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.

1.4.10 - 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 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 logic

  • Update MAX_NUM_REQUESTS_AT_A_TIME to 25

  • Update default chunk_size in annotate() methods to 1000

  • Make __validate_and_sanitize_input_data() method public (now it’s a 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