Update docs

[emmleroy]

Summary

This PR updates the docs for quant-aq/cli and fixes various bugs

Changes

• Updated Usage section of docs
• Updated API Reference
• Example notebook in notebooks/example.ipynb

Bug fixes

• Merge command now collapses duplicated columns if they are identical
• Flagging and expunging requires schema validation

Previewing docs

• docs are built upon release in gh-actions but they can be previewed by pulling the branch and running
  $ poetry run sphinx-build -b html -E docs docs/_build
$ open docs/_build/index.html

Questions for Review

• merge_files() operates on files, but maybe this should operate on pandas DataFrames instead (i.e. merge_dataframes()) --> in the notebook example, we save the previous output to a temporary csv file before merging.

[dhhagan]

I think this generally looks good, except that I believe we're missing all of the API docs for the actual library itself, no? We should make sure the actual underlying library is documented, probably alongside quantaq-cli under "API Reference".

[dhhagan]

This should probably be a dev dep, no?

[emmleroy]

moved jupyter to dev deps in 14da369!

[codecov]

Codecov Report

❌ Patch coverage is 91.91176% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 91.74%. Comparing base (8f1fbf6) to head (23f2ab6).
⚠️ Report is 1 commits behind head on emmleroy-v1.0.0.

Files with missing lines	Patch %	Lines
quantaq_cli/toolkit/merge.py	75.00%	8 Missing ⚠️
quantaq_cli/toolkit/flag.py	85.71%	2 Missing ⚠️
quantaq_cli/cli.py	90.90%	1 Missing ⚠️

Additional details and impacted files

@@                 Coverage Diff                 @@
##           emmleroy-v1.0.0      #34      +/-   ##
===================================================
+ Coverage            91.39%   91.74%   +0.35%     
===================================================
  Files                   23       24       +1     
  Lines                 1162     1260      +98     
===================================================
+ Hits                  1062     1156      +94     
- Misses                 100      104       +4     

Flag	Coverage Δ
unittests	91.74% <91.91%> (+0.35%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines	Coverage Δ
quantaq_cli/__init__.py	100.00% <100.00%> (ø)
quantaq_cli/log.py	59.09% <100.00%> (ø)
quantaq_cli/toolkit/__init__.py	100.00% <100.00%> (ø)
quantaq_cli/toolkit/expunge.py	85.71% <ø> (+6.54%)	⬆️
quantaq_cli/toolkit/resample.py	87.50% <ø> (ø)
tests/test_clean.py	100.00% <100.00%> (ø)
tests/test_expunge.py	92.30% <100.00%> (+0.08%)	⬆️
tests/test_flag.py	100.00% <100.00%> (ø)
tests/test_merge.py	100.00% <100.00%> (ø)
tests/test_resample.py	100.00% <100.00%> (ø)
... and 3 more

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[emmleroy]

I think this generally looks good, except that I believe we're missing all of the API docs for the actual library itself, no? We should make sure the actual underlying library is documented, probably alongside quantaq-cli under "API Reference".

Actually there is an updated API Reference! It's just that the docs site only builds/deploys upon release by gh-actions. You can still preview the updated docs by downloading the static build here: https://github.com/quant-aq/cli/actions/runs/29425224822/artifacts/8346972632