pyobo 0.12.10__tar.gz → 0.12.12__tar.gz

{pyobo-0.12.10 → pyobo-0.12.12}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.10
+Version: 0.12.12
 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
@@ -55,10 +55,15 @@ Requires-Dist: nih-reporter-downloader>=0.0.1
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
 Requires-Dist: obographs>=0.0.8
+Requires-Dist: sssom-pydantic>=0.1.1
 Requires-Dist: psycopg2-binary ; extra == 'drugcentral'
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
+Requires-Dist: grape ; extra == 'grape'
+Requires-Dist: embiggen ; extra == 'grape'
+Requires-Dist: ensmallen ; extra == 'grape'
 Requires-Dist: protmapper ; extra == 'pid'
+Requires-Dist: pykeen ; extra == 'pykeen'
 Requires-Dist: scispacy ; python_full_version < '3.13' and extra == 'scispacy'
 Requires-Dist: spacy ; python_full_version < '3.13' and extra == 'scispacy'
 Requires-Dist: scipy<1.11 ; python_full_version < '3.13' and extra == 'scispacy'
@@ -74,7 +79,9 @@ Project-URL: Repository, https://github.com/biopragmatics/pyobo.git
 Provides-Extra: drugcentral
 Provides-Extra: gilda
 Provides-Extra: gilda-slim
+Provides-Extra: grape
 Provides-Extra: pid
+Provides-Extra: pykeen
 Provides-Extra: scispacy
 Provides-Extra: sources
 Description-Content-Type: text/markdown
@@ -516,20 +523,6 @@ Alternatively, install using pip:
 $ python3 -m pip install -e .
 ```
 
-### Updating Package Boilerplate
-
-This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
-guidelines, documentation configuration) up-to-date with the upstream
-cookiecutter package. Install cruft with either `uv tool install cruft` or
-`python3 -m pip install cruft` then run:
-
-```console
-$ cruft update
-```
-
-More info on Cruft's update command is available
-[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
-
 ### 🥼 Testing
 
 After cloning the repository and installing `tox` with
@@ -567,8 +560,21 @@ only that Sphinx can build the documentation in an isolated environment (i.e.,
 with `tox -e docs-test`) but also that
 [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
 
+</details>
+
+## 🧑‍💻 For Maintainers
+
+<details>
+  <summary>See maintainer instructions</summary>
+
+### Initial Configuration
+
 #### Configuring ReadTheDocs
 
+[ReadTheDocs](https://readthedocs.org) is an external documentation hosting
+service that integrates with GitHub's CI/CD. Do the following for each
+repository:
+
 1. Log in to ReadTheDocs with your GitHub account to install the integration at
    https://readthedocs.org/accounts/login/?next=/dashboard/
 2. Import your project by navigating to https://readthedocs.org/dashboard/import
@@ -577,12 +583,10 @@ with `tox -e docs-test`) but also that
    (i.e., with spaces and capital letters)
 4. Click next, and you're good to go!
 
-### 📦 Making a Release
-
-#### Configuring Zenodo
+#### Configuring Archival on Zenodo
 
 [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
-to each release of your package.
+to each release of your package. Do the following for each repository:
 
 1. Log in to Zenodo via GitHub with this link:
    https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
@@ -602,10 +606,10 @@ the DOI for the release and link to the Zenodo record for it.
 
 #### Registering with the Python Package Index (PyPI)
 
-You only have to do the following steps once.
+The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can
+be easily installed with `pip`, `uv`, and equivalent tools.
 
-1. Register for an account on the
-   [Python Package Index (PyPI)](https://pypi.org/account/register)
+1. Register for an account [here](https://pypi.org/account/register)
 2. Navigate to https://pypi.org/manage/account and make sure you have verified
    your email address. A verification email might not have been sent by default,
    so you might have to click the "options" dropdown next to your address to get
@@ -616,9 +620,11 @@ You only have to do the following steps once.
    2-factor authentication
 4. Issue an API token from https://pypi.org/manage/account/token
 
+This only needs to be done once per developer.
+
 #### Configuring your machine's connection to PyPI
 
-You have to do the following steps once per machine.
+This needs to be done once per machine.
 
 ```console
 $ uv tool install keyring
@@ -628,6 +634,8 @@ $ keyring set https://test.pypi.org/legacy/ __token__
 
 Note that this deprecates previous workflows using `.pypirc`.
 
+### 📦 Making a Release
+
 #### Uploading to PyPI
 
 After installing the package in development mode and installing `tox` with
@@ -665,4 +673,18 @@ This script does the following:
 
 This will trigger Zenodo to assign a DOI to your release as well.
 
+### Updating Package Boilerplate
+
+This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
+guidelines, documentation configuration) up-to-date with the upstream
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
 </details>

{pyobo-0.12.10 → pyobo-0.12.12}/README.md

@@ -435,20 +435,6 @@ Alternatively, install using pip:
 $ python3 -m pip install -e .
 ```
 
-### Updating Package Boilerplate
-
-This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
-guidelines, documentation configuration) up-to-date with the upstream
-cookiecutter package. Install cruft with either `uv tool install cruft` or
-`python3 -m pip install cruft` then run:
-
-```console
-$ cruft update
-```
-
-More info on Cruft's update command is available
-[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
-
 ### 🥼 Testing
 
 After cloning the repository and installing `tox` with
@@ -486,8 +472,21 @@ only that Sphinx can build the documentation in an isolated environment (i.e.,
 with `tox -e docs-test`) but also that
 [ReadTheDocs can build it too](https://docs.readthedocs.io/en/stable/pull-requests.html).
 
+</details>
+
+## 🧑‍💻 For Maintainers
+
+<details>
+  <summary>See maintainer instructions</summary>
+
+### Initial Configuration
+
 #### Configuring ReadTheDocs
 
+[ReadTheDocs](https://readthedocs.org) is an external documentation hosting
+service that integrates with GitHub's CI/CD. Do the following for each
+repository:
+
 1. Log in to ReadTheDocs with your GitHub account to install the integration at
    https://readthedocs.org/accounts/login/?next=/dashboard/
 2. Import your project by navigating to https://readthedocs.org/dashboard/import
@@ -496,12 +495,10 @@ with `tox -e docs-test`) but also that
    (i.e., with spaces and capital letters)
 4. Click next, and you're good to go!
 
-### 📦 Making a Release
-
-#### Configuring Zenodo
+#### Configuring Archival on Zenodo
 
 [Zenodo](https://zenodo.org) is a long-term archival system that assigns a DOI
-to each release of your package.
+to each release of your package. Do the following for each repository:
 
 1. Log in to Zenodo via GitHub with this link:
    https://zenodo.org/oauth/login/github/?next=%2F. This brings you to a page
@@ -521,10 +518,10 @@ the DOI for the release and link to the Zenodo record for it.
 
 #### Registering with the Python Package Index (PyPI)
 
-You only have to do the following steps once.
+The [Python Package Index (PyPI)](https://pypi.org) hosts packages so they can
+be easily installed with `pip`, `uv`, and equivalent tools.
 
-1. Register for an account on the
-   [Python Package Index (PyPI)](https://pypi.org/account/register)
+1. Register for an account [here](https://pypi.org/account/register)
 2. Navigate to https://pypi.org/manage/account and make sure you have verified
    your email address. A verification email might not have been sent by default,
    so you might have to click the "options" dropdown next to your address to get
@@ -535,9 +532,11 @@ You only have to do the following steps once.
    2-factor authentication
 4. Issue an API token from https://pypi.org/manage/account/token
 
+This only needs to be done once per developer.
+
 #### Configuring your machine's connection to PyPI
 
-You have to do the following steps once per machine.
+This needs to be done once per machine.
 
 ```console
 $ uv tool install keyring
@@ -547,6 +546,8 @@ $ keyring set https://test.pypi.org/legacy/ __token__
 
 Note that this deprecates previous workflows using `.pypirc`.
 
+### 📦 Making a Release
+
 #### Uploading to PyPI
 
 After installing the package in development mode and installing `tox` with
@@ -584,4 +585,18 @@ This script does the following:
 
 This will trigger Zenodo to assign a DOI to your release as well.
 
+### Updating Package Boilerplate
+
+This project uses `cruft` to keep boilerplate (i.e., configuration, contribution
+guidelines, documentation configuration) up-to-date with the upstream
+cookiecutter package. Install cruft with either `uv tool install cruft` or
+`python3 -m pip install cruft` then run:
+
+```console
+$ cruft update
+```
+
+More info on Cruft's update command is available
+[here](https://github.com/cruft/cruft?tab=readme-ov-file#updating-a-project).
+
 </details>

{pyobo-0.12.10 → pyobo-0.12.12}/pyproject.toml

@@ -1,10 +1,10 @@
 [build-system]
-requires = ["uv_build>=0.6.6,<1.0"]
+requires = ["uv_build>=0.9.6,<1.0"]
 build-backend = "uv_build"
 
 [project]
 name = "pyobo"
-version = "0.12.10"
+version = "0.12.12"
 description = "A python package for handling and generating OBO"
 readme = "README.md"
 authors = [
@@ -89,6 +89,7 @@ dependencies = [
     "typing_extensions",
     "rdflib",
     "obographs>=0.0.8",
+    "sssom_pydantic>=0.1.1",
 ]
 
 # see https://peps.python.org/pep-0735/ and https://docs.astral.sh/uv/concepts/dependencies/#dependency-groups
@@ -102,6 +103,7 @@ docs = [
     "sphinx-rtd-theme>=3.0",
     "sphinx-click", 
     "sphinx_automodapi",
+    "sphinx_toolbox",
 ]
 lint = [
     "ruff",
@@ -139,8 +141,8 @@ bump = [
     "bump-my-version",
 ]
 build = [
-    "uv",
-    "uv-build",
+    "uv>=0.9.6",
+    "uv-build>=0.9.6",
 ]
 release = [
     { include-group = "build" },
@@ -174,6 +176,14 @@ scispacy = [
     "spacy; python_version <= '3.12'",
     "scipy<1.11; python_version <= '3.12'",
 ]
+pykeen = [
+    "pykeen",
+]
+grape = [
+    "grape",
+    "embiggen",
+    "ensmallen",
+]
 
 # 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/
@@ -305,7 +315,7 @@ known-first-party = [
 docstring-code-format = true
 
 [tool.bumpversion]
-current_version = "0.12.10"
+current_version = "0.12.12"
 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-0.12.10 → pyobo-0.12.12}/src/pyobo/__init__.py

@@ -14,6 +14,7 @@ from .api import (
     get_filtered_relations_df,
     get_filtered_xrefs,
     get_graph,
+    get_graph_embeddings_df,
     get_hierarchy,
     get_id_definition_mapping,
     get_id_multirelations_mapping,
@@ -37,6 +38,7 @@ from .api import (
     get_obsolete,
     get_primary_curie,
     get_primary_identifier,
+    get_primary_reference,
     get_properties,
     get_properties_df,
     get_property,
@@ -44,6 +46,7 @@ from .api import (
     get_relation,
     get_relation_mapping,
     get_relations_df,
+    get_semantic_mappings,
     get_species,
     get_sssom_df,
     get_subhierarchy,
@@ -114,6 +117,7 @@ __all__ = [
     "get_filtered_relations_df",
     "get_filtered_xrefs",
     "get_graph",
+    "get_graph_embeddings_df",
     "get_grounder",
     "get_hierarchy",
     "get_id_definition_mapping",
@@ -139,6 +143,7 @@ __all__ = [
     "get_ontology",
     "get_primary_curie",
     "get_primary_identifier",
+    "get_primary_reference",
     "get_properties",
     "get_properties_df",
     "get_property",
@@ -149,6 +154,7 @@ __all__ = [
     "get_scispacy_entities",
     "get_scispacy_entity_linker",
     "get_scispacy_knowledgebase",
+    "get_semantic_mappings",
     "get_species",
     "get_sssom_df",
     "get_subhierarchy",

{pyobo-0.12.10 → pyobo-0.12.12}/src/pyobo/api/__init__.py

@@ -5,10 +5,16 @@ from .alts import (
     get_id_to_alts,
     get_primary_curie,
     get_primary_identifier,
+    get_primary_reference,
 )
 from .combine import get_literal_mappings_subset
 from .edges import get_edges, get_edges_df, get_graph
-from .embedding import get_text_embedding, get_text_embedding_similarity, get_text_embeddings_df
+from .embedding import (
+    get_graph_embeddings_df,
+    get_text_embedding,
+    get_text_embedding_similarity,
+    get_text_embeddings_df,
+)
 from .hierarchy import (
     get_ancestors,
     get_children,
@@ -59,6 +65,7 @@ from .typedefs import get_typedef_df
 from .xrefs import (
     get_filtered_xrefs,
     get_mappings_df,
+    get_semantic_mappings,
     get_sssom_df,
     get_xref,
     get_xrefs,
@@ -80,6 +87,7 @@ __all__ = [
     "get_filtered_relations_df",
     "get_filtered_xrefs",
     "get_graph",
+    "get_graph_embeddings_df",
     "get_hierarchy",
     "get_id_definition_mapping",
     "get_id_multirelations_mapping",
@@ -105,6 +113,7 @@ __all__ = [
     "get_ontology",
     "get_primary_curie",
     "get_primary_identifier",
+    "get_primary_reference",
     "get_priority_curie",
     "get_properties",
     "get_properties_df",
@@ -113,6 +122,7 @@ __all__ = [
     "get_relation",
     "get_relation_mapping",
     "get_relations_df",
+    "get_semantic_mappings",
     "get_species",
     "get_sssom_df",
     "get_subhierarchy",

{pyobo-0.12.10 → pyobo-0.12.12}/src/pyobo/api/alts.py

@@ -20,6 +20,7 @@ __all__ = [
     "get_id_to_alts",
     "get_primary_curie",
     "get_primary_identifier",
+    "get_primary_reference",
 ]
 
 logger = logging.getLogger(__name__)
@@ -61,13 +62,13 @@ def get_alts_to_id(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> Mapping[
     }
 
 
-def get_primary_curie(
+def get_primary_reference(
     prefix: str | curies.Reference | curies.ReferenceTuple,
     identifier: str | None = None,
     /,
     **kwargs: Unpack[GetOntologyKwargs],
-) -> str | None:
-    """Get the primary curie for an entity."""
+) -> curies.ReferenceTuple | None:
+    """Get the primary reference for an entity."""
     reference = _get_pi(prefix, identifier)
     try:
         primary_identifier = get_primary_identifier(reference, **kwargs)
@@ -76,7 +77,20 @@ def get_primary_curie(
             raise
         # this happens on invalid prefix. maybe revise?
         return None
-    return f"{reference.prefix}:{primary_identifier}"
+    return curies.ReferenceTuple(reference.prefix, primary_identifier)
+
+
+def get_primary_curie(
+    prefix: str | curies.Reference | curies.ReferenceTuple,
+    identifier: str | None = None,
+    /,
+    **kwargs: Unpack[GetOntologyKwargs],
+) -> str | None:
+    """Get the primary curie for an entity."""
+    reference = get_primary_reference(prefix, identifier, **kwargs)
+    if reference is None:
+        return None
+    return reference.curie
 
 
 def get_primary_identifier(