visualifyjs 2.5.3-2.dev → 3.0.0

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 (252) hide show
  1. package/.claude/mem/TIMELINE.md +36 -0
  2. package/.claude/mem/notes/2026-02-11-3d-visualization-docs-fix-external-script-solution.md +24 -0
  3. package/.claude/mem/notes/2026-02-11-3d-visualization-docs-fix-session-summary.md +43 -0
  4. package/.claude/mem/notes/2026-02-11-cli-fix-editor-command-alias.md +26 -0
  5. package/.claude/mem/notes/2026-02-11-phase-3-developer-experience-completed.md +51 -0
  6. package/.claude/mem/notes/2026-02-11-phase-4-web-workers-implementation-complete.md +59 -0
  7. package/.claude/mem/notes/2026-02-11-visualify-phase-2-3d-visualization-complete.md +50 -0
  8. package/.claude/mem/notes/2026-02-11-visualify-phase-2-committed-ready-for-phase-3.md +33 -0
  9. package/.claude/mem/notes/2026-02-11-visualify-phase-3-complete-developer-experience.md +52 -0
  10. package/.claude/mem/notes/2026-02-11-visualify-repository-cleanup-complete.md +28 -0
  11. package/.claude/mem/notes/2026-02-18-codebase-cleanup-docsify-plugin-documentation.md +37 -0
  12. package/.claude/mem/notes/2026-02-19-css-grid-layout-fix-displaycontents-on-vcontroller.md +18 -0
  13. package/.claude/mem/notes/2026-02-19-docsify-plugin-fixes-latex-and-visualify-code-bloc.md +26 -0
  14. package/.claude/mem/notes/2026-02-19-page-mode-docs-update-decisions.md +23 -0
  15. package/.claude/mem/notes/2026-02-19-react-context-infinite-re-render-loop-fix-pattern.md +31 -0
  16. package/.claude/mem/notes/2026-02-19-version-300-bump-and-build-fixes.md +32 -0
  17. package/.claude/mem/notes/2026-02-19-visualify-build-deployment-architecture-bug-fixes.md +25 -0
  18. package/.claude/mem/notes/2026-02-19-visualify-dist-iife-self-contained-build-config.md +30 -0
  19. package/.claude/mem/notes/2026-02-19-visualify-infinite-loop-i18n-fixes.md +31 -0
  20. package/.claude/mem/notes/2026-02-19-visualify-v3-bundle-splitting-docs-restructuring.md +32 -0
  21. package/.claude/mem/notes/2026-02-20-bundle-externalization-final-architecture.md +29 -0
  22. package/.claude/mem/notes/2026-02-20-chromium-page-fix-unstable-keys-and-double-event-b.md +27 -0
  23. package/.claude/mem/notes/2026-02-20-console-cleanup-bundle-optimization-commit.md +20 -0
  24. package/.claude/mem/notes/2026-02-20-dotbio-dot-plot-fix-useeffect-dependency.md +21 -0
  25. package/.claude/mem/notes/2026-02-20-public-folder-cleanup-and-readme-rewrite.md +25 -0
  26. package/.claude/mem/notes/2026-02-20-v300-release-and-beta-channel-strategy.md +29 -0
  27. package/.claude/mem/notes/2026-02-20-visium-background-image-unknown-legend-fix.md +19 -0
  28. package/.claude/mem/notes/2026-02-20-visualify-cdn-loader-bundle-externalization.md +34 -0
  29. package/.claude/mem/sessions/session-2026-02-20-031524.md +54 -0
  30. package/.claude/settings.local.json +21 -0
  31. package/.github/workflows/static.yml.bak +51 -51
  32. package/.sisyphus/boulder.json +65 -0
  33. package/.sisyphus/plans/phase-4-advanced-optimizations.md +217 -0
  34. package/LICENSE +674 -674
  35. package/README.md +94 -59
  36. package/config-overrides.js +31 -31
  37. package/dist/stats.html +4949 -0
  38. package/dist/visualify-3d.esm.js +1 -0
  39. package/dist/visualify-3d.js +1 -0
  40. package/dist/visualify-core.esm.js +1 -0
  41. package/dist/visualify-core.js +1 -0
  42. package/dist/visualify-docs.esm.js +1 -0
  43. package/dist/visualify-docs.js +1 -0
  44. package/dist/visualify-loader.js +1 -0
  45. package/dist/visualify-pages.esm.js +1 -0
  46. package/dist/visualify-pages.js +1 -0
  47. package/dist/visualify-portal.esm.js +1 -0
  48. package/dist/visualify-portal.js +1 -0
  49. package/dist/visualify-shared.js +26571 -0
  50. package/dist/visualify.js +1 -188
  51. package/docs/CHANGELOG.md +148 -0
  52. package/docs/cli/commands.md +513 -0
  53. package/docs/configuration/visualify-json.md +474 -0
  54. package/docs/docs/3d-visualization.md +374 -0
  55. package/docs/docs/CLI.md +303 -34
  56. package/docs/docs/README.md +65 -65
  57. package/docs/docs/Rechart/bar.md +190 -190
  58. package/docs/docs/Rechart/funnel.md +241 -241
  59. package/docs/docs/Rechart/line.md +355 -355
  60. package/docs/docs/Rechart/pie.md +225 -225
  61. package/docs/docs/Rechart/radar.md +253 -253
  62. package/docs/docs/Rechart/scatter.md +298 -298
  63. package/docs/docs/_404.md +51 -51
  64. package/docs/docs/_coverpage.md +11 -11
  65. package/docs/docs/_sidebar.md +54 -44
  66. package/docs/docs/components/dotBio.md +87 -34
  67. package/docs/docs/components/echart.md +171 -82
  68. package/docs/docs/components/html.md +61 -34
  69. package/docs/docs/components/macaron.md +156 -145
  70. package/docs/docs/components/markdown.md +42 -0
  71. package/docs/docs/components/more.md +183 -142
  72. package/docs/docs/components/plotly.md +132 -62
  73. package/docs/docs/components/scatterL.md +171 -70
  74. package/docs/docs/components/visium.md +112 -57
  75. package/docs/docs/configuration.md +121 -121
  76. package/docs/docs/deploy.md +31 -31
  77. package/docs/docs/docsify-plugin.md +655 -0
  78. package/docs/docs/hmr.md +165 -0
  79. package/docs/docs/i18n.md +332 -0
  80. package/docs/docs/log.md +30 -9
  81. package/docs/docs/more-pages.md +23 -23
  82. package/docs/docs/quickstart.md +148 -124
  83. package/docs/docs/rechart-attributes.md +74 -74
  84. package/docs/docs/rechart-basic-usage.md +160 -162
  85. package/docs/docs/theme.md +5 -5
  86. package/docs/docs/typescript.md +306 -0
  87. package/docs/docs/visual-editor.md +359 -0
  88. package/docs/index.html +85 -71
  89. package/docs/manifest.json +23 -23
  90. package/docs/migration/v3-migration.md +392 -0
  91. package/docs/static/css/fluff-stuff.css +169 -169
  92. package/docs/static/css/font-awesome.min.css +4 -4
  93. package/docs/static/css/visualify.css +6 -25
  94. package/docs/static/js/3d-viz-examples.js +181 -0
  95. package/docs/static/js/configuration.js +630 -448
  96. package/docs/static/js/visualify.js +1 -188
  97. package/package.json +106 -84
  98. package/rollup.config.mjs +766 -76
  99. package/src/_css/404.css +115 -115
  100. package/src/_css/App.css +37 -37
  101. package/src/_css/autoSuggestion.css +26 -26
  102. package/src/_css/circular-progress.css +32 -32
  103. package/src/_css/index.css +36 -36
  104. package/src/_css/modern.css +350 -25
  105. package/src/_media/corner.svg +8 -8
  106. package/src/_media/download.svg +3 -3
  107. package/src/_media/logo.svg +14 -14
  108. package/src/_test/App.test.js +15 -15
  109. package/src/_utils/reportWebVitals.js +13 -13
  110. package/src/a11y/README.md +177 -0
  111. package/src/a11y/aria-labels.js +339 -0
  112. package/src/a11y/color-contrast.js +535 -0
  113. package/src/a11y/index.js +197 -0
  114. package/src/a11y/keyboard-nav.js +523 -0
  115. package/src/a11y/styles.css +165 -0
  116. package/src/cli/commands/dev.js +214 -0
  117. package/src/cli/commands/docs.js +521 -0
  118. package/src/cli/commands/edit.js +379 -0
  119. package/src/cli/commands/init.js +213 -0
  120. package/src/cli/commands/portal.js +236 -0
  121. package/src/cli/dev-server.js +530 -0
  122. package/src/cli/hmr.js +456 -0
  123. package/src/cli/index.js +180 -0
  124. package/src/cli/utils/config.js +207 -0
  125. package/src/cli/utils/logger.js +241 -0
  126. package/src/config/defaults.ts +122 -0
  127. package/src/config/index.ts +72 -0
  128. package/src/config/loader.ts +478 -0
  129. package/src/config/schema.ts +227 -0
  130. package/src/config/validator.ts +337 -0
  131. package/src/core/appContext.js +34 -27
  132. package/src/core/components/Bar.js +383 -0
  133. package/src/core/components/Bar3D.js +473 -0
  134. package/src/core/components/LargeDatasetChart.js +296 -0
  135. package/src/core/components/Line3D.js +310 -0
  136. package/src/core/components/Scatter.js +392 -188
  137. package/src/core/components/Scatter3D.js +455 -0
  138. package/src/core/components/ScatterBio.js +601 -572
  139. package/src/core/components/Surface3D.js +326 -0
  140. package/src/core/components/ThreeCustom.js +648 -0
  141. package/src/core/components/ThreeScene.js +459 -0
  142. package/src/core/components/VisiumPlot.js +191 -165
  143. package/src/core/components/browser.js +42 -42
  144. package/src/core/components/dotplot.js +413 -413
  145. package/src/core/components/html.js +29 -29
  146. package/src/core/components/list.js +178 -178
  147. package/src/core/components/macaron.js +206 -201
  148. package/src/core/components/markdown.js +56 -56
  149. package/src/core/components/parser.scatterBio.js +582 -587
  150. package/src/core/components/ratio.js +82 -80
  151. package/src/core/components/scatterL.js +206 -173
  152. package/src/core/components/searchbar.js +156 -131
  153. package/src/core/components/selection.js +310 -193
  154. package/src/core/components/timeline.js +236 -281
  155. package/src/core/components/visium.js +114 -97
  156. package/src/core/data-processor.js +413 -0
  157. package/src/core/fetch/condfetch.js +82 -82
  158. package/src/core/fetch/fetch.js +92 -92
  159. package/src/core/fetch/json.js +29 -29
  160. package/src/core/fetch/vfetch.js +42 -42
  161. package/src/core/hmr-client.js +724 -0
  162. package/src/core/liveEditor.js +44 -44
  163. package/src/core/modules/codeEditorWithPreview.js +104 -104
  164. package/src/core/modules/echarts/common.js +20 -20
  165. package/src/core/modules/echarts/gl.js +228 -0
  166. package/src/core/modules/echarts/presetHandler.js +41 -41
  167. package/src/core/modules/echarts/presets/esodev.chromium.js +172 -172
  168. package/src/core/modules/echarts/presets/esodev.codex.js +130 -130
  169. package/src/core/modules/echarts/presets/esodev.visium.js +123 -123
  170. package/src/core/modules/echarts/presets/mmtrbc.js +186 -186
  171. package/src/core/modules/echarts.js +70 -71
  172. package/src/core/modules/echartsUtils.js +43 -43
  173. package/src/core/modules/echartswitcher.js +227 -152
  174. package/src/core/modules/replotly/presetHandler.js +24 -24
  175. package/src/core/modules/replotly/presets/minimum.js +18 -18
  176. package/src/core/modules/replotly/presets/mmtrbc.dot.js +114 -114
  177. package/src/core/modules/replotly/presets/mmtrbc.violin.js +100 -100
  178. package/src/core/modules/replotly.js +74 -71
  179. package/src/core/modules/threejs/Camera.js +373 -0
  180. package/src/core/modules/threejs/Lighting.js +459 -0
  181. package/src/core/modules/threejs/Renderer.js +364 -0
  182. package/src/core/modules/threejs/Scene.js +266 -0
  183. package/src/core/modules/threejs/index.js +155 -0
  184. package/src/core/pages/404.js +50 -50
  185. package/src/core/pages/error.js +27 -27
  186. package/src/core/pages/jsonPage.js +62 -62
  187. package/src/core/pages/loading.js +44 -44
  188. package/src/core/parser/echart.data.js +204 -183
  189. package/src/core/parser/echart.features.js +125 -125
  190. package/src/core/parser/echart.general.js +147 -147
  191. package/src/core/parser/echart.hilbert.js +57 -57
  192. package/src/core/parser/echart.parser.js +210 -210
  193. package/src/core/parser/echart.series.js +67 -67
  194. package/src/core/parser/echart.types.js +76 -76
  195. package/src/core/parser/plotly.config.js +10 -10
  196. package/src/core/parser/plotly.data.js +132 -132
  197. package/src/core/parser/plotly.layout.js +9 -9
  198. package/src/core/parser/plotly.violin.js +18 -18
  199. package/src/core/recharts.js +361 -62
  200. package/src/core/router/alias.js +49 -49
  201. package/src/core/router/jsonRouter.js +31 -31
  202. package/src/core/themes/modern.js +32 -32
  203. package/src/core/themes/themeSelector.js +33 -33
  204. package/src/core/visualify.js +213 -47
  205. package/src/core/widgets/circularProgress.js +23 -23
  206. package/src/core/widgets/controller.js +116 -83
  207. package/src/core/widgets/errorBoundary.js +36 -36
  208. package/src/core/widgets/footer.js +185 -177
  209. package/src/core/widgets/header.js +238 -234
  210. package/src/core/widgets/layout/Grid.js +31 -31
  211. package/src/core/widgets/layout.js +36 -36
  212. package/src/core/widgets/mapping.js +56 -42
  213. package/src/core/workers/data-worker.js +349 -0
  214. package/src/core/workers/worker-pool.js +396 -0
  215. package/src/docsify/bundle.js +215 -0
  216. package/src/docsify/markdown.js +271 -0
  217. package/src/docsify/plugin.js +268 -0
  218. package/src/editor/README.md +172 -0
  219. package/src/editor/components/ChartBuilder.jsx +341 -0
  220. package/src/editor/components/ChartTypeSidebar.jsx +91 -0
  221. package/src/editor/components/Editor.jsx +367 -0
  222. package/src/editor/components/Preview.jsx +446 -0
  223. package/src/editor/components/PropertyPanel.jsx +468 -0
  224. package/src/editor/components/StatusBar.jsx +85 -0
  225. package/src/editor/context/EditorContext.js +248 -0
  226. package/src/editor/hooks/useDebounce.js +32 -0
  227. package/src/editor/index.js +315 -0
  228. package/src/editor/styles/editor.css +637 -0
  229. package/src/editor/utils/chartValidator.js +263 -0
  230. package/src/entries/charts3d.js +70 -0
  231. package/src/entries/core.js +78 -0
  232. package/src/entries/docs.js +154 -0
  233. package/src/entries/pages.js +93 -0
  234. package/src/entries/portal.js +204 -0
  235. package/src/entries/shared.js +50 -0
  236. package/src/i18n/formatters.js +455 -0
  237. package/src/i18n/index.js +169 -0
  238. package/src/i18n/locales/ar.json +137 -0
  239. package/src/i18n/locales/de.json +137 -0
  240. package/src/i18n/locales/en.json +137 -0
  241. package/src/i18n/locales/es.json +137 -0
  242. package/src/i18n/locales/he.json +137 -0
  243. package/src/i18n/locales/zh.json +137 -0
  244. package/src/i18n/rtl.css +183 -0
  245. package/src/index.js +82 -62
  246. package/src/loader.js +103 -0
  247. package/src/setupTests.js +5 -5
  248. package/tsconfig.json +51 -0
  249. package/types/charts.d.ts +569 -0
  250. package/types/components.d.ts +441 -0
  251. package/types/config.d.ts +199 -0
  252. package/types/index.d.ts +353 -0
package/package.json CHANGED
@@ -1,84 +1,106 @@
1
- {
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- "name": "visualifyjs",
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- "version": "2.5.3-2.dev",
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- "main": "dist/visualify.js",
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- "homepage": "https://visualify.pharmacy.arizona.edu",
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- "license": "GNU General Public License v3.0",
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- "description": "Visualify is a web-based platform for visualizing and analyzing large-scale omics data.",
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- "keywords": [
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- "visualization",
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- "analysis",
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- "web",
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- "platform"
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- ],
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- "dependencies": {
15
- "@testing-library/jest-dom": "^5.17.0",
16
- "@testing-library/react": "^13.4.0",
17
- "@testing-library/user-event": "^13.5.0",
18
- "ace-builds": "^1.32.0",
19
- "axios": "^1.6.2",
20
- "bootstrap": "^5.3.2",
21
- "dompurify": "^3.0.6",
22
- "echarts": "^5.4.3",
23
- "echarts-for-react": "^3.0.2",
24
- "hilbert": "^2.0.0",
25
- "lodash": "^4.17.21",
26
- "react": "^18.2.0",
27
- "react-ace": "^10.1.0",
28
- "react-bootstrap": "^2.9.1",
29
- "react-dom": "^18.2.0",
30
- "react-markdown": "^9.0.1",
31
- "react-plotly.js": "^2.6.0",
32
- "react-router-dom": "^6.20.0",
33
- "react-scripts": "5.0.1",
34
- "react-select": "^5.8.0",
35
- "remark": "^15.0.1",
36
- "remark-html": "^16.0.1",
37
- "web-vitals": "^2.1.4"
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- },
39
- "scripts": {
40
- "rollup": "rollup -c",
41
- "start": "react-app-rewired start",
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- "build": "npm run rollup & react-app-rewired build",
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- "test": "react-app-rewired test",
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- "eject": "react-scripts eject"
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- },
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- "eslintConfig": {
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- "extends": [
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- "react-app",
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- "react-app/jest"
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- ]
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- },
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- "browserslist": {
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- "production": [
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- ">0.2%",
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- "not dead",
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- "not op_mini all"
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- ],
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- "development": [
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- "last 1 chrome version",
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- "last 1 firefox version",
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- "last 1 safari version"
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- ]
63
- },
64
- "devDependencies": {
65
- "@babel/core": "^7.23.5",
66
- "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
67
- "@babel/preset-env": "^7.23.5",
68
- "@babel/preset-react": "^7.23.3",
69
- "@rollup/plugin-babel": "^6.0.4",
70
- "@rollup/plugin-commonjs": "^25.0.7",
71
- "@rollup/plugin-image": "^3.0.3",
72
- "@rollup/plugin-json": "^6.0.1",
73
- "@rollup/plugin-node-resolve": "^15.2.3",
74
- "@rollup/plugin-replace": "^5.0.5",
75
- "@rollup/plugin-terser": "^0.4.4",
76
- "@rollup/plugin-url": "^8.0.2",
77
- "babel-plugin-inline-react-svg": "^2.0.2",
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- "react-app-rewired": "^2.2.1",
79
- "rollup": "^2.79.1",
80
- "rollup-plugin-css-only": "^4.5.2",
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- "rollup-plugin-polyfill-node": "^0.13.0",
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- "rollup-plugin-postcss": "^4.0.2"
83
- }
84
- }
1
+ {
2
+ "name": "visualifyjs",
3
+ "version": "3.0.0",
4
+ "main": "dist/visualify.js",
5
+ "homepage": "https://visualify.pharmacy.arizona.edu",
6
+ "license": "GNU General Public License v3.0",
7
+ "description": "Visualify is a web-based platform for visualizing and analyzing large-scale omics data.",
8
+ "bin": {
9
+ "visualify": "./src/cli/index.js"
10
+ },
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+ "keywords": [
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+ "visualization",
13
+ "analysis",
14
+ "web",
15
+ "platform"
16
+ ],
17
+ "dependencies": {
18
+ "@react-three/drei": "^9.0.0",
19
+ "@react-three/fiber": "^8.15.0",
20
+ "@testing-library/jest-dom": "^5.17.0",
21
+ "@testing-library/react": "^13.4.0",
22
+ "@testing-library/user-event": "^13.5.0",
23
+ "ace-builds": "^1.32.0",
24
+ "axios": "^1.6.2",
25
+ "bootstrap": "^5.3.2",
26
+ "chalk": "^4.1.2",
27
+ "chokidar": "^3.5.3",
28
+ "commander": "^11.1.0",
29
+ "docsify": "^4.13.1",
30
+ "docsify-cli": "^4.4.4",
31
+ "dompurify": "^3.0.6",
32
+ "echarts": "^5.4.3",
33
+ "echarts-for-react": "^3.0.2",
34
+ "echarts-gl": "^2.0.9",
35
+ "express": "^4.18.2",
36
+ "hilbert": "^2.0.0",
37
+ "i18next": "^25.8.5",
38
+ "i18next-browser-languagedetector": "^8.2.0",
39
+ "lodash": "^4.17.21",
40
+ "plotly.js": "^3.3.1",
41
+ "react": "^18.2.0",
42
+ "react-ace": "^10.1.0",
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+ "react-bootstrap": "^2.9.1",
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+ "react-dom": "^18.2.0",
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+ "react-i18next": "^16.5.4",
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+ "react-markdown": "^9.0.1",
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+ "react-plotly.js": "^2.6.0",
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+ "react-router-dom": "^6.20.0",
49
+ "react-scripts": "5.0.1",
50
+ "react-select": "^5.8.0",
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+ "react-toastify": "^11.0.5",
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+ "remark": "^15.0.1",
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+ "remark-html": "^16.0.1",
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+ "three": "^0.160.0",
55
+ "web-vitals": "^2.1.4",
56
+ "ws": "^8.14.2"
57
+ },
58
+ "scripts": {
59
+ "rollup": "rollup -c",
60
+ "rollup:dev": "NODE_ENV=development rollup -c",
61
+ "start": "react-app-rewired start",
62
+ "build": "npm run rollup & react-app-rewired build",
63
+ "test": "react-app-rewired test",
64
+ "eject": "react-scripts eject"
65
+ },
66
+ "eslintConfig": {
67
+ "extends": [
68
+ "react-app",
69
+ "react-app/jest"
70
+ ]
71
+ },
72
+ "browserslist": {
73
+ "production": [
74
+ ">0.2%",
75
+ "not dead",
76
+ "not op_mini all"
77
+ ],
78
+ "development": [
79
+ "last 1 chrome version",
80
+ "last 1 firefox version",
81
+ "last 1 safari version"
82
+ ]
83
+ },
84
+ "devDependencies": {
85
+ "@babel/core": "^7.23.5",
86
+ "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
87
+ "@babel/preset-env": "^7.23.5",
88
+ "@babel/preset-react": "^7.23.3",
89
+ "@rollup/plugin-babel": "^6.0.4",
90
+ "@rollup/plugin-commonjs": "^25.0.7",
91
+ "@rollup/plugin-image": "^3.0.3",
92
+ "@rollup/plugin-json": "^6.0.1",
93
+ "@rollup/plugin-node-resolve": "^15.2.3",
94
+ "@rollup/plugin-replace": "^5.0.5",
95
+ "@rollup/plugin-terser": "^0.4.4",
96
+ "@rollup/plugin-url": "^8.0.2",
97
+ "babel-plugin-inline-react-svg": "^2.0.2",
98
+ "react-app-rewired": "^2.2.1",
99
+ "rollup": "^2.79.1",
100
+ "rollup-plugin-css-only": "^4.5.2",
101
+ "rollup-plugin-polyfill-node": "^0.13.0",
102
+ "rollup-plugin-postcss": "^4.0.2",
103
+ "rollup-plugin-visualizer": "^6.0.5",
104
+ "typescript": "^4.9.5"
105
+ }
106
+ }