Merge PyChaste into Chaste develop

.github/workflows/pychaste-conda-tests.yml

@@ -0,0 +1,90 @@
+name: PyChaste conda tests
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - "**"
+
+# Limit concurrent runs to one per branch
+concurrency:
+  group: pychaste-conda-tests-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pychaste-conda-tests:
+    if: ${{ !contains(github.event.pull_request.labels.*.name, 'ci:off') }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+
+    runs-on: ubuntu-latest
+
+    env:
+      CHASTE_TEST_OUTPUT: ${{ github.workspace }}/testoutput
+
+    defaults:
+      run:
+        shell: bash -el {0} # -l needed to activate conda
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Make build and test directories
+        run: |
+          mkdir -p build
+          mkdir -p ${CHASTE_TEST_OUTPUT}
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y castxml clang cmake xvfb
+
+      - name: Setup Miniconda Python ${{ matrix.python-version }}
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          auto-update-conda: true
+          use-mamba: true
+          miniforge-version: latest
+          environment-file: pychaste/src/py/conda/environment.yml
+          python-version: ${{ matrix.python-version }}
+          channels: conda-forge,pychaste
+
+      - name: Configure PyChaste
+        run: |
+          cmake \
+            -DChaste_ENABLE_PYCHASTE=ON \
+            -DCMAKE_BUILD_TYPE=Release \
+            -DCMAKE_INSTALL_PREFIX="${CONDA_PREFIX}" \
+            -DCMAKE_PREFIX_PATH="${CONDA_PREFIX}" \
+            -DCMAKE_LIBRARY_PATH="${CONDA_PREFIX}/lib" \
+            -DBUILD_SHARED_LIBS=ON \
+            -DBOOST_ROOT="${CONDA_PREFIX}" \
+            -DHDF5_C_COMPILER_EXECUTABLE="${CONDA_PREFIX}/bin/h5pcc" \
+            -DPETSC_DIR="${CONDA_PREFIX}" \
+            -DPYTHON_EXECUTABLE="$(which python)" \
+            -DVTK_DIR="${CONDA_PREFIX}" \
+            -DXERCESC_INCLUDE="${CONDA_PREFIX}/include" \
+            -DXERCESC_LIBRARY="${CONDA_PREFIX}/lib/libxerces-c.so" \
+            -DXSD_EXECUTABLE="${CONDA_PREFIX}/bin/xsd" \
+            ..
+        working-directory: build
+
+      - name: Build PyChaste
+        run: |
+          make -j $(nproc) pychaste
+        working-directory: build
+
+      - name: Install PyChaste
+        run: |
+          python3 -m pip install -v pychaste/package
+        working-directory: build
+
+      - name: Run PyChaste tests
+        run: |
+          xvfb-run --server-args="-screen 0 1024x768x24" \
+            ctest -j $(nproc) -L pychaste --output-on-failure
+        working-directory: build

.github/workflows/pychaste-ubuntu-tests.yml

@@ -0,0 +1,89 @@
+name: PyChaste Ubuntu tests
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - "**"
+
+# Limit concurrent runs to one per branch
+concurrency:
+  group: pychaste-ubuntu-tests-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pychaste-ubuntu-tests:
+    if: ${{ !contains(github.event.pull_request.labels.*.name, 'ci:off') }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-22.04", "ubuntu-24.04"]
+
+    runs-on: ${{ matrix.os }}
+
+    env:
+      CHASTE_TEST_OUTPUT: ${{ github.workspace }}/testoutput
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Make build and test directories
+        run: |
+          mkdir -p build
+          mkdir -p ${CHASTE_TEST_OUTPUT}
+
+      - name: Install Chaste dependencies
+        run: |
+          codename=$(cat /etc/os-release | grep VERSION_CODENAME | cut -d= -f2)
+          sudo wget -O /usr/share/keyrings/chaste.asc https://chaste.github.io/chaste.asc
+          echo "deb [signed-by=/usr/share/keyrings/chaste.asc] https://chaste.github.io/ubuntu ${codename}/" \
+            | sudo tee -a /etc/apt/sources.list.d/chaste.list
+          sudo apt-get update
+          sudo apt-get install -y chaste-dependencies
+
+      - name: Install extra PyChaste dependencies
+        run: |
+          for vtk_ver in $(seq 7 9); do
+            installed=1
+            dpkg -s "libvtk${vtk_ver}-dev" || installed=0
+            if [ "${installed}" -eq 1 ]; then
+              break
+            fi
+          done
+
+          sudo apt-get install -y \
+            castxml \
+            clang \
+            python3-matplotlib \
+            python3-mpi4py \
+            python3-notebook \
+            python3-numpy \
+            python3-petsc4py-real \
+            python3-pip \
+            python3-vtk${vtk_ver} \
+            python3-xvfbwrapper \
+            xvfb
+
+      - name: Configure PyChaste
+        run: |
+          cmake -DCMAKE_BUILD_TYPE=Release -DChaste_ENABLE_PYCHASTE=ON ..
+        working-directory: build
+
+      - name: Build PyChaste
+        run: |
+          make -j $(nproc) pychaste
+        working-directory: build
+
+      - name: Install PyChaste
+        run: |
+          PIP_BREAK_SYSTEM_PACKAGES=1 \
+          python3 -m pip install -v --user pychaste/package
+        working-directory: build
+
+      - name: Run PyChaste tests
+        run: |
+          xvfb-run --server-args="-screen 0 1024x768x24" \
+            ctest -j $(nproc) -L pychaste --output-on-failure
+        working-directory: build

.github/workflows/update-pychaste-tutorials.yml

@@ -0,0 +1,77 @@
+name: Update pychaste tutorials
+
+on:
+  pull_request:
+    branches:
+      - '**'
+  push:
+    branches:
+      - develop
+  workflow_dispatch:
+
+jobs:
+
+  generate-tutorial-markdown:
+    runs-on: ubuntu-latest
+    if: ${{ !contains(github.event.pull_request.labels.*.name, 'ci:off') }}
+    steps:
+      - name: checkout Chaste
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch all history in order to get revision info for tutorial files
+
+      - name: setup python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: install dependencies
+        run: |
+          python -m pip install jupyterlab
+
+      - name: generate pychaste tutorial markdown
+        run: |
+          python GeneratePyChasteTutorials.py
+        working-directory: python/infra
+
+      - name: upload archive files
+        uses: actions/upload-artifact@v4
+        with:
+          name: pychaste-tutorial-markdown
+          path: |
+            pychaste/src/py/doc/tutorial/*.md
+
+  upload-to-website:
+    needs: generate-tutorial-markdown
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+    steps:
+      - name: Download pychaste-tutorial-markdown
+        uses: actions/download-artifact@v4
+        with:
+          name: pychaste-tutorial-markdown
+          path: pychaste/src/py/doc/tutorial
+
+      - name: Checkout website repository
+        uses: actions/checkout@v4
+        with:
+          repository: Chaste/Chaste.github.io
+          token: ${{ secrets.WEBSITE_ACCESS }}
+          path: chaste-website
+          fetch-depth: 0  # Fetch all history for all tags and branches
+
+      - name: Display structure of downloaded files
+        run: ls -R
+
+      - name: Copy markdown to website repository
+        run: |
+          cp pychaste/src/py/doc/tutorial/*.md chaste-website/site/content/pychaste/tutorials
+
+      - name: Commit and push if changed
+        run: |
+          git config user.name "github-action"
+          git config user.email "github-action"
+          git add --all
+          git commit -m "update pychaste tutorials" || echo "No changes to commit"
+          git push
+        working-directory: chaste-website

.gitignore

@@ -25,7 +25,7 @@ _local/
 # Temporary build folders for dynamically loaded models
 /heart/dynamic/tmp_*_*
 /heart/dynamic/luo_rudy_1991_dyn.*
-/codegen_python3_venv
+/chaste_python3_venv
 **/__pycache__/
 
 # Local hostconfig