pyobo 0.12.1__tar.gz → 0.12.2__tar.gz

{pyobo-0.12.1 → pyobo-0.12.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.1
+Version: 0.12.2
 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
@@ -39,13 +39,14 @@ Requires-Dist: cachier
 Requires-Dist: pystow>=0.7.0
 Requires-Dist: bioversions>=0.8.0
 Requires-Dist: bioregistry>=0.12.7
-Requires-Dist: bioontologies>=0.7.1
+Requires-Dist: bioontologies>=0.7.2
 Requires-Dist: ssslm>=0.0.13
 Requires-Dist: zenodo-client>=0.3.6
 Requires-Dist: class-resolver>=0.6.0
 Requires-Dist: psycopg2-binary
 Requires-Dist: pydantic>=2.0
 Requires-Dist: curies>=0.10.13
+Requires-Dist: curies-processing>=0.1.0
 Requires-Dist: python-dateutil
 Requires-Dist: networkx>=3.4
 Requires-Dist: drugbank-downloader
@@ -395,19 +396,6 @@ class MyTestCase(unittest.TestCase):
           pyobo.get_name("chebi", "1234")
 ```
 
-## Preprocessing CURIEs, URIs, and unqualified identifiers
-
-In order to normalize references and identify resources, PyOBO uses the
-[Bioregistry](https://github.com/bioregistry/bioregistry). It used to be a part
-of PyOBO, but has since been externalized for more general reuse.
-
-At
-[src/pyobo/identifier_utils/preprocessing.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/src/pyobo/identifier_utils/preprocessing.json)
-is the curated set of pre-processing rules. These are used in combination with
-the `curies` package to do pre-processing steps on CURIEs, URIs, and unqualified
-identifiers beyond what is possible with the Bioregistry. See
-https://curies.readthedocs.io/en/latest/preprocessing.html.
-
 ## Troubleshooting
 
 The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO

{pyobo-0.12.1 → pyobo-0.12.2}/README.md

@@ -324,19 +324,6 @@ class MyTestCase(unittest.TestCase):
           pyobo.get_name("chebi", "1234")
 ```
 
-## Preprocessing CURIEs, URIs, and unqualified identifiers
-
-In order to normalize references and identify resources, PyOBO uses the
-[Bioregistry](https://github.com/bioregistry/bioregistry). It used to be a part
-of PyOBO, but has since been externalized for more general reuse.
-
-At
-[src/pyobo/identifier_utils/preprocessing.json](https://github.com/pyobo/pyobo/blob/master/src/pyobo/src/pyobo/identifier_utils/preprocessing.json)
-is the curated set of pre-processing rules. These are used in combination with
-the `curies` package to do pre-processing steps on CURIEs, URIs, and unqualified
-identifiers beyond what is possible with the Bioregistry. See
-https://curies.readthedocs.io/en/latest/preprocessing.html.
-
 ## Troubleshooting
 
 The OBO Foundry seems to be pretty unstable with respect to the URLs to OBO

{pyobo-0.12.1 → pyobo-0.12.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "pyobo"
-version = "0.12.1"
+version = "0.12.2"
 description = "A python package for handling and generating OBO"
 readme = "README.md"
 authors = [
@@ -72,13 +72,14 @@ dependencies = [
     "pystow>=0.7.0",
     "bioversions>=0.8.0",
     "bioregistry>=0.12.7",
-    "bioontologies>=0.7.1",
+    "bioontologies>=0.7.2",
     "ssslm>=0.0.13",
     "zenodo-client>=0.3.6",
     "class_resolver>=0.6.0",
     "psycopg2-binary",
     "pydantic>=2.0",
     "curies>=0.10.13",
+    "curies-processing>=0.1.0",
     "python-dateutil",
     "networkx>=3.4",
     # Resource Downloaders
@@ -288,7 +289,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.12.1"
+current_version = "0.12.2"
 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-0.12.1 → pyobo-0.12.2}/src/pyobo/getters.py

@@ -20,7 +20,6 @@ from typing import Any, TypeVar
 import bioregistry
 import click
 import pystow.utils
-from bioontologies import robot
 from tabulate import tabulate
 from tqdm.auto import tqdm
 from typing_extensions import Unpack
@@ -160,6 +159,8 @@ def get_ontology(
     elif ontology_format == "obo":
         pass  # all gucci
     elif ontology_format == "owl":
+        from bioontologies import robot
+
         _converted_obo_path = path.with_suffix(".obo")
         if prefix in REQUIRES_NO_ROBOT_CHECK:
             robot_check = False

{pyobo-0.12.1 → pyobo-0.12.2}/src/pyobo/identifier_utils/__init__.py

@@ -1,5 +1,7 @@
 """Extract registry information."""
 
+from curies_processing import get_rules
+
 from .api import (
     DefaultCoercionError,
     EmptyStringError,
@@ -13,7 +15,6 @@ from .api import (
     standardize_ec,
     wrap_norm_prefix,
 )
-from .preprocessing import get_rules
 from .relations import ground_relation
 
 __all__ = [

{pyobo-0.12.1 → pyobo-0.12.2}/src/pyobo/identifier_utils/api.py

@@ -12,10 +12,10 @@ from bioregistry import NormalizedNamableReference as Reference
 from bioregistry.constants import FailureReturnType
 from curies import ReferenceTuple
 from curies.preprocessing import BlocklistError, PreprocessingConverter
+from curies_processing import get_rules
 from pydantic import ValidationError
 from typing_extensions import Doc
 
-from .preprocessing import get_rules
 from .relations import ground_relation
 
 __all__ = [

{pyobo-0.12.1 → pyobo-0.12.2}/src/pyobo/obographs.py

@@ -4,6 +4,7 @@ from __future__ import annotations
 
 import logging
 from collections.abc import Iterable
+from typing import TYPE_CHECKING
 
 import bioregistry
 from bioontologies.obograph import (
@@ -16,12 +17,14 @@ from bioontologies.obograph import (
     Synonym,
     Xref,
 )
-from bioontologies.robot import ParseResults
 from tqdm import tqdm
 
 from pyobo.struct import Obo, OBOLiteral, Reference, Term
 from pyobo.struct.typedef import definition_source, is_a
 
+if TYPE_CHECKING:
+    from bioontologies.robot import ParseResults
+
 __all__ = [
     "graph_from_obo",
     "parse_results_from_obo",
@@ -33,6 +36,8 @@ logger = logging.getLogger(__name__)
 def parse_results_from_obo(obo: Obo) -> ParseResults:
     """Get parse results from an OBO graph."""
     graph = graph_from_obo(obo)
+    from bioontologies.robot import ParseResults
+
     return ParseResults(graph_document=GraphDocument(graphs=[graph]))
 
 

{pyobo-0.12.1 → pyobo-0.12.2}/src/pyobo/sources/credit.py

@@ -7,7 +7,7 @@ from collections.abc import Iterable
 
 from more_itertools import chunked
 
-from pyobo.struct import Obo, Term
+from pyobo.struct import CHARLIE_TERM, HUMAN_TERM, Obo, Reference, Term, default_reference
 from pyobo.utils.path import ensure_path
 
 __all__ = [
@@ -16,6 +16,12 @@ __all__ = [
 
 url = "https://api.github.com/repos/CASRAI-CRedIT/Dictionary/contents/Picklists/Contributor%20Roles"
 PREFIX = "credit"
+ROOT = default_reference(prefix=PREFIX, identifier="contributor-role", name="contributor role")
+ROOT_TERM = (
+    Term(reference=ROOT)
+    .append_contributor(CHARLIE_TERM)
+    .append_xref(Reference(prefix="cro", identifier="0000000"))
+)
 
 
 class CreditGetter(Obo):
@@ -23,6 +29,7 @@ class CreditGetter(Obo):
 
     ontology = PREFIX
     static_version = "2022"
+    root_terms = [ROOT]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
@@ -34,14 +41,16 @@ def get_terms(force: bool = False) -> list[Term]:
     path = ensure_path(PREFIX, url=url, name="picklist-api.json", force=force)
     with open(path) as f:
         data = json.load(f)
-    terms = []
+    terms = [
+        CHARLIE_TERM,
+        HUMAN_TERM,
+        ROOT_TERM,
+    ]
     for x in data:
-        name = x["name"].removesuffix(".md").lower()
-
         pp = ensure_path(PREFIX, "picklist", url=x["download_url"], backend="requests")
         with open(pp) as f:
             header, *rest = f.read().splitlines()
-            name = header = header.removeprefix("# Contributor Roles/")
+            name = header.removeprefix("# Contributor Roles/")
             dd = {k.removeprefix("## "): v for k, v in chunked(rest, 2)}
             identifier = (
                 dd["Canonical URL"]
@@ -50,7 +59,9 @@ def get_terms(force: bool = False) -> list[Term]:
             )
             desc = dd["Short definition"]
             terms.append(
-                Term.from_triple(prefix=PREFIX, identifier=identifier, name=name, definition=desc)
+                Term.from_triple(
+                    prefix=PREFIX, identifier=identifier, name=name, definition=desc
+                ).append_parent(ROOT)
             )
 
     return terms

{pyobo-0.12.1 → pyobo-0.12.2}/src/pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.1"
+VERSION = "0.12.2"
 
 
 def get_git_hash() -> str: