v1.0.0

What's Changed

BGCFlow version 1.0.0 by release by @matinnuhamunada in #348

New Features

• Database Schema Update: Upgraded to bgcflow database schema 0.3.1.
• Custom Taxon Parameter: Enabled parameter to change taxon in antiSMASH.
• antiSMASH Parameters: Added new parameters for antiSMASH based on the antiSMASH database 4 paper.

Fixes

• BGC Downstream Preparation:
  • Updated the BGC genome preparation script to handle unusual input formats (for example, includes ":" in the metadata) which breaks BiG-SCAPE.
  • Changed input requirements and corrected issues to ensure all changes are properly registered.
  • Reincluded full antiSMASH genbanks for downstream processes.
  • Modified the get_antismash_inputs function to correctly retrieve region genbanks.
• lsabgc: Updated lsabgc to version 1.52
• CheckM: Pinned numpy to version 1.26.4 for compatibility with CheckM.
• Recognized Formats: Included .gbff as a recognized format.

Documentation

• Citation Update: Updated the citation information to the BGCFlow publication at NAR.

Tests

• Action Corrections:
  • Micromamba Version: Fixed the Micromamba version in tests.
  • Snakemake Version: Ensured tests use the Snakemake version from the wrapper.
  • NCBI Metadata: Updated the expected NCBI metadata for tests.
  • Build Test Updates: Dropped build tests for antiSMASH 6 and lsabgc.
  • Setuptools Compatibility: Pinned setuptools to versions below 70.0.0.

Full Changelog: v0.9.3...v1.0.0