run precommit, align with pep8 naming convention

biocypher/_core.py

@@ -286,9 +286,7 @@ def write_nodes(
         else:
             tnodes = nodes
         # write node files
-        return self._writer.write_nodes(
-            tnodes, batch_size=batch_size
-        )
+        return self._writer.write_nodes(tnodes, batch_size=batch_size)
 
     def write_edges(self, edges, batch_size: int = int(1e6)) -> bool:
         """

biocypher/write/_batch_writer.py

@@ -6,8 +6,8 @@
 import re
 import glob
 
-from more_itertools import peekable
 from rdflib import Graph
+from more_itertools import peekable
 
 from biocypher._create import BioCypherEdge, BioCypherNode, BioCypherRelAsNode
 from biocypher._logger import logger
@@ -119,7 +119,7 @@ def __init__(
         db_host: str = None,
         db_port: str = None,
         rdf_format: str = None,
-        rdf_namespaces: dict = {}
+        rdf_namespaces: dict = {},
     ):
         """
 
@@ -199,10 +199,10 @@ class contains all methods expected by a bach writer instance, some of
 
             db_port:
                 The database port.
-            
+
             rdf_format:
                 The format of RDF.
-            
+
             rdf_namespaces:
                 The namespaces for RDF.
         """

biocypher/write/_write.py

@@ -14,11 +14,11 @@
 """
 
 from biocypher._logger import logger
+from biocypher.write.graph._rdf import _RDFWriter
 from biocypher.write.graph._neo4j import _Neo4jBatchWriter
 from biocypher.write.graph._arangodb import _ArangoDBBatchWriter
 from biocypher.write.relational._sqlite import _SQLiteBatchWriter
 from biocypher.write.relational._postgresql import _PostgreSQLBatchWriter
-from biocypher.write.graph._rdf import _RDFwriter
 
 logger.debug(f"Loading module {__name__}.")
 
@@ -44,8 +44,8 @@
     "ArangoDB": _ArangoDBBatchWriter,
     "sqlite": _SQLiteBatchWriter,
     "sqlite3": _SQLiteBatchWriter,
-    "rdf": _RDFwriter,
-    "RDF": _RDFwriter,
+    "rdf": _RDFWriter,
+    "RDF": _RDFWriter,
 }
 
 
@@ -105,6 +105,6 @@ def get_writer(
             db_user=dbms_config.get("user"),  # psql
             db_password=dbms_config.get("password"),  # psql
             db_port=dbms_config.get("port"),  # psql
-            rdf_format= dbms_config.get("rdf_format"), # rdf
-            rdf_namespaces= dbms_config.get("rdf_namespaces")# rdf
+            rdf_format=dbms_config.get("rdf_format"),  # rdf
+            rdf_namespaces=dbms_config.get("rdf_namespaces"),  # rdf
         )