From 24f1e7c732c3b6300f3c70c7f5d5aa600065cf33 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 08:58:29 +0100
Subject: [PATCH 01/20] building source distribution works

---
 CMakeLists.txt                           | 10 ++++++
 pycode/memilio-simulation/CMakeLists.txt |  9 -----
 pycode/memilio-simulation/pyproject.toml | 39 --------------------
 pyproject.toml                           | 45 +++++++++++++++++++++++-
 4 files changed, 54 insertions(+), 49 deletions(-)
 create mode 100644 CMakeLists.txt
 delete mode 100644 pycode/memilio-simulation/pyproject.toml

diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000000..15b092d12f
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,10 @@
+cmake_minimum_required(VERSION 3.13)
+project(memilio-simulation)
+
+set(CMAKE_CXX_STANDARD "20")
+set(CMAKE_CXX_STANDARD_REQUIRED "20")
+
+# add in C++ library
+add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/cpp ${CMAKE_CURRENT_BINARY_DIR}/cpp EXCLUDE_FROM_ALL)
+
+add_subdirectory(pycode/memilio-simulation)
\ No newline at end of file
diff --git a/pycode/memilio-simulation/CMakeLists.txt b/pycode/memilio-simulation/CMakeLists.txt
index f54390d920..94ae9184b0 100644
--- a/pycode/memilio-simulation/CMakeLists.txt
+++ b/pycode/memilio-simulation/CMakeLists.txt
@@ -1,9 +1,3 @@
-cmake_minimum_required(VERSION 3.13)
-project(memilio-python)
-
-set(CMAKE_CXX_STANDARD "20")
-set(CMAKE_CXX_STANDARD_REQUIRED "20")
-
 option(MEMILIO_USE_BUNDLED_PYBIND11 "Use pybind11 bundled with this library." ON)
 mark_as_advanced(MEMILIO_USE_BUNDLED_PYBIND11)
 
@@ -52,9 +46,6 @@ else()
     find_package(pybind11 REQUIRED)
 endif()
 
-# add in C++ library
-add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/../../cpp ${CMAKE_CURRENT_BINARY_DIR}/cpp EXCLUDE_FROM_ALL)
-
 # a list of all "LINKED_LIBRARIES" that are given to add_pymio_module. will contain duplicates
 # used for wheel installation
 set(PYMIO_MEMILIO_LIBS_LIST)
diff --git a/pycode/memilio-simulation/pyproject.toml b/pycode/memilio-simulation/pyproject.toml
deleted file mode 100644
index d7bc24b90f..0000000000
--- a/pycode/memilio-simulation/pyproject.toml
+++ /dev/null
@@ -1,39 +0,0 @@
-[build-system]
-requires = [
-  "scikit-build-core>=0.9.0",
-  "setuptools>=68",
-  "wheel"
-]
-build-backend = "scikit_build_core.build"
-
-[project]
-name = "memilio-simulation"
-version = "1.0.0"
-description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
-readme = "README.md"
-requires-python = ">=3.8"
-license = { text = "Apache-2.0" }
-authors = [{ name = "MEmilio Team" }]
-maintainers = [
-  { email = "martin.kuehn@dlr.de" }
-]
-dependencies = [
-  # smaller numpy versions cause a security issue, 1.25 does not work together with pyfakefs
-  "numpy>=1.22,!=1.25.*",
-  # smaller pandas versions contain a bug that sometimes prevents reading
-  "pandas>=2.0.0"
-]
-
-[project.optional-dependencies]
-dev = []
-
-[project.urls]
-Homepage = "https://github.com/SciCompMod/memilio"
-Team = "https://memilio.readthedocs.io/en/latest/team.html"
-
-[tool.scikit-build]
-cmake.version = ">=3.13"
-cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
-wheel.packages = ["memilio"]
-wheel.install-dir = "memilio/simulation"
-build-dir = "../build/memilio-simulation"
diff --git a/pyproject.toml b/pyproject.toml
index 2f12cc6b19..fec49ef467 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -3,4 +3,47 @@ max-line-length = 79
 
 [tool.pyright]
 include = ["pycode"]
-exclude = ["pycode/memilio-simulation"]
\ No newline at end of file
+exclude = ["pycode/memilio-simulation"]
+
+[build-system]
+requires = [
+  "scikit-build-core>=0.9.0",
+  "setuptools>=68",
+  "wheel"
+]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "memilio-simulation"
+version = "1.0.0"
+description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
+readme = "README.md"
+requires-python = ">=3.8"
+license = { text = "Apache-2.0" }
+authors = [{ name = "MEmilio Team" }]
+maintainers = [
+  { email = "martin.kuehn@dlr.de" }
+]
+dependencies = [
+  # smaller numpy versions cause a security issue, 1.25 does not work together with pyfakefs
+  "numpy>=1.22,!=1.25.*",
+  # smaller pandas versions contain a bug that sometimes prevents reading
+  "pandas>=2.0.0"
+]
+
+[project.optional-dependencies]
+dev = []
+
+[project.urls]
+Homepage = "https://github.com/SciCompMod/memilio"
+Team = "https://memilio.readthedocs.io/en/latest/team.html"
+
+[tool.scikit-build]
+cmake.version = ">=3.13"
+cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
+wheel.packages = ["memilio"]
+wheel.install-dir = "memilio/simulation"
+build-dir = "../build/memilio-simulation"
+
+[tool.setuptools]
+packages = ["pycode/memilio-simulation"]

From 467748305f3c4177e31f93ef9427f4558724244c Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 14:57:47 +0100
Subject: [PATCH 02/20] try building wheels with ci

---
 .github/workflows/build_wheels.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)
 create mode 100644 .github/workflows/build_wheels.yml

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
new file mode 100644
index 0000000000..a948125dce
--- /dev/null
+++ b/.github/workflows/build_wheels.yml
@@ -0,0 +1,19 @@
+name: Build wheels
+
+on: [pull_request, release]
+
+jobs:
+  build_wheels:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: pypa/cibuildwheel@v2.16
+
+      - uses: actions/upload-artifact@v4
+        with:
+          path: ./wheelhouse/*.whl
\ No newline at end of file

From fe6706c5e9c4a25e363bec1963c27c8c92a18e73 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 15:36:51 +0100
Subject: [PATCH 03/20] [ci skip] try only ubuntu

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

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index a948125dce..48e4bccd64 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v4

From 6b35ba7483365380b8d07a6c2ef0a7e0562cad8c Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 23 Feb 2026 15:38:38 +0100
Subject: [PATCH 04/20] test

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

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 48e4bccd64..3c7019f73d 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -1,4 +1,4 @@
-name: Build wheels
+name: Build wheels 
 
 on: [pull_request, release]
 

From 369342fe5af1de461657fba4679444833539bc7b Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 13:36:22 +0100
Subject: [PATCH 05/20] require higher pybind version

---
 .github/workflows/epidata_main.yml | 294 ++++++-------
 .github/workflows/main.yml         | 660 ++++++++++++++---------------
 .github/workflows/message_bot.yml  | 226 +++++-----
 pyproject.toml                     |   1 +
 4 files changed, 591 insertions(+), 590 deletions(-)

diff --git a/.github/workflows/epidata_main.yml b/.github/workflows/epidata_main.yml
index 3cd8fea21b..e8e84dd564 100644
--- a/.github/workflows/epidata_main.yml
+++ b/.github/workflows/epidata_main.yml
@@ -1,158 +1,158 @@
-name: Epidata-CI
+# name: Epidata-CI
 
-on: 
-  schedule:
-    - cron: "40 1 * * *"
-  push:
-    branches:
-      - 'main'
-    tags:
-      - version-*
-    paths:
-      - '**/memilio-epidata/**'
-      - '.github/**'
-  pull_request:
-    types: [opened, reopened, synchronize, ready_for_review]
-    paths:
-      - '**/memilio-epidata/**'
-      - '.github/**'
-  workflow_dispatch:
+# on: 
+#   schedule:
+#     - cron: "40 1 * * *"
+#   push:
+#     branches:
+#       - 'main'
+#     tags:
+#       - version-*
+#     paths:
+#       - '**/memilio-epidata/**'
+#       - '.github/**'
+#   pull_request:
+#     types: [opened, reopened, synchronize, ready_for_review]
+#     paths:
+#       - '**/memilio-epidata/**'
+#       - '.github/**'
+#   workflow_dispatch:
 
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - uses: actions/setup-python@v5
-      with:
-        python-version: 3.12
-    - uses: pre-commit/action@v3.0.1
+# jobs:
+#   pre-commit:
+#     runs-on: ubuntu-latest
+#     steps:
+#     - uses: actions/checkout@v4
+#     - uses: actions/setup-python@v5
+#       with:
+#         python-version: 3.12
+#     - uses: pre-commit/action@v3.0.1
 
-  build-py-epidata:
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: epidata
+#   build-py-epidata:
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: epidata
 
-  build-py-plot:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: plot
+#   build-py-plot:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: plot
 
-  test-py-epidata:
-    needs: build-py-epidata
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with: 
-          version: ${{ matrix.version }}
-          package: epidata
-          coverage: ON
+#   test-py-epidata:
+#     needs: build-py-epidata
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with: 
+#           version: ${{ matrix.version }}
+#           package: epidata
+#           coverage: ON
 
-  test-py-plot:
-    if: github.event.pull_request.draft == false
-    needs: [build-py-plot, build-py-epidata]
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with: 
-          version: ${{ matrix.version }}
-          package: plot
-          coverage: ON 
+#   test-py-plot:
+#     if: github.event.pull_request.draft == false
+#     needs: [build-py-plot, build-py-epidata]
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with: 
+#           version: ${{ matrix.version }}
+#           package: plot
+#           coverage: ON 
 
-  merge-artifacts:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        packages: [epidata, plot]
-    needs: [test-py-plot, test-py-epidata]
-    steps:
-      - name: merge epidata reports
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-py-coverage-reports-${{ matrix.packages }}
-          pattern: test-py-coverage-reports-${{ matrix.packages }}-*
+#   merge-artifacts:
+#     runs-on: ubuntu-latest
+#     strategy:
+#       matrix:
+#         packages: [epidata, plot]
+#     needs: [test-py-plot, test-py-epidata]
+#     steps:
+#       - name: merge epidata reports
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-py-coverage-reports-${{ matrix.packages }}
+#           pattern: test-py-coverage-reports-${{ matrix.packages }}-*
 
-  test-pylint-epidata:
-    needs: build-py-epidata
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-pylint
-        with:
-          package: epidata
+#   test-pylint-epidata:
+#     needs: build-py-epidata
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-pylint
+#         with:
+#           package: epidata
 
-  test-pylint-plot:
-    needs: build-py-plot
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-pylint
-        with:
-          package: plot
+#   test-pylint-plot:
+#     needs: build-py-plot
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-pylint
+#         with:
+#           package: plot
 
-  download-data:
-    needs: build-py-epidata
-    runs-on: ubuntu-latest
-    continue-on-error: true
-    steps:
-      - uses: actions/checkout@v4
-      - name: Install dependencies
-        run: |
-          sudo apt-get -qq update
-          sudo apt-get -qq -y install python3-pip gnupg
-          python -m pip install --upgrade pip
-      - name: Download Python Wheels
-        uses: actions/download-artifact@v4
-        with:
-          name: python-wheels-epidata
-          path: pycode/wheelhouse
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - name: Install Python Wheels
-        run: |
-          for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
-          for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
-      - name: Download Data
-        run: |
-          mkdir -p data_dl
-          getcasedata -o data_dl --no-progress-indicators
-          getpopuldata -o data_dl --no-progress-indicators
-          getjhdata -o data_dl --no-progress-indicators
-          getdividata -o data_dl --no-progress-indicators
-          getcommutermobility -o data_dl --no-progress-indicators
-          getvaccinationdata -o data_dl --no-progress-indicators
-          gethospitalizationdata -o data_dl --no-progress-indicators
-      - name: Upload Data
-        uses: actions/upload-artifact@v4
-        with:
-          name: data
-          path: |
-            data_dl/*.json
-            data_dl/Germany/*.json
-            data_dl/Spain/*.json
-            data_dl/France/*.json
-            data_dl/Italy*.json
-            data_dl/SouthKorea/*.json
-            data_dl/US/*.json
-            data_dl/China/*.json
-          retention-days: 1
+#   download-data:
+#     needs: build-py-epidata
+#     runs-on: ubuntu-latest
+#     continue-on-error: true
+#     steps:
+#       - uses: actions/checkout@v4
+#       - name: Install dependencies
+#         run: |
+#           sudo apt-get -qq update
+#           sudo apt-get -qq -y install python3-pip gnupg
+#           python -m pip install --upgrade pip
+#       - name: Download Python Wheels
+#         uses: actions/download-artifact@v4
+#         with:
+#           name: python-wheels-epidata
+#           path: pycode/wheelhouse
+#       - name: Set up Python 3.12
+#         uses: actions/setup-python@v5
+#         with:
+#           python-version: 3.12
+#       - name: Install Python Wheels
+#         run: |
+#           for pkg in `ls pycode/wheelhouse/*cp312*.whl`; do python -m pip install $pkg; done # packages that contain native extensions are version specific
+#           for pkg in `ls pycode/wheelhouse/*py3*.whl`; do python -m pip install $pkg; done # pure python packages are not version specific
+#       - name: Download Data
+#         run: |
+#           mkdir -p data_dl
+#           getcasedata -o data_dl --no-progress-indicators
+#           getpopuldata -o data_dl --no-progress-indicators
+#           getjhdata -o data_dl --no-progress-indicators
+#           getdividata -o data_dl --no-progress-indicators
+#           getcommutermobility -o data_dl --no-progress-indicators
+#           getvaccinationdata -o data_dl --no-progress-indicators
+#           gethospitalizationdata -o data_dl --no-progress-indicators
+#       - name: Upload Data
+#         uses: actions/upload-artifact@v4
+#         with:
+#           name: data
+#           path: |
+#             data_dl/*.json
+#             data_dl/Germany/*.json
+#             data_dl/Spain/*.json
+#             data_dl/France/*.json
+#             data_dl/Italy*.json
+#             data_dl/SouthKorea/*.json
+#             data_dl/US/*.json
+#             data_dl/China/*.json
+#           retention-days: 1
           
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index b87795d7bd..4bafd6e343 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -1,355 +1,355 @@
-name: CI
+# name: CI
 
 
-on:
-  schedule:
-    - cron: "40 2 * * *"
-  push:
-    branches:
-      - "main"
-    tags:
-      - version-*
-    paths-ignore:
-      - "**/memilio-epidata/**"
-  pull_request:
-    types: [opened, reopened, synchronize, ready_for_review]
-    paths-ignore:
-      - "**/memilio-epidata/**"
-  workflow_dispatch:
+# on:
+#   schedule:
+#     - cron: "40 2 * * *"
+#   push:
+#     branches:
+#       - "main"
+#     tags:
+#       - version-*
+#     paths-ignore:
+#       - "**/memilio-epidata/**"
+#   pull_request:
+#     types: [opened, reopened, synchronize, ready_for_review]
+#     paths-ignore:
+#       - "**/memilio-epidata/**"
+#   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.workflow }}-${{ github.ref_name }}-${{ github.event.pull_request.number || github.run_id }}
-  cancel-in-progress: true
+# concurrency:
+#   group: ${{ github.workflow }}-${{ github.ref_name }}-${{ github.event.pull_request.number || github.run_id }}
+#   cancel-in-progress: true
 
-jobs:
-  pre-commit:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
-      - uses: pre-commit/action@v3.0.1
+# jobs:
+#   pre-commit:
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: actions/setup-python@v5
+#         with:
+#           python-version: 3.12
+#       - uses: pre-commit/action@v3.0.1
 
-  build-cpp-gcc_clang:
-    if: github.event.pull_request.draft == false
-    strategy:
-      matrix:
-        compiler: ["gcc", "clang"]
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "ubuntu-latest"
-          - version: "min"
-            os: "ubuntu-22.04"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-build
-        with:
-          compiler: ${{ matrix.compiler }}
-          config: ${{ matrix.config }}
-          version: ${{ matrix.version }}
-          coverage: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }} # `c && t || f` is (usually) equivalent to `c ? t : f`
-          sanitizers: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }}
+#   build-cpp-gcc_clang:
+#     if: github.event.pull_request.draft == false
+#     strategy:
+#       matrix:
+#         compiler: ["gcc", "clang"]
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "ubuntu-latest"
+#           - version: "min"
+#             os: "ubuntu-22.04"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-build
+#         with:
+#           compiler: ${{ matrix.compiler }}
+#           config: ${{ matrix.config }}
+#           version: ${{ matrix.version }}
+#           coverage: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }} # `c && t || f` is (usually) equivalent to `c ? t : f`
+#           sanitizers: ${{ (matrix.compiler == 'gcc' && matrix.config == 'Debug' && matrix.version == 'latest') && 'ON' || 'OFF' }}
 
-  build-cpp-gcc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-build
-        with:
-          compiler: gcc
-          version: latest
-          config: Release
-          optional-dependencies: OFF
+#   build-cpp-gcc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-build
+#         with:
+#           compiler: gcc
+#           version: latest
+#           config: Release
+#           optional-dependencies: OFF
 
-  build-cpp-gcc-openmp:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-build
-        with:
-          compiler: gcc
-          version: latest
-          config: Release
-          openmp: ON
+#   build-cpp-gcc-openmp:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-build
+#         with:
+#           compiler: gcc
+#           version: latest
+#           config: Release
+#           openmp: ON
 
-  build-cpp-msvc:
-    if: github.event.pull_request.draft == false
-    strategy:
-      matrix:
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "windows-2025"
-          - version: "min"
-            os: "windows-2022"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-build
-        with:
-          config: ${{ matrix.config }}
-          version: ${{ matrix.version }}
+#   build-cpp-msvc:
+#     if: github.event.pull_request.draft == false
+#     strategy:
+#       matrix:
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "windows-2025"
+#           - version: "min"
+#             os: "windows-2022"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-build
+#         with:
+#           config: ${{ matrix.config }}
+#           version: ${{ matrix.version }}
 
-  build-cpp-msvc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    runs-on: windows-2025
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-build
-        with:
-          config: Release
-          version: latest
-          optional-dependencies: OFF
+#   build-cpp-msvc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     runs-on: windows-2025
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-build
+#         with:
+#           config: Release
+#           version: latest
+#           optional-dependencies: OFF
 
-  test-cpp-gcc_clang:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc_clang
-    strategy:
-      matrix:
-        compiler: ["gcc", "clang"]
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "ubuntu-latest"
-          - version: "min"
-            os: "ubuntu-22.04"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-test
-        with:
-          artifact-pattern: ${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
-          coverage: ${{ (matrix.compiler == 'gcc' && matrix.version == 'latest' && matrix.config == 'Debug') && 'ON' || 'OFF' }}
+#   test-cpp-gcc_clang:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc_clang
+#     strategy:
+#       matrix:
+#         compiler: ["gcc", "clang"]
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "ubuntu-latest"
+#           - version: "min"
+#             os: "ubuntu-22.04"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-test
+#         with:
+#           artifact-pattern: ${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
+#           coverage: ${{ (matrix.compiler == 'gcc' && matrix.version == 'latest' && matrix.config == 'Debug') && 'ON' || 'OFF' }}
  
-  test-cpp-gcc-sbml:
-      if: github.event.pull_request.draft == false
-      needs: build-cpp-gcc_clang
-      runs-on: ubuntu-latest
-      steps:
-        - uses: actions/checkout@v4
-        - uses: ./.github/actions/sbml-test
+#   test-cpp-gcc-sbml:
+#       if: github.event.pull_request.draft == false
+#       needs: build-cpp-gcc_clang
+#       runs-on: ubuntu-latest
+#       steps:
+#         - uses: actions/checkout@v4
+#         - uses: ./.github/actions/sbml-test
 
-  merge-test-artifacts:
-    needs: [test-cpp-gcc_clang, test-cpp-msvc, test-py-surrogatemodel]
-    runs-on: ubuntu-latest
-    steps:
-      - name: merge-coverage-artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-cpp-coverage-reports
-          pattern: test-cpp-coverage-reports-*
-      - name: merge-linux-artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-cpp-linux-report
-          pattern: test-cpp-linux-report-*
-      - name: merge-windows-artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-cpp-win-report
-          pattern: test-cpp-win-report-*
-      - name: merge python reports
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: test-py-coverage-reports-surrogatemodel
-          pattern: test-py-coverage-reports-surrogatemodel-*
+#   merge-test-artifacts:
+#     needs: [test-cpp-gcc_clang, test-cpp-msvc, test-py-surrogatemodel]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - name: merge-coverage-artifacts
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-cpp-coverage-reports
+#           pattern: test-cpp-coverage-reports-*
+#       - name: merge-linux-artifacts
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-cpp-linux-report
+#           pattern: test-cpp-linux-report-*
+#       - name: merge-windows-artifacts
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-cpp-win-report
+#           pattern: test-cpp-win-report-*
+#       - name: merge python reports
+#         uses: actions/upload-artifact/merge@v4
+#         with:
+#           name: test-py-coverage-reports-surrogatemodel
+#           pattern: test-py-coverage-reports-surrogatemodel-*
 
-  test-cpp-gcc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc-no-optional-deps
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-test
-        with:
-          artifact-pattern: gcc-latest-Release
-          optional-deps: OFF
+#   test-cpp-gcc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc-no-optional-deps
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-test
+#         with:
+#           artifact-pattern: gcc-latest-Release
+#           optional-deps: OFF
 
-  test-cpp-gcc-openmp:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc-openmp
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
-    env:
-      OMP_NUM_THREADS: 4
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-test
-        with:
-          artifact-pattern: gcc-latest-Release
-          num-repeat: 10
-          openmp: ON
+#   test-cpp-gcc-openmp:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc-openmp
+#     runs-on: ubuntu-latest
+#     timeout-minutes: 30
+#     env:
+#       OMP_NUM_THREADS: 4
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-test
+#         with:
+#           artifact-pattern: gcc-latest-Release
+#           num-repeat: 10
+#           openmp: ON
 
-  test-cpp-msvc:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-msvc
-    strategy:
-      matrix:
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "windows-2025"
-          - version: "min"
-            os: "windows-2022"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-test
-        with:
-          artifact-pattern: msvc-${{ matrix.version }}-${{ matrix.config }}
+#   test-cpp-msvc:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-msvc
+#     strategy:
+#       matrix:
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "windows-2025"
+#           - version: "min"
+#             os: "windows-2022"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-test
+#         with:
+#           artifact-pattern: msvc-${{ matrix.version }}-${{ matrix.config }}
 
-  test-cpp-msvc-no-optional-deps:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-msvc-no-optional-deps
-    runs-on: windows-2025
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-test
-        with:
-          artifact-pattern: msvc-latest-Release
-          optional-deps: OFF
+#   test-cpp-msvc-no-optional-deps:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-msvc-no-optional-deps
+#     runs-on: windows-2025
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-test
+#         with:
+#           artifact-pattern: msvc-latest-Release
+#           optional-deps: OFF
 
-  run_examples-cpp-gcc_clang:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-gcc_clang
-    strategy:
-      matrix:
-        compiler: ["gcc", "clang"]
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "ubuntu-latest"
-          - version: "min"
-            os: "ubuntu-22.04"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/linux-run_examples
-        with:
-          build-artifact: build-cpp-linux-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
+#   run_examples-cpp-gcc_clang:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-gcc_clang
+#     strategy:
+#       matrix:
+#         compiler: ["gcc", "clang"]
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "ubuntu-latest"
+#           - version: "min"
+#             os: "ubuntu-22.04"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/linux-run_examples
+#         with:
+#           build-artifact: build-cpp-linux-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.config }}
 
-  run_examples-cpp-msvc:
-    if: github.event.pull_request.draft == false
-    needs: build-cpp-msvc
-    strategy:
-      matrix:
-        config: ["Debug", "Release"]
-        version: ["latest", "min"]
-        include:
-          - version: "latest"
-            os: "windows-2025"
-          - version: "min"
-            os: "windows-2022"
-    runs-on: ${{ matrix.os }}
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/windows-run_examples
-        with:
-          build-artifact: build-cpp-windows-msvc-${{ matrix.version }}-${{ matrix.config }}
+#   run_examples-cpp-msvc:
+#     if: github.event.pull_request.draft == false
+#     needs: build-cpp-msvc
+#     strategy:
+#       matrix:
+#         config: ["Debug", "Release"]
+#         version: ["latest", "min"]
+#         include:
+#           - version: "latest"
+#             os: "windows-2025"
+#           - version: "min"
+#             os: "windows-2022"
+#     runs-on: ${{ matrix.os }}
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/windows-run_examples
+#         with:
+#           build-artifact: build-cpp-windows-msvc-${{ matrix.version }}-${{ matrix.config }}
 
-  build-py-generation:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: generation
+#   build-py-generation:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: generation
 
-  build-py-simulation:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: simulation
+#   build-py-simulation:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: simulation
 
-  build-py-surrogatemodel:
-    if: github.event.pull_request.draft == false
-    runs-on: ubuntu-latest
-    container: quay.io/pypa/manylinux_2_28_x86_64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/build-py
-        with:
-          package: surrogatemodel
+#   build-py-surrogatemodel:
+#     if: github.event.pull_request.draft == false
+#     runs-on: ubuntu-latest
+#     container: quay.io/pypa/manylinux_2_28_x86_64
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/build-py
+#         with:
+#           package: surrogatemodel
 
-  test-py-generation:
-    if: github.event.pull_request.draft == false
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    needs: build-py-generation
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with:
-          package: generation
+#   test-py-generation:
+#     if: github.event.pull_request.draft == false
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     needs: build-py-generation
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with:
+#           package: generation
 
-  test-py-simulation:
-    if: github.event.pull_request.draft == false
-    needs: build-py-simulation
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with:
-          package: simulation
+#   test-py-simulation:
+#     if: github.event.pull_request.draft == false
+#     needs: build-py-simulation
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with:
+#           package: simulation
 
-  test-py-surrogatemodel:
-    if: github.event.pull_request.draft == false
-    needs: [build-py-surrogatemodel, build-py-simulation]
-    strategy:
-      matrix: 
-        version: ["3.8", "3.12"]
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: ./.github/actions/test-py
-        with:
-          version: ${{ matrix.version }}
-          package: surrogatemodel
-          coverage: ON
+#   test-py-surrogatemodel:
+#     if: github.event.pull_request.draft == false
+#     needs: [build-py-surrogatemodel, build-py-simulation]
+#     strategy:
+#       matrix: 
+#         version: ["3.8", "3.12"]
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - uses: ./.github/actions/test-py
+#         with:
+#           version: ${{ matrix.version }}
+#           package: surrogatemodel
+#           coverage: ON
 
-  codecov:
-    if: github.event.pull_request.draft == false
-    needs: merge-test-artifacts
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Install dependencies
-        run: |
-          sudo apt-get -qq update
-          sudo apt-get -qq -y install git curl
-      - name: Download python coverage report
-        uses: actions/download-artifact@v4
-        with:
-          name: test-py-coverage-reports-surrogatemodel
-      - name: Download cpp coverage report
-        uses: actions/download-artifact@v4
-        with:
-          name: test-cpp-coverage-reports
-      - name: Deploy to codecov.io
-        uses: codecov/codecov-action@v3
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
-          directory: ./coverage_python
-          files: ./coverage_python/**,./coverage.info
-          verbose: true
+#   codecov:
+#     if: github.event.pull_request.draft == false
+#     needs: merge-test-artifacts
+#     runs-on: ubuntu-latest
+#     steps:
+#       - uses: actions/checkout@v4
+#       - name: Install dependencies
+#         run: |
+#           sudo apt-get -qq update
+#           sudo apt-get -qq -y install git curl
+#       - name: Download python coverage report
+#         uses: actions/download-artifact@v4
+#         with:
+#           name: test-py-coverage-reports-surrogatemodel
+#       - name: Download cpp coverage report
+#         uses: actions/download-artifact@v4
+#         with:
+#           name: test-cpp-coverage-reports
+#       - name: Deploy to codecov.io
+#         uses: codecov/codecov-action@v3
+#         with:
+#           token: ${{ secrets.CODECOV_TOKEN }}
+#           directory: ./coverage_python
+#           files: ./coverage_python/**,./coverage.info
+#           verbose: true
diff --git a/.github/workflows/message_bot.yml b/.github/workflows/message_bot.yml
index cd4f322ca1..55fdb1545d 100644
--- a/.github/workflows/message_bot.yml
+++ b/.github/workflows/message_bot.yml
@@ -1,134 +1,134 @@
-# .github/workflows/discussion-monitor.yml
-name: Discussion Monitor
+# # .github/workflows/discussion-monitor.yml
+# name: Discussion Monitor
 
-on:
-  schedule:
-    - cron: '0 9 * * *'
+# on:
+#   schedule:
+#     - cron: '0 9 * * *'
 
 
-jobs:
-  check-discussions:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      discussions: read
-    steps:
-    - name: Check for new discussions
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
-      run: |
-        npm install @octokit/rest
-        cat > check.js << 'EOF'
-        const { Octokit } = require('@octokit/rest');
+# jobs:
+#   check-discussions:
+#     runs-on: ubuntu-latest
+#     permissions:
+#       contents: read
+#       discussions: read
+#     steps:
+#     - name: Check for new discussions
+#       env:
+#         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+#         MATTERMOST_WEBHOOK_URL: ${{ secrets.MATTERMOST_WEBHOOK_URL }}
+#       run: |
+#         npm install @octokit/rest
+#         cat > check.js << 'EOF'
+#         const { Octokit } = require('@octokit/rest');
 
-        const octokit = new Octokit({ auth: process.env.GITHUB_TOKEN });
+#         const octokit = new Octokit({ auth: process.env.GITHUB_TOKEN });
 
-        async function check() {
-          const since = new Date();
-          since.setHours(since.getHours() - 25);
+#         async function check() {
+#           const since = new Date();
+#           since.setHours(since.getHours() - 25);
           
-          const [owner, repo] = process.env.GITHUB_REPOSITORY.split('/');
-          console.log(`Checking discussions for ${owner}/${repo}`);
+#           const [owner, repo] = process.env.GITHUB_REPOSITORY.split('/');
+#           console.log(`Checking discussions for ${owner}/${repo}`);
           
-          try {
-            const response = await octokit.graphql(`
-              query { 
-                repository(owner: "${owner}", name: "${repo}") {
-                  discussions(first: 10, orderBy: {field: CREATED_AT, direction: DESC}) {
-                    nodes { 
-                      createdAt
-                      title
-                      url
-                      number
-                      author {
-                        login
-                      }
-                      category {
-                        name
-                        emoji
-                      }
-                    }
-                  }
-                }
-              }
-            `);
+#           try {
+#             const response = await octokit.graphql(`
+#               query { 
+#                 repository(owner: "${owner}", name: "${repo}") {
+#                   discussions(first: 10, orderBy: {field: CREATED_AT, direction: DESC}) {
+#                     nodes { 
+#                       createdAt
+#                       title
+#                       url
+#                       number
+#                       author {
+#                         login
+#                       }
+#                       category {
+#                         name
+#                         emoji
+#                       }
+#                     }
+#                   }
+#                 }
+#               }
+#             `);
             
-            console.log('Full GraphQL response:', JSON.stringify(response, null, 2));
+#             console.log('Full GraphQL response:', JSON.stringify(response, null, 2));
             
-            if (!response || !response.repository) {
-              console.log('Repository not found or discussions not enabled');
-              console.log('Response keys:', Object.keys(response || {}));
-              return;
-            }
+#             if (!response || !response.repository) {
+#               console.log('Repository not found or discussions not enabled');
+#               console.log('Response keys:', Object.keys(response || {}));
+#               return;
+#             }
 
-            if (!response.repository.discussions) {
-              console.log('Discussions not available for this repository');
-              return;
-            }
+#             if (!response.repository.discussions) {
+#               console.log('Discussions not available for this repository');
+#               return;
+#             }
             
-            const newDiscussions = response.repository.discussions.nodes.filter(
-              d => new Date(d.createdAt) > since
-            );
+#             const newDiscussions = response.repository.discussions.nodes.filter(
+#               d => new Date(d.createdAt) > since
+#             );
             
-            console.log(`Found ${newDiscussions.length} new discussions`);
+#             console.log(`Found ${newDiscussions.length} new discussions`);
             
-            if (newDiscussions.length > 0) {
-              let message;
+#             if (newDiscussions.length > 0) {
+#               let message;
               
-              if (newDiscussions.length === 1) {
-                const discussion = newDiscussions[0];
-                message = {
-                  text: `${discussion.category.emoji || '💬'} New Discussion on ${owner}/${repo}
+#               if (newDiscussions.length === 1) {
+#                 const discussion = newDiscussions[0];
+#                 message = {
+#                   text: `${discussion.category.emoji || '💬'} New Discussion on ${owner}/${repo}
 
-        **[${discussion.title}](${discussion.url})**
+#         **[${discussion.title}](${discussion.url})**
 
-        👤 **Author:** ${discussion.author.login}
-        📂 **Category:** ${discussion.category.name}
-        🔢 **Discussion #${discussion.number}**`,
-                  username: "GitHub Discussion Bot",
-                  icon_emoji: ":github:"
-                };
-              } else {
-                const discussionList = newDiscussions.map(d => 
-                  `- ${d.category.emoji || '💬'} **[${d.title}](${d.url})** by ${d.author.login}`
-                ).join('\n');
+#         👤 **Author:** ${discussion.author.login}
+#         📂 **Category:** ${discussion.category.name}
+#         🔢 **Discussion #${discussion.number}**`,
+#                   username: "GitHub Discussion Bot",
+#                   icon_emoji: ":github:"
+#                 };
+#               } else {
+#                 const discussionList = newDiscussions.map(d => 
+#                   `- ${d.category.emoji || '💬'} **[${d.title}](${d.url})** by ${d.author.login}`
+#                 ).join('\n');
                 
-                message = {
-                  text: `🎉 ${newDiscussions.length} New Discussions on ${owner}/${repo}
+#                 message = {
+#                   text: `🎉 ${newDiscussions.length} New Discussions on ${owner}/${repo}
 
-        ${discussionList}
+#         ${discussionList}
 
-        ---
-        *Check out the latest discussions above!*`,
-                  username: "GitHub Discussion Bot",
-                  icon_emoji: ":github:"
-                };
-              }
+#         ---
+#         *Check out the latest discussions above!*`,
+#                   username: "GitHub Discussion Bot",
+#                   icon_emoji: ":github:"
+#                 };
+#               }
               
-              const response = await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
-                method: 'POST',
-                headers: { 'Content-Type': 'application/json' },
-                body: JSON.stringify(message)
-              });
-              console.log('Mattermost notification sent');
-            }
-          } catch (error) {
-            console.error('Error details:', error);
-            if (process.env.MATTERMOST_WEBHOOK_URL) {
-              await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
-                method: 'POST',
-                headers: { 'Content-Type': 'application/json' },
-                body: JSON.stringify({ 
-                  text: '⚠️ **GitHub Discussion Bot Error**\nThere was an error checking discussions. Please check the workflow logs.',
-                  username: "GitHub Discussion Bot",
-                  icon_emoji: ":warning:"
-                })
-              });
-            }
-          }
-        }
+#               const response = await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
+#                 method: 'POST',
+#                 headers: { 'Content-Type': 'application/json' },
+#                 body: JSON.stringify(message)
+#               });
+#               console.log('Mattermost notification sent');
+#             }
+#           } catch (error) {
+#             console.error('Error details:', error);
+#             if (process.env.MATTERMOST_WEBHOOK_URL) {
+#               await fetch(process.env.MATTERMOST_WEBHOOK_URL, {
+#                 method: 'POST',
+#                 headers: { 'Content-Type': 'application/json' },
+#                 body: JSON.stringify({ 
+#                   text: '⚠️ **GitHub Discussion Bot Error**\nThere was an error checking discussions. Please check the workflow logs.',
+#                   username: "GitHub Discussion Bot",
+#                   icon_emoji: ":warning:"
+#                 })
+#               });
+#             }
+#           }
+#         }
 
-        check().catch(console.error);
-        EOF
-        node check.js
+#         check().catch(console.error);
+#         EOF
+#         node check.js
diff --git a/pyproject.toml b/pyproject.toml
index fec49ef467..e9b66a9e66 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,6 +10,7 @@ requires = [
   "scikit-build-core>=0.9.0",
   "setuptools>=68",
   "wheel"
+  "pybind11>=2.11.2"
 ]
 build-backend = "scikit_build_core.build"
 

From c13105fbc38cd9e9de949ce6b17b83f05c591870 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 13:39:51 +0100
Subject: [PATCH 06/20] add comma

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

diff --git a/pyproject.toml b/pyproject.toml
index e9b66a9e66..2f298e1118 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@ exclude = ["pycode/memilio-simulation"]
 requires = [
   "scikit-build-core>=0.9.0",
   "setuptools>=68",
-  "wheel"
+  "wheel",
   "pybind11>=2.11.2"
 ]
 build-backend = "scikit_build_core.build"

From e25c2184b4ebe7b209d0c51d55db3215d1a9af6a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 14:37:35 +0100
Subject: [PATCH 07/20] skip some pypy versions

---
 pyproject.toml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/pyproject.toml b/pyproject.toml
index 2f298e1118..cc1c221201 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -48,3 +48,7 @@ build-dir = "../build/memilio-simulation"
 
 [tool.setuptools]
 packages = ["pycode/memilio-simulation"]
+
+[tool.cibuildwheel]
+# Disable building PyPy 3.8 and 3.9 wheels on all platforms
+skip = ["pp38-*", "pp39-*"]

From 69a5b96a3aaaee6832cd02d7cb59553c166673c6 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 14:57:57 +0100
Subject: [PATCH 08/20] skip all pypy versions

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

diff --git a/pyproject.toml b/pyproject.toml
index cc1c221201..e491bed7aa 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,5 +50,5 @@ build-dir = "../build/memilio-simulation"
 packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
-# Disable building PyPy 3.8 and 3.9 wheels on all platforms
-skip = ["pp38-*", "pp39-*"]
+# Disable building PyPy wheels on all platforms
+skip = ["pp*"]

From 73a7fbc453d3d0a3d3964b6277c54648e813b949 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 15:49:51 +0100
Subject: [PATCH 09/20] skip musllinux

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e491bed7aa..d34c2f6c2f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,4 +51,5 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*"]
+skip = ["pp*", "*musllinux*"]
+skip = ["*_i686"] # these work, skip for further testing

From 6ca71df7af474c4c0591e71769861e085879897a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 15:52:09 +0100
Subject: [PATCH 10/20] fix

---
 pyproject.toml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d34c2f6c2f..6358fafdec 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -51,5 +51,4 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*"]
-skip = ["*_i686"] # these work, skip for further testing
+skip = ["pp*", "*musllinux*", "*_i686"] # "*_i686" works, skip for now for further testing

From 265a58c9c5d355f3a2df614d6dfbce974d5eb9ae Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 16:16:34 +0100
Subject: [PATCH 11/20] test windows

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

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index 3c7019f73d..aaa02519cf 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [windows-latest]
 
     steps:
       - uses: actions/checkout@v4

From 22c73cbcb42b02c710ffb6f0379540a8e2f327b0 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Wed, 25 Feb 2026 16:45:36 +0100
Subject: [PATCH 12/20] skip win32

---
 pyproject.toml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 6358fafdec..d3eb152a96 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,8 +9,7 @@ exclude = ["pycode/memilio-simulation"]
 requires = [
   "scikit-build-core>=0.9.0",
   "setuptools>=68",
-  "wheel",
-  "pybind11>=2.11.2"
+  "wheel"
 ]
 build-backend = "scikit_build_core.build"
 
@@ -51,4 +50,4 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*", "*_i686"] # "*_i686" works, skip for now for further testing
+skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing

From 02edbf2d3bb79a25b6c113d600e4836322175cb0 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 09:20:20 +0100
Subject: [PATCH 13/20] test macos

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

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index aaa02519cf..a4ef4c49d9 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -7,7 +7,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [windows-latest]
+        os: [macos-latest]
 
     steps:
       - uses: actions/checkout@v4

From a1d4085d3e847f9df138cd13bceb37f6e2b81476 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 09:57:00 +0100
Subject: [PATCH 14/20] skip macosx_arm64

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

diff --git a/pyproject.toml b/pyproject.toml
index d3eb152a96..b709e83ee8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,4 +50,4 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
+skip = ["pp*", "*musllinux*", "*_i686", "*-win32", "*-macosx_arm64"] # "*_i686" works, skip for now for further testing

From 59e454a3705dd92875c260d12eade58744c3c2f6 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:14:00 +0100
Subject: [PATCH 15/20] test

---
 pyproject.toml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b709e83ee8..066f2c4ee4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,4 +50,5 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-skip = ["pp*", "*musllinux*", "*_i686", "*-win32", "*-macosx_arm64"] # "*_i686" works, skip for now for further testing
+build = ["*-macosx_x86_64", "*-macosx_universal2"]
+skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing

From b4febe3c088d2a4c8b3ef2e1601a8da8da390e7a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:19:02 +0100
Subject: [PATCH 16/20] test

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 066f2c4ee4..254f60d429 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -50,5 +50,7 @@ packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable building PyPy wheels on all platforms
-build = ["*-macosx_x86_64", "*-macosx_universal2"]
+build-verbosity = 3
 skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
+
+

From 6f2ac0a461b302925eabd45b1356d28fc79caccc Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 11:34:05 +0100
Subject: [PATCH 17/20] build sdist in ci

---
 .github/workflows/build_wheels.yml | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index a4ef4c49d9..dcd949973a 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -3,11 +3,25 @@ name: Build wheels
 on: [pull_request, release]
 
 jobs:
+
+  build_sdist: 
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        path: dist/*.tar.gz
+
+
   build_wheels:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macos-latest]
+        os: [ubuntu-latest]
 
     steps:
       - uses: actions/checkout@v4

From 4b9ce8df99dd38f83cbebb5defa8781d9d881382 Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 12:06:54 +0100
Subject: [PATCH 18/20] add names for artifacts

---
 .github/workflows/build_wheels.yml | 2 ++
 pyproject.toml                     | 3 +--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index dcd949973a..f7711d163d 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -14,6 +14,7 @@ jobs:
 
     - uses: actions/upload-artifact@v4
       with:
+        name: sdist
         path: dist/*.tar.gz
 
 
@@ -30,4 +31,5 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.os }}
           path: ./wheelhouse/*.whl
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index 254f60d429..ec05c47a80 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -49,8 +49,7 @@ build-dir = "../build/memilio-simulation"
 packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
-# Disable building PyPy wheels on all platforms
-build-verbosity = 3
+# Disable some wheels
 skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
 
 

From 9747c8c3eb7149f7beb0d93b5f52bb7e0568a22f Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Fri, 27 Feb 2026 15:32:20 +0100
Subject: [PATCH 19/20] also include other python packages

---
 .github/workflows/build_wheels.yml |  2 +-
 pyproject.toml                     | 34 +++++++++++++++---------------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
index f7711d163d..d8ca6d7bec 100644
--- a/.github/workflows/build_wheels.yml
+++ b/.github/workflows/build_wheels.yml
@@ -22,7 +22,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest]
+        os: [ubuntu-latest, windows_latest]
 
     steps:
       - uses: actions/checkout@v4
diff --git a/pyproject.toml b/pyproject.toml
index ec05c47a80..260a1a979d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,20 +1,5 @@
-[tool.autopep8]
-max-line-length = 79
-
-[tool.pyright]
-include = ["pycode"]
-exclude = ["pycode/memilio-simulation"]
-
-[build-system]
-requires = [
-  "scikit-build-core>=0.9.0",
-  "setuptools>=68",
-  "wheel"
-]
-build-backend = "scikit_build_core.build"
-
 [project]
-name = "memilio-simulation"
+name = "memilio"
 version = "1.0.0"
 description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
@@ -38,6 +23,14 @@ dev = []
 Homepage = "https://github.com/SciCompMod/memilio"
 Team = "https://memilio.readthedocs.io/en/latest/team.html"
 
+[build-system]
+requires = [
+  "scikit-build-core>=0.9.0",
+  "setuptools>=68",
+  "wheel"
+]
+build-backend = "scikit_build_core.build"
+
 [tool.scikit-build]
 cmake.version = ">=3.13"
 cmake.args = ["-DMEMILIO_BUILD_SHARED_LIBS:BOOL=ON"]
@@ -46,10 +39,17 @@ wheel.install-dir = "memilio/simulation"
 build-dir = "../build/memilio-simulation"
 
 [tool.setuptools]
-packages = ["pycode/memilio-simulation"]
+packages = ["pycode/memilio-epidata","pycode/memilio-generation","pycode/memilio-plot","pycode/memilio-simulation","pycode/memilio-surrogatemodel"]
 
 [tool.cibuildwheel]
 # Disable some wheels
 skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
 
+[tool.autopep8]
+max-line-length = 79
+
+[tool.pyright]
+include = ["pycode"]
+exclude = ["pycode/memilio-simulation"]
+
 

From 77bab936db076c3e30819f1f6d992a8bd239455a Mon Sep 17 00:00:00 2001
From: Anna Wendler <106674756+annawendler@users.noreply.github.com>
Date: Mon, 2 Mar 2026 13:18:43 +0100
Subject: [PATCH 20/20] update

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

diff --git a/pyproject.toml b/pyproject.toml
index 260a1a979d..f97d9e91e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [project]
-name = "memilio"
+name = "memilio-simulation"
 version = "1.0.0"
-description = "Part of MEmilio project, python bindings to the C++ libraries that contain the models and simulations."
+description = "Part of MEmilio project, Python bindings to the C++ libraries that contain the models and simulations."
 readme = "README.md"
 requires-python = ">=3.8"
 license = { text = "Apache-2.0" }
@@ -39,11 +39,11 @@ wheel.install-dir = "memilio/simulation"
 build-dir = "../build/memilio-simulation"
 
 [tool.setuptools]
-packages = ["pycode/memilio-epidata","pycode/memilio-generation","pycode/memilio-plot","pycode/memilio-simulation","pycode/memilio-surrogatemodel"]
+packages = ["pycode/memilio-simulation"]
 
 [tool.cibuildwheel]
 # Disable some wheels
-skip = ["pp*", "*musllinux*", "*_i686", "*-win32"] # "*_i686" works, skip for now for further testing
+skip = ["pp*", "*musllinux*", "*-win32"] 
 
 [tool.autopep8]
 max-line-length = 79