Cleaning some of the folders

src/nomad_auto_xrd/example_uploads/getting_started/auto-xrd-analysis.ipynb

@@ -1,28 +1,13 @@
 {
  "cells": [
   {
-   "cell_type": "code",
-   "execution_count": 8,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [
-    {
-     "ename": "ImportError",
-     "evalue": "cannot import name 'AnalysisSettings' from 'nomad_auto_xrd.auto_xrd_analysis' (/home/pepe_marquez/NOMAD/nomad/plugins/nomad-auto-xrd/src/nomad_auto_xrd/auto_xrd_analysis.py)",
-     "output_type": "error",
-     "traceback": [
-      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[0;31mImportError\u001b[0m                               Traceback (most recent call last)",
-      "Cell \u001b[0;32mIn[8], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[38;5;28;01mfrom\u001b[39;00m \u001b[38;5;21;01mnomad_auto_xrd\u001b[39;00m\u001b[38;5;21;01m.\u001b[39;00m\u001b[38;5;21;01mauto_xrd_analysis\u001b[39;00m \u001b[38;5;28;01mimport\u001b[39;00m (\n\u001b[1;32m      2\u001b[0m     AnalysisSettings,\n\u001b[1;32m      3\u001b[0m     run_analysis_existing_spectra,\n\u001b[1;32m      4\u001b[0m     run_analysis_with_patterns_archive,\n\u001b[1;32m      5\u001b[0m )\n",
-      "\u001b[0;31mImportError\u001b[0m: cannot import name 'AnalysisSettings' from 'nomad_auto_xrd.auto_xrd_analysis' (/home/pepe_marquez/NOMAD/nomad/plugins/nomad-auto-xrd/src/nomad_auto_xrd/auto_xrd_analysis.py)"
-     ]
-    }
-   ],
    "source": [
-    "from nomad_auto_xrd.auto_xrd_analysis import (\n",
-    "    AnalysisSettings,\n",
-    "    run_analysis_existing_spectra,\n",
-    "    run_analysis_with_patterns_archive,\n",
-    ")\n"
+    "# Running Auto XRD Analysis\n",
+    "\n",
+    "We can now run inference in our train models. We will data coming from a NOMAD archive in \n",
+    "the first example and the mdoels that we have in the archive."
    ]
   },
   {
@@ -32,15 +17,28 @@
    "outputs": [],
    "source": [
     "# from nomad_auto_xrd.auto_xrd_analysis import run_analysis\n",
-    "\n",
-    "settings = AnalysisSettings(\n",
-    "    # structure_references_directory='References',\n",
-    "    # xrd_model='Models/XRD_Model.h5',\n",
-    "    max_phases=5,\n",
-    "    min_confidence=30,\n",
-    "    include_pdf=True,\n",
+    "from nomad_auto_xrd.auto_xrd_analysis import (\n",
+    "    AnalysisSettings,\n",
+    "    run_analysis_existing_spectra,\n",
+    "    run_analysis_with_patterns_archive,\n",
     ")\n",
-    "run_analysis_with_patterns_archive(settings, 'model_metadata.archive.json', 'xrd_archive.json', 'custom_results.json')"
+    "\n",
+    "settings = AnalysisSettings()\n",
+    "run_analysis_with_patterns_archive(\n",
+    "    settings,\n",
+    "    'model_metadata.archive.json',\n",
+    "    'xrd_archive.json',\n",
+    "    'custom_results.json'\n",
+    "    )"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Optionally, we can run it as it is classically done in AutoXRD, specifying the model path,\n",
+    "the path to the cif files and the path to the folder where the patterns are located in \n",
+    "`.xy` format. We can also override the default parameters of the model."
    ]
   },
   {
@@ -49,6 +47,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "\n",
     "settings = AnalysisSettings(\n",
     "    structure_references_directory='References',\n",
     "    patterns_folder_directory='Spectra',\n",
@@ -57,7 +56,10 @@
     "    min_confidence=30,\n",
     "    include_pdf=True,\n",
     ")\n",
-    "run_analysis_existing_spectra(settings, 'model_metadata.archive.json', 'custom_results.json')"
+    "run_analysis_existing_spectra(\n",
+    "    settings,\n",
+    "    'model_metadata.archive.json',\n",
+    "    'custom_results.json')"
    ]
   }
  ],