pyobo 0.10.11__py3-none-any.whl → 0.11.0__py3-none-any.whl

pyobo/sources/dictybase_gene.py

@@ -1,12 +1,10 @@
-# -*- coding: utf-8 -*-
-
 """Converter for dictyBase gene.
 
 Note that normal dictybase idenififers are for sequences
 """
 
 import logging
-from typing import Iterable
+from collections.abc import Iterable
 
 import pandas as pd
 from tqdm.auto import tqdm

pyobo/sources/drugbank.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Convert DrugBank to OBO.
 
 Run with ``python -m pyobo.sources.drugbank``
@@ -8,14 +6,15 @@ Run with ``python -m pyobo.sources.drugbank``
 import datetime
 import itertools as itt
 import logging
+from collections.abc import Iterable, Mapping
 from functools import lru_cache
-from typing import Any, Dict, Iterable, Mapping, Optional
+from typing import Any, Optional
 from xml.etree import ElementTree
 
 import pystow
 from tqdm.auto import tqdm
 
-from ..getters import NoBuild
+from ..getters import NoBuildError
 from ..struct import Obo, Reference, Term
 from ..struct.typedef import has_inchi, has_salt, has_smiles
 from ..utils.cache import cached_pickle
@@ -139,7 +138,7 @@ def _make_term(drug_info: Mapping[str, Any]) -> Term:
     return term
 
 
-@lru_cache()
+@lru_cache
 def get_xml_root(version: Optional[str] = None) -> ElementTree.Element:
     """Get the DrugBank XML parser root.
 
@@ -152,7 +151,7 @@ def get_xml_root(version: Optional[str] = None) -> ElementTree.Element:
         username = pystow.get_config("pyobo", "drugbank_username", raise_on_missing=True)
         password = pystow.get_config("pyobo", "drugbank_password", raise_on_missing=True)
     except ConfigError as e:
-        raise NoBuild from e
+        raise NoBuildError from e
 
     element = parse_drugbank(version=version, username=username, password=password)
     return element.getroot()
@@ -167,7 +166,7 @@ smiles_template = f"{ns}calculated-properties/{ns}property[{ns}kind='SMILES']/{n
 def _extract_drug_info(drug_xml: ElementTree.Element) -> Mapping[str, Any]:
     """Extract information from an XML element representing a drug."""
     # assert drug_xml.tag == f'{ns}drug'
-    row: Dict[str, Any] = {
+    row: dict[str, Any] = {
         "type": drug_xml.get("type"),
         "drugbank_id": drug_xml.findtext(f"{ns}drugbank-id[@primary='true']"),
         "cas": drug_xml.findtext(f"{ns}cas-number"),

pyobo/sources/drugbank_salt.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Convert DrugBank Salts to OBO.
 
 Run with ``python -m pyobo.sources.drugbank_salt``
@@ -10,11 +8,12 @@ Get relations between drugbank salts and drugbank parents with
 .. code-block:: python
 
     import pyobo
-    df = pyobo.get_filtered_relations_df('drugbank', 'obo:has_salt')
+
+    df = pyobo.get_filtered_relations_df("drugbank", "obo:has_salt")
 """
 
 import logging
-from typing import Iterable
+from collections.abc import Iterable
 
 from .drugbank import iterate_drug_info
 from ..struct import Obo, Reference, Term

pyobo/sources/drugcentral.py

@@ -1,11 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """Get DrugCentral as OBO."""
 
 import logging
 from collections import defaultdict
+from collections.abc import Iterable
 from contextlib import closing
-from typing import DefaultDict, Iterable, List
 
 import bioregistry
 import psycopg2
@@ -25,9 +23,9 @@ PREFIX = "drugcentral"
 HOST = "unmtid-dbs.net"
 PORT = 5433
 USER = "drugman"
-PASSWORD = "dosage"
+PASSWORD = "dosage"  # noqa:S105
 DBNAME = "drugcentral"
-PARAMS = dict(dbname=DBNAME, user=USER, password=PASSWORD, host=HOST, port=PORT)
+PARAMS = {"dbname": DBNAME, "user": USER, "password": PASSWORD, "host": HOST, "port": PORT}
 
 
 class DrugCentralGetter(Obo):
@@ -58,7 +56,7 @@ def iter_terms() -> Iterable[Term]:
         with closing(conn.cursor()) as cur:
             cur.execute("SELECT struct_id, id_type, identifier FROM public.identifier")
             rows = cur.fetchall()
-            xrefs: DefaultDict[str, List[Reference]] = defaultdict(list)
+            xrefs: defaultdict[str, list[Reference]] = defaultdict(list)
             for drugcentral_id, prefix, identifier in tqdm(
                 rows, unit_scale=True, desc="loading xrefs"
             ):
@@ -76,7 +74,7 @@ def iter_terms() -> Iterable[Term]:
                 )
         with closing(conn.cursor()) as cur:
             cur.execute("SELECT id, name FROM public.synonyms")
-            synonyms: DefaultDict[str, List[Synonym]] = defaultdict(list)
+            synonyms: defaultdict[str, list[Synonym]] = defaultdict(list)
             for drugcentral_id, synonym in cur.fetchall():
                 synonyms[str(drugcentral_id)].append(Synonym(name=synonym))
 

pyobo/sources/expasy.py

@@ -1,10 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """Convert ExPASy to OBO."""
 
 import logging
 from collections import defaultdict
-from typing import Any, Dict, Iterable, Mapping, Optional, Set, Tuple
+from collections.abc import Iterable, Mapping
+from typing import Any, Optional
 
 from .utils import get_go_mapping
 from ..struct import Obo, Reference, Synonym, Term
@@ -76,7 +75,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
     with open(tree_path) as file:
         tree = get_tree(file)
 
-    terms: Dict[str, Term] = {}
+    terms: dict[str, Term] = {}
     child_to_parents = defaultdict(list)
     for ec_code, data in tree.items():
         terms[ec_code] = Term(
@@ -176,7 +175,7 @@ def normalize_expasy_id(expasy_id: str) -> str:
     return expasy_id.replace(" ", "")
 
 
-def give_edge(unnormalized_ec_code: str) -> Tuple[int, Optional[str], str]:
+def give_edge(unnormalized_ec_code: str) -> tuple[int, Optional[str], str]:
     """Return a (parent, child) tuple for given id."""
     levels = [x for x in unnormalized_ec_code.replace(" ", "").replace("-", "").split(".") if x]
     level = len(levels)
@@ -227,7 +226,7 @@ def get_database(lines: Iterable[str]) -> Mapping:
     for groups in _group_by_id(lines):
         _, expasy_id = groups[0]
 
-        ec_data_entry: Dict[str, Any] = {
+        ec_data_entry: dict[str, Any] = {
             "concept": {
                 "namespace": PREFIX,
                 "identifier": expasy_id,
@@ -269,11 +268,11 @@ def get_database(lines: Iterable[str]) -> Mapping:
                         continue
                     uniprot_id, uniprot_accession = uniprot_entry.split(",")
                     ec_data_entry["proteins"].append(  # type:ignore
-                        dict(
-                            namespace="uniprot",
-                            name=uniprot_accession,
-                            identifier=uniprot_id,
-                        )
+                        {
+                            "namespace": "uniprot",
+                            "name": uniprot_accession,
+                            "identifier": uniprot_id,
+                        }
                     )
 
         rv[expasy_id] = ec_data_entry
@@ -300,7 +299,7 @@ def _group_by_id(lines):
     return groups
 
 
-def get_ec2go(version: str) -> Mapping[str, Set[Tuple[str, str]]]:
+def get_ec2go(version: str) -> Mapping[str, set[tuple[str, str]]]:
     """Get the EC mapping to GO activities."""
     url = "http://current.geneontology.org/ontology/external2go/ec2go"
     path = ensure_path(PREFIX, url=url, name="ec2go.tsv", version=version)

pyobo/sources/famplex.py

@@ -1,10 +1,8 @@
-# -*- coding: utf-8 -*-
-
 """Converter for FamPlex."""
 
 import logging
 from collections import defaultdict
-from typing import Iterable, List, Mapping, Tuple
+from collections.abc import Iterable, Mapping
 
 import bioregistry
 from pystow.utils import get_commit
@@ -62,7 +60,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
         dtype=str,
         force=force,
     )
-    id_to_definition: Mapping[str, Tuple[str, str]] = {
+    id_to_definition: Mapping[str, tuple[str, str]] = {
         identifier: (definition, provenance)
         for identifier, provenance, definition in definitions_df.values
     }
@@ -140,7 +138,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
         yield term
 
 
-def _get_xref_df(version: str) -> Mapping[str, List[Reference]]:
+def _get_xref_df(version: str) -> Mapping[str, list[Reference]]:
     base_url = f"https://raw.githubusercontent.com/sorgerlab/famplex/{version}"
     xrefs_url = f"{base_url}/equivalences.csv"
     xrefs_df = ensure_df(PREFIX, url=xrefs_url, version=version, header=None, sep=",", dtype=str)

pyobo/sources/flybase.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 """Converter for FlyBase Genes."""
 
 import logging
-from typing import Iterable, Mapping, Set
+from collections.abc import Iterable, Mapping
 
 import pandas as pd
 from tqdm.auto import tqdm
@@ -68,7 +66,7 @@ def _get_definitions(version: str, force: bool = False) -> Mapping[str, str]:
     return dict(df.values)
 
 
-def _get_human_orthologs(version: str, force: bool = False) -> Mapping[str, Set[str]]:
+def _get_human_orthologs(version: str, force: bool = False) -> Mapping[str, set[str]]:
     url = (
         f"http://ftp.flybase.net/releases/FB{version}/precomputed_files/"
         f"orthologs/dmel_human_orthologs_disease_fb_{version}.tsv.gz"

pyobo/sources/geonames.py

@@ -1,7 +1,9 @@
 """Get terms from geonames."""
 
+from __future__ import annotations
+
 import logging
-from typing import Collection, Iterable, Mapping
+from collections.abc import Collection, Iterable, Mapping
 
 import pandas as pd
 from pystow.utils import read_zipfile_csv
@@ -146,15 +148,7 @@ def get_code_to_admin2(
     return code_to_admin2
 
 
-def get_cities(
-    code_to_country,
-    code_to_admin1,
-    code_to_admin2,
-    *,
-    minimum_population: int = 100_000,
-    force: bool = False,
-) -> Mapping[str, Term]:
-    """Get a mapping from city code to term."""
+def _get_cities_df(force: bool = False) -> pd.DataFrame:
     columns = [
         "geonames_id",
         "name",
@@ -184,7 +178,19 @@ def get_cities(
         names=columns,
         dtype=str,
     )
+    return cities_df
+
 
+def get_cities(
+    code_to_country,
+    code_to_admin1,
+    code_to_admin2,
+    *,
+    minimum_population: int = 100_000,
+    force: bool = False,
+) -> Mapping[str, Term]:
+    """Get a mapping from city code to term."""
+    cities_df = _get_cities_df(force=force)
     cities_df = cities_df[cities_df.population.astype(int) > minimum_population]
     cities_df.synonyms = cities_df.synonyms.str.split(",")
 
@@ -235,5 +241,17 @@ def get_cities(
     return terms
 
 
+def get_city_to_country() -> dict[str, str]:
+    """Get a mapping from city GeoNames to country GeoNames id."""
+    rv = {}
+    code_to_country = get_code_to_country()
+    cities_df = _get_cities_df()
+    for city_geonames_id, country_code in cities_df[["geonames_id", "country_code"]].values:
+        if pd.isna(city_geonames_id) or pd.isna(country_code):
+            continue
+        rv[city_geonames_id] = code_to_country[country_code].identifier
+    return rv
+
+
 if __name__ == "__main__":
     GeonamesGetter().write_default(write_obo=True, force=True)

pyobo/sources/gmt_utils.py

@@ -1,12 +1,11 @@
-# -*- coding: utf-8 -*-
-
 """GMT utilities."""
 
+from collections.abc import Iterable
 from pathlib import Path
-from typing import Iterable, Set, Tuple, Union
+from typing import Union
 
-GMTSummary = Tuple[str, str, Set[str]]
-WikiPathwaysGMTSummary = Tuple[str, str, str, str, str, Set[str]]
+GMTSummary = tuple[str, str, set[str]]
+WikiPathwaysGMTSummary = tuple[str, str, str, str, str, set[str]]
 
 
 def parse_gmt_file(path: Union[str, Path]) -> Iterable[GMTSummary]:
@@ -20,7 +19,7 @@ def parse_gmt_file(path: Union[str, Path]) -> Iterable[GMTSummary]:
             yield _process_line(line)
 
 
-def _process_line(line: str) -> Tuple[str, str, Set[str]]:
+def _process_line(line: str) -> tuple[str, str, set[str]]:
     """Return the pathway name, url, and gene sets associated.
 
     :param line: gmt file line

pyobo/sources/go.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Gene Ontology."""
 
 from pyobo import get_descendants
@@ -14,13 +12,13 @@ __all__ = [
 def is_biological_process(identifier: str) -> bool:
     """Return if the given GO identifier is a biological process.
 
-    >>> is_biological_process('0006915')
+    >>> is_biological_process("0006915")
     True
-    >>> is_biological_process('GO:0006915')
+    >>> is_biological_process("GO:0006915")
     True
-    >>> is_molecular_function('0006915')
+    >>> is_molecular_function("0006915")
     False
-    >>> is_cellular_component('0006915')
+    >>> is_cellular_component("0006915")
     False
     """
     return _is_descendant(identifier, "0008150")

pyobo/sources/gwascentral_phenotype.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 """Converter for GWAS Central Phenotypes."""
 
 import json
-from typing import Iterable
+from collections.abc import Iterable
 
 from tqdm.auto import tqdm, trange
 

pyobo/sources/gwascentral_study.py

@@ -1,10 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """Converter for GWAS Central."""
 
 import logging
 import tarfile
-from typing import Iterable, Optional
+from collections.abc import Iterable
+from typing import Optional
 from xml.etree import ElementTree
 
 from pyobo.struct import Obo, Reference, Term, has_part

pyobo/sources/hgnc.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Converter for HGNC."""
 
 import itertools as itt
@@ -7,13 +5,14 @@ import json
 import logging
 import typing
 from collections import Counter, defaultdict
+from collections.abc import Iterable
 from operator import attrgetter
-from typing import DefaultDict, Dict, Iterable, Optional
+from typing import Optional
 
-import bioversions
 from tabulate import tabulate
 from tqdm.auto import tqdm
 
+from pyobo.api.utils import get_version
 from pyobo.struct import (
     Obo,
     Reference,
@@ -238,12 +237,12 @@ def get_obo(*, force: bool = False) -> Obo:
     return HGNCGetter(force=force)
 
 
-def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Term]:  # noqa:C901
+def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Term]:
     """Get HGNC terms."""
     if version is None:
-        version = bioversions.get_version("hgnc")
+        version = get_version("hgnc")
     unhandled_entry_keys: typing.Counter[str] = Counter()
-    unhandle_locus_types: DefaultDict[str, Dict[str, Term]] = defaultdict(dict)
+    unhandle_locus_types: defaultdict[str, dict[str, Term]] = defaultdict(dict)
     path = ensure_path(
         PREFIX,
         url=DEFINITIONS_URL_FMT.format(version=version),
@@ -459,8 +458,8 @@ def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Te
                 headers=["hgnc_id", "name", "obsolete", "link", "provenance"],
                 tablefmt="github",
             )
-            print(f"## {k} ({len(v)})", file=file)  # noqa: T201
-            print(t, "\n", file=file)  # noqa: T201
+            print(f"## {k} ({len(v)})", file=file)
+            print(t, "\n", file=file)
 
     unhandle_locus_type_counter = Counter(
         {locus_type: len(d) for locus_type, d in unhandle_locus_types.items()}

pyobo/sources/hgncgenefamily.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 """Converter for HGNC Gene Families."""
 
 from collections import defaultdict
-from typing import Iterable, List, Mapping
+from collections.abc import Iterable, Mapping
 
 import pandas as pd
 
@@ -50,7 +48,7 @@ def get_obo(force: bool = False) -> Obo:
     return HGNCGroupGetter(force=force)
 
 
-def get_hierarchy(force: bool = False) -> Mapping[str, List[str]]:
+def get_hierarchy(force: bool = False) -> Mapping[str, list[str]]:
     """Get the HGNC Gene Families hierarchy as a dictionary."""
     path = ensure_path(PREFIX, url=HIERARCHY_URL, force=force)
     df = pd.read_csv(path, dtype={"parent_fam_id": str, "child_fam_id": str})

pyobo/sources/icd10.py

@@ -1,12 +1,11 @@
-# -*- coding: utf-8 -*-
-
 """Convert ICD-10 to OBO.
 
 Run with python -m pyobo.sources.icd10 -v
 """
 
 import logging
-from typing import Any, Iterable, Mapping, Set
+from collections.abc import Iterable, Mapping
+from typing import Any
 
 import click
 from more_click import verbose_option
@@ -57,7 +56,7 @@ def iter_terms() -> Iterable[Term]:
     chapter_urls = res_json["child"]
     tqdm.write(f"there are {len(chapter_urls)} chapters")
 
-    visited_identifiers: Set[str] = set()
+    visited_identifiers: set[str] = set()
     for identifier in get_child_identifiers(ICD10_TOP_LEVEL_URL, res_json):
         yield from visiter(
             identifier,

pyobo/sources/icd11.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Convert ICD11 to OBO.
 
 Run with python -m pyobo.sources.icd11 -v
@@ -8,7 +6,8 @@ Run with python -m pyobo.sources.icd11 -v
 import json
 import logging
 import os
-from typing import Any, Iterable, Mapping, Set
+from collections.abc import Iterable, Mapping
+from typing import Any
 
 import click
 from more_click import verbose_option
@@ -67,7 +66,7 @@ def iterate_icd11() -> Iterable[Term]:
 
     tqdm.write(f'There are {len(res_json["child"])} top level entities')
 
-    visited_identifiers: Set[str] = set()
+    visited_identifiers: set[str] = set()
     for identifier in get_child_identifiers(ICD11_TOP_LEVEL_URL, res_json):
         yield from visiter(
             identifier,

pyobo/sources/icd_utils.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Utilities or interacting with the ICD API.
 
 Want to get your own API cliend ID and client secret?
@@ -11,8 +9,9 @@ Want to get your own API cliend ID and client secret?
 import datetime
 import json
 import os
+from collections.abc import Iterable, Mapping
 from pathlib import Path
-from typing import Any, Callable, Iterable, List, Mapping, Set, Union
+from typing import Any, Callable, Union
 
 import pystow
 import requests
@@ -20,7 +19,7 @@ from cachier import cachier
 from pystow.config_api import ConfigError
 from tqdm.auto import tqdm
 
-from ..getters import NoBuild
+from ..getters import NoBuildError
 from ..struct import Term
 
 TOKEN_URL = "https://icdaccessmanagement.who.int/connect/token"  # noqa:S105
@@ -43,7 +42,7 @@ def _get_entity(endpoint: str, identifier: str):
     return res.json()
 
 
-def get_child_identifiers(endpoint: str, res_json: Mapping[str, Any]) -> List[str]:
+def get_child_identifiers(endpoint: str, res_json: Mapping[str, Any]) -> list[str]:
     """Ge the child identifiers."""
     return [url[len(endpoint) :].lstrip("/") for url in res_json.get("child", [])]
 
@@ -55,7 +54,7 @@ def get_icd_api_headers() -> Mapping[str, str]:
         icd_client_id = pystow.get_config("pyobo", "icd_client_id", raise_on_missing=True)
         icd_client_secret = pystow.get_config("pyobo", "icd_client_secret", raise_on_missing=True)
     except ConfigError as e:
-        raise NoBuild from e
+        raise NoBuildError from e
 
     grant_type = "client_credentials"
     body_params = {"grant_type": grant_type}
@@ -73,7 +72,7 @@ def get_icd_api_headers() -> Mapping[str, str]:
 
 def visiter(
     identifier: str,
-    visited_identifiers: Set[str],
+    visited_identifiers: set[str],
     directory: Union[str, Path],
     *,
     endpoint: str,

pyobo/sources/interpro.py

@@ -1,9 +1,7 @@
-# -*- coding: utf-8 -*-
-
 """Converter for InterPro."""
 
 from collections import defaultdict
-from typing import DefaultDict, Iterable, List, Mapping, Set, Tuple
+from collections.abc import Iterable, Mapping
 
 from .utils import get_go_mapping
 from ..struct import Obo, Reference, Term
@@ -82,7 +80,7 @@ def iter_terms(*, version: str, proteins: bool = False, force: bool = False) ->
         yield term
 
 
-def get_interpro_go_df(version: str, force: bool = False) -> Mapping[str, Set[Tuple[str, str]]]:
+def get_interpro_go_df(version: str, force: bool = False) -> Mapping[str, set[tuple[str, str]]]:
     """Get InterPro to Gene Ontology molecular function mapping."""
     url = f"https://ftp.ebi.ac.uk/pub/databases/interpro/releases/{version}/interpro2go"
     path = ensure_path(PREFIX, url=url, name="interpro2go.tsv", version=version, force=force)
@@ -98,7 +96,7 @@ def get_interpro_tree(version: str, force: bool = False):
 
 
 def _parse_tree_helper(lines: Iterable[str]):
-    rv1: DefaultDict[str, List[str]] = defaultdict(list)
+    rv1: defaultdict[str, list[str]] = defaultdict(list)
     previous_depth, previous_id = 0, ""
     stack = [previous_id]
 

pyobo/sources/itis.py

@@ -1,13 +1,11 @@
-# -*- coding: utf-8 -*-
-
 """Converter for the Integrated Taxonomic Information System (ITIS)."""
 
 import os
 import shutil
 import sqlite3
 import zipfile
+from collections.abc import Iterable
 from contextlib import closing
-from typing import Iterable
 
 from pyobo.struct import Obo, Reference, Term
 from pyobo.utils.io import multidict

pyobo/sources/kegg/__init__.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """KEGG Databases."""
 
 from .genes import KEGGGeneGetter

pyobo/sources/kegg/api.py

@@ -1,10 +1,9 @@
-# -*- coding: utf-8 -*-
-
 """API utilities for KEGG."""
 
 import urllib.error
+from collections.abc import Mapping
 from dataclasses import dataclass
-from typing import Mapping, Optional
+from typing import Optional
 
 from pyobo import Reference, Term, ensure_path
 from pyobo.struct import from_species
@@ -132,7 +131,7 @@ def _ensure_conv_genome_helper(
             version=version,
         )
         with path_rv.open("w") as file:
-            print(file=file)  # noqa: T201
+            print(file=file)
         return path_rv.as_posix()
     except FileNotFoundError:
         return None

pyobo/sources/kegg/genes.py

@@ -1,12 +1,11 @@
-# -*- coding: utf-8 -*-
-
 """Convert KEGG Genes to OBO.
 
 Run with ``python -m pyobo.sources.kegg.genes``
 """
 
 import logging
-from typing import Iterable, Optional
+from collections.abc import Iterable
+from typing import Optional
 
 import click
 from more_click import verbose_option
@@ -90,7 +89,7 @@ def _make_terms(
                 )
                 continue
             if ";" in line:
-                *_extras, name = [part.strip() for part in extras.split(";")]
+                *_extras, name = (part.strip() for part in extras.split(";"))
             else:
                 name = extras
 

pyobo/sources/kegg/genome.py

@@ -1,12 +1,10 @@
-# -*- coding: utf-8 -*-
-
 """Convert KEGG Genome to OBO.
 
 Run with ``python -m pyobo.sources.kegg.genome``
 """
 
 import logging
-from typing import Iterable
+from collections.abc import Iterable
 
 from tqdm.auto import tqdm