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.
1.5.1 - 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
topreprocessing`
Moved all preprocessing-related code to
preprocessing
submoduleAdded a
postprocessing
submoduleAdded a
visualization
submoduleRenamed
scanpy
optional dependencies tovis
(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 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
CASClient
Add sync POST method (using requests) to CASAPIService
Add
CHANGELOG.rst
fileAdd 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 25Update default
chunk_size
inannotate_anndata()
methods to 1000Make
__validate_and_sanitize_input_data
method public (now it isvalidate_and_sanitize_input_data()
) inCASClient
Update backend API url to point to the new API endpoints depending on the environment
Update
pyproject.toml
file to include scanpy optional dependenciesRestructure data_preparation into a module
Removed
Remove docs generation from CI/CD pipeline
File Structure Changes
Add
CHANGELOG.rst
fileAdd
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
, andproduction.py
filesAdd cas/version.py file
Add
cellarium/cas/data_preparation
directory, including__init__.py
,callbacks.py
,sanitizer.py
andvalidator.py`
filesAdd
tests/unit/test_data_preparation_callbacks.py
fileAdd
cellarium/cas/constants.py
fileRemove
.github/actions/docs
folder (docs are now hosted on readthedocs)
Notes
Users will need a new API token to use this version