rsynthbio 3.0.0

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 modality parameter (“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 with api_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)