chore!: upgrade to jquery 3 (#1169)

* fix: jquery-migrate 1.4.1 deprecations

* wip: update jQuery to v3

* fixup

* chore!: remove biojs

* chore: update dependencies

* feat: update katex to v0.16

* feat: update mf-parser to v3.6.0

* chore: update eslint config

* feat: update fontawesome to v7.0.0

* feat: update mathjs to v14.6.0

* chore: do not update conventional-changelog

* chore: remove unused d3-hierarchy

* feat: update mime-types to v3.0.1

* feat: update semver to v7.7.2

* chore: update dependencies

* feat: update superagent to v10.2.3

* chore: update dependencies

* feat: update jsbarcode to v3.12.1

* refactor: move fancytree to npm dependencies

* refactor: move numeral to npm dependencies

* feat: update leaflet to v1.9.4 and move it to package.json

* refactor: move moment to npm dependencies

* refactor: move marked to npm dependencies

* refactor: move pouchdb to npm dependencies

* refactor: move papaparse to npm dependencies and update to v5

* refactor: move requirejs to npm dependencies

* refactor: move json-chart to npm dependencies

* chore: update dependencies

* fix: use correct debug version

* chore: update dependencies

* chore: update dependencies

* chore: update dependencies

* chore: update eslint config

* fixup: correct fancytree import

* chore: fix build

do not use superagent in init bundle and remove phantom babel dependency

* fix: use newer version of jquery.event.drag and jquery.event.drop modules

Those are compatible with jquery 3

* fix: update position of select fields in libform's group table element
There is a breaking change in jquery in how offset positions are calculated. Previously using jquery method `offsetParent()`, now using native `offsetParent` instead which considers different offset parents.

* chore: eslint fix

* fix: restore closing of color selector on palette select

* docs: better testcase slick grid update preferences

* docs: dedupe testcase

* docs: remove non-working testcase which relies on visualizer-helper

* docs: move slickgrid testcases to slickgrid folder

* docs: add slickgrid reorder rows testcase

* docs: add failing panzoom example

* fix: update panzoom to a version compatible with jquery v3

* chore: jquery-mousewheel is no longer needed with panzoom update

* docs: add panzoom overlay example in testcase

* docs: better fancytree testcase

* docs: remove dummy testcase

the dummy_module module does not exist anymore

* fix: correct show / hide column implementation

* fix: do not load removed jquery-mouswheel in loading_plot

* fix: remove fabtastic dependency

Change color picker in favor of spectrum everywhere

fixes canvas_matrix, pie_chart, leaflet, dendrogram, loading_plot and spectra_displayer

* docs: improve slickgrid testcases

* fix: correct jquery updating breaking well-plate module

* fix: correct use of `this` in $.Deferred

* docs: update phylogram testcases

* fix: correct hexagonal chart module

* docs: add panzoom example with SVG

* fix: correct reference to module id

* fixup: refactor and correct canvas matrix drag handling

Remove jquery dependency jquery.threedubmedia

* fix(pie_chart_jit): do not use non-existing configuration options

* fix: resolve race condition which can lead to failed module instantiation

The problem is problably related to jquery changing their promise implementation to be spec compliant.

To reproduce:
- Instantiate code editor
- Instantiate code executor

Results (most of the time) in a crash, or a code executor component which does not have a label on its button.

* chore: remove log and unused var

* update dependencies

* fixup: cleanup event listener in matrix module

* fix: correct loading date in slick editor and use native date picker instead of jquery UI

* chore: fix jquery deprecations in drag and drop module

* chore: remove console.log

---------

Co-authored-by: Daniel Kostro <kostro.d@gmail.com>

Author: targos

.ncurc.yml

@@ -4,3 +4,7 @@ reject:
   - delay
   # Now ESM and depends on top-level await.
   - tempfile
+  # Version 7 had breaking changes not worth the effort.
+  - conventional-changelog
+  # Version 2.0.3 made a breaking change with whitespaces: https://github.com/slab/quill/issues/4509
+  - quill

bower.json

@@ -12,61 +12,36 @@
   },
   "license": "MIT",
   "dependencies": {
-    "ace": "ajaxorg/ace-builds#v1.4.6",
-    "async": "2.1.4",
-    "babel-standalone": "6.19.0",
-    "bowser": "1.0.0",
+    "ace": "ajaxorg/ace-builds#v1.43.2",
     "chroma-js": "1.1.1",
     "ckeditor": "4.7.3",
     "colors": "3.0.0",
     "d3": "3.5.17",
-    "d3-plugins": "cheminfo/d3-plugins#ea652308c616f3accde0a418f7ccc6254a932985",
     "eventEmitter": "^5.2.3",
-    "fancytree": "2.20.0",
-    "farbtastic": "2.0.0-alpha.1",
-    "fetch": "2.0.1",
     "file-saver.js": "cheminfo-js/file-saver.js#6a90cb37e56fbb110f03c70c90ebceb9312650db",
     "flag-icon-css": "2.8.0",
     "jit": "2.0.2",
     "jqgrid_edit": "git://github.com/NPellet/jqGrid#4.5.6",
-    "jquery": "2.2.4",
-    "jquery-cookie": "1.4.1",
-    "jquery-mousewheel": "3.1.13",
     "jquery-qrcode": "cheminfo/jquery-qrcode#efece6cf4e32d1151436a146a2ac0e2197e0837b",
     "jquery-tmpl": "BorisMoore/jquery-tmpl#vBeta1.0.0",
-    "jquery-ui": "1.12.1",
-    "jquery.panzoom": "cheminfo/jquery.panzoom#626f65a0180211aafc9b5d57696ac56350be6bf1",
-    "jquery.threedubmedia": "git://github.com/threedubmedia/jquery.threedubmedia",
-    "jsbarcode": "3.5.7",
+    "jquery.panzoom": "cheminfo/jquery.panzoom#8fea7dc6539cc414419818956d8102ed47dea94b",
     "jsgraph": "2.2.36",
     "jsme": "bcdc8f0d475eb72c2d75d20afae0b7ca4ebde273",
     "jsmol": "v1.2.0",
-    "json-chart": "1.1.0",
-    "jsoneditor": "5.5.11",
     "jszip": "3.1.3",
-    "leaflet": "1.0.2",
-    "leaflet-omnivore": "0.3.2",
     "lodash": "4.17.5",
     "loglevel": "1.4.1",
-    "marked": "0.3.6",
     "ml": "0.2.1",
-    "modernizr": "2.8.3",
-    "moment": "2.17.1",
-    "moment-duration-format": "~1.3.0",
     "nmr-simulation": "0.2.1",
     "notifyjs": "0.4.2",
-    "numeral": "2.0.6",
-    "onde": "cheminfo/onde#126c1571a3b212abbefb5351ad9b192cef35e7a1",
-    "papa-parse": "4.1.2",
-    "pouchdb": "3.3.1",
-    "requirejs": "2.3.6",
+    "onde": "cheminfo/onde#9ed3407d02ca323b8dce8d2456eb54b49a804344",
     "select2": "4.0.3",
     "setImmediate": "YuzuJS/setImmediate#1.0.5",
     "slickgrid": "cheminfo/SlickGrid#6423d3d4c9e09180ad83a9166d149e3e4124320d",
-    "spectrum": "1.8.0",
-    "sprintf": "1.0.3",
+    "spectrum": "101b05c1d977fbc529ae4c3b6865b1f7ab70c6e0",
+    "sprintf": "1.1.3",
     "threejs": "r71",
-    "ui-contextmenu": "1.14.0",
+    "ui-contextmenu": "1.18.1",
     "uri.js": "1.18.4",
     "web-animations-js": "2.2.2",
     "x2js": "1.2.0",
@@ -75,7 +50,6 @@
   },
   "resolutions": {
     "jsgraph": "2.2.36",
-    "jquery": "2.2.4",
     "eventEmitter": "^5.1.0"
   },
   "private": true

eslint.config.mjs

@@ -22,6 +22,9 @@ export default defineConfig(
   {
     rules: {
       'unicorn/consistent-function-scoping': 'off',
+      'unicorn/no-array-reverse': 'off',
+      'unicorn/no-array-sort': 'off',
+      'unicorn/no-immediate-mutation': 'off',
       'unicorn/no-this-assignment': 'off',
       'unicorn/prefer-code-point': 'off',
       'unicorn/prefer-default-parameters': 'off',

gruntfile.js

@@ -191,22 +191,11 @@ module.exports = function (grunt) {
             cwd: './src/components/',
             src: [
               './d3/d3*',
-              [
-                './fancytree/dist/jquery.fancytree*.js',
-                './fancytree/dist/skin-lion/*',
-              ],
               [
                 './jqgrid_edit/js/*.js',
                 './jqgrid_edit/js/i18n/grid.locale-en.js',
                 './jqgrid_edit/css/*.css',
               ],
-              './jquery/dist/*',
-              [
-                './jquery-ui/ui/*.js',
-                './jquery-ui/ui/effects/*.js',
-                './jquery-ui/ui/widgets/*.js',
-                './jquery-ui/themes/base/**',
-              ],
               './threejs/build/three.min.js',
               './ace/src/**',
               [
@@ -219,66 +208,38 @@ module.exports = function (grunt) {
                 './ckeditor/plugins/**',
                 './ckeditor/config.js',
               ],
-              './farbtastic/src/farbtastic.js',
-              './jquery.threedubmedia/event.drag/jquery.event.drag.js',
               './sprintf/dist/**',
-              './requirejs/require.js',
               './x2js/xml2json*',
-              [
-                './leaflet/dist/**',
-                './leaflet-omnivore/leaflet-omnivore.min.js',
-              ],
-              './jsoneditor/dist/**',
               './jit/Jit/**/*',
               './ui-contextmenu/jquery.ui-contextmenu*',
-              './papa-parse/papaparse*',
               './colors/css/colors.min.css',
-              './pouchdb/dist/**',
               './uri.js/src/*.js',
               './onde/src/*',
               ['./spectrum/spectrum.js', './spectrum/spectrum.css'],
-              './superagent/superagent.js',
-              './modernizr/modernizr.js',
               './lodash/dist/**',
-              './bowser/bowser*',
-              './jquery-cookie/jquery.cookie.js',
               './chemcalc/lib.js',
               './jsgraph/dist/**',
               './jsme/**',
               './jsmol/**',
               './jcampconverter/*',
-              './jsbarcode/dist/*.js',
               './slickgrid/**',
               './ml/dist/*',
               './jquery-tmpl/**',
               './setImmediate/setImmediate.js',
               './chroma-js/chroma*',
-              './async/dist/**',
               './loglevel/dist/**',
-              './marked/lib/marked.js',
               './highlight.js/build/highlight.pack.js',
               './jquery.panzoom/dist/*.js',
-              './jquery-mousewheel/*.js',
               './select2/dist/**',
               './jszip/dist/**',
               './file-saver.js/*.js',
-              './json-chart/dist/*',
-              './d3-plugins/**',
-              './mime-types/**',
               './notifyjs/dist/**',
               './web-animations-js/*.js',
               './web-animations-js/*.js.map',
-              './moment/moment*',
-              './moment-duration-format/lib/moment-duration-format.js',
-              './numeral/numeral*',
               './flag-icon-css/css/flag-icon.min.css',
               './flag-icon-css/flags/**',
               './jquery-qrcode/jquery.qrcode.min.js',
-              './mathjs/dist/**',
               './nmr-simulation/**',
-              './katex/dist/**',
-              './babel-standalone/**',
-              './fetch/fetch.js',
               './js-yaml/dist/**',
               './canvg/dist/**',
               './eventEmitter/*.js',
@@ -289,18 +250,36 @@ module.exports = function (grunt) {
             expand: true,
             cwd: './node_modules',
             src: [
-              './katex/dist/**',
               './angularplasmid/dist/**',
-              './mathjs/dist/math.min.js',
-              './mathjs/dist/math.min.map',
+              './jquery/dist/*',
+              [
+                './jquery.fancytree/dist/modules/jquery.fancytree*.js',
+                './jquery.fancytree/dist/skin-lion/*',
+              ],
+              ['./jquery-ui/dist/*.js', './jquery-ui/themes/base/**'],
+              './jsbarcode/dist/*.js',
+              './jsoneditor/dist/**',
+              './jquery-migrate/dist/*',
+              './katex/dist/**',
+              [
+                './leaflet/dist/**',
+                './@mapbox/leaflet-omnivore/leaflet-omnivore.min.js',
+              ],
+              './marked/lib/marked.js',
+              './mathjs/lib/browser/**',
+              './moment/moment.js',
+              './moment-duration-format/lib/moment-duration-format.js',
+              './numeral/min/numeral.min.js',
               './openchemlib/dist/**',
+              './papaparse/papaparse*',
+              './pouchdb/dist/**',
               [
                 './quill/dist/*.js*',
                 './quill/dist/*.css',
                 './quill-resize-module/dist/resize.*',
                 './quill-table-better/dist/quill-table-better.*',
               ],
-              './d3-hierarchy/dist/d3-hierarchy.min.js',
+              './requirejs/require.js',
               './@fortawesome/fontawesome-free/css/all.min.css',
               './@fortawesome/fontawesome-free/webfonts/*',
             ],
@@ -459,7 +438,7 @@ module.exports = function (grunt) {
           modules: [
             {
               name: 'init',
-              exclude: ['babel', 'lodash'],
+              exclude: ['lodash'],
             },
           ],
         },