pyvcell-mbsolver 1.0.0__tar.gz

pyvcell_mbsolver-1.0.0/.github/workflows/build-and-release.yml

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+name: Build and Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-2022]
+        include:
+          - os: ubuntu-latest
+            artifact_prefix: linux
+          - os: macos-latest
+            artifact_prefix: macos
+          - os: windows-2022
+            artifact_prefix: windows
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Configure git for private submodule
+        run: |
+          git config --global url."https://x-access-token:${{ secrets.SUBMODULE_TOKEN }}@github.com/".insteadOf "https://github.com/"
+        shell: bash
+
+      - name: Initialize submodules
+        run: git submodule update --init --recursive
+        shell: bash
+
+      # Ubuntu dependencies
+      - name: Install Ubuntu dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake libhdf5-dev python3-dev python3-pip pybind11-dev libboost-dev libcurl4-openssl-dev
+          pip3 install pybind11
+
+      # macOS dependencies
+      - name: Install macOS dependencies
+        if: runner.os == 'macOS'
+        run: |
+          brew install cmake hdf5 python pybind11 boost curl
+
+      # Windows dependencies
+      - name: Setup vcpkg (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          pip install pybind11 pytest
+          git clone --depth 1 https://github.com/microsoft/vcpkg.git "$env:RUNNER_TEMP\vcpkg"
+          & "$env:RUNNER_TEMP\vcpkg\bootstrap-vcpkg.bat"
+          Add-Content -Path $env:GITHUB_ENV -Value "VCPKG_ROOT=$env:RUNNER_TEMP\vcpkg"
+          
+          # Export Python Executable Path for CMake
+          $pyExe = & python -c "import sys; print(sys.executable)"
+          Add-Content -Path $env:GITHUB_ENV -Value "PYTHON_EXE=$pyExe"
+
+      # REMOVED: ilammy/msvc-dev-cmd step to prevent environment variable contamination
+
+      - name: Install dependencies with vcpkg (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $manifest = @{
+              name = "vcell-mbsolver-deps"
+              version = "0.1.0"
+              "builtin-baseline" = "d59510da59a2ee8b943509998b63da7b472d93cf"
+              dependencies = @(
+                  @{ name = "hdf5"; features = @("cpp") },
+                  "boost",
+                  "pybind11",
+                  "pthread",
+                  "curl"
+              )
+          } | ConvertTo-Json -Depth 5
+          
+          Set-Content -Path "vcpkg.json" -Value $manifest
+          
+          $vcpkg = "$env:VCPKG_ROOT\vcpkg.exe"
+          & $vcpkg install --triplet x64-windows --clean-after-build
+          if ($LASTEXITCODE -ne 0) { exit 1 }
+
+      # Configure CMake
+      - name: Configure CMake (Ubuntu/macOS)
+        if: runner.os != 'Windows'
+        run: |
+          cmake -S . -B build -DCMAKE_BUILD_TYPE=Release -DOPTION_TARGET_MESSAGING=ON
+
+      - name: Configure CMake (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          $vcpkgRoot = $env:VCPKG_ROOT
+          $instPrefix = "$vcpkgRoot/installed/x64-windows" -replace '\\','/'
+          $vcpkgToolchain = "$vcpkgRoot/scripts/buildsystems/vcpkg.cmake" -replace '\\','/'
+          
+          $pyRoot = $env:pythonLocation -replace '\\','/'
+          $pyInclude = "$pyRoot/include"
+          $pyLib = "$pyRoot/libs/python310.lib"
+
+          cmake -S . -B build -G "Visual Studio 17 2022" -A x64 `
+            -DCMAKE_BUILD_TYPE=Release `
+            -DOPTION_TARGET_MESSAGING=OFF `
+            -DCMAKE_TOOLCHAIN_FILE="$vcpkgToolchain" `
+            -DVCPKG_TARGET_TRIPLET="x64-windows" `
+            -DCMAKE_PREFIX_PATH="$instPrefix" `
+            -DHDF5_ROOT="$instPrefix" `
+            -DPYTHON_EXECUTABLE="$($env:PYTHON_EXE -replace '\\','/')" `
+            -DPYTHON_INCLUDE_DIR="$pyInclude" `
+            -DPYTHON_LIBRARY="$pyLib"
+
+          if ($LASTEXITCODE -ne 0) { exit 1 }
+
+      # Build
+      - name: Build (Ubuntu/macOS)
+        if: runner.os != 'Windows'
+        run: cmake --build build --parallel
+
+      - name: Build (Windows)
+        if: runner.os == 'Windows'
+        run: cmake --build build --config Release --parallel
+        shell: pwsh
+
+      # Run tests
+      - name: Install test dependencies
+        run: pip install pytest
+        shell: bash
+
+      - name: Run tests (Ubuntu/macOS)
+        if: runner.os != 'Windows'
+        run: |
+          cd build
+          ctest --output-on-failure -j$(nproc)
+
+      - name: Run tests (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          cd build
+          ctest --output-on-failure -C Release --parallel $env:NUMBER_OF_PROCESSORS
+          if ($LASTEXITCODE -ne 0) { exit 1 }
+
+      # Prepare artifacts
+      - name: Prepare artifacts (Ubuntu/macOS)
+        if: runner.os != 'Windows'
+        run: |
+          mkdir -p artifacts
+          cp build/bin/MovingBoundarySolver artifacts/MovingBoundarySolver-${{ matrix.artifact_prefix }}
+          cp build/bin/libMovingBoundaryLib.a artifacts/libMovingBoundaryLib-${{ matrix.artifact_prefix }}.a
+          cp build/bin/vcellmbsolver_py*.so artifacts/ 2>/dev/null || true
+
+      # RESTORED: Output tracking targets build/bin/Release/ for the native MSVC multi-config compiler
+      - name: Prepare artifacts (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          New-Item -ItemType Directory -Path artifacts -Force | Out-Null
+          Copy-Item -Path build\bin\Release\MovingBoundarySolver.exe -Destination artifacts\MovingBoundarySolver-${{ matrix.artifact_prefix }}.exe -Force
+          Copy-Item -Path build\bin\Release\MovingBoundaryLib.lib -Destination artifacts\MovingBoundaryLib-${{ matrix.artifact_prefix }}.lib -Force
+          Get-ChildItem -Path build\bin\Release\vcellmbsolver_py*.pyd -ErrorAction SilentlyContinue | ForEach-Object {
+            Copy-Item -Path $_.FullName -Destination artifacts\ -Force
+          }
+
+      - name: Upload artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.artifact_prefix }}-artifacts
+          path: artifacts/
+          retention-days: 1
+
+  release:
+    name: Create Release
+    needs: build
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download all artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: all-artifacts
+
+      - name: Create Release
+        uses: softprops/action-gh-release@v1
+        with:
+          files: all-artifacts/**/*
+          draft: false
+          prerelease: false
+          generate_release_notes: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Display release info
+        run: |
+          echo "Release created successfully!"
+          find all-artifacts -type f -exec echo "  - {}" \;

pyvcell_mbsolver-1.0.0/.github/workflows/wheels.yml

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+name: Wheels
+
+on:
+  push:
+    branches: [main]
+    tags: ['v*']
+  pull_request:
+  workflow_dispatch:
+    inputs:
+      testpypi:
+        description: "Dry run: publish built wheels + sdist to TestPyPI"
+        type: boolean
+        default: false
+
+# Cancel superseded runs on the same ref.
+concurrency:
+  group: wheels-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_wheels:
+    name: Wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # macOS : macos-15-intel (x86_64) + macos-15 (arm64)
+        # Linux : ubuntu-latest (x86_64) + ubuntu-24.04-arm (arm64)
+        # Windows is intentionally absent: the bundled FronTier library does not
+        # compile under MSVC (Unix/GCC code — POINT/boolean clash with the
+        # Windows SDK, GCC anonymous-struct tags). Windows users can build from
+        # the sdist under WSL or use the Linux wheels. See the README.
+        os: [macos-15-intel, macos-15, ubuntu-latest, ubuntu-24.04-arm]
+
+    steps:
+      # vcell-messaging / vcell-expressionparser are PRIVATE submodules, so the
+      # default GITHUB_TOKEN cannot fetch them. Authenticate with SUBMODULE_TOKEN
+      # the same way build-and-release.yml does.
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Configure git for private submodules
+        shell: bash
+        run: |
+          git config --global url."https://x-access-token:${{ secrets.SUBMODULE_TOKEN }}@github.com/".insteadOf "https://github.com/"
+
+      - name: Initialize submodules
+        shell: bash
+        run: git submodule update --init --recursive
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.4.0
+        env:
+          CIBW_ARCHS: native
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+          retention-days: 7
+
+  make_sdist:
+    name: Source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+      - name: Configure git for private submodules
+        shell: bash
+        run: |
+          git config --global url."https://x-access-token:${{ secrets.SUBMODULE_TOKEN }}@github.com/".insteadOf "https://github.com/"
+      - name: Initialize submodules
+        shell: bash
+        run: git submodule update --init --recursive
+      - name: Build sdist
+        run: pipx run build --sdist
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+          retention-days: 7
+
+  # Dry run: manually trigger this workflow (Actions tab → Run workflow, or
+  # `gh workflow run wheels.yml -f testpypi=true`) to publish to TestPyPI.
+  # Requires a TestPyPI trusted publisher for this repo + workflow + the
+  # `testpypi` environment (see README). skip-existing avoids a hard failure
+  # if that version was already uploaded in a previous dry run.
+  publish-testpypi:
+    name: Publish to TestPyPI (dry run)
+    needs: [build_wheels, make_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && inputs.testpypi
+    environment: testpypi
+    permissions:
+      id-token: write          # OIDC token for trusted publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
+
+  # Real publish: dormant until a v* tag is pushed AND the PyPI project has a
+  # trusted publisher configured for this repo + workflow (see README). Normal
+  # pushes/PRs only produce downloadable wheel artifacts above.
+  publish:
+    name: Publish to PyPI
+    needs: [build_wheels, make_sdist]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    environment: pypi
+    permissions:
+      id-token: write          # OIDC token for trusted publishing
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          path: dist
+          merge-multiple: true
+      - uses: pypa/gh-action-pypi-publish@release/v1

pyvcell_mbsolver-1.0.0/.gitignore

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+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Linker files
+*.ilk
+
+# Debugger Files
+*.pdb
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+*.so.*
+
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Build directories
+build/
+Build/
+build-*/
+
+# CMake generated files
+CMakeFiles/
+CMakeCache.txt
+cmake_install.cmake
+Makefile
+install_manifest.txt
+compile_commands.json
+
+# Temporary files
+*.tmp
+*.log
+*.bak
+*.swp
+
+# vcpkg
+vcpkg_installed/
+
+# debug information files
+*.dwo
+
+# test output & cache
+Testing/
+.cache/
+.pytest_cache/
+
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Python packaging / wheel build
+dist/
+wheelhouse/
+*.whl
+*.egg-info/
+_skbuild/

pyvcell_mbsolver-1.0.0/.gitmodules

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+[submodule "vcell-messaging"]
+	path = vcell-messaging
+	url = https://github.com/virtualcell/vcell-messaging.git
+[submodule "vcell-expressionparser"]
+	path = vcell-expressionparser
+	url = https://github.com/virtualcell/vcell-expressionparser.git

pyvcell_mbsolver-1.0.0/.idea/.gitignore

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+# Default ignored files
+/shelf/
+/workspace.xml
+# Editor-based HTTP Client requests
+/httpRequests/
+# Ignored default folder with query files
+/queries/
+# Datasource local storage ignored files
+/dataSources/
+/dataSources.local.xml