[pre-commit.ci] pre-commit autoupdate (#439)

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

updates:
- [github.com/psf/black-pre-commit-mirror: 25.12.0 → 26.1.0](psf/black-pre-commit-mirror@25.12.0...26.1.0)

* [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

@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.12.0
+    rev: 26.1.0
     hooks:
     - id: black
 -   repo: https://github.com/pre-commit/pre-commit-hooks

graphein/grn/parse_regnetwork.py

@@ -46,10 +46,8 @@ def _download_RegNetwork(
     # Ping server to check if file is available
     ping_result = ping("regnetworkweb.org")
     if not ping_result:
-        log.warning(
-            "RegNetwork is not available. Please check your internet \
-            connection or verify at: http://www.regnetworkweb.org"
-        )
+        log.warning("RegNetwork is not available. Please check your internet \
+            connection or verify at: http://www.regnetworkweb.org")
 
     mouse_url = "https://regnetworkweb.org/download/mouse.zip"
 

graphein/protein/features/nodes/dssp.py

@@ -244,10 +244,8 @@ def add_dssp_feature(G: nx.Graph, feature: str) -> nx.Graph:
 
             G.nodes[n][feature] = dssp_df.loc[residue, feature]
         """
-        raise NameError(
-            f"DSSP residue features ({feature}) \
-            cannot be added to atom granularity graph"
-        )
+        raise NameError(f"DSSP residue features ({feature}) \
+            cannot be added to atom granularity graph")
 
     else:
         nx.set_node_attributes(G, dict(dssp_df[feature]), feature)

graphein/protein/graphs.py

@@ -914,10 +914,8 @@ def _mp_graph_constructor(
     :return: Protein structure graph or ``None`` if an error is encountered.
     :rtype: Union[nx.Graph, None]
     """
-    log.info(
-        f"Constructing graph for: {args[0]}. Chain selection: {args[1]}. \
-            Model index: {args[2]}"
-    )
+    log.info(f"Constructing graph for: {args[0]}. Chain selection: {args[1]}. \
+            Model index: {args[2]}")
     func = partial(construct_graph, config=config)
     try:
         if source == "pdb_code":
@@ -936,10 +934,8 @@ def _mp_graph_constructor(
             )
 
     except Exception as ex:
-        log.info(
-            f"Graph construction error (PDB={args[0]})! \
-                {traceback.format_exc()}"
-        )
+        log.info(f"Graph construction error (PDB={args[0]})! \
+                {traceback.format_exc()}")
         log.info(ex)
         return None
 
@@ -1232,10 +1228,8 @@ def compute_secondary_structure_graph(
                 ss_list[u], ss_list[v], kind=d["kind"], source=f"{u}_{v}"
             )
         except KeyError as e:
-            log.debug(
-                f"Edge {u}-{v} not added to secondary structure graph. \
-                Reason: {e} not in graph"
-            )
+            log.debug(f"Edge {u}-{v} not added to secondary structure graph. \
+                Reason: {e} not in graph")
 
     # Remove self-loops if necessary.
     # Checks for equality between nodes in a given edge.

graphein/protein/utils.py

@@ -238,10 +238,8 @@ def download_pdb(
                 new_pdb, out_dir, format=format, overwrite=overwrite
             )
         except KeyError:
-            log.warning(
-                f"PDB {pdb_code} not found. Possibly too large; large \
-                    structures are only provided as mmCIF files."
-            )
+            log.warning(f"PDB {pdb_code} not found. Possibly too large; large \
+                    structures are only provided as mmCIF files.")
             return
 
     # Check if PDB already exists