pyobo 0.12.5__tar.gz → 0.12.6__tar.gz

{pyobo-0.12.5 → pyobo-0.12.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.5
+Version: 0.12.6
 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
@@ -30,7 +30,6 @@ Requires-Dist: tqdm
 Requires-Dist: pyyaml
 Requires-Dist: pandas
 Requires-Dist: requests
-Requires-Dist: protmapper
 Requires-Dist: more-itertools
 Requires-Dist: more-click>=0.0.2
 Requires-Dist: humanize
@@ -43,7 +42,6 @@ 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>=0.10.17
 Requires-Dist: curies-processing>=0.1.2
@@ -57,8 +55,11 @@ Requires-Dist: nih-reporter-downloader>=0.0.1
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
 Requires-Dist: obographs>=0.0.8
+Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
+Requires-Dist: protmapper ; extra == 'pid'
+Requires-Dist: pyobo[drugcentral,pid] ; extra == 'sources'
 Maintainer: Charles Tapley Hoyt
 Maintainer-email: Charles Tapley Hoyt <cthoyt@gmail.com>
 Requires-Python: >=3.10
@@ -67,8 +68,11 @@ Project-URL: Documentation, https://pyobo.readthedocs.io
 Project-URL: Funding, https://github.com/sponsors/cthoyt
 Project-URL: Homepage, https://github.com/biopragmatics/pyobo
 Project-URL: Repository, https://github.com/biopragmatics/pyobo.git
+Provides-Extra: drugcentral
 Provides-Extra: gilda
 Provides-Extra: gilda-slim
+Provides-Extra: pid
+Provides-Extra: sources
 Description-Content-Type: text/markdown
 
 <!--

{pyobo-0.12.5 → pyobo-0.12.6}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "uv_build"
 
 [project]
 name = "pyobo"
-version = "0.12.5"
+version = "0.12.6"
 description = "A python package for handling and generating OBO"
 readme = "README.md"
 authors = [
@@ -63,7 +63,6 @@ dependencies = [
     "pyyaml",
     "pandas",
     "requests",
-    "protmapper",
     "more_itertools",
     "more_click>=0.0.2",
     "humanize",
@@ -76,7 +75,6 @@ dependencies = [
     "ssslm>=0.0.13",
     "zenodo-client>=0.3.6",
     "class_resolver>=0.6.0",
-    "psycopg2-binary",
     "pydantic>=2.0",
     "curies>=0.10.17",
     "curies-processing>=0.1.2",
@@ -158,6 +156,15 @@ gilda = [
 gilda-slim = [
     "ssslm[gilda-slim]",
 ]
+sources = [
+    "pyobo[drugcentral,pid]",
+]
+drugcentral =[
+    "psycopg2-binary",
+]
+pid = [
+    "protmapper",
+]
 
 # See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#urls
 # and also https://packaging.python.org/en/latest/specifications/well-known-project-urls/
@@ -289,7 +296,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.12.5"
+current_version = "0.12.6"
 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-0.12.5 → pyobo-0.12.6}/src/pyobo/cli/database.py

@@ -6,6 +6,7 @@ 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
@@ -97,12 +98,17 @@ def _update_database_kwargs(kwargs: DatabaseKwargs) -> DatabaseKwargs:
 
 
 @database_annotate
+@click.option("--eager-versions", is_flag=True)
 @click.pass_context
-def build(ctx: click.Context, **kwargs: Unpack[DatabaseKwargs]) -> None:
+def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Build all databases."""
     # if no_strict and zenodo:
     #    click.secho("Must be strict before uploading", fg="red")
     #    sys.exit(1)
+
+    if eager_versions:
+        bioversions.get_rows(use_tqdm=True)
+
     with logging_redirect_tqdm():
         click.secho("Collecting metadata and building", fg="cyan", bold=True)
         # note that this is the only one that needs a force=force

{pyobo-0.12.5 → pyobo-0.12.6}/src/pyobo/identifier_utils/api.py

@@ -287,7 +287,9 @@ def wrap_norm_prefix(f):
                 raise ValueError(f"Invalid prefix: {prefix.prefix}")
             prefix = ReferenceTuple(norm_prefix, prefix.identifier)
         else:
-            raise TypeError
+            raise TypeError(
+                f"prefix should be given as a string or reference object. Got {type(prefix)} {prefix}"
+            )
         return f(prefix, *args, **kwargs)
 
     return _wrapped

{pyobo-0.12.5 → pyobo-0.12.6}/src/pyobo/sources/drugcentral.py

@@ -6,7 +6,6 @@ from collections.abc import Iterable
 from contextlib import closing
 
 import bioregistry
-import psycopg2
 from pydantic import ValidationError
 from tqdm.auto import tqdm
 
@@ -42,6 +41,8 @@ class DrugCentralGetter(Obo):
 
 def iter_terms() -> Iterable[Term]:
     """Iterate over DrugCentral terms."""
+    import psycopg2
+
     with closing(psycopg2.connect(**PARAMS)) as conn:
         with closing(conn.cursor()) as cur:
             cur.execute(

{pyobo-0.12.5 → pyobo-0.12.6}/src/pyobo/sources/spdx.py

@@ -55,11 +55,15 @@ def _get_term(record: dict[str, Any]) -> Term | None:
     except ValidationError:
         tqdm.write(f"invalid: {record['licenseId']}")
         return None
-    term = Term(
-        reference=reference,
-        is_obsolete=True if record.get("isDeprecatedLicenseId") else None,
-        # type="Instance",
-    ).append_parent(ROOT)
+    term = (
+        Term(
+            reference=reference,
+            is_obsolete=True if record.get("isDeprecatedLicenseId") else None,
+            # type="Instance",
+        )
+        .append_parent(ROOT)
+        .append_synonym(record["licenseId"])
+    )
     if record.get("isOsiApproved"):
         term.annotate_boolean(IS_OSI, True)
     if record.get("isFsfLibre"):
@@ -82,4 +86,4 @@ class SPDXLicenseGetter(Obo):
 
 
 if __name__ == "__main__":
-    SPDXLicenseGetter.cli(["--obo", "--owl", "--rewrite"])
+    SPDXLicenseGetter.cli()

{pyobo-0.12.5 → pyobo-0.12.6}/src/pyobo/struct/struct.py

@@ -8,6 +8,7 @@ import json
 import logging
 import os
 import sys
+import tempfile
 import warnings
 from collections import ChainMap, defaultdict
 from collections.abc import Callable, Collection, Iterable, Iterator, Mapping, Sequence
@@ -1021,6 +1022,15 @@ class Obo:
         ofn = get_ofn_from_obo(self)
         ofn.write_funowl(path)
 
+    def write_owl(self, path: str | Path) -> None:
+        """Write OWL, by first outputting OFN then converting with ROBOT."""
+        from bioontologies import robot
+
+        with tempfile.TemporaryDirectory() as directory:
+            ofn_path = Path(directory).joinpath("tmp.ofn")
+            self.write_ofn(ofn_path)
+            robot.convert(ofn_path, path)
+
     def write_rdf(self, path: str | Path) -> None:
         """Write as Turtle RDF."""
         from .functional.obo_to_functional import get_ofn_from_obo

{pyobo-0.12.5 → pyobo-0.12.6}/src/pyobo/utils/misc.py

@@ -3,7 +3,7 @@
 from __future__ import annotations
 
 import logging
-from collections.abc import Callable
+from collections.abc import Callable, Iterable
 from datetime import datetime
 
 import bioversions.utils
@@ -46,6 +46,8 @@ VERSION_PREFIXES = [
     "http://w3id.org/nfdi4ing/metadata4ing/",  # like http://w3id.org/nfdi4ing/metadata4ing/1.3.1
     "http://www.semanticweb.com/OntoRxn/",  # like http://www.semanticweb.com/OntoRxn/0.2.5
     "https://w3id.org/lehrplan/ontology/",  # like in https://w3id.org/lehrplan/ontology/1.0.0-4
+    "http://www.ebi.ac.uk/swo/version/",  # http://www.ebi.ac.uk/swo/version/6.0
+    "https://w3id.org/emi/version/",
 ]
 VERSION_PREFIX_SPLITS = [
     "http://www.ebi.ac.uk/efo/releases/v",
@@ -193,18 +195,23 @@ def _prioritize_version(
     return None
 
 
-def _get_version_from_artifact(prefix: str) -> str | None:
+def _get_getter_urls(prefix: str) -> Iterable[tuple[OntologyFormat, str]]:
     # assume that all possible files that can be downloaded
     # are in sync and have the same version
-    for ontology_format, func in ONTOLOGY_GETTERS:
-        url = func(prefix)
+    for ontology_format, get_url_func in ONTOLOGY_GETTERS:
+        url = get_url_func(prefix)
         if url is None:
             continue
+        yield ontology_format, url
+
+
+def _get_version_from_artifact(prefix: str) -> str | None:
+    for ontology_format, url in _get_getter_urls(prefix):
         # Try to peak into the file to get the version without fully downloading
-        version_func = VERSION_GETTERS.get(ontology_format)
-        if version_func is None:
+        get_version_func = VERSION_GETTERS.get(ontology_format)
+        if get_version_func is None:
             continue
-        version = version_func(prefix, url)
+        version = get_version_func(prefix, url)
         if version:
             return cleanup_version(version, prefix=prefix)
     return None

{pyobo-0.12.5 → pyobo-0.12.6}/src/pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.5"
+VERSION = "0.12.6"
 
 
 def get_git_hash() -> str: