v0.17.1

Highlights

Two correctness and usability fixes for atb query and atb download.

• --sample-file is fast again. atb query --sample-file now uses the SQLite index instead of falling back to a full-table scan, so it runs as fast as --samples (a minute-plus → ~0.1s for the reporter's 10 accessions). (#19)
• Clearer download vs. data directories. The --data-dir help no longer implies it controls where genomes are downloaded, and atb download --output-dir now shows its real default path and the config key that changes it. (#20)

Fixed

• atb query --sample-file now uses the fast SQLite index path instead of scanning the whole table. The index lookup read only the --samples slice and ignored accessions loaded from --sample-file, so a file-based query fell back to a full scan — the reporter's --sample-file run had not finished after a minute, versus ~0.1s for the same 10 accessions passed via --samples. Both sources are now merged and de-duplicated through Filters.SampleAccessions() before building the sample_accession IN (...) clause, so --sample-file and --samples perform identically. (#19)
• atb directory help no longer conflates the metadata index with genome downloads. --data-dir (and $ATB_DATA_DIR) govern only the local metadata index; atb download writes assemblies to the separate download.output_dir (-o/--output-dir). The --data-dir help now reads "directory for the local metadata index", and atb download --output-dir shows its effective default path and the download.output_dir config key. (#20)

Full changelog: v0.17.0...v0.17.1