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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)

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.