[pre-commit.ci] pre-commit autoupdate (#363)

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.1.1
     hooks:
     - id: black
 -   repo: https://github.com/pre-commit/pre-commit-hooks

graphein/cli.py

@@ -1,4 +1,5 @@
 """Command line interface for graphein."""
+
 import pathlib
 import pickle
 

graphein/grn/edges.py

@@ -1,4 +1,5 @@
 """Functions for adding edges to Gene Regulatory Networks from various sources."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>, Ramon Vinas

graphein/grn/features/node_features.py

@@ -1,4 +1,5 @@
 """Node featurisation utilities for Gene Regulatory Networks."""
+
 from typing import Any, Dict
 
 from bioservices import HGNC, UniProt

graphein/grn/graphs.py

@@ -1,4 +1,5 @@
 """Graph construction utilities for Gene Regulatory Networks."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>, Ramon Vinas
@@ -152,11 +153,11 @@ def edge_ann_fn(u, v, d):
     print(g.edges(data=True))
 
     edge_colors = [
-        "r"
-        if g[u][v]["kind"] == {"trrust"}
-        else "b"
-        if g[u][v]["kind"] == {"regnetwork"}
-        else "y"
+        (
+            "r"
+            if g[u][v]["kind"] == {"trrust"}
+            else "b" if g[u][v]["kind"] == {"regnetwork"} else "y"
+        )
         for u, v in g.edges()
     ]
 

graphein/grn/parse_regnetwork.py

@@ -1,4 +1,5 @@
 """Functions for parsing GRNs from RegNetwork."""
+
 # %%
 # Graphein
 # Author: Ramon Vinas, Arian Jamasb <arian@jamasb.io>

graphein/grn/parse_trrust.py

@@ -1,4 +1,5 @@
 """Utilities for parsing the TRRUST database."""
+
 # %%
 # Graphein
 # Author: Ramon Vinas, Arian Jamasb <arian@jamasb.io>

graphein/ml/conversion.py

@@ -1,5 +1,6 @@
 """Utilities for converting Graphein Networks to Geometric Deep Learning formats.
 """
+
 # %%
 # Graphein
 # Author: Kexin Huang, Arian Jamasb <arian@jamasb.io>

graphein/ml/datasets/foldcomp_dataset.py

@@ -1,4 +1,5 @@
 """Utilities for loading FoldComp databases for deep learning."""
+
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>
 # License: MIT

graphein/ml/datasets/torch_geometric_dataset.py

@@ -1,4 +1,5 @@
 """Pytorch Geometric Dataset classes for Protein Graphs."""
+
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>
 # License: MIT
@@ -164,9 +165,9 @@ def __init__(
         elif self.uniprot_ids:
             self.structures = uniprot_ids
         self.af_version = af_version
-        self.bad_pdbs: List[
-            str
-        ] = []  # list of pdb codes that failed to download
+        self.bad_pdbs: List[str] = (
+            []
+        )  # list of pdb codes that failed to download
 
         # Labels & Chains
         self.graph_label_map = graph_label_map
@@ -265,9 +266,11 @@ def process(self):
 
         if self.chain_selection_map:
             chain_selections = [
-                self.chain_selection_map[pdb]
-                if pdb in self.chain_selection_map.keys()
-                else "all"
+                (
+                    self.chain_selection_map[pdb]
+                    if pdb in self.chain_selection_map.keys()
+                    else "all"
+                )
                 for pdb in self.structures
             ]
         else:

graphein/ml/diffusion.py

@@ -6,6 +6,7 @@
 and returns a 2D xarray.
 These arrays can then be stacked to generate a diffusion tensor.
 """
+
 from typing import Dict
 
 import networkx as nx

graphein/ml/utils.py

@@ -1,4 +1,5 @@
 """ML utility Functions for working with graphs."""
+
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>
 # License: MIT

graphein/ml/visualisation.py

@@ -1,4 +1,5 @@
 """Visualisation utils for ML."""
+
 from __future__ import annotations
 
 import itertools

graphein/molecule/atoms.py

@@ -5,6 +5,7 @@
 
 These include various collections of standard atom types used molecule-focussed ML
 """
+
 # Graphein
 # Author: Eric J. Ma, Arian Jamasb <arian@jamasb.io>
 # License: MIT

graphein/molecule/chembl.py

@@ -1,4 +1,5 @@
 """Functions for retrieving molecular data from ChEMBL."""
+
 from typing import Any, Dict
 
 import networkx as nx

graphein/molecule/config.py

@@ -1,4 +1,5 @@
 """Base Config object for use with Molecule Graph Construction."""
+
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>
 # License: MIT

graphein/molecule/edges/atomic.py

@@ -1,4 +1,5 @@
 """Functions for computing atomic structure of molecules."""
+
 import networkx as nx
 
 # %%

graphein/molecule/features/edges/bonds.py

@@ -1,4 +1,5 @@
 """Functions for computing atomic features for molecules."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>

graphein/molecule/features/graph/molecule.py

@@ -1,4 +1,5 @@
 """Functions for featurising Small Molecule Graphs."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>

graphein/molecule/features/nodes/atom_type.py

@@ -1,4 +1,5 @@
 """Functions for featurising Small Molecule Graphs."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>, Yuanqi Du

graphein/molecule/graphs.py

@@ -1,4 +1,5 @@
 """Functions for working with Small Molecule Graphs."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>, Eric Ma, Charlie Harris

graphein/molecule/utils.py

@@ -4,6 +4,7 @@
 
 Junction tree code adapted from Wengong Jin https://github.com/wengong-jin/icml18-jtnn
 """
+
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>
 # License: MIT

graphein/molecule/visualisation.py

@@ -2,6 +2,7 @@
 
 Plotting functions for molecules wrap the methods defined on protein graphs and provide sane defaults.
 """
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>

graphein/molecule/zinc.py

@@ -2,6 +2,7 @@
 
 Adapted from smilite (https://github.com/rasbt/smilite) by Sebastian Raschka.
 """
+
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>
 # License: MIT

graphein/ppi/config.py

@@ -26,18 +26,18 @@ class STRINGConfig(BaseModel):
     """
 
     species: Optional[int] = 9606  # NCBI taxon identifiers
-    required_score: Optional[
-        int
-    ] = 50  # threshold of significance to include a interaction, a number between 0 and 1000 (default depends on the network)
-    network_type: Optional[
-        str
-    ] = "functional"  # network type: functional (default), physical
-    add_nodes: Optional[
-        int
-    ] = 0  # adds a number of proteins to the network based on their confidence score, e.g., extends the interaction neighborhood of selected proteins to desired value
-    show_query_node_labels: Optional[
-        bool
-    ] = 0  # when available use submitted names in the preferredName column when (0 or 1) (default:0)
+    required_score: Optional[int] = (
+        50  # threshold of significance to include a interaction, a number between 0 and 1000 (default depends on the network)
+    )
+    network_type: Optional[str] = (
+        "functional"  # network type: functional (default), physical
+    )
+    add_nodes: Optional[int] = (
+        0  # adds a number of proteins to the network based on their confidence score, e.g., extends the interaction neighborhood of selected proteins to desired value
+    )
+    show_query_node_labels: Optional[bool] = (
+        0  # when available use submitted names in the preferredName column when (0 or 1) (default:0)
+    )
 
 
 class BioGridConfig(BaseModel):
@@ -82,58 +82,58 @@ class BioGridConfig(BaseModel):
     :type throughputTag: str, optional
     """
 
-    searchNames: Optional[
-        bool
-    ] = True  # If ‘true’, the interactor OFFICIAL_SYMBOL will be examined for a match with the geneList.
+    searchNames: Optional[bool] = (
+        True  # If ‘true’, the interactor OFFICIAL_SYMBOL will be examined for a match with the geneList.
+    )
     max: Optional[int] = 10000  # Number of results to fetch
-    interSpeciesExcluded: Optional[
-        bool
-    ] = True  # If ‘true’, interactions with interactors from different species will be excluded.
-    selfInteractionsExcluded: Optional[
-        bool
-    ] = False  # If ‘true’, interactions with one interactor will be excluded.
-    evidenceList: Optional[
-        str
-    ] = ""  # Any interaction evidence with its Experimental System in the list will be excluded from the results unless includeEvidence is set to true.
-    includeEvidence: Optional[
-        bool
-    ] = False  # If set to true, any interaction evidence with its Experimental System in the evidenceList will be included in the result
-    searchIds: Optional[
-        bool
-    ] = True  # If ‘true’, the interactor ENTREZ_GENE, ORDERED LOCUS and SYSTEMATIC_NAME (orf) will be examined for a match with the geneList.
-    searchNames: Optional[
-        bool
-    ] = True  # If ‘true’, the interactor OFFICIAL_SYMBOL will be examined for a match with the geneList.
-    searchSynonyms: Optional[
-        bool
-    ] = True  # If ‘true’, the interactor SYNONYMS will be examined for a match with the geneList.
-    searchBiogridIds: Optional[
-        bool
-    ] = True  # If ‘true’, the entries in 'GENELIST' will be compared to BIOGRID internal IDS which are provided in all Tab2 formatted files.
-    additionalIdentifierTypes: Optional[
-        str
-    ] = ""  # Identifier types on this list are examined for a match with the geneList.
-    excludeGenes: Optional[
-        bool
-    ] = False  # If ‘true’, interactions containing genes in the geneList will be excluded from the results.
-    includeInteractors: Optional[
-        bool
-    ] = True  # If ‘true’, in addition to interactions between genes on the geneList, interactions will also be fetched which have only one interactor on the geneList
-    includeInteractorInteractions: Optional[
-        bool
-    ] = False  # If ‘true’ interactions between the geneList’s first order interactors will be included.
-    pubmedList: Optional[
-        str
-    ] = ""  # Interactions will be fetched whose Pubmed Id is/ is not in this list, depending on the value of excludePubmeds.
-    excludePubmeds: Optional[
-        bool
-    ] = False  # If ‘false’, interactions with Pubmed ID in pubmedList will be included in the results; if ‘true’ they will be excluded.
-    htpThreshold: Optional[
-        int
-    ] = 20  # Interactions whose Pubmed ID has more than this number of interactions will be excluded from the results. Ignored if excludePubmeds is ‘false’.
-    throughputTag: Optional[
-        str
-    ] = "any"  # If set to 'low or 'high', only interactions with 'Low throughput' or 'High throughput' in the 'throughput' field will be returned.
+    interSpeciesExcluded: Optional[bool] = (
+        True  # If ‘true’, interactions with interactors from different species will be excluded.
+    )
+    selfInteractionsExcluded: Optional[bool] = (
+        False  # If ‘true’, interactions with one interactor will be excluded.
+    )
+    evidenceList: Optional[str] = (
+        ""  # Any interaction evidence with its Experimental System in the list will be excluded from the results unless includeEvidence is set to true.
+    )
+    includeEvidence: Optional[bool] = (
+        False  # If set to true, any interaction evidence with its Experimental System in the evidenceList will be included in the result
+    )
+    searchIds: Optional[bool] = (
+        True  # If ‘true’, the interactor ENTREZ_GENE, ORDERED LOCUS and SYSTEMATIC_NAME (orf) will be examined for a match with the geneList.
+    )
+    searchNames: Optional[bool] = (
+        True  # If ‘true’, the interactor OFFICIAL_SYMBOL will be examined for a match with the geneList.
+    )
+    searchSynonyms: Optional[bool] = (
+        True  # If ‘true’, the interactor SYNONYMS will be examined for a match with the geneList.
+    )
+    searchBiogridIds: Optional[bool] = (
+        True  # If ‘true’, the entries in 'GENELIST' will be compared to BIOGRID internal IDS which are provided in all Tab2 formatted files.
+    )
+    additionalIdentifierTypes: Optional[str] = (
+        ""  # Identifier types on this list are examined for a match with the geneList.
+    )
+    excludeGenes: Optional[bool] = (
+        False  # If ‘true’, interactions containing genes in the geneList will be excluded from the results.
+    )
+    includeInteractors: Optional[bool] = (
+        True  # If ‘true’, in addition to interactions between genes on the geneList, interactions will also be fetched which have only one interactor on the geneList
+    )
+    includeInteractorInteractions: Optional[bool] = (
+        False  # If ‘true’ interactions between the geneList’s first order interactors will be included.
+    )
+    pubmedList: Optional[str] = (
+        ""  # Interactions will be fetched whose Pubmed Id is/ is not in this list, depending on the value of excludePubmeds.
+    )
+    excludePubmeds: Optional[bool] = (
+        False  # If ‘false’, interactions with Pubmed ID in pubmedList will be included in the results; if ‘true’ they will be excluded.
+    )
+    htpThreshold: Optional[int] = (
+        20  # Interactions whose Pubmed ID has more than this number of interactions will be excluded from the results. Ignored if excludePubmeds is ‘false’.
+    )
+    throughputTag: Optional[str] = (
+        "any"  # If set to 'low or 'high', only interactions with 'Low throughput' or 'High throughput' in the 'throughput' field will be returned.
+    )
 
 
 class PPIGraphConfig(BaseModel):

graphein/ppi/edges.py

@@ -1,4 +1,5 @@
 """Functions for adding edges to a PPI Graph from parsed STRING & BIOGRID API call outputs."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>, Ramon Vinas

graphein/ppi/features/node_features.py

@@ -1,4 +1,5 @@
 """Functions for adding nodes features to a PPI Graph."""
+
 # %%
 # Graphein
 # Author: Ramon Vinas, Arian Jamasb <arian@jamasb.io>
@@ -71,11 +72,11 @@ def add_sequence_to_nodes(n: str, d: Dict[str, Any]):
 
     print(nx.get_node_attributes(g, "sequence"))
     edge_colors = [
-        "r"
-        if g[u][v]["kind"] == {"string"}
-        else "b"
-        if g[u][v]["kind"] == {"biogrid"}
-        else "y"
+        (
+            "r"
+            if g[u][v]["kind"] == {"string"}
+            else "b" if g[u][v]["kind"] == {"biogrid"} else "y"
+        )
         for u, v in g.edges()
     ]
 

graphein/ppi/graph_metadata.py

@@ -1,4 +1,5 @@
 """Functions for adding metadata to PPI Graphs from STRING and BIOGRID."""
+
 # %%
 # Graphein
 # Author: Arian Jamasb <arian@jamasb.io>, Ramon Vinas