Use scikit build core

.gitignore

@@ -1,4 +1,13 @@
 *.so
 *.o
 *.mod
+*.whl
+__pycache__/
+*.py[cod]
+.pytest_cache/
+.venv/
+uv.lock
 _psiesta.c
+build/
+builddir
+Siesta.pc

CMakeLists.txt

@@ -0,0 +1,97 @@
+cmake_minimum_required(VERSION 3.20)
+
+project(
+  PSiesta
+  VERSION 0.3.0
+  LANGUAGES C Fortran
+)
+
+include(FetchContent)
+include(GNUInstallDirs)
+
+option(PSIESTA_FETCH_SIESTA "Fetch/build Siesta as a CMake subproject" ON)
+option(PSIESTA_USE_SYSTEM_SIESTA "Use an installed Siesta CMake package" OFF)
+set(PSIESTA_SIESTA_SOURCE_DIR "" CACHE PATH "Existing Siesta source checkout")
+set(PSIESTA_SIESTA_GIT_REPOSITORY "https://gitlab.com/siesta-project/siesta.git" CACHE STRING "Siesta git repository")
+set(PSIESTA_SIESTA_GIT_TAG "master" CACHE STRING "Siesta git tag, branch, or commit")
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
+find_package(MPI REQUIRED COMPONENTS C Fortran)
+
+execute_process(
+  COMMAND "${Python_EXECUTABLE}" -c "import numpy; print(numpy.get_include())"
+  OUTPUT_VARIABLE NumPy_INCLUDE_DIR
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+  COMMAND_ERROR_IS_FATAL ANY
+)
+
+find_program(CYTHON_EXECUTABLE cython REQUIRED)
+
+if(PSIESTA_USE_SYSTEM_SIESTA)
+  find_package(SIESTA CONFIG REQUIRED)
+elseif(PSIESTA_SIESTA_SOURCE_DIR)
+  set(SIESTA_TESTS OFF CACHE BOOL "" FORCE)
+  set(SIESTA_INSTALL OFF CACHE BOOL "" FORCE)
+  set(SIESTA_WITH_MPI ON CACHE BOOL "" FORCE)
+  set(SIESTA_WITH_PEXSI OFF CACHE BOOL "" FORCE)
+  set(SIESTA_SHARED_LIBS OFF CACHE BOOL "" FORCE)
+  add_subdirectory("${PSIESTA_SIESTA_SOURCE_DIR}" "${CMAKE_BINARY_DIR}/_deps/siesta-build")
+elseif(PSIESTA_FETCH_SIESTA)
+  set(SIESTA_TESTS OFF CACHE BOOL "" FORCE)
+  set(SIESTA_INSTALL OFF CACHE BOOL "" FORCE)
+  set(SIESTA_WITH_MPI ON CACHE BOOL "" FORCE)
+  set(SIESTA_WITH_PEXSI OFF CACHE BOOL "" FORCE)
+  set(SIESTA_SHARED_LIBS OFF CACHE BOOL "" FORCE)
+  FetchContent_Declare(
+    siesta
+    GIT_REPOSITORY "${PSIESTA_SIESTA_GIT_REPOSITORY}"
+    GIT_TAG "${PSIESTA_SIESTA_GIT_TAG}"
+  )
+  FetchContent_MakeAvailable(siesta)
+else()
+  message(FATAL_ERROR "Set one of PSIESTA_USE_SYSTEM_SIESTA, PSIESTA_SIESTA_SOURCE_DIR, or PSIESTA_FETCH_SIESTA")
+endif()
+
+set(_siesta_target "")
+foreach(candidate IN ITEMS SIESTA::libsiesta SIESTA.libsiesta SIESTA-libsiesta siesta.libsiesta siesta-libsiesta)
+  if(TARGET "${candidate}")
+    set(_siesta_target "${candidate}")
+    break()
+  endif()
+endforeach()
+if(NOT _siesta_target)
+  message(FATAL_ERROR "Could not find the upstream Siesta libsiesta CMake target")
+endif()
+message(STATUS "Using Siesta target: ${_siesta_target}")
+
+set(_psiesta_c "${CMAKE_CURRENT_BINARY_DIR}/psiesta/_psiesta.c")
+add_custom_command(
+  OUTPUT "${_psiesta_c}"
+  COMMAND "${CMAKE_COMMAND}" -E make_directory "${CMAKE_CURRENT_BINARY_DIR}/psiesta"
+  COMMAND "${CYTHON_EXECUTABLE}" -3 "${CMAKE_CURRENT_SOURCE_DIR}/psiesta/_psiesta.pyx" -o "${_psiesta_c}"
+  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/psiesta/_psiesta.pyx"
+  VERBATIM
+)
+
+Python_add_library(_psiesta MODULE
+  "${_psiesta_c}"
+  "${CMAKE_CURRENT_SOURCE_DIR}/psiesta/c_bindings/fpsiesta.f90"
+  WITH_SOABI
+)
+
+target_include_directories(_psiesta PRIVATE "${NumPy_INCLUDE_DIR}")
+target_link_libraries(_psiesta PRIVATE
+  "${_siesta_target}"
+  MPI::MPI_C
+  MPI::MPI_Fortran
+)
+
+install(TARGETS _psiesta LIBRARY DESTINATION psiesta)
+install(FILES
+  "psiesta/__init__.py"
+  "psiesta/ase.py"
+  "psiesta/psiesta.py"
+  DESTINATION psiesta
+)

README.md

@@ -65,15 +65,70 @@ You should use a Siesta version later than the git master as of 2020-06-10, as a
 
 ## Obtaining source, building and installing
 You can obtain the source by simply cloning this repository.
-To build, you must have a properly set up `arch.make` for Siesta in your Obj-dir, and you must have at least compiled Siesta there (see the note above for a patched Siesta).
-You can then run `OBJ=/my/custom/siesta/Obj/ python3 setup.py install [--user] [--prefix=<prefix>]` (or use `build` instead of `install`) to build PSiesta.
-The setup.py-file makes use of Siesta's own `Makefile` (which includes your `arch.make`) in combination with `--dry-run` to extract the compilation and link arguments.
-It *should* work for both intel and gnu compilers, but be aware that LTO can complicate things, and ensure that any external libraries that are used (eg. flook) are compiled with `-fPIC`.
 
-On some platforms it is necessary to link more libraries than Siesta is otherwise compiled with. It is currently a little unclear why, but in one case I needed to use `EXTRA_COMP_ARGS="-lmkl_avx512 -lmkl_def"` (which the setup.py-file will recognize).
+The current build uses scikit-build-core and CMake. By default, CMake fetches upstream Siesta and builds it as a subproject, using Siesta's native CMake build.
 
-As noted above, you should use a Siesta version later than the git master as of 2020-06-10.
+For development, the recommended environment is Nix for native dependencies and uv for Python dependencies. Nix provides the native scientific build stack, including C, C++, and Fortran compilers, OpenMPI compiler wrappers, CMake, Ninja, BLAS/LAPACK, ScaLAPACK, NetCDF C/Fortran, HDF5, FFTW, libxc, readline, zlib, curl, and `uv`. uv manages Python build isolation and dependencies from `pyproject.toml`.
 
+Install Nix with flakes enabled, then run commands inside the development shell:
+
+```bash
+nix develop
+```
+
+Or run a single command inside it:
+
+```bash
+nix develop -c <command>
+```
+
+Check the shell with:
+
+```bash
+nix develop -c sh -c 'cc --version && mpicc --version && mpifort --version && cmake --version && uv --version'
+```
+
+Build the wheel with:
+
+```bash
+nix develop -c uv build --wheel
+```
+
+This produces a wheel in `dist/`. Build output is written under `build/`.
+
+You can point at an existing Siesta checkout with:
+
+```bash
+nix develop -c uv build --wheel --config-setting=cmake.define.PSIESTA_SIESTA_SOURCE_DIR=/path/to/siesta
+```
+
+Local build artifacts can be removed with:
+
+```bash
+rm -rf build dist
+```
+
+## Smoke tests
+
+The test suite contains lightweight technical smoke tests. They are not intended
+to validate scientific accuracy; they only check that the Python extension
+imports, MPI starts, Siesta launches as a library, and simple H/H2 force calls
+return finite energy, force, and stress arrays.
+
+The calculation tests use `tests/fixtures/H.psml`.
+
+Run the tests from the Nix development shell with:
+
+```bash
+nix develop -c mpirun -n 1 uv run python -m mpi4py -m pytest -q
+```
+
+The Nix development shell exports OpenMPI's library directory so uv's isolated
+Python environment and `mpi4py` can locate `libmpi.so`.
+
+The smoke calculations deliberately use very loose settings, including a tiny
+basis, low mesh cutoff, one SCF step, and `SCF.MustConverge false`, so warnings
+about unconverged SCF are expected.
 
 ## Behaviour
 See also [the SiestaSubroutine readme](https://gitlab.com/siesta-project/siesta/tree/master/Util/SiestaSubroutine/README).
@@ -88,5 +143,4 @@ It will also prepend some settings to your fdf-file: Notably `MD.TypeOfRun force
 * Only a few properties can currently be fetched directly via the bindings. Other properties must be obtained via the output-files.
   Feel free to create an issue if you'd like something in particular built-in, or send a PR if you've implemented it already.
 * You don't get an exception when eg. the fdf-file contains an error. Instead, the whole process dies.
-  This is because on error, Siesta calls `abort()` to "helpfully" crash and spit out a stacktrace.
-  TODO: Can we catch sigabrt and raise a Python exception with the stacktrace instead?
+  This is because on error, Siesta intentionally kills itself which unfortunately includes the Python process.

flake.nix

@@ -0,0 +1,53 @@
+{
+  description = "PSiesta development shell";
+
+  inputs.nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
+
+  outputs = { nixpkgs, ... }:
+    let
+      systems = [ "x86_64-linux" "aarch64-linux" ];
+      forAllSystems = nixpkgs.lib.genAttrs systems;
+    in
+    {
+      devShells = forAllSystems (system:
+        let
+          pkgs = import nixpkgs { inherit system; };
+        in
+        {
+          default = pkgs.mkShell {
+            packages = with pkgs; [
+              stdenv.cc
+              gfortran
+              cmake
+              ninja
+              pkg-config
+              git
+
+              openmpi
+              blas
+              lapack
+              scalapack
+              curl
+              hdf5
+              netcdf
+              netcdffortran
+              fftw
+              libxc
+              readline
+              zlib
+
+              uv
+            ];
+
+            shellHook = ''
+              export CC=mpicc
+              export CXX=mpicxx
+              export FC=mpifort
+              export F77=mpifort
+              export F90=mpifort
+              export LD_LIBRARY_PATH=${pkgs.openmpi}/lib:$LD_LIBRARY_PATH
+            '';
+          };
+        });
+    };
+}

pyproject.toml

@@ -0,0 +1,28 @@
+[build-system]
+requires = ["scikit-build-core", "cython", "numpy"]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "psiesta"
+version = "0.3.0"
+description = "Run Siesta as a subroutine in Python, with ASE bindings"
+readme = "README.md"
+requires-python = ">=3.9"
+authors = [{ name = "Jonas Lundholm Bertelsen" }]
+dependencies = ["numpy", "mpi4py", "ase", "sisl"]
+
+[project.urls]
+Homepage = "https://github.com/jonaslb/psiesta"
+
+[dependency-groups]
+dev = ["pytest"]
+
+[tool.uv]
+default-groups = ["dev"]
+
+[tool.scikit-build]
+minimum-version = "0.10"
+build-dir = "build/{wheel_tag}"
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]