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Setting up Docker image and Jupyter book build and deploy on GitHub
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‎.binder/Dockerfile‎

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### ###
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################################################################################
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FROM registry.gitlab.inria.fr/mgenet/dolfin_warp-tutorials:latest
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# FROM registry.gitlab.inria.fr/mgenet/dolfin_warp-tutorials:latest
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FROM ghcr.io/mgenet/dolfin_warp-tutorials:latest
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# Copy repo into the image, cf. https://mybinder.readthedocs.io/en/latest/tutorials/dockerfile.html. MG20230531: OMG this copies from the "build context", cf. https://stackoverflow.com/questions/73156067/where-does-the-copy-command-in-docker-copy-from; here it seems to be the repo itself.
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ARG NB_USER=jovyan

‎.github/workflows/build_and_deploy_jupyter_book.yml‎

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on:
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- push
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jobs:
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build_and_deploy_jupyter_book:
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runs-on: ubuntu-latest
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permissions:
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pages: write
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id-token: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@main
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- name: Build Jupyter Book
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run: |
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pip install -U jupyter-book
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jupyter-book clean .
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jupyter-book build .
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- name: Upload artifact
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uses: actions/upload-pages-artifact@main
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with:
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path: "_build/html"
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- name: Deploy Jupyter Book to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@main

‎.github/workflows/build_and_push_docker_image.yml‎

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on:
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- push
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jobs:
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build_and_push_docker_image:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@main
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- name: Prepare build
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run: |
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rm -rf ${{github.workspace}}/.binder
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cp ${{github.workspace}}/.repo2docker/* ${{github.workspace}}/.
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- name: Build and push docker image
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uses: jupyterhub/repo2docker-action@master
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with:
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DOCKER_USERNAME: ${{github.actor}}
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DOCKER_PASSWORD: ${{secrets.GITHUB_TOKEN}}
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DOCKER_REGISTRY: ghcr.io

‎.github/workflows/mirror_to_gitlab.yml‎

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on:
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- push
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- delete
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jobs:
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mirror_to_gitlab:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@main
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with:
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fetch-depth: 0
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- name: Sync repo
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uses: wangchucheng/git-repo-sync@master
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with:
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target-url: https://gitlab.inria.fr/mgenet/dolfin_warp-tutorials
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target-username: mgenet
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target-token: ${{secrets.GITLAB_TOKEN}}

‎.gitlab-ci.yml‎

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tags:
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- ci.inria.fr
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- large
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# image: registry.gitlab.inria.fr/inria-ci/docker/ubuntu:20.04
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image: ubuntu:20.04
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script:
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- apt update; DEBIAN_FRONTEND=noninteractive apt install -y ca-certificates curl git gnupg lsb-release mercurial python3 python3-pip tzdata

‎.repo2docker/environment-old.yml‎

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################################################################################
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### ###
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### Created by Martin Genet ###
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### ###
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### École Polytechnique, Palaiseau, France ###
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### ###
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################################################################################
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name: notebook
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channels:
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- conda-forge
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- defaults
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dependencies:
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# python
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# - mpi4py=3.1.3 # MG20220906: To avoid mpi warnings in FEniCS, cf. https://fenicsproject.discourse.group/t/runtimewarning-mpi4py-mpi-file-size-changed-may-indicate-binary-incompatibility-expected-32-from-c-header-got-40-from-pyobject-def-compile-class-cpp-data-mpi-comm-mpi-comm-world/6496 # MG20220906: Note that 3.0.3 leads to a `RuntimeError: Error when importing mpi4py`, but 3.1.3 seems to work.
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- numpy=1.21.6 # MG20221220: later numpy versions seem incompatible with itkwidgets 0.32
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- python=3.8.15
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- scipy=1.9.3
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- sympy=1.9
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- traitlets=5.6.0 # MG20221220: later traitlets versions seem incompatible with itkwidgets 0.32, cf. https://github.com/InsightSoftwareConsortium/itkwidgets/issues/588
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# jupyter
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- ipydatawidgets=4.3.2
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- ipywidgets=7.6.5 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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- itkwidgets=0.32.6
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# MG20240123: Specified all these versions based on the 2023 build to get ipywidgets and itkwidgets to properly interact
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- jupyter=1.0.0
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- jupyter_client=7.4.8
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- jupyter_console=6.4.4
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- jupyter_contrib_core=0.4.0
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- jupyter_contrib_nbextensions=0.5.1
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- jupyter_core=5.1.3
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- jupyter_highlight_selected_word=0.2.0
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- jupyter_latex_envs=1.4.6
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- jupyter_nbextensions_configurator=0.4.1
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- jupyter_server=2.0.6
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- jupyter_server_terminals=0.4.3
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# MG20240123: Specified all these versions based on the 2023 build to get ipywidgets and itkwidgets to properly interact
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- jupyterlab=3.5.2 # MG20230602: This seems to be needed as well, otherwise jupyter does not start on binder
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- notebook=6.4.6 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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- traitlets=5.6.0 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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# coding stuff
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- git=2.39.0
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# computing stuff
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- expat=2.5 # MG20241020: expat > 2.5 seems to break vtkXMLDataParser, cf. https://gitlab.kitware.com/vtk/vtk/-/issues/19258
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- fenics=2019.1.0
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- meshio=5.3.4
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- vtk=9.0.3 # MG20201223: Need to correspond to the environment variable CPATH # MG20220628: Apparently there is some kind of conflict between vtk9.1 & libstdc++.so.6 in Ubuntu 20.04… # MG20221220: Apparently there is some kind of conflict between vtk9.1 & itkwidgets 0.32…
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# plotting stuff
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- matplotlib=3.6.2
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- gnuplot=5.4.3
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- pip
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- pip:
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# python
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# - zstd
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# computing stuff
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- gmsh==4.11.0
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# tracking stuff
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- dolfin_warp
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variables:
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CPATH: /srv/conda/envs/notebook/include/vtk-9.0

‎.repo2docker/environment.yml‎

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- defaults
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dependencies:
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# python
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- mpi4py=3.1.3 # MG20220906: To avoid mpi warnings in FEniCS, cf. https://fenicsproject.discourse.group/t/runtimewarning-mpi4py-mpi-file-size-changed-may-indicate-binary-incompatibility-expected-32-from-c-header-got-40-from-pyobject-def-compile-class-cpp-data-mpi-comm-mpi-comm-world/6496 # MG20220906: Note that 3.0.3 leads to a `RuntimeError: Error when importing mpi4py`, but 3.1.3 seems to work.
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# dolfin_warp
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- expat=2.5
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- fenics=2019.1.0
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- gnuplot=5.4
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- matplotlib=3.5
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- meshio=5.3
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- mpi4py=3.1.3
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- numpy=1.21.6 # MG20221220: later numpy versions seem incompatible with itkwidgets 0.32
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- python=3.8
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- pandas=1.3
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- python=3.10
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- scipy=1.9
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- sympy=1.9
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- vtk=9.2
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# jupyter
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- ipywidgets=7.6 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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- itkwidgets=0.32
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- ipydatawidgets=4.3.2
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- ipywidgets=7.6.5 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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- itkwidgets=0.32.6
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# MG20240123: Specified all these versions based on the 2023 build to get ipywidgets and itkwidgets to properly interact
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- jupyter=1.0.0
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- jupyter_client=7.4.8
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- jupyter_server=2.0.6
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- jupyter_server_terminals=0.4.3
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# MG20240123: Specified all these versions based on the 2023 build to get ipywidgets and itkwidgets to properly interact
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- jupyterlab=3.5 # MG20230602: This seems to be needed as well, otherwise jupyter does not start on binder
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- notebook=6.4 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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# coding stuff
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- git=2.39
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# computing stuff
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- expat=2.5
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- fenics=2019.1.0
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- vtk=9.0 # MG20201223: Need to correspond to the environment variable CPATH # MG20220628: Apparently there is some kind of conflict between vtk9.1 & libstdc++.so.6 in Ubuntu 20.04… # MG20221220: Apparently there is some kind of conflict between vtk9.1 & itkwidgets 0.32…
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# plotting stuff
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- matplotlib=3.5
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- gnuplot=5.4
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- jupyterlab=3.5.2 # MG20230602: This seems to be needed as well, otherwise jupyter does not start on binder
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- notebook=6.4.6 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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- traitlets=5.6.0 # MG20221226: cf. https://github.com/InsightSoftwareConsortium/itkwidgets/pull/590/files # MG20230601: Somehow this is still needed, despite the updated itkwidgets version…
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- pip
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- pip:
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# python
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- numpy==1.21.6 # MG20240605: meshio seems to be installing a newer numpy…
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- zstd
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# computing stuff
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- gmsh==4.9.0
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- meshio==5.3.4
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# tracking stuff
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- dolfin_warp
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variables:
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CPATH: /srv/conda/envs/notebook/include/vtk-9.0
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CPATH: /srv/conda/envs/notebook/include/vtk-9.2

‎.repo2docker/postBuild‎

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echo "alias ll=\"ls -l\"" >> ~/.bash_aliases
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echo "alias la=\"ls -la\"" >> ~/.bash_aliases
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export CPATH=$CPATH:"/srv/conda/envs/notebook/include/vtk-9.2"
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rm ~/apt.txt
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rm ~/environment.yml
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rm ~/postBuild

‎README.md‎

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# Welcome to the dolfin_warp tutorials!
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Main library can be found at https://gitlab.inria.fr/mgenet/dolfin_warp
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Main library can be found at https://github.com/mgenet/dolfin_warp
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Interactive tutorials can be found at https://mgenet.gitlabpages.inria.fr/dolfin_warp-tutorials/index.html.
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Interactive tutorials can be found at https://mgenet.github.io/dolfin_warp-tutorials.

‎index.md‎

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# Welcome to the dolfin_warp tutorials!
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Main library can be found at [https://gitlab.inria.fr/mgenet/dolfin_warp](https://gitlab.inria.fr/mgenet/dolfin_warp).
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Main library can be found at [https://github.com/mgenet/dolfin_warp](https://github.com/mgenet/dolfin_warp).
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Tutorials can be browsed statically but also interactively—to start a session and run the code just click on the rocket icon at the top of a tutorial page and then click on Binder.

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