Formatting

.gitignore

@@ -173,4 +173,7 @@ notebooks/tmp
 *.pickle
 
 # wandb
-wandb/
+wandb/
+
+# ruff
+.ruff_cache/

.pre-commit-config.yaml

@@ -17,14 +17,14 @@ repos:
           - --maxkb=2048
       - id: requirements-txt-fixer
 
-  # - repo: https://github.com/astral-sh/ruff-pre-commit
-  #   rev: v0.4.4
-  #   hooks:
-  #     - id: ruff
-  #       args: [ --fix ]
-  #     - id: ruff-format
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
 
-  # - repo: https://github.com/numpy/numpydoc
-  #   rev: v1.6.0
-  #   hooks:
-  #     - id: numpydoc-validation
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.6.0
+    hooks:
+      - id: numpydoc-validation

pyproject.toml

@@ -92,7 +92,8 @@ wrap-descriptions = 79
 
 [tool.ruff]
 target-version = "py310"
-extend-include = ["*.ipynb"]
+#extend-include = ["*.ipynb"]
+extend-exclude = ["test", "tutorials", "notebooks"]
 line-length = 79  # PEP 8 standard for maximum line length
 
 [tool.ruff.format]
@@ -128,7 +129,7 @@ ignore = [
 [tool.ruff.lint.pydocstyle]
 convention = "numpy"
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["F403"]
 
 [tool.setuptools.dynamic]

topobenchmarkx/data/utils/__init__.py

@@ -1,11 +1,12 @@
+# numpydoc ignore=GL08
 from .utils import (
-    ensure_serializable,
-    generate_zero_sparse_connectivity,
-    get_complex_connectivity,
-    load_cell_complex_dataset,
-    load_manual_graph,
-    load_simplicial_dataset,
-    make_hash,
+    ensure_serializable,  # noqa: F401
+    generate_zero_sparse_connectivity,  # noqa: F401
+    get_complex_connectivity,  # noqa: F401
+    load_cell_complex_dataset,  # noqa: F401
+    load_manual_graph,  # noqa: F401
+    load_simplicial_dataset,  # noqa: F401
+    make_hash,  # noqa: F401
 )
 
 utils_functions = [
@@ -14,12 +15,14 @@
     "load_cell_complex_dataset",
     "load_simplicial_dataset",
     "load_manual_graph",
+    "make_hash",
+    "ensure_serializable",
 ]
 
-from .split_utils import (
-    load_coauthorship_hypergraph_splits,
-    load_inductive_splits,
-    load_transductive_splits,
+from .split_utils import (  # noqa: E402
+    load_coauthorship_hypergraph_splits,  # noqa: F401
+    load_inductive_splits,  # noqa: F401
+    load_transductive_splits,  # noqa: F401
 )
 
 split_helper_functions = [
@@ -28,10 +31,10 @@
     "load_transductive_splits",
 ]
 
-from .io_utils import (
-    download_file_from_drive,
-    load_hypergraph_pickle_dataset,
-    read_us_county_demos,
+from .io_utils import (  # noqa: E402
+    download_file_from_drive,  # noqa: F401
+    load_hypergraph_pickle_dataset,  # noqa: F401
+    read_us_county_demos,  # noqa: F401
 )
 
 io_helper_functions = [

topobenchmarkx/transforms/data_manipulations/keep_selected_data_fields.py

@@ -1,7 +1,10 @@
+# numpydoc ignore=GL08,PR01,RT01
 import torch_geometric
 
 
-class KeepSelectedDataFields(torch_geometric.transforms.BaseTransform):
+class KeepSelectedDataFields(
+    torch_geometric.transforms.BaseTransform
+):  # numpydoc ignore=PR01
     r"""A transform that keeps only the selected fields of the input data.
 
     Args:
@@ -16,7 +19,9 @@ def __init__(self, **kwargs):
     def __repr__(self) -> str:
         return f"{self.__class__.__name__}(type={self.type!r}, parameters={self.parameters!r})"
 
-    def forward(self, data: torch_geometric.data.Data):
+    def forward(
+        self, data: torch_geometric.data.Data
+    ):  # numpydoc ignore=GL08,PR01,RT01
         r"""Apply the transform to the input data.
 
         Args:
@@ -30,7 +35,7 @@ def forward(self, data: torch_geometric.data.Data):
             + self.parameters["preserved_fields"]
         )
 
-        for key in data.keys():
+        for key in data:
             if key not in fields_to_keep:
                 del data[key]
         return data