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 "cells": [
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   "source": [
    "name = '2015-12-11-meeting-summary'\n",
    "title = 'Introducing Git'\n",
    "tags = 'git, github, version control'\n",
    "author = 'Denis Sergeev'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from nb_tools import connect_notebook_to_post\n",
    "from IPython.core.display import HTML\n",
    "\n",
    "html = connect_notebook_to_post(name, title, tags, author)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Today we talked about git and its functionality for managing code, text documents and other building blocks of our research."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We followed a very good tutorial created by [**Software Carpentry**](http://swcarpentry.github.io/git-novice/). There are hundreds of other resources available online, for example, [**Git Real**](http://gitreal.codeschool.com/)."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Hence, this post is not trying to be yet another git tutorial. Instead, below is just a brief recap of what commands were covered during the meeting."
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Setting Up Git"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Set up your name and email so that each time you contribute to a project your commit has an author"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git config --global user.name \"Python UEA\"`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git config --global user.email \"python@uea.ac.uk\"`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Creating a Repository"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create a new directory for a project"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`mkdir myproject`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Go into the newly created directory"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`cd myproject`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Make the directory a Git repository"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git init`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Check status of the repository"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git status`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Tracking Changes"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Add a Python script to the repo (make the file staged for commit)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git add awesome_script.py`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Commit changes with a meaningful message"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git commit -m \"Add awesome script written in Python\"`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Exploring History"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Commits history"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git log`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Comparing different versions of files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "List all untracked changes in the repository"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git diff`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Differences with “head minus one”, i.e. previous, commit"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git diff HEAD~1 awesome_script.py`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Differences with a specific commit"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git diff <unique commit id> awesome_script.py`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Ignoring Things"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create a .gitignore file and put '*.pyc' line in it telling git will to ignore all Python bytecode files"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`echo '*.pyc' >> .gitignore`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Include .gitignore in the repository"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git add .gitignore`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git commit -m \"Add .gitignore file\"`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git status`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Remotes in GitHub"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git remote add origin git@github.com:<username>/<repository_name>.git`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`git push -u origin master`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Issue on Grace"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "If you use git on [Grace](http://rscs.uea.ac.uk/high-performance-computing) and have tried `git push` to a GitHub repository, you have probably encountered the following error:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`fatal: unable to access 'https://github.com/***/***/': error:0D0C50A1:asn1 encoding routines:ASN1_item_verify:unknown message digest algorithm`"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "One of the possible solutions here is to switch off SSL verification by adding the following line in your .bashrc file:"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "`export GIT_SSL_NO_VERIFY=true`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
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