Merge pull request #217 from Exabyte-io/feauture/SOF-7549-1

chore: add wave viewer + other fixes

Author: timurbazhirov

other/materials_designer/create_adatom_defect.ipynb

@@ -205,14 +205,9 @@
   {
    "cell_type": "code",
    "source": [
-    "import time\n",
-    "import json\n",
-    "import ipywidgets\n",
-    "\n",
     "from mat3ra.made.tools.build.defect import create_defects\n",
     "\n",
-    "slab_with_adatom = create_defects(defect_configurations)\n",
-    "\n"
+    "slab_with_adatom = create_defects(defect_configurations)"
    ],
    "metadata": {
     "collapsed": false
@@ -231,35 +226,15 @@
    },
    "id": "462549d016073446"
   },
-  {
-   "metadata": {},
-   "cell_type": "code",
-   "source": "",
-   "id": "5e8e68df02b876cf",
-   "outputs": [],
-   "execution_count": null
-  },
-  {
-   "metadata": {},
-   "cell_type": "code",
-   "source": [
-    "visualize(materials=[slab,slab_with_adatom], title=\"Material with adatom defects\", rotation=\"-90x\", viewer=\"wave\"\n",
-    "          )"
-   ],
-   "id": "2159b0765a0c88c8",
-   "outputs": [],
-   "execution_count": null
-  },
   {
    "metadata": {},
    "cell_type": "code",
    "source": [
     "from utils.visualize import visualize_materials as visualize\n",
     "\n",
     "visualize([{\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defects\"},\n",
-    "           {\"material\": slab, \"title\": \"Original material\"},\n",
-    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defects\"}], viewer=\"wave\"\n",
+    "           {\"material\": slab_with_adatom, \"title\": f\"Material with adatom defects\"}],\n",
+    "          viewer=\"wave\"\n",
     "          )"
    ],
    "id": "256b07fb2dd39ae2",

other/materials_designer/custom_transformation.ipynb

@@ -136,6 +136,7 @@
    "source": [
     "from utils.jupyterlite import set_materials, download_content_to_file\n",
     "\n",
+    "new_material.name = \"Custom Transformed Material\"\n",
     "set_materials(new_material)\n",
     "# for idx, material in enumerate(new_materials):\n",
     "#   download_content_to_file(new_materials, f\"new_material_{idx}.json\")"

other/materials_designer/import_materials_from_files.ipynb

@@ -241,7 +241,7 @@
     "\n",
     "materials = [Material(esse_entry) for esse_entry in esse_entries]\n",
     "\n",
-    "visualize_materials(materials)"
+    "visualize_materials(materials, viewer=\"wave\")"
    ],
    "outputs": [],
    "execution_count": null

other/materials_designer/import_materials_from_standata.ipynb

@@ -36,11 +36,12 @@
     "\n",
     "if sys.platform == \"emscripten\":\n",
     "    import micropip\n",
-    "  \n",
+    "\n",
     "    await micropip.install('mat3ra-api-examples', deps=False)\n",
     "    await micropip.install('mat3ra-utils')\n",
     "    await micropip.install('mat3ra-standata')\n",
-    "    from utils.jupyterlite import install_packages\n",
+    "    from mat3ra.utils.jupyterlite.packages import install_packages\n",
+    "\n",
     "    await install_packages(\"\")"
    ],
    "metadata": {
@@ -65,6 +66,7 @@
    "cell_type": "code",
    "source": [
     "from mat3ra.standata.materials import Materials\n",
+    "\n",
     "Materials.get_names()"
    ],
    "metadata": {

other/materials_designer/specific_examples/perturbation_ripple_graphene.ipynb

@@ -277,7 +277,7 @@
   },
   {
    "cell_type": "code",
-   "source": "visualize(material_with_custom_perturbation, viewer=\"wave\")WW",
+   "source": "visualize(material_with_custom_perturbation, viewer=\"wave\")",
    "metadata": {
     "collapsed": false
    },