Mars v0.1.4 Release Notes

Release Date: TBD

Overview

This release includes bug fixes and improvements.

--mzML flag alias: The --mzml option now also accepts --mzML (matching the file extension casing) across all commands (calibrate, qc, apply).
Unquoted wildcards: Shell-expanded wildcards now work without quotes. For example, mars calibrate --mzml *.mzML works the same as mars calibrate --mzml "*.mzML".
Positional file arguments: mzML files can now be passed as positional arguments without the --mzml flag, e.g., mars calibrate *.mzML --prism-csv report.csv.
Repeatable --mzml: The --mzml option can be specified multiple times to pass individual files, e.g., --mzml a.mzML --mzml b.mzML.

(No bug fixes this version)

The --mzml option now uses multiple=True internally, accepting one or more values.
All three subcommands (calibrate, qc, apply) accept a trailing [INPUT_FILES]... positional argument for mzML file paths.

Fully backward compatible with v0.1.3
Supported spectral library formats:
- blib (BiblioSpec)
- PRISM CSV
- DIA-NN parquet (report-lib.parquet + report.parquet)
Output mzML files are compatible with:
- DIA-NN
- SeeMS (ProteoWizard)
- MSConvert
- Skyline
- Other standard mzML readers

pip install --upgrade mars-ms