v0.6.0

.github/workflows/build-publish.yml

@@ -27,43 +27,54 @@ concurrency:
 env:
   # Directory that will be published on github pages
   PUBLISH_DIR: ./_build/html
-
+  HDF5_MPI: "ON"
+  HDF5_DIR: "/usr/local/"
+  DISPLAY: ":99.0"
+  DEB_PYTHON_INSTALL_LAYOUT: deb_system
 
 # A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
   # This workflow contains a single job called "build"
   test:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: ghcr.io/jorgensd/dolfinx-tutorial:v0.5.1
-
+    container: ghcr.io/fenics/dolfinx/lab:v0.6.0-r1
     env:
-      HDF5_MPI: "ON"
-      CC: mpicc
-      HDF5_DIR: "/usr/local/"
-      DISPLAY: ":99.0"
       PYVISTA_OFF_SCREEN: true
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - uses: actions/checkout@v3
 
+      # Upgrade setuptools and pip
+      # https://github.com/pypa/setuptools/issues/3269#issuecomment-1254507377
+      - name: Install apt dependencies and upgrade pip
+        run: |
+          apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb
+          python3 -m pip install -U "setuptools<=65.5.1" pip pkgconfig
+
+      # Install `h5py`
+      # https://github.com/hl5py/h5py/issues/2222
+      - name: Install h5py and pip requirements
+        run: |
+          python3 -m pip install cython
+          python3 -m pip install --no-build-isolation --no-binary=h5py h5py
+          python3 -m pip install --no-cache-dir -r docker/requirements.txt --upgrade
+
+
       - name: Test complex notebooks in parallel
         run: |
           export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$PKG_CONFIG_PATH
           export PETSC_ARCH=linux-gnu-complex-32
           export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
-          pip3 uninstall pyvista -y
-          pip3 install pyvista --upgrade
           python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
           cd chapter1
+          python3 complex_mode.py
           mpirun -n 2 python3 complex_mode.py
 
-
-      - name: Install dependencies
-        run: pip3 install notebook nbconvert jupyter-book --upgrade
+
       - name: Test notebooks in parallel
         run: |
           python3 -c "from pyvista import start_xvfb; start_xvfb(0.1)"
@@ -102,24 +113,39 @@ jobs:
   build-book:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: ghcr.io/jorgensd/dolfinx-tutorial:v0.5.1
-
+    container: ghcr.io/fenics/dolfinx/lab:v0.6.0-r1
+   
     env:
-      HDF5_MPI: "ON"
-      CC: mpicc
-      HDF5_DIR: "/usr/local/"
-      DISPLAY: ":99.0"
+      PYVISTA_TRAME_SERVER_PROXY_PREFIX: '/proxy/'
+      PYVISTA_TRAME_SERVER_PROXY_ENABLED: "True"
       PYVISTA_OFF_SCREEN: false
-      PYVISTA_JUPYTER_BACKEND: "static"
+      PYVISTA_JUPYTER_BACKEND: "panel"
+
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
+
       - uses: actions/checkout@v3
-      # Runs a single command using the runners shell
+
+      # Upgrade setuptools and pip
+      # https://github.com/pypa/setuptools/issues/3269#issuecomment-1254507377
+      - name: Install apt dependencies and upgrade pip
+        run: |
+          apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb
+          python3 -m pip install -U "setuptools<=65.5.1" pip pkgconfig
+
+      # Install `h5py`
+      # https://github.com/hl5py/h5py/issues/2222
+      - name: Install h5py and pip requirements
+        run: |
+          python3 -m pip install cython
+          python3 -m pip install --no-build-isolation --no-binary=h5py h5py
+          python3 -m pip install --no-cache-dir -r docker/requirements.txt jupyter-book --upgrade 
+
+
       - name: Build the book
         run: 
-          jupyter-book build  -W .
+          jupyter-book build .
 
       - name: Upload book
         uses: actions/upload-pages-artifact@v1
@@ -147,4 +173,4 @@ jobs:
 
         - name: Deploy to GitHub Pages
           id: deployment
-          uses: actions/deploy-pages@v1
+          uses: actions/deploy-pages@v1

.github/workflows/nightly.yml

@@ -27,23 +27,31 @@ jobs:
     env:
       HDF5_MPI: "ON"
       PYVISTA_OFF_SCREEN: true
-
+      DISPLAY: ":99.0"
+      PYVISTA_JUPYTER_BACKEND: panel
+
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         # Workaround for scheduling to work
         with:
           ref: dokken/release
 
-      - name: Install dependencies
+      # Upgrade setuptools and pip
+      # https://github.com/pypa/setuptools/issues/3269#issuecomment-1254507377
+      - name: Install apt dependencies and upgrade pip
+        run: |
+          apt-get update && apt-get install -y libgl1-mesa-glx libxrender1 xvfb
+          python3 -m pip install -U "setuptools<=65.5.1" pip pkgconfig
+
+      # Install `h5py`
+      # https://github.com/hl5py/h5py/issues/2222
+      - name: Install h5py and pip requirements
         run: |
-          pip3 install --upgrade pip setuptools
-          CC=mpicc HDF_MPI="ON" HDF5_DIR="/usr/local/" pip3 install --no-cache-dir -r docker/requirements.txt
-          pip3 uninstall pyvista -y
-          pip3 install pyvista --upgrade --user
-          apt-get -qq update
-          apt-get install -y libgl1-mesa-dev xvfb nodejs
+          python3 -m pip install cython
+          python3 -m pip install --no-build-isolation --no-binary=h5py h5py
+          python3 -m pip install --no-cache-dir -r docker/requirements.txt --upgrade
 
       - name: Test complex notebooks in parallel
         run: |
@@ -52,6 +60,7 @@ jobs:
           export PYTHONPATH=/usr/local/dolfinx-complex/lib/python3.10/dist-packages:$PYTHONPATH
           export LD_LIBRARY_PATH=/usr/local/dolfinx-complex/lib:$LD_LIBRARY_PATH
           cd chapter1
+          python3 complex_mode.py
           mpirun -n 2 python3 complex_mode.py
 
       - name: Test real notebooks in parallel
@@ -84,4 +93,4 @@ jobs:
 
       - name: Test building the book
         run: 
-          PYVISTA_JUPYTER_BACKEND=static PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
+          PYVISTA_OFF_SCREEN=false jupyter-book build  -W .

.github/workflows/publish_docker.yml

@@ -0,0 +1,52 @@
+on:
+  push:
+    branches:
+      - "!*"
+    tags:
+      - "v*"
+
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v2
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@v2
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v4
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          push: true
+          file: docker/Dockerfile
+          platforms: linux/amd64,linux/arm64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

Dockerfile

@@ -1,4 +1,4 @@
-FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.5.1
+FROM ghcr.io/jorgensd/dolfinx-tutorial:v0.6.0
 
 # create user with a home directory
 ARG NB_USER