Generate complete Python and C++ API documentation with checked CI

[spraharsh]

Get a working docs page that is nice to look at

[codecov-commenter]

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 71.44%. Comparing base (f208883) to head (419f06c).
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Additional details and impacted files

@@            Coverage Diff             @@
##             main     #184      +/-   ##
==========================================
- Coverage   72.85%   71.44%   -1.42%     
==========================================
  Files         201      138      -63     
  Lines       16471     9833    -6638     
  Branches     1242     1242              
==========================================
- Hits        12000     7025    -4975     
+ Misses       4073     2413    -1660     
+ Partials      398      395       -3     

Flag	Coverage Δ
cpp	?
python	71.44% <ø> (+0.11%)	⬆️

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

Files with missing lines	Coverage Δ
pele/accept_tests/__init__.py	100.00% <ø> (ø)
pele/amber/read_amber.py	0.00% <ø> (ø)
pele/angleaxis/__init__.py	100.00% <ø> (ø)
pele/angleaxis/aamindist.py	75.36% <ø> (ø)
pele/angleaxis/rigidbody.py	78.45% <ø> (ø)
pele/basinhopping.py	72.22% <ø> (ø)
pele/distance/__init__.py	100.00% <ø> (ø)
pele/landscape/__init__.py	100.00% <ø> (ø)
pele/mc.py	65.00% <ø> (ø)
pele/mindist/minpermdist_stochastic.py	86.76% <ø> (ø)
... and 23 more

... and 63 files with indirect coverage changes

---

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[spraharsh]

@codex review

[chatgpt-codex-connector]

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-10-12T01:33:21.407702Z	8493971	Manual request

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• Comment "@codex review" or "@codex security review".

Codex reacts with 👀 while any review is running, comments if it has suggestions, and reacts with 👍 once all reviews finish with no findings.

[chatgpt-codex-connector]

Codex Review: Didn't find any major issues. Hooray!

Reviewed commit: 8493971531

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".