All notable changes to Cellarium CAS client will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Add :meth:`annotate_matrix_cell_type_summary_statistics_strategy` method to :class:`CASClient`
- Add :meth:`annotate_matrix_cell_type_ontology_aware_strategy` method to :class:`CASClient`
- Deprecate :meth:`annotate_anndata`, :meth:`annotate_anndata_file`, :meth:`annotate_10x_h5_file`, :meth:`search_anndata`, and :meth:`search_10x_h5_file`, methods in :class:`CASClient`
- No changes in file structure
- Fix total mrna umis for normalized data
- Handle different matrix types in the data preparation callbacks
- Update unit tests for the data preparation callbacks
- Increase client HTTP request timeouts
- Include kNN search method (#49)
- Include get cells by IDs method (#49)
- Include helper methods for visualization and demo
- Add model name validation method to :class:`clients.CASClient`
- Add sync POST method (using requests) to :class:`services.CASAPIService`
- Add CHANGELOG.rst file
- Add settings module that chooses the correct settings file based on the environment according to current git version. Since now package will use development settings if it's tagged as a pre-release (alpha, beta, or release candidate (rc)), and production settings otherwise.
- Add version determination based on git tags
- Add callback methods to data_preparation module. Include total total_mrna_umis calculation as a callback before data sanitization
- Reorganize :class:`CASClient` methods: factor out sharding logic
- Update MAX_NUM_REQUESTS_AT_A_TIME to 25
- Update default chunk_size in :meth:`annotate` methods to 1000
- Make :meth:`__validate_and_sanitize_input_data` method public (now it's a :meth:`validate_and_sanitize_input_data`) in CASClient
- Update backend API url to point to the new API endpoints depending on the environment
- Update pyproject.toml file to include scanpy optional dependencies
- Restructure data_preparation into a module
- Remove docs generation from CI/CD pipeline
- Add CHANGELOG.rst file
- Add requirements/scanpy.txt file (optional requirements for scanpy related demos)
- Add cellarium/cas/scanpy_utils.py (Not necessary for the client methods, but useful for the demo)
- Add cellarium/cas/settings directory, including __init__.py, base.py, development.py, and production.py files
- Add cas/version.py file
- Add cellarium/cas/data_preparation directory, including __init__.py, callbacks.py, sanitizer.py and validator.py files
- Add tests/unit/test_data_preparation_callbacks.py file
- Add cellarium/cas/constants.py file
- Remove .github/actions/docs folder (docs are now hosted on readthedocs)
- Users will need a new API token to use this version