Merge pull request #177 from compomics/main

pull main in spectrum-feature-generator

.github/workflows/publish.yml

@@ -54,7 +54,7 @@ jobs:
       - name: Install package and dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install --only-binary :all: . pyinstaller
+          pip install --only-binary :all: .[ionmob] pyinstaller
 
       - name: Install Inno Setup
         uses: crazy-max/ghaction-chocolatey@v3
@@ -83,3 +83,43 @@ jobs:
           tag: ${{ github.ref }}
           file_glob: true
           file: dist/*.exe
+
+  docker-image:
+    runs-on: ubuntu-latest
+    permissions:
+      packages: write
+      contents: read
+      attestations: write
+      id-token: write
+    steps:
+      - name: Check out the repo
+        uses: actions/checkout@v4
+
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ghcr.io/${{ github.repository }}
+
+      - name: Build and push Docker images
+        id: push
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-name: ghcr.io/${{ github.repository }}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true

.github/workflows/test.yml

@@ -55,7 +55,7 @@ jobs:
       - name: Install package and dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install --only-binary :all: . pyinstaller
+          pip install --only-binary :all: .[ionmob] pyinstaller
 
       - name: Install Inno Setup
         uses: crazy-max/ghaction-chocolatey@v1

ms2rescore.spec

@@ -16,6 +16,8 @@ project = "ms2rescore"
 bundle_name = "ms2rescore"
 bundle_identifier = f"{bundle_name}.{__version__}"
 
+extra_requirements = {"ionmob"}
+
 # Requirements config
 skip_requirements_regex = r"^(?:.*\..*)"
 
@@ -28,6 +30,7 @@ requirements = {
     if "; extra ==" not in req  # Exclude optional dependencies
 }
 requirements.update([project, "xgboost"])
+requirements.update(extra_requirements)
 
 hidden_imports = set()
 datas = []

ms2rescore/__init__.py

@@ -1,6 +1,6 @@
 """MS²Rescore: Sensitive PSM rescoring with predicted MS² peak intensities and RTs."""
 
-__version__ = "3.1.0"
+__version__ = "3.1.1"
 
 from warnings import filterwarnings
 

ms2rescore/gui/app.py

@@ -383,6 +383,9 @@ def get(self) -> Dict:
             config["deeplc"] = deeplc_config
         if ionmob_enabled:
             config["ionmob"] = ionmob_config
+        if im2deep_enabled:
+            config["im2deep"] = im2deep_config
+
         return config
 
 

ms2rescore/rescoring_engines/percolator.py

@@ -88,7 +88,7 @@ def rescore(
         "decoy-results-proteins": output_file_root + ".percolator.decoy.proteins.pout",
         "weights": output_file_root + ".percolator.weights.tsv",
         "verbose": LOG_LEVEL_MAP[log_level],
-        "num-threads": processes,
+        "num-threads": min(processes, 128),  # Higher values not supported by Percolator
         "post-processing-tdc": True,
     }
     if percolator_kwargs: