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v0.4.0

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@pgarrett-scripps pgarrett-scripps released this 10 Apr 18:37
v0.4.0
5d3c3d6

What's Changed

Breaking Changes

  • write_ms2_file, write_mgf_file, and write_mzml_file now take a single dataclass argument (Ms2Args, MgfArgs, MzmlArgs) instead of many individual keyword arguments.
# before
write_mzml_file("/path/to/foo.d", output_file="foo.mzML", top_n_peaks=150)

# after
from tdfextractor import MzmlArgs, write_mzml_file
write_mzml_file(MzmlArgs(analysis_dir="/path/to/foo.d", output_file="foo.mzML", top_n_peaks=150))

Added

  • New tdfextractor.args module with BaseExtractorArgs, Ms2Args, MgfArgs, MzmlArgs, EncodingBitWidth, CompressionName
  • write_ms2_file and write_mgf_file added to public API
  • --workers arg for parallel processing of multiple .d folders
  • --min/--max-precursor-rt now also bounds MS1 frames in mzML output
  • py.typed PEP 561 marker (typed package)
  • Full test suite with session-scoped fixtures and slow marker

Fixed

  • Renamed mgf_exctractor.py → mgf_extractor.py (typo)
  • Fixed StateTransitionWarning from psims (missing instrumentConfigurationList in mzML header)
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