Closed yuxuanzhuang closed 1 month ago
Hello @yuxuanzhuang! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:
package/MDAnalysis/lib/util.py
:Line 2587:1: W293 blank line contains whitespace
package/MDAnalysis/topology/PSFParser.py
:Line 255:9: E731 do not assign a lambda expression, use a def
testsuite/MDAnalysisTests/topology/test_psf.py
:Line 162:1: E302 expected 2 blank lines, found 1 Line 165:51: W292 no newline at end of file
Hi @yuxuanzhuang! 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/9296711606/job/25585650663
Please note: The black
linter is purely informational, you can safely ignore these outcomes if there are no flake8 failures!
All modified and coverable lines are covered by tests :white_check_mark:
Project coverage is 93.17%. Comparing base (
81062f3
) to head (34810e6
).
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@hmacdope please look after this PR! Thank you!
(As always, if it gets too much please say something an un-assign yourself.)
Fixes #2053 #4189
Changes made in this Pull Request:
In CHARMM PSF, residue identifiers (resids) can be any string, as discussed in https://github.com/MDAnalysis/mdanalysis/issues/2053#issuecomment-1984023249. Tools like CHARMM-GUI and psfgen often modify resids by including insertion codes from PDB files or converting large resids to hexadecimal numbers for placement in the resid block.
We should support reading it and this update aligns with the approach used by VMD for reading the leading number (atoi as in C) from string-like resids.
PR Checklist
Developers certificate of origin
📚 Documentation preview 📚: https://mdanalysis--4582.org.readthedocs.build/en/4582/