Update Python in CI (#147)

Author: RMeli

.github/workflows/flake8.yml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/mypy.yml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
 
     steps:
     - uses: actions/checkout@v4

.github/workflows/pytest.yml

@@ -23,19 +23,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [macOS-latest, ubuntu-latest, windows-latest]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: ["3.11", "3.12", "3.13", "3.14"]
         chemlib: [obabel, rdkit]
         graphlib: [nogt, all]
         exclude:
           # graph-tool does not work on Windows
           - {os: "windows-latest", graphlib: "all"}
           # Don't run without graph-tool on Ubuntu and macOS
           - {os: "ubuntu-latest", graphlib: "nogt"}
-          - {os: "macOS-latest", graphlib: "nogt"}
-        include:
-          - {os: "macOS-14", graphlib: "all", chemlib: "obabel", python-version: "3.12"}
-          - {os: "macOS-14", graphlib: "all", chemlib: "rdkit", python-version: "3.12"}
+          - {os: "macos-latest", graphlib: "nogt"}
+          # Open Babel has not been updated for Python 3.13 and 3.14
+          - {chemlib: "obabel", python-version: "3.13"}
+          - {chemlib: "obabel", python-version: "3.14"}
 
     steps:
     - uses: actions/checkout@v4

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ exclude: |
             )$
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v6.0.0
     hooks:
     - id: check-json
     - id: check-merge-conflict
@@ -14,20 +14,20 @@ repos:
     - id: end-of-file-fixer
     - id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 25.12.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/flake8
-    rev: 7.1.1
+    rev: 7.3.0
     hooks:
     -   id: flake8
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.13.2
+    rev: 7.0.0
     hooks:
     -   id: isort
         args: ["--profile", "black"]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.1
+    rev: v1.19.1
     hooks:
     -   id: mypy
         additional_dependencies: [types-requests]

spyrmsd/graphs/gt.py

@@ -14,7 +14,7 @@
 
 
 # TODO: Implement all graph-tool supported types
-def _c_type(numpy_dtype):
+def _c_type(numpy_dtype: np.dtype) -> str:
     """
     Get C type compatible with graph-tool from numpy dtype
 
@@ -89,19 +89,17 @@ def graph_from_adjacency_matrix(
         warnings.warn(warn_disconnected_graph)
 
     if aprops is not None:
-        if not isinstance(aprops, np.ndarray):
-            aprops = np.array(aprops)
+        aprops_ = np.asarray(aprops)
+        assert aprops_.shape[0] == num_vertices
 
-        assert aprops.shape[0] == num_vertices
-
-        ptype: str = _c_type(aprops.dtype)  # Get C type
-        vprop = G.new_vertex_property(ptype, vals=aprops)  # Create property map
+        ptype: str = _c_type(aprops_.dtype)  # Get C type
+        vprop = G.new_vertex_property(ptype, vals=aprops_)  # Create property map
         G.vertex_properties["aprops"] = vprop  # Set property map
 
     return G
 
 
-def match_graphs(G1, G2) -> List[Tuple[List[int], List[int]]]:
+def match_graphs(G1, G2) -> List[Tuple[np.ndarray, np.ndarray]]:
     """
     Compute graph isomorphisms.