Cif reader

[hp115]

Fixes #

Changes made in this Pull Request:

PR Checklist

• Tests?
• Docs?
• CHANGELOG updated?
• Issue raised/referenced?

Developers certificate of origin

• I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.

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📚 Documentation preview 📚: https://mdanalysis--4681.org.readthedocs.build/en/4681/

[pep8speaks]

Hello @hp115! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file package/MDAnalysis/coordinates/CIF.py:

Line 29:80: E501 line too long (98 > 79 characters)
Line 30:80: E501 line too long (113 > 79 characters)
Line 44:1: E303 too many blank lines (4)
Line 65:80: E501 line too long (80 > 79 characters)
Line 79:1: W293 blank line contains whitespace
Line 80:5: E303 too many blank lines (3)
Line 89:1: W391 blank line at end of file

• In the file package/MDAnalysis/coordinates/PDBx.py:

Line 28:80: E501 line too long (98 > 79 characters)
Line 29:80: E501 line too long (113 > 79 characters)
Line 47:5: E303 too many blank lines (2)
Line 57:80: E501 line too long (80 > 79 characters)
Line 61:37: E128 continuation line under-indented for visual indent
Line 61:80: E501 line too long (80 > 79 characters)
Line 69:9: E731 do not assign a lambda expression, use a def
Line 73:80: E501 line too long (81 > 79 characters)
Line 74:13: E731 do not assign a lambda expression, use a def
Line 101:1: W391 blank line at end of file

• In the file package/MDAnalysis/topology/PDBxParser.py:

Line 102:13: E122 continuation line missing indentation or outdented
Line 103:9: E122 continuation line missing indentation or outdented

• In the file testsuite/MDAnalysisTests/coordinates/test_cif.py:

Line 1:14: W291 trailing whitespace
Line 6:1: E303 too many blank lines (3)
Line 8:1: E302 expected 2 blank lines, found 1
Line 8:10: W292 no newline at end of file

Comment last updated at 2024-08-23 15:11:23 UTC

[github-actions]

Linter Bot Results:

Hi @hp115! Thanks for making this PR. We linted your code and found the following:

Some issues were found with the formatting of your code.

Code Location	Outcome
main package	⚠️ Possible failure
testsuite	⚠️ Possible failure

Please have a look at the darker-main-code and darker-test-code steps here for more details: https://github.com/MDAnalysis/mdanalysis/actions/runs/10528066841/job/29172710356

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Please note: The black linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!

[orbeckst]

@richardjgowers / @hmacdope would one of you assign the PR to yourself to look after it? You both seem to have an interest in it.

[tylerjereddy]

for clarity, this is a new MPL-2.0 license dependency we'd be adding.

[IAlibay]

We would need to make this optional.

[tylerjereddy]

Shouldn't be too hard to draft tests based on other coordinate readers and some small test files.

[tylerjereddy]

A bit unfortunate we need a manual CPython loop over each coordinate. I don't see an obvious alternative from poking around. Gemmi is 90 % C++ it seems, so one might think they could return an appropriate buffer somehow, but that's probably an upstream matter and would likely want to focus on correctness here for now.

[RMeli]

I removed the [WIP] tag and converted it to draft, which better signals that this is still ongoing work.

[orbeckst]

This PR is superseded by PR #4712 which uses gemmi and is close to being merged.