Merge pull request #2 from virtualcell/python-module

pyvcell_fvsolver Python module

.github/workflows/cd.yml

@@ -104,6 +104,7 @@ jobs:
           -G Ninja \
           -DCMAKE_C_COMPILER=/opt/homebrew/opt/llvm/bin/clang \
           -DCMAKE_CXX_COMPILER=/opt/homebrew/opt/llvm/bin/clang++ \
+          -DOPTION_TARGET_PYTHON_BINDING=OFF \
           -DOPTION_MINGW=ON \
           -DOPTION_TARGET_MESSAGING=OFF \
           -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
@@ -128,6 +129,7 @@ jobs:
           -G Ninja \
           -DCMAKE_C_COMPILER=/usr/local/opt/llvm/bin/clang \
           -DCMAKE_CXX_COMPILER=/usr/local/opt/llvm/bin/clang++ \
+          -DOPTION_TARGET_PYTHON_BINDING=OFF \
           -DOPTION_MINGW=ON \
           -DOPTION_TARGET_MESSAGING=OFF \
           -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
@@ -205,6 +207,7 @@ jobs:
           -G Ninja \
           -DCMAKE_C_COMPILER="clang.exe" \
           -DCMAKE_CXX_COMPILER="clang++.exe" \
+          -DOPTION_TARGET_PYTHON_BINDING=OFF \
           -DOPTION_TARGET_MESSAGING=OFF \
           -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
           -DOPTION_TARGET_FV_SOLVER=ON \
@@ -253,6 +256,7 @@ jobs:
 
           cmake \
           -G Ninja \
+          -DOPTION_TARGET_PYTHON_BINDING=OFF \
           -DOPTION_TARGET_MESSAGING=OFF \
           -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
           -DOPTION_TARGET_FV_SOLVER=ON \

.github/workflows/conda.yml

@@ -0,0 +1,50 @@
+name: Conda
+
+on:
+  workflow_dispatch:
+#  push:
+#    branches:
+#      - master
+#  pull_request:
+
+jobs:
+  build:
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [ubuntu-latest, macos-13, macos-14, windows-latest]
+        python-version: ["3.8", "3.11"]
+
+    runs-on: ${{ matrix.platform }}
+
+    # The setup-miniconda action needs this to activate miniconda
+    defaults:
+      run:
+        shell: "bash -l {0}"
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Get conda
+        uses: conda-incubator/[email protected]
+        with:
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge
+
+      - name: Prepare
+        run: conda install conda-build conda-verify pytest
+
+      - name: Build
+        run: conda build conda.recipe
+
+      - name: Install
+        run: conda install -c ${CONDA_PREFIX}/conda-bld/ .
+
+      - name: Test
+        run: pytest tests
+
+      - name: Setup tmate session
+        uses: mxschmitt/action-tmate@v3
+        if: ${{ failure() }}
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/enscripten.yaml

@@ -0,0 +1,60 @@
+name: WASM
+
+on:
+  workflow_dispatch:
+#  pull_request:
+#    branches:
+#    - master
+
+concurrency:
+  group: "${{ github.workflow }}-${{ github.ref }}"
+  cancel-in-progress: true
+
+jobs:
+  build-wasm-emscripten:
+    name: Pyodide
+    runs-on: ubuntu-22.04
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: true
+        fetch-depth: 0
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.11"
+
+    - name: Install pyodide-build
+      run: pip install pyodide-build==0.23.4
+
+    - name: Compute emsdk version
+      id: compute-emsdk-version
+      run: |
+        pyodide xbuildenv install --download
+        EMSCRIPTEN_VERSION=$(pyodide config get emscripten_version)
+        echo "emsdk-version=$EMSCRIPTEN_VERSION" >> $GITHUB_OUTPUT
+
+    - uses: mymindstorm/setup-emsdk@v14
+      with:
+        version: ${{ steps.compute-emsdk-version.outputs.emsdk-version }}
+        actions-cache-folder: emsdk-cache
+
+    # A future version of pyodide may switch to -fwasm-exceptions
+    - name: Build
+      run: CFLAGS=-fexceptions LDFLAGS=-fexceptions pyodide build
+
+    - uses: actions/upload-artifact@v4
+      with:
+        path: dist/*.whl
+
+    - uses: actions/setup-node@v4
+      with:
+        node-version: 18
+
+    - name: Set up Pyodide virtual environment
+      run: |
+        pyodide venv .venv-pyodide
+        .venv-pyodide/bin/pip install $(echo -n dist/*.whl)[test]
+
+    - name: Test
+      run: .venv-pyodide/bin/pytest

.github/workflows/pip.yml

@@ -0,0 +1,143 @@
+name: "Pip"
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - master
+
+jobs:
+  build:
+    name: Build with Pip
+    runs-on: ${{ matrix.platform }}
+    strategy:
+      fail-fast: false
+      matrix:
+        platform: [windows-latest, macos-13, macos-14, ubuntu-latest]
+#        python-version: ["3.7", "3.12", "pypy-3.9"]
+        python-version: ["3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install Intel MacOS dependencies
+      if: matrix.platform == 'macos-13'
+      shell: bash
+      run: |
+        brew install boost
+        brew install hdf5
+        brew install ninja
+        
+        brew install llvm
+        echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
+        source /Users/runner/.bash_profile
+        
+        gcc --version
+        gfortran --version
+        cmake --version
+        brew info boost
+        brew info hdf5
+
+
+    - name: Install ARM MacOS dependencies
+      if: matrix.platform == 'macos-14'
+      shell: bash
+      run: |
+        brew install boost
+        brew install hdf5
+        brew install ninja
+        
+        brew install llvm
+        echo 'export PATH="/opt/homebrew/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
+        ln -s /opt/homebrew/bin/gfortran-14 /usr/local/bin/gfortran
+        
+        gcc --version
+        gfortran --version
+        cmake --version
+        brew info boost
+        brew info hdf5
+
+
+    - name: Install Windows Dependencies
+      if: matrix.platform == 'windows-latest'
+      uses: msys2/setup-msys2@v2
+      with:
+        msystem: CLANG64
+        update: true
+        install: >
+          zip
+          git
+          mingw-w64-clang-x86_64-curl
+          mingw-w64-clang-x86_64-toolchain
+          mingw-w64-clang-x86_64-flang
+          mingw-w64-clang-x86_64-cmake
+          mingw-w64-clang-x86_64-boost
+          mingw-w64-clang-x86_64-hdf5
+          mingw-w64-clang-x86_64-libzip
+          mingw-w64-clang-x86_64-zlib
+          mingw-w64-clang-x86_64-libaec
+          mingw-w64-clang-x86_64-python-pip-tools
+
+
+    - name: Install Linux Dependencies
+      if: matrix.platform == 'ubuntu-latest'
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libboost-all-dev
+        sudo apt-get install -y libhdf5-dev
+        sudo apt-get install -y ninja-build
+        
+        gcc --version
+        gfortran --version
+        cmake --version
+        dpkg -s libboost-all-dev
+        dpkg -s libhdf5-dev
+
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "${{ matrix.python-version }}"
+
+    - name: Build and install macos-13
+      run: |
+        PATH="/usr/local/opt/llvm/bin:$PATH"
+        pip install --verbose .
+      if: matrix.platform == 'macos-13'
+
+    - name: Build and install macos-14
+      run: |
+        PATH="/opt/homebrew/opt/llvm/bin:$PATH"
+        pip install --verbose .
+      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" .
+      if: matrix.platform == 'windows-latest'
+
+    - name: Build and install ubuntu-latest
+      run: |
+        platform=linux
+        pip install --verbose .
+      if: matrix.platform == 'ubuntu-latest'
+
+    - name: Test not windows
+      run: |
+        pip install pytest
+        pytest
+      if: matrix.platform != 'windows-latest'
+
+    - name: Test on windows
+      shell: msys2 {0}
+      run: |
+        pip install pytest
+        pytest
+      if: matrix.platform == 'windows-latest'
+
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ failure() }}
+      with:
+        github-token: ${{ secrets.GITHUB_TOKEN }}