anndata2cas add accession_columns parameter

[hkir-dev]

Anndata2cas is automatically generating accession IDs from the hash of the cells belonging to the cell set. However in some cases (in the anndata or spreadsheet) there are already pre-calculated accession ids in the dataset. This update enables users to identify accession columns and utilise those instead of generating new accessions.

Also parent_cell_set_name doesn't exist in the CAS schema, so deleted it from the json output.

[Copilot]

Pull Request Overview

This PR updates anndata2cas to support using pre-calculated accession IDs by introducing an accession_columns parameter while removing the now-unsupported parent_cell_set_name field. Key changes include updating tests to reflect schema changes, modifying conversion utility functions to accept an accession mapping, and adding a new MappedAccessionManager to handle predefined accession IDs.

Reviewed Changes

Copilot reviewed 10 out of 10 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
src/test/spreadsheet_to_cas_test.py	Updated expected annotation length in the test to match the removal of parent_cell_set_name.
src/test/conversion_utils_test.py	Commented out parent_cell_set_name test case as it is no longer part of the schema.
src/cas/utils/conversion_utils.py	Added an accession mapping parameter to generate_parent_cell_lookup and created create_accession_mapping.
src/cas/anndata_to_cas.py	Updated function signature and logic to pass accession_columns and use the new accession mapping.
src/cas/accession/*.py	Updated accession manager implementations to accept an extra cellset_name parameter.
src/cas/main.py & docs/cli.md	Updated CLI options and documentation for the new accession_columns parameter.