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Changelog

Source: NEWS.md

rsynthbio 3.0.0

CRAN release: 2025-10-15

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)