Cypella

The main changes in this release is the overhaul of the 'report' API, which works much more nicely internally. Now, several kinds of reports are available on the command line, including:

• goat-cli taxon hist
• goat-cli taxon cat-hist
• goat-cli taxon scatter to be implemented! Once Rich does the hard work!

These commands echo the output used in the GoaT website to create the histogram and categorical histogram plots, which are really nice! You can tweak all the options you would be able to on the website.

In addition, there's a new flag on search -x or --exclude. You must supply one or more variable yourself for this to work. This flag excludes a row if it contains at least one missing or ancestral value. This is nice if you want to be absolutely sure you are only getting direct results back. See the difference for yourself between these two commands:

goat-cli taxon search -dt 'Eukaryota' -v 'c_value, ploidy'
goat-cli taxon search -dt 'Eukaryota' -v 'c_value, ploidy' -x

All versions of dependencies have been updated to the latest. This required quite the overhaul in the main command line parser dependency, clap.

Full git changelog below:

• Accurate help message for -x/exclude. Tue, 22 Nov 2022 18:44:04 +0000
• No panic on scatterplot invocation. Tue, 22 Nov 2022 18:33:08 +0000
• Update docs, and fix broken doc links. Tue, 22 Nov 2022 18:23:24 +0000
• Update variables 22.11.22 and bunp version. Tue, 22 Nov 2022 18:18:56 +0000
• Make clippy happier. Tue, 22 Nov 2022 18:18:14 +0000
• Fix links in README.md Tue, 8 Nov 2022 20:23:31 +0000
• Better description for function & update docs. Tue, 8 Nov 2022 19:38:35 +0000
• Update docs. Tue, 8 Nov 2022 18:01:25 +0000
• Update tabled dependency. Tue, 8 Nov 2022 17:33:01 +0000
• Update variable data for 07.11.22. Mon, 7 Nov 2022 23:27:25 +0000
• Update variable data for 07.11.22. Mon, 7 Nov 2022 23:23:03 +0000
• Update indicatif and clap dependencies. Mon, 7 Nov 2022 23:18:09 +0000
• Fixes #11. Add exclude as a flag to only return direct results (i.e. omit missing and ancestral values). Mon, 7 Nov 2022 23:13:17 +0000
• Update docs in report.rs Mon, 7 Nov 2022 21:33:29 +0000
• Add static lifetime to scale types. Tue, 18 Oct 2022 17:19:16 +0100
• Version update. Update dependencies (mainly clap). Update variables. Fri, 30 Sep 2022 18:03:02 +0100
• Remove empty file. Wed, 28 Sep 2022 17:31:27 +0100
• Add categorical histogram. Wed, 28 Sep 2022 17:28:04 +0100
• Major re-write of report API. Histogram reports added. Sat, 24 Sep 2022 21:04:47 +0100
• Update variables. Minor changes to get_vars.bash to get sed to run on Mac again. Sat, 17 Sep 2022 11:33:42 +0100
• rm .DS_Store Thu, 14 Jul 2022 18:28:27 +0100
• Update GoaT variables. Some need fixing. Thu, 14 Jul 2022 18:28:06 +0100

Arum

This release is quite big and breaking. As there are multiple indexes of the data in GoaT, we have introduced a structure to allow for changes indexes on the command line. The API currently looks like:

• goat-cli taxon <subcommand> for the taxon index
• goat-cli assembly <subcommand> for the assembly index

Thank you to @rjchallis for suggesting this change.

Other changes of note include removing --all flag from searches and counts, adding support for tax_lineage(), and fixing longstanding bug in the progress bars.

The official binary name is now goat-cli.

As always, please test and help us debug! I'm sure things have slipped through the net.

Full git changelog below:

• goat taxon/assembly search/count get -U flag to print the GoaT URL to the terminal window. Fri, 1 Jul 2022 16:06:47 +0100
• Change App name to goat-cli too. Fri, 1 Jul 2022 15:17:36 +0100
• Change binary name to goat-cli, in line with docs & crates.io. Fri, 1 Jul 2022 15:16:26 +0100
• Update docs. Fri, 1 Jul 2022 14:07:11 +0100
• Merge pull request #14 from genomehubs/assembly Fri, 1 Jul 2022 13:48:21 +0100
• Add goat-cli assembly lookup implementation. Thu, 30 Jun 2022 16:55:09 +0100
• Add goat-cli assembly lookup bare bones. Thu, 30 Jun 2022 13:55:32 +0100
• Version increase. Remove thiserror dep. Thu, 30 Jun 2022 09:27:51 +0100
• Update docs. Wed, 29 Jun 2022 17:27:20 +0100
• Remove up redundant files. Wed, 29 Jun 2022 17:23:33 +0100
• Variables and expressions work for assembly. Wed, 29 Jun 2022 17:21:46 +0100
• Adding assembly variables. Wed, 29 Jun 2022 16:31:36 +0100
• Working version of goat-cli assembly. Wed, 29 Jun 2022 15:26:40 +0100
• Add IndexType enum. Tue, 28 Jun 2022 12:00:22 +0100
• Change CLI to add taxon/assembly super-sub commands. Tue, 28 Jun 2022 10:00:09 +0100
• Update docs. Mon, 27 Jun 2022 16:59:44 +0100
• Code now compiles. Mon, 27 Jun 2022 16:58:42 +0100
• Remove all from flag options. Refactor field building. Mon, 27 Jun 2022 15:43:05 +0100
• Print expression works as expected now. Wed, 22 Jun 2022 17:10:56 +0100
• Fixes #13. Now a 15 random alphanumeric character string appends each query. Wed, 22 Jun 2022 16:22:57 +0100
• Fixes #9. Add support for tax_lineage. First pass anyway. Mon, 20 Jun 2022 14:54:00 +0100
• Update tabled dependency. Mon, 20 Jun 2022 13:53:57 +0100
• Remove record. Mon, 20 Jun 2022 10:18:06 +0100
• Fixes #12. Change record endpoint to report. Mon, 20 Jun 2022 10:16:10 +0100
• Fixes #8. API updated to version 2. Mon, 20 Jun 2022 09:56:49 +0100
• Make code more maintainable. Module system refactored. Fri, 22 Apr 2022 11:24:32 +0100
• New README.md image Fri, 22 Apr 2022 09:46:42 +0100

Nianhochloa

New minor release for tutorials.

• Suggestions in --expression not only in variable, but also in the value.
• This extends to type checking, and more useful errors in --expression.
• Minor addition to help, showing some links.

Thomsonaria

Another small release. Fixes a few bugs, adds a couple of features.

• Suggestions are now added to -v, --variable and -e, --expression flags, if there is a typo or a near miss.
• goat-cli newick now works (again). Small typo in URL generation.
• goat-cli lookup now returns search queries for multiple taxa correctly. Also accepts a file of taxids/taxa now.
• Documentation added.

This is the release that now appears on crates.io.

Sonderothamnus

• Fixes some parsing bugs
• Add progress bar as an option, not as an enforced feature. This means return times are quicker for smaller queries.
• Fix the binary name in clap as goat-cli was being used.

Bryocarpum

Minor release.

• Add some more enumerations to the keywords of some variables.
• Update tabled dependency.
• In line with the release on crates.io.

Pigafetta

This release updates only the author list.

Synandra

This release will be the first to be published on conda.

Additions:

• Reformat and edits to the command line argument parser
• Better error handling throughout
• Finalised expression, variable, and taxon rank parsers
• Small errors and bugs fixed
• Add GC percent as flag

Sacculina

This release add progress bars to hefty searches, in addition to a few more variables included in search.

0.1.2

Checks complete for Rust 1.56.1.