Fix for writing non-unique site labels in CifWriter

[stefsmeets]

This PR addresses an issue where the Structure contains non-unique user-defined labels causing duplicate labels in the cif file. It achieves this by adding a warning when writing such a cif file. There is also a new method that helps circumvent the issue by relabeling sites, suffixing _1, _2, ..., _n for duplicates.

Closes #3761

Summary

Major changes:

• feature 1: Add SiteCollection.relabel_sites() method that suffixes _$NUM for duplicate labels
• fix 1: Warn user when writing non-unique atom site labels in CifWriter

Todos

• Check written labels make sense in tests

Checklist

• Google format doc strings added. Check with ruff.
• Type annotations included. Check with mypy.
• Tests added for new features/fixes.
• If applicable, new classes/functions/modules have duecredit @due.dcite decorators to reference relevant papers by DOI (example)

Tip: Install pre-commit hooks to auto-check types and linting before every commit:

pip install -U pre-commit
pre-commit install

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Commits

Files that changed from the base of the PR and between d2257a5 and 3201e04.

Walkthrough

The recent updates in pymatgen involve modifications to the CifWriter to ensure unique atom site labels in CIF files, addressing issues with non-unique and incorrectly rewritten labels. This includes a method update in cif.py for checking and conditionally updating site labels, alongside a new test in test_cif.py to validate these changes.

Changes

File	Change Summary
pymatgen/io/cif.py, tests/io/test_cif.py	Updated __init__ in cif.py to ensure unique atom_site_label. Added test_cif_writer_non_unique_labels in test_cif.py.
pymatgen/core/structure.py	Added relabel_sites method to Structure class for ensuring unique site labels.
tests/core/test_structure.py	Added test_relabel_sites to test the relabel_sites function.

Assessment against linked issues

Objective	Addressed	Explanation
Ensure unique atom_site_label in CIF files (#3761)	✅	The addition of relabel_sites method in Structure class ensures unique labels, addressing the issue of non-unique labels in CIF files.
Prevent CifWriter from rewriting unique atom labels (#3772)	✅	The update in CifWriter to ensure label uniqueness now prevents the issue of rewriting unique atom labels, aligning with the expected behavior.

Possibly related issues

• Issue Atom labels in CIF file are silently rewritten by CifWriter #3772: This issue describes a problem where CifWriter was rewriting unique atom labels, which should now be addressed by the updated handling of label uniqueness in the CifWriter class. This ensures that already unique labels are not altered unnecessarily.

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[stefsmeets]

This PR is ready. I'm a bit puzzled why the test fails...:

E       FileNotFoundError: [Errno 2] No such file or directory: '/home/runner/work/pymatgen/pymatgen/tests/files/garnet.cif'

[fxcoudert]

Wondering: why make the situation asymmetric? i.e. in the case of your four Ca1 atoms, one will remain Ca1 while the others will become Ca1_1, Ca1_2, …

[janosh]

i think @fxcoudert has a point. in case of relabeling, let's sequentially suffix all duplicate site labels for consistency.

How about an option to CifWriter to make labels unique.

this also sounds sensible to give the user control over relabeling behavior

[stefsmeets]

A matter of taste I presume :-)

Adding an option and making sure the first atom is also labeled may be a bit more involved. I will have a go at tackling #3772 as well in this PR then.

[janosh]

A matter of taste I presume :-)

very true! hopefully, adding an option can make everyone happy. maybe make it deduplicate_site_labels: Literal["sequential", None] = "sequential" so it's easy to add additional options in the future.

[stefsmeets]

maybe make it deduplicate_site_labels: Literal["sequential", None] = "sequential"

In that case I think this would be better as a method on Structure to make it generally available, together with a warning in CifWriter (one of the other suggestions in the issue). The label duplication happens only if the user passed a structure with custom labels and does not specify symprec which avoids this path.

[janosh]

In that case I think this would be better as a method on Structure to make it generally available

sure

together with a warning in CifWriter (one of the other suggestions in the issue).

definitely. a warning that the labels were suffixed with a link to the spec to explain why this was done would be great!

[coderabbitai]

Actionable comments posted: 4

[janosh]

thanks @stefsmeets, very nice work!