Add scaffolding for SBML and python wrappers

.flake8

@@ -0,0 +1,11 @@
+[flake8]
+max_line_length = 120
+
+exclude =
+    __pycache__,
+    .git,
+    .github,
+    .venv,
+    build,
+    output,
+    venv,

.github/workflows/test-force-example.yml

@@ -0,0 +1,65 @@
+name: Test Force Example
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+
+concurrency:
+  group: test-force-example-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-force-example:
+    runs-on: ubuntu-latest
+
+    container:
+      image: chaste/base
+      options: --user root
+
+    env:
+      CHASTE_SOURCE_DIR: /tmp/Chaste
+      CHASTE_BUILD_DIR: /tmp/build
+      CHASTE_TEST_OUTPUT: /tmp/testoutput
+      PROJECT_DIR: /tmp/myproject
+
+    steps:
+      - name: Checkout template
+        uses: actions/checkout@v7
+
+      - name: Checkout Chaste source
+        run: |
+          git clone --depth 1 --branch develop https://github.com/Chaste/Chaste.git "${CHASTE_SOURCE_DIR}"
+          git config --global --add safe.directory "${CHASTE_SOURCE_DIR}"
+
+      - name: Create test project
+        run: |
+          cp -r . ${{ env.PROJECT_DIR }}
+          cd ${{ env.PROJECT_DIR }}
+          # Yes to proceed, Yes to cell_based, No to crypt/heart/lung, Yes to Python bindings, No to SBML, Yes to confirm
+          printf 'y\ny\nn\nn\nn\ny\nn\ny\n' | python3 setup_project.py
+
+      - name: Add MyForce to the project bindings
+        run: |
+          cd ${{ env.PROJECT_DIR }}
+          cp examples/my_force/MyForce.hpp examples/my_force/MyForce.cpp src/
+          sed -i.bak 's/^source_includes:$/&\n  - MyForce.hpp/' dynamic/config.yaml
+          sed -i.bak 's/^    classes:$/&\n      - name: MyForce/' dynamic/config.yaml
+          # Import PyChaste's module and declare AbstractForce as an external base
+          sed -i.bak 's/^  - name: all$/&\n    imports:/' dynamic/config.yaml
+          sed -i.bak 's/^    imports:$/&\n      - chaste._pychaste_all/' dynamic/config.yaml
+          sed -i.bak 's/^      - chaste._pychaste_all$/&\n    external_bases:/' dynamic/config.yaml
+          sed -i.bak 's/^    external_bases:$/&\n      - AbstractForce/' dynamic/config.yaml
+
+      - name: Configure
+        run: ${{ env.PROJECT_DIR }}/scripts/configure.sh
+
+      - name: Compile
+        run: ${{ env.PROJECT_DIR }}/scripts/compile.sh
+
+      - name: Install
+        run: ${{ env.PROJECT_DIR }}/scripts/bindings_install.sh
+
+      - name: Run the MyForce simulation from Python
+        run: ${{ env.PROJECT_DIR }}/.virtualenv/bin/python ${{ env.PROJECT_DIR }}/examples/my_force/run_my_force.py

.github/workflows/test-project.yml

@@ -0,0 +1,50 @@
+name: Test Project
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+
+concurrency:
+  group: test-project-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-project:
+    runs-on: ubuntu-latest
+
+    container:
+      image: chaste/base
+      options: --user root
+
+    env:
+      CHASTE_SOURCE_DIR: /tmp/Chaste
+      CHASTE_BUILD_DIR: /tmp/build
+      CHASTE_TEST_OUTPUT: /tmp/testoutput
+      PROJECT_DIR: /tmp/myproject
+
+    steps:
+      - name: Checkout template
+        uses: actions/checkout@v7
+
+      - name: Checkout Chaste source
+        run: |
+          git clone --depth 1 --branch develop https://github.com/Chaste/Chaste.git "${CHASTE_SOURCE_DIR}"
+          git config --global --add safe.directory "${CHASTE_SOURCE_DIR}"
+
+      - name: Create test project
+        run: |
+          cp -r . ${{ env.PROJECT_DIR }}
+          cd ${{ env.PROJECT_DIR }}
+          # Prompt defaults (no components, no Python bindings, no SBML), yes to confirm
+          printf '\n\n\n\n\nn\nn\ny\n' | python3 setup_project.py
+
+      - name: Configure
+        run: ${{ env.PROJECT_DIR }}/scripts/configure.sh
+
+      - name: Compile
+        run: ${{ env.PROJECT_DIR }}/scripts/compile.sh
+
+      - name: Test
+        run: ${{ env.PROJECT_DIR }}/scripts/test.sh

.github/workflows/test-python-project.yml

@@ -0,0 +1,64 @@
+name: Test Python Project
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+
+concurrency:
+  group: test-python-project-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-python-project:
+    runs-on: ubuntu-latest
+
+    container:
+      image: chaste/base
+      options: --user root
+
+    env:
+      CHASTE_SOURCE_DIR: /tmp/Chaste
+      CHASTE_BUILD_DIR: /tmp/build
+      CHASTE_TEST_OUTPUT: /tmp/testoutput
+      PROJECT_DIR: /tmp/myproject
+
+    steps:
+      - name: Checkout template
+        uses: actions/checkout@v7
+
+      - name: Checkout Chaste source
+        run: |
+          git clone --depth 1 --branch develop https://github.com/Chaste/Chaste.git "${CHASTE_SOURCE_DIR}"
+          git config --global --add safe.directory "${CHASTE_SOURCE_DIR}"
+
+      - name: Create test project
+        run: |
+          cp -r . ${{ env.PROJECT_DIR }}
+          cd ${{ env.PROJECT_DIR }}
+          # Yes to Python bindings, no to SBML, yes to final confirmation
+          printf '\n\n\n\n\ny\nn\ny\n' | python3 setup_project.py
+
+      - name: Configure
+        run: |
+          ${{ env.PROJECT_DIR }}/scripts/configure.sh
+
+      - name: Compile
+        run: |
+          ${{ env.PROJECT_DIR }}/scripts/compile.sh
+
+      - name: Install
+        run: |
+          ${{ env.PROJECT_DIR }}/scripts/bindings_install.sh
+
+      - name: Test Python bindings
+        run: |
+          ${{ env.PROJECT_DIR }}/.virtualenv/bin/python -c "
+          import myproject
+          h = myproject.Hello_myproject('Hello from Python!')
+          message = h.GetMessage()
+          assert message == 'Hello from Python!', f'Expected \"Hello from Python!\" but got \"{message}\"'
+          print(f'GetMessage() returned: {message}')
+          print('Test passed!')
+          "

.github/workflows/test-sbml-project.yml

@@ -0,0 +1,66 @@
+name: Test SBML Project
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+    branches: ["**"]
+
+concurrency:
+  group: test-sbml-project-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test-sbml-project:
+    runs-on: ubuntu-latest
+
+    container:
+      image: chaste/base
+      options: --user root
+
+    env:
+      CHASTE_SOURCE_DIR: /tmp/Chaste
+      CHASTE_BUILD_DIR: /tmp/build
+      CHASTE_TEST_OUTPUT: /tmp/testoutput
+      PROJECT_DIR: /tmp/myproject
+
+    steps:
+      - name: Checkout template
+        uses: actions/checkout@v7
+
+      - name: Checkout Chaste source
+        run: |
+          git clone --depth 1 --branch develop https://github.com/Chaste/Chaste.git "${CHASTE_SOURCE_DIR}"
+          git config --global --add safe.directory "${CHASTE_SOURCE_DIR}"
+
+      - name: Install clang-format and curl
+        run: apt-get update && apt-get install -y clang-format curl
+
+      - name: Create test project
+        run: |
+          cp -r . ${{ env.PROJECT_DIR }}
+          cd ${{ env.PROJECT_DIR }}
+          # Prompt defaults for proceed/components/no-python-bindings, yes to SBML, yes to confirm
+          printf '\n\n\n\n\n\ny\ny\n' | python3 setup_project.py
+
+      - name: Install SBML code generator
+        run: ${{ env.PROJECT_DIR }}/scripts/sbml_install.sh
+
+      - name: Import the Goldbeter 1991 model
+        run: |
+          cd ${{ env.PROJECT_DIR }}
+          # Use the vendored model (examples/goldbeter_1991/Goldbeter1991.xml) so the
+          # job does not depend on reaching BioModels at run time.
+          cp examples/goldbeter_1991/Goldbeter1991.xml .
+          .virtualenv/bin/chaste-sbml generate Goldbeter1991.xml --model-type srn --output-dir src/
+          cp examples/goldbeter_1991/TestGoldbeter1991SbmlSrnModel.hpp test/
+          echo "TestGoldbeter1991SbmlSrnModel.hpp" >> test/ContinuousTestPack.txt
+
+      - name: Configure
+        run: ${{ env.PROJECT_DIR }}/scripts/configure.sh
+
+      - name: Compile
+        run: ${{ env.PROJECT_DIR }}/scripts/compile.sh
+
+      - name: Test
+        run: ${{ env.PROJECT_DIR }}/scripts/test.sh

.gitignore

@@ -1,2 +1,42 @@
 build/
+output/
 
+.vscode/
+
+.DS_Store
+Thumbs.db
+
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+.eggs/
+.virtualenv/
+.venv/
+venv/
+env/
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+
+# C++
+*.o
+*.obj
+*.lo
+*.slo
+*.a
+*.lib
+*.so
+*.dylib
+*.dll
+*.exe
+*.out
+*.gch
+*.pch
+
+# CMake
+CMakeCache.txt
+CMakeFiles/
+cmake_install.cmake
+CTestTestfile.cmake
+compile_commands.json

CMakeLists.txt

@@ -52,3 +52,7 @@ find_package(Chaste COMPONENTS continuum_mechanics global io linalg mesh ode pde
 # Change the project name in the line below to match the folder this file is in,
 # i.e. the name of your project.
 chaste_do_project(template_project)
+
+if(Chaste_ENABLE_PYCHASTE AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/dynamic")
+    add_subdirectory(dynamic)
+endif()