Entire code base reformat with black. Added github workflow for ci.

[ejolly]

Also added vscode settings and recommended extensions

[codecov]

Codecov Report

Merging #379 (b16a029) into master (da5f37d) will decrease coverage by 0.11%.
The diff coverage is 74.16%.

❗ Current head b16a029 differs from pull request most recent head 86534f3. Consider uploading reports for the commit 86534f3 to get more accurate results

@@            Coverage Diff             @@
##           master     #379      +/-   ##
==========================================
- Coverage   70.47%   70.36%   -0.12%     
==========================================
  Files          31       31              
  Lines        5528     5520       -8     
==========================================
- Hits         3896     3884      -12     
- Misses       1632     1636       +4     

Impacted Files	Coverage Δ
nltools/data/brain_data.py	66.76% <ø> (ø)
nltools/datasets.py	0.00% <0.00%> (ø)
nltools/plotting.py	8.76% <0.00%> (ø)
nltools/stats.py	65.83% <ø> (-0.53%)	⬇️
nltools/tests/test_file_reader.py	100.00% <ø> (ø)
nltools/external/srm.py	75.86% <46.42%> (-0.24%)	⬇️
nltools/prefs.py	59.37% <47.36%> (ø)
nltools/utils.py	67.27% <47.36%> (ø)
nltools/analysis.py	51.77% <47.61%> (ø)
nltools/data/design_matrix.py	72.13% <53.48%> (-0.28%)	⬇️
... and 28 more

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[ejolly]

@ljchang This is ready to merge in. All tests are passing except for one which I think you might be able to fix. Any chance you can take a quick look: https://github.com/cosanlab/nltools/runs/2171188010?check_suite_focus=true#step:6:47

We're also having some weird platform issues around MAXINT on Windows, but fine on Ubuntu and macOS. As of now we don't support Python 3.9 as of yet because several of our dependencies are not Python 3.9 ready either. But 3.9 is still new enough that that's ok I think.

Also our sphinx auto-gallery all builds without errors now and I can hook it up to deploy somewhere. Did you still want to use readthedocs or should I switch it to github pages?

The total list of changes include:

• switching all CI to github actions which does the following:
  • checks code formatting via black and will kill build if a commit or PR isn't formatted
  • runs pytest with parallelization
  • runs code-coverage and pushes to coveralls.io
  • in a parallel to all of the above, sets up a separate system to that installs the package and uses it to build the docs including the auto-gallery. Then it builds the HTML and can be pushed somewhere (e.g. github pages, readthedocs, netlify)
• removing pretty much all traces of Python 2 code (e.g. from __future__ imports), six, etc
• Fixes support Path objects #369
• Fixes check that input to stats.fdr is between 0 and 1 #364
• Starts on Major refactoring #377
• Pins our max pandas version to < 1.2, because deepdish needs to support it first for all our .h5 support

[ljchang]

I'll start looking through code, I would like to move documentation to github if possible, sick of debugging RTD.

Is sphinx-gallery building on github actions? if so, that's awesome!

[ejolly]

ok @ljchang I fixed that failing test by giving our simulator classes a random seed and just pinning it for testing purposes. Also docs work great on gh-pages! https://cosanlab.github.io/nltools/

Did you want to setup up a custom domain? Will probably merge this PR in shortly.