Use new uv package manager to install deps in CI

.github/workflows/test.yml

@@ -33,14 +33,17 @@ jobs:
           cache: pip
           cache-dependency-path: pyproject.toml
 
+      - name: Install uv
+        run: pip install uv
+
       - name: Install dependencies
         run: |
-          pip install cython
+          uv pip install cython --system
           # install ase from main branch until FrechetCellFilter is released
-          # TODO remove pip install git+https://gitlab.com/ase/ase
-          pip install git+https://gitlab.com/ase/ase
+          # TODO remove uv pip install git+https://gitlab.com/ase/ase
           python setup.py build_ext --inplace
-          pip install -e .[test]
+          uv pip install -e .[test] --system
+          uv pip install --upgrade 'ase@git+https://gitlab.com/ase/ase' --system
 
       - name: Run Tests
         run: pytest --capture=no --cov --cov-report=xml .

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ default_install_hook_types: [pre-commit, commit-msg]
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.0
     hooks:
       - id: ruff
         args: [--fix]
@@ -46,7 +46,7 @@ repos:
           - svelte
 
   - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v9.0.0-beta.0
+    rev: v9.0.0-beta.1
     hooks:
       - id: eslint
         types: [file]

chgnet/graph/graph.py

@@ -186,9 +186,9 @@ def add_edge(self, center_index, neighbor_index, image, distance) -> None:
                     # is the reverse of our DE
                     if added_DE == this_directed_edge:
                         # Add UDE index to this DE
-                        this_directed_edge.info[
-                            "undirected_edge_index"
-                        ] = added_DE.info["undirected_edge_index"]
+                        this_directed_edge.info["undirected_edge_index"] = (
+                            added_DE.info["undirected_edge_index"]
+                        )
 
                         # At the center node, draw edge with this DE
                         self.nodes[center_index].add_neighbor(

chgnet/model/model.py

@@ -807,7 +807,9 @@ def from_graphs(
             else:
                 strain = None
                 lattice = graph.lattice
-            volumes.append(torch.dot(lattice[0], torch.cross(lattice[1], lattice[2])))
+            volumes.append(
+                torch.dot(lattice[0], torch.linalg.cross(lattice[1], lattice[2]))
+            )
             strains.append(strain)
 
             # Bonds

pyproject.toml

@@ -99,6 +99,7 @@ ignore = [
     "EM",
     "ERA001",  # found commented out code
     "FBT001",  # Boolean positional argument in function
+    "ISC001",
     "FBT002",  # Boolean keyword argument in function
     "NPY002",  # TODO replace legacy np.random.seed
     "PLR",     # pylint refactor

site/make_docs.py

@@ -3,6 +3,7 @@
 - prettier badges linking to source code on GitHub
 - remove bold tags since they break inline code.
 """
+
 from __future__ import annotations
 
 import json