Merge pull request #127 from phyloref/upgrade-to-es6

This PR upgrades newick-js to v1.2.1, which requires some minor changes to how we call it. Newick-js v1.2.1 no longer works with Node.js v10.x, which makes sense -- it was EOL in April 2021. So this PR also removes that from the Node.js versions we test against.

.github/workflows/tests.yml

@@ -13,7 +13,7 @@ jobs:
 
     strategy:
       matrix:
-        node-version: [10.x, 12.x, 14.x]
+        node-version: [12.x, 14.x]
 
     steps:
     - uses: actions/checkout@v2

CHANGELOG.md

@@ -4,6 +4,8 @@ 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]
+- 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.

package.json

@@ -36,7 +36,7 @@
     "jsonld": "^5.0.0",
     "lodash": "^4.17.20",
     "moment": "^2.27.0",
-    "newick-js": "1.1.1",
+    "newick-js": "^1.2.1",
     "retus": "^1.1.1",
     "yargs": "^15.4.1"
   },

src/wrappers/PhylogenyWrapper.js

@@ -5,7 +5,7 @@
 const { has } = require('lodash');
 
 /** Used to parse Newick strings. */
-const parseNewick = require('newick-js').parse;
+const newickJs = require('newick-js');
 
 /** OWL terms to be used here. */
 const owlterms = require('../utils/owlterms');
@@ -73,9 +73,9 @@ class PhylogenyWrapper {
       });
     }
 
-    // Finally, try parsing it with parseNewick and see if we get an error.
+    // Finally, try parsing it with newickJs.parse() and see if we get an error.
     try {
-      parseNewick(newickTrimmed);
+      newickJs.parse(newickTrimmed);
     } catch (ex) {
       errors.push({
         title: 'Error parsing phylogeny',
@@ -152,7 +152,7 @@ class PhylogenyWrapper {
     // - 'both': Return node labels on both internal and terminal nodes.
 
     // Parse the phylogeny (will throw an exception if parsing failed).
-    const { graph } = parseNewick(this.phylogeny.newick || '()');
+    const { graph } = newickJs.parse(this.phylogeny.newick || '()');
     const [vertices, arcs] = graph;
 
     if (nodeType === 'both') {
@@ -252,7 +252,7 @@ class PhylogenyWrapper {
     // This method provides a similar facility using the newick-js library.
     //
     // Throws an exception if the Newick could not be parsed.
-    const { graph, root, rootWeight } = parseNewick(newick);
+    const { graph, root, rootWeight } = newickJs.parse(newick);
     const [, arcs] = graph;
 
     // Go through the arcs, assigning 'children' to the appropriate parent node.