isort and black

rxnutils/chem/cgr.py

@@ -4,9 +4,9 @@
 import warnings
 from typing import List
 
-from CGRtools.files.SDFrw import SDFRead
-from CGRtools.containers.reaction import ReactionContainer
 from CGRtools.containers.molecule import MoleculeContainer
+from CGRtools.containers.reaction import ReactionContainer
+from CGRtools.files.SDFrw import SDFRead
 from rdkit import Chem
 
 from rxnutils.chem.reaction import ChemicalReaction

rxnutils/chem/reaction.py

@@ -1,19 +1,16 @@
 """Module containing a class to handle chemical reactions"""
 import hashlib
-from typing import List, Tuple, Optional, Dict, Any
+from typing import Any, Dict, List, Optional, Tuple
 
 import wrapt_timeout_decorator
+from rdchiral import template_extractor as extractor
 from rdkit import Chem
 from rdkit.Chem import AllChem
-from rdchiral import template_extractor as extractor
 
-from rxnutils.chem.rinchi import rinchi_api
 from rxnutils.chem import utils
+from rxnutils.chem.rinchi import rinchi_api
 from rxnutils.chem.template import ReactionTemplate
-from rxnutils.chem.utils import (
-    reassign_rsmi_atom_mapping,
-    split_smiles_from_reaction,
-)
+from rxnutils.chem.utils import reassign_rsmi_atom_mapping, split_smiles_from_reaction
 
 
 class ReactionException(Exception):

rxnutils/chem/rinchi/download_rinchi.py

@@ -1,9 +1,9 @@
 """Module for downloading InChI Trust Reaction InChI."""
+import logging
 import os
-import sys
 import stat
+import sys
 from zipfile import ZipFile
-import logging
 
 import requests
 

rxnutils/chem/rinchi/rinchi_api.py

@@ -1,16 +1,15 @@
 """Module containing an API to the Reaction InChI program"""
 import logging
 import os
-import sys
 import subprocess
+import sys
 import tempfile
 from collections import namedtuple
 
 from rdkit.Chem import AllChem
 
 from rxnutils.chem.rinchi import download_rinchi
-from rxnutils.chem.rinchi.download_rinchi import RInChIError, PLATFORM2FOLDER
-
+from rxnutils.chem.rinchi.download_rinchi import PLATFORM2FOLDER, RInChIError
 
 RInChIStructure = namedtuple(
     "RInChI", "rinchi rauxinfo long_rinchikey short_rinchikey web_rinchikey"

rxnutils/chem/template.py

@@ -1,18 +1,17 @@
 """Module containing useful representations of templates
 """
-import re
 import hashlib
 import logging
+import re
 from collections import defaultdict
 from itertools import permutations
-from typing import List, Dict, Set, Iterator, Tuple, Any
+from typing import Any, Dict, Iterator, List, Set, Tuple
 
 import numpy as np
 import rdchiral.main as rdc
-from xxhash import xxh32
 from rdkit import Chem, DataStructs
 from rdkit.Chem import AllChem, SanitizeFlags  # pylint: disable=all
-
+from xxhash import xxh32
 
 DELIM_REGEX_STR = r"[&:\]]"
 AROMATIC_REGEX_STR = r"&a" + DELIM_REGEX_STR

rxnutils/chem/utils.py

@@ -1,11 +1,9 @@
 """Module containing various chemical utility routines"""
-import logging
 import functools
+import logging
 from typing import List, Tuple
 
-
 import rdchiral.template_extractor
-
 from rdkit import Chem
 from rdkit.Chem import AllChem
 from rdkit.Chem.MolStandardize import rdMolStandardize

rxnutils/data/base_pipeline.py

@@ -1,15 +1,14 @@
 """Module containing base class for data pipelines
 """
-import os
 import math
+import os
 from pathlib import Path
+from typing import List, Tuple
 
 import pandas as pd
 from metaflow import FlowSpec, Parameter
 
-from typing import List, Tuple
-
-from rxnutils.data.batch_utils import create_csv_batches, combine_csv_batches
+from rxnutils.data.batch_utils import combine_csv_batches, create_csv_batches
 
 # This is hack to only import the validation_runner if rxnmapper is not installed
 try:

rxnutils/data/mapping_pipeline.py

@@ -4,7 +4,7 @@
 """
 from pathlib import Path
 
-from metaflow import step, Parameter
+from metaflow import Parameter, step
 
 from rxnutils.data.base_pipeline import DataBaseFlow
 from rxnutils.data.mapping import main as map_data

rxnutils/data/ord/import_ord_dataset.py

@@ -1,9 +1,9 @@
 """
 Module containing script to import ORD dataset to a CSV file
 """
-import re
 import argparse
 import os
+import re
 from collections import defaultdict
 from typing import Optional, Sequence
 

rxnutils/data/ord/preparation_pipeline.py

@@ -6,7 +6,7 @@
 import os
 from pathlib import Path
 
-from metaflow import step, Parameter
+from metaflow import Parameter, step
 
 from rxnutils.data.base_pipeline import DataPreparationBaseFlow
 from rxnutils.data.ord.import_ord_dataset import main as import_data

rxnutils/data/uspto/download.py

@@ -1,14 +1,13 @@
 """Module containing a script to download USPTO files Figshare
 """
-import os
 import argparse
+import os
 from pathlib import Path
 from typing import Optional, Sequence
 
-import tqdm
-import requests
 import py7zr
-
+import requests
+import tqdm
 
 FILES_TO_DOWNLOAD = [
     {

rxnutils/data/uspto/preparation_pipeline.py

@@ -8,8 +8,8 @@
 from metaflow import step
 
 from rxnutils.data.base_pipeline import DataPreparationBaseFlow
-from rxnutils.data.uspto.download import main as download_uspto
 from rxnutils.data.uspto.combine import main as combine_uspto
+from rxnutils.data.uspto.download import main as download_uspto
 
 
 class UsptoDataPreparationFlow(DataPreparationBaseFlow):

rxnutils/data/uspto/uspto_yield.py

@@ -9,8 +9,8 @@
 
 from dataclasses import dataclass
 
-import pandas as pd
 import numpy as np
+import pandas as pd
 
 
 @dataclass

rxnutils/pipeline/actions/reaction_mod.py

@@ -18,9 +18,9 @@
 from rxnutils.chem.disconnection_sites.tag_converting import convert_atom_map_tag
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
+    desalt_molecules,
     neutralize_molecules,
     remove_atom_mapping,
-    desalt_molecules,
 )
 from rxnutils.pipeline.base import ReactionActionMixIn, action, global_apply
 

rxnutils/pipeline/actions/reaction_props.py

@@ -5,7 +5,7 @@
 import os
 from collections import defaultdict
 from dataclasses import dataclass
-from typing import ClassVar, List, Set, Tuple, Optional
+from typing import ClassVar, List, Optional, Set, Tuple
 
 import pandas as pd
 from rdkit import Chem, RDLogger
@@ -14,20 +14,16 @@
 from rdkit.Chem.rdMolDescriptors import CalcNumRings
 from rdkit.Chem.rdmolops import FindPotentialStereo
 
-from rxnutils.pipeline.base import (
-    action,
-    global_apply,
-    ReactionActionMixIn,
-)
+from rxnutils.chem.cgr import CondensedGraphReaction
+from rxnutils.chem.reaction import ChemicalReaction
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
     has_atom_mapping,
     join_smiles_from_reaction,
     reaction_centres,
     split_smiles_from_reaction,
 )
-from rxnutils.chem.reaction import ChemicalReaction
-from rxnutils.chem.cgr import CondensedGraphReaction
+from rxnutils.pipeline.base import ReactionActionMixIn, action, global_apply
 
 rd_logger = RDLogger.logger()
 rd_logger.setLevel(RDLogger.CRITICAL)

rxnutils/pipeline/actions/templates.py

@@ -1,16 +1,16 @@
 """Module containing template validation actions"""
 from __future__ import annotations
+
 from dataclasses import dataclass
-from typing import ClassVar, Set, Sequence
+from typing import ClassVar, Sequence, Set
 
 import pandas as pd
-from rdkit import RDLogger
-from rdkit import Chem
+from rdkit import Chem, RDLogger
 from rdkit.Chem import AllChem
 
-from rxnutils.pipeline.base import action, global_apply
 from rxnutils.chem.template import ReactionTemplate
 from rxnutils.chem.utils import split_smiles_from_reaction
+from rxnutils.pipeline.base import action, global_apply
 
 rd_logger = RDLogger.logger()
 rd_logger.setLevel(RDLogger.CRITICAL)

rxnutils/pipeline/base.py

@@ -1,16 +1,15 @@
 """Module containing routines for the validation framework"""
 from __future__ import annotations
-from typing import Any
-from typing import Callable
-from typing import Dict, Optional, Tuple, List
+
 from collections import defaultdict
 from dataclasses import fields
+from typing import Any, Callable, Dict, List, Optional, Tuple
 
 import pandas as pd
 import swifter  # noqa #pylint: disable=unused-import
 from tqdm import tqdm
 
-from rxnutils.chem.utils import split_smiles_from_reaction, join_smiles_from_reaction
+from rxnutils.chem.utils import join_smiles_from_reaction, split_smiles_from_reaction
 
 ActionType = Callable[[pd.DataFrame], pd.DataFrame]
 

rxnutils/pipeline/runner.py

@@ -1,18 +1,19 @@
 """Module containg routines and interface to run pipelines"""
 import argparse
-from typing import Dict, Any, Optional, Sequence
+from typing import Any, Dict, Optional, Sequence
 
-import yaml
 import pandas as pd
+import yaml
+
+import rxnutils.pipeline.actions.dataframe_mod  # noqa
 
 # imports needed to register all the actions
 # pylint: disable=unused-import
 import rxnutils.pipeline.actions.reaction_mod  # noqa
 import rxnutils.pipeline.actions.reaction_props  # noqa
 import rxnutils.pipeline.actions.templates  # noqa
-import rxnutils.pipeline.actions.dataframe_mod  # noqa
-from rxnutils.pipeline.base import create_action, global_apply, list_actions
 from rxnutils.data.batch_utils import read_csv_batch
+from rxnutils.pipeline.base import create_action, global_apply, list_actions
 
 
 def run_pipeline(

rxnutils/routes/base.py

@@ -5,22 +5,22 @@
 """
 
 import warnings
-from typing import Dict, Any, List, Callable, Tuple, Set, Union
 from copy import deepcopy
 from operator import itemgetter
+from typing import Any, Callable, Dict, List, Set, Tuple, Union
 
 import pandas as pd
 from PIL.Image import Image as PilImage
 from rdkit import Chem
 
-from rxnutils.pipeline.actions.reaction_mod import NameRxn, RxnMapper
-from rxnutils.routes.image import RouteImageFactory
 from rxnutils.chem.augmentation import single_reactant_augmentation
 from rxnutils.chem.utils import (
     atom_mapping_numbers,
-    split_smiles_from_reaction,
     join_smiles_from_reaction,
+    split_smiles_from_reaction,
 )
+from rxnutils.pipeline.actions.reaction_mod import NameRxn, RxnMapper
+from rxnutils.routes.image import RouteImageFactory
 from rxnutils.routes.utils.validation import validate_dict
 
 

rxnutils/routes/comparison.py

@@ -1,16 +1,15 @@
 """ Contains routines for computing route similarities
 """
 import functools
-from typing import Any, Callable, Dict, Sequence, Tuple, List, Set
+from typing import Any, Callable, Dict, List, Sequence, Set, Tuple
 
 import numpy as np
 
-from rxnutils.chem.utils import atom_mapping_numbers
 from rxnutils.chem.reaction import ChemicalReaction
+from rxnutils.chem.utils import atom_mapping_numbers
 from rxnutils.routes.base import SynthesisRoute
 from rxnutils.routes.ted.distances_calculator import ted_distances_calculator
 
-
 RouteDistancesCalculator = Callable[[Sequence[SynthesisRoute]], np.ndarray]
 
 

rxnutils/routes/image.py

@@ -11,16 +11,7 @@
 
 if TYPE_CHECKING:
     # pylint: disable=ungrouped-imports
-    from typing import (
-        Any,
-        Callable,
-        Optional,
-        Dict,
-        List,
-        Sequence,
-        Tuple,
-        Union,
-    )
+    from typing import Any, Callable, Dict, List, Optional, Sequence, Tuple, Union
 
     PilColor = Union[str, Tuple[int, int, int]]
     FrameColors = Optional[Dict[bool, PilColor]]

rxnutils/routes/readers.py

@@ -1,15 +1,14 @@
 """Routines for reading routes from various formats"""
 
 import copy
-from typing import Sequence, List, Dict, Any
+from typing import Any, Dict, List, Sequence
 
 import pandas as pd
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
-from rxnutils.routes.base import SynthesisRoute
-from rxnutils.routes.base import smiles2inchikey
-from rxnutils.chem.utils import split_smiles_from_reaction, join_smiles_from_reaction
+from rxnutils.chem.utils import join_smiles_from_reaction, split_smiles_from_reaction
+from rxnutils.routes.base import SynthesisRoute, smiles2inchikey
 
 
 def read_reaction_lists(filename: str) -> List[SynthesisRoute]:

rxnutils/routes/retro_bleu/__init__.py

@@ -1,4 +1,4 @@
 from rxnutils.routes.retro_bleu.scoring import (
-    ngram_overlap_score,
+    ngram_overlap_score,  # noqa
     retro_bleu_score,
-)  # noqa
+)

rxnutils/routes/retro_bleu/ngram_collection.py

@@ -8,6 +8,7 @@
 """
 
 from __future__ import annotations
+
 import json
 from dataclasses import dataclass
 from typing import Any, Set, Tuple