Fix tutorial data for Colab

Author: ElliottKasoar

docs/source/tutorials/cli/geomopt.ipynb

@@ -93,7 +93,7 @@
     "from ase.io import write\n",
     "from weas_widget import WeasWidget\n",
     "\n",
-    "Path(\"data\").mkdir(exist_ok=True)\n",
+    "Path(\"../data\").mkdir(exist_ok=True)\n",
     "\n",
     "NaCl = bulk(\"NaCl\", \"rocksalt\", a=5.63, cubic=True)\n",
     "NaCl[0].position = [1.5, 1.5, 1.5]\n",

docs/source/tutorials/cli/md.ipynb

@@ -44,6 +44,21 @@
     "# get_ipython().kernel.do_shutdown(restart=True)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# from data_tutorials.data import get_data\n",
+    "\n",
+    "# get_data(\n",
+    "#     url=\"https://raw.githubusercontent.com/stfc/janus-core/main/docs/source/tutorials/data/\",\n",
+    "#     filename=[\"NaCl-1040.extxyz\"],\n",
+    "#     folder=\"../data\",\n",
+    "# )"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -52,15 +67,17 @@
    },
    "outputs": [],
    "source": [
+    "from pathlib import Path\n",
+    "\n",
     "from ase.build import bulk\n",
     "from ase.io import read, write\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
     "from weas_widget import WeasWidget\n",
-    "from janus_core.helpers.stats import Stats\n",
-    "from janus_core.processing import post_process\n",
     "import yaml\n",
     "\n",
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt"
+    "from janus_core.helpers.stats import Stats\n",
+    "from janus_core.processing import post_process"
    ]
   },
   {
@@ -80,6 +97,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "Path(\"../data\").mkdir(exist_ok=True)\n",
+    "\n",
     "NaCl = bulk(\"NaCl\", \"rocksalt\", a=5.63, cubic=True)\n",
     "NaCl = NaCl * (2, 2, 2)\n",
     "write(\"../data/NaCl.xyz\", NaCl)\n",

docs/source/tutorials/python/neb.ipynb

@@ -36,45 +36,45 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "You can toggle the following to investigate different models:"
+    "## Set up environment (optional)\n",
+    "\n",
+    "These steps are required for Google Colab, but may work on other systems too:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "id": "TF-EiWxyuMc7"
+   },
    "outputs": [],
    "source": [
-    "model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-0b3\"}\n",
-    "# model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-mpa-0\"}\n",
-    "# model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-omat-0\"}\n",
-    "# model_params = {\"arch\": \"chgnet\"}\n",
-    "# model_params = {\"arch\": \"sevennet\"}"
+    "# import locale\n",
+    "# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
+    "\n",
+    "# ! pip uninstall torch torchaudio torchvision transformers numpy -y\n",
+    "# ! uv pip install janus-core[all] data-tutorials torch==2.5.1 --system\n",
+    "# get_ipython().kernel.do_shutdown(restart=True)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Set up environment (optional)\n",
-    "\n",
-    "These steps are required for Google Colab, but may work on other systems too:"
+    "You can toggle the following to investigate different models:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {
-    "id": "TF-EiWxyuMc7"
-   },
+   "metadata": {},
    "outputs": [],
    "source": [
-    "# import locale\n",
-    "# locale.getpreferredencoding = lambda: \"UTF-8\"\n",
-    "\n",
-    "# ! pip uninstall torch torchaudio torchvision transformers numpy -y\n",
-    "# ! uv pip install janus-core[all] data-tutorials torch==2.5.1 --system\n",
-    "# get_ipython().kernel.do_shutdown(restart=True)"
+    "model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-0b3\"}\n",
+    "# model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-mpa-0\"}\n",
+    "# model_params = {\"arch\": \"mace_mp\", \"model\": \"medium-omat-0\"}\n",
+    "# model_params = {\"arch\": \"chgnet\"}\n",
+    "# model_params = {\"arch\": \"sevennet\"}"
    ]
   },
   {