pyobo 0.10.12__py3-none-any.whl → 0.11.0__py3-none-any.whl

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

@@ -3,7 +3,7 @@
 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

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
@@ -7,8 +5,9 @@ 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
 
 from tabulate import tabulate
 from tqdm.auto import tqdm
@@ -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 = 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
 

pyobo/sources/kegg/pathway.py

@@ -1,5 +1,3 @@
-# -*- coding: utf-8 -*-
-
 """Convert KEGG Pathways to OBO.
 
 Run with ``python -m pyobo.sources.kegg.pathway``
@@ -8,8 +6,9 @@ Run with ``python -m pyobo.sources.kegg.pathway``
 import logging
 import urllib.error
 from collections import defaultdict
+from collections.abc import Iterable, Mapping
 from functools import partial
-from typing import Iterable, List, Mapping, Tuple, Union
+from typing import Union
 
 from tqdm.auto import tqdm
 from tqdm.contrib.concurrent import thread_map
@@ -76,7 +75,7 @@ def iter_terms(version: str, skip_missing: bool = True) -> Iterable[Term]:
         )
 
 
-def _get_link_pathway_map(path: str) -> Mapping[str, List[str]]:
+def _get_link_pathway_map(path: str) -> Mapping[str, list[str]]:
     rv = defaultdict(list)
     with open(path) as file:
         for line in file:
@@ -110,7 +109,7 @@ def _iter_genome_terms(
         list_pathway_lines = [line.strip() for line in file]
     for line in list_pathway_lines:
         line = line.strip()
-        pathway_id, name = [part.strip() for part in line.split("\t")]
+        pathway_id, name = (part.strip() for part in line.split("\t"))
         pathway_id = pathway_id[len("path:") :]
 
         terms[pathway_id] = term = Term.from_triple(
@@ -149,7 +148,7 @@ def _iter_genome_terms(
 
 def iter_kegg_pathway_paths(
     version: str, skip_missing: bool = True
-) -> Iterable[Union[Tuple[KEGGGenome, str, str], Tuple[None, None, None]]]:
+) -> Iterable[Union[tuple[KEGGGenome, str, str], tuple[None, None, None]]]:
     """Get paths for the KEGG Pathway files."""
     genomes = list(iter_kegg_genomes(version=version, desc="KEGG Pathways"))
     func = partial(_process_genome, version=version, skip_missing=skip_missing)

pyobo/sources/mesh.py

@@ -1,17 +1,16 @@
-# -*- coding: utf-8 -*-
-
 """Parser for the MeSH descriptors."""
 
 import datetime
 import itertools as itt
 import logging
 import re
-from typing import Any, Collection, Dict, Iterable, List, Mapping, Optional, Set, Tuple
+from collections.abc import Collection, Iterable, Mapping
+from typing import Any, Optional
 from xml.etree.ElementTree import Element
 
 from tqdm.auto import tqdm
 
-from pyobo.api.utils import get_version
+from pyobo.api.utils import safe_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
@@ -70,7 +69,7 @@ def get_tree_to_mesh_id(version: str) -> Mapping[str, str]:
 
 def get_terms(version: str, force: bool = False) -> Iterable[Term]:
     """Get MeSH OBO terms."""
-    mesh_id_to_term: Dict[str, Term] = {}
+    mesh_id_to_term: dict[str, Term] = {}
 
     descriptors = ensure_mesh_descriptors(version=version, force=force)
     supplemental_records = ensure_mesh_supplemental_records(version=version, force=force)
@@ -80,8 +79,8 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
         name = entry["name"]
         definition = entry.get("scope_note")
 
-        xrefs: List[Reference] = []
-        synonyms: Set[str] = set()
+        xrefs: list[Reference] = []
+        synonyms: set[str] = set()
         for concept in entry["concepts"]:
             synonyms.add(concept["name"])
             for term in concept["terms"]:
@@ -107,7 +106,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
 
 def ensure_mesh_descriptors(
     version: str, force: bool = False, force_process: bool = False
-) -> List[Mapping[str, Any]]:
+) -> list[Mapping[str, Any]]:
     """Get the parsed MeSH dictionary, and cache it if it wasn't already."""
 
     @cached_json(path=prefix_directory_join(PREFIX, name="desc.json", version=version), force=force)
@@ -133,7 +132,7 @@ def get_supplemental_url(version: str) -> str:
     return f"https://nlmpubs.nlm.nih.gov/projects/mesh/{version}/xmlmesh/supp{version}.gz"
 
 
-def ensure_mesh_supplemental_records(version: str, force: bool = False) -> List[Mapping[str, Any]]:
+def ensure_mesh_supplemental_records(version: str, force: bool = False) -> list[Mapping[str, Any]]:
     """Get the parsed MeSH dictionary, and cache it if it wasn't already."""
 
     @cached_json(path=prefix_directory_join(PREFIX, name="supp.json", version=version), force=force)
@@ -147,11 +146,11 @@ def ensure_mesh_supplemental_records(version: str, force: bool = False) -> List[
     return _inner()
 
 
-def get_descriptor_records(element: Element, id_key: str, name_key) -> List[Dict[str, Any]]:
+def get_descriptor_records(element: Element, id_key: str, name_key) -> list[dict[str, Any]]:
     """Get MeSH descriptor records."""
     logger.info("extract MeSH descriptors, concepts, and terms")
 
-    rv: List[Dict[str, Any]] = [
+    rv: list[dict[str, Any]] = [
         get_descriptor_record(descriptor, id_key=id_key, name_key=name_key)
         for descriptor in tqdm(element, desc="Getting MeSH Descriptors", unit_scale=True)
     ]
@@ -204,7 +203,7 @@ def get_descriptor_record(
     element: Element,
     id_key: str,
     name_key: str,
-) -> Dict[str, Any]:
+) -> dict[str, Any]:
     """Get descriptor records from the main element.
 
     :param element: An XML element
@@ -228,13 +227,13 @@ def get_descriptor_record(
     return rv
 
 
-def get_concept_records(element: Element) -> List[Mapping[str, Any]]:
+def get_concept_records(element: Element) -> list[Mapping[str, Any]]:
     """Get concepts from a record."""
     return [get_concept_record(e) for e in element.findall("ConceptList/Concept")]
 
 
-def _get_xrefs(element: Element) -> List[Tuple[str, str]]:
-    raw_registry_numbers: List[str] = sorted(
+def _get_xrefs(element: Element) -> list[tuple[str, str]]:
+    raw_registry_numbers: list[str] = sorted(
         {e.text for e in element.findall("RelatedRegistryNumberList/RegistryNumber") if e.text}
     )
     registry_number = element.findtext("RegistryNumber")
@@ -267,7 +266,7 @@ def get_concept_record(element: Element) -> Mapping[str, Any]:
     if scope_note is not None:
         scope_note = scope_note.replace("\\n", "\n").strip()
 
-    rv: Dict[str, Any] = {
+    rv: dict[str, Any] = {
         "concept_ui": element.findtext("ConceptUI"),
         "name": element.findtext("ConceptName/String"),
         "terms": get_term_records(element),
@@ -286,7 +285,7 @@ def get_concept_record(element: Element) -> Mapping[str, Any]:
     return rv
 
 
-def get_term_records(element: Element) -> List[Mapping[str, Any]]:
+def get_term_records(element: Element) -> list[Mapping[str, Any]]:
     """Get all of the terms for a concept."""
     return [get_term_record(term) for term in element.findall("TermList/Term")]
 
@@ -307,7 +306,7 @@ def _text_or_bust(element: Element, name: str) -> str:
     return n
 
 
-def _get_descriptor_qualifiers(descriptor: Element) -> List[Mapping[str, str]]:
+def _get_descriptor_qualifiers(descriptor: Element) -> list[Mapping[str, str]]:
     return [
         {
             "qualifier_ui": _text_or_bust(qualifier, "QualifierUI"),
@@ -321,7 +320,7 @@ def _get_descriptor_qualifiers(descriptor: Element) -> List[Mapping[str, str]]:
 
 def get_mesh_category_curies(
     letter: str, *, skip: Optional[Collection[str]] = None, version: Optional[str] = None
-) -> List[str]:
+) -> list[str]:
     """Get the MeSH LUIDs for a category, by letter (e.g., "A").
 
     :param letter: The MeSH tree, A for anatomy, C for disease, etc.
@@ -332,8 +331,7 @@ def get_mesh_category_curies(
     .. seealso:: https://meshb.nlm.nih.gov/treeView
     """
     if version is None:
-        version = get_version("mesh")
-        assert version is not None
+        version = safe_get_version("mesh")
     tree_to_mesh = get_tree_to_mesh_id(version=version)
     rv = []
     for i in range(1, 100):