zip_clean.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Clean up Notebooks and Zip (before uploading to GitHub)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "#pip install --upgrade nbstripout"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!nbstripout --install"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# !nbstripout"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# pip install clean_ipynb"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Clean Output from Notebooks Using `nbstripout`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "# !nbstripout -h"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash\n",
    "# The string `{}' is replaced by the current file name being processed\n",
    "find ./ -type f -name \"*.ipynb\" -exec nbstripout \"{}\" \\;"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Archive Directories"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "dirs = [\n",
    "    \"1_python\",\n",
    "    \"2_pandas\",\n",
    "    \"3_scipy\",\n",
    "    \"4_scikit-learn\"\n",
    "]\n",
    "\n",
    "for directory in dirs:\n",
    "    \n",
    "    zip_path = '-r ./zip_archives/{}.zip ./{} -x \"*/.*\"'.format(directory, directory)\n",
    "    \n",
    "    if directory is \"08_bioinfo_python\":\n",
    "        zip_path = '-r ./zip_archives/{}.zip ./{} -x \\*.snakemake\\* -x \"*/.*\"'.format(directory, directory)\n",
    "    elif directory is \"10_databases\":\n",
    "        zip_path = '-r ./zip_archives/{}.zip ./{} -x \\datasets\\* -x \"*/.*\"'.format(directory, directory)\n",
    "\n",
    "    print(zip_path)\n",
    "    !zip {zip_path}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!ls -ls ./zip_archives/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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