Add jupyter notebooks for code instruction

notebooks/MultipleDicotPipeline.ipynb

@@ -0,0 +1,136 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from sleap_roots.series import find_all_series, Series\n",
+    "from sleap_roots.trait_pipelines import MultipleDicotPipeline, Pipeline\n",
+    "\n",
+    "import numpy as np\n",
+    "import matplotlib.pyplot as plt\n",
+    "import pandas as pd\n",
+    "import json\n",
+    "import os\n",
+    "\n",
+    "from typing import List\n",
+    "from pathlib import Path"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Current directory: C:\\repos\\sleap-roots\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Get the current working directory\n",
+    "current_directory = os.getcwd()\n",
+    "\n",
+    "# Print the current working directory\n",
+    "print(\"Current directory:\", current_directory)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Updated current directory: C:\\repos\\sleap-roots\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Use this cell when you want to change the current working directory\n",
+    "\n",
+    "# Define the directory you want to change to\n",
+    "new_directory = \"C:/repos/sleap-roots\"\n",
+    "\n",
+    "# Change the current working directory\n",
+    "os.chdir(new_directory)\n",
+    "\n",
+    "# Get the updated current working directory\n",
+    "updated_directory = os.getcwd()\n",
+    "\n",
+    "# Print the updated current working directory\n",
+    "print(\"Updated current directory:\", updated_directory)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 15,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Change these variables for your own data\n",
+    "csv_path = \"tests/data/multiple_arabidopsis_11do/merged_proofread_samples_03122024.csv\" # For sample information (count, group)\n",
+    "folder_path = \"tests/data/multiple_arabidopsis_11do\" # Location of h5 files and predictions\n",
+    "primary_name = \"primary\" # For loading primary root predictions\n",
+    "lateral_name = \"lateral\" # For loading lateral root predictions"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[]"
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "# Find all h5 files in the folder\n",
+    "all_h5s = find_all_series(folder_path)\n",
+    "all_h5s"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "sleap_roots",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

pyproject.toml

@@ -35,6 +35,11 @@ dynamic = ["version", "readme"]
 version = {attr = "sleap_roots.__version__"}
 readme = {file = ["README.md"], content-type="text/markdown"}
 
+[tool.setuptools.packages.find]
+include = ["sleap_roots"]  # Include only the sleap_roots package
+exclude = ["notebooks"]  # Exclude the notebooks directory
+namespaces = false
+
 [project.optional-dependencies]
 dev = [
     "pytest",