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Given the following text description, write Python code to implement the functionality described below step by step
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Description:
 Version control for fun and profit
Step1:  A repository
Step2:  And this is pretty much the essence of Git!
First things first
Step3:  And how you will edit text files (it will often ask you to edit messages and other information, and thus wants to know how you like to edit your files)
Step4:  Set git to use the credential memory cache so we don't have to retype passwords too frequently. On Linux, you should run the following (note that this requires git version 1.7.10 or newer)
Step5:  Github offers in its help pages instructions on how to configure the credentials helper for Mac OSX and Windows.
Stage 1
Step6:  git init
Step7:  Note
Step8:  Now let's edit our first file in the test directory with a text editor... I'm doing it programatically here for automation purposes, but you'd normally be editing by hand
Step9:  git add
Step10:  We can now ask git about what happened with status
Step11:  git commit
Step12:  In the commit above, we  used the -m flag to specify a message at the command line.  If we don't do that, git will open the editor we specified in our configuration above and require that we enter a message.  By default, git refuses to record changes that don't have a message to go along with them (though you can obviously 'cheat' by using an empty or meaningless string
Step13:  git diff
Step14:  And now we can ask git what is different
Step15:  The cycle of git virtue
Step16:  git log revisited
First, let's see what the log shows us now
Step17:  Sometimes it's handy to see a very summarized version of the log
Step18:  Git supports aliases
Step19:  git mv and rm
Step20:  Note that these changes must be committed too, to become permanent!  In git's world, until something hasn't been committed, it isn't permanently recorded anywhere.
Step21:  And git rm works in a similar fashion.
Exercise
Add a new file file2.txt, commit it, make some changes to it, commit them again, and then remove it (and don't forget to commit this last step!).
Local user, branching
What is a branch?  Simply a label for the 'current' commit in a sequence of ongoing commits
Step22:  We are now going to try two different routes of development
Step23:  Using remotes as a single user
We are now going to introduce the concept of a remote repository
Step24:  Since the above cell didn't produce any output after the git remote -v call, it means we have no remote repositories configured.  We will now proceed to do so.  Once logged into GitHub, go to the new repository page and make a repository called test.  Do not check the box that says Initialize this repository with a README, since we already have an existing repository here.  That option is useful when you're starting first at Github and don't have a repo made already on a local computer.
We can now follow the instructions from the next page
Step25:  Let's see the remote situation again
Step26:  We can now see this repository publicly on github.
Let's see how this can be useful for backup and syncing work between two different computers.  I'll simulate a 2nd computer by working in a different directory...
Step27:  Let's now make some changes in one 'computer' and synchronize them on the second.
Step28:  Now we put this new work up on the github server so it's available from the internet
Step29:  Now let's fetch that work from machine #1
Step30:  An important aside
Step31:  And now we go back to the master branch, where we change the same file
Step32:  So now let's see what happens if we try to merge the trouble branch into master
Step33:  Let's see what git has put into our file
Step34:  At this point, we go into the file with a text editor, decide which changes to keep, and make a new commit that records our decision.  I've now made the edits, in this case I decided that both pieces of text were useful, but integrated them with some changes
Step35:  Let's then make our new commit
Step36:  Note
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Python Code:
ls
Explanation: Version control for fun and profit: the tool you didn't know you needed. From personal workflows to open collaboration
Note: this tutorial was particularly modeled, and therefore owes a lot, to the excellent materials offered in:
"Git for Scientists: A Tutorial" by John McDonnell 
Emanuele Olivetti's lecture notes and exercises from the G-Node summer school on Advanced Scientific Programming in Python.
In particular I've reused the excellent images from the Pro Git book that John had already selected and downloaded, as well as some of his outline.  But this version of the tutorial aims to be 100% reproducible by being executed directly as an IPython notebook and is hosted itself on github so that others can more easily make improvements to it by collaborating on Github.  Many thanks to John and Emanuele for making their materials available online.
After writing this document, I discovered J.R. Johansson's tutorial on version control that is also written as a fully reproducible notebook and is also aimed at a scientific audience.  It has a similar spirit to this one, and is part of his excellent series Lectures on Scientific Computing with Python that is entirely available as IPython Notebooks.
Wikipedia
“Revision control, also known as version control, source control
or software configuration management (SCM), is the
management of changes to documents, programs, and other
information stored as computer files.”
Reproducibility?
Tracking and recreating every step of your work
In the software world: it's called Version Control!
What do (good) version control tools give you?
Peace of mind (backups)
Freedom (exploratory branching)
Collaboration (synchronization)
Git is an enabling technology: Use version control for everything
Paper writing (never get paper_v5_john_jane_final_oct22_really_final.tex by email again!)
Grant writing
Everyday research
Teaching (never accept an emailed homework assignment again!)
Teaching courses with Git
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<img src="https://raw.github.com/fperez/reprosw/master/fig/indefero_projects_notes.png" width="100%">
Annotated history of each student's worfklow (and backup!)
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<img src="https://raw.github.com/fperez/reprosw/master/fig/indefero_projects1.png" width="100%">
The plan for this tutorial
This tutorial is structured in the following way: we will begin with a brief overview of key concepts you need to understand in order for git to really make sense.  We will then dive into hands-on work: after a brief interlude into necessary configuration we will discuss 5 "stages of git" with scenarios of increasing sophistication and complexity, introducing the necessary commands for each stage:
Local, single-user, linear workflow
Single local user, branching
Using remotes as a single user
Remotes for collaborating in a small team
Full-contact github: distributed collaboration with large teams
In reality, this tutorial only covers stages 1-4, since for #5 there are many software develoment-oriented tutorials and documents of very high quality online.  But most scientists start working alone with a few files or with a small team, so I feel it's important to build first the key concepts and practices based on problems scientists encounter in their everyday life and without the jargon of the software world.  Once you've become familiar with 1-4, the excellent tutorials that exist about collaborating on github on open-source projects should make sense.
Very high level picture: an overview of key concepts
The commit: a snapshot of work at a point in time
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<img src="https://raw.github.com/fperez/reprosw/master/fig/commit_anatomy.png">
Credit: ProGit book, by Scott Chacon, CC License.
End of explanation
import sha
# Our first commit
data1 = 'This is the start of my paper2.'
meta1 = 'date: 1/1/12'
hash1 = sha.sha(data1 + meta1).hexdigest()
print 'Hash:', hash1
# Our second commit, linked to the first
data2 = 'Some more text in my paper...'
meta2 = 'date: 1/2/12'
# Note we add the parent hash here!
hash2 = sha.sha(data2 + meta2 + hash1).hexdigest()
print 'Hash:', hash2
Explanation: A repository: a group of linked commits
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<img src="https://raw.github.com/fperez/reprosw/master/fig/threecommits.png" >
Note: these form a Directed Acyclic Graph (DAG), with nodes identified by their hash.
A hash: a fingerprint of the content of each commit and its parent
End of explanation
%%bash
git config --global user.name "Fernando Perez"
git config --global user.email "Fernando.Perez@berkeley.edu"
Explanation: And this is pretty much the essence of Git!
First things first: git must be configured before first use
The minimal amount of configuration for git to work without pestering you is to tell it who you are:
End of explanation
%%bash
# Put here your preferred editor. If this is not set, git will honor
# the $EDITOR environment variable
git config --global core.editor /usr/bin/jed  # my lightweight unix editor
# On Windows Notepad will do in a pinch, I recommend Notepad++ as a free alternative
# On the mac, you can set nano or emacs as a basic option
# And while we're at it, we also turn on the use of color, which is very useful
git config --global color.ui "auto"
Explanation: And how you will edit text files (it will often ask you to edit messages and other information, and thus wants to know how you like to edit your files):
End of explanation
%%bash 
git config --global credential.helper cache
# Set the cache to timeout after 2 hours (setting is in seconds)
git config --global credential.helper 'cache --timeout=7200'
Explanation: Set git to use the credential memory cache so we don't have to retype passwords too frequently. On Linux, you should run the following (note that this requires git version 1.7.10 or newer):
End of explanation
!git
Explanation: Github offers in its help pages instructions on how to configure the credentials helper for Mac OSX and Windows.
Stage 1: Local, single-user, linear workflow
Simply type git to see a full list of all the 'core' commands.  We'll now go through most of these via small practical exercises:
End of explanation
%%bash
rm -rf test
git init test
Explanation: git init: create an empty repository
End of explanation
%%bash
cd test
ls
%%bash
cd test
ls -la
%%bash
cd test
ls -l .git
Explanation: Note: all these cells below are meant to be run by you in a terminal  where  you change once to the test directory and continue working there.
Since we are putting all of them here in a single notebook for the purposes of the tutorial, they will all be prepended with the first two lines:
%%bash
cd test
that tell IPython to do that each time.  But you should ignore those two lines and type the rest of each cell yourself in your terminal.
Let's look at what git did:
End of explanation
%%bash
cd test
echo "My first bit of text" > file1.txt
Explanation: Now let's edit our first file in the test directory with a text editor... I'm doing it programatically here for automation purposes, but you'd normally be editing by hand
End of explanation
%%bash
cd test
git add file1.txt
Explanation: git add: tell git about this new file
End of explanation
%%bash
cd test
git status
Explanation: We can now ask git about what happened with status:
End of explanation
%%bash
cd test
git commit -a -m"This is our first commit"
Explanation: git commit: permanently record our changes in git's database
For now, we are always going to call git commit either with the -a option or with specific filenames (git commit file1 file2...).  This delays the discussion of an aspect of git called the index (often referred to also as the 'staging area') that we will cover later.  Most everyday work in regular scientific practice doesn't require understanding the extra moving parts that the index involves, so on a first round we'll bypass it.  Later on we will discuss how to use it to achieve more fine-grained control of what and how git records our actions.
End of explanation
%%bash
cd test
git log
Explanation: In the commit above, we  used the -m flag to specify a message at the command line.  If we don't do that, git will open the editor we specified in our configuration above and require that we enter a message.  By default, git refuses to record changes that don't have a message to go along with them (though you can obviously 'cheat' by using an empty or meaningless string: git only tries to facilitate best practices, it's not your nanny).
git log: what has been committed so far
End of explanation
%%bash
cd test
echo "And now some more text..." >> file1.txt
Explanation: git diff: what have I changed?
Let's do a little bit more work... Again, in practice you'll be editing the files by hand, here we do it via shell commands for the sake of automation (and therefore the reproducibility of this tutorial!)
End of explanation
%%bash
cd test
git diff
Explanation: And now we can ask git what is different:
End of explanation
%%bash
cd test
git commit -a -m"I have made great progress on this critical matter."
Explanation: The cycle of git virtue: work, commit, work, commit, ...
End of explanation
%%bash
cd test
git log
Explanation: git log revisited
First, let's see what the log shows us now:
End of explanation
%%bash
cd test
git log --oneline --topo-order --graph
Explanation: Sometimes it's handy to see a very summarized version of the log:
End of explanation
%%bash
cd test
# We create our alias (this saves it in git's permanent configuration file):
git config --global alias.slog "log --oneline --topo-order --graph"
# And now we can use it
git slog
Explanation: Git supports aliases: new names given to command combinations. Let's make this handy shortlog an alias, so we only have to type git slog and see this compact log:
End of explanation
%%bash
cd test
git mv file1.txt file-newname.txt
git status
Explanation: git mv and rm: moving and removing files
While git add is used to add fils to the list git tracks, we must also tell it if we want their  names to change or for it to stop tracking them.  In familiar Unix fashion, the mv and rm git commands do precisely this:
End of explanation
%%bash
cd test
git commit -a -m"I like this new name better"
echo "Let's look at the log again:"
git slog
Explanation: Note that these changes must be committed too, to become permanent!  In git's world, until something hasn't been committed, it isn't permanently recorded anywhere.
End of explanation
%%bash
cd test
git status
ls
Explanation: And git rm works in a similar fashion.
Exercise
Add a new file file2.txt, commit it, make some changes to it, commit them again, and then remove it (and don't forget to commit this last step!).
Local user, branching
What is a branch?  Simply a label for the 'current' commit in a sequence of ongoing commits:
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<img src="https://raw.github.com/fperez/reprosw/master/fig/masterbranch.png" >
There can be multiple branches alive at any point in time; the working directory is the state of a special pointer called HEAD.  In this example there are two branches, master and testing, and testing is the currently active branch since it's what HEAD points to:
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<img src="https://raw.github.com/fperez/reprosw/master/fig/HEAD_testing.png" >
Once new commits are made on a branch, HEAD and the branch label move with the new commits:
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<img src="https://raw.github.com/fperez/reprosw/master/fig/branchcommit.png" >
This allows the history of both branches to diverge:
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<img src="https://raw.github.com/fperez/reprosw/master/fig/mergescenario.png" >
But based on this graph structure, git can compute the necessary information to merge the divergent branches back and continue with a unified line of development:
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<img src="https://raw.github.com/fperez/reprosw/master/fig/mergeaftermath.png" >
Let's now illustrate all of this with a concrete example.  Let's get our bearings first:
End of explanation
%%bash
cd test
git branch experiment
git checkout experiment
%%bash
cd test
echo "Some crazy idea" > experiment.txt
git add experiment.txt
git commit -a -m"Trying something new"
git slog
%%bash
cd test
git checkout master
git slog
%%bash
cd test
echo "All the while, more work goes on in master..." >> file-newname.txt
git commit -a -m"The mainline keeps moving"
git slog
%%bash
cd test
ls
%%bash
cd test
git merge experiment
git slog
Explanation: We are now going to try two different routes of development: on the master branch we will add one file and on the experiment branch, which we will create, we will add a different one.  We will then merge the experimental branch into master.
End of explanation
%%bash
cd test
ls
echo "Let's see if we have any remote repositories here:"
git remote -v
Explanation: Using remotes as a single user
We are now going to introduce the concept of a remote repository: a pointer to another copy of the repository that lives on a different location.  This can be simply a different path on the filesystem or a server on the internet.
For this discussion, we'll be using remotes hosted on the GitHub.com service, but you can equally use other services like BitBucket or Gitorious as well as host your own.
End of explanation
%%bash
cd test
git remote add origin https://github.com/fperez/test.git
git push -u origin master
Explanation: Since the above cell didn't produce any output after the git remote -v call, it means we have no remote repositories configured.  We will now proceed to do so.  Once logged into GitHub, go to the new repository page and make a repository called test.  Do not check the box that says Initialize this repository with a README, since we already have an existing repository here.  That option is useful when you're starting first at Github and don't have a repo made already on a local computer.
We can now follow the instructions from the next page:
End of explanation
%%bash
cd test
git remote -v
Explanation: Let's see the remote situation again:
End of explanation
%%bash
# Here I clone my 'test' repo but with a different name, test2, to simulate a 2nd computer
git clone https://github.com/fperez/test.git test2
cd test2
pwd
git remote -v
Explanation: We can now see this repository publicly on github.
Let's see how this can be useful for backup and syncing work between two different computers.  I'll simulate a 2nd computer by working in a different directory...
End of explanation
%%bash
cd test2  # working on computer #2
echo "More new content on my experiment" >> experiment.txt
git commit -a -m"More work, on machine #2"
Explanation: Let's now make some changes in one 'computer' and synchronize them on the second.
End of explanation
%%bash
cd test2
git push
Explanation: Now we put this new work up on the github server so it's available from the internet
End of explanation
%%bash
cd test
git pull
Explanation: Now let's fetch that work from machine #1:
End of explanation
%%bash
cd test
git branch trouble
git checkout trouble
echo "This is going to be a problem..." >> experiment.txt
git commit -a -m"Changes in the trouble branch"
Explanation: An important aside: conflict management
While git is very good at merging, if two different branches modify the same file in the same location, it simply can't decide which change should prevail.  At that point, human intervention is necessary to make the decision.  Git will help you by marking the location in the file that has a problem, but it's up to you to resolve the conflict.  Let's see how that works by intentionally creating a conflict.
We start by creating a branch and making a change to our experiment file:
End of explanation
%%bash
cd test
git checkout master
echo "More work on the master branch..." >> experiment.txt
git commit -a -m"Mainline work"
Explanation: And now we go back to the master branch, where we change the same file:
End of explanation
%%bash
cd test
git merge trouble
Explanation: So now let's see what happens if we try to merge the trouble branch into master:
End of explanation
%%bash
cd test
cat experiment.txt
Explanation: Let's see what git has put into our file:
End of explanation
%%bash
cd test
cat experiment.txt
Explanation: At this point, we go into the file with a text editor, decide which changes to keep, and make a new commit that records our decision.  I've now made the edits, in this case I decided that both pieces of text were useful, but integrated them with some changes:
End of explanation
%%bash
cd test
git commit -a -m"Completed merge of trouble, fixing conflicts along the way"
git slog
Explanation: Let's then make our new commit:
End of explanation
from IPython.display import YouTubeVideo
YouTubeVideo('U8GBXvdmHT4')
Explanation: Note: While it's a good idea to understand the basics of fixing merge conflicts by hand, in some cases you may find the use of an automated tool useful.  Git supports multiple merge tools: a merge tool is a piece of software that conforms to a basic interface and knows how to merge two files into a new one.  Since these are typically graphical tools, there are various to choose from for the different operating systems, and as long as they obey a basic command structure, git can work with any of them.
Collaborating on github with a small team
Single remote with shared access: we are going to set up a shared collaboration with one partner (the person sitting next to you).  This will show the basic workflow of collaborating on a project with a small team where everyone has write privileges to the same repository.  
Note for SVN users: this is similar to the classic SVN workflow, with the distinction that commit and push are separate steps.  SVN, having no local repository, commits directly to the shared central resource, so to a first approximation you can think of svn commit as being synonymous with git commit; git push.
We will have two people, let's call them Alice and Bob, sharing a repository.  Alice will be the owner of the repo and she will give Bob write privileges.  
We begin with a simple synchronization example, much like we just did above, but now between two people instead of one person.  Otherwise it's the same:
Bob clones Alice's repository.
Bob makes changes to a file and commits them locally.
Bob pushes his changes to github.
Alice pulls Bob's changes into her own repository.
Next, we will have both parties make non-conflicting changes each, and commit them locally.  Then both try to push their changes:
Alice adds a new file, alice.txt to the repo and commits.
Bob adds bob.txt and commits.
Alice pushes to github.
Bob tries to push to github.  What happens here?
The problem is that Bob's changes create a commit that conflicts with Alice's, so git refuses to apply them.  It forces Bob to first do the merge on his machine, so that if there is a conflict in the merge, Bob deals with the conflict manually (git could try to do the merge on the server, but in that case if there's a conflict, the server repo would be left in a conflicted state without a human to fix things up).  The solution is for Bob to first pull the changes (pull in git is really fetch+merge), and then push again.
Full-contact github: distributed collaboration with large teams
Multiple remotes and merging based on pull request workflow: this is beyond the scope of this brief tutorial, so we'll simply discuss how it works very briefly, illustrating it with the activity on the IPython github repository.
Other useful commands
show
reflog
rebase
tag
Git resources
Introductory materials
There are lots of good tutorials and introductions for Git, which you
can easily find yourself; this is just a short list of things I've found
useful.  For a beginner, I would recommend the following 'core' reading list, and
below I mention a few extra resources:
The smallest, and in the style of this tuorial: git - the simple guide
contains 'just the basics'.  Very quick read.
The concise Git Reference: compact but with
    all the key ideas. If you only read one document, make it this one.
In my own experience, the most useful resource was Understanding Git
Conceptually.
Git has a reputation for being hard to use, but I have found that with a
clear view of what is actually a very simple internal design, its
behavior is remarkably consistent, simple and comprehensible.
For more detail, see the start of the excellent Pro
    Git online book, or similarly the early
    parts of the Git community book. Pro
    Git's chapters are very short and well illustrated; the community
    book tends to have more detail and has nice screencasts at the end
    of some sections.
If you are really impatient and just want a quick start, this visual git tutorial
may be sufficient. It is nicely illustrated with diagrams that show what happens on the filesystem.
For windows users, an Illustrated Guide to Git on Windows is useful in that
it contains also some information about handling SSH (necessary to interface with git hosted on remote servers when collaborating) as well
as screenshots of the Windows interface.
Cheat sheets
:   Two different
    cheat
    sheets
    in PDF format that can be printed for frequent reference.
Beyond the basics
At some point, it will pay off to understand how git itself is built.  These two documents, written in a similar spirit, 
are probably the most useful descriptions of the Git architecture short of diving into the actual implementation.  They walk you through
how you would go about building a version control system with a little story. By the end you realize that Git's model is almost
an inevitable outcome of the proposed constraints:
The Git parable by Tom Preston-Werner.
Git foundations by Matthew Brett.
Git ready
:   A great website of posts on specific git-related topics, organized
    by difficulty.
QGit: an excellent Git GUI
:   Git ships by default with gitk and git-gui, a pair of Tk graphical
    clients to browse a repo and to operate in it. I personally have
    found qgit to be nicer and
    easier to use. It is available on modern linux distros, and since it
    is based on Qt, it should run on OSX and Windows.
Git Magic
:   Another book-size guide that has useful snippets.
The learning center at Github
:   Guides on a number of topics, some specific to github hosting but
    much of it of general value.
A port of the Hg book's beginning
:   The Mercurial book has a reputation
    for clarity, so Carl Worth decided to
    port its introductory chapter
    to Git. It's a nicely written intro, which is possible in good
    measure because of how similar the underlying models of Hg and Git
    ultimately are.
Intermediate tips
:   A set of tips that contains some very valuable nuggets, once you're
    past the basics.
Finally, if you prefer a video presentation, this 1-hour tutorial prepared by the GitHub educational team will walk you through the entire process:
End of explanation
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