deploy PyPI 0.1.1 with Smoldyn and memory fixes

.github/workflows/cd.yml

@@ -41,14 +41,24 @@ jobs:
         with:
           images: "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}"
 
-      - name: Build and push Docker image
+      - name: Build and Push Docker image
         uses: docker/build-push-action@v5
+        if: github.event_name == 'release' && github.event.action == 'published'
         with:
           context: .
           push: true
           tags: ${{ steps.meta.outputs.tags }}
           labels: ${{ steps.meta.outputs.labels }}
 
+      - name: Only Build Docker image
+        uses: docker/build-push-action@v5
+        if: github.event_name != 'release' || github.event.action != 'published'
+        with:
+          context: .
+          push: false
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
   native-build:
     name:
       native-build-${{ matrix.platform }}
@@ -80,16 +90,19 @@ jobs:
           echo 'export PATH="/usr/local/opt/llvm/bin:$PATH"' >> /Users/runner/.bash_profile
           source /Users/runner/.bash_profile
           ln -s $(which gfortran-14) /usr/local/bin/gfortran
+
+          python3 -m pip install h5py numpy
 
           gcc --version
           gfortran --version
           cmake --version
           brew info boost
           brew info hdf5
 
-      - name: Install ARM MacOS dependencies
+      - name: Install ARM MacOS dependencies Part 1
         if: matrix.platform == 'macos-14'
         shell: bash
+
         run: |
           brew install boost
           brew install hdf5
@@ -107,6 +120,11 @@ jobs:
           brew info boost
           brew info hdf5
 
+      - name: Install ARM MacOS dependencies Part 2
+        if: matrix.platform == 'macos-14'
+        run: |
+          /opt/homebrew/bin/python3 -m pip install h5py --break-system-packages
+
       - name: Build Macos ARM
         if: matrix.platform == 'macos-14'
         run: |
@@ -117,17 +135,19 @@ jobs:
           cd build
 
           export PATH="/opt/homebrew/opt/llvm/bin:$PATH"
-
+
+          # General Build
           cmake \
           -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 \
+          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
           -DOPTION_TARGET_FV_SOLVER=ON \
           -DOPTION_TARGET_DOCS=ON \
+          -DOPTION_TARGET_TESTS=ON \
           -B . -S ..
 
           ninja
@@ -150,9 +170,10 @@ jobs:
           -DOPTION_TARGET_PYTHON_BINDING=OFF \
           -DOPTION_MINGW=ON \
           -DOPTION_TARGET_MESSAGING=OFF \
-          -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
+          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
           -DOPTION_TARGET_FV_SOLVER=ON \
           -DOPTION_TARGET_DOCS=ON \
+          -DOPTION_TARGET_TESTS=ON \
           -B . -S ..
 
           ninja
@@ -185,15 +206,18 @@ jobs:
 #          limit-access-to-actor: false
 
 
-      - name: Install Windows Dependencies
+      - name: Install Windows Dependencies #Part 1
         if: matrix.platform == 'windows-latest'
         uses: msys2/setup-msys2@v2
         with:
           msystem: CLANG64
           update: true
           install: >
+            python3
+            python-pip
             zip
             git
+            mingw-w64-clang-x86_64-python-h5py
             mingw-w64-clang-x86_64-curl
             mingw-w64-clang-x86_64-toolchain
             mingw-w64-clang-x86_64-flang
@@ -204,6 +228,12 @@ jobs:
             mingw-w64-clang-x86_64-zlib
             mingw-w64-clang-x86_64-libaec
 
+#      - name: Install Windows Dependencies Part 2
+#        if: matrix.platform == 'windows-latest'
+#        shell: msys2 {0}
+#        run: |
+#          pip install h5py --break-system-packages
+
 #      - name: Setup tmate session
 #        uses: mxschmitt/action-tmate@v3
 #        with:
@@ -227,9 +257,10 @@ jobs:
           -DCMAKE_CXX_COMPILER="clang++.exe" \
           -DOPTION_TARGET_PYTHON_BINDING=OFF \
           -DOPTION_TARGET_MESSAGING=OFF \
-          -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
+          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
           -DOPTION_TARGET_FV_SOLVER=ON \
           -DOPTION_TARGET_DOCS=OFF \
+          -DOPTION_TARGET_TESTS=ON \
           -B . -S ..
 
           ninja -j 1
@@ -256,7 +287,8 @@ jobs:
         if: matrix.platform == 'ubuntu-latest'
         run: |
           sudo apt-get update
-          sudo apt-get install -y libboost-all-dev libhdf5-dev libzip-dev libbz2-dev ninja-build
+          sudo apt-get install -y python3-pip libboost-all-dev libhdf5-dev libzip-dev libbz2-dev ninja-build
+          python3 -m pip install h5py numpy
 
           gcc --version
           gfortran --version
@@ -277,9 +309,10 @@ jobs:
           -G Ninja \
           -DOPTION_TARGET_PYTHON_BINDING=OFF \
           -DOPTION_TARGET_MESSAGING=OFF \
-          -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
+          -DOPTION_TARGET_SMOLDYN_SOLVER=ON \
           -DOPTION_TARGET_FV_SOLVER=ON \
           -DOPTION_TARGET_DOCS=ON \
+          -DOPTION_TARGET_TESTS=ON \
           -B . -S ..
 
           ninja
@@ -372,5 +405,5 @@ jobs:
         if: ${{ failure() }}
         uses: mxschmitt/action-tmate@v3
         with:
-          limit-access-to-actor: false
+          limit-access-to-actor: true
 

.github/workflows/pip.yml

@@ -17,14 +17,18 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        #platform: [ windows-latest, macos-13, macos-14, ubuntu-latest ]
-        platform: [ macos-13, macos-14, ubuntu-latest ]
+        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"
+        exclude:
+          - platform: windows-latest
+            python-version: "3.9"
+          - platform: windows-latest
+            python-version: "3.10"
+          - platform: windows-latest
+            python-version: "3.11"
+          - platform: windows-latest
+            python-version: "3.12"
 
     steps:
     - uses: actions/checkout@v4
@@ -94,7 +98,59 @@ jobs:
           mingw-w64-clang-x86_64-libaec
           mingw-w64-clang-x86_64-python-pip-tools
 
+    - name: Fix windows python version for python3.10
+      if: matrix.platform == 'windows-latest' && matrix.python-version == '3.10'
+      shell: msys2 {0}
+      run: |
+        echo "Preparing files for installation"
+        pacman -Sy --noconfirm mingw-w64-clang-x86_64-python-pip
+        echo "Downloading old archives"
+        curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python3.10-3.10.5-1-any.pkg.tar.zst
+        curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python-pip-23.1.2-1-any.pkg.tar.zst
+        echo "Installing Python 3.10"
+        pacman -U --noconfirm mingw-w64-clang-x86_64-python3.10-3.10.5-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python3.10 | grep bin/python
+        echo "Installing Corresponding Pip"
+        pacman -U --noconfirm mingw-w64-clang-x86_64-python-pip-23.1.2-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python-pip | grep bin/pip
+        echo "Attempting to create python symlink"
+        ln -sf /clang64/bin/python3.10.exe /clang64/bin/python3
+        /clang64/bin/python3 --version
+
+    - name: Fix windows python version for python3.11
+      if: matrix.platform == 'windows-latest' && matrix.python-version == '3.11'
+      shell: msys2 {0}
+      run: |
+        echo "Preparing files for installation"
+        pacman -Sy --noconfirm mingw-w64-x86_64-python-pip
+        echo "Downloading old archives"
+        curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python3.11-3.11.4-1-any.pkg.tar.zst
+        curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python-pip-23.3.2-1-any.pkg.tar.zst
+        echo "Installing Python 3.11"
+        pacman -U --noconfirm mingw-w64-clang-x86_64-python3.11-3.11.4-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python3.11 | grep bin/python
+        echo "Installing Corresponding Pip"
+        pacman -U --noconfirm mingw-w64-clang-x86_64-python-pip-23.3.2-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python-pip | grep bin/pip
+        echo "Attempting to create python symlink..."
+        ln -sf /clang64/bin/python3.11.exe /clang64/bin/python3
+        /clang64/bin/python3 --version
+
+    - name: Fix windows python version for python3.12
+      if: matrix.platform == 'windows-latest' && matrix.python-version == '3.12'
+      shell: msys2 {0}
+      run: |
+        echo "Preparing files for installation"
+        pacman -Sy --noconfirm mingw-w64-x86_64-python-pip
+        echo "Downloading old archives"
+        curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python3.12-3.12.7-1-any.pkg.tar.zst
+        curl -LO https://repo.msys2.org/mingw/clang64/mingw-w64-clang-x86_64-python-pip-25.0.1-1-any.pkg.tar.zst
+        echo "Installing Python 3.12"
+        pacman -U --noconfirm mingw-w64-clang-x86_64-python3.12-3.12.7-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python3.12 | grep bin/python
+        echo "Installing Corresponding Pip"
+        pacman -U --noconfirm mingw-w64-clang-x86_64-python-pip-25.0.1-1-any.pkg.tar.zst && pacman -Ql mingw-w64-clang-x86_64-python-pip | grep bin/pip
+        echo "Attempting to create python symlink"
+        ln -sf /clang64/bin/python3.12.exe /clang64/bin/python3
+        /clang64/bin/python3 --version
+
     - uses: actions/setup-python@v5
+      if: matrix.platform != 'windows-latest'
       with:
         python-version: "${{ matrix.python-version }}"
 
@@ -124,24 +180,26 @@ jobs:
     - name: Build and install windows-latest
       shell: msys2 {0}
       run: |
-        pip wheel --verbose -Ccmake.define.CMAKE_C_COMPILER="clang.exe" -Ccmake.define.CMAKE_CXX_COMPILER="clang++.exe" . -w dist
-        pip install delvewheel
+        which python3
+        python3 --version
+        python3 -m pip wheel --verbose -Ccmake.define.CMAKE_C_COMPILER="clang.exe" -Ccmake.define.CMAKE_CXX_COMPILER="clang++.exe" . -w dist
+        python3 -m 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
+        python3 -m pip install dist/*.whl
       if: matrix.platform == 'windows-latest'
 
     - name: Build and install manylinux for python 3.9
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
-           /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
-           /opt/python/cp39-cp39/bin/pip wheel /io/ -w /io/dist && \
-           auditwheel repair /io/dist/*.whl -w /io/dist/"
+            /bin/bash -c \
+            "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
+            /opt/python/cp39-cp39/bin/pip wheel /io/ -w /io/dist && \
+            auditwheel repair --disable-isa-ext-check /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
@@ -150,10 +208,10 @@ jobs:
     - name: Build and install manylinux for python 3.10
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
-           /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
-           /opt/python/cp310-cp310/bin/pip wheel /io/ -w /io/dist && \
-           auditwheel repair /io/dist/*.whl -w /io/dist/"
+            /bin/bash -c \
+            "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
+            /opt/python/cp310-cp310/bin/pip wheel /io/ -w /io/dist && \
+            auditwheel repair --disable-isa-ext-check /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
@@ -162,10 +220,10 @@ jobs:
     - name: Build and install manylinux for python 3.11
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
-           /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
-           /opt/python/cp311-cp311/bin/pip wheel /io/ -w /io/dist && \
-           auditwheel repair /io/dist/*.whl -w /io/dist/"
+            /bin/bash -c \
+            "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
+            /opt/python/cp311-cp311/bin/pip wheel /io/ -w /io/dist && \
+            auditwheel repair --disable-isa-ext-check /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
@@ -174,10 +232,10 @@ jobs:
     - name: Build and install manylinux for python 3.12
       run: |
         docker run --rm -v $(pwd):/io quay.io/pypa/manylinux_2_34_x86_64 \
-           /bin/bash -c \
-           "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
-           /opt/python/cp312-cp312/bin/pip wheel /io/ -w /io/dist && \
-           auditwheel repair /io/dist/*.whl -w /io/dist/"
+            /bin/bash -c \
+            "yum install -y boost-devel hdf5-devel libzip-devel bzip2-devel ninja-build openssl-devel xz-devel && \
+            /opt/python/cp312-cp312/bin/pip wheel /io/ -w /io/dist && \
+            auditwheel repair --disable-isa-ext-check /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
@@ -192,8 +250,10 @@ jobs:
     - name: Test on windows
       shell: msys2 {0}
       run: |
-        pip install pytest
-        pytest
+        which python3
+        python3 --version
+        python3 -m pip install pytest
+        python3 -m pytest
       if: matrix.platform == 'windows-latest'
 
     - name: set wheel_file and artifact_name environment vars (non-windows)
@@ -225,7 +285,7 @@ jobs:
       uses: mxschmitt/action-tmate@v3
       if: ${{ failure() }}
       with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
+        limit-access-to-actor: true
 
   publish-to-pypi:
     name: Publish to PyPI
@@ -266,6 +326,5 @@ jobs:
       uses: mxschmitt/action-tmate@v3
       if: ${{ failure() }}
       with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        limit-access-to-actor: false
+        limit-access-to-actor: true
 

.gitignore

@@ -28,3 +28,14 @@ tests/__pycache__/
 *.whl
 
 VCell/tests/testFiles/output/
+
+VCell/tests/smoke/*.fvinput
+VCell/tests/smoke/*.hdf5
+VCell/tests/smoke/*.log
+VCell/tests/smoke/*.meshmetrics
+VCell/tests/smoke/*.zip
+
+VCell/tests/testFiles/input/Smoldyn/*.zip
+VCell/tests/testFiles/input/Smoldyn/*.log
+VCell/tests/testFiles/input/Smoldyn/*.hdf5
+VCell/tests/testFiles/input/Smoldyn/*.smoldynOutput

CMakeLists.txt

@@ -1,4 +1,8 @@
 cmake_minimum_required(VERSION 3.22)
+
+set (CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
 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)
@@ -37,9 +41,6 @@ else()
 	set(OPTION_VCELL ON)
 endif ()
 
-set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 set(OPTION_USE_OPENGL OFF CACHE BOOL "")