czbenchmarks.cli.resolve_reference
==================================

.. py:module:: czbenchmarks.cli.resolve_reference


Attributes
----------

.. autoapisummary::

   czbenchmarks.cli.resolve_reference.ANNDATA_REF_PREFIX


Classes
-------

.. autoapisummary::

   czbenchmarks.cli.resolve_reference.AnnDataReference


Functions
---------

.. autoapisummary::

   czbenchmarks.cli.resolve_reference.is_anndata_reference
   czbenchmarks.cli.resolve_reference.resolve_value_recursively
   czbenchmarks.cli.resolve_reference.resolve_task_parameters


Module Contents
---------------

.. py:data:: ANNDATA_REF_PREFIX
   :value: '@'


.. py:class:: AnnDataReference(/, **data: Any)

   Bases: :py:obj:`pydantic.BaseModel`


   DataRef represents a structured reference to a specific slot or field within an AnnData object.
   References are denoted by a leading '@' and can point to various AnnData attributes:
       - '@X'                → adata.X (main data matrix)
       - '@obs'              → adata.obs (entire observations DataFrame)
       - '@obs:cell_type'    → adata.obs["cell_type"] (specific column in obs)
       - '@obsm:X_pca'       → adata.obsm["X_pca"] (specific key in obsm)
       - '@layers:counts'    → adata.layers["counts"] (specific layer)
       - '@var:gene_symbols' → adata.var["gene_symbols"] (specific column in var)
       - '@varm:some_key'    → adata.varm["some_key"] (specific key in varm)
       - '@uns:some_key'     → adata.uns["some_key"] (specific key in uns)
   .. attribute:: space

      The AnnData attribute to reference ('X', 'obs', 'obsm', 'var', 'varm', 'layers', 'uns').

      :type: str

   .. attribute:: key

      The key or column name within the specified space, if applicable.

      :type: Optional[str]

   .. method:: parse(value

      str) -> DataRef:
      Parse a string reference (e.g., '@obs:cell_type') into a DataRef instance.

   .. method:: resolve(adata

      AnnData) -> Any:
      Resolve the reference against a given AnnData object, returning the referenced data.

   :raises ValueError: If the reference format is invalid or unsupported.
   :raises KeyError: If the specified key does not exist in the referenced AnnData attribute.

   Create a new model by parsing and validating input data from keyword arguments.

   Raises [`ValidationError`][pydantic_core.ValidationError] if the input data cannot be
   validated to form a valid model.

   `self` is explicitly positional-only to allow `self` as a field name.


   .. py:attribute:: space
      :type:  str


   .. py:attribute:: key
      :type:  Optional[str]
      :value: None



   .. py:method:: parse(ref_string: str) -> AnnDataReference
      :staticmethod:



   .. py:method:: resolve(anndata: anndata.AnnData) -> Any


.. py:function:: is_anndata_reference(value: Any) -> bool

.. py:function:: resolve_value_recursively(value: Any, anndata: anndata.AnnData) -> Any

.. py:function:: resolve_task_parameters(task_params: dict[str, Any], anndata: anndata.AnnData) -> dict[str, Any]