From feaf75edd8d435fbb0ff95a08b8efe74dace431e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Feb 2025 00:00:10 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 24.10.0 → 25.1.0](https://github.com/psf/black/compare/24.10.0...25.1.0)
- [github.com/pycqa/isort: 5.13.2 → 6.0.0](https://github.com/pycqa/isort/compare/5.13.2...6.0.0)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 6855c315..29ccabc3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -9,7 +9,7 @@ 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
@@ -17,6 +17,6 @@ repos:
     hooks:
     - id: flake8
 -   repo: https://github.com/pycqa/isort
-    rev: 5.13.2
+    rev: 6.0.0
     hooks:
     - id: isort

From c16d8e1cd304db3685b3a35a669a22777b67d444 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 4 Feb 2025 00:00:31 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 graphein/ml/conversion.py  | 3 +--
 graphein/molecule/utils.py | 2 +-
 graphein/rna/nussinov.py   | 2 +-
 graphein/utils/utils.py    | 2 +-
 4 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/graphein/ml/conversion.py b/graphein/ml/conversion.py
index 2cb013d0..993c9626 100644
--- a/graphein/ml/conversion.py
+++ b/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
diff --git a/graphein/molecule/utils.py b/graphein/molecule/utils.py
index 4be3ed9e..193a542f 100644
--- a/graphein/molecule/utils.py
+++ b/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.
 
diff --git a/graphein/rna/nussinov.py b/graphein/rna/nussinov.py
index 5c5a8d00..7db836b0 100644
--- a/graphein/rna/nussinov.py
+++ b/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
diff --git a/graphein/utils/utils.py b/graphein/utils/utils.py
index 700eda56..8f2500a8 100644
--- a/graphein/utils/utils.py
+++ b/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