run pre-commit hooks

Author: sfluegel05

chebifier/cli.py

@@ -1,10 +1,8 @@
-import importlib.resources
-
 import click
-import yaml
 
 from chebifier.model_registry import ENSEMBLES
 
+
 @click.group()
 def cli():
     """Command line interface for Chebifier."""

chebifier/ensemble/base_ensemble.py

@@ -1,3 +1,4 @@
+import importlib
 import os
 import time
 from pathlib import Path
@@ -6,13 +7,17 @@
 import torch
 import tqdm
 import yaml
-import importlib
 
 from chebifier.check_env import check_package_installed
 from chebifier.hugging_face import download_model_files
 from chebifier.inconsistency_resolution import PredictionSmoother
 from chebifier.prediction_models.base_predictor import BasePredictor
-from chebifier.utils import get_disjoint_files, load_chebi_graph, get_default_configs, process_config
+from chebifier.utils import (
+    get_default_configs,
+    get_disjoint_files,
+    load_chebi_graph,
+    process_config,
+)
 
 
 class BaseEnsemble:
@@ -37,8 +42,8 @@ def __init__(
 
         with (
             importlib.resources.files("chebifier")
-                    .joinpath("model_registry.yml")
-                    .open("r") as f
+            .joinpath("model_registry.yml")
+            .open("r") as f
         ):
             model_registry = yaml.safe_load(f)
 

chebifier/inconsistency_resolution.py

@@ -1,8 +1,9 @@
 import csv
 import os
-import torch
 from pathlib import Path
 
+import torch
+
 
 def get_disjoint_groups(disjoint_files):
     if disjoint_files is None:

chebifier/model_registry.py

@@ -4,15 +4,15 @@
     WMVwithPPVNPVEnsemble,
 )
 from chebifier.prediction_models import (
+    ChEBILookupPredictor,
     ChemlogPeptidesPredictor,
     ElectraPredictor,
     ResGatedPredictor,
-    ChEBILookupPredictor,
 )
 from chebifier.prediction_models.c3p_predictor import C3PPredictor
 from chebifier.prediction_models.chemlog_predictor import (
-    ChemlogXMolecularEntityPredictor,
     ChemlogOrganoXCompoundPredictor,
+    ChemlogXMolecularEntityPredictor,
 )
 
 ENSEMBLES = {

chebifier/prediction_models/chemlog_predictor.py

@@ -2,8 +2,8 @@
 
 import tqdm
 
-from .base_predictor import BasePredictor
 from .. import modelwise_smiles_lru_cache
+from .base_predictor import BasePredictor
 
 AA_DICT = {
     "A": "L-alanine",

chebifier/utils.py

@@ -1,13 +1,13 @@
 import importlib.resources
 import os
+import pickle
 
+import fastobo
 import networkx as nx
 import requests
-import fastobo
 import yaml
 
 from chebifier.hugging_face import download_model_files
-import pickle
 
 
 def load_chebi_graph(filename=None):
@@ -131,8 +131,8 @@ def get_default_configs():
     print(f"Using default ensemble configuration from {default_config_name}")
     with (
         importlib.resources.files("chebifier")
-            .joinpath(default_config_name)
-            .open("r") as f
+        .joinpath(default_config_name)
+        .open("r") as f
     ):
         return yaml.safe_load(f)