v0.5.0

This release include some major functionality changes:

• Download via NCBI REST API for gbsketch. Input file no longer uses ftp_path.
• add --n-simultaneous-downloads parameter, and allow up to 10 if using an API KEY with gbsketch
• Allow merged & ranged sketching in urlsketch
• Enable building skipmer signatures (skipm1n3, skipm2n3; sourmash experimental addition)

And some nice UX updates:

• use input csv as default base filename for --fail and --checksum-fail
• ignore extra columns in gbsketch input CSV

It also fixes a bug where directsketch zips did not properly record n_hashes and thus did not get properly summarized via sourmash sig summarize.

This release includes first content contributions from @ctb 🎉 .

What's Changed

Functionality updates

• MRG: modify n simultaneous downloads; update buildutils by @bluegenes in #154
• MRG: add skipmer sketching by @bluegenes in #159
• MRG: fix manifest n_hashes + test by @bluegenes in #171
• MRG: Enable merged sigs, sequence range selection in urlsketch by @bluegenes in #161
• MRG: batched zip reporting - notify after finishing batch to be clearer by @bluegenes in #179
• MRG: download via NCBI REST API by @bluegenes in #181
• MRG: doc rerunning failures by @bluegenes in #184
• MRG: set n-simultaneous-downloads to 9 if api key provided by @ctb in #194
• MRG: provide default failed filenames based on CSV by @ctb in #195
• MRG: ignore extra columns in gbsketch input CSV by @ctb in #188

Developer updates

• MRG: remove BuildParams, filter via manifest / Select approaches by @bluegenes in #127
• try fixing ci by @bluegenes in #157
• upd sourmash core to 0.17.2 by @bluegenes in #156
• bump version; add ctb to authors by @bluegenes in #199

dependabot

• Bump tokio from 1.40.0 to 1.41.0 by @dependabot in #130
• Bump pyo3 from 0.22.5 to 0.23.3 by @dependabot in #151
• Bump tokio from 1.41.0 to 1.42.0 by @dependabot in #150
• Bump reqwest from 0.12.8 to 0.12.9 by @dependabot in #136
• Bump regex from 1.11.0 to 1.11.1 by @dependabot in #133
• Bump tokio-util from 0.7.12 to 0.7.13 by @dependabot in #149
• Bump anyhow from 1.0.90 to 1.0.94 by @dependabot in #152
• Bump serde_json from 1.0.132 to 1.0.134 by @dependabot in #162
• Update pytest-cov requirement from <6.0,>=2.12 to >=2.12,<7.0 by @dependabot in #135
• Bump anyhow from 1.0.94 to 1.0.95 by @dependabot in #163
• Bump reqwest from 0.12.9 to 0.12.12 by @dependabot in #169
• Bump serde from 1.0.216 to 1.0.217 by @dependabot in #167
• Bump tokio from 1.42.0 to 1.43.0 by @dependabot in #176
• Bump pyo3 from 0.23.3 to 0.23.4 by @dependabot in #178
• Bump serde_json from 1.0.134 to 1.0.135 by @dependabot in #177
• Bump serde_json from 1.0.135 to 1.0.137 by @dependabot in #190
• Bump getset from 0.1.3 to 0.1.4 by @dependabot in #197
• Bump openssl from 0.10.68 to 0.10.69 by @dependabot in #196

Full Changelog: v0.4.1...v0.5.0