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.github/workflows/quarto.yaml

@@ -0,0 +1,25 @@
+on:
+  workflow_dispatch:
+  push:
+    branches: main
+
+name: Quarto Publish
+
+jobs:
+  build-deploy:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v3
+
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Render and Publish
+        uses: quarto-dev/quarto-actions/publish@v2
+        with:
+          target: gh-pages
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

README.md

@@ -9,9 +9,10 @@ This is the development repository of educational training materials we are buil
 
 ## Quickstart [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/espm-157/nasa-topst-env-justice?quickstart=1)
 
-Click _Open in GitHub Codespaces_ to try out this respository in a GitHub-hosted cloud instance.  This instance provides both VSCode or RStudio environments with most necessary packages already installed.  This environment can also be accessed in a local VSCode as a devcontainer or as a [Docker image](https://github.com/boettiger-lab/nasa-topst-env-justice/pkgs/container/nasa-tops).
+Click _Open in GitHub Codespaces_ to try out this repository in a GitHub-hosted cloud instance.  This instance provides both VSCode or RStudio environments with most necessary packages already installed.  This environment can also be accessed in a local VSCode as a [devcontainer](https://code.visualstudio.com/docs/devcontainers/containers) or as a [Docker image](https://github.com/boettiger-lab/nasa-topst-env-justice/pkgs/container/nasa-tops).
+
+Open [intro.ipynb](stac.ipynb) (_Python_) or [intro.qmd](intro.qmd) (_R_) notebooks to get started.  
 
-Open [intro.ipynb](stac.ipynb) (Python) or [intro.qmd](intro.qmd) (R) notebooks to get started.  
 
 ## Abstract
 

_quarto.yml

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+project:
+  type: website
+  output-dir: docs
+execute:
+  freeze: auto
+
+website:
+  sidebar:
+    style: "docked"
+    search: true
+    contents:
+      - file: index.qmd
+        icon: house
+        text: About
+      - text: JuypterHub
+        icon: pc-display-horizontal
+        href: https://openscapes.2i2c.cloud/
+      - icon: book
+        text: Catalog
+        href: https://radiantearth.github.io/stac-browser/#/external/raw.githubusercontent.com/schmidtDSE/biodiversity-catalog/main/stac/v1/catalog.json?.language=en
+      - icon: github
+        text: GitHub repo
+        href: https://github.com/boettiger-lab/nasa-topst-env-justice
+      - icon: globe-americas
+        text: Author Homepage
+        href: https://carlboettiger.info
+      - section: Examples
+        contents:
+          - text: Computing Environments
+            href: contents/computing-environment.qmd

contents/computing-environment.qmd

@@ -0,0 +1,86 @@
+---
+title: "Computing Environments"
+format: html
+---
+
+
+# Portable Reproducibility :onion:
+
+Noam Ross says that good reproducibility is like an onion :onion: -- it comes
+in many layers.  There's a purpose to containerized environments deployed on
+cloud-hosted virtual machines.  And we believe students should be able to leverage
+those things, easily and rapidly deploying cloud-hosted images, and will get
+to that here. But reproducibility doesn't often involve reconstructing many GB
+virtual computing environments from scratch.  Most of the time, we just want
+to copy-paste a few lines of code and expect it to work. Many layers lie between
+these two extremes -- from package dependencies and system dependencies to
+containers, orchestration, metadata, even hardware requirements.  
+
+In many cases, it should be sufficient to copy-paste code from the examples shown
+here into your preferred computational environment -- it's okay to grab just what
+you need, you don't have to take the whole onion. But it is also our goal to make
+it as easy as possible to grab the whole onion and take it where you want it --
+be that a local VSCode editor on your laptop, or an RStudio Server instance 
+running up on Microsoft Azure cloud.  
+
+## On the cloud: Codespaces
+
+By clicking the "open in codespaces" button on the README in GitHub, users
+will be placed into a free cloud-based virtual machine running a VSCode editor
+in their web browser.  
+This includes specific versions of R and python packages, the 
+latest releases of the OSGeo C libraries GDAL, PROJ, and GEOS that power
+many spatial operations in both languages.  These elements are pre-compiled
+in a Docker container based on the latest Ubuntu LTS release (22.04 at
+the time of writing), which itself is build according to the [Dockerfile](https://github.com/boettiger-lab/nasa-topst-env-justice/blob/main/.devcontainer/Dockerfile) 
+found in this repository using [a GitHub Action](https://github.com/boettiger-lab/nasa-topst-env-justice/actions/workflows/docker-image.yml).
+The [devcontainer.json configuration](https://github.com/boettiger-lab/nasa-topst-env-justice/blob/main/.devcontainer/devcontainer.json) will also set 
+up relevant VSCode extensions for working with python and R, including 
+interactivity for both Jupyter and Quarto notebooks.  Additionally, it will
+provide access to an RStudio Server environment on an embedded port for users
+who prefer that editor to VSCode.
+
+## Locally: VSCode
+
+Open this repository in a local [Visual Studio Code editor](https://code.visualstudio.com/) on a Mac, Linux, or Windows
+laptop and you will probably be prompted "Do you want to open this in project 
+in a Dev Container?" If you agree, VSCode will attempt to use a local Docker 
+installation to pull a container with much of the required software already
+installed. This uses the same Docker container and enables all the same 
+extensions in VSCode, including RStudio server on the embedded port.
+
+Of course, users can open this project in a local VSCode or any other favorite editor
+without opening in the devcontainer. The user assumes responsibility to install necessary software,
+i.e. the packages listed in `requirements.txt` or `install.R`.  Note that 
+doing so does not ensure that the same version of system libraries like GDAL,
+PROJ, or GEOS will necessarily be used. For most operations this should
+not matter, but users on older versions of GDAL may encounter
+worse performance or other difficulties.
+
+## Anywhere: Docker
+
+We can sidesteps elements specific to the VSCode editor defined in the
+[`devcontainer.json` configuration](https://github.com/boettiger-lab/nasa-topst-env-justice/blob/main/.devcontainer/devcontainer.json)
+while still leveraging the same system libraries and pre-built packages.
+For example, a user could also choose to run (or extend) 
+the underlying docker container independently, e.g.
+
+```bash
+docker run --rm -ti ghcr.io/boettiger-lab/nasa-tops:latest bash
+```
+
+which opens a bash terminal inside the container. This approach is also
+compatible with most HPC setups using [singularity](https://rocker-project.org/use/singularity.html) instead of docker.
+
+Some users may not be familiar with editing and running code entirely from a bash shell, so the container also includes RStudio server and thus can be run to launch RStudio in an open port instead,
+
+```bash
+docker run -d -p 8787:8787 --user root -e DISABLE_AUTH=true \
+  ghcr.io/boettiger-lab/nasa-tops:latest
+```
+
+and visit `http://localhost:8787` to connect. 
+
+
+
+

index.qmd

@@ -0,0 +1,15 @@
+---
+title: "NASA TOPS-T Module"
+format: html
+---
+
+
+<img align="right" src="https://zenodo.org/record/7742997/files/Tops_Badge_Nasa.png" width="150" alt="Transform to Open Science Logo that shows a top as a rocket taking off and the text Transform to Open Science in the white vapor plume around the launch site">
+
+[![Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+[![Docker Image :whale2:](https://github.com/boettiger-lab/nasa-topst-env-justice/actions/workflows/docker-image.yml/badge.svg)](https://github.com/boettiger-lab/nasa-topst-env-justice/actions/workflows/docker-image.yml)
+
+
+---
+
+[![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/espm-157/nasa-topst-env-justice?quickstart=1)

intro.qmd

@@ -0,0 +1,6 @@
+---
+title: "Introduction: R"
+format: html
+---
+
+