visualifyjs 2.5.3-2.dev → 2.5.3-9-dev

package/docs/theme.md

@@ -0,0 +1,3 @@
+# Theme
+
+## Modern

package/package.json

@@ -1,84 +1,75 @@
-{
-    "name": "visualifyjs",
-    "version": "2.5.3-2.dev",
-    "main": "dist/visualify.js",
-    "homepage": "https://visualify.pharmacy.arizona.edu",
-    "license": "GNU General Public License v3.0",
-    "description": "Visualify is a web-based platform for visualizing and analyzing large-scale omics data.",
-    "keywords": [
-        "visualization",
-        "analysis",
-        "web",
-        "platform"
-    ],
-    "dependencies": {
-        "@testing-library/jest-dom": "^5.17.0",
-        "@testing-library/react": "^13.4.0",
-        "@testing-library/user-event": "^13.5.0",
-        "ace-builds": "^1.32.0",
-        "axios": "^1.6.2",
-        "bootstrap": "^5.3.2",
-        "dompurify": "^3.0.6",
-        "echarts": "^5.4.3",
-        "echarts-for-react": "^3.0.2",
-        "hilbert": "^2.0.0",
-        "lodash": "^4.17.21",
-        "react": "^18.2.0",
-        "react-ace": "^10.1.0",
-        "react-bootstrap": "^2.9.1",
-        "react-dom": "^18.2.0",
-        "react-markdown": "^9.0.1",
-        "react-plotly.js": "^2.6.0",
-        "react-router-dom": "^6.20.0",
-        "react-scripts": "5.0.1",
-        "react-select": "^5.8.0",
-        "remark": "^15.0.1",
-        "remark-html": "^16.0.1",
-        "web-vitals": "^2.1.4"
-    },
-    "scripts": {
-        "rollup": "rollup -c",
-        "start": "react-app-rewired start",
-        "build": "npm run rollup & react-app-rewired build",
-        "test": "react-app-rewired test",
-        "eject": "react-scripts eject"
-    },
-    "eslintConfig": {
-        "extends": [
-            "react-app",
-            "react-app/jest"
-        ]
-    },
-    "browserslist": {
-        "production": [
-            ">0.2%",
-            "not dead",
-            "not op_mini all"
-        ],
-        "development": [
-            "last 1 chrome version",
-            "last 1 firefox version",
-            "last 1 safari version"
-        ]
-    },
-    "devDependencies": {
-        "@babel/core": "^7.23.5",
-        "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
-        "@babel/preset-env": "^7.23.5",
-        "@babel/preset-react": "^7.23.3",
-        "@rollup/plugin-babel": "^6.0.4",
-        "@rollup/plugin-commonjs": "^25.0.7",
-        "@rollup/plugin-image": "^3.0.3",
-        "@rollup/plugin-json": "^6.0.1",
-        "@rollup/plugin-node-resolve": "^15.2.3",
-        "@rollup/plugin-replace": "^5.0.5",
-        "@rollup/plugin-terser": "^0.4.4",
-        "@rollup/plugin-url": "^8.0.2",
-        "babel-plugin-inline-react-svg": "^2.0.2",
-        "react-app-rewired": "^2.2.1",
-        "rollup": "^2.79.1",
-        "rollup-plugin-css-only": "^4.5.2",
-        "rollup-plugin-polyfill-node": "^0.13.0",
-        "rollup-plugin-postcss": "^4.0.2"
-    }
+{
+    "name": "visualifyjs",
+    "version": "2.5.3-9-dev+24.2.5",
+    "main": "dist/visualify.js",
+    "dependencies": {
+        "@testing-library/jest-dom": "^5.17.0",
+        "@testing-library/react": "^13.4.0",
+        "@testing-library/user-event": "^13.5.0",
+        "ace-builds": "^1.32.0",
+        "axios": "^1.6.2",
+        "bootstrap": "^5.3.2",
+        "dompurify": "^3.0.6",
+        "echarts": "^5.4.3",
+        "echarts-for-react": "^3.0.2",
+        "hilbert": "^2.0.0",
+        "lodash": "^4.17.21",
+        "react": "^18.2.0",
+        "react-ace": "^10.1.0",
+        "react-bootstrap": "^2.9.1",
+        "react-dom": "^18.2.0",
+        "react-markdown": "^9.0.1",
+        "react-plotly.js": "^2.6.0",
+        "react-router-dom": "^6.20.0",
+        "react-scripts": "5.0.1",
+        "react-select": "^5.8.0",
+        "remark": "^15.0.1",
+        "remark-html": "^16.0.1",
+        "web-vitals": "^2.1.4"
+    },
+    "scripts": {
+        "rollup": "rollup -c",
+        "start": "react-app-rewired start",
+        "build": "npm run rollup & react-app-rewired build",
+        "test": "react-app-rewired test",
+        "eject": "react-scripts eject"
+    },
+    "eslintConfig": {
+        "extends": [
+            "react-app",
+            "react-app/jest"
+        ]
+    },
+    "browserslist": {
+        "production": [
+            ">0.2%",
+            "not dead",
+            "not op_mini all"
+        ],
+        "development": [
+            "last 1 chrome version",
+            "last 1 firefox version",
+            "last 1 safari version"
+        ]
+    },
+    "devDependencies": {
+        "@babel/core": "^7.23.5",
+        "@babel/plugin-proposal-private-property-in-object": "^7.21.11",
+        "@babel/preset-env": "^7.23.5",
+        "@babel/preset-react": "^7.23.3",
+        "@rollup/plugin-babel": "^6.0.4",
+        "@rollup/plugin-commonjs": "^25.0.7",
+        "@rollup/plugin-image": "^3.0.3",
+        "@rollup/plugin-json": "^6.0.1",
+        "@rollup/plugin-node-resolve": "^15.2.3",
+        "@rollup/plugin-replace": "^5.0.5",
+        "@rollup/plugin-terser": "^0.4.4",
+        "@rollup/plugin-url": "^8.0.2",
+        "babel-plugin-inline-react-svg": "^2.0.2",
+        "react-app-rewired": "^2.2.1",
+        "rollup": "^2.79.1",
+        "rollup-plugin-css-only": "^4.5.2",
+        "rollup-plugin-polyfill-node": "^0.13.0",
+        "rollup-plugin-postcss": "^4.0.2"
+    }
 }

package/rollup.config.mjs

@@ -1,76 +1,76 @@
-/*
- * @Author       : Lihao leolihao@arizona.edu
- * @Date         : 2023-12-01 12:51:04
- * @FilePath     : /visualifyjs/rollup.config.mjs
- * @Description  :
- * Copyright (c) 2023 by Lihao (leolihao@arizona.edu), All Rights Reserved.
- */
-// rollup.config.js
-import resolve from '@rollup/plugin-node-resolve';
-import commonjs from '@rollup/plugin-commonjs';
-import babel from '@rollup/plugin-babel';
-import replace from '@rollup/plugin-replace';
-import terser from '@rollup/plugin-terser';
-import json from '@rollup/plugin-json';
-import postcss from 'rollup-plugin-postcss';
-import nodePolyfills from 'rollup-plugin-polyfill-node';
-import image from '@rollup/plugin-image';
-import inlineReactSvg from 'babel-plugin-inline-react-svg';
-import url from '@rollup/plugin-url';
-
-//import css from 'rollup-plugin-css-only';
-
-function onwarn(warning, warn) {
-    if (warning.code === 'MODULE_LEVEL_DIRECTIVE') {
-        return;
-    }
-    warn(warning);
-}
-
-export default {
-    input: 'src/index.js',
-    output: [{
-            dir: 'dist/',
-            format: 'esm',
-            entryFileNames: 'visualify.js',
-            inlineDynamicImports: true,
-            sourcemap: false,
-        },
-        {
-            dir: 'docs/static/js',
-            format: 'esm',
-            entryFileNames: 'visualify.js',
-            inlineDynamicImports: true,
-            sourcemap: false,
-        },
-    ],
-    plugins: [
-        replace({
-            preventAssignment: true,
-            'process.env.NODE_ENV': JSON.stringify('production'),
-        }),
-        resolve({ browser: true }),
-        babel({
-            exclude: 'node_modules/**',
-            babelHelpers: 'bundled',
-            presets: ['@babel/preset-env', '@babel/preset-react'],
-            plugins: [inlineReactSvg],
-        }),
-        postcss({
-            extensions: ['.css'],
-            inject: true,
-            minimize: true,
-        }),
-        url({
-            include: ['**/*.svg'], // Only SVG files
-            limit: 0, // 0 bytes
-            emitFiles: true,
-        }),
-        commonjs(),
-        terser(),
-        json(),
-        nodePolyfills(),
-        image(),
-    ],
-    onwarn,
+/*
+ * @Author       : Lihao leolihao@arizona.edu
+ * @Date         : 2023-12-01 12:51:04
+ * @FilePath     : /visualifyjs/rollup.config.mjs
+ * @Description  :
+ * Copyright (c) 2023 by Lihao (leolihao@arizona.edu), All Rights Reserved.
+ */
+// rollup.config.js
+import resolve from '@rollup/plugin-node-resolve';
+import commonjs from '@rollup/plugin-commonjs';
+import babel from '@rollup/plugin-babel';
+import replace from '@rollup/plugin-replace';
+import terser from '@rollup/plugin-terser';
+import json from '@rollup/plugin-json';
+import postcss from 'rollup-plugin-postcss';
+import nodePolyfills from 'rollup-plugin-polyfill-node';
+import image from '@rollup/plugin-image';
+import inlineReactSvg from 'babel-plugin-inline-react-svg';
+import url from '@rollup/plugin-url';
+
+//import css from 'rollup-plugin-css-only';
+
+function onwarn(warning, warn) {
+    if (warning.code === 'MODULE_LEVEL_DIRECTIVE') {
+        return;
+    }
+    warn(warning);
+}
+
+export default {
+    input: 'src/index.js',
+    output: [{
+            dir: 'dist/',
+            format: 'esm',
+            entryFileNames: 'visualify.js',
+            inlineDynamicImports: true,
+            sourcemap: false,
+        },
+        {
+            dir: 'docs/static/js',
+            format: 'esm',
+            entryFileNames: 'visualify.js',
+            inlineDynamicImports: true,
+            sourcemap: false,
+        },
+    ],
+    plugins: [
+        replace({
+            preventAssignment: true,
+            'process.env.NODE_ENV': JSON.stringify('production'),
+        }),
+        resolve({ browser: true }),
+        babel({
+            exclude: 'node_modules/**',
+            babelHelpers: 'bundled',
+            presets: ['@babel/preset-env', '@babel/preset-react'],
+            plugins: [inlineReactSvg],
+        }),
+        postcss({
+            extensions: ['.css'],
+            inject: true,
+            minimize: true,
+        }),
+        url({
+            include: ['**/*.svg'], // Only SVG files
+            limit: 0, // 0 bytes
+            emitFiles: true,
+        }),
+        commonjs(),
+        terser(),
+        json(),
+        nodePolyfills(),
+        image(),
+    ],
+    onwarn,
 };

package/src/_css/404.css

@@ -1,116 +1,116 @@
-* {
-    -webkit-box-sizing: border-box;
-    box-sizing: border-box;
-}
-
-body.colorlib-body {
-    padding: 0;
-    margin: 0;
-}
-
-#colorlib-notfound {
-    min-height: 60vh;
-    /* Ensures that the container takes at least the full viewport height */
-    position: relative;
-    display: flex;
-    flex-direction: column;
-    /* Stack children vertically */
-    justify-content: center;
-    /* Center children vertically */
-    align-items: center;
-    /* Center children horizontally */
-    padding: 3rem 1rem;
-    /* Add some padding around */
-}
-
-.colorlib-notfound {
-    max-width: 767px;
-    width: -moz-fit-content;
-    width: fit-content;
-    line-height: 1.4;
-    padding: 0 15px;
-    text-align: center;
-    /* Center the text */
-}
-
-.colorlib-notfound .colorlib-notfound-404 {
-    position: relative;
-    height: 150px;
-    line-height: 150px;
-    margin-bottom: 25px;
-}
-
-.colorlib-notfound .colorlib-notfound-404 h1 {
-    font-family: 'Titillium Web', sans-serif;
-    font-size: 186px;
-    font-weight: 900;
-    margin: 0;
-    text-transform: uppercase;
-    background: url('../_media/404.png') no-repeat center;
-    -webkit-background-clip: text;
-    background-clip: text;
-    -webkit-text-fill-color: transparent;
-    background-size: cover;
-}
-
-.colorlib-notfound h2 {
-    font-family: 'Titillium Web', sans-serif;
-    font-size: 26px;
-    font-weight: 700;
-    margin: 0;
-}
-
-.colorlib-notfound p {
-    font-family: 'Montserrat', sans-serif;
-    font-size: 14px;
-    font-weight: 500;
-    margin-bottom: 0;
-    text-transform: uppercase;
-}
-
-.colorlib-notfound a {
-    font-family: 'Titillium Web', sans-serif;
-    display: inline-block;
-    text-transform: uppercase;
-    color: #fff;
-    text-decoration: none;
-    background: #5c91fe;
-    padding: 10px 40px;
-    font-size: 14px;
-    font-weight: 700;
-    border-radius: 1px;
-    margin-top: 15px;
-    -webkit-transition: 0.2s all;
-    transition: 0.2s all;
-}
-
-.colorlib-notfound a:hover {
-    opacity: 0.8;
-}
-
-.colorlib-copyrigh {
-    font-size: 0.8rem;
-    text-align: center;
-    margin-top: 20px;
-    width: 100%;
-    position: absolute;
-    /* Make it break out of the flexbox */
-    bottom: 10px;
-    /* Position it at the bottom of the page */
-}
-
-@media only screen and (max-width: 767px) {
-    .colorlib-notfound .colorlib-notfound-404 {
-        height: 110px;
-        line-height: 110px;
-    }
-    .colorlib-notfound .colorlib-notfound-404 h1 {
-        font-size: 120px;
-    }
-}
-
-@media only screen and (max-height: 600px) {
-    #colorlib-notfound {
-        min-height: 100vh;
-    }
+* {
+    -webkit-box-sizing: border-box;
+    box-sizing: border-box;
+}
+
+body.colorlib-body {
+    padding: 0;
+    margin: 0;
+}
+
+#colorlib-notfound {
+    min-height: 60vh;
+    /* Ensures that the container takes at least the full viewport height */
+    position: relative;
+    display: flex;
+    flex-direction: column;
+    /* Stack children vertically */
+    justify-content: center;
+    /* Center children vertically */
+    align-items: center;
+    /* Center children horizontally */
+    padding: 3rem 1rem;
+    /* Add some padding around */
+}
+
+.colorlib-notfound {
+    max-width: 767px;
+    width: -moz-fit-content;
+    width: fit-content;
+    line-height: 1.4;
+    padding: 0 15px;
+    text-align: center;
+    /* Center the text */
+}
+
+.colorlib-notfound .colorlib-notfound-404 {
+    position: relative;
+    height: 150px;
+    line-height: 150px;
+    margin-bottom: 25px;
+}
+
+.colorlib-notfound .colorlib-notfound-404 h1 {
+    font-family: 'Titillium Web', sans-serif;
+    font-size: 186px;
+    font-weight: 900;
+    margin: 0;
+    text-transform: uppercase;
+    background: url('../_media/404.png') no-repeat center;
+    -webkit-background-clip: text;
+    background-clip: text;
+    -webkit-text-fill-color: transparent;
+    background-size: cover;
+}
+
+.colorlib-notfound h2 {
+    font-family: 'Titillium Web', sans-serif;
+    font-size: 26px;
+    font-weight: 700;
+    margin: 0;
+}
+
+.colorlib-notfound p {
+    font-family: 'Montserrat', sans-serif;
+    font-size: 14px;
+    font-weight: 500;
+    margin-bottom: 0;
+    text-transform: uppercase;
+}
+
+.colorlib-notfound a {
+    font-family: 'Titillium Web', sans-serif;
+    display: inline-block;
+    text-transform: uppercase;
+    color: #fff;
+    text-decoration: none;
+    background: #5c91fe;
+    padding: 10px 40px;
+    font-size: 14px;
+    font-weight: 700;
+    border-radius: 1px;
+    margin-top: 15px;
+    -webkit-transition: 0.2s all;
+    transition: 0.2s all;
+}
+
+.colorlib-notfound a:hover {
+    opacity: 0.8;
+}
+
+.colorlib-copyrigh {
+    font-size: 0.8rem;
+    text-align: center;
+    margin-top: 20px;
+    width: 100%;
+    position: absolute;
+    /* Make it break out of the flexbox */
+    bottom: 10px;
+    /* Position it at the bottom of the page */
+}
+
+@media only screen and (max-width: 767px) {
+    .colorlib-notfound .colorlib-notfound-404 {
+        height: 110px;
+        line-height: 110px;
+    }
+    .colorlib-notfound .colorlib-notfound-404 h1 {
+        font-size: 120px;
+    }
+}
+
+@media only screen and (max-height: 600px) {
+    #colorlib-notfound {
+        min-height: 100vh;
+    }
 }

package/src/_css/App.css

@@ -1,38 +1,38 @@
-.App {
-    text-align: center;
-}
-
-.App-logo {
-    height: 20vmin;
-    pointer-events: none;
-}
-
-@media (prefers-reduced-motion: no-preference) {
-    .App-logo {
-        animation: App-logo-spin infinite 20s linear;
-    }
-}
-
-.App-header {
-    background-color: #282c34;
-    min-height: 10vh;
-    display: flex;
-    flex-direction: column;
-    align-items: center;
-    justify-content: center;
-    font-size: calc(10px + 2vmin);
-    color: white;
-}
-
-.App-link {
-    color: #61dafb;
-}
-
-@keyframes App-logo-spin {
-    from {
-        transform: rotate(0deg);
-    }
-    to {
-        transform: rotate(360deg);
-    }
+.App {
+    text-align: center;
+}
+
+.App-logo {
+    height: 20vmin;
+    pointer-events: none;
+}
+
+@media (prefers-reduced-motion: no-preference) {
+    .App-logo {
+        animation: App-logo-spin infinite 20s linear;
+    }
+}
+
+.App-header {
+    background-color: #282c34;
+    min-height: 10vh;
+    display: flex;
+    flex-direction: column;
+    align-items: center;
+    justify-content: center;
+    font-size: calc(10px + 2vmin);
+    color: white;
+}
+
+.App-link {
+    color: #61dafb;
+}
+
+@keyframes App-logo-spin {
+    from {
+        transform: rotate(0deg);
+    }
+    to {
+        transform: rotate(360deg);
+    }
 }