Python discussion: tools, pypi/conda, etc

[sckott]

chat with @tefirman on 2024-02-15

• conda: have a section discussing conda - suggest that folks maintaining packages should consider submitting their package to conda b/c conda is heavily used in our bioinformatics
• pyproject.toml file: steer people towards it for sure
• packaging tools:
  • https://packaging.python.org/en/latest/guides/tool-recommendations/
  • https://docs.conda.io/projects/conda-build/en/latest/user-guide/tutorials/build-pkgs.html
• docstring formatting: really important to include. styling of docstrings, tell them what way we prefer (taylor likes https://google.github.io/styleguide/pyguide.html#38-comments-and-docstrings). text editor support vs code: https://marketplace.visualstudio.com/items?itemName=njpwerner.autodocstring
  • maybe put under Style chapter
• python versions:
  • absolutely do not use python2
  • strong preference for python3.9 or greater
• security? maybe talk about things like https://socket.dev/ for their repos

[sckott]

updates on 2024-10-21

• given conda's pricing situation, maybe discourage conda use?
• given uv starting to get so much adoption, perhaps only talk about uv with respect to tooling just to have one golden path?