update im2deep version, fix docstring

.github/workflows/publish.yml

@@ -44,23 +44,22 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
           python-version: "3.11"
+          enable-cache: true
 
       - 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
+        run: uv sync --group installer
 
       - name: Install Inno Setup
         uses: crazy-max/ghaction-chocolatey@v3
         with:
-          args: install innosetup -y --allow-unofficial --force
+          args: install innosetup -y --allow-unofficial
 
       - name: Run pyinstaller
-        run: pyinstaller ./ms2rescore.spec --clean --noconfirm
+        run: uv run pyinstaller ./ms2rescore.spec --clean --noconfirm
 
       - name: Test built exe
         run: dist/ms2rescore/ms2rescore.exe

.github/workflows/test.yml

@@ -45,35 +45,32 @@ jobs:
         run: uv run ms2rescore --help
 
   test-windows-installer:
-    # Only run on push to main (e.g., after PR merge)
-    if: ${{ github.ref == 'refs/heads/main' }}
     runs-on: windows-latest
     steps:
       - uses: actions/checkout@v4
 
-      - uses: actions/setup-python@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
         with:
-          python-version: "3.12"
+          python-version: "3.11"
+          enable-cache: true
 
       - 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,idxml] pyinstaller
+        run: uv sync --group installer
 
       - name: Install Inno Setup
         uses: crazy-max/ghaction-chocolatey@v1
         with:
-          args: install innosetup -y --allow-unofficial --force
+          args: install innosetup -y --allow-unofficial
 
       - name: Run pyinstaller
-        run: pyinstaller ./ms2rescore.spec --clean --noconfirm
+        run: uv run pyinstaller ./ms2rescore.spec --clean --noconfirm
 
       - name: Test built exe
         run: dist/ms2rescore/ms2rescore.exe
 
       - name: Run Inno Setup
-        run: ISCC.exe ./ms2rescore_innosetup.iss /DAppVersion=${{  github.ref_name }}
+        run: ISCC.exe ./ms2rescore_innosetup.iss /DAppVersion=test-build
 
       - name: Upload artifact
         uses: actions/upload-artifact@v4

ms2rescore.spec

@@ -46,7 +46,9 @@ while requirements:
     module_version = importlib.metadata.version(re.match(r"^[\w\-]+", requirement)[0])
     try:
         datas_, binaries_, hidden_imports_ = collect_all(requirement, include_py_files=True)
-    except ImportError:
+    except (ImportError, RuntimeError) as e:
+        # Skip packages that fail to collect (e.g., xgboost.testing requires hypothesis)
+        print(f"Warning: Failed to collect {requirement}: {e}")
         continue
     datas += datas_
     hidden_imports_ = set(hidden_imports_)

ms2rescore/feature_generators/im2deep.py

@@ -150,7 +150,7 @@ def make_calibration_df(psm_list_df: pd.DataFrame, threshold: float = 0.25) -> p
             DataFrame with PSMs.
         threshold
             Percentage of highest scoring identified target PSMs to use for calibration,
-            default 0.95.
+            default 0.25.
 
         Returns
         -------

pyproject.toml

@@ -19,6 +19,7 @@ authors = [
     { name = "Ralf Gabriels", email = "ralf@gabriels.dev" },
     { name = "Arthur Declercq", email = "arthur.declercq@ugent.be" },
     { name = "Ana Sílvia C. Silva" },
+    { name = "Robbe Devreese" },
     { name = "Robbin Bouwmeester" },
     { name = "Louise Buur" },
 ]
@@ -37,12 +38,12 @@ dependencies = [
     "customtkinter>=5,<6",
     "deeplc>=3.1",
     "deeplcretrainer",
-    "im2deep>=0.3.1",
+    "im2deep>=1.1",
     "jinja2>=3",
     "lxml>=4.5",
     "mokapot==0.10",                     # 0.11.0 will introduce API changes
     "ms2pip>=4.0.0",
-    "ms2rescore_rs>=0.4.3",
+    "ms2rescore_rs>=0.4",
     "numpy>=1.25",
     "packaging>=25.0",
     "pandas>=1",
@@ -71,6 +72,14 @@ docs = [
     "sphinx-autobuild",
     "toml",
 ]
+installer = [
+    # Pinned dependencies for reproducible Windows installer builds
+    "pyinstaller",
+    "pyopenms==3.3",
+    "ionmob>=0.2",
+    "tensorflow",
+    "im2deep==1.1.1",
+]
 
 [project.urls]
 GitHub = "https://github.com/compomics/ms2rescore"