rsynthbio 3.0.2
Major Changes
- Async API Support: Migrated to async API model matching the Python
pysynthbio implementation
predict_query() now uses an asynchronous workflow: submit → poll → download - Added automatic status polling with configurable intervals and timeouts
- New parameters:
poll_interval_seconds (default: 2),poll_timeout_seconds (default: 900)
- Single-Cell Support: Added support for single-cell RNA-seq data via the “single-cell” modality
get_valid_query() now accepts a modalityparameter (“bulk” or “single-cell”) get_valid_modalities() now returns both “bulk” and “single-cell” - Updated
MODEL_MODALITIES to include both modalities
- GEM-1 Model: rsynthbio now works with the GEM-1 model from Synthesize Bio
- Older versions of Synthesize Bio models are no longer supported
Breaking Changes
- API Base URL Changed:
API_BASE_URL is now https://app.synthesize.bio (base URL only, not versioned endpoint)
- Parameter Changes in
predict_query():
- Removed
raw_response parameter
- Removed
url parameter (replaced withapi_base_url)
- Added
poll_interval_seconds parameter
- Added
poll_timeout_seconds parameter
- Added
return_download_url parameter
New Functions
resolve_api_slug(): Maps modality to API endpoint slug (internal)start_model_query(): Initiates async model query (internal)poll_model_query(): Polls status endpoint until completion (internal)get_json(): Fetches results from signed download URL (internal)transform_result_to_frames(): Converts JSON to data frames (internal)
Bug Fixes
- Fixed metadata handling for queries with empty metadata fields
- Improved error messages for failed queries (now shows error message instead of error URL)
- Better handling of single-cell count data format (dict vs list)
Documentation
- Updated README.md to explain async API behavior
- Updated vignettes with async workflow examples
- Added examples for both bulk and single-cell modalities
- Clarified polling timeout and interval configuration
Tests
- Added comprehensive test suite mirroring Python implementation
- Added live API tests for both bulk and single-cell modalities
- Added tests for invalid metadata validation
- Added mocked async workflow tests (success, failure, timeout scenarios)