Merge pull request #400 from pyt-team/frantzen/test-python-3.13

Test against Python 3.13

.github/workflows/test.yml

@@ -22,14 +22,14 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  build:
+  pytest:
     runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         flavor: ["dev", "all"]
 
     steps:

pyproject.toml

@@ -71,7 +71,6 @@ all = [
     "TopoNetX[doc, dev]",
 
     # optional packages that are not required to run the library
-    "gudhi",
     "hypernetx < 2.0.0",
     "spharapy"
 ]

test/classes/test_simplicial_complex.py

@@ -1,5 +1,7 @@
 """Test simplicial complex class."""
 
+from unittest.mock import Mock
+
 import networkx as nx
 import numpy as np
 import pytest
@@ -10,11 +12,6 @@
 from toponetx.classes.simplicial_complex import SimplicialComplex
 from toponetx.datasets.mesh import stanford_bunny
 
-try:
-    from gudhi import SimplexTree
-except ImportError:
-    SimplexTree = None
-
 try:
     import hypernetx as hnx
 except ImportError:
@@ -819,13 +816,31 @@ def test_to_combinatorial_complex(self):
         assert len(result.cells) == len(expected_result.cells)
         assert len(result.nodes) == len(expected_result.nodes)
 
-    @pytest.mark.skipif(
-        SimplexTree is None, reason="Optional dependency 'gudhi' not installed."
-    )
     def test_from_gudhi(self):
         """Create a SimplicialComplex from a Gudhi SimplexTree and compare the number of simplices."""
-        tree = SimplexTree()
-        tree.insert([1, 2, 3, 5])
+        gudhi_simplices = [
+            ([1, 2, 3, 5], 0.0),
+            ([1, 2, 3], 0.0),
+            ([1, 2, 5], 0.0),
+            ([1, 2], 0.0),
+            ([1, 3, 5], 0.0),
+            ([1, 3], 0.0),
+            ([1, 5], 0.0),
+            ([1], 0.0),
+            ([2, 3, 5], 0.0),
+            ([2, 3], 0.0),
+            ([2, 5], 0.0),
+            ([2], 0.0),
+            ([3, 5], 0.0),
+            ([3], 0.0),
+            ([5], 0.0),
+        ]
+        tree = Mock(["get_skeleton", "dimension"])
+        tree.get_skeleton.side_effect = lambda i: (
+            s for s in gudhi_simplices if len(s[0]) <= i + 1
+        )
+        tree.dimension.return_value = 3
+
         expected_result = SimplicialComplex()
         expected_result.add_simplex((1, 2, 3, 5))
         result = SimplicialComplex.from_gudhi(tree)