higlass 1.13.1 → 1.13.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (244) hide show
  1. package/README.md +0 -2
  2. package/app/globals.d.ts +4 -4
  3. package/app/missing-types.d.ts +3 -3
  4. package/app/scripts/AddTrackDialog.jsx +1 -0
  5. package/app/scripts/AddTrackPositionMenu.jsx +17 -4
  6. package/app/scripts/Annotations1dTrack.js +1 -0
  7. package/app/scripts/Annotations2dTrack.js +1 -0
  8. package/app/scripts/ArrowheadDomainsTrack.js +1 -0
  9. package/app/scripts/Autocomplete.jsx +2 -0
  10. package/app/scripts/AxisPixi.js +1 -0
  11. package/app/scripts/BarTrack.js +1 -0
  12. package/app/scripts/BedLikeTrack.js +1 -0
  13. package/app/scripts/Button.jsx +1 -0
  14. package/app/scripts/CNVIntervalTrack.js +1 -0
  15. package/app/scripts/CenterTiledPlot.jsx +1 -0
  16. package/app/scripts/CenterTrack.jsx +1 -0
  17. package/app/scripts/Chromosome2DAnnotations.js +1 -0
  18. package/app/scripts/Chromosome2DLabels.js +1 -0
  19. package/app/scripts/ChromosomeGrid.js +1 -0
  20. package/app/scripts/ChromosomeInfo.js +1 -0
  21. package/app/scripts/CloseTrackMenu.jsx +1 -0
  22. package/app/scripts/CombinedTrack.js +1 -0
  23. package/app/scripts/ConfigTrackMenu.jsx +1 -0
  24. package/app/scripts/ConfigViewMenu.jsx +1 -0
  25. package/app/scripts/ConfigureSeriesMenu.jsx +1 -0
  26. package/app/scripts/ContextMenuContainer.jsx +1 -0
  27. package/app/scripts/ContextMenuItem.jsx +1 -0
  28. package/app/scripts/Cross.jsx +1 -0
  29. package/app/scripts/CrossRule.js +1 -0
  30. package/app/scripts/CustomTrackDialog.jsx +5 -0
  31. package/app/scripts/Dialog.jsx +1 -0
  32. package/app/scripts/DivergentBarTrack.js +1 -0
  33. package/app/scripts/DragListeningDiv.jsx +1 -0
  34. package/app/scripts/DraggableDiv.jsx +1 -0
  35. package/app/scripts/ExportLinkDialog.jsx +1 -0
  36. package/app/scripts/FixedTrack.jsx +1 -0
  37. package/app/scripts/GalleryTracks.jsx +1 -0
  38. package/app/scripts/GenomePositionSearchBox.jsx +2 -0
  39. package/app/scripts/HeatmapOptions.jsx +1 -0
  40. package/app/scripts/HeatmapTiledPixiTrack.js +1 -0
  41. package/app/scripts/HiGlassComponent.jsx +1 -0
  42. package/app/scripts/HiGlassTrackComponent.jsx +1 -0
  43. package/app/scripts/Horizontal1dHeatmapTrack.js +1 -0
  44. package/app/scripts/Horizontal2DDomainsTrack.js +1 -0
  45. package/app/scripts/HorizontalChromosomeLabels.js +1 -0
  46. package/app/scripts/HorizontalGeneAnnotationsTrack.js +1 -0
  47. package/app/scripts/HorizontalHeatmapTrack.js +1 -0
  48. package/app/scripts/HorizontalItem.jsx +1 -0
  49. package/app/scripts/HorizontalLine1DPixiTrack.js +1 -0
  50. package/app/scripts/HorizontalMultivecTrack.js +1 -0
  51. package/app/scripts/HorizontalPoint1DPixiTrack.js +1 -0
  52. package/app/scripts/HorizontalRule.js +1 -0
  53. package/app/scripts/HorizontalTiled1DPixiTrack.js +1 -0
  54. package/app/scripts/HorizontalTiledPlot.jsx +1 -0
  55. package/app/scripts/HorizontalTrack.jsx +1 -0
  56. package/app/scripts/Id2DTiledPixiTrack.js +1 -0
  57. package/app/scripts/IdHorizontal1DTiledPixiTrack.js +1 -0
  58. package/app/scripts/IdVertical1DTiledPixiTrack.js +1 -0
  59. package/app/scripts/LeftAxisTrack.js +1 -0
  60. package/app/scripts/LeftTrackModifier.js +1 -0
  61. package/app/scripts/ListWrapper.jsx +2 -0
  62. package/app/scripts/MapboxTilesTrack.js +1 -0
  63. package/app/scripts/Modal.jsx +1 -0
  64. package/app/scripts/MoveableTrack.jsx +1 -0
  65. package/app/scripts/NestedContextMenu.jsx +1 -0
  66. package/app/scripts/OSMTileIdsTrack.js +1 -0
  67. package/app/scripts/OSMTilesTrack.js +1 -0
  68. package/app/scripts/OverlayTrack.js +1 -0
  69. package/app/scripts/PixiTrack.js +0 -1
  70. package/app/scripts/PlotTypeChooser.jsx +1 -0
  71. package/app/scripts/PopupMenu.jsx +1 -0
  72. package/app/scripts/RasterTilesTrack.js +1 -0
  73. package/app/scripts/RuleMixin.js +1 -0
  74. package/app/scripts/SVGTrack.js +1 -0
  75. package/app/scripts/SearchField.js +1 -0
  76. package/app/scripts/SeriesListItems.jsx +1 -0
  77. package/app/scripts/SeriesListMenu.jsx +1 -0
  78. package/app/scripts/SeriesListSubmenuMixin.jsx +1 -0
  79. package/app/scripts/SketchInlinePicker.jsx +1 -0
  80. package/app/scripts/SortableList.jsx +2 -0
  81. package/app/scripts/SquareMarkersTrack.js +1 -0
  82. package/app/scripts/Tiled1DPixiTrack.js +1 -0
  83. package/app/scripts/TiledPixiTrack.js +1 -0
  84. package/app/scripts/TiledPlot.jsx +3 -0
  85. package/app/scripts/TilesetFinder.jsx +1 -0
  86. package/app/scripts/TopAxisTrack.js +1 -0
  87. package/app/scripts/Track.js +0 -1
  88. package/app/scripts/TrackArea.jsx +1 -0
  89. package/app/scripts/TrackControl.jsx +1 -0
  90. package/app/scripts/TrackRenderer.jsx +0 -1
  91. package/app/scripts/UnknownPixiTrack.js +1 -0
  92. package/app/scripts/ValueIntervalTrack.js +1 -0
  93. package/app/scripts/VerticalItem.jsx +1 -0
  94. package/app/scripts/VerticalRule.js +1 -0
  95. package/app/scripts/VerticalTiled1DPixiTrack.js +1 -0
  96. package/app/scripts/VerticalTiledPlot.jsx +1 -0
  97. package/app/scripts/VerticalTrack.jsx +1 -0
  98. package/app/scripts/ViewConfigEditor.jsx +1 -0
  99. package/app/scripts/ViewContextMenu.jsx +1 -0
  100. package/app/scripts/ViewHeader.jsx +1 -0
  101. package/app/scripts/ViewportTracker2D.js +1 -0
  102. package/app/scripts/ViewportTracker2DPixi.js +1 -0
  103. package/app/scripts/ViewportTrackerHorizontal.js +1 -0
  104. package/app/scripts/ViewportTrackerVertical.js +1 -0
  105. package/app/scripts/api.js +1 -0
  106. package/app/scripts/configs/available-track-types.js +1 -0
  107. package/app/scripts/configs/colormaps.js +1 -0
  108. package/app/scripts/configs/datatype-to-track-type.js +1 -0
  109. package/app/scripts/configs/default-tracks-for-datatype.js +0 -1
  110. package/app/scripts/configs/dense-data-extrema-config.js +1 -0
  111. package/app/scripts/configs/globals.js +1 -0
  112. package/app/scripts/configs/index.js +1 -0
  113. package/app/scripts/configs/positions-by-datatype.js +1 -0
  114. package/app/scripts/configs/primitives.js +0 -1
  115. package/app/scripts/configs/themes.js +1 -0
  116. package/app/scripts/configs/tracks-info-by-type.js +0 -1
  117. package/app/scripts/configs/tracks-info.js +0 -1
  118. package/app/scripts/d3-context-menu.js +1 -0
  119. package/app/scripts/data-fetchers/DataFetcher.js +193 -153
  120. package/app/scripts/data-fetchers/genbank-fetcher.js +205 -87
  121. package/app/scripts/data-fetchers/index.js +1 -0
  122. package/app/scripts/data-fetchers/local-tile-fetcher.js +37 -4
  123. package/app/scripts/hglib.jsx +1 -0
  124. package/app/scripts/hocs/with-modal.jsx +2 -0
  125. package/app/scripts/hocs/with-pub-sub.jsx +2 -0
  126. package/app/scripts/hocs/with-theme.jsx +2 -0
  127. package/app/scripts/icons.jsx +7 -0
  128. package/app/scripts/mixwith.js +1 -0
  129. package/app/scripts/options-info.js +1 -0
  130. package/app/scripts/plugins/available-for-plugins.js +1 -0
  131. package/app/scripts/plugins/get-data-fetcher.js +1 -0
  132. package/app/scripts/plugins/index.js +1 -0
  133. package/app/scripts/services/chrom-info.js +1 -0
  134. package/app/scripts/services/dom-event.js +1 -0
  135. package/app/scripts/services/element-resize-listener.js +1 -0
  136. package/app/scripts/services/index.js +1 -0
  137. package/app/scripts/services/tile-proxy.js +15 -11
  138. package/app/scripts/services/worker.js +161 -84
  139. package/app/scripts/symbol.js +1 -0
  140. package/app/scripts/test-helpers/index.js +1 -0
  141. package/app/scripts/test-helpers/test-helpers.jsx +1 -0
  142. package/app/scripts/track-utils.js +1 -0
  143. package/app/scripts/types.ts +59 -22
  144. package/app/scripts/utils/DenseDataExtrema1D.js +32 -19
  145. package/app/scripts/utils/DenseDataExtrema2D.js +51 -31
  146. package/app/scripts/utils/LruCache.js +1 -0
  147. package/app/scripts/utils/abs-to-chr.js +0 -1
  148. package/app/scripts/utils/accessor-transposition.js +0 -2
  149. package/app/scripts/utils/add-arrays.js +0 -2
  150. package/app/scripts/utils/add-class.js +0 -1
  151. package/app/scripts/utils/add-event-listener-once.js +0 -2
  152. package/app/scripts/utils/background-task-scheduler.js +0 -2
  153. package/app/scripts/utils/base64-to-canvas.js +0 -2
  154. package/app/scripts/utils/chr-to-abs.js +0 -2
  155. package/app/scripts/utils/chrom-info-bisector.js +0 -1
  156. package/app/scripts/utils/clone-event.js +0 -2
  157. package/app/scripts/utils/color-domain-to-rgba-array.js +1 -0
  158. package/app/scripts/utils/color-to-hex.js +0 -1
  159. package/app/scripts/utils/color-to-rgba.js +0 -1
  160. package/app/scripts/utils/data-to-genomic-loci.js +0 -1
  161. package/app/scripts/utils/debounce.js +0 -2
  162. package/app/scripts/utils/dec-to-hex-str.js +0 -1
  163. package/app/scripts/utils/dict-from-tuples.js +0 -2
  164. package/app/scripts/utils/dict-items.js +0 -2
  165. package/app/scripts/utils/dict-keys.js +0 -2
  166. package/app/scripts/utils/dict-values.js +0 -2
  167. package/app/scripts/utils/download.js +0 -2
  168. package/app/scripts/utils/expand-combined-tracks.js +1 -0
  169. package/app/scripts/utils/fill-in-min-widths.js +1 -0
  170. package/app/scripts/utils/flatten.js +1 -0
  171. package/app/scripts/utils/for-each.js +0 -1
  172. package/app/scripts/utils/forward-event.js +0 -1
  173. package/app/scripts/utils/genome-loci-to-pixels.js +0 -1
  174. package/app/scripts/utils/genomic-range-to-chromosome-chunks.js +0 -2
  175. package/app/scripts/utils/get-aggregation-function.js +6 -12
  176. package/app/scripts/utils/get-default-track-for-datatype.js +1 -0
  177. package/app/scripts/utils/get-element-dim.js +0 -1
  178. package/app/scripts/utils/get-higlass-components.js +1 -0
  179. package/app/scripts/utils/get-track-by-uid.js +1 -0
  180. package/app/scripts/utils/get-track-conf-from-hgc.js +1 -0
  181. package/app/scripts/utils/get-track-obj-by-id.js +1 -0
  182. package/app/scripts/utils/get-track-position-by-uid.js +1 -0
  183. package/app/scripts/utils/get-xylofon.js +1 -0
  184. package/app/scripts/utils/gradient.js +0 -2
  185. package/app/scripts/utils/has-class.js +0 -2
  186. package/app/scripts/utils/has-parent.js +1 -0
  187. package/app/scripts/utils/hex-string-to-int.js +0 -1
  188. package/app/scripts/utils/index.js +0 -1
  189. package/app/scripts/utils/interval-tree.js +1 -0
  190. package/app/scripts/utils/into-the-void.js +0 -1
  191. package/app/scripts/utils/is-track-or-child-track.js +0 -1
  192. package/app/scripts/utils/is-track-range-selectable.js +0 -1
  193. package/app/scripts/utils/is-within.js +0 -2
  194. package/app/scripts/utils/lat-to-y.js +0 -2
  195. package/app/scripts/utils/lng-to-x.js +0 -1
  196. package/app/scripts/utils/load-chrom-infos.js +1 -0
  197. package/app/scripts/utils/map.js +0 -1
  198. package/app/scripts/utils/max-non-zero.js +0 -1
  199. package/app/scripts/utils/max.js +0 -1
  200. package/app/scripts/utils/min-non-zero.js +0 -1
  201. package/app/scripts/utils/min.js +0 -1
  202. package/app/scripts/utils/mod.js +0 -1
  203. package/app/scripts/utils/ndarray-assign.js +1 -0
  204. package/app/scripts/utils/ndarray-flatten.js +1 -0
  205. package/app/scripts/utils/ndarray-to-list.js +1 -0
  206. package/app/scripts/utils/numericify-version.js +0 -1
  207. package/app/scripts/utils/obj-vals.js +1 -0
  208. package/app/scripts/utils/or.js +0 -1
  209. package/app/scripts/utils/parse-chromsizes-rows.js +0 -2
  210. package/app/scripts/utils/pixi-text-to-svg.js +1 -0
  211. package/app/scripts/utils/q.js +1 -0
  212. package/app/scripts/utils/rad-to-deg.js +0 -1
  213. package/app/scripts/utils/range-query-2d.js +1 -0
  214. package/app/scripts/utils/reduce.js +1 -0
  215. package/app/scripts/utils/rel-to-abs-chrom-pos.js +0 -2
  216. package/app/scripts/utils/remove-class.js +0 -1
  217. package/app/scripts/utils/reset-d3-brush-style.js +0 -2
  218. package/app/scripts/utils/rgb-to-hex.js +0 -2
  219. package/app/scripts/utils/scales-center-and-k.js +0 -2
  220. package/app/scripts/utils/scales-to-genome-loci.js +0 -1
  221. package/app/scripts/utils/segments-to-rows.js +1 -0
  222. package/app/scripts/utils/selected-items-to-cum-weights.js +0 -1
  223. package/app/scripts/utils/selected-items-to-size.js +0 -1
  224. package/app/scripts/utils/show-mouse-position.js +0 -1
  225. package/app/scripts/utils/some.js +0 -1
  226. package/app/scripts/utils/sum.js +0 -1
  227. package/app/scripts/utils/svg-line.js +1 -0
  228. package/app/scripts/utils/throttle-and-debounce.js +0 -1
  229. package/app/scripts/utils/tile-to-canvas.js +0 -1
  230. package/app/scripts/utils/timeout.js +0 -1
  231. package/app/scripts/utils/to-void.js +0 -1
  232. package/app/scripts/utils/total-track-pixel-height.js +0 -1
  233. package/app/scripts/utils/trim-trailing-slash.js +0 -1
  234. package/app/scripts/utils/type-guards.js +0 -2
  235. package/app/scripts/utils/value-to-color.js +0 -1
  236. package/app/scripts/utils/visit-positioned-tracks.js +0 -1
  237. package/app/scripts/utils/visit-tracks.js +0 -1
  238. package/dist/esm.html +13 -14
  239. package/dist/hglib.css +1 -1724
  240. package/dist/hglib.js +122661 -28
  241. package/dist/hglib.min.js +116 -119
  242. package/dist/higlass.mjs +122643 -28
  243. package/dist/index.html +5 -6
  244. package/package.json +25 -18
package/dist/index.html CHANGED
@@ -14,12 +14,11 @@
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  overflow: hidden;
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  }
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  </style>
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- <link rel="stylesheet" href="./hglib.css">
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- <script src="https://unpkg.com/react@17/umd/react.production.min.js"></script>
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- <script src="https://unpkg.com/react-dom@17/umd/react-dom.production.min.js"></script>
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- <script src="https://unpkg.com/pixi.js@6/dist/browser/pixi.min.js"></script>
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- <script src="./hglib.min.js"></script>
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-
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+ <script src="https://unpkg.com/react@17/umd/react.production.min.js"></script>
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+ <script src="https://unpkg.com/react-dom@17/umd/react-dom.production.min.js"></script>
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+ <script src="https://unpkg.com/pixi.js@6/dist/browser/pixi.min.js"></script>
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+ <script src="./hglib.min.js"></script>
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+
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  </head>
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  <body>
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "higlass",
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- "version": "1.13.1",
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+ "version": "1.13.3",
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  "description": "HiGlass Hi-C / genomic / large data viewer",
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  "author": "Peter Kerpedjiev <pkerpedjiev@gmail.com>",
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  "main": "dist/hglib.js",
@@ -10,7 +10,8 @@
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  "exports": {
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  ".": {
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  "import": "./dist/higlass.mjs"
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- }
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+ },
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+ "./dist/*": "./dist/*"
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  },
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  "files": [
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  "app",
@@ -25,13 +26,11 @@
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  "scripts": {
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  "test": "wtr",
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  "start": "vite",
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- "build": "vite build",
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- "optimize": "vite optimize",
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- "compile": "npm run build && node ./scripts/compile.mjs && zip -r dist.zip dist",
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+ "build": "node ./scripts/build.mjs",
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+ "compile": "npm run build && zip -r dist.zip dist",
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  "typecheck": "tsc",
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- "format": "prettier --ignore-path=.gitignore --write \"**/*.{mjs,js,jsx}\"",
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- "lint": "prettier --ignore-path=.gitignore --check \"**/*.{mjs,js,jsx}\" && eslint --ignore-path=.gitignore \"**/*.{mjs,js,jsx}\"",
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- "precommit": "NODE_ENV=production lint-staged"
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+ "format": "prettier --ignore-path=.gitignore --write \"**/*.{mjs,js,jsx,ts}\"",
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+ "lint": "prettier --ignore-path=.gitignore --check \"**/*.{mjs,js,jsx,ts}\" && eslint --ignore-path=.gitignore \"**/*.{mjs,js,jsx}\""
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  },
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  "repository": {
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  "type": "git",
@@ -70,15 +69,12 @@
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  "pub-sub-es": "^2.0.1",
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  "react-checkbox-tree": "^1.7.3",
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  "react-color": "^2.13.8",
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- "react-contextmenu": "^2.9.2",
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  "react-grid-layout": "^0.16.6",
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- "react-resizable": "^1.8.0",
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  "react-simple-code-editor": "^0.9.10",
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  "react-sortable-hoc": "^1.10.1",
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  "reactcss": "^1.2.3",
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  "robust-point-in-polygon": "^1.0.3",
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  "slugid": "^3.2.0",
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- "stream": "0.0.2",
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  "url-parse": "^1.4.3",
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  "vkbeautify": "^0.99.3"
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  },
@@ -88,25 +84,36 @@
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  "react-dom": "^16.6.3 || ^17.0.0 || ^18.0.0"
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  },
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  "devDependencies": {
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- "@babel/core": "^7.20.12",
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- "@babel/plugin-transform-classes": "^7.20.7",
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+ "@babel/core": "^7.23.3",
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+ "@babel/plugin-transform-classes": "^7.23.3",
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+ "@babel/preset-react": "^7.23.3",
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  "@types/d3-array": "^2.7.1",
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+ "@types/d3-axis": "^2.0.0",
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+ "@types/d3-brush": "^2.1.0",
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+ "@types/d3-color": "^2.0.0",
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+ "@types/d3-drag": "^2.0.0",
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+ "@types/d3-dsv": "^2.0.0",
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  "@types/d3-format": "^2.0.0",
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+ "@types/d3-geo": "^2.0.1",
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+ "@types/d3-queue": "^3.0.7",
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+ "@types/d3-request": "^1.0.6",
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  "@types/d3-scale": "^4.0.2",
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  "@types/d3-selection": "^2.0.0",
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  "@types/d3-transition": "^3.0.1",
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  "@types/d3-zoom": "^3.0.0",
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+ "@types/ndarray": "^1.0.13",
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+ "@types/pako": "^2.0.2",
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  "@types/prop-types": "^15.7.3",
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  "@types/react": "^17.0.2",
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  "@types/react-dom": "^17.0.2",
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- "@vitejs/plugin-react": "^2.0.1",
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+ "@vitejs/plugin-react": "^4.2.0",
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  "@web/test-runner": "^0.17.2",
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  "@web/test-runner-puppeteer": "^0.14.1",
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  "@wojtekmaj/enzyme-adapter-react-17": "^0.6.7",
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  "ajv-cli": "^5.0.0",
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  "chai": "^4.3.4",
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  "enzyme": "^3.4.1",
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- "esbuild": "^0.19.4",
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+ "esbuild": "^0.19.8",
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  "eslint": "^8.23.0",
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  "eslint-config-airbnb": "^19.0.4",
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  "eslint-config-prettier": "^8.5.0",
@@ -115,14 +122,14 @@
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  "eslint-plugin-react": "^7.31.8",
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  "eslint-plugin-react-hooks": "^4.6.0",
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  "pixi.js": "^6.5.2",
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- "postcss": "^8.4.6",
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- "postcss-scss": "^4.0.4",
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  "prettier": "^2.5.1",
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  "react": "^17.0.2",
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  "react-dom": "^17.0.2",
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  "sass": "^1.54.5",
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  "tinyspy": "^1.0.2",
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  "typescript": "^5.2.2",
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- "vite": "^3.0.9"
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+ "vite": "^5.0.3",
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+ "vite-plugin-babel": "^1.1.3",
133
+ "vite-plugin-css-injected-by-js": "^3.3.0"
127
134
  }
128
135
  }