StaticFetcher() Implementation + from_pdb() refactor

[jauy123]

Fixes #5429 and #5431

Changes made in this Pull Request:

• Implements fetch.fetchers.StaticFetcher()
• Refactors fetch.pdb.from_pdb() to use StaticFetchers()

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes / no
From comment: #5436 (comment)

Per AI policy, I'm declaring that I used in AI in primary two ways: IDE autocomplete and help with reviewing the docstring used for the documentation to make it look more professional.

The one notable exception is that I used AI to help me draft test_multiple_downloads_existing_database and test_existing_database in testsuite/MDAnalysisTests/fetch/test_static_fetcher.py

I prompt is "Is there a unique way to determine the hash in order if two files are exactly the same including modification time in python using the standard library"

It gave code that used os.stat(), so I googled it and found pathlib.Path.stat().st_mtime in the official [docs](https://docs.python.org/3/library/pathlib.html#pathlib.Path.stat) which I then used manually for test_existing_database and test_multiple_downloads_existing_database with no AI.

PR Checklist

• Issue raised/referenced?
• Tests updated/added?
• Documentation updated/added?
• package/CHANGELOG file updated?
• Is your name in package/AUTHORS? (If it is not, add it!)
• LLM/AI disclosure was updated.

Developers Certificate of Origin

I certify that I can submit this code contribution as described in the Developer Certificate of Origin, under the MDAnalysis LICENSE.

[jauy123]

Per AI policy, I'm declaring that I used in AI in primary two ways: IDE autocomplete and help with reviewing the docstring used for the documentation to make it look more professional.

The one notable exception is that I used AI to help me draft test_multiple_downloads_existing_database and test_existing_database in testsuite/MDAnalysisTests/fetch/test_static_fetcher.py

I prompt is "Is there a unique way to determine the hash in order if two files are exactly the same including modification time in python using the standard library"

It gave code that used os.stat(), so I googled it and found pathlib.Path.stat().st_mtime in the official docs which I then used manually for test_existing_database and test_multiple_downloads_existing_database with no AI.

[jauy123]

By the way, I don't know why tests are failing for this? The tests that are failing aren't from my code. It is stuff like MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDATAWriter_molecule_tag which are failing which I didn't touch at all from my end.

I been running my tests (not the whole test suite) locally with pytest-cov on my end, and they aren't failing there.

[orbeckst]

The failing tests are, as far as I can tell, #5382

[yuxuanzhuang]

Looks like there's test failures related to the fetcher FAILED testsuite/MDAnalysisTests/fetch/test_static_fetcher.py::test_write_registry - ModuleNotFoundError: pooch is needed as a dependency for Fetchers. Could you try to fix it?

I will take a look at the other parts of the code today.

[jauy123]

Looks like there's test failures related to the fetcher FAILED testsuite/MDAnalysisTests/fetch/test_static_fetcher.py::test_write_registry - ModuleNotFoundError: pooch is needed as a dependency for Fetchers. Could you try to fix it?

I will take a look at the other parts of the code today.

There shouldn't be. I added pooch as a proper dependency in #4943 in .github/actions/setup-deps/action.yaml, package/requirements.txt, and package/pyproject.toml. I can't even see that error on the github actions because of the preexisting error that @orbeckst mentioned

[jauy123]

Otherwise, I feel like my code here is ready for review. One of the linters is angry about a superficial pass, but that is intentional in the design. At the current moment, StaticFetcher() is in its most completed state with all the features that seem to be needed, and from_pdb() is going to be the archetypical for the other from_ convenience functions.