From 226071741f78f0d68e406d28d43242ac20066a10 Mon Sep 17 00:00:00 2001
From: "Ryan M. Moore" <rmm1047@gmail.com>
Date: Mon, 6 Jan 2025 17:59:15 -0500
Subject: [PATCH] Add S5 env check

---
 Submodule_5/Submodule_5_Env_Check.ipynb | 106 ++++++++++++++++++++++++
 1 file changed, 106 insertions(+)
 create mode 100644 Submodule_5/Submodule_5_Env_Check.ipynb

diff --git a/Submodule_5/Submodule_5_Env_Check.ipynb b/Submodule_5/Submodule_5_Env_Check.ipynb
new file mode 100644
index 0000000..328b5c5
--- /dev/null
+++ b/Submodule_5/Submodule_5_Env_Check.ipynb
@@ -0,0 +1,106 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Environment Check -- Submodule 5\n",
+    "\n",
+    "If this notebook runs successfully, then all the required packages for Submodule 4 are properly installed.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Requirement already satisfied: jupyterquiz in /home/ryan/miniconda3/envs/nigms_sandbox_ud__submodule_4_exported/lib/python3.9/site-packages (2.8.1)\n",
+      "Note: you may need to restart the kernel to use updated packages.\n",
+      "OK!\n"
+     ]
+    }
+   ],
+   "source": [
+    "import os\n",
+    "import warnings\n",
+    "from collections import Counter\n",
+    "\n",
+    "import deepchem as dc\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "import seaborn as sns\n",
+    "import tensorflow as tf\n",
+    "from IPython.display import YouTubeVideo\n",
+    "from jupyterquiz import display_quiz\n",
+    "from keras.callbacks import EarlyStopping\n",
+    "from keras.layers import (\n",
+    "    LSTM,\n",
+    "    Bidirectional,\n",
+    "    Conv1D,\n",
+    "    Dense,\n",
+    "    Dropout,\n",
+    "    Embedding,\n",
+    "    Flatten,\n",
+    "    Input,\n",
+    "    MaxPooling1D,\n",
+    ")\n",
+    "from keras.models import Model, Sequential\n",
+    "from keras.preprocessing.sequence import pad_sequences\n",
+    "from keras.regularizers import l2\n",
+    "from scipy import interp\n",
+    "from sklearn import metrics\n",
+    "from sklearn.base import clone\n",
+    "from sklearn.metrics import auc, classification_report, confusion_matrix, roc_curve\n",
+    "from sklearn.model_selection import train_test_split\n",
+    "from sklearn.preprocessing import LabelEncoder, StandardScaler, label_binarize\n",
+    "from tensorflow.keras.utils import to_categorical\n",
+    "\n",
+    "sns.set_style(\"darkgrid\")\n",
+    "\n",
+    "%matplotlib inline\n",
+    "\n",
+    "print(\"OK!\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Set up conda environment\n",
+    "\n",
+    "If the above code returned any errors, then either 1. not all the required packages are installed, or 2. incorrect versions of one of more of the packages are installed.\n",
+    "\n",
+    "We recommend that you use conda to set up an environment for this submodule.\n",
+    "\n",
+    "```\n",
+    "# Create conda environment\n",
+    "conda env create -f conda_env_submodule_5_exported.yml\n",
+    "\n",
+    "# Activate the environment\n",
+    "conda activate nigms_sandbox_ud__submodule_5_exported\n",
+    "\n",
+    "# Register the kernel\n",
+    "python -m ipykernel install --user \\\n",
+    "    --name=nigms_sandbox_ud__submodule_5_exported \\\n",
+    "    --display-name \"Python (nigms_sandbox_ud__submodule_5_exported)\"\n",
+    "```\n",
+    "\n",
+    "Then, when starting the notebook, select the `Python (nigms_sandbox_ud__submodule_5_exported)` kernel from the list.\n",
+    "\n",
+    "Note that you may need to restart Jupyter Lab for these changes to take effect.\n"
+   ]
+  }
+ ],
+ "metadata": {
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}