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OCNS / CompNeuroCookBook

Software development guidelines, maintained by the INCF/OCNS Software Working Group
https://ocns.github.io/CompNeuroCookBook/index.html
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References for Python guidelines #4

Closed sanjayankur31 closed 1 year ago

sanjayankur31 commented 3 years ago

Please collect Python specific bits here.

sanjayankur31 commented 3 years ago
sanjayankur31 commented 3 years ago
brenthuisman commented 3 years ago

Python docstrings and Sphinx: Napoleon Doxygen/Sphinx integration: Breathe, Exhale Doxygen alternative: https://www.copperspice.com/docs/doxypress/index.html

mstimberg commented 3 years ago

Very relevant initiative in general: https://www.pyopensci.org/ Here their requirements for packages they review: https://www.pyopensci.org/contributing-guide/authoring/overview.html I like their approach of having good/better/best recommendations (I think I mentioned this somewhere already, but at the time I did not have the link at hand) – it avoids making recommendations/requirements feel unachievable for "common researchers" (of the form "you definitely need to provide a docker container, make sure to set up your own testing server, so you can test run your software on exotic hardware, and if your lines are longer than 79 character, don't even bother publishing it").

sanjayankur31 commented 3 years ago

Looks very good. I'll update my WIP to use this system. Not been able to find a lot of time to work on these yet, unfortunately.

sanjayankur31 commented 3 years ago

Structuring Your Project — The Hitchhiker's Guide to Python

For new projects

mstimberg commented 3 years ago

A forthcoming book (also freely available under CC license): Research Software Engineering with Python

mstimberg commented 3 years ago

"This is a tutorial with a template for packaging, testing, documenting, and publishing scientific Python code." scientific-python-cookiecutter

mstimberg commented 2 years ago

Writing good research code

This repo contains the slides and code for a presentation on writing research software I first gave in January 2021 to the PhD students in neuro at Harvard. It's a compendium of 5 lessons I learned the hard way about writing research code that won't bite back.

https://github.com/patrickmineault/research_code

mstimberg commented 2 years ago

Patrick Mineault now turned the material from my previous comment into a handbook: https://goodresearch.dev