Update to ruff 0.8

pyt-team · Dec 3, 2024 · 6142b71 · 6142b71
1 parent 3540143
commit 6142b71
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.8.1
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

diff --git a/pyproject.toml b/pyproject.toml
@@ -111,7 +111,7 @@ select = [
     "SLOT", # slot rules
     "SIM", # code simplifications
     "TID", # tidy imports
-    "TCH", # type checking rules
+    "TC", # type checking rules
     "PTH", # use pathlib
     "PD", # pandas rules
     "PLC", # pylint conventions

diff --git a/toponetx/algorithms/components.py b/toponetx/algorithms/components.py
@@ -10,10 +10,10 @@
 from toponetx.classes.combinatorial_complex import CombinatorialComplex
 
 __all__ = [
-    "s_connected_components",
-    "s_component_subcomplexes",
-    "connected_components",
     "connected_component_subcomplexes",
+    "connected_components",
+    "s_component_subcomplexes",
+    "s_connected_components",
 ]
 
 # In this module, only cell complexes, combinatorial complexes and colored

diff --git a/toponetx/algorithms/distance.py b/toponetx/algorithms/distance.py
@@ -11,7 +11,7 @@
 from toponetx.classes.hyperedge import HyperEdge
 from toponetx.exception import TopoNetXNoPath
 
-__all__ = ["distance", "cell_distance"]
+__all__ = ["cell_distance", "distance"]
 
 # In this module, only cell complexes, combinatorial complexes and colored
 # hypergraphs are supported.

diff --git a/toponetx/algorithms/distance_measures.py b/toponetx/algorithms/distance_measures.py
@@ -8,7 +8,7 @@
 from toponetx.classes.colored_hypergraph import ColoredHyperGraph
 from toponetx.classes.combinatorial_complex import CombinatorialComplex
 
-__all__ = ["node_diameters", "cell_diameters", "diameter", "cell_diameter"]
+__all__ = ["cell_diameter", "cell_diameters", "diameter", "node_diameters"]
 
 # In this module, only cell complexes, combinatorial complexes and colored
 # hypergraphs are supported.

diff --git a/toponetx/algorithms/spectrum.py b/toponetx/algorithms/spectrum.py
@@ -13,16 +13,16 @@
 from toponetx.classes.simplicial_complex import SimplicialComplex
 
 __all__ = [
-    "hodge_laplacian_eigenvectors",
-    "set_hodge_laplacian_eigenvector_attrs",
     "_normalize",
+    "cell_complex_adjacency_spectrum",
+    "cell_complex_hodge_laplacian_spectrum",
+    "combinatorial_complex_adjacency_spectrum",
+    "hodge_laplacian_eigenvectors",
     "laplacian_beltrami_eigenvectors",
     "laplacian_spectrum",
-    "cell_complex_hodge_laplacian_spectrum",
-    "simplicial_complex_hodge_laplacian_spectrum",
-    "cell_complex_adjacency_spectrum",
+    "set_hodge_laplacian_eigenvector_attrs",
     "simplicial_complex_adjacency_spectrum",
-    "combinatorial_complex_adjacency_spectrum",
+    "simplicial_complex_hodge_laplacian_spectrum",
 ]
 
 
@@ -42,11 +42,11 @@ def _normalize(f: dict[Any, Any]) -> dict[Any, Any]:
     minf = min(f.values())
     maxf = max(f.values())
     f_normalized = {}
-    for v in f:
+    for key, value in f.items():
         if minf == maxf:
-            f_normalized[v] = 0
+            f_normalized[key] = 0
         else:
-            f_normalized[v] = (f[v] - minf) / (maxf - minf)
+            f_normalized[key] = (value - minf) / (maxf - minf)
 
     return f_normalized
 

diff --git a/toponetx/classes/__init__.py b/toponetx/classes/__init__.py
@@ -21,22 +21,22 @@
 from .simplicial_complex import SimplicialComplex
 
 __all__ = [
-    "CellComplex",
-    "Cell",
-    "CombinatorialComplex",
-    "ColoredHyperGraph",
     "Atom",
     "AtomView",
+    "Cell",
+    "CellComplex",
+    "CellView",
+    "ColoredHyperEdgeView",
+    "ColoredHyperGraph",
+    "CombinatorialComplex",
     "Complex",
     "HyperEdge",
     "HyperEdgeView",
-    "ColoredHyperEdgeView",
-    "CellView",
-    "SimplexView",
     "NodeView",
+    "Path",
+    "PathComplex",
     "PathView",
     "Simplex",
+    "SimplexView",
     "SimplicialComplex",
-    "Path",
-    "PathComplex",
 ]
diff --git a/toponetx/classes/reportviews.py b/toponetx/classes/reportviews.py
@@ -17,12 +17,12 @@
 
 __all__ = [
     "AtomView",
-    "HyperEdgeView",
-    "ColoredHyperEdgeView",
     "CellView",
-    "SimplexView",
+    "ColoredHyperEdgeView",
+    "HyperEdgeView",
     "NodeView",
     "PathView",
+    "SimplexView",
 ]
 
 T_Atom = TypeVar("T_Atom", bound=Atom)

diff --git a/toponetx/datasets/graph.py b/toponetx/datasets/graph.py
@@ -12,7 +12,7 @@
 from toponetx.classes.simplicial_complex import SimplicialComplex
 from toponetx.transform.graph_to_simplicial_complex import graph_to_clique_complex
 
-__all__ = ["karate_club", "coauthorship"]
+__all__ = ["coauthorship", "karate_club"]
 
 DIR = Path(__file__).parent
 

diff --git a/toponetx/datasets/mesh.py b/toponetx/datasets/mesh.py
@@ -11,7 +11,7 @@
 from toponetx.classes.cell_complex import CellComplex
 from toponetx.classes.simplicial_complex import SimplicialComplex
 
-__all__ = ["stanford_bunny", "shrec_16", "coseg"]
+__all__ = ["coseg", "shrec_16", "stanford_bunny"]
 
 DIR = Path(__file__).parent
 SHREC_DS_MAP = {

diff --git a/toponetx/exception.py b/toponetx/exception.py
@@ -1,10 +1,10 @@
 """Base errors and exceptions for TopoNetX."""
 
 __all__ = [
-    "TopoNetXException",
     "TopoNetXAlgorithmError",
-    "TopoNetXUnfeasible",
+    "TopoNetXException",
     "TopoNetXNoPath",
+    "TopoNetXUnfeasible",
 ]
 
 

diff --git a/toponetx/generators/classic_cell_complexes.py b/toponetx/generators/classic_cell_complexes.py
@@ -3,7 +3,7 @@
 from toponetx.classes import CellComplex
 from toponetx.classes.cell import Cell
 
-__all__ = ["single_cell_complex", "pyrmaid_complex"]
+__all__ = ["pyrmaid_complex", "single_cell_complex"]
 
 
 def single_cell_complex(n: int) -> CellComplex:

diff --git a/toponetx/generators/random_simplicial_complexes.py b/toponetx/generators/random_simplicial_complexes.py
@@ -11,8 +11,8 @@
 
 __all__ = [
     "linial_meshulam_complex",
-    "random_clique_complex",
     "multiparameter_linial_meshulam_complex",
+    "random_clique_complex",
 ]
 
 

diff --git a/toponetx/readwrite/atomlist.py b/toponetx/readwrite/atomlist.py
@@ -10,9 +10,9 @@
 
 __all__ = [
     "generate_atomlist",
-    "write_atomlist",
     "load_from_atomlist",
     "parse_atomlist",
+    "write_atomlist",
 ]
 
 

diff --git a/toponetx/readwrite/serialization.py b/toponetx/readwrite/serialization.py
@@ -3,7 +3,7 @@
 import pickle
 from pathlib import Path
 
-__all__ = ["to_pickle", "load_from_pickle"]
+__all__ = ["load_from_pickle", "to_pickle"]
 
 
 def to_pickle(obj, filename: str) -> None:

diff --git a/toponetx/utils/normalization.py b/toponetx/utils/normalization.py
@@ -6,19 +6,19 @@
 from scipy.sparse import csr_matrix, diags
 
 __all__ = [
-    "compute_laplacian_normalized_matrix",
-    "compute_x_laplacian_normalized_matrix",
-    "compute_kipf_adjacency_normalized_matrix",
-    "compute_xu_asymmetric_normalized_matrix",
-    "compute_bunch_normalized_matrices",
-    "_compute_B1_normalized_matrix",
     "_compute_B1T_normalized_matrix",
-    "_compute_B2_normalized_matrix",
+    "_compute_B1_normalized_matrix",
     "_compute_B2T_normalized_matrix",
+    "_compute_B2_normalized_matrix",
     "_compute_D1",
     "_compute_D2",
     "_compute_D3",
     "_compute_D5",
+    "compute_bunch_normalized_matrices",
+    "compute_kipf_adjacency_normalized_matrix",
+    "compute_laplacian_normalized_matrix",
+    "compute_x_laplacian_normalized_matrix",
+    "compute_xu_asymmetric_normalized_matrix",
 ]
 
 

diff --git a/toponetx/utils/structure.py b/toponetx/utils/structure.py
@@ -30,11 +30,11 @@
 from scipy.sparse import csr_matrix
 
 __all__ = [
-    "sparse_array_to_neighborhood_list",
+    "compute_set_incidence",
+    "incidence_to_adjacency",
     "neighborhood_list_to_neighborhood_dict",
     "sparse_array_to_neighborhood_dict",
-    "incidence_to_adjacency",
-    "compute_set_incidence",
+    "sparse_array_to_neighborhood_list",
 ]
 
 

diff --git a/tutorials/01_simplicial_complexes.ipynb b/tutorials/01_simplicial_complexes.ipynb
@@ -18,14 +18,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "1d48b70e",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from IPython import display\n",
+    "from IPython.display import Image\n",
     "\n",
-    "display.Image(\"sc.png\")"
+    "Image(\"sc.png\")"
    ]
   },
   {

diff --git a/tutorials/02_cell_complexes.ipynb b/tutorials/02_cell_complexes.ipynb
@@ -18,16 +18,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "b4b84db3",
    "metadata": {},
    "outputs": [],
    "source": [
-    "from IPython import display\n",
+    "from IPython.display import Image\n",
     "\n",
-    "import toponetx\n",
+    "import toponetx as tnx\n",
     "\n",
-    "display.Image(\"cc.png\")"
+    "Image(\"cc.png\")"
    ]
   },
   {
@@ -141,12 +141,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "id": "a48e579f",
    "metadata": {},
    "outputs": [],
    "source": [
-    "example_1 = toponetx.CellComplex()\n",
+    "example_1 = tnx.CellComplex()\n",
     "print(example_1)\n",
     "\n",
     "example_1.add_cell([1, 2], rank=1)\n",
@@ -180,12 +180,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "866efb53",
    "metadata": {},
    "outputs": [],
    "source": [
-    "example_2 = toponetx.CellComplex()\n",
+    "example_2 = tnx.CellComplex()\n",
     "print(example_2)\n",
     "\n",
     "example_2.add_cell([1, 2, 3], rank=2)\n",

diff --git a/tutorials/03_combinatorial_complexes.ipynb b/tutorials/03_combinatorial_complexes.ipynb
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "8cd070d7",
    "metadata": {},
    "outputs": [
@@ -35,11 +35,11 @@
     }
    ],
    "source": [
-    "from IPython import display\n",
+    "from IPython.display import Image\n",
     "\n",
-    "import toponetx\n",
+    "import toponetx as tnx\n",
     "\n",
-    "display.Image(\"ccc.png\")"
+    "Image(\"ccc.png\")"
    ]
   },
   {
@@ -135,7 +135,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "id": "0ce2f1f7",
    "metadata": {},
    "outputs": [
@@ -152,7 +152,7 @@
     }
    ],
    "source": [
-    "example = toponetx.CombinatorialComplex()\n",
+    "example = tnx.CombinatorialComplex()\n",
     "\n",
     "example.add_cell([1, 2], rank=1)\n",
     "print(example)\n",

diff --git a/tutorials/04_colored_hypergraphs.ipynb b/tutorials/04_colored_hypergraphs.ipynb
@@ -18,7 +18,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "8cd070d7",
    "metadata": {},
    "outputs": [
@@ -35,9 +35,9 @@
     }
    ],
    "source": [
-    "from IPython import display\n",
+    "from IPython.display import Image\n",
     "\n",
-    "display.Image(\"chg.png\")"
+    "Image(\"chg.png\")"
    ]
   },
   {
@@ -54,7 +54,9 @@
    "id": "24d69d5e",
    "metadata": {},
    "outputs": [],
-   "source": "import toponetx as tnx"
+   "source": [
+    "import toponetx as tnx"
+   ]
   },
   {
    "cell_type": "markdown",