Topics to cover in Collaboration

[dcsoto]

Main tools to cover:

• [x] Share notebooks: static (GitHub, NBViewer, Kyso), interactive (Binder, Google Colab), comparative (NBreview) D
• [x] Share code: Git branching, simple GitFlow, code review (good reviewing practices) and good coding practices (linter, style guides) B
• [x] Share pipelines: workflows (Bash scripts, Make, Snakemake, Nextflow) D
• [x] Make tests: test correctness (pytest), test coverage (codecov), implement test pipeline (tox, Travis CI, GitHub actions) B
• [x] Make papers: Tools for collaborative manuscript writing (Manubot, Overleaf, Authorea, GDocs, Office 365) D

[dcsoto]

Share pipelines:

• Bash scripts (set -eo pipefail more info here)

[dcsoto]

Consider adding in this section:

• Common workflow language
• Citation Style Language
• Writing manuscript in LaTeX or R Markdown (https://github.com/svmiller/svm-r-markdown-templates)

[dcsoto]

Let's add a supplementary figure with an example of a wrong github branching structure and a right one.

[dcsoto]

I just realized there is a GitHub command line utility to avoid using the desktop application, maybe we want to include something about it briefly! Here there is more information: https://cli.github.com/

[BenjaSanchez]

@dcsoto great! will add it to the code section ;)