set up jupyter book for IGARSS 2024 Pangeo & Copernicus tutorial

.binder/environment.yml

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+name: igarss2024
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - jupyter-book
+  - matplotlib
+  - numpy
+  - ghp-import
+  - xarray
+  - cftime
+  - netcdf4
+  - h5netcdf
+  - cartopy
+  - holoviews
+  - hvplot
+  - geoviews
+  - cartopy
+  - geopandas
+  - pooch
+  - fsspec
+  - s3fs
+  - git
+  - jupyterlab-git
+  - "nodejs>=16,<17"
+  - jupyterlab-myst>=2.0.0
+  - pip:
+      - wget
+      - sphinx-exercise
+      - jupytext
+      - nbgitpuller
+      - mystmd

.github/workflows/deploy.yml

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+name: deploy
+
+on:
+  # Trigger the workflow on push to main branch and tutorial path
+  push:
+    branches:
+      - main
+    paths:
+      - docs/**
+
+# This job installs dependencies, build the jupyter notebook, and pushes it to `render`, a new `branch`
+jobs:
+  build:
+    name: Setup
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up conda and dependencies
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: .binder/environment.yml
+          environment-name: gfts
+          condarc: |
+            channels:
+              - conda-forge
+      # Build the book
+      - name: Build the jupyter book
+        run: |
+          jupyter-book build docs
+      # Deploy the book's HTML to gh-pages branch
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: docs/_build/html
+          force_orphan: true

docs/_config.yml

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+#######################################################################################
+# A default configuration that will be loaded for all jupyter books
+# See the documentation for help and more options:
+# https://jupyterbook.org/customize/config.html
+
+#######################################################################################
+# Book settings
+title: Global Fish Tracking System (GFTS) - DESP use case # The title of the book. Will be placed in the left navbar.
+author: Pangeo # The author of the book
+copyright: "2023" # Copyright year to be placed in the footer
+logo: "./images/pangeo-logo.png" # A path to the book logo
+only_build_toc_files: true
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: force
+  timeout: 1000
+
+# Add a launch button on a specific binder instance
+launch_buttons:
+  notebook_interface: "jupyterlab"
+  binderhub_url: "https://notebooks.gesis.org/binder/" # The URL for your BinderHub (e.g., https://mybinder.org)
+  jupyterhub_url: "http://pangeo-eosc.vm.fedcloud.eu/jupyterhub/" # The URL for your JupyterHub. (e.g., https://datahub.berkeley.edu)
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: gfts.tex
+
+# 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/destination-earth/DestinE_ESA_GFTS # Online location of your book
+  path_to_book: docs # Optional path to your book, relative to the repository root
+  branch: main # Which branch of the repository should be used when creating links (optional)
+
+# 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
+
+sphinx:
+  config:
+    html_js_files:
+      - https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js
+  extra_extensions:
+    - sphinx_exercise

docs/_toc.yml

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+format: jb-book
+root: intro
+parts:
+  - caption: About
+    chapters:
+      - file: agenda

docs/agenda.md

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+# Agenda
+
+TODO

docs/conf.py

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+###############################################################################
+# Auto-generated by `jupyter-book config`
+# If you wish to continue using _config.yml, make edits to that file and
+# re-generate this one.
+###############################################################################
+author = "Pangeo"
+bibtex_bibfiles = ["references.bib"]
+comments_config = {"hypothesis": False, "utterances": False}
+copyright = "2023"
+exclude_patterns = ["**.ipynb_checkpoints", ".DS_Store", "Thumbs.db", "_build"]
+extensions = [
+    "sphinx_togglebutton",
+    "sphinx_copybutton",
+    "myst_nb",
+    "jupyter_book",
+    "sphinx_thebe",
+    "sphinx_comments",
+    "sphinx_external_toc",
+    "sphinx.ext.intersphinx",
+    "sphinx_design",
+    "sphinx_book_theme",
+    "sphinx_exercise",
+    "sphinxcontrib.bibtex",
+    "sphinx_jupyterbook_latex",
+    "sphinx_multitoc_numbering",
+]
+external_toc_exclude_missing = True
+external_toc_path = "_toc.yml"
+html_baseurl = ""
+html_favicon = ""
+html_js_files = [
+    "https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"
+]
+html_logo = "./images/pangeo-logo.png"
+html_sourcelink_suffix = ""
+html_theme = "sphinx_book_theme"
+html_theme_options = {
+    "search_bar_text": "Search this book...",
+    "launch_buttons": {
+        "notebook_interface": "jupyterlab",
+        "binderhub_url": "https://notebooks.gesis.org/binder/",
+        "jupyterhub_url": "http://pangeo-eosc.vm.fedcloud.eu/jupyterhub/",
+        "thebe": False,
+        "colab_url": "",
+    },
+    "path_to_docs": "docs",
+    "repository_url": "https://github.com/pangeo-data/pangeo-igarss2024",
+    "repository_branch": "main",
+    "extra_footer": "",
+    "home_page_in_toc": True,
+    "announcement": "",
+    "analytics": {"google_analytics_id": ""},
+    "use_repository_button": True,
+    "use_edit_page_button": False,
+    "use_issues_button": True,
+}
+html_title = "Earthly marvels revealed: Pangeo, AI, and Copernicus in action"
+latex_engine = "pdflatex"
+myst_enable_extensions = [
+    "colon_fence",
+    "dollarmath",
+    "linkify",
+    "substitution",
+    "tasklist",
+]
+myst_url_schemes = ["mailto", "http", "https"]
+nb_execution_allow_errors = False
+nb_execution_cache_path = ""
+nb_execution_excludepatterns = []
+nb_execution_in_temp = False
+nb_execution_mode = "force"
+nb_execution_timeout = 1000
+nb_output_stderr = "show"
+numfig = True
+pygments_style = "sphinx"
+suppress_warnings = ["myst.domains"]
+use_jupyterbook_latex = True
+use_multitoc_numbering = True

docs/intro.md

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+---
+# File metadata may be provided as frontmatter YAML
+title: Earthly marvels revealed - Pangeo, AI, and Copernicus in action
+subtitle: IGARSS 2024
+description: this tutorial will provide a comprehensive introduction along with hands-on examples to help you understand how these technologies can be used for Earth science data analysis and interpretation.
+date: 2024-04-09
+authors:
+  - id: annefou
+    name: Anne Fouilloux
+    orcid: 0000-0002-1784-2920
+    corresponding: false
+    roles:
+      - Pangeo
+    affiliations:
+      - simula
+  - id: tinaok
+    name: Tina Erica Odaka
+    orcid: 0000-0002-1500-0156
+    corresponding: false
+    roles:
+      - Pangeo
+    affiliations:
+      - ifremer
+affiliations:
+  - id: simula
+    name: Simula Research Laboratory
+    city: Oslo
+    country: Norway
+    url: https://www.simula.no
+    ror: https://ror.org/00vn06n10
+  - id: ifremer
+    name: IFREMER
+    city: Brest
+    country: France
+    url: https://www.ifremer.fr
+    ror: https://ror.org/044jxhp58
+tags:
+  - pangeo
+  - copernicus
+  - AI
+  - machine-learning
+thumbnail: images/pangeo-logo.png
+---
+
+#  Earthly marvels revealed: Pangeo, AI, and Copernicus in action 
+
++++ {"part":"abstract"}
+
+% The article should include an abstract block at the beginning. The block is delimited by `+++` before and after, and you must specify `"part": "abstract"` as JSON metadata on the block opener. This metadata is required for recognizing the content of this cell as the abstract.
+% The abstract should begin with a short description of the problem addressed, briefly describe the new data or analyses, then briefly state the main conclusion(s) and how they are supported, and address any uncertainty.
+
+This tutorial will provide a comprehensive introduction along with hands-on examples to help you understand how these technologies can be used for Earth science data analysis and interpretation.
+
++++
+
+# Overview
+
+TODO