Sourmash-plugin-directsketch

What's Changed

This release includes a bugfix where using a zipfile without an explicit path would yield an error (118). The remaining changes are internal, including adding parameter string validation and improving the sketching utilities for potential use in other plugins.

* MRG: refactor sketching utilities by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/112
* MRG: validate param strings by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/114
* MRG: update sourmash core to 0.16.0 by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/115
* MRG: fix bug in zip paths if output provided in current dir by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/121
* bump to 0.4.1 by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/128


dependabot
* Bump reqwest from 0.12.7 to 0.12.8 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/110
* Bump futures from 0.3.30 to 0.3.31 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/111
* Bump pyo3 from 0.22.3 to 0.22.5 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/122
* Bump anyhow from 1.0.89 to 1.0.90 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/126
* Bump serde_json from 1.0.128 to 1.0.132 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/124
* Bump openssl from 0.10.66 to 0.10.68 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/125

**Full Changelog**: https://github.com/sourmash-bio/sourmash_plugin_directsketch/compare/v0.4.0...v0.4.1

This release introduces two new parameters:
- `--checksum-failures` - an output file to log any failures with the checksum file download and parsing or any md5sum mismatches. Required for `gbsketch`
- `--batch-size` - enables writing smaller, batched zipfiles. This is recommended for large database generation, as batches allow restart after unexpected failure. It also should address some issues arising from extremely large zips.

Under the hood, this release also introduces a standardized sketching building framework that may be useful outside of this plugin.

What's Changed

* MRG: report checksum file download failures by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/92
* MRG: add generic support for signature building by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/101
* MRG: improve restart by optionally writing batched zipfiles by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/102
* MRG: fix ci by moving install from `mambaforge` --> `miniforge` by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/106
* bump to v0.4.0 by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/109

Dependabot
- `sourmash-core`:
* Bump sourmash from 0.14.0 to 0.14.1 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/62
* Bump sourmash from 0.14.1 to 0.15.0 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/75
* Bump sourmash from 0.15.0 to 0.15.1 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/87
* Bump sourmash from 0.15.1 to 0.15.2 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/103
- `simple-error`:
* Bump simple-error from 0.3.0 to 0.3.1 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/59
- `reqwest`:
* Bump reqwest from 0.12.4 to 0.12.5 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/60
* Bump reqwest from 0.12.5 to 0.12.7 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/88
- `lazy_static`:
* Bump lazy_static from 1.4.0 to 1.5.0 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/61
- `pyo3`:
* Bump pyo3 from 0.21.2 to 0.22.0 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/64
* Bump pyo3 from 0.22.0 to 0.22.1 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/66
* Bump pyo3 from 0.22.1 to 0.22.2 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/73
* Bump pyo3 from 0.22.2 to 0.22.3 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/99
- `serde_json`:
* Bump serde_json from 1.0.117 to 1.0.119 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/63
* Bump serde_json from 1.0.119 to 1.0.120 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/67
- `serde`:
* Bump serde from 1.0.203 to 1.0.204 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/65
- `tokio`:
* Bump tokio from 1.38.0 to 1.38.1 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/74
* Bump tokio from 1.38.1 to 1.40.0 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/91
- `pytest`:
* Update pytest requirement from <8.3.0,>=6.2.4 to >=6.2.4,<8.4.0 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/71
- `openssl`:
* Bump openssl from 0.10.64 to 0.10.66 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/72
- `regex`:
* Bump regex from 1.10.5 to 1.10.6 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/80
* Bump regex from 1.10.6 to 1.11.0 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/104
- `anyhow`:
* Bump anyhow from 1.0.86 to 1.0.89 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/100




**Full Changelog**: https://github.com/sourmash-bio/sourmash_plugin_directsketch/compare/v0.3.2...v0.4.0

What's Changed
* MRG: update to sourmash-rs core r0.14.0 by ctb in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/52
* MRG: set zip permissions to 644 by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/53
* MRG: enable dayhoff, hp sketching by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/55
* bump version to 0.3.2 by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/54

Dependabot
* Bump tokio from 1.37.0 to 1.38.0 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/46
* Bump serde from 1.0.202 to 1.0.203 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/45

* Bump regex from 1.10.4 to 1.10.5 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/51


New Contributors
* ctb made their first contribution in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/52

**Full Changelog**: https://github.com/sourmash-bio/sourmash_plugin_directsketch/compare/v0.3.1...v0.3.2

- 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 https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/36
* add `urlsketch` command by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/34

Dependabot and version updates
* Bump anyhow from 1.0.83 to 1.0.86 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/39
* Bump serde from 1.0.201 to 1.0.202 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/38
* Bump camino from 1.1.6 to 1.1.7 by dependabot in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/37
* bump version to 0.3.1 by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/43


**Full Changelog**: https://github.com/sourmash-bio/sourmash_plugin_directsketch/compare/v0.3.0...v0.3.1

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 https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/29
* prevent unneccesary downloads by also setting genomes-only/proteomes-only via params if not keeping fastas by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/30
* do not require signature output file if not sketching by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/31


**Full Changelog**: https://github.com/sourmash-bio/sourmash_plugin_directsketch/compare/v0.2.3...v0.3.0

What's Changed
* fix ci by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/6
* revert channel sizes by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/23
* bump version to 0.2.3 by bluegenes in https://github.com/sourmash-bio/sourmash_plugin_directsketch/pull/24


**Full Changelog**: https://github.com/sourmash-bio/sourmash_plugin_directsketch/compare/v0.2.2...v0.2.3