v1.8.0 - Robust Reference Handling

What's New

Highlights

• New CLI flags for explicit reference paths (--nuc-ref, --aa-ref)
• Environment variable support (NUC_REF, AA_REF)
• XDG-compliant caching for LAPIS-fetched references (~/.cache/sr2silo/references/)
• Major documentation overhaul with new logo and improved structure

Features

• Add --nuc-ref and --aa-ref CLI flags for explicit reference file paths
• Support NUC_REF and AA_REF environment variables for reference configuration
• Use ~/.cache/sr2silo/references/ for LAPIS-fetched references (XDG-compliant)
• Move timeline_columns.yml inside package using importlib.resources
• Add NUC_REF/AA_REF support to Snakemake workflow
• Workflow conda environment now includes sr2silo>=1.8.0

Reference Resolution Priority

1. CLI flags (--nuc-ref, --aa-ref)
2. Environment variables (NUC_REF, AA_REF)
3. LAPIS auto-fetch with caching

Bug Fixes

• Fix full URL path for multi-virus reference directories
• Fix non-user specific path handling
• Handle Snakemake exit codes for smarter job resubmission

Documentation

• Overhaul MkDocs documentation with new logo and styling
• Streamline README
• Add new API documentation pages (process, schema, vpipe)

Breaking Changes

• Genomic references moved from resources/references/ to examples/references/

Full Changelog: v1.7.0...v1.8.0