Add database adapter for reference

.readthedocs.yml

@@ -19,5 +19,5 @@ build:
     - asdf install uv latest
     - asdf global uv latest
     - uv venv $READTHEDOCS_VIRTUALENV_PATH
-    - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH UV_PREVIEW=1 uv pip install .[docs,pandas,flask,fastapi,rdflib]
+    - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH UV_PREVIEW=1 uv pip install .[docs,pandas,flask,fastapi,rdflib,sqlmodels,sqlalchemy]
     - python -m sphinx -T -b html -d docs/_build/doctrees -D language=en docs/source $READTHEDOCS_OUTPUT/html

docs/source/conf.py

@@ -239,15 +239,18 @@
 # Note: don't add trailing slashes, since sphinx adds "/objects.inv" to the end
 intersphinx_mapping = {
     "python": ("https://docs.python.org/3", None),
-    "bioregistry": ("https://bioregistry.readthedocs.io/en/stable/", None),
-    "pandas": ("https://pandas.pydata.org/docs/", None),
-    "flask": ("https://flask.palletsprojects.com/", None),
-    "pydantic": ("https://docs.pydantic.dev/latest/", None),
+    "bioregistry": ("https://bioregistry.readthedocs.io/en/stable", None),
+    "pandas": ("https://pandas.pydata.org/docs", None),
+    "flask": ("https://flask.palletsprojects.com/en/stable", None),
+    "pydantic": ("https://docs.pydantic.dev/latest", None),
     # "fastapi": ("https://fastapi.tiangolo.com/", None),
     # "gunicorn": ("https://docs.gunicorn.org/", None),
     # "uvicorn": ("https://www.uvicorn.org/", None),
-    "prefixmaps": ("https://linkml.io/prefixmaps/", None),
-    "rdflib": ("https://rdflib.readthedocs.io/en/stable/", None),
+    "prefixmaps": ("https://linkml.io/prefixmaps", None),
+    "rdflib": ("https://rdflib.readthedocs.io/en/stable", None),
+    "sssom": ("https://mapping-commons.github.io/sssom-py", None),
+    # "sqlalchemy": ("https://docs.sqlalchemy.org/en/20", None),
+    # "sqlmodel": ("https://sqlmodel.tiangolo.com", None),
 }
 
 autoclass_content = "both"

docs/source/database.rst

@@ -0,0 +1,6 @@
+Database
+========
+
+.. automodapi:: curies.database
+    :no-inheritance-diagram:
+    :no-heading:

docs/source/index.rst

@@ -69,3 +69,4 @@ The most recent code and data can be installed directly from GitHub with:
     typing
     w3c
     preprocessing
+    database

pyproject.toml

@@ -69,6 +69,12 @@ tests = [
 pandas = [
     "pandas",
 ]
+sqlalchemy = [
+    "sqlalchemy",
+]
+sqlmodel = [
+    "sqlmodel",
+]
 flask = [
     "flask",
     "defusedxml",

src/curies/api.py

@@ -429,6 +429,10 @@ def __eq__(self, other: Any) -> bool:
             and self.identifier == other.identifier
         )
 
+    def __composite_values__(self) -> tuple[str, str]:
+        """Return values appropriate for :func:`sqlalchemy.orm.composite`."""
+        return self.prefix, self.identifier
+
     @property
     def curie(self) -> str:
         """Get the reference as a CURIE string.
@@ -485,7 +489,7 @@ class NamableReference(Reference):
     model_config = ConfigDict(frozen=True)
 
     @classmethod
-    def from_curie(  # type:ignore
+    def from_curie(
         cls,
         curie: str,
         name: str | None = None,
@@ -2244,7 +2248,7 @@ def pd_compress(
         :param ambiguous: If true, consider the column as containing either CURIEs or URIs.
         """
         pre_func = self.compress_or_standardize if ambiguous else self.compress
-        func = partial(pre_func, strict=strict, passthrough=passthrough)  # type:ignore
+        func = partial(pre_func, strict=strict, passthrough=passthrough)
         df[column if target_column is None else target_column] = df[column].map(func)
 
     def pd_expand(
@@ -2267,7 +2271,7 @@ def pd_expand(
         :param ambiguous: If true, consider the column as containing either CURIEs or URIs.
         """
         pre_func = self.expand_or_standardize if ambiguous else self.expand
-        func = partial(pre_func, strict=strict, passthrough=passthrough)  # type:ignore
+        func = partial(pre_func, strict=strict, passthrough=passthrough)
         df[column if target_column is None else target_column] = df[column].map(func)
 
     def pd_standardize_prefix(
@@ -2370,7 +2374,7 @@ def file_compress(
         :param ambiguous: If true, consider the column as containing either CURIEs or URIs.
         """
         pre_func = self.compress_or_standardize if ambiguous else self.compress
-        func = partial(pre_func, strict=strict, passthrough=passthrough)  # type:ignore
+        func = partial(pre_func, strict=strict, passthrough=passthrough)
         self._file_helper(func, path=path, column=column, sep=sep, header=header)
 
     def file_expand(
@@ -2396,7 +2400,7 @@ def file_expand(
         :param ambiguous: If true, consider the column as containing either CURIEs or URIs.
         """
         pre_func = self.expand_or_standardize if ambiguous else self.expand
-        func = partial(pre_func, strict=strict, passthrough=passthrough)  # type:ignore
+        func = partial(pre_func, strict=strict, passthrough=passthrough)
         self._file_helper(func, path=path, column=column, sep=sep, header=header)
 
     @staticmethod