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cboettig committed Oct 22, 2024
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36 changes: 0 additions & 36 deletions .github/workflows/book.yml

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63 changes: 63 additions & 0 deletions .github/workflows/deploy.yml
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# This file was created automatically with `myst init --gh-pages` 🪄 💚

name: MyST GitHub Pages Deploy
on:
push:
# Runs on pushes targeting the default branch
branches: [main]
env:
# `BASE_URL` determines the website is served from, including CSS & JS assets
# You may need to change this to `BASE_URL: ''`
BASE_URL: '' #/${{ github.event.repository.name }}

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
contents: read
pages: write
id-token: write
# 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:
environment:
name: github-pages
url: ${{ steps.deployment.outputs.page_url }}
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4

- name: Setup Pages
uses: actions/configure-pages@v3

- uses: actions/setup-node@v4
with:
node-version: 18.x

- name: Install MyST Markdown
run: npm install -g mystmd

- name: Build HTML Assets
run: myst build --html

- name: Upload artifact
uses: actions/upload-pages-artifact@v3
with:
path: './_build/html'

#- name: Wait for artifact finalization
# run: sleep 30

- name: List uploaded artifacts
run: |
echo "Listing artifacts..."
curl -H "Authorization: Bearer ${{ secrets.GITHUB_TOKEN }}" \
"https://api.github.com/repos/${{ github.repository }}/actions/artifacts"
- name: Deploy to GitHub Pages
id: deployment
uses: actions/deploy-pages@v4
env:
ACTIONS_STEP_DEBUG: true
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13 changes: 6 additions & 7 deletions index.md
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Expand Up @@ -12,18 +12,17 @@ title: "ESPM-157: Data Science in Global Change Ecology"
</center>


::::{grid}
:gutter: 3
::::{grid} 1 1 2 2

:::{grid-item-card} Instructor Team
{material-regular}`person;2em;sd-text-primary` [Carl Boettiger](https://carlboettiger.info) [OH: 9a Friday by appt](https://berkeley.zoom.us/my/cboettig)
{material-regular}`person;2em;sd-text-primary` Amanda Wik, TA.
{material-regular}`person;2em;sd-text-primary` Tyler Bernard, TA. [OH: 11:30a Fridays](https://calendly.com/tgbernard19-berkeley/office-hours-2)
👤 [Carl Boettiger](https://carlboettiger.info) [OH: 9a Friday by appt](https://berkeley.zoom.us/my/cboettig)
👤 Amanda Wik, TA.
👤 Tyler Bernard, TA. [OH: 11:30a Fridays](https://calendly.com/tgbernard19-berkeley/office-hours-2)
:::

:::{grid-item-card} Logistics
{material-regular}`account_balance;2em;sd-text-primary` Wheeler 212
{material-regular}`calendar_month;2em;sd-text-primary` Mon/Weds noon-2pm
🏛 Wheeler 212
📅 Mon/Weds noon-2pm
:::

::::
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41 changes: 41 additions & 0 deletions myst.yml
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# See docs at: https://mystmd.org/guide/frontmatter
version: 1
project:
title: "Data Science for Global Change Ecology"
# description:
# keywords: []
# authors: []
github: https://github.com/espm-157/website
# To autogenerate a Table of Contents, run "myst init --write-toc"
license:
code: MIT
content: CC-BY-4.0
jupyter:
lite: true
toc:
# Auto-generated by `myst init --write-toc`
- file: index.md
- title: Overview
children:
- file: overview/syllabus.md
- file: overview/schedule.md
- title: Textbook
children:
- file: reading/00-preface.md
- file: reading/01-github-jupyter.md
- file: reading/02-visualization-basics.ipynb
- file: reading/03-data-access.md
- file: reading/04-transform.ipynb
- file: reading/05-ibis-1.ipynb
- file: reading/06-ibis-2.ipynb
- file: reading/06-ibis-3.ipynb
- file: reading/07-ibis-4.ipynb

site:
template: book-theme
options:
favicon: logo.png
logo: hex.png
title: "Data Science for Global Change Ecology"
domains:
- espm-157.carlboettiger.info
71 changes: 35 additions & 36 deletions overview/schedule.md
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# {material-regular}`view_module` Module Overview
# 🧰 Module Overview


::::{grid}
:gutter: 3

:::{grid-item-card} {material-regular}`device_thermostat;2em` Module 1: Global Climate Change
:::{grid-item-card} 🌡 Module 1: Global Climate Change
:columns: 6

{material-regular}`article;1.5em;sd-text-info` [Mann et al (1998)](https://doi.org/10.1038/33859)
{material-regular}`handyman;1.5em;sd-text-primary` Concepts: Tabular data, git
{material-regular}`auto_graph;1.5em;sd-text-warning` Communication: declarative visualization, jupyter notebooks
🖺 [Mann et al (1998)](https://doi.org/10.1038/33859)
🛠 Concepts: Tabular data, git
Communication: declarative visualization, jupyter notebooks

+++
<a href="https://github.com/espm-157/climate-python-template"><i class="i-simpleicons github"></i> climate template </a>

:::

:::{grid-item-card} {material-regular}`directions_boat;2em` Module 2: Global Fisheries Collapse
:::{grid-item-card} 🐟 Module 2: Global Fisheries Collapse
:columns: 6

{material-regular}`article;1.5em;sd-text-info` [Worm et al (2006)](https://doi.org/10.1126/science.1132294)
{material-regular}`handyman;1.5em;sd-text-primary` Concepts: Relational databases
{material-regular}`auto_graph;1.5em;sd-text-warning` Communication: Myst, pdf/LaTeX, html outputs
🖺 [Worm et al (2006)](https://doi.org/10.1126/science.1132294)
🛠 Concepts: Relational databases
📈 Communication: Myst, pdf/LaTeX, html outputs

+++
<a href="https://github.com/espm-157/fish-python-template"><i class="i-simpleicons github"></i> fish template </a>

:::

:::{grid-item-card} {material-regular}`satellite_alt;2em` Module 3: Environmental Justice
:::{grid-item-card} 🛰 Module 3: Environmental Justice
:columns: 6



{material-regular}`article;1.5em;sd-text-info` [Schell et al (2020)](https://doi.org/10.1126/science.aay4497)
{material-regular}`handyman;1.5em;sd-text-primary` Concepts: Geospatial data structures + analysis
{material-regular}`auto_graph;1.5em;sd-text-warning` Communication: Geospatial visualziation
🖺 [Schell et al (2020)](https://doi.org/10.1126/science.aay4497)
🛠 Concepts: Geospatial data structures + analysis
📈 Communication: Geospatial visualziation

+++
<a href="https://github.com/espm-157/spatial-python-template"><i class="i-simpleicons github"></i> spatial template </a>

:::

:::{grid-item-card} {material-regular}`smart_toy;2em` Module 4: Language Models and Decision support tools?
:::{grid-item-card} 🤖 Module 4: Language Models and Decision support tools?
:columns: 6

{material-regular}`article;1.5em;sd-text-info` TBD
{material-regular}`handyman;1.5em;sd-text-primary` LLMs, RAG,
{material-regular}`auto_graph;1.5em;sd-text-warning` `streamlit`, reactive design
🖺 TBD
🛠 LLMs, RAG,
📈 `streamlit`, reactive design

+++
<a href="https://github.com/espm-157/llm-python-template"><i class="i-simpleicons github"></i> llm template </a>
Expand All @@ -63,26 +63,25 @@



# {material-regular}`calendar_month` Weekly Plan
# 📅 Weekly Plan

Hold on tight and don't put too much faith in this.


Week | Module | Topics | Reading links
---------|---------------------------------------------|----------------------------|-------------------------
week 1 | {material-regular}`device_thermostat;1.5em` | GitHub, JupyterHub | [{material-regular}`book;1.5em;sd-text-info`](/reading/01-github-jupyter/)
week 2 | {material-regular}`device_thermostat;1.5em` | viz: `seaborn` | [{material-regular}`book;1.5em;sd-text-info`](/reading/02-visualization-basics/)
week 3 | {material-regular}`device_thermostat;1.5em` | data: `pandas` / `ibis` | [{material-regular}`book;1.5em;sd-text-info`](/reading/03-data-access/)
week 4 | {material-regular}`device_thermostat;1.5em` | Collab, PRs, CI | [{material-regular}`book;1.5em;sd-text-info`](/reading/04-transform/)
week 5 | {material-regular}`directions_boat;1.5em` | Module intro | [{material-regular}`book;1.5em;sd-text-info`](/reading/05-ibis-1/)
week 6 | {material-regular}`directions_boat;1.5em` | RDBs, joins | [{material-regular}`book;1.5em;sd-text-info`](/reading/05-ibis-2/)
week 7 | {material-regular}`directions_boat;1.5em` | discovery | [{material-regular}`book;1.5em;sd-text-info`](/reading/05-ibis-3/)
week 8 | {material-regular}`satellite_alt;1.5em` | spatial data types | [{material-regular}`book;1.5em;sd-text-info`](#)
week 9 | {material-regular}`satellite_alt;1.5em` | spatial data viz | [{material-regular}`book;1.5em;sd-text-info`](#)
week 10 | {material-regular}`satellite_alt;1.5em` | spatial data analysis | [{material-regular}`book;1.5em;sd-text-info`](#)
week 11 | {material-regular}`satellite_alt;1.5em` | putting it together | [{material-regular}`book;1.5em;sd-text-info`](#)
week 12 | {material-regular}`smart_toy;1.5em` | LLMs | [{material-regular}`book;1.5em`](#)
week 13 | {material-regular}`smart_toy;1.5em` | LLMs+RAG? | [{material-regular}`book;1.5em`](#)
week 14 | {material-regular}`smart_toy;1.5em` | `streamlit` | [{material-regular}`book;1.5em`](#)
week 15 | {material-regular}`school;1.5em` | Final Projects | [{material-regular}`book;1.5em`](#)

Week | Module | Topics | Reading links
---------|--------|----------------------------|-------------------------
week 1 | 🌡 | GitHub, JupyterHub | [{📖](/reading/01-github-jupyter/)
week 2 | 🌡 | viz: `seaborn` | [{📖](/reading/02-visualization-basics/)
week 3 | 🌡 | data: `pandas` / `ibis` | [{📖](/reading/03-data-access/)
week 4 | 🌡 | Collab, PRs, CI | [{📖](/reading/04-transform/)
week 5 | 🐟 | Module intro | [{📖](/reading/05-ibis-1/)
week 6 | 🐟 | RDBs, joins | [{📖](/reading/05-ibis-2/)
week 7 | 🐟 | discovery | [{📖](/reading/05-ibis-3/)
week 8 | 🛰 | spatial data types | [{📖](#)
week 9 | 🛰 | spatial data viz | [{📖](#)
week 10 | 🛰 | spatial data analysis | [{📖](#)
week 11 | 🛰 | putting it together | [{📖](#)
week 12 | 🤖 | LLMs | [{📖](#)
week 13 | 🤖 | LLMs+RAG? | [{📖](#)
week 14 | 🤖 | `streamlit` | [{📖](#)
week 15 | 🎓 | Final Projects | [{📖](#)
2 changes: 1 addition & 1 deletion overview/syllabus.md
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# {material-regular}`gavel` Syllabus
# Syllabus

**ESPM-157: Data Science in Global Change Ecology**

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4 changes: 2 additions & 2 deletions reading/01-github-jupyter.md
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Expand Up @@ -49,11 +49,11 @@ There's a few one-time setup steps we need to work with Git and GitHub from Jupy

Try to `clone` our "authentication" repo, <https://github.com/espm-157-f24/auth> into your Jupyterhub using the Clone Repository button from the Git menu (left side). (We will review this together in class).

![](/_static/img/git-clone.png)
![](https://github.com/espm-157/website/blob/main/_static/img/git-clone.png?raw=true)

Then use the "File" menu on the left side to open the `auth` folder and then opn the Jupyter Notebook, `github-login.ipynb`. Try running the cell in that notebook.

![](/_static/img/file-menu.png)
![](https://github.com/espm-157/website/blob/main/_static/img/file-menu.png?raw=true)


Tada! You have authenticated with GitHub on your Jupyterhub. In future, you will only need to re-open this login notebook to authenticate, as it will remain on your JupyterHub.
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8 changes: 4 additions & 4 deletions reading/02-visualization-basics.ipynb

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14 changes: 7 additions & 7 deletions reading/04-transform.ipynb

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