update MVS Stories app and deploy scripts (#1574)

* update MVS Stories app and deploy scripts

* reorder changelog

.gitignore

@@ -1,4 +1,5 @@
 build/
+deploy/
 lib/
 docs/site/
 

CHANGELOG.md

@@ -4,6 +4,13 @@ All notable changes to this project will be documented in this file, following t
 Note that since we don't clearly distinguish between a public and private interfaces there will be changes in non-major versions that are potentially breaking. If we make breaking changes to less used interfaces we will highlight it in here.
 
 ## [Unreleased]
+- [Breaking] Renamed some color schemes ('inferno' -> 'inferno-no-black', 'magma' -> 'magma-no-black', 'turbo' -> 'turbo-no-black', 'rainbow' -> 'simple-rainbow')
+- [Breaking] `Box3D.nearestIntersectionWithRay` -> `nearestIntersectionWithRay3D` (use `Ray3D`)
+- [Breaking] `Plane3D.distanceToSpher3D` -> `distanceToSphere3D` (fix spelling)
+- [Breaking] fix typo `MarchinCubes` -> `MarchingCubes`
+- [Breaking] `PluginContext.initViewer/initContainer/mount` are now async and have been renamed to include `Async` postfix
+- [Breaking] Add `Volume.instances` support and a `VolumeInstances` transform to dynamically assign it
+  - This change is breaking because all volume objects require the `instances` field now.
 - Update production build to use `esbuild`
 - Emit explicit paths in `import`s in `lib/`
 - Fix outlines on opaque elements using illumination mode
@@ -21,7 +28,6 @@ Note that since we don't clearly distinguish between a public and private interf
   - Support `matrix` on transform params
   - Add `instance` node type
   - Support transforming and instancing of structures, components, and volumes
-- [Breaking] Renamed some color schemes ('inferno' -> 'inferno-no-black', 'magma' -> 'magma-no-black', 'turbo' -> 'turbo-no-black', 'rainbow' -> 'simple-rainbow')
 - Added new color schemes, synchronized with D3.js ('inferno', 'magma', 'turbo', 'rainbow', 'sinebow', 'warm', 'cool', 'cubehelix-default', 'category-10', 'observable-10', 'tableau-10')
 - Snapshot Markdown improvements
   - Add `MarkdownExtensionManager` (`PluginContext.managers.markdownExtensions`)
@@ -34,21 +40,16 @@ Note that since we don't clearly distinguish between a public and private interf
 - Fix isosurface compute shader normals when transformation matrix is applied to volume
 - Symmetry operator naming for spacegroup symmetry - parenthesize multi-character indices (1_111-1 -> 1_(11)1(-1))
 - Add `SymmetryOperator.instanceId` that corresponds to a canonical operator name (e.g. ASM-1, ASM-X0-1 for assemblies, 1_555, 1_(11)1(-1) for crystals)
-- [Breaking] `PluginContext.initViewer/initContainer/mount` are now async and have been renamed to include `Async` postfix
 - Mol2 Reader
     - Fix column count parsing
     - Add support for substructure
 - Fix shader error when clipping flags are set without clip objects present
-- [Breaking] Add `Volume.instances` support and a `VolumeInstances` transform to dynamically assign it
-  - This change is breaking because all volume objects require the `instances` field now.
 - Fix wrong group count calculation on geometry update (#1562)
 - Fix wrong instance index in `calcMeshColorSmoothing`
 - Add `Ray3D` object and helpers
-- [Breaking] `Box3D.nearestIntersectionWithRay` -> `nearestIntersectionWithRay3D` (use `Ray3D`)
-- [Breaking] `Plane3D.distanceToSpher3D` -> `distanceToSphere3D` (fix spelling)
-- [Breaking] fix typo `MarchinCubes` -> `MarchingCubes`
 - Volume slice representation: add `relativeX/Y/Z` options for dimension
 - Add `StructureInstances` transform
+- Add `story-id` URL arg support to `mvs-stories` app
 
 ## [v4.18.0] - 2025-06-08
 - MolViewSpec extension:

README.md

@@ -190,9 +190,14 @@ To get syntax highlighting for shader files add the following to Visual Code's s
     npm publish
 
 ## Deploy
+To prepare apps and demos for https://molstar.org deploy, run:
+
     npm run test
-    npm run build
+    npm run deploy:local
-    node ./scripts/deploy.js # currently updates the viewer on molstar.org/viewer
+
+To commit these changes remotely to the `molstar/molstar.github.io` repo:
+
+    npm run deploy:remote
 
 ## Contributing
 Just open an issue or make a pull request. All contributions are welcome.

package.json

@@ -18,7 +18,8 @@
     "lint-fix": "eslint . --fix",
     "test": "npm install --no-save \"gl@^6.0.2\" && npm run lint && jest",
     "jest": "jest",
-    "clean": "node ./scripts/clean.js",
+    "clean": "node ./scripts/clean.js --all",
+    "clean:build": "node ./scripts/clean.js --build",
     "build": "npm run build:apps && npm run build:lib",
     "build:apps": "node ./scripts/build.mjs -a -e --prd",
     "build:lib": "concurrently \"tsc --incremental\" \"tsc --build tsconfig.commonjs.json --incremental\" && npm run build:lib-extra",
@@ -31,6 +32,8 @@
     "dev:examples": "node ./scripts/build.mjs -e",
     "dev:browser-tests": "node ./scripts/build.mjs -bt",
     "serve": "http-server -p 1338 -g",
+    "deploy:local": "npm run clean:build && npm run build:apps && node ./scripts/deploy.js --local",
+    "deploy:remote": "npm run clean:build && npm run build:apps && node ./scripts/deploy.js",
     "model-server": "node lib/commonjs/servers/model/server.js",
     "model-server-watch": "nodemon --watch lib lib/commonjs/servers/model/server.js",
     "volume-server-test": "node lib/commonjs/servers/volume/server.js --idMap em 'test/${id}.mdb' --defaultPort 1336",

scripts/clean.js

@@ -6,6 +6,7 @@
 
 const fs = require('fs');
 const path = require('path');
+const argparse = require('argparse');
 
 function removeDir(dirPath) {
     for (const ent of fs.readdirSync(dirPath)) {
@@ -24,11 +25,29 @@ function remove(entryPath) {
         fs.unlinkSync(entryPath);
 }
 
-const toClean = [
+const argParser = new argparse.ArgumentParser({
-    path.resolve(__dirname, '../build'),
+    add_help: true,
-    path.resolve(__dirname, '../lib'),
+    description: 'Clean Script'
-    path.resolve(__dirname, '../tsconfig.tsbuildinfo'),
+});
-];
+argParser.add_argument('--build', { required: false, action: 'store_true' });
+argParser.add_argument('--lib', { required: false, action: 'store_true' });
+argParser.add_argument('--all', { required: false, action: 'store_true' });
+const args = argParser.parse_args();
+
+const toClean = [];
+
+if (args.build || args.all) {
+    toClean.push(path.resolve(__dirname, '../build'));
+    toClean.push(path.resolve(__dirname, '../deploy/data'));
+}
+if (args.lib || args.all) {
+    toClean.push(
+        path.resolve(__dirname, '../lib'),
+        path.resolve(__dirname, '../tsconfig.tsbuildinfo'),
+    );
+}
+
+console.log('\n###', 'cleaning', toClean.join(', '));
 
 toClean.forEach(ph => {
     if (fs.existsSync(ph)) {

scripts/deploy.js

@@ -2,20 +2,24 @@
  * Copyright (c) 2019-2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
  *
  * @author Alexander Rose <alexander.rose@weirdbyte.de>
+ * @author David Sehnal <david.sehnal@gmail.com>
  */
 
 const git = require('simple-git');
 const path = require('path');
 const fs = require("fs");
 const fse = require("fs-extra");
+const argparse = require('argparse');
 
 const VERSION = require(path.resolve(__dirname, '../package.json')).version;
+const MVS_STORIES_VERSION = require(path.resolve(__dirname, '../src/apps/mvs-stories/version.ts')).VERSION;
 
 const remoteUrl = "https://github.com/molstar/molstar.github.io.git";
 const dataDir = path.resolve(__dirname, '../data/');
 const buildDir = path.resolve(__dirname, '../build/');
-const deployDir = path.resolve(buildDir, 'deploy/');
+const deployDir = path.resolve(__dirname, '../deploy/');
-const localPath = path.resolve(deployDir, 'molstar.github.io/');
+const localPath = path.resolve(deployDir, 'data/');
+const repositoryPath = path.resolve(deployDir, 'molstar.github.io/');
 
 const analyticsTag = /<!-- __MOLSTAR_ANALYTICS__ -->/g;
 const analyticsCode = `<!-- Cloudflare Web Analytics --><script defer src='https://static.cloudflareinsights.com/beacon.min.js' data-cf-beacon='{"token": "c414cbae2d284ea995171a81e4a3e721"}'></script><!-- End Cloudflare Web Analytics --><iframe src="https://web3dsurvey.com/collector-iframe.html" style="width: 1px; height: 1px;"></iframe>`;
@@ -80,54 +84,106 @@ function copyMe() {
     addAnalytics(path.resolve(meDeployPath, 'index.html'));
 }
 
+function copyMVSStories() {
+    console.log('\n###', 'copy MVS stories files');
+    const mvsStoriesBuildPath = path.resolve(buildDir, 'mvs-stories/');
+    const mvsStoriesDeployPath = path.resolve(localPath, `stories-viewer/v${MVS_STORIES_VERSION}/`);
+    fse.copySync(mvsStoriesBuildPath, mvsStoriesDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(mvsStoriesDeployPath, 'index.html'));
+
+    // TODO: add PWA
+    // addManifest(path.resolve(mvsStoriesDeployPath, 'index.html'));
+    // addPwa(path.resolve(mvsStoriesDeployPath, 'index.html'));
+}
+
+function copyDemo(name) {
+    console.log('\n###', `copy demo files for ${name}`);
+    const demoBuildPath = path.resolve(buildDir, `examples/${name}/`);
+    const demoDeployPath = path.resolve(localPath, `demos/${name}/`);
+    fse.copySync(demoBuildPath, demoDeployPath, { overwrite: true });
+    addAnalytics(path.resolve(demoDeployPath, 'index.html'));
+}
+
 function copyDemos() {
     console.log('\n###', 'copy demos files');
-    const lightingBuildPath = path.resolve(buildDir, 'examples/lighting/');
+    copyDemo('lighting');
-    const lightingDeployPath = path.resolve(localPath, 'demos/lighting/');
+    copyDemo('alpha-orbitals');
-    fse.copySync(lightingBuildPath, lightingDeployPath, { overwrite: true });
+    copyDemo('mvs-stories');
-    addAnalytics(path.resolve(lightingDeployPath, 'index.html'));
-
-    const orbitalsBuildPath = path.resolve(buildDir, 'examples/alpha-orbitals/');
-    const orbitalsDeployPath = path.resolve(localPath, 'demos/alpha-orbitals/');
-    fse.copySync(orbitalsBuildPath, orbitalsDeployPath, { overwrite: true });
-    addAnalytics(path.resolve(orbitalsDeployPath, 'index.html'));
 }
 
 function copyFiles() {
     try {
         copyViewer();
         copyMe();
+        copyMVSStories();
         copyDemos();
     } catch (e) {
         console.error(e);
     }
 }
 
+function copyToRepository() {
+    console.log('\n###', 'copy repository files');
+    fse.copySync(localPath, repositoryPath, { overwrite: true });
+}
+
+function syncRepository() {
+    console.log('\n###', 'sync repository');
+    if (!fs.existsSync(path.resolve(repositoryPath, '.git/'))) {
+        console.log('\n###', 'clone repository');
+        git()
+            .outputHandler(log)
+            .clone(remoteUrl, repositoryPath)
+            .fetch(['--all'])
+            .exec(copyToRepository);
+    } else {
+        console.log('\n###', 'update repository');
+        git()
+            .outputHandler(log)
+            .fetch(['--all'])
+            .reset(['--hard', 'origin/master'])
+            .exec(copyToRepository);
+    }
+}
+
+function commit() {
+    console.log('\n###', 'commit changes');
+    git()
+        .outputHandler(log)
+        .add(['-A'])
+        .commit(`Updated Apps and Demos
+- Mol* version: ${VERSION}
+- MVS Stories version: ${MVS_STORIES_VERSION}`)
+        .push();
+}
+
 if (!fs.existsSync(localPath)) {
     console.log('\n###', 'create localPath');
     fs.mkdirSync(localPath, { recursive: true });
 }
 
-process.chdir(localPath);
+const argParser = new argparse.ArgumentParser({
+    add_help: true,
+    description: 'Mol* Deploy'
+});
+argParser.add_argument('--local',{
+    help: 'Do not commit to remote repository.',
+    required: false,
+    action: 'store_true',
+});
+const args = argParser.parse_args();
 
-if (!fs.existsSync(path.resolve(localPath, '.git/'))) {
+copyFiles();
-    console.log('\n###', 'clone repository');
+
-    git()
+if (args.local) {
-        .outputHandler(log)
+    process.exit(0);
-        .clone(remoteUrl, localPath)
+}
-        .fetch(['--all'])
+
-        .exec(copyFiles)
+if (!fs.existsSync(repositoryPath)) {
-        .add(['-A'])
+    console.log('\n###', 'create repositoryPath');
-        .commit('updated viewer & demos')
+    fs.mkdirSync(repositoryPath, { recursive: true });
-        .push();
+}
-} else {
+
-    console.log('\n###', 'update repository');
+process.chdir(repositoryPath);
-    git()
+syncRepository();
-        .outputHandler(log)
+commit();
-        .fetch(['--all'])
-        .reset(['--hard', 'origin/master'])
-        .exec(copyFiles)
-        .add(['-A'])
-        .commit('updated viewer & demos')
-        .push();
-}

src/apps/mvs-stories/index.html

@@ -76,6 +76,7 @@
 
     <script>
         var urlParams = new URLSearchParams(window.location.search);
+        var storyId = urlParams.get('story-id');
         var storyUrl = urlParams.get('story-url');
         var format = urlParams.get('data-format');
 
@@ -84,11 +85,13 @@
         //     storyUrl = 'https://raw.githubusercontent.com/molstar/molstar/master/examples/mvs/kinase-story.mvsj';
         // }
 
-        mvsStories.loadFromURL(
+        if (storyId) {
-            storyUrl,
+            mvsStories.loadFromID(storyId, { contextName: 'story1' });
-            { format: format || 'mvsj', contextName: 'story1' },
+        } else if (storyUrl) {
-        );
+            mvsStories.loadFromURL(storyUrl, { format: format || 'mvsj', contextName: 'story1' });
+        }
     </script>
+    <!-- __MOLSTAR_ANALYTICS__ -->
 </body>
 
 </html>

src/apps/mvs-stories/index.tsx

@@ -37,4 +37,15 @@ export function loadFromData(data: MVSData | string | Uint8Array, options?: { fo
     }, 0);
 }
 
+function getStoryUrlFromId(id: string, format: 'mvsx' | 'mvsj' = 'mvsj') {
+    return `https://stories.molstar.org/api/story/${id}/data`;
+}
+
+export function loadFromID(id: string, options?: { format?: 'mvsx' | 'mvsj', contextName?: string }) {
+    loadFromURL(
+        getStoryUrlFromId(id, options?.format),
+        { format: options?.format ?? 'mvsj', contextName: options?.contextName },
+    );
+}
+
 export { MVSData };

src/apps/mvs-stories/version.ts

@@ -0,0 +1,7 @@
+/**
+ * Copyright (c) 2025 mol* contributors, licensed under MIT, See LICENSE file for more info.
+ *
+ * @author David Sehnal <david.sehnal@gmail.com>
+ */
+
+export const VERSION = 1;

src/examples/mvs-stories/index.html

@@ -118,6 +118,7 @@
             window.initStories();
         }, 0);
     </script>
+    <!-- __MOLSTAR_ANALYTICS__ -->
 </body>
 
 </html>