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.

1.7.5 - 2026-04-03

Changed

• Sorting of top-k calls now uses (depth, score) as the sort key, ensuring ties in depth are broken by score

• get_most_granular_top_k_calls, compute_most_granular_top_k_calls_single, and compute_most_granular_top_k_calls_cluster now accept a use_shortest_path parameter (default True) to control whether shortest or longest ontology path lengths are used when ranking cell type calls

• Added get_shortest_path_lengths_from_target method to CellOntologyCache for computing shortest-path depths in the cell ontology graph

• Relaxed upper bound on requests dependency (>=2.31)

• Updated biopython dependency to >=1.87

• Linting is now only run on Python 3.12 in the CI matrix to avoid duplicate failures

• Fixed mutable default argument in insert_cas_ontology_aware_response_into_adata (CellOntologyCache is now instantiated lazily)

Fixed

• Fixed incorrect mock type in unit tests (aiohttp.ClientResponse replaced with requests.Response where appropriate)

1.7.4 - 2025-09-23

Changed

• Refactored PyPI publishing into a dedicated publish-pypi.yaml workflow; removed the old pypi-deploy composite action

• Simplified the main CI workflow (main-workflow.yaml) to remove manual PyPI dispatch options

1.7.3 - 2025-09-11

Fixed

• Pinned scanpy per Python version (<1.10.0 for Python < 3.12, <1.12.0 for Python >= 3.12)

• Pinned biopython==1.85 for reproducible visualization installs

1.7.2 - 2025-09-10

Changed

• Added Python 3.12 support; split dependency pins by Python version for anndata, numpy, pandas, typing-extensions, and owlready2

• Pinned dash==2.17.1 and dash-bootstrap-components==1.6.0 in visualization requirements

• Simplified tox configuration to a single py environment

• Removed unused Python version entries from gh-actions tox config

Fixed

• Fixed float32 conversion for adata.raw.X by restoring via raw.to_adata() before casting

1.7.1 - 2024-10-25

Changed

• Improved quota status message formatting: weekly quota, reset date, and lifetime quota are now printed on separate lines

1.7.0 - 2024-10-25

Changed

• Client now displays user quota on initialization

• Added low-quota warning feedback link when remaining lifetime quota falls below threshold

• Feedback link is also shown when a quota-exceeded error is raised for users without a quota increase

• Added quota_increased field handling throughout quota checks

1.6.0 - 2024-10-08

Changed

• Added ability to enforce lifetime quotas

• Dependency vulnerability checks are performed by unit testing github action

• Improved handling of different root nodes in the circular tree plot visualization Dash App

Fixed

• Logging now uses Python logging

1.5.1 - 2024-09-09

Changed

• Added ability to render documentation locally

• PR tests will now fail when doc is invalid

• Fixed bugs in documentation navigation

• Update Cell Type Ontology to the version used in cellxgene schema v5

• Explicitly typed all objects returned from the client

Fixed

• Added a pre-sanitization step to fix an issue where non-float32 anndata matrices would be submitted to CAS and fail

• Removed unused method parameters

1.4.13 - 2024-09-06

Warning: This version was compromised due to a wrong commit being tagged. It is not a proper release version. Please use version 1.5.1 or later.

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