pyobo 0.10.10__py3-none-any.whl → 0.10.12__py3-none-any.whl

pyobo/xrefdb/sources/__init__.py

@@ -7,7 +7,7 @@ from functools import lru_cache
 from typing import Callable, Iterable, Mapping, Optional
 
 import pandas as pd
-from pkg_resources import iter_entry_points
+from class_resolver import FunctionResolver
 from tqdm.auto import tqdm
 
 __all__ = [
@@ -19,10 +19,13 @@ __all__ = [
 
 logger = logging.getLogger(__name__)
 
+XrefGetter = Callable[[], pd.DataFrame]
+
 
 @lru_cache()
-def _get_xref_plugins() -> Mapping[str, Callable[[], pd.DataFrame]]:
-    return {entry.name: entry.load() for entry in iter_entry_points(group="pyobo.xrefs")}
+def _get_xref_plugins() -> Mapping[str, XrefGetter]:
+    resolver: FunctionResolver[XrefGetter] = FunctionResolver.from_entrypoint("pyobo.xrefs")
+    return resolver.lookup_dict
 
 
 def has_xref_plugin(prefix: str) -> bool:

pyobo/xrefdb/sources/chembl.py

@@ -4,9 +4,9 @@
 
 from typing import Optional
 
-import bioversions
 import pandas as pd
 
+from pyobo.api.utils import get_version
 from pyobo.constants import (
     PROVENANCE,
     SOURCE_ID,
@@ -26,7 +26,7 @@ def get_chembl_compound_equivalences_raw(
 ) -> pd.DataFrame:
     """Get the chemical representations raw dataframe."""
     if version is None:
-        version = bioversions.get_version("chembl")
+        version = get_version("chembl")
 
     base_url = f"ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_{version}"
     url = f"{base_url}/chembl_{version}_chemreps.txt.gz"
@@ -36,7 +36,7 @@ def get_chembl_compound_equivalences_raw(
 def get_chembl_compound_equivalences(version: Optional[str] = None) -> pd.DataFrame:
     """Get ChEMBL chemical equivalences."""
     if version is None:
-        version = bioversions.get_version("chembl")
+        version = get_version("chembl")
 
     df = get_chembl_compound_equivalences_raw(version=version)
     rows = []
@@ -55,7 +55,7 @@ def get_chembl_compound_equivalences(version: Optional[str] = None) -> pd.DataFr
 def get_chembl_protein_equivalences(version: Optional[str] = None) -> pd.DataFrame:
     """Get ChEMBL protein equivalences."""
     if version is None:
-        version = bioversions.get_version("chembl")
+        version = get_version("chembl")
 
     url = f"ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_{version}/chembl_uniprot_mapping.txt"
     df = ensure_df(
@@ -75,7 +75,7 @@ def get_chembl_protein_equivalences(version: Optional[str] = None) -> pd.DataFra
 def get_chembl_xrefs_df(version: Optional[str] = None) -> pd.DataFrame:
     """Get all ChEBML equivalences."""
     if version is None:
-        version = bioversions.get_version("chembl")
+        version = get_version("chembl")
 
     return pd.concat(
         [

pyobo/xrefdb/sources/pubchem.py

@@ -4,9 +4,9 @@
 
 from typing import Optional
 
-import bioversions
 import pandas as pd
 
+from ...api.utils import get_version
 from ...constants import XREF_COLUMNS
 from ...sources.pubchem import _get_pubchem_extras_url, get_pubchem_id_to_mesh_id
 
@@ -18,7 +18,8 @@ __all__ = [
 def get_pubchem_mesh_df(version: Optional[str] = None) -> pd.DataFrame:
     """Get PubChem Compound-MeSH xrefs."""
     if version is None:
-        version = bioversions.get_version("pubchem")
+        version = get_version("pubchem")
+        assert version is not None
     cid_mesh_url = _get_pubchem_extras_url(version, "CID-MeSH")
     return pd.DataFrame(
         [

pyobo/xrefdb/sources/wikidata.py

@@ -81,11 +81,18 @@ def iter_wikidata_mappings(
             json.dump(rows, file, indent=2)
 
     for row in rows:
-        wikidata_id = row["wikidata_id"]["value"][len("http://wikidata.org/entity/") :]
+        wikidata_id = _removeprefix(row["wikidata_id"]["value"], "http://www.wikidata.org/entity/")
+        wikidata_id = _removeprefix(wikidata_id, "http://wikidata.org/entity/")
         entity_id = row["id"]["value"]
         yield wikidata_id, entity_id
 
 
+def _removeprefix(s, prefix):
+    if s.startswith(prefix):
+        return s[len(prefix) :]
+    return s
+
+
 HEADERS = {
     "User-Agent": f"pyobo/{get_version()}",
 }

{pyobo-0.10.10.dist-info → pyobo-0.10.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.10.10
+Version: 0.10.12
 Summary: Handling and writing OBO
 Home-page: https://github.com/pyobo/pyobo
 Download-URL: https://github.com/pyobo/pyobo/releases
@@ -19,16 +19,16 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3 :: Only
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
-Requires-Python: >=3.8
+Requires-Python: >=3.9
 License-File: LICENSE
-Requires-Dist: obonet >=0.3.0
+Requires-Dist: obonet>=0.3.0
 Requires-Dist: click
 Requires-Dist: tqdm
 Requires-Dist: pyyaml
@@ -36,37 +36,37 @@ Requires-Dist: pandas
 Requires-Dist: requests
 Requires-Dist: protmapper
 Requires-Dist: more-itertools
-Requires-Dist: more-click >=0.0.2
+Requires-Dist: more-click>=0.0.2
 Requires-Dist: humanize
 Requires-Dist: tabulate
 Requires-Dist: cachier
-Requires-Dist: pystow >=0.2.7
-Requires-Dist: bioversions >=0.5.202
-Requires-Dist: bioregistry >=0.10.20
-Requires-Dist: bioontologies >=0.4.0
-Requires-Dist: zenodo-client >=0.0.5
+Requires-Dist: pystow>=0.2.7
+Requires-Dist: bioversions>=0.5.202
+Requires-Dist: bioregistry>=0.10.20
+Requires-Dist: bioontologies>=0.4.0
+Requires-Dist: zenodo-client>=0.0.5
 Requires-Dist: class-resolver
 Requires-Dist: psycopg2-binary
 Requires-Dist: drugbank-downloader
 Requires-Dist: chembl-downloader
-Requires-Dist: umls-downloader >=0.1.3
+Requires-Dist: umls-downloader>=0.1.3
 Requires-Dist: typing-extensions
 Provides-Extra: agrovoc
-Requires-Dist: rdflib ; extra == 'agrovoc'
+Requires-Dist: rdflib; extra == "agrovoc"
 Provides-Extra: docs
-Requires-Dist: sphinx ; extra == 'docs'
-Requires-Dist: sphinx-rtd-theme ; extra == 'docs'
-Requires-Dist: sphinx-click ; extra == 'docs'
-Requires-Dist: sphinx-automodapi ; extra == 'docs'
+Requires-Dist: sphinx<8.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme; extra == "docs"
+Requires-Dist: sphinx-click; extra == "docs"
+Requires-Dist: sphinx-automodapi; extra == "docs"
 Provides-Extra: tests
-Requires-Dist: coverage ; extra == 'tests'
-Requires-Dist: pytest ; extra == 'tests'
+Requires-Dist: coverage; extra == "tests"
+Requires-Dist: pytest; extra == "tests"
 Provides-Extra: web
-Requires-Dist: flask ; extra == 'web'
-Requires-Dist: bootstrap-flask ; extra == 'web'
-Requires-Dist: flask-admin ; extra == 'web'
-Requires-Dist: flasgger ; extra == 'web'
-Requires-Dist: psutil ; extra == 'web'
+Requires-Dist: flask; extra == "web"
+Requires-Dist: bootstrap-flask; extra == "web"
+Requires-Dist: flask-admin; extra == "web"
+Requires-Dist: flasgger; extra == "web"
+Requires-Dist: psutil; extra == "web"
 
 PyOBO
 =====

{pyobo-0.10.10.dist-info → pyobo-0.10.12.dist-info}/RECORD

@@ -1,28 +1,28 @@
 pyobo/__init__.py,sha256=mZ96iZ-5ucxe2eLBi0xuSKaa2ZfeInaSR5Ajc_NkvUo,1862
 pyobo/__main__.py,sha256=cQjBabQ2wlFKcv54PFdt0SgPXNeb3oWneuOHaBgHx1Q,108
-pyobo/aws.py,sha256=EUXsN_sQEOWOV2oZXrVrkO8R6Zo_JJHGeGzzWWgpvzo,5948
-pyobo/constants.py,sha256=gj8xSUmCO0rU-eGXHOW7Vix3SAHl50cLAM3HXuoAFt4,2200
+pyobo/aws.py,sha256=oSy4qqHlCpuSyGhDeslrPtc_N0JDhRoGKWjw8RBmyNE,5976
+pyobo/constants.py,sha256=khE82G0qbKjyBSSSKnJSQFZDmn1Rhn06quKg9XbZzZ4,3047
 pyobo/getters.py,sha256=37e7pcTqU-uVjx_XctT9pJMn7zaazsNfcyWoe7KMHi0,15565
-pyobo/gilda_utils.py,sha256=9rzlOkmq2MFac2sJ7b-XHS6UTSTiOM_rRk_xzt-uJiI,7582
-pyobo/identifier_utils.py,sha256=y4eFbJJQGoGe0HKRqQoUc_3tani22W_K4z7OZFL6Z0E,3659
+pyobo/gilda_utils.py,sha256=cUv1WaZtzvu6Eb33ua4XShXXYcoD5StoEhNn3WcXN9c,8180
+pyobo/identifier_utils.py,sha256=Ivjai_uBk2Qodo1y6RTej4FjqT6lSGnZxgwRNnt-zPk,4484
 pyobo/mocks.py,sha256=R-4W3Rm5NarIHfNjxurbvBYsLHXt6jmDb6THMUt6K1w,2432
 pyobo/normalizer.py,sha256=OHME2CDQSZYSbqmP-L_-4nxete9W9mtAjUzXVs1hnjU,8293
 pyobo/obographs.py,sha256=JKE0a7e-gmxqdJoeX2zb_xQ6Tv5PAe60YhnIpAvrrYg,3758
 pyobo/plugins.py,sha256=dXWGoFuQktNeQUWSJlPz2a7FeLysggc9ry6auEZdw98,1227
-pyobo/reader.py,sha256=3VTWQMmA-AHi3RdA2jb48d2deXO-lYKqXbcMa9Qhi_4,21271
+pyobo/reader.py,sha256=sCC8RCUysmyVQRy8g_YJHLswr0BzQhxUJMMhe350l9A,21272
 pyobo/resource_utils.py,sha256=JBcJRihZhNwp78-qWZPrzSCGoYfyOjzBwMkfmOkO_no,4289
-pyobo/version.py,sha256=S2agZOhWCaqxb1jQk8O_DDd5X86GPoXvcBAAxtmCpsc,978
+pyobo/version.py,sha256=-M7dCNE1QohvaQ27gU5nWrB8AJHFKX5mla7gvx3HugI,978
 pyobo/api/__init__.py,sha256=Hq8p5uPW8fFYG2KfLqUsHhtLkTPqE4TqItGkedZzvXM,1326
-pyobo/api/alts.py,sha256=xmAb-gGQCJ9MbaFvoNK6E-V0B3TV9hxulkfbkHIvOso,2617
-pyobo/api/hierarchy.py,sha256=2KtyTkqOKJzejNqVvlhPQD_w0fKzrOQp1BSx-Ina3t0,9413
-pyobo/api/metadata.py,sha256=62E7j0ZW3vYK2Rh-R7NCMKnChbYjZwPjVDoaE1AsCOc,1070
-pyobo/api/names.py,sha256=m_5UjixlUS10FCrlmNoNJ8pI_z-YB2xqgROGvPGIQBY,7661
+pyobo/api/alts.py,sha256=fa516S9uWVgMIXR5KbYu70KFpvfOD7Not2iEYFB8C_4,2844
+pyobo/api/hierarchy.py,sha256=o69jARrh9UXbzLsnXjW8Rs0kfQahvc22BlwcE7nAnFI,9527
+pyobo/api/metadata.py,sha256=py8Pv_Mmy31itziRaucWibGvWF6vOhF4Ofj1kFMk_vQ,1148
+pyobo/api/names.py,sha256=qf_YjV631lyXezSyd3vW43kxP_Z1rSdU_VH3S2BZ8ZA,8405
 pyobo/api/properties.py,sha256=BKqUgN8nTpYrc0fROdaGGkptELgjbGT6TC_N2X8FIQM,7813
-pyobo/api/relations.py,sha256=VEQCQjPamehyGaL-wFzUYH9OeVq9pVzj70sl9K3ttKw,5996
-pyobo/api/species.py,sha256=xRPRoD6n1wcDaqlC_tHLw3rKMWa4razWsSPNa228g_4,2181
-pyobo/api/typedefs.py,sha256=TqNZ8_5ntw6PXwvqIlHtMHqD7l2jWwHn48vccUPbJiI,1061
-pyobo/api/utils.py,sha256=jxisiISIUtoW_SfNa3eOVTkEYP5ygYHaFTDibmMO7UE,1059
-pyobo/api/xrefs.py,sha256=p2ZdAcCOVnaRUQezGH3i0cTj2wVH-0mhSae98YVrMOQ,5942
+pyobo/api/relations.py,sha256=oAjslceGPLPUDT4keOJQCFBt_BXOqhCgSYZ2d-IjO34,6217
+pyobo/api/species.py,sha256=RvTrC39yskueQyAplbcmqjHnL-t3QqggjBJcs5swgVU,2249
+pyobo/api/typedefs.py,sha256=Vb1wvWDWLZu-FchYFs03wMEzS3RUPUsLxvyPNlHBcYE,1157
+pyobo/api/utils.py,sha256=cpYzdGiFmgWJB5PeelyIfFyDdUflmmAS2h_M65SGztc,1245
+pyobo/api/xrefs.py,sha256=oy5ZSoeEpcJfjDfSCBwUx3LJEykqbpBwNrMhfhiyYlY,6020
 pyobo/apps/__init__.py,sha256=iACi86TkTiGxwneGmfaudZOIEqZ45YjPXng7XjPE38Y,72
 pyobo/apps/cli.py,sha256=gnXBAaESw1T1BvgMpTv-0P26hM2vKCAXPy0SOskgUwU,335
 pyobo/apps/gilda/__init__.py,sha256=jpLIHJOmR_66tdXXUWFP9NiZnpQKvjv5YpCJWoAKnUI,54
@@ -42,7 +42,7 @@ pyobo/cli/__init__.py,sha256=ReL2NlPx_GEljszzkjIKKAK6BC3KAuHli9pFU1YmgXQ,96
 pyobo/cli/aws.py,sha256=ySuCV9JkOjelXLhcIgeHWReFSLh2n5zvGddNsfM1B8o,989
 pyobo/cli/cli.py,sha256=0Vibj_1LnkI8pfkK8U7r5eSRspR9VkH2OH4DwcHzA2M,3616
 pyobo/cli/database.py,sha256=5MCAbMClxYpPxZ83GilcsjjNs3zPjM7rHjqsBPfDGRM,10106
-pyobo/cli/lookup.py,sha256=zTSLZ2eu8Zl-zyGporm5f_pVKZaFSU8VgR8qA9hUkQU,10069
+pyobo/cli/lookup.py,sha256=1tjSaEaMxntGNxoe4tm8Gs2dQjFDTAH3oyrC_1xIrco,10160
 pyobo/cli/utils.py,sha256=n8HVfJMEai0_4hDntbQPDZpqqZIPMNX_-kZ2cCyakss,1370
 pyobo/registries/__init__.py,sha256=P4UmjPFFYkQ_YrXcM5NMT9VF45pHLBqavcmZ7jPwpNQ,417
 pyobo/registries/metaregistry.json,sha256=ssjWlc3fqQBw0V4wwVZBeW-4Y_B_RkIEc0ooOFeiKJQ,12865
@@ -52,11 +52,11 @@ pyobo/resources/ncbitaxon.py,sha256=kyJDMGm8qIpIpckN6NSGovCBDacG1qGYTIpvJ--HXhM,
 pyobo/resources/ncbitaxon.tsv.gz,sha256=43zHjnVt62TA4_lV58X-FCPdMDfLg1B1PvZSr_Xy9hY,22981954
 pyobo/resources/ro.py,sha256=_CYD90vftMZvu8Rj6H9kOiw6wRBbs1LWmCl-HToxMIg,1484
 pyobo/resources/ro.tsv,sha256=YvlBLPAKy2w4IheYzO9ox1Yg6WkHdMVzMQTikIlECog,26586
-pyobo/sources/__init__.py,sha256=uG7If-_xo4GfuvQ43yVQFBDUjYMGwmm5o3vyAm0Qqow,3783
+pyobo/sources/__init__.py,sha256=Fxsxq4ahr5wJbqR6-v9W-Rp1bjbcsr81q6RMq6eCMq0,3836
 pyobo/sources/agrovoc.py,sha256=J425AyyOVAeqeyN5MhmAR9OtJom41GDvKArfyz1iIU8,795
-pyobo/sources/antibodyregistry.py,sha256=5i2qRhGgyi11Ke9xrHU1NRFxD3xMCnHQWWKh9fQCXDs,3178
-pyobo/sources/biogrid.py,sha256=Rr5gSLmOK95YPm2cYcFbGLDm3LWNckLvlarmbSIP-5M,3290
-pyobo/sources/ccle.py,sha256=KqqVokOq0HYE980plNa3987O1ixLkpcC0j9rYoQIM70,2963
+pyobo/sources/antibodyregistry.py,sha256=bA84wQBInOqAKGA7YZI3pq4vIqSx2rWuIOUuTwrpdmQ,3332
+pyobo/sources/biogrid.py,sha256=fqKE6oRC_dgHuKLPZf6cnadg-cCOejaexDjGdoVQmrs,3325
+pyobo/sources/ccle.py,sha256=RwsrFTVOUAySvS2helFbSNAsmiCX3Zs8PiZUeRoGA0I,3023
 pyobo/sources/cgnc.py,sha256=hCjFv05_aS2_Mn5Qb9VGLKGcOY87rEXZ6jH7r6WgUeg,2336
 pyobo/sources/chebi.py,sha256=7t5CaykOWXMQ9JRW8x1g_gsZhygCdjR2MGRYTFLEiTs,1230
 pyobo/sources/chembl.py,sha256=MG_bTilUwhhkeuTA3owLn1gro1QicMyGGfcd-48NGgE,2296
@@ -64,6 +64,7 @@ pyobo/sources/civic_gene.py,sha256=SUwlb1PXwVVB-XQanyI7tRbPMGaDNiB-CXNry_idAZY,1
 pyobo/sources/complexportal.py,sha256=nhEaUzw4riuN31OLiwpGffj66YMCeLigekblTWGk3nk,6022
 pyobo/sources/conso.py,sha256=ZLQ_T5EgrcuX9q6kCBKCwfGzAEVxgN6xADl-LKzJtbk,2460
 pyobo/sources/cpt.py,sha256=x8P15D9UX5Fwf6bmeVsU1DAFJvZ22rxVPy5ur-GUk_Q,1482
+pyobo/sources/credit.py,sha256=UD_QYfSBvWOejsLaN28WpN2ci_aozPHI7mf1Wbk0uwE,2008
 pyobo/sources/cvx.py,sha256=FZAghQxkefWsxT1nTTUb56NgteRbAmawpOo3IdAfPAQ,2836
 pyobo/sources/depmap.py,sha256=VuZduDgCduiAHPLwPDXgWpxhMSOZCC4UsxFdj7hNkYQ,3656
 pyobo/sources/dictybase_gene.py,sha256=EgWBwUZ83ev7x5Lp_nUkgSq2zumkDjJ7_13m3f6kJz0,2564
@@ -73,38 +74,38 @@ pyobo/sources/drugcentral.py,sha256=05mGolBIyKCxAYzpH9LY_ZQrTVnizup2JUiWi2wW9OI,
 pyobo/sources/expasy.py,sha256=Ul6DFtHKw3fU1ec93c9f29kXxod2Rn-jPWOYl1xrRa8,10051
 pyobo/sources/famplex.py,sha256=bn3WaJdrDf9BxsG9vnnnnGOwCrnrJ-vTMxOnxgrtUb4,5816
 pyobo/sources/flybase.py,sha256=0-BCNsp-L-CgGPN9VdJec6-8e4-fJuzaZAZiNra3ZUQ,5768
-pyobo/sources/geonames.py,sha256=XpSc-_6653MrjunVJhqbHHLtkT8kmbJZzfRuF6DoWU8,7929
+pyobo/sources/geonames.py,sha256=SU5i1_UWjnCKLz4yWKZThSJp5dqJdNXj9VL-wWUeiNg,8554
 pyobo/sources/gmt_utils.py,sha256=NAWyUZ1p1HcO8RPL9mEEcL9KoaBDPuU-tbyG2QLb98k,1401
 pyobo/sources/go.py,sha256=IJul9eAXxKifZiWKJL1Dl9PFDFdoPMQ0ZVydzhnRtX0,1275
 pyobo/sources/gwascentral_phenotype.py,sha256=dCzyw_jbmhol69Li0g2ocMQJRqjoV2fZM_pno6i7xyA,1889
 pyobo/sources/gwascentral_study.py,sha256=_YH9TRWsCOHjOrJ2pAqQ7fi_HmF1WbMmTUj5iqWDUwY,2812
-pyobo/sources/hgnc.py,sha256=kVxVIv4LIy_H_rvVQbwvj3Jn6KmLwpk-XRn5jkpnjN4,15951
+pyobo/sources/hgnc.py,sha256=VDiHNbGms3xUyAPjRvkFxGfzR7Jdi2CG5HEtKzM1EGA,15960
 pyobo/sources/hgncgenefamily.py,sha256=o7gCI5raXkCMr8ONfAZpRW7PtsZ8lkRC4T1kEjTxBn4,3645
 pyobo/sources/icd10.py,sha256=KhenR1U8LvZQF97mRZIoSEE_daKcJ2hTJ41BQU7SNuM,2286
 pyobo/sources/icd11.py,sha256=04nLt-Lr64hAroOLH4OP-iNbuIjBk-mYcg-Ib34zgMM,2834
 pyobo/sources/icd_utils.py,sha256=c1Xkk9YAyKQ-vvnPud5GKq5ygZVbd1j0NFSml3RjQZ0,3155
 pyobo/sources/interpro.py,sha256=sWla5FDOkzA8elzeNHXOMD0nEVIbNK7jg4UZ0Zp7BfI,4934
 pyobo/sources/itis.py,sha256=LXS4MTL7OMmdfo-ypoF75UJkePw7VnHDrgq10RF_VUk,2967
-pyobo/sources/mesh.py,sha256=w06h1p0qeLUyNKEGLIqSdQXDtA4yqdfwnaAxF-4Xbr8,12048
+pyobo/sources/mesh.py,sha256=bERu2apELBxM4DVA-ViuJZzNfaL0dvrNZfPRQFWyPAA,12163
 pyobo/sources/mgi.py,sha256=c0CiiH_LolAFdHPNu1lpLeAzHq20wVLyOrLRTkLYxhY,5766
 pyobo/sources/mirbase.py,sha256=NMqZfT7CbbetqCV-KdGjHJmz2uM5QvdF_M1BxKi1ZCw,6349
 pyobo/sources/mirbase_constants.py,sha256=X7KhJDp1saGrdBwUR9fQSWwebzns5f-mEF4qWSETs2k,2023
 pyobo/sources/mirbase_family.py,sha256=Yj3oXaeBWDxcmBKnvOl0q_7nzlye5EXhSJPWlV3YpT8,2167
 pyobo/sources/mirbase_mature.py,sha256=nvWcQVDMBucPu6v5DLFb_W_9fz_J_Id7HZrilkUhaFI,1504
-pyobo/sources/msigdb.py,sha256=YKgFyPgYKdYQtu22P69IVyLeBsLfgNyaNOl7q0Sy8IU,5019
+pyobo/sources/msigdb.py,sha256=o5thqA4-4GzUE3PUIEad-iznYh6NNLKqkSXCbea_rZM,5021
 pyobo/sources/ncbigene.py,sha256=qipZEaaXop289vRro_NS8BB0_t-c738lJItWSjzD7PI,5055
-pyobo/sources/npass.py,sha256=t8TDdxpfvvXYo8VczT4ngoSspPAdPJuLKigvHZ9OHrE,2805
+pyobo/sources/npass.py,sha256=AnZTNCsV4JD5tPCenoU4RyBxnEmVk_tA_4rbni99KcY,2814
 pyobo/sources/omim_ps.py,sha256=uULW_1gmYIE66O85GdLCGbdmsi9qxcS7tZziOny0wc0,1020
 pyobo/sources/pathbank.py,sha256=yhdS4BCbGxQf0o3HCGzL2cYRY7zyvHvDzzSBkkezoog,4989
 pyobo/sources/pfam.py,sha256=aHXdXmoG6xyNkScHft_xYe4J2DzRr22EinyfjpmwEj4,1846
 pyobo/sources/pfam_clan.py,sha256=hjJ0UUEcrNoaQVWbXZ_EaTWFo4iB9VG9Sp6pcO90gxY,1340
 pyobo/sources/pid.py,sha256=ZEbiYpbZL9_aOCEJWw0I3H5f7Q2RhQuNy5PUZfs0orU,4570
 pyobo/sources/pombase.py,sha256=nRMxk2FuQZv6KnL8LBxqZbVtvynvneLe39i5V3dYAtw,3601
-pyobo/sources/pubchem.py,sha256=arIX53mvCWRghLJkeh9iTPUU_lQJ8SSTm-pOK8KBqbE,5289
+pyobo/sources/pubchem.py,sha256=ZnbRh1hCSAVawfVCNSy43kvIBXslq4lX8OlArnbo5sE,5282
 pyobo/sources/reactome.py,sha256=H-hMMrbf2mElOLDu_hYZgurYLYTZvrQ7E1dyvaWKvSM,5084
-pyobo/sources/rgd.py,sha256=CbtDDIrBQ7ZA0GK6BcorxYBeaJazo3D1gMot588cA0E,5397
-pyobo/sources/rhea.py,sha256=vfmDFo11LdxuIfo3LZ7n5X942IjO-U9iX4l-CGTMjb0,7772
-pyobo/sources/ror.py,sha256=g4UxcEYJ4RW_imqna3T6GnAxRp058L7MJFDmZjstYdo,6123
+pyobo/sources/rgd.py,sha256=v-4xH5w2C58J_hRI5V8Eof7EiTPofVlIwFA-3c2jyhg,5397
+pyobo/sources/rhea.py,sha256=nt2j7LMiuKM7zaVflSUoWNj7J8EnsRVfigFK9XXuNRg,7781
+pyobo/sources/ror.py,sha256=Omu5DYStYoUyenEfNOwsQZbmZTZQZ0DvToXrT3pLFYc,7364
 pyobo/sources/sgd.py,sha256=DOcRxEJGrHEOsaIiWat2x9ER2HnfnU3l8lqr3IktblA,2150
 pyobo/sources/slm.py,sha256=ai_Zp0tqBIanMZ7q7b5x6w9KdTTCEqA4PhX0ToaF594,3804
 pyobo/sources/utils.py,sha256=tmCGXGxHVrYkS5E1-k2SZqL8H4Tv8dFrkoIEJ0xzVmQ,1119
@@ -126,7 +127,7 @@ pyobo/sources/umls/get_synonym_types.py,sha256=5u1ZEl8gp_StuQxrasvHK4S0DyVWdgp_r
 pyobo/sources/umls/synonym_types.tsv,sha256=z--ngeAqA_Kk8ft2YD8qOU_XUxhnTxF0OhL8jRd5xqo,8551
 pyobo/sources/umls/umls.py,sha256=C3UXVd1iSlj5TC6Ib1T1oDIyJ4pIveNeGPK8ORkRtG4,4318
 pyobo/sources/uniprot/__init__.py,sha256=dsL0BvfMn3O_swtNhzQpjJUlP56NUBCcjSYdFvRlwmI,225
-pyobo/sources/uniprot/uniprot.py,sha256=WVSxy6cDPYu5S69_V5_dzRdsU6aSVm-rFXvmEcuk8eI,6105
+pyobo/sources/uniprot/uniprot.py,sha256=FNfLttMPFnYL8DECoa1I6j4qAxg6nRo_VzLqFYkDOYM,6114
 pyobo/sources/uniprot/uniprot_ptm.py,sha256=ze1cf0_kkqslhS-lXa7EdfasV4reUDp6niJat6yymT8,3551
 pyobo/ssg/__init__.py,sha256=Q5vYmk1LZwriShmA3TcYZ1Z1yiyjTWItcGxep5Fi2pw,5390
 pyobo/ssg/base.html,sha256=_vldUCa-gL2YTNY6GgAuxNT3TgaED585vF_q7TrrjYs,2844
@@ -135,8 +136,8 @@ pyobo/ssg/term.html,sha256=QU6piGOq4dq8zlNhJvLFxqFjhVQyWlkiG31I0Sg5frg,3559
 pyobo/ssg/typedef.html,sha256=KrdqzB6xjt689bG33D26AL-11JrvNuEkoxNNI-EG-Tg,2038
 pyobo/struct/__init__.py,sha256=F5iav-0rnkLrldDxDPVeDt4zd1tXYBKICoKODJBk_kQ,671
 pyobo/struct/reference.py,sha256=U2qHIANj_0XhSxh7UBaXUiOXWtVjtyIBeDQ03heWuxA,5712
-pyobo/struct/struct.py,sha256=bkZv5H_sZFaWQr3cXA5F6JQbqg_OtVfMBV4mS10aHKk,54398
-pyobo/struct/typedef.py,sha256=spRRFWV-lV7yOU6HHnxAAFA-4ap6bm3l27KV-bmdLlc,13498
+pyobo/struct/struct.py,sha256=oSEocxLlb4o51-qPhYu8Mi74S4w1FfaEDR8332wW124,54425
+pyobo/struct/typedef.py,sha256=IbYBL_FpTQqlZBsC8tq-DqD_mfGvfUaJz02gMIjtPO0,13900
 pyobo/struct/utils.py,sha256=-XHuCETp7jPNhjHCW72gikaKoaiTPTNhDK5BZYyJsVw,815
 pyobo/utils/__init__.py,sha256=wXtcjcasWRBtJdTSMCC3jT8yFG8ZkQC-Xdh9lLiQDAo,42
 pyobo/utils/cache.py,sha256=bmuEE0DyppY6szNEzkS1tLLKfsLIrHQFhp0P-q94KFs,2677
@@ -144,26 +145,25 @@ pyobo/utils/io.py,sha256=GiOittPhSJKc-acmj6h3DGSvLnPDntRIiUhjuCEUwj8,4756
 pyobo/utils/iter.py,sha256=VyISqr04Pg2xLSLJhypUuZnh7WzxVmpp3MsASCuL8Tk,1475
 pyobo/utils/misc.py,sha256=WfvJ_AGge8plp9IIlAGiahPxoCiWAow4t_-ncr7AjwY,2857
 pyobo/utils/ndex_utils.py,sha256=gxmGfR_O-ZMOsBil_YFSn99x_Fvatg7O8s9iZp4Iy10,2351
-pyobo/utils/path.py,sha256=-IVv_0H4Q790-ymmLdOlFgFSDuDubh9jZpPtDQzf-hI,3931
+pyobo/utils/path.py,sha256=ZNJ3aOZT9xqyk8NSQ1jZLtTB5goFPlquVYAwvuGEkVQ,3972
 pyobo/xrefdb/__init__.py,sha256=0W6AuvghFHQ1zY-Dq26z8V_MRC9xL39aWqLb-JbU8T8,74
-pyobo/xrefdb/bengo.py,sha256=DUhvdWvjNg2rfa99x3pfkonKERmylbt06u5GLlTZ10Q,1312
 pyobo/xrefdb/canonicalizer.py,sha256=gtwOoOMmBSCnXrlGfAyuryhT16F87I9HAOd2wi0O7I0,7421
 pyobo/xrefdb/priority.py,sha256=QfaKJ4U_6d1JlVZX_vM1s6T35bdc1-PiQH3--WTLAK0,1203
 pyobo/xrefdb/xrefs_pipeline.py,sha256=I0zsukpuOBIBIM2vh4K3A0UuaI6l56qt3is8NAzYTaU,6219
-pyobo/xrefdb/sources/__init__.py,sha256=2eRNhpQJsPN4vTwFrk2j8RK34P6GSh7_tWIRoPJrpGI,1587
+pyobo/xrefdb/sources/__init__.py,sha256=uM3g-OyOCsz7dINGcBkcqBs4lYwogTQhX3BZj1Bz5zo,1647
 pyobo/xrefdb/sources/biomappings.py,sha256=110puNUl0CbIBXFovEpMeW25QsnIetteWPmCCQ00s3Q,919
 pyobo/xrefdb/sources/cbms2019.py,sha256=neUfZsmLEi0kNKaOHtMCpnCyvcc4VD1KX88ldhLjYoo,2843
-pyobo/xrefdb/sources/chembl.py,sha256=cYjZwwS8NXsunjeHxGziUvZomMw9qdwUkCjxX0GvQKc,2662
+pyobo/xrefdb/sources/chembl.py,sha256=NyxfELxPE2uB0UPBzs27DcRFun7Wu9ZWy1bNsIX2bS0,2635
 pyobo/xrefdb/sources/compath.py,sha256=IS6kgkVTYQHgy3gm6GhrHkfUStfjd0z5W_w8KrWb5Rs,2334
 pyobo/xrefdb/sources/famplex.py,sha256=pAbfFjRs_tPuxTJWJqvPT5p3ZKIqtgT0xqn2GizJ3-4,1833
 pyobo/xrefdb/sources/gilda.py,sha256=aYMFXMbDKB-_HqPMzEIUhvz6YahJiuyAcNgo2KfFalk,1070
 pyobo/xrefdb/sources/intact.py,sha256=F0z6WrOwI79aZSuM5MsvQwzqoyzh9J0UuB4Mseoj9X8,2966
 pyobo/xrefdb/sources/ncit.py,sha256=unoIKJqdcfitTc6pU9P1SxJ1w8ax0iDjvEOlqe64nCY,3745
-pyobo/xrefdb/sources/pubchem.py,sha256=GaqgqtSV-T_P-900nL3alPx_ZB36MlmnEepOnZMONA4,780
-pyobo/xrefdb/sources/wikidata.py,sha256=bOI2zUkkLbmXvOMJZmVWq1xKlMCuL_3l1NVsaoJr1x4,3387
-pyobo-0.10.10.dist-info/LICENSE,sha256=GRbxxtZEWtZiFGDENk1gntCQK4HEJYYbylEJEwpSLao,1076
-pyobo-0.10.10.dist-info/METADATA,sha256=rzbhrEqNk6WZVG-Z6qDwkOaobEwleVjGz5m-tSB3Zqg,20046
-pyobo-0.10.10.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-pyobo-0.10.10.dist-info/entry_points.txt,sha256=Du5V6qw_T917Z5ZoMhLTTJoolK7kkVuUWkdE7aJWea0,669
-pyobo-0.10.10.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
-pyobo-0.10.10.dist-info/RECORD,,
+pyobo/xrefdb/sources/pubchem.py,sha256=m6I_zYUGDe27EKhyNvjMSy1hpRcUURc7fuTxiTy8xlg,821
+pyobo/xrefdb/sources/wikidata.py,sha256=vrrbOBIIQimrghzishZ6yyE1L_ARgJDCoAogqfuUYDY,3585
+pyobo-0.10.12.dist-info/LICENSE,sha256=GRbxxtZEWtZiFGDENk1gntCQK4HEJYYbylEJEwpSLao,1076
+pyobo-0.10.12.dist-info/METADATA,sha256=WNna9-0XS_htOC_zl7-jLF05KGsjmau8rwTnUoLqQ-8,20031
+pyobo-0.10.12.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+pyobo-0.10.12.dist-info/entry_points.txt,sha256=Du5V6qw_T917Z5ZoMhLTTJoolK7kkVuUWkdE7aJWea0,669
+pyobo-0.10.12.dist-info/top_level.txt,sha256=oVdkT-pbiGoSdGSQplXFuP1KQGJNf4GdRC65jn6y9t0,6
+pyobo-0.10.12.dist-info/RECORD,,

{pyobo-0.10.10.dist-info → pyobo-0.10.12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

pyobo/xrefdb/bengo.py

@@ -1,44 +0,0 @@
-# -*- coding: utf-8 -*-
-
-"""Pipeline for building a large ontology graph."""
-
-import logging
-
-import bioregistry
-import networkx as nx
-from tqdm.auto import tqdm
-
-from pyobo import get_hierarchy
-from pyobo.getters import SKIP
-from pyobo.resource_utils import ensure_inspector_javert_df
-
-logger = logging.getLogger(__name__)
-
-
-def bens_magical_ontology(use_tqdm: bool = True) -> nx.DiGraph:
-    """Make a super graph containing is_a, part_of, and xref relationships."""
-    rv = nx.DiGraph()
-
-    df = ensure_inspector_javert_df()
-    for source_ns, source_id, target_ns, target_id, provenance in df.values:
-        rv.add_edge(
-            f"{source_ns}:{source_id}",
-            f"{target_ns}:{target_id}",
-            relation="xref",
-            provenance=provenance,
-        )
-
-    logger.info("getting hierarchies")
-    it = tqdm(sorted(bioregistry.read_registry()), desc="Entries", disable=not use_tqdm)
-    for prefix in it:
-        if bioregistry.is_deprecated(prefix) or prefix in SKIP:
-            continue
-        if use_tqdm:
-            it.set_postfix({"prefix": prefix})
-
-        hierarchy = get_hierarchy(prefix, include_has_member=True, include_part_of=True)
-        rv.add_edges_from(hierarchy.edges(data=True))
-
-    # TODO include translates_to, transcribes_to, and has_variant
-
-    return rv