Implementation of from_DOI()

[jauy123]

Fixes #5434

Changes made in this Pull Request:

• Implements from_DOI using StaticFetcher()

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: no

PR Checklist

• [ x] Issue raised/referenced?
• [ x] 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.

[read-the-docs-community]

Documentation build overview

📚 MDAnalysis | 🛠️ Build #34026638 | 📁 Comparing 9a269d4 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

[codecov]

Codecov Report

❌ Patch coverage is 96.59864% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 93.88%. Comparing base (83bc9a2) to head (9a269d4).
⚠️ Report is 5 commits behind head on develop.

Files with missing lines	Patch %	Lines
package/MDAnalysis/fetch/fetchers.py	96.74%	3 Missing and 1 partial ⚠️
package/MDAnalysis/fetch/pdb.py	95.65%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #5454      +/-   ##
===========================================
+ Coverage    93.87%   93.88%   +0.01%     
===========================================
  Files          182      183       +1     
  Lines        22510    22650     +140     
  Branches      3202     3228      +26     
===========================================
+ Hits         21131    21265     +134     
- Misses         917      921       +4     
- Partials       462      464       +2     

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[jauy123]

This diverged from #5436 using StaticFetcher as a base.

[jauy123]

docs still need to be changed and updated

[jauy123]

docs for from_DOI is done

[orbeckst]

Whatever I said on PR #5457 also applies for the common StaticFetcher code here. I assume that once one of these gets merged, the other gets updated accordingly.

More generally though it sounds to me that the original way we thought about organizing fetchers in sub-modules by format (or source) is not useful. The from_xxx() designates the source, the files argument determines the files, so the sub-module (namely, fetch.pdb) is not relevant or really confusing. Perhaps you already have a plan to reorganize everything once the current PRs are merged but if not, I'd suggest to just ditch fetch.pdb and make the fetch_xxx() functions directly available from MDAnalysis.fetch.

[orbeckst]

It's a bit confusing that this lives under fetch.pdb.from_doi() given that it can download any kind of files. The semantics are unclear because when I get a psf I do not "fetch a pdb-formatted file from a DOI".

Perhaps all these functions make more sense directly under fetch, at least fetch.from_doi(..., file="AdK.psf") does not spell a contradictory sentence.