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]

Docs need to be reupdated, but the code itself feel like it is in a completed state.

[read-the-docs-community]

Documentation build overview

📚 MDAnalysis | 🛠️ Build #34026146 | 📁 Comparing 32715ca against latest (83bc9a2)

  🔍 Preview build  

10 files changed · + 2 added · ± 8 modified

+ Added

• documentation_pages/fetchers/fetchers.html
• _modules/MDAnalysis/fetch/fetchers.html

± Modified

• genindex.html
• index.html
• py-modindex.html
• _modules/index.html
• documentation_pages/fetchers_modules.html
• documentation_pages/analysis/wbridge_analysis.html
• documentation_pages/fetchers/PDB.html
• _modules/MDAnalysis/fetch/pdb.html

[yuxuanzhuang]

I think the code is in pretty good shape. I will add more comments related to the code.

For the documentation, it would be helpful to add an overview page at package/doc/sphinx/source/documentation_pages/fetchers_modules.rst that includes:

1. Usage examples.
2. A list of the available fetchers.

See package/doc/sphinx/source/documentation_pages/converters.rst for an example.

[yuxuanzhuang]

Checking whether a requested file is present in the registry should not require scanning the entire cache directory. That is error-prone since unrelated cache files can also cause false failures; it also adds unnecessary I/O.

[jauy123]

check_registry() might be a misleading name. This method is meant to return all files not in the self.cache_path per the docstring

Return paths relative to :attr:`cache_path` for cache files that are
missing from the registry.

I originally made it when I was refactoring the fetch() method where it would toss error to prevent unintentional update of the registry (which would be a security issue)

        if LOAD_FROM_CACHE:
            registry_dictionary = self.read_registry(db_path)
            missing_files_list = self.check_registry(
                db_path, files=list(requested_files)
            )

            if len(missing_files_list) != 0:
                MISSING_FILES = True

        if MISSING_FILES and not APPEND_DATABASE:
            raise ValueError(
                "fetch() is requesting files not found in the registry. "
                + f"The missing files are {missing_files_list}. "
                + "To fix this, please set append_db=True to append the "
                + "registry."
            )

[jauy123]

This method could be renamed because it's not really checking like return a True or False