Update changelog; bump version

compomics · Mar 29, 2024 · f09bdff · f09bdff
1 parent 21521c6
commit f09bdff
Show file tree

Hide file tree

Showing 3 changed files with 23 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,23 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.8.1] - 2024-03-29
+
+### 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`)
+
 ## [0.8.0] - 2024-03-27
 
 ### Added
@@ -37,16 +54,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [0.7.2] - 2023-11-29
 
 ### Fixed
+
 - `io.xtandem`: Fixed bug when extracting run name (introduced in v0.7.0)
 
 ## [0.7.1] - 2023-10-30
 
 ### Added
-- Tests: Added tests for _format_number_as_string function
+
+- 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)

diff --git a/README.rst b/README.rst
@@ -99,7 +99,7 @@ Supported file formats
  `Percolator tab <https://github.com/percolator/percolator/wiki/Interface>`_                                           ``percolator``           ✅              ✅
  Proteome Discoverer MSF                                                                                               ``proteome_discoverer``  ✅              ❌
  `Sage <https://github.com/lazear/sage/blob/v0.12.0/DOCS.md#interpreting-sage-output>`_                                ``sage``                 ✅              ❌
- TIMScore Parquet                                                                                                      ``timscore``             ✅              ❌
+ ProteoScape Parquet                                                                                                   ``proteoscape``          ✅              ❌
  `TSV <https://psm-utils.readthedocs.io/en/stable/api/psm_utils.io/#module-psm_utils.io.tsv>`_                         ``tsv``                  ✅              ✅
  `X!Tandem XML <https://www.thegpm.org/tandem/>`_                                                                      ``xtandem``              ✅              ❌
 ===================================================================================================================== ======================== =============== ===============

diff --git a/psm_utils/__init__.py b/psm_utils/__init__.py
@@ -1,6 +1,6 @@
 """Common utilities for parsing and handling PSMs, and search engine results."""
 
-__version__ = "0.8.0"
+__version__ = "0.8.1"
 
 from warnings import filterwarnings