bioregistry 0.13.4__tar.gz → 0.13.5__tar.gz

{bioregistry-0.13.4 → bioregistry-0.13.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: bioregistry
-Version: 0.13.4
+Version: 0.13.5
 Summary: Integrated registry of biological databases and nomenclatures
 Keywords: snekpack,cookiecutter,databases,biological databases,biomedical databases,persistent identifiers
 Author: Charles Tapley Hoyt

{bioregistry-0.13.4 → bioregistry-0.13.5}/pyproject.toml

@@ -10,7 +10,7 @@ markers = [
 
 [project]
 name = "bioregistry"
-version = "0.13.4"
+version = "0.13.5"
 description = "Integrated registry of biological databases and nomenclatures"
 readme = "README.md"
 authors = [
@@ -254,7 +254,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.13.4"
+current_version = "0.13.5"
 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}",

{bioregistry-0.13.4 → bioregistry-0.13.5}/src/bioregistry/__init__.py

@@ -1,6 +1,11 @@
 """Extract registry information."""
 
-from .collection_api import get_collection, get_context
+from .collection_api import (
+    get_collection,
+    get_collection_prefixes,
+    get_collection_resources,
+    get_context,
+)
 from .metaresource_api import (
     get_registry,
     get_registry_description,
@@ -176,6 +181,8 @@ __all__ = [
     "get_bioregistry_iri",
     "get_canonical_for",
     "get_collection",
+    "get_collection_prefixes",
+    "get_collection_resources",
     "get_contact",
     "get_contact_email",
     "get_contact_github",

bioregistry-0.13.5/src/bioregistry/collection_api.py

@@ -0,0 +1,84 @@
+"""API for collections."""
+
+from __future__ import annotations
+
+from typing import Literal, overload
+
+from .resource_manager import manager
+from .schema import Collection, Context, Resource
+
+__all__ = [
+    "get_collection",
+    "get_collection_prefixes",
+    "get_collection_resources",
+    "get_context",
+]
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_collection(identifier: str, *, strict: Literal[True] = ...) -> Collection: ...
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_collection(identifier: str, *, strict: Literal[False] = ...) -> Collection | None: ...
+
+
+def get_collection(identifier: str, *, strict: bool = False) -> Collection | None:
+    """Get the collection entry for the given identifier."""
+    rv = manager.collections.get(identifier)
+    if rv is not None:
+        return rv
+    if strict:
+        raise KeyError
+    return None
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_collection_prefixes(identifier: str, *, strict: Literal[True] = ...) -> list[str]: ...
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_collection_prefixes(
+    identifier: str, *, strict: Literal[False] = ...
+) -> list[str] | None: ...
+
+
+def get_collection_prefixes(identifier: str, *, strict: bool = False) -> list[str] | None:
+    """Get collection prefixes."""
+    rv = manager.collections.get(identifier)
+    if rv is not None:
+        return rv.resources
+    if strict:
+        raise KeyError(f"no collection exists: {identifier}. try: {set(manager.collections)}")
+    return None
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_collection_resources(identifier: str, *, strict: Literal[True] = ...) -> list[Resource]: ...
+
+
+# docstr-coverage:excused `overload`
+@overload
+def get_collection_resources(
+    identifier: str, *, strict: Literal[False] = ...
+) -> list[Resource] | None: ...
+
+
+def get_collection_resources(identifier: str, *, strict: bool = False) -> list[Resource] | None:
+    """Get collection resources."""
+    rv = manager.collections.get(identifier)
+    if rv is not None:
+        return [manager.registry[r] for r in rv.resources]
+    if strict:
+        raise KeyError(f"no collection exists: {identifier}. try: {set(manager.collections)}")
+    return None
+
+
+def get_context(identifier: str) -> Context | None:
+    """Get the context for the given identifier."""
+    return manager.get_context(identifier)

{bioregistry-0.13.4 → bioregistry-0.13.5}/src/bioregistry/constants.py

@@ -214,7 +214,7 @@ INTERNAL_KEY = "bioregistry"
 INTERNAL_PIP = "bioregistry"
 INTERNAL_LABEL = "Bioregistry"
 INTERNAL_REPOSITORY_SLUG = "biopragmatics/bioregistry"
-INTERNAL_REPOSITORY_PAGES = "https://biopragmatics.io/bioregistry"
+INTERNAL_REPOSITORY_PAGES = "https://biopragmatics.github.io/bioregistry"
 INTERNAL_REPOSITORY = f"https://github.com/{INTERNAL_REPOSITORY_SLUG}"
 INTERNAL_REPOSITORY_BLOB = f"https://github.com/{INTERNAL_REPOSITORY_SLUG}/blob/main"
 INTERNAL_REPOSITORY_RAW = f"https://raw.githubusercontent.com/{INTERNAL_REPOSITORY_SLUG}/main"