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https://github.com/michaelakridge-noaa/open-science-codespaces

Zero Setup Open Science Codespaces. Quick and Easy Github Codespaces for RStudio, Tidyverse, Shiny, Python and more.
https://github.com/michaelakridge-noaa/open-science-codespaces

codespaces data-science devcontainer docker docker-compose geospatial jupyter-notebook python r rocker rstudio shiny streamlit tidyverse

Last synced: about 5 hours ago
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Zero Setup Open Science Codespaces. Quick and Easy Github Codespaces for RStudio, Tidyverse, Shiny, Python and more.

Host: GitHub
URL: https://github.com/michaelakridge-noaa/open-science-codespaces
Owner: MichaelAkridge-NOAA
License: other
Created: 2023-10-19T01:39:02.000Z (over 1 year ago)
Default Branch: main
Last Pushed: 2024-09-10T01:07:07.000Z (5 months ago)
Last Synced: 2024-09-10T04:28:43.597Z (5 months ago)
Topics: codespaces, data-science, devcontainer, docker, docker-compose, geospatial, jupyter-notebook, python, r, rocker, rstudio, shiny, streamlit, tidyverse
Language: Shell
Homepage:
Size: 5.63 MB
Stars: 15
Watchers: 3
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE.md

Awesome Lists containing this project

README

        # Open Science Codespaces



Quick & Easy Cloud Working Environments(Codespaces). This repo setups Github Codespaces for R/RStudio, python and more. These can be used for

- Reproducible Science Setups

- Workshops

- Portable Development

- and more!

### Contact: [email protected]

### Presentation: 

- Checkout a recent Presentation on Codespaces for Open Science  

### List of Codespaces

1. ### **[R Codespaces](#r-codespaces)**

    - RStudio

    - Tidyverse

    - Verse

    - Geospatial

    - Shiny Server

    - How to: [Install extra R Packages into Codespace](#faq-how-do-i-to-install-extra-packages-see-examples)

    - Codespace Example: [Environmental Data Summary (EDS) Project](https://github.com/MichaelAkridge-NOAA/ncei_eds_codespace)

2. ### **[Python Codespaces](#python-codespaces)**

    - [Python Codespaces](#links-to-various-python-based-codespaces)

    - Codespace Example: [Python Streamlit Web App | Data Explorer & Viz Tool](#python-codespaces)

4. ### **[Resources, Links & More Info](#resources-more-info)**

    - [Codespace Designer Tool ](#codespace-designer-tool)

    - [General Info about Codespaces/Docker](#general-info-about-codespacesdocker)

    - [Python Links](#python-links)

    - [R Links](#r-links)

# R Codespaces

Just click the button below to quickly start a codespace:

| Codespace   | QuickStart Link  | Description | 

| ----------- | ----------- |----------- |

| RStudio | [![Open RStudio in GitHub Codespaces](./docs/badge_rstudio.png)](https://codespaces.new/MichaelAkridge-NOAA/Open-Science-Codespaces?devcontainer_path=.devcontainer%2Frstudio%2Fdevcontainer.json)   |  Adds RStudio Server. Install R from source and set RSPM as default CRAN mirror	|

| RStudio Tidyverse | [![Open in GitHub Codespaces](./docs/badge_rstudio_tidyverse.png)](https://codespaces.new/MichaelAkridge-NOAA/Open-Science-Codespaces?devcontainer_path=.devcontainer%2Frstudio-tidyverse%2Fdevcontainer.json)   |Adds tidyverse packages & devtools. R packages for data science | 

| RStudio Verse | [![Open in GitHub Codespaces](./docs/badge_rstudio_tidyverse.png)](https://codespaces.new/MichaelAkridge-NOAA/Open-Science-Codespaces?devcontainer_path=.devcontainer%2Frstudio-verse%2Fdevcontainer.json)  | Adds tex & publishing-related package to tidyverse | 

| RStudio Geospatial |   [![Open in GitHub Codespaces](./docs/badge_rstudio_geospatial.png)](https://codespaces.new/MichaelAkridge-NOAA/Open-Science-Codespaces?devcontainer_path=.devcontainer%2Frstudio-geospatial%2Fdevcontainer.json)   | Adds geospatial packages | 

| RStudio Shiny Server| [![Open in GitHub Codespaces](./docs/badge_rstudio_shiny.png)](https://codespaces.new/MichaelAkridge-NOAA/Open-Science-Codespaces?devcontainer_path=.devcontainer%2Frstudio-shiny%2Fdevcontainer.json)   | Adds shiny server | 

### FAQ: How do I to install extra packages? See examples:

- [RStudio & Install R Packages via Dev Container Features ](.devcontainer/rstudio-example-01/)

- [RStudio & Install R Packages via dockerfile ](.devcontainer/rstudio-example-02/)

- [RStudio & Install R Packages via install.R File ](.devcontainer/rstudio-example-05/)

### Screenshots 



  

  

  



***

# [Environmental Data Summary (EDS) Codespace](https://github.com/MichaelAkridge-NOAA/ncei_eds_codespace)

[![Open RStudio in GitHub Codespaces](./docs/badge_rstudio.png)](https://codespaces.new/MichaelAkridge-NOAA/ncei_eds_codespace?quickstart=1)

RStudio Github Codespace with EDS project files. The EDS allows users to download/filter/extract/summarize large amounts of gridded and tabular data given user-defined time stamps and geographical coordinates. The various external environmental data summarized at individual survey sites can aid scientists to assess and understand how living marine resources are impacted by the environmental variabilities. 

## [(Learn More)](https://github.com/MichaelAkridge-NOAA/ncei_eds_codespace)

![](https://github.com/MichaelAkridge-NOAA/ncei_eds_codespace/blob/0db0a17a5ac59a0a77fb52568dd1841b45b5213b/docs/02.png)

***

# Python Codespaces

## Streamlit Python App Codespace Example | Data Explorer & Viz Tool

[![Open in GitHub Codespaces](./docs/badge_python.png)](https://codespaces.new/MichaelAkridge-NOAA/Open-Science-Codespaces?devcontainer_path=.devcontainer%2Fpython-streamlit-app-example%2Fdevcontainer.json)

- Exploratory Data Analysis & Visualization Tool. 

- Allows users to explore and visualize recent NOAA's National Coral Reef Monitoring Program(NCRMP) data or upload their own.

- This codespace example runs a python Streamlit App with Pygwalker(https://github.com/Kanaries/pygwalker) for data analysis and data visualization.

![](./docs/py_data_tool_00.png)

![](./docs/py_data_tool_01.png)

## Links to various python based codespaces.

| Codespace  | QuickStart Link | Description | 

| ----------- | ----------- |----------- |

|Streamlit Python App Codespace Example | [![Open in GitHub Codespaces](./docs/badge_python.png)](https://codespaces.new/MichaelAkridge-NOAA/Open-Science-Codespaces?devcontainer_path=.devcontainer%2Fpython-streamlit-app-example%2Fdevcontainer.json) | Data Explorer & Viz Tool App| 

| Jupyter Notebook  | [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/github/codespaces-jupyter)  |[github/codespaces-jupter](https://github.com/github/codespaces-jupyter) | 

| Jupyter Data Science  | [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/devcontainers-community/templates-jupyter-datascience-notebooks) |[devcontainers-community/jupyter-datascience-notebooks](https://github.com/devcontainers-community/templates-jupyter-datascience-notebooks) | 

| Flask  | [![Open in GitHub Codespaces](https://github.com/codespaces/badge.svg)](https://codespaces.new/github/codespaces-flask) | [github/codespaces-flask](https://github.com/github/codespaces-flask)| 

| Anaconda  |  | [devcontainers/templates/anaconda](https://github.com/devcontainers/templates/tree/main/src/anaconda)| 

| Datascience Py & R  |   | [microsoft/datascience-py-r](https://github.com/microsoft/datascience-py-r)| 

***

# Resources & More Info

## Codespace Designer Tool 



- Link: https://michaelakridge-noaa.github.io/codespace-designer/

- Use to configure a GitHub Codespace environment

- Powered by Github Pages to help design a codespace devcontainer file with NMFS-Opensci data science images

## General Info about Codespaces/Docker

- About Github Codespaces: https://github.com/features/codespaces

- About using images, dockerfiles, compose, and devcontainers: https://containers.dev/guide/dockerfile

- About Docker: https://docs.docker.com/

## Python Links

- Streamlit (https://streamlit.io/) turns data scripts into shareable web apps

- Pygwalker(https://github.com/Kanaries/pygwalker)  for data analysis and data visualization

## R Links

- The R codespaces use the images from the Rocker Project. For more info, please visit:

  - https://rocker-project.org/images/

  - https://hub.docker.com/u/rocker

----------

#### Disclaimer

This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project content is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.

##### License

See the [LICENSE.md](./LICENSE.md) for details