[aaronkanzer]

pymzml 2.7.0 cannot read the m/z or intensity array of any spectrum that uses MS-Numpress.

import pymzml
spec = next(iter(pymzml.run.Reader("small-composite-test.mzML")))  # msconvert output, galaxyp test data
spec.mz

• MS:1002312 (linear) and MS:1002314 (slof) raise AttributeError: 'Spectrum' object has no attribute 'calling_instance'.
• MS:1002313 (pic) and the three "followed by zlib compression" terms MS:1002746, MS:1002747 and MS:1002748 raise ValueError: Unsupported data type: None.

Why:

• _decodeNumpress_to_array still looks up self.calling_instance.OT. calling_instance was removed in 174193e (2023) when Spectrum got its own obo_translator, and nothing sets it anymore.
• _decode_to_numpy only checks for the linear and slof names, not pic or the "followed by zlib" names. Those terms are all children of MS:1000572 (binary data compression type) in the PSI-MS CV, and msconvert and OpenMS write them.
• When numpress is used, _get_encoding_parameters returns d_type = None on purpose, but _decode_to_numpy then always reaches raise ValueError(f"Unsupported data type: {data_type}"), even after a successful decode.

#332 looks like the same problem for the "followed by zlib" term.

Fix: map the six numpress CV names (plus the legacy ms-np-* names) to their method, zlib-decompress first when the term says so, and return the decoded float64 array directly. The pure Python MSNumpress fallback is stateful (MSNumpress(bytearray).decode_linear()), so it is called that way when pynumpress is not installed.

Tested:

• New tests/numpress_spectrum_test.py covers linear, pic, slof and the three zlib variants, with pynumpress and with the Python fallback. It fails on dev (8 subtests) and passes with the fix.
• Five real numpress files (two msconvert outputs from galaxyp test data and three OpenMS TOPP test files, 42 spectra in all) now give m/z and intensity arrays identical to pyteomics.
• Full suite: before 135 passed, 2 failed, 3 skipped. After: 137 passed, 2 failed, 3 skipped. The 2 failures are plot_spec_test.py and fail the same way before and after, because plotly is not installed.
• black --check pymzml is clean (black 26.5.1, as in CI).

Note: the legacy MS_Spectrum class in spec.py keeps its own copy of the old decoding code. Reader does not use it, so this PR leaves it alone.

[sonarqubecloud]

Quality Gate passed

Issues
1 New issue
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud