Use isort (#720)

* Use isort

* lint

* exclude generated files

* black

.github/workflows/cleanup.yml

@@ -46,6 +46,9 @@ jobs:
       - name: Run black
         run: |
           black --check .
+      - name: Run isort
+        run: |
+          isort --check .
       - name: Run pylint
         run: |
           pylint -j 0 -v examples ord_schema *.py

badges/reactions.py

@@ -22,9 +22,9 @@
 """
 import glob
 import os
-import requests
 
 import docopt
+import requests
 
 from ord_schema import message_helpers
 from ord_schema.logging import get_logger

ord_schema/__init__.py

@@ -14,8 +14,8 @@
 """Generic helpers for ord_schema, including common message types."""
 from typing import Union
 
-from google.protobuf import descriptor
 import google.protobuf.message  # pytype: disable=import-error
+from google.protobuf import descriptor
 
 from ord_schema.proto import reaction_pb2
 

ord_schema/frozen_message_test.py

@@ -19,10 +19,8 @@
 
 import pytest
 
-from ord_schema import frozen_message
-from ord_schema import message_helpers
-from ord_schema.proto import reaction_pb2
-from ord_schema.proto import test_pb2
+from ord_schema import frozen_message, message_helpers
+from ord_schema.proto import reaction_pb2, test_pb2
 
 
 def _freeze(message) -> frozen_message.FrozenMessage:

ord_schema/macros/solutions.py

@@ -14,8 +14,8 @@
 """Macros for programmatic message creation."""
 from typing import Optional, Union
 
-from ord_schema.proto import reaction_pb2
 from ord_schema import units
+from ord_schema.proto import reaction_pb2
 
 UNITS_RESOLVER = units.UnitResolver()
 CONCENTRATION_RESOLVER = units.UnitResolver(units.CONCENTRATION_UNIT_SYNONYMS, forbidden_units={})

ord_schema/macros/solutions_test.py

@@ -17,9 +17,9 @@
 import pytest
 from google.protobuf import text_format
 
-from ord_schema.proto import reaction_pb2
-from ord_schema.macros import solutions
 from ord_schema import validations
+from ord_schema.macros import solutions
+from ord_schema.proto import reaction_pb2
 
 
 def test_simple_solution():

ord_schema/macros/workups.py

@@ -43,8 +43,8 @@
 """
 from collections.abc import Iterable
 
-from ord_schema.proto import reaction_pb2
 from ord_schema import units
+from ord_schema.proto import reaction_pb2
 
 UNITS_RESOLVER = units.UnitResolver()
 CONCENTRATION_RESOLVER = units.UnitResolver(units.CONCENTRATION_UNIT_SYNONYMS)

ord_schema/message_helpers.py

@@ -26,16 +26,15 @@
 import pandas as pd
 import requests
 from google import protobuf  # pytype: disable=import-error
-from google.protobuf import json_format
 from google.protobuf import text_format  # pytype: disable=import-error
+from google.protobuf import json_format
 from rdkit import Chem
 from rdkit.Chem import rdChemReactions
 from werkzeug import security
 
 import ord_schema
 from ord_schema import units
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 _COMPOUND_IDENTIFIER_LOADERS = {
     reaction_pb2.CompoundIdentifier.SMILES: Chem.MolFromSmiles,

ord_schema/message_helpers_test.py

@@ -18,13 +18,11 @@
 
 import pandas as pd
 import pytest
-from google.protobuf import json_format
-from google.protobuf import text_format
+from google.protobuf import json_format, text_format
 from rdkit import Chem
 
 from ord_schema import message_helpers
-from ord_schema.proto import reaction_pb2
-from ord_schema.proto import test_pb2
+from ord_schema.proto import reaction_pb2, test_pb2
 
 _BENZENE_MOLBLOCK = """241
   -OEChem-07232015262D

ord_schema/orm/database.py

@@ -13,14 +13,14 @@
 # limitations under the License.
 
 """Functions for creating/managing the PostgreSQL database."""
-import time
 import os
+import time
 from unittest.mock import patch
 
 from sqlalchemy import cast, delete, func, select, text, update
 from sqlalchemy.dialects.postgresql import insert
 from sqlalchemy.engine import Engine
-from sqlalchemy.exc import OperationalError, NotSupportedError
+from sqlalchemy.exc import NotSupportedError, OperationalError
 from sqlalchemy.orm import Session
 
 from ord_schema.logging import get_logger

ord_schema/orm/mappers.py

@@ -35,17 +35,15 @@
 from google.protobuf.descriptor import Descriptor, FieldDescriptor
 from google.protobuf.message import Message
 from inflection import underscore
-from sqlalchemy import Boolean, Column, Enum, Float, Integer, ForeignKey, LargeBinary, String, Text
+from sqlalchemy import Boolean, Column, Enum, Float, ForeignKey, Integer, LargeBinary, String, Text
 from sqlalchemy.dialects.postgresql import ARRAY
 from sqlalchemy.orm import relationship
 
 import ord_schema.orm.rdkit_mappers  # pylint: disable=unused-import
 from ord_schema import message_helpers
 from ord_schema.logging import get_logger
 from ord_schema.orm import Base
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
-
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 logger = get_logger(__name__)
 

ord_schema/orm/mappers_test.py

@@ -14,6 +14,7 @@
 
 """Tests for ord_schema.orm.mappers."""
 import os
+
 import pytest
 
 from ord_schema.message_helpers import load_message

ord_schema/orm/rdkit_mappers_test.py

@@ -16,6 +16,7 @@
 import pytest
 from sqlalchemy import select
 from sqlalchemy.exc import ProgrammingError
+
 from ord_schema.orm.mappers import Mappers
 from ord_schema.orm.rdkit_mappers import FingerprintType, RDKitMol
 

ord_schema/orm/scripts/add_datasets.py

@@ -31,10 +31,10 @@
 """
 import os
 import time
+from concurrent.futures import ProcessPoolExecutor
 from functools import partial
 from glob import glob
 from hashlib import md5
-from concurrent.futures import ProcessPoolExecutor
 
 from docopt import docopt
 from rdkit import RDLogger

ord_schema/proto/dataset_pb2_test.py

@@ -15,8 +15,7 @@
 
 import pytest
 
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 
 @pytest.fixture

ord_schema/resolvers.py

@@ -14,14 +14,14 @@
 """Name/string resolution to structured messages or identifiers."""
 import email.message
 import re
+import urllib.error
 import urllib.parse
 import urllib.request
-import urllib.error
 
 from rdkit import Chem
 
-from ord_schema.logging import get_logger
 from ord_schema import message_helpers
+from ord_schema.logging import get_logger
 from ord_schema.proto import reaction_pb2
 
 logger = get_logger(__name__)

ord_schema/scripts/build_dataset.py

@@ -29,11 +29,9 @@
 
 import docopt
 
+from ord_schema import message_helpers, validations
 from ord_schema.logging import get_logger
-from ord_schema import message_helpers
-from ord_schema import validations
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 logger = get_logger(__name__)
 

ord_schema/scripts/build_dataset_test.py

@@ -17,10 +17,8 @@
 import docopt
 import pytest
 
-from ord_schema import message_helpers
-from ord_schema import validations
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema import message_helpers, validations
+from ord_schema.proto import dataset_pb2, reaction_pb2
 from ord_schema.scripts import build_dataset
 
 

ord_schema/scripts/enumerate_dataset.py

@@ -24,9 +24,8 @@
 """
 import docopt
 
+from ord_schema import message_helpers, templating
 from ord_schema.logging import get_logger
-from ord_schema import message_helpers
-from ord_schema import templating
 
 logger = get_logger(__name__)
 

ord_schema/scripts/enumerate_dataset_test.py

@@ -18,10 +18,8 @@
 import pandas as pd
 import pytest
 
-from ord_schema import message_helpers
-from ord_schema import validations
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema import message_helpers, validations
+from ord_schema.proto import dataset_pb2, reaction_pb2
 from ord_schema.scripts import enumerate_dataset
 
 

ord_schema/scripts/parse_uspto.py

@@ -43,12 +43,9 @@
 from rdkit import RDLogger
 
 import ord_schema
+from ord_schema import message_helpers, units, validations
 from ord_schema.logging import get_logger
-from ord_schema import message_helpers
-from ord_schema import units
-from ord_schema import validations
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 logger = get_logger(__name__)
 RDLogger.DisableLog("rdApp.*")  # Disable RDKit logging.

ord_schema/scripts/process_dataset.py

@@ -56,10 +56,8 @@
 import github
 from rdkit import RDLogger
 
+from ord_schema import message_helpers, updates, validations
 from ord_schema.logging import get_logger
-from ord_schema import message_helpers
-from ord_schema import updates
-from ord_schema import validations
 from ord_schema.proto import dataset_pb2
 
 logger = get_logger(__name__)

ord_schema/scripts/process_dataset_test.py

@@ -21,11 +21,9 @@
 import pytest
 from rdkit import RDLogger
 
+from ord_schema import message_helpers, validations
 from ord_schema.logging import get_logger
-from ord_schema import message_helpers
-from ord_schema import validations
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 from ord_schema.scripts import process_dataset
 
 logger = get_logger(__name__)

ord_schema/scripts/validate_dataset.py

@@ -27,9 +27,8 @@
 import docopt
 from rdkit import RDLogger
 
+from ord_schema import message_helpers, validations
 from ord_schema.logging import get_logger
-from ord_schema import message_helpers
-from ord_schema import validations
 from ord_schema.proto import dataset_pb2
 
 logger = get_logger(__name__)

ord_schema/scripts/validate_dataset_test.py

@@ -17,10 +17,8 @@
 import docopt
 import pytest
 
-from ord_schema import message_helpers
-from ord_schema import validations
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema import message_helpers, validations
+from ord_schema.proto import dataset_pb2, reaction_pb2
 from ord_schema.scripts import validate_dataset
 
 

ord_schema/templating.py

@@ -29,9 +29,7 @@
 
 import ord_schema
 from ord_schema import validations
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
-
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 # pylint: disable=too-many-branches
 

ord_schema/templating_test.py

@@ -19,8 +19,7 @@
 from rdkit import Chem
 
 from ord_schema import templating
-from ord_schema.proto import reaction_pb2
-from ord_schema.proto import dataset_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 
 @pytest.fixture

ord_schema/units.py

@@ -14,7 +14,7 @@
 """Helpers for translating strings with units."""
 
 import re
-from typing import Optional, Type, Union, Tuple
+from typing import Optional, Tuple, Type, Union
 
 import numpy as np
 

ord_schema/updates.py

@@ -17,8 +17,7 @@
 import re
 import uuid
 
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 _COMPOUND_STRUCTURAL_IDENTIFIERS = [
     reaction_pb2.CompoundIdentifier.SMILES,

ord_schema/updates_test.py

@@ -16,8 +16,7 @@
 import pytest
 
 from ord_schema import updates
-from ord_schema.proto import reaction_pb2
-from ord_schema.proto import dataset_pb2
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 
 class TestUpdateReaction:

ord_schema/validations.py

@@ -18,18 +18,17 @@
 import re
 import warnings
 from collections.abc import Mapping
-from typing import Any, Optional
 from enum import IntEnum
+from typing import Any, Optional
 
 from dateutil import parser
 from rdkit import Chem
 from rdkit import __version__ as RDKIT_VERSION
 
 import ord_schema
-from ord_schema.logging import get_logger
 from ord_schema import message_helpers
-from ord_schema.proto import dataset_pb2
-from ord_schema.proto import reaction_pb2
+from ord_schema.logging import get_logger
+from ord_schema.proto import dataset_pb2, reaction_pb2
 
 logger = get_logger(__name__)