Fix #124: Support pathlib.Path in loadStructure and add test

[kwagoner94]

This PR resolves #124 by adding support for pathlib.Path inputs in loadStructure.

Summary:

• Adds os.fspath(filename) to allow str, pathlib.Path, and os.PathLike file inputs.
• Updates the docstring to clarify accepted types.
• Adds a new unit test (test_cif_pathlib) to verify that loadStructure accepts Path objects.
• Confirmed functionality with both automated and manual tests.

Note:

Some unrelated tests are failing due to YappsSyntaxError now being raised by PyCifRW instead of StructureFormatError. These issues predate this change and are unrelated to the fix provided here.

[sbillinge]

Thanks so much for this @kwagoner94

Couple of comments

1. is it possible you don't have pre-commit running locally? It looks as if pre-commit had to make changes in the CI which usually indicates that. Please check the scikit-package docs, but you are missing a pre-commit install command that must be run in your local repo.
2. Things are in a bit of a precarious state because CI is not running because we have migrated our release scripts in the latest version of scikit-package. We must merge a fix to skpkg: use scikit-package v0.1.0 to restandarlize package #126 before we can merge anything else. Do you want to take that one? You will have to follow the instructions for migrating a package to scikit-package level 5

Again, thanks so much for the fix. I see it was done carefully and I appreciate the detailed info you shared in the comments etc..... excellent! I can tell that things are going to go well!

[sbillinge]

@kwagoner94 you mentioned failing tests coming from an update in pyCIFrw. Please could you create an issue for someone to fix that? Failing tests are usually a high priority so we want to address that also with some urgency. We may want to merge that before we merge this also, but after #123

[kwagoner94]

@sbillinge I’ve created a new issue to track the YappsSyntaxError test failures.

As for pre-commit, you’re right — I hadn’t set it up properly. It’s now installed and configured locally. Let me know if you'd prefer that I push a new commit with the pre-commit fixes now, or wait until #126 is merged and then rebase.

I’m also happy to take on #126 and help migrate the repo to scikit-package level 5.

[sbillinge]

@sbillinge I’ve created a new issue to track the YappsSyntaxError test failures.

👍

As for pre-commit, you’re right — I hadn’t set it up properly. It’s now installed and configured locally. Let me know if you'd prefer that I push a new commit with the pre-commit fixes now, or wait until #126 is merged and then rebase.

I think this PR is pretty clean so no worries. You will have to sync your local from your fork if there are any more commits you have to push (no worries if not). We don't rebase btw, we want to keep a linear commit history.

I’m also happy to take on #126 and help migrate the repo to scikit-package level 5.

Yes, please! Could you do that?