build python wheels for all platforms

.github/workflows/cd.yml

@@ -1,6 +1,14 @@
 name: CD
 
-on: [push, workflow_dispatch]
+on: 
+  pull_request:
+  push:
+    branches:
+      - master
+  release:
+    types:
+      - published
+
 
 env:
   REGISTRY: ghcr.io

.github/workflows/pip.yml

@@ -6,6 +6,9 @@ on:
   push:
     branches:
       - master
+  release:
+    types:
+      - published
 
 jobs:
   build:
@@ -14,9 +17,14 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        platform: [windows-latest, macos-13, macos-14, ubuntu-latest]
-#        python-version: ["3.7", "3.12", "pypy-3.9"]
-        python-version: ["3.12"]
+        #platform: [ windows-latest, macos-13, macos-14, ubuntu-latest ]
+        platform: [ macos-13, macos-14, ubuntu-latest ]
+        python-version: ["3.9","3.10","3.11","3.12"]
+#        exclude:
+#          - platform: windows-latest
+#            python-version: "3.9"
+#          - platform: windows-latest
+#            python-version: "3.12"
 
     steps:
     - uses: actions/checkout@v4
@@ -79,49 +87,94 @@ jobs:
           mingw-w64-clang-x86_64-libaec
           mingw-w64-clang-x86_64-python-pip-tools
 
-
-    - name: Install Linux Dependencies
-      if: matrix.platform == 'ubuntu-latest'
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y libboost-all-dev
-        sudo apt-get install -y libhdf5-dev
-        sudo apt-get install -y ninja-build
-
-        gcc --version
-        gfortran --version
-        cmake --version
-        dpkg -s libboost-all-dev
-        dpkg -s libhdf5-dev
-
-
     - uses: actions/setup-python@v5
       with:
         python-version: "${{ matrix.python-version }}"
 
     - name: Build and install macos-13
       run: |
+        export MACOSX_DEPLOYMENT_TARGET=13.0
         PATH="/usr/local/opt/llvm/bin:$PATH"
-        pip install --verbose .
+        pip wheel . -w dist
+        ls -al dist
+        pip install delocate
+        delocate-listdeps dist/*.whl
+        delocate-wheel -v dist/*.whl
+        pip install dist/*.whl
       if: matrix.platform == 'macos-13'
 
     - name: Build and install macos-14
       run: |
         PATH="/opt/homebrew/opt/llvm/bin:$PATH"
-        pip install --verbose .
+        pip wheel . -w dist
+        ls -al dist
+        pip install delocate
+        delocate-listdeps dist/*.whl
+        delocate-wheel -v dist/*.whl
+        pip install dist/*.whl
       if: matrix.platform == 'macos-14'
 
     - name: Build and install windows-latest
       shell: msys2 {0}
       run: |
-        pip install --verbose -Ccmake.define.CMAKE_C_COMPILER="clang.exe" -Ccmake.define.CMAKE_CXX_COMPILER="clang++.exe" .
+        pip wheel --verbose -Ccmake.define.CMAKE_C_COMPILER="clang.exe" -Ccmake.define.CMAKE_CXX_COMPILER="clang++.exe" . -w dist
+        pip install delvewheel
+        for wheel_file in dist/*.whl; do
+          echo "not inspecting $wheel_file"
+          echo "delvewheel needed -v $wheel_file"
+          echo "not repairing $wheel_file"
+          echo "delvewheel repair -v $wheel_file"
+        done
+        pip install dist/*.whl
       if: matrix.platform == 'windows-latest'
 
-    - name: Build and install ubuntu-latest
+    - name: Build and install manylinux for python 3.9
+      run: |
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+           /bin/bash -c \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
+           /opt/python/cp39-cp39/bin/pip wheel /io/ -w /io/dist && \
+           auditwheel repair /io/dist/*.whl -w /io/dist/"
+        echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
+        sudo rm -rf dist/*-linux_x86_64.whl
+        pip install dist/*.whl
+      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.9'
+
+    - name: Build and install manylinux for python 3.10
+      run: |
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+           /bin/bash -c \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
+           /opt/python/cp310-cp310/bin/pip wheel /io/ -w /io/dist && \
+           auditwheel repair /io/dist/*.whl -w /io/dist/"
+        echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
+        sudo rm -rf dist/*-linux_x86_64.whl
+        pip install dist/*.whl
+      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.10'
+
+    - name: Build and install manylinux for python 3.11
+      run: |
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+           /bin/bash -c \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
+           /opt/python/cp311-cp311/bin/pip wheel /io/ -w /io/dist && \
+           auditwheel repair /io/dist/*.whl -w /io/dist/"
+        echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
+        sudo rm -rf dist/*-linux_x86_64.whl
+        pip install dist/*.whl
+      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.11'
+
+    - name: Build and install manylinux for python 3.12
       run: |
-        platform=linux
-        pip install --verbose .
-      if: matrix.platform == 'ubuntu-latest'
+        docker run --rm -v $(pwd):/io quay.io/pypa/manylinux2014_x86_64 \
+           /bin/bash -c \
+           "yum install -y boost-devel hdf5-devel ninja-build && \
+           /opt/python/cp312-cp312/bin/pip wheel /io/ -w /io/dist && \
+           auditwheel repair /io/dist/*.whl -w /io/dist/"
+        echo "keeping only the manylinux wheels, remove those with -linux_x86_64.whl in the name"
+        sudo rm -rf dist/*-linux_x86_64.whl
+        pip install dist/*.whl
+      if: matrix.platform == 'ubuntu-latest' && matrix.python-version == '3.12'
 
     - name: Test not windows
       run: |
@@ -136,8 +189,75 @@ jobs:
         pytest
       if: matrix.platform == 'windows-latest'
 
+    - name: set wheel_file and artifact_name environment vars (non-windows)
+      if: matrix.platform != 'windows-latest'
+      run: |
+        for wheel_file in dist/*.whl; do
+          echo "Uploading $wheel_file"
+          echo "wheel_file=$wheel_file" >> $GITHUB_ENV
+          echo "artifact_name=$(basename $wheel_file)" >> $GITHUB_ENV
+        done
+
+    - name: set wheel_file and artifact_name environment vars (windows)
+      if: matrix.platform == 'windows-latest'
+      shell: pwsh
+      run: |
+        foreach ($wheel_file in Get-ChildItem -Path dist -Filter *.whl) {
+          Write-Output "Uploading $wheel_file"
+          echo "wheel_file=$wheel_file" | Out-File -Append -FilePath $env:GITHUB_ENV -Encoding utf8
+          echo "artifact_name=$(Split-Path $wheel_file -Leaf)" | Out-File -Append -FilePath $env:GITHUB_ENV -Encoding utf8
+        }
+
+    - name: Upload wheel file
+      uses: actions/upload-artifact@v4
+      with:
+        name: ${{ env.artifact_name }}
+        path: ${{ env.wheel_file }}
+
     - name: Setup tmate session
       uses: mxschmitt/action-tmate@v3
       if: ${{ failure() }}
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
+
+  publish-to-pypi:
+    name: Publish to PyPI
+    needs: build
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release' && github.event.action == 'published'
+    environment: pypi
+    permissions:
+      id-token: write
+
+    steps:
+    - name: download all artifacts (wheels and executables)
+      uses: actions/download-artifact@v4
+      with:
+        path: dist_temp/
+
+    - name: Install Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.12'
+
+    - name: Publish wheels to PyPI
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+      run: |
+        pip install twine
+        mkdir dist
+        echo "current directory is $(pwd)"
+        ls -al dist*
+        echo "absolute paths of wheels:"
+        find dist_temp -type f -name '*.whl' -exec sh -c 'echo "$(realpath {})"/' \;
+        echo "moving wheels to dist directory"
+        find dist_temp -type f -name '*.whl' -exec sh -c 'mv "$(realpath {})" dist/' \;
+        twine upload --repository pypi dist/*.whl
+
+    - name: Setup tmate session for PyPI upload failure
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ failure() }}
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}
+

.github/workflows/wheels.yml

@@ -1,4 +1,4 @@
-name: Wheels
+name: "Wheels"
 
 on:
   workflow_dispatch:
@@ -107,7 +107,7 @@ jobs:
           mingw-w64-clang-x86_64-libzip
           mingw-w64-clang-x86_64-zlib
           mingw-w64-clang-x86_64-libaec
-
+          mingw-w64-clang-x86_64-python-pip-tools
 
     - name: Install Linux Dependencies
       if: matrix.os == 'ubuntu-latest'
@@ -123,9 +123,40 @@ jobs:
         dpkg -s libboost-all-dev
         dpkg -s libhdf5-dev
 
+    # Used to host cibuildwheel
+    - uses: actions/setup-python@v5
+
+    - name: Install cibuildwheel
+      run: python -m pip install cibuildwheel==2.18.1
+
+    - name: build wheel on macos-13
+      if: matrix.os == 'macos-13'
+      run: |
+        export PATH="/usr/local/opt/llvm/bin:$PATH"
+        python -m cibuildwheel --output-dir wheelhouse
+      env:
+        CIBW_ARCHS: native
+
+    - name: build wheel on macos-14
+      if: matrix.os == 'macos-14'
+      run: |
+        export PATH="/opt/homebrew/opt/llvm/bin:$PATH"
+        python -m cibuildwheel --output-dir wheelhouse
+      env:
+        CIBW_ARCHS: native
+
+    - name: build wheel on windows-latest
+      if: matrix.os == 'windows-latest'
+      shell: msys2 {0}
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
+      env:
+        CIBW_ARCHS: native
 
     - name: build wheel
-      uses: pypa/[email protected]
+      if: matrix.os == 'ubuntu-latest'
+      run: |
+        python -m cibuildwheel --output-dir wheelhouse
       env:
         CIBW_ARCHS: native
 

.gitignore

@@ -17,5 +17,12 @@
 /.idea/
 /nfsim/
 /all_solvers/*
+/.venv/
+/venv/
 
 .DS_Store
+/dist/
+
+tests/__pycache__/
+
+*.whl

CMakeLists.txt

@@ -3,6 +3,7 @@ option(OPTION_TARGET_PYTHON_BINDING "build Python bindings" ON)
 option(OPTION_TARGET_MESSAGING "Messaging (requires libcurl)" off)
 option(OPTION_TARGET_DOCS "Generate Doxygen documentation" off)
 option(OPTION_TARGET_FV_SOLVER on)
+option(OPTION_TARGET_TESTS "Build tests" off)
 option(OPTION_VCELL "Compile Smoldyn for VCell" ON)
 option(OPTION_NSV "Compile Smoldyn with NextSubvolume functionality" OFF)
 option(OPTION_USE_OPENGL "Build with OpenGL support" OFF)
@@ -217,7 +218,7 @@ if (OPTION_TARGET_PYTHON_BINDING)
 	find_package(pybind11 CONFIG REQUIRED)
 
 	# Add a library using FindPython's tooling (pybind11 also provides a helper like this)
-	python_add_library(_core MODULE src/main.cpp src/SolverMain.cpp src/SolverMain.h WITH_SOABI)
+	python_add_library(_core MODULE src/main.cpp WITH_SOABI)
 	target_link_libraries(_core PRIVATE vcell pybind11::headers)
 
 	# This is passing in the version as a define just as an example
@@ -226,35 +227,4 @@ if (OPTION_TARGET_PYTHON_BINDING)
 	# The install directory is the output (wheel) directory
 	install(TARGETS _core DESTINATION pyvcell_fvsolver)
 
-else(OPTION_TARGET_PYTHON_BINDING)
-
-	include(FetchContent)
-	FetchContent_Declare(
-			googletest
-			URL https://github.com/google/googletest/archive/03597a01ee50ed33e9dfd640b249b4be3799d395.zip
-	)
-	if (WINDOWS)
-		# For Windows: Prevent overriding the parent project's compiler/linker settings
-		set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
-	endif()
-
-	FetchContent_MakeAvailable(googletest)
-	enable_testing()
-
-	get_cmake_property(_variableNames VARIABLES)
-	list (SORT _variableNames)
-	foreach (_variableName ${_variableNames})
-		message(STATUS "${_variableName}=${${_variableName}}")
-	endforeach()
-
-	include(CMakePrintHelpers)
-	cmake_print_variables(OPTION_TARGET_MESSAGING
-			OPTION_TARGET_DOCS
-			OPTION_TARGET_FV_SOLVER
-			OPTION_TARGET_LIBSMOLDYN OPTION_TARGET_VCELL OPTION_TARGET_NSV )
-	cmake_print_variables(CMAKE_CXX_FLAGS CMAKE_C_FLAGS CMAKE_Fortran_FLAGS)
-	cmake_print_variables(CMAKE_SYSTEM_NAME WINDOWS WIN32 MINGW APPLE ARCH_64bit ARCH_32bit)
-	cmake_print_variables(CMAKE_CPP_COMPILER CMAKE_C_COMPILER CMAKE_CXX_COMPILER CMAKE_Fortran_COMPILER)
-	cmake_print_variables(HAVE_ZLIB)
-
 endif (OPTION_TARGET_PYTHON_BINDING)

README.md

@@ -8,9 +8,11 @@
 ![CI](https://github.com/virtualcell/vcell-solvers/actions/workflows/cd.yml/badge.svg)
 
 # vcell-fvsolver
-Virtual Cell solvers [virtualcell/vcell-solvers](https://github.com/virtualcell/vcell-solvers) is a collection of numerical simulation codes used in the Virtual Cell framework [virtualcell/vcell](https://github.com/virtualcell/vcell)).
+Virtual Cell Finite Volume solver [virtualcell/vcell-fvsolver](https://github.com/virtualcell/vcell-fvsolver) 
+is a reaction-diffusion-advection PDE solver for computational cell biology. 
+This solver is used within the Virtual Cell modeling and simulation application [virtualcell/vcell](https://github.com/virtualcell/vcell) 
+and as a component in the Virtual Cell Python API [virtualcell/pyvcell](https://github.com/virtualcell/pyvcell) (coming soon).
 
-
 ## The Virtual Cell Project
 The Virtual Cell is a modeling and simulation framework for computational biology.  For details see http://vcell.org and http://github.com/virtualcell.
 
@@ -27,4 +29,4 @@ and generates the output files (.log, .zip, .mesh, .meshmetrics, .hdf5).  The
 .functions file is not used by the solver, but is helpful for interpreting the 
 results in the context of the original model.
 
-This package is intented to be used by the Virtual Cell Python API, pyvcell (coming soon).
+This package is intended to be used by the Virtual Cell Python API [virtualcell/pyvcell](https://github.com/virtualcell/pyvcell) (coming soon).