Modernize infrastructure

[jGaboardi]

This PR:

• resolves migrate docs to GH Pages? #42
• resolves Modernize infrastructure  #43
• resolves add a codecov config file #44
  • swaps out setup.* for pyproject.toml
  • adopt setuptools_scm
  • ruff lints more strictly
  • adds pre-commit-config
  • cleans and reruns notebooks
  • remove old/superfluous files
    • all setup*.* (and related) files
    • all docs/{build,generated}* files (this accounts for the huge file diff)
  • adopts pytest over unittest
  • revamps docs & ensure docs build locally (and beautifully)
  • etc.

@martinfleis this isn't complete, but how's looking so far? Some questions/comments:

• Do we want to address migrate docs to GH Pages? #42 in this PR and add an action for it? And if so, shall we remove the RTD yaml?
• Should I put a release action in here even though we won't be able to use it yet?
• Anything obvious I am missing here?

[codecov]

Codecov Report

Merging #45 (593c7e6) into main (7939ea9) will increase coverage by 1.9%.
The diff coverage is 83.8%.

@@           Coverage Diff           @@
##            main     #45     +/-   ##
=======================================
+ Coverage   69.8%   71.7%   +1.9%     
=======================================
  Files          9       8      -1     
  Lines        999     760    -239     
=======================================
- Hits         697     545    -152     
+ Misses       302     215     -87     

Files	Coverage Δ
spglm/__init__.py	100.0% <100.0%> (ø)
spglm/family.py	84.3% <100.0%> (+2.1%)	⬆️
spglm/glm.py	97.0% <100.0%> (ø)
spglm/iwls.py	83.6% <100.0%> (+1.2%)	⬆️
spglm/varfuncs.py	77.4% <100.0%> (ø)
spglm/base.py	46.2% <66.7%> (+0.8%)	⬆️
spglm/links.py	63.3% <81.0%> (ø)
spglm/utils.py	48.1% <50.0%> (+20.2%)	⬆️

... and 1 file with indirect coverage changes

[martinfleis]

Great job!

[jGaboardi]

@martinfleis I think this PR is ready for review now. I have added the docs and release workflows, event though the release will not work until we get access to PyPI/spglm.

[martinfleis]

readthedocs.yml can go, so we don't build the docs twice, now that we have the action. Otherwise looks good, though it is a bit pain to review this :D.

[jGaboardi]

readthedocs.yml can go, so we don't build the docs twice, now that we have the action. Otherwise looks good, though it is a bit pain to review this :D.

No good deed goes unpunished. 🤣

[jGaboardi]

@martinfleis And it's been a long time since I've set up the GH-Pages stuff. Not sure I did it correctly... In Setting/Pages I simply changed the branch to main/root, but that doesn't feel right...

[martinfleis]

I've never done it (momepy still runs on RTD and its own domain) but you'll need to point it to gh-pages/root. But gh-pages branch does not exist yet. Not sure if the action will create it or it needs to be created and populated manually first.

[jGaboardi]

Perhaps @knaaptime can advise? But also, once this is reviewed and merged I can simply do some trial and error v1.1.0rcXX tag & releases (which will fail) to get the doc build sorted.

[knaaptime]

pretty sure the action will create the branch if necessary

[martinfleis]

@jGaboardi it seems that you should have all the rights you need to setup the publishing action with a token, right?

[jGaboardi]

@jGaboardi it seems that you should have all the rights you need to setup the publishing action with a token, right?

Yep, I just set that up right now. So once this PR is reviewed and merged we can give v1.1.0rc1 a go.

[martinfleis]

@jGaboardi What is the status here?

[jGaboardi]

Waiting for a review.