Merge remote-tracking branch 'origin/main' into simo-11-patch-1

Author: jorgensd

.github/actions/install-dependencies/action.yml

@@ -1,17 +1,10 @@
 name: Install dependencies
 
-
 runs:
   using: composite
   steps:
       - name: Install apt dependencies and upgrade pip
         shell: bash -el {0}
         run: |
           apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb
-          python3 -m pip install -U pip
-      # Install `h5py` master branch
-      # https://github.com/hl5py/h5py/issues/2222
-      - name: Install h5py and pip requirements
-        shell: bash -el {0}
-        run: |
-          python3 -m pip install --no-binary=h5py git+https://github.com/h5py/h5py@master
+          python3 -m pip install -U pip

.github/workflows/book_stable.yml

@@ -15,13 +15,13 @@ env:
 jobs:
   build-book:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.6.0-r1
+    container: ghcr.io/fenics/dolfinx/lab:v0.7.2
 
     env:
       PYVISTA_TRAME_SERVER_PROXY_PREFIX: "/proxy/"
       PYVISTA_TRAME_SERVER_PROXY_ENABLED: "True"
       PYVISTA_OFF_SCREEN: false
-      PYVISTA_JUPYTER_BACKEND: "panel"
+      PYVISTA_JUPYTER_BACKEND: "html"
 
     steps:
       - uses: actions/checkout@v4
@@ -30,7 +30,7 @@ jobs:
         uses: ./.github/actions/install-dependencies
 
       - name: Install book deps
-        run: python3 -m pip install -r docker/requirements.txt
+        run: python3 -m pip install --no-binary=h5py .
 
       - name: Build the book
         run: jupyter-book build . -W

.github/workflows/deploy.yml

@@ -44,7 +44,7 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Setup Pages
-        uses: actions/configure-pages@v2
+        uses: actions/configure-pages@v4
 
       - name: Download docs artifact
         uses: actions/download-artifact@v3
@@ -53,10 +53,10 @@ jobs:
           path: "./public"
 
       - name: Upload page artifact
-        uses: actions/upload-pages-artifact@v1
+        uses: actions/upload-pages-artifact@v2
         with:
           path: "./public"
 
       - name: Deploy coverage report to GH Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v3

.github/workflows/publish_docker.yml

@@ -44,7 +44,7 @@ jobs:
       - name: Build and push Docker image
         uses: docker/build-push-action@v3
         with:
-          context: ./docker
+          context: .
           push: true
           file: docker/Dockerfile
           platforms: linux/amd64,linux/arm64

.github/workflows/test_nightly.yml

@@ -17,7 +17,7 @@ jobs:
   test-nightly:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: dolfinx/lab:nightly
+    container: ghcr.io/fenics/dolfinx/lab:nightly
 
     env:
       HDF5_MPI: "ON"
@@ -42,7 +42,7 @@ jobs:
         uses: ./.github/actions/install-dependencies
 
       - name: Install requirements
-        run: python3 -m pip install --no-cache-dir -r docker/requirements.txt --upgrade
+        run: python3 -m pip install --no-cache-dir --no-binary=h5py . --upgrade
 
       - name: Test complex notebooks in parallel
         run: |

.github/workflows/test_stable.yml

@@ -20,7 +20,7 @@ jobs:
   test:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.6.0-r1
+    container: ghcr.io/fenics/dolfinx/lab:v0.7.2
     env:
       PYVISTA_OFF_SCREEN: true
 
@@ -32,12 +32,12 @@ jobs:
 
       - name: Install additional deps
         run: |
-          python3 -m pip install -r docker/requirements.txt
+          python3 -m pip install --no-binary=h5py .
 
       - name: Test complex notebooks in parallel
         run: |
           export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
-          export PETSC_ARCH=linux-gnu-complex-32
+          export PETSC_ARCH=linux-gnu-complex128-32
           export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
           python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"

.gitignore

@@ -8,4 +8,5 @@ _build
 **/.cache
 *.png
 *.pvtu
-*.msh
+*.msh
+*.bp

Changelog.md

@@ -1,18 +1,32 @@
 # Changelog
 
-## main
-- No changes
+## v0.7.2
+ - Change pyvista backend to `html`, using Pyvista main branch
+ - Using DOLFINx v0.7.2 https://github.com/FEniCS/dolfinx/releases/tag/v0.7.2 as base
+
+## v0.7.1
+ - No API changes, release due to various bug-fixes from the 0.7.0 release, see:
+   https://github.com/FEniCS/dolfinx/releases/tag/v0.7.1 for more information
+
+## v0.7.0
+
+- Renamed `dolfinx.graph.create_adjacencylist` to `dolfinx.graph.adjacencylist`
+- Renamed `dolfinx.plot.create_vtk_mesh` to `dolfinx.plot.vtk_mesh`
+- `dolfinx.geometry.BoundingBoxTree` has been changed to `dolfinx.geometry.bb_tree`
+- `create_mesh` with Meshio has been modified. Note that you now need to pass dtype `np.int32` to the cell_data.
+- Update dolfinx petsc API. Now one needs to explicitly import `dolfinx.fem.petsc` and `dolfinx.fem.nls`, as PETSc is no longer a strict requirement. Replace `petsc4py.PETSc.ScalarType` with `dolfinx.default_scalar_type` in demos where we do not use `petsc4py` explicitly.
 
 ## v0.6.0
+
 - Remove `ipygany` and `pythreejs` as plotting backends. Using `panel`.
 - Add gif-output to [chapter2/diffusion_code] and [chapter2/hyperelasticity].
 - Replace `dolfinx.fem.Function.geometric_dimension` with `len(dolfinx.fem.Function)`
 - Improve [chapter2/ns_code2] to have better splitting scheme and density.
 - Improve mesh quality in [chapter3/em].
 - `jit_params` and `form_compiler_params` renamed to `*_options`.
 
-
 ## v0.5.0
+
 - Using new GMSH interface in DOLFINx (`dolfinx.io.gmshio`) in all demos using GMSH
 - Added a section on custom Newton-solvers, see [chapter4/newton-solver].
 - Various minor DOLFINx API updates. `dolfinx.mesh.compute_boundary_facets` -> `dolfinx.mesh.exterior_facet_indices` with slightly different functionality. Use `dolfinx.mesh.MeshTagsMetaClass.find` instead of `mt.indices[mt.values==value]`.
@@ -21,9 +35,11 @@
 - Add example of how to use `DOLFINx` in complex mode, see [chapter1/complex_mode].
 
 ## 0.4.1
+
 - No changes
 
 ## 0.4.0 (05.02.2021)
+
 - All `pyvista` plotting has been rewritten to use `ipygany` and `pythreejs` as well as using a cleaner interface.
 - `dolfinx.plot.create_vtk_topology` has been renamed to `dolfinx.plot.create_vtk_mesh` and can now be directly used as input to `pyvista.UnstructuredGrid`.
 - `dolfinx.fem.Function.compute_point_values` has been deprecated. Interpolation into a CG-1 is now the way of getting vertex values.
@@ -34,14 +50,14 @@
 - Various API changes relating to the import structure of DOLFINx
 
 ## 0.3.0 (09.09.2021)
+
 - Major improvements in [Form compiler parameters](chapter4/compiler_parameters), using pandas and seaborn for visualization of speed-ups gained using form compiler parameters.
 - API change: `dolfinx.cpp.la.scatter_forward(u.x)` -> `u.x.scatter_forward`
 - Various plotting updates due to new version of pyvista.
 - Updating of the [Hyperelasticity demo](chapter2/hyperelasticity), now using DOLFINx wrappers to create the non-linear problem
 - Internal updates due to bumping of jupyter-book versions
 - Various typos and capitalizations fixed by @mscroggs in [PR 35](https://github.com/jorgensd/dolfinx-tutorial/pull/35).
 
-
-
 ## 0.1.0 (11.05.2021)
-- First tagged release of DOLFINx Tutorial, compatible with [DOLFINx 0.1.0](https://github.com/FEniCS/dolfinx/releases/tag/0.1.0).
+
+- First tagged release of DOLFINx Tutorial, compatible with [DOLFINx 0.1.0](https://github.com/FEniCS/dolfinx/releases/tag/0.1.0).

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.6.0.post0
+FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.7.2
 
 # create user with a home directory
 ARG NB_USER=jovyan

README.md

@@ -16,18 +16,24 @@ Any code added to the tutorial should work in parallel.
 
 Alternatively, if you want to add a separate chapter, a Jupyter notebook can be added to a pull request, without integrating it into the tutorial. If so, the notebook will be reviewed and modified to be included in the tutorial.
 
+## Dependencies
+It is adviced to use a pre-installed version of DOLFINx, for instance through conda or docker. Remaining dependencies can be installed with
+```bash
+python3 -m pip install --no-binary=h5py -e .
+```
+
 # Docker images
 Docker images for this tutorial can be found in the [packages tab](https://github.com/jorgensd/dolfinx-tutorial/pkgs/container/dolfinx-tutorial) 
 
-Additional requirements on top of the `dolfinx/lab:nightly` images can be found at [Dockerfile](docker/Dockerfile) and [requirements.txt](docker/requirements.txt)
+Additional requirements on top of the `dolfinx/lab:nightly` images can be found at [Dockerfile](docker/Dockerfile) and [pyproject.toml](./pyproject.toml)
 
 ##
 An image building DOLFINx, Basix, UFL and FFCx from source can be built using:
 ```bash
 cd docker
-docker build -f LocalDockerfile -t local_lab_env .
+docker build -f ./docker/Dockerfile -t local_lab_env .
 ```
-and run
+from the root of this repository, and run
 ```bash
  docker run --rm -ti -v $(pwd):/root/shared -w /root/shared  --init -p 8888:8888 local_lab_env
  ```

_config.yml

@@ -8,7 +8,7 @@ logo: fenics_logo.png
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
 execute:
-  execute_notebooks: force
+  execute_notebooks: cache
 
   # Set timeout for any example to 20 minutes
   timeout: 1800
@@ -35,6 +35,11 @@ sphinx:
   config:
     html_last_updated_fmt: "%b %d, %Y"
     suppress_warnings: ["mystnb.unknown_mime_type"]
+
+    # To avoid warning about default changing due to
+    # https://github.com/pydata/pydata-sphinx-theme/issues/1492
+    # html_theme_options:
+    #   navigation_with_keys: false
 parse:
   myst_enable_extensions:
     - "amsmath"