Merge branch 'master' into patch-1

.devcontainer/devcontainers.json

@@ -0,0 +1,13 @@
+{
+    "postCreateCommand": "nvm install 16.16.0 && npm run build",
+    "customizations": {
+        "vscode": {
+            "extensions": [
+                "ritwickdey.LiveServer",
+                "github.vscode-github-actions",
+                "GitHub.vscode-pull-request-github",
+                "waderyan.gitblame"
+            ]
+        }
+    }
+}

.github/workflows/CI.yml

@@ -12,19 +12,27 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
+
       - uses: actions/setup-node@v3
         with:
-          node-version: lts/*
-      - name: Build
-        run: |
-          npm i npm@latest
-          npm install
+          node-version: 20
+
+      # As our package has a postInstall script, which in turn calls `npm run build`, hence we do not need a explicit job for that
+      - name: Install Dependencies & Build 3dmol.js
+        run: npm install 
+
       - name: Test    
         run: npm test
+
       - name: Coverage
         env:
-          NODE_OPTIONS: "--max_old_space_size=8192"      
+          NODE_OPTIONS: "--max_old_space_size=8192"   
+        # coverage has trouble fetching data for some reason in the CI,
+        # I don't actually care about the test results (that's tested above)
+        # so ignore any failure here
         run: npm run cover
+        continue-on-error: true
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
 

.github/workflows/CodeQL-Analysis.yml

@@ -0,0 +1,58 @@
+name: "CodeQL"
+
+on:
+  workflow_dispatch:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  analyze:
+    name: Analyze
+    runs-on: ubuntu-latest
+    permissions:
+      actions: read
+      contents: read
+      security-events: write
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: [ 'javascript', 'python' ]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+
+    - uses: actions/setup-node@v3
+      with:
+        cache: npm
+        node-version: 20
+
+    - name: Cache NPM Dependencies
+      id: cache-npm
+      uses: actions/cache@v3
+      env:
+        cache-name: cache-node-modules
+      with:
+        path: node_modules
+        key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }}
+
+    # For CodeQL, we don't need to generate tests or doc, hence running only install
+    - name: Install Dependencies
+      run: npm install --ignore-scripts
+
+    # Build for dev and prod
+    - name: Build 3dmol.js
+      run: |
+        npm run build:dev
+        npm run build:prod
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v2
+      with:
+        languages: ${{ matrix.language }}
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v2

.github/workflows/dependency-review.yml

@@ -0,0 +1,19 @@
+name: Dependency Review
+on: [ pull_request ]
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
+    cancel-in-progress: true
+
+permissions:
+    contents: read
+
+jobs:
+  review:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Dependency Review
+        uses: actions/dependency-review-action@v3

.github/workflows/npm-publish.yml

@@ -0,0 +1,56 @@
+# This workflow will run tests using node and then publish a package to GitHub Packages when a release is created
+# For more information see: https://docs.github.com/en/actions/publishing-packages/publishing-nodejs-packages
+
+name: Node.js Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+        with:
+          cache: npm
+          node-version: 20
+
+      - uses: actions/cache@v3
+        with:
+          # npm cache files are stored in `~/.npm` on Linux/macOS
+          path: ~/.npm
+          key: ${{ runner.os }}-build-${{ hashFiles('**/package-lock.json') }}
+      - run: npm ci
+      - run: npm test
+
+  publish-npm:
+    needs: build
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-node@v3
+        with:
+          cache: npm
+          node-version: 20
+          registry-url: https://registry.npmjs.org/
+
+      - name: Cache NPM Dependencies
+        id: cache-npm
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-node-modules
+        with:
+          path: node_modules
+          key: ${{ runner.os }}-node-${{ hashFiles('package-lock.json') }}
+
+      - name: Check Cache & Install Dependencies
+        if: ${{ steps.cache-npm.outputs.cache-hit != 'true' }}
+        run: npm ci
+
+      - run: npm publish
+        env:
+          NODE_AUTH_TOKEN: ${{secrets.npm_token}}

.npmignore

@@ -1,4 +1,3 @@
-/tests
 /node_modules
 /tmp
 /coverage
@@ -8,6 +7,20 @@ script.map
 .settings
 .ipynb
 
+CODE_OF_CONDUCT.md
+CONTRIBUTING.md
+doc.md
+echo.cgi
+examples/
+index.html
+learning-environment/
+paper/
+py3Dmol/
+tests/
+track/
+tutorials/
+/viewer.*
+
 #Ignoring Virtual Environments for the Active Learning Environment Project
 .env
 .venv

CITATION.cff

@@ -0,0 +1,29 @@
+cff-version: 1.2.0
+title: '3Dmol.js: molecular visualization with WebGL'
+message: If you use 3Dmol.js, please cite our Bioinformatics paper
+type: software
+authors:
+  - given-names: David
+    family-names: Koes
+    email: [email protected]
+    affiliation: University of Pittsburgh
+    orcid: 'https://orcid.org/0000-0002-6892-6614'
+  - given-names: Nicholas
+    family-names: Rego
+    affiliation: University of Pittsburgh
+    orcid: 'https://orcid.org/0000-0002-3164-6803'
+identifiers:
+  - type: doi
+    value: 10.1093/bioinformatics/btu829
+repository-code: 'https://github.com/3dmol/3Dmol.js'
+url: 'https://3dmol.org/'
+abstract: >-
+  3Dmol.js is a modern, object-oriented JavaScript library
+  that uses the latest web technologies to provide
+  interactive, hardware-accelerated three-dimensional
+  representations of molecular data without the need to
+  install browser plugins or Java. 3Dmol.js provides a full
+  featured API for developers as well as a straightforward
+  declarative interface that lets users easily share and
+  embed molecular data in websites.
+license: BSD-3-Clause

CONTRIBUTING.md

@@ -8,7 +8,7 @@
 
  ## Feature Request
 
- 1. Please go through the 3Dmol.js [js documentation](http://3dmol.org/doc/index.html) to check whether the feature is already present.
+ 1. Please go through the 3Dmol.js [js documentation](https://3dmol.org/doc/index.html) to check whether the feature is already present.
  2. Ensure that the feature request is new and is not already proposed.
  3. If the feature request is new, follow the feature request template to submit an issue.
  4. Please close your issue when you think it has been adequately resolved.

codecov.yml

@@ -0,0 +1,18 @@
+coverage:
+  status:
+    project:
+      default:
+        # basic
+        target: auto
+        threshold: 0.05%
+        base: auto 
+        flags: 
+          - unit
+        paths: 
+          - "src"
+       # advanced settings
+        branches: 
+          - master
+        if_ci_failed: error #success, failure, error, ignore
+        informational: false
+        only_pulls: false

doc.md

@@ -15,20 +15,21 @@
 </script>
 
 3Dmol.js is an object-oriented, WebGL based JavaScript library for online molecular visualization - No Java required!
-With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications. Features include:
+With 3Dmol.js, you can add beautifully rendered molecular visualizations to your web applications. 
 
-* support for pdb, sdf, mol2, xyz, and cube formats
-* parallelized molecular surface computation
-* sphere, stick, line, cross, cartoon, and surface styles
-* atom property based selection and styling
-* labels
-* clickable interactivity with molecular data
-* geometric shapes including spheres and arrows
+Features include:
+
+- Support for pdb, sdf, mol2, xyz, and cube formats
+- Parallelized molecular surface computation
+- Sphere, stick, line, cross, cartoon, and surface styles
+- Atom property based selection and styling
+- Labels
+- Clickable interactivity with molecular data
+- Geometric shapes including spheres and arrows
 
 ## Getting Started
 
-Molecular data can be shared and visualized without writing any HTML
- using only a declarative URL specification and our hosted viewer (see {@tutorial url}).
+Molecular data can be shared and visualized without writing any HTML using only a declarative URL specification and our hosted viewer (see {@tutorial url}).
 
 Viewers can be quickly embedded in any HTML document using just two lines of source code (see {@tutorial embeddable}).
 
@@ -64,11 +65,11 @@ An un-minified file is also provided for debugging purposes:
 
 #### Method 2: using a CDN
 
-The files hosted by 3Dmol.org closely track the development version and so will change frequently. If you desire more stability you may copy the files into your own project or, alternatively, we host release snapshots on the <a href="https://cdnjs.com/libraries/3Dmol">cdnjs</a> content delivery network (note that you must specify the release version).
+The files hosted by 3Dmol.org closely track the development version and so will change frequently. If you desire more stability you may copy the files into your own project or, alternatively, we host release snapshots on the <a href="https://cdnjs.com/libraries/3Dmol">cdnjs</a> content delivery network (note that you must specify the release version). **Do not use the CDN minified version** (3Dmol-min.min.js).  The CDN autominifier does not generate correct code and `3Dmol-min.js` is alread minified.
 
 ```{@lang html}
-<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/1.8.0/3Dmol-min.js"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/1.8.0/3Dmol.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol-min.js"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/3Dmol/2.0.1/3Dmol.js"></script>
 ```
 
 Using the CDN will likely provide the best network performance to your users, but features will lag behind the development branch as we only plan to tag new releases a few times a year.