Add script for meshing

.github/workflows/build_docs.yml

@@ -7,17 +7,19 @@ on:
   workflow_dispatch:
 
 env:
-  DEB_PYTHON_INSTALL_LAYOUT: deb_system
+  HDF5_MPI: "ON"
+  HDF5_DIR: "/usr/local/"
   DISPLAY: ":99.0"
-  CI: 1
+  DEB_PYTHON_INSTALL_LAYOUT: deb_system
+  LIBGL_ALWAYS_SOFTWARE: 1
 
 jobs:
 
   build:
     runs-on: ubuntu-22.04
+    container: ghcr.io/fenics/dolfinx/lab:stable
     env:
       PUBLISH_DIR: ./_build/html
-      DISPLAY: ":99.0"
       PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"
       PYVISTA_TRAME_SERVER_PROXY_ENABLED: "True"
       PYVISTA_OFF_SCREEN: false
@@ -28,12 +30,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Install dependencies for pyvista
-        run: sudo apt-get update && sudo apt-get install -y libgl1-mesa-dev xvfb
-
-      - name: Setup python
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.12
+        run: apt-get update && apt-get install -y libxrender1 xvfb
 
       - name: Install dependencies
         run: python3 -m pip install ".[docs]"

.github/workflows/test.yml

@@ -14,27 +14,44 @@ jobs:
       fail-fast: false
       matrix:
         python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-latest, macos-latest]
 
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v5
+
+    - name: Cache conda
+      uses: actions/cache@v3
+      env:
+        # Increase this value to reset cache if environment.yml has not changed
+        CACHE_NUMBER: 0
+      with:
+        path: ~/conda_pkgs_dir
+        key:
+          ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-py-${{ matrix.python-version }}${{
+          hashFiles('environment.yml') }}
+
+    - uses: conda-incubator/setup-miniconda@v3
       with:
         python-version: ${{ matrix.python-version }}
-        allow-prereleases: true
+        auto-update-conda: false
+        channels: conda-forge
+        activate-environment: mri2mesh
+        environment-file: environment.yml
 
     - name: Install mri2mesh
+      shell: bash -el {0}
       run: |
         python -m pip install -e ".[test]"
 
     - name: Test with pytest
+      shell: bash -el {0}
       run: |
         python -m pytest --cov=mri2mesh --cov-report html --cov-report xml --cov-report term-missing -v
 
     - name: Coverage report
       if: matrix.python-version == '3.10' && matrix.os == 'ubuntu-latest'
+      shell: bash -el {0}
       run: |
         python3 -m coverage report | sed 's/^/    /' >> $GITHUB_STEP_SUMMARY
         python3 -m coverage json

.pre-commit-config.yaml

@@ -29,6 +29,7 @@ repos:
       - id: mypy
         files: ^src/|^tests/
         args: ["--config-file", "pyproject.toml"]
+        additional_dependencies: ['types-toml', 'types-PyYAML']
 
 
   - repo: https://github.com/kynan/nbstripout

_toc.yml

@@ -5,6 +5,7 @@ parts:
   - caption: Examples
     chapters:
     - file: "examples/synthseg.ipynb"
+    - file: "examples/cli.ipynb"
   - caption: Community
     chapters:
       - file: "CONTRIBUTING"

environment.yml

@@ -0,0 +1,20 @@
+name: mri2mesh
+channels:
+  - conda-forge
+dependencies:
+  - numpy
+  - fenics-dolfinx
+  - ipython
+  - matplotlib
+  - pyvista
+  - scikit-image
+  - meshio
+  - h5py
+  - seaborn
+  - nibabel
+  - imageio-ffmpeg
+  - napari
+  - jupyter
+  - pip
+  - pip:
+    - wildmeshing