Merge branch 'main' of https://github.com/geo-smart/mind-the-chl-gap

.github/workflows/deploy.yml

@@ -0,0 +1,53 @@
+name: deploy-book
+
+on:
+  # Trigger the workflow on push to main branch and book dir
+  push:
+    branches:
+      - main
+    paths:
+      - book/**
+env:
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  deploy-book:
+    runs-on: ubuntu-latest
+    # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+    permissions:
+      pages: write
+      id-token: write
+    steps:
+      - uses: actions/checkout@v3
+
+      # 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
+
+      # 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@v2
+        with:
+          path: "book/_build/html"
+
+      # Deploy the book's HTML to GitHub Pages
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2

.gitignore

@@ -99,6 +99,7 @@ venv.bak/
 
 # mkdocs documentation
 /site
+/book/_build
 
 # mypy
 .mypy_cache/
@@ -109,3 +110,8 @@ venv.bak/
 *.hdf5
 *.nc
 *.tif
+
+# misc
+*.Rproj
+.Rproj.user
+.DS_Store

CONDUCT.md

@@ -0,0 +1,44 @@
+
+# Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team. The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4).

CONTRIBUTING.md

@@ -0,0 +1,22 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! 
+
+## Report Bugs or Questions
+
+Report bugs and questions using GitHub issues.
+
+## Contribute
+
+Ready to contribute? Here's how to set up `sample-jupyterbook-repository` for local development.
+
+1. Fork the repo on GitHub.
+2. Clone your fork locally.
+3. Install your local copy into a virtualenv, e.g., using `conda`.
+4. Create a branch for local development and make changes locally.
+5. Commit your changes and push your branch to GitHub.
+6. Submit a pull request through the GitHub website.
+
+## Code of Conduct
+
+Please note that the book project is released with a [Contributor Code of Conduct](CONDUCT.md). By contributing to this project you agree to abide by its terms.

README.md

@@ -1,23 +1,44 @@
 # mind-the-chl-gap
 
-### Neural network models for Chloraphyll-a gap-filling for remote-sensing products
+#### Neural network models for Chloraphyll-a gap-filling for remote-sensing products
 
-### Collaborators
+### 2024 GeoSMART Hackweek team:
 
-* 2024 [Shridhar Sinha](https://www.linkedin.com/in/shridhar-sinha-5b7125184/), University of Washington, Paul G. Allen School of Computer Science & Engineering, [email protected]
-* 2024 Yifei Hang, University of Washington, Applied & Computational Mathematical Sciences, [email protected]
-* 2023 [Jiarui Yu](https://www.linkedin.com/in/jiarui-yu-0b0ab522b/), University of Washington, Applied & Computational Mathematical Sciences
-* 2023 [Minh Phan](https://www.linkedin.com/in/minhphan03/), University of Washington, Applied & Computational Mathematical Sciences
-* mentor [Elizabeth Eli Holmes](https://eeholmes.github.io/), NOAA Fisheries, UW SAFS
+* Shridhar Sinha
+* Ares
+* Gabe
+* Qi
+* Andy
+* Eli
+* Robin
+
+### Hackweek notes
 
-2024 GeoSMART Hackweek team:
+Image to use for GPU if you need tensorflow `quay.io/pangeo/ml-notebook:2024.08.18`
 
 [Pitch slide](https://docs.google.com/presentation/d/1YfBLkspba2hRz5pTHG9OF3o9WHv-yNemZDq2QKFCme0/edit?usp=sharing)
 [Zotero library](https://www.zotero.org/groups/5595561/safs-interns-/library)
 [Google doc](https://docs.google.com/document/d/1ADjtPFMy5mDxWJ_jhFhUWaBvjSd54YAfcc3d6araPCs/edit?usp=sharing)
 
-* Shridhar Sinha
-* come join!
+The IO dataset is an analysis ready gridded zarr file for the Indian Ocean. It is in the Cryo hub. Load with
+```
+import xarray as xr
+ds = xr.open_zarr("~/shared-public/mind_the_chl_gap/IO.zarr")
+```
+- Copernicus level 3 Chl-a (globColour) `ds["CHL_cmes-level3"]`
+- Copernicus level 4 Chl-a (globColour) `ds["CHL_cmes-gapfree"]`
+- Environmental variables: SST, E-W & N-S surface wind, surface air temp, E-W & N-S currents, sea surface anomaly, mean ocean mixed layer thickness, salinity, bathymetry, 
+- 0.25 degree grid. So large but that makes it easier to work with.
+- 1972 to 2022 but Chl is 1997-2022
+
+
+### SAFS Varanasi Interns on this project
+
+* 2024 [Shridhar Sinha](https://www.linkedin.com/in/shridhar-sinha-5b7125184/), University of Washington, Paul G. Allen School of Computer Science & Engineering, [email protected]
+* 2024 Yifei Hang, University of Washington, Applied & Computational Mathematical Sciences, [email protected]
+* 2023 [Jiarui Yu](https://www.linkedin.com/in/jiarui-yu-0b0ab522b/), University of Washington, Applied & Computational Mathematical Sciences
+* 2023 [Minh Phan](https://www.linkedin.com/in/minhphan03/), University of Washington, Applied & Computational Mathematical Sciences
+* mentor [Elizabeth Eli Holmes](https://eeholmes.github.io/), NOAA Fisheries, UW SAFS
 
 
 ## Problem
@@ -60,18 +81,6 @@ The overarching goal for this hackweek is to compare physics informed neural net
 - perform sensitivity analysis to quantify the importance of each co-located environmental variable. We have not done that yet for any of our models.
 - use a model without Chl-a as a predictor variable and create Chl-a predictions for 1972 to present.
 
-### Data
-[Our dataset](https://safs-varanasi-internship.github.io/indian-ocean-zarr/) is an analysis ready gridded zarr file for the Indian Ocean. Load with
-```
-import xarray as xr
-ds = xr.open_zarr("~/shared-public/mind_the_chl_gap/IO.zarr")
-```
-- Copernicus level 3 Chl-a (globColour) `ds["CHL_cmes-level3"]`
-- Copernicus level 4 Chl-a (globColour) `ds["CHL_cmes-gapfree"]`
-- Environmental variables: SST, E-W & N-S surface wind, surface air temp, E-W & N-S currents, sea surface anomaly, mean ocean mixed layer thickness, salinity, bathymetry, 
-- 0.25 degree grid. So large but that makes it easier to work with.
-- 1972 to 2022 but Chl is 1997-2022
-
 ### Notebooks
 
 TBD. Will add to the notebooks folder before the hackweek starts.
@@ -89,4 +98,7 @@ We use fake clouds to create a test set for each image. Each image has missing v
 |:--:| 
 | *Both green + yellow have been observed for this image. For predicting, we treat the green as missing (fake clouds). We use the yellow as our observations that help inform our estimates. We predict the green and compare our predictions to the actual observations for the green pixels.* |
 
+## Building the book
+
+See the `README.md` in the `book` directory.
 

book/README.md

@@ -0,0 +1,31 @@
+# Jupyter Book
+
+Everything is here.
+
+`_config.yml` is set to not render the notebooks. So make sure to save in rendered format.
+
+### GitHub Action
+
+There is a GitHub Action that should build the book whenever there is a push to the `book` directory. 
+
+Set Pages to use a GitHub Action. If the Action does not run, then you will need to debug. Click on the Action that did not build and click on the part that had a problem.
+
+### Build locally and push to GitHub
+
+Do `pip install ghp-import` if needed. Then build book and push to GitHub. Set Pages to use `gh-pages` branch (which is going to disable deploying from the GitHub Action). These commands are run within the `book` directory.
+
+```
+cd /book
+jupyter-book build . --keep-going
+ghp-import -n -p -f _build/html
+```
+
+### Building Locally
+
+1. Open a terminal.
+2. Run `jupyter-book clean book/` to remove any existing builds
+3. Run `jupyter-book build book/`
+
+A fully-rendered HTML version of the book will be built in `book/_build/html/`.
+
+

book/_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                       : Mind the CHL Gap  # The title of the book
+author                      : geo-smart HackWeek  # The author of the book
+copyright                   : "2024"  # Copyright year to be placed in the footer
+logo                        : logo.jpg  # A path to the book logo
+
+# Whether to reexecute notebooks on each build.
+# See https://jupyterbook.org/content/execute.html
+execute:
+  execute_notebooks: off
+
+# 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/geo-smart/mind-the-chl-gap/book  # Online location of your book
+  path_to_book: 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)
+
+# 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

book/_toc.yml

@@ -0,0 +1,12 @@
+# Table of contents
+# Learn more at https://jupyterbook.org/customize/toc.html
+
+format: jb-book
+root: intro
+chapters:
+  - file: notebooks/IO_Zarr.md
+    title: Indian Ocean dataset
+  - file: notebooks/background.md
+    title: Background
+  - file: notebooks/IO_Zarr_visualizations.ipynb
+    title: Data visualizations

book/intro.md

@@ -0,0 +1,25 @@
+# Home
+
+## Neural network models for Chloraphyll-a gap-filling for remote-sensing products
+
+2024 GeoSMART Hackweek:
+
+[Pitch slide](https://docs.google.com/presentation/d/1YfBLkspba2hRz5pTHG9OF3o9WHv-yNemZDq2QKFCme0/edit?usp=sharing)
+[Zotero library](https://www.zotero.org/groups/5595561/safs-interns-/library)
+[Google doc](https://docs.google.com/document/d/1ADjtPFMy5mDxWJ_jhFhUWaBvjSd54YAfcc3d6araPCs/edit?usp=sharing)
+
+
+### Collaborators
+
+| Name | Affiliation | Role | email |
+| ------------- | ------------- | ------------- | ------------- |
+| [Elizabeth Eli Holmes](https://eeholmes.github.io/) | NOAA Fisheries, University of Washington SAFS| SAFS Varanasi mentor | [email protected] |
+[Shridhar Sinha](https://www.linkedin.com/in/shridhar-sinha-5b7125184/)  | University of Washington, Paul G. Allen School of Computer Science & Engineering | 2024 SAFS Varanasi Intern | [email protected] |
+| Yifei Hang  | University of Washington, Applied & Computational Mathematical Sciences | 2024 SAFS Varanasi Intern | [email protected] |
+| [Jiarui Yu](https://www.linkedin.com/in/jiarui-yu-0b0ab522b/) | University of Washington, Applied & Computational Mathematical Sciences | 2023 SAFS Varanasi Intern |  |
+| [Minh Phan](https://www.linkedin.com/in/minhphan03/)  | University of Washington, Applied & Computational Mathematical Sciences | 2023 SAFS Varanasi Intern |  |
+| Ares | | geo-smart HackWeek 2024 | |
+| Gabe | | geo-smart HackWeek 2024 | |
+| Qi Ge | | geo-smart HackWeek 2024 | |
+| Andy Barrett | | geo-smart HackWeek 2024 | |
+| Robin Clancy | | geo-smart HackWeek 2024 | |