12-CommandLine.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# Command Line\n",
    "\n",
    "- command line & shell commands\n",
    "- file paths (absolute and relative)\n",
    "- scripts and modules"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "Jupyter Notebooks are a helpful tool, but they're _bulky_."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## File Systems"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "Computers use a hierarchical file systems that organizes files & folders.\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "When you click through the folders (directories) on your computer, you're interacting with this hierarchical system."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Command Line"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "A <b>command line interface</b> is a way to interact with a computer through written commands.\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "The command line allows us to:\n",
    "\n",
    "- create files\n",
    "- edit files\n",
    "- run python scripts\n",
    "- etc.\n",
    "\n",
    "...without clicking on anything."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### The Terminal\n",
    "\n",
    "The **terminal** is where you can type these commands into the command line.\n",
    "\n",
    "Accessing the terminal...\n",
    "\n",
    "- possible on your computer\n",
    "    - Windows: \"Command Prompt\"\n",
    "    - Mac or Linux: \"Terminal\"\n",
    "- and on datahub"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Shell Commands\n",
    "\n",
    "...can be run in the terminal _and_ Jupyter notebooks\n",
    "\n",
    "In jupyter Notebooks, do this by starting with `!`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Check current directory\n",
    "(note that this command will be `cd` (without anything afterwards) on Windows machines and `pwd` on Linux/Mac pachines)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "# print working directory\n",
    "!cd\n",
    "# on datahub this would be:\n",
    "# !pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## An important aside: File Paths"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "The specific location of a file or folder on your computer. </div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "When using a Graphical User Interface (GUI), you click on directories to access subdirectories and finally find the file you're interested in."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "When using the command line, you specify a file's path explicitly with text. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Absolute vs. Relative Paths\n",
    "\n",
    "The two ways to specify the path to your file of interest allow for flexibility in programming."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "#### Absolute Paths"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "<b>Absolute paths</b> specify the <b>full</b> path for a given file system (starting from the root directory). \n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "**root** specifies the 'highest' directory in the file structure (the start).\n",
    "\n",
    "An absolute file path starts with a slash `/` (in Mac OS and Linux) or a drive letter and backslash `C:\\` (in Windows) specifying the root directory.\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "## absolute path\n",
    "## this is specific to my computer\n",
    "## look at the path output above for you computer\n",
    "!cd\n",
    "# on datahub this would be:\n",
    "# !pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Relative Paths"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "<b>Relative paths</b> specify the path to a file from your <b>current working directory</b> (where your computer is working right now). \n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "Note that directories are separated with `\\` in Windows and `/` in Linux and Mac OS"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# remind us of our current working directory\n",
    "!cd\n",
    "# on datahub this would be:\n",
    "# !pwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# relative path\n",
    "# this is specific to my computer\n",
    "!dir ..\\winter_2025\n",
    "# on datahub this would be:\n",
    "# !ls ../winter_2025"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "\n",
    "- `..` specify you want to move one directory up in your hierarchy\n",
    "- `\\fall_2024` specifies the path to the directory I want to list files in\n",
    "- each directory is separated with a backslash or slash (`\\` or `/`)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "This **relative** path does _not_ start with a leading slash (b/c it's not an absolute path)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Class Question #1\n",
    "\n",
    "Given the following file structure: \n",
    "\n",
    "- `/`\n",
    "    - `scripts/`\n",
    "        - cool_thing.py\n",
    "        - super_cool_thing.py\n",
    "    - `images/`\n",
    "        - image1.png\n",
    "        - image2.png\n",
    "    - `notebooks/`\n",
    "        - 00_intro.ipynb\n",
    "        - 01_variables.ipynb\n",
    "    \n",
    "\n",
    "If your current working directory is `notebooks`, what is the **absolute path** to `cool_thing.py`?\n",
    "\n",
    "- A) `/scripts/cool_thing.py`\n",
    "- B) `scripts/cool_thing.py`\n",
    "- C) `cool_thing.py`\n",
    "- D) `../scripts/cool_thing.py`\n",
    "- E) ¯\\\\\\_(ツ)\\_/¯"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Class Question #2\n",
    "\n",
    "Given the same file structure: \n",
    "\n",
    "- `/`\n",
    "    - `scripts/`\n",
    "        - cool_thing.py\n",
    "        - super_cool_thing.py\n",
    "    - `images/`\n",
    "        - image1.png\n",
    "        - image2.png\n",
    "    - `notebooks/`\n",
    "        - 00_intro.ipynb\n",
    "        - 01_variables.ipynb\n",
    "    \n",
    "\n",
    "If your current working directory is `notebooks`, what is the **relative path** to `cool_thing.py`?\n",
    "\n",
    "- A) `/notebooks/../scripts/cool_thing.py`\n",
    "- B) `scripts/cool_thing.py`\n",
    "- C) `/scripts/cool_thing.py`\n",
    "- D) `../scripts/cool_thing.py`\n",
    "- E) ¯\\\\\\_(ツ)\\_/¯"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Shell Commands\n",
    "\n",
    "...can be run in the terminal _and_ Jupyter notebooks"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Check current directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# print working directory\n",
    "!cd\n",
    "# on datahub this would be:\n",
    "# !pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Change directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# change directory \n",
    "!cd ..\\winter_2025\n",
    "# same on datahub"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "outputs": [],
   "source": [
    "# which directory are we in now?\n",
    "!cd\n",
    "# on datahub this would be:\n",
    "# !pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### List files in a directory\n",
    "`dir` in Windows, `ls` in Linux/Mac"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "scrolled": true,
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# list files (list segments)\n",
    "!dir\n",
    "# on datahub this would be:\n",
    "# !ls"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### More Shell Commands"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Make a new directory"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# make directory \n",
    "!mkdir dir_name\n",
    "# same on datahub"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Create a file\n",
    "Works in Linux/Mac, not in Windows"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# create an empty file (this will work on Linux/Mac/datahub but not in Windows)\n",
    "!touch new_file.py "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Move a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "# move file\n",
    "# notice the relative file path\n",
    "!move new_file.py dir_name\\\n",
    "# on datahub this would be:\n",
    "# !mv new_file.py dir_name\\"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### And Some More"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Print out a message"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "!echo Hello World!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "#### Print the contents of a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "outputs": [],
   "source": [
    "!type dir_name\\new_file.py\n",
    "# on datahub this would be:\n",
    "# !cat dir_name/new_file.py"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "notes"
    }
   },
   "source": [
    "#### Open to see and edit contents of a file"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "slideshow": {
     "slide_type": "notes"
    }
   },
   "outputs": [],
   "source": [
    "# will not work on datahub\n",
    "!open dir_name/new_file.py"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "#### Class Question #4\n",
    "\n",
    "Which creates a file?     \n",
    "   \n",
    "- A) `mkdir`\n",
    "- B) `pwd`\n",
    "- C) `cd`\n",
    "- D) `touch`\n",
    "- E) `cat`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Windows Command Prompt\n",
    "\n",
    "- `dir` : lists files in current directory\n",
    "- `move` : moves a file\n",
    "- `copy` : copies a file\n",
    "- `rename` : renames a file\n",
    "- `type` : can be used to print out a file\n",
    "    \n",
    "Note that `pwd`, `cd`, `mkdir`, `echo` are all the same in Windows command prompt and Linux/Mac terminal.\n",
    "\n",
    "If you want to make a new empty file, you can do:\n",
    "\n",
    "`echo '' > my_file.py`\n",
    "\n",
    "^This construction puts an empty string into a file. If the filename is not found, it will create a new (empty) file."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Linux/Mac Command Prompt\n",
    "\n",
    "- `ls` or `ls -l` : lists files in current directory\n",
    "- `mv` : moves a file or renames it if you move to a new name in the same directory\n",
    "- `cp` : copies a file\n",
    "- `cat` : can be used to print out a file\n",
    "- `touch` : creates an empty file\n",
    "    \n",
    "Note that `pwd`, `cd`, `mkdir`, `echo` are all the same in Windows command prompt and Linux/Mac terminal.\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Python Files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "Python files are plain-text files, with Python code in them, that can be executed and/or imported from.\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "### Script vs. Module File"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "### Scripts"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "A <b>script</b> is a Python file that can be run to execute a particular task. \n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "### Module Files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "A <b>module</b> file is a file with Python code (typically functions & classes) that we can import and use.\n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "Remember: if you're writing code, you cannot just click through to the file you want. You need to specify _using code_ where the file you want is. \n",
    "\n",
    "This is where understanding file paths is critically important."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Text Editors"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "<div class=\"alert alert-success\">\n",
    "Text-editors are programs made for editing text. Many text-editors are designed for writing code specifically. \n",
    "</div>"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "notes"
    }
   },
   "source": [
    "### Terminal Based Text Editors\n",
    "\n",
    "There are text editors designed to be used within a terminal, such as `vim`, `emacs`, or `nano`. "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "notes"
    }
   },
   "source": [
    "#### vim\n",
    "\n",
    "`vim` is a terminal based text-editor. Type `vim filename` in command line to open a file in vim. \n",
    "\n",
    "`vim` has different modes:\n",
    "\n",
    "- click `escape` + `i` to enter edit mode (insert mode). \n",
    "    - This will let you write text / code into the file\n",
    "- To escape vim, press `escape` then type `:wq` and enter to save and quit vim\n",
    "    - If you want to exit without saving, you can do `:!q` to force quit without saving"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "fragment"
    }
   },
   "source": [
    "### Non-Terminal Text Editors\n",
    "\n",
    "For writing code (outside of notebooks and the terminal), you probably want a code focused stand-alone text editor, like `Sublime`.  If you are doing more extensive Python coding, you may want `PyCharm` instead."
   ]
  },
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   "source": [
    "## Executing Python Files"
   ]
  },
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   "source": [
    "From the command line, you can execute a Python script using the `python` command:\n",
    "\n",
    "`python dir_name/new_file.py`"
   ]
  },
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   "source": [
    "#### Class Question #5\n",
    "\n",
    "To create a file and see its contents, which command line commands would you use (and in which order)?    \n",
    "   \n",
    "- A) `mkdir` -> `cd`\n",
    "- B) `pwd` -> `ls`\n",
    "- C) `cd` -> `pwd`\n",
    "- D) `touch` -> `cat`\n",
    "- E) `cat` -> `touch`"
   ]
  },
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   "source": [
    "#### Class Question #6\n",
    "\n",
    "Given the file structure from earlier: \n",
    "\n",
    "- `/`\n",
    "    - `scripts/`\n",
    "        - cool_thing.py\n",
    "        - super_cool_thing.py\n",
    "    - `images/`\n",
    "        - image1.png\n",
    "        - image2.png\n",
    "    - `notebooks/`\n",
    "        - 00_intro.ipynb\n",
    "        - 01_variables.ipynb\n",
    "\n",
    "Your currently working within `notebooks` and you want to execute the code in 'cool_thing.py' from the command line. How would you do that?\n",
    "\n",
    "\n",
    "- A) `python cool_thing.py` \n",
    "- B) `python ../notebooks/cool_thing.py` \n",
    "- C) `python ../scripts/cool_thing.py` \n",
    "- D) `python ../cool_thing.py` \n",
    "- E) ¯\\\\\\_(ツ)\\_/¯ "
   ]
  }
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