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

.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

@@ -17,7 +17,7 @@ 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"
@@ -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:v0.7.1
+    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 +1,9 @@
 # Changelog
 
+## 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 +16,24 @@ 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

@@ -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"

docker/Dockerfile

@@ -1,6 +1,6 @@
 # Execute from root of repo as: docker buildx build --platform=linux/arm64,linux/amd64 -f docker/Dockerfile ./docker/ --progress=plain
 
-FROM ghcr.io/fenics/dolfinx/lab:v0.7.1
+FROM ghcr.io/fenics/dolfinx/lab:v0.7.2
 ARG TARGETPLATFORM
 
 
@@ -29,8 +29,8 @@ RUN echo ${TARGETPLATFORM}
 RUN if [ "$TARGETPLATFORM" = "linux/arm64" ]; then python3 -m pip install "https://github.com/finsberg/vtk-aarch64/releases/download/vtk-9.2.6-cp310/vtk-9.2.6.dev0-cp310-cp310-linux_aarch64.whl"; fi
 RUN if [ "$TARGETPLATFORM" = "linux/amd64" ]; then python3 -m pip install vtk; fi
 
-ADD requirements.txt /tmp/requirements.txt
-RUN python3 -m pip install --no-cache-dir -v -r requirements.txt
+ADD pyproject.toml /tmp/pyproject.toml
+RUN python3 -m pip install --no-cache-dir --no-binary=h5py -v pyproject.toml
 RUN python3 -m pip cache purge
 RUN jupyter lab build
 ENTRYPOINT ["jupyter", "lab", "--ip", "0.0.0.0", "--no-browser", "--allow-root"]

fem.md

@@ -40,13 +40,13 @@ The tutorial uses several dependencies for meshing, plotting and timings. A comp
 To use the notebooks in this tutorial with DOLFINx on your own computer, you should use the docker image using the following command:
 
 ```bash
-  docker run --init -p 8888:8888 -v "$(pwd)":/root/shared ghcr.io/jorgensd/dolfinx-tutorial:v0.7.1
+  docker run --init -p 8888:8888 -v "$(pwd)":/root/shared ghcr.io/jorgensd/dolfinx-tutorial:v0.7.2
 ```
 
 This image can also be used as a normal docker container by adding:
 
 ```bash
-  docker run --ti -v "$(pwd)":/root/shared  --entrypoint="/bin/bash" ghcr.io/jorgensd/dolfinx-tutorial:v0.7.1
+  docker run --ti -v "$(pwd)":/root/shared  --entrypoint="/bin/bash" ghcr.io/jorgensd/dolfinx-tutorial:v0.7.2
 ```
 
 The tutorials can also be exported as a notebook or PDF by clicking the ![Download](save.png)-symbol in the top right corner of the relevant tutorial. The notebook can in turn be used with a Python kernel which has DOLFINx.
@@ -58,7 +58,7 @@ The [Dockerfile](https://github.com/FEniCS/dolfinx/blob/main/docker/Dockerfile)
 provides a definitive build recipe. As the DOLFINx docker images are hosted at Docker-hub, one can directly access the image:
 
 ```
-docker run dolfinx/dolfinx:v0.7.1
+docker run dolfinx/dolfinx:v0.7.2
 ```
 
 There are several ways of customizing a docker container, such as mounting volumes/sharing folder, setting a working directory, sharing graphical interfaces etc. See `docker run --help` for an extensive list.

pyproject.toml

@@ -0,0 +1,27 @@
+[build-system]
+requires = ["setuptools>=64.4.0", "wheel", "pip>=22.3"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "DOLFINx_Tutorial"
+version = "0.7.2"
+dependencies = ["jupyter-book",
+# Pin docutils due to https://github.com/executablebooks/jupyter-book/issues/1970#issuecomment-1466051277
+"docutils==0.17.1",
+"meshio",
+"h5py",
+"seaborn",
+"pandas",
+"tqdm",
+"pyvista[all]@git+https://github.com/pyvista/pyvista",
+"fenics-dolfinx>=0.7.0"
+]
+
+[project.optional-dependencies]
+dev = [
+    "pdbpp",
+    "ipython",
+]
+
+[tool.setuptools]
+packages = []