Adaptive mesh refinement with NetGen (#266)

* Add amr demo

* Update CI

* Update pyproject.toml

* Simplify dockerfile as vtk is now on pypi on linux arch

* Fix indent

* Make netgen optional as it is not on pypi on linux/arm

* Build netgen from source

Author: jorgensd

.github/workflows/book_stable.yml

@@ -26,7 +26,7 @@ jobs:
       PYVISTA_JUPYTER_BACKEND: "html"
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Install common packages
         uses: ./.github/actions/install-dependencies

.github/workflows/deploy.yml

@@ -35,7 +35,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Setup Pages
         uses: actions/configure-pages@v5

.github/workflows/publish_docker.yml

@@ -28,7 +28,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Log in to the Container registry
         uses: docker/login-action@v3

.github/workflows/test_nightly.yml

@@ -27,15 +27,15 @@ jobs:
       LIBGL_ALWAYS_SOFTWARE: 1
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
 
       - name: Special handling of some installation
         uses: ./.github/actions/install-dependencies
 
       - name: Install requirements
         run: |
-          python3 -m pip install --break-system-packages -U pip setuptools pkgconfig
-          python3 -m pip install --no-build-isolation --break-system-packages --no-cache-dir --no-binary=h5py . --upgrade
+          python3 -m pip install --break-system-packages -U pip setuptools pkgconfig poetry-core
+          python3 -m pip install --no-build-isolation --break-system-packages --no-cache-dir --no-binary=h5py .[netgen] --upgrade
 
       - name: Test building the book
         run: PYVISTA_OFF_SCREEN=false jupyter-book build  -W .

.github/workflows/test_stable.yml

@@ -21,15 +21,16 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           ref: release
 
       - uses: ./.github/actions/install-dependencies
 
       - name: Install additional deps
         run: |
-          python3 -m pip install --no-binary=h5py .
+          python3 -m pip install -U pip setuptools pkgconfig poetry-core
+          python3 -m pip install --no-binary=h5py .[netgen]
 
       - name: Test complex notebooks in parallel
         working-directory: chapter1

_toc.yml

@@ -16,6 +16,7 @@ parts:
         sections:
           - file: chapter1/membrane_code
           - file: chapter1/membrane_paraview
+
   - caption: A Gallery of finite element solvers
     chapters:
       - file: chapter2/intro
@@ -39,6 +40,7 @@ parts:
       - file: chapter2/helmholtz
         sections:
           - file: chapter2/helmholtz_code
+      - file: chapter2/amr
 
   - caption: Subdomains and boundary conditions
     chapters: