Merge pull request #188 from wilhelm-lab/release/0.8.1

WassimG · web-flow · commit 26c5b3cd828d · 2025-06-11T14:51:13.000+02:00
release/0.8.1
diff --git a/.cookietemple.yml b/.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: 0.8.0
+version: 0.8.1
 license: MIT
diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml
@@ -1,5 +1,5 @@
-name-template: "0.8.0 " # <<COOKIETEMPLE_FORCE_BUMP>>
-tag-template: 0.8.0 # <<COOKIETEMPLE_FORCE_BUMP>>
+name-template: "0.8.1 " # <<COOKIETEMPLE_FORCE_BUMP>>
+tag-template: 0.8.1 # <<COOKIETEMPLE_FORCE_BUMP>>
 exclude-labels:
     - "skip-changelog"
 
diff --git a/.github/workflows/build_package.yml b/.github/workflows/build_package.yml
@@ -16,7 +16,7 @@ jobs:
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.3.0
+              uses: actions/setup-python@v5.6.0
               with:
                   python-version: ${{ matrix.python }}
 
diff --git a/.github/workflows/main_master_branch_protection.yml b/.github/workflows/main_master_branch_protection.yml
@@ -40,9 +40,9 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Set up Python
-              uses: actions/setup-python@v5.3.0
+              uses: actions/setup-python@v5.6.0
               with:
-                  python-version: "3.13"
+                  python-version: "3.11"
             # PRs to the repository master branch are only ok if coming from any patch or release branch
             - name: Install mlf-core
               run: pip install mlf-core
diff --git a/.github/workflows/publish_docs.yml b/.github/workflows/publish_docs.yml
@@ -11,7 +11,7 @@ jobs:
               name: Check out source-code repository
 
             - name: Setup Python
-              uses: actions/setup-python@v5.3.0
+              uses: actions/setup-python@v5.6.0
               with:
                   python-version: 3.13
 
diff --git a/.github/workflows/publish_package.yml b/.github/workflows/publish_package.yml
@@ -15,7 +15,7 @@ jobs:
                   fetch-depth: 2
 
             - name: Set up Python
-              uses: actions/setup-python@v5.3.0
+              uses: actions/setup-python@v5.6.0
               with:
                   python-version: "3.13"
 
diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
@@ -117,7 +117,7 @@ jobs:
               uses: actions/checkout@v4
 
             - name: Set up Python ${{ matrix.python-version }}
-              uses: actions/setup-python@v5.3.0
+              uses: actions/setup-python@v5.6.0
               with:
                   python-version: ${{ matrix.python-version }}
 
@@ -150,7 +150,7 @@ jobs:
                   print("::set-output name=result::{}".format(result))
 
             - name: Restore pre-commit cache
-              uses: actions/cache@v4.2.0
+              uses: actions/cache@v4.2.3
               if: matrix.session == 'pre-commit'
               with:
                   path: ~/.cache/pre-commit
@@ -184,7 +184,7 @@ jobs:
               uses: actions/checkout@v4
 
             - name: Set up Python 3.13
-              uses: actions/setup-python@v5.3.0
+              uses: actions/setup-python@v5.6.0
               with:
                   python-version: "3.13"
 
@@ -213,4 +213,4 @@ jobs:
               run: nox --force-color --session=coverage -- xml -i
 
             - name: Upload coverage report
-              uses: codecov/codecov-action@v5.4.0
+              uses: codecov/codecov-action@v5.4.3
diff --git a/.github/workflows/sync_project.yml b/.github/workflows/sync_project.yml
@@ -10,7 +10,7 @@ jobs:
         runs-on: ubuntu-latest
         steps:
             - name: Setup Python
-              uses: actions/setup-python@v5.3.0
+              uses: actions/setup-python@v5.6.0
               with:
                   python-version: "3.13"
 
diff --git a/cookietemple.cfg b/cookietemple.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.0
+current_version = 0.8.1
 
 [bumpversion_files_whitelisted]
 init_file = spectrum_fundamentals/__init__.py
diff --git a/docs/conf.py b/docs/conf.py
@@ -52,9 +52,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "0.8.0"
+version = "0.8.1"
 # The full version, including alpha/beta/rc tags.
-release = "0.8.0"
+release = "0.8.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "spectrum_fundamentals"
-version = "0.8.0"  # <<COOKIETEMPLE_FORCE_BUMP>>
+version = "0.8.1"  # <<COOKIETEMPLE_FORCE_BUMP>>
 description = "Fundamental functions, annotation pipeline and constants for oktoberfest"
 authors = ["Wilhelmlab at Technical University of Munich"]
 license = "MIT"
diff --git a/spectrum_fundamentals/__init__.py b/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__ = "0.8.0"
+__version__ = "0.8.1"
 
 import logging
 import logging.handlers
diff --git a/spectrum_fundamentals/__main__.py b/spectrum_fundamentals/__main__.py
@@ -5,7 +5,7 @@
 
 
 @click.command()
-@click.version_option(version="0.8.0", message=click.style("spectrum_fundamentals Version: 0.8.0"))
+@click.version_option(version="0.8.1", message=click.style("spectrum_fundamentals Version: 0.8.1"))
 def main() -> None:
     """spectrum_fundamentals."""
 
diff --git a/spectrum_fundamentals/fragments.py b/spectrum_fundamentals/fragments.py
@@ -29,7 +29,7 @@ def _get_modifications(peptide_sequence: str, custom_mods: Optional[Dict[str, fl
     :param custom_mods: mapping of custom UNIMOD string identifiers ('[UNIMOD:xyz]') to their mass
     :return: modification_deltas
     """
-    modification_deltas = {}
+    modification_deltas: dict[int, float] = {}
     offset = 1  # shift position of mod start in seq by one to the left to reflect position of aa
     if peptide_sequence.startswith("["):  # n-term mod => seq must be [UNIMOD:xyz]-X...
         offset = 2  # need to add one more offset, because of the dash '-', n_terminal stored at -1
@@ -44,7 +44,10 @@ def _get_modifications(peptide_sequence: str, custom_mods: Optional[Dict[str, fl
 
     for match in matches:
         start_pos, end_pos = match.span()
-        modification_deltas[start_pos - offset] = mod_masses[match.group()]
+        if (start_pos - offset) in modification_deltas.keys():
+            modification_deltas[start_pos - offset] += mod_masses[match.group()]
+        else:
+            modification_deltas[start_pos - offset] = mod_masses[match.group()]
         offset += end_pos - start_pos
 
     return modification_deltas
