Apply pytest suggestions from scientific python

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.4.10
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

pyproject.toml

@@ -30,6 +30,7 @@ dependencies=[
     "networkx",
     "numpy",
     "pandas",
+    "pyarrow",
     "requests",
     "scipy",
     "trimesh",
@@ -125,7 +126,15 @@ disable_error_code = ["import-untyped"]
 plugins = "numpy.typing.mypy_plugin"
 
 [tool.pytest.ini_options]
-addopts = "--capture=no"
+minversion = "7.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+filterwarnings = [
+    "error",
+    "ignore::scipy.sparse._base.SparseEfficiencyWarning",
+]
+log_cli_level = "info"
+testpaths = ["test"]
 
 [tool.coverage.report]
 exclude_lines = ["pragma: not covered", "@overload"]

test/classes/test_simplex.py

@@ -28,11 +28,7 @@ def test_simplex_creation(self):
 
     def test_simplex_sign(self):
         """Test simplex sign method."""
-        s = Simplex(
-            [
-                1,
-            ]
-        )
+        s = Simplex([1])
         with pytest.raises(NotImplementedError):
             s.sign(face=1)
 
@@ -73,15 +69,18 @@ def test__contains__(self):
 
     def test_construct_tree(self):
         """Test the construct_tree property of the simplex."""
-        s = Simplex((1, 2, 3), construct_tree=True)
-        assert len(s.boundary) == 3
+        with pytest.warns(DeprecationWarning):
+            s = Simplex((1, 2, 3), construct_tree=True)
+        with pytest.warns(DeprecationWarning):
+            assert len(s.boundary) == 3
 
         s = Simplex((1, 2, 3), construct_tree=False)
-        assert len(s.boundary) == 3
+        with pytest.warns(DeprecationWarning):
+            assert len(s.boundary) == 3
 
     def test_getting_and_setting_items(self):
         """Test getting and setting items in the simplex."""
-        s = Simplex((1, 2, 3), construct_tree=True)
+        s = Simplex((1, 2, 3))
         s["weight"] = 1
         assert s["weight"] == 1
 

toponetx/classes/cell_complex.py

@@ -790,9 +790,7 @@ def add_cell(
                     if not isinstance(cell, list):
                         cell = list(cell)
 
-                    if self.is_insertable_cycle(
-                        cell, check_skeleton=check_skeleton, warnings_dis=True
-                    ):
+                    if self.is_insertable_cycle(cell, check_skeleton):
                         edges_cell = set(zip_longest(cell, cell[1:] + [cell[0]]))
                         self._G.add_edges_from(edges_cell)
                         self._insert_cell(Cell(cell, regular=self._regular), **attr)

toponetx/classes/simplicial_complex.py

@@ -463,12 +463,11 @@ def remove_maximal_simplex(self, simplex: Collection) -> None:
         if simplex_ in self._simplex_set.faces_dict[len(simplex_) - 1]:
             if self.is_maximal(simplex):
                 del self._simplex_set.faces_dict[len(simplex_) - 1][simplex_]
-                faces = Simplex(simplex_).faces
+                faces = self.get_boundaries([simplex_])
                 for s in faces:
                     if len(s) == len(simplex_):
                         continue
 
-                    s = s.elements
                     self._simplex_set.faces_dict[len(s) - 1][s]["membership"] -= {
                         simplex_
                     }