v0.7.3

Minor new features:

• add taxonomy output via sourmash tax on the gather results (#100)
• add a gather-only summary step (#99)
• update to use sourmash picklists and manifests for significant decrease in disk space, increase in speed (#94, #103)
• make missing config options clearer (#102)
• add CLI usage info (#90)
• re-try logscale and gridlines to new figure 10 (#87)
• add per-genome coverage & abundance reporting (#85)

Developer fixes:

• add sourmash to the papermill environment (#111)
• Update Snakemake version (#106)
• update dependencies in setup.py and environment.yml (#89)

Documentation updates:

• change default targets and update help docs (#101)
• fix README for new targets (#109)

v0.7.2

Update to sourmash 4.1.1, downgrade sra-tools, use lower-memory signature outputs, and output a prefetch CSV (#83).

v0.7.1

Many significant improvements to internals; no major new features.

• use fasterq-dump instead of fastq-dump to enable multithreaded downloads (#75)
• usesourmash prefetch from sourmash v4.1.0 (#68)
• use scratch instead of tmp (#76)
• use fastp instead of trimmomatic (#72)
• use temp directory so snakemake automatically deletes temp files (#71)
• add mamba to environment yml; update sourmash to 4.x (#74)
• update sourmash and screed versions; turn on python -Werror (#67)

v0.7

New features

• Add more reporting for output read/kmer stats (#56); add tests for new reporting (#65)

Fixes, updates, and refactors

• Fix abundance calculations (#64)
• GitHub actions update; sync with screed setup (#58)
• Change ftp to https for genome downloads (#57)
• Adjust memory requirements; update README with quickstart tutorial, memory requirements and other text (#54)

v0.6.1

Fix issues for a non-developer install.

v0.6

Provide an end-to-end workflow with checkpoints; many minor improvements.

v0.5

Much cleaning, more good. Testing, also good.

v0.4

Add prefetching of containment matches to speed up gather (#16)
Add tests and github actions for CI (#19)

v0.3.2

minor fixes to installation, updates to README.

v0.3.1

Minor fixes to docs, setup.py.