From 808da8cab2c8569eef3b428683b956ad580bc304 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 15 Oct 2021 13:06:41 -0400 Subject: [PATCH 1/6] Updated packages with `npm update`. --- package-lock.json | 1914 ++++++++++++++++++++++----------------------- 1 file changed, 955 insertions(+), 959 deletions(-) diff --git a/package-lock.json b/package-lock.json index a590bf4e..66d7b0e7 100644 --- a/package-lock.json +++ b/package-lock.json @@ -37,29 +37,38 @@ } }, "node_modules/@babel/code-frame": { - "version": "7.12.13", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.12.13.tgz", - "integrity": "sha512-HV1Cm0Q3ZrpCR93tkWOYiuYIgLxZXZFVG2VgK+MBWjUqZTundupbfx2aXarXuw5Ko5aMcjtJgbSs4vUGBS5v6g==", + "version": "7.15.8", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.15.8.tgz", + "integrity": "sha512-2IAnmn8zbvC/jKYhq5Ki9I+DwjlrtMPUCH/CpHvqI4dNnlwHwsxoIhlc8WcYY5LSYknXQtAlFYuHfqAFCvQ4Wg==", "dev": true, "dependencies": { - "@babel/highlight": "^7.12.13" + "@babel/highlight": "^7.14.5" + }, + "engines": { + "node": ">=6.9.0" } }, "node_modules/@babel/helper-validator-identifier": { - 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"strip-ansi": "^6.0.0" + "strip-ansi": "^6.0.1" } }, "strip-ansi": { - "version": "6.0.0", - "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.0.tgz", - "integrity": "sha512-AuvKTrTfQNYNIctbR1K/YGTR1756GycPsg7b9bdV9Duqur4gv6aKqHXah67Z8ImS7WEz5QVcOtlfW2rZEugt6w==", + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-6.0.1.tgz", + "integrity": "sha512-Y38VPSHcqkFrCpFnQ9vuSXmquuv5oXOKpGeT6aGrr3o3Gc9AlVa6JBfUSOCnbxGGZF+/0ooI7KrPuUSztUdU5A==", + "dev": true, "requires": { - "ansi-regex": "^5.0.0" + "ansi-regex": "^5.0.1" } } } @@ -9680,6 +9675,7 @@ "version": "18.1.3", "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-18.1.3.tgz", "integrity": "sha512-o50j0JeToy/4K6OZcaQmW6lyXXKhq7csREXcDwk2omFPJEwUNOVtJKvmDr9EI1fAJZUyZcRF7kxGBWmRXudrCQ==", + "dev": true, "requires": { "camelcase": "^5.0.0", "decamelize": "^1.2.0" From 924c4451dd9a6bab07292beed9842cc82e7dbf59 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 15 Oct 2021 13:07:13 -0400 Subject: [PATCH 2/6] Sorted scripts in package.json. --- package.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/package.json b/package.json index da4ae49d..1dfbc9e0 100644 --- a/package.json +++ b/package.json @@ -24,13 +24,13 @@ "resolve": "bin/resolve.js" }, "scripts": { - "lint": "eslint \"src/**/*.js\" \"test/**/*.js\" \"**/*.json\"", - "pretest": "npm run lint", - "test": "mocha --recursive", "docs": "esdoc", - "resolve": "node bin/resolve.js", "generate-every-topology": "every-topology-testing/generate-topologies.js", - "phyx2owl": "node bin/phyx2owl.js" + "lint": "eslint \"src/**/*.js\" \"test/**/*.js\" \"**/*.json\"", + "phyx2owl": "node bin/phyx2owl.js", + "resolve": "node bin/resolve.js", + "pretest": "npm run lint", + "test": "mocha --recursive" }, "dependencies": { "jsonld": "^5.0.0", From 1a33e15428b0270f6853e60f232fd4d863d57515 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 15 Oct 2021 13:21:13 -0400 Subject: [PATCH 3/6] Updated CHANGELOG. --- CHANGELOG.md | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index bcfffc3d..0cd2d0a2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,18 @@ The format is based on [Keep a Changelog] and this project adheres to [Semantic ## [Unreleased] +## [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 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 @@ -40,7 +52,8 @@ release of this package was based on [commit 14d2c3d5d1] in that repository. - 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. - [Unreleased]: https://github.com/phyloref/phyx.js/compare/v0.2.0...master + [Unreleased]: https://github.com/phyloref/phyx.js/compare/v1.0.1...master + [1.0.1]: https://github.com/phyloref/phyx.js/compare/v1.0.0...v1.0.1 [1.0.0]: https://github.com/phyloref/phyx.js/compare/v0.2.1...v1.0.0 [0.2.1]: https://github.com/phyloref/phyx.js/compare/v0.2.0...v0.2.1 [0.2.0]: https://github.com/phyloref/phyx.js/compare/v0.1.2...v0.2.0 From fed5956ffaa97ddadbf652a485d8f34c1b1672f7 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 15 Oct 2021 13:25:43 -0400 Subject: [PATCH 4/6] Updated timeout to 60s as 20s was timing out on GitHub Actions. --- test/jphyloref.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/jphyloref.js b/test/jphyloref.js index 8c005d3e..96da3890 100644 --- a/test/jphyloref.js +++ b/test/jphyloref.js @@ -56,7 +56,7 @@ describe('JPhyloRef', function () { .filter(filename => filename.endsWith('.nq')) .forEach((filename) => { it(`testing ${filename}`, function () { - this.timeout(20000); + this.timeout(60000); // Start JPhyloRef to test filename. const filePath = path.resolve(__dirname, 'examples', 'correct', filename); From 124734cca522d64068fdfe90edf21e400cdd2847 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 15 Oct 2021 13:28:19 -0400 Subject: [PATCH 5/6] Updated CHANGELOG. --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0cd2d0a2..50372d51 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ The format is based on [Keep a Changelog] and this project adheres to [Semantic - 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 From 8464a8644622025ee8a8505cf089e9df43eb4d55 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 18 Oct 2021 15:47:31 -0400 Subject: [PATCH 6/6] Updated version number. --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 1dfbc9e0..2062d7e9 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@phyloref/phyx", - "version": "1.0.0", + "version": "1.0.1", "description": "Classes and methods that help read and manipulate components of Phyloreference Exchange (PHYX) format files", "keywords": [ "phylogenetics",