v1.0.1

Fixed

• io.percolator: Fix and improve ScanNr inferring and writing
• io.percolator: Infer style from file extension if not provided (enables dynamic style determination in, for instance, convert function).

v1.0.0

Added

• peptidoform: Allow comparison between a peptidoform and a peptidoform string; allow direct indexing with square brackets, which indexes or slices parsed_sequence (in #89)

Fixed

• io.tsv: Avoid flooding logs when reading a different file format by raising exception when three consecutive rows could not be parsed (in #88)

v0.9.1

Fixed

• io.xtandem: Fix parsing PSMs and complete protein names in XTandem (by @julianu in #83)
• io.tsv: Fix warning formatting when parsing TSV (by @paretje in #85)
• io: Fix support for mzIdentML and pepXML files from Comet (by @paretje in #87)

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New Contributors

• @julianu made their first contribution in #83

Full Changelog: v0.9.0...0.9.1

Important

This version was not correctly released to PyPI.

v0.9.0

Added

• io: Read and write support for writing PSMs to Apache Parquet for efficient storage of PSM lists.
• io.sage: Support for Sage results in Parquet format (new SageParquetReader, renamed SageReader to SageTSVReader).

Changed

• Upgrade Pydantic dependency to v2. The PSM spectrum_id field is now always coerced to a string.
• io.proteoscape: Use pyarrow to iteratively read from Parquet instead of first reading an entire dataframe with Pandas.
• io.sage: Update compatibility to Sage v0.14
• Remove temporary patch for caching Proforma modification resolvers (now in Pyteomics v4.7.2).

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Full Changelog: v0.8.3...v0.9.0

v0.8.3

Added

• Speed up mass calculation for large datasets by caching Proforma modification resolvers.
  Temporary patch until implemented in Pyteomics (see levitsky/pyteomics#147).

Changed

• Project infrastructure changes: Switch from Flit to Setuptools, use Ruff for linting on GitHub Actions, fix CodeCov.

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Full Changelog: v0.8.2...v0.8.3

v0.8.2

Added

• io.proteoscape: Parse filename into PSM run field.

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Full Changelog: v0.8.1...v0.8.2

v0.8.1

Added

• io.proteoscape: Allow ProteoScapeReader instantiation from Pandas DataFrame and access PSM by index.

Fixed

• Remove accidental print statement.
• io.idxml: Fixed parenthesis in type hint

Changed

• io.idxml: Filter OPENMS_DATA_PATH warnings (see CompOmics/ms2rescore#129 and OpenMS/OpenMS#7418)
• io.proteoscape: Rename module from TIMScore to ProteoScape.
• io.proteoscape: Use correct search engine score (x_corr_score instead of tims_score)

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Full Changelog: v0.8.0...v0.8.1

v0.8.0

Added

• io.timscore: Add support for TIMScore Parquet files.

Fixed

• Fixed _csv.Error: field larger than field limit (131072) for very large fields when reading CSV-based PSM files.
• Pinned Pyteomics version to avoid pickling issues in multithreading (to be investigated)

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Full Changelog: v0.7.4...v0.8.0

v0.7.4

Added

• Peptidoform: Support adding and applying global terminal modifications. For now using a
  workaround while waiting for official support and an implementation in Pyteomics. See
  HUPO-PSI/ProForma#6.

Full Changelog: v0.7.3...v0.7.4

v0.7.3

Changed

• io.xtandem: Parse double mass modifications as double modification instead of merging and summing mass shifts into a single modification.
• io.xtandem: Avoid float formatting issues when parsing modification mass label.
• io.xtandem: Parse all proteins into protein_list instead of only the first one.
• io.tsv: Log error instead of raising exception when a TSV row cannot be parsed.

Full Changelog: v0.7.2...v0.7.3