Merge pull request #73 from MannLabs/update_documentation

Update documentation

Author: sophiamaedler

docs/doctrees/environment.pickle

@@ -2,28 +2,19 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "id": "9f0c563a-3f1b-4b1c-8738-1b29c4a94375",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "WARNING:root:Temp mmap arrays are written to /tmp/temp_mmap_bl8redu9. Cleanup of this folder is OS dependant, and might need to be triggered manually!\n",
-      "/fs/home/maedler/.local/miniconda3/envs/SPARCS_complete/lib/python3.11/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
-      "  from .autonotebook import tqdm as notebook_tqdm\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "import os\n",
-    "from sparcstools.parse import PhenixParser"
+    "os.environ['JAVA_HOME'] = \"/Users/sophia/mambaforge/envs/scPortrait/lib/jvm\"\n",
+    "from scportrait.tools.parse import PhenixParser"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "id": "97859949-245f-4411-b696-35984d0de19f",
    "metadata": {},
    "outputs": [],
@@ -83,9 +74,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "SPARCS_complete",
+   "display_name": "scPortrait",
    "language": "python",
-   "name": "sparcs_complete"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -97,7 +88,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.0"
+   "version": "3.10.0"
   }
  },
  "nbformat": 4,