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

1.2.1 - 2025-07-28

• PR #152: Upraded packages using npm upgrade.

1.2.0 - 2025-03-10

• PR #138: Added normalization methods so that Phyx objects can be normalized.
• PR #139: upgraded NPM packages and minor test fixes
• PR #143: Replaced dwc:basisOfRecord to basisOfRecord
• PR #144: Add links to our npmjs URL
• PR #148: Correct empty occurenceID so that it is blank, not urn:catalog:::

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.