Changelog
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.
1.4.5 - 2024-06-03
Added
Add optional parameter to the client constructor to set the CAS API URL
1.4.4 - 2024-05-02
Added
Add
annotate_matrix_cell_type_summary_statistics_strategy()
method toCASClient
Add
annotate_matrix_cell_type_ontology_aware_strategy()
method toCASClient
Changed
Deprecate
annotate_anndata()
,annotate_anndata_file()
,annotate_10x_h5_file()
,search_anndata()
, andsearch_10x_h5_file()
, methods inCASClient
File Structure Changes
No changes in file structure
1.4.3 - 2024-03-18
Added
Fix total mrna umis for normalized data
Changed
Handle different matrix types in the data preparation callbacks
Update unit tests for the data preparation callbacks
1.4.2 - 2024-03-12
Changed
Increase client HTTP request timeouts
1.4.1 - 2024-02-15
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
clients.CASClient
Add sync POST method (using requests) to
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
Changed
Reorganize
CASClient
methods: factor out sharding logicUpdate MAX_NUM_REQUESTS_AT_A_TIME to 25
Update default chunk_size in
annotate()
methods to 1000Make
__validate_and_sanitize_input_data()
method public (now it’s avalidate_and_sanitize_input_data()
) in CASClientUpdate 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