Merge remote-tracking branch 'origin/master' into imessage

.github/workflows/build-extension.yml

@@ -1,9 +1,6 @@
 name: Build extension
 
 on:
-  push:
-    branches:
-    - '*'
   pull_request:
     branches:
     - '*'
@@ -14,11 +11,15 @@ jobs:
     steps:
     - name: Checkout
       uses: actions/checkout@v3
-    - name: Install node
+
+    - name: Set up Node.js
       uses: actions/setup-node@v3
       with:
-       node-version: '20.x'
-       npm-version: '10.9.0'
+        node-version: 'lts/*'
+
+    - name: Install Yarn
+      run: corepack enable
+
     - name: Install Python
       uses: actions/setup-python@v4
       with:
@@ -37,6 +38,7 @@ jobs:
     - name: Get yarn cache directory path
       id: yarn-cache-dir-path
       run: echo "::set-output name=dir::$(yarn cache dir)"
+
     - name: Setup yarn cache
       uses: actions/cache@v3
       id: yarn-cache
@@ -48,9 +50,10 @@ jobs:
 
     - name: Install dependencies
       run: python -m pip install -U jupyterlab jupyter_packaging jupyterlab_widgets
+
     - name: Use existing lockfile
       run: yarn install --frozen-lockfile
+
     - name: Build the extension
       working-directory: js
-      run: |
-        npm install
+      run: npm install

.github/workflows/test.yml

@@ -1,7 +1,6 @@
 name: Test
 
 on:
-  push:
   pull_request:
   workflow_dispatch:
 
@@ -44,6 +43,20 @@ jobs:
         python-version: ${{ matrix.python-version }}
         use-only-tar-bz2: false  # https://github.com/conda-incubator/setup-miniconda/issues/264
 
+    - name: Set up Node.js
+      uses: actions/setup-node@v3
+      with:
+        node-version: 'lts/*'
+
+    - name: Install Yarn
+      run: corepack enable
+
+    - name: Build labextension
+      run: |
+        cd js
+        npm install
+        cd ..
+
     - name: Run tests
       run: |
         python -m pytest -vs tests --cov=nglview --cov-report=html --disable-pytest-warnings

MANIFEST.in

@@ -1,6 +1,6 @@
 include nglview/datafiles/*
-recursive-include nglview/static *.*
-recursive-include nglview/staticlab *.*
+recursive-include nglview/nbextension *.*
+recursive-include nglview/labextension *.*
 include nglview/theme/*
 include LICENSE README.md DEVELOPMENT.md CHANGELOG.md
 include setup.py

devtools/create_labextension_symlink.py

@@ -0,0 +1,56 @@
+import os
+import sys
+import argparse
+from pathlib import Path
+
+
+def get_extension_paths():
+    base_dir = Path(sys.prefix)
+    nglview_js_widgets = "nglview-js-widgets"
+    nbextension_dest = base_dir / "share" / "jupyter" / "nbextensions" / nglview_js_widgets
+    labextension_dest = base_dir / "share" / "jupyter" / "labextensions" / nglview_js_widgets
+    return nbextension_dest, labextension_dest
+
+
+def create_symlink(source, destination):
+    try:
+        if os.path.islink(destination):
+            os.remove(destination)
+        os.symlink(source, destination)
+        print(f"Created symlink: {destination} -> {source}")
+    except OSError as e:
+        print(f"Failed to create symlink: {e}", file=sys.stderr)
+
+
+def remove_symlink(destination):
+    try:
+        if os.path.islink(destination):
+            os.remove(destination)
+            print(f"Removed symlink: {destination}")
+        else:
+            print(f"No symlink to remove at: {destination}")
+    except OSError as e:
+        print(f"Failed to remove symlink: {e}", file=sys.stderr)
+
+
+def main():
+    parser = argparse.ArgumentParser(description="Create or remove symlinks for nbextension and labextension.")
+    parser.add_argument('-d', '--delete', action='store_true', help="Remove the symlinks instead of creating them.")
+    args = parser.parse_args()
+
+    nbextension_dest, labextension_dest = get_extension_paths()
+
+    base_dir = Path(__file__).resolve().parent.parent
+    nbextension_source = base_dir / 'nglview' / 'nbextension'
+    labextension_source = base_dir / 'nglview' / 'labextension'
+
+    if args.delete:
+        remove_symlink(nbextension_dest)
+        remove_symlink(labextension_dest)
+    else:
+        create_symlink(nbextension_source, nbextension_dest)
+        create_symlink(labextension_source, labextension_dest)
+
+
+if __name__ == "__main__":
+    main()

devtools/release.py

@@ -1,19 +1,5 @@
 #!/usr/bin/env python
 
-"""
-Steps:
-    - cd nglview/static
-    - git rm -rf ./*
-
-    - cd nglview/staticlab
-    - git rm -rf ./*
-
-    - cd js
-    - npm install
-    - cd ../nglview
-    - git add static staticlab
-"""
-
 import subprocess
 import sys
 from pathlib import Path

js/DEVELOPMENT.md

@@ -0,0 +1,2 @@
+yarn==1.22.19
+node==22.11.0

js/package.json

@@ -35,7 +35,7 @@
   },
   "scripts": {
     "prepublish": "yarn build:prod && webpack && yarn run copy:labextension",
-    "copy:labextension": "cp -r nglview-js-widgets/labextension/* ../nglview/staticlab/",
+    "copy:labextension": "mkdir -p ../nglview/labextension && cp -r nglview-js-widgets/labextension/* ../nglview/labextension/",
     "build": "yarn run build:lib && yarn run build:labextension:dev",
     "build:prod": "yarn run build:lib && yarn run build:labextension",
     "build:labextension": "jupyter labextension build .",
@@ -52,6 +52,7 @@
     "watch": "run-p watch:src watch:labextension",
     "watch:src": "tsc -w",
     "watch:labextension": "jupyter labextension watch .",
+    "watch:install": "nodemon --watch src/widget_ngl.ts --exec 'npm install'",
     "test": "mocha"
   },
   "dependencies": {
@@ -89,7 +90,8 @@
     "webpack": "^5.96.1",
     "webpack-cli": "^5.1.4",
     "babel-loader": "^8.2.2",
-    "@babel/plugin-transform-object-rest-spread": "^7.14.5"
+    "@babel/plugin-transform-object-rest-spread": "^7.14.5",
+    "nodemon": "^2.0.22"
   },
   "sideEffects": [
     "style/*.css",

js/src/widget_ngl.ts

@@ -266,13 +266,16 @@ export
         }, this);
 
         this.stage.viewerControls.signals.changed.add(function () {
-            this.serialize_camera_orientation();
+            setTimeout(() => {
+                // https://github.com/nglviewer/nglview/issues/948#issuecomment-898121063
+                this.serialize_camera_orientation();
+            }, 100);
+
             var m = this.stage.viewerControls.getOrientation();
             if (that._synced_model_ids.length > 0 && that._ngl_focused == 1) {
                 that._synced_model_ids.forEach(async function (mid) {
                     var model = await that.model.widget_manager.get_model(mid)
                     for (var k in model.views) {
-                        var pview = model.views[k];
                         var view = await model.views[k]
                         if (view.uuid != that.uuid) {
                             view.stage.viewerControls.orient(m);

js/webpack.config.js

@@ -30,7 +30,7 @@ module.exports = [
         entry: './lib/extension.js',
         output: {
             filename: 'extension.js',
-            path: path.resolve(__dirname, '..', 'nglview', 'static'),
+            path: path.resolve(__dirname, '..', 'nglview', 'nbextension'),
             libraryTarget: 'amd'
         },
         mode: 'production'
@@ -44,7 +44,7 @@ module.exports = [
         entry: './lib/index.js',
         output: {
             filename: 'index.js',
-            path: path.resolve(__dirname, '..', 'nglview', 'static'),
+            path: path.resolve(__dirname, '..', 'nglview', 'nbextension'),
             libraryTarget: 'amd'
         },
         devtool: 'source-map',

nglview/__init__.py

@@ -35,7 +35,7 @@
 def _jupyter_nbextension_paths():
     return [{
         'section': 'notebook',
-        'src': 'static',
+        'src': 'nbextension',
         'dest': 'nglview-js-widgets',
         'require': 'nglview-js-widgets/extension'
     }]

nglview/widget.py

@@ -63,17 +63,15 @@ def wrap_2(*args, **kwargs):
 
 
 def write_html(fp, views, frame_range=None):
-    # type: (str, List[NGLWidget]) -> None
-    """EXPERIMENTAL. Likely will be changed.
-
-    Make html file to display a list of views. For further options, please
-    check `ipywidgets.embed` module.
+    """
+    Write html file to display a list of views.
 
     Parameters
     ----------
     fp : str or file handle
     views : a DOMWidget view or a list of views.
     frame_range : None or a tuple of int
+        if None, do not serialize coordinates
 
     Examples
     --------
@@ -286,6 +284,8 @@ def on_change_layout(change):
     def _set_serialization(self, frame_range=None):
         self._ngl_serialize = True
         resource = self._ngl_coordinate_resource
+        if frame_range is None and self._trajlist:
+            print("frame_range is not provided. Do not serialize coordinates. Default to use current frame.")
         if frame_range is not None:
             for t_index, traj in enumerate(self._trajlist):
                 resource[t_index] = []

notebooks/orientation.ipynb

@@ -0,0 +1,119 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "id": "82035655-b580-4e4d-86bf-5a90563c2840",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "c7cd4ef8a8ca410c96f8cad4d48928b2",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "NGLWidget()"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import nglview as nv\n",
+    "\n",
+    "view = nv.demo()\n",
+    "view"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "id": "7bf1502e-ce30-4b5c-9a72-5a2360322c82",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view.control.rotate([0.6, -0.4, 0.3, -0.4])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "id": "d07a8c2b-806d-42c6-b841-e49460688348",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "nv.write_html('index.html', view)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "id": "f397830a-2c05-4275-bdbe-40e0b58f621a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!open index.html"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "id": "5c00397d-cdd4-4196-91e4-fb55d98774a0",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[65.20023905320915,\n",
+       " -93.88834423662117,\n",
+       " 5.2160191242567215,\n",
+       " 0,\n",
+       " -31.29611474554039,\n",
+       " 13.040047810641841,\n",
+       " -93.88834423662117,\n",
+       " 0,\n",
+       " 88.67232511236445,\n",
+       " 31.29611474554039,\n",
+       " -5.216019124256737,\n",
+       " 0,\n",
+       " -37.284461975097656,\n",
+       " -42.47041130065918,\n",
+       " -44.55349826812744,\n",
+       " 1]"
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "view._camera_orientation"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.12.7"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}