Fix RELION & RELION5 star file import for ChimeraX 1.10.1#53
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Use pandas type to work with newer versions
The RELION5 star-file reader had the same np.issubdtype(df.dtypes[key], np.number) check that fails on pandas StringDtype columns under ChimeraX 1.10.1 (issue #43). Use pandas' is_numeric_dtype here too so RELION5 imports are covered by the same fix. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Fixes #43. Supersedes #44.
Problem
ChimeraX 1.10.1 ships a newer pandas where the
starfilereader returns string columns (e.g.rlnMicrographName) as the pandas extensionStringDtypeinstead of numpyobject.np.issubdtype()only understands numpy dtypes, so classifying the "additional" columns during import raises:Fix
Replace the check with pandas' public
pd.api.types.is_numeric_dtype(), which correctly handles both numpy dtypes and pandas extension dtypes.The identical check existed in both star-file readers, so the fix is applied in both:
src/io/RELION/RELIONParticleData.py— original fix by @bwmr (from Fix Relion Star file import for ChimeraX 1.10.1 #44)src/io/RELION5/RELION5ParticleData.py— the RELION5 reader had the same line and would crash the same way on RELION5 star filesCredit to @bwmr for the root-cause analysis and the original fix in #43/#44; their commit is preserved here. This PR bundles the matching RELION5 fix so #43 is fully resolved (rebased onto current
main, which now includes #39 and #52).🤖 Generated with Claude Code