cloud_env_setup.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Cloud environment setup\n",
    "\n",
    "<table align=\"left\">\n",
    "\n",
    "  <td>\n",
    "    <a href=\"https://github.com/verily-src/workbench-examples/blob/main/cloud_env_setup.ipynb\">\n",
    "      <img src=\"https://cloud.google.com/ml-engine/images/github-logo-32px.png\" alt=\"GitHub logo\">\n",
    "      View on GitHub\n",
    "    </a>\n",
    "  </td>\n",
    "  <td>\n",
    "    <a href=\"https://console.cloud.google.com/vertex-ai/workbench/deploy-notebook?download_url=https://github.com/verily-src/workbench-examples/main/cloud_env_setup.ipynb\">\n",
    "      <img src=\"https://lh3.googleusercontent.com/UiNooY4LUgW_oTvpsNhPpQzsstV5W8F7rYgxgGBD85cWJoLmrOzhVs_ksK_vgx40SHs7jCqkTkCk=e14-rj-sc0xffffff-h130-w32\" alt=\"Vertex AI logo\">\n",
    "      Open in a Verily Workbench notebook instance\n",
    "    </a>\n",
    "  </td>                                                                                               \n",
    "</table>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "tvgnzT1CKxrO"
   },
   "source": [
    "## Overview\n",
    "\n",
    "This notebook sets up some reasonable defaults for your cloud environment. Add more setup to this notebook to meet your needs."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "id": "d975e698c9a4"
   },
   "source": [
    "### Objective\n",
    "\n",
    "Perform common environment setup tasks including:\n",
    "\n",
    "1. Configuring the user name and email address to use for your git commits.\n",
    "1. Creating a directory on this machine for Python virtual environments used in Verily Workbench tutorials.\n",
    "\n",
    "#### How to run this notebook\n",
    "\n",
    "Run this notebook cell by cell to set up your cloud environment. You can select `Run` > `Run All Cells` from the Jupyter menu bar after editing the optional defaults.\n",
    "All setup steps are optional, but recommended so that your environment is compatible with the Verily Workbench tutorials.\n",
    "\n",
    "#### Costs\n",
    "\n",
    "This notebook takes less than a minute to run, which will typically cost less than $0.01 of compute time on your cloud environment."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setup and configuration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "if not os.getenv('GOOGLE_CLOUD_PROJECT'):\n",
    "    raise Exception('Expected environment variables are not available. Please let workbench-support@verily.com know.')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Set up source control"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Edit the cloud environment's [git configuration](https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration) to tell git the name and email address to use for **all** your commits. This is optional. If the name and email address are not configured globally, JupyterLab will prompt for them upon the first commit to a newly cloned repository.\n",
    "\n",
    "<div class=\"alert alert-block alert-info\">\n",
    "<b>Tip:</b> Also <a href=\"https://support.workbench.verily.com/docs/guides/cloud_environments/git_integrations/#set-up-an-ssh-key\">set up the Verily Workbench-provided GitHub SSH key</a> for convenient interaction with source control.\n",
    "</div>\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# [Optional] EDIT THIS CELL If you wish to set your name and email address for all git repositories, change these\n",
    "# values to be correct for you. All other cells in this notebook work fine unchanged.\n",
    "\n",
    "# Uncomment the following line if you want to use your Workbench email address as your Git email address.\n",
    "#GIT_EMAIL = os.environ['WORKBENCH_USER_EMAIL']\n",
    "GIT_EMAIL = None\n",
    "\n",
    "GIT_NAME = None"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!git config --global --list"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "if GIT_NAME is not None:\n",
    "    !git config --global user.name \"{GIT_NAME}\"\n",
    "\n",
    "if GIT_EMAIL is not None:\n",
    "    !git config --global user.email \"{GIT_EMAIL}\"\n",
    "\n",
    "!git config --global --list | grep user"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Specify any other useful [git configuration](https://git-scm.com/book/en/v2/Customizing-Git-Git-Configuration)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# [Optional] EDIT THIS CELL If you wish to set the text editor when using git\n",
    "# in the terminal instead of via the JupyterLab git extension.\n",
    "\n",
    "# !git config --global core.editor emacs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Create a local directory for Python virtual environments\n",
    "\n",
    "Several of the Verily Workbench tutorials create [Python virtual environments](https://docs.python.org/3/tutorial/venv.html). They will all be placed in this subdirectory.\n",
    "\n",
    "> A virtual environment is a Python tool for dependency management and project isolation. They allow Python site packages (third party libraries) to be installed locally in an isolated directory for a particular project, as opposed to being installed globally (i.e. as part of a system-wide Python) [[1]](https://towardsdatascience.com/virtual-environments-104c62d48c54#:~:text=A%20virtual%20environment%20is%20a,a%20system%2Dwide%20Python)."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!mkdir -p ~/venvs"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Provenance\n",
    "\n",
    "Generate information about this notebook environment and the packages installed."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!date"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Conda and pip installed packages:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!conda env export"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "JupyterLab extensions:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!jupyter labextension list"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Number of cores:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!grep ^processor /proc/cpuinfo | wc -l"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Memory:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "!grep \"^MemTotal:\" /proc/meminfo"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "---\n",
    "Copyright 2024 Verily Life Sciences LLC\n",
    "\n",
    "Use of this source code is governed by a BSD-style   \n",
    "license that can be found in the LICENSE file or at   \n",
    "https://developers.google.com/open-source/licenses/bsd"
   ]
  }
 ],
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