Run linting changes (isort and black) to pass Github linting test

src/pyobo/api/utils.py

@@ -7,8 +7,8 @@
 
 import bioversions
 
-from ..utils.path import prefix_directory_join
 from ..constants import VERSION_PINS
+from ..utils.path import prefix_directory_join
 
 __all__ = [
     "get_version",

src/pyobo/constants.py

@@ -2,20 +2,15 @@
 
 """Constants for PyOBO."""
 
+import json
 import logging
-import re
 import os
-import json
-import click
+import re
 
+import click
 import pystow
 
-__all__ = [
-    "RAW_DIRECTORY",
-    "DATABASE_DIRECTORY",
-    "SPECIES_REMAPPING",
-    "VERSION_PINS"
-]
+__all__ = ["RAW_DIRECTORY", "DATABASE_DIRECTORY", "SPECIES_REMAPPING", "VERSION_PINS"]
 
 logger = logging.getLogger(__name__)
 
@@ -112,18 +107,20 @@
         VERSION_PINS = json.loads(VERSION_PINS_STR)
         for k, v in VERSION_PINS.items():
             if not isinstance(k, str) or not isinstance(v, str):
-                logger.error("The prefix and version name must both be "
-                                 "strings")
+                logger.error("The prefix and version name must both be " "strings")
             VERSION_PINS = {}
             break
 except ValueError as e:
-    logger.error("The value for the environment variable VERSION_PINS"
-                     " must be a valid JSON string")
+    logger.error(
+        "The value for the environment variable VERSION_PINS" " must be a valid JSON string"
+    )
     VERSION_PINS = {}
 
-click.echo(f"These are the resource versions that are pinned.\n{VERSION_PINS}. "
-           f"\nPyobo will download the latest version of a resource if it's "
-           f"not pinned.\nIf you want to use a specific version of a "
-           f"resource, edit your VERSION_PINS environmental "
-           f"variable which is a JSON string to include a prefix and version "
-           f"name.")
+click.echo(
+    f"These are the resource versions that are pinned.\n{VERSION_PINS}. "
+    f"\nPyobo will download the latest version of a resource if it's "
+    f"not pinned.\nIf you want to use a specific version of a "
+    f"resource, edit your VERSION_PINS environmental "
+    f"variable which is a JSON string to include a prefix and version "
+    f"name."
+)

src/pyobo/sources/antibodyregistry.py

@@ -10,8 +10,8 @@
 from tqdm.auto import tqdm
 
 from pyobo import Obo, Term
-from pyobo.utils.path import ensure_df
 from pyobo.api.utils import get_version
+from pyobo.utils.path import ensure_df
 
 __all__ = [
     "AntibodyRegistryGetter",

src/pyobo/sources/biogrid.py

@@ -7,10 +7,10 @@
 
 import pandas as pd
 
+from pyobo.api.utils import get_version
 from pyobo.resources.ncbitaxon import get_ncbitaxon_id
 from pyobo.utils.cache import cached_mapping
 from pyobo.utils.path import ensure_df, prefix_directory_join
-from pyobo.api.utils import get_version
 
 PREFIX = "biogrid"
 BASE_URL = "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive"

src/pyobo/sources/hgnc.py

@@ -10,10 +10,10 @@
 from operator import attrgetter
 from typing import DefaultDict, Dict, Iterable, Optional
 
-
 from tabulate import tabulate
 from tqdm.auto import tqdm
 
+from pyobo.api.utils import get_version
 from pyobo.struct import (
     Obo,
     Reference,
@@ -29,7 +29,6 @@
 )
 from pyobo.struct.typedef import exact_match
 from pyobo.utils.path import ensure_path, prefix_directory_join
-from pyobo.api.utils import get_version
 
 __all__ = [
     "HGNCGetter",

src/pyobo/sources/mesh.py

@@ -11,12 +11,12 @@
 
 from tqdm.auto import tqdm
 
+from pyobo.api.utils import get_version
 from pyobo.identifier_utils import standardize_ec
 from pyobo.struct import Obo, Reference, Synonym, Term
 from pyobo.utils.cache import cached_json, cached_mapping
 from pyobo.utils.io import parse_xml_gz
 from pyobo.utils.path import ensure_path, prefix_directory_join
-from pyobo.api.utils import get_version
 
 __all__ = [
     "MeSHGetter",

src/pyobo/sources/pubchem.py

@@ -5,16 +5,15 @@
 import logging
 from typing import Iterable, Mapping, Optional
 
-
 import pandas as pd
 from bioregistry.utils import removeprefix
 from tqdm.auto import tqdm
 
 from ..api import get_name_id_mapping
+from ..api.utils import get_version
 from ..struct import Obo, Reference, Synonym, Term
 from ..utils.iter import iterate_gzips_together
 from ..utils.path import ensure_df, ensure_path
-from ..api.utils import get_version
 
 __all__ = [
     "PubChemCompoundGetter",

src/pyobo/sources/rhea.py

@@ -7,6 +7,7 @@
 
 import pystow
 
+from pyobo.api.utils import get_version
 from pyobo.struct import Obo, Reference, Term
 from pyobo.struct.typedef import (
     TypeDef,
@@ -20,7 +21,6 @@
     reaction_enabled_by_molecular_function,
 )
 from pyobo.utils.path import ensure_df
-from pyobo.api.utils import get_version
 
 if TYPE_CHECKING:
     import rdflib

src/pyobo/sources/uniprot/uniprot.py

@@ -9,12 +9,12 @@
 from tqdm.auto import tqdm
 
 from pyobo import Obo, Reference
+from pyobo.api.utils import get_version
 from pyobo.constants import RAW_MODULE
 from pyobo.identifier_utils import standardize_ec
 from pyobo.struct import Term, derives_from, enables, from_species, participates_in
 from pyobo.struct.typedef import gene_product_of, located_in, molecularly_interacts_with
 from pyobo.utils.io import open_reader
-from pyobo.api.utils import get_version
 
 PREFIX = "uniprot"
 BASE_URL = "https://rest.uniprot.org/uniprotkb/stream"

src/pyobo/struct/struct.py

@@ -56,6 +56,7 @@
     term_replaced_by,
 )
 from .utils import comma_separate, obo_escape_slim
+from ..api.utils import get_version
 from ..constants import (
     DATE_FORMAT,
     NCBITAXON_PREFIX,
@@ -68,7 +69,6 @@
 from ..utils.io import multidict, write_iterable_tsv
 from ..utils.misc import obo_to_owl
 from ..utils.path import get_prefix_obo_path, prefix_directory_join
-from ..api.utils import get_version
 
 __all__ = [
     "Synonym",

src/pyobo/xrefdb/sources/chembl.py

@@ -6,6 +6,7 @@
 
 import pandas as pd
 
+from pyobo.api.utils import get_version
 from pyobo.constants import (
     PROVENANCE,
     SOURCE_ID,
@@ -15,7 +16,6 @@
     XREF_COLUMNS,
 )
 from pyobo.utils.path import ensure_df
-from pyobo.api.utils import get_version
 
 CHEMBL_COMPOUND_PREFIX = "chembl.compound"
 CHEMBL_TARGET_PREFIX = "chembl.target"

src/pyobo/xrefdb/sources/pubchem.py

@@ -6,9 +6,9 @@
 
 import pandas as pd
 
+from ...api.utils import get_version
 from ...constants import XREF_COLUMNS
 from ...sources.pubchem import _get_pubchem_extras_url, get_pubchem_id_to_mesh_id
-from ...api.utils import get_version
 
 __all__ = [
     "get_pubchem_mesh_df",