Recent Releases of pyprophet
pyprophet - PyProphet 3.0.1
What's Changed
- fix pypdf out of date by @jcharkow in https://github.com/PyProphet/pyprophet/pull/150
Full Changelog: https://github.com/PyProphet/pyprophet/compare/3.0.0...3.0.1
- Python
Published by singjc 7 months ago
pyprophet - PyProphet 3.0.0
Release Highlights (Major Version Update)
This release introduces significant structural changes to improve modularity:
Introduced I/O Module: I/O logic is now modularized by file type (e.g., SQLite .osw, Parquet), to support new parquet format support.
Configurable Data Classes: Core algorithms (scoring, IPF, levels contexts) now use configuration dataclasses for cleaner parameter management and easier extension.
Click CLI Restructure: Command chaining has been removed to enable grouped subcommands (e.g., peptide, protein, peptidoform) for better CLI organization.
Deprecation Notice: Original flat subcommands remain for backwards compatibility but will be removed in a future release.
Added readthedocs for API and CLI documentation
Added linear SVM classifier model for scoring module.
All existing functionality should continue to work as is. Please report any issues if any.
What's Changed
- Patch/pq memory opt by @singjc in https://github.com/PyProphet/pyprophet/pull/141
- Refactor/codebase by @singjc in https://github.com/PyProphet/pyprophet/pull/142
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.3.4...3.0.0
- Python
Published by singjc 8 months ago
pyprophet - PyProphet 2.3.4
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.3.3...2.3.4
- Python
Published by singjc 10 months ago
pyprophet - PyProphet 2.3.3
What's Changed
- add: export sqMass to parquet by @singjc in https://github.com/PyProphet/pyprophet/pull/138
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.3.2...2.3.3
- Python
Published by singjc 10 months ago
pyprophet - PyProphet 2.3.2
Fix Dockerfile pyprophet installation. Previously used setup.py, but changed over to pyproject.toml, so installation needed to be changed to use pip install Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.3.1...2.3.2
- Python
Published by singjc 10 months ago
pyprophet - PyProphet 2.3.1
What's Changed
- Add: Full parquet support for scoring and inference by @singjc in https://github.com/PyProphet/pyprophet/pull/137
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.3.0...2.3.1
- Python
Published by singjc 10 months ago
pyprophet - PyProphet 2.3.0
What's Changed
- Continous Integration Tests by @jcharkow in https://github.com/PyProphet/pyprophet/pull/129
- fix: export parquet peptide global level by @jcharkow in https://github.com/PyProphet/pyprophet/pull/130
- feature: transition level string in precursor level export by @jcharkow in https://github.com/PyProphet/pyprophet/pull/132
- Feature: Alignment Scoring and Across Run IPF by @singjc in https://github.com/PyProphet/pyprophet/pull/133
- update: merge osw post scoring method to merge feature alignment tables if present by @singjc in https://github.com/PyProphet/pyprophet/pull/134
- fix: ipf transfer confidence method by @singjc in https://github.com/PyProphet/pyprophet/pull/135
- Add/glycoinference by @singjc in https://github.com/PyProphet/pyprophet/pull/136
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.9...2.3.0
- Python
Published by singjc 11 months ago
pyprophet - PyProphet 2.2.9
What's Changed
- Patch/export parquet by @jcharkow in https://github.com/PyProphet/pyprophet/pull/128
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.8...2.2.9
- Python
Published by singjc over 1 year ago
pyprophet - PyProphet 2.2.8
What's Changed
- Update Report with PP plot by @singjc in https://github.com/PyProphet/pyprophet/pull/127
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.7...2.2.8
- Python
Published by singjc over 1 year ago
pyprophet - PyProphet 2.2.7
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.6...2.2.7
- Python
Published by singjc over 1 year ago
pyprophet - PyProphet 2.2.6
What's Changed
- [FIX] deprecation warning with pandas by @jcharkow in https://github.com/PyProphet/pyprophet/pull/121
- Fix broken osw tests and report/deprecation warnings by @singjc in https://github.com/PyProphet/pyprophet/pull/118
- Feature/speedup parquet export by @jcharkow in https://github.com/PyProphet/pyprophet/pull/126
- Feature/split by @singjc in https://github.com/PyProphet/pyprophet/pull/123
- [ADD] peptide sequence specific filtering for sqMass and OSW filtering by @singjc in https://github.com/PyProphet/pyprophet/pull/122
New Contributors
- @jcharkow made their first contribution in https://github.com/PyProphet/pyprophet/pull/121
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.5...2.2.6
- Python
Published by singjc over 1 year ago
pyprophet - PyProphet 2.2.5
What's Changed
- Fix/ipf np int by @singjc in https://github.com/PyProphet/pyprophet/pull/115
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.4...2.2.5
- Python
Published by grosenberger almost 3 years ago
pyprophet - PyProphet 2.2.4
What's Changed
- Update/main score selection by @singjc in https://github.com/PyProphet/pyprophet/pull/114
- [FIX] PyPDF2 3.0.0 deprecation of PdfFileMerger, PdfFileReader to Pdf… by @singjc in https://github.com/PyProphet/pyprophet/pull/112
- Fix/apply weights by @singjc in https://github.com/PyProphet/pyprophet/pull/113
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.3...2.2.4
- Python
Published by grosenberger about 3 years ago
pyprophet - PyProphet 2.2.3
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.2...2.2.3
- Python
Published by grosenberger about 3 years ago
pyprophet - PyProphet 2.2.2
What's Changed
- ADD: export before scoring with MS1MS2 scores by @oliveralka in https://github.com/PyProphet/pyprophet/pull/87
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.1...2.2.2
- Python
Published by grosenberger about 3 years ago
pyprophet - PyProphet 2.2.1
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.2.0...2.2.1
- Python
Published by grosenberger about 3 years ago
pyprophet - PyProphet 2.2.0
What's Changed
- [MINOR] Docker file end bind mount point by @singjc in https://github.com/PyProphet/pyprophet/pull/109
- Feature/filter osw by @singjc in https://github.com/PyProphet/pyprophet/pull/108
- Feature/dynamic main score by @singjc in https://github.com/PyProphet/pyprophet/pull/110
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.1.12...2.2.0
- Python
Published by grosenberger about 3 years ago
pyprophet - PyProphet 2.1.12
What's Changed
- [MINOR] Add exception handling for when applying weights and not spec… by @singjc in https://github.com/PyProphet/pyprophet/pull/107
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.1.11...2.1.12
- Python
Published by grosenberger over 3 years ago
pyprophet - PyProphet 2.1.11
What's Changed
- [FEATURE] Separate color blind friendly feature into separate PR from … by @singjc in https://github.com/PyProphet/pyprophet/pull/102
- [ADD] Add pi0estimation extended error help into separate PR from PR … by @singjc in https://github.com/PyProphet/pyprophet/pull/103
Full Changelog: https://github.com/PyProphet/pyprophet/compare/2.1.10...2.1.11
- Python
Published by grosenberger over 3 years ago