Update Actions and Enable Dependabot for GH Actions

.github/dependabot.yml

@@ -0,0 +1,8 @@
+# Set update schedule for GitHub Actions
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "monthly"

.github/workflows/docker.yml

@@ -14,12 +14,12 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.12'
 
     - name: Install build dependencies
       run: |
@@ -31,26 +31,26 @@ jobs:
         python -m build --wheel .
 
     - name: Set up QEMU
-      uses: docker/setup-qemu-action@v2
+      uses: docker/setup-qemu-action@v3
 
     - name: Set up Docker Buildx
-      uses: docker/setup-buildx-action@v2
+      uses: docker/setup-buildx-action@v3
 
     - name: Login to the GitHub Container Registry
-      uses: docker/login-action@v1
+      uses: docker/login-action@v3
       with:
         registry: ${{ env.REGISTRY }}
         username: ${{ github.actor }}
         password: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Extract metadata for Docker
       id: meta
-      uses: docker/metadata-action@v3
+      uses: docker/metadata-action@v5
       with:
         images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
 
     - name: Push the Docker image to the GHCR
-      uses: docker/build-push-action@v3
+      uses: docker/build-push-action@v6
       with:
         context: .
         push: true

.github/workflows/lint.yml

@@ -10,11 +10,11 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - name: Setup Python 3.10
-        uses: actions/setup-python@v4
+      - uses: actions/checkout@v4
+      - name: Setup Python 3.12
+        uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install Ruff
         run: |
@@ -24,3 +24,7 @@ jobs:
       - name: Lint/Check format with Ruff
         run: |
           ruff check . --output-format=github
+
+      - name: Check formatting with Ruff
+        run: |
+          ruff format --check .

.github/workflows/publish.yml

@@ -9,11 +9,11 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.10'
+        python-version: '3.12'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/tests.yml

@@ -17,33 +17,27 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
         os: [ubuntu-latest, windows-latest, macos-latest]
         experimental: [false,]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest pytest-cov wheel
+        pip install pytest pytest-cov wheel
         pip install -e .
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Run unit and system tests
       run: |
         pytest -v --cov=mokapot tests/
     - name: Upload coverage to codecov
-      uses: codecov/codecov-action@v3
+      uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         fail_ci_if_error: true

mokapot/confidence.py

@@ -488,7 +488,7 @@ def assign_confidence(
     psms: list[OnDiskPsmDataset],
     max_workers,
     scores=None,
-    descs: list[bool] | None=None,
+    descs: list[bool] | None = None,
     eval_fdr=0.01,
     dest_dir: Path | None = None,
     file_root: str = "",

mokapot/config.py

@@ -76,7 +76,9 @@ def _parser():
         "--verify_pin",
         type=bool,
         default=True,
-        help="Verify that PIN input files are valid TSVs. If not convert them.",
+        help=(
+            "Verify that PIN input files are valid TSVs. If not convert them."
+        ),
     )
 
     parser.add_argument(
@@ -399,8 +401,8 @@ def _parser():
         default=None,
         type=Path,
         help="Optionally, sets a path to an MSAID sqlite result database "
-             "for writing outputs to. If not set (None), results are "
-             "written in the standard TSV format.",
+        "for writing outputs to. If not set (None), results are "
+        "written in the standard TSV format.",
     )
 
     return parser

mokapot/mokapot.py

@@ -62,13 +62,13 @@ def main(main_args=None):
     logging.info("=================")
     if config.verify_pin:
         for path_pin in config.psm_files:
-            with open(path_pin, 'r') as f_pin:
+            with open(path_pin, "r") as f_pin:
                 valid_tsv = is_valid_tsv(f_pin)
             if not valid_tsv:
                 logging.info(f"{path_pin} invalid tsv, converting")
                 path_tsv = f"{path_pin}.tsv"
-                with open(path_pin, 'r') as f_pin:
-                    with open(path_tsv, 'a') as f_tsv:
+                with open(path_pin, "r") as f_pin:
+                    with open(path_tsv, "a") as f_tsv:
                         pin_to_valid_tsv(f_in=f_pin, f_out=f_tsv)
                 shutil.move(path_tsv, path_pin)