Skeletons

.github/workflows/build_and_publish.yml

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+# This is a basic workflow to help you get started with Actions
+name: Build and publish
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [main]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+  # Weekly build on Mondays at 8 am
+  schedule:
+    - cron: "0 8 * * 1"
+
+# 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"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: dokken92/dolfinx_custom:15072022
+
+    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 $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      # - name: Test complex notebooks in parallel
+      #   run: |
+      #     export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$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
+
+
+      - 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)"
+
+      # Runs a single command using the runners shell
+      - name: Build the book
+        run: |
+          PYVISTA_JUPYTER_BACKEND=static PYVISTA_OFF_SCREEN=false jupyter-book build  -W .
+
+      # Push book to HTML to github pages
+      - name: GitHub Pages action
+          uses: peaceiris/actions-gh-pages@v3.5.9
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build/html

.github/workflows/test-build.yml

@@ -0,0 +1,61 @@
+# This is a basic workflow to help you get started with Actions
+name: Test tutorial against DOLFINx main branch
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events but only for the master branch
+  push:
+    branches: [main]
+  pull_request:
+    branches:
+      - main
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+  # Test every day at 9 am
+  schedule:
+    - cron: "* 9 * * 1"
+
+# 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-against-master:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+    container: dolfinx/lab
+
+    env:
+      HDF5_MPI: "ON"
+      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 $GITHUB_WORKSPACE, so your job can access it
+      - uses: actions/checkout@v2
+
+      - name: Install dependencies
+        run: |
+          pip3 install --upgrade pip setuptools
+          CC=mpicc HDF_MPI="ON" HDF5_DIR="/usr/local" pip3 install --no-cache-dir -r deps/requirements.txt
+          apt-get -qq update
+          apt-get install -y libgl1-mesa-dev xvfb nodejs
+          apt-get clean
+          rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+          jupyter nbextension enable --py --sys-prefix ipygany 
+          rm -rf /usr/local/share/.cache/*
+          jupyter-book -h
+
+      # - name: Test complex notebooks in parallel
+      #   run: |
+      #     export PKG_CONFIG_PATH=/usr/local/dolfinx-complex/lib/pkgconfig:$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
+
+      # - name: Test real notebooks in parallel
+      #   run: |
+
+      - name: Test building the book
+        run: 
+          PYVISTA_JUPYTER_BACKEND=static PYVISTA_OFF_SCREEN=false jupyter-book build  -W .

.gitignore

@@ -127,3 +127,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Jupybook
+_build/*

Dockerfile

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+FROM dokken92/dolfinx_custom:15072022
+
+# create user with a home directory
+ARG NB_USER
+ARG NB_UID=1000
+ENV USER ${NB_USER}
+ENV HOME /home/${NB_USER}
+
+# Copy home directory for usage in binder
+WORKDIR ${HOME}
+COPY . ${HOME}
+USER root
+RUN chown -R ${NB_UID} ${HOME}
+
+USER ${NB_USER}
+ENTRYPOINT []

README.md

@@ -1,2 +1,71 @@
 # fenics22-tutorial
+
 Tutorial for the FEniCS [22 conference](https://fenicsproject.org/fenics-2022/) in San Diego
+
+
+## Adding a tutorial to the book
+
+Add a chapter to `_toc.yml`.
+
+Inside the Jupyter notebook, go to `Property Inspector` (the two cogwheels in the top right corner of JupyterLab)
+and add the following as notebook metadata:
+```yml
+ "metadata": {
+  "jupytext": {
+   "formats": "ipynb,py:light"
+  },
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.4"
+  }
+ }
+```
+This will choose the default kernel in the `dolfinx/lab` docker image, and automatically convert the notebooks to a `.py` file at saving.
+
+If you want to use complex numbers, change:
+```bash
+ "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+```
+to
+```bash
+  "kernelspec": {
+   "display_name": "Python 3 (DOLFINx complex)",
+   "language": "python",
+   "name": "python3-complex"
+  },
+```
+
+
+## Create slides from your notebook
+
+You can use `nbconvert` (`pip3 install nbconvert`) to convert the `.ipynb` to a presentation.
+The command to run is:
+```bash
+jupyter nbconvert example.ipynb --to html --template reveal
+```
+
+To change what is rendered on each slide, you can change the notebook metadata,
+which is in `Property Inspector` (the two cogwheels in the top right corner of JupyterLab), and change the `Slide Type` to `Slide` to start a new slide. If you want to add the cell below to the same slide, change the type to `-`.
+
+If a cell should be revealed with `Right Arrow`, choose `Fragment`.
+
+If you want a sub-slide, i.e. navigating downwards with arrows when rendering the presentation, change the type to `Sub-Slide`.
+
+If a cell should be ignored in presentation mode, set it to `Notes`.

_config.yml

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+# Book settings
+# Learn more at https://jupyterbook.org/customize/config.html
+
+title: FEniCS 22 tutorial
+author: The FEniCS project
+logo: logo.jpeg
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+
+# Set timeout for any example to 20 minutes
+timeout: 1800
+
+# Add a bibtex file so that we can create citations
+bibtex_bibfiles:
+  - references.bib
+
+# Information about where the book exists on the web
+repository:
+  url: https://github.com/jorgensd/fenics22-tutorial # Online location of your book
+  path_to_book: . # Optional path to your book, relative to the repository root
+  branch: main # Which branch of the repository should be used when creating links (optional)
+
+parse:
+  myst_enable_extensions:
+    - "amsmath"
+    - "colon_fence"
+    - "deflist"
+    - "dollarmath"
+    - "html_admonition"
+    - "html_image"
+    - "linkify"
+    - "replacements"
+    - "smartquotes"
+    - "substitution"
+
+# Add GitHub buttons to your book
+# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
+html:
+  use_issues_button: true
+  use_repository_button: true
+  use_edit_page_button: true
+
+exclude_patterns: [README.md]

_toc.yml

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+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: intro
+chapters:
+- file: example

deps/requirements.txt

@@ -0,0 +1,33 @@
+# Various jupyterlab components
+setuptools
+jupyterhub
+jupyterlab
+jupyter-book
+
+# Notebook conversion
+nbconvert
+
+# Meshio
+# meshio
+# --no-binary=h5py
+# h5py
+
+# Visualization with pandas
+# seaborn
+# pandas
+
+# Visualization with Pyvista 
+# matplotlib
+
+# Until VTK is released with wheels for python 3.10
+--find-links https://wheels.pyvista.org/
+pyvista
+
+pythreejs
+ipygany
+
+# Progress bar
+# tqdm
+
+# To resolve black dependency conflict
+# click