Merge pull request #1 from osscar-org/develop

Version 0.1.0a2

.github/workflows/heroku_deploy.yml

@@ -0,0 +1,24 @@
+
+name: Deploy on Heroku
+
+on:
+  workflow_dispatch:
+    inputs:
+      name:
+        description: 'Deploy on Heroku'
+        required: true
+        default: 'Deploy on Heroku'
+  push:
+    branches:
+      - develop
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: akhileshns/[email protected] # This is the action
+        with:
+          heroku_api_key: ${{secrets.HEROKU_API_KEY}}
+          heroku_app_name: "osscar-widget-bzvisualizer" #Must be unique in Heroku
+          heroku_email: "[email protected]"

.github/workflows/python-package.yml

@@ -0,0 +1,40 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Python package
+
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |    
+        python -m pip install --upgrade pip
+        python -m pip install -e .
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        # pytest

.github/workflows/python-publish.yml

@@ -0,0 +1,31 @@
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Build and publish
+      env:
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload dist/*

Procfile

@@ -0,0 +1 @@
+web: voila --template=osscar --VoilaConfiguration.enable_nbextensions=True --VoilaConfiguration.file_whitelist="['.*']" example/bzvisualizer-example.ipynb --port=$PORT --no-browser --MappingKernelManager.cull_interval=60 --MappingKernelManager.cull_idle_timeout=120 --MappingKernelManager.cull_busy=True 

example/bzvisualizer-example.ipynb

@@ -0,0 +1,75 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "hindu-movement",
+   "metadata": {},
+   "source": [
+    "## **A Jupyter widget to visualize the 1st Brillouin zone**\n",
+    "\n",
+    "<hr style=\"height:1px;border:none;color:#cccccc;background-color:#cccccc;\" />"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "particular-companion",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from widget_bzvisualizer import BZVisualizer\n",
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "great-number",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lattice = np.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "constant-techno",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "w = BZVisualizer(lattice, [[0.0, 0.0, 0.0]], [1], True)\n",
+    "display(w)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "north-moisture",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.9.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

js/lib/BZVisualizer.js

@@ -528,15 +528,44 @@ var BZVisualizer = function (showAxes, showBVectors, showPathpoints, useSVGRende
                 new THREE.Vector3(p2[0], p2[1], p2[2]));
             var line = new THREE.Line(geometry, line_material);
             line.material.linewidth = 4;
+            line.name = "pathvectors";
             scene.add(line);
         });
 
+        // update the path vectors
+        this.update_pathVector = function (pathVector) {
+            var vectors = scene.getObjectByName('pathvectors');
+            while (vectors) {
+                vectors = scene.getObjectByName('pathvectors');
+                scene.remove(vectors);
+            };
+
+            pathVector.forEach(function (linespec) {
+                label1 = linespec[0];
+                label2 = linespec[1];
+                p1 = special_points[label1];
+                p2 = special_points[label2];
+
+                var geometry = new THREE.Geometry();
+                geometry.vertices.push(
+                    new THREE.Vector3(p1[0], p1[1], p1[2]));
+                geometry.vertices.push(
+                    new THREE.Vector3(p2[0], p2[1], p2[2]));
+                var line = new THREE.Line(geometry, line_material);
+                line.material.linewidth = 4;
+                line.name = "pathvectors";
+                scene.add(line);
+            });
+
+            render();
+        };
+
 
         if (showPathpoints) {
             kpoints_abs = jsondata['explicit_kpoints_abs'];
             for (var idx in kpoints_abs) {
                 pos = kpoints_abs[idx];
-                radius = 0.01 * max_b_length;
+                radius = 0.008 * max_b_length;
 
                 var sphere_geometry = new THREE.SphereGeometry(
                     radius, 16, 16);
@@ -582,7 +611,7 @@ var BZVisualizer = function (showAxes, showBVectors, showPathpoints, useSVGRende
 
         // canvas3d.addEventListener('dblclick', bz_switch_enable);
 
-        var toggle_visiblity = function (event) {
+        toggle_visibility = function (event) {
             if (bz_material.opacity === 0.0) {
                 bz_material.opacity = 0.3;
                 bz_material.needsUpdate = true;
@@ -594,7 +623,19 @@ var BZVisualizer = function (showAxes, showBVectors, showPathpoints, useSVGRende
             render();
         }
 
-        canvas3d.addEventListener('dblclick', toggle_visiblity);
+        this.set_visibility = function (faceColor) {
+            if (faceColor) {
+                bz_material.opacity = 0.3;
+                bz_material.needsUpdate = true;
+            } else {
+                bz_material.opacity = 0.0;
+                bz_material.needsUpdate = true;
+            };
+
+            render();
+        }
+
+        // canvas3d.addEventListener('dblclick', toggle_visibility);
 
         this.update_kpts = function (kpoints_abs) {
             var kpt = scene.getObjectByName('kpts');
@@ -605,7 +646,7 @@ var BZVisualizer = function (showAxes, showBVectors, showPathpoints, useSVGRende
 
             for (var idx in kpoints_abs) {
                 pos = kpoints_abs[idx];
-                radius = 0.01 * max_b_length;
+                radius = 0.008 * max_b_length;
 
                 var sphere_geometry = new THREE.SphereGeometry(
                     radius, 16, 16);

js/lib/example.js

@@ -45,27 +45,49 @@ var BrillouinZoneView = widgets.DOMWidgetView.extend({
         this.BZVisualizer = new BZVisualizer(true, true, true, false);
     },
 
+    events: {
+        'dblclick': 'toggle_faceColor',
+    },
+
     // Defines how the widget gets rendered into the DOM
     render: function () {
         // Observe changes in the value traitlet in Python, and define
         // a custom callback.
         this.model.on('change:kpts', this.kpts_changed, this);
+        this.model.on('change:face_color', this.faceColor_changed, this);
+        this.model.on('change:path_vectors', this.vectors_changed, this);
 
         this.el.innerHTML = '<div class="BZ-widget" id="' + this.canvasID + '"></div>'
             + '<div id="' + this.infoID + '"></div>';
 
         var jsondata = this.model.get('jsondata');
+        var faceColor = this.model.get('face_color');
 
         that = this;
         $(document).ready(function () {
-            that.BZVisualizer.loadBZ(canvasID=that.canvasID, infoID=that.infoID, jsondata=jsondata);
+            that.BZVisualizer.loadBZ(canvasID = that.canvasID, infoID = that.infoID, jsondata = jsondata);
+            that.BZVisualizer.set_visibility(faceColor);
         });
     },
 
+    toggle_faceColor: function () {
+        const faceColor = this.model.get('face_color');
+        this.model.set('face_color', !faceColor);
+        this.touch();
+    },
+
     kpts_changed: function () {
-        console.log("This function has been triggled here***********");
         const kpts = this.model.get('kpts');
         this.BZVisualizer.update_kpts(kpts);
+    },
+
+    vectors_changed: function () {
+        const vectors = this.model.get('path_vectors');
+        this.BZVisualizer.update_pathVector(vectors);
+    },
+
+    faceColor_changed: function () {
+        this.BZVisualizer.set_visibility(this.model.get('face_color'));
     }
 });
 

requirements.txt

@@ -0,0 +1,3 @@
+voila==0.2.7 
+voila-osscar-template==0.2.8
+widget-bzvisualizer==0.1.0a1

widget_bzvisualizer/_version.py

@@ -1,5 +1,5 @@
 # Module version
-version_info = (0, 1, 0, 'alpha', 1)
+version_info = (0, 1, 0, 'alpha', 2)
 
 # Module version stage suffix map
 _specifier_ = {'alpha': 'a', 'beta': 'b', 'candidate': 'rc', 'final': ''}

widget_bzvisualizer/example.py

@@ -1,5 +1,5 @@
 import ipywidgets as widgets
-from traitlets import Unicode, Dict, List
+from traitlets import Unicode, Dict, List, Bool
 import seekpath
 from seekpath.brillouinzone.brillouinzone import get_BZ
 import numpy as np
@@ -43,7 +43,13 @@ class BZVisualizer(widgets.DOMWidget):
     # The jsondata for the Brillouin zone
     jsondata = Dict().tag(sync=True)
 
-    def __init__(self, cell, positions, numbers):
+    # Show the BZ surface
+    face_color = Bool(True).tag(sync=True)
+
+    # The path vectors
+    path_vectors = List().tag(sync=True)
+
+    def __init__(self, cell, positions, numbers, face_color=True):
         if type(cell) == np.ndarray:
             cell = cell.tolist()
 
@@ -53,7 +59,7 @@ def __init__(self, cell, positions, numbers):
         if type(numbers) == np.ndarray:
             numbers = numbers.tolist()
 
-        super().__init__(cell = cell, positions=positions, numbers=numbers)
+        super().__init__(cell = cell, positions=positions, numbers=numbers, face_color=face_color)
 
         system = (np.array(cell), np.array(positions), np.array(numbers))
         res = seekpath.getpaths.get_path(system, with_time_reversal=False)
@@ -100,4 +106,5 @@ def __init__(self, cell, positions, numbers):
             raise AssertionError("Got different reciprocal cells...")
 
         self.jsondata = response
-        self.kpts = self.jsondata['explicit_kpoints_abs']
+        self.kpts = self.jsondata['explicit_kpoints_abs']
+        self.path_vectors = self.jsondata['path']