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v0.6.0 (#95)
* Updates for JIT-options * Update various plots and other minor things * Resolve meshsize issue at the right part of the ring (x>0,y=0) on page /chapter3/em.html #111 * Repin nbconvert. Resolve Issue on chapter2/ns_code2.html #105 * Add new docker workflow for publishing images on tagging * Resolve Issue on page /chapter3/neumann_dirichlet_code.html #91 * Change jupyter backend to trame * Pin setuptools as long as we don't have new ffcx sub release
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‎.github/workflows/build-publish.yml

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

‎.github/workflows/nightly.yml

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

‎.github/workflows/publish_docker.yml

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

‎Dockerfile

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

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