From e3994fc0306156a53543bad3bb2e09b6c7a949fd Mon Sep 17 00:00:00 2001
From: Louie <hessellundlouie@gmail.com>
Date: Wed, 4 Dec 2024 15:29:06 +0100
Subject: [PATCH] Move notebook to docs/source/notebooks folder

---
 .../notebooks}/Latent_var_notebook.ipynb      | 69 ++++++++++++-------
 1 file changed, 44 insertions(+), 25 deletions(-)
 rename {pyhgf/model => docs/source/notebooks}/Latent_var_notebook.ipynb (99%)

diff --git a/pyhgf/model/Latent_var_notebook.ipynb b/docs/source/notebooks/Latent_var_notebook.ipynb
similarity index 99%
rename from pyhgf/model/Latent_var_notebook.ipynb
rename to docs/source/notebooks/Latent_var_notebook.ipynb
index b7df6353d..659241c10 100644
--- a/pyhgf/model/Latent_var_notebook.ipynb
+++ b/docs/source/notebooks/Latent_var_notebook.ipynb
@@ -2,12 +2,12 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "import sys\n",
-    "from IPython.utils import io"
+    "from IPython.utils import io # I made a change - Is this visible in Github?"
    ]
   },
   {
@@ -24,7 +24,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 80,
+   "execution_count": 18,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -45,9 +45,21 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 19,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "ename": "NameError",
+     "evalue": "name 'jax' is not defined",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mNameError\u001b[0m                                 Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[19], line 2\u001b[0m\n\u001b[0;32m      1\u001b[0m \u001b[38;5;66;03m# Disable JIT compilation globally\u001b[39;00m\n\u001b[1;32m----> 2\u001b[0m \u001b[43mjax\u001b[49m\u001b[38;5;241m.\u001b[39mconfig\u001b[38;5;241m.\u001b[39mupdate(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mjax_disable_jit\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mFalse\u001b[39;00m) \u001b[38;5;66;03m# True - If I want the compiler disabled.\u001b[39;00m\n",
+      "\u001b[1;31mNameError\u001b[0m: name 'jax' is not defined"
+     ]
+    }
+   ],
    "source": [
     "# Disable JIT compilation globally\n",
     "jax.config.update(\"jax_disable_jit\", False) # True - If I want the compiler disabled."
@@ -55,7 +67,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 62,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +83,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 63,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -122,10 +134,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.sources.Source at 0x19f37284770>"
+       "<graphviz.sources.Source at 0x209b3f58da0>"
       ]
      },
-     "execution_count": 63,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -136,7 +148,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 68,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -154,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 69,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
@@ -205,10 +217,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.sources.Source at 0x19f3bb46cc0>"
+       "<graphviz.sources.Source at 0x209b3ff1eb0>"
       ]
      },
-     "execution_count": 69,
+     "execution_count": 7,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -219,7 +231,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 64,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -229,7 +241,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 65,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -249,7 +261,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 25,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -262,7 +274,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 54,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -272,7 +284,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 55,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -292,7 +304,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 71,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -310,7 +322,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 72,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
@@ -361,10 +373,10 @@
        "</svg>\n"
       ],
       "text/plain": [
-       "<graphviz.sources.Source at 0x19f3cb872c0>"
+       "<graphviz.sources.Source at 0x209b7c81730>"
       ]
      },
-     "execution_count": 72,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -375,7 +387,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 73,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -386,7 +398,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 81,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -396,7 +408,7 @@
      "traceback": [
       "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[1;31mKeyError\u001b[0m                                  Traceback (most recent call last)",
-      "Cell \u001b[1;32mIn[81], line 17\u001b[0m\n\u001b[0;32m     15\u001b[0m l_a \u001b[38;5;241m=\u001b[39m attributes[\u001b[38;5;241m1\u001b[39m][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexpected_mean\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[0;32m     16\u001b[0m w_b \u001b[38;5;241m=\u001b[39m attributes[\u001b[38;5;241m2\u001b[39m][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexpected_mean\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m---> 17\u001b[0m l_b \u001b[38;5;241m=\u001b[39m \u001b[43mattributes\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m]\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexpected_mean\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[0;32m     19\u001b[0m \u001b[38;5;66;03m# the decision function\u001b[39;00m\n\u001b[0;32m     20\u001b[0m p_a \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mexp(beta \u001b[38;5;241m*\u001b[39m (w_a \u001b[38;5;241m-\u001b[39m l_a)) \u001b[38;5;241m/\u001b[39m (\n\u001b[0;32m     21\u001b[0m     np\u001b[38;5;241m.\u001b[39mexp(beta \u001b[38;5;241m*\u001b[39m (w_a \u001b[38;5;241m-\u001b[39m l_a)) \u001b[38;5;241m+\u001b[39m np\u001b[38;5;241m.\u001b[39mexp(beta \u001b[38;5;241m*\u001b[39m (w_b \u001b[38;5;241m-\u001b[39m l_b))\n\u001b[0;32m     22\u001b[0m )\n",
+      "Cell \u001b[1;32mIn[16], line 17\u001b[0m\n\u001b[0;32m     15\u001b[0m l_a \u001b[38;5;241m=\u001b[39m attributes[\u001b[38;5;241m1\u001b[39m][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexpected_mean\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[0;32m     16\u001b[0m w_b \u001b[38;5;241m=\u001b[39m attributes[\u001b[38;5;241m2\u001b[39m][\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexpected_mean\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[1;32m---> 17\u001b[0m l_b \u001b[38;5;241m=\u001b[39m \u001b[43mattributes\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m]\u001b[49m[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mexpected_mean\u001b[39m\u001b[38;5;124m\"\u001b[39m]\n\u001b[0;32m     19\u001b[0m \u001b[38;5;66;03m# the decision function\u001b[39;00m\n\u001b[0;32m     20\u001b[0m p_a \u001b[38;5;241m=\u001b[39m np\u001b[38;5;241m.\u001b[39mexp(beta \u001b[38;5;241m*\u001b[39m (w_a \u001b[38;5;241m-\u001b[39m l_a)) \u001b[38;5;241m/\u001b[39m (\n\u001b[0;32m     21\u001b[0m     np\u001b[38;5;241m.\u001b[39mexp(beta \u001b[38;5;241m*\u001b[39m (w_a \u001b[38;5;241m-\u001b[39m l_a)) \u001b[38;5;241m+\u001b[39m np\u001b[38;5;241m.\u001b[39mexp(beta \u001b[38;5;241m*\u001b[39m (w_b \u001b[38;5;241m-\u001b[39m l_b))\n\u001b[0;32m     22\u001b[0m )\n",
       "\u001b[1;31mKeyError\u001b[0m: 3"
      ]
     }
@@ -448,6 +460,13 @@
     "    )\n",
     "responses = jnp.asarray(responses)  # vector of responses"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {