Updates compatible with nightly branch of DOLFINx (#156)

* Replace VectorElement and FiniteElement with `basix.ufl.element`.
Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace`

* More updates

* And more

* Last vector element updates

* Bump pyvista and dolfinx to v0.7.2 (#159)

* Bump pyvista and dolfinx to v0.7.2

* remove -r

* Add further pyvista deps

* Bump versions

* Update petsc solver and pc links. Resolves #143 (#160)

* Fix typo and issue Issue on page /fem.html #122 (#161)

* Compute entity-cell connectivity before calling locate_dofs_topological.
Remove soon to be deprecated pyvista syntax for updating time dependent fields.
Fix range->np.arange conversion

* Update backend in workflow

* Fix broken link (#140) + http:// to https:// (#162)

* Run book build prior to parallel run

* Add back write frame

Author: jorgensd

.github/workflows/book_stable.yml

@@ -15,13 +15,13 @@ env:
 jobs:
   build-book:
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.7.1
+    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

@@ -17,13 +17,13 @@ jobs:
   test-nightly:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: ghcr.io/fenics/dolfinx/lab:v0.7.1
+    container: ghcr.io/fenics/dolfinx/lab:nightly
 
     env:
       HDF5_MPI: "ON"
       PYVISTA_OFF_SCREEN: true
       DISPLAY: ":99.0"
-      PYVISTA_JUPYTER_BACKEND: panel
+      PYVISTA_JUPYTER_BACKEND: html
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
@@ -42,7 +42,10 @@ 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 building the book
+        run: PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
 
       - name: Test complex notebooks in parallel
         run: |
@@ -82,9 +85,6 @@ jobs:
           mpirun -n 2 python3 compiler_parameters.py
           mpirun -n 2 python3 newton-solver.py
 
-      - name: Test building the book
-        run: PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
-
       - uses: actions/upload-artifact@v3
         with:
           name: webpage

.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:v0.7.1
+    container: ghcr.io/fenics/dolfinx/lab:v0.7.2
     env:
       PYVISTA_OFF_SCREEN: true
 
@@ -32,7 +32,7 @@ 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: |

.gitignore

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

Changelog.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## Release
+ - Replace all `ufl.FiniteElement` and `ufl.VectorElement` with the appropriate `basix.ufl.element`
+ - Replace `dolfinx.fem.FunctionSpace` with `dolfinx.fem.functionspace`
+
+## 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

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.7.1
+FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.7.2
 
 # create user with a home directory
 ARG NB_USER=jovyan

README.md

@@ -16,18 +16,26 @@ 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.
 
+Note that every chapter is written as an IPython notebook and a Python file. These are kept in sync by jupytext. See [their notes](https://jupytext.readthedocs.io/en/latest/install.html#jupytext-commands-in-jupyterlab) on how to keep them in sync.
+
+## 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

@@ -38,8 +38,8 @@ sphinx:
 
     # To avoid warning about default changing due to
     # https://github.com/pydata/pydata-sphinx-theme/issues/1492
-    html_theme_options:
-      navigation_with_keys: false
+    # html_theme_options:
+    #   navigation_with_keys: false
 parse:
   myst_enable_extensions:
     - "amsmath"

chapter1/complex_mode.ipynb

@@ -6,7 +6,7 @@
 #       extension: .py
 #       format_name: light
 #       format_version: '1.5'
-#       jupytext_version: 1.14.7
+#       jupytext_version: 1.15.2
 #   kernelspec:
 #     display_name: Python 3 (DOLFINx complex)
 #     language: python
@@ -47,7 +47,7 @@
 from mpi4py import MPI
 import numpy as np
 mesh = dolfinx.mesh.create_unit_square(MPI.COMM_WORLD, 10, 10)
-V = dolfinx.fem.FunctionSpace(mesh, ("Lagrange", 1))
+V = dolfinx.fem.functionspace(mesh, ("Lagrange", 1))
 u_r = dolfinx.fem.Function(V, dtype=np.float64) 
 u_r.interpolate(lambda x: x[0])
 u_c = dolfinx.fem.Function(V, dtype=np.complex128)

chapter1/complex_mode.py

@@ -4,7 +4,7 @@ Authors: Hans Petter Langtangen, Anders Logg
 
 Adapted to FEniCSx by Jørgen S. Dokken 
 
-The goal of this tutorial is to solve one of the most basic PDEs, the Poisson equations, with a few lines of code in FEniCSx. We start by introducing the most fundamental FEniCSx objects, such as `Function`, `FunctionSpace`, `TrialFunction` and `TestFunction`, and learn how to write a basic PDE solver. 
+The goal of this tutorial is to solve one of the most basic PDEs, the Poisson equations, with a few lines of code in FEniCSx. We start by introducing the most fundamental FEniCSx objects, such as `Function`, `functionspace`, `TrialFunction` and `TestFunction`, and learn how to write a basic PDE solver. 
 This will include:
 - How to formulate a mathematical variational problem
 - How to apply boundary conditions