simcoon 1.10.0__tar.gz

simcoon-1.10.0/.github/workflows/build-doc.yml

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+name: Documentation
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ documentation, master ]
+  pull_request:
+    branches: [ documentation, master ]
+
+env:
+  USE_CACHE: "true"
+
+jobs:
+  build-doc:
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -el {0}
+    
+    steps:
+      - uses: actions/checkout@v6
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: simcoon-doc
+          python-version: "3.12"
+          environment-file: environment.yml
+          channels: conda-forge,set3mah
+
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+
+      - name: Cache Conda env
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.CONDA }}/envs
+          key: conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('environment_doc.yml') }}-${{ env.CACHE_NUMBER }}
+        env:
+          # Increase this value to reset cache if environment.yml has not changed
+          CACHE_NUMBER: 0
+        id: cache
+
+      - name: Prepare conda environment
+        shell: bash -l {0}
+        run: |
+          conda config --env --add channels conda-forge
+          conda config --env --add channels set3mah          
+          conda config --env --set channel_priority strict    
+
+      - name: Update environment
+        run: |
+          conda env update -n simcoon-doc -f environment_doc.yml
+        if: steps.cache.outputs.cache-hit != 'true' 
+
+      - name: Remove broken LaTeX from Conda env
+        run: |
+          # Remove or move conda-provided LaTeX binaries only if present in the
+          # conda environment. Move to a .bak instead of deleting to be safe.
+          for bin in latex mktexfmt tlmgr; do
+            if [ -x "${CONDA_PREFIX}/bin/${bin}" ]; then
+              echo "Removing ${CONDA_PREFIX}/bin/${bin}"
+              rm -f "${CONDA_PREFIX}/bin/${bin}" || true
+            fi
+          done
+          hash -r
+
+      - name: Install minimal TeX Live for Matplotlib
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            texlive-latex-base \
+            texlive-latex-extra \
+            texlive-fonts-recommended \
+            dvipng \
+            cm-super \
+            doxygen
+
+      - name: Install Python package
+        shell: bash -l {0}
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install .
+
+      # - name: Cache Sphinx-Gallery Examples
+      #   uses: actions/cache@v4
+      #   if: env.USE_CACHE == 'true'
+      #   with:
+      #     path: examples/
+      #     key: doc-examples-${{ hashFiles('python-setup/simcoon/__version__.py') }}
+
+      - name: Cache Sphinx build directory
+        uses: actions/cache@v4
+        if: env.USE_CACHE == 'true'
+        with:
+          path: docs/_build/
+          key: doc-build-${{ hashFiles('python-setup/simcoon/__version__.py') }}-${{ hashFiles('docs/Doxyfile') }}
+
+      - name: Generate Doxygen XML for C++ API
+        run: |
+          cd docs
+          mkdir -p _build/doxygen
+          doxygen Doxyfile
+          echo "Doxygen XML generated successfully"
+
+      - name: Build Documentation
+        run: |
+          cd docs
+          sphinx-build -b html . _build/html
+
+      - name: Upload HTML documentation
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: docs-build
+          path:
+            docs/_build/html/
+            
+      # Deploy to simcoon-docs/main only for master branch
+      - name: Deploy HTML documentation (master branch)
+        if: ${{ github.ref == 'refs/heads/master' }}
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          personal_token: ${{ secrets.SIMCOON_DOC_TOKEN }}
+          external_repository: 3MAH/simcoon-docs
+          publish_branch: main
+          publish_dir: ./docs/_build/html
+          force_orphan: true
+
+      # Deploy to simcoon-docs/PRXX for each pull request
+      - name: Deploy HTML documentation (pull request)
+        if: ${{ github.event_name == 'pull_request' }}
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          personal_token: ${{ secrets.SIMCOON_DOC_TOKEN }}
+          external_repository: 3MAH/simcoon-docs
+          publish_branch: PR${{ github.event.pull_request.number }}
+          publish_dir: ./docs/_build/html
+          force_orphan: true

simcoon-1.10.0/.github/workflows/build.yml

@@ -0,0 +1,74 @@
+name: Python Build & Test
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+  actions: read
+
+jobs:
+  build-and-test:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            sys-package-install-command: |
+              sudo apt-get update
+              sudo apt-get install -y libarmadillo-dev ninja-build
+          - os: macos-latest
+            sys-package-install-command: brew install armadillo ninja
+          - os: windows-latest
+            sys-package-install-command: vcpkg install armadillo
+            setup-env-command: |
+              echo "CMAKE_TOOLCHAIN_FILE=C:\vcpkg\scripts\buildsystems\vcpkg.cmake" >> $env:GITHUB_ENV
+
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Install system dependencies
+        if: matrix.sys-package-install-command != ''
+        run: ${{ matrix.sys-package-install-command }}
+
+      - name: Setup environment
+        if: matrix.setup-env-command
+        run: ${{ matrix.setup-env-command }}
+
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v7
+
+      - name: Editable install
+        run: |
+          uv venv
+          uv pip install scikit-build-core pybind11 numpy
+          uv pip install -e .[dev]
+
+      - name: Verify cmake rebuild works (Unix)
+        if: runner.os != 'Windows'
+        run: |
+          touch src/Continuum_mechanics/Functions/constitutive.cpp
+          cmake --build build/cp*
+          # Verify import works after cmake rebuild (should not trigger another build)
+          uv run python -c "import simcoon" 2>&1 | tee import.log
+          if grep -q "Building CXX" import.log; then
+            echo "ERROR: Import should not trigger rebuild after cmake --build"
+            exit 1
+          fi
+
+      - name: Verify auto-rebuild on import (Unix)
+        if: runner.os != 'Windows'
+        run: |
+          touch src/Continuum_mechanics/Functions/contimech.cpp
+          uv run python -c "import simcoon" 2>&1 | tee rebuild.log
+          grep -q "Building CXX" rebuild.log || (echo "ERROR: Auto-rebuild did not trigger cmake" && exit 1)
+
+      - name: Run Python tests
+        run: uv run pytest

simcoon-1.10.0/.github/workflows/ci.yml

@@ -0,0 +1,91 @@
+name: Build & Test
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+  actions: read
+
+jobs:
+  build-and-test:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: Linux
+            runner: ubuntu-latest
+            environment-file: environment.yml
+            shell: bash -l {0}
+          - os: MacOS
+            runner: macos-latest
+            environment-file: environment_arm64.yml
+            shell: bash -l {0}
+          - os: Windows
+            runner: windows-latest
+            environment-file: environment_win.yml
+            shell: pwsh
+
+    defaults:
+      run:
+        shell: ${{ matrix.shell }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniconda-version: "latest"
+          activate-environment: foo
+          python-version: "3.14"
+          environment-file: ${{ matrix.environment-file }}
+          channels: conda-forge,set3mah
+
+      - name: Prepare conda environment (Unix)
+        if: runner.os != 'Windows'
+        run: |
+          conda config --env --add channels conda-forge
+          conda config --env --add channels set3mah
+          conda config --env --set channel_priority strict
+
+      - name: Build (Unix)
+        if: runner.os != 'Windows'
+        run: |
+          cmake -S . -B build -G Ninja \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DCMAKE_INCLUDE_PATH=$CONDA_PREFIX/include \
+            -DCMAKE_LIBRARY_PATH=$CONDA_PREFIX/lib \
+            -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX \
+            -Wno-dev
+          cmake --build build
+
+      - name: Build (Windows)
+        if: runner.os == 'Windows'
+        run: |
+          cmake -S . -B build `
+              -DCMAKE_BUILD_TYPE=Release `
+              -DCMAKE_INSTALL_PREFIX="$env:CONDA_PREFIX/Library" `
+              -Wno-dev
+          cmake --build build --config Release
+
+      - name: Tests (Unix)
+        if: runner.os != 'Windows'
+        run: ctest --test-dir build --output-on-failure
+
+      - name: Tests (Windows)
+        if: runner.os == 'Windows'
+        run: ctest --test-dir build -C Release --output-on-failure -VV
+
+      - name: Upload test logs as artifact
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-logs-${{ matrix.os }}
+          path: build/Testing/Temporary/LastTest.log
+          retention-days: 7

simcoon-1.10.0/.github/workflows/conda-packaging.yml

@@ -0,0 +1,192 @@
+name: Conda packaging
+
+on:
+  workflow_dispatch:
+    inputs:
+      upload:
+        description: 'Upload packages to Anaconda'
+        type: boolean
+        default: true
+  workflow_call:
+    inputs:
+      upload:
+        description: 'Upload packages to Anaconda'
+        type: boolean
+        default: true
+      ref:
+        description: 'Git ref to checkout'
+        type: string
+        required: false
+    secrets:
+      ANACONDA_API_TOKEN:
+        required: false
+  pull_request:
+    paths:
+      - 'conda.recipe/**'
+      - '.github/workflows/conda-packaging.yml'
+      - 'environment*.yml'
+
+permissions:
+  contents: read
+  actions: read
+
+jobs:
+  build:
+    name: ${{ matrix.os }}
+    runs-on: ${{ matrix.runner }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: Linux
+            runner: ubuntu-latest
+            target-platform: linux-64
+          - os: MacOS
+            runner: macos-latest
+            target-platform: osx-arm64
+          - os: Windows
+            runner: windows-latest
+            target-platform: win-64
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          ref: ${{ inputs.ref || github.ref }}
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          miniforge-version: latest
+          activate-environment: packaging
+          auto-update-conda: true
+          conda-solver: libmamba
+
+      - name: Conda build
+        shell: bash -l {0}
+        run: |
+          conda install -y conda-build conda-index
+          conda build conda.recipe -c conda-forge -c set3mah --output-folder .
+          # Index output folder to make it a valid conda channel
+          python -m conda_index .
+
+      - name: Install and verify package structure (Unix)
+        if: runner.os != 'Windows'
+        shell: bash -l {0}
+        run: |
+          # Create fresh environment and install the built package using local channel
+          conda create -n test-install -y python simcoon -c file://$PWD -c conda-forge -c set3mah
+
+          # Get the test environment prefix
+          TEST_PREFIX=$(conda run -n test-install printenv CONDA_PREFIX)
+          echo "Test environment: $TEST_PREFIX"
+
+          echo "=== Verifying conda package structure ==="
+
+          # Check C++ library in $PREFIX/lib
+          echo "Checking libsimcoon in \$PREFIX/lib..."
+          if [ -f "$TEST_PREFIX/lib/libsimcoon.so" ] || [ -f "$TEST_PREFIX/lib/libsimcoon.dylib" ]; then
+            echo "✓ libsimcoon found in \$PREFIX/lib"
+            ls -la $TEST_PREFIX/lib/libsimcoon*
+          else
+            echo "✗ ERROR: libsimcoon NOT found in \$PREFIX/lib"
+            exit 1
+          fi
+
+          # Check headers in $PREFIX/include
+          echo "Checking headers in \$PREFIX/include/simcoon..."
+          if [ -d "$TEST_PREFIX/include/simcoon" ]; then
+            echo "✓ Headers found in \$PREFIX/include/simcoon"
+            ls $TEST_PREFIX/include/simcoon/ | head -5
+          else
+            echo "✗ ERROR: Headers NOT found in \$PREFIX/include/simcoon"
+            exit 1
+          fi
+
+          # Check CMake config
+          echo "Checking CMake config..."
+          if [ -f "$TEST_PREFIX/lib/cmake/simcoon/simcoonConfig.cmake" ]; then
+            echo "✓ CMake config found"
+          else
+            echo "✗ ERROR: CMake config NOT found"
+            exit 1
+          fi
+
+          # Check Python module in site-packages
+          echo "Checking Python module..."
+          SITE_PACKAGES=$(conda run -n test-install python -c "import sysconfig; print(sysconfig.get_path('purelib'))")
+          if [ -f "$SITE_PACKAGES/simcoon/_core.so" ] || ls "$SITE_PACKAGES/simcoon"/_core.cpython*.so 1>/dev/null 2>&1; then
+            echo "✓ _core.so found in site-packages/simcoon"
+          else
+            echo "✗ ERROR: _core.so NOT found in site-packages/simcoon"
+            ls -la $SITE_PACKAGES/simcoon/ || true
+            exit 1
+          fi
+
+          # Verify _core links to system libsimcoon (not bundled)
+          echo "Checking _core RPATH..."
+          SIMMIT_PATH=$(find $SITE_PACKAGES/simcoon -name "_core*.so" | head -1)
+          if [ -n "$SIMMIT_PATH" ]; then
+            if command -v readelf &> /dev/null; then
+              readelf -d "$SIMMIT_PATH" | grep -E "(RPATH|RUNPATH)" || echo "(no RPATH/RUNPATH found)"
+            elif command -v otool &> /dev/null; then
+              otool -l "$SIMMIT_PATH" | grep -A2 LC_RPATH || echo "(no LC_RPATH found)"
+            fi
+          fi
+
+          # Verify libsimcoon is NOT bundled in site-packages
+          echo "Checking libsimcoon is NOT bundled in site-packages..."
+          if [ -f "$SITE_PACKAGES/simcoon/libsimcoon.so" ] || [ -f "$SITE_PACKAGES/simcoon/libsimcoon.dylib" ]; then
+            echo "✗ WARNING: libsimcoon found in site-packages (should only be in \$PREFIX/lib)"
+            ls -la $SITE_PACKAGES/simcoon/libsimcoon* || true
+          else
+            echo "✓ libsimcoon correctly NOT bundled in site-packages"
+          fi
+
+          # Test import
+          echo "Testing Python import..."
+          conda run -n test-install python -c "import simcoon; import simcoon._core; print('✓ Import successful')"
+
+      - name: Install and verify package structure (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          # Create fresh environment and install the built package using local channel
+          $localChannel = "file:///" + ($PWD.Path -replace '\\', '/')
+          conda create -n test-install -y python simcoon -c $localChannel -c conda-forge -c set3mah
+
+          # Get the test environment prefix
+          $envInfo = conda info --envs | Select-String "test-install"
+          $TEST_PREFIX = ($envInfo -split '\s+')[1]
+          Write-Host "Test environment: $TEST_PREFIX"
+
+          Write-Host "=== Verifying conda package structure ==="
+
+          # Check C++ library
+          Write-Host "Checking simcoon.dll..."
+          if (Test-Path "$TEST_PREFIX\Library\bin\simcoon.dll") {
+            Write-Host "✓ simcoon.dll found in Library/bin"
+          } else {
+            Write-Host "✗ ERROR: simcoon.dll NOT found"
+            exit 1
+          }
+
+          # Check headers
+          Write-Host "Checking headers..."
+          if (Test-Path "$TEST_PREFIX\Library\include\simcoon") {
+            Write-Host "✓ Headers found"
+          } else {
+            Write-Host "✗ ERROR: Headers NOT found"
+            exit 1
+          }
+
+          # Test import
+          Write-Host "Testing Python import..."
+          conda run -n test-install python -c "import simcoon; import simcoon._core; print('Import successful')"
+
+      - name: Upload to Anaconda
+        if: inputs.upload
+        shell: bash -l {0}
+        env:
+          ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}
+        run: |
+          conda install -y anaconda-client
+          anaconda upload ${{ matrix.target-platform }}/*.conda --force --no-progress

simcoon-1.10.0/.github/workflows/release.yml

@@ -0,0 +1,22 @@
+name: Release
+
+on:
+  release:
+    types: [published]
+  push:
+    tags:
+      - 'v*'
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: 'Tag to release (e.g., v1.0.0)'
+        required: true
+
+jobs:
+  conda-packaging:
+    uses: ./.github/workflows/conda-packaging.yml
+    with:
+      upload: true
+      ref: ${{ inputs.tag || github.ref }}
+    secrets:
+      ANACONDA_API_TOKEN: ${{ secrets.ANACONDA_API_TOKEN }}

simcoon-1.10.0/.github/workflows/wheels.yml

@@ -0,0 +1,144 @@
+name: Build Wheels
+
+on:
+  workflow_dispatch:
+    inputs:
+      publish_testpypi:
+        description: 'Publish to TestPyPI'
+        type: boolean
+        default: false
+      publish_pypi:
+        description: 'Publish to PyPI'
+        type: boolean
+        default: false
+  push:
+    tags:
+      - "v*"
+  pull_request:
+    branches: [master]
+    paths:
+      - ".github/workflows/wheels.yml"
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  # =========================================================================
+  # Build source distribution
+  # =========================================================================
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: astral-sh/setup-uv@v7
+
+      - name: Build sdist
+        run: uvx --from build pyproject-build --sdist
+
+      - uses: actions/upload-artifact@v5
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+  # =========================================================================
+  # Build wheels on all platforms
+  # =========================================================================
+  build_wheels:
+    name: Wheels on ${{ matrix.os }} (${{ matrix.cibw_archs }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          # Linux x86_64
+          - os: ubuntu-latest
+            cibw_archs: "x86_64"
+
+          # Linux aarch64 (native ARM runner)
+          - os: ubuntu-24.04-arm
+            cibw_archs: "aarch64"
+
+          # macOS Apple Silicon only
+          - os: macos-latest
+            cibw_archs: "arm64"
+
+          # Windows x64
+          - os: windows-latest
+            cibw_archs: "AMD64"
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.3
+        env:
+          CIBW_ARCHS: ${{ matrix.cibw_archs }}
+
+      - uses: actions/upload-artifact@v5
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ matrix.cibw_archs }}
+          path: ./wheelhouse/*.whl
+
+  # =========================================================================
+  # Publish to TestPyPI (manual trigger)
+  # =========================================================================
+  publish_testpypi:
+    name: Publish to TestPyPI
+    needs: [build_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && github.event.inputs.publish_testpypi == 'true'
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/simcoon
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v6
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/
+
+  # =========================================================================
+  # Publish to PyPI (release tags OR manual trigger)
+  # =========================================================================
+  publish_pypi:
+    name: Publish to PyPI
+    needs: [build_sdist, build_wheels]
+    runs-on: ubuntu-latest
+    # Logic: Run if it's a v* tag push OR if manually triggered via dispatch with checkbox
+    if: >-
+      (github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')) ||
+      (github.event_name == 'workflow_dispatch' && github.event.inputs.publish_pypi == 'true')
+    environment:
+      name: pypi
+      url: https://pypi.org/p/simcoon
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v6
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - name: Display artifacts
+        run: ls -la dist/
+
+      - uses: pypa/gh-action-pypi-publish@release/v1

simcoon-1.10.0/.gitignore

@@ -0,0 +1,14 @@
+
+.DS_Store
+
+build/
+build_coverage/
+*.egg-info/
+**/__pycache__/
+
+*.dll
+*.pyd
+*.exp
+*.lib
+*.pdb
+*.exe