22,4 +22,5 @@ ELSE (APPLE)
     SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}")
 ENDIF (APPLE)
 
+SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES INSTALL_RPATH "$ORIGIN/..;$ORIGIN/../../../nvidia/cufft/lib;$ORIGIN/../../../nvidia/cuda_nvrtc/lib;")
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
new file mode 100755
index 0000000000..70b8f95d13
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
@@ -0,0 +1,38 @@
+#! /bin/bash
+
+set -e
+set -x
+
+# Install dependencies with yum
+dnf install -y doxygen zip opencl-headers ocl-icd tree
+
+# # Install CUDA (nothing)
+
+# # Install HIP
+# export HIP_VERSION=6
+# yum install -y epel-release
+# yum install -y https://repo.radeon.com/amdgpu-install/6.2.2/el/8.10/amdgpu-install-6.2.60202-1.el8.noarch.rpm
+# yum install -y rocm-device-libs hip-devel hip-runtime-amd hipcc
+
+# Configure build with Cmake
+mkdir -p build
+cd build
+cmake .. \
+    -DCMAKE_INSTALL_PREFIX=${HOME}/openmm-install \
+    -DCMAKE_CXX_FLAGS='-D_GLIBCXX_USE_CXX11_ABI=0' \
+    -DOPENMM_BUILD_OPENCL_LIB=ON \
+    -DOPENCL_INCLUDE_DIR=/usr/include/CL \
+    -DOPENCL_LIBRARY=/usr/lib64/libOpenCL.so.1
+
+tree .
+
+# Build OpenMM
+make -j4 install
+make -j4 PythonInstall
+
+# Build wheel
+export LD_LIBRARY_PATH=${HOME}/openmm-install/lib
+export OPENMM_INCLUDE_PATH=../openmmapi/include
+tree ./python
+
+ls -l ../openmmapi/
\ No newline at end of file
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh
new file mode 100755
index 0000000000..ac32543d6d
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh
@@ -0,0 +1,124 @@
+#! /bin/bash
+
+set -e
+set -x
+
+dnf install -y doxygen
+
+
+if [ "$CIBW_ARCHS" != "aarch64" ]; then
+
+    # Install CUDA 11.8:
+    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
+
+    dnf install --setopt=obsoletes=0 -y \
+        cuda-nvcc-11-8-11.8.89-1 \
+        cuda-cudart-devel-11-8-11.8.89-1 \
+        libcurand-devel-11-8-10.3.0.86-1 \
+        libcudnn9-devel-cuda-11-9.8.0.87-1 \
+        libcublas-devel-11-8-11.11.3.6-1 \
+        libnccl-devel-2.15.5-1+cuda11.8 \
+        libcusparse-devel-11-8-11.7.5.86-1 \
+        libcusolver-devel-11-8-11.4.1.48-1 \
+        gcc-toolset-11
+
+    ln -s cuda-11.8 /usr/local/cuda
+    ln -s /opt/rh/gcc-toolset-11/root/usr/bin/gcc /usr/local/cuda/bin/gcc
+    ln -s /opt/rh/gcc-toolset-11/root/usr/bin/g++ /usr/local/cuda/bin/g++
+
+    export CUDA_HOME="/usr/local/cuda"
+    export WITH_CUDA=1
+
+    
+    # Configure pip to use PyTorch extra-index-url for CUDA 11.8
+    mkdir -p $HOME/.config/pip
+    echo "[global]
+extra-index-url = https://download.pytorch.org/whl/cu118" > $HOME/.config/pip/pip.conf
+    
+fi
+
+
+# OpenMM Compilation starting here
+
+CMAKE_FLAGS="${CMAKE_ARGS} -DCMAKE_BUILD_TYPE=Release"
+if [[ "$with_test_suite" == "true" ]]; then
+    CMAKE_FLAGS+=" -DBUILD_TESTING=ON -DOPENMM_BUILD_OPENCL_TESTS=ON"
+else
+    CMAKE_FLAGS+=" -DBUILD_TESTING=OFF"
+fi
+
+
+if [[ "$target_platform" == linux* ]]; then
+    SHLIB_EXT=".so"
+    # CFLAGS
+    # JRG: Had to add -ldl to prevent linking errors (dlopen, etc)
+    MINIMAL_CFLAGS+=" -O3 -ldl"
+    CFLAGS+=" $MINIMAL_CFLAGS"
+    CXXFLAGS+=" $MINIMAL_CFLAGS"
+
+    # CUDA is enabled in these platforms
+    if [[ "$target_platform" == linux-64 || "$target_platform" == linux-ppc64le ]]; then
+        # # CUDA_HOME is defined by nvcc metapackage
+        CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=${CUDA_HOME}"
+        # CUDA tests won't build, disable for now
+        # See https://github.com/openmm/openmm/issues/2258#issuecomment-462223634
+        CMAKE_FLAGS+=" -DOPENMM_BUILD_CUDA_TESTS=OFF"
+        # shadow some CMAKE_ARGS bits that interfere with CUDA detection
+        CMAKE_FLAGS+=" -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=BOTH"
+    fi
+
+    # OpenCL ICD
+    CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=${PREFIX}/include"
+    CMAKE_FLAGS+=" -DOPENCL_LIBRARY=${PREFIX}/lib/libOpenCL${SHLIB_EXT}"
+
+elif [[ "$target_platform" == osx* ]]; then
+    SHLIB_EXT=".dylib"
+    if [[ "$opencl_impl" == khronos ]]; then
+        CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=${PREFIX}/include"
+        CMAKE_FLAGS+=" -DOPENCL_LIBRARY=${PREFIX}/lib/libOpenCL${SHLIB_EXT}"
+    fi
+    # When using opencl_impl == apple, CMake will auto-locate it, so no need to provide the flags
+    # On Conda Forge, this will result in:
+    #   /Applications/Xcode_12.app/Contents/Developer/Platforms/MacOSX.platform/Developer/...
+    #   ...SDKs/MacOSX10.9.sdk/System/Library/Frameworks/OpenCL.framework
+    # On local builds, it might be:
+    #   /System/Library/Frameworks/OpenCL.framework/OpenCL
+fi
+
+# Set location for FFTW3 on both linux and mac
+CMAKE_FLAGS+=" -DFFTW_INCLUDES=${PREFIX}/include/"
+CMAKE_FLAGS+=" -DFFTW_LIBRARY=${PREFIX}/lib/libfftw3f${SHLIB_EXT}"
+CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=${PREFIX}/lib/libfftw3f_threads${SHLIB_EXT}"
+# Disambiguate swig location
+CMAKE_FLAGS+=" -DSWIG_EXECUTABLE=$(which swig)"
+
+# Build in subdirectory and install.
+mkdir -p build
+cd build
+cmake ${CMAKE_FLAGS} ..
+make -j$CPU_COUNT
+make -j$CPU_COUNT install PythonInstall
+
+# Put examples into an appropriate subdirectory.
+mkdir -p ${PREFIX}/share/openmm/
+mv ${PREFIX}/examples ${PREFIX}/share/openmm/
+
+# Fix some overlinking warnings/errors
+for lib in ${PREFIX}/lib/plugins/*${SHLIB_EXT}; do
+    ln -s $lib ${PREFIX}/lib/$(basename $lib) || true
+done
+
+if [[ "$with_test_suite" == "true" ]]; then
+    mkdir -p ${PREFIX}/share/openmm/tests/
+    # BSD find vs GNU find: -executable is only available in GNU find
+    # +0111 is somehow equivalent in BSD, but that's not compatible in GNU
+    # so we use different commands for each...
+    if [[ "$target_platform" == osx* ]]; then
+        find . -name "Test*" -perm +0111 -type f \
+            -exec python $RECIPE_DIR/patch_osx_tests.py "{}" \; \
+            -exec cp "{}" $PREFIX/share/openmm/tests/ \;
+    else
+        find . -name "Test*" -executable -type f -exec cp "{}" $PREFIX/share/openmm/tests/ \;
+    fi
+    cp -r python/tests $PREFIX/share/openmm/tests/python
+fi
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh
new file mode 100755
index 0000000000..cc9e212c5a
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh
@@ -0,0 +1,31 @@
+#! /bin/bash
+
+set -e
+set -x
+
+
+if [ "$CIBW_ARCHS" != "aarch64" ]; then
+
+    # Install CUDA 12.4:
+    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
+
+    dnf install --setopt=obsoletes=0 -y \
+        cuda-nvcc-12-4-12.4.131-1 \
+        cuda-cudart-devel-12-4-12.4.127-1 \
+        libcurand-devel-12-4-10.3.5.147-1 \
+        libcudnn9-devel-cuda-12-9.1.0.70-1 \
+        libcublas-devel-12-4-12.4.5.8-1 \
+        libnccl-devel-2.21.5-1+cuda12.4 \
+        libcusparse-devel-12-4-12.3.1.170-1 \
+        libcusolver-devel-12-4-11.6.1.9-1 \
+        gcc-toolset-13
+
+    ln -s cuda-12.4 /usr/local/cuda
+    ln -s /opt/rh/gcc-toolset-13/root/usr/bin/gcc /usr/local/cuda/bin/gcc
+    ln -s /opt/rh/gcc-toolset-13/root/usr/bin/g++ /usr/local/cuda/bin/g++
+
+    export CUDA_HOME="/usr/local/cuda"
+    export WITH_CUDA=1
+    
+fi
+
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
new file mode 100755
index 0000000000..e69de29bb2
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh
new file mode 100755
index 0000000000..1785227133
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+
+# Create pip directory if it doesn't exist
+mkdir -p "C:\ProgramData\pip"
+
+# Create pip.ini file with PyTorch CPU index
+echo "[global]
+extra-index-url = https://download.pytorch.org/whl/cpu" > "C:\ProgramData\pip\pip.ini"
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh
new file mode 100755
index 0000000000..3bf768f08d
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh
@@ -0,0 +1,19 @@
+#! /bin/bash
+
+set -e
+set -x
+
+CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8"
+curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_522.06_windows.exe
+./cuda.exe -s nvcc_11.8 cudart_11.8 cublas_dev_11.8 curand_dev_11.8 cusparse_dev_11.8 cusolver_dev_11.8 thrust_11.8
+rm cuda.exe
+
+export WITH_CUDA=1
+export CUDA_HOME="$CUDA_ROOT"
+
+# Create pip directory if it doesn't exist
+mkdir -p "C:\ProgramData\pip"
+
+# Create pip.ini file with PyTorch CUDA 11.8 index
+echo "[global]
+extra-index-url = https://download.pytorch.org/whl/cu118" > "C:\ProgramData\pip\pip.ini"
\ No newline at end of file
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh
new file mode 100755
index 0000000000..7b441f93e0
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh
@@ -0,0 +1,19 @@
+#! /bin/bash
+
+set -e
+set -x
+
+CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4"
+curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
+./cuda.exe -s nvcc_12.4 cudart_12.4 cublas_dev_12.4 curand_dev_12.4 cusparse_dev_12.4 cusolver_dev_12.4
+rm cuda.exe
+
+export WITH_CUDA=1
+export CUDA_HOME="$CUDA_ROOT"
+
+# Create pip directory if it doesn't exist
+mkdir -p "C:\ProgramData\pip"
+
+# Create pip.ini file with PyTorch CUDA 12.4 index
+echo "[global]
+extra-index-url = https://download.pytorch.org/whl/cu124" > "C:\ProgramData\pip\pip.ini"
\ No newline at end of file
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
new file mode 100644
index 0000000000..6a3b8b33b0
--- /dev/null
+++ b/wrappers/python/pyproject.toml
@@ -0,0 +1,47 @@
+[project]
+name = "OpenMM"
+description = "Python wrapper for OpenMM (a C++ MD package)"
+authors = [{ name = "Peter Eastman", email = "peastman@stanford.edu" }]
+readme = "README.md"
+license = "PSF-2.0"
+requires-python = ">=3.8"
+dynamic = ["version"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+]
+dependencies = [
+  "numpy"
+]
+
+[project.urls]
+"Homepage" = "https://openmm.org"
+"Bug Tracker" = "https://github.com/openmm/openmm/issues"
+"Download URL" = "https://openmm.org"
+
+[tool.setuptools_scm]
+
+[tool.setuptools.packages.find]
+include = ["openmm*"]
+
+
+[tool.setuptools.exclude-package-data]
+"*" = ["*.c", "*.cpp", "*.h", "*.cuh", "*.cu", ".gitignore"]
+
+[build-system]
+requires = ["setuptools>=64", "setuptools-scm>=8", "numpy", "cython"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.cibuildwheel]
+skip = ["cp38-*", "pp*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
+test-requires = ["pytest"]
+test-command = "pytest {project}/tests"
+manylinux-x86_64-image = "manylinux_2_28"
+manylinux-aarch64-image = "manylinux_2_28"
+environment-pass = ["CIBW_ARCHS"]
+# container-engine = "docker; create_args: --gpus all"
+
+# [tool.cibuildwheel.macos]
+# repair-wheel-command = [
+#   "delocate-wheel --ignore-missing-dependencies --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
+# ]
\ No newline at end of file
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 05c958e0ad..9453641d11 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -84,13 +84,14 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
     """
 
     cnt = """
+import os
 # THIS FILE IS GENERATED FROM OPENMM SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
 full_version = '%(full_version)s'
 git_revision = '%(git_revision)s'
 release = %(isrelease)s
-openmm_library_path = r'%(path)s'
+openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "OpenMM.libs", "lib"))
 
 if not release:
     version = full_version
@@ -127,16 +128,6 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                            build_info=BUILD_INFO):
     from setuptools import Extension
     setupKeywords = {}
-    setupKeywords["name"]              = "OpenMM"
-    setupKeywords["version"]           = "%s.%s.%s%s" % (major_version_num,
-                                                       minor_version_num,
-                                                       build_info,
-                                                       os.getenv('VERSION_SUFFIX', ''))
-    setupKeywords["author"]            = "Peter Eastman"
-    setupKeywords["license"]           = \
-    "Python Software Foundation License (BSD-like)"
-    setupKeywords["url"]               = "https://openmm.org"
-    setupKeywords["download_url"]      = "https://openmm.org"
     setupKeywords["packages"]          = [
                                           "simtk",
                                           "simtk.unit",
@@ -151,21 +142,6 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                                           "openmm.app.internal.pdbx",
                                           "openmm.app.internal.pdbx.reader",
                                           "openmm.app.internal.pdbx.writer"]
-    setupKeywords["data_files"]        = []
-    setupKeywords["package_data"]      = {"openmm" : [],
-                                          "openmm.app" : ['data/*.xml', 'data/*.pdb', 'data/amber14/*.xml', 'data/charmm36/*.xml', 'data/implicit/*.xml'],
-                                          "openmm.app.internal" : []}
-    setupKeywords["install_requires"]  = ["numpy"]
-    setupKeywords["platforms"]         = ["Linux", "Mac OS X", "Windows"]
-    setupKeywords["description"]       = \
-    "Python wrapper for OpenMM (a C++ MD package)"
-    setupKeywords["long_description"]  = \
-    """OpenMM is a toolkit for molecular simulation. It can be used either as a
-    stand-alone application for running simulations, or as a library you call
-    from your own code. It provides a combination of extreme flexibility
-    (through custom forces and integrators), openness, and high performance
-    (especially on recent GPUs) that make it truly unique among simulation codes.
-    """
 
     define_macros = [('MAJOR_VERSION', major_version_num),
                      ('MINOR_VERSION', minor_version_num)]
@@ -191,7 +167,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     if not openmm_lib_path:
         reportError("Set OPENMM_LIB_PATH to point to the lib directory for OpenMM")
 
-    extra_compile_args=['-std=c++11']
+    extra_compile_args=['-std=c++11', '-D_GLIBCXX_USE_CXX11_ABI=0']
     extra_link_args=[]
     if platform.system() == "Windows":
         define_macros.append( ('WIN32', None) )
@@ -199,6 +175,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         define_macros.append( (' _MSC_VER', None) )
         extra_compile_args.append('/EHsc')
     else:
+        extra_link_args += ['-Wl,-rpath,$ORIGIN/../OpenMM.libs/lib']
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++']
             extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', openmm_lib_path]

From 7fce7cf3a180e1f30f310678112fa53c365c1b50 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 15:15:01 +0300
Subject: [PATCH 02/75] cpu build working

---
 wrappers/python/MANIFEST.in                   |  3 ++-
 .../prepare_build_environment_linux_cpu.sh    | 19 +++++++++++--------
 wrappers/python/pyproject.toml                | 16 +++++++++++-----
 wrappers/python/setup.py                      |  4 ++--
 4 files changed, 26 insertions(+), 16 deletions(-)

diff --git a/wrappers/python/MANIFEST.in b/wrappers/python/MANIFEST.in
index c9af15ab45..df2d446845 100644
--- a/wrappers/python/MANIFEST.in
+++ b/wrappers/python/MANIFEST.in
@@ -8,4 +8,5 @@ recursive-include src       *.txt *.py *.i *.c *.cxx *.h *.sh Doxyfile
 prune src/swig_doxygen/doxygen/html
 prune src/swig_doxygen/doxygen/xml
 global-exclude CMakeLists.txt
-
+graft openmm/include
+graft openmm/lib
\ No newline at end of file
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
index 70b8f95d13..55c64f0472 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
@@ -4,7 +4,7 @@ set -e
 set -x
 
 # Install dependencies with yum
-dnf install -y doxygen zip opencl-headers ocl-icd tree
+dnf install -y doxygen zip opencl-headers ocl-icd
 
 # # Install CUDA (nothing)
 
@@ -16,23 +16,26 @@ dnf install -y doxygen zip opencl-headers ocl-icd tree
 
 # Configure build with Cmake
 mkdir -p build
+mkdir -p openmm-install
 cd build
 cmake .. \
-    -DCMAKE_INSTALL_PREFIX=${HOME}/openmm-install \
+    -DCMAKE_INSTALL_PREFIX=openmm-install \
     -DCMAKE_CXX_FLAGS='-D_GLIBCXX_USE_CXX11_ABI=0' \
     -DOPENMM_BUILD_OPENCL_LIB=ON \
     -DOPENCL_INCLUDE_DIR=/usr/include/CL \
     -DOPENCL_LIBRARY=/usr/lib64/libOpenCL.so.1
 
-tree .
-
 # Build OpenMM
 make -j4 install
 make -j4 PythonInstall
 
+cd ..
+
 # Build wheel
-export LD_LIBRARY_PATH=${HOME}/openmm-install/lib
-export OPENMM_INCLUDE_PATH=../openmmapi/include
-tree ./python
+export LD_LIBRARY_PATH=openmm-install/lib
+
+cp -r build/python/* wrappers/python/
+cp -r build/openmm-install/include wrappers/python/openmm/
+cp -r build/openmm-install/lib wrappers/python/openmm/
+
 
-ls -l ../openmmapi/
\ No newline at end of file
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 6a3b8b33b0..07ecb8b641 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -19,28 +19,34 @@ dependencies = [
 "Download URL" = "https://openmm.org"
 
 [tool.setuptools_scm]
+root = "../.."
 
 [tool.setuptools.packages.find]
 include = ["openmm*"]
 
 
-[tool.setuptools.exclude-package-data]
-"*" = ["*.c", "*.cpp", "*.h", "*.cuh", "*.cu", ".gitignore"]
+# [tool.setuptools.exclude-package-data]
+# "*" = ["*.c", "*.cpp", "*.h", "*.cuh", "*.cu", ".gitignore"]
 
 [build-system]
-requires = ["setuptools>=64", "setuptools-scm>=8", "numpy", "cython"]
+requires = ["setuptools>=78", "setuptools-scm>=8", "numpy", "cython"]
 build-backend = "setuptools.build_meta"
 
 
 [tool.cibuildwheel]
 skip = ["cp38-*", "pp*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
 test-requires = ["pytest"]
-test-command = "pytest {project}/tests"
+test-command = "cd {project}/wrappers/python/tests; pytest ."
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
-environment-pass = ["CIBW_ARCHS"]
+environment-pass = ["CIBW_ARCHS", "OPENMM_INCLUDE_PATH", "OPENMM_LIB_PATH", "LD_LIBRARY_PATH"]
 # container-engine = "docker; create_args: --gpus all"
 
+[tool.cibuildwheel.linux]
+repair-wheel-command = [
+  "auditwheel repair --exclude libOpenMM.so --exclude libOpenMMCUDA.so --exclude libOpenMMHIP.so --exclude libOpenMMOpenCL.so --exclude libOpenMMDrude.so --exclude libOpenMMAmoeba.so --exclude libOpenMMRPMD.so --exclude libOpenCL.so.1 --exclude libcuda.so.1 --exclude libcufft.so.11 --exclude libcufft.so.10 --exclude libnvrtc.so.11.2 --exclude libnvrtc.so.12 --exclude libhiprtc.so.6 --exclude libamdhip64.so.6 -w {dest_dir} {wheel}",
+]
+
 # [tool.cibuildwheel.macos]
 # repair-wheel-command = [
 #   "delocate-wheel --ignore-missing-dependencies --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 9453641d11..e6b072a0d1 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -91,7 +91,7 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
 full_version = '%(full_version)s'
 git_revision = '%(git_revision)s'
 release = %(isrelease)s
-openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "OpenMM.libs", "lib"))
+openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "lib"))
 
 if not release:
     version = full_version
@@ -175,7 +175,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         define_macros.append( (' _MSC_VER', None) )
         extra_compile_args.append('/EHsc')
     else:
-        extra_link_args += ['-Wl,-rpath,$ORIGIN/../OpenMM.libs/lib']
+        extra_link_args += ['-Wl,-rpath,$ORIGIN/lib']
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++']
             extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', openmm_lib_path]

From db005cd2c0067a3de1e1e0deeae1958a1d97e588 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 15:33:57 +0300
Subject: [PATCH 03/75] cleanup the installation

---
 wrappers/python/MANIFEST.in                           |  4 ++--
 .../prepare_build_environment_linux_cpu.sh            |  2 +-
 wrappers/python/openmm/__init__.py                    | 11 ++++++-----
 wrappers/python/pyproject.toml                        |  2 +-
 wrappers/python/setup.py                              |  8 ++------
 5 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/wrappers/python/MANIFEST.in b/wrappers/python/MANIFEST.in
index df2d446845..a97adf6cbc 100644
--- a/wrappers/python/MANIFEST.in
+++ b/wrappers/python/MANIFEST.in
@@ -8,5 +8,5 @@ recursive-include src       *.txt *.py *.i *.c *.cxx *.h *.sh Doxyfile
 prune src/swig_doxygen/doxygen/html
 prune src/swig_doxygen/doxygen/xml
 global-exclude CMakeLists.txt
-graft openmm/include
-graft openmm/lib
\ No newline at end of file
+graft openmm/lib
+prune include
\ No newline at end of file
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
index 55c64f0472..fa154ed944 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
@@ -35,7 +35,7 @@ cd ..
 export LD_LIBRARY_PATH=openmm-install/lib
 
 cp -r build/python/* wrappers/python/
-cp -r build/openmm-install/include wrappers/python/openmm/
+cp -r build/openmm-install/include wrappers/python/
 cp -r build/openmm-install/lib wrappers/python/openmm/
 
 
diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index 26a1a2aeaf..3141065085 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -9,14 +9,15 @@
 
 import os, os.path
 import sys
-from . import version
 
+
+openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'lib'))
 if sys.platform == 'win32':
     _path = os.environ['PATH']
     os.environ['PATH'] = r'%(lib)s;%(lib)s\plugins;%(path)s' % {
-        'lib': version.openmm_library_path, 'path': _path}
+        'lib': openmm_library_path, 'path': _path}
     try:
-        with os.add_dll_directory(version.openmm_library_path):
+        with os.add_dll_directory(openmm_library_path):
             from . import _openmm
     except:
         pass
@@ -26,8 +27,8 @@
 from openmm.mtsintegrator import MTSIntegrator, MTSLangevinIntegrator
 from openmm.amd import AMDIntegrator, AMDForceGroupIntegrator, DualAMDIntegrator
 
-if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(version.openmm_library_path):
-    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(version.openmm_library_path, 'plugins'))
+if os.getenv('OPENMM_PLUGIN_DIR') is None and os.path.isdir(openmm_library_path):
+    pluginLoadedLibNames = Platform.loadPluginsFromDirectory(os.path.join(openmm_library_path, 'plugins'))
 else:
     pluginLoadedLibNames = Platform.loadPluginsFromDirectory(Platform.getDefaultPluginsDirectory())
 
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 07ecb8b641..80b40ac56e 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -39,7 +39,7 @@ test-requires = ["pytest"]
 test-command = "cd {project}/wrappers/python/tests; pytest ."
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
-environment-pass = ["CIBW_ARCHS", "OPENMM_INCLUDE_PATH", "OPENMM_LIB_PATH", "LD_LIBRARY_PATH"]
+environment-pass = ["CIBW_ARCHS"]
 # container-engine = "docker; create_args: --gpus all"
 
 [tool.cibuildwheel.linux]
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index e6b072a0d1..f1409d5471 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -160,12 +160,8 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                 libraries[ii]="%s_d" % libraries[ii]
                 sys.stdout.write("%s\n" % libraries[ii])
 
-    openmm_include_path = os.getenv('OPENMM_INCLUDE_PATH')
-    if not openmm_include_path:
-        reportError("Set OPENMM_INCLUDE_PATH to point to the include directory for OpenMM")
-    openmm_lib_path = os.getenv('OPENMM_LIB_PATH')
-    if not openmm_lib_path:
-        reportError("Set OPENMM_LIB_PATH to point to the lib directory for OpenMM")
+    openmm_include_path = 'include'
+    openmm_lib_path = 'openmm/lib'
 
     extra_compile_args=['-std=c++11', '-D_GLIBCXX_USE_CXX11_ABI=0']
     extra_link_args=[]

From d8bace0f078fa8e033d44af6a8b4bb63936e585c Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 16:26:56 +0300
Subject: [PATCH 04/75] time to test it on all OSs

---
 .github/workflows/publish.yml                 |  81 ++++++++++++
 .../prepare_build_environment_linux.sh        |  62 +++++++++
 .../prepare_build_environment_linux_cpu.sh    |  41 ------
 .../prepare_build_environment_linux_cu118.sh  | 124 ------------------
 .../prepare_build_environment_linux_cu124.sh  |  31 -----
 .../prepare_build_environment_osx.sh          |  13 ++
 .../prepare_build_environment_windows.sh      |  49 +++++++
 .../prepare_build_environment_windows_cpu.sh  |   8 --
 ...prepare_build_environment_windows_cu118.sh |  19 ---
 ...prepare_build_environment_windows_cu124.sh |  19 ---
 wrappers/python/pyproject.toml                |   4 +-
 11 files changed, 207 insertions(+), 244 deletions(-)
 create mode 100644 .github/workflows/publish.yml
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
 delete mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
 delete mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh
 delete mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh
 create mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
 delete mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh
 delete mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh
 delete mode 100755 wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
new file mode 100644
index 0000000000..4a81d3f51c
--- /dev/null
+++ b/.github/workflows/publish.yml
@@ -0,0 +1,81 @@
+name: Build wheels and publish
+
+on:
+  workflow_dispatch:
+  workflow_call:
+  push:
+
+jobs:
+  build:
+    name: Build wheels on ${{ matrix.os }}-${{ matrix.cuda }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-2019, macos-latest]
+        accelerator: [cpu, cu118, cu124, hip]
+        exclude:
+          - os: ubuntu-24.04-arm
+            accelerator: cu118
+          - os: ubuntu-24.04-arm
+            accelerator: cu124
+          - os: macos-latest
+            accelerator: cu118
+          - os: macos-latest
+            accelerator: cu124
+
+    steps:
+      - name: Free space of Github Runner (otherwise it will fail by running out of disk)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+          sudo rm -rf "/usr/local/share/boost"
+          sudo rm -rf "/usr/local/.ghcup"
+          sudo rm -rf "/usr/local/julia1.9.2"
+          sudo rm -rf "/usr/local/lib/android"
+          sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.23.0
+
+      - name: Activate MSVC
+        uses: ilammy/msvc-dev-cmd@v1
+        if: matrix.os == 'windows-2019'
+
+      - name: Build wheels
+        if: matrix.os != 'windows-2019'
+        shell: bash -l {0}
+        run: |
+          if [[ "${{ runner.os }}" == "Linux" ]]; then
+            export CIBW_ARCHS="${{ matrix.os == 'ubuntu-24.04-arm' && 'aarch64' || 'auto64' }}"
+          fi
+          python -m cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
+          CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
+          CUDA_VERSION: ${{ matrix.accelerator }}
+          ACCELERATOR: ${{ matrix.accelerator }}
+          CIBW_BUILD: "cp310-*"
+
+      - name: Build wheels
+        if: matrix.os == 'windows-2019'
+        shell: cmd # Use cmd on Windows to avoid bash environment taking priority over MSVC variables
+        run: python -m cibuildwheel --output-dir wheelhouse
+        env:
+          CIBW_BEFORE_ALL_WINDOWS: "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
+          DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
+          CUDA_VERSION: ${{ matrix.accelerator }}
+          ACCELERATOR: ${{ matrix.accelerator }}
+          CIBW_BUILD: "cp310-*"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.accelerator }}-cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
new file mode 100755
index 0000000000..c7ba69faf3
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -0,0 +1,62 @@
+#! /bin/bash
+
+set -e
+set -x
+
+# Install dependencies with yum
+dnf install -y doxygen zip opencl-headers ocl-icd
+
+if [ "$ACCELERATOR" == "cu118" ]; then
+    # Install CUDA 11.8
+    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
+
+    dnf install --setopt=obsoletes=0 -y \
+        cuda-compiler-11-8-11.8.0-1 \
+        cuda-libraries-11-8-11.8.0-1 \
+        cuda-libraries-devel-11-8-11.8.0-1
+        
+    ln -s cuda-11.8 /usr/local/cuda
+
+    export CUDA_HOME="/usr/local/cuda"
+fi
+
+if [ "$ACCELERATOR" == "cu124" ]; then
+    # Install CUDA 12.4
+    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
+
+    dnf install --setopt=obsoletes=0 -y \
+        cuda-compiler-12-4-12.4.1-1 \
+        cuda-libraries-12-4-12.4.1-1 \
+        cuda-libraries-devel-12-4-12.4.1-1
+
+    ln -s cuda-12.4 /usr/local/cuda
+
+    export CUDA_HOME="/usr/local/cuda"
+fi
+
+if [ "$ACCELERATOR" == "hip" ]; then
+    # Install HIP 6.2
+    dnf install -y https://repo.radeon.com/amdgpu-install/6.2.2/el/8.10/amdgpu-install-6.2.60202-1.el8.noarch.rpm
+    dnf install -y rocm-device-libs hip-devel hip-runtime-amd hipcc
+fi
+
+# Configure build with Cmake
+mkdir -p build
+mkdir -p openmm-install
+cd build
+cmake .. \
+    -DCMAKE_INSTALL_PREFIX=openmm-install \
+    -DCMAKE_CXX_FLAGS='-D_GLIBCXX_USE_CXX11_ABI=0' \
+    -DOPENMM_BUILD_OPENCL_LIB=ON \
+    -DOPENCL_INCLUDE_DIR=/usr/include/CL \
+    -DOPENCL_LIBRARY=/usr/lib64/libOpenCL.so.1
+
+# Build OpenMM
+make -j4 install
+make -j4 PythonInstall
+
+cd ..
+
+cp -r build/python/* wrappers/python/
+cp -r build/openmm-install/include wrappers/python/
+cp -r build/openmm-install/lib wrappers/python/openmm/
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
deleted file mode 100755
index fa154ed944..0000000000
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cpu.sh
+++ /dev/null
@@ -1,41 +0,0 @@
-#! /bin/bash
-
-set -e
-set -x
-
-# Install dependencies with yum
-dnf install -y doxygen zip opencl-headers ocl-icd
-
-# # Install CUDA (nothing)
-
-# # Install HIP
-# export HIP_VERSION=6
-# yum install -y epel-release
-# yum install -y https://repo.radeon.com/amdgpu-install/6.2.2/el/8.10/amdgpu-install-6.2.60202-1.el8.noarch.rpm
-# yum install -y rocm-device-libs hip-devel hip-runtime-amd hipcc
-
-# Configure build with Cmake
-mkdir -p build
-mkdir -p openmm-install
-cd build
-cmake .. \
-    -DCMAKE_INSTALL_PREFIX=openmm-install \
-    -DCMAKE_CXX_FLAGS='-D_GLIBCXX_USE_CXX11_ABI=0' \
-    -DOPENMM_BUILD_OPENCL_LIB=ON \
-    -DOPENCL_INCLUDE_DIR=/usr/include/CL \
-    -DOPENCL_LIBRARY=/usr/lib64/libOpenCL.so.1
-
-# Build OpenMM
-make -j4 install
-make -j4 PythonInstall
-
-cd ..
-
-# Build wheel
-export LD_LIBRARY_PATH=openmm-install/lib
-
-cp -r build/python/* wrappers/python/
-cp -r build/openmm-install/include wrappers/python/
-cp -r build/openmm-install/lib wrappers/python/openmm/
-
-
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh
deleted file mode 100755
index ac32543d6d..0000000000
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu118.sh
+++ /dev/null
@@ -1,124 +0,0 @@
-#! /bin/bash
-
-set -e
-set -x
-
-dnf install -y doxygen
-
-
-if [ "$CIBW_ARCHS" != "aarch64" ]; then
-
-    # Install CUDA 11.8:
-    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
-
-    dnf install --setopt=obsoletes=0 -y \
-        cuda-nvcc-11-8-11.8.89-1 \
-        cuda-cudart-devel-11-8-11.8.89-1 \
-        libcurand-devel-11-8-10.3.0.86-1 \
-        libcudnn9-devel-cuda-11-9.8.0.87-1 \
-        libcublas-devel-11-8-11.11.3.6-1 \
-        libnccl-devel-2.15.5-1+cuda11.8 \
-        libcusparse-devel-11-8-11.7.5.86-1 \
-        libcusolver-devel-11-8-11.4.1.48-1 \
-        gcc-toolset-11
-
-    ln -s cuda-11.8 /usr/local/cuda
-    ln -s /opt/rh/gcc-toolset-11/root/usr/bin/gcc /usr/local/cuda/bin/gcc
-    ln -s /opt/rh/gcc-toolset-11/root/usr/bin/g++ /usr/local/cuda/bin/g++
-
-    export CUDA_HOME="/usr/local/cuda"
-    export WITH_CUDA=1
-
-    
-    # Configure pip to use PyTorch extra-index-url for CUDA 11.8
-    mkdir -p $HOME/.config/pip
-    echo "[global]
-extra-index-url = https://download.pytorch.org/whl/cu118" > $HOME/.config/pip/pip.conf
-    
-fi
-
-
-# OpenMM Compilation starting here
-
-CMAKE_FLAGS="${CMAKE_ARGS} -DCMAKE_BUILD_TYPE=Release"
-if [[ "$with_test_suite" == "true" ]]; then
-    CMAKE_FLAGS+=" -DBUILD_TESTING=ON -DOPENMM_BUILD_OPENCL_TESTS=ON"
-else
-    CMAKE_FLAGS+=" -DBUILD_TESTING=OFF"
-fi
-
-
-if [[ "$target_platform" == linux* ]]; then
-    SHLIB_EXT=".so"
-    # CFLAGS
-    # JRG: Had to add -ldl to prevent linking errors (dlopen, etc)
-    MINIMAL_CFLAGS+=" -O3 -ldl"
-    CFLAGS+=" $MINIMAL_CFLAGS"
-    CXXFLAGS+=" $MINIMAL_CFLAGS"
-
-    # CUDA is enabled in these platforms
-    if [[ "$target_platform" == linux-64 || "$target_platform" == linux-ppc64le ]]; then
-        # # CUDA_HOME is defined by nvcc metapackage
-        CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=${CUDA_HOME}"
-        # CUDA tests won't build, disable for now
-        # See https://github.com/openmm/openmm/issues/2258#issuecomment-462223634
-        CMAKE_FLAGS+=" -DOPENMM_BUILD_CUDA_TESTS=OFF"
-        # shadow some CMAKE_ARGS bits that interfere with CUDA detection
-        CMAKE_FLAGS+=" -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=BOTH"
-    fi
-
-    # OpenCL ICD
-    CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=${PREFIX}/include"
-    CMAKE_FLAGS+=" -DOPENCL_LIBRARY=${PREFIX}/lib/libOpenCL${SHLIB_EXT}"
-
-elif [[ "$target_platform" == osx* ]]; then
-    SHLIB_EXT=".dylib"
-    if [[ "$opencl_impl" == khronos ]]; then
-        CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=${PREFIX}/include"
-        CMAKE_FLAGS+=" -DOPENCL_LIBRARY=${PREFIX}/lib/libOpenCL${SHLIB_EXT}"
-    fi
-    # When using opencl_impl == apple, CMake will auto-locate it, so no need to provide the flags
-    # On Conda Forge, this will result in:
-    #   /Applications/Xcode_12.app/Contents/Developer/Platforms/MacOSX.platform/Developer/...
-    #   ...SDKs/MacOSX10.9.sdk/System/Library/Frameworks/OpenCL.framework
-    # On local builds, it might be:
-    #   /System/Library/Frameworks/OpenCL.framework/OpenCL
-fi
-
-# Set location for FFTW3 on both linux and mac
-CMAKE_FLAGS+=" -DFFTW_INCLUDES=${PREFIX}/include/"
-CMAKE_FLAGS+=" -DFFTW_LIBRARY=${PREFIX}/lib/libfftw3f${SHLIB_EXT}"
-CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=${PREFIX}/lib/libfftw3f_threads${SHLIB_EXT}"
-# Disambiguate swig location
-CMAKE_FLAGS+=" -DSWIG_EXECUTABLE=$(which swig)"
-
-# Build in subdirectory and install.
-mkdir -p build
-cd build
-cmake ${CMAKE_FLAGS} ..
-make -j$CPU_COUNT
-make -j$CPU_COUNT install PythonInstall
-
-# Put examples into an appropriate subdirectory.
-mkdir -p ${PREFIX}/share/openmm/
-mv ${PREFIX}/examples ${PREFIX}/share/openmm/
-
-# Fix some overlinking warnings/errors
-for lib in ${PREFIX}/lib/plugins/*${SHLIB_EXT}; do
-    ln -s $lib ${PREFIX}/lib/$(basename $lib) || true
-done
-
-if [[ "$with_test_suite" == "true" ]]; then
-    mkdir -p ${PREFIX}/share/openmm/tests/
-    # BSD find vs GNU find: -executable is only available in GNU find
-    # +0111 is somehow equivalent in BSD, but that's not compatible in GNU
-    # so we use different commands for each...
-    if [[ "$target_platform" == osx* ]]; then
-        find . -name "Test*" -perm +0111 -type f \
-            -exec python $RECIPE_DIR/patch_osx_tests.py "{}" \; \
-            -exec cp "{}" $PREFIX/share/openmm/tests/ \;
-    else
-        find . -name "Test*" -executable -type f -exec cp "{}" $PREFIX/share/openmm/tests/ \;
-    fi
-    cp -r python/tests $PREFIX/share/openmm/tests/python
-fi
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh
deleted file mode 100755
index cc9e212c5a..0000000000
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux_cu124.sh
+++ /dev/null
@@ -1,31 +0,0 @@
-#! /bin/bash
-
-set -e
-set -x
-
-
-if [ "$CIBW_ARCHS" != "aarch64" ]; then
-
-    # Install CUDA 12.4:
-    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
-
-    dnf install --setopt=obsoletes=0 -y \
-        cuda-nvcc-12-4-12.4.131-1 \
-        cuda-cudart-devel-12-4-12.4.127-1 \
-        libcurand-devel-12-4-10.3.5.147-1 \
-        libcudnn9-devel-cuda-12-9.1.0.70-1 \
-        libcublas-devel-12-4-12.4.5.8-1 \
-        libnccl-devel-2.21.5-1+cuda12.4 \
-        libcusparse-devel-12-4-12.3.1.170-1 \
-        libcusolver-devel-12-4-11.6.1.9-1 \
-        gcc-toolset-13
-
-    ln -s cuda-12.4 /usr/local/cuda
-    ln -s /opt/rh/gcc-toolset-13/root/usr/bin/gcc /usr/local/cuda/bin/gcc
-    ln -s /opt/rh/gcc-toolset-13/root/usr/bin/g++ /usr/local/cuda/bin/g++
-
-    export CUDA_HOME="/usr/local/cuda"
-    export WITH_CUDA=1
-    
-fi
-
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
index e69de29bb2..bc417b6056 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
@@ -0,0 +1,13 @@
+brew install doxygen
+
+mkdir build
+cd build
+cmake .. -DCMAKE_INSTALL_PREFIX=openmm-install
+make -j4 install
+make -j4 PythonInstall
+
+cd ..
+
+cp -r build/python/* wrappers/python/
+cp -r build/openmm-install/include wrappers/python/
+cp -r build/openmm-install/lib wrappers/python/openmm/
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
new file mode 100755
index 0000000000..8d1ef94ec9
--- /dev/null
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -0,0 +1,49 @@
+#! /bin/bash
+
+set -e
+set -x
+
+if [ "$ACCELERATOR" == "cu118" ]; then
+    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8"
+    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_522.06_windows.exe
+    ./cuda.exe -s nvcc_11.8 nvrtc_11.8 nvrtc_dev_11.8 cudart_11.8 cufft_11.8 cufft_dev_11.8 opencl_11.8 cuda_profiler_api_11.8
+    rm cuda.exe
+fi
+
+if [ "$ACCELERATOR" == "cu124" ]; then
+    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4"
+    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
+    ./cuda.exe -s nvcc_12.4 nvrtc_12.4 nvrtc_dev_12.4 cudart_12.4 cufft_12.4 cufft_dev_12.4 opencl_12.4 cuda_profiler_api_12.4
+    rm cuda.exe
+fi
+
+if [ "$ACCELERATOR" == "hip" ]; then
+    curl.exe --output HIP.exe --url https://download.amd.com/developer/eula/rocm-hub/AMD-Software-PRO-Edition-24.Q3-Win10-Win11-For-HIP.exe
+    ./HIP.exe -install
+    rm HIP.exe
+fi
+
+# Configure build with Cmake
+mkdir -p build
+mkdir -p openmm-install
+cd build
+cmake -G "NMake Makefiles JOM" \
+    -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX=openmm-install \
+    -DCMAKE_PREFIX_PATH="openmm-install;C:\Program Files\AMD\ROCm\6.1" \
+    -DCMAKE_CXX_COMPILER=cl.exe \
+    -DCMAKE_C_COMPILER=cl.exe \
+    -DOPENCL_INCLUDE_DIR="${CUDA_ROOT}/include" \
+    -DOPENCL_LIBRARY="${CUDA_ROOT}/lib/x64/OpenCL.lib" \
+    -DHIP_PLATFORM=amd \
+    ..
+
+# Build OpenMM
+make -j4 install
+make -j4 PythonInstall
+
+cd ..
+
+cp -r build/python/* wrappers/python/
+cp -r build/openmm-install/include wrappers/python/
+cp -r build/openmm-install/lib wrappers/python/openmm/
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh
deleted file mode 100755
index 1785227133..0000000000
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cpu.sh
+++ /dev/null
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-# Create pip directory if it doesn't exist
-mkdir -p "C:\ProgramData\pip"
-
-# Create pip.ini file with PyTorch CPU index
-echo "[global]
-extra-index-url = https://download.pytorch.org/whl/cpu" > "C:\ProgramData\pip\pip.ini"
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh
deleted file mode 100755
index 3bf768f08d..0000000000
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu118.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#! /bin/bash
-
-set -e
-set -x
-
-CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8"
-curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_522.06_windows.exe
-./cuda.exe -s nvcc_11.8 cudart_11.8 cublas_dev_11.8 curand_dev_11.8 cusparse_dev_11.8 cusolver_dev_11.8 thrust_11.8
-rm cuda.exe
-
-export WITH_CUDA=1
-export CUDA_HOME="$CUDA_ROOT"
-
-# Create pip directory if it doesn't exist
-mkdir -p "C:\ProgramData\pip"
-
-# Create pip.ini file with PyTorch CUDA 11.8 index
-echo "[global]
-extra-index-url = https://download.pytorch.org/whl/cu118" > "C:\ProgramData\pip\pip.ini"
\ No newline at end of file
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh
deleted file mode 100755
index 7b441f93e0..0000000000
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows_cu124.sh
+++ /dev/null
@@ -1,19 +0,0 @@
-#! /bin/bash
-
-set -e
-set -x
-
-CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4"
-curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
-./cuda.exe -s nvcc_12.4 cudart_12.4 cublas_dev_12.4 curand_dev_12.4 cusparse_dev_12.4 cusolver_dev_12.4
-rm cuda.exe
-
-export WITH_CUDA=1
-export CUDA_HOME="$CUDA_ROOT"
-
-# Create pip directory if it doesn't exist
-mkdir -p "C:\ProgramData\pip"
-
-# Create pip.ini file with PyTorch CUDA 12.4 index
-echo "[global]
-extra-index-url = https://download.pytorch.org/whl/cu124" > "C:\ProgramData\pip\pip.ini"
\ No newline at end of file
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 80b40ac56e..fe667e338a 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -39,8 +39,8 @@ test-requires = ["pytest"]
 test-command = "cd {project}/wrappers/python/tests; pytest ."
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
-environment-pass = ["CIBW_ARCHS"]
-# container-engine = "docker; create_args: --gpus all"
+environment-pass = ["ACCELERATOR"]
+container-engine = "docker; create_args: --gpus all"
 
 [tool.cibuildwheel.linux]
 repair-wheel-command = [

From f097d519065b3beb526b7c35c1d4efc7c30de7ec Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 16:29:36 +0300
Subject: [PATCH 05/75] wront path

---
 .github/workflows/publish.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 4a81d3f51c..021bc4a371 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -19,10 +19,14 @@ jobs:
             accelerator: cu118
           - os: ubuntu-24.04-arm
             accelerator: cu124
+          - os: ubuntu-24.04-arm
+            accelerator: hip
           - os: macos-latest
             accelerator: cu118
           - os: macos-latest
             accelerator: cu124
+          - os: macos-latest
+            accelerator: hip
 
     steps:
       - name: Free space of Github Runner (otherwise it will fail by running out of disk)
@@ -52,11 +56,7 @@ jobs:
       - name: Build wheels
         if: matrix.os != 'windows-2019'
         shell: bash -l {0}
-        run: |
-          if [[ "${{ runner.os }}" == "Linux" ]]; then
-            export CIBW_ARCHS="${{ matrix.os == 'ubuntu-24.04-arm' && 'aarch64' || 'auto64' }}"
-          fi
-          python -m cibuildwheel --output-dir wheelhouse
+        run: python -m cibuildwheel wrappers/python/ --output-dir wheelhouse
         env:
           CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
           CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
@@ -67,7 +67,7 @@ jobs:
       - name: Build wheels
         if: matrix.os == 'windows-2019'
         shell: cmd # Use cmd on Windows to avoid bash environment taking priority over MSVC variables
-        run: python -m cibuildwheel --output-dir wheelhouse
+        run: python -m cibuildwheel wrappers/python/ --output-dir wheelhouse
         env:
           CIBW_BEFORE_ALL_WINDOWS: "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building

From e76d87be990484510dd58993ea041149d64e73f3 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 16:46:00 +0300
Subject: [PATCH 06/75] fixes

---
 .github/workflows/publish.yml                          | 10 +++++++++-
 .../prepare_build_environment_osx.sh                   |  2 +-
 .../prepare_build_environment_windows.sh               |  4 ++--
 3 files changed, 12 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 021bc4a371..51d5731fbd 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -7,7 +7,7 @@ on:
 
 jobs:
   build:
-    name: Build wheels on ${{ matrix.os }}-${{ matrix.cuda }}
+    name: Build wheels on ${{ matrix.os }}-${{ matrix.accelerator }}
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -53,6 +53,14 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
         if: matrix.os == 'windows-2019'
 
+      - name: "Install OpenCL"
+        uses: Jimver/cuda-toolkit@v0.2.16
+        if: matrix.os == 'windows-2019'
+        id: cuda-toolkit
+        with:
+          method: "network"
+          sub-packages: '["opencl"]'
+
       - name: Build wheels
         if: matrix.os != 'windows-2019'
         shell: bash -l {0}
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
index bc417b6056..6053766898 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
@@ -1,4 +1,4 @@
-brew install doxygen
+brew install doxygen swig
 
 mkdir build
 cd build
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 8d1ef94ec9..50822cc02d 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -6,14 +6,14 @@ set -x
 if [ "$ACCELERATOR" == "cu118" ]; then
     CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_522.06_windows.exe
-    ./cuda.exe -s nvcc_11.8 nvrtc_11.8 nvrtc_dev_11.8 cudart_11.8 cufft_11.8 cufft_dev_11.8 opencl_11.8 cuda_profiler_api_11.8
+    ./cuda.exe -s nvcc_11.8 nvrtc_11.8 nvrtc_dev_11.8 cudart_11.8 cufft_11.8 cufft_dev_11.8 cuda_profiler_api_11.8
     rm cuda.exe
 fi
 
 if [ "$ACCELERATOR" == "cu124" ]; then
     CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
-    ./cuda.exe -s nvcc_12.4 nvrtc_12.4 nvrtc_dev_12.4 cudart_12.4 cufft_12.4 cufft_dev_12.4 opencl_12.4 cuda_profiler_api_12.4
+    ./cuda.exe -s nvcc_12.4 nvrtc_12.4 nvrtc_dev_12.4 cudart_12.4 cufft_12.4 cufft_dev_12.4 cuda_profiler_api_12.4
     rm cuda.exe
 fi
 

From a886cabae8da35d7a20ae66706d88c7e38157b68 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 16:51:13 +0300
Subject: [PATCH 07/75] ignore missing deps on OSX

---
 wrappers/python/pyproject.toml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index fe667e338a..75d4cfa245 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -47,7 +47,7 @@ repair-wheel-command = [
   "auditwheel repair --exclude libOpenMM.so --exclude libOpenMMCUDA.so --exclude libOpenMMHIP.so --exclude libOpenMMOpenCL.so --exclude libOpenMMDrude.so --exclude libOpenMMAmoeba.so --exclude libOpenMMRPMD.so --exclude libOpenCL.so.1 --exclude libcuda.so.1 --exclude libcufft.so.11 --exclude libcufft.so.10 --exclude libnvrtc.so.11.2 --exclude libnvrtc.so.12 --exclude libhiprtc.so.6 --exclude libamdhip64.so.6 -w {dest_dir} {wheel}",
 ]
 
-# [tool.cibuildwheel.macos]
-# repair-wheel-command = [
-#   "delocate-wheel --ignore-missing-dependencies --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
-# ]
\ No newline at end of file
+[tool.cibuildwheel.macos]
+repair-wheel-command = [
+  "delocate-wheel --ignore-missing-dependencies --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
+]
\ No newline at end of file

From 28f6353483fabf475477c87d896f4e08d9c0ebba Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 16:55:03 +0300
Subject: [PATCH 08/75] jom for Windows

---
 .github/workflows/publish.yml                               | 6 ++++++
 .../prepare_build_environment_windows.sh                    | 4 ++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 51d5731fbd..7e25897c26 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -61,6 +61,12 @@ jobs:
           method: "network"
           sub-packages: '["opencl"]'
 
+      - name: "Install dependencies with choco"
+        uses: crazy-max/ghaction-chocolatey@v3
+        if: matrix.os == 'windows-2019'
+        with:
+          args: install doxygen.install jom
+
       - name: Build wheels
         if: matrix.os != 'windows-2019'
         shell: bash -l {0}
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 50822cc02d..53b244e2c6 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -39,8 +39,8 @@ cmake -G "NMake Makefiles JOM" \
     ..
 
 # Build OpenMM
-make -j4 install
-make -j4 PythonInstall
+jom -j 4 install
+jom -j 4 PythonInstall
 
 cd ..
 

From cde2efa474236c67dff5fffb08b2178e92c7a2c6 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 16:58:44 +0300
Subject: [PATCH 09/75] no gpus on CI

---
 wrappers/python/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 75d4cfa245..44b00b537c 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -40,7 +40,7 @@ test-command = "cd {project}/wrappers/python/tests; pytest ."
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
 environment-pass = ["ACCELERATOR"]
-container-engine = "docker; create_args: --gpus all"
+# container-engine = "docker; create_args: --gpus all"
 
 [tool.cibuildwheel.linux]
 repair-wheel-command = [

From 2918023b5b464f9fc0ceb918708d7fc29243a481 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 17:14:52 +0300
Subject: [PATCH 10/75] include the includes. continue on error for OSX

---
 wrappers/python/MANIFEST.in                                | 2 +-
 .../prepare_build_environment_linux.sh                     | 2 +-
 .../cibuildwheel_support/prepare_build_environment_osx.sh  | 7 ++++++-
 .../prepare_build_environment_windows.sh                   | 2 +-
 4 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/wrappers/python/MANIFEST.in b/wrappers/python/MANIFEST.in
index a97adf6cbc..12cc448ab9 100644
--- a/wrappers/python/MANIFEST.in
+++ b/wrappers/python/MANIFEST.in
@@ -9,4 +9,4 @@ prune src/swig_doxygen/doxygen/html
 prune src/swig_doxygen/doxygen/xml
 global-exclude CMakeLists.txt
 graft openmm/lib
-prune include
\ No newline at end of file
+graft openmm/include
\ No newline at end of file
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
index c7ba69faf3..260044592f 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -58,5 +58,5 @@ make -j4 PythonInstall
 cd ..
 
 cp -r build/python/* wrappers/python/
-cp -r build/openmm-install/include wrappers/python/
+cp -r build/openmm-install/include wrappers/python/openmm/
 cp -r build/openmm-install/lib wrappers/python/openmm/
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
index 6053766898..f527c3dc24 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh
@@ -1,3 +1,8 @@
+#! /bin/bash
+
+set -e
+set -x
+
 brew install doxygen swig
 
 mkdir build
@@ -9,5 +14,5 @@ make -j4 PythonInstall
 cd ..
 
 cp -r build/python/* wrappers/python/
-cp -r build/openmm-install/include wrappers/python/
+cp -r build/openmm-install/include wrappers/python/openmm/
 cp -r build/openmm-install/lib wrappers/python/openmm/
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 53b244e2c6..864e35ac9b 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -45,5 +45,5 @@ jom -j 4 PythonInstall
 cd ..
 
 cp -r build/python/* wrappers/python/
-cp -r build/openmm-install/include wrappers/python/
+cp -r build/openmm-install/include wrappers/python/openmm/
 cp -r build/openmm-install/lib wrappers/python/openmm/

From 88f6ea516cf248d841e28c49532b30545a79cfee Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 17:17:50 +0300
Subject: [PATCH 11/75] fix windows opencl path

---
 .github/workflows/publish.yml                                 | 1 +
 .../cibuildwheel_support/prepare_build_environment_windows.sh | 4 ++--
 wrappers/python/pyproject.toml                                | 2 +-
 3 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 7e25897c26..264170d772 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -88,6 +88,7 @@ jobs:
           CUDA_VERSION: ${{ matrix.accelerator }}
           ACCELERATOR: ${{ matrix.accelerator }}
           CIBW_BUILD: "cp310-*"
+          OPENCL_PATH: "${{steps.cuda-toolkit.outputs.CUDA_PATH}}"
 
       - uses: actions/upload-artifact@v4
         with:
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 864e35ac9b..714ec53cff 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -33,8 +33,8 @@ cmake -G "NMake Makefiles JOM" \
     -DCMAKE_PREFIX_PATH="openmm-install;C:\Program Files\AMD\ROCm\6.1" \
     -DCMAKE_CXX_COMPILER=cl.exe \
     -DCMAKE_C_COMPILER=cl.exe \
-    -DOPENCL_INCLUDE_DIR="${CUDA_ROOT}/include" \
-    -DOPENCL_LIBRARY="${CUDA_ROOT}/lib/x64/OpenCL.lib" \
+    -DOPENCL_INCLUDE_DIR="${OPENCL_PATH}/include" \
+    -DOPENCL_LIBRARY="${OPENCL_PATH}/lib/x64/OpenCL.lib" \
     -DHIP_PLATFORM=amd \
     ..
 
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 44b00b537c..8312e5b2b8 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -39,7 +39,7 @@ test-requires = ["pytest"]
 test-command = "cd {project}/wrappers/python/tests; pytest ."
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
-environment-pass = ["ACCELERATOR"]
+environment-pass = ["ACCELERATOR", "OPENCL_PATH"]
 # container-engine = "docker; create_args: --gpus all"
 
 [tool.cibuildwheel.linux]

From 00ef6e1c2c1c98243cd0a7ff506c174412c392c3 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 17:26:19 +0300
Subject: [PATCH 12/75] forgot one path

---
 wrappers/python/setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index f1409d5471..8b0de0e3bd 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -160,7 +160,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                 libraries[ii]="%s_d" % libraries[ii]
                 sys.stdout.write("%s\n" % libraries[ii])
 
-    openmm_include_path = 'include'
+    openmm_include_path = 'openmm/include'
     openmm_lib_path = 'openmm/lib'
 
     extra_compile_args=['-std=c++11', '-D_GLIBCXX_USE_CXX11_ABI=0']

From 11a5de8648dfc06f5a704982a5193a904bc47b4b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 17:35:20 +0300
Subject: [PATCH 13/75] fix OSX rpath

---
 wrappers/python/setup.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 8b0de0e3bd..e28494cfa6 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -91,7 +91,6 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
 full_version = '%(full_version)s'
 git_revision = '%(git_revision)s'
 release = %(isrelease)s
-openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "lib"))
 
 if not release:
     version = full_version
@@ -119,8 +118,7 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
         a.write(cnt % {'version': version,
                        'full_version' : full_version,
                        'git_revision' : git_revision,
-                       'isrelease': str(IS_RELEASED),
-                       'path': os.getenv('OPENMM_LIB_PATH')})
+                       'isrelease': str(IS_RELEASED)})
 
 
 def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
@@ -174,7 +172,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         extra_link_args += ['-Wl,-rpath,$ORIGIN/lib']
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++']
-            extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', openmm_lib_path]
+            extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', f'@loader_path/{openmm_lib_path}']
             if 'MACOSX_DEPLOYMENT_TARGET' not in os.environ and platform.processor() != 'arm':
                 extra_compile_args += ['-mmacosx-version-min=10.7']
                 extra_link_args += ['-mmacosx-version-min=10.7']

From ec96e89d59061731ad4ee77aaf286e89a1054f35 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 17:49:52 +0300
Subject: [PATCH 14/75] fixes for windows and osx

---
 wrappers/python/pyproject.toml | 5 ++++-
 wrappers/python/setup.py       | 2 +-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 8312e5b2b8..6dc30b944b 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -36,12 +36,15 @@ build-backend = "setuptools.build_meta"
 [tool.cibuildwheel]
 skip = ["cp38-*", "pp*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
 test-requires = ["pytest"]
-test-command = "cd {project}/wrappers/python/tests; pytest ."
+test-command = "cd {project}/wrappers/python/tests && pytest ."
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
 environment-pass = ["ACCELERATOR", "OPENCL_PATH"]
 # container-engine = "docker; create_args: --gpus all"
 
+[tool.cibuildwheel.windows]
+test-command = "cd {project}\\wrappers\\python\\tests && pytest ."
+
 [tool.cibuildwheel.linux]
 repair-wheel-command = [
   "auditwheel repair --exclude libOpenMM.so --exclude libOpenMMCUDA.so --exclude libOpenMMHIP.so --exclude libOpenMMOpenCL.so --exclude libOpenMMDrude.so --exclude libOpenMMAmoeba.so --exclude libOpenMMRPMD.so --exclude libOpenCL.so.1 --exclude libcuda.so.1 --exclude libcufft.so.11 --exclude libcufft.so.10 --exclude libnvrtc.so.11.2 --exclude libnvrtc.so.12 --exclude libhiprtc.so.6 --exclude libamdhip64.so.6 -w {dest_dir} {wheel}",
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index e28494cfa6..3946c292a6 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -169,7 +169,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         define_macros.append( (' _MSC_VER', None) )
         extra_compile_args.append('/EHsc')
     else:
-        extra_link_args += ['-Wl,-rpath,$ORIGIN/lib']
+        extra_link_args += ['-Wl']
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++']
             extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', f'@loader_path/{openmm_lib_path}']

From 22cd17faf5574647c2f87f1affb73e319ab16ed9 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 17:56:03 +0300
Subject: [PATCH 15/75] osx fix

---
 wrappers/python/setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 3946c292a6..b4297eef71 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -172,7 +172,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         extra_link_args += ['-Wl']
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++']
-            extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', f'@loader_path/{openmm_lib_path}']
+            extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', '@loader_path/lib']
             if 'MACOSX_DEPLOYMENT_TARGET' not in os.environ and platform.processor() != 'arm':
                 extra_compile_args += ['-mmacosx-version-min=10.7']
                 extra_link_args += ['-mmacosx-version-min=10.7']

From 93290a25f13a5ad9fabd619b85a0fb733881e7dd Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 17:57:36 +0300
Subject: [PATCH 16/75] cleanup

---
 wrappers/python/setup.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index b4297eef71..1440c76854 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -169,7 +169,6 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         define_macros.append( (' _MSC_VER', None) )
         extra_compile_args.append('/EHsc')
     else:
-        extra_link_args += ['-Wl']
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++']
             extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', '@loader_path/lib']

From 91d1e4da669f63517bda43c65f20d5be9b506919 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 18:07:55 +0300
Subject: [PATCH 17/75] rpath for linux

---
 wrappers/python/setup.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 1440c76854..669303cd66 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -169,6 +169,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
         define_macros.append( (' _MSC_VER', None) )
         extra_compile_args.append('/EHsc')
     else:
+        extra_link_args += ['-Wl,-rpath,$ORIGIN/lib']
         if platform.system() == 'Darwin':
             extra_compile_args += ['-stdlib=libc++']
             extra_link_args += ['-stdlib=libc++', '-Wl', '-rpath', '@loader_path/lib']

From 0cd5007a268974d30ef8187e31b917765e01f450 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 19:14:35 +0300
Subject: [PATCH 18/75] test file paths relative to the test folder

---
 wrappers/python/tests/TestAmberInpcrdFile.py  |  15 ++-
 wrappers/python/tests/TestAmberPrmtopFile.py  |  38 +++---
 wrappers/python/tests/TestCharmmFiles.py      | 125 +++++++++---------
 .../python/tests/TestCheckpointReporter.py    |   6 +-
 wrappers/python/tests/TestDcdFile.py          |  10 +-
 wrappers/python/tests/TestDesmondDMSFile.py   |  10 +-
 wrappers/python/tests/TestForceField.py       |  50 +++----
 wrappers/python/tests/TestGenerators.py       |   4 +-
 wrappers/python/tests/TestGromacsGroFile.py   |   5 +-
 wrappers/python/tests/TestGromacsTopFile.py   |  32 +++--
 wrappers/python/tests/TestIntegrators.py      |  18 ++-
 wrappers/python/tests/TestModeller.py         |  22 +--
 .../python/tests/TestNumpyCompatibility.py    |   5 +-
 wrappers/python/tests/TestPdbFile.py          |  16 ++-
 wrappers/python/tests/TestPdbReporter.py      |  11 +-
 wrappers/python/tests/TestPdbxFile.py         |  21 +--
 wrappers/python/tests/TestPickle.py           |   8 +-
 wrappers/python/tests/TestSimulation.py       |  18 ++-
 .../python/tests/TestStateDataReporter.py     |   3 +-
 wrappers/python/tests/TestTopology.py         |   6 +-
 wrappers/python/tests/TestXtcFile.py          |  17 ++-
 21 files changed, 253 insertions(+), 187 deletions(-)

diff --git a/wrappers/python/tests/TestAmberInpcrdFile.py b/wrappers/python/tests/TestAmberInpcrdFile.py
index c93d3687e6..a1aa863964 100644
--- a/wrappers/python/tests/TestAmberInpcrdFile.py
+++ b/wrappers/python/tests/TestAmberInpcrdFile.py
@@ -1,3 +1,4 @@
+import os
 import unittest
 from validateConstraints import *
 from openmm.app import *
@@ -15,13 +16,15 @@ def compareByElement(array1, array2, cmp):
         cmp(x, y)
 
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestAmberInpcrdFile(unittest.TestCase):
     """Test the Amber inpcrd file parser"""
 
     def test_CrdVelBox(self):
         """ Test parsing ASCII restarts with crds, vels, and box """
         cmp = self.assertAlmostEqual
-        inpcrd = AmberInpcrdFile('systems/crds_vels_box.rst7')
+        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crds_vels_box.rst7'))
         self.assertEqual(len(inpcrd.positions), 2101)
         compareByElement(inpcrd.positions[-1].value_in_unit(angstroms),
                          [3.5958082, 8.4176792, -8.2954064], cmp)
@@ -35,7 +38,7 @@ def test_NetCDF(self):
         """ Test NetCDF restart file parsing """
         cmp = self.assertAlmostEqual
 
-        inpcrd = AmberInpcrdFile('systems/amber.ncrst')
+        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'amber.ncrst'))
         self.assertEqual(len(inpcrd.positions), 2101)
         compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
                          [6.82122492718229, 6.6276250662042, -8.51668999892245],
@@ -48,24 +51,24 @@ def test_NetCDF(self):
 
     def test_CrdBox(self):
         """ Test parsing ASCII restarts with only crds and box """
-        inpcrd = AmberInpcrdFile('systems/crds_box.rst7')
+        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crds_box.rst7'))
         self.assertEqual(len(inpcrd.positions), 18660)
         self.assertTrue(inpcrd.velocities is None)
         self.assertTrue(inpcrd.boxVectors is not None)
 
     def test_CrdVel(self):
-        inpcrd = AmberInpcrdFile('systems/crds_vels.rst7')
+        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crds_vels.rst7'))
         self.assertTrue(inpcrd.boxVectors is None)
         self.assertTrue(inpcrd.velocities is not None)
 
     def test_CrdOnly(self):
-        inpcrd = AmberInpcrdFile('systems/crdsonly.rst7')
+        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crdsonly.rst7'))
         self.assertTrue(inpcrd.boxVectors is None)
         self.assertTrue(inpcrd.velocities is None)
 
     def test_CrdBoxTruncoct(self):
         # Check that the box vectors come out correct.
-        inpcrd = AmberInpcrdFile('systems/tz2.truncoct.rst7')
+        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'tz2.truncoct.rst7'))
         ac = Vec3(42.4388485, 0.0, 0.0) * angstroms
         bc = Vec3(-14.146281691908937, 40.011730483685835, 0.0) * angstroms
         cc = Vec3(-14.146281691908937, -20.0058628205162, 34.651176446201672) * angstroms
diff --git a/wrappers/python/tests/TestAmberPrmtopFile.py b/wrappers/python/tests/TestAmberPrmtopFile.py
index 5f8678542d..4e9e769bc5 100644
--- a/wrappers/python/tests/TestAmberPrmtopFile.py
+++ b/wrappers/python/tests/TestAmberPrmtopFile.py
@@ -7,17 +7,19 @@
 from openmm.unit import *
 import openmm.app.element as elem
 
-inpcrd1 = AmberInpcrdFile('systems/alanine-dipeptide-explicit.inpcrd')
-inpcrd3 = AmberInpcrdFile('systems/ff14ipq.rst7')
-inpcrd4 = AmberInpcrdFile('systems/Mg_water.inpcrd')
-inpcrd7 = AmberInpcrdFile('systems/18protein.rst7')
-prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
-prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
-prmtop3 = AmberPrmtopFile('systems/ff14ipq.parm7', periodicBoxVectors=inpcrd3.boxVectors)
-prmtop4 = AmberPrmtopFile('systems/Mg_water.prmtop', periodicBoxVectors=inpcrd4.boxVectors)
-prmtop5 = AmberPrmtopFile('systems/tz2.truncoct.parm7')
-prmtop6 = AmberPrmtopFile('systems/gaffwat.parm7')
-prmtop7 = AmberPrmtopFile('systems/18protein.parm7', periodicBoxVectors=inpcrd7.boxVectors)
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
+inpcrd1 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.inpcrd'))
+inpcrd3 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'ff14ipq.rst7'))
+inpcrd4 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'Mg_water.inpcrd'))
+inpcrd7 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', '18protein.rst7'))
+prmtop1 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.prmtop'))
+prmtop2 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.prmtop'))
+prmtop3 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'ff14ipq.parm7'), periodicBoxVectors=inpcrd3.boxVectors)
+prmtop4 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'Mg_water.prmtop'), periodicBoxVectors=inpcrd4.boxVectors)
+prmtop5 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'tz2.truncoct.parm7'))
+prmtop6 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'gaffwat.parm7'))
+prmtop7 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', '18protein.parm7'), periodicBoxVectors=inpcrd7.boxVectors)
 
 class TestAmberPrmtopFile(unittest.TestCase):
 
@@ -307,14 +309,14 @@ def test_ImplicitSolventForces(self):
         nonbondedMethod = [NoCutoff, CutoffNonPeriodic, CutoffNonPeriodic, NoCutoff, NoCutoff]
         salt = [0.0, 0.0, 0.5, 0.5, 0.0]*(moles/liter)
         file = ['HCT_NoCutoff', 'OBC1_NonPeriodic', 'OBC2_NonPeriodic_Salt', 'GBn_NoCutoff_Salt', 'GBn2_NoCutoff']
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         for i in range(5):
             system = prmtop2.createSystem(implicitSolvent=solventType[i], nonbondedMethod=nonbondedMethod[i], implicitSolventSaltConc=salt[i])
             integrator = VerletIntegrator(0.001)
             context = Context(system, integrator, Platform.getPlatform("Reference"))
             context.setPositions(pdb.positions)
             state1 = context.getState(getForces=True)
-            with open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml') as infile:
+            with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit-forces', file[i]+'.xml')) as infile:
                 state2 = XmlSerializer.deserialize(infile.read())
             for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
                 diff = norm(f1-f2)
@@ -375,8 +377,8 @@ def test_with_dcd_reporter(self):
 
     def testChamber(self):
         """Test a prmtop file created with Chamber."""
-        prmtop = AmberPrmtopFile('systems/ala3_solv.parm7')
-        crd = CharmmCrdFile('systems/ala3_solv.crd')
+        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'ala3_solv.parm7'))
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
         system = prmtop.createSystem()
         for i,f in enumerate(system.getForces()):
             f.setForceGroup(i)
@@ -414,8 +416,8 @@ def testGBneckRadii(self):
 
     def testNucleicGBParametes(self):
         """Test that correct GB parameters are used for nucleic acids."""
-        prmtop = AmberPrmtopFile('systems/DNA_mbondi3.prmtop')
-        inpcrd = AmberInpcrdFile('systems/DNA_mbondi3.inpcrd')
+        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'DNA_mbondi3.prmtop'))
+        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'DNA_mbondi3.inpcrd'))
         sanderEnergy = [-19223.87993545, -19527.40433175, -19788.1070698]
         for solvent, expectedEnergy in zip([OBC2, GBn, GBn2], sanderEnergy):
             system = prmtop.createSystem(implicitSolvent=solvent, gbsaModel=None)
@@ -456,7 +458,7 @@ def testAmberCMAP(self):
 
     def testEPConstraints(self):
         """Test different types of constraints when using extra particles"""
-        prmtop = AmberPrmtopFile('systems/peptide_with_tip4p.prmtop')
+        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'peptide_with_tip4p.prmtop'))
         for constraints in (HBonds, AllBonds):
             system = prmtop.createSystem(constraints=constraints)
             integrator = VerletIntegrator(0.001*picoseconds)
diff --git a/wrappers/python/tests/TestCharmmFiles.py b/wrappers/python/tests/TestCharmmFiles.py
index 7ac43e13a4..a66943a13c 100644
--- a/wrappers/python/tests/TestCharmmFiles.py
+++ b/wrappers/python/tests/TestCharmmFiles.py
@@ -14,6 +14,9 @@
 else:
     from cStringIO import StringIO
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestCharmmFiles(unittest.TestCase):
 
     """Test the GromacsTopFile.createSystem() method."""
@@ -22,12 +25,13 @@ def setUp(self):
         """Set up the tests by loading the input files."""
 
         # alanine tripeptide; no waters
-        self.psf_c = CharmmPsfFile('systems/ala_ala_ala.psf')
-        self.psf_x = CharmmPsfFile('systems/ala_ala_ala.xpsf')
-        self.psf_v = CharmmPsfFile('systems/ala_ala_ala.vpsf')
+        self.psf_c = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.psf'))
+        self.psf_x = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.xpsf'))
+        self.psf_v = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.vpsf'))
         self.params = CharmmParameterSet(
-                            'systems/charmm22.rtf', 'systems/charmm22.par')
-        self.pdb = PDBFile('systems/ala_ala_ala.pdb')
+                            os.path.join(curr_dir, 'systems', 'charmm22.rtf'),
+                            os.path.join(curr_dir, 'systems', 'charmm22.par'))
+        self.pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
 
     def test_NonbondedMethod(self):
         """Test both non-periodic methods for the systems"""
@@ -103,9 +107,9 @@ def test_HydrogenMass(self):
     def test_DrudeMass(self):
         """Test that setting the mass of Drude particles works correctly."""
 
-        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
-        crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
-        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'))
         system = psf.createSystem(params, drudeMass=0)
         trueMass = [system.getParticleMass(i) for i in range(system.getNumParticles())]
         drudeMass = 0.3*amu
@@ -130,10 +134,10 @@ def test_DrudeMass(self):
     def test_NBFIX(self):
         """Tests CHARMM systems with NBFIX Lennard-Jones modifications"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv.psf', unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500)*angstroms)
-        crd = CharmmCrdFile('systems/ala3_solv.crd')
-        params = CharmmParameterSet('systems/par_all36_prot.prm',
-                                    'systems/toppar_water_ions.str')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv.psf'), unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500)*angstroms)
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_prot.prm'),
+                                    os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
 
         # Turn off charges so we only test the Lennard-Jones energies
         for a in psf.atom_list:
@@ -154,9 +158,11 @@ def test_NBFIX(self):
     def test_NBFIX14(self):
         """Tests CHARMM systems with NBFIX modifications to 1-4 interactions"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/chl1.psf')
-        crd = CharmmCrdFile('systems/chl1.crd')
-        params = CharmmParameterSet('systems/par_all36_lipid.prm', 'systems/par_all36_cgenff.prm', 'systems/toppar_all36_lipid_cholesterol.str')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'chl1.psf'))
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'chl1.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_lipid.prm'),
+                                   os.path.join(curr_dir, 'systems', 'par_all36_cgenff.prm'),
+                                   os.path.join(curr_dir, 'systems', 'toppar_all36_lipid_cholesterol.str'))
 
         # Turn off charges so we only test the Lennard-Jones energies
         for a in psf.atom_list:
@@ -178,9 +184,10 @@ def test_NBFIX14(self):
     def test_NBThole(self):
         """Tests CHARMM system with NBTHole"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/cyt-gua-cyt.psf')
-        crd = CharmmCrdFile('systems/cyt-gua-cyt.crd')
-        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str','systems/toppar_drude_nucleic_acid_2017b.str')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'cyt-gua-cyt.psf'))
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'cyt-gua-cyt.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'),
+                                   os.path.join(curr_dir, 'systems', 'toppar_drude_nucleic_acid_2017b.str'))
         # Box dimensions (cubic box)
         psf.setBox(30.0*angstroms, 30.0*angstroms, 30.0*angstroms)
 
@@ -197,7 +204,7 @@ def test_NBThole(self):
 
     def test_PSFSetUnitCellDimensions(self):
         """Test that setting the box via unit cell dimensions works correctly."""
-        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
 
         # Orthorhombic
         psf.setBox(2.1*nanometer, 2.3*nanometer, 2.4*nanometer)
@@ -228,9 +235,9 @@ def test_PSFSetUnitCellDimensions(self):
     def test_Drude(self):
         """Test CHARMM systems with Drude force field"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
-        crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
-        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'))
         # Box dimensions (cubic box)
         psf.setBox(33.2*angstroms, 33.2*angstroms, 33.2*angstroms)
 
@@ -248,10 +255,10 @@ def test_Drude(self):
     def test_Lonepair(self):
         """Test the lonepair facilities, in particular the colinear type of lonepairs"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/chlb_cgenff.psf')
-        crd = CharmmCrdFile('systems/chlb_cgenff.crd')
-        params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
-                                    'systems/par_all36_cgenff.prm')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'chlb_cgenff.psf'))
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'chlb_cgenff.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'top_all36_cgenff.rtf'),
+                                   os.path.join(curr_dir, 'systems', 'par_all36_cgenff.prm'))
         plat = Platform.getPlatform('Reference')
         system = psf.createSystem(params)
         con = Context(system, VerletIntegrator(2*femtoseconds), plat)
@@ -270,7 +277,7 @@ def test_Lonepair(self):
 
     def test_InsCode(self):
         """ Test the parsing of PSF files that contain insertion codes in their residue numbers """
-        psf = CharmmPsfFile('systems/4TVP-dmj_wat-ion.psf')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', '4TVP-dmj_wat-ion.psf'))
         self.assertEqual(len(list(psf.topology.atoms())), 66264)
         self.assertEqual(len(list(psf.topology.residues())), 20169)
         self.assertEqual(len(list(psf.topology.bonds())), 46634)
@@ -278,11 +285,11 @@ def test_InsCode(self):
     def testSystemOptions(self):
         """ Test various options in CharmmPsfFile.createSystem """
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv.psf',
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv.psf'),
                             periodicBoxVectors=(Vec3(32.7119500, 0, 0)*angstroms, Vec3(0, 32.9959600, 0)*angstroms, Vec3(0, 0, 33.0071500)*angstroms))
-        crd = CharmmCrdFile('systems/ala3_solv.crd')
-        params = CharmmParameterSet('systems/par_all36_prot.prm',
-                                    'systems/toppar_water_ions.str')
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_prot.prm'),
+                                   os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
 
         # Check some illegal options
         self.assertRaises(ValueError, lambda:
@@ -314,10 +321,10 @@ def test_ImplicitSolventForces(self):
             context = Context(system, integrator, Platform.getPlatform("Reference"))
             context.setPositions(self.pdb.positions)
             state1 = context.getState(getForces=True)
-            #out = open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml', 'w')
+            #out = open(os.path.join(curr_dir, 'systems', 'ala-ala-ala-implicit-forces', file[i]+'.xml'), 'w')
             #out.write(XmlSerializer.serialize(state1))
             #out.close()
-            with open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml') as xml:
+            with open(os.path.join(curr_dir, 'systems', 'ala-ala-ala-implicit-forces', file[i]+'.xml')) as xml:
                 state2 = XmlSerializer.deserialize(xml.read())
             for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
                 diff = norm(f1-f2)
@@ -326,11 +333,11 @@ def test_ImplicitSolventForces(self):
     def test_PermissiveRead(self):
         """Compare permissive and strict reading of Charmm parameters"""
 
-        psf = CharmmPsfFile('systems/5dhfr_cube.psf')
-        pdb = PDBFile('systems/5dhfr_cube.pdb')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', '5dhfr_cube.psf'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', '5dhfr_cube.pdb'))
 
-        params_strict     = CharmmParameterSet('systems/par_all22_prot_with_mass.inp')
-        params_permissive = CharmmParameterSet('systems/par_all22_prot.inp', permissive=True)
+        params_strict     = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all22_prot_with_mass.inp'))
+        params_permissive = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all22_prot.inp'), permissive=True)
         # Box dimensions (found from bounding box)
         psf.setBox(62.23*angstroms, 62.23*angstroms, 62.23*angstroms)
 
@@ -361,7 +368,7 @@ def test_PermissiveRead(self):
     
     def test_Impropers(self):
         """Test CHARMM improper torsions."""
-        psf = CharmmPsfFile('systems/improper.psf')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'improper.psf'))
         system = psf.createSystem(self.params)
         force = [f for f in system.getForces() if isinstance(f, CustomTorsionForce)][0]
         group = force.getForceGroup()
@@ -508,7 +515,7 @@ def test_Residues(self):
         hoh = ["O", "H1", "H2"]
         pot = ["POT"]
         cla = ["CLA"]
-        psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'charmm-solvated', 'isa_wat.3_kcl.m14.psf'))
         for residue in psf.topology.residues():
             atoms = [atom.name for atom in residue.atoms()]
             if residue.name == "M14":
@@ -525,11 +532,11 @@ def test_Residues(self):
     def test_NoLongRangeCorrection(self):
         """Test that long range correction is disabled."""
         parameters = CharmmParameterSet(
-            'systems/charmm-solvated/envi.str',
-            'systems/charmm-solvated/m14.rtf',
-            'systems/charmm-solvated/m14.prm'
+            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'envi.str'),
+            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.rtf'),
+            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.prm')
         )
-        psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'charmm-solvated', 'isa_wat.3_kcl.m14.psf'))
         psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
         system = psf.createSystem(parameters, nonbondedMethod=PME)
         for force in system.getForces():
@@ -541,20 +548,20 @@ def test_NoLongRangeCorrection(self):
     def test_NoPsfWarning(self):
         """Test that PSF warning is not thrown."""
         parameters = CharmmParameterSet(
-            'systems/charmm-solvated/envi.str',
-            'systems/charmm-solvated/m14.rtf',
-            'systems/charmm-solvated/m14.prm'
+            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'envi.str'),
+            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.rtf'),
+            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.prm')
         )
         with warnings.catch_warnings():
             warnings.simplefilter("error", CharmmPSFWarning)
-            psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
+            psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'charmm-solvated', 'isa_wat.3_kcl.m14.psf'))
             psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
             psf.createSystem(parameters, nonbondedMethod=PME)
 
     def test_NBXMod(self):
         """Test that all values of NBXMod are interpreted correctly."""
-        crd = CharmmCrdFile('systems/ala_ala_ala.crd')
-        with open('systems/charmm22.par') as parfile:
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.crd'))
+        with open(os.path.join(curr_dir, 'systems', 'charmm22.par')) as parfile:
             par = parfile.read()
         # The following values were computed with CHARMM.
         modeEnergy = {0: 754318.20507, 1: 754318.20507, 2: 908.35224, 3: 59.65279, 4: -241.12856, 5: 39.13169}
@@ -562,7 +569,7 @@ def test_NBXMod(self):
             with tempfile.NamedTemporaryFile(suffix='.par', mode='w', delete=False) as parfile:
                 parfile.write(par.replace('nbxmod  5', 'nbxmod %d' % nbxmod))
                 parfile.close()
-                params = CharmmParameterSet('systems/charmm22.rtf', parfile.name)
+                params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'charmm22.rtf'), parfile.name)
                 os.remove(parfile.name)
             system = self.psf_c.createSystem(params, nonbondedMethod=NoCutoff)
             context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatform('Reference'))
@@ -572,9 +579,9 @@ def test_NBXMod(self):
 
     def test_Nonbonded_Exclusion(self):
         """Test that the 1-2, 1-3 and 1-4 pairs are correctly excluded or scaled."""
-        psf = CharmmPsfFile('systems/MoS2.psf')
-        pdb = PDBFile('systems/MoS2.pdb')
-        params = CharmmParameterSet('systems/MoS2.prm')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'MoS2.psf'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'MoS2.pdb'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'MoS2.prm'))
         system = psf.createSystem(params, nonbondedMethod=NoCutoff)
         context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
@@ -584,8 +591,8 @@ def test_Nonbonded_Exclusion(self):
 
     def test_Constraints(self):
         """Test that bond and angles constraints are correctly added into the system"""
-        psf = CharmmPsfFile('systems/water_methanol.psf')
-        params = CharmmParameterSet('systems/water_methanol.prm')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'water_methanol.psf'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'water_methanol.prm'))
         # the system is made of one water molecule and one methanol molecule
         hBonds_water = [[0, 1], [1, 2]]
         hAngles_water = [[0, 2]]
@@ -619,11 +626,11 @@ def test_Constraints(self):
     def test_Constraints_charmm(self):
         """Tests that CHARMM and OpenMM implementation of CHARMM force field produce the same constraints and energy"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv.psf',
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv.psf'),
                             unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500) * angstroms)
-        crd = CharmmCrdFile('systems/ala3_solv.crd')
-        params = CharmmParameterSet('systems/par_all36_prot.prm',
-                                    'systems/toppar_water_ions.str')
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_prot.prm'),
+                                   os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
         plat = Platform.getPlatform('Reference')
         system_charmm = psf.createSystem(params, nonbondedMethod=PME,
                                   nonbondedCutoff=8 * angstroms)
diff --git a/wrappers/python/tests/TestCheckpointReporter.py b/wrappers/python/tests/TestCheckpointReporter.py
index aac1e35582..7a4d35b2d4 100644
--- a/wrappers/python/tests/TestCheckpointReporter.py
+++ b/wrappers/python/tests/TestCheckpointReporter.py
@@ -5,12 +5,14 @@
 import openmm as mm
 from openmm import unit
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 
 class TestCheckpointReporter(unittest.TestCase):
     def setUp(self):
-        with open('systems/alanine-dipeptide-implicit.pdb') as f:
+        with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb')) as f:
             pdb = app.PDBFile(f)
-        forcefield = app.ForceField('amber99sbildn.xml')
+        forcefield = app.ForceField(os.path.join(curr_dir, 'systems', 'amber99sbildn.xml'))
         system = forcefield.createSystem(pdb.topology,
             nonbondedMethod=app.CutoffNonPeriodic, nonbondedCutoff=1.0*unit.nanometers,
             constraints=app.HBonds)
diff --git a/wrappers/python/tests/TestDcdFile.py b/wrappers/python/tests/TestDcdFile.py
index 048da3af73..42e8d19b0d 100644
--- a/wrappers/python/tests/TestDcdFile.py
+++ b/wrappers/python/tests/TestDcdFile.py
@@ -6,6 +6,8 @@
 from random import random
 import os
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 
 def _read_dcd_header(file):
     import struct
@@ -21,7 +23,7 @@ class TestDCDFile(unittest.TestCase):
     def test_dcd(self):
         """ Test the DCD file """
         fname = tempfile.mktemp(suffix='.dcd')
-        pdbfile = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         natom = len(list(pdbfile.topology.atoms()))
         with open(fname, 'wb') as f:
             dcd = app.DCDFile(f, pdbfile.topology, 0.001)
@@ -32,7 +34,7 @@ def test_dcd(self):
     def testLongTrajectory(self):
         """Test writing a trajectory that has more than 2^31 steps."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdbfile = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         natom = len(list(pdbfile.topology.atoms()))
         with open(fname, 'wb') as f:
             dcd = app.DCDFile(f, pdbfile.topology, 0.001, interval=1000000000)
@@ -43,7 +45,7 @@ def testLongTrajectory(self):
     def testAppend(self):
         """Test appending to an existing trajectory."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         
@@ -87,7 +89,7 @@ def testAppend(self):
     def testAtomSubset(self):
         """Test writing a DCD file containing a subset of atoms"""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
 
diff --git a/wrappers/python/tests/TestDesmondDMSFile.py b/wrappers/python/tests/TestDesmondDMSFile.py
index fbe7c0bb6c..9fede1a8b9 100644
--- a/wrappers/python/tests/TestDesmondDMSFile.py
+++ b/wrappers/python/tests/TestDesmondDMSFile.py
@@ -5,21 +5,23 @@
 from openmm.unit import *
 import openmm.app.element as elem
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestDesmondDMSFile(unittest.TestCase):
     def setUp(self):
         """Set up the tests by loading the input files."""
 
         # alanine dipeptide with explicit water
-        path = os.path.join(os.path.dirname(__file__), 'systems/alanine-dipeptide-explicit-amber99SBILDN-tip3p.dms')
+        path = os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit-amber99SBILDN-tip3p.dms')
         self.dms = DesmondDMSFile(path)
 
         #nabumetone OPLS force field
-        path = os.path.join(os.path.dirname(__file__), 'systems/bcd-nabumetone_lig.dms')
+        path = os.path.join(curr_dir, 'systems', 'bcd-nabumetone_lig.dms')
         self.dms_opls1 = DesmondDMSFile(path)
         
         #beta-cyclodextrin/nabumetone complex OPLS force field
-        path1 = os.path.join(os.path.dirname(__file__), 'systems/bcd-nabumetone_lig.dms')
-        path2 = os.path.join(os.path.dirname(__file__), 'systems/bcd-nabumetone_rcpt.dms')
+        path1 = os.path.join(curr_dir, 'systems', 'bcd-nabumetone_lig.dms')
+        path2 = os.path.join(curr_dir, 'systems', 'bcd-nabumetone_rcpt.dms')
         self.dms_opls2 = DesmondDMSFile([path1,path2])
     
     def test_NonbondedMethod(self):
diff --git a/wrappers/python/tests/TestForceField.py b/wrappers/python/tests/TestForceField.py
index 3b0376bf95..8c5c48ed5b 100644
--- a/wrappers/python/tests/TestForceField.py
+++ b/wrappers/python/tests/TestForceField.py
@@ -14,6 +14,9 @@
 import os
 import warnings
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method."""
 
@@ -23,13 +26,13 @@ def setUp(self):
 
         """
         # alanine dipeptide with explicit water
-        self.pdb1 = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         self.forcefield1 = ForceField('amber99sb.xml', 'tip3p.xml')
         self.topology1 = self.pdb1.topology
         self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))
 
         # alanine dipeptide with implicit water
-        self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        self.pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')
 
 
@@ -258,7 +261,7 @@ def test_DrudeMass(self):
         """Test that setting the mass of Drude particles works correctly."""
 
         forcefield = ForceField('charmm_polar_2013.xml')
-        pdb = PDBFile('systems/ala_ala_ala.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
         modeller = Modeller(pdb.topology, pdb.positions)
         modeller.addExtraParticles(forcefield)
         system = forcefield.createSystem(modeller.topology, drudeMass=0)
@@ -297,13 +300,13 @@ def test_UnusedArgs(self):
     def test_Forces(self):
         """Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
 
-        pdb = PDBFile('systems/lysozyme-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'lysozyme-implicit.pdb'))
         system = self.forcefield2.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001)
         context = Context(system, integrator)
         context.setPositions(pdb.positions)
         state1 = context.getState(getForces=True)
-        with open('systems/lysozyme-implicit-forces.xml') as input:
+        with open(os.path.join(curr_dir, 'systems', 'lysozyme-implicit-forces.xml')) as input:
             state2 = XmlSerializer.deserialize(input.read())
         numDifferences = 0
         for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
@@ -327,7 +330,7 @@ def test_ImplicitSolventForces(self):
             context.setPositions(self.pdb2.positions)
             state1 = context.getState(getForces=True)
             if file[i] is not None:
-                with open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml') as infile:
+                with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit-forces', file[i]+'.xml')) as infile:
                     state2 = XmlSerializer.deserialize(infile.read())
                 for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
                     diff = norm(f1-f2)
@@ -607,7 +610,7 @@ def test_residueMatcher(self):
         ff = ForceField(StringIO(xml))
 
         # Load a water box.
-        prmtop = AmberPrmtopFile('systems/water-box-216.prmtop')
+        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'water-box-216.prmtop'))
         top = prmtop.topology
         
         # Building a System should fail, because two templates match each residue.
@@ -1103,10 +1106,9 @@ def test_CMAPTorsionGeneratorMapAssignment(self):
     def test_LennardJonesGenerator(self):
         """ Test the LennardJones generator"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ions.psf')
-        pdb = PDBFile('systems/ions.pdb')
-        params = CharmmParameterSet('systems/toppar_water_ions.str'
-                                    )
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ions.psf'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ions.pdb'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
 
         # Box dimensions (found from bounding box)
         psf.setBox(12.009*angstroms,   12.338*angstroms,   11.510*angstroms)
@@ -1266,7 +1268,7 @@ def test_ImpropersOrdering(self):
  </PeriodicTorsionForce>
 </ForceField>
 """
-        pdb = PDBFile('systems/impropers_ordering_tetrapeptide.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'impropers_ordering_tetrapeptide.pdb'))
         # ff1 uses default ordering of impropers, ff2 uses "amber" for the one
         # problematic improper
         ff1 = ForceField('amber99sbildn.xml')
@@ -1316,7 +1318,7 @@ def test_ImpropersOrdering_smirnoff(self):
   </Residues>
 </ForceField>
 """
-        pdb = PDBFile('systems/formaldehyde.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'formaldehyde.pdb'))
         # ff1 uses default ordering of impropers, ff2 uses "amber" for the one
         # problematic improper
         ff = ForceField(StringIO(xml))
@@ -1335,7 +1337,7 @@ def test_ImpropersOrdering_smirnoff(self):
 
     def test_Disulfides(self):
         """Test that various force fields handle disulfides correctly."""
-        pdb = PDBFile('systems/bpti.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'bpti.pdb'))
         for ff in ['amber99sb.xml', 'amber14-all.xml', 'charmm36.xml', 'amberfb15.xml', 'amoeba2013.xml']:
             forcefield = ForceField(ff)
             system = forcefield.createSystem(pdb.topology)
@@ -1370,7 +1372,7 @@ def test_IdenticalTemplates(self):
 
     def test_CharmmPolar(self):
         """Test the CHARMM polarizable force field."""
-        pdb = PDBFile('systems/ala_ala_ala_drude.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala_drude.pdb'))
         pdb.topology.setUnitCellDimensions(Vec3(3, 3, 3))
         ff = ForceField('charmm_polar_2019.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1.2*nanometers)
@@ -1452,7 +1454,7 @@ def test_InitializationScript(self):
     def test_Glycam(self):
         """Test computing energy with GLYCAM."""
         ff = ForceField('amber14/protein.ff14SB.xml', 'amber14/GLYCAM_06j-1.xml')
-        pdb = PDBFile('systems/glycopeptide.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
         system = ff.createSystem(pdb.topology)
         for i, f in enumerate(system.getForces()):
             f.setForceGroup(i)
@@ -1474,7 +1476,7 @@ def test_Glycam(self):
 
     def test_CustomNonbondedGenerator(self):
         """ Test the CustomNonbondedForce generator"""
-        pdb = PDBFile('systems/ions.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ions.pdb'))
         xml = """
 <ForceField>
  <AtomTypes>
@@ -1520,7 +1522,7 @@ def test_CustomNonbondedGenerator(self):
         self.assertAlmostEqual(energy1, energy2)
 
     def test_OpcEnergy(self):
-        pdb = PDBFile('systems/opcbox.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'opcbox.pdb'))
         topology, positions = pdb.topology, pdb.positions
         self.assertEqual(len(positions), 864)
         forcefield = ForceField('opc.xml')
@@ -1554,7 +1556,7 @@ def test_OpcEnergy(self):
         self.assertTrue(abs(energy1 - energy2) < energy_tolerance)
 
     def test_Opc3Energy(self):
-        pdb = PDBFile('systems/opc3box.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'opc3box.pdb'))
         topology, positions = pdb.topology, pdb.positions
         self.assertEqual(len(positions), 648)
         forcefield = ForceField('opc3.xml')
@@ -1596,7 +1598,7 @@ def setUp(self):
 
         """
 
-        self.pdb1 = PDBFile('systems/amoeba-ion-in-water.pdb')
+        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'amoeba-ion-in-water.pdb'))
         self.forcefield1 = ForceField('amoeba2013.xml')
         self.topology1 = self.pdb1.topology
 
@@ -1670,14 +1672,14 @@ def test_RigidWater(self):
     def test_Forces(self):
         """Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
 
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         forcefield = ForceField('amoeba2013.xml', 'amoeba2013_gk.xml')
         system = forcefield.createSystem(pdb.topology, polarization='direct')
         integrator = VerletIntegrator(0.001)
         context = Context(system, integrator, Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         state1 = context.getState(getForces=True)
-        with open('systems/alanine-dipeptide-amoeba-forces.xml') as input:
+        with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-amoeba-forces.xml')) as input:
             state2 = XmlSerializer.deserialize(input.read())
         for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
             diff = norm(f1-f2)
@@ -1700,7 +1702,7 @@ def computeAmoeba18Energies(self, filename):
 
     def test_Amoeba18BPTI(self):
         """Test that AMOEBA18 computes energies correctly for BPTI."""
-        energies = self.computeAmoeba18Energies('systems/bpti.pdb')
+        energies = self.computeAmoeba18Energies(os.path.join(curr_dir, 'systems', 'bpti.pdb'))
 
         # Compare to values computed with Tinker.
 
@@ -1717,7 +1719,7 @@ def test_Amoeba18BPTI(self):
 
     def test_Amoeba18Nucleic(self):
         """Test that AMOEBA18 computes energies correctly for DNA and RNA."""
-        energies = self.computeAmoeba18Energies('systems/nucleic.pdb')
+        energies = self.computeAmoeba18Energies(os.path.join(curr_dir, 'systems', 'nucleic.pdb'))
 
         # Compare to values computed with Tinker.
 
diff --git a/wrappers/python/tests/TestGenerators.py b/wrappers/python/tests/TestGenerators.py
index 8a67347cfa..28506267f6 100644
--- a/wrappers/python/tests/TestGenerators.py
+++ b/wrappers/python/tests/TestGenerators.py
@@ -13,12 +13,14 @@
 import os
 import warnings
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestGenerators(unittest.TestCase):
     """Test the various generators found in forcefield.py."""
 
     def setUp(self):
         # alanine dipeptide with implicit water
-        self.pdb1 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
 
 
     def test_CustomHbondGenerator(self):
diff --git a/wrappers/python/tests/TestGromacsGroFile.py b/wrappers/python/tests/TestGromacsGroFile.py
index b18107bde0..2413362465 100644
--- a/wrappers/python/tests/TestGromacsGroFile.py
+++ b/wrappers/python/tests/TestGromacsGroFile.py
@@ -3,13 +3,16 @@
 from openmm import *
 from openmm.unit import *
 import openmm.app.element as elem
+import os
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestGromacsGroFile(unittest.TestCase):
     """Test the Gromacs GRO file parser"""
  
     def test_Triclinic(self):
         """Test parsing a file that describes a triclinic box."""
-        gro = GromacsGroFile('systems/triclinic.gro')
+        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'triclinic.gro'))
         self.assertEqual(len(gro.positions), 8)
         expectedPositions = [
             Vec3(1.744, 2.788, 3.162),
diff --git a/wrappers/python/tests/TestGromacsTopFile.py b/wrappers/python/tests/TestGromacsTopFile.py
index 08ab6ecb2c..9d6bc3ef45 100644
--- a/wrappers/python/tests/TestGromacsTopFile.py
+++ b/wrappers/python/tests/TestGromacsTopFile.py
@@ -6,9 +6,13 @@
 from openmm.app.gromacstopfile import _defaultGromacsIncludeDir
 import openmm.app.element as elem
 from numpy.testing import assert_allclose
+import os
 
 GROMACS_INCLUDE = _defaultGromacsIncludeDir()
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 @unittest.skipIf(not os.path.exists(GROMACS_INCLUDE), 'GROMACS is not installed')
 class TestGromacsTopFile(unittest.TestCase):
 
@@ -18,7 +22,7 @@ def setUp(self):
         """Set up the tests by loading the input files."""
 
         # alanine dipeptide with explicit water
-        self.top1 = GromacsTopFile('systems/explicit.top', unitCellDimensions=Vec3(6.223, 6.223, 6.223)*nanometers)
+        self.top1 = GromacsTopFile(os.path.join(curr_dir, 'systems', 'explicit.top'), unitCellDimensions=Vec3(6.223, 6.223, 6.223)*nanometers)
 
     def test_NonbondedMethod(self):
         """Test all six options for the nonbondedMethod parameter."""
@@ -38,8 +42,8 @@ def test_NonbondedMethod(self):
 
     def test_ff99SBILDN(self):
         """ Test Gromacs topology #define replacement as used in ff99SB-ILDN """
-        top = GromacsTopFile('systems/aidilnaaaaa.top')
-        gro = GromacsGroFile('systems/aidilnaaaaa.gro')
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'aidilnaaaaa.top'))
+        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'aidilnaaaaa.gro'))
         system = top.createSystem()
         for force in system.getForces():
             if isinstance(force, PeriodicTorsionForce):
@@ -52,8 +56,8 @@ def test_ff99SBILDN(self):
 
     def test_SMOG(self):
         """ Test to ensure that SMOG models can be run without problems """
-        top = GromacsTopFile('systems/2ci2.pdb.top')
-        gro = GromacsGroFile('systems/2ci2.pdb.gro')
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', '2ci2.pdb.top'))
+        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', '2ci2.pdb.gro'))
         system = top.createSystem()
 
         context = Context(system, VerletIntegrator(1*femtosecond),
@@ -64,8 +68,8 @@ def test_SMOG(self):
 
     def test_ionic(self):
         """Test simulating an ionic liquid"""
-        gro = GromacsGroFile('systems/ionic.gro')
-        top = GromacsTopFile('systems/ionic.top', periodicBoxVectors=gro.getPeriodicBoxVectors())
+        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'ionic.gro'))
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'ionic.top'), periodicBoxVectors=gro.getPeriodicBoxVectors())
         system = top.createSystem(nonbondedMethod=PME, nonbondedCutoff=1.2)
         for f in system.getForces():
             if isinstance(f, CustomNonbondedForce):
@@ -94,7 +98,7 @@ def test_Cutoff(self):
 
     def test_SwitchingFunction(self):
         """Test using a switching function."""
-        top = GromacsTopFile('systems/ionic.top')
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'ionic.top'))
         for distance in (None, 0.8*nanometers):
             system = top.createSystem(nonbondedMethod=CutoffNonPeriodic, switchDistance=distance)
             for f in system.getForces():
@@ -158,8 +162,8 @@ def test_HydrogenMass(self):
     def test_VirtualParticle(self):
         """Test virtual particle works correctly."""
 
-        top = GromacsTopFile('systems/bnz.top')
-        gro = GromacsGroFile('systems/bnz.gro')
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'bnz.top'))
+        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'bnz.gro'))
         for atom in top.topology.atoms():
             if atom.name.startswith('C'):
                 self.assertEqual(elem.carbon, atom.element)
@@ -182,7 +186,7 @@ def test_VirtualParticle(self):
 
     def test_Vsite3Func1(self):
         """Test a three particle virtual site."""
-        top = GromacsTopFile('systems/tip4pew.top')
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'tip4pew.top'))
         system = top.createSystem()
         self.assertEqual(3, system.getNumConstraints())
         self.assertTrue(system.isVirtualSite(3))
@@ -197,7 +201,7 @@ def test_Vsite3Func1(self):
 
     def test_Vsite3Func4(self):
         """Test a three particle virtual site."""
-        top = GromacsTopFile('systems/tip5p.top')
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'tip5p.top'))
         system = top.createSystem()
         self.assertEqual(3, system.getNumConstraints())
         for i in (3, 4):
@@ -217,8 +221,8 @@ def test_Vsite3Func4(self):
     def test_GROMOS(self):
         """Test a system using the GROMOS 54a7 force field."""
 
-        top = GromacsTopFile('systems/1ppt.top')
-        gro = GromacsGroFile('systems/1ppt.gro')
+        top = GromacsTopFile(os.path.join(curr_dir, 'systems', '1ppt.top'))
+        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', '1ppt.gro'))
         system = top.createSystem()
         for i, f in enumerate(system.getForces()):
             f.setForceGroup(i)
diff --git a/wrappers/python/tests/TestIntegrators.py b/wrappers/python/tests/TestIntegrators.py
index cff603b4d2..7855ab805a 100644
--- a/wrappers/python/tests/TestIntegrators.py
+++ b/wrappers/python/tests/TestIntegrators.py
@@ -6,6 +6,10 @@
 from openmm.app import *
 from openmm.unit import *
 import math, random
+import os
+
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestIntegrators(unittest.TestCase):
     """Test Python Integrator classes"""
@@ -13,7 +17,7 @@ class TestIntegrators(unittest.TestCase):
     def testMTSIntegratorExplicit(self):
         """Test the MTS integrator on an explicit solvent system"""
         # Create a periodic solvated system with PME
-        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -100,7 +104,7 @@ def testMTSIntegratorConstraints(self):
     def testBadGroups(self):
         """Test the MTS integrator with bad force group substeps."""
         # Create a periodic solvated system with PME
-        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -124,7 +128,7 @@ def testBadGroups(self):
     def testMTSLangevinIntegrator(self):
         """Test the MTSLangevinIntegrator on an explicit solvent system"""
         # Create a periodic solvated system with PME
-        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -188,7 +192,7 @@ def get_final_velocities(nsubsteps):
 
     def testNoseHooverIntegrator(self):
         """Test partial thermostating in the NoseHooverIntegrator (only API)"""
-        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -203,9 +207,9 @@ def testNoseHooverIntegrator(self):
     def testDrudeNoseHooverIntegrator(self):
         """Test the DrudeNoseHooverIntegrator"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
-        crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
-        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str')
+        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
+        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.crd'))
+        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'))
         # Box dimensions (cubic box)
         psf.setBox(33.2*angstroms, 33.2*angstroms, 33.2*angstroms)
 
diff --git a/wrappers/python/tests/TestModeller.py b/wrappers/python/tests/TestModeller.py
index 33d085a715..1e75b5ca13 100644
--- a/wrappers/python/tests/TestModeller.py
+++ b/wrappers/python/tests/TestModeller.py
@@ -6,29 +6,33 @@
 from openmm.app import *
 from openmm import *
 from openmm.unit import *
+import os
 
 if sys.version_info >= (3, 0):
     from io import StringIO
 else:
     from cStringIO import StringIO
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestModeller(unittest.TestCase):
     """ Test the Modeller class. """
 
     def setUp(self):
         # load the alanine dipeptide pdb file
-        self.pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        self.pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         self.topology_start = self.pdb.topology
         self.positions = self.pdb.positions
         self.forcefield = ForceField('amber10.xml', 'tip3p.xml')
 
         # load the T4-lysozyme-L99A receptor pdb file
-        self.pdb2 = PDBFile('systems/lysozyme-implicit.pdb')
+        self.pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'lysozyme-implicit.pdb'))
         self.topology_start2 = self.pdb2.topology
         self.positions2 = self.pdb2.positions
 
         # load the metallothionein pdb file
-        self.pdb3 =  PDBFile('systems/1T2Y.pdb')
+        self.pdb3 =  PDBFile(os.path.join(curr_dir, 'systems', '1T2Y.pdb'))
         self.topology_start3 = self.pdb3.topology
         self.positions3 = self.pdb3.positions
 
@@ -134,7 +138,7 @@ def test_add(self):
         """ Test the add() method. """
 
         # load the methanol-box pdb file
-        pdb2 = PDBFile('systems/methanol-box.pdb')
+        pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'methanol-box.pdb'))
         topology_toAdd = pdb2.topology
         positions_toAdd = pdb2.positions
 
@@ -969,7 +973,7 @@ def test_addHydrogenspH11(self):
 
     def test_addHydrogensGlycam(self):
         """Test adding hydrogens for GLYCAM."""
-        pdb = PDBFile('systems/glycopeptide.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
         Modeller.loadHydrogenDefinitions('glycam-hydrogens.xml')
         modeller = Modeller(pdb.topology, pdb.positions)
         hydrogens = [a for a in modeller.topology.atoms() if a.element == element.hydrogen]
@@ -987,7 +991,7 @@ def test_addHydrogensGlycam(self):
 
     def test_addSpecificHydrogens(self):
         """Test specifying exactly which hydrogens to add."""
-        pdb = PDBFile('systems/glycopeptide.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
         variants = [None]*pdb.topology.getNumResidues()
         for residue in pdb.topology.residues():
             if residue.name != 'ALA':
@@ -1185,7 +1189,7 @@ def test_multiSiteIon(self):
     def test_addMembrane(self):
         """Test adding a membrane to a realistic system."""
 
-        mol = PDBxFile('systems/gpcr.cif')
+        mol = PDBxFile(os.path.join(curr_dir, 'systems', 'gpcr.cif'))
         modeller = Modeller(mol.topology, mol.positions)
         ff = ForceField('amber14-all.xml', 'amber14/tip3p.xml')
 
@@ -1235,7 +1239,7 @@ def test_bondTypeAndOrderPreserved(self):
         """
 
         # Given: an isolated molecule
-        pdb = PDBFile("systems/alanine-dipeptide-implicit.pdb")
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         topology, positions = pdb.topology, pdb.positions
         topology.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5) * nanometers)
         # with some bonds carrying type and order information
@@ -1282,7 +1286,7 @@ def test_bondTypeAndOrderPreserved(self):
         self.assertIn((Double, 2.0), [(b.type, b.order) for b in modeller.topology.bonds()])
 
         # When (6): add a modeller (which also bears some bond info)
-        to_add = PDBFile('systems/methanol-box.pdb')
+        to_add = PDBFile(os.path.join(curr_dir, 'systems', 'methanol-box.pdb'))
         topology_to_add = to_add.topology
         positions_to_add = to_add.positions
         # add a dummy bond to the "to_add" system to check that it also is preserved
diff --git a/wrappers/python/tests/TestNumpyCompatibility.py b/wrappers/python/tests/TestNumpyCompatibility.py
index 46b55a6ba0..7f7fb5a8d5 100644
--- a/wrappers/python/tests/TestNumpyCompatibility.py
+++ b/wrappers/python/tests/TestNumpyCompatibility.py
@@ -2,6 +2,7 @@
 from openmm import app
 import openmm as mm
 from openmm import unit
+import os
 try:
     import numpy as np
     NUMPY_IMPORT_FAILED = False
@@ -9,11 +10,13 @@
     NUMPY_IMPORT_FAILED = True
 
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 @unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyCompatibility(unittest.TestCase):
 
     def setUp(self):
-        prmtop = app.AmberPrmtopFile('systems/water-box-216.prmtop')
+        prmtop = app.AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'water-box-216.prmtop'))
 
         system = prmtop.createSystem(nonbondedMethod=app.PME,
                                      nonbondedCutoff=0.9*unit.nanometers,
diff --git a/wrappers/python/tests/TestPdbFile.py b/wrappers/python/tests/TestPdbFile.py
index 430ce3b048..d1ee6022c9 100644
--- a/wrappers/python/tests/TestPdbFile.py
+++ b/wrappers/python/tests/TestPdbFile.py
@@ -5,6 +5,10 @@
 from openmm.unit import *
 import openmm.app.element as elem
 from io import StringIO
+import os
+
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 
 class TestPdbFile(unittest.TestCase):
@@ -12,7 +16,7 @@ class TestPdbFile(unittest.TestCase):
 
     def test_Triclinic(self):
         """Test parsing a file that describes a triclinic box."""
-        pdb = PDBFile('systems/triclinic.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'triclinic.pdb'))
         self.assertEqual(len(pdb.positions), 8)
         expectedPositions = [
             Vec3(1.744, 2.788, 3.162),
@@ -56,7 +60,7 @@ def compareFiles(pdb1, pdb2):
                 self.assertEqual(atom1.name, atom2.name)
                 self.assertEqual(atom1.residue.name, atom2.residue.name)
 
-        pdb1 = PDBFile('systems/triclinic.pdb')
+        pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'triclinic.pdb'))
 
         # First try writing to an open file object.
 
@@ -78,13 +82,13 @@ def compareFiles(pdb1, pdb2):
 
     def test_BinaryStream(self):
         """Test reading a stream that was opened in binary mode."""
-        with open('systems/triclinic.pdb', 'rb') as infile:
+        with open(os.path.join(curr_dir, 'systems', 'triclinic.pdb'), 'rb') as infile:
             pdb = PDBFile(infile)
         self.assertEqual(len(pdb.positions), 8)
 
     def test_ExtraParticles(self):
         """Test reading, and writing and re-reading of a file containing extra particle atoms."""
-        pdb = PDBFile('systems/tip5p.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'tip5p.pdb'))
         for atom in pdb.topology.atoms():
             if atom.index > 2:
                 self.assertEqual(None, atom.element)
@@ -99,7 +103,7 @@ def test_ExtraParticles(self):
     def test_AltLocs(self):
         """Test reading a file that includes AltLocs"""
         for filename in ['altlocs.pdb', 'altlocs2.pdb']:
-            pdb = PDBFile(f'systems/{filename}')
+            pdb = PDBFile(os.path.join(curr_dir, 'systems', filename))
             self.assertEqual(1, pdb.topology.getNumResidues())
             self.assertEqual(19, pdb.topology.getNumAtoms())
             self.assertEqual(19, len(pdb.positions))
@@ -107,7 +111,7 @@ def test_AltLocs(self):
 
     def test_FormalCharges(self):
         """Test reading, and writing and re-reading of a file containing formal charges."""
-        pdb = PDBFile('systems/formal-charges.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'formal-charges.pdb'))
         for atom in pdb.topology.atoms():
             if atom.index == 8:
                 self.assertEqual(+1, atom.formalCharge)
diff --git a/wrappers/python/tests/TestPdbReporter.py b/wrappers/python/tests/TestPdbReporter.py
index 68bc4b84c7..c117749fd3 100644
--- a/wrappers/python/tests/TestPdbReporter.py
+++ b/wrappers/python/tests/TestPdbReporter.py
@@ -7,6 +7,9 @@
 import os
 import gc
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 def assertVecAlmostEqual(p1, p2, tol=1e-7):
     unit = p1.unit
     p1 = p1.value_in_unit(unit)
@@ -19,7 +22,7 @@ def assertVecAlmostEqual(p1, p2, tol=1e-7):
 
 class TestPDBReporter(unittest.TestCase):
     def setUp(self):
-        self.pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        self.pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         self.forcefield = app.ForceField('amber99sbildn.xml','tip3p.xml')
         self.system = self.forcefield.createSystem(self.pdb.topology, nonbondedMethod=app.CutoffNonPeriodic, constraints=app.HBonds)
 
@@ -117,7 +120,7 @@ def testBondSubset(self):
 
         # use a testcase that has CONECT records in the input pdb file
         ff = app.ForceField('amber14/protein.ff14SB.xml', 'amber14/GLYCAM_06j-1.xml','amber14/tip3pfb.xml')
-        pdb = app.PDBFile('systems/glycopeptide.pdb')
+        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
 
         # add in water molecules
         modeller = app.Modeller(pdb.topology, pdb.positions)
@@ -157,7 +160,7 @@ def testBondSubset(self):
 
 class TestPDBxReporter(unittest.TestCase):
     def setUp(self):
-        self.pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        self.pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         self.forcefield = app.ForceField('amber99sbildn.xml','tip3p.xml')
         self.system = self.forcefield.createSystem(self.pdb.topology, nonbondedMethod=app.CutoffNonPeriodic, constraints=app.HBonds)
 
@@ -255,7 +258,7 @@ def testBondSubset(self):
 
         # use a testcase that has CONECT records in the input pdb file
         ff = app.ForceField('amber14/protein.ff14SB.xml', 'amber14/GLYCAM_06j-1.xml','amber14/tip3pfb.xml')
-        pdb = app.PDBFile('systems/glycopeptide.pdb')
+        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
 
         # add in water molecules
         modeller = app.Modeller(pdb.topology, pdb.positions)
diff --git a/wrappers/python/tests/TestPdbxFile.py b/wrappers/python/tests/TestPdbxFile.py
index 711c5739c7..c1b7de6063 100644
--- a/wrappers/python/tests/TestPdbxFile.py
+++ b/wrappers/python/tests/TestPdbxFile.py
@@ -7,13 +7,16 @@
 import os
 from io import StringIO
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestPdbxFile(unittest.TestCase):
     """Test the PDBx/mmCIF file parser"""
 
     def test_FormatConversion(self):
         """Test conversion from PDB to PDBx"""
 
-        mol = PDBFile('systems/ala_ala_ala.pdb')
+        mol = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
         with tempfile.TemporaryDirectory() as tempdir:
             filename = os.path.join(tempdir, 'temp.pdbx')
             PDBxFile.writeFile(mol.topology, mol.positions, filename, keepIds=True)
@@ -25,7 +28,7 @@ def test_FormatConversion(self):
 
     def test_Triclinic(self):
         """Test parsing a file that describes a triclinic box."""
-        pdb = PDBxFile('systems/triclinic.pdbx')
+        pdb = PDBxFile(os.path.join(curr_dir, 'systems', 'triclinic.pdbx'))
         self.assertEqual(len(pdb.positions), 8)
         expectedPositions = [
             Vec3(1.744, 2.788, 3.162),
@@ -66,11 +69,11 @@ def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
 
     def testReporterImplicit(self):
         """ Tests the PDBxReporter without PBC """
-        parm = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
+        parm = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.prmtop'))
         system = parm.createSystem()
         sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
                          Platform.getPlatform('Reference'))
-        sim.context.setPositions(PDBFile('systems/alanine-dipeptide-implicit.pdb').getPositions())
+        sim.context.setPositions(PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb')).getPositions())
         sim.reporters.append(PDBxReporter('test.cif', 1))
         sim.step(10)
         pdb = PDBxFile('test.cif')
@@ -98,11 +101,11 @@ def assertAlmostEqualVec(self, vec1, vec2, *args, **kwargs):
 
     def testReporterExplicit(self):
         """ Tests the PDBxReporter with PBC """
-        parm = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
+        parm = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.prmtop'))
         system = parm.createSystem(nonbondedCutoff=1.0, nonbondedMethod=PME)
         sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
                          Platform.getPlatform('Reference'))
-        orig_pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        orig_pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         sim.context.setPositions(orig_pdb.getPositions())
         sim.context.setPeriodicBoxVectors(*parm.topology.getPeriodicBoxVectors())
         sim.reporters.append(PDBxReporter('test.cif', 1))
@@ -132,7 +135,7 @@ def testReporterExplicit(self):
 
     def testBonds(self):
         """Test reading and writing a file that includes bonds."""
-        pdb = PDBFile('systems/methanol_ions.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'methanol_ions.pdb'))
         output = StringIO()
         PDBxFile.writeFile(pdb.topology, pdb.positions, output)
         input = StringIO(output.getvalue())
@@ -146,7 +149,7 @@ def testBonds(self):
 
     def testMultiChain(self):
         """Test reading and writing a file that includes multiple chains"""
-        cif_ori = PDBxFile('systems/multichain.pdbx')
+        cif_ori = PDBxFile(os.path.join(curr_dir, 'systems', 'multichain.pdbx'))
 
         output = StringIO()
         PDBxFile.writeFile(cif_ori.topology, cif_ori.positions, output, keepIds=True)
@@ -162,7 +165,7 @@ def testMultiChain(self):
 
     def testInsertionCodes(self):
         """Test reading a file that uses insertion codes."""
-        pdbx = PDBxFile('systems/insertions.pdbx')
+        pdbx = PDBxFile(os.path.join(curr_dir, 'systems', 'insertions.pdbx'))
         residues = list(pdbx.topology.residues())
         self.assertEqual(7, len(residues))
         names = ['PHE', 'ASP', 'LYS', 'ILE', 'LYS', 'ASN', 'TRP']
diff --git a/wrappers/python/tests/TestPickle.py b/wrappers/python/tests/TestPickle.py
index b019aa114b..eade637963 100644
--- a/wrappers/python/tests/TestPickle.py
+++ b/wrappers/python/tests/TestPickle.py
@@ -8,6 +8,10 @@
 import openmm.app.forcefield as forcefield
 import copy
 import pickle
+import os
+
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestPickle(unittest.TestCase):
     """Pickling / deepcopy of OpenMM objects."""
@@ -18,13 +22,13 @@ def setUp(self):
 
         """
         # alanine dipeptide with explicit water
-        self.pdb1 = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         self.forcefield1 = ForceField('amber99sb.xml', 'tip3p.xml')
         self.topology1 = self.pdb1.topology
         self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))
 
         # alalnine dipeptide with implicit water
-        self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        self.pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')
 
     def check_copy(self, object, object_copy):
diff --git a/wrappers/python/tests/TestSimulation.py b/wrappers/python/tests/TestSimulation.py
index 68ba979670..b6b7797836 100644
--- a/wrappers/python/tests/TestSimulation.py
+++ b/wrappers/python/tests/TestSimulation.py
@@ -4,13 +4,17 @@
 from openmm import *
 from openmm.app import *
 from openmm.unit import *
+import os
+
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestSimulation(unittest.TestCase):
     """Test the Simulation class"""
 
     def testCheckpointing(self):
         """Test that checkpointing works correctly."""
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -44,7 +48,7 @@ def testCheckpointing(self):
 
     def testLoadFromXML(self):
         """ Test creating a Simulation from XML files """
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -67,7 +71,7 @@ def testLoadFromXML(self):
 
     def testSaveState(self):
         """Test that saving States works correctly."""
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -100,7 +104,7 @@ def testSaveState(self):
 
     def testStep(self):
         """Test the step() method."""
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -123,7 +127,7 @@ def testStep(self):
 
     def testRunForClockTime(self):
         """Test the runForClockTime() method."""
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -167,7 +171,7 @@ def testRunForClockTime(self):
 
     def testWrappedCoordinates(self):
         """Test generating reports with and without wrapped coordinates."""
-        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=CutoffPeriodic, constraints=HBonds)
         integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
@@ -199,7 +203,7 @@ def report(self, simulation, state):
 
     def testMinimizationReporter(self):
         """Test invoking a reporter during minimization."""
-        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
diff --git a/wrappers/python/tests/TestStateDataReporter.py b/wrappers/python/tests/TestStateDataReporter.py
index cacdae066b..d6df5283b4 100644
--- a/wrappers/python/tests/TestStateDataReporter.py
+++ b/wrappers/python/tests/TestStateDataReporter.py
@@ -5,10 +5,11 @@
 from openmm import unit
 import os
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestStateDataReporter(unittest.TestCase):
     def setUp(self):
-        self.pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        self.pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         self.forcefield = app.ForceField('amber99sbildn.xml')
         self.system = self.forcefield.createSystem(self.pdb.topology, nonbondedMethod=app.CutoffNonPeriodic, constraints=app.HBonds)
 
diff --git a/wrappers/python/tests/TestTopology.py b/wrappers/python/tests/TestTopology.py
index a2b6db23ee..936b51f620 100644
--- a/wrappers/python/tests/TestTopology.py
+++ b/wrappers/python/tests/TestTopology.py
@@ -5,12 +5,16 @@
 from openmm import *
 from openmm.unit import *
 import openmm.app.element as elem
+import os
 if sys.version_info >= (3, 0):
     from io import StringIO
 else:
     from cStringIO import StringIO
 
 
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
+
 class TestTopology(unittest.TestCase):
     """Test the Topology object"""
 
@@ -25,7 +29,7 @@ def check_pdbfile(self, pdbfilename, natoms, nres, nchains):
 
     def test_getters(self):
         """Test getters for number of atoms, residues, chains."""
-        self.check_pdbfile('systems/1T2Y.pdb', 271, 25, 1)
+        self.check_pdbfile(os.path.join(curr_dir, 'systems', '1T2Y.pdb'), 271, 25, 1)
 
     def test_bondtype_singleton(self):
         """ Tests that the bond types are really singletons """
diff --git a/wrappers/python/tests/TestXtcFile.py b/wrappers/python/tests/TestXtcFile.py
index 2d905ccf14..fcd118517f 100644
--- a/wrappers/python/tests/TestXtcFile.py
+++ b/wrappers/python/tests/TestXtcFile.py
@@ -10,12 +10,15 @@
 import numpy as np
 from openmm.app.internal.xtc_utils import read_xtc
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestXtcFile(unittest.TestCase):
     def test_xtc_triclinic(self):
         """Test the XTC file by writing a trajectory and reading it back. Using a triclinic box"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
+            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             pdbfile.topology.setUnitCellDimensions([10, 10, 10])
             natom = len(list(pdbfile.topology.atoms()))
@@ -57,7 +60,7 @@ def test_xtc_cubic(self):
         """Test the XTC file by writing a trajectory and reading it back. Using a cubic box"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
+            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             pdbfile.topology.setUnitCellDimensions([10, 10, 10])
             natom = len(list(pdbfile.topology.atoms()))
@@ -95,7 +98,7 @@ def test_xtc_box_from_topology(self):
         """Test the XTC file by writing a trajectory and reading it back. Letting the box be set from the topology"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
+            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             unitCell = mm.Vec3(random(), random(), random()) * unit.nanometers
             pdbfile.topology.setUnitCellDimensions(unitCell)
@@ -139,7 +142,7 @@ def test_xtc_small(self):
         """Test the XTC file by writing a trajectory and reading it back. Using a system size below the compression threshold"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile("systems/ions.pdb")
+            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'ions.pdb'))
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             pdbfile.topology.setUnitCellDimensions([10, 10, 10])
             natom = len(list(pdbfile.topology.atoms()))
@@ -181,7 +184,7 @@ def testLongTrajectory(self):
         """Test writing a trajectory that has more than 2^31 steps."""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
+            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
             natom = len(list(pdbfile.topology.atoms()))
             xtc = app.XTCFile(fname, pdbfile.topology, 0.001, interval=1000000000)
             for i in range(5):
@@ -196,7 +199,7 @@ def testAppend(self):
         """Test appending to an existing trajectory."""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdb = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
+            pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
             ff = app.ForceField("amber99sb.xml", "tip3p.xml")
             system = ff.createSystem(pdb.topology)
 
@@ -249,7 +252,7 @@ def testAtomSubset(self):
         """Test writing an XTC file containing a subset of atoms"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdb = app.PDBFile("systems/alanine-dipeptide-explicit.pdb")
+            pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
             ff = app.ForceField("amber99sb.xml", "tip3p.xml")
             system = ff.createSystem(pdb.topology)
 

From b9923947c8c02ee309b0e119be54114de4005f83 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 19:18:35 +0300
Subject: [PATCH 19/75] minor mistake

---
 wrappers/python/tests/TestCheckpointReporter.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/tests/TestCheckpointReporter.py b/wrappers/python/tests/TestCheckpointReporter.py
index 7a4d35b2d4..70fe152486 100644
--- a/wrappers/python/tests/TestCheckpointReporter.py
+++ b/wrappers/python/tests/TestCheckpointReporter.py
@@ -12,7 +12,7 @@ class TestCheckpointReporter(unittest.TestCase):
     def setUp(self):
         with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb')) as f:
             pdb = app.PDBFile(f)
-        forcefield = app.ForceField(os.path.join(curr_dir, 'systems', 'amber99sbildn.xml'))
+        forcefield = app.ForceField('amber99sbildn.xml')
         system = forcefield.createSystem(pdb.topology,
             nonbondedMethod=app.CutoffNonPeriodic, nonbondedCutoff=1.0*unit.nanometers,
             constraints=app.HBonds)

From 5a3f39f01b2ca0f5d8bf7d5211ee3dd96dbcb0bb Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 19:19:39 +0300
Subject: [PATCH 20/75] pytest run from main dir

---
 wrappers/python/pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 6dc30b944b..b130888631 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -36,14 +36,14 @@ build-backend = "setuptools.build_meta"
 [tool.cibuildwheel]
 skip = ["cp38-*", "pp*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
 test-requires = ["pytest"]
-test-command = "cd {project}/wrappers/python/tests && pytest ."
+test-command = "pytest {project}/wrappers/python/tests"
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
 environment-pass = ["ACCELERATOR", "OPENCL_PATH"]
 # container-engine = "docker; create_args: --gpus all"
 
 [tool.cibuildwheel.windows]
-test-command = "cd {project}\\wrappers\\python\\tests && pytest ."
+test-command = "pytest {project}\\wrappers\\python\\tests"
 
 [tool.cibuildwheel.linux]
 repair-wheel-command = [

From 4a5b441ed7ae21d9087f9dc501fce6fac47b319b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 7 Apr 2025 19:31:45 +0300
Subject: [PATCH 21/75] missing curr_dir

---
 wrappers/python/tests/TestForceField.py | 20 ++++++++++----------
 wrappers/python/tests/TestPatches.py    |  7 +++++--
 2 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/wrappers/python/tests/TestForceField.py b/wrappers/python/tests/TestForceField.py
index 8c5c48ed5b..2a19b06677 100644
--- a/wrappers/python/tests/TestForceField.py
+++ b/wrappers/python/tests/TestForceField.py
@@ -681,7 +681,7 @@ def simpleTemplateGenerator(forcefield, residue):
         #
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
         # Add the residue template generator.
@@ -703,7 +703,7 @@ def simpleTemplateGenerator(forcefield, residue):
         # Test all systems with separate ForceField objects.
         for test in tests:
             # Load the PDB file.
-            pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
+            pdb = PDBFile(os.path.join(curr_dir, 'systems', test['pdb_filename']))
             # Create a ForceField object.
             forcefield = ForceField(StringIO(simple_ffxml_contents))
             # Add the residue template generator.
@@ -719,7 +719,7 @@ def simpleTemplateGenerator(forcefield, residue):
         forcefield.registerTemplateGenerator(simpleTemplateGenerator)
         for test in tests:
             # Load the PDB file.
-            pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
+            pdb = PDBFile(os.path.join(curr_dir, 'systems', test['pdb_filename']))
             # Parameterize system.
             system = forcefield.createSystem(pdb.topology, nonbondedMethod=test['nonbondedMethod'])
             # TODO: Test energies are finite?
@@ -728,7 +728,7 @@ def test_getUnmatchedResidues(self):
         """Test retrieval of list of residues for which no templates are available."""
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
         # Get list of unmatched residues.
@@ -739,7 +739,7 @@ def test_getUnmatchedResidues(self):
         self.assertEqual(unmatched_residues[0].id, '163')
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('tip3p.xml')
         # Get list of unmatched residues.
@@ -757,7 +757,7 @@ def test_generateTemplatesForUnmatchedResidues(self):
         #
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'nacl-water.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('tip3p.xml')
         # Get list of unmatched residues.
@@ -800,7 +800,7 @@ def test_generateTemplatesForUnmatchedResidues(self):
         #
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
         # Get list of unique unmatched residues.
@@ -820,7 +820,7 @@ def test_getMatchingTemplates(self):
         """Test retrieval of list of templates that match residues in a topology."""
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml')
         # Get list of matching residue templates.
@@ -873,7 +873,7 @@ def test_Wildcard(self):
 
     def test_ScalingFactorCombining(self):
         """ Tests that FFs can be combined if their scaling factors are very close """
-        forcefield = ForceField('amber99sb.xml', os.path.join('systems', 'test_amber_ff.xml'))
+        forcefield = ForceField('amber99sb.xml', os.path.join(curr_dir, 'systems', 'test_amber_ff.xml'))
         # This would raise an exception if it didn't work
 
     def test_MultipleFilesandForceTags(self):
@@ -1251,7 +1251,7 @@ def test_IgnoreExternalBonds(self):
 
     def test_Includes(self):
         """Test using a ForceField that includes other files."""
-        forcefield = ForceField(os.path.join('systems', 'ff_with_includes.xml'))
+        forcefield = ForceField(os.path.join(curr_dir, 'systems', 'ff_with_includes.xml'))
         self.assertTrue(len(forcefield._atomTypes) > 10)
         self.assertTrue('spce-O' in forcefield._atomTypes)
         self.assertTrue('HOH' in forcefield._templates)
diff --git a/wrappers/python/tests/TestPatches.py b/wrappers/python/tests/TestPatches.py
index 1a3db2e322..d5cac60774 100644
--- a/wrappers/python/tests/TestPatches.py
+++ b/wrappers/python/tests/TestPatches.py
@@ -10,6 +10,9 @@
     from io import StringIO
 import os
 
+
+curr_dir = os.path.dirname(os.path.abspath(__file__))
+
 class TestPatches(unittest.TestCase):
     """Test ForceFields that use patches."""
 
@@ -260,7 +263,7 @@ def testAlaAlaAla(self):
  </NonbondedForce>
 </ForceField>"""
         ff = ForceField(StringIO(xml))
-        pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
         system = ff.createSystem(pdb.topology)
         nb = system.getForce(0)
         expectedCharges = [0.1414, 0.2719, 0.2719, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603, 0.5973, -0.5679,
@@ -270,7 +273,7 @@ def testAlaAlaAla(self):
             self.assertEqual(expectedCharges[i], nb.getParticleParameters(i)[0].value_in_unit(elementary_charge))
 
     def testDisulfidePatch(self):
-        pdb = PDBFile(os.path.join('systems', 'bpti.pdb'))
+        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'bpti.pdb'))
         ff = ForceField('amber99sb.xml')
         system1 = ff.createSystem(pdb.topology)
         

From 8b00683770e27fa1fe7847df8514a9fed257cc1b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 09:29:54 +0300
Subject: [PATCH 22/75] try installing the right CUDA version to set the path
 correctly

---
 .github/workflows/publish.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 264170d772..8c042c0dbc 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -58,6 +58,7 @@ jobs:
         if: matrix.os == 'windows-2019'
         id: cuda-toolkit
         with:
+          cuda: ${{ matrix.accelerator == 'cu118' && '11.8' || '12.4' }}
           method: "network"
           sub-packages: '["opencl"]'
 
@@ -87,8 +88,8 @@ jobs:
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           CUDA_VERSION: ${{ matrix.accelerator }}
           ACCELERATOR: ${{ matrix.accelerator }}
-          CIBW_BUILD: "cp310-*"
           OPENCL_PATH: "${{steps.cuda-toolkit.outputs.CUDA_PATH}}"
+          CIBW_BUILD: "cp310-*"
 
       - uses: actions/upload-artifact@v4
         with:

From 5872d4a90935c63f5e74b09816611ab4e071f24a Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 09:56:34 +0300
Subject: [PATCH 23/75] manually install opencl

---
 .github/workflows/publish.yml                      | 14 ++------------
 .../prepare_build_environment_windows.sh           |  8 +++++++-
 2 files changed, 9 insertions(+), 13 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 8c042c0dbc..7b62d191df 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -53,15 +53,6 @@ jobs:
         uses: ilammy/msvc-dev-cmd@v1
         if: matrix.os == 'windows-2019'
 
-      - name: "Install OpenCL"
-        uses: Jimver/cuda-toolkit@v0.2.16
-        if: matrix.os == 'windows-2019'
-        id: cuda-toolkit
-        with:
-          cuda: ${{ matrix.accelerator == 'cu118' && '11.8' || '12.4' }}
-          method: "network"
-          sub-packages: '["opencl"]'
-
       - name: "Install dependencies with choco"
         uses: crazy-max/ghaction-chocolatey@v3
         if: matrix.os == 'windows-2019'
@@ -75,7 +66,7 @@ jobs:
         env:
           CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
           CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
-          CUDA_VERSION: ${{ matrix.accelerator }}
+          # CUDA_VERSION: ${{ matrix.accelerator }}
           ACCELERATOR: ${{ matrix.accelerator }}
           CIBW_BUILD: "cp310-*"
 
@@ -86,9 +77,8 @@ jobs:
         env:
           CIBW_BEFORE_ALL_WINDOWS: "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
-          CUDA_VERSION: ${{ matrix.accelerator }}
+          # CUDA_VERSION: ${{ matrix.accelerator }}
           ACCELERATOR: ${{ matrix.accelerator }}
-          OPENCL_PATH: "${{steps.cuda-toolkit.outputs.CUDA_PATH}}"
           CIBW_BUILD: "cp310-*"
 
       - uses: actions/upload-artifact@v4
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 714ec53cff..78aed39aad 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -23,6 +23,12 @@ if [ "$ACCELERATOR" == "hip" ]; then
     rm HIP.exe
 fi
 
+# Download and extract OpenCL
+curl --netrc-optional -L -nv -o OpenCL-SDK.zip https://github.com/KhronosGroup/OpenCL-SDK/releases/download/v2024.10.24/OpenCL-SDK-v2024.10.24-Win-x64.zip
+unzip OpenCL-SDK.zip
+OPENCL_PATH="$(pwd)/OpenCL-SDK-v2024.10.24-Win-x64"
+
+
 # Configure build with Cmake
 mkdir -p build
 mkdir -p openmm-install
@@ -34,7 +40,7 @@ cmake -G "NMake Makefiles JOM" \
     -DCMAKE_CXX_COMPILER=cl.exe \
     -DCMAKE_C_COMPILER=cl.exe \
     -DOPENCL_INCLUDE_DIR="${OPENCL_PATH}/include" \
-    -DOPENCL_LIBRARY="${OPENCL_PATH}/lib/x64/OpenCL.lib" \
+    -DOPENCL_LIBRARY="${OPENCL_PATH}/lib/OpenCL.lib" \
     -DHIP_PLATFORM=amd \
     ..
 

From f43034ec4fab994f29e21bfd188ba2ee3e65eb3d Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 10:32:20 +0300
Subject: [PATCH 24/75] set CUDA_PATH on Windows builds

---
 .github/workflows/publish.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 7b62d191df..c3fac0ee81 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -66,7 +66,6 @@ jobs:
         env:
           CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
           CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
-          # CUDA_VERSION: ${{ matrix.accelerator }}
           ACCELERATOR: ${{ matrix.accelerator }}
           CIBW_BUILD: "cp310-*"
 
@@ -77,8 +76,8 @@ jobs:
         env:
           CIBW_BEFORE_ALL_WINDOWS: "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
-          # CUDA_VERSION: ${{ matrix.accelerator }}
           ACCELERATOR: ${{ matrix.accelerator }}
+          CUDA_PATH: ${{ matrix.accelerator == 'cu118' && 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8' || 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4' }}
           CIBW_BUILD: "cp310-*"
 
       - uses: actions/upload-artifact@v4

From e159b8c0c16ff88659217e4f9ad279160e186375 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 11:01:30 +0300
Subject: [PATCH 25/75] full workflow

---
 .github/workflows/publish.yml  | 84 ++++++++++++++++++++++++++++++++--
 .github/workflows/workflow.yml |  9 ++++
 2 files changed, 90 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/workflow.yml

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index c3fac0ee81..6fa465ea8d 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -3,7 +3,6 @@ name: Build wheels and publish
 on:
   workflow_dispatch:
   workflow_call:
-  push:
 
 jobs:
   build:
@@ -67,7 +66,6 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
           CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
           ACCELERATOR: ${{ matrix.accelerator }}
-          CIBW_BUILD: "cp310-*"
 
       - name: Build wheels
         if: matrix.os == 'windows-2019'
@@ -78,9 +76,89 @@ jobs:
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           ACCELERATOR: ${{ matrix.accelerator }}
           CUDA_PATH: ${{ matrix.accelerator == 'cu118' && 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8' || 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4' }}
-          CIBW_BUILD: "cp310-*"
 
       - uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.accelerator }}-cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
+
+  publish-to-accelera-pypi:
+    name: >-
+      Publish Python 🐍 distribution 📦 to Acellera PyPI
+    needs:
+      - build
+    runs-on: ubuntu-latest
+    permissions: # Needed for GCP authentication
+      contents: "read"
+      id-token: "write"
+    strategy:
+      fail-fast: false
+      matrix:
+        accelerator: [cpu, cu118, cu124, hip]
+
+    steps:
+      - uses: actions/checkout@v4 # Needed for GCP authentication for some reason
+
+      - name: Set up Cloud SDK
+        uses: google-github-actions/auth@v2
+        with:
+          workload_identity_provider: ${{ secrets.GCP_WORKLOAD_IDENTITY_PROVIDER }}
+          service_account: ${{ secrets.GCP_PYPI_SERVICE_ACCOUNT }}
+
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          pattern: "${{ matrix.accelerator }}-cibw-wheels*"
+          path: dist/
+          merge-multiple: true
+
+      - name: Publish distribution 📦 to Acellera PyPI
+        run: |
+          pip install build twine keyring keyrings.google-artifactregistry-auth
+          pip install -U packaging
+          twine upload --repository-url https://us-central1-python.pkg.dev/pypi-packages-455608/${{ matrix.accelerator }} dist/* --verbose --skip-existing
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+      - build
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write # IMPORTANT: mandatory for sigstore
+
+    steps:
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          path: dist/
+          merge-multiple: true
+
+      - name: Sign the dists with Sigstore
+        uses: sigstore/gh-action-sigstore-python@v3.0.0
+        with:
+          inputs: >-
+            ./dist/*.whl
+
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        run: >-
+          gh release create
+          "$GITHUB_REF_NAME"
+          --repo "$GITHUB_REPOSITORY"
+          --notes ""
+
+      - name: Upload artifact signatures to GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ github.token }}
+        # Upload to GitHub Release using the `gh` CLI.
+        # `dist/` contains the built packages, and the
+        # sigstore-produced signatures and certificates.
+        run: >-
+          gh release upload
+          "$GITHUB_REF_NAME" dist/**
+          --repo "$GITHUB_REPOSITORY"
diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
new file mode 100644
index 0000000000..45eab0be08
--- /dev/null
+++ b/.github/workflows/workflow.yml
@@ -0,0 +1,9 @@
+name: Whole
+
+on: [push]
+
+jobs:
+  publish:
+    if: startsWith(github.event.ref, 'refs/tags/v')
+    uses: ./.github/workflows/publish.yml
+    secrets: inherit

From 865d989692f4f2210b029717e57f55bb3848c21b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 11:24:25 +0300
Subject: [PATCH 26/75] quick test with just 3.10

---
 .github/workflows/publish.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 6fa465ea8d..ea5b967e8f 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -66,6 +66,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
           CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
           ACCELERATOR: ${{ matrix.accelerator }}
+          CIBW_BUILD: "cp310-*"
 
       - name: Build wheels
         if: matrix.os == 'windows-2019'
@@ -76,6 +77,7 @@ jobs:
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           ACCELERATOR: ${{ matrix.accelerator }}
           CUDA_PATH: ${{ matrix.accelerator == 'cu118' && 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8' || 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4' }}
+          CIBW_BUILD: "cp310-*"
 
       - uses: actions/upload-artifact@v4
         with:

From 2ec36e4c1e7255e0fae70c21a6a6f45b8caf93a0 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 12:14:09 +0300
Subject: [PATCH 27/75] build all versions

---
 .github/workflows/publish.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index ea5b967e8f..6fa465ea8d 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -66,7 +66,6 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
           CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
           ACCELERATOR: ${{ matrix.accelerator }}
-          CIBW_BUILD: "cp310-*"
 
       - name: Build wheels
         if: matrix.os == 'windows-2019'
@@ -77,7 +76,6 @@ jobs:
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           ACCELERATOR: ${{ matrix.accelerator }}
           CUDA_PATH: ${{ matrix.accelerator == 'cu118' && 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8' || 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4' }}
-          CIBW_BUILD: "cp310-*"
 
       - uses: actions/upload-artifact@v4
         with:

From 20bc5d6ceae233803634855b802fe92813b128a6 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 12:57:44 +0300
Subject: [PATCH 28/75] can't use setuptools versioning since it will be
 inconsistent with the C++ version

---
 .github/workflows/publish.yml  | 2 ++
 CMakeLists.txt                 | 2 +-
 wrappers/python/pyproject.toml | 5 +----
 wrappers/python/setup.py       | 4 ++++
 4 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 6fa465ea8d..363acf7b76 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -66,6 +66,7 @@ jobs:
           CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
           CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
           ACCELERATOR: ${{ matrix.accelerator }}
+          VERSION_SUFFIX: "rc1"
 
       - name: Build wheels
         if: matrix.os == 'windows-2019'
@@ -76,6 +77,7 @@ jobs:
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           ACCELERATOR: ${{ matrix.accelerator }}
           CUDA_PATH: ${{ matrix.accelerator == 'cu118' && 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8' || 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4' }}
+          VERSION_SUFFIX: "rc1"
 
       - uses: actions/upload-artifact@v4
         with:
diff --git a/CMakeLists.txt b/CMakeLists.txt
index f7f6ffce49..1aae41d343 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -157,7 +157,7 @@ ENDIF (NOT CMAKE_CXX_FLAGS_RELEASE)
 SET(OPENMM_LIBRARY_NAME OpenMM)
 SET(OPENMM_MAJOR_VERSION 8)
 SET(OPENMM_MINOR_VERSION 2)
-SET(OPENMM_BUILD_VERSION 0)
+SET(OPENMM_BUILD_VERSION 1)
 
 ADD_DEFINITIONS(-DOPENMM_LIBRARY_NAME=${OPENMM_LIBRARY_NAME}
                 -DOPENMM_MAJOR_VERSION=${OPENMM_MAJOR_VERSION}
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index b130888631..bb3890c33f 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -18,9 +18,6 @@ dependencies = [
 "Bug Tracker" = "https://github.com/openmm/openmm/issues"
 "Download URL" = "https://openmm.org"
 
-[tool.setuptools_scm]
-root = "../.."
-
 [tool.setuptools.packages.find]
 include = ["openmm*"]
 
@@ -39,7 +36,7 @@ test-requires = ["pytest"]
 test-command = "pytest {project}/wrappers/python/tests"
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
-environment-pass = ["ACCELERATOR", "OPENCL_PATH"]
+environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 # container-engine = "docker; create_args: --gpus all"
 
 [tool.cibuildwheel.windows]
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 669303cd66..c882289192 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -126,6 +126,10 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                            build_info=BUILD_INFO):
     from setuptools import Extension
     setupKeywords = {}
+    setupKeywords["version"]           = "%s.%s.%s%s" % (major_version_num,
+                                                       minor_version_num,
+                                                       build_info,
+                                                       os.getenv('VERSION_SUFFIX', ''))
     setupKeywords["packages"]          = [
                                           "simtk",
                                           "simtk.unit",

From 2d7344c4475042b9d03169facc3329789f2471d0 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 16:18:25 +0300
Subject: [PATCH 29/75] add runtime requirements for CUDA packages

---
 wrappers/python/setup.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index c882289192..651b41d7c1 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -84,7 +84,6 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
     """
 
     cnt = """
-import os
 # THIS FILE IS GENERATED FROM OPENMM SETUP.PY
 short_version = '%(version)s'
 version = '%(version)s'
@@ -145,6 +144,15 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                                           "openmm.app.internal.pdbx.reader",
                                           "openmm.app.internal.pdbx.writer"]
 
+    setupKeywords["install_requires"] = ["numpy"]
+    if os.getenv("ACCELERATOR", "") in ("cu118", "cu124"):
+        cuda_ver = os.getenv("ACCELERATOR", "")[2:4]
+        setupKeywords["install_requires"] += [f'nvidia-cuda-runtime-cu{cuda_ver}',
+                                              f'nvidia-cuda-nvcc-cu{cuda_ver}',
+                                              f'nvidia-cuda-nvrtc-cu{cuda_ver}',
+                                              f'nvidia-cuda-cupti-cu{cuda_ver}',
+                                              f'nvidia-cufft-cu{cuda_ver}']
+
     define_macros = [('MAJOR_VERSION', major_version_num),
                      ('MINOR_VERSION', minor_version_num)]
 

From c46457a3f1d32ba3264b0545beebb66298bb4864 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Tue, 8 Apr 2025 18:35:08 +0300
Subject: [PATCH 30/75] get dependencies dynamically

---
 wrappers/python/pyproject.toml | 5 +----
 wrappers/python/setup.py       | 2 ++
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index bb3890c33f..054c9ab25a 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -5,13 +5,10 @@ authors = [{ name = "Peter Eastman", email = "peastman@stanford.edu" }]
 readme = "README.md"
 license = "PSF-2.0"
 requires-python = ">=3.8"
-dynamic = ["version"]
+dynamic = ["version", "dependencies"]
 classifiers = [
   "Programming Language :: Python :: 3",
 ]
-dependencies = [
-  "numpy"
-]
 
 [project.urls]
 "Homepage" = "https://openmm.org"
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 651b41d7c1..a0fd098990 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -85,6 +85,8 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
 
     cnt = """
 # THIS FILE IS GENERATED FROM OPENMM SETUP.PY
+from openmm import openmm_library_path
+
 short_version = '%(version)s'
 version = '%(version)s'
 full_version = '%(full_version)s'

From b53e180a9413a1a31bce243a4433d912ee8e2313 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 17 Apr 2025 12:56:03 +0300
Subject: [PATCH 31/75] cuda 12.6 releases

---
 .github/workflows/publish.yml                      |  6 +++++-
 .../prepare_build_environment_linux.sh             | 14 ++++++++++++++
 .../prepare_build_environment_windows.sh           |  7 +++++++
 3 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 363acf7b76..fb07d42e71 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -12,18 +12,22 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, ubuntu-24.04-arm, windows-2019, macos-latest]
-        accelerator: [cpu, cu118, cu124, hip]
+        accelerator: [cpu, cu118, cu124, cu126, hip]
         exclude:
           - os: ubuntu-24.04-arm
             accelerator: cu118
           - os: ubuntu-24.04-arm
             accelerator: cu124
+          - os: ubuntu-24.04-arm
+            accelerator: cu126
           - os: ubuntu-24.04-arm
             accelerator: hip
           - os: macos-latest
             accelerator: cu118
           - os: macos-latest
             accelerator: cu124
+          - os: macos-latest
+            accelerator: cu126
           - os: macos-latest
             accelerator: hip
 
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
index 260044592f..dd4e2c658e 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -34,6 +34,20 @@ if [ "$ACCELERATOR" == "cu124" ]; then
     export CUDA_HOME="/usr/local/cuda"
 fi
 
+if [ "$ACCELERATOR" == "cu126" ]; then
+    # Install CUDA 12.6
+    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
+
+    dnf install --setopt=obsoletes=0 -y \
+        cuda-compiler-12-6-12.6.3-1 \
+        cuda-libraries-12-6-12.6.3-1 \
+        cuda-libraries-devel-12-6-12.6.3-1
+
+    ln -s cuda-12.6 /usr/local/cuda
+
+    export CUDA_HOME="/usr/local/cuda"
+fi
+
 if [ "$ACCELERATOR" == "hip" ]; then
     # Install HIP 6.2
     dnf install -y https://repo.radeon.com/amdgpu-install/6.2.2/el/8.10/amdgpu-install-6.2.60202-1.el8.noarch.rpm
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 78aed39aad..3cbeba0112 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -17,6 +17,13 @@ if [ "$ACCELERATOR" == "cu124" ]; then
     rm cuda.exe
 fi
 
+if [ "$ACCELERATOR" == "cu126" ]; then
+    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.6"
+    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.6.0/local_installers/cuda_12.6.0_551.61_windows.exe
+    ./cuda.exe -s nvcc_12.6 nvrtc_12.6 nvrtc_dev_12.6 cudart_12.6 cufft_12.6 cufft_dev_12.6 cuda_profiler_api_12.6
+    rm cuda.exe
+fi
+
 if [ "$ACCELERATOR" == "hip" ]; then
     curl.exe --output HIP.exe --url https://download.amd.com/developer/eula/rocm-hub/AMD-Software-PRO-Edition-24.Q3-Win10-Win11-For-HIP.exe
     ./HIP.exe -install

From ac28a564d4486ac65ce44586e1e144120f40ae8d Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 17 Apr 2025 15:03:00 +0300
Subject: [PATCH 32/75] correct build

---
 .../cibuildwheel_support/prepare_build_environment_windows.sh   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 3cbeba0112..59631f16ee 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -19,7 +19,7 @@ fi
 
 if [ "$ACCELERATOR" == "cu126" ]; then
     CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.6"
-    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.6.0/local_installers/cuda_12.6.0_551.61_windows.exe
+    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.6.0/local_installers/cuda_12.6.0_560.76_windows.exe
     ./cuda.exe -s nvcc_12.6 nvrtc_12.6 nvrtc_dev_12.6 cudart_12.6 cufft_12.6 cufft_dev_12.6 cuda_profiler_api_12.6
     rm cuda.exe
 fi

From 9a6652453b588812ef7a66ca68c2c28e3317d5ab Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 17 Apr 2025 16:06:34 +0300
Subject: [PATCH 33/75] forgot the upload part

---
 .github/workflows/publish.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index fb07d42e71..2c43f30352 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -100,7 +100,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        accelerator: [cpu, cu118, cu124, hip]
+        accelerator: [cpu, cu118, cu124, cu126, hip]
 
     steps:
       - uses: actions/checkout@v4 # Needed for GCP authentication for some reason

From 9705b682a0f596c3c6ba68b8b7210c7ca8fe4b30 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 17 Apr 2025 16:23:44 +0300
Subject: [PATCH 34/75] add simtk also to the package

---
 wrappers/python/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 054c9ab25a..fb5317154e 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -16,7 +16,7 @@ classifiers = [
 "Download URL" = "https://openmm.org"
 
 [tool.setuptools.packages.find]
-include = ["openmm*"]
+include = ["openmm*", "simtk*"]
 
 
 # [tool.setuptools.exclude-package-data]

From 1284ed1afc66928f209a664c316f93da8b9bf0b3 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 24 Apr 2025 13:34:29 +0300
Subject: [PATCH 35/75] switch to CXX11_ABI=1 since pytorch also moved to it
 and we need to keep compatibility between the two for openmm-torch

---
 .../cibuildwheel_support/prepare_build_environment_linux.sh     | 2 +-
 wrappers/python/setup.py                                        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
index dd4e2c658e..81d807cdf0 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -60,7 +60,7 @@ mkdir -p openmm-install
 cd build
 cmake .. \
     -DCMAKE_INSTALL_PREFIX=openmm-install \
-    -DCMAKE_CXX_FLAGS='-D_GLIBCXX_USE_CXX11_ABI=0' \
+    -DCMAKE_CXX_FLAGS='-D_GLIBCXX_USE_CXX11_ABI=1' \
     -DOPENMM_BUILD_OPENCL_LIB=ON \
     -DOPENCL_INCLUDE_DIR=/usr/include/CL \
     -DOPENCL_LIBRARY=/usr/lib64/libOpenCL.so.1
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index a0fd098990..2ff27a8da7 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -175,7 +175,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     openmm_include_path = 'openmm/include'
     openmm_lib_path = 'openmm/lib'
 
-    extra_compile_args=['-std=c++11', '-D_GLIBCXX_USE_CXX11_ABI=0']
+    extra_compile_args=['-std=c++11', '-D_GLIBCXX_USE_CXX11_ABI=1']
     extra_link_args=[]
     if platform.system() == "Windows":
         define_macros.append( ('WIN32', None) )

From 527b9772d2192642edc32ab30f4f1a1bdb9b89ba Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 24 Apr 2025 13:48:46 +0300
Subject: [PATCH 36/75] cuda 12.8 release

---
 .github/workflows/publish.yml                        |  8 ++++----
 .../prepare_build_environment_linux.sh               | 12 ++++++------
 .../prepare_build_environment_windows.sh             |  8 ++++----
 3 files changed, 14 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 2c43f30352..8b9458e5c0 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -12,14 +12,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, ubuntu-24.04-arm, windows-2019, macos-latest]
-        accelerator: [cpu, cu118, cu124, cu126, hip]
+        accelerator: [cpu, cu118, cu124, cu128, hip]
         exclude:
           - os: ubuntu-24.04-arm
             accelerator: cu118
           - os: ubuntu-24.04-arm
             accelerator: cu124
           - os: ubuntu-24.04-arm
-            accelerator: cu126
+            accelerator: cu128
           - os: ubuntu-24.04-arm
             accelerator: hip
           - os: macos-latest
@@ -27,7 +27,7 @@ jobs:
           - os: macos-latest
             accelerator: cu124
           - os: macos-latest
-            accelerator: cu126
+            accelerator: cu128
           - os: macos-latest
             accelerator: hip
 
@@ -100,7 +100,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        accelerator: [cpu, cu118, cu124, cu126, hip]
+        accelerator: [cpu, cu118, cu124, cu128, hip]
 
     steps:
       - uses: actions/checkout@v4 # Needed for GCP authentication for some reason
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
index 81d807cdf0..ebcf7ea65d 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -34,16 +34,16 @@ if [ "$ACCELERATOR" == "cu124" ]; then
     export CUDA_HOME="/usr/local/cuda"
 fi
 
-if [ "$ACCELERATOR" == "cu126" ]; then
-    # Install CUDA 12.6
+if [ "$ACCELERATOR" == "cu128" ]; then
+    # Install CUDA 12.8
     dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
 
     dnf install --setopt=obsoletes=0 -y \
-        cuda-compiler-12-6-12.6.3-1 \
-        cuda-libraries-12-6-12.6.3-1 \
-        cuda-libraries-devel-12-6-12.6.3-1
+        cuda-compiler-12-8-12.8.1-1 \
+        cuda-libraries-12-8-12.8.1-1 \
+        cuda-libraries-devel-12-8-12.8.1-1
 
-    ln -s cuda-12.6 /usr/local/cuda
+    ln -s cuda-12.8 /usr/local/cuda
 
     export CUDA_HOME="/usr/local/cuda"
 fi
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 59631f16ee..e0503b2f65 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -17,10 +17,10 @@ if [ "$ACCELERATOR" == "cu124" ]; then
     rm cuda.exe
 fi
 
-if [ "$ACCELERATOR" == "cu126" ]; then
-    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.6"
-    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.6.0/local_installers/cuda_12.6.0_560.76_windows.exe
-    ./cuda.exe -s nvcc_12.6 nvrtc_12.6 nvrtc_dev_12.6 cudart_12.6 cufft_12.6 cufft_dev_12.6 cuda_profiler_api_12.6
+if [ "$ACCELERATOR" == "cu128" ]; then
+    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8"
+    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_572.61_windows.exe
+    ./cuda.exe -s nvcc_12.8 nvrtc_12.8 nvrtc_dev_12.8 cudart_12.8 cufft_12.8 cufft_dev_12.8 cuda_profiler_api_12.8
     rm cuda.exe
 fi
 

From e53385bab5162f1dc72274c625a68bb563d447fd Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 25 Apr 2025 10:34:58 +0300
Subject: [PATCH 37/75] more cuda versions to be compatible with pytorch
 releases

---
 .github/workflows/publish.yml                 |  9 +++++---
 .../prepare_build_environment_linux.sh        | 22 ++++++++++++-------
 .../prepare_build_environment_windows.sh      | 17 +++++++-------
 wrappers/python/setup.py                      |  2 +-
 4 files changed, 29 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 8b9458e5c0..cea30b8d00 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -12,12 +12,14 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, ubuntu-24.04-arm, windows-2019, macos-latest]
-        accelerator: [cpu, cu118, cu124, cu128, hip]
+        accelerator: [cpu, cu118, cu124, cu126, cu128, hip]
         exclude:
           - os: ubuntu-24.04-arm
             accelerator: cu118
           - os: ubuntu-24.04-arm
             accelerator: cu124
+          - os: ubuntu-24.04-arm
+            accelerator: cu126
           - os: ubuntu-24.04-arm
             accelerator: cu128
           - os: ubuntu-24.04-arm
@@ -26,6 +28,8 @@ jobs:
             accelerator: cu118
           - os: macos-latest
             accelerator: cu124
+          - os: macos-latest
+            accelerator: cu126
           - os: macos-latest
             accelerator: cu128
           - os: macos-latest
@@ -80,7 +84,6 @@ jobs:
           CIBW_BEFORE_ALL_WINDOWS: "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           ACCELERATOR: ${{ matrix.accelerator }}
-          CUDA_PATH: ${{ matrix.accelerator == 'cu118' && 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8' || 'C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4' }}
           VERSION_SUFFIX: "rc1"
 
       - uses: actions/upload-artifact@v4
@@ -100,7 +103,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        accelerator: [cpu, cu118, cu124, cu128, hip]
+        accelerator: [cpu, cu118, cu124, cu126, cu128, hip]
 
     steps:
       - uses: actions/checkout@v4 # Needed for GCP authentication for some reason
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
index ebcf7ea65d..2120cec828 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -18,9 +18,7 @@ if [ "$ACCELERATOR" == "cu118" ]; then
     ln -s cuda-11.8 /usr/local/cuda
 
     export CUDA_HOME="/usr/local/cuda"
-fi
-
-if [ "$ACCELERATOR" == "cu124" ]; then
+elif [ "$ACCELERATOR" == "cu124" ]; then
     # Install CUDA 12.4
     dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
 
@@ -32,9 +30,19 @@ if [ "$ACCELERATOR" == "cu124" ]; then
     ln -s cuda-12.4 /usr/local/cuda
 
     export CUDA_HOME="/usr/local/cuda"
-fi
+elif [ "$ACCELERATOR" == "cu126" ]; then
+    # Install CUDA 12.6
+    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
+
+    dnf install --setopt=obsoletes=0 -y \
+        cuda-compiler-12-6-12.6.3-1 \
+        cuda-libraries-12-6-12.6.3-1 \
+        cuda-libraries-devel-12-6-12.6.3-1
 
-if [ "$ACCELERATOR" == "cu128" ]; then
+    ln -s cuda-12.4 /usr/local/cuda
+
+    export CUDA_HOME="/usr/local/cuda"
+elif [ "$ACCELERATOR" == "cu128" ]; then
     # Install CUDA 12.8
     dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
 
@@ -46,9 +54,7 @@ if [ "$ACCELERATOR" == "cu128" ]; then
     ln -s cuda-12.8 /usr/local/cuda
 
     export CUDA_HOME="/usr/local/cuda"
-fi
-
-if [ "$ACCELERATOR" == "hip" ]; then
+elif [ "$ACCELERATOR" == "hip" ]; then
     # Install HIP 6.2
     dnf install -y https://repo.radeon.com/amdgpu-install/6.2.2/el/8.10/amdgpu-install-6.2.60202-1.el8.noarch.rpm
     dnf install -y rocm-device-libs hip-devel hip-runtime-amd hipcc
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index e0503b2f65..71ffbae87b 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -8,23 +8,22 @@ if [ "$ACCELERATOR" == "cu118" ]; then
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_522.06_windows.exe
     ./cuda.exe -s nvcc_11.8 nvrtc_11.8 nvrtc_dev_11.8 cudart_11.8 cufft_11.8 cufft_dev_11.8 cuda_profiler_api_11.8
     rm cuda.exe
-fi
-
-if [ "$ACCELERATOR" == "cu124" ]; then
+elif [ "$ACCELERATOR" == "cu124" ]; then
     CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
     ./cuda.exe -s nvcc_12.4 nvrtc_12.4 nvrtc_dev_12.4 cudart_12.4 cufft_12.4 cufft_dev_12.4 cuda_profiler_api_12.4
     rm cuda.exe
-fi
-
-if [ "$ACCELERATOR" == "cu128" ]; then
+elif [ "$ACCELERATOR" == "cu126" ]; then
+    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.6"
+    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.6.0/local_installers/cuda_12.6.0_560.76_windows.exe
+    ./cuda.exe -s nvcc_12.6 nvrtc_12.6 nvrtc_dev_12.6 cudart_12.6 cufft_12.6 cufft_dev_12.6 cuda_profiler_api_12.6
+    rm cuda.exe
+elif [ "$ACCELERATOR" == "cu128" ]; then
     CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_572.61_windows.exe
     ./cuda.exe -s nvcc_12.8 nvrtc_12.8 nvrtc_dev_12.8 cudart_12.8 cufft_12.8 cufft_dev_12.8 cuda_profiler_api_12.8
     rm cuda.exe
-fi
-
-if [ "$ACCELERATOR" == "hip" ]; then
+elif [ "$ACCELERATOR" == "hip" ]; then
     curl.exe --output HIP.exe --url https://download.amd.com/developer/eula/rocm-hub/AMD-Software-PRO-Edition-24.Q3-Win10-Win11-For-HIP.exe
     ./HIP.exe -install
     rm HIP.exe
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 2ff27a8da7..2a0f43b81b 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -147,7 +147,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                                           "openmm.app.internal.pdbx.writer"]
 
     setupKeywords["install_requires"] = ["numpy"]
-    if os.getenv("ACCELERATOR", "") in ("cu118", "cu124"):
+    if os.getenv("ACCELERATOR", "").startswith("cu"):
         cuda_ver = os.getenv("ACCELERATOR", "")[2:4]
         setupKeywords["install_requires"] += [f'nvidia-cuda-runtime-cu{cuda_ver}',
                                               f'nvidia-cuda-nvcc-cu{cuda_ver}',

From 485911ae4a60e1cff9b65452e6b990c3903dd2aa Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 25 Apr 2025 11:03:46 +0300
Subject: [PATCH 38/75] fix test file paths

---
 wrappers/python/tests/TestDcdFile.py  | 4 ++--
 wrappers/python/tests/TestPdbxFile.py | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/wrappers/python/tests/TestDcdFile.py b/wrappers/python/tests/TestDcdFile.py
index d2e9869f29..e7bdbc0696 100644
--- a/wrappers/python/tests/TestDcdFile.py
+++ b/wrappers/python/tests/TestDcdFile.py
@@ -133,7 +133,7 @@ def testAtomSubset(self):
     def testAppendAtomCountMismatch(self):
         """Test that appending to a DCD file with a different number of atoms raises an error."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
+        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
 
@@ -166,7 +166,7 @@ def testAppendAtomCountMismatch(self):
     def testAppendLongCommentBlock(self):
         """Test appending to an existing trajectory with a long comment block."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
+        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
 
diff --git a/wrappers/python/tests/TestPdbxFile.py b/wrappers/python/tests/TestPdbxFile.py
index 5ddd391009..38f0d6f43f 100644
--- a/wrappers/python/tests/TestPdbxFile.py
+++ b/wrappers/python/tests/TestPdbxFile.py
@@ -149,7 +149,7 @@ def testBonds(self):
 
     def testChemCompBonds(self):
         """Test creating bonds based on chem_comp_bond records."""
-        pdb = PDBxFile('systems/6mvz.cif')
+        pdb = PDBxFile(os.path.join(curr_dir, 'systems', '6mvz.cif'))
 
         def bondCount(res1, atom1, res2, atom2):
             count = 0

From 81a5b6df31dfb64437547977291aff0408829e9b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 28 Apr 2025 16:23:12 +0300
Subject: [PATCH 39/75] fix cuda detection on Windows

---
 .../prepare_build_environment_windows.sh         | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 71ffbae87b..dd10df9951 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -4,25 +4,33 @@ set -e
 set -x
 
 if [ "$ACCELERATOR" == "cu118" ]; then
-    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_522.06_windows.exe
     ./cuda.exe -s nvcc_11.8 nvrtc_11.8 nvrtc_dev_11.8 cudart_11.8 cufft_11.8 cufft_dev_11.8 cuda_profiler_api_11.8
     rm cuda.exe
+    # Move CUDA folder to a path without spaces
+    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8" /c/CUDA
+    export CUDA_PATH="/c/CUDA"
 elif [ "$ACCELERATOR" == "cu124" ]; then
-    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
     ./cuda.exe -s nvcc_12.4 nvrtc_12.4 nvrtc_dev_12.4 cudart_12.4 cufft_12.4 cufft_dev_12.4 cuda_profiler_api_12.4
     rm cuda.exe
+    # Move CUDA folder to a path without spaces
+    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4" /c/CUDA
+    export CUDA_PATH="/c/CUDA"
 elif [ "$ACCELERATOR" == "cu126" ]; then
-    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.6"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.6.0/local_installers/cuda_12.6.0_560.76_windows.exe
     ./cuda.exe -s nvcc_12.6 nvrtc_12.6 nvrtc_dev_12.6 cudart_12.6 cufft_12.6 cufft_dev_12.6 cuda_profiler_api_12.6
     rm cuda.exe
+    # Move CUDA folder to a path without spaces
+    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.6" /c/CUDA
+    export CUDA_PATH="/c/CUDA"
 elif [ "$ACCELERATOR" == "cu128" ]; then
-    CUDA_ROOT="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8"
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_572.61_windows.exe
     ./cuda.exe -s nvcc_12.8 nvrtc_12.8 nvrtc_dev_12.8 cudart_12.8 cufft_12.8 cufft_dev_12.8 cuda_profiler_api_12.8
     rm cuda.exe
+    # Move CUDA folder to a path without spaces
+    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8" /c/CUDA
+    export CUDA_PATH="/c/CUDA"
 elif [ "$ACCELERATOR" == "hip" ]; then
     curl.exe --output HIP.exe --url https://download.amd.com/developer/eula/rocm-hub/AMD-Software-PRO-Edition-24.Q3-Win10-Win11-For-HIP.exe
     ./HIP.exe -install

From d74f35335acad36a467104c440825f39c69ffc85 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 12:08:50 +0300
Subject: [PATCH 40/75] run tests from inside test folder

---
 .github/workflows/publish.yml  | 3 ---
 wrappers/python/pyproject.toml | 7 +++++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index cea30b8d00..7de2cab4f3 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -71,8 +71,6 @@ jobs:
         shell: bash -l {0}
         run: python -m cibuildwheel wrappers/python/ --output-dir wheelhouse
         env:
-          CIBW_BEFORE_ALL_LINUX: "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
-          CIBW_BEFORE_ALL_MACOS: "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
           ACCELERATOR: ${{ matrix.accelerator }}
           VERSION_SUFFIX: "rc1"
 
@@ -81,7 +79,6 @@ jobs:
         shell: cmd # Use cmd on Windows to avoid bash environment taking priority over MSVC variables
         run: python -m cibuildwheel wrappers/python/ --output-dir wheelhouse
         env:
-          CIBW_BEFORE_ALL_WINDOWS: "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           ACCELERATOR: ${{ matrix.accelerator }}
           VERSION_SUFFIX: "rc1"
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index fb5317154e..dc8a5ad4b4 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -30,21 +30,24 @@ build-backend = "setuptools.build_meta"
 [tool.cibuildwheel]
 skip = ["cp38-*", "pp*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
 test-requires = ["pytest"]
-test-command = "pytest {project}/wrappers/python/tests"
+test-command = "cd {project}/wrappers/python/tests; pytest"
 manylinux-x86_64-image = "manylinux_2_28"
 manylinux-aarch64-image = "manylinux_2_28"
 environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 # container-engine = "docker; create_args: --gpus all"
 
 [tool.cibuildwheel.windows]
-test-command = "pytest {project}\\wrappers\\python\\tests"
+before-all = "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
+test-command = "cd {project}/wrappers/python/tests; pytest"
 
 [tool.cibuildwheel.linux]
+before-all = "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"
 repair-wheel-command = [
   "auditwheel repair --exclude libOpenMM.so --exclude libOpenMMCUDA.so --exclude libOpenMMHIP.so --exclude libOpenMMOpenCL.so --exclude libOpenMMDrude.so --exclude libOpenMMAmoeba.so --exclude libOpenMMRPMD.so --exclude libOpenCL.so.1 --exclude libcuda.so.1 --exclude libcufft.so.11 --exclude libcufft.so.10 --exclude libnvrtc.so.11.2 --exclude libnvrtc.so.12 --exclude libhiprtc.so.6 --exclude libamdhip64.so.6 -w {dest_dir} {wheel}",
 ]
 
 [tool.cibuildwheel.macos]
+before-all = "wrappers/python/cibuildwheel_support/prepare_build_environment_osx.sh"
 repair-wheel-command = [
   "delocate-wheel --ignore-missing-dependencies --require-archs {delocate_archs} -w {dest_dir} -v {wheel}",
 ]
\ No newline at end of file

From ca87f331c2231e4bfdda1d3cb5a066e9f324bb72 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 12:09:51 +0300
Subject: [PATCH 41/75] undo path changes in OpenMM tests

---
 wrappers/python/tests/TestAmberInpcrdFile.py  |  15 +--
 wrappers/python/tests/TestAmberPrmtopFile.py  |  38 +++---
 wrappers/python/tests/TestCharmmFiles.py      | 125 +++++++++---------
 .../python/tests/TestCheckpointReporter.py    |   4 +-
 wrappers/python/tests/TestDcdFile.py          |  14 +-
 wrappers/python/tests/TestDesmondDMSFile.py   |  10 +-
 wrappers/python/tests/TestForceField.py       |  70 +++++-----
 wrappers/python/tests/TestGenerators.py       |   4 +-
 wrappers/python/tests/TestGromacsGroFile.py   |   5 +-
 wrappers/python/tests/TestGromacsTopFile.py   |  32 ++---
 wrappers/python/tests/TestIntegrators.py      |  18 +--
 wrappers/python/tests/TestModeller.py         |  22 ++-
 .../python/tests/TestNumpyCompatibility.py    |   5 +-
 wrappers/python/tests/TestPatches.py          |   7 +-
 wrappers/python/tests/TestPdbFile.py          |  16 +--
 wrappers/python/tests/TestPdbReporter.py      |  11 +-
 wrappers/python/tests/TestPdbxFile.py         |  23 ++--
 wrappers/python/tests/TestPickle.py           |   8 +-
 wrappers/python/tests/TestSimulation.py       |  18 +--
 .../python/tests/TestStateDataReporter.py     |   3 +-
 wrappers/python/tests/TestTopology.py         |   6 +-
 wrappers/python/tests/TestXtcFile.py          |  17 +--
 22 files changed, 201 insertions(+), 270 deletions(-)

diff --git a/wrappers/python/tests/TestAmberInpcrdFile.py b/wrappers/python/tests/TestAmberInpcrdFile.py
index a1aa863964..c93d3687e6 100644
--- a/wrappers/python/tests/TestAmberInpcrdFile.py
+++ b/wrappers/python/tests/TestAmberInpcrdFile.py
@@ -1,4 +1,3 @@
-import os
 import unittest
 from validateConstraints import *
 from openmm.app import *
@@ -16,15 +15,13 @@ def compareByElement(array1, array2, cmp):
         cmp(x, y)
 
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestAmberInpcrdFile(unittest.TestCase):
     """Test the Amber inpcrd file parser"""
 
     def test_CrdVelBox(self):
         """ Test parsing ASCII restarts with crds, vels, and box """
         cmp = self.assertAlmostEqual
-        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crds_vels_box.rst7'))
+        inpcrd = AmberInpcrdFile('systems/crds_vels_box.rst7')
         self.assertEqual(len(inpcrd.positions), 2101)
         compareByElement(inpcrd.positions[-1].value_in_unit(angstroms),
                          [3.5958082, 8.4176792, -8.2954064], cmp)
@@ -38,7 +35,7 @@ def test_NetCDF(self):
         """ Test NetCDF restart file parsing """
         cmp = self.assertAlmostEqual
 
-        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'amber.ncrst'))
+        inpcrd = AmberInpcrdFile('systems/amber.ncrst')
         self.assertEqual(len(inpcrd.positions), 2101)
         compareByElement(inpcrd.positions[0].value_in_unit(angstroms),
                          [6.82122492718229, 6.6276250662042, -8.51668999892245],
@@ -51,24 +48,24 @@ def test_NetCDF(self):
 
     def test_CrdBox(self):
         """ Test parsing ASCII restarts with only crds and box """
-        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crds_box.rst7'))
+        inpcrd = AmberInpcrdFile('systems/crds_box.rst7')
         self.assertEqual(len(inpcrd.positions), 18660)
         self.assertTrue(inpcrd.velocities is None)
         self.assertTrue(inpcrd.boxVectors is not None)
 
     def test_CrdVel(self):
-        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crds_vels.rst7'))
+        inpcrd = AmberInpcrdFile('systems/crds_vels.rst7')
         self.assertTrue(inpcrd.boxVectors is None)
         self.assertTrue(inpcrd.velocities is not None)
 
     def test_CrdOnly(self):
-        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'crdsonly.rst7'))
+        inpcrd = AmberInpcrdFile('systems/crdsonly.rst7')
         self.assertTrue(inpcrd.boxVectors is None)
         self.assertTrue(inpcrd.velocities is None)
 
     def test_CrdBoxTruncoct(self):
         # Check that the box vectors come out correct.
-        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'tz2.truncoct.rst7'))
+        inpcrd = AmberInpcrdFile('systems/tz2.truncoct.rst7')
         ac = Vec3(42.4388485, 0.0, 0.0) * angstroms
         bc = Vec3(-14.146281691908937, 40.011730483685835, 0.0) * angstroms
         cc = Vec3(-14.146281691908937, -20.0058628205162, 34.651176446201672) * angstroms
diff --git a/wrappers/python/tests/TestAmberPrmtopFile.py b/wrappers/python/tests/TestAmberPrmtopFile.py
index 4e9e769bc5..5f8678542d 100644
--- a/wrappers/python/tests/TestAmberPrmtopFile.py
+++ b/wrappers/python/tests/TestAmberPrmtopFile.py
@@ -7,19 +7,17 @@
 from openmm.unit import *
 import openmm.app.element as elem
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
-inpcrd1 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.inpcrd'))
-inpcrd3 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'ff14ipq.rst7'))
-inpcrd4 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'Mg_water.inpcrd'))
-inpcrd7 = AmberInpcrdFile(os.path.join(curr_dir, 'systems', '18protein.rst7'))
-prmtop1 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.prmtop'))
-prmtop2 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.prmtop'))
-prmtop3 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'ff14ipq.parm7'), periodicBoxVectors=inpcrd3.boxVectors)
-prmtop4 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'Mg_water.prmtop'), periodicBoxVectors=inpcrd4.boxVectors)
-prmtop5 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'tz2.truncoct.parm7'))
-prmtop6 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'gaffwat.parm7'))
-prmtop7 = AmberPrmtopFile(os.path.join(curr_dir, 'systems', '18protein.parm7'), periodicBoxVectors=inpcrd7.boxVectors)
+inpcrd1 = AmberInpcrdFile('systems/alanine-dipeptide-explicit.inpcrd')
+inpcrd3 = AmberInpcrdFile('systems/ff14ipq.rst7')
+inpcrd4 = AmberInpcrdFile('systems/Mg_water.inpcrd')
+inpcrd7 = AmberInpcrdFile('systems/18protein.rst7')
+prmtop1 = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
+prmtop2 = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
+prmtop3 = AmberPrmtopFile('systems/ff14ipq.parm7', periodicBoxVectors=inpcrd3.boxVectors)
+prmtop4 = AmberPrmtopFile('systems/Mg_water.prmtop', periodicBoxVectors=inpcrd4.boxVectors)
+prmtop5 = AmberPrmtopFile('systems/tz2.truncoct.parm7')
+prmtop6 = AmberPrmtopFile('systems/gaffwat.parm7')
+prmtop7 = AmberPrmtopFile('systems/18protein.parm7', periodicBoxVectors=inpcrd7.boxVectors)
 
 class TestAmberPrmtopFile(unittest.TestCase):
 
@@ -309,14 +307,14 @@ def test_ImplicitSolventForces(self):
         nonbondedMethod = [NoCutoff, CutoffNonPeriodic, CutoffNonPeriodic, NoCutoff, NoCutoff]
         salt = [0.0, 0.0, 0.5, 0.5, 0.0]*(moles/liter)
         file = ['HCT_NoCutoff', 'OBC1_NonPeriodic', 'OBC2_NonPeriodic_Salt', 'GBn_NoCutoff_Salt', 'GBn2_NoCutoff']
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         for i in range(5):
             system = prmtop2.createSystem(implicitSolvent=solventType[i], nonbondedMethod=nonbondedMethod[i], implicitSolventSaltConc=salt[i])
             integrator = VerletIntegrator(0.001)
             context = Context(system, integrator, Platform.getPlatform("Reference"))
             context.setPositions(pdb.positions)
             state1 = context.getState(getForces=True)
-            with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit-forces', file[i]+'.xml')) as infile:
+            with open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml') as infile:
                 state2 = XmlSerializer.deserialize(infile.read())
             for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
                 diff = norm(f1-f2)
@@ -377,8 +375,8 @@ def test_with_dcd_reporter(self):
 
     def testChamber(self):
         """Test a prmtop file created with Chamber."""
-        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'ala3_solv.parm7'))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
+        prmtop = AmberPrmtopFile('systems/ala3_solv.parm7')
+        crd = CharmmCrdFile('systems/ala3_solv.crd')
         system = prmtop.createSystem()
         for i,f in enumerate(system.getForces()):
             f.setForceGroup(i)
@@ -416,8 +414,8 @@ def testGBneckRadii(self):
 
     def testNucleicGBParametes(self):
         """Test that correct GB parameters are used for nucleic acids."""
-        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'DNA_mbondi3.prmtop'))
-        inpcrd = AmberInpcrdFile(os.path.join(curr_dir, 'systems', 'DNA_mbondi3.inpcrd'))
+        prmtop = AmberPrmtopFile('systems/DNA_mbondi3.prmtop')
+        inpcrd = AmberInpcrdFile('systems/DNA_mbondi3.inpcrd')
         sanderEnergy = [-19223.87993545, -19527.40433175, -19788.1070698]
         for solvent, expectedEnergy in zip([OBC2, GBn, GBn2], sanderEnergy):
             system = prmtop.createSystem(implicitSolvent=solvent, gbsaModel=None)
@@ -458,7 +456,7 @@ def testAmberCMAP(self):
 
     def testEPConstraints(self):
         """Test different types of constraints when using extra particles"""
-        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'peptide_with_tip4p.prmtop'))
+        prmtop = AmberPrmtopFile('systems/peptide_with_tip4p.prmtop')
         for constraints in (HBonds, AllBonds):
             system = prmtop.createSystem(constraints=constraints)
             integrator = VerletIntegrator(0.001*picoseconds)
diff --git a/wrappers/python/tests/TestCharmmFiles.py b/wrappers/python/tests/TestCharmmFiles.py
index a66943a13c..7ac43e13a4 100644
--- a/wrappers/python/tests/TestCharmmFiles.py
+++ b/wrappers/python/tests/TestCharmmFiles.py
@@ -14,9 +14,6 @@
 else:
     from cStringIO import StringIO
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestCharmmFiles(unittest.TestCase):
 
     """Test the GromacsTopFile.createSystem() method."""
@@ -25,13 +22,12 @@ def setUp(self):
         """Set up the tests by loading the input files."""
 
         # alanine tripeptide; no waters
-        self.psf_c = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.psf'))
-        self.psf_x = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.xpsf'))
-        self.psf_v = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.vpsf'))
+        self.psf_c = CharmmPsfFile('systems/ala_ala_ala.psf')
+        self.psf_x = CharmmPsfFile('systems/ala_ala_ala.xpsf')
+        self.psf_v = CharmmPsfFile('systems/ala_ala_ala.vpsf')
         self.params = CharmmParameterSet(
-                            os.path.join(curr_dir, 'systems', 'charmm22.rtf'),
-                            os.path.join(curr_dir, 'systems', 'charmm22.par'))
-        self.pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
+                            'systems/charmm22.rtf', 'systems/charmm22.par')
+        self.pdb = PDBFile('systems/ala_ala_ala.pdb')
 
     def test_NonbondedMethod(self):
         """Test both non-periodic methods for the systems"""
@@ -107,9 +103,9 @@ def test_HydrogenMass(self):
     def test_DrudeMass(self):
         """Test that setting the mass of Drude particles works correctly."""
 
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'))
+        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
+        crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
+        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str')
         system = psf.createSystem(params, drudeMass=0)
         trueMass = [system.getParticleMass(i) for i in range(system.getNumParticles())]
         drudeMass = 0.3*amu
@@ -134,10 +130,10 @@ def test_DrudeMass(self):
     def test_NBFIX(self):
         """Tests CHARMM systems with NBFIX Lennard-Jones modifications"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv.psf'), unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500)*angstroms)
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_prot.prm'),
-                                    os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
+        psf = CharmmPsfFile('systems/ala3_solv.psf', unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500)*angstroms)
+        crd = CharmmCrdFile('systems/ala3_solv.crd')
+        params = CharmmParameterSet('systems/par_all36_prot.prm',
+                                    'systems/toppar_water_ions.str')
 
         # Turn off charges so we only test the Lennard-Jones energies
         for a in psf.atom_list:
@@ -158,11 +154,9 @@ def test_NBFIX(self):
     def test_NBFIX14(self):
         """Tests CHARMM systems with NBFIX modifications to 1-4 interactions"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'chl1.psf'))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'chl1.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_lipid.prm'),
-                                   os.path.join(curr_dir, 'systems', 'par_all36_cgenff.prm'),
-                                   os.path.join(curr_dir, 'systems', 'toppar_all36_lipid_cholesterol.str'))
+        psf = CharmmPsfFile('systems/chl1.psf')
+        crd = CharmmCrdFile('systems/chl1.crd')
+        params = CharmmParameterSet('systems/par_all36_lipid.prm', 'systems/par_all36_cgenff.prm', 'systems/toppar_all36_lipid_cholesterol.str')
 
         # Turn off charges so we only test the Lennard-Jones energies
         for a in psf.atom_list:
@@ -184,10 +178,9 @@ def test_NBFIX14(self):
     def test_NBThole(self):
         """Tests CHARMM system with NBTHole"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'cyt-gua-cyt.psf'))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'cyt-gua-cyt.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'),
-                                   os.path.join(curr_dir, 'systems', 'toppar_drude_nucleic_acid_2017b.str'))
+        psf = CharmmPsfFile('systems/cyt-gua-cyt.psf')
+        crd = CharmmCrdFile('systems/cyt-gua-cyt.crd')
+        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str','systems/toppar_drude_nucleic_acid_2017b.str')
         # Box dimensions (cubic box)
         psf.setBox(30.0*angstroms, 30.0*angstroms, 30.0*angstroms)
 
@@ -204,7 +197,7 @@ def test_NBThole(self):
 
     def test_PSFSetUnitCellDimensions(self):
         """Test that setting the box via unit cell dimensions works correctly."""
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
+        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
 
         # Orthorhombic
         psf.setBox(2.1*nanometer, 2.3*nanometer, 2.4*nanometer)
@@ -235,9 +228,9 @@ def test_PSFSetUnitCellDimensions(self):
     def test_Drude(self):
         """Test CHARMM systems with Drude force field"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'))
+        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
+        crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
+        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str')
         # Box dimensions (cubic box)
         psf.setBox(33.2*angstroms, 33.2*angstroms, 33.2*angstroms)
 
@@ -255,10 +248,10 @@ def test_Drude(self):
     def test_Lonepair(self):
         """Test the lonepair facilities, in particular the colinear type of lonepairs"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'chlb_cgenff.psf'))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'chlb_cgenff.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'top_all36_cgenff.rtf'),
-                                   os.path.join(curr_dir, 'systems', 'par_all36_cgenff.prm'))
+        psf = CharmmPsfFile('systems/chlb_cgenff.psf')
+        crd = CharmmCrdFile('systems/chlb_cgenff.crd')
+        params = CharmmParameterSet('systems/top_all36_cgenff.rtf',
+                                    'systems/par_all36_cgenff.prm')
         plat = Platform.getPlatform('Reference')
         system = psf.createSystem(params)
         con = Context(system, VerletIntegrator(2*femtoseconds), plat)
@@ -277,7 +270,7 @@ def test_Lonepair(self):
 
     def test_InsCode(self):
         """ Test the parsing of PSF files that contain insertion codes in their residue numbers """
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', '4TVP-dmj_wat-ion.psf'))
+        psf = CharmmPsfFile('systems/4TVP-dmj_wat-ion.psf')
         self.assertEqual(len(list(psf.topology.atoms())), 66264)
         self.assertEqual(len(list(psf.topology.residues())), 20169)
         self.assertEqual(len(list(psf.topology.bonds())), 46634)
@@ -285,11 +278,11 @@ def test_InsCode(self):
     def testSystemOptions(self):
         """ Test various options in CharmmPsfFile.createSystem """
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv.psf'),
+        psf = CharmmPsfFile('systems/ala3_solv.psf',
                             periodicBoxVectors=(Vec3(32.7119500, 0, 0)*angstroms, Vec3(0, 32.9959600, 0)*angstroms, Vec3(0, 0, 33.0071500)*angstroms))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_prot.prm'),
-                                   os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
+        crd = CharmmCrdFile('systems/ala3_solv.crd')
+        params = CharmmParameterSet('systems/par_all36_prot.prm',
+                                    'systems/toppar_water_ions.str')
 
         # Check some illegal options
         self.assertRaises(ValueError, lambda:
@@ -321,10 +314,10 @@ def test_ImplicitSolventForces(self):
             context = Context(system, integrator, Platform.getPlatform("Reference"))
             context.setPositions(self.pdb.positions)
             state1 = context.getState(getForces=True)
-            #out = open(os.path.join(curr_dir, 'systems', 'ala-ala-ala-implicit-forces', file[i]+'.xml'), 'w')
+            #out = open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml', 'w')
             #out.write(XmlSerializer.serialize(state1))
             #out.close()
-            with open(os.path.join(curr_dir, 'systems', 'ala-ala-ala-implicit-forces', file[i]+'.xml')) as xml:
+            with open('systems/ala-ala-ala-implicit-forces/'+file[i]+'.xml') as xml:
                 state2 = XmlSerializer.deserialize(xml.read())
             for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
                 diff = norm(f1-f2)
@@ -333,11 +326,11 @@ def test_ImplicitSolventForces(self):
     def test_PermissiveRead(self):
         """Compare permissive and strict reading of Charmm parameters"""
 
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', '5dhfr_cube.psf'))
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', '5dhfr_cube.pdb'))
+        psf = CharmmPsfFile('systems/5dhfr_cube.psf')
+        pdb = PDBFile('systems/5dhfr_cube.pdb')
 
-        params_strict     = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all22_prot_with_mass.inp'))
-        params_permissive = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all22_prot.inp'), permissive=True)
+        params_strict     = CharmmParameterSet('systems/par_all22_prot_with_mass.inp')
+        params_permissive = CharmmParameterSet('systems/par_all22_prot.inp', permissive=True)
         # Box dimensions (found from bounding box)
         psf.setBox(62.23*angstroms, 62.23*angstroms, 62.23*angstroms)
 
@@ -368,7 +361,7 @@ def test_PermissiveRead(self):
     
     def test_Impropers(self):
         """Test CHARMM improper torsions."""
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'improper.psf'))
+        psf = CharmmPsfFile('systems/improper.psf')
         system = psf.createSystem(self.params)
         force = [f for f in system.getForces() if isinstance(f, CustomTorsionForce)][0]
         group = force.getForceGroup()
@@ -515,7 +508,7 @@ def test_Residues(self):
         hoh = ["O", "H1", "H2"]
         pot = ["POT"]
         cla = ["CLA"]
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'charmm-solvated', 'isa_wat.3_kcl.m14.psf'))
+        psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
         for residue in psf.topology.residues():
             atoms = [atom.name for atom in residue.atoms()]
             if residue.name == "M14":
@@ -532,11 +525,11 @@ def test_Residues(self):
     def test_NoLongRangeCorrection(self):
         """Test that long range correction is disabled."""
         parameters = CharmmParameterSet(
-            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'envi.str'),
-            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.rtf'),
-            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.prm')
+            'systems/charmm-solvated/envi.str',
+            'systems/charmm-solvated/m14.rtf',
+            'systems/charmm-solvated/m14.prm'
         )
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'charmm-solvated', 'isa_wat.3_kcl.m14.psf'))
+        psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
         psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
         system = psf.createSystem(parameters, nonbondedMethod=PME)
         for force in system.getForces():
@@ -548,20 +541,20 @@ def test_NoLongRangeCorrection(self):
     def test_NoPsfWarning(self):
         """Test that PSF warning is not thrown."""
         parameters = CharmmParameterSet(
-            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'envi.str'),
-            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.rtf'),
-            os.path.join(curr_dir, 'systems', 'charmm-solvated', 'm14.prm')
+            'systems/charmm-solvated/envi.str',
+            'systems/charmm-solvated/m14.rtf',
+            'systems/charmm-solvated/m14.prm'
         )
         with warnings.catch_warnings():
             warnings.simplefilter("error", CharmmPSFWarning)
-            psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'charmm-solvated', 'isa_wat.3_kcl.m14.psf'))
+            psf = CharmmPsfFile('systems/charmm-solvated/isa_wat.3_kcl.m14.psf')
             psf.setBox(3.0584*nanometers,3.0584*nanometers,3.0584*nanometers)
             psf.createSystem(parameters, nonbondedMethod=PME)
 
     def test_NBXMod(self):
         """Test that all values of NBXMod are interpreted correctly."""
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.crd'))
-        with open(os.path.join(curr_dir, 'systems', 'charmm22.par')) as parfile:
+        crd = CharmmCrdFile('systems/ala_ala_ala.crd')
+        with open('systems/charmm22.par') as parfile:
             par = parfile.read()
         # The following values were computed with CHARMM.
         modeEnergy = {0: 754318.20507, 1: 754318.20507, 2: 908.35224, 3: 59.65279, 4: -241.12856, 5: 39.13169}
@@ -569,7 +562,7 @@ def test_NBXMod(self):
             with tempfile.NamedTemporaryFile(suffix='.par', mode='w', delete=False) as parfile:
                 parfile.write(par.replace('nbxmod  5', 'nbxmod %d' % nbxmod))
                 parfile.close()
-                params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'charmm22.rtf'), parfile.name)
+                params = CharmmParameterSet('systems/charmm22.rtf', parfile.name)
                 os.remove(parfile.name)
             system = self.psf_c.createSystem(params, nonbondedMethod=NoCutoff)
             context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatform('Reference'))
@@ -579,9 +572,9 @@ def test_NBXMod(self):
 
     def test_Nonbonded_Exclusion(self):
         """Test that the 1-2, 1-3 and 1-4 pairs are correctly excluded or scaled."""
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'MoS2.psf'))
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'MoS2.pdb'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'MoS2.prm'))
+        psf = CharmmPsfFile('systems/MoS2.psf')
+        pdb = PDBFile('systems/MoS2.pdb')
+        params = CharmmParameterSet('systems/MoS2.prm')
         system = psf.createSystem(params, nonbondedMethod=NoCutoff)
         context = Context(system, VerletIntegrator(1*femtoseconds), Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
@@ -591,8 +584,8 @@ def test_Nonbonded_Exclusion(self):
 
     def test_Constraints(self):
         """Test that bond and angles constraints are correctly added into the system"""
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'water_methanol.psf'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'water_methanol.prm'))
+        psf = CharmmPsfFile('systems/water_methanol.psf')
+        params = CharmmParameterSet('systems/water_methanol.prm')
         # the system is made of one water molecule and one methanol molecule
         hBonds_water = [[0, 1], [1, 2]]
         hAngles_water = [[0, 2]]
@@ -626,11 +619,11 @@ def test_Constraints(self):
     def test_Constraints_charmm(self):
         """Tests that CHARMM and OpenMM implementation of CHARMM force field produce the same constraints and energy"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv.psf'),
+        psf = CharmmPsfFile('systems/ala3_solv.psf',
                             unitCellDimensions=Vec3(32.7119500, 32.9959600, 33.0071500) * angstroms)
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'par_all36_prot.prm'),
-                                   os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
+        crd = CharmmCrdFile('systems/ala3_solv.crd')
+        params = CharmmParameterSet('systems/par_all36_prot.prm',
+                                    'systems/toppar_water_ions.str')
         plat = Platform.getPlatform('Reference')
         system_charmm = psf.createSystem(params, nonbondedMethod=PME,
                                   nonbondedCutoff=8 * angstroms)
diff --git a/wrappers/python/tests/TestCheckpointReporter.py b/wrappers/python/tests/TestCheckpointReporter.py
index 70fe152486..aac1e35582 100644
--- a/wrappers/python/tests/TestCheckpointReporter.py
+++ b/wrappers/python/tests/TestCheckpointReporter.py
@@ -5,12 +5,10 @@
 import openmm as mm
 from openmm import unit
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 
 class TestCheckpointReporter(unittest.TestCase):
     def setUp(self):
-        with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb')) as f:
+        with open('systems/alanine-dipeptide-implicit.pdb') as f:
             pdb = app.PDBFile(f)
         forcefield = app.ForceField('amber99sbildn.xml')
         system = forcefield.createSystem(pdb.topology,
diff --git a/wrappers/python/tests/TestDcdFile.py b/wrappers/python/tests/TestDcdFile.py
index e7bdbc0696..2bf54907c1 100644
--- a/wrappers/python/tests/TestDcdFile.py
+++ b/wrappers/python/tests/TestDcdFile.py
@@ -7,8 +7,6 @@
 import os
 import struct
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 
 def _read_dcd_header(file):
     with open(file, "r+b") as f:
@@ -22,7 +20,7 @@ class TestDCDFile(unittest.TestCase):
     def test_dcd(self):
         """ Test the DCD file """
         fname = tempfile.mktemp(suffix='.dcd')
-        pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdbfile = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
         natom = len(list(pdbfile.topology.atoms()))
         with open(fname, 'wb') as f:
             dcd = app.DCDFile(f, pdbfile.topology, 0.001)
@@ -33,7 +31,7 @@ def test_dcd(self):
     def testLongTrajectory(self):
         """Test writing a trajectory that has more than 2^31 steps."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdbfile = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
         natom = len(list(pdbfile.topology.atoms()))
         with open(fname, 'wb') as f:
             dcd = app.DCDFile(f, pdbfile.topology, 0.001, interval=1000000000)
@@ -44,7 +42,7 @@ def testLongTrajectory(self):
     def testAppend(self):
         """Test appending to an existing trajectory."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         
@@ -88,7 +86,7 @@ def testAppend(self):
     def testAtomSubset(self):
         """Test writing a DCD file containing a subset of atoms"""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
 
@@ -133,7 +131,7 @@ def testAtomSubset(self):
     def testAppendAtomCountMismatch(self):
         """Test that appending to a DCD file with a different number of atoms raises an error."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
 
@@ -166,7 +164,7 @@ def testAppendAtomCountMismatch(self):
     def testAppendLongCommentBlock(self):
         """Test appending to an existing trajectory with a long comment block."""
         fname = tempfile.mktemp(suffix='.dcd')
-        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = app.ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
 
diff --git a/wrappers/python/tests/TestDesmondDMSFile.py b/wrappers/python/tests/TestDesmondDMSFile.py
index 9fede1a8b9..fbe7c0bb6c 100644
--- a/wrappers/python/tests/TestDesmondDMSFile.py
+++ b/wrappers/python/tests/TestDesmondDMSFile.py
@@ -5,23 +5,21 @@
 from openmm.unit import *
 import openmm.app.element as elem
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestDesmondDMSFile(unittest.TestCase):
     def setUp(self):
         """Set up the tests by loading the input files."""
 
         # alanine dipeptide with explicit water
-        path = os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit-amber99SBILDN-tip3p.dms')
+        path = os.path.join(os.path.dirname(__file__), 'systems/alanine-dipeptide-explicit-amber99SBILDN-tip3p.dms')
         self.dms = DesmondDMSFile(path)
 
         #nabumetone OPLS force field
-        path = os.path.join(curr_dir, 'systems', 'bcd-nabumetone_lig.dms')
+        path = os.path.join(os.path.dirname(__file__), 'systems/bcd-nabumetone_lig.dms')
         self.dms_opls1 = DesmondDMSFile(path)
         
         #beta-cyclodextrin/nabumetone complex OPLS force field
-        path1 = os.path.join(curr_dir, 'systems', 'bcd-nabumetone_lig.dms')
-        path2 = os.path.join(curr_dir, 'systems', 'bcd-nabumetone_rcpt.dms')
+        path1 = os.path.join(os.path.dirname(__file__), 'systems/bcd-nabumetone_lig.dms')
+        path2 = os.path.join(os.path.dirname(__file__), 'systems/bcd-nabumetone_rcpt.dms')
         self.dms_opls2 = DesmondDMSFile([path1,path2])
     
     def test_NonbondedMethod(self):
diff --git a/wrappers/python/tests/TestForceField.py b/wrappers/python/tests/TestForceField.py
index 38a50ce598..009811807f 100644
--- a/wrappers/python/tests/TestForceField.py
+++ b/wrappers/python/tests/TestForceField.py
@@ -14,9 +14,6 @@
 import os
 import warnings
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestForceField(unittest.TestCase):
     """Test the ForceField.createSystem() method."""
 
@@ -26,13 +23,13 @@ def setUp(self):
 
         """
         # alanine dipeptide with explicit water
-        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        self.pdb1 = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         self.forcefield1 = ForceField('amber99sb.xml', 'tip3p.xml')
         self.topology1 = self.pdb1.topology
         self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))
 
         # alanine dipeptide with implicit water
-        self.pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')
 
 
@@ -261,7 +258,7 @@ def test_DrudeMass(self):
         """Test that setting the mass of Drude particles works correctly."""
 
         forcefield = ForceField('charmm_polar_2013.xml')
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
+        pdb = PDBFile('systems/ala_ala_ala.pdb')
         modeller = Modeller(pdb.topology, pdb.positions)
         modeller.addExtraParticles(forcefield)
         system = forcefield.createSystem(modeller.topology, drudeMass=0)
@@ -300,13 +297,13 @@ def test_UnusedArgs(self):
     def test_Forces(self):
         """Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
 
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'lysozyme-implicit.pdb'))
+        pdb = PDBFile('systems/lysozyme-implicit.pdb')
         system = self.forcefield2.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001)
         context = Context(system, integrator)
         context.setPositions(pdb.positions)
         state1 = context.getState(getForces=True)
-        with open(os.path.join(curr_dir, 'systems', 'lysozyme-implicit-forces.xml')) as input:
+        with open('systems/lysozyme-implicit-forces.xml') as input:
             state2 = XmlSerializer.deserialize(input.read())
         numDifferences = 0
         for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
@@ -330,7 +327,7 @@ def test_ImplicitSolventForces(self):
             context.setPositions(self.pdb2.positions)
             state1 = context.getState(getForces=True)
             if file[i] is not None:
-                with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit-forces', file[i]+'.xml')) as infile:
+                with open('systems/alanine-dipeptide-implicit-forces/'+file[i]+'.xml') as infile:
                     state2 = XmlSerializer.deserialize(infile.read())
                 for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
                     diff = norm(f1-f2)
@@ -610,7 +607,7 @@ def test_residueMatcher(self):
         ff = ForceField(StringIO(xml))
 
         # Load a water box.
-        prmtop = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'water-box-216.prmtop'))
+        prmtop = AmberPrmtopFile('systems/water-box-216.prmtop')
         top = prmtop.topology
         
         # Building a System should fail, because two templates match each residue.
@@ -681,7 +678,7 @@ def simpleTemplateGenerator(forcefield, residue):
         #
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
         # Add the residue template generator.
@@ -703,7 +700,7 @@ def simpleTemplateGenerator(forcefield, residue):
         # Test all systems with separate ForceField objects.
         for test in tests:
             # Load the PDB file.
-            pdb = PDBFile(os.path.join(curr_dir, 'systems', test['pdb_filename']))
+            pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
             # Create a ForceField object.
             forcefield = ForceField(StringIO(simple_ffxml_contents))
             # Add the residue template generator.
@@ -719,7 +716,7 @@ def simpleTemplateGenerator(forcefield, residue):
         forcefield.registerTemplateGenerator(simpleTemplateGenerator)
         for test in tests:
             # Load the PDB file.
-            pdb = PDBFile(os.path.join(curr_dir, 'systems', test['pdb_filename']))
+            pdb = PDBFile(os.path.join('systems', test['pdb_filename']))
             # Parameterize system.
             system = forcefield.createSystem(pdb.topology, nonbondedMethod=test['nonbondedMethod'])
             # TODO: Test energies are finite?
@@ -728,7 +725,7 @@ def test_getUnmatchedResidues(self):
         """Test retrieval of list of residues for which no templates are available."""
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml', 'tip3p.xml')
         # Get list of unmatched residues.
@@ -739,7 +736,7 @@ def test_getUnmatchedResidues(self):
         self.assertEqual(unmatched_residues[0].id, '163')
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('tip3p.xml')
         # Get list of unmatched residues.
@@ -757,7 +754,7 @@ def test_generateTemplatesForUnmatchedResidues(self):
         #
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'nacl-water.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'nacl-water.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('tip3p.xml')
         # Get list of unmatched residues.
@@ -800,7 +797,7 @@ def test_generateTemplatesForUnmatchedResidues(self):
         #
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'T4-lysozyme-L99A-p-xylene-implicit.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml', 'tip3p.xml', StringIO(simple_ffxml_contents))
         # Get list of unique unmatched residues.
@@ -820,7 +817,7 @@ def test_getMatchingTemplates(self):
         """Test retrieval of list of templates that match residues in a topology."""
 
         # Load the PDB file.
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
         # Create a ForceField object.
         forcefield = ForceField('amber99sb.xml')
         # Get list of matching residue templates.
@@ -873,7 +870,7 @@ def test_Wildcard(self):
 
     def test_ScalingFactorCombining(self):
         """ Tests that FFs can be combined if their scaling factors are very close """
-        forcefield = ForceField('amber99sb.xml', os.path.join(curr_dir, 'systems', 'test_amber_ff.xml'))
+        forcefield = ForceField('amber99sb.xml', os.path.join('systems', 'test_amber_ff.xml'))
         # This would raise an exception if it didn't work
 
     def test_MultipleFilesandForceTags(self):
@@ -1106,9 +1103,10 @@ def test_CMAPTorsionGeneratorMapAssignment(self):
     def test_LennardJonesGenerator(self):
         """ Test the LennardJones generator"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ions.psf'))
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ions.pdb'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_water_ions.str'))
+        psf = CharmmPsfFile('systems/ions.psf')
+        pdb = PDBFile('systems/ions.pdb')
+        params = CharmmParameterSet('systems/toppar_water_ions.str'
+                                    )
 
         # Box dimensions (found from bounding box)
         psf.setBox(12.009*angstroms,   12.338*angstroms,   11.510*angstroms)
@@ -1251,7 +1249,7 @@ def test_IgnoreExternalBonds(self):
 
     def test_Includes(self):
         """Test using a ForceField that includes other files."""
-        forcefield = ForceField(os.path.join(curr_dir, 'systems', 'ff_with_includes.xml'))
+        forcefield = ForceField(os.path.join('systems', 'ff_with_includes.xml'))
         self.assertTrue(len(forcefield._atomTypes) > 10)
         self.assertTrue('spce-O' in forcefield._atomTypes)
         self.assertTrue('HOH' in forcefield._templates)
@@ -1268,7 +1266,7 @@ def test_ImpropersOrdering(self):
  </PeriodicTorsionForce>
 </ForceField>
 """
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'impropers_ordering_tetrapeptide.pdb'))
+        pdb = PDBFile('systems/impropers_ordering_tetrapeptide.pdb')
         # ff1 uses default ordering of impropers, ff2 uses "amber" for the one
         # problematic improper
         ff1 = ForceField('amber99sbildn.xml')
@@ -1318,7 +1316,7 @@ def test_ImpropersOrdering_smirnoff(self):
   </Residues>
 </ForceField>
 """
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'formaldehyde.pdb'))
+        pdb = PDBFile('systems/formaldehyde.pdb')
         # ff1 uses default ordering of impropers, ff2 uses "amber" for the one
         # problematic improper
         ff = ForceField(StringIO(xml))
@@ -1337,7 +1335,7 @@ def test_ImpropersOrdering_smirnoff(self):
 
     def test_Disulfides(self):
         """Test that various force fields handle disulfides correctly."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'bpti.pdb'))
+        pdb = PDBFile('systems/bpti.pdb')
         for ff in ['amber99sb.xml', 'amber14-all.xml', 'amber19-all.xml', 'charmm36.xml', 'charmm36_2024.xml', 'amberfb15.xml', 'amoeba2013.xml']:
             forcefield = ForceField(ff)
             system = forcefield.createSystem(pdb.topology)
@@ -1372,7 +1370,7 @@ def test_IdenticalTemplates(self):
 
     def test_CharmmPolar(self):
         """Test the CHARMM polarizable force field."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala_drude.pdb'))
+        pdb = PDBFile('systems/ala_ala_ala_drude.pdb')
         pdb.topology.setUnitCellDimensions(Vec3(3, 3, 3))
         ff = ForceField('charmm_polar_2019.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME, nonbondedCutoff=1.2*nanometers)
@@ -1454,7 +1452,7 @@ def test_InitializationScript(self):
     def test_Glycam(self):
         """Test computing energy with GLYCAM."""
         ff = ForceField('amber14/protein.ff14SB.xml', 'amber14/GLYCAM_06j-1.xml')
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
+        pdb = PDBFile('systems/glycopeptide.pdb')
         system = ff.createSystem(pdb.topology)
         for i, f in enumerate(system.getForces()):
             f.setForceGroup(i)
@@ -1476,7 +1474,7 @@ def test_Glycam(self):
 
     def test_CustomNonbondedGenerator(self):
         """ Test the CustomNonbondedForce generator"""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ions.pdb'))
+        pdb = PDBFile('systems/ions.pdb')
         xml = """
 <ForceField>
  <AtomTypes>
@@ -1522,7 +1520,7 @@ def test_CustomNonbondedGenerator(self):
         self.assertAlmostEqual(energy1, energy2)
 
     def test_OpcEnergy(self):
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'opcbox.pdb'))
+        pdb = PDBFile('systems/opcbox.pdb')
         topology, positions = pdb.topology, pdb.positions
         self.assertEqual(len(positions), 864)
         forcefield = ForceField('opc.xml')
@@ -1556,7 +1554,7 @@ def test_OpcEnergy(self):
         self.assertTrue(abs(energy1 - energy2) < energy_tolerance)
 
     def test_Opc3Energy(self):
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'opc3box.pdb'))
+        pdb = PDBFile('systems/opc3box.pdb')
         topology, positions = pdb.topology, pdb.positions
         self.assertEqual(len(positions), 648)
         forcefield = ForceField('opc3.xml')
@@ -1598,7 +1596,7 @@ def setUp(self):
 
         """
 
-        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'amoeba-ion-in-water.pdb'))
+        self.pdb1 = PDBFile('systems/amoeba-ion-in-water.pdb')
         self.forcefield1 = ForceField('amoeba2013.xml')
         self.topology1 = self.pdb1.topology
 
@@ -1672,14 +1670,14 @@ def test_RigidWater(self):
     def test_Forces(self):
         """Compute forces and compare them to ones generated with a previous version of OpenMM to ensure they haven't changed."""
 
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         forcefield = ForceField('amoeba2013.xml', 'amoeba2013_gk.xml')
         system = forcefield.createSystem(pdb.topology, polarization='direct')
         integrator = VerletIntegrator(0.001)
         context = Context(system, integrator, Platform.getPlatform('Reference'))
         context.setPositions(pdb.positions)
         state1 = context.getState(getForces=True)
-        with open(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-amoeba-forces.xml')) as input:
+        with open('systems/alanine-dipeptide-amoeba-forces.xml') as input:
             state2 = XmlSerializer.deserialize(input.read())
         for f1, f2, in zip(state1.getForces().value_in_unit(kilojoules_per_mole/nanometer), state2.getForces().value_in_unit(kilojoules_per_mole/nanometer)):
             diff = norm(f1-f2)
@@ -1702,7 +1700,7 @@ def computeAmoeba18Energies(self, filename):
 
     def test_Amoeba18BPTI(self):
         """Test that AMOEBA18 computes energies correctly for BPTI."""
-        energies = self.computeAmoeba18Energies(os.path.join(curr_dir, 'systems', 'bpti.pdb'))
+        energies = self.computeAmoeba18Energies('systems/bpti.pdb')
 
         # Compare to values computed with Tinker.
 
@@ -1719,7 +1717,7 @@ def test_Amoeba18BPTI(self):
 
     def test_Amoeba18Nucleic(self):
         """Test that AMOEBA18 computes energies correctly for DNA and RNA."""
-        energies = self.computeAmoeba18Energies(os.path.join(curr_dir, 'systems', 'nucleic.pdb'))
+        energies = self.computeAmoeba18Energies('systems/nucleic.pdb')
 
         # Compare to values computed with Tinker.
 
diff --git a/wrappers/python/tests/TestGenerators.py b/wrappers/python/tests/TestGenerators.py
index 28506267f6..8a67347cfa 100644
--- a/wrappers/python/tests/TestGenerators.py
+++ b/wrappers/python/tests/TestGenerators.py
@@ -13,14 +13,12 @@
 import os
 import warnings
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestGenerators(unittest.TestCase):
     """Test the various generators found in forcefield.py."""
 
     def setUp(self):
         # alanine dipeptide with implicit water
-        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        self.pdb1 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
 
 
     def test_CustomHbondGenerator(self):
diff --git a/wrappers/python/tests/TestGromacsGroFile.py b/wrappers/python/tests/TestGromacsGroFile.py
index 2413362465..b18107bde0 100644
--- a/wrappers/python/tests/TestGromacsGroFile.py
+++ b/wrappers/python/tests/TestGromacsGroFile.py
@@ -3,16 +3,13 @@
 from openmm import *
 from openmm.unit import *
 import openmm.app.element as elem
-import os
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestGromacsGroFile(unittest.TestCase):
     """Test the Gromacs GRO file parser"""
  
     def test_Triclinic(self):
         """Test parsing a file that describes a triclinic box."""
-        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'triclinic.gro'))
+        gro = GromacsGroFile('systems/triclinic.gro')
         self.assertEqual(len(gro.positions), 8)
         expectedPositions = [
             Vec3(1.744, 2.788, 3.162),
diff --git a/wrappers/python/tests/TestGromacsTopFile.py b/wrappers/python/tests/TestGromacsTopFile.py
index 9d6bc3ef45..08ab6ecb2c 100644
--- a/wrappers/python/tests/TestGromacsTopFile.py
+++ b/wrappers/python/tests/TestGromacsTopFile.py
@@ -6,13 +6,9 @@
 from openmm.app.gromacstopfile import _defaultGromacsIncludeDir
 import openmm.app.element as elem
 from numpy.testing import assert_allclose
-import os
 
 GROMACS_INCLUDE = _defaultGromacsIncludeDir()
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 @unittest.skipIf(not os.path.exists(GROMACS_INCLUDE), 'GROMACS is not installed')
 class TestGromacsTopFile(unittest.TestCase):
 
@@ -22,7 +18,7 @@ def setUp(self):
         """Set up the tests by loading the input files."""
 
         # alanine dipeptide with explicit water
-        self.top1 = GromacsTopFile(os.path.join(curr_dir, 'systems', 'explicit.top'), unitCellDimensions=Vec3(6.223, 6.223, 6.223)*nanometers)
+        self.top1 = GromacsTopFile('systems/explicit.top', unitCellDimensions=Vec3(6.223, 6.223, 6.223)*nanometers)
 
     def test_NonbondedMethod(self):
         """Test all six options for the nonbondedMethod parameter."""
@@ -42,8 +38,8 @@ def test_NonbondedMethod(self):
 
     def test_ff99SBILDN(self):
         """ Test Gromacs topology #define replacement as used in ff99SB-ILDN """
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'aidilnaaaaa.top'))
-        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'aidilnaaaaa.gro'))
+        top = GromacsTopFile('systems/aidilnaaaaa.top')
+        gro = GromacsGroFile('systems/aidilnaaaaa.gro')
         system = top.createSystem()
         for force in system.getForces():
             if isinstance(force, PeriodicTorsionForce):
@@ -56,8 +52,8 @@ def test_ff99SBILDN(self):
 
     def test_SMOG(self):
         """ Test to ensure that SMOG models can be run without problems """
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', '2ci2.pdb.top'))
-        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', '2ci2.pdb.gro'))
+        top = GromacsTopFile('systems/2ci2.pdb.top')
+        gro = GromacsGroFile('systems/2ci2.pdb.gro')
         system = top.createSystem()
 
         context = Context(system, VerletIntegrator(1*femtosecond),
@@ -68,8 +64,8 @@ def test_SMOG(self):
 
     def test_ionic(self):
         """Test simulating an ionic liquid"""
-        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'ionic.gro'))
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'ionic.top'), periodicBoxVectors=gro.getPeriodicBoxVectors())
+        gro = GromacsGroFile('systems/ionic.gro')
+        top = GromacsTopFile('systems/ionic.top', periodicBoxVectors=gro.getPeriodicBoxVectors())
         system = top.createSystem(nonbondedMethod=PME, nonbondedCutoff=1.2)
         for f in system.getForces():
             if isinstance(f, CustomNonbondedForce):
@@ -98,7 +94,7 @@ def test_Cutoff(self):
 
     def test_SwitchingFunction(self):
         """Test using a switching function."""
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'ionic.top'))
+        top = GromacsTopFile('systems/ionic.top')
         for distance in (None, 0.8*nanometers):
             system = top.createSystem(nonbondedMethod=CutoffNonPeriodic, switchDistance=distance)
             for f in system.getForces():
@@ -162,8 +158,8 @@ def test_HydrogenMass(self):
     def test_VirtualParticle(self):
         """Test virtual particle works correctly."""
 
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'bnz.top'))
-        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', 'bnz.gro'))
+        top = GromacsTopFile('systems/bnz.top')
+        gro = GromacsGroFile('systems/bnz.gro')
         for atom in top.topology.atoms():
             if atom.name.startswith('C'):
                 self.assertEqual(elem.carbon, atom.element)
@@ -186,7 +182,7 @@ def test_VirtualParticle(self):
 
     def test_Vsite3Func1(self):
         """Test a three particle virtual site."""
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'tip4pew.top'))
+        top = GromacsTopFile('systems/tip4pew.top')
         system = top.createSystem()
         self.assertEqual(3, system.getNumConstraints())
         self.assertTrue(system.isVirtualSite(3))
@@ -201,7 +197,7 @@ def test_Vsite3Func1(self):
 
     def test_Vsite3Func4(self):
         """Test a three particle virtual site."""
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', 'tip5p.top'))
+        top = GromacsTopFile('systems/tip5p.top')
         system = top.createSystem()
         self.assertEqual(3, system.getNumConstraints())
         for i in (3, 4):
@@ -221,8 +217,8 @@ def test_Vsite3Func4(self):
     def test_GROMOS(self):
         """Test a system using the GROMOS 54a7 force field."""
 
-        top = GromacsTopFile(os.path.join(curr_dir, 'systems', '1ppt.top'))
-        gro = GromacsGroFile(os.path.join(curr_dir, 'systems', '1ppt.gro'))
+        top = GromacsTopFile('systems/1ppt.top')
+        gro = GromacsGroFile('systems/1ppt.gro')
         system = top.createSystem()
         for i, f in enumerate(system.getForces()):
             f.setForceGroup(i)
diff --git a/wrappers/python/tests/TestIntegrators.py b/wrappers/python/tests/TestIntegrators.py
index 7855ab805a..cff603b4d2 100644
--- a/wrappers/python/tests/TestIntegrators.py
+++ b/wrappers/python/tests/TestIntegrators.py
@@ -6,10 +6,6 @@
 from openmm.app import *
 from openmm.unit import *
 import math, random
-import os
-
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestIntegrators(unittest.TestCase):
     """Test Python Integrator classes"""
@@ -17,7 +13,7 @@ class TestIntegrators(unittest.TestCase):
     def testMTSIntegratorExplicit(self):
         """Test the MTS integrator on an explicit solvent system"""
         # Create a periodic solvated system with PME
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -104,7 +100,7 @@ def testMTSIntegratorConstraints(self):
     def testBadGroups(self):
         """Test the MTS integrator with bad force group substeps."""
         # Create a periodic solvated system with PME
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -128,7 +124,7 @@ def testBadGroups(self):
     def testMTSLangevinIntegrator(self):
         """Test the MTSLangevinIntegrator on an explicit solvent system"""
         # Create a periodic solvated system with PME
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -192,7 +188,7 @@ def get_final_velocities(nsubsteps):
 
     def testNoseHooverIntegrator(self):
         """Test partial thermostating in the NoseHooverIntegrator (only API)"""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         ff = ForceField('amber99sbildn.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=PME)
 
@@ -207,9 +203,9 @@ def testNoseHooverIntegrator(self):
     def testDrudeNoseHooverIntegrator(self):
         """Test the DrudeNoseHooverIntegrator"""
         warnings.filterwarnings('ignore', category=CharmmPSFWarning)
-        psf = CharmmPsfFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.psf'))
-        crd = CharmmCrdFile(os.path.join(curr_dir, 'systems', 'ala3_solv_drude.crd'))
-        params = CharmmParameterSet(os.path.join(curr_dir, 'systems', 'toppar_drude_master_protein_2013e.str'))
+        psf = CharmmPsfFile('systems/ala3_solv_drude.psf')
+        crd = CharmmCrdFile('systems/ala3_solv_drude.crd')
+        params = CharmmParameterSet('systems/toppar_drude_master_protein_2013e.str')
         # Box dimensions (cubic box)
         psf.setBox(33.2*angstroms, 33.2*angstroms, 33.2*angstroms)
 
diff --git a/wrappers/python/tests/TestModeller.py b/wrappers/python/tests/TestModeller.py
index 3caddc88d7..068cfcc1ad 100644
--- a/wrappers/python/tests/TestModeller.py
+++ b/wrappers/python/tests/TestModeller.py
@@ -6,33 +6,29 @@
 from openmm.app import *
 from openmm import *
 from openmm.unit import *
-import os
 
 if sys.version_info >= (3, 0):
     from io import StringIO
 else:
     from cStringIO import StringIO
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestModeller(unittest.TestCase):
     """ Test the Modeller class. """
 
     def setUp(self):
         # load the alanine dipeptide pdb file
-        self.pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        self.pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         self.topology_start = self.pdb.topology
         self.positions = self.pdb.positions
         self.forcefield = ForceField('amber10.xml', 'tip3p.xml')
 
         # load the T4-lysozyme-L99A receptor pdb file
-        self.pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'lysozyme-implicit.pdb'))
+        self.pdb2 = PDBFile('systems/lysozyme-implicit.pdb')
         self.topology_start2 = self.pdb2.topology
         self.positions2 = self.pdb2.positions
 
         # load the metallothionein pdb file
-        self.pdb3 =  PDBFile(os.path.join(curr_dir, 'systems', '1T2Y.pdb'))
+        self.pdb3 =  PDBFile('systems/1T2Y.pdb')
         self.topology_start3 = self.pdb3.topology
         self.positions3 = self.pdb3.positions
 
@@ -138,7 +134,7 @@ def test_add(self):
         """ Test the add() method. """
 
         # load the methanol-box pdb file
-        pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'methanol-box.pdb'))
+        pdb2 = PDBFile('systems/methanol-box.pdb')
         topology_toAdd = pdb2.topology
         positions_toAdd = pdb2.positions
 
@@ -973,7 +969,7 @@ def test_addHydrogenspH11(self):
 
     def test_addHydrogensGlycam(self):
         """Test adding hydrogens for GLYCAM."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
+        pdb = PDBFile('systems/glycopeptide.pdb')
         Modeller.loadHydrogenDefinitions('glycam-hydrogens.xml')
         modeller = Modeller(pdb.topology, pdb.positions)
         hydrogens = [a for a in modeller.topology.atoms() if a.element == element.hydrogen]
@@ -991,7 +987,7 @@ def test_addHydrogensGlycam(self):
 
     def test_addSpecificHydrogens(self):
         """Test specifying exactly which hydrogens to add."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
+        pdb = PDBFile('systems/glycopeptide.pdb')
         variants = [None]*pdb.topology.getNumResidues()
         for residue in pdb.topology.residues():
             if residue.name != 'ALA':
@@ -1237,7 +1233,7 @@ def test_multiSiteIon(self):
     def test_addMembrane(self):
         """Test adding a membrane to a realistic system."""
 
-        mol = PDBxFile(os.path.join(curr_dir, 'systems', 'gpcr.cif'))
+        mol = PDBxFile('systems/gpcr.cif')
         modeller = Modeller(mol.topology, mol.positions)
         ff = ForceField('amber14-all.xml', 'amber14/tip3p.xml')
 
@@ -1287,7 +1283,7 @@ def test_bondTypeAndOrderPreserved(self):
         """
 
         # Given: an isolated molecule
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile("systems/alanine-dipeptide-implicit.pdb")
         topology, positions = pdb.topology, pdb.positions
         topology.setUnitCellDimensions(Vec3(3.5, 3.5, 3.5) * nanometers)
         # with some bonds carrying type and order information
@@ -1334,7 +1330,7 @@ def test_bondTypeAndOrderPreserved(self):
         self.assertIn((Double, 2.0), [(b.type, b.order) for b in modeller.topology.bonds()])
 
         # When (6): add a modeller (which also bears some bond info)
-        to_add = PDBFile(os.path.join(curr_dir, 'systems', 'methanol-box.pdb'))
+        to_add = PDBFile('systems/methanol-box.pdb')
         topology_to_add = to_add.topology
         positions_to_add = to_add.positions
         # add a dummy bond to the "to_add" system to check that it also is preserved
diff --git a/wrappers/python/tests/TestNumpyCompatibility.py b/wrappers/python/tests/TestNumpyCompatibility.py
index 7f7fb5a8d5..46b55a6ba0 100644
--- a/wrappers/python/tests/TestNumpyCompatibility.py
+++ b/wrappers/python/tests/TestNumpyCompatibility.py
@@ -2,7 +2,6 @@
 from openmm import app
 import openmm as mm
 from openmm import unit
-import os
 try:
     import numpy as np
     NUMPY_IMPORT_FAILED = False
@@ -10,13 +9,11 @@
     NUMPY_IMPORT_FAILED = True
 
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 @unittest.skipIf(NUMPY_IMPORT_FAILED, 'Numpy is not installed')
 class TestNumpyCompatibility(unittest.TestCase):
 
     def setUp(self):
-        prmtop = app.AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'water-box-216.prmtop'))
+        prmtop = app.AmberPrmtopFile('systems/water-box-216.prmtop')
 
         system = prmtop.createSystem(nonbondedMethod=app.PME,
                                      nonbondedCutoff=0.9*unit.nanometers,
diff --git a/wrappers/python/tests/TestPatches.py b/wrappers/python/tests/TestPatches.py
index d5cac60774..1a3db2e322 100644
--- a/wrappers/python/tests/TestPatches.py
+++ b/wrappers/python/tests/TestPatches.py
@@ -10,9 +10,6 @@
     from io import StringIO
 import os
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestPatches(unittest.TestCase):
     """Test ForceFields that use patches."""
 
@@ -263,7 +260,7 @@ def testAlaAlaAla(self):
  </NonbondedForce>
 </ForceField>"""
         ff = ForceField(StringIO(xml))
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'ala_ala_ala.pdb'))
         system = ff.createSystem(pdb.topology)
         nb = system.getForce(0)
         expectedCharges = [0.1414, 0.2719, 0.2719, 0.2719, 0.0337, 0.0823, 0.0337, 0.0603, 0.0603, 0.0603, 0.5973, -0.5679,
@@ -273,7 +270,7 @@ def testAlaAlaAla(self):
             self.assertEqual(expectedCharges[i], nb.getParticleParameters(i)[0].value_in_unit(elementary_charge))
 
     def testDisulfidePatch(self):
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'bpti.pdb'))
+        pdb = PDBFile(os.path.join('systems', 'bpti.pdb'))
         ff = ForceField('amber99sb.xml')
         system1 = ff.createSystem(pdb.topology)
         
diff --git a/wrappers/python/tests/TestPdbFile.py b/wrappers/python/tests/TestPdbFile.py
index d1ee6022c9..430ce3b048 100644
--- a/wrappers/python/tests/TestPdbFile.py
+++ b/wrappers/python/tests/TestPdbFile.py
@@ -5,10 +5,6 @@
 from openmm.unit import *
 import openmm.app.element as elem
 from io import StringIO
-import os
-
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 
 class TestPdbFile(unittest.TestCase):
@@ -16,7 +12,7 @@ class TestPdbFile(unittest.TestCase):
 
     def test_Triclinic(self):
         """Test parsing a file that describes a triclinic box."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'triclinic.pdb'))
+        pdb = PDBFile('systems/triclinic.pdb')
         self.assertEqual(len(pdb.positions), 8)
         expectedPositions = [
             Vec3(1.744, 2.788, 3.162),
@@ -60,7 +56,7 @@ def compareFiles(pdb1, pdb2):
                 self.assertEqual(atom1.name, atom2.name)
                 self.assertEqual(atom1.residue.name, atom2.residue.name)
 
-        pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'triclinic.pdb'))
+        pdb1 = PDBFile('systems/triclinic.pdb')
 
         # First try writing to an open file object.
 
@@ -82,13 +78,13 @@ def compareFiles(pdb1, pdb2):
 
     def test_BinaryStream(self):
         """Test reading a stream that was opened in binary mode."""
-        with open(os.path.join(curr_dir, 'systems', 'triclinic.pdb'), 'rb') as infile:
+        with open('systems/triclinic.pdb', 'rb') as infile:
             pdb = PDBFile(infile)
         self.assertEqual(len(pdb.positions), 8)
 
     def test_ExtraParticles(self):
         """Test reading, and writing and re-reading of a file containing extra particle atoms."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'tip5p.pdb'))
+        pdb = PDBFile('systems/tip5p.pdb')
         for atom in pdb.topology.atoms():
             if atom.index > 2:
                 self.assertEqual(None, atom.element)
@@ -103,7 +99,7 @@ def test_ExtraParticles(self):
     def test_AltLocs(self):
         """Test reading a file that includes AltLocs"""
         for filename in ['altlocs.pdb', 'altlocs2.pdb']:
-            pdb = PDBFile(os.path.join(curr_dir, 'systems', filename))
+            pdb = PDBFile(f'systems/{filename}')
             self.assertEqual(1, pdb.topology.getNumResidues())
             self.assertEqual(19, pdb.topology.getNumAtoms())
             self.assertEqual(19, len(pdb.positions))
@@ -111,7 +107,7 @@ def test_AltLocs(self):
 
     def test_FormalCharges(self):
         """Test reading, and writing and re-reading of a file containing formal charges."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'formal-charges.pdb'))
+        pdb = PDBFile('systems/formal-charges.pdb')
         for atom in pdb.topology.atoms():
             if atom.index == 8:
                 self.assertEqual(+1, atom.formalCharge)
diff --git a/wrappers/python/tests/TestPdbReporter.py b/wrappers/python/tests/TestPdbReporter.py
index 81e7b930d3..852d891c27 100644
--- a/wrappers/python/tests/TestPdbReporter.py
+++ b/wrappers/python/tests/TestPdbReporter.py
@@ -7,9 +7,6 @@
 import os
 import gc
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 def assertVecAlmostEqual(p1, p2, tol=1e-7):
     unit = p1.unit
     p1 = p1.value_in_unit(unit)
@@ -22,7 +19,7 @@ def assertVecAlmostEqual(p1, p2, tol=1e-7):
 
 class TestPDBReporter(unittest.TestCase):
     def setUp(self):
-        self.pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        self.pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
         self.forcefield = app.ForceField('amber99sbildn.xml','tip3p.xml')
         self.system = self.forcefield.createSystem(self.pdb.topology, nonbondedMethod=app.CutoffNonPeriodic, constraints=app.HBonds)
 
@@ -120,7 +117,7 @@ def testBondSubset(self):
 
         # use a testcase that has CONECT records in the input pdb file
         ff = app.ForceField('amber14/protein.ff14SB.xml', 'amber14/GLYCAM_06j-1.xml','amber14/tip3pfb.xml')
-        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
+        pdb = app.PDBFile('systems/glycopeptide.pdb')
 
         # add in water molecules
         modeller = app.Modeller(pdb.topology, pdb.positions)
@@ -160,7 +157,7 @@ def testBondSubset(self):
 
 class TestPDBxReporter(unittest.TestCase):
     def setUp(self):
-        self.pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        self.pdb = app.PDBFile('systems/alanine-dipeptide-explicit.pdb')
         self.forcefield = app.ForceField('amber99sbildn.xml','tip3p.xml')
         self.system = self.forcefield.createSystem(self.pdb.topology, nonbondedMethod=app.CutoffNonPeriodic, constraints=app.HBonds)
 
@@ -258,7 +255,7 @@ def testBondSubset(self):
 
         # use a testcase that has CONECT records in the input pdb file
         ff = app.ForceField('amber14/protein.ff14SB.xml', 'amber14/GLYCAM_06j-1.xml','amber14/tip3pfb.xml')
-        pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'glycopeptide.pdb'))
+        pdb = app.PDBFile('systems/glycopeptide.pdb')
 
         # add in water molecules
         modeller = app.Modeller(pdb.topology, pdb.positions)
diff --git a/wrappers/python/tests/TestPdbxFile.py b/wrappers/python/tests/TestPdbxFile.py
index 38f0d6f43f..7ba276fb3c 100644
--- a/wrappers/python/tests/TestPdbxFile.py
+++ b/wrappers/python/tests/TestPdbxFile.py
@@ -7,16 +7,13 @@
 import os
 from io import StringIO
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestPdbxFile(unittest.TestCase):
     """Test the PDBx/mmCIF file parser"""
 
     def test_FormatConversion(self):
         """Test conversion from PDB to PDBx"""
 
-        mol = PDBFile(os.path.join(curr_dir, 'systems', 'ala_ala_ala.pdb'))
+        mol = PDBFile('systems/ala_ala_ala.pdb')
         with tempfile.TemporaryDirectory() as tempdir:
             filename = os.path.join(tempdir, 'temp.pdbx')
             PDBxFile.writeFile(mol.topology, mol.positions, filename, keepIds=True)
@@ -28,7 +25,7 @@ def test_FormatConversion(self):
 
     def test_Triclinic(self):
         """Test parsing a file that describes a triclinic box."""
-        pdb = PDBxFile(os.path.join(curr_dir, 'systems', 'triclinic.pdbx'))
+        pdb = PDBxFile('systems/triclinic.pdbx')
         self.assertEqual(len(pdb.positions), 8)
         expectedPositions = [
             Vec3(1.744, 2.788, 3.162),
@@ -69,11 +66,11 @@ def assertVecAlmostEqual(self, p1, p2, tol=1e-7):
 
     def testReporterImplicit(self):
         """ Tests the PDBxReporter without PBC """
-        parm = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.prmtop'))
+        parm = AmberPrmtopFile('systems/alanine-dipeptide-implicit.prmtop')
         system = parm.createSystem()
         sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
                          Platform.getPlatform('Reference'))
-        sim.context.setPositions(PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb')).getPositions())
+        sim.context.setPositions(PDBFile('systems/alanine-dipeptide-implicit.pdb').getPositions())
         sim.reporters.append(PDBxReporter('test.cif', 1))
         sim.step(10)
         pdb = PDBxFile('test.cif')
@@ -101,11 +98,11 @@ def assertAlmostEqualVec(self, vec1, vec2, *args, **kwargs):
 
     def testReporterExplicit(self):
         """ Tests the PDBxReporter with PBC """
-        parm = AmberPrmtopFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.prmtop'))
+        parm = AmberPrmtopFile('systems/alanine-dipeptide-explicit.prmtop')
         system = parm.createSystem(nonbondedCutoff=1.0, nonbondedMethod=PME)
         sim = Simulation(parm.topology, system, VerletIntegrator(1*femtoseconds),
                          Platform.getPlatform('Reference'))
-        orig_pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        orig_pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         sim.context.setPositions(orig_pdb.getPositions())
         sim.context.setPeriodicBoxVectors(*parm.topology.getPeriodicBoxVectors())
         sim.reporters.append(PDBxReporter('test.cif', 1))
@@ -135,7 +132,7 @@ def testReporterExplicit(self):
 
     def testBonds(self):
         """Test reading and writing a file that includes bonds."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'methanol_ions.pdb'))
+        pdb = PDBFile('systems/methanol_ions.pdb')
         output = StringIO()
         PDBxFile.writeFile(pdb.topology, pdb.positions, output)
         input = StringIO(output.getvalue())
@@ -149,7 +146,7 @@ def testBonds(self):
 
     def testChemCompBonds(self):
         """Test creating bonds based on chem_comp_bond records."""
-        pdb = PDBxFile(os.path.join(curr_dir, 'systems', '6mvz.cif'))
+        pdb = PDBxFile('systems/6mvz.cif')
 
         def bondCount(res1, atom1, res2, atom2):
             count = 0
@@ -186,7 +183,7 @@ def bondCount(res1, atom1, res2, atom2):
 
     def testMultiChain(self):
         """Test reading and writing a file that includes multiple chains"""
-        cif_ori = PDBxFile(os.path.join(curr_dir, 'systems', 'multichain.pdbx'))
+        cif_ori = PDBxFile('systems/multichain.pdbx')
 
         output = StringIO()
         PDBxFile.writeFile(cif_ori.topology, cif_ori.positions, output, keepIds=True)
@@ -202,7 +199,7 @@ def testMultiChain(self):
 
     def testInsertionCodes(self):
         """Test reading a file that uses insertion codes."""
-        pdbx = PDBxFile(os.path.join(curr_dir, 'systems', 'insertions.pdbx'))
+        pdbx = PDBxFile('systems/insertions.pdbx')
         residues = list(pdbx.topology.residues())
         self.assertEqual(7, len(residues))
         names = ['PHE', 'ASP', 'LYS', 'ILE', 'LYS', 'ASN', 'TRP']
diff --git a/wrappers/python/tests/TestPickle.py b/wrappers/python/tests/TestPickle.py
index eade637963..b019aa114b 100644
--- a/wrappers/python/tests/TestPickle.py
+++ b/wrappers/python/tests/TestPickle.py
@@ -8,10 +8,6 @@
 import openmm.app.forcefield as forcefield
 import copy
 import pickle
-import os
-
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestPickle(unittest.TestCase):
     """Pickling / deepcopy of OpenMM objects."""
@@ -22,13 +18,13 @@ def setUp(self):
 
         """
         # alanine dipeptide with explicit water
-        self.pdb1 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        self.pdb1 = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         self.forcefield1 = ForceField('amber99sb.xml', 'tip3p.xml')
         self.topology1 = self.pdb1.topology
         self.topology1.setUnitCellDimensions(Vec3(2, 2, 2))
 
         # alalnine dipeptide with implicit water
-        self.pdb2 = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        self.pdb2 = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         self.forcefield2 = ForceField('amber99sb.xml', 'amber99_obc.xml')
 
     def check_copy(self, object, object_copy):
diff --git a/wrappers/python/tests/TestSimulation.py b/wrappers/python/tests/TestSimulation.py
index b6b7797836..68ba979670 100644
--- a/wrappers/python/tests/TestSimulation.py
+++ b/wrappers/python/tests/TestSimulation.py
@@ -4,17 +4,13 @@
 from openmm import *
 from openmm.app import *
 from openmm.unit import *
-import os
-
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestSimulation(unittest.TestCase):
     """Test the Simulation class"""
 
     def testCheckpointing(self):
         """Test that checkpointing works correctly."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -48,7 +44,7 @@ def testCheckpointing(self):
 
     def testLoadFromXML(self):
         """ Test creating a Simulation from XML files """
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -71,7 +67,7 @@ def testLoadFromXML(self):
 
     def testSaveState(self):
         """Test that saving States works correctly."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -104,7 +100,7 @@ def testSaveState(self):
 
     def testStep(self):
         """Test the step() method."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -127,7 +123,7 @@ def testStep(self):
 
     def testRunForClockTime(self):
         """Test the runForClockTime() method."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = VerletIntegrator(0.001*picoseconds)
@@ -171,7 +167,7 @@ def testRunForClockTime(self):
 
     def testWrappedCoordinates(self):
         """Test generating reports with and without wrapped coordinates."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-explicit.pdb')
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology, nonbondedMethod=CutoffPeriodic, constraints=HBonds)
         integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
@@ -203,7 +199,7 @@ def report(self, simulation, state):
 
     def testMinimizationReporter(self):
         """Test invoking a reporter during minimization."""
-        pdb = PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        pdb = PDBFile('systems/alanine-dipeptide-implicit.pdb')
         ff = ForceField('amber99sb.xml', 'tip3p.xml')
         system = ff.createSystem(pdb.topology)
         integrator = LangevinIntegrator(300*kelvin, 1/picosecond, 0.002*picoseconds)
diff --git a/wrappers/python/tests/TestStateDataReporter.py b/wrappers/python/tests/TestStateDataReporter.py
index d6df5283b4..cacdae066b 100644
--- a/wrappers/python/tests/TestStateDataReporter.py
+++ b/wrappers/python/tests/TestStateDataReporter.py
@@ -5,11 +5,10 @@
 from openmm import unit
 import os
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
 
 class TestStateDataReporter(unittest.TestCase):
     def setUp(self):
-        self.pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+        self.pdb = app.PDBFile('systems/alanine-dipeptide-implicit.pdb')
         self.forcefield = app.ForceField('amber99sbildn.xml')
         self.system = self.forcefield.createSystem(self.pdb.topology, nonbondedMethod=app.CutoffNonPeriodic, constraints=app.HBonds)
 
diff --git a/wrappers/python/tests/TestTopology.py b/wrappers/python/tests/TestTopology.py
index 936b51f620..a2b6db23ee 100644
--- a/wrappers/python/tests/TestTopology.py
+++ b/wrappers/python/tests/TestTopology.py
@@ -5,16 +5,12 @@
 from openmm import *
 from openmm.unit import *
 import openmm.app.element as elem
-import os
 if sys.version_info >= (3, 0):
     from io import StringIO
 else:
     from cStringIO import StringIO
 
 
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
-
 class TestTopology(unittest.TestCase):
     """Test the Topology object"""
 
@@ -29,7 +25,7 @@ def check_pdbfile(self, pdbfilename, natoms, nres, nchains):
 
     def test_getters(self):
         """Test getters for number of atoms, residues, chains."""
-        self.check_pdbfile(os.path.join(curr_dir, 'systems', '1T2Y.pdb'), 271, 25, 1)
+        self.check_pdbfile('systems/1T2Y.pdb', 271, 25, 1)
 
     def test_bondtype_singleton(self):
         """ Tests that the bond types are really singletons """
diff --git a/wrappers/python/tests/TestXtcFile.py b/wrappers/python/tests/TestXtcFile.py
index fcd118517f..2d905ccf14 100644
--- a/wrappers/python/tests/TestXtcFile.py
+++ b/wrappers/python/tests/TestXtcFile.py
@@ -10,15 +10,12 @@
 import numpy as np
 from openmm.app.internal.xtc_utils import read_xtc
 
-
-curr_dir = os.path.dirname(os.path.abspath(__file__))
-
 class TestXtcFile(unittest.TestCase):
     def test_xtc_triclinic(self):
         """Test the XTC file by writing a trajectory and reading it back. Using a triclinic box"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             pdbfile.topology.setUnitCellDimensions([10, 10, 10])
             natom = len(list(pdbfile.topology.atoms()))
@@ -60,7 +57,7 @@ def test_xtc_cubic(self):
         """Test the XTC file by writing a trajectory and reading it back. Using a cubic box"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             pdbfile.topology.setUnitCellDimensions([10, 10, 10])
             natom = len(list(pdbfile.topology.atoms()))
@@ -98,7 +95,7 @@ def test_xtc_box_from_topology(self):
         """Test the XTC file by writing a trajectory and reading it back. Letting the box be set from the topology"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             unitCell = mm.Vec3(random(), random(), random()) * unit.nanometers
             pdbfile.topology.setUnitCellDimensions(unitCell)
@@ -142,7 +139,7 @@ def test_xtc_small(self):
         """Test the XTC file by writing a trajectory and reading it back. Using a system size below the compression threshold"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'ions.pdb'))
+            pdbfile = app.PDBFile("systems/ions.pdb")
             # Set some arbitrary size for the unit cell so that a box is included in the trajectory
             pdbfile.topology.setUnitCellDimensions([10, 10, 10])
             natom = len(list(pdbfile.topology.atoms()))
@@ -184,7 +181,7 @@ def testLongTrajectory(self):
         """Test writing a trajectory that has more than 2^31 steps."""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdbfile = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+            pdbfile = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
             natom = len(list(pdbfile.topology.atoms()))
             xtc = app.XTCFile(fname, pdbfile.topology, 0.001, interval=1000000000)
             for i in range(5):
@@ -199,7 +196,7 @@ def testAppend(self):
         """Test appending to an existing trajectory."""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-implicit.pdb'))
+            pdb = app.PDBFile("systems/alanine-dipeptide-implicit.pdb")
             ff = app.ForceField("amber99sb.xml", "tip3p.xml")
             system = ff.createSystem(pdb.topology)
 
@@ -252,7 +249,7 @@ def testAtomSubset(self):
         """Test writing an XTC file containing a subset of atoms"""
         with tempfile.TemporaryDirectory() as temp:
             fname = os.path.join(temp, 'traj.xtc')
-            pdb = app.PDBFile(os.path.join(curr_dir, 'systems', 'alanine-dipeptide-explicit.pdb'))
+            pdb = app.PDBFile("systems/alanine-dipeptide-explicit.pdb")
             ff = app.ForceField("amber99sb.xml", "tip3p.xml")
             system = ff.createSystem(pdb.topology)
 

From 01ef012b5f5f275934493be332be350be26f7ef3 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 12:23:42 +0300
Subject: [PATCH 42/75] fix CI test issues

---
 .github/workflows/workflow.yml     | 2 ++
 wrappers/python/openmm/__init__.py | 1 +
 wrappers/python/setup.py           | 4 ++--
 3 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 45eab0be08..f3fb10801e 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -1,4 +1,6 @@
 name: Whole
+permissions:
+  contents: read
 
 on: [push]
 
diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index 3141065085..367f3a4928 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -9,6 +9,7 @@
 
 import os, os.path
 import sys
+from . import version
 
 
 openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'lib'))
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 2a0f43b81b..40c407aa22 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -172,8 +172,8 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                 libraries[ii]="%s_d" % libraries[ii]
                 sys.stdout.write("%s\n" % libraries[ii])
 
-    openmm_include_path = 'openmm/include'
-    openmm_lib_path = 'openmm/lib'
+    openmm_include_path = os.getenv('OPENMM_INCLUDE_PATH', 'openmm/include')
+    openmm_lib_path = os.getenv('OPENMM_LIB_PATH', 'openmm/lib')
 
     extra_compile_args=['-std=c++11', '-D_GLIBCXX_USE_CXX11_ABI=1']
     extra_link_args=[]

From 516cc0a4c64e457d988e0453316847d39b8f70b9 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 12:32:17 +0300
Subject: [PATCH 43/75] delay import to solve circular import issue

---
 wrappers/python/openmm/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index 367f3a4928..f829168ee9 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -9,7 +9,6 @@
 
 import os, os.path
 import sys
-from . import version
 
 
 openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'lib'))
@@ -41,3 +40,5 @@
 class OpenMMException(Exception):
     """This is the class used for all exceptions thrown by the C++ library."""
     pass
+
+from . import version

From 510a234acbf430329993b5f5a0ed1ac201053de0 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 12:40:01 +0300
Subject: [PATCH 44/75] include data files in the package

---
 wrappers/python/MANIFEST.in | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/wrappers/python/MANIFEST.in b/wrappers/python/MANIFEST.in
index 12cc448ab9..b26a0dc0e7 100644
--- a/wrappers/python/MANIFEST.in
+++ b/wrappers/python/MANIFEST.in
@@ -9,4 +9,10 @@ prune src/swig_doxygen/doxygen/html
 prune src/swig_doxygen/doxygen/xml
 global-exclude CMakeLists.txt
 graft openmm/lib
-graft openmm/include
\ No newline at end of file
+graft openmm/include
+include openmm/app/data/*.xml
+include openmm/app/data/*.pdb
+include openmm/app/data/amber14/*.xml
+include openmm/app/data/amber19/*.xml
+include openmm/app/data/charmm36/*.xml
+include openmm/app/data/implicit/*.xml
\ No newline at end of file

From 556e93f219504abca99601265ef0f9d416d00a88 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 13:06:09 +0300
Subject: [PATCH 45/75] resolve github warning

---
 .github/workflows/publish.yml  | 2 ++
 wrappers/python/pyproject.toml | 5 -----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 7de2cab4f3..83028c26ab 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -8,6 +8,8 @@ jobs:
   build:
     name: Build wheels on ${{ matrix.os }}-${{ matrix.accelerator }}
     runs-on: ${{ matrix.os }}
+    permissions:
+      contents: read
     strategy:
       fail-fast: false
       matrix:
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index dc8a5ad4b4..824872a874 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -18,15 +18,10 @@ classifiers = [
 [tool.setuptools.packages.find]
 include = ["openmm*", "simtk*"]
 
-
-# [tool.setuptools.exclude-package-data]
-# "*" = ["*.c", "*.cpp", "*.h", "*.cuh", "*.cu", ".gitignore"]
-
 [build-system]
 requires = ["setuptools>=78", "setuptools-scm>=8", "numpy", "cython"]
 build-backend = "setuptools.build_meta"
 
-
 [tool.cibuildwheel]
 skip = ["cp38-*", "pp*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
 test-requires = ["pytest"]

From f1c37838b337bbc55df8c6442af7877e9cfafaae Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 13:12:19 +0300
Subject: [PATCH 46/75] cleanup

---
 wrappers/python/MANIFEST.in | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/wrappers/python/MANIFEST.in b/wrappers/python/MANIFEST.in
index b26a0dc0e7..12cc448ab9 100644
--- a/wrappers/python/MANIFEST.in
+++ b/wrappers/python/MANIFEST.in
@@ -9,10 +9,4 @@ prune src/swig_doxygen/doxygen/html
 prune src/swig_doxygen/doxygen/xml
 global-exclude CMakeLists.txt
 graft openmm/lib
-graft openmm/include
-include openmm/app/data/*.xml
-include openmm/app/data/*.pdb
-include openmm/app/data/amber14/*.xml
-include openmm/app/data/amber19/*.xml
-include openmm/app/data/charmm36/*.xml
-include openmm/app/data/implicit/*.xml
\ No newline at end of file
+graft openmm/include
\ No newline at end of file

From d6bcc3c91debe87b16c9b340dae47c5193c840dc Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 13:14:10 +0300
Subject: [PATCH 47/75] actions permissions

---
 .github/workflows/workflow.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index f3fb10801e..45eab0be08 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -1,6 +1,4 @@
 name: Whole
-permissions:
-  contents: read
 
 on: [push]
 

From 5346fdf8b5ce7478781eb771bfbfe72c2372b10d Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 13:37:03 +0300
Subject: [PATCH 48/75] fix windows path for cd

---
 wrappers/python/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 824872a874..7a80969145 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -33,7 +33,7 @@ environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 
 [tool.cibuildwheel.windows]
 before-all = "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
-test-command = "cd {project}/wrappers/python/tests; pytest"
+test-command = "cd {project}\\wrappers\\python\\tests; pytest"
 
 [tool.cibuildwheel.linux]
 before-all = "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"

From 51edeaf430884fc025f344adb286609a239b9c2b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 13:52:36 +0300
Subject: [PATCH 49/75] fix windows again?

---
 wrappers/python/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 7a80969145..7a3f52628c 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -33,7 +33,7 @@ environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 
 [tool.cibuildwheel.windows]
 before-all = "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
-test-command = "cd {project}\\wrappers\\python\\tests; pytest"
+test-command = "cd {project}\\wrappers\\python\\tests && pytest"
 
 [tool.cibuildwheel.linux]
 before-all = "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"

From 501b42ad938fee5c5763c9cce36864cf7cff6e86 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 14:11:13 +0300
Subject: [PATCH 50/75] fix windows again?

---
 wrappers/python/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 7a3f52628c..a40db6fcb3 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -33,7 +33,7 @@ environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 
 [tool.cibuildwheel.windows]
 before-all = "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
-test-command = "cd {project}\\wrappers\\python\\tests && pytest"
+test-command = "cd {project}\\wrappers\\python\\tests && pytest {project}\\wrappers\\python\\tests"
 
 [tool.cibuildwheel.linux]
 before-all = "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"

From 347bfb9e345f0bc7496b950374e91efcd3ce6ba7 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 15:49:47 +0300
Subject: [PATCH 51/75] symlink the test files into current directory hoping
 windows pytest might work

---
 .../cibuildwheel_support/prepare_build_environment_windows.sh   | 2 ++
 wrappers/python/pyproject.toml                                  | 2 +-
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index dd10df9951..2daae832b2 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -67,3 +67,5 @@ cd ..
 cp -r build/python/* wrappers/python/
 cp -r build/openmm-install/include wrappers/python/openmm/
 cp -r build/openmm-install/lib wrappers/python/openmm/
+
+ln -s wrappers/python/tests/systems .
\ No newline at end of file
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index a40db6fcb3..37e1d1d521 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -33,7 +33,7 @@ environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 
 [tool.cibuildwheel.windows]
 before-all = "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
-test-command = "cd {project}\\wrappers\\python\\tests && pytest {project}\\wrappers\\python\\tests"
+test-command = "pytest {project}/wrappers/python/tests"
 
 [tool.cibuildwheel.linux]
 before-all = "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"

From 60a31684aa996b6a72ed80495b88458181729b58 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 16:31:29 +0300
Subject: [PATCH 52/75] ls the symlink

---
 .../cibuildwheel_support/prepare_build_environment_windows.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 2daae832b2..eaac2db247 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -68,4 +68,6 @@ cp -r build/python/* wrappers/python/
 cp -r build/openmm-install/include wrappers/python/openmm/
 cp -r build/openmm-install/lib wrappers/python/openmm/
 
-ln -s wrappers/python/tests/systems .
\ No newline at end of file
+ln -s wrappers/python/tests/systems .
+
+ls -la ./systems/
\ No newline at end of file

From 112392d67bd6b6ee30a8c26cca9397078aac5573 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 16:48:58 +0300
Subject: [PATCH 53/75] try with cp

---
 .../cibuildwheel_support/prepare_build_environment_windows.sh   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index eaac2db247..f2ed63cdd9 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -68,6 +68,6 @@ cp -r build/python/* wrappers/python/
 cp -r build/openmm-install/include wrappers/python/openmm/
 cp -r build/openmm-install/lib wrappers/python/openmm/
 
-ln -s wrappers/python/tests/systems .
+cp -r wrappers/python/tests/systems .
 
 ls -la ./systems/
\ No newline at end of file

From 1c19a5160a48e70aede8be08399060b0428fa8ca Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 23 May 2025 16:50:12 +0300
Subject: [PATCH 54/75] try cping right before the pytest

---
 .../cibuildwheel_support/prepare_build_environment_windows.sh | 4 ----
 wrappers/python/pyproject.toml                                | 2 +-
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index f2ed63cdd9..dd10df9951 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -67,7 +67,3 @@ cd ..
 cp -r build/python/* wrappers/python/
 cp -r build/openmm-install/include wrappers/python/openmm/
 cp -r build/openmm-install/lib wrappers/python/openmm/
-
-cp -r wrappers/python/tests/systems .
-
-ls -la ./systems/
\ No newline at end of file
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 37e1d1d521..86c0f91cd6 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -33,7 +33,7 @@ environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 
 [tool.cibuildwheel.windows]
 before-all = "bash wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh"
-test-command = "pytest {project}/wrappers/python/tests"
+test-command = "cp -r {project}/wrappers/python/tests/systems . && pytest {project}/wrappers/python/tests"
 
 [tool.cibuildwheel.linux]
 before-all = "wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh"

From 061fab2933a9b73b2eadefbab5411359c839333b Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 26 May 2025 15:22:43 +0300
Subject: [PATCH 55/75] conda publishing

---
 .github/workflows/conda_publish.yaml          | 250 ++++++++++++++++++
 conda_package/README.md                       |  10 +
 conda_package/recipe/build_openmm.bat         |  44 +++
 conda_package/recipe/build_openmm.sh          |  85 ++++++
 conda_package/recipe/meta.yaml                | 145 ++++++++++
 conda_package/recipe/patch_osx_tests.py       |  22 ++
 conda_package/recipe/test_openmm.bat          | 107 ++++++++
 conda_package/recipe/test_openmm.sh           |  91 +++++++
 conda_package/scripts/setup_cuda.ps1          | 102 +++++++
 ...sion11numpy1.22python3.10.____cpython.yaml |  44 +++
 ...rsion11numpy1.22python3.9.____cpython.yaml |  44 +++
 ...sion11numpy1.23python3.11.____cpython.yaml |  44 +++
 ...sion11numpy1.26python3.12.____cpython.yaml |  44 +++
 ...sion12numpy1.22python3.10.____cpython.yaml |  44 +++
 ...rsion12numpy1.22python3.9.____cpython.yaml |  44 +++
 ...sion12numpy1.23python3.11.____cpython.yaml |  44 +++
 ...sion12numpy1.26python3.12.____cpython.yaml |  44 +++
 ...pencl_implapplepython3.10.____cpython.yaml |  43 +++
 ...opencl_implapplepython3.9.____cpython.yaml |  43 +++
 ...ncl_implkhronospython3.10.____cpython.yaml |  43 +++
 ...encl_implkhronospython3.9.____cpython.yaml |  43 +++
 ...pencl_implapplepython3.11.____cpython.yaml |  43 +++
 ...ncl_implkhronospython3.11.____cpython.yaml |  43 +++
 ...pencl_implapplepython3.12.____cpython.yaml |  43 +++
 ...ncl_implkhronospython3.12.____cpython.yaml |  43 +++
 ...pencl_implapplepython3.10.____cpython.yaml |  43 +++
 ...opencl_implapplepython3.9.____cpython.yaml |  43 +++
 ...ncl_implkhronospython3.10.____cpython.yaml |  43 +++
 ...encl_implkhronospython3.9.____cpython.yaml |  43 +++
 ...pencl_implapplepython3.11.____cpython.yaml |  43 +++
 ...ncl_implkhronospython3.11.____cpython.yaml |  43 +++
 ...pencl_implapplepython3.12.____cpython.yaml |  43 +++
 ...ncl_implkhronospython3.12.____cpython.yaml |  43 +++
 ...on12.0numpy1.22python3.10.____cpython.yaml |  29 ++
 ...ion12.0numpy1.22python3.9.____cpython.yaml |  29 ++
 ...on12.0numpy1.23python3.11.____cpython.yaml |  29 ++
 ...on12.0numpy1.26python3.12.____cpython.yaml |  29 ++
 ...on11.8numpy1.22python3.10.____cpython.yaml |  29 ++
 ...ion11.8numpy1.22python3.9.____cpython.yaml |  29 ++
 ...on11.8numpy1.23python3.11.____cpython.yaml |  29 ++
 ...on11.8numpy1.26python3.12.____cpython.yaml |  29 ++
 41 files changed, 2128 insertions(+)
 create mode 100644 .github/workflows/conda_publish.yaml
 create mode 100644 conda_package/README.md
 create mode 100644 conda_package/recipe/build_openmm.bat
 create mode 100644 conda_package/recipe/build_openmm.sh
 create mode 100644 conda_package/recipe/meta.yaml
 create mode 100644 conda_package/recipe/patch_osx_tests.py
 create mode 100644 conda_package/recipe/test_openmm.bat
 create mode 100644 conda_package/recipe/test_openmm.sh
 create mode 100644 conda_package/scripts/setup_cuda.ps1
 create mode 100644 conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.10.____cpython.yaml
 create mode 100644 conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.9.____cpython.yaml
 create mode 100644 conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.23python3.11.____cpython.yaml
 create mode 100644 conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.26python3.12.____cpython.yaml
 create mode 100644 conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.10.____cpython.yaml
 create mode 100644 conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.9.____cpython.yaml
 create mode 100644 conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.23python3.11.____cpython.yaml
 create mode 100644 conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.26python3.12.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.10.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.9.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.23opencl_implapplepython3.11.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.26opencl_implapplepython3.12.____cpython.yaml
 create mode 100644 conda_package/variants/osx_64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.10.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.9.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.23opencl_implapplepython3.11.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.26opencl_implapplepython3.12.____cpython.yaml
 create mode 100644 conda_package/variants/osx_arm64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.10.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.9.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.23python3.11.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.26python3.12.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.10.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.9.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.23python3.11.____cpython.yaml
 create mode 100644 conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.26python3.12.____cpython.yaml

diff --git a/.github/workflows/conda_publish.yaml b/.github/workflows/conda_publish.yaml
new file mode 100644
index 0000000000..041f668991
--- /dev/null
+++ b/.github/workflows/conda_publish.yaml
@@ -0,0 +1,250 @@
+name: Test code and publish package
+
+on:
+  push:
+    tags:
+    - 'v*'
+
+jobs:
+  deploy_linux_cuda11:
+    strategy:
+      fail-fast: false
+      matrix:
+        config_file:
+          [
+            "conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.9.____cpython.yaml",
+            "conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.10.____cpython.yaml",
+            "conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.23python3.11.____cpython.yaml",
+            "conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.26python3.12.____cpython.yaml",
+          ]
+
+    runs-on: ubuntu-latest
+    container: quay.io/condaforge/linux-anvil-cuda:11.8
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Build openmm package
+        shell: bash -l {0}
+        run: |
+          git config --global --add safe.directory '*'
+          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
+        env:
+          OPENMM_VERSION: ${{ github.ref_name }}
+          OPENMM_COMMIT: ${{ github.sha }}
+
+      - name: Upload to conda
+        shell: bash -l {0}
+        run: |
+          /opt/conda/bin/anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/linux-64/openmm-*.tar.bz2 --skip-existing
+
+  deploy_linux_cuda12:
+    strategy:
+      fail-fast: false
+      matrix:
+        config_file:
+          [
+            "conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.9.____cpython.yaml",
+            "conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.10.____cpython.yaml",
+            "conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.23python3.11.____cpython.yaml",
+            "conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.26python3.12.____cpython.yaml",
+          ]
+
+    runs-on: ubuntu-latest
+    container: quay.io/condaforge/linux-anvil-cos7-x86_64
+
+    steps:
+      - uses: actions/checkout@v1
+
+      - name: Build openmm package
+        shell: bash -l {0}
+        run: |
+          git config --global --add safe.directory '*'
+          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
+        env:
+          OPENMM_VERSION: ${{ github.ref_name }}
+          OPENMM_COMMIT: ${{ github.sha }}
+
+      - name: Upload to conda
+        shell: bash -l {0}
+        run: |
+          /opt/conda/bin/anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/linux-64/openmm-*.tar.bz2 --skip-existing
+
+  deploy_osx_64:
+    strategy:
+      fail-fast: false
+      matrix:
+        config_file:
+          [
+            "conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.9.____cpython.yaml",
+            "conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.9.____cpython.yaml",
+            "conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml",
+            "conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml",
+            "conda_package/variants/osx_64_numpy1.23opencl_implapplepython3.11.____cpython.yaml",
+            "conda_package/variants/osx_64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml",
+            "conda_package/variants/osx_64_numpy1.26opencl_implapplepython3.12.____cpython.yaml",
+            "conda_package/variants/osx_64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml",
+          ]
+    runs-on: macos-13
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: ../deploy-env
+          python-version: "3.10"
+
+      - name: Build openmm package
+        shell: bash -l {0}
+        run: |
+          git config --global --add safe.directory '*'
+          conda install anaconda-client conda-build
+          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
+        env:
+          OPENMM_VERSION: ${{ github.ref_name }}
+          OPENMM_COMMIT: ${{ github.sha }}
+
+      - name: Upload to conda
+        shell: bash -l {0}
+        run: |
+          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.conda --skip-existing
+
+  deploy_osx_arm64:
+    strategy:
+      fail-fast: false
+      matrix:
+        config_file:
+          [
+            "conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.10.____cpython.yaml",
+            "conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.9.____cpython.yaml",
+            "conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml",
+            "conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml",
+            "conda_package/variants/osx_arm64_numpy1.23opencl_implapplepython3.11.____cpython.yaml",
+            "conda_package/variants/osx_arm64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml",
+            "conda_package/variants/osx_arm64_numpy1.26opencl_implapplepython3.12.____cpython.yaml",
+            "conda_package/variants/osx_arm64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml",
+          ]
+    runs-on: macos-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: ../deploy-env
+          python-version: "3.10"
+
+      - name: Build openmm package
+        shell: bash -l {0}
+        run: |
+          git config --global --add safe.directory '*'
+          conda install anaconda-client conda-build
+          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
+        env:
+          OPENMM_VERSION: ${{ github.ref_name }}
+          OPENMM_COMMIT: ${{ github.sha }}
+
+      - name: Upload to conda
+        shell: bash -l {0}
+        run: |
+          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.conda --skip-existing
+
+  deploy_win_64_cuda11:
+    strategy:
+      fail-fast: false
+      matrix:
+        config_file:
+          [
+            "conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.10.____cpython.yaml",
+            "conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.9.____cpython.yaml",
+            "conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.23python3.11.____cpython.yaml",
+            "conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.26python3.12.____cpython.yaml",
+          ]
+    runs-on: windows-2022
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: ../deploy-env
+          python-version: "3.10"
+          channels: conda-forge
+
+      - name: Add msbuild to PATH
+        uses: microsoft/setup-msbuild@v2
+
+      - name: Setup CUDA Toolkit
+        id: cuda-toolkit
+        shell: pwsh
+        run: scripts/setup_cuda.ps1
+        env:
+          INPUT_CUDA_VERSION: 11.8.0
+
+      - name: Build openmm package
+        shell: bash -l {0}
+        run: |
+          git config --global --add safe.directory '*'
+          conda install anaconda-client conda-build
+          conda clean --all -y
+          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
+        env:
+          OPENMM_VERSION: ${{ github.ref_name }}
+          OPENMM_COMMIT: ${{ github.sha }}
+
+      - name: Upload to conda
+        shell: bash -l {0}
+        run: |
+          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.tar.bz2 --skip-existing
+
+  deploy_win_64_cuda12:
+    strategy:
+      fail-fast: false
+      matrix:
+        config_file:
+          [
+            "conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.10.____cpython.yaml",
+            "conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.9.____cpython.yaml",
+            "conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.23python3.11.____cpython.yaml",
+            "conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.26python3.12.____cpython.yaml",
+          ]
+    runs-on: windows-2022
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: ../deploy-env
+          python-version: "3.10"
+
+      - name: Add msbuild to PATH
+        uses: microsoft/setup-msbuild@v2
+
+      - name: Setup CUDA Toolkit
+        id: cuda-toolkit
+        shell: pwsh
+        run: scripts/setup_cuda.ps1
+        env:
+          INPUT_CUDA_VERSION: 12.0.0
+
+      - name: Build openmm package
+        shell: bash -l {0}
+        run: |
+          git config --global --add safe.directory '*'
+          conda install anaconda-client conda-build
+          conda clean --all -y
+          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
+        env:
+          OPENMM_VERSION: ${{ github.ref_name }}
+          OPENMM_COMMIT: ${{ github.sha }}
+
+      - name: Upload to conda
+        shell: bash -l {0}
+        run: |
+          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.tar.bz2 --skip-existing
diff --git a/conda_package/README.md b/conda_package/README.md
new file mode 100644
index 0000000000..bf4b2743d3
--- /dev/null
+++ b/conda_package/README.md
@@ -0,0 +1,10 @@
+# OpeMM Feedstock by Acellera
+
+This is a partial fork of the conda-forge feedstock for OpenMM.
+The idea is to be able to quickly create OpenMM release candidates from specific commits without having to wait for an official OpenMM release.
+
+To create a new release you need to:
+
+1. Open the recipe/meta.yaml file and change the package version at the top of the file.
+2. Update the git_rev version in the meta.yaml file in the source section to point to the desired commit.
+3. Push your changes
diff --git a/conda_package/recipe/build_openmm.bat b/conda_package/recipe/build_openmm.bat
new file mode 100644
index 0000000000..04fcdc30ca
--- /dev/null
+++ b/conda_package/recipe/build_openmm.bat
@@ -0,0 +1,44 @@
+@echo on
+
+mkdir build
+cd build
+
+set "CUDA_TOOLKIT_ROOT_DIR=%CUDA_PATH:\=/%"
+
+if "%with_test_suite%"=="true" (
+    set "CMAKE_FLAGS=-DBUILD_TESTING=ON  -DOPENMM_BUILD_CUDA_TESTS=ON  -DOPENMM_BUILD_OPENCL_TESTS=ON"
+) else (
+    set "CMAKE_FLAGS=-DBUILD_TESTING=OFF -DOPENMM_BUILD_CUDA_TESTS=OFF -DOPENMM_BUILD_OPENCL_TESTS=OFF"
+)
+
+cmake.exe .. -G "NMake Makefiles JOM" ^
+    -DCMAKE_BUILD_TYPE=Release ^
+    -DCMAKE_INSTALL_PREFIX="%LIBRARY_PREFIX%" ^
+    -DCMAKE_PREFIX_PATH="%LIBRARY_PREFIX%" ^
+    -DCUDA_TOOLKIT_ROOT_DIR="%CUDA_TOOLKIT_ROOT_DIR%" ^
+    -DOPENCL_INCLUDE_DIR="%LIBRARY_INC%" ^
+    -DOPENCL_LIBRARY="%LIBRARY_LIB%\opencl.lib" ^
+    %CMAKE_FLAGS% ^
+    || goto :error
+
+jom -j %NUMBER_OF_PROCESSORS% || goto :error
+jom -j %NUMBER_OF_PROCESSORS% install || goto :error
+jom -j %NUMBER_OF_PROCESSORS% PythonInstall || goto :error
+
+:: Better location for examples
+mkdir %LIBRARY_PREFIX%\share\openmm || goto :error
+move %LIBRARY_PREFIX%\examples %LIBRARY_PREFIX%\share\openmm || goto :error
+
+if "%with_test_suite%"=="true" (
+    mkdir %LIBRARY_PREFIX%\share\openmm\tests\ || goto :error
+    find . -name "Test*" -type f -exec cp "{}" %LIBRARY_PREFIX%\share\openmm\tests\ ; || goto :error
+    robocopy /E python\tests\ %LIBRARY_PREFIX%\share\openmm\tests\python
+    if %errorlevel% GTR 1 ( exit /b %errorlevel% )
+)
+
+
+goto :EOF
+
+:error
+echo Failed with error #%errorlevel%.
+exit /b %errorlevel%
diff --git a/conda_package/recipe/build_openmm.sh b/conda_package/recipe/build_openmm.sh
new file mode 100644
index 0000000000..1ad92c63a8
--- /dev/null
+++ b/conda_package/recipe/build_openmm.sh
@@ -0,0 +1,85 @@
+#!/bin/bash
+
+set -ex
+
+
+CMAKE_FLAGS="${CMAKE_ARGS} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_TYPE=Release"
+if [[ "$with_test_suite" == "true" ]]; then
+    CMAKE_FLAGS+=" -DBUILD_TESTING=ON -DOPENMM_BUILD_OPENCL_TESTS=ON"
+else
+    CMAKE_FLAGS+=" -DBUILD_TESTING=OFF"
+fi
+
+
+if [[ "$target_platform" == linux* ]]; then
+    # CFLAGS
+    # JRG: Had to add -ldl to prevent linking errors (dlopen, etc)
+    MINIMAL_CFLAGS+=" -O3 -ldl"
+    CFLAGS+=" $MINIMAL_CFLAGS"
+    CXXFLAGS+=" $MINIMAL_CFLAGS"
+
+    # CUDA is enabled in these platforms
+    if [[ "$target_platform" == linux-64 || "$target_platform" == linux-ppc64le ]]; then
+        # # CUDA_HOME is defined by nvcc metapackage
+        CMAKE_FLAGS+=" -DCUDA_TOOLKIT_ROOT_DIR=${CUDA_HOME}"
+        # CUDA tests won't build, disable for now
+        # See https://github.com/openmm/openmm/issues/2258#issuecomment-462223634
+        CMAKE_FLAGS+=" -DOPENMM_BUILD_CUDA_TESTS=OFF"
+        # shadow some CMAKE_ARGS bits that interfere with CUDA detection
+        CMAKE_FLAGS+=" -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=BOTH"
+    fi
+
+    # OpenCL ICD
+    CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=${PREFIX}/include"
+    CMAKE_FLAGS+=" -DOPENCL_LIBRARY=${PREFIX}/lib/libOpenCL${SHLIB_EXT}"
+
+elif [[ "$target_platform" == osx* ]]; then
+    if [[ "$opencl_impl" == khronos ]]; then
+        CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=${PREFIX}/include"
+        CMAKE_FLAGS+=" -DOPENCL_LIBRARY=${PREFIX}/lib/libOpenCL${SHLIB_EXT}"
+    fi
+    # When using opencl_impl == apple, CMake will auto-locate it, so no need to provide the flags
+    # On Conda Forge, this will result in:
+    #   /Applications/Xcode_12.app/Contents/Developer/Platforms/MacOSX.platform/Developer/...
+    #   ...SDKs/MacOSX10.9.sdk/System/Library/Frameworks/OpenCL.framework
+    # On local builds, it might be:
+    #   /System/Library/Frameworks/OpenCL.framework/OpenCL
+fi
+
+# Set location for FFTW3 on both linux and mac
+CMAKE_FLAGS+=" -DFFTW_INCLUDES=${PREFIX}/include/"
+CMAKE_FLAGS+=" -DFFTW_LIBRARY=${PREFIX}/lib/libfftw3f${SHLIB_EXT}"
+CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=${PREFIX}/lib/libfftw3f_threads${SHLIB_EXT}"
+# Disambiguate swig location
+CMAKE_FLAGS+=" -DSWIG_EXECUTABLE=$(which swig)"
+
+# Build in subdirectory and install.
+mkdir -p build
+cd build
+cmake ${CMAKE_FLAGS} ${SRC_DIR}
+make -j$CPU_COUNT
+make -j$CPU_COUNT install PythonInstall
+
+# Put examples into an appropriate subdirectory.
+mkdir -p ${PREFIX}/share/openmm/
+mv ${PREFIX}/examples ${PREFIX}/share/openmm/
+
+# Fix some overlinking warnings/errors
+for lib in ${PREFIX}/lib/plugins/*${SHLIB_EXT}; do
+    ln -s $lib ${PREFIX}/lib/$(basename $lib) || true
+done
+
+if [[ "$with_test_suite" == "true" ]]; then
+    mkdir -p ${PREFIX}/share/openmm/tests/
+    # BSD find vs GNU find: -executable is only available in GNU find
+    # +0111 is somehow equivalent in BSD, but that's not compatible in GNU
+    # so we use different commands for each...
+    if [[ "$target_platform" == osx* ]]; then
+        find . -name "Test*" -perm +0111 -type f \
+            -exec python $RECIPE_DIR/patch_osx_tests.py "{}" \; \
+            -exec cp "{}" $PREFIX/share/openmm/tests/ \;
+    else
+        find . -name "Test*" -executable -type f -exec cp "{}" $PREFIX/share/openmm/tests/ \;
+    fi
+    cp -r python/tests $PREFIX/share/openmm/tests/python
+fi
diff --git a/conda_package/recipe/meta.yaml b/conda_package/recipe/meta.yaml
new file mode 100644
index 0000000000..af1de683d3
--- /dev/null
+++ b/conda_package/recipe/meta.yaml
@@ -0,0 +1,145 @@
+{% set name = "openmm" %}
+{% set version = environ.get("OPENMM_VERSION", "")[1:] %}
+{% set build = 0 %}
+{% set with_test_suite = "false" %}
+#{% set with_test_suite = "true" %}  # [(osx and arm64)]
+
+{% if cuda_compiler_version in (None, "None", True, False) %}
+{% set cuda_major = 0 %}
+{% else %}
+{% set cuda_major = environ.get("cuda_compiler_version", "11.8").split(".")[0] | int %}
+{% endif %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  git_url: https://github.com/Acellera/{{ name }}.git
+  git_rev: {{ environ.get("OPENMM_COMMIT", "") }}
+
+build:
+  number: {{ build }}
+  string: "py{{ PY_VER.replace('.', '') }}h{{ PKG_HASH }}_{{ build }}_{{ opencl_impl }}"  # [osx]
+  track_features:  # make Apple OpenCL low priority
+    - openmm_opencl_apple  # [osx and (opencl_impl == 'apple')]
+  skip: true  # [(cuda_compiler_version in (undefined, 'None') and (linux64 or win)) or ((cuda_compiler_version != '10.2') and (ppc64le))]
+  # see https://github.com/conda-forge/openmm-feedstock/pull/143#issuecomment-2429793569
+  skip: true  # [aarch64 and (cuda_compiler_version == '11.8')]
+  script_env:
+    - CONFIG
+    - CUDA_HOME  # [ppc64le]
+  missing_dso_whitelist:
+    - "*/libcuda.*"    # [linux]
+    - "*/libOpenCL.*"  # [unix]
+    - "*/nvcuda.dll"   # [win]
+  script:
+    - env with_test_suite={{ with_test_suite }} bash {{ RECIPE_DIR }}/build_openmm.sh   # [unix]
+    - set with_test_suite={{ with_test_suite }} &&   {{ RECIPE_DIR }}\build_openmm.bat  # [win]
+
+requirements:
+  build:
+    - python                                 # [build_platform != target_platform]
+    - cross-python_{{ target_platform }}     # [build_platform != target_platform]
+    - cython                                 # [build_platform != target_platform]
+    - numpy                                  # [build_platform != target_platform]
+    - swig                                   # [build_platform != target_platform]
+    - {{ compiler('c') }}
+    - {{ stdlib("c") }}
+    - {{ compiler('cxx') }}
+    - {{ compiler('cuda') }}  # [(linux or win) and cuda_compiler != "None"]
+    - cuda-version {{ cuda_compiler_version }}  # [(cuda_compiler_version or "None") != "None"]
+    - {{ cdt('mesa-libgl-devel') }}  # [linux]
+    - cmake
+    - make  # [unix]
+    - jom  # [win]
+    # needed for Python wrappers
+    - doxygen
+{% if with_test_suite == 'true' %}
+    - conda-build  # [osx]
+    - m2-findutils  # [win]
+    - m2-coreutils  # [win]
+{% endif %}
+
+  host:
+    - python
+    - swig
+    - pthread-stubs
+    - lxml
+    - numpy
+    - cython
+    - setuptools
+    # OpenCL ICD
+    - ocl-icd  # [linux]
+    - khronos-opencl-icd-loader  # [win or (osx and opencl_impl == 'khronos')]
+    - cuda-version {{ cuda_compiler_version }}  # [(cuda_compiler_version or "None") != "None"]
+    {% if cuda_major >= 12 %}
+    - libcufft-dev  # [linux or win]
+    - cuda-profiler-api  # [linux or win]
+    - cuda-nvrtc-dev  # [linux or win]
+    # No cuda-driver-dev in windows
+    - cuda-driver-dev  # [linux]
+    {% endif %}
+  run:
+    - python
+    - numpy
+    - scipy <1.14
+    # OpenCL ICD
+    - ocl-icd  # [linux]
+    - ocl-icd-system  # [linux]
+    - khronos-opencl-icd-loader  # [win or (osx and opencl_impl == 'khronos')]
+    - ocl_icd_wrapper_apple      # [osx and opencl_impl == 'khronos']
+
+  run_constrained:
+    - khronos-opencl-icd-loader  ==9999999999  # [osx and opencl_impl == 'apple']
+    - ocl_icd_wrapper_apple      ==9999999999  # [osx and opencl_impl == 'apple']
+
+test:
+  requires:
+    # - git
+    - pocl      # [linux]
+    {% if cuda_major >= 12 %}
+    # No cuda-driver-dev nor cuda-compat in windows
+    - cuda-driver-dev  # [linux]
+    - cuda-compat  # [linux]
+    {% endif %}
+{% if with_test_suite == 'true' %}
+    - pytest
+    - pytest-xdist
+{% endif %}
+  files:
+    - test_openmm.sh   # [unix]
+    - test_openmm.bat  # [win]
+  imports:
+    - openmm
+  commands:
+    - env with_test_suite={{ with_test_suite }} bash test_openmm.sh   # [unix]
+    - set with_test_suite={{ with_test_suite }} && .\test_openmm.bat  # [win]
+
+about:
+  home: http://openmm.org
+  license: LGPL-3.0-or-later
+  license_family: LGPL
+  license_file:
+    - docs-source/licenses/Licenses.txt
+    - docs-source/licenses/LGPL.txt
+    - docs-source/licenses/GPL.txt
+  summary: A high performance toolkit for molecular simulation.
+
+  description: |
+    OpenMM is a toolkit for molecular simulation. It can be used either as a
+    stand-alone application for running simulations, or as a library you call
+    from your own code. It provides a combination of extreme flexibility
+    (through custom forces and integrators), openness, and high performance
+    (especially on recent GPUs) that make it truly unique among simulation
+    codes. OpenMM is MIT licensed with some LGPL portions (CUDA and OpenCL
+    platforms).
+  doc_url: http://docs.openmm.org
+  dev_url: https://github.com/openmm/openmm
+
+extra:
+  recipe-maintainers:
+    - mikemhenry
+    - jchodera
+    - jaimergp
+    - peastman
diff --git a/conda_package/recipe/patch_osx_tests.py b/conda_package/recipe/patch_osx_tests.py
new file mode 100644
index 0000000000..8ddbe86b9e
--- /dev/null
+++ b/conda_package/recipe/patch_osx_tests.py
@@ -0,0 +1,22 @@
+import os
+import sys
+from pathlib import Path
+from conda_build.os_utils import macho
+
+
+def name_callback(path, dylib):
+    prefix = os.environ["SRC_DIR"]
+    if prefix.endswith("/"):
+        prefix = prefix[:-1]
+
+    if dylib["name"].startswith(prefix):
+        return f"@rpath/{Path(dylib['name']).name}"
+
+
+def main(path):
+    dylibs = macho.otool(path)
+    macho.install_name_change(path, None, name_callback, dylibs, verbose=True)
+
+
+if __name__ == "__main__":
+    main(sys.argv[1])
\ No newline at end of file
diff --git a/conda_package/recipe/test_openmm.bat b/conda_package/recipe/test_openmm.bat
new file mode 100644
index 0000000000..1930ed6bb2
--- /dev/null
+++ b/conda_package/recipe/test_openmm.bat
@@ -0,0 +1,107 @@
+@echo on
+
+:: Are we running on CI? CONFIG is defined for the whole Azure pipeline
+:: and we are bringing it in through `script_env` in meta.yaml
+if not "%CONFIG%"=="" set CI="True"
+
+:: Existence tests
+if not exist %LIBRARY_LIB%/OpenMM.lib exit 1
+if not exist %LIBRARY_LIB%/plugins/OpenMMCPU.lib exit 1
+if not exist %LIBRARY_LIB%/plugins/OpenMMPME.lib exit 1
+if not exist %LIBRARY_LIB%/plugins/OpenMMOpenCL.lib exit 1
+if not exist %LIBRARY_LIB%/plugins/OpenMMCUDA.lib exit 1
+
+:: Debug silent errors in plugin loading
+python -c "import openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
+
+:: Check that hardcoded library path was correctly replaced by conda-build
+python -c "import os, openmm.version as v; print(v.openmm_library_path); assert os.path.isdir(v.openmm_library_path), 'Directory does not exist'" || goto :error
+
+:: Check all platforms
+python -m openmm.testInstallation
+
+:: On CI, Windows will only see 2 platforms because the driver nvcuda.dll is missing and that throws a 126 error
+:: We expect that people running this locally will have Nvidia properly installed, so they should all platforms (4)
+if "%CI%"=="" (
+    set n_platforms=4
+) else (
+    set n_platforms=2
+)
+python -c "from openmm import Platform as P; n = P.getNumPlatforms(); assert n == %n_platforms%, f'n_platforms ({n}) != %n_platforms%'" || goto :error
+
+:: Now let's run a little MD
+cd %LIBRARY_PREFIX%/share/openmm/examples
+python benchmark.py --test=rf --seconds=10 --platform=Reference || goto :error
+python benchmark.py --test=rf --seconds=10 --platform=CPU || goto :error
+if "%CI%"=="" (
+    python benchmark.py --test=rf --seconds=10 --platform=CUDA  || goto :error
+    python benchmark.py --test=rf --seconds=10 --platform=OpenCL  || goto :error
+)
+
+:: Check version metadata looks ok, only for final releases, RCs are not checked!
+:: See https://stackoverflow.com/a/7006016/3407590 for substring checks in CMD
+if x%PKG_VERSION:rc=%==x%PKG_VERSION% (
+    if x%PKG_VERSION:beta=%==x%PKG_VERSION% (
+	if x%PKG_VERSION:dev=%==x%PKG_VERSION% (
+            python -c "from openmm import Platform; v = Platform.getOpenMMVersion(); assert '%PKG_VERSION%' in (v, v+'.0'), v + '!=%PKG_VERSION%'"  || goto :error
+            for /f "usebackq tokens=1" %%a in (`git ls-remote https://github.com/openmm/openmm.git %PKG_VERSION%`) do (
+            python -c "from openmm.version import git_revision; r = git_revision; assert r == '%%a', r + '!=%%a'" || goto :error
+         )
+	)
+    )
+) else (
+    echo "!!! WARNING !!!"
+    echo "This is a release candidate build (%PKG_VERSION%). Please check versions and git hashes manually!"
+)
+
+
+(set \n=^
+%=This hack is required to store newlines=%
+)
+
+:: Run the full test suite, if requested
+if "%with_test_suite%"=="true" (
+    SETLOCAL EnableDelayedExpansion
+    @echo off
+    cd %LIBRARY_PREFIX%\share\openmm\tests
+
+    :: Start with C++ tests
+    if not "%CI%"=="" (
+        del /Q /F TestCuda* TestOpenCL*
+    )
+    set count=0
+    set exitcode=0
+    set summary=
+    FOR %%F IN ( Test* ) do (
+        set testexe=%%~F
+        set /a count=!count!+1
+        echo;
+        echo #!count!: !testexe!
+        .\!testexe!
+        set thisexitcode=!errorlevel!
+        set summary=!summary!
+        if not "!thisexitcode!"=="0" ( set "summary=!summary!#!count! !testexe!\n!" )
+        set /a exitcode=!exitcode!+!thisexitcode!
+    )
+    if not "!exitcode!"=="0" (
+        echo;
+        echo ------------
+        echo Failed tests
+        echo ------------
+        echo;
+        echo !summary!
+        exit /b !exitcode!
+    )
+    @echo on
+    :: Python unit tests
+    cd python
+    python -m pytest -v -n %CPU_COUNT% || goto :error
+
+    ENDLOCAL
+)
+
+goto :EOF
+
+:error
+echo Failed with error #%errorlevel%.
+exit /b %errorlevel%
diff --git a/conda_package/recipe/test_openmm.sh b/conda_package/recipe/test_openmm.sh
new file mode 100644
index 0000000000..13f760b389
--- /dev/null
+++ b/conda_package/recipe/test_openmm.sh
@@ -0,0 +1,91 @@
+#!/bin/bash
+set -ex
+with_cuda="no"
+
+# Existence tests
+test -f $PREFIX/lib/libOpenMM$SHLIB_EXT
+test -f $PREFIX/lib/plugins/libOpenMMCPU$SHLIB_EXT
+test -f $PREFIX/lib/plugins/libOpenMMPME$SHLIB_EXT
+test -f $PREFIX/lib/plugins/libOpenMMOpenCL$SHLIB_EXT
+if [[ "$target_platform" == linux-64 || "$target_platform" == linux-ppc64le ]]; then
+    with_cuda="yes"
+    test -f $PREFIX/lib/plugins/libOpenMMCUDA$SHLIB_EXT
+fi
+
+## Do they work properly?
+# Debug silent errors in plugin loading
+python -c "import openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
+# Check that hardcoded library path was correctly replaced by conda-build
+python -c "import os, openmm.version as v; print(v.openmm_library_path); assert os.path.isdir(v.openmm_library_path), 'Directory does not exist'"
+
+# Check all platforms
+if [[ "$target_platform" == linux-ppc64le || "$target_platform" == linux-aarch64 ]]; then
+    python -m openmm.testInstallation || true  # OpenCL will fail but that's ok
+else
+    python -m openmm.testInstallation
+fi
+if [[ $with_cuda == yes ]]; then
+    # Linux64 / PPC see all 4 platforms, but CUDA is not usable because there's no GPU there
+    n_platforms=4
+else
+    # MacOS / ARM only see 3 because CUDA is not available there
+    n_platforms=3
+fi
+# testing cuda 12 changes, see https://github.com/conda-forge/openmm-feedstock/pull/108#issuecomment-1692190752
+#python -c "from openmm import Platform as P; n = P.getNumPlatforms(); assert n == $n_platforms, f'n_platforms ({n}) != $n_platforms'"
+
+# Run a small MD
+cd ${PREFIX}/share/openmm/examples
+python benchmark.py --test=rf --seconds=10 --platform=Reference
+python benchmark.py --test=rf --seconds=10 --platform=CPU
+if [[ -z ${CI-} ]]; then  # Run only outside CI, assuming there will be a GPU there
+    python benchmark.py --test=rf --seconds=10 --platform=OpenCL
+    if [[ $with_cuda == yes ]]; then
+        python benchmark.py --test=rf --seconds=10 --platform=CUDA
+    fi
+fi
+
+# Check version metadata looks ok, only for final releases, RCs are not checked!
+if [[ ${PKG_VERSION} != *"rc"* && ${PKG_VERSION} != *"beta"* && ${PKG_VERSION} != *"dev"* ]]; then
+    python -c "from openmm import Platform; v = Platform.getOpenMMVersion(); assert \"$PKG_VERSION\" in (v, v+'.0'), v + \"!=$PKG_VERSION\""
+    git_revision=$(git ls-remote https://github.com/openmm/openmm.git $PKG_VERSION | awk '{ print $1}')
+    python -c "from openmm.version import git_revision; r = git_revision; assert r == \"$git_revision\", r + \"!=$git_revision\""
+else
+    echo "!!! WARNING !!!"
+    echo "This is a release candidate build ($PKG_VERSION). Please check versions and git hashes manually!"
+fi
+
+if [[ $with_test_suite == "true" ]]; then
+    cd $PREFIX/share/openmm/tests
+    set +ex
+
+    # C++ tests
+    summary=""; exitcode=0; count=0;
+    for f in Test*; do
+        if [[ -n ${CI-} && ( $f == *Cuda* || $f == *OpenCL* ) ]]; then continue; fi
+        ((count+=1))
+        echo -e "\n#$count: $f"
+        # Retry three times so stochastic tests have a chance
+        attempts=0
+        while true; do
+            ./${f}
+            thisexitcode=$?
+            ((attempts+=1))
+            if [[ $thisexitcode == 0 || $attempts == 3 ]]; then break; fi
+        done
+        if [[ $thisexitcode != 0 ]]; then summary+="\n#$count ${f}"; fi
+        ((exitcode+=$thisexitcode))
+    done
+    if [[ $exitcode != 0 ]]; then
+        echo "------------"
+        echo "Failed tests"
+        echo "------------"
+        echo -e "${summary}"
+        exit $exitcode
+    fi
+
+    # Python tests
+    set -ex
+    cd python
+    python -m pytest -v -n $CPU_COUNT
+fi
diff --git a/conda_package/scripts/setup_cuda.ps1 b/conda_package/scripts/setup_cuda.ps1
new file mode 100644
index 0000000000..8029aa3be1
--- /dev/null
+++ b/conda_package/scripts/setup_cuda.ps1
@@ -0,0 +1,102 @@
+$CUDA_VERSION_FULL = $env:INPUT_CUDA_VERSION # v12.5.0 or v11.8.0 or v12.0.0
+
+# Make sure CUDA_VERSION_FULL is set and valid, otherwise error.
+# Validate CUDA version, extracting components via regex
+$cuda_ver_matched = $CUDA_VERSION_FULL -match "^(?<major>[1-9][0-9]*)\.(?<minor>[0-9]+)\.(?<patch>[0-9]+)$"
+if(-not $cuda_ver_matched){
+    Write-Output "Invalid CUDA version specified, <major>.<minor>.<patch> required. '$CUDA_VERSION_FULL'."
+    exit 1
+}
+$CUDA_MAJOR=$Matches.major
+$CUDA_MINOR=$Matches.minor
+$CUDA_PATCH=$Matches.patch
+
+Write-Output "Selected CUDA version: $CUDA_VERSION_FULL"
+
+$src = "cuda"
+$dst = "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v$($CUDA_MAJOR).$($CUDA_MINOR)"
+$installer = "cuda.exe"
+
+if ($CUDA_VERSION_FULL -eq "12.5.0") {
+    $downloadUrl = "https://developer.download.nvidia.com/compute/cuda/12.5.0/local_installers/cuda_12.5.0_555.85_windows.exe"
+} elseif ($CUDA_VERSION_FULL -eq "12.0.0") {
+    $downloadUrl = "https://developer.download.nvidia.com/compute/cuda/12.0.0/local_installers/cuda_12.0.0_527.41_windows.exe"
+} elseif ($CUDA_VERSION_FULL -eq "11.8.0") {
+    $downloadUrl = "https://developer.download.nvidia.com/compute/cuda/11.8.0/local_installers/cuda_11.8.0_522.06_windows.exe"
+} else {
+    Write-Output "Unsupported CUDA version specified"
+    exit 1
+}
+
+# Download cuda
+Write-Output "Downloading CUDA from: $downloadUrl"
+if (-not (Test-Path -Path $installer)) {
+    Write-Output "Downloading CUDA installer..."
+    # If the file does not exist, download it
+    & "C:\msys64\usr\bin\wget" $downloadUrl -O $installer -q
+}
+
+# Extract cuda
+if (-not (Test-Path -Path $src -Type Container)) {
+    # Extract CUDA using 7-Zip
+    Write-Output "Extracting CUDA using 7-Zip..."
+    mkdir "$src"
+    & 'C:\Program Files\7-Zip\7z' x $installer -o"$src"
+}
+
+# Create destination directory if it doesn't exist
+if (-Not (Test-Path -Path $dst)) {
+    Write-Output "Creating destination directory: $dst"
+    New-Item -Path $dst -ItemType Directory
+}
+
+# Get directories to process from the source path
+$directories = Get-ChildItem -Directory -Path $src
+$whitelist = @("CUDA_Toolkit_Release_Notes.txt", "DOCS", "EULA.txt", "LICENSE", "README", "version.json")
+
+foreach ($dir in $directories) {
+    # Get all subdirectories and files in the current directory
+    $items = Get-ChildItem -Path (Join-Path $src $dir.Name)
+
+    foreach ($item in $items) {
+        if ($item.PSIsContainer) {
+            # If the item is a directory, copy its contents
+            Write-Output "Copying contents of directory $($item.FullName) to $dst"
+            Copy-Item -Path "$($item.FullName)\*" -Destination $dst -Recurse -Force
+        } else {
+            if ($whitelist -contains $item.Name) {
+                Write-Output "Copying file $($item.FullName) to $dst"
+                Copy-Item -Path $item.FullName -Destination $dst -Force
+            }
+        }
+    }
+}
+
+# Add msbuild cuda extensions
+$msBuildExtensions = (Get-ChildItem  "$src\visual_studio_integration\CUDAVisualStudioIntegration\extras\visual_studio_integration\MSBuildExtensions").fullname
+(Get-ChildItem 'C:\Program Files\Microsoft Visual Studio\2022\*\MSBuild\Microsoft\VC\*\BuildCustomizations').FullName | ForEach-Object { 
+    $destination = $_
+    $msBuildExtensions | ForEach-Object {
+        $extension = $_
+        Copy-Item $extension -Destination $destination -Force
+        Write-Output "Copied $extension to $destination"
+    }
+}
+
+# Add to Github env
+Write-Output "Setting environment variables for GitHub Actions..."
+
+Write-Output "CUDA_PATH=$dst"
+Write-Output "CUDA_PATH_V$($CUDA_MAJOR)_$($CUDA_MINOR)=$dst"
+Write-Output "CUDA_PATH_VX_Y=CUDA_PATH_V$($CUDA_MAJOR)_$($CUDA_MINOR)"
+Write-Output "CUDA_VERSION=$CUDA_VERSION_FULL"
+
+Write-Output "CUDA_PATH=$dst" >> $env:GITHUB_ENV
+Write-Output "CUDA_PATH_V$($CUDA_MAJOR)_$($CUDA_MINOR)=$dst" >> $env:GITHUB_ENV
+Write-Output "CUDA_PATH_VX_Y=CUDA_PATH_V$($CUDA_MAJOR)_$($CUDA_MINOR)" >> $env:GITHUB_ENV
+Write-Output "CudaToolkitDir=$dst" >> $env:GITHUB_ENV
+Write-Output "CMAKE_CUDA_COMPILER=$dst\bin\nvcc.exe" >> $env:GITHUB_ENV
+Write-Output "NVCC_APPEND_FLAGS=-allow-unsupported-compiler" >> $env:GITHUB_ENV
+
+Write-Output "CUDA_VERSION=$CUDA_VERSION_FULL" >> $env:GITHUB_ENV
+Write-Output "Setup completed."
diff --git a/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.10.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.10.____cpython.yaml
new file mode 100644
index 0000000000..6b185941c8
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.10.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '11'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '11'
+docker_image:
+- quay.io/condaforge/linux-anvil-cuda:11.8
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.9.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.9.____cpython.yaml
new file mode 100644
index 0000000000..9ad9e134e0
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.22python3.9.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '11'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '11'
+docker_image:
+- quay.io/condaforge/linux-anvil-cuda:11.8
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.23python3.11.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.23python3.11.____cpython.yaml
new file mode 100644
index 0000000000..d8ab21ac73
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.23python3.11.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '11'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '11'
+docker_image:
+- quay.io/condaforge/linux-anvil-cuda:11.8
+numpy:
+- '1.23'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.26python3.12.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.26python3.12.____cpython.yaml
new file mode 100644
index 0000000000..f7ca5554e2
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version11cuda_compilernvcccuda_compiler_version11.8cxx_compiler_version11numpy1.26python3.12.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '11'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '11'
+docker_image:
+- quay.io/condaforge/linux-anvil-cuda:11.8
+numpy:
+- '1.26'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.10.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.10.____cpython.yaml
new file mode 100644
index 0000000000..50c3797f71
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.10.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '12'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '12'
+docker_image:
+- quay.io/condaforge/linux-anvil-cos7-x86_64
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.9.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.9.____cpython.yaml
new file mode 100644
index 0000000000..0b8971faaf
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.22python3.9.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '12'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '12'
+docker_image:
+- quay.io/condaforge/linux-anvil-cos7-x86_64
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.23python3.11.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.23python3.11.____cpython.yaml
new file mode 100644
index 0000000000..2bd7f50443
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.23python3.11.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '12'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '12'
+docker_image:
+- quay.io/condaforge/linux-anvil-cos7-x86_64
+numpy:
+- '1.23'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.26python3.12.____cpython.yaml b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.26python3.12.____cpython.yaml
new file mode 100644
index 0000000000..66671ce7dd
--- /dev/null
+++ b/conda_package/variants/linux_64_c_compiler_version12cuda_compilercuda-nvcccuda_compiler_version12.0cxx_compiler_version12numpy1.26python3.12.____cpython.yaml
@@ -0,0 +1,44 @@
+c_compiler:
+- gcc
+c_compiler_version:
+- '12'
+c_stdlib:
+- sysroot
+c_stdlib_version:
+- '2.17'
+cdt_name:
+- cos7
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- gxx
+cxx_compiler_version:
+- '12'
+docker_image:
+- quay.io/condaforge/linux-anvil-cos7-x86_64
+numpy:
+- '1.26'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- linux-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+  - c_stdlib_version
+  - cdt_name
+  - cuda_compiler
+  - cuda_compiler_version
+  - docker_image
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.10.____cpython.yaml b/conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.10.____cpython.yaml
new file mode 100644
index 0000000000..f147e53caa
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.10.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.22'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.9.____cpython.yaml b/conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.9.____cpython.yaml
new file mode 100644
index 0000000000..6a659ea44a
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.22opencl_implapplepython3.9.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.22'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml b/conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml
new file mode 100644
index 0000000000..881b77e905
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.22'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml b/conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml
new file mode 100644
index 0000000000..604c27a1b5
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.22'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.23opencl_implapplepython3.11.____cpython.yaml b/conda_package/variants/osx_64_numpy1.23opencl_implapplepython3.11.____cpython.yaml
new file mode 100644
index 0000000000..66526dc731
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.23opencl_implapplepython3.11.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.23'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml b/conda_package/variants/osx_64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml
new file mode 100644
index 0000000000..7a41b6ed89
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.23'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.26opencl_implapplepython3.12.____cpython.yaml b/conda_package/variants/osx_64_numpy1.26opencl_implapplepython3.12.____cpython.yaml
new file mode 100644
index 0000000000..4ed488532d
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.26opencl_implapplepython3.12.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.26'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml b/conda_package/variants/osx_64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml
new file mode 100644
index 0000000000..d642f02219
--- /dev/null
+++ b/conda_package/variants/osx_64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '10.13'
+MACOSX_SDK_VERSION:
+- '10.13'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '10.13'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- x86_64-apple-darwin13.4.0
+numpy:
+- '1.26'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- osx-64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.10.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.10.____cpython.yaml
new file mode 100644
index 0000000000..46289cb78a
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.10.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.22'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.9.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.9.____cpython.yaml
new file mode 100644
index 0000000000..e68ce0782b
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.22opencl_implapplepython3.9.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.22'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml
new file mode 100644
index 0000000000..e8cb0c3b99
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.10.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.22'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml
new file mode 100644
index 0000000000..5751f6c3f1
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.22opencl_implkhronospython3.9.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.22'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.23opencl_implapplepython3.11.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.23opencl_implapplepython3.11.____cpython.yaml
new file mode 100644
index 0000000000..ec02403c92
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.23opencl_implapplepython3.11.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.23'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml
new file mode 100644
index 0000000000..2561123ed5
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.23opencl_implkhronospython3.11.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.23'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.26opencl_implapplepython3.12.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.26opencl_implapplepython3.12.____cpython.yaml
new file mode 100644
index 0000000000..f43b3e9898
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.26opencl_implapplepython3.12.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.26'
+opencl_impl:
+- apple
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/osx_arm64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml b/conda_package/variants/osx_arm64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml
new file mode 100644
index 0000000000..5d03516237
--- /dev/null
+++ b/conda_package/variants/osx_arm64_numpy1.26opencl_implkhronospython3.12.____cpython.yaml
@@ -0,0 +1,43 @@
+MACOSX_DEPLOYMENT_TARGET:
+- '11.0'
+MACOSX_SDK_VERSION:
+- '11.0'
+c_compiler:
+- clang
+c_compiler_version:
+- '18'
+c_stdlib:
+- macosx_deployment_target
+c_stdlib_version:
+- '11.0'
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- None
+cuda_compiler_version:
+- None
+cxx_compiler:
+- clangxx
+cxx_compiler_version:
+- '18'
+macos_machine:
+- arm64-apple-darwin20.0.0
+numpy:
+- '1.26'
+opencl_impl:
+- khronos
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- osx-arm64
+zip_keys:
+- - c_compiler_version
+  - cxx_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.10.____cpython.yaml b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.10.____cpython.yaml
new file mode 100644
index 0000000000..660e26a5a1
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.10.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.9.____cpython.yaml b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.9.____cpython.yaml
new file mode 100644
index 0000000000..bb509a35c3
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.22python3.9.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.23python3.11.____cpython.yaml b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.23python3.11.____cpython.yaml
new file mode 100644
index 0000000000..fb6c253b15
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.23python3.11.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.23'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.26python3.12.____cpython.yaml b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.26python3.12.____cpython.yaml
new file mode 100644
index 0000000000..5aee6a6b3c
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilercuda-nvcccuda_compiler_version12.0numpy1.26python3.12.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- cuda-nvcc
+cuda_compiler_version:
+- '12.0'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.26'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.10.____cpython.yaml b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.10.____cpython.yaml
new file mode 100644
index 0000000000..e10dc24ff2
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.10.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.10.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.9.____cpython.yaml b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.9.____cpython.yaml
new file mode 100644
index 0000000000..1c4db9181b
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.9.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.22'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.9.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.23python3.11.____cpython.yaml b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.23python3.11.____cpython.yaml
new file mode 100644
index 0000000000..978ba439a4
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.23python3.11.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.23'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.11.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy
diff --git a/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.26python3.12.____cpython.yaml b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.26python3.12.____cpython.yaml
new file mode 100644
index 0000000000..e6432be9d2
--- /dev/null
+++ b/conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.26python3.12.____cpython.yaml
@@ -0,0 +1,29 @@
+c_compiler:
+- vs2019
+c_stdlib:
+- vs
+channel_sources:
+- conda-forge
+channel_targets:
+- conda-forge main
+cuda_compiler:
+- nvcc
+cuda_compiler_version:
+- '11.8'
+cxx_compiler:
+- vs2019
+numpy:
+- '1.26'
+pin_run_as_build:
+  python:
+    min_pin: x.x
+    max_pin: x.x
+python:
+- 3.12.* *_cpython
+target_platform:
+- win-64
+zip_keys:
+- - cuda_compiler
+  - cuda_compiler_version
+- - python
+  - numpy

From bca93836a9aa549a2d21a86ce8836e566eba7a1e Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 28 May 2025 12:37:56 +0300
Subject: [PATCH 56/75] better naming of cuda openmm packages

---
 conda_package/recipe/meta.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/conda_package/recipe/meta.yaml b/conda_package/recipe/meta.yaml
index af1de683d3..4b20bd0973 100644
--- a/conda_package/recipe/meta.yaml
+++ b/conda_package/recipe/meta.yaml
@@ -20,6 +20,7 @@ source:
 
 build:
   number: {{ build }}
+  string: "cuda{{ cuda_compiler_version | replace('.', '') }}py{{ PY_VER.replace('.', '') }}h{{ PKG_HASH }}_{{ build }}"  # [cuda_compiler_version != "None"]
   string: "py{{ PY_VER.replace('.', '') }}h{{ PKG_HASH }}_{{ build }}_{{ opencl_impl }}"  # [osx]
   track_features:  # make Apple OpenCL low priority
     - openmm_opencl_apple  # [osx and (opencl_impl == 'apple')]

From 1f7e0962b1761e5f34c8448c8917d86f3a1e5e37 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 28 May 2025 12:40:45 +0300
Subject: [PATCH 57/75] merge workflows

---
 .github/workflows/conda_publish.yaml | 5 ++---
 .github/workflows/workflow.yml       | 7 ++++++-
 2 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/conda_publish.yaml b/.github/workflows/conda_publish.yaml
index 041f668991..a631a770fa 100644
--- a/.github/workflows/conda_publish.yaml
+++ b/.github/workflows/conda_publish.yaml
@@ -1,9 +1,8 @@
 name: Test code and publish package
 
 on:
-  push:
-    tags:
-    - 'v*'
+  workflow_dispatch:
+  workflow_call:
 
 jobs:
   deploy_linux_cuda11:
diff --git a/.github/workflows/workflow.yml b/.github/workflows/workflow.yml
index 45eab0be08..e4035831cc 100644
--- a/.github/workflows/workflow.yml
+++ b/.github/workflows/workflow.yml
@@ -3,7 +3,12 @@ name: Whole
 on: [push]
 
 jobs:
-  publish:
+  publish_pypi:
     if: startsWith(github.event.ref, 'refs/tags/v')
     uses: ./.github/workflows/publish.yml
     secrets: inherit
+
+  publish_conda:
+    if: startsWith(github.event.ref, 'refs/tags/v')
+    uses: ./.github/workflows/conda_publish.yml
+    secrets: inherit

From 6b8ee9a48232018a2ed8512cb02e635322c245c3 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 28 May 2025 12:43:01 +0300
Subject: [PATCH 58/75] rename yaml

---
 .github/workflows/{conda_publish.yaml => conda_publish.yml} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename .github/workflows/{conda_publish.yaml => conda_publish.yml} (100%)

diff --git a/.github/workflows/conda_publish.yaml b/.github/workflows/conda_publish.yml
similarity index 100%
rename from .github/workflows/conda_publish.yaml
rename to .github/workflows/conda_publish.yml

From 2709892018d7124c4d2252acf8b69c9bbad4efe3 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 28 May 2025 13:29:07 +0300
Subject: [PATCH 59/75] fallback if openmm_library_path is not in openmm/lib to
 search in env/lib instead

---
 wrappers/python/openmm/__init__.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index f829168ee9..ebaddbb872 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -12,6 +12,13 @@
 
 
 openmm_library_path = os.path.abspath(os.path.join(os.path.dirname(__file__), 'lib'))
+if not os.path.exists(openmm_library_path):
+    # The conda package installs all the libraries in the env/lib directory
+    import site
+
+    sp_dir = site.getsitepackages()[0]
+    openmm_library_path = os.path.abspath(os.path.join(sp_dir, '..', '..'))
+
 if sys.platform == 'win32':
     _path = os.environ['PATH']
     os.environ['PATH'] = r'%(lib)s;%(lib)s\plugins;%(path)s' % {

From 2a58d6dba398d2e6abe0e9f311156c55413caf91 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 28 May 2025 13:47:24 +0300
Subject: [PATCH 60/75] try to make both setup.py and pyproject.toml work at
 the same time

---
 wrappers/python/setup.py | 17 ++++++++++++++++-
 1 file changed, 16 insertions(+), 1 deletion(-)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 40c407aa22..1f1e2b228e 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -146,7 +146,22 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                                           "openmm.app.internal.pdbx.reader",
                                           "openmm.app.internal.pdbx.writer"]
 
-    setupKeywords["install_requires"] = ["numpy"]
+    setupKeywords["data_files"]        = []
+    setupKeywords["package_data"]      = {"openmm" : [],
+                                          "openmm.app" : ['data/*.xml', 'data/*.pdb', 'data/amber14/*.xml', 'data/amber19/*.xml', 'data/charmm36/*.xml', 'data/implicit/*.xml'],
+                                          "openmm.app.internal" : []}
+    setupKeywords["install_requires"]  = ["numpy"]
+    setupKeywords["platforms"]         = ["Linux", "Mac OS X", "Windows"]
+    setupKeywords["description"]       = \
+    "Python wrapper for OpenMM (a C++ MD package)"
+    setupKeywords["long_description"]  = \
+    """OpenMM is a toolkit for molecular simulation. It can be used either as a
+    stand-alone application for running simulations, or as a library you call
+    from your own code. It provides a combination of extreme flexibility
+    (through custom forces and integrators), openness, and high performance
+    (especially on recent GPUs) that make it truly unique among simulation codes.
+    """
+
     if os.getenv("ACCELERATOR", "").startswith("cu"):
         cuda_ver = os.getenv("ACCELERATOR", "")[2:4]
         setupKeywords["install_requires"] += [f'nvidia-cuda-runtime-cu{cuda_ver}',

From 12d57d76feb639ee514ba940d6a18be664d2c278 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 28 May 2025 13:58:42 +0300
Subject: [PATCH 61/75] fix windows

---
 .github/workflows/conda_publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index a631a770fa..c6596474f6 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -180,7 +180,7 @@ jobs:
       - name: Setup CUDA Toolkit
         id: cuda-toolkit
         shell: pwsh
-        run: scripts/setup_cuda.ps1
+        run: conda_package/scripts/setup_cuda.ps1
         env:
           INPUT_CUDA_VERSION: 11.8.0
 
@@ -228,7 +228,7 @@ jobs:
       - name: Setup CUDA Toolkit
         id: cuda-toolkit
         shell: pwsh
-        run: scripts/setup_cuda.ps1
+        run: conda_package/scripts/setup_cuda.ps1
         env:
           INPUT_CUDA_VERSION: 12.0.0
 

From f66212344c0f6b34c907a05b4aff82c9dcad1451 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 29 May 2025 13:30:16 +0300
Subject: [PATCH 62/75] test fix for conda windows builds

---
 .github/workflows/testwindows.yml  | 46 ++++++++++++++++++++++++++++++
 wrappers/python/openmm/__init__.py |  4 +++
 2 files changed, 50 insertions(+)
 create mode 100644 .github/workflows/testwindows.yml

diff --git a/.github/workflows/testwindows.yml b/.github/workflows/testwindows.yml
new file mode 100644
index 0000000000..31da7657f9
--- /dev/null
+++ b/.github/workflows/testwindows.yml
@@ -0,0 +1,46 @@
+name: Test code and publish package
+
+on:
+  push:
+
+jobs:
+  deploy_win_64_cuda11:
+    strategy:
+      fail-fast: false
+      matrix:
+        config_file:
+          [
+            "conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.10.____cpython.yaml",
+          ]
+    runs-on: windows-2022
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: ../deploy-env
+          python-version: "3.10"
+          channels: conda-forge
+
+      - name: Add msbuild to PATH
+        uses: microsoft/setup-msbuild@v2
+
+      - name: Setup CUDA Toolkit
+        id: cuda-toolkit
+        shell: pwsh
+        run: conda_package/scripts/setup_cuda.ps1
+        env:
+          INPUT_CUDA_VERSION: 11.8.0
+
+      - name: Build openmm package
+        shell: bash -l {0}
+        run: |
+          git config --global --add safe.directory '*'
+          conda install anaconda-client conda-build
+          conda clean --all -y
+          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
+        env:
+          OPENMM_VERSION: ${{ github.ref_name }}
+          OPENMM_COMMIT: ${{ github.sha }}
diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index ebaddbb872..9316d30a38 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -18,6 +18,10 @@
 
     sp_dir = site.getsitepackages()[0]
     openmm_library_path = os.path.abspath(os.path.join(sp_dir, '..', '..'))
+    if sys.platform == 'win32':
+        # Don't move this in the next if below. it should only happen on conda packages where
+        # lib is not under the package root.
+        openmm_library_path = os.path.join(openmm_library_path, '..', 'Library', 'lib')
 
 if sys.platform == 'win32':
     _path = os.environ['PATH']

From ae2e068b4d456b960b0694cfbf0cdccfa7220394 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 29 May 2025 15:07:31 +0300
Subject: [PATCH 63/75] some debugging prints

---
 wrappers/python/openmm/__init__.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index 9316d30a38..a2ec86c1a2 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -23,14 +23,18 @@
         # lib is not under the package root.
         openmm_library_path = os.path.join(openmm_library_path, '..', 'Library', 'lib')
 
+print(f"XXX_OPENMM_LIBRARY_PATH: {openmm_library_path}")
 if sys.platform == 'win32':
+    print("XXX_WINDOWS!!!")
     _path = os.environ['PATH']
     os.environ['PATH'] = r'%(lib)s;%(lib)s\plugins;%(path)s' % {
         'lib': openmm_library_path, 'path': _path}
     try:
         with os.add_dll_directory(openmm_library_path):
             from . import _openmm
+        print("WORKED!!!")
     except:
+        print("FAILED!!!")
         pass
 
 from openmm.openmm import *

From 8c191d6b5dd1c4f96a8af28ad541fb4a0e7e5dfb Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 29 May 2025 15:50:04 +0300
Subject: [PATCH 64/75] fix the directory

---
 wrappers/python/openmm/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index a2ec86c1a2..46f31a7e3e 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -21,7 +21,7 @@
     if sys.platform == 'win32':
         # Don't move this in the next if below. it should only happen on conda packages where
         # lib is not under the package root.
-        openmm_library_path = os.path.join(openmm_library_path, '..', 'Library', 'lib')
+        openmm_library_path = os.path.join(openmm_library_path, 'Library', 'lib')
 
 print(f"XXX_OPENMM_LIBRARY_PATH: {openmm_library_path}")
 if sys.platform == 'win32':

From 9a4f0091152ff07c7cd19866f743fa4646e29d34 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 29 May 2025 16:21:06 +0300
Subject: [PATCH 65/75] windows handles site-packages differently

---
 wrappers/python/openmm/__init__.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index 46f31a7e3e..5fa13784ff 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -16,12 +16,11 @@
     # The conda package installs all the libraries in the env/lib directory
     import site
 
-    sp_dir = site.getsitepackages()[0]
-    openmm_library_path = os.path.abspath(os.path.join(sp_dir, '..', '..'))
+    openmm_library_path = os.path.abspath(os.path.join(site.getsitepackages()[0], '..', '..'))
     if sys.platform == 'win32':
         # Don't move this in the next if below. it should only happen on conda packages where
         # lib is not under the package root.
-        openmm_library_path = os.path.join(openmm_library_path, 'Library', 'lib')
+        openmm_library_path = os.path.join(os.path.dirname(__file__), '..', '..', '..', 'Library', 'lib')
 
 print(f"XXX_OPENMM_LIBRARY_PATH: {openmm_library_path}")
 if sys.platform == 'win32':

From bc5af824ad467d2c1b144759b3691465961b2962 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 29 May 2025 16:51:01 +0300
Subject: [PATCH 66/75] fixed windows, removing debugging

---
 .github/workflows/testwindows.yml  | 46 ------------------------------
 wrappers/python/openmm/__init__.py |  4 ---
 2 files changed, 50 deletions(-)
 delete mode 100644 .github/workflows/testwindows.yml

diff --git a/.github/workflows/testwindows.yml b/.github/workflows/testwindows.yml
deleted file mode 100644
index 31da7657f9..0000000000
--- a/.github/workflows/testwindows.yml
+++ /dev/null
@@ -1,46 +0,0 @@
-name: Test code and publish package
-
-on:
-  push:
-
-jobs:
-  deploy_win_64_cuda11:
-    strategy:
-      fail-fast: false
-      matrix:
-        config_file:
-          [
-            "conda_package/variants/win_64_cuda_compilernvcccuda_compiler_version11.8numpy1.22python3.10.____cpython.yaml",
-          ]
-    runs-on: windows-2022
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - uses: conda-incubator/setup-miniconda@v3
-        with:
-          miniconda-version: "latest"
-          activate-environment: ../deploy-env
-          python-version: "3.10"
-          channels: conda-forge
-
-      - name: Add msbuild to PATH
-        uses: microsoft/setup-msbuild@v2
-
-      - name: Setup CUDA Toolkit
-        id: cuda-toolkit
-        shell: pwsh
-        run: conda_package/scripts/setup_cuda.ps1
-        env:
-          INPUT_CUDA_VERSION: 11.8.0
-
-      - name: Build openmm package
-        shell: bash -l {0}
-        run: |
-          git config --global --add safe.directory '*'
-          conda install anaconda-client conda-build
-          conda clean --all -y
-          conda build conda_package/recipe/ --variant-config-files ${{ matrix.config_file }} --output-folder ./pkg/ --no-include-recipe --no-anaconda-upload -c conda-forge
-        env:
-          OPENMM_VERSION: ${{ github.ref_name }}
-          OPENMM_COMMIT: ${{ github.sha }}
diff --git a/wrappers/python/openmm/__init__.py b/wrappers/python/openmm/__init__.py
index 5fa13784ff..b593a81d3d 100644
--- a/wrappers/python/openmm/__init__.py
+++ b/wrappers/python/openmm/__init__.py
@@ -22,18 +22,14 @@
         # lib is not under the package root.
         openmm_library_path = os.path.join(os.path.dirname(__file__), '..', '..', '..', 'Library', 'lib')
 
-print(f"XXX_OPENMM_LIBRARY_PATH: {openmm_library_path}")
 if sys.platform == 'win32':
-    print("XXX_WINDOWS!!!")
     _path = os.environ['PATH']
     os.environ['PATH'] = r'%(lib)s;%(lib)s\plugins;%(path)s' % {
         'lib': openmm_library_path, 'path': _path}
     try:
         with os.add_dll_directory(openmm_library_path):
             from . import _openmm
-        print("WORKED!!!")
     except:
-        print("FAILED!!!")
         pass
 
 from openmm.openmm import *

From 6692c994396e27295b1d6505e523c11f523f01dd Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Thu, 29 May 2025 17:43:39 +0300
Subject: [PATCH 67/75] correct package extension

---
 .github/workflows/conda_publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/conda_publish.yml b/.github/workflows/conda_publish.yml
index c6596474f6..4207ce5b7a 100644
--- a/.github/workflows/conda_publish.yml
+++ b/.github/workflows/conda_publish.yml
@@ -198,7 +198,7 @@ jobs:
       - name: Upload to conda
         shell: bash -l {0}
         run: |
-          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.tar.bz2 --skip-existing
+          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.conda --skip-existing
 
   deploy_win_64_cuda12:
     strategy:
@@ -246,4 +246,4 @@ jobs:
       - name: Upload to conda
         shell: bash -l {0}
         run: |
-          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.tar.bz2 --skip-existing
+          anaconda -t ${{ secrets.ANACONDA_TOKEN_BASIC }} upload -u acellera pkg/*/openmm-*.conda --skip-existing

From c057bb2497ef99b5dd2e18a2ce90ecc5445b7df2 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Fri, 30 May 2025 11:19:09 +0300
Subject: [PATCH 68/75] update release candidate version in CI

---
 .github/workflows/publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 83028c26ab..41fb377755 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -74,7 +74,7 @@ jobs:
         run: python -m cibuildwheel wrappers/python/ --output-dir wheelhouse
         env:
           ACCELERATOR: ${{ matrix.accelerator }}
-          VERSION_SUFFIX: "rc1"
+          VERSION_SUFFIX: "rc2"
 
       - name: Build wheels
         if: matrix.os == 'windows-2019'
@@ -83,7 +83,7 @@ jobs:
         env:
           DISTUTILS_USE_SDK: "1" # Windows requires this to use vc for building
           ACCELERATOR: ${{ matrix.accelerator }}
-          VERSION_SUFFIX: "rc1"
+          VERSION_SUFFIX: "rc2"
 
       - uses: actions/upload-artifact@v4
         with:

From 6810a6998760dc3a0122e2e0012df1bfb6618983 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 13 Aug 2025 11:32:52 +0300
Subject: [PATCH 69/75] public PyPI unofficial OpenMM version for cuda 11.8 and
 12.0 only

---
 .github/workflows/publish.yml                 | 93 +++++++++++++------
 .../prepare_build_environment_linux.sh        | 12 +++
 .../prepare_build_environment_windows.sh      |  7 ++
 wrappers/python/setup.py                      |  4 +
 4 files changed, 86 insertions(+), 30 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 41fb377755..70d79e614a 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -14,26 +14,30 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, ubuntu-24.04-arm, windows-2019, macos-latest]
-        accelerator: [cpu, cu118, cu124, cu126, cu128, hip]
+        accelerator: [cpu, cu118, cu120, hip] #cu124, cu126, cu128, hip]
         exclude:
           - os: ubuntu-24.04-arm
             accelerator: cu118
           - os: ubuntu-24.04-arm
-            accelerator: cu124
-          - os: ubuntu-24.04-arm
-            accelerator: cu126
-          - os: ubuntu-24.04-arm
-            accelerator: cu128
+            accelerator: cu120
+          # - os: ubuntu-24.04-arm
+          #   accelerator: cu124
+          # - os: ubuntu-24.04-arm
+          #   accelerator: cu126
+          # - os: ubuntu-24.04-arm
+          #   accelerator: cu128
           - os: ubuntu-24.04-arm
             accelerator: hip
           - os: macos-latest
             accelerator: cu118
           - os: macos-latest
-            accelerator: cu124
-          - os: macos-latest
-            accelerator: cu126
-          - os: macos-latest
-            accelerator: cu128
+            accelerator: cu120
+          # - os: macos-latest
+          #   accelerator: cu124
+          # - os: macos-latest
+          #   accelerator: cu126
+          # - os: macos-latest
+          #   accelerator: cu128
           - os: macos-latest
             accelerator: hip
 
@@ -90,29 +94,22 @@ jobs:
           name: ${{ matrix.accelerator }}-cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
-  publish-to-accelera-pypi:
+  publish-to-public-pypi:
     name: >-
-      Publish Python 🐍 distribution 📦 to Acellera PyPI
+      Publish Python 🐍 distribution 📦 to PyPI
     needs:
       - build
     runs-on: ubuntu-latest
-    permissions: # Needed for GCP authentication
-      contents: "read"
-      id-token: "write"
+    environment:
+      name: pypi
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
     strategy:
       fail-fast: false
       matrix:
-        accelerator: [cpu, cu118, cu124, cu126, cu128, hip]
+        accelerator: [cpu, cu118, cu120, hip] #cu124, cu126, cu128, hip]
 
     steps:
-      - uses: actions/checkout@v4 # Needed for GCP authentication for some reason
-
-      - name: Set up Cloud SDK
-        uses: google-github-actions/auth@v2
-        with:
-          workload_identity_provider: ${{ secrets.GCP_WORKLOAD_IDENTITY_PROVIDER }}
-          service_account: ${{ secrets.GCP_PYPI_SERVICE_ACCOUNT }}
-
       - name: Download all the dists
         uses: actions/download-artifact@v4
         with:
@@ -120,11 +117,47 @@ jobs:
           path: dist/
           merge-multiple: true
 
-      - name: Publish distribution 📦 to Acellera PyPI
-        run: |
-          pip install build twine keyring keyrings.google-artifactregistry-auth
-          pip install -U packaging
-          twine upload --repository-url https://us-central1-python.pkg.dev/pypi-packages-455608/${{ matrix.accelerator }} dist/* --verbose --skip-existing
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PUBLIC_PYPI_API_TOKEN }}
+          skip-existing: true
+
+  # publish-to-accelera-pypi:
+  #   name: >-
+  #     Publish Python 🐍 distribution 📦 to Acellera PyPI
+  #   needs:
+  #     - build
+  #   runs-on: ubuntu-latest
+  #   permissions: # Needed for GCP authentication
+  #     contents: "read"
+  #     id-token: "write"
+  #   strategy:
+  #     fail-fast: false
+  #     matrix:
+  #       accelerator: [cpu, cu118, cu120, hip] #cu124, cu126, cu128, hip]
+
+  #   steps:
+  #     - uses: actions/checkout@v4 # Needed for GCP authentication for some reason
+
+  #     - name: Set up Cloud SDK
+  #       uses: google-github-actions/auth@v2
+  #       with:
+  #         workload_identity_provider: ${{ secrets.GCP_WORKLOAD_IDENTITY_PROVIDER }}
+  #         service_account: ${{ secrets.GCP_PYPI_SERVICE_ACCOUNT }}
+
+  #     - name: Download all the dists
+  #       uses: actions/download-artifact@v4
+  #       with:
+  #         pattern: "${{ matrix.accelerator }}-cibw-wheels*"
+  #         path: dist/
+  #         merge-multiple: true
+
+  #     - name: Publish distribution 📦 to Acellera PyPI
+  #       run: |
+  #         pip install build twine keyring keyrings.google-artifactregistry-auth
+  #         pip install -U packaging
+  #         twine upload --repository-url https://us-central1-python.pkg.dev/pypi-packages-455608/${{ matrix.accelerator }} dist/* --verbose --skip-existing
 
   github-release:
     name: >-
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
index 2120cec828..9a87136b8b 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -17,6 +17,18 @@ if [ "$ACCELERATOR" == "cu118" ]; then
         
     ln -s cuda-11.8 /usr/local/cuda
 
+    export CUDA_HOME="/usr/local/cuda"
+elif [ "$ACCELERATOR" == "cu120" ]; then
+    # Install CUDA 12.0
+    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
+
+    dnf install --setopt=obsoletes=0 -y \
+        cuda-compiler-12-0-12.0.1-1 \
+        cuda-libraries-12-0-12.0.1-1 \
+        cuda-libraries-devel-12-0-12.0.1-1
+
+    ln -s cuda-12.0 /usr/local/cuda
+
     export CUDA_HOME="/usr/local/cuda"
 elif [ "$ACCELERATOR" == "cu124" ]; then
     # Install CUDA 12.4
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index dd10df9951..22d6e45769 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -10,6 +10,13 @@ if [ "$ACCELERATOR" == "cu118" ]; then
     # Move CUDA folder to a path without spaces
     mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.8" /c/CUDA
     export CUDA_PATH="/c/CUDA"
+elif [ "$ACCELERATOR" == "cu120" ]; then
+    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.0.0/local_installers/cuda_12.0.0_527.41_windows.exe
+    ./cuda.exe -s nvcc_12.0 nvrtc_12.0 nvrtc_dev_12.0 cudart_12.0 cufft_12.0 cufft_dev_12.0 cuda_profiler_api_12.0
+    rm cuda.exe
+    # Move CUDA folder to a path without spaces
+    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.0" /c/CUDA
+    export CUDA_PATH="/c/CUDA"
 elif [ "$ACCELERATOR" == "cu124" ]; then
     curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
     ./cuda.exe -s nvcc_12.4 nvrtc_12.4 nvrtc_dev_12.4 cudart_12.4 cufft_12.4 cufft_dev_12.4 cuda_profiler_api_12.4
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 0b5971a4c6..01523a5d1a 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -162,8 +162,12 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     (especially on recent GPUs) that make it truly unique among simulation codes.
     """
 
+    setupKeywords["name"] = "openmm-unofficial-cpu"
+    if os.getenv("ACCELERATOR", "").startswith("hip"):
+        setupKeywords["name"] = "openmm-unofficial-hip"
     if os.getenv("ACCELERATOR", "").startswith("cu"):
         cuda_ver = os.getenv("ACCELERATOR", "")[2:4]
+        setupKeywords["name"] = f"openmm-unofficial-cu{cuda_ver}"
         setupKeywords["install_requires"] += [f'nvidia-cuda-runtime-cu{cuda_ver}',
                                               f'nvidia-cuda-nvcc-cu{cuda_ver}',
                                               f'nvidia-cuda-nvrtc-cu{cuda_ver}',

From d37a039a270329a7352f7b8aa574b9b9f4a6e717 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 13 Aug 2025 11:37:11 +0300
Subject: [PATCH 70/75] update windows version

---
 .github/workflows/publish.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index 70d79e614a..a35569ff16 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, ubuntu-24.04-arm, windows-2019, macos-latest]
+        os: [ubuntu-latest, ubuntu-24.04-arm, windows-2022, macos-latest]
         accelerator: [cpu, cu118, cu120, hip] #cu124, cu126, cu128, hip]
         exclude:
           - os: ubuntu-24.04-arm
@@ -64,16 +64,16 @@ jobs:
 
       - name: Activate MSVC
         uses: ilammy/msvc-dev-cmd@v1
-        if: matrix.os == 'windows-2019'
+        if: matrix.os == 'windows-2022'
 
       - name: "Install dependencies with choco"
         uses: crazy-max/ghaction-chocolatey@v3
-        if: matrix.os == 'windows-2019'
+        if: matrix.os == 'windows-2022'
         with:
           args: install doxygen.install jom
 
       - name: Build wheels
-        if: matrix.os != 'windows-2019'
+        if: matrix.os != 'windows-2022'
         shell: bash -l {0}
         run: python -m cibuildwheel wrappers/python/ --output-dir wheelhouse
         env:
@@ -81,7 +81,7 @@ jobs:
           VERSION_SUFFIX: "rc2"
 
       - name: Build wheels
-        if: matrix.os == 'windows-2019'
+        if: matrix.os == 'windows-2022'
         shell: cmd # Use cmd on Windows to avoid bash environment taking priority over MSVC variables
         run: python -m cibuildwheel wrappers/python/ --output-dir wheelhouse
         env:

From bfb62120a02e9ed576ee580b04582a90e7cd9d93 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 13 Aug 2025 15:21:14 +0300
Subject: [PATCH 71/75] placeholder package name since pyproject doesn't allow
 dynamic package names

---
 .github/workflows/publish.yml        |  2 +-
 conda_package/recipe/test_openmm.bat |  2 +-
 conda_package/recipe/test_openmm.sh  |  2 +-
 wrappers/python/pyproject.toml       |  6 ++----
 wrappers/python/setup.py             | 17 ++++++++++++++---
 5 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index a35569ff16..b841968132 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -60,7 +60,7 @@ jobs:
           python-version: "3.13"
 
       - name: Install cibuildwheel
-        run: python -m pip install cibuildwheel==2.23.0
+        run: python -m pip install cibuildwheel==3.1.3
 
       - name: Activate MSVC
         uses: ilammy/msvc-dev-cmd@v1
diff --git a/conda_package/recipe/test_openmm.bat b/conda_package/recipe/test_openmm.bat
index 1930ed6bb2..e732530991 100644
--- a/conda_package/recipe/test_openmm.bat
+++ b/conda_package/recipe/test_openmm.bat
@@ -30,7 +30,7 @@ if "%CI%"=="" (
 python -c "from openmm import Platform as P; n = P.getNumPlatforms(); assert n == %n_platforms%, f'n_platforms ({n}) != %n_platforms%'" || goto :error
 
 :: Now let's run a little MD
-cd %LIBRARY_PREFIX%/share/openmm/examples
+cd %LIBRARY_PREFIX%/share/openmm/examples/benchmarks
 python benchmark.py --test=rf --seconds=10 --platform=Reference || goto :error
 python benchmark.py --test=rf --seconds=10 --platform=CPU || goto :error
 if "%CI%"=="" (
diff --git a/conda_package/recipe/test_openmm.sh b/conda_package/recipe/test_openmm.sh
index 13f760b389..663016e9bb 100644
--- a/conda_package/recipe/test_openmm.sh
+++ b/conda_package/recipe/test_openmm.sh
@@ -35,7 +35,7 @@ fi
 #python -c "from openmm import Platform as P; n = P.getNumPlatforms(); assert n == $n_platforms, f'n_platforms ({n}) != $n_platforms'"
 
 # Run a small MD
-cd ${PREFIX}/share/openmm/examples
+cd ${PREFIX}/share/openmm/examples/benchmarks
 python benchmark.py --test=rf --seconds=10 --platform=Reference
 python benchmark.py --test=rf --seconds=10 --platform=CPU
 if [[ -z ${CI-} ]]; then  # Run only outside CI, assuming there will be a GPU there
diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index 86c0f91cd6..dac970f7cf 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -1,5 +1,5 @@
 [project]
-name = "OpenMM"
+name = "PLACEHOLDER"
 description = "Python wrapper for OpenMM (a C++ MD package)"
 authors = [{ name = "Peter Eastman", email = "peastman@stanford.edu" }]
 readme = "README.md"
@@ -23,11 +23,9 @@ requires = ["setuptools>=78", "setuptools-scm>=8", "numpy", "cython"]
 build-backend = "setuptools.build_meta"
 
 [tool.cibuildwheel]
-skip = ["cp38-*", "pp*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
+skip = ["cp38-*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
 test-requires = ["pytest"]
 test-command = "cd {project}/wrappers/python/tests; pytest"
-manylinux-x86_64-image = "manylinux_2_28"
-manylinux-aarch64-image = "manylinux_2_28"
 environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]
 # container-engine = "docker; create_args: --gpus all"
 
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 01523a5d1a..d4ee0fb955 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -122,6 +122,16 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
                        'isrelease': str(IS_RELEASED)})
 
 
+def _replace_name(name):
+    import pathlib
+    
+    pyproject_path = pathlib.Path(__file__).parent / "pyproject.toml"
+    with open(pyproject_path, 'r') as f:
+        pyproject_text = f.read()
+    pyproject_text = pyproject_text.replace("PLACEHOLDER", name)
+    with open(pyproject_path, 'w') as f:
+        f.write(pyproject_text)
+
 def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
                            minor_version_num=MINOR_VERSION_NUM,
                            build_info=BUILD_INFO):
@@ -162,12 +172,13 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     (especially on recent GPUs) that make it truly unique among simulation codes.
     """
 
-    setupKeywords["name"] = "openmm-unofficial-cpu"
+    if os.getenv("ACCELERATOR", "").startswith("cpu"):
+        _replace_name("openmm-unofficial-cpu")
     if os.getenv("ACCELERATOR", "").startswith("hip"):
-        setupKeywords["name"] = "openmm-unofficial-hip"
+        _replace_name("openmm-unofficial-hip")
     if os.getenv("ACCELERATOR", "").startswith("cu"):
         cuda_ver = os.getenv("ACCELERATOR", "")[2:4]
-        setupKeywords["name"] = f"openmm-unofficial-cu{cuda_ver}"
+        _replace_name(f"openmm-unofficial-cu{cuda_ver}")
         setupKeywords["install_requires"] += [f'nvidia-cuda-runtime-cu{cuda_ver}',
                                               f'nvidia-cuda-nvcc-cu{cuda_ver}',
                                               f'nvidia-cuda-nvrtc-cu{cuda_ver}',

From 88facdb2ce536e0eef5e29a782c0dafcc97b44a9 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 13 Aug 2025 16:31:09 +0300
Subject: [PATCH 72/75] disable hip for now

---
 .github/workflows/publish.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
index b841968132..063b53eb3d 100644
--- a/.github/workflows/publish.yml
+++ b/.github/workflows/publish.yml
@@ -14,7 +14,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, ubuntu-24.04-arm, windows-2022, macos-latest]
-        accelerator: [cpu, cu118, cu120, hip] #cu124, cu126, cu128, hip]
+        accelerator: [cpu, cu118, cu120] #, cu124, cu126, cu128, hip]
         exclude:
           - os: ubuntu-24.04-arm
             accelerator: cu118
@@ -107,7 +107,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        accelerator: [cpu, cu118, cu120, hip] #cu124, cu126, cu128, hip]
+        accelerator: [cpu, cu118, cu120] #, hip, cu124, cu126, cu128]
 
     steps:
       - name: Download all the dists

From 997aaccb96f82685e7b556a5adf2342a1f1e743a Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Mon, 25 Aug 2025 15:53:33 +0300
Subject: [PATCH 73/75] don't build for 3.14t release candidate

---
 wrappers/python/pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/wrappers/python/pyproject.toml b/wrappers/python/pyproject.toml
index dac970f7cf..54734e9fe4 100644
--- a/wrappers/python/pyproject.toml
+++ b/wrappers/python/pyproject.toml
@@ -23,7 +23,7 @@ requires = ["setuptools>=78", "setuptools-scm>=8", "numpy", "cython"]
 build-backend = "setuptools.build_meta"
 
 [tool.cibuildwheel]
-skip = ["cp38-*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
+skip = ["cp38-*", "cp314t-*", "*win32", "*armv7l", "*_i686", "*_ppc64le", "*_s390x", "*_universal2", "*-musllinux_*"]
 test-requires = ["pytest"]
 test-command = "cd {project}/wrappers/python/tests; pytest"
 environment-pass = ["ACCELERATOR", "VERSION_SUFFIX"]

From 9f0909f270bccbd083023a8161ae12be11b41287 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 27 Aug 2025 11:39:16 +0300
Subject: [PATCH 74/75] updated the runtime dependencies

---
 .../prepare_build_environment_linux.sh        | 36 -------------------
 .../prepare_build_environment_windows.sh      | 21 -----------
 wrappers/python/setup.py                      | 17 ++++++---
 3 files changed, 12 insertions(+), 62 deletions(-)

diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
index 9a87136b8b..27d09164e8 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_linux.sh
@@ -29,42 +29,6 @@ elif [ "$ACCELERATOR" == "cu120" ]; then
 
     ln -s cuda-12.0 /usr/local/cuda
 
-    export CUDA_HOME="/usr/local/cuda"
-elif [ "$ACCELERATOR" == "cu124" ]; then
-    # Install CUDA 12.4
-    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
-
-    dnf install --setopt=obsoletes=0 -y \
-        cuda-compiler-12-4-12.4.1-1 \
-        cuda-libraries-12-4-12.4.1-1 \
-        cuda-libraries-devel-12-4-12.4.1-1
-
-    ln -s cuda-12.4 /usr/local/cuda
-
-    export CUDA_HOME="/usr/local/cuda"
-elif [ "$ACCELERATOR" == "cu126" ]; then
-    # Install CUDA 12.6
-    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
-
-    dnf install --setopt=obsoletes=0 -y \
-        cuda-compiler-12-6-12.6.3-1 \
-        cuda-libraries-12-6-12.6.3-1 \
-        cuda-libraries-devel-12-6-12.6.3-1
-
-    ln -s cuda-12.4 /usr/local/cuda
-
-    export CUDA_HOME="/usr/local/cuda"
-elif [ "$ACCELERATOR" == "cu128" ]; then
-    # Install CUDA 12.8
-    dnf config-manager --add-repo https://developer.download.nvidia.com/compute/cuda/repos/rhel8/x86_64/cuda-rhel8.repo
-
-    dnf install --setopt=obsoletes=0 -y \
-        cuda-compiler-12-8-12.8.1-1 \
-        cuda-libraries-12-8-12.8.1-1 \
-        cuda-libraries-devel-12-8-12.8.1-1
-
-    ln -s cuda-12.8 /usr/local/cuda
-
     export CUDA_HOME="/usr/local/cuda"
 elif [ "$ACCELERATOR" == "hip" ]; then
     # Install HIP 6.2
diff --git a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
index 22d6e45769..80dad2620a 100755
--- a/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
+++ b/wrappers/python/cibuildwheel_support/prepare_build_environment_windows.sh
@@ -17,27 +17,6 @@ elif [ "$ACCELERATOR" == "cu120" ]; then
     # Move CUDA folder to a path without spaces
     mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.0" /c/CUDA
     export CUDA_PATH="/c/CUDA"
-elif [ "$ACCELERATOR" == "cu124" ]; then
-    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.4.0/local_installers/cuda_12.4.0_551.61_windows.exe
-    ./cuda.exe -s nvcc_12.4 nvrtc_12.4 nvrtc_dev_12.4 cudart_12.4 cufft_12.4 cufft_dev_12.4 cuda_profiler_api_12.4
-    rm cuda.exe
-    # Move CUDA folder to a path without spaces
-    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.4" /c/CUDA
-    export CUDA_PATH="/c/CUDA"
-elif [ "$ACCELERATOR" == "cu126" ]; then
-    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.6.0/local_installers/cuda_12.6.0_560.76_windows.exe
-    ./cuda.exe -s nvcc_12.6 nvrtc_12.6 nvrtc_dev_12.6 cudart_12.6 cufft_12.6 cufft_dev_12.6 cuda_profiler_api_12.6
-    rm cuda.exe
-    # Move CUDA folder to a path without spaces
-    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.6" /c/CUDA
-    export CUDA_PATH="/c/CUDA"
-elif [ "$ACCELERATOR" == "cu128" ]; then
-    curl --netrc-optional -L -nv -o cuda.exe https://developer.download.nvidia.com/compute/cuda/12.8.1/local_installers/cuda_12.8.1_572.61_windows.exe
-    ./cuda.exe -s nvcc_12.8 nvrtc_12.8 nvrtc_dev_12.8 cudart_12.8 cufft_12.8 cufft_dev_12.8 cuda_profiler_api_12.8
-    rm cuda.exe
-    # Move CUDA folder to a path without spaces
-    mv "/c/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v12.8" /c/CUDA
-    export CUDA_PATH="/c/CUDA"
 elif [ "$ACCELERATOR" == "hip" ]; then
     curl.exe --output HIP.exe --url https://download.amd.com/developer/eula/rocm-hub/AMD-Software-PRO-Edition-24.Q3-Win10-Win11-For-HIP.exe
     ./HIP.exe -install
diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index d4ee0fb955..913ddbac73 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -179,11 +179,18 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     if os.getenv("ACCELERATOR", "").startswith("cu"):
         cuda_ver = os.getenv("ACCELERATOR", "")[2:4]
         _replace_name(f"openmm-unofficial-cu{cuda_ver}")
-        setupKeywords["install_requires"] += [f'nvidia-cuda-runtime-cu{cuda_ver}',
-                                              f'nvidia-cuda-nvcc-cu{cuda_ver}',
-                                              f'nvidia-cuda-nvrtc-cu{cuda_ver}',
-                                              f'nvidia-cuda-cupti-cu{cuda_ver}',
-                                              f'nvidia-cufft-cu{cuda_ver}']
+        if cuda_ver == "12":
+            setupKeywords["install_requires"] += ['nvidia-cuda-runtime-cu12==12.4.99',
+                                                  'nvidia-cuda-nvcc-cu12==12.4.99',
+                                                  'nvidia-cuda-nvrtc-cu12==12.4.99',
+                                                  'nvidia-cuda-cupti-cu12==12.4.99',
+                                                  'nvidia-cufft-cu12==11.2.3.18']
+        elif cuda_ver == "11":
+            setupKeywords["install_requires"] += ['nvidia-cuda-runtime-cu11==11.8.89',
+                                                  'nvidia-cuda-nvcc-cu11==11.8.89',
+                                                  'nvidia-cuda-nvrtc-cu11==11.8.89',
+                                                  'nvidia-cuda-cupti-cu11==11.8.87',
+                                                  'nvidia-cufft-cu11==10.9.0.58']
 
     define_macros = [('MAJOR_VERSION', major_version_num),
                      ('MINOR_VERSION', minor_version_num)]

From 1e7b3d66a3d0509b357d54a30411b3c3c7543d44 Mon Sep 17 00:00:00 2001
From: Stefan Doerr <stefdoerr@gmail.com>
Date: Wed, 27 Aug 2025 12:13:25 +0300
Subject: [PATCH 75/75] back to not hard-coding the cuda deps

---
 wrappers/python/setup.py | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
index 913ddbac73..28d261150d 100644
--- a/wrappers/python/setup.py
+++ b/wrappers/python/setup.py
@@ -179,18 +179,12 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
     if os.getenv("ACCELERATOR", "").startswith("cu"):
         cuda_ver = os.getenv("ACCELERATOR", "")[2:4]
         _replace_name(f"openmm-unofficial-cu{cuda_ver}")
-        if cuda_ver == "12":
-            setupKeywords["install_requires"] += ['nvidia-cuda-runtime-cu12==12.4.99',
-                                                  'nvidia-cuda-nvcc-cu12==12.4.99',
-                                                  'nvidia-cuda-nvrtc-cu12==12.4.99',
-                                                  'nvidia-cuda-cupti-cu12==12.4.99',
-                                                  'nvidia-cufft-cu12==11.2.3.18']
-        elif cuda_ver == "11":
-            setupKeywords["install_requires"] += ['nvidia-cuda-runtime-cu11==11.8.89',
-                                                  'nvidia-cuda-nvcc-cu11==11.8.89',
-                                                  'nvidia-cuda-nvrtc-cu11==11.8.89',
-                                                  'nvidia-cuda-cupti-cu11==11.8.87',
-                                                  'nvidia-cufft-cu11==10.9.0.58']
+        setupKeywords["install_requires"] += [f'nvidia-cuda-runtime-cu{cuda_ver}',
+                                              f'nvidia-cuda-nvcc-cu{cuda_ver}',
+                                              f'nvidia-cuda-nvrtc-cu{cuda_ver}',
+                                              f'nvidia-cuda-cupti-cu{cuda_ver}',
+                                              f'nvidia-cufft-cu{cuda_ver}']
+
 
     define_macros = [('MAJOR_VERSION', major_version_num),
                      ('MINOR_VERSION', minor_version_num)]