------------------
Added
~~~~~
- 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:`~.CASClient`
- Add sync POST method (using requests) to 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
Changed
~~~~~~~
- Reorganize :class:`~.CASClient` methods: factor out sharding logic
- Update ``MAX_NUM_REQUESTS_AT_A_TIME`` to 25
- Update default ``chunk_size`` in :meth:`~.CASClient.annotate_anndata` methods to 1000
- Make ``__validate_and_sanitize_input_data`` method public (now it is :meth:`~.CASClient.validate_and_sanitize_input_data`) in :class:`~.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
Removed
~~~~~~~
- Remove docs generation from CI/CD pipeline
File Structure Changes
~~~~~~~~~~~~~~~~~~~~~~
- 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)
Notes
~~~~~
- Users will need a new API token to use this version