Default to Python 3.12, add idxml extra, upgrade DeepLC ≥ 3.1, and fix ignored profile config parameter

.github/workflows/publish.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Install uv and set the Python version
         uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           enable-cache: true
 
       - name: Install the project

.github/workflows/test.yml

@@ -23,8 +23,9 @@ jobs:
     needs: check-python-package
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
     steps:
       - uses: actions/checkout@v4
 
@@ -52,13 +53,13 @@ jobs:
 
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install package and dependencies
         run: |
           # Using pip to ensure proper environment discovery by PyInstaller
           python -m pip install --upgrade pip
-          pip install --only-binary :all: .[ionmob] pyinstaller
+          pip install --only-binary :all: .[ionmob,idxml] pyinstaller
 
       - name: Install Inno Setup
         uses: crazy-max/ghaction-chocolatey@v1

Dockerfile

@@ -31,7 +31,7 @@ ADD ms2rescore /ms2rescore/ms2rescore
 
 # Install the project and its dependencies using the lockfile and settings
 RUN --mount=type=cache,target=/root/.cache/uv \
-    uv sync --no-dev
+    uv sync --no-dev --all-extras
 
 # Place executables in the environment at the front of the path
 ENV PATH="/ms2rescore/.venv/bin:$PATH"

ms2rescore/__init__.py

@@ -19,6 +19,14 @@
     module="psims.mzmlb",
 )
 
+# Attempt to suppress pyopenms warning about OPENMS_DATA_PATH already set
+filterwarnings(
+    "ignore",
+    message="Warning: OPENMS_DATA_PATH environment variable already exists.*",
+    category=UserWarning,
+    module="pyopenms",
+)
+
 from ms2rescore._version import get_version  # noqa: E402
 from ms2rescore.config_parser import parse_configurations  # noqa: E402
 from ms2rescore.core import rescore  # noqa: E402

ms2rescore/__main__.py

@@ -247,7 +247,7 @@ def main(tims=False):
 
     # Run MS²Rescore
     try:
-        if cli_args.profile:
+        if config["ms2rescore"]["profile"]:
             profiled_rescore = profile(rescore, config["ms2rescore"]["output_path"])
             profiled_rescore(configuration=config)
         else:

pyproject.toml

@@ -30,12 +30,12 @@ classifiers = [
     "Topic :: Scientific/Engineering :: Bio-Informatics",
     "Development Status :: 5 - Production/Stable",
 ]
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 dependencies = [
     "cascade-config>=0.4.0",
     "click>=7",
     "customtkinter>=5,<6",
-    "deeplc>=3.0,<3.1",
+    "deeplc>=3.1",
     "deeplcretrainer",
     "im2deep>=0.3.1",
     "jinja2>=3",
@@ -55,6 +55,7 @@ dependencies = [
 
 [project.optional-dependencies]
 ionmob = ["ionmob>=0.2", "tensorflow"]
+idxml = ["pyopenms>=3.3"]
 
 [dependency-groups]
 dev = ["ruff", "black", "pytest>=8.4.2", "pytest-cov", "pre-commit>=4.3.0"]