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

v0.7.2

Fixed

• io.xtandem: Fixed bug when extracting run name (introduced in v0.7.0) (#63)

v0.7.1

Added

• Tests: Added tests for _format_number_as_string function
• Tests: Added more test cases for peptidoform.rename_modifications for mass modifications
• io.xtandem: To parse run value, fall back to PSM file name if run name cannot be parsed from label field

Fixed

• peptidoform.rename_modifications: Fixed mapping of negative mass modifications
• io.xtandem: Fixed regular expression to parse run value fom XML label field
• io.idxml: Fix handling multiple types in rescoring_features when writing (fixes #60)

Full Changelog: v0.7.0...v0.7.1

v0.7.0

Added

• io.idxml: Write support for idXML files, including merging an existing idXML with a PSMList 🎉
• io.xtandem: New argument score_key to select which score to parse as PSM.score.
• io.xtandem: Parse run name from X!Tandem PSM files
• Docs: Add intersphinx links to other package documentation pages.

Changed

• io.idxml: Use pyOpenMS instead of Pyteomics for reading idXML (~5x faster⚡)

Fixed

• Fix reading of pepXML files without RT
• Fixed Black formatting throughout project