OpenSWATH XIC parquet reader

[jcharkow]

Description

This adds a reader for OpenSWATH XICs in .parquet format in the new pyprophet. Specifically this relies on the parquet export here PyProphet/pyprophet#158 since it requires transition annotation columns.

Fixes # (issue)

Type of change

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)

How Has This Been Tested?

Tests have been added.
API Documentation has been updated.
I do not believe any additional documentation is required because it is the same format as the other readers.

Checklist:

• My code follows the style guidelines of this project
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules

Contents (#188)

Other

• add reader for OSW parquet chromatograms
• update api docs
• assemble transitionGroups rather than chromatogram list
• fix: update tests and control for when no chromatograms found

Uncategorised!

• add fragment ion annotation reading
• remove unneeded imports
• add tests for OSW parquet XICs
• add readme on how chromatograms parquet were created
• apply copilot suggestions
• add util method for numpress decompression
• Merge branch 'dev' into osw_parquet_chrom_reader
• Merge branch 'dev' into osw_parquet_chrom_reader
• apply singjc suggestions

[Copilot]

Pull Request Overview

This PR adds a new reader for OpenSWATH XICs (Extracted Ion Chromatograms) stored in parquet format, specifically designed to work with parquet exports from pyprophet that include transition annotation columns.

Key changes:

• Implements OpenSwathXICParquetLoader and OpenSwathXICParquetAccess classes for reading parquet-formatted chromatograms
• Adds comprehensive test coverage for the new functionality
• Updates API documentation to include the new loader

Reviewed Changes

Copilot reviewed 8 out of 21 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
massdash/loaders/access/OpenSwathXICParquetAccess.py	Core access class for reading parquet chromatogram data with compression handling
massdash/loaders/OpenSwathXICParquetLoader.py	Loader class implementing the chromatogram loading interface
test/loaders/test_OpenSwathXICParquetLoader.py	Tests for the parquet loader functionality
test/loaders/access/test_OpenSwathXICParquetAccess.py	Tests for the parquet access class
massdash/loaders/__init__.py	Export registration for the new loader
massdash/loaders/access/__init__.py	Export registration for the new access class
docs/API.rst	Documentation updates for the new classes

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[jcharkow]

@singjc can I merge this?

[singjc]

Looks good. I made some minor suggestions which you can commit, and then had one question about returning None instead of throwing a message telling the user there was not XIC data for a requested peptide charge.

You can go ahead an merge

[singjc]

Is there an instance where we would want to return none, instead of throwing a message stating that no data was found for this peptide precursor?

[jcharkow]

This is the behaviour that is used in the SqMassLoader so I did it this way for consistency. I believe I implemented it this way because an empty Datatframe is returned for the loadTransitionGroupDf() method so this is somewhat consistent with that.

I could change the behaviour for both of them if you think that would be more appropriate.

massdash/massdash/loaders/SqMassLoader.py

Lines 82 to 83 in a0e48a9

	if transitionMetaInfo.empty:
	return None

[jcharkow]

I think that I will merge with the currently functionality for now (pending tests passing) and we I can create a separate PR with the new behaviour if you think we should change it.