Activate additional ruff rules

conftest.py

@@ -1,10 +1,10 @@
 """Configure our testing suite."""
 
-import networkx
-import numpy
+import networkx as nx
+import numpy as np
 import pytest
 
-import toponetx
+import toponetx as tnx
 
 
 @pytest.fixture(autouse=True)
@@ -26,6 +26,6 @@ def doctest_default_imports(doctest_namespace):
     doctest_namespace : dict
         The namespace of the doctest.
     """
-    doctest_namespace["np"] = numpy
-    doctest_namespace["nx"] = networkx
-    doctest_namespace["tnx"] = toponetx
+    doctest_namespace["np"] = np
+    doctest_namespace["nx"] = nx
+    doctest_namespace["tnx"] = tnx

docs/conf.py

@@ -3,7 +3,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "TopoNetX"
-copyright = "2022-2023, PyT-Team, Inc."
+copyright = "2022-2023, PyT-Team, Inc."  # noqa: A001
 author = "PyT-Team Authors"
 language = "en"
 
@@ -66,7 +66,7 @@
             "url": "https://github.com/pyt-team/TopoNetX",
             "icon": "fa-brands fa-github",
             "type": "fontawesome",
-        }
+        },
     ],
     "use_edit_page_button": True,
 }

pyproject.toml

@@ -80,9 +80,6 @@ all = [
 documentation="https://pyt-team.github.io/toponetx/"
 source="https://github.com/pyt-team/TopoNetX/"
 
-[tool.ruff]
-extend-include = ["*.ipynb"]
-
 [tool.ruff.format]
 docstring-code-format = true
 
@@ -92,23 +89,50 @@ select = [
     "E", # code style
     "W", # warnings
     "I", # import order
+    "D", # pydocstyle rules
     "UP", # pyupgrade rules
+    "YTT", # flake8-2020 rules
+    "S", # bandit rules
+    "BLE", # blind except
     "B", # bugbear rules
+    "A", # builtin shadowing
+    "COM", # comma rules
+    "C4", # comprehensions
+    "DTZ", # datetime rules
+    "T10", # debugger calls
+    "FA", # future annotations
+    "ISC", # implicit str concatenation
+    "ICN", # import conventions
+    "LOG", # logging rules
+    "G", # logging format rules
     "PIE", # pie rules
     "Q", # quote rules
+    "RSE", # raise rules
     "RET", # return rules
+    "SLOT", # slot rules
     "SIM", # code simplifications
+    "TID", # tidy imports
+    "TCH", # type checking rules
+    "PTH", # use pathlib
+    "PD", # pandas rules
+    "PLC", # pylint conventions
+    "PLE", # pylint errors
+    "FLY", # flynt
     "NPY", # numpy rules
     "PERF", # performance rules
+    "FURB", # refurb
     "RUF", # miscellaneous rules
 ]
 ignore = [
     "E501",    # line too long
+    "COM812",  # trailing commas; conflict with `ruff format`
+    "ISC001",  # implicitly single-line str concat; conflict with `ruff format`
     "PERF203", # allow try-except within loops
 ]
 
 [tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F403"]
+"test/**.py" = ["S101"]
 
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"

test/classes/test_colored_hypergraph.py

@@ -147,9 +147,9 @@ def test_chg_getitem(self):
 
         # invalid inputs should raise `KeyError`s as well
         with pytest.raises(KeyError):
-            _ = CHG[tuple()]
+            _ = CHG[()]
         with pytest.raises(KeyError):
-            _ = CHG[(tuple(), 0)]
+            _ = CHG[((), 0)]
 
     def test_add_cell(self):
         """Test adding a cell to a CHG."""

test/test_tutorials.py

@@ -1,8 +1,8 @@
 """Unit tests for the tutorials."""
 
-import glob
 import subprocess
 import tempfile
+from pathlib import Path
 
 import pytest
 
@@ -28,11 +28,11 @@ def _exec_tutorial(path):
             tmp_file.name,
             path,
         ]
-        subprocess.check_call(args)
+        subprocess.check_call(args)  # noqa: S603
 
 
 TUTORIALS_DIR = "tutorials"
-paths = sorted(glob.glob(f"{TUTORIALS_DIR}/*.ipynb"))
+paths = sorted(Path(TUTORIALS_DIR).glob("*.ipynb"))
 
 
 @pytest.mark.parametrize("path", paths)

toponetx/algorithms/distance.py

@@ -86,7 +86,7 @@ def distance(
     try:
         return nx.shortest_path_length(G, rowdict[source], rowdict[target])
     except nx.NetworkXNoPath as exc:
-        raise TopoNetXNoPath() from exc
+        raise TopoNetXNoPath from exc
 
 
 def cell_distance(
@@ -172,4 +172,4 @@ def cell_distance(
     try:
         return nx.shortest_path_length(G, cell_dict[source], cell_dict[target])
     except nx.NetworkXNoPath as exc:
-        raise TopoNetXNoPath() from exc
+        raise TopoNetXNoPath from exc

toponetx/classes/cell.py

@@ -76,8 +76,8 @@ def __init__(self, elements: Collection, regular: bool = True, **kwargs) -> None
             for e in self._boundary:
                 if e[0] in _adjdict:
                     raise ValueError(
-                        f" Node {e[0]} is repeated multiple times in the input cell."
-                        + " Input cell violates the cell complex regularity condition."
+                        f"Node {e[0]} is repeated multiple times in the input cell. "
+                        "Input cell violates the cell complex regularity condition."
                     )
                 _adjdict[e[0]] = e[1]
         else:

toponetx/classes/cell_complex.py

@@ -324,9 +324,9 @@ def __iter__(self) -> Iterator:
             Iterator over nodes.
         """
         return chain(
-            map(lambda x: (x,), self.nodes),
+            ((x,) for x in self.nodes),
             self.edges,
-            map(lambda cell: tuple(cell), self.cells),
+            (tuple(cell) for cell in self.cells),
         )
 
     def __contains__(self, item) -> bool:
@@ -624,7 +624,7 @@ def cell_neighbors(self, cell, s: int = 1):
         list
             List of cell neighbors.
         """
-        raise NotImplementedError()
+        raise NotImplementedError
 
     def remove_node(self, node: Hashable) -> None:
         """Remove the given node from the cell complex.

toponetx/classes/colored_hypergraph.py

@@ -1355,7 +1355,7 @@ def from_trimesh(cls, mesh: trimesh.Trimesh):
         >>> CHG = tnx.ColoredHyperGraph.from_trimesh(mesh)
         >>> CHG.nodes
         """
-        raise NotImplementedError()
+        raise NotImplementedError
 
     def restrict_to_cells(self, cell_set):
         """Construct a Colored Hypergraph using a subset of the cells.

toponetx/classes/combinatorial_complex.py

@@ -599,13 +599,13 @@ def _CCC_condition(self, hyperedge_: set, rank: int) -> None:
                     if rank > e_rank and existing_hyperedge.issuperset(hyperedge_):
                         raise ValueError(
                             "a violation of the combinatorial complex condition:"
-                            + f"the hyperedge {existing_hyperedge} in the complex has rank {e_rank} is larger than {rank}, the rank of the input hyperedge {hyperedge_} "
+                            f"the hyperedge {existing_hyperedge} in the complex has rank {e_rank} is larger than {rank}, the rank of the input hyperedge {hyperedge_} "
                         )
 
                     if rank < e_rank and hyperedge_.issuperset(existing_hyperedge):
                         raise ValueError(
                             "violation of the combinatorial complex condition : "
-                            + f"the hyperedge {existing_hyperedge} in the complex has rank {e_rank} is smaller than {rank}, the rank of the input hyperedge {hyperedge_} "
+                            f"the hyperedge {existing_hyperedge} in the complex has rank {e_rank} is smaller than {rank}, the rank of the input hyperedge {hyperedge_} "
                         )
 
     def _add_hyperedge(self, hyperedge, rank, **attr):

toponetx/classes/simplex.py

@@ -126,7 +126,6 @@ def construct_simplex_tree(elements: Collection) -> frozenset["Simplex"]:
         frozenset[Simplex]
             The set of faces of the simplex.
         """
-
         faceset = set()
         for r in range(len(elements), 0, -1):
             for face in combinations(elements, r):
@@ -165,7 +164,7 @@ def sign(self, face) -> int:
         face : Simplex
             A face of the simplex.
         """
-        raise NotImplementedError()
+        raise NotImplementedError
 
     @property
     @deprecated(

toponetx/classes/simplicial_complex.py

@@ -877,7 +877,10 @@ def incidence_matrix(
                 values.append((-1) ** i)
                 face = frozenset(simplex).difference({left_out})
                 idx_faces.append(simplex_dict_d_minus_1[tuple(sorted(face))])
-        assert len(values) == (rank + 1) * len(simplex_dict_d)
+
+        if len(values) != (rank + 1) * len(simplex_dict_d):
+            raise RuntimeError("Error in computing the incidence matrix.")
+
         boundary = csr_matrix(
             (values, (idx_faces, idx_simplices)),
             dtype=np.float32,
@@ -1313,8 +1316,7 @@ def add_elements_from_nx_graph(self, G: nx.Graph) -> None:
         G : networkx.Graph
             A networkx graph instance.
         """
-        _simplices = list(G.edges) + list(map(lambda n: [n], G.nodes))
-
+        _simplices = [[n] for n in G.nodes] + list(G.edges)
         self.add_simplices_from(_simplices)
 
     def restrict_to_simplices(self, cell_set) -> Self:

toponetx/datasets/graph.py

@@ -184,7 +184,8 @@ def coauthorship() -> SimplicialComplex:
 
     if not dataset_file.exists():
         r = requests.get(
-            "https://github.com/pyt-team/topological-datasets/raw/main/resources/coauthorship.npy"
+            "https://github.com/pyt-team/topological-datasets/raw/main/resources/coauthorship.npy",
+            timeout=10,
         )
         with dataset_file.open("wb") as f:
             f.write(r.content)

toponetx/datasets/mesh.py

@@ -78,7 +78,8 @@ def stanford_bunny(
 
     if not dataset_file.exists():
         r = requests.get(
-            "https://github.com/pyt-team/topological-datasets/raw/main/resources/bunny.obj"
+            "https://github.com/pyt-team/topological-datasets/raw/main/resources/bunny.obj",
+            timeout=10,
         )
         with dataset_file.open("wb") as f:
             f.write(r.content)
@@ -145,7 +146,7 @@ def shrec_16(size: Literal["full", "small"] = "full"):
 
     if not training.exists() or not testing.exists():
         print(f"downloading shrec 16 {size} dataset...\n")
-        r = requests.get(url)
+        r = requests.get(url, timeout=10)
         with zipfile.ZipFile(BytesIO(r.content)) as zip_ref:
             zip_ref.extractall(DIR)
         print("done!")
@@ -211,7 +212,7 @@ def coseg(data: Literal["alien", "vase", "chair"] = "alien"):
 
     if not unziped_file.exists():
         print(f"downloading {data} dataset...\n")
-        r = requests.get(url)
+        r = requests.get(url, timeout=10)
         with zipfile.ZipFile(BytesIO(r.content)) as zip_ref:
             zip_ref.extractall(DIR)
         print("done!")

toponetx/datasets/utils.py

@@ -45,13 +45,13 @@ def load_ppi():
     ]
     proteins = "%0d".join(protein_list)
     url = f"https://string-db.org/api/tsv/network?identifiers={proteins}&species=9606"
-    r = requests.get(url)
+    r = requests.get(url, timeout=10)
 
     lines = r.text.split("\n")
     data = [line.split("\t") for line in lines]
-    df = pd.DataFrame(data[1:-1], columns=data[0])
+    protein_df = pd.DataFrame(data[1:-1], columns=data[0])
 
-    interactions = df[["preferredName_A", "preferredName_B", "score"]]
+    interactions = protein_df[["preferredName_A", "preferredName_B", "score"]]
 
     G = nx.Graph(name="Protein Interaction Graph")
     interactions = np.array(interactions)

toponetx/readwrite/serialization.py

@@ -1,6 +1,7 @@
 """Read and write complexes as pickled objects."""
 
 import pickle
+from pathlib import Path
 
 __all__ = ["to_pickle", "load_from_pickle"]
 
@@ -12,10 +13,10 @@ def to_pickle(obj, filename: str) -> None:
     ----------
     obj : object
         Object to write.
-    filename : str
+    filename : Path or str
         Filename.
     """
-    with open(filename, "wb") as f:
+    with Path(filename).open("wb") as f:
         pickle.dump(obj, f)
 
 
@@ -24,13 +25,13 @@ def load_from_pickle(filepath):
 
     Parameters
     ----------
-    filepath : str
+    filepath : Path or str
         Filepath.
 
     Returns
     -------
     object
         Object.
     """
-    with open(filepath, "rb") as f:
-        return pickle.load(f)
+    with Path(filepath).open("rb") as f:
+        return pickle.load(f)  # noqa: S301

toponetx/utils/normalization.py

@@ -65,7 +65,9 @@ def compute_x_laplacian_normalized_matrix(L: csr_matrix, Lx: csr_matrix) -> csr_
     This function normalizes the up or down Laplacian matrices by dividing them
     by the largest eigenvalue of the Laplacian matrix.
     """
-    assert L.shape[0] == L.shape[1]
+    if not L.shape[0] == L.shape[1]:
+        raise ValueError("Laplacian matrix must be square.")
+
     topeig = spl.eigsh(L.asfptype(), k=1, which="LM", return_eigenvectors=False)[0]
     return Lx * (1.0 / topeig)