more flake8 fixes

src/pathme/normalize_names.py

@@ -10,8 +10,8 @@
 
 from pathme.constants import REACTOME, WIKIPATHWAYS
 from pathme.pybel_utils import multi_relabel
-from pybel import BELGraph
 
+from pybel import BELGraph
 from pybel.dsl import Abundance, BiologicalProcess, CentralDogma, ListAbundance, Reaction, MicroRna, Protein
 
 logger = logging.getLogger(__name__)

src/pathme/pybel_utils.py

@@ -7,14 +7,13 @@
 
 from pybel import BELGraph
 from pybel.dsl import BaseEntity
-
 from pybel_tools.node_utils import list_abundance_cartesian_expansion, reaction_cartesian_expansion
 
 logger = logging.getLogger(__name__)
 
 
 def flatten_complex_nodes(graph: BELGraph) -> None:
-    """Flatten complex nodes"""
+    """Flatten complex nodes."""
     logger.info("Flat complexes and composites")
     list_abundance_cartesian_expansion(graph)
     reaction_cartesian_expansion(graph)

src/pathme/reactome/rdf_sparql.py

@@ -12,10 +12,10 @@
 from pathme.constants import REACTOME_BEL
 from pathme.reactome.convert_to_bel import convert_to_bel
 from pathme.utils import get_pathway_statitics, parse_rdf, query_result_to_dict
+
 from pybel import to_pickle
 from rdflib import URIRef
 from rdflib.namespace import DC, DCTERMS, Namespace, OWL, RDF, RDFS, SKOS, XSD
-
 from tqdm import tqdm
 
 log = logging.getLogger(__name__)
@@ -232,9 +232,9 @@ def _get_pathway_components(pathway_uri: rdflib.URIRef, rdf_graph: rdflib.Graph)
         Dict[str, Dict[str, Union[str, Set[str]]]], List[Dict[str, Union[str, Set[str]]]]]:
     """Get components (nodes and interactions) for a given pathway.
 
-     :param pathway_uri: URI reference of the queried pathway
-     :param rdf_graph: RDF Reactome Universe graph object
-     :return: returns the pathway components as entities (Proteins, Complex, SmallMolecule...) and proteins (their links)
+    :param pathway_uri: URI reference of the queried pathway
+    :param rdf_graph: RDF Reactome Universe graph object
+    :return: returns the pathway components as entities (Proteins, Complex, SmallMolecule...) and proteins (their links)
     """
     interactions = {}
     nodes = {}

src/pathme/utils.py

@@ -195,7 +195,7 @@ def query_result_to_dict(entries, **kwargs) -> Dict[str, Dict[str, Dict[str, str
                 else:
                     entries_dict[id_key][label] = new_value
 
-    if len(entries_dict) == 1 and kwargs.get('id_dict') == False:
+    if len(entries_dict) == 1 and kwargs.get('id_dict') is False:
         return list(entries_dict.values())[0]
 
     elif not entries and 'attr_empty' in kwargs:
@@ -206,7 +206,7 @@ def query_result_to_dict(entries, **kwargs) -> Dict[str, Dict[str, Dict[str, str
             for attr in attr_empty
         }
 
-    if kwargs.get('ids_argument') == True:
+    if kwargs.get('ids_argument') is True:
         return entries_dict_ids_argument(entries_dict)
 
     else:

src/pathme/wikipathways/convert_to_bel.py

@@ -9,6 +9,7 @@
 from bio2bel_hgnc import Manager
 from pybel import BELGraph
 from pybel.dsl import BaseEntity, abundance, activity, bioprocess, complex_abundance, gene, protein, rna
+
 from .utils import check_multiple, evaluate_wikipathways_metadata, get_valid_gene_identifier
 from ..constants import ACTIVITY_ALLOWED_MODIFIERS, HGNC
 from ..utils import add_bel_metadata, parse_id_uri

src/pathme/wikipathways/rdf_sparql.py

@@ -76,12 +76,10 @@
    ?uri_id rdf:type ?uri_type .
 
    optional {?uri_id dcterms:identifier ?dc_identifier .}
-   
    optional {?uri_id wp:bdbHgncSymbol ?hgnc_uri .}
    optional {?uri_id wp:bdbEnsembl ?ensembl_uri .}
    optional {?uri_id wp:bdbEntrezGene ?ncbigene_uri .}
    optional {?uri_id wp:bdbUniprot ?uniprot_uri .}
-   
    optional {?uri_id wp:bdbChEBI ?chebi_uri .}
    optional {?uri_id wp:bdbChemspider ?chemspider_uri .}
    optional {?uri_id wp:bdbPubChem ?pubchem_uri .}
@@ -202,7 +200,7 @@ def _get_interactions(rdf_graph: rdflib.Graph) -> Dict[str, Dict]:
 
 
 def _get_pathway_components(graph) -> Tuple[
-    Dict[str, Dict[str, Dict[str, str]]], Dict[str, Dict[str, Dict[str, str]]], Dict[str, Dict[str, Dict[str, str]]]]:
+        Dict[str, Dict[str, Dict[str, str]]], Dict[str, Dict[str, Dict[str, str]]], Dict[str, Dict[str, Dict[str, str]]]]:
     """Get all components in data structures from a RDF pathway network.
 
     :param graph: RDF graph object
@@ -215,7 +213,7 @@ def _get_pathway_components(graph) -> Tuple[
 
 
 def get_wp_statistics(resource_files, resource_folder, hgnc_manager) -> Tuple[
-    Dict[str, Dict[str, int]], Dict[str, Dict[str, Dict[str, int]]]]:
+        Dict[str, Dict[str, int]], Dict[str, Dict[str, Dict[str, int]]]]:
     """Load WikiPathways RDF to BELGraph.
 
     :param iter[str] resource_files: RDF file path