Update pymatgen example

Author: ml-evs

notebooks/demonstration-pymatgen-for-optimade-queries.ipynb

@@ -68,57 +68,17 @@
     },
     {
       "cell_type": "code",
-      "execution_count": 103,
+      "execution_count": null,
       "metadata": {
         "colab": {
           "base_uri": "https://localhost:8080/"
         },
         "id": "qU7Uolip7N-g",
         "outputId": "b756287e-3d19-444d-f91c-c4aea6c440a6"
       },
-      "outputs": [
-        {
-          "name": "stdout",
-          "output_type": "stream",
-          "text": [
-            "Requirement already satisfied: pymatgen in /usr/local/lib/python3.7/dist-packages (2022.0.14)\n",
-            "Requirement already satisfied: pybtex in /usr/local/lib/python3.7/dist-packages (0.24.0)\n",
-            "Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (3.7.4.3)\n",
-            "Requirement already satisfied: matplotlib>=1.5 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (3.2.2)\n",
-            "Requirement already satisfied: requests in /usr/local/lib/python3.7/dist-packages (from pymatgen) (2.23.0)\n",
-            "Requirement already satisfied: plotly>=4.5.0 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (5.3.1)\n",
-            "Requirement already satisfied: tabulate in /usr/local/lib/python3.7/dist-packages (from pymatgen) (0.8.9)\n",
-            "Requirement already satisfied: sympy in /usr/local/lib/python3.7/dist-packages (from pymatgen) (1.7.1)\n",
-            "Requirement already satisfied: spglib>=1.9.9.44 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (1.16.2)\n",
-            "Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from pymatgen) (1.1.5)\n",
-            "Requirement already satisfied: uncertainties>=3.1.4 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (3.1.6)\n",
-            "Requirement already satisfied: networkx>=2.2 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (2.6.2)\n",
-            "Requirement already satisfied: monty>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (2021.8.17)\n",
-            "Requirement already satisfied: scipy>=1.5.0 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (1.7.1)\n",
-            "Requirement already satisfied: numpy>=1.20.1 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (1.21.2)\n",
-            "Requirement already satisfied: ruamel.yaml>=0.15.6 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (0.17.16)\n",
-            "Requirement already satisfied: palettable>=3.1.1 in /usr/local/lib/python3.7/dist-packages (from pymatgen) (3.3.0)\n",
-            "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=1.5->pymatgen) (0.10.0)\n",
-            "Requirement already satisfied: python-dateutil>=2.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=1.5->pymatgen) (2.8.2)\n",
-            "Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=1.5->pymatgen) (2.4.7)\n",
-            "Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.7/dist-packages (from matplotlib>=1.5->pymatgen) (1.3.1)\n",
-            "Requirement already satisfied: six in /usr/local/lib/python3.7/dist-packages (from cycler>=0.10->matplotlib>=1.5->pymatgen) (1.15.0)\n",
-            "Requirement already satisfied: tenacity>=6.2.0 in /usr/local/lib/python3.7/dist-packages (from plotly>=4.5.0->pymatgen) (8.0.1)\n",
-            "Requirement already satisfied: ruamel.yaml.clib>=0.1.2 in /usr/local/lib/python3.7/dist-packages (from ruamel.yaml>=0.15.6->pymatgen) (0.2.6)\n",
-            "Requirement already satisfied: future in /usr/local/lib/python3.7/dist-packages (from uncertainties>=3.1.4->pymatgen) (0.16.0)\n",
-            "Requirement already satisfied: latexcodec>=1.0.4 in /usr/local/lib/python3.7/dist-packages (from pybtex) (2.0.1)\n",
-            "Requirement already satisfied: PyYAML>=3.01 in /usr/local/lib/python3.7/dist-packages (from pybtex) (3.13)\n",
-            "Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.7/dist-packages (from pandas->pymatgen) (2018.9)\n",
-            "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.7/dist-packages (from requests->pymatgen) (2021.5.30)\n",
-            "Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /usr/local/lib/python3.7/dist-packages (from requests->pymatgen) (1.24.3)\n",
-            "Requirement already satisfied: chardet<4,>=3.0.2 in /usr/local/lib/python3.7/dist-packages (from requests->pymatgen) (3.0.4)\n",
-            "Requirement already satisfied: idna<3,>=2.5 in /usr/local/lib/python3.7/dist-packages (from requests->pymatgen) (2.10)\n",
-            "Requirement already satisfied: mpmath>=0.19 in /usr/local/lib/python3.7/dist-packages (from sympy->pymatgen) (1.2.1)\n"
-          ]
-        }
-      ],
+      "outputs": [],
       "source": [
-        "!pip install pymatgen pybtex"
+        "%pip install pymatgen pybtex"
       ]
     },
     {
@@ -319,7 +279,9 @@
       ],
       "source": [
         "opt = OptimadeRester()\n",
-        "opt.refresh_aliases()"
+        "opt.refresh_aliases()\n",
+        "\n",
+        "latest_aliases = opt.aliases"
       ]
     },
     {
@@ -343,7 +305,7 @@
       },
       "outputs": [],
       "source": [
-        "opt = OptimadeRester([\"mp\", \"mcloud.2dstructures\"],timeout=10)"
+        "opt = OptimadeRester([\"mp\", \"https://aiida.materialscloud.org/mc2d/optimade\"]],timeout=10)"
       ]
     },
     {
@@ -1407,12 +1369,18 @@
       "provenance": []
     },
     "kernelspec": {
-      "display_name": "Python 3",
+      "display_name": "Python 3.9.12 ('optimade_39')",
+      "language": "python",
       "name": "python3"
     },
     "language_info": {
       "name": "python",
-      "version": "3.9.7"
+      "version": "3.9.12"
+    },
+    "vscode": {
+      "interpreter": {
+        "hash": "aba44ae4de6e4ad6c6ed049de3bd37f83e5fa31c56eecbd2c7dd1c3d1baa4d3b"
+      }
     }
   },
   "nbformat": 4,