Remove snowflake from dependencies, documentation and code.#489
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jsstevenson
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Jun 24, 2026
| "anyio", | ||
| "bioutils", | ||
| "biocommons.seqrepo", | ||
| "pyjwt[crypto]", |
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what's the gist here? was this previously provided by something else and it's needed for the JWT authentication stuff?
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pyjwt was previously a transitive dependency of snowflake. JWT authorization defined in anyvar.restapi.auth requires. So it was added back in.
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Remove Snowflake storage backend
Summary
Removes the Snowflake object-store backend from AnyVar — including the
backend implementation, the
snowflake-sqlalchemydependency, allSnowflake-specific ORM hooks, tests, and documentation.
The Postgres, DuckDB, and stateless (
NoObjectStore) backends areuntouched.
Motivation
The Snowflake backend is no longer needed. Removing it eliminates a
heavy SQLAlchemy dialect dependency, simplifies the ORM layer (which had
dialect-specific
with_variant(...)calls and a conditional__table_args__), and reduces the surface area of the storageabstraction.
Breaking changes
ANYVAR_STORAGE_URI="snowflake://..."is no longer supported.create_storage()now raises the same genericValueError("URI scheme snowflake is not implemented")it raises forany other unrecognized scheme.
snowflake-sqlalchemydependency is removed frompyproject.toml.pytest.mark.snowflakemarker is no longer registered.Changes
Deleted files
src/anyvar/storage/snowflake.py—SnowflakeObjectStore,privatelink dialect monkey-patch,
@compiles(Insert, "snowflake")PARSE_JSON helper.
tests/unit/storage/test_snowflake.py,tests/unit/storage/test_snowflake_dyntable.py.docs/source/configuration/snowflake.rst.docs/source/api/api/storage/anyvar.storage.snowflake.rst(autosummary stub).
Modified files
pyproject.toml— droppedsnowflake-sqlalchemy~=1.8.2and thesnowflake:pytest marker.src/anyvar/anyvar.py— removed the"snowflake"branch increate_storage()and the matching docstring entry.src/anyvar/storage/orm.pySnowflakeVARIANTTypeDecorator..with_variant(SnowflakeVARIANT, "snowflake")fromVrsObject.vrs_object,Allele.state,Extension.value(theJSON()/JSONBvariants remain).VariationMapping.__table_args__; theUniqueConstraintit applied only to Snowflake is gone.json,urlparse,Dialect,UniqueConstraint,TypeDecorator,snowflake.sqlalchemy.snowdialect,DEFAULT_STORAGE_URI).tests/conftest.py—all_dbsno longer includes"snowflake".docs/source/configuration/index.rst,docs/source/configuration/storage.rst,docs/source/api/index.rst— removed Snowflake bullets, toctreeentries, and autosummary entries.