doc: add notebooks for tutorials

.gitignore

@@ -65,3 +65,4 @@ perfs_benchmark.log
 .env
 bench/
 .chromnn
+*.keras

docs/source/tutorials/integrating-multiomics.ipynb

@@ -0,0 +1,91 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Integrating multi-omics data with `momics`\n",
+    "\n",
+    "`momics` excels at managing multi-omics data. It allows you to store and retrieve data from a variety of sources. Here, we will see how to create, manage and query local repositories using `momics`.\n",
+    "\n",
+    "## Creating a local `momics` repository"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "momics :: INFO :: 2024-10-21 09:31:58,466 :: Purged yeast_CNN_data.momics\n",
+      "momics :: INFO :: 2024-10-21 09:31:58,471 :: Created yeast_CNN_data.momics\n",
+      "momics :: INFO :: 2024-10-21 09:32:01,936 :: Genome sequence ingested in 3.4528s.\n",
+      "momics :: INFO :: 2024-10-21 09:32:03,193 :: 2 tracks ingested in 1.2557s.\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "<momics.momics.Momics at 0x7f1d7c0dc1f0>"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "from momics.momics import Momics\n",
+    "\n",
+    "## Creating repository\n",
+    "Momics(\"yeast_CNN_data.momics\").remove()  # Purging existing files\n",
+    "repo = Momics(\"yeast_CNN_data.momics\")  # Creating a brand new repository\n",
+    "\n",
+    "## Registering chromosome sizes\n",
+    "## We will get chromosome sizes from a local fasta file.\n",
+    "from pyfaidx import Fasta\n",
+    "\n",
+    "f = Fasta(\"/data/momics/S288c.fa\")\n",
+    "chrom_lengths = {chrom: len(seq) for chrom, seq in zip(f.keys(), f.values())}\n",
+    "\n",
+    "repo.ingest_chroms(chrom_lengths, genome_version=\"S288c\")\n",
+    "repo.chroms()\n",
+    "\n",
+    "## Registering sequence\n",
+    "repo.ingest_sequence(\"/data/momics/S288c.fa\")\n",
+    "\n",
+    "## Registering genomic tracks\n",
+    "repo.ingest_tracks(\n",
+    "    {\n",
+    "        \"ATAC\": \"/data/momics/S288c_atac.bw\",\n",
+    "        \"MNase\": \"/data/momics/S288c_mnase.bw\",\n",
+    "    }\n",
+    ")"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.10.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}