chore: refactor pytest fixtures and sync pyproject.toml and pre-commit file with main

[cadenmyers13]

The manual edits are in conftest.py, pyproject.toml, .pre-commit-config.yaml, and small FIXME's so black and docformatter agree. All other edits are from docformatter and should mirror the edits made in PR #184

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 79.07%. Comparing base (0b16bfd) to head (d2c26d6).
⚠️ Report is 1 commits behind head on v3.3.0.

Additional details and impacted files

@@            Coverage Diff             @@
##           v3.3.0     #188      +/-   ##
==========================================
- Coverage   79.08%   79.07%   -0.02%     
==========================================
  Files          25       25              
  Lines        3821     3818       -3     
==========================================
- Hits         3022     3019       -3     
  Misses        799      799              

Files with missing lines	Coverage Δ
tests/conftest.py	92.21% <100.00%> (-0.69%)	⬇️
tests/test_builder.py	100.00% <ø> (ø)
tests/test_characteristicfunctions.py	12.38% <ø> (+0.11%)	⬆️
tests/test_constraint.py	98.30% <ø> (ø)
tests/test_equation.py	100.00% <ø> (ø)
tests/test_fitrecipe.py	99.85% <ø> (ø)
tests/test_literals.py	99.17% <ø> (ø)
tests/test_objcrystparset.py	10.27% <ø> (ø)
tests/test_profile.py	99.52% <ø> (ø)
tests/test_recipeorganizer.py	99.73% <ø> (ø)
... and 2 more

🚀 New features to boost your workflow:

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

[cadenmyers13]

@sbillinge ready for review. The manual edits here are copied over from main (with the exception of the FIXME's).

[sbillinge]

@cadenmyers13 this won't merge for some reason. It is saying it is out of date with head or something like that

[sbillinge]

Btw I don't remember why we are using v3.3.0 as our base branch
Does anyone remember?

[stevenhua0320]

I got the reason why we previously open this branch, it is because at that time we were busy with the CamelCase deprecation job and we decide open a branch to perform all the actions there and then when we are done with this we would merge v3.3.0 into main. But seems that in the meanwhile there is some commits that are merged to main.

[cadenmyers13]

@sbillinge what @stevenhua0320 said ^^^

this won't merge for some reason. It is saying it is out of date with head or something like that

That is odd, this is what it looks like on my end:

I pushed an empty commit. did that fix it?

[stevenhua0320]

If still the issue persists, the safest thing we could do is to revert the changes on main with pre-commit and python 3.14 bump. Those two PRs we could redo it after this branch be merged.

[sbillinge]

OK, that seemed to have fixed it. It merged successfully now.

[sbillinge]

@cadenmyers13 @stevenhua0320 does it make sense to merge main into this branch? Please check that this won't break anything, but I think it should just be a couple of edits.

Then how do we test this before merging into main and releasing? I guess that if all tests are passing and all tutorial examples in diffpy.cmi are passing in an env that contains this version, then we can feel secure enough to merge it into main and make a release?

[stevenhua0320]

@sbillinge I think we could merge main to this one as the main brancn only did the pre-commit job, if it conflicts then we would revert those changes and ask @danielsirakov to perform the pre-commit update action on this branch. To make sure that everything is running correctly, I think what you propose is what we need to do next after the pre-commit and version update are done.

[sbillinge]

@stevenhua0320 please could you guide this through. Please assign tasks to different people who have the requisite skills to do them but shepherd this to completion

[cadenmyers13]

@stevenhua0320 I can take care of merging main into v3.3.0 since I've done most of the work on v3.3.0.

Then how do we test this before merging into main and releasing? I guess that if all tests are passing and all tutorial examples in diffpy.cmi are passing in an env that contains this version, then we can feel secure enough to merge it into main and make a release?

@sbillinge Because we did the deprecation slowly on v3.3.0 I feel confident that we haven't broken anything. But yes, all tests passing means we're good. Running the cmi scripts on this branch will probably have to be something done locally. I can do that (and will confirm) when the PR merging into main comes.

[sbillinge]

Not sure I understand. Are you asking me to merge 3.3.0 into main? If you can confirm that you think it is ready I will do that and you can test the examples?

[cadenmyers13]

@sbillinge Yeah we will merge v3.3.0 into main. I'll take care of it