pyobo 0.12.11__py3-none-any.whl → 0.12.12__py3-none-any.whl

pyobo/api/xrefs.py

@@ -9,7 +9,7 @@ import curies
 import pandas as pd
 from curies import ReferenceTuple
 from sssom_pydantic import SemanticMapping
-from sssom_pydantic.io import parse_record, parse_row
+from sssom_pydantic.io import row_to_semantic_mapping
 from typing_extensions import Unpack
 
 from .utils import get_version_from_kwargs
@@ -124,12 +124,7 @@ def get_semantic_mappings(
     )
     if converter is None:
         converter = get_converter()
-    rv = []
-    for _, row in df.iterrows():
-        record = parse_row(row.to_dict())
-        mapping = parse_record(record, converter=converter)
-        rv.append(mapping)
-    return rv
+    return [row_to_semantic_mapping(row, converter=converter) for _, row in df.iterrows()]
 
 
 def get_mappings_df(

pyobo/cli/cli.py

@@ -6,10 +6,7 @@ from collections.abc import Iterable
 from functools import lru_cache
 from operator import itemgetter
 
-import bioregistry
 import click
-import humanize
-from tabulate import tabulate
 
 from .database import main as database_main
 from .lookup import lookup
@@ -59,6 +56,9 @@ def clean(remove_obo: bool):
 @main.command()
 def ls():
     """List how big all of the OBO files are."""
+    import humanize
+    from tabulate import tabulate
+
     entries = [(prefix, os.path.getsize(path)) for prefix, path in _iter_cached_obo()]
     entries = [
         (prefix, humanize.naturalsize(size), "✅" if not has_nomenclature_plugin(prefix) else "❌")
@@ -69,6 +69,8 @@ def ls():
 
 def _iter_cached_obo() -> Iterable[tuple[str, str]]:
     """Iterate over cached OBO paths."""
+    import bioregistry
+
     for prefix in os.listdir(RAW_DIRECTORY):
         if prefix in GLOBAL_SKIP or _has_no_download(prefix) or bioregistry.is_deprecated(prefix):
             continue
@@ -83,6 +85,8 @@ def _iter_cached_obo() -> Iterable[tuple[str, str]]:
 
 def _has_no_download(prefix: str) -> bool:
     """Return if the prefix is not available."""
+    import bioregistry
+
     prefix_norm = bioregistry.normalize_prefix(prefix)
     return prefix_norm is not None and prefix_norm in _no_download()
 
@@ -90,6 +94,8 @@ def _has_no_download(prefix: str) -> bool:
 @lru_cache(maxsize=1)
 def _no_download() -> set[str]:
     """Get the list of prefixes not available as OBO."""
+    import bioregistry
+
     return {resource.prefix for resource in bioregistry.resources() if not resource.has_download()}
 
 

pyobo/cli/database.py

@@ -5,29 +5,11 @@ import warnings
 from collections.abc import Iterable
 from pathlib import Path
 
-import bioregistry
-import bioversions
 import click
 from more_click import verbose_option
 from tqdm.contrib.logging import logging_redirect_tqdm
 from typing_extensions import Unpack
-from zenodo_client import update_zenodo
-
-from .database_utils import (
-    IterHelperHelperDict,
-    _iter_alts,
-    _iter_definitions,
-    _iter_edges,
-    _iter_mappings,
-    _iter_names,
-    _iter_properties,
-    _iter_relations,
-    _iter_species,
-    _iter_synonyms,
-    _iter_typedefs,
-    _iter_xrefs,
-    iter_helper_helper,
-)
+
 from .utils import (
     Clickable,
     directory_option,
@@ -48,7 +30,6 @@ from ..constants import (
     TYPEDEFS_RECORD,
     DatabaseKwargs,
 )
-from ..getters import db_output_helper, get_ontology
 
 __all__ = [
     "main",
@@ -107,6 +88,8 @@ def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwa
     #    sys.exit(1)
 
     if eager_versions:
+        import bioversions
+
         bioversions.get_rows(use_tqdm=True)
 
     with logging_redirect_tqdm():
@@ -143,6 +126,9 @@ def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwa
 @database_annotate
 def cache(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Cache all things."""
+    from .database_utils import iter_helper_helper
+    from ..getters import get_ontology
+
     if zenodo:
         click.echo("no zenodo for caching")
 
@@ -156,9 +142,13 @@ def cache(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-metadata dump."""
+    import bioregistry
+
+    from .database_utils import IterHelperHelperDict, iter_helper_helper
     from ..api import get_metadata
+    from ..getters import db_output_helper
 
-    def _iter_metadata(
+    def _iter_metadata_internal(
         **kwargs: Unpack[IterHelperHelperDict],
     ) -> Iterable[tuple[str, str, str, bool]]:
         for prefix, data in iter_helper_helper(get_metadata, **kwargs):
@@ -166,7 +156,7 @@ def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             logger.debug(f"[{prefix}] using version {version}")
             yield prefix, version, data["date"], bioregistry.is_deprecated(prefix)
 
-    it = _iter_metadata(**kwargs)
+    it = _iter_metadata_internal(**kwargs)
     db_output_helper(
         it,
         "metadata",
@@ -181,6 +171,9 @@ def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-name dump."""
+    from .database_utils import _iter_names
+    from ..getters import db_output_helper
+
     it = _iter_names(**kwargs)
     with logging_redirect_tqdm():
         paths = db_output_helper(
@@ -190,6 +183,8 @@ def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4020486
         update_zenodo(OOH_NA_NA_RECORD, paths)
 
@@ -197,6 +192,9 @@ def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def species(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-species dump."""
+    from .database_utils import _iter_species
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_species(**kwargs)
         paths = db_output_helper(
@@ -206,6 +204,8 @@ def species(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/5334738
         update_zenodo(SPECIES_RECORD, paths)
 
@@ -221,6 +221,9 @@ def _extend_skip_set(kwargs: DatabaseKwargs, skip_set: set[str]) -> None:
 @database_annotate
 def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-definition dump."""
+    from .database_utils import _iter_definitions
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome", "umls"})
         it = _iter_definitions(**kwargs)
@@ -231,6 +234,8 @@ def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4637061
         update_zenodo(DEFINITIONS_RECORD, paths)
 
@@ -238,6 +243,9 @@ def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
 @database_annotate
 def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the typedef prefix-identifier-name dump."""
+    from .database_utils import _iter_typedefs
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"ncbigene", "kegg.pathway", "kegg.genes", "kegg.genome"})
         it = _iter_typedefs(**kwargs)
@@ -249,6 +257,8 @@ def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4644013
         update_zenodo(TYPEDEFS_RECORD, paths)
 
@@ -256,6 +266,9 @@ def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-alt-id dump."""
+    from .database_utils import _iter_alts
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome", "umls"})
         it = _iter_alts(**kwargs)
@@ -266,6 +279,8 @@ def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> Non
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021476
         update_zenodo(ALTS_DATA_RECORD, paths)
 
@@ -273,6 +288,9 @@ def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> Non
 @database_annotate
 def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-synonym dump."""
+    from .database_utils import _iter_synonyms
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome"})
         it = _iter_synonyms(**kwargs)
@@ -283,6 +301,8 @@ def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021482
         update_zenodo(SYNONYMS_RECORD, paths)
 
@@ -290,6 +310,9 @@ def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the relation dump."""
+    from .database_utils import _iter_relations
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_relations(**kwargs)
         paths = db_output_helper(
@@ -307,6 +330,8 @@ def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4625167
         update_zenodo(RELATIONS_RECORD, paths)
 
@@ -314,6 +339,9 @@ def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -
 @database_annotate
 def edges(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the edges dump."""
+    from .database_utils import _iter_edges
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_edges(**kwargs)
         db_output_helper(
@@ -334,6 +362,9 @@ def edges(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the properties dump."""
+    from .database_utils import _iter_properties
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_properties(**kwargs)
         paths = db_output_helper(
@@ -344,6 +375,8 @@ def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4625172
         update_zenodo(PROPERTIES_RECORD, paths)
 
@@ -351,6 +384,9 @@ def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
 @database_annotate
 def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-xref dump."""
+    from .database_utils import _iter_xrefs
+    from ..getters import db_output_helper
+
     warnings.warn("Use pyobo.database.mappings instead", DeprecationWarning, stacklevel=2)
     with logging_redirect_tqdm():
         it = _iter_xrefs(**kwargs)
@@ -362,6 +398,8 @@ def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021477
         update_zenodo(JAVERT_RECORD, paths)
 
@@ -369,6 +407,9 @@ def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def mappings(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the SSSOM dump."""
+    from .database_utils import _iter_mappings
+    from ..getters import db_output_helper
+
     columns = [
         "subject_id",
         "object_id",

pyobo/cli/lookup.py

@@ -4,7 +4,6 @@ import json
 import sys
 from collections.abc import Mapping
 
-import bioregistry
 import click
 from more_click import verbose_option
 from typing_extensions import Unpack
@@ -18,30 +17,7 @@ from .utils import (
     strict_option,
     version_option,
 )
-from ..api import (
-    get_ancestors,
-    get_descendants,
-    get_filtered_properties_df,
-    get_filtered_relations_df,
-    get_filtered_xrefs,
-    get_hierarchy,
-    get_id_definition_mapping,
-    get_id_name_mapping,
-    get_id_species_mapping,
-    get_id_synonyms_mapping,
-    get_id_to_alts,
-    get_ids,
-    get_mappings_df,
-    get_metadata,
-    get_name,
-    get_properties_df,
-    get_relations_df,
-    get_typedef_df,
-    get_xrefs_df,
-)
 from ..constants import LookupKwargs
-from ..getters import get_ontology
-from ..struct.reference import _parse_str_or_curie_or_uri
 
 __all__ = [
     "lookup",
@@ -75,6 +51,10 @@ identifier_option = click.option("-i", "--identifier")
 @click.option("-t", "--target")
 def xrefs(target: str, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through xrefs for the given namespace to the second given namespace."""
+    import bioregistry
+
+    from ..api import get_filtered_xrefs, get_xrefs_df
+
     if target:
         target_norm = bioregistry.normalize_prefix(target)
         filtered_xrefs = get_filtered_xrefs(xref_prefix=target_norm, **kwargs)
@@ -91,6 +71,10 @@ def xrefs(target: str, **kwargs: Unpack[LookupKwargs]) -> None:
 @click.option("-t", "--target")
 def mappings(include_names: bool, target: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through mappings for the given namespace."""
+    import bioregistry
+
+    from ..api import get_mappings_df
+
     mappings_df = get_mappings_df(names=include_names, **kwargs)
     if target:
         target_norm = bioregistry.normalize_prefix(target)
@@ -106,6 +90,8 @@ def mappings(include_names: bool, target: str | None, **kwargs: Unpack[LookupKwa
 @lookup_annotate
 def metadata(**kwargs: Unpack[LookupKwargs]) -> None:
     """Print the metadata for the given namespace."""
+    from ..api import get_metadata
+
     metadata = get_metadata(**kwargs)
     click.echo(json.dumps(metadata, indent=2))
 
@@ -113,6 +99,8 @@ def metadata(**kwargs: Unpack[LookupKwargs]) -> None:
 @lookup_annotate
 def ids(**kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers of entities in the given namespace."""
+    from ..api import get_ids
+
     id_list = get_ids(**kwargs)
     if not id_list:
         click.secho("no data", fg="red")
@@ -124,6 +112,8 @@ def ids(**kwargs: Unpack[LookupKwargs]) -> None:
 @identifier_option
 def names(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and names of entities in the given namespace."""
+    from ..api import get_id_name_mapping
+
     id_to_name = get_id_name_mapping(**kwargs)
     _help_page_mapping(id_to_name, identifier=identifier)
 
@@ -132,6 +122,8 @@ def names(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
 @identifier_option
 def species(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and species of entities in the given namespace."""
+    from ..api import get_id_species_mapping
+
     id_to_species = get_id_species_mapping(**kwargs)
     _help_page_mapping(id_to_species, identifier=identifier)
 
@@ -140,6 +132,8 @@ def species(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
 @identifier_option
 def definitions(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and definitions of entities in the given namespace."""
+    from ..api import get_id_definition_mapping
+
     id_to_definition = get_id_definition_mapping(**kwargs)
     _help_page_mapping(id_to_definition, identifier=identifier)
 
@@ -147,6 +141,8 @@ def definitions(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
 @lookup_annotate
 def typedefs(**kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and names of typedefs in the given namespace."""
+    from ..api import get_typedef_df
+
     df = get_typedef_df(**kwargs)
     echo_df(df)
 
@@ -168,6 +164,8 @@ def _help_page_mapping(id_to_name: Mapping[str, str], *, identifier: str | None
 @identifier_option
 def synonyms(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the synonyms for entities in the given namespace."""
+    from ..api import get_id_synonyms_mapping
+
     id_to_synonyms = get_id_synonyms_mapping(**kwargs)
     if identifier is None:
         click.echo_via_pager(
@@ -198,6 +196,11 @@ def relations(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through the relations for entities in the given namespace."""
+    import bioregistry
+
+    from ..api import get_filtered_relations_df, get_relations_df
+    from ..struct.reference import _parse_str_or_curie_or_uri
+
     if relation is None:
         relations_df = get_relations_df(**kwargs)
         if summarize:
@@ -232,6 +235,8 @@ def hierarchy(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through the hierarchy for entities in the namespace."""
+    from ..api import get_hierarchy
+
     h = get_hierarchy(
         include_part_of=include_part_of,
         include_has_member=include_has_member,
@@ -250,6 +255,8 @@ def ancestors(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Look up ancestors."""
+    from ..api import get_ancestors, get_name
+
     # note, prefix is passed via kwargs
     ancestors = get_ancestors(identifier=identifier, **kwargs)
     for ancestor in sorted(ancestors or []):
@@ -263,6 +270,8 @@ def descendants(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Look up descendants."""
+    from ..api import get_descendants, get_name
+
     # note, prefix is passed via kwargs
     descendants = get_descendants(identifier=identifier, **kwargs)
     for descendant in sorted(descendants or []):
@@ -276,6 +285,8 @@ def properties(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through the properties for entities in the given namespace."""
+    from ..api import get_filtered_properties_df, get_properties_df
+
     if key is None:
         properties_df = get_properties_df(**kwargs)
     else:
@@ -290,6 +301,8 @@ def alts(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through alt ids in a namespace."""
+    from ..api import get_id_to_alts
+
     id_to_alts = get_id_to_alts(**kwargs)
     _help_page_mapping(id_to_alts, identifier=identifier)
 
@@ -297,6 +310,8 @@ def alts(
 @lookup_annotate
 def prefixes(**kwargs: Unpack[LookupKwargs]) -> None:
     """Page through prefixes appearing in an ontology."""
+    from ..getters import get_ontology
+
     ontology = get_ontology(**kwargs)
     for prefix in sorted(ontology._get_prefixes(), key=str.casefold):
         click.echo(prefix)

pyobo/cli/utils.py

@@ -1,15 +1,19 @@
 """Utilities for the CLI."""
 
+from __future__ import annotations
+
 import datetime
 import pathlib
 from collections.abc import Callable
-from typing import TypeVar
+from typing import TYPE_CHECKING, TypeVar
 
 import click
-import pandas as pd
 
 from ..constants import DATABASE_DIRECTORY
 
+if TYPE_CHECKING:
+    import pandas as pd
+
 __all__ = [
     "Clickable",
     "directory_option",

pyobo/constants.py

@@ -8,7 +8,6 @@ from collections.abc import Callable
 from pathlib import Path
 from typing import Literal, NamedTuple, TypeAlias
 
-import bioregistry
 import pystow
 from typing_extensions import NotRequired, TypedDict
 
@@ -247,11 +246,35 @@ class OntologyPathPack(NamedTuple):
     path: Path
 
 
+def _get_obo_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_obo_download(prefix)
+
+
+def _get_owl_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_owl_download(prefix)
+
+
+def _get_json_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_json_download(prefix)
+
+
+def _get_rdf_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_rdf_download(prefix)
+
+
 #: Functions that get ontology files. Order matters in this list,
 #: since order implicitly defines priority
 ONTOLOGY_GETTERS: list[tuple[OntologyFormat, Callable[[str], str | None]]] = [
-    ("obo", bioregistry.get_obo_download),
-    ("owl", bioregistry.get_owl_download),
-    ("json", bioregistry.get_json_download),
-    ("rdf", bioregistry.get_rdf_download),
+    ("obo", _get_obo_download),
+    ("owl", _get_owl_download),
+    ("json", _get_json_download),
+    ("rdf", _get_rdf_download),
 ]

pyobo/ner/api.py

@@ -32,6 +32,7 @@ def get_grounder(
     grounder_cls: type[gilda.Grounder] | None = None,
     versions: None | str | Iterable[str | None] | dict[str, str] = None,
     skip_obsolete: bool = False,
+    raise_on_missing: bool = False,
     **kwargs: Unpack[GetOntologyKwargs],
 ) -> ssslm.Grounder:
     """Get a grounder for the given prefix(es)."""
@@ -46,6 +47,8 @@ def get_grounder(
             continue
         else:
             if not literal_mappings:
+                if raise_on_missing:
+                    raise ValueError(f"no literal mappings were loaded for {prefix}")
                 logger.warning("[%s] no literal mappings loaded", prefix)
             all_literal_mappings.extend(literal_mappings)
 

pyobo/ner/scispacy_utils.py

@@ -227,6 +227,8 @@ def get_scispacy_entities(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> I
     # TODO reuse labels, synonyms, and definitions cache
     ontology = get_ontology(prefix, **kwargs)
     for term in ontology:
+        if not term.name or term.prefix != ontology.ontology:
+            continue
         yield Entity(
             concept_id=term.curie,
             canonical_name=term.name,

pyobo/plugins.py

@@ -4,8 +4,10 @@ from __future__ import annotations
 
 from collections.abc import Callable, Iterable, Mapping
 from functools import lru_cache
+from typing import TYPE_CHECKING
 
-from .struct import Obo
+if TYPE_CHECKING:
+    from .struct import Obo
 
 __all__ = [
     "has_nomenclature_plugin",

pyobo/struct/obo/reader.py

@@ -345,7 +345,7 @@ def _get_terms(
         _process_equivalent_to(term, data, ontology_prefix=ontology_prefix, strict=strict)
         _process_disjoint_from(term, data, ontology_prefix=ontology_prefix, strict=strict)
         _process_consider(term, data, ontology_prefix=ontology_prefix, strict=strict)
-        _process_comment(term, data, ontology_prefix=ontology_prefix, strict=strict)
+        _process_comment(term, data)
         _process_description(term, data, ontology_prefix=ontology_prefix, strict=strict)
         _process_creation_date(term, data)
 
@@ -367,7 +367,7 @@ def _process_description(term: Stanza, data, *, ontology_prefix: str, strict: bo
             )
 
 
-def _process_comment(term: Stanza, data, *, ontology_prefix: str, strict: bool) -> None:
+def _process_comment(term: Stanza, data) -> None:
     if comment := data.get("comment"):
         term.append_comment(comment)
 
@@ -902,7 +902,7 @@ def iterate_typedefs(
         _process_equivalent_to(typedef, data, ontology_prefix=ontology_prefix, strict=strict)
         _process_disjoint_from(typedef, data, ontology_prefix=ontology_prefix, strict=strict)
         _process_consider(typedef, data, ontology_prefix=ontology_prefix, strict=strict)
-        _process_comment(typedef, data, ontology_prefix=ontology_prefix, strict=strict)
+        _process_comment(typedef, data)
         _process_description(typedef, data, ontology_prefix=ontology_prefix, strict=strict)
         _process_creation_date(typedef, data)
 

pyobo/struct/typedef.py

@@ -26,6 +26,7 @@ __all__ = [
     "from_species",
     "gene_product_member_of",
     "has_contributor",
+    "has_creator",
     "has_dbxref",
     "has_depiction",
     "has_end_date",
@@ -319,6 +320,8 @@ has_end_date = TypeDef(
 
 has_title = TypeDef(reference=v.has_title, is_metadata_tag=True)
 has_license = TypeDef(reference=v.has_license, is_metadata_tag=True)
+has_creator = TypeDef(reference=v.has_creator, is_metadata_tag=True)
+
 has_description = TypeDef(reference=v.has_description, is_metadata_tag=True)
 obo_autogenerated_by = TypeDef(reference=v.obo_autogenerated_by, is_metadata_tag=True)
 obo_has_format_version = TypeDef(reference=v.obo_has_format_version, is_metadata_tag=True)

pyobo/struct/vocabulary.py

@@ -41,6 +41,7 @@ mapping_has_justification = Reference(
 )
 mapping_has_confidence = Reference(prefix="sssom", identifier="confidence", name="has confidence")
 has_contributor = _c(_v.has_contributor)
+has_creator = Reference(prefix="dcterms", identifier="creator", name="creator")
 has_source = _c(_v.has_source)
 has_date = _c(_v.has_date)
 has_dbxref = _c(_v.has_dbxref)
@@ -89,6 +90,7 @@ mentions = Reference(prefix="mito", identifier="mentions", name="mentions")
 
 has_description = _c(_v.has_description)
 has_license = _c(_v.has_license)
+has_license = _c(_v.has_license)
 has_title = _c(_v.has_title)
 
 has_homepage = Reference(prefix="foaf", identifier="homepage", name="has homepage")

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.11"
+VERSION = "0.12.12"
 
 
 def get_git_hash() -> str:

{pyobo-0.12.11.dist-info → pyobo-0.12.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.11
+Version: 0.12.12
 Summary: A python package for handling and generating OBO
 Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
 Author: Charles Tapley Hoyt
@@ -55,7 +55,7 @@ Requires-Dist: nih-reporter-downloader>=0.0.1
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
 Requires-Dist: obographs>=0.0.8
-Requires-Dist: sssom-pydantic
+Requires-Dist: sssom-pydantic>=0.1.1
 Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
@@ -523,20 +523,6 @@ Alternatively, install using pip:
 $ python3 -m pip install -e .
 ```
 
-### Updating Package Boilerplate
-
-This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
-guidelines, documentation configuration) up-to-date with the upstream
-cookiecutter package. Install cruft with either `uv tool install cruft` or
-`python3 -m pip install cruft` then run:
-
-```console
-$ cruft update
-```
-
-More info on Cruft's update command is available
-[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
-
 ### 🥼 Testing
 
 After cloning the repository and installing `tox` with
@@ -574,8 +560,21 @@ only that Sphinx can build the documentation in an isolated environment (i.e.,
 with `tox -e docs-test`) but also that
 [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
 
+</details>
+
+## 🧑‍💻 For Maintainers
+
+<details>
+  <summary>See maintainer instructions</summary>
+
+### Initial Configuration
+
 #### Configuring ReadTheDocs
 
+[ReadTheDocs](https://readthedocs.org) is an external documentation hosting
+service that integrates with GitHub's CI/CD. Do the following for each
+repository:
+
 1. Log in to ReadTheDocs with your GitHub account to install the integration at
    https://readthedocs.org/accounts/login/?next=/dashboard/
 2. Import your project by navigating to https://readthedocs.org/dashboard/import
@@ -584,12 +583,10 @@ with `tox -e docs-test`) but also that
    (i.e., with spaces and capital letters)
 4. Click next, and you're good to go!
 
-### 📦 Making a Release
-
-#### Configuring Zenodo
+#### Configuring Archival on Zenodo
 
 [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
-to each release of your package.
+to each release of your package. Do the following for each repository:
 
 1. Log in to Zenodo via GitHub with this link:
    https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
@@ -609,10 +606,10 @@ the DOI for the release and link to the Zenodo record for it.
 
 #### Registering with the Python Package Index (PyPI)
 
-You only have to do the following steps once.
+The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can
+be easily installed with `pip`, `uv`, and equivalent tools.
 
-1. Register for an account on the
-   [Python Package Index (PyPI)](https://pypi.org/account/register)
+1. Register for an account [here](https://pypi.org/account/register)
 2. Navigate to https://pypi.org/manage/account and make sure you have verified
    your email address. A verification email might not have been sent by default,
    so you might have to click the "options" dropdown next to your address to get
@@ -623,9 +620,11 @@ You only have to do the following steps once.
    2-factor authentication
 4. Issue an API token from https://pypi.org/manage/account/token
 
+This only needs to be done once per developer.
+
 #### Configuring your machine's connection to PyPI
 
-You have to do the following steps once per machine.
+This needs to be done once per machine.
 
 ```console
 $ uv tool install keyring
@@ -635,6 +634,8 @@ $ keyring set https://test.pypi.org/legacy/ __token__
 
 Note that this deprecates previous workflows using `.pypirc`.
 
+### 📦 Making a Release
+
 #### Uploading to PyPI
 
 After installing the package in development mode and installing `tox` with
@@ -672,4 +673,18 @@ This script does the following:
 
 This will trigger Zenodo to assign a DOI to your release as well.
 
+### Updating Package Boilerplate
+
+This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
+guidelines, documentation configuration) up-to-date with the upstream
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
 </details>

{pyobo-0.12.11.dist-info → pyobo-0.12.12.dist-info}/RECORD

@@ -14,14 +14,14 @@ pyobo/api/relations.py,sha256=Kebguj5khScU2c0Pm8dJrewu8je9DnKlNenRtmYWGKI,5875
 pyobo/api/species.py,sha256=YxzJeClfuKI-pjYLpu5797jdDeyTkXpjQDgdmc9MKwo,2376
 pyobo/api/typedefs.py,sha256=HTui0kl_VELxgji0vfBr-NBG3zrrpCU8tmuQOSWK6fw,1262
 pyobo/api/utils.py,sha256=SCMsy4QyYVhn-QK0h90Ef1XUMbyHKR1fvteRESzs-bk,5192
-pyobo/api/xrefs.py,sha256=oQ7D2p9mrzb-LtLkXlJ_LYRArs5eqq9Zwwx9_0Yov_o,6053
+pyobo/api/xrefs.py,sha256=szsPOMwkKmfDRb7CNgyEoe7hRQK8aX1Vm6Vcz0FYN2w,5956
 pyobo/cli/__init__.py,sha256=pTiLuzjjpi0P69yVjQ2kE6nBUmZuYFnqdJNDZLDkgvk,71
-pyobo/cli/cli.py,sha256=5bY_7ZVZOoHwhZtCxx-AYL5ybyBzjS65NU5v5X9DsLA,2842
-pyobo/cli/database.py,sha256=grPVG1d78yhog5lvEAu3wwHkBASKhtmabwmvx49WRIc,12121
+pyobo/cli/cli.py,sha256=lyN_Hi5Hf2jyCUXjD87pG7RU3g7TnbBiOd8o-PMqIEw,2904
+pyobo/cli/database.py,sha256=iq4-eJ_8Kgim0MMnSqf1wu2hvHDZk9BWNMVuwykz2Ko,13407
 pyobo/cli/database_utils.py,sha256=jQ7qSg-oZk-Q-RC121NkUbqXeNg0K8fV96igXaK3ra4,5540
-pyobo/cli/lookup.py,sha256=GxG753GXnDRf-N9JRWKRmQC5XiN8fEN5l1le5C3jHHY,9163
-pyobo/cli/utils.py,sha256=nmtXsxG0TWEIjjIe-jh_aqzr09bTN7-NHFifuHGzME0,1738
-pyobo/constants.py,sha256=vqaf3xj0Sv39PETE3PJuuZ5SZTpoprsngKOzwpca1CU,7129
+pyobo/cli/lookup.py,sha256=-Tz6E3OP6HBPipVqSrMn7LyzrezbT0pngeDExF5uyn4,9467
+pyobo/cli/utils.py,sha256=SfW9JC8olzp4AcAsDodMPdgHfteeXq0Ngd8yQ2kzOMA,1812
+pyobo/constants.py,sha256=K3d8gjfty6zVc3nUBX32oVQX7tzFxnEkGCO1THlC5Qw,7564
 pyobo/getters.py,sha256=exZNjlseRoWhshQYArWwN2KLvkk4NmCQnHM88YUYf-w,18340
 pyobo/gilda_utils.py,sha256=uThAArALSNzJi-hrR9lUvtQci5VIw4Cqq2L6mtkp0Ko,1990
 pyobo/identifier_utils/__init__.py,sha256=iSHAZhOwqWZmYpOfpXNLuKouSYj7ZSViaX7BF5uT8so,793
@@ -34,10 +34,10 @@ pyobo/identifier_utils/relations/data_rdf.json,sha256=T1PNoYwrqgwDVLtfmj7L5e0Sq0
 pyobo/identifier_utils/relations/data_rdfs.json,sha256=bjpxZte3g4WvrGJsmHuAJN_cg_faxqIa9tCL7auHdqQ,86
 pyobo/mocks.py,sha256=j545K9P_DPsDBuYHDrhyTLjmlPoNlRdEtcRlLhXlbXI,2440
 pyobo/ner/__init__.py,sha256=7Os84d8_gZktUxyUW9Tn2dW33rYFWSO8cviJJef-ZeE,373
-pyobo/ner/api.py,sha256=dy51kXQbfx7C8ZIwxlsu78HjsdYtdgdkbF0KuaDJoG4,2396
+pyobo/ner/api.py,sha256=a_wMpzIbRdBeK3UaMsklzL44T4Q7a9gtV3tzDrqBEX0,2555
 pyobo/ner/normalizer.py,sha256=pdvwFG9elriK83FKqjQfT2s-ZuC-QZZuMPudjfay21w,954
-pyobo/ner/scispacy_utils.py,sha256=4NRGJ1JJB-OmlVthHhyms1iPMwJYrkVMQP1jgZfJ18U,8170
-pyobo/plugins.py,sha256=wEr-NpyZ7Z6uEr0uGDNOeXLOGZokGbFmo3e-z2PNKJM,1232
+pyobo/ner/scispacy_utils.py,sha256=13oQi4R5ikbg3xkzU0L46zno-Acq3BtjdtLm5eiBKjw,8253
+pyobo/plugins.py,sha256=DJFJ3Eogb0snTUz22w6I56Yn2Ys0OOXK1dJJgzpyCOM,1287
 pyobo/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pyobo/resource_utils.py,sha256=bloSKbHfMLz0hB8AkhMkfLOGqw6FyO8CEU6LNg0PVMk,4406
 pyobo/resources/__init__.py,sha256=Q9nik7HgpICCON7GEKpbw3z9ZIM7NFJwoGNpepkn2nA,38
@@ -184,7 +184,7 @@ pyobo/struct/functional/obo_to_functional.py,sha256=65OmttFto-tm6-7T0RQlgIKo34sw
 pyobo/struct/functional/ontology.py,sha256=-a8jx-61NsI3dgCBEYNP-VeswAy8wWxLBlAEFMJucyI,9342
 pyobo/struct/functional/utils.py,sha256=c-XG2SJ7ChYtz7KU3K0F-T6ocMjYevei0WxlkfkkmtE,3487
 pyobo/struct/obo/__init__.py,sha256=xJAFJ4yueWBQv3BrtTuHHJ7AzOqCgOuHgKY4RQocsW0,157
-pyobo/struct/obo/reader.py,sha256=fzh1YiNblhmA4rfehOO37WmCfi2r5I4R72ubWwmK4eE,50799
+pyobo/struct/obo/reader.py,sha256=HJ4u1c2ScA-2qxKhyKIZZo8RI2QOUSXwushK9FZGdrQ,50664
 pyobo/struct/obo/reader_utils.py,sha256=UyQVTQhXbhZ9fCizZg26o5TmeHis9-qZMKvQFwIBRgo,4423
 pyobo/struct/obograph/__init__.py,sha256=B4rNP9OCTnMXm8YpQ0rar1swn4GIw9b4gQD-IVuqHyw,452
 pyobo/struct/obograph/export.py,sha256=yk3MHulDM_SMohfwiFdeB62-XGJ2ZNgRUZGjGjiyonY,9945
@@ -193,9 +193,9 @@ pyobo/struct/obograph/utils.py,sha256=je0kSkC24MU9pWRHq1_K-J5jWhjWESY6NI3TpZqvZ_
 pyobo/struct/reference.py,sha256=qgwTa-0VIoDklQ7LjlYH-mf2WG0_uO7KlHt0PSBail4,11744
 pyobo/struct/struct.py,sha256=-JaApTZ7e50bRJ2dXPdAVuJ0ElIVJIJ-HHRsVdaiMxM,96291
 pyobo/struct/struct_utils.py,sha256=tqaUOYKfM3NAa9NfIrWUbaEFJuSOi05_fXPh1cNMY2w,40911
-pyobo/struct/typedef.py,sha256=X5eDKtFsuXXbmFxAS3GxNHQaES5s6UyowAI7_c8Qcao,13364
+pyobo/struct/typedef.py,sha256=9qO09bK641t_N37wGHuX9WpYRwUaApk1AhlS9hjLwek,13453
 pyobo/struct/utils.py,sha256=zkpOE42JQIfkN0rc5qNENK03VIKmkf_57tHojMJK71Y,906
-pyobo/struct/vocabulary.py,sha256=87VqrkU1BrarSW4C2sVbe3qnkn-4jwztCOrnBXy5Ujs,5262
+pyobo/struct/vocabulary.py,sha256=wY_wlV17NyoPQZMiCkf72GL4bIB9gwTHIoMlx7W8Cf4,5375
 pyobo/utils/__init__.py,sha256=CANSY8vGq_6v8rWhWRIdnk-Wo5LA2R9Wjg1nqbWqLOw,17
 pyobo/utils/cache.py,sha256=x7Dnw8vHYsoslXWiV9L9ZdTu5ZueIR1ki5Ncdpb7H10,3136
 pyobo/utils/io.py,sha256=QTvGjNDkaIf78Tca23B5RW_aVweKiSsxmgwSKXcMSNo,3921
@@ -203,9 +203,9 @@ pyobo/utils/iter.py,sha256=rYRbbaFJHxMaE0yU-rQZoCagYIrtev09uY0mxFkf5zY,1524
 pyobo/utils/misc.py,sha256=499pencyDqW9_xm0H0Cq0FhOw0MoNoq-9IVQTKh-eaE,7992
 pyobo/utils/ndex_utils.py,sha256=EokCWS00Wrk_4y8ldeQuUyaaC6yNzBg3DagUl-J2czY,2326
 pyobo/utils/path.py,sha256=snV58UHxHO6GI2QPPE46ssR4RWozaw83V59sS_I9BY8,4109
-pyobo/version.py,sha256=v0j2YjxitLkr27imJK-XFpLZk5UCOkggapvETMVWd4I,927
-pyobo-0.12.11.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
-pyobo-0.12.11.dist-info/WHEEL,sha256=Pi5uDq5Fdo_Rr-HD5h9BiPn9Et29Y9Sh8NhcJNnFU1c,79
-pyobo-0.12.11.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
-pyobo-0.12.11.dist-info/METADATA,sha256=pUsxtOFil50llmHEkOeZi_NcSwly-ezHUMZyZ1EJ2YM,22340
-pyobo-0.12.11.dist-info/RECORD,,
+pyobo/version.py,sha256=Eu_AwMBgCNMCmdFFfIt2yVQpL91vAj4m086WEmjvn6g,927
+pyobo-0.12.12.dist-info/licenses/LICENSE,sha256=QcgJZKGxlW5BwBNnCBL8VZLVtRvXs81Ch9lJRQSIpJg,1076
+pyobo-0.12.12.dist-info/WHEEL,sha256=UH59_qNuDUAa1VxQvC6fxmbl24EMw6DOIlT1yp8oeuU,78
+pyobo-0.12.12.dist-info/entry_points.txt,sha256=ANgzvuwF_9_1ipCoxJtbBM6A4i2Mkt39gMPzQO6hvGs,42
+pyobo-0.12.12.dist-info/METADATA,sha256=mC0mNzJrMLuFLelXKTY04R8Dm1nlU5rcXZsBA_M3YYI,22783
+pyobo-0.12.12.dist-info/RECORD,,

{pyobo-0.12.11.dist-info → pyobo-0.12.12.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: uv 0.8.17
+Generator: uv 0.9.6
 Root-Is-Purelib: true
 Tag: py3-none-any