newgene / reusable-data-best-practices Public

A collaborative guidebook for informatics playbook

The live version is rendered at:

Any new commit push to this repo will trigger a rebuild, so you will see the latest changes from the above URL.

Chapter Template [DRAFT]

Each chapter should have the following sections:

Section Description Intended audience The chapters will cover heterogeous and not necessarily overlapping target audiences; therefore please include a short description to ensure readers’ time is wisely spent. Current version / status Guidance tbd, but some indication of whether the draft is early, actively soliciting comments, or ready to implement Lessons learned / summary This section is optional but encouraged in chapters where the source of truth for the majority of the content is external (Incorporated here by reference only) Why this is important Description of the problem and vision for what best practices will address or make possible Status and feedback mechanisms What stage is it in the development process? (See options below). Description and links for how people can comment, or contribute — whether via Google form or GitHub issue etc. Takeaway List A bulleted list of things you can read and implement (similar to top 10 PLoS Top 10 articles). Deep dive into takeaways Each item should include specific examples that demonstrate that practice XYZ is possible and offer some insight and evidence as to why doing it one way (vs. another) is better. Acknowledgements Key sources and or contributors. Note that references are most easily incorporated as hyperlinks rather than footnotes. This also makes it easier to read.

Chapter status

Chapter status What is in it What the stage means Stub Outline with importance and audience specified Open for high-level comments Early draft Outline and preliminary content Open for community contributions Ready for comment Mature draft Actively soliciting more in-depth community feedback Implementation-ready Mature draft revised in light of input Ready to be implemented, and evolved according to real world experince with it

Add google document to chapters

main.py allows you to convert a google document to a markdown file and add it to chapters. To use this run python main.py . The images will be downloaded to docs/_static and the document will be added to docs/chapters .

Instruction for making changes

  • This project requires credentials.json for the google doc apis to work. This has to be at the root folder of the project. See here how to get the credentials.json https://developers.google.com/docs/api/quickstart/js.

for the google doc apis to work. This has to be at the root folder of the project. See here how to get the https://developers.google.com/docs/api/quickstart/js. Every Sphinx related files are under docs folder.

  • index.rst file is the the top-level index page.
  • Each chapter goes under docs/chapters folder. They are markdown files.
  • If you need to include static contents (pictures, css, js files), put it under docs/_static folder.

How to create a new chapter

Create a new chapter file with the .md extension under docs/chapters. Typically you can name it as chapter_[number]_[brief name].md .

extension under docs/chapters. Typically you can name it as . Add your content in Markdown format in this file.

  • If you need to add a media file, upload it to docs/_static folder first, and then reference it in your markdown text.
  • Once you are done with the content (you can always come back to make changes later), add the reference to your new chapter file in docs/index.rst file.
  • Every time you commit your changes to github, after a few minutes, your changes will be compiled automatically and rendered on the live documentation site.

Option 1: Edit directly on github

Option 2: Clone the repo and edit locally and then push the changes

Useful resources:

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