Exhibition widget and a more sane repr for closed UniverseWidget

auto_widget.py

@@ -0,0 +1,161 @@
+#!/usr/bin/env python
+"""
+
+Assumes the following environment:
+
+    export BROWSER=/path/to/chrome/executable
+
+    pip install selenium
+
+And that a chromedriver version matching BROWSER
+is in the PATH. (See install-chromedriver.sh)
+
+Note:
+    Hit enter to pass a failure to load extension
+    and continue the test. Not sure why disable-extensions
+    does not suppress that pop-up.
+
+"""
+import os
+import uuid
+import shutil
+from time import sleep
+import subprocess as sp
+
+from selenium import webdriver
+from selenium.webdriver.support import expected_conditions as EC
+from selenium.webdriver.common.action_chains import ActionChains
+from selenium.webdriver.common.by import By
+from selenium.webdriver.common.keys import Keys
+from selenium.webdriver.support.wait import WebDriverWait
+from selenium.webdriver.chrome.options import Options
+
+
+PORT = 8889
+TOKEN = str(uuid.uuid4())
+
+
+def start_notebook_server():
+    os.makedirs(TOKEN, exist_ok=True)
+    return sp.Popen(['jupyter', 'notebook',
+                     f'--NotebookApp.port={PORT}',
+                     f'--NotebookApp.token={TOKEN}'],
+                     stdout=sp.PIPE, stderr=sp.PIPE,
+                     cwd=TOKEN)
+
+
+def click_by_css(driver, wait, css):
+    wait.until(
+        EC.presence_of_element_located((By.CSS_SELECTOR, css))
+    )
+    [obj] = driver.find_elements_by_css_selector(css)
+    obj.click()
+
+
+def run_notebook_widget():
+    options = Options()
+
+    options.binary_location = os.getenv('BROWSER')
+    options.add_argument('--no-sandbox')
+    options.add_argument('--disable-extensions')
+    options.add_argument('--disable-dev-shm-usage')
+
+    capabilities = {
+        'browserName': 'chrome',
+        'chromeOptions': {
+            'useAutomationExtension': False,
+            'args': ['--disable-extensions'],
+        }
+    }
+
+    notebook = f'http://localhost:{PORT}/?token={TOKEN}'
+
+    with webdriver.Chrome(options=options, desired_capabilities=capabilities) as driver:
+        wait = WebDriverWait(driver, 10)
+        driver.get(notebook)
+        print("hack to get around failed to load extension window")
+        ActionChains(driver).key_down(Keys.ENTER).key_up(Keys.ENTER).perform()
+
+        # click on new notebook dropdown
+        click_by_css(driver, wait, '#new-dropdown-button')
+        # primary notebook server window
+        initial_handles = driver.window_handles
+        # spawns new notebook
+        click_by_css(driver, wait, '#kernel-python3 > a')
+
+        # wait for new notebook
+        wait.until(
+            lambda driver: len(initial_handles) != len(driver.window_handles)
+        )
+        # switch to new notebook
+        driver.switch_to.window(driver.window_handles[1])
+
+        # select the first input cell
+        cell = '#notebook-container > div > div.input > div.inner_cell > div.input_area'
+        click_by_css(driver, wait, cell)
+
+        # input some text
+        run = 'import exatomic; exatomic.widgets.widget_base.Scene()'
+        ActionChains(driver).send_keys(run).perform()
+        [cell] = driver.find_elements_by_css_selector(cell)
+
+        # execute the cell
+        (ActionChains(driver).key_down(Keys.SHIFT).key_down(Keys.ENTER)
+                             .key_up(Keys.SHIFT).key_up(Keys.ENTER).perform())
+        print('should show widget now')
+
+        # touch the rendered canvas
+        scene = ('#notebook-container > div.cell.code_cell.rendered.unselected > div.output_wrapper '
+                 '> div.output > div > div.output_subarea.jupyter-widgets-view > div > canvas')
+        click_by_css(driver, wait, scene)
+
+        print('interacted with scene')
+
+        # shut down the new notebook
+        menu = '#filelink'
+        click_by_css(driver, wait, menu)
+        print('clicked on file menu button')
+
+        current_handles = driver.window_handles
+        close = '#close_and_halt > a'
+        click_by_css(driver, wait, close)
+        print('clicked on close and halt')
+
+        # may trigger "Leave without saving? alert"
+        wait.until(EC.alert_is_present())
+        driver.switch_to.alert.accept()
+        print('caught alert about unsaved notebook')
+
+        # wait until second notebook window is closed
+        wait.until(
+            lambda driver: len(current_handles) != len(driver.window_handles)
+        )
+
+        # switch back to server home window
+        driver.switch_to.window(driver.window_handles[0])
+        shutdown = '#shutdown'
+        print('closing notebook server down from UI')
+        click_by_css(driver, wait, shutdown)
+        driver.close()
+        print('closed server home window')
+
+
+if __name__ == '__main__':
+    print("""\
+Assumes the following environment:
+
+    export BROWSER=/path/to/chrome/executable
+
+    pip install selenium
+
+May get a "Failed to load extension" pop-up when
+starting chrome via selenium. By hitting enter,
+the test will continue and should run to completion.
+""")
+    server = start_notebook_server()
+    try:
+        sleep(0.2)
+        run_notebook_widget()
+    finally:
+        server.kill()
+        shutil.rmtree(TOKEN)

exatomic/widgets/__init__.py

@@ -3,3 +3,64 @@
 # Distributed under the terms of the Apache License 2.0
 
 from .widget import TensorContainer, DemoContainer, DemoUniverse, UniverseWidget
+
+def exhibition_widget():
+    """An exhibition widget from static resources
+    that contains enough data to demonstrate numerous pieces
+    of functionality in the UniverseWidget.
+
+    Control each scene individually by selecting active
+    scenes based on the index of their layout reading
+    left to right, top to bottom. The Camera tab allows
+    for linking cameras across scenes. The Fill tab
+    controls the atomic display model and Axis will display
+    a unit vector (defaults to the origin).
+
+    Returns:
+        UniverseWidget featuring the application.
+            scene 0: trajectory animation (Animate tab)
+            scene 1: orbital isosurfaces (Fields, Contours tabs)
+            scene 2: NMR shielding tensor (Tensor tab)
+
+    Note:
+        All scenes are active by default and not all required
+        data are exposed in each scene. Therefore, "unselect"
+        active scenes in the Active Scenes tab (at least until
+        there is better exception handling on the JS side).
+
+    Note:
+        This widget provides test cases for marching cubes
+        (and marching squares) over 3D (2D) scalar fields, animated
+        trajectories, and plotting parametric surfaces, but
+        not all at the same time. The aim is to provide a
+        complex enough test case that covers a good portion of
+        the JS code so that updates can be checked (albeit in
+        a time-consuming manner). It may also serve to uncover
+        python-related bugs related to a UniverseWidget housing
+        multiple independent UniverseScenes.
+
+    Note:
+        The use of an entire tensor table is not well supported
+        by the application yet. The aim is to improve functionality
+        to be similar to the functionality for isosurfaces.
+
+    """
+    import exatomic
+    from exatomic import gaussian
+
+    trj_file = 'H2O.traj.xyz'
+    orb_file = 'g09-ch3nh2-631g.out'
+    nmr_file = 'g16-nitromalonamide-6-31++g-nmr.out'
+
+    trj = exatomic.XYZ(
+        exatomic.base.resource(trj_file)).to_universe()
+
+    orb = gaussian.Output(
+        exatomic.base.resource(orb_file)).to_universe()
+    orb.add_molecular_orbitals()
+
+    nmr = gaussian.Output(
+        exatomic.base.resource(nmr_file)).to_universe()
+    nmr.tensor = nmr.nmr_shielding
+
+    return exatomic.UniverseWidget(trj, orb, nmr)

exatomic/widgets/tests/test_widgets.py

@@ -16,6 +16,13 @@
 H 0.0 0.0  0.35
 '''
 
+class TestExhibitionWidget(TestCase):
+
+    def test_exhibition_widget(self):
+        import exatomic
+        w = exatomic.widgets.exhibition_widget()
+        self.assertEqual(len(w.scenes), 3)
+
 class TestDemoContainer(TestCase):
     def setUp(self):
         self.box = DemoContainer()

exatomic/widgets/widget.py

@@ -574,6 +574,9 @@ def _axis(b):
 
         return mainopts
 
+    def __repr__(self):
+        return self.__class__.__name__ + f'({len(self.scenes)},closed)'
+
     def __init__(self, *unis, **kwargs):
         scenekwargs = kwargs.pop('scenekwargs', {})
         #scenekwargs.update({'uni': True, 'test': False})

exatomic/widgets/widget_base.py

@@ -25,6 +25,26 @@
                            _vboxlo, _bboxlo, _ListDict,
                            Folder, GUIBox, gui_field_widgets)
 
+@register
+class Scene(DOMWidget):
+    _model_module_version = Unicode(__js_version__).tag(sync=True)
+    _view_module_version = Unicode(__js_version__).tag(sync=True)
+    _view_module = Unicode('exatomic').tag(sync=True)
+    _model_module = Unicode('exatomic').tag(sync=True)
+    _model_name = Unicode('SceneModel').tag(sync=True)
+    _view_name = Unicode('SceneView').tag(sync=True)
+    _inited = Bool(False).tag(sync=True)
+    flag = Bool(True).tag(sync=True)
+
+
+    def close(self):
+        self.send({'type': 'close'})
+        super().close()
+
+    def _handle_custom_msg(self, msg, callback):
+        if msg['type'] == 'init':
+            self._inited = True
+
 
 @register
 class ExatomicScene(DOMWidget):

install-chromedriver.sh

@@ -0,0 +1,38 @@
+#!/usr/bin/env bash
+
+echo """
+Installer script to set up chromedriver for selenium
+on WSL. This allows for running selenium automated
+browser tests.
+
+Needs approximately the following in the bash environment:
+
+    export DISPLAY=:0
+    export BROWSER=/mnt/c/Program\ Files\ \(x86\)/Google/Chrome/Application/chrome.exe
+
+Depending on chrome version, please update CHROME_SUFFIX.
+If on latest, CHROME_SUFFIX can be "".
+"""
+
+CHROME_WINDOWS_MAJOR_VER=84
+CHROME_SUFFIX="_${CHROME_WINDOWS_MAJOR_VER}"
+
+
+CHROME_DRIVER_VERSION=$(curl -sS https://chromedriver.storage.googleapis.com/LATEST_RELEASE${CHROME_SUFFIX})
+CHROME_DRIVER_ARTIFACT=chromedriver_linux64.zip
+CHROME_DRIVER_DEST=/usr/local/bin/chromedriver
+
+# Clean workspace
+rm ./$CHROME_DRIVER_ARTIFACT
+sudo rm $CHROME_DRIVER_DEST
+
+# Install dependencies
+sudo apt-get install -y openjdk-8-jre-headless xvfb libxi6 libgconf-2-4
+
+# Install chromedriver
+wget -N https://chromedriver.storage.googleapis.com/$CHROME_DRIVER_VERSION/$CHROME_DRIVER_ARTIFACT -P ./
+unzip ./$CHROME_DRIVER_ARTIFACT -d ./
+rm ./$CHROME_DRIVER_ARTIFACT
+sudo mv -f ./chromedriver $CHROME_DRIVER_DEST
+sudo chown root:root $CHROME_DRIVER_DEST
+sudo chmod 0755 $CHROME_DRIVER_DEST

js/.eslintrc.js

@@ -5,17 +5,35 @@ module.exports = {
     es2020: true,
   },
   extends: [
+    'eslint:recommended',
     'airbnb-base',
+    'plugin:@typescript-eslint/recommended',
   ],
   parserOptions: {
     ecmaVersion: 11,
     sourceType: 'module',
   },
   rules: {
-      indent: ["error", 4],
-      semi: [2, "never"],
-      'max-classes-per-file': ["error", 4]
+      indent: ['error', 4],
+      semi: [2, 'never'],
+      'no-console': 'off',
+      'max-classes-per-file': ['error', 4],
+      'no-bitwise': ['error', { 'allow': ['>>', '<<', '&'] } ],
+      '@typescript-eslint/no-explicit-any': 'off',
+      '@typescript-eslint/member-delimiter-style': ['error', {
+          'multiline': {
+              'delimiter': 'none'
+          }
+      }],
   },
+  // TODO : typescript indent checking is buggy
+  // '@typescript-eslint/indent': ['error', 4],
+  overrides: [{
+      'files': ['*.ts'],
+      'rules': {
+          indent: 'off',
+      }
+  }],
   settings: {
     'import/resolver': {
       node: {
@@ -24,4 +42,4 @@ module.exports = {
       }
     }
   }
-};
+}

js/package.json

@@ -28,6 +28,7 @@
     "watch": "webpack -d -w"
   },
   "devDependencies": {
+    "@typescript-eslint/eslint-plugin": "^3.6.1",
     "@typescript-eslint/parser": "^3.6.0",
     "babel-eslint": "^10.1.0",
     "eslint": "^7.4.0",

js/src/base.js

@@ -8,9 +8,6 @@ JavaScript "frontend" complement of exatomic"s Universe
 for use within the Jupyter notebook interface.
 */
 
-// eslint-disable-next-line
-import * as util from './util'
-
 const widgets = require('@jupyter-widgets/base')
 const control = require('@jupyter-widgets/controls')
 const three = require('./appthree')
@@ -20,8 +17,6 @@ const ver = require('../package.json').version
 const semver = `^${ver}`
 // eslint-disable-next-line no-console
 console.log(`exatomic JS version: ${semver}`)
-// eslint-disable-next-line no-console
-console.log('typescript module', util)
 
 export class ExatomicBoxModel extends control.BoxModel {
     defaults() {