Add logging control

[mikemhenry]

Checklist

• Added a news entry

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

Fixes #1499

[codecov]

Codecov Report

❌ Patch coverage is 99.29078% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.00%. Comparing base (3648154) to head (1989f58).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/tests/utils/test_log_control.py	99.56%	1 Missing ⚠️
openfe/utils/logging_control.py	97.61%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1585      +/-   ##
==========================================
- Coverage   95.33%   93.00%   -2.34%     
==========================================
  Files         183      184       +1     
  Lines       15770    16033     +263     
==========================================
- Hits        15035    14911     -124     
- Misses        735     1122     +387     

Flag	Coverage Δ
fast-tests	93.00% <99.29%> (?)
slow-tests	?

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[mikemhenry]

pre-commit.ci autofix

[mikemhenry]

pre-commit.ci autofix

[mikemhenry]

pre-commit.ci autofix

[mikemhenry]

didn't fix the build:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/ext/autosummary/generate.py", line 503, in generate_autosummary_docs
    name, obj, parent, modname = import_by_name(entry.name)
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/ext/autosummary/__init__.py", line 655, in import_by_name
    raise ImportExceptionGroup('no module named %s' % ' or '.join(tried), exceptions)
sphinx.ext.autosummary.ImportExceptionGroup: no module named openfe.AlchemicalNetwork
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/events.py", line 97, in emit
    results.append(listener.handler(self.app, *args))
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/ext/autosummary/__init__.py", line 814, in process_generate_options
    generate_autosummary_docs(genfiles, suffix=suffix, base_path=app.srcdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/ext/autosummary/generate.py", line 508, in generate_autosummary_docs
    name, obj, parent, modname = import_ivar_by_name(entry.name)
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/ext/autosummary/__init__.py", line 712, in import_ivar_by_name
    real_name, obj, parent, modname = import_by_name(name, prefixes)
                                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/ext/autosummary/__init__.py", line 655, in import_by_name
    raise ImportExceptionGroup('no module named %s' % ' or '.join(tried), exceptions)
sphinx.ext.autosummary.ImportExceptionGroup: no module named openfe
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/cmd/build.py", line 293, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/application.py", line 272, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/application.py", line 343, in _init_builder
    self.events.emit('builder-inited')
  File "/home/docs/checkouts/readthedocs.org/user_builds/openfe/conda/1585/lib/python3.11/site-packages/sphinx/events.py", line 108, in emit
    raise ExtensionError(__("Handler %r for event %r threw an exception") %
sphinx.errors.ExtensionError: Handler <function process_generate_options at 0x77d92c224680> for event 'builder-inited' threw an exception (exception: no module named openfe)
Extension error (sphinx.ext.autosummary):
Handler <function process_generate_options at 0x77d92c224680> for event 'builder-inited' threw an exception (exception: no module named openfe)

I'll investigate this more once I get the FAQ doc finished

[mikemhenry]

This is what it looks like:

[mikemhenry]

Not sure if we need a news entry or not

[mikemhenry]

ez link to new docs:
https://openfe--1585.org.readthedocs.build/en/1585/guide/troubleshooting.html#jax-warnings

[IAlibay]

This looks good to me, but please let @atravitz have a look before merging.

[mikemhenry]

Do we want to prefix these classes with a _ to keep them private? Do we want this control in the public API?

[atravitz]

Not sure if we need a news entry or not

I'm in favor of a news entry that points to the new docs, since people have been raising this as a bug and might look for it in a CHANGELOG.

[mikemhenry]

hmm, @atravitz ruff wants to change this:

-from . import custom_typing
-from . import logging_control
+from . import custom_typing, logging_control

Maybe b/c its relative it is being weird, but I would rather have these on separate lines or

from . import (
    custom_typing, 
    logging_control,
)

so that the diff will be clean if we want to add more (or remove one)

[mikemhenry]

It looks like it was happy when I manually did it in this style:

from . import (
    custom_typing,
    logging_control,
)

not sure if we can automate that or not

[mikemhenry]

need to add the news bit still

[atravitz]

It looks like it was happy when I manually did it in this style:

from . import (
    custom_typing,
    logging_control,
)

not sure if we can automate that or not

I don't have a super strong opinion about this, the way you have it here is good though.

[atravitz]

Do we want to prefix these classes with a _ to keep them private? Do we want this control in the public API?

I like the idea of having it user facing at some point (could be helpful for colab headaches?). But let's make them private for now - we can always make them public in a follow-up PR.

[github-actions]

No API break detected ✅

[mikemhenry]

@atravitz Sounds good! Renamed everything

[atravitz]

looks great!