Docs/701 pathfinder

[mitzimorris]

Submission Checklist

• Run unit tests
• Declare copyright holder and open-source license: see below

Summary

Added references to Pathfinder throughout docs and docstrings in code.

(Note: Sphinx documentation builds, but page api.rst triggers complaint about bad anonymous reference. cannot track down the problem, but the documentation looks good on my machine. discussion on Sphinx issue tracker says basically "too much preprocessing going on". sphinx-doc/sphinx#6036 (comment))

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company): Columbia University

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)

[mitzimorris]

failing because of stanio?

[WardBrian]

where are you seeing failures from stanio?

[codecov-commenter]

Codecov Report

Merging #707 (3ba5f11) into develop (d4839e0) will decrease coverage by 0.13%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##           develop     #707      +/-   ##
===========================================
- Coverage    79.72%   79.60%   -0.13%     
===========================================
  Files           25       50      +25     
  Lines         3793     7590    +3797     
===========================================
+ Hits          3024     6042    +3018     
- Misses         769     1548     +779     

see 33 files with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[mitzimorris]

where are you seeing failures from stanio?

not a problem - I was concerned it might be because running mypy locally produces these errors:

mypy cmdstanpy
cmdstanpy/utils/json.py:4: error: Cannot find implementation or library stub for module named "stanio"  [import]
cmdstanpy/stanfit/metadata.py:6: error: Cannot find implementation or library stub for module named "stanio"  [import]
cmdstanpy/stanfit/metadata.py:6: note: See https://mypy.readthedocs.io/en/stable/running_mypy.html#missing-imports
cmdstanpy/utils/data_munging.py:7: error: Cannot find implementation or library stub for module named "stanio"  [import]
Found 3 errors in 3 files (checked 25 source files)

maybe my local setup is defective somehow?

[mitzimorris]

Windows tests failing - can't compile models - PCH header problems? Boost problems?

[WardBrian]

Windows tests were broken by this release of the Github Actions OS images. They bumped Mingw from 11.2 to 12.2, so we need similar flags set as RTools 43.

I have a temporary fix in #691 but it probably deserves a closer look

[mitzimorris]

regarding RTools, install_cxx_toolchain installs RTools 4.0. bump that to 4.3? (and update installation docs)

[WardBrian]

We should probably do that at some point, I'm hoping we can figure out a way that doesn't require this extra config first (stan-dev/math#2948)

[WardBrian]

Thanks for this, a lot of much-needed cleanups

[mitzimorris]

ready for re-review.

[WardBrian]

Thank you!

[WardBrian]

We know the failures aren't from this PR so I think it's all safe to merge