Merge remote-tracking branch 'pmg/master' into ppd-to-json

Author: CompRhys

.github/workflows/lint.yml

@@ -31,8 +31,5 @@ jobs:
           uv run ruff check .
           uv run ruff format --check .
 
-      - name: mypy
-        run: uv run mypy -p pymatgen
-
       - name: pyright
         run: uv run pyright src

.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.3
+    rev: v0.14.7
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.18.2
+    rev: v1.19.0
     hooks:
       - id: mypy
         entry: mypy -p pymatgen
@@ -50,7 +50,7 @@ repos:
       - id: blacken-docs
 
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.45.0
+    rev: v0.46.0
     hooks:
       - id: markdownlint
         # MD013: line too long
@@ -61,7 +61,7 @@ repos:
         args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.1
+    rev: 0.8.2
     hooks:
       - id: nbstripout
         args: [--drop-empty-cells, --keep-output]

pyproject.toml

@@ -98,9 +98,9 @@ ase = ["ase>=3.23.0"]
 # electronic_structure = ["fdint>=2.0.2"]
 matcalc = [
     "matcalc>=0.4.0; python_version<'3.13'",
-    "matgl>=1.2.7; python_version<'3.13'",
+    "matgl>=2.0.4; python_version<'3.13'",
 ]
-mlp = ["matgl>=1.2.7 ; python_version<'3.13'"]
+mlp = ["matgl>=2.0.4 ; python_version<'3.13'"]
 numba = ["numba>=0.55; python_version<'3.14'"]
 numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 optional = [

src/pymatgen/analysis/adsorption.py

@@ -22,7 +22,7 @@
 from pymatgen.util.coord import in_coord_list_pbc
 
 if TYPE_CHECKING:
-    import matplotlib.pyplot as plt
+    from matplotlib.axes import Axes
     from numpy.typing import ArrayLike
     from typing_extensions import Self
 
@@ -636,7 +636,7 @@ def reorient_z(structure):
 
 def plot_slab(
     slab: Slab,
-    ax: plt.Axes,
+    ax: Axes,
     scale=0.8,
     repeat=5,
     window=1.5,

src/pymatgen/analysis/chemenv/connectivity/structure_connectivity.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import collections
+import collections.abc
 import logging
 from typing import TYPE_CHECKING