Changelog

All notable changes to this library will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

1.1.1 - 2023-08-01

PR #133: Add guards to some usages of phyloref.internalSpecifiers/phyloref.externalSpecifiers.
PR #136: Improved GitHub test action, including changing Node versions.
PR #127: Upgraded Newick.js to ^1.2.1. This means that we no longer support Node.js v10.x, which end-of-lifed on April 30, 2021.

1.1.0 - 2023-05-11

PR #129: Added curator notes to phylorefs and phylogenies.
PR #128: Added citation to README and a CITATION.CFF file.
PR #125: Added curator information as contributors to Phyx file.

1.0.1 - 2021-10-15

Created a tutorial for using phyx.js, including:
- PR #99: Add tutorial.
- PR #103: Improve integration of the tutorial.
- PR #109: Add resolve.js instructions to Introduction tutorial.
Improvements to README files, including:
- PR #108: Added links to published JSON-LD contexts and JSON schemas.
- PR #110: Added note that Binder cannot be used.
- PR #111: Changes link to tutorials to directory.
PR #106: Fixed typo in resolve.js.
Updated timeout to 60s as 20s was timing out on GitHub Actions.
Updated NPM packages and resorted packages in package.json.

1.0.0 - 2021-03-16

Many changes across the entire library.
Two new scripts: bin/phyx2owl.js for converting a Phyx file into OWL/JSON-LD and bin/resolve.js to resolve a Phyx file on the Open Tree of Life.
Incorporation of JPhyloRef into testing.
Fixed a bug in which phyloref and phylogeny @id values were being overwritten when generating JSON-LD.
Added scripts to generate every possible topology from n=2 to n=6 with expected resolution and to test them with JPhyloRef.

0.2.1 - 2019-08-15

Updated all NPM packages to their latest version.
Fixed a bug in which node's types were not being correctly set to obo:CDAO_0000140.

0.2.0 - 2019-07-18

Changed

The single index.js has been split into multiple files, one per class, with documentation using ESdocs (#21).
Added support for generating "model 2.0" ontologies, which can be reasoned over in an OWL 2 EL reasoner such as Elk (#4). As part of this change, specifiers have been changed so that they are taxonomic units, rather than containing taxonomic units and a new Phyx context file has been created (#19).
Taxonomic units have been cleaned up, are clearly typed, and taxonomic names now include nomenclatural codes (#18) and support trinomial names (#22).

0.1.2 - 2019-02-08

Added

Moved Phyx context file for JSON-LD into this repository from the Curation Tool and changed URI to point to it.

0.1.1 - 2019-02-06

Added

A replacement for the Phylotree.js Newick parser.

0.1.0 - 2019-01-27

Added

Transfered initial code from the Phyloreference Curation Tool. The initial release of this package was based on commit 14d2c3d5d1 in that repository.

Changed

Replaced references to the phylotree library with the newick-js library.
Made other changes to the initial code as needed to work as an independent NPM package.