Merge pull request #148 from wilhelm-lab/release/0.7.6

Release/0.7.6

Author: WassimG

.cookietemple.yml

@@ -15,5 +15,5 @@ full_name: Victor Giurcoiu
 email: victor.giurcoiu@tum.de
 project_name: spectrum_fundamentals
 project_short_description: Fundamentals public repo
-version: 0.7.5
+version: 0.7.6
 license: MIT

.github/release-drafter.yml

@@ -1,5 +1,5 @@
-name-template: "0.7.5 " # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.7.5 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.7.6 " # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.7.6 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 

cookietemple.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.7.5
+current_version = 0.7.6
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_fundamentals/__init__.py

docs/conf.py

@@ -52,9 +52,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.7.5"
+version = "0.7.6"
 # The full version, including alpha/beta/rc tags.
-release = "0.7.5"
+release = "0.7.6"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spectrum_fundamentals"
-version = "0.7.5"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.7.6"  # <<COOKIETEMPLE_FORCE_BUMP>>
 description = "Fundamental functions, annotation pipeline and constants for oktoberfest"
 authors = ["Wilhelmlab at Technical University of Munich"]
 license = "MIT"

spectrum_fundamentals/__init__.py

@@ -5,7 +5,7 @@
 __author__ = """The Oktoberfest development team (Wilhelmlab at Technical University of Munich)"""
 __copyright__ = f"Copyright {datetime.now():%Y}, Wilhelmlab at Technical University of Munich"
 __license__ = "MIT"
-__version__ = "0.7.5"
+__version__ = "0.7.6"
 
 import logging
 import logging.handlers

spectrum_fundamentals/__main__.py

@@ -5,7 +5,7 @@
 
 
 @click.command()
-@click.version_option(version="0.7.5", message=click.style("spectrum_fundamentals Version: 0.7.5"))
+@click.version_option(version="0.7.6", message=click.style("spectrum_fundamentals Version: 0.7.6"))
 def main() -> None:
     """spectrum_fundamentals."""
 

spectrum_fundamentals/metrics/percolator.py

@@ -444,7 +444,7 @@ def _reorder_columns_for_percolator(self):
         new_columns = first_columns + sorted(mid_columns) + last_columns
         self.metrics_val = self.metrics_val[new_columns]
 
-    def calc(self):
+    def calc(self):  # noqa: C901
         """Adds percolator metadata and feature columns to metrics_val based on PSM metadata."""
         self.add_common_features()
         self.target_decoy_labels = self.metadata["REVERSE"].apply(Percolator.get_target_decoy_label).to_numpy()
@@ -464,6 +464,11 @@ def calc(self):
             if self.neutral_loss_flag:
                 self.metrics_val["ANNOTATED_NL_COUNT"] = self.metadata["ANNOTATED_NL_COUNT"]
                 self.metrics_val["EXPECTED_NL_COUNT"] = self.metadata["EXPECTED_NL_COUNT"]
+                columns_to_remove = []
+                for col in self.metrics_val.columns:
+                    if "vs_predicted" in col:
+                        columns_to_remove.append(col)
+                self.metrics_val.drop(columns=columns_to_remove, inplace=True)
             if self.drop_miss_cleavage_flag:
                 self.metrics_val.drop(columns=["missedCleavages", "KR"], inplace=True)
             if self.xl: