Merge pull request ScienceCore#73 from jnywong/folder-structure

Update folder structure ScienceCore#72

.github/workflows/deploy_jupyter_book.yml

@@ -0,0 +1,59 @@
+name: deploy-jupyter-book
+
+# Run this when the main branch changes
+on:
+  push:
+    branches:
+    - main
+    # If your git repository has the Jupyter Book within some-subfolder next to
+    # unrelated files, you can make this run only if a file within that specific
+    # folder has been modified.
+    #
+    paths:
+    - book/**
+
+# This job installs dependencies, builds the book, and pushes it to `gh-pages`
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+    - uses: actions/checkout@v4
+
+    # Install dependencies
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.11
+
+    - name: Install dependencies
+      run: |
+        pip install -r requirements.txt
+
+    # (optional) Cache your executed notebooks between runs
+    # if you have in your conf.yml:
+    # execute:
+    #   execute_notebooks: cache
+    - name: cache executed notebooks
+      uses: actions/cache@v3
+      with:
+        path: _build/.jupyter_cache
+        key: jupyter-book-cache-${{ hashFiles('requirements.txt') }}
+
+    # Build the book
+    - name: Build the book
+      run: |
+        jupyter-book build ./book
+
+    # Upload the book's HTML as an artifact
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v3
+      with:
+        path: "./book/_build/html"
+
+    # Deploy the book's HTML to GitHub Pages
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v4

book/01_Open_Science/Open_Science_Intro.md

@@ -12,7 +12,7 @@ jupyter:
     name: python3
 ---
 
-## About this tutorial
+# About this tutorial
 
 This tutorial is part of a project which focuses on leveraging the vast amount of Earth science data available through the NASA Earthdata Cloud to better understand and forecast environmental risks such as wildfire, drought, and floods. At its core, this project embodies the principles of open science, aiming to make data, methods, and findings accessible to all. 
 We aim to equip learners with the skills to analyze, visualize, and report on data related to these critical environmental risks through open science-based workflows and the use of cloud-based data computing.
@@ -24,7 +24,7 @@ We aim to equip learners with the skills to analyze, visualize, and report on da
 
 <!-- #region -->
 
-<img src="../assets/image165.png" width="800">
+![](../assets/image165.png)
 
 ### Availability of Open Science Resources:
 
@@ -47,7 +47,7 @@ We aim to equip learners with the skills to analyze, visualize, and report on da
 - And much more..
 
 
-<img src="../assets/image377.jpg" width="800">
+![](../assets/image377.jpg)
 
 <!-- #endregion -->
 
@@ -64,7 +64,7 @@ We aim to equip learners with the skills to analyze, visualize, and report on da
 
 Scientific knowledge, or research products, take the form of:
 
-<img src="../assets/image5.png" width="500">
+![](../assets/image5.png)
 
 ### What is data?
 
@@ -98,7 +98,7 @@ Results capture the different research outputs of the scientific process. Public
 Products are created throughout the scientific process that are needed to enable others to reproduce the findings. The products of research include data, code, analysis pipelines, papers, and more!
 
 
-<img src="../assets/image7.jpeg" width="800">
+![](../assets/image7.jpeg)
 
 
 

book/02_Geospatial_fundamentals/2_Selecting_an_AOI.md

@@ -12,6 +12,8 @@ jupyter:
     name: python3
 ---
 
+# Selecting an AOI
+
 Selecting and modifying Areas of Interest (AOIs) is an important part of geospatial data analysis workflows. The Python ecosystem of libraries provide a number ways to do this, some of which will be explored and demonstrated in this notebook. In particular, we will demonstrate the following: 
 1. How to specify AOIs in different ways
 2. How to use `geopandas` to load shapely geometries, visualize them, and perform operations such as `intersection`

book/03_Geospatial_data_files/geographic_data_formats.md

@@ -12,7 +12,7 @@ Line data is used to represent linear features. Common examples would be rivers,
 **Polygon data**
 Polygons are used to represent areas such as the boundary of a city (on a large scale map), lake, or forest.  Polygon features are two dimensional and therefore can be used to measure the area and perimeter of a geographic feature.^1^
 
-![points-lines-polygons-vector-data-types](../../assets/points-lines-polygons-vector-data-types.png)
+![points-lines-polygons-vector-data-types](../assets/points-lines-polygons-vector-data-types.png)
 
 <p style="text-align: center;">This image shows the three vector types: points, lines and polygons. Source: National Ecological Observatory Network.
 </p>

book/04_NASA_Earthdata/0_Configuracion_inicial.md

@@ -32,7 +32,7 @@ Para acceder al 2i2c Hub seguí estos sencillos pasos:
 ## 2- ¿Cómo utilizar el Earthdata de la NASA?
 
 
-#### Breve introducción
+### Breve introducción
 
 El programa **Earth Science Data Systems (ESDS)**, **Programa de Sistemas de Datos de Ciencias de la Tierra** de la NASA, supervisa el ciclo de vida de los datos científicos de la Tierra de todas sus misiones de observación de la Tierra, desde su adquisición hasta su procesamiento y distribución.
 

book/07_Wildfire_analysis/Retrieving_Disturbance_Data.md

@@ -12,6 +12,8 @@ jupyter:
     name: python3
 ---
 
+# Retrieving Disturbance Data
+
 The [OPERA DIST-HLS data product](https://lpdaac.usgs.gov/documents/1766/OPERA_DIST_HLS_Product_Specification_V1.pdf) can be used to study the impacts and evolution of wildfires at a large scale. In this notebook, we will retrieve data associated with the [2023 Greece wildfires](https://en.wikipedia.org/wiki/2023_Greece_wildfires) to understand its evolution and extent. We will also generate a time series visualization of the event.
 
 In particular, we will be examining the area around the city of [Alexandroupolis](https://en.wikipedia.org/wiki/Alexandroupolis) which was severely impacted by the wildfires, resulting in loss of lives, property, and forested areas.

book/_config.yml

@@ -3,22 +3,15 @@
 
 title: Reproducibly Analysing Wildfire, Drought, and Flood Risk with NASA Earthdata Cloud
 author: 2i2c / MetaDocencia
-logo: logo.png
+logo: assets/TOPS.png
+# Auto-exclude files not in the toc
+only_build_toc_files: true
 
 # Force re-execution of notebooks on each build.
 # See https://jupyterbook.org/content/execute.html
 execute:
   execute_notebooks: force
 
-# 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/ScienceCore/climaterisk  # Online location of your book
@@ -30,7 +23,6 @@ repository:
 html:
   use_issues_button: true
   use_repository_button: true
-
   use_multitoc_numbering: false
 
 launch_buttons:

book/_toc.yml

@@ -4,37 +4,31 @@
 format: jb-book
 root: intro
 parts:
-  - caption: About this Module
+  - caption: Open Science
     chapters:
-    - file: about_the_tutorial/disenio_leccion
-    - file: about_the_tutorial/Assessment_Activities
-    - file: about_the_tutorial/Learner_Personas
-    - file: about_the_tutorial/Module_Objectives
-    - file: about_the_tutorial/Outcomes
-    - file: about_the_tutorial/Requirements
-
-  - caption: Flood Module
+    - file: 01_Open_Science/Open_Science_Intro
+
+  - caption: Geospatial fundamentals
+    chapters:
+    - file: 02_Geospatial_fundamentals/2_Selecting_an_AOI
+    - file: 02_Geospatial_fundamentals/remote-sensing
+
+  - caption: Geospatial data files
+    chapters:
+    - file: 03_Geospatial_data_files/geographic_data_formats
+
+  - caption: NASA EarthData
     chapters:
-    - file: remote-sensing
-    - file: earthdata-cloud
-    - file: flood
-    - file: 1_Getting_Started_text
-    - file: 1_Getting_Started
-    - file: 1_ES_Primeros_pasos
-    - file: notebooks/2_ES_Flood
-    - file: SLIDES-NASA-TOPS-setup
-    - file: SLIDES-NASA-TOPS-flood
+    - file: 04_NASA_Earthdata/0_Initial_Setup
+    - file: 04_NASA_Earthdata/0_Configuracion_inicial
 
-  - caption: Drought Module
+  - caption: Wildfire Analysis
     chapters:
-    - file: drought
+    - file: 07_Wildfire_analysis/Retrieving_Disturbance_Data
+    - file: 07_Wildfire_analysis/Wildfire
 
-  - caption: Wildfire Module
+  - caption: Flood Analysis
     chapters:
-    - file: wildfire
-
-  - caption: Appendix
-    chapters: 
-    - file: proposal
-      title: TOPS-T Proposal
+    - file: 08_Flood_analysis/3_Retrieving_FloodData
+    - file: 08_Flood_analysis/flood
 

book/intro.md

@@ -2,7 +2,6 @@
 
 ![](assets/banner.jpg)
 
-
 GitHub Repo: https://github.com/ScienceCore/climaterisk