For version 4.0, the CLI was reimplemented in node. This should make it easier to install for users and easier to maintain for developers.

All commands use the same syntax, so switching shouldn't be a big problem. For a detailed list of changes, see #172

This release adds support for the new unipept protinfo command. More information can be found here: https://unipept.ugent.be/clidocs/protinfo.

• [Fixed] an issue with the uniprot command due to a change with the UniProtKB website

• [Added] psych as an explicit dependency, hopefully fixing #120

This release switches to the Unipept API v2. There are only minimal changes, but scripts using the output of this tool might break (which is why we bumped the major version number).

More specifically, when requesting the full lineages there are some changes to the ranks that are returned: strain was added and some uncommon ranks such as parvorder were removed. The exact details can be found in this pull request: unipept/unipept#1409

• [Updated] dependencies
• [Improved] explicit support ruby 3.0 and 3.1
• [Removed] support for ruby 2.5 and 2.6

• [Fixed] a small bug related to the batch size

• Add the taxa2tree command to generate a hierarchical json of the taxonomy. The command can also return an HTML view that shows a visualisation.

• Follow redirects for requests

Added pept2interpro, updated dependencies and fixed some bug where not all functional annotations were returned (#63).