From ccd96b4c0f5994f2c303804aed7fe09568b96486 Mon Sep 17 00:00:00 2001
From: Kedi Cao <kedic715@gmail.com>
Date: Tue, 4 Mar 2025 17:42:45 +0100
Subject: [PATCH] clear notebook output
---
.../read_numbers_in_bar_graph.py.ipynb | 73 +------------------
1 file changed, 2 insertions(+), 71 deletions(-)
diff --git a/snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb b/snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb
index 2668ad7..bdf36a9 100644
--- a/snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb
+++ b/snakemodules/notebooks/read_numbers_in_bar_graph.py.ipynb
@@ -2,71 +2,10 @@
"cells": [
{
"cell_type": "code",
- "execution_count": 5,
- "id": "e346a6bb-0831-404d-9a4c-b7e8fa48c426",
- "metadata": {},
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "Name: ipython\n",
- "Version: 9.0.0\n",
- "Summary: IPython: Productive Interactive Computing\n",
- "Home-page: https://ipython.org\n",
- "Author: The IPython Development Team\n",
- "Author-email: ipython-dev@python.org\n",
- "License: BSD-3-Clause\n",
- "Location: /home/kedic/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages\n",
- "Requires: decorator, ipython-pygments-lexers, jedi, matplotlib-inline, pexpect, prompt_toolkit, pygments, stack_data, traitlets\n",
- "Required-by: ipykernel, ipywidgets, jupyter-console\n",
- "Note: you may need to restart the kernel to use updated packages.\n"
- ]
- }
- ],
- "source": [
- "pip show ipython"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": 6,
+ "execution_count": null,
"id": "8f2c7f1e",
"metadata": {},
- "outputs": [
- {
- "ename": "ModuleNotFoundError",
- "evalue": "No module named 'IPython.extensions.deduperreload'",
- "output_type": "error",
- "traceback": [
- "\u001b[31m---------------------------------------------------------------------------\u001b[39m",
- "\u001b[31mModuleNotFoundError\u001b[39m Traceback (most recent call last)",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:62\u001b[39m, in \u001b[36mExtensionManager.load_extension\u001b[39m\u001b[34m(self, module_str)\u001b[39m\n\u001b[32m 61\u001b[39m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[32m---> \u001b[39m\u001b[32m62\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_load_extension\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodule_str\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 63\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mModuleNotFoundError\u001b[39;00m:\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:77\u001b[39m, in \u001b[36mExtensionManager._load_extension\u001b[39m\u001b[34m(self, module_str)\u001b[39m\n\u001b[32m 76\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m module_str \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m sys.modules:\n\u001b[32m---> \u001b[39m\u001b[32m77\u001b[39m mod = \u001b[43mimport_module\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodule_str\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 78\u001b[39m mod = sys.modules[module_str]\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/importlib/__init__.py:90\u001b[39m, in \u001b[36mimport_module\u001b[39m\u001b[34m(name, package)\u001b[39m\n\u001b[32m 89\u001b[39m level += \u001b[32m1\u001b[39m\n\u001b[32m---> \u001b[39m\u001b[32m90\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_bootstrap\u001b[49m\u001b[43m.\u001b[49m\u001b[43m_gcd_import\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m[\u001b[49m\u001b[43mlevel\u001b[49m\u001b[43m:\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpackage\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlevel\u001b[49m\u001b[43m)\u001b[49m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:1387\u001b[39m, in \u001b[36m_gcd_import\u001b[39m\u001b[34m(name, package, level)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:1360\u001b[39m, in \u001b[36m_find_and_load\u001b[39m\u001b[34m(name, import_)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:1324\u001b[39m, in \u001b[36m_find_and_load_unlocked\u001b[39m\u001b[34m(name, import_)\u001b[39m\n",
- "\u001b[31mModuleNotFoundError\u001b[39m: No module named 'autoreload'",
- "\nDuring handling of the above exception, another exception occurred:\n",
- "\u001b[31mModuleNotFoundError\u001b[39m Traceback (most recent call last)",
- "\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[6]\u001b[39m\u001b[32m, line 1\u001b[39m\n\u001b[32m----> \u001b[39m\u001b[32m1\u001b[39m \u001b[43mget_ipython\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\u001b[43m.\u001b[49m\u001b[43mrun_line_magic\u001b[49m\u001b[43m(\u001b[49m\u001b[33;43m'\u001b[39;49m\u001b[33;43mload_ext\u001b[39;49m\u001b[33;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[33;43m'\u001b[39;49m\u001b[33;43mautoreload\u001b[39;49m\u001b[33;43m'\u001b[39;49m\u001b[43m)\u001b[49m\n\u001b[32m 2\u001b[39m get_ipython().run_line_magic(\u001b[33m'\u001b[39m\u001b[33mautoreload\u001b[39m\u001b[33m'\u001b[39m, \u001b[33m'\u001b[39m\u001b[33m2\u001b[39m\u001b[33m'\u001b[39m)\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/interactiveshell.py:2478\u001b[39m, in \u001b[36mInteractiveShell.run_line_magic\u001b[39m\u001b[34m(self, magic_name, line, _stack_depth)\u001b[39m\n\u001b[32m 2476\u001b[39m kwargs[\u001b[33m'\u001b[39m\u001b[33mlocal_ns\u001b[39m\u001b[33m'\u001b[39m] = \u001b[38;5;28mself\u001b[39m.get_local_scope(stack_depth)\n\u001b[32m 2477\u001b[39m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m.builtin_trap:\n\u001b[32m-> \u001b[39m\u001b[32m2478\u001b[39m result = \u001b[43mfn\u001b[49m\u001b[43m(\u001b[49m\u001b[43m*\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 2480\u001b[39m \u001b[38;5;66;03m# The code below prevents the output from being displayed\u001b[39;00m\n\u001b[32m 2481\u001b[39m \u001b[38;5;66;03m# when using magics with decorator @output_can_be_silenced\u001b[39;00m\n\u001b[32m 2482\u001b[39m \u001b[38;5;66;03m# when the last Python token in the expression is a ';'.\u001b[39;00m\n\u001b[32m 2483\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(fn, magic.MAGIC_OUTPUT_CAN_BE_SILENCED, \u001b[38;5;28;01mFalse\u001b[39;00m):\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/magics/extension.py:33\u001b[39m, in \u001b[36mExtensionMagics.load_ext\u001b[39m\u001b[34m(self, module_str)\u001b[39m\n\u001b[32m 31\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m module_str:\n\u001b[32m 32\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m UsageError(\u001b[33m'\u001b[39m\u001b[33mMissing module name.\u001b[39m\u001b[33m'\u001b[39m)\n\u001b[32m---> \u001b[39m\u001b[32m33\u001b[39m res = \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43mshell\u001b[49m\u001b[43m.\u001b[49m\u001b[43mextension_manager\u001b[49m\u001b[43m.\u001b[49m\u001b[43mload_extension\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodule_str\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 35\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m res == \u001b[33m'\u001b[39m\u001b[33malready loaded\u001b[39m\u001b[33m'\u001b[39m:\n\u001b[32m 36\u001b[39m \u001b[38;5;28mprint\u001b[39m(\u001b[33m\"\u001b[39m\u001b[33mThe \u001b[39m\u001b[38;5;132;01m%s\u001b[39;00m\u001b[33m extension is already loaded. To reload it, use:\u001b[39m\u001b[33m\"\u001b[39m % module_str)\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:66\u001b[39m, in \u001b[36mExtensionManager.load_extension\u001b[39m\u001b[34m(self, module_str)\u001b[39m\n\u001b[32m 64\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m module_str \u001b[38;5;129;01min\u001b[39;00m BUILTINS_EXTS:\n\u001b[32m 65\u001b[39m BUILTINS_EXTS[module_str] = \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[32m---> \u001b[39m\u001b[32m66\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_load_extension\u001b[49m\u001b[43m(\u001b[49m\u001b[33;43m\"\u001b[39;49m\u001b[33;43mIPython.extensions.\u001b[39;49m\u001b[33;43m\"\u001b[39;49m\u001b[43m \u001b[49m\u001b[43m+\u001b[49m\u001b[43m \u001b[49m\u001b[43mmodule_str\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 67\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/core/extensions.py:77\u001b[39m, in \u001b[36mExtensionManager._load_extension\u001b[39m\u001b[34m(self, module_str)\u001b[39m\n\u001b[32m 75\u001b[39m \u001b[38;5;28;01mwith\u001b[39;00m \u001b[38;5;28mself\u001b[39m.shell.builtin_trap:\n\u001b[32m 76\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m module_str \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m sys.modules:\n\u001b[32m---> \u001b[39m\u001b[32m77\u001b[39m mod = \u001b[43mimport_module\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmodule_str\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 78\u001b[39m mod = sys.modules[module_str]\n\u001b[32m 79\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m._call_load_ipython_extension(mod):\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/importlib/__init__.py:90\u001b[39m, in \u001b[36mimport_module\u001b[39m\u001b[34m(name, package)\u001b[39m\n\u001b[32m 88\u001b[39m \u001b[38;5;28;01mbreak\u001b[39;00m\n\u001b[32m 89\u001b[39m level += \u001b[32m1\u001b[39m\n\u001b[32m---> \u001b[39m\u001b[32m90\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43m_bootstrap\u001b[49m\u001b[43m.\u001b[49m\u001b[43m_gcd_import\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m[\u001b[49m\u001b[43mlevel\u001b[49m\u001b[43m:\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpackage\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlevel\u001b[49m\u001b[43m)\u001b[49m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:1387\u001b[39m, in \u001b[36m_gcd_import\u001b[39m\u001b[34m(name, package, level)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:1360\u001b[39m, in \u001b[36m_find_and_load\u001b[39m\u001b[34m(name, import_)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:1331\u001b[39m, in \u001b[36m_find_and_load_unlocked\u001b[39m\u001b[34m(name, import_)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:935\u001b[39m, in \u001b[36m_load_unlocked\u001b[39m\u001b[34m(spec)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap_external>:999\u001b[39m, in \u001b[36mexec_module\u001b[39m\u001b[34m(self, module)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m<frozen importlib._bootstrap>:488\u001b[39m, in \u001b[36m_call_with_frames_removed\u001b[39m\u001b[34m(f, *args, **kwds)\u001b[39m\n",
- "\u001b[36mFile \u001b[39m\u001b[32m~/workflow_dev/popinSnake/.snakemake/conda/69c6e6c50cd0e118bb8c803e51bd5c48_/lib/python3.12/site-packages/IPython/extensions/autoreload.py:110\u001b[39m\n\u001b[32m 108\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mIPython\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mcore\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m magic_arguments\n\u001b[32m 109\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mIPython\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mcore\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mmagic\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m Magics, magics_class, line_magic\n\u001b[32m--> \u001b[39m\u001b[32m110\u001b[39m \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01mIPython\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mextensions\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mdeduperreload\u001b[39;00m\u001b[34;01m.\u001b[39;00m\u001b[34;01mdeduperreload\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[38;5;28;01mimport\u001b[39;00m DeduperReloader\n\u001b[32m 112\u001b[39m __skip_doctest__ = \u001b[38;5;28;01mTrue\u001b[39;00m\n\u001b[32m 114\u001b[39m \u001b[38;5;66;03m# -----------------------------------------------------------------------------\u001b[39;00m\n\u001b[32m 115\u001b[39m \u001b[38;5;66;03m# Copyright (C) 2000 Thomas Heller\u001b[39;00m\n\u001b[32m 116\u001b[39m \u001b[38;5;66;03m# Copyright (C) 2008 Pauli Virtanen <pav@iki.fi>\u001b[39;00m\n\u001b[32m (...)\u001b[39m\u001b[32m 127\u001b[39m \u001b[38;5;66;03m# Imports\u001b[39;00m\n\u001b[32m 128\u001b[39m \u001b[38;5;66;03m# -----------------------------------------------------------------------------\u001b[39;00m\n",
- "\u001b[31mModuleNotFoundError\u001b[39m: No module named 'IPython.extensions.deduperreload'"
- ]
- }
- ],
+ "outputs": [],
"source": [
"%load_ext autoreload\n",
"%autoreload 2"
@@ -75,14 +14,6 @@
{
"cell_type": "code",
"execution_count": null,
- "id": "5ebc1c0a-0d55-430e-988f-ea6521abcfdb",
- "metadata": {},
- "outputs": [],
- "source": []
- },
- {
- "cell_type": "code",
- "execution_count": 2,
"id": "e9cb92ab-fc91-4311-a745-3a03e0fbde3c",
"metadata": {},
"outputs": [],
--
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