v0.3.2

What's Changed

• MRG: update to sourmash-rs core r0.14.0 by @ctb in #52
• MRG: set zip permissions to 644 by @bluegenes in #53
• MRG: enable dayhoff, hp sketching by @bluegenes in #55
• bump version to 0.3.2 by @bluegenes in #54

Dependabot

• Bump tokio from 1.37.0 to 1.38.0 by @dependabot in #46

• Bump serde from 1.0.202 to 1.0.203 by @dependabot in #45

• Bump regex from 1.10.4 to 1.10.5 by @dependabot in #51

New Contributors

• @ctb made their first contribution in #52

Full Changelog: v0.3.1...v0.3.2

v0.3.1

• fixes URL formatting bug in failure output
• adds new urlsketch command
• changes failure output format for both gbsketch, urlsketch. The new header is: accession,name,moltype,md5sum,download_filename,url, which matches the urlsketch input format.

What's Changed

• fix url printing by @bluegenes in #36
• add urlsketch command by @bluegenes in #34

Dependabot and version updates

• Bump anyhow from 1.0.83 to 1.0.86 by @dependabot in #39
• Bump serde from 1.0.201 to 1.0.202 by @dependabot in #38
• Bump camino from 1.1.6 to 1.1.7 by @dependabot in #37
• bump version to 0.3.1 by @bluegenes in #43

Full Changelog: v0.3.0...v0.3.1

v0.3.0

This release fixes a bug where the wrong version may be downloaded #27.

The input format has changed slightly! Required columns are now: accession,name,ftp_path. ftp_path column name must be present, but column can be empty.

• if ftp_path is provided, it is used as the path for finding files associated with the accession. Otherwise, gbsketch will build the ftp_path from the accession.

What's Changed

• optionally use ftp_path input for gbsketch by @bluegenes in #29
• prevent unneccesary downloads by also setting genomes-only/proteomes-only via params if not keeping fastas by @bluegenes in #30
• do not require signature output file if not sketching by @bluegenes in #31

Full Changelog: v0.2.3...v0.3.0

v0.2.3

What's Changed

• fix ci by @bluegenes in #6
• revert channel sizes by @bluegenes in #23
• bump version to 0.2.3 by @bluegenes in #24

Full Changelog: v0.2.2...v0.2.3

v0.2.2

Bugfix Release

• fix a bug where md5sum file error caused directsketch to hang

What's Changed

• fix error handling by @bluegenes in #19
• Bump serde from 1.0.200 to 1.0.201 by @dependabot in #12
• Bump anyhow from 1.0.82 to 1.0.83 by @dependabot in #11
• Bump serde_json from 1.0.116 to 1.0.117 by @dependabot in #10

New Contributors

• @dependabot made their first contribution in #12

Full Changelog: v0.2.1...v0.2.2

v0.2.1

What's Changed

• changed progress reporting back from 5% --> 1%; adjusted to reflect start times better
• remove interval delay by @bluegenes in #16

Full Changelog: v0.2.0...v0.2.1

v0.2.0

Major changes:

• #8 - actually use tokio threading, fully asynchronous file downloading + writing
• #9 - download md5sums and check them prior to sketching
• #14 - make sure we return an error if the md5sum can't be downloaded (rather than just continuing)
• #15 - safer tokio thread/runtime setting while still allowing pytest to run multiple iterations at once

Benchmarking shows this structure is much faster

software/version	command	acc details	time	max RAM
v0.1.0	gbsketch	9 fungal	6min	156 MB
main (v0.2.0)	gbsketch	9 fungal	10s	156 MB
v0.1.0	gbsketch	49 fungal	58min	1.5 GB
main (v0.2.0)	gbsketch	49 fungal	1min 26s	1.6GB
main(v0.2.0)	gbsketch	243 fungal	4min	1.16GB

What's Changed

• check md5sums by @bluegenes in #9
• WIP: fully async with tokio threading by @bluegenes in #8
• return error if downloading md5sums fails by @bluegenes in #14
• safer tokio thread setting by @bluegenes in #15

Full Changelog: v0.1.0...v0.2.0

v0.1.0

Initial Release