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.

1.4.12 - 2024-08-01

Changed

Removed references to the development environment in the client code
Updated client documentation
Updated the demo notebook’s documentation

1.4.11 - 2024-07-24

Added

Added docstrings in visualization and exposed it to sphinx docs

1.4.10 - 2024-07-23

Fixed

Bug fix in the circular tree plot visualization Dash App

1.4.9 - 2024-07-22

Added

Added circular tree plot visualization Dash App

Changed

Renamed data_preparation to preprocessing`
Moved all preprocessing-related code to preprocessing submodule
Added a postprocessing submodule
Added a visualization submodule
Renamed scanpy optional dependencies to vis (for all visualization-related dependencies)

1.4.8 - 2024-07-22

Changed

Decrease MAX_NUM_REQUESTS_AT_A_TIME to 8

1.4.7 - 2024-07-09

Added

Add check in client initialization to ensure the current version of the client code is compatbile with the selected CAS server

1.4.6 - 2024-06-12

Added

Add text requesting feedback at the end of calls with instructions on opting out of feedback requests

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 to CASClient
Add annotate_matrix_cell_type_ontology_aware_strategy() method to CASClient

Changed

Deprecate annotate_anndata(), annotate_anndata_file(), annotate_10x_h5_file(), search_anndata(), and search_10x_h5_file(), methods in CASClient

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 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 CASClient methods: factor out sharding logic
Update MAX_NUM_REQUESTS_AT_A_TIME to 25
Update default chunk_size in annotate_anndata() methods to 1000
Make __validate_and_sanitize_input_data method public (now it is 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

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