Fix numpy 2.4 scalar conversion error

[chemonke]

Code of Conduct

Description

See #156

Related issues or pull requests

Fixes #156 , test now passes.

Pull Request Checklist

• Added a note about the modification or contribution to the ./docs/sources/CHANGELOG.md file (if applicable)
• Added appropriate unit test functions in the ./biopandas/*/tests directories (if applicable)
• Modify documentation in the corresponding Jupyter Notebook under biopandas/docs/sources/ (if applicable)
• Ran PYTHONPATH='.' pytest ./biopandas -sv and make sure that all unit tests pass (for small modifications, it might be sufficient to only run the specific test file, e.g., PYTHONPATH='.' pytest ./biopandas/classifier/tests/test_stacking_cv_classifier.py -sv)
• Checked for style issues by running flake8 ./biopandas

[a-r-j]

Hi @chemonke thanks for the contribution. Do you mind checking out the failing test?

[Copilot]

Pull request overview

This PR addresses NumPy 2.4+ compatibility issues in BioPandas structure parsing, primarily fixing an MMTF parsing failure caused by stricter scalar conversion rules, and improving amino3to1 residue boundary detection across PDB/MMTF/mmCIF.

Changes:

• Fix NumPy 2.4+ TypeError in mmtf_to_df by extracting a scalar index from np.argwhere(...).
• Make amino3to1 residue grouping more robust by including chain IDs and safely handling missing insertion codes.
• Add a changelog entry describing the update (needs alignment with the PR’s actual fixes).

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
docs/CHANGELOG.md	Adds a release note entry for the change (currently misaligned with the PR’s primary fix).
biopandas/pdb/pandas_pdb.py	Updates amino3to1 residue boundary key to include chain_id and tolerate missing insertion codes.
biopandas/mmtf/pandas_mmtf.py	Fixes NumPy 2.4 scalar conversion in mmtf_to_df; updates amino3to1 residue boundary key similarly.
biopandas/mmcif/pandas_mmcif.py	Updates amino3to1 residue boundary key to include chain + insertion handling for mmCIF.

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[chemonke]

I'll have a look at it tomorrow when I'm home again.

[chemonke]

Full disclosure: my background is in chemistry, and I haven't finished my data science degree yet, so I'm basically a beginner.

I don't expect any problems from the indexing change in b4b69b1.

But the test__construct_df() series seems odd to me. Was it ever intended behavior to convert None to a str? What I did in 89e961f seems a bit hacky, maybe the test should be rewritten?