Refactoring #245
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Refactoring #245
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…into spectrum-feature-generator
…into spectrum-feature-generator
…into spectrum-feature-generator
…trum-feature-generator
pull main in spectrum-feature-generator
…pectrum-feature-generator
…mics/ms2rescore into spectrum-feature-generator
…mics/ms2rescore into spectrum-feature-generator
…rator * origin/main: Use np.fromiter for generators Implement requested changes (.copy; use generators) Urgent fix in im2deep.py require ms2rescore-rs version with file type check move file type check to ms2rescore_rs Pin DeepLC version to <3.1, avoiding calibration bug Refactor parsing of spectrum data: - Clearer logging when parsing precursor info from spectrum files - Always check if PSMs match with spectra based on observed precursor m/z (if available in PSM list) - Always raise error if not all PSMs can be found in spectrum file(s), before MS²PIP - Provide example PSM IDs from both PSM and spectrum file when matching fails. - Move all code to parse_spectra
rustyms 0.9.0a3 requires python 3.11, while we support 3.9.
As mumble hasn't been published on pypi yet, use a git dependency for now.
im2deep.utils was introduced in 0.3.0. CompOmics/IM2Deep@0a4bc9d
…pectrum-feature-generator
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