pyobo 0.12.12__tar.gz → 0.12.13__tar.gz

{pyobo-0.12.12 → pyobo-0.12.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.12
+Version: 0.12.13
 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

{pyobo-0.12.12 → pyobo-0.12.13}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "pyobo"
-version = "0.12.12"
+version = "0.12.13"
 description = "A python package for handling and generating OBO"
 readme = "README.md"
 authors = [
@@ -315,7 +315,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.12.12"
+current_version = "0.12.13"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?(?:\\+(?P<build>[0-9A-Za-z-]+(?:\\.[0-9A-Za-z-]+)*))?"
 serialize = [
     "{major}.{minor}.{patch}-{release}+{build}",

{pyobo-0.12.12 → pyobo-0.12.13}/src/pyobo/sources/chebi.py

@@ -3,7 +3,7 @@
 from collections.abc import Mapping
 
 from ..api import get_filtered_properties_mapping, get_filtered_relations_df
-from ..struct import Reference, TypeDef
+from ..struct.typedef import has_role
 from ..utils.io import multisetdict
 
 __all__ = [
@@ -28,9 +28,6 @@ def get_chebi_smiles_id_mapping() -> Mapping[str, str]:
     return {v: k for k, v in get_chebi_id_smiles_mapping().items()}
 
 
-has_role = TypeDef(reference=Reference(prefix="chebi", identifier="has_role"))
-
-
 def get_chebi_role_to_children() -> Mapping[str, set[tuple[str, str]]]:
     """Get the ChEBI role to children mapping."""
     df = get_filtered_relations_df("chebi", relation=has_role)

{pyobo-0.12.12 → pyobo-0.12.13}/src/pyobo/struct/struct_utils.py

@@ -1020,6 +1020,8 @@ def _format_obo_trailing_modifiers(
                     right = f'"{obo_escape_slim(value)}"'
                 else:
                     right = value
+            case _:
+                raise TypeError(f"invalid prop value: {type(prop.value)} - {prop.value}")
         modifiers.append((left, right))
     inner = ", ".join(f"{key}={value}" for key, value in modifiers)
     return " {" + inner + "}"

{pyobo-0.12.12 → pyobo-0.12.13}/src/pyobo/struct/typedef.py

@@ -18,6 +18,7 @@ __all__ = [
     "contributes_to_condition",
     "default_typedefs",
     "derives_from_organism",
+    "directly_regulates_activity_of",
     "editor_note",
     "enables",
     "ends",
@@ -46,15 +47,20 @@ __all__ = [
     "has_successor",
     "has_taxonomy_rank",
     "is_a",
+    "is_agonist_of",
+    "is_antagonist_of",
+    "is_inverse_agonist_of",
     "located_in",
     "mapping_has_confidence",
     "mapping_has_justification",
     "match_typedefs",
     "member_of",
     "narrow_match",
+    "negatively_regulates",
     "orthologous",
     "part_of",
     "participates_in",
+    "positively_regulates",
     "related_match",
     "role_of",
     "see_also",
@@ -267,6 +273,19 @@ has_functional_parent = TypeDef(
     reference=Reference(prefix="ro", identifier="0018038", name="has functional parent"),
 )
 
+positively_regulates = TypeDef(
+    Reference(prefix="RO", identifier="0002213", name="positively regulates")
+)
+negatively_regulates = TypeDef(
+    Reference(prefix="RO", identifier="0002212", name="negatively regulates")
+)
+is_agonist_of = TypeDef.from_triple("RO", "0018027", "is agonist of")
+is_inverse_agonist_of = TypeDef.from_triple("RO", "0018028", "is inverse agonist of")
+is_antagonist_of = TypeDef.from_triple("RO", "0018029", "is antagonist of")
+directly_regulates_activity_of = TypeDef.from_triple(
+    "RO", "0002448", "directly regulates activity of"
+)
+
 is_mentioned_by = TypeDef(
     reference=v.is_mentioned_by,
     is_metadata_tag=True,

{pyobo-0.12.12 → pyobo-0.12.13}/src/pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.12"
+VERSION = "0.12.13"
 
 
 def get_git_hash() -> str: