Clean up directory structure & convert notebooks to .md files

[dhavide]

Roughly speaking, this is what is needed:

• Convert all existing notebook (i.e., .ipynb) files to Markdown(.md) files, e.g.,

  jupytext notebook.ipynb --output notebook.md
  # Equivalently,
  # jupytext notebook.ipynb -o notebook.md

  The current environment.yaml file includes jupytext so try updating your environment if jupytext is not installed locally.

  To be safe, make sure that the files are converted correctly by doing a round-trip conversion and using diff to ensure that the original .ipynb file is restored correctly. There will be some differences (e.g., in cell labels) but those can safely be ignored.

• Introduce a directory structure that looks something like this:
  
  (use numbered directories in sequence according to the diagram so that the intended order is clear, e.g., 01_Open_Science/, 02_Geospatial_fundamentals/, etc. Use the sequence as in the diagram for now; that may change later).
  Move MarkDown files (and whatever else) into the appropriate directories. This may break relative links to, e.g., image files in the assets folder. Check to make sure these links are correct before checking in.

• Use a directory called, e.g., scratch to store files that currently do not have an obvious place; they most likely have a future use.

[jnywong]

Heya 👋 Let me know if I can help with this one @JFormoso – seems like a pretty fundamental infrastructure issue that needs attention before work on #40 can start.

[JFormoso]

Hi @dhavide and @jnywong! This is what I got so far, I am not sure about the location of many of the files, such as the nb to select AOI, and remote sensing, which I included in geospatial fundamentals. Also, many notebooks seem to be placeholders.
This is the current structure:

│ .gitignore
│ apt.txt
│ CONDUCT.md
│ CONTRIBUTING.md
│ environment.yml
│ LICENSE
│ README.md
│ requirements.txt
│
├───.github
│ └───workflows
│ build.yml
│ deploy.yml
│
├───assets
│ 2i2c_login.png
│ 2i2c_logo.png
│ banner.jpg
│ banner_with_person.jpg
│ climate_risks_cloud_data_filled.png
│ climate_risks_cloud_data_filled.svg
│ climate_risks_cloud_data_line.png
│ climate_risks_cloud_data_line.svg
│ climate_risks_drought_color.png
│ climate_risks_drought_filled.png
│ climate_risks_drought_filled.svg
│ climate_risks_drought_line.png
│ climate_risks_drought_line.svg
│ climate_risks_fire_color.png
│ climate_risks_fire_filled.png
│ climate_risks_fire_filled.svg
│ climate_risks_fire_line.png
│ climate_risks_fire_line.svg
│ climate_risks_flood_color.png
│ climate_risks_flood_filled.png
│ climate_risks_flood_filled.svg
│ climate_risks_flood_line.png
│ climate_risks_flood_line.svg
│ climate_risks_remote_sensing_filled.png
│ climate_risks_remote_sensing_filled.svg
│ climate_risks_remote_sensing_line.png
│ climate_risks_remote_sensing_line.svg
│ earthdata_login.png
│ earthdata_profile2.png
│ earthdata_profile_old.png
│ image165.png
│ image377.jpg
│ image5.png
│ image7.jpeg
│ logo.png
│ MD_logo.png
│ points-lines-polygons-vector-data-types.png
│ SETUP1.png
│ start_server.png
│ TOPS.png
│ work_environment_jupyter_lab.png
│
└───book
│ _config.yml
│ _toc.yml
│
├───01_Open_Science
│ Open_Science_Intro.md
│ Open_Science_Intro_Slides.md
│
├───02_Geospatial_fundamentals
│ 2_Selecting_an_AOI.md
│ remote-sensing.md
│
├───03_Geospatial_data_files
│ geographic_data_formats.md
│
├───04_NASA_Earthdata
│ 0_Configuracion_inicial.md
│ 0_Initial_Setup.md
│ 1_Getting_Started.md
│ earthdata-cloud.md
│
├───05_2i2c_Hub
├───06_Python_APIs
├───07_Wildfire_analysis
│ Retrieving_Disturbance_Data.md
│ Wildfire.md
│
├───08_Flood_analysis
│ 3_Retrieving_FloodData.md
│ flood.md
│
└───09_Scratch
│ .netrc
│ 4_Analyzing_Datasets.md
│ 5_Manipulating_and_Visualizing_Datasets.md
│ drought.md
│ intro.md
│ proposal.md
│ references.bib
│ SLIDES-NASA-TOPS-flood-EN.md
│ SLIDES-NASA-TOPS-flood-ES.md
│
├───about_the_tutorial
│ Assessment_Activities.md
│ disenio_leccion.md
│ Learner_Personas.md
│ Module_Objectives.md
│ Outcomes.md
│ Requirements.md
│
└───notebooks
2_ES_Flood.md

Let me know what I need to change.

Regarding the files, I converted all files to .md, did the round-trip conversion, use diff to check if the conversion was done properly.

[PatriLoto]

Hi @JFormoso and @dhavide .I just wanted to let you know that the files 1_Getting_Started_text.md
and earthdata-cloud.md are no longer needed because their contents are included in the Initial_setup.md file.

[JFormoso]

Thanks Patri, I'll correct that!

[jnywong]

Hey @JFormoso I'm happy with this directory structure! The assets directory will need to move into the book folder for the Jupyter Book to find the image files however.

Can I double-check that the 09_Scratch/intro.md should be the "homepage" for the tutorial?

[JFormoso]

Hi @jnywong I really don't know if the intro.md file is the future homepage. All ask at Friday's meeting. I made the changes you suggested, I am not sure if the pull request shows them or how to merge that. Let me know!

[jnywong]

Closed by pull requests #70 and #73