diff --git a/tests/print_random_number.py b/tests/print_random_number.py
new file mode 100644
index 0000000000000000000000000000000000000000..a105a4fb95f717678d2091beb3ac1512fdc87912
--- /dev/null
+++ b/tests/print_random_number.py
@@ -0,0 +1,3 @@
+print(203)
+with open("output/data.txt", "w") as handle:
+ handle.write(203)
diff --git a/tests/test_jupyter.ipynb b/tests/test_jupyter.ipynb
new file mode 100644
index 0000000000000000000000000000000000000000..e3faca2f32a017f780d0874e37f8c087a762775b
--- /dev/null
+++ b/tests/test_jupyter.ipynb
@@ -0,0 +1,331 @@
+{
+ "cells": [
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "id": "a5c6949c-da6a-40ab-aec7-de4534582ab2",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import nbformat as nbf\n",
+ "import sys\n",
+ "import os\n",
+ "from pathlib import Path\n",
+ "\n",
+ "import nbformat\n",
+ "import time\n",
+ "from nbconvert.preprocessors import ExecutePreprocessor\n",
+ "\n",
+ "from nbconvert.nbconvertapp import NbConvertApp\n",
+ "from ipylab import JupyterFrontEnd"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "id": "e4dd4791-5e5b-4fa7-89f1-8a9e574c300e",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "1\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(1)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "id": "e983e571-58f5-4310-8584-064fe4ac3570",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "2\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(2)"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 24,
+ "id": "b28fb6d3-faa9-4788-86a1-4ec0d1026aa8",
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "def check_execution_order(notebook_path,\n",
+ " check_all_executed=False,\n",
+ " check_all_except_last_executed=True,\n",
+ " check_top_to_bottom=False,\n",
+ " check_in_order=True,\n",
+ " exclude_last_cell=False):\n",
+ " ntbk = nbf.read(notebook_path, nbf.NO_CONVERT)\n",
+ "\n",
+ " # extract all code cells (disregard markdown, raw and others), then extract the execution order\n",
+ " output_cells = [cell for cell in ntbk.cells if cell[\"cell_type\"] == \"code\"]\n",
+ " # remove empty cells\n",
+ " non_empty_cells = [cell for cell in output_cells if cell[\"source\"] != \"\"]\n",
+ " execution_counts = [cell[\"execution_count\"] for cell in non_empty_cells]\n",
+ "\n",
+ " def _all_none(item_list):\n",
+ " return all([i is None for i in item_list])\n",
+ "\n",
+ " # return early if no cells were executed\n",
+ " if _all_none(execution_counts):\n",
+ " return True\n",
+ "\n",
+ " pass_check = [True]\n",
+ "\n",
+ " def _check_all_executed(execution_counts: list) -> bool:\n",
+ " \"\"\"Check all cells were executed.\n",
+ "\n",
+ " Parameters\n",
+ " ----------\n",
+ " execution_counts : list\n",
+ " execution_counts\n",
+ "\n",
+ " Returns\n",
+ " -------\n",
+ " bool\n",
+ " \"\"\"\n",
+ " return not None in execution_counts\n",
+ "\n",
+ " def _check_in_order(execution_counts: list) -> bool:\n",
+ " \"\"\"Check that execution counts that aren't None go from 1 to N.\n",
+ "\n",
+ " Parameters\n",
+ " ----------\n",
+ " execution_counts : list\n",
+ " execution counts\n",
+ "\n",
+ " Returns\n",
+ " -------\n",
+ " bool\n",
+ " \"\"\"\n",
+ " print(execution_counts)\n",
+ " execution_counts = [x for x in execution_counts if x is not None]\n",
+ " count_range = len(execution_counts)\n",
+ " if exclude_last_cell:\n",
+ " count_range = count_range - 1\n",
+ " is_in_order = all([execution_counts[i] < execution_counts[i + 1] for i in range(count_range - 1)])\n",
+ " return is_in_order\n",
+ "\n",
+ " if check_in_order:\n",
+ " pass_check.append(_check_in_order(execution_counts))\n",
+ "\n",
+ " if check_all_executed:\n",
+ " pass_check.append(_check_all_executed(execution_counts))\n",
+ " \n",
+ " if check_all_except_last_executed:\n",
+ " pass_check.append(_check_all_executed(execution_counts[:-1]))\n",
+ "\n",
+ " if check_top_to_bottom:\n",
+ " pass_check.append(\n",
+ " _check_all_executed(execution_counts) and _check_in_order(execution_counts)\n",
+ " )\n",
+ " return all(pass_check)\n",
+ "\n",
+ "\n",
+ "def save_ipynb():\n",
+ " app = JupyterFrontEnd()\n",
+ " print(\"Saving\", end=\"\")\n",
+ " # note: docmanager:save doesn't lock the python thread until saving is completed.\n",
+ " # Sometimes, new changes aren't completely saved before checks are performed.\n",
+ " # Waiting for 0.1 seconds seems to prevent that.\n",
+ " app.commands.execute('docmanager:save')\n",
+ " time.sleep(0.1)\n",
+ " print(\"\")\n",
+ "\n",
+ "\n",
+ "def reload_notebook():\n",
+ " app = JupyterFrontEnd()\n",
+ " app.commands.execute('docmanager:reload')\n",
+ "\n",
+ "\n",
+ "def wait_for_user(message):\n",
+ " proceed = input(message + \" Y/n\")\n",
+ " if proceed.lower() == \"y\" or proceed == \"\":\n",
+ " return True\n",
+ " else:\n",
+ " return False\n",
+ "\n",
+ "\n",
+ "def clear_and_rerun_notebook(notebook_filename, force_rerun=False, timeout=600):\n",
+ " if \"nbconvert_call\" in sys.argv:\n",
+ " print(\"Finished rerun\")\n",
+ " return\n",
+ "\n",
+ " save_ipynb()\n",
+ " time.sleep(1)\n",
+ "\n",
+ " is_in_order = check_execution_order(notebook_filename)\n",
+ "\n",
+ " if is_in_order and not force_rerun:\n",
+ " print(\"Notebook was already executed in order.\")\n",
+ " return\n",
+ " else:\n",
+ " rerun_confirmed_bool = wait_for_user(\"Notebook was not in order, rerun notebook now?\")\n",
+ " if not rerun_confirmed_bool and not force_rerun:\n",
+ " print(\"Aborting.\")\n",
+ " return\n",
+ "\n",
+ " print(\"Rerunning.\")\n",
+ " with open(notebook_filename) as f:\n",
+ " nb = nbformat.read(f, as_version=4)\n",
+ "\n",
+ " ep = ExecutePreprocessor(timeout=timeout, kernel_name='python3', extra_arguments=[\"nbconvert_call\"])\n",
+ " ep.preprocess(nb, )\n",
+ "\n",
+ " with open(notebook_filename, 'w', encoding='utf-8') as f:\n",
+ " nbformat.write(nb, f)\n",
+ "\n",
+ " reload_notebook()\n",
+ "\n",
+ "\n",
+ "def convert_ipynb(filepath, formats=None):\n",
+ " if formats is None:\n",
+ " formats = [\"html\", \"python\"]\n",
+ " app = NbConvertApp()\n",
+ " app.initialize()\n",
+ " output_root_directory = os.path.join(r\"C:\\Users\\ronal\\PycharmProjects\\git_lfs_test_2\", \"results\",\n",
+ " os.path.basename(filepath.replace('.', '_')))\n",
+ " for format in formats:\n",
+ " app.export_format = format\n",
+ " app.notebooks = [filepath]\n",
+ " app.output_base = os.path.join(output_root_directory, os.path.basename(filepath.replace('.ipynb', '')))\n",
+ " if not os.path.exists(output_root_directory):\n",
+ " os.makedirs(output_root_directory)\n",
+ " app.start()\n",
+ "\n",
+ "\n",
+ "\n",
+ "def export_all_figures():\n",
+ " import junix\n",
+ "\n",
+ " for file in os.listdir(git_repo.working_dir):\n",
+ " if file.endswith(\"ipynb\"):\n",
+ " file_without_extension = Path(file).stem\n",
+ " images = junix.export_images(filepath=os.path.join(git_repo.working_dir, file),\n",
+ " output_dir=os.path.join(git_repo.working_dir, \"results\",\n",
+ " file.replace(\".\", \"_\")),\n",
+ " prefix=file_without_extension)\n",
+ " convert_ipynb(filepath=os.path.join(git_repo.working_dir, file), formats=[\"html\"])\n"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 27,
+ "id": "99404052-11f1-499b-a23f-4a90ed917300",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Saving\n",
+ "[13, 14, 15, 24, None, 25, 26]\n"
+ ]
+ },
+ {
+ "name": "stdin",
+ "output_type": "stream",
+ "text": [
+ "Notebook was not in order, rerun notebook now? Y/n n\n"
+ ]
+ },
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Aborting.\n"
+ ]
+ }
+ ],
+ "source": [
+ "clear_and_rerun_notebook(\"test_jupyter.ipynb\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 28,
+ "id": "fec9df11-5622-49d8-8e08-c6e8bbe73dfd",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Saving\n",
+ "[13, 14, 15, 24, 27, None, 26]\n"
+ ]
+ },
+ {
+ "data": {
+ "text/plain": [
+ "False"
+ ]
+ },
+ "execution_count": 28,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "save_ipynb()\n",
+ "time.sleep(1)\n",
+ "check_execution_order(\"test_jupyter.ipynb\")"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 29,
+ "id": "81841f17-c8d7-4a1e-b13d-d3f5a19adfd4",
+ "metadata": {},
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "Saving\n",
+ "[13, 14, 15, 24, 27, 28, None]\n",
+ "Notebook was already executed in order.\n"
+ ]
+ }
+ ],
+ "source": [
+ "clear_and_rerun_notebook(\"test_jupyter.ipynb\")"
+ ]
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3 (ipykernel)",
+ "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": "3.12.0"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/token instructions.png b/token instructions.png
new file mode 100644
index 0000000000000000000000000000000000000000..b1959f92dde40566c8aac588cf7ba90a26d6441f
Binary files /dev/null and b/token instructions.png differ