Merge pull request #55 from annefou/jupyter-book

add generation of jupyter book

.github/workflows/deploy.yml

@@ -0,0 +1,40 @@
+name: deploy
+
+on:
+  # Trigger the workflow on push to main branch and tutorial path
+  push:
+    branches:
+      - main
+    paths:
+      - lectures/**
+
+# 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: ./environment.yml
+          environment-name: cubes-and-clouds
+          condarc: |
+            channels:
+              - conda-forge
+      # Build the book
+      - name: Build the jupyter book
+        run: |
+          jupyter-book build lectures
+      # 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: lectures/_build/html
+          force_orphan: true

environment.yml

@@ -3,6 +3,7 @@ channels:
   - defaults
   - conda-forge
 dependencies:
+  - python=3.11
   - numpy
   - pandas
   - matplotlib
@@ -20,7 +21,9 @@ dependencies:
   - pystac
   - pip
   - pip:
+    - jupyter-book
+    - sphinx-exercise
     - rio_stac
     - scikit-learn
     - openeo-processes-dask[implementations]
-    - openeo-pg-parser-networkx
+    - openeo-pg-parser-networkx

lectures/1.3_openscience/1.3.3_openscienceineo.md

@@ -37,7 +37,7 @@ Howard Butler, a director of the Open-Source Geospatial Foundation, said about t
 - **Code:** Workflows and Code can easily be shared on EO Cloud Platforms. There are openly available tutorial notebooks. Workflows can be shared as user defined processes and be reused by the community. There are user forums that share solutions and snippets. OpenEO, a standardized processing API for EO in the cloud, allows code to be portable between different cloud platforms. This increases reprodicibility, collaboration and prevents vendor locks.
   - **To Do: Image Slider:** openEO Platform Forum, Tutorial Notebooks Microsoft Planetary Computer, User Defined Processes openEO,
 
-- **Results:** There are multiple ways to share results created in EO cloud platforms. Ideally they can be ingested into the platform and be made available as collections for other users directly upon creation. If the result comes with appropiate metadata (e.g. according to the STAC specification) they can easily be registered in publicly avialable STAC Catalogues. Cloud Native Data Formats (described in more detail in lesson [2.4 Formats and Performance](2.4_formats_and_performance)), like cloud optimized geotiff, are accessible via https requests. So instead of sharing a file, only a URL pointing to the file is shared.
+- **Results:** There are multiple ways to share results created in EO cloud platforms. Ideally they can be ingested into the platform and be made available as collections for other users directly upon creation. If the result comes with appropiate metadata (e.g. according to the STAC specification) they can easily be registered in publicly avialable STAC Catalogues. Cloud Native Data Formats (described in more detail in lesson [2.4 Formats and Performance](../2.4_formats_and_performance/2.4_formats_and_performance.md)), like cloud optimized geotiff, are accessible via https requests. So instead of sharing a file, only a URL pointing to the file is shared.
   - **To Do: Image Slider**: Collection in a Platform, STAC Catalogue, Link to a COG
 
 - **Publication:** If a publication is built on top of results produced in an EO cloud platform, the results and code can easily be linked to the publication in one of the forms described aboved. For example, you can publish your openEO process graph and link to it, and provide a link to a STAC Catalogue where the results are accessible.

lectures/2.3_data_access/2.3_data_access.md

@@ -1,8 +1,8 @@
-## Access EO Data from the Cloud
+# Access EO Data from the Cloud
 
 Using a cloud provider for accessing data, and in this specific scenario Earth Observation data, could improve your productivity a lot. To get the most out of it, we will provide you some important insights.
 
-### Learning objectives
+## Learning objectives
 
 - In this lecture you will learn the usage and peculiarities of the main data operators commonly available on cloud platforms like:
   - Data loading

lectures/9.9_master_asi_conae/test/s1.ipynb

@@ -1,5 +1,13 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "1addb5d4-3779-465d-916c-2ecdc3e6acf0",
+   "metadata": {},
+   "source": [
+    "# S1"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,

lectures/_config.yml

@@ -0,0 +1,37 @@
+#######################################################################################
+# 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                       : Cubes & Clouds - Cloud Native Open Data Sciences for Earth Observation  # The title of the book. Will be placed in the left navbar.
+author                      : ESA  # The author of the book
+copyright                   : "2024"  # Copyright year to be placed in the footer
+logo                        : logo.png  # A path to the book logo
+
+# Force re-execution of notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: false
+
+# Define the name of the latex output file for PDF builds
+latex:
+  latex_documents:
+    targetname: book.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/EO-College/cubes-and-clouds  # Online location of your book
+  path_to_book: lectures  # 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

lectures/_toc.yml

@@ -0,0 +1,64 @@
+format: jb-book
+root: README
+parts:
+  - caption: Setup
+    chapters:
+    - file: 0_introduction/0_introduction
+    - file: 0_introduction/exercises/0_login
+  - caption: Concepts
+    chapters:
+    - file: 1.1_intro_platform/1.1_intro_platform
+    - file: 1.2_data_cube/1.2_data_cube
+    - file: 1.3_openscience/1.3.1_openscienceandfair
+      sections:
+      - file: 1.3_openscience/1.3.3_openscienceineo
+      - file: 1.3_openscience/1.3.2_opendataopensource
+  - caption: Discovery and metadata
+    chapters:
+    - file: 2.1_data_discovery/2.1_data_discovery
+    - file: 2.2_data_properties/2.2_data_properties
+  - caption: Data access with OpenEO
+    chapters:
+    - file: 2.3_data_access/2.3_data_access
+      sections:
+      - file: 2.3_data_access/exercises/23_data_access_lazy_loading
+      - file: 2.3_data_access/exercises/23_data_access_reduce
+      - file: 2.3_data_access/exercises/23_data_access_filter
+      - file: 2.3_data_access/exercises/23_data_access_resample
+      - file: 2.3_data_access/exercises/23_data_access_aggregate
+      - file: 2.3_data_access/exercises/23_data_access_apply
+  - caption: Data formats for achieving scalability
+    chapters:
+    - file: 2.4_formats_and_performance/2.4_formats_and_performance
+  - caption: Process & Share
+    chapters:
+    - file: 3.1_data_processing/3.1_data_processing
+      title: Data processing
+      sections:
+      - file: 3.1_data_processing/3.1_exercises/31_data_processing
+        title: Basic EO workflow
+      - file: 3.1_data_processing/3.1_exercises/_alternatives/31_data_processing_stac
+        title: EO workflow with STAC
+      - file: 3.1_data_processing/3.1_exercises/_alternatives/31_data_processing_openEO_Platform
+        title: EO workflow with openEO
+      - file: 3.1_data_processing/3.1_exercises/_alternatives/34_data_sharing_aoi_test
+        title: Data sharing and publishing
+    - file: 3.2_validation/3.2_validation
+      title: Validation
+      sections:
+      - file: 3.2_validation/3.2_exercises/32_validation
+        title: Exercise validation
+    - file: 3.3_data_sharing/3.3_data_sharing
+      title: Data sharing
+      sections:
+      - file: 3.3_data_sharing/3.3_exercises/33_data_sharing
+        title: Exercise data sharing
+  - caption: Additional materials
+    chapters:
+    - file: 9.9_master_asi_conae/s2_sca
+      sections:
+      - file: 9.9_master_asi_conae/test/s1
+      - file: 9.9_master_asi_conae/test/s2_snowcover_test
+      - file: 9.9_master_asi_conae/test/test_s1_s3
+      - file: 9.9_mar_asi_conae/test/test_s1_s3
+      - file: 9.9_master_asi_conae/test/s3_ndsi