[pre-commit.ci] pre-commit autoupdate (#417)

* [pre-commit.ci] pre-commit autoupdate

updates:
- [github.com/psf/black: 24.10.0 → 25.1.0](psf/black@24.10.0...25.1.0)
- [github.com/pycqa/isort: 5.13.2 → 6.0.0](PyCQA/isort@5.13.2...6.0.0)

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -9,14 +9,14 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
     - id: black
 -   repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
     - id: flake8
 -   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
     - id: isort

graphein/ml/conversion.py

@@ -1,5 +1,4 @@
-"""Utilities for converting Graphein Networks to Geometric Deep Learning formats.
-"""
+"""Utilities for converting Graphein Networks to Geometric Deep Learning formats."""
 
 # %%
 # Graphein

graphein/molecule/utils.py

@@ -337,7 +337,7 @@ def get_mol_weight(mol: Union[nx.Graph, Chem.Mol]) -> float:
 
 @requires_python_libs("rdkit")
 def get_qed_score(
-    mol: Union[nx.Graph, rdkit.Chem.rdchem.Mol]
+    mol: Union[nx.Graph, rdkit.Chem.rdchem.Mol],
 ) -> Union[float, None]:
     """Computes the Quantitative Estimate of Druglikeness (QED) score for a molecule or molecular graph.
 

graphein/rna/nussinov.py

@@ -1,5 +1,5 @@
 """Nussinov algorithm for computing RNA secondary structure adopted from
-adopted from https://github.com/cgoliver/Nussinov/blob/master/nussinov.py """
+adopted from https://github.com/cgoliver/Nussinov/blob/master/nussinov.py"""
 
 # %%
 # Graphein

graphein/utils/utils.py

@@ -358,7 +358,7 @@ def ping(host: str) -> bool:
 
 
 def parse_aggregation_type(
-    aggregation_type: Literal["sum", "mean", "max", "min", "median"]
+    aggregation_type: Literal["sum", "mean", "max", "min", "median"],
 ) -> Callable:
     """Returns an aggregation function by name