Configure Renovate

.github/workflows/CI.yaml

@@ -1,27 +1,40 @@
-name: PUSH
+name: CI
 
-on: [push]
+on:
+  push:
+    branches: [main]
+  pull_request:
+  workflow_dispatch:
 
 jobs:
-  build:
-
+  tests:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9","3.10","3.11","3.12"]
+        pixi-env: ["py39", "py310", "py311", "py312"]
+
+    steps:
+      - uses: actions/checkout@v5
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+      - name: Run tests
+        run: pixi run -e ${{ matrix.pixi-env }} pytest
 
+  precommit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+      - name: Run prek
+        run: pixi run -e lint prek run --all-files
+
+  tests_complete:
+    name: All tests
+    if: always()
+    needs: [tests, precommit]
+    runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v5
-    - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v6
-      with:
-        python-version: ${{ matrix.python-version }}
-    - name: Install package
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install -r requirements/requirements-test.txt
-        python -m pip install pytest
-        python -m pip install .
-    - name: Test with pytest
-      run: |
-        python -m pytest
+      - run: jq --exit-status 'all(.result == "success")' <<< '${{ toJson(needs) }}'
+      - name: Done
+        run: echo "Done."

.github/workflows/prek-update.yml

@@ -0,0 +1,24 @@
+name: Prek Update
+
+on:
+  schedule:
+    - cron: "0 0 1 */3 *"
+  workflow_dispatch:
+
+jobs:
+  prek-update:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v5
+      - name: Set up pixi
+        uses: prefix-dev/setup-pixi@v0.8.1
+      - name: Run prek update
+        run: pixi run -e lint prek update
+      - name: Create pull request
+        uses: peter-evans/create-pull-request@v7
+        with:
+          commit-message: "chore: prek update"
+          title: "chore: update pre-commit hooks"
+          body: "Automated prek update."
+          branch: "automation/prek-update"
+          labels: "dependencies"

.pre-commit-config.yaml

@@ -1,6 +1,3 @@
-ci:
-  autoupdate_schedule: quarterly
-
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: 'v4.5.0'

.ruff.toml

@@ -1,4 +1,5 @@
-target-version = "py38"
+target-version = "py39"
+line-length = 90
 
 [lint]
 select = [

WaterNetworkAnalysis/WaterNetworkAnalysis.py

@@ -786,8 +786,7 @@ def align_trajectory(
         raise Exception(exception_string)
     if align_target_file_name in {trajectory, topology}:
         exception_string = (
-            "align_target_file_name name cannot be the same as "
-            "trajectory or topology"
+            "align_target_file_name name cannot be the same as " "trajectory or topology"
         )
         raise Exception(exception_string)
     if topology is not None:
@@ -1067,23 +1066,23 @@ def read_results_and_make_pdb(
 
 
 def is_pdb_file(filepath: str) -> bool:
-    """
-    Return True if `filepath` is probably a PDB (by extension or by peeking at contents).
-    If it’s binary (like XTC/DCD), this will return False safely.
+    """Return True if `filepath` is probably a PDB.
+
+    If it's binary (like XTC/DCD), this will return False safely.
     """
     ext = os.path.splitext(filepath)[1].lower()
     if ext in {".pdb", ".ent", ".pdb1", ".pdb2"}:
         return True
 
     # If extension isn't a known PDB, peek at first few lines:
     try:
-        with open(filepath, "r", encoding="utf-8") as f:
+        with open(filepath, encoding="utf-8") as f:
             for _ in range(10):
                 line = next(f)
                 if line.startswith(("ATOM  ", "HETATM", "HEADER", "TITLE")):
                     return True
-    except (UnicodeDecodeError, IOError, StopIteration):
-        # If it fails to decode (binary), or can't open, it’s not a PDB.
+    except (UnicodeDecodeError, OSError, StopIteration):
+        # If it fails to decode (binary), or can't open, it's not a PDB.
         return False
 
     return False