Lint fixes

Author: shyuep

.github/workflows/lint.yml

@@ -11,15 +11,16 @@ jobs:
         python-version: [3.11]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Install uv with python version.
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v8
       with:
         python-version: ${{ matrix.python-version }}
         enable-cache: true
         cache-dependency-glob: "uv.lock"
     - name: Install dependencies
       run: |
+        uv pip install dgl==2.4.0 -f https://data.dgl.ai/wheels/torch-2.4/repo.html
         uv sync --group lint
 
     - name: ruff

.github/workflows/test.yml

@@ -29,9 +29,9 @@ jobs:
       PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
     - name: Install uv with python version.
-      uses: astral-sh/setup-uv@v5
+      uses: astral-sh/setup-uv@v8
       with:
         python-version: ${{ matrix.python-version }}
         enable-cache: true
@@ -45,7 +45,7 @@ jobs:
         uv run pytest tests --cov=maml
     - name: Upload coverage reports to Codecov
       if: matrix.os == 'ubuntu-latest'
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v6
       env:
         CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
@@ -57,9 +57,9 @@ jobs:
       # For pypi trusted publishing
       id-token: write
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - name: Install uv with python version.
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v8
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true

src/maml/apps/bowsr/model/dft.py

@@ -73,7 +73,7 @@ def predict_energy(self, structure: Structure):
 
             compat = MaterialsProjectCompatibility()
             vrun = Vasprun("vasprun.xml")
-            entry = compat.process_entry(vrun.get_computed_entry())
+            entry = compat.process_entry(vrun.get_computed_entry())  # type: ignore[arg-type]
             return (
                 entry.energy  # type: ignore[union-attr]
                 - sum(elements[el]["energy_per_atom"] * amt for el, amt in el_amt_dict.items())

src/maml/apps/bowsr/optimizer.py

@@ -94,7 +94,7 @@ def atoms_crowded(structure: Structure, cutoff_distance: float = 1.1) -> bool:
     """
     distance_matrix = copy(structure.distance_matrix)
     distance_matrix[distance_matrix == 0] = np.inf
-    return np.min(distance_matrix) < cutoff_distance
+    return bool(np.min(distance_matrix) < cutoff_distance)
 
 
 class BayesianOptimizer:

src/maml/utils/_dummy.py

@@ -10,8 +10,8 @@
 DUMMY_OBJECTS = {
     "str": "H2O",
     "composition": Composition("H2O"),
-    "structure": Structure(Lattice.cubic(3.167), ["Mo", "Mo"], [[0, 0, 0], [0.5, 0.5, 0.5]]),
-    "molecule": Molecule(["C", "O"], [[0, 0, 0], [1, 0, 0]]),
+    "structure": Structure(Lattice.cubic(3.167), ["Mo", "Mo"], [[0, 0, 0], [0.5, 0.5, 0.5]]),  # type: ignore[arg-type]
+    "molecule": Molecule(["C", "O"], [[0, 0, 0], [1, 0, 0]]),  # type: ignore[arg-type]
 }