v1.0.0

1.0.0 - 2026-07-24

First stable release. genome-dl resolves and downloads genome assemblies from
NCBI, written as a drop-in replacement for ncbi-genome-download. Resolution and
metadata come from the NCBI Datasets v2 REST API (immune to the
assembly_summary.txt column breakage that retired ngd); sequence files are
downloaded directly from the NCBI FTP site, where they are already gzipped and
md5-verifiable.

Added

• Three ways to select assemblies (exactly one required): --accession for a
  single accession, --accessions for a file of accessions (one per line), and
  --species for a taxon name.

• Taxon queries with --section {refseq,genbank,all}, --assembly-level
  (complete,chromosome,scaffold,contig or all), and --limit (the first N
  assemblies in NCBI relevance order, reference genome first; 0 for all).

• 13 downloadable formats via --formats (comma-separated, or all), each
  written flat as {ACCESSION}.{ext}:

  Format	Output extension
  fasta	.fna.gz
  genbank	.gbff.gz
  wgs	.wgsmaster.gbff.gz
  gff	.gff.gz
  gtf	.gtf.gz
  protein	.faa.gz
  genpept	.gpff.gz
  cds	.cds.fna.gz
  translated-cds	.translated_cds.faa.gz
  rna	.rna.fna.gz
  feature-table	.feature_table.txt.gz
  assembly-report	.assembly_report.txt
  assembly-stats	.assembly_stats.txt

• Version-pin policy. A versionless accession selects the current version; an
  explicit outdated pin (e.g. GCF_x.1 when .2 is current) is refused by
  default with a message naming the current version, and honored exactly with
  --allow-outdated. Suppressed versions always error.

• Integrity checks. Every download is verified against the FTP
  md5checksums.txt manifest and its Content-Length; --ignore skips md5 but
  still guards against truncated streams. --force re-downloads existing files.

• Concurrent, resilient downloads. --cpus parallel FTP workers with a
  per-file retry loop (--max-attempts, --sleep backoff). Transient errors
  (5xx, rate-limits, connection drops) are retried; permanent errors (4xx) fail
  fast. Partial successes are kept and reported. Ctrl-C cancels queued work and
  lets in-flight files finish (press again to force-quit).

• Run outputs. A metadata TSV (columns adapt to the infraspecific fields
  present in the run), a human-readable run summary, and a machine-readable JSON
  report. --json emits the report to stdout for piping; --dry-run lists
  targets without downloading.

• API key support via the NCBI_API_KEY environment variable, which raises
  the Datasets API rate limit from 5 to 10 requests/second. The key is never
  written to output files or attached to FTP traffic.

• Ergonomics. --outdir/--prefix for output location and naming,
  --progress for a live progress display, and --silent/--verbose log
  levels. Case-insensitive and de-duplicated --formats/--assembly-level.

• Exit-code contract for scripting: 0 success, 1 validation / API /
  download error, 2 not found / empty result / unrecognized taxon, 3 partial
  download.

Requirements

• Python 3.11–3.13.