Edit your .login file on saxon to include the following line:

if ("`hostname`" == "saxon.stat.duke.edu") then
    eval `keychain --eval id_rsa`
endif

The first time you login you will be asked for the passphrase, after that you will not need to reenter it unless saxon gets restarted.

• Simple formal system for tracking all changes to a project

• Time machine for your projects
  • Track blame and/or praise
  • Remove the fear of breaking things

• Learning curve is steep, but when you need it you REALLY need it

• Distributed
  • Work online or offline
  • Collaborate with large groups
• Popular and Successful
  • Active development
  • Shiny new tools and ecosystems
  • Fast

• Tracks any type of file

• Branching
  • Smarter merges

We want to let git know who we are so there are some simple configuration options we should setup.

Let's first tell git who we are, and what editor we want to use.

$ git config --global user.name "Colin Rundel"
$ git config --global user.email "rundel@gmail.com"
$ git config --global color.ui true
$ git config --global core.editor nano
$ git config --global push.default matching

We also want to set this up on saxon too, so

$ ssh cr173@saxon.stat.duke.edu
[cr173@saxon ~]$ git config --global user.name "Colin Rundel"
...

$ git clone git@github.com:Sta523-Fa14/ExampleTeam.git
Cloning into 'ExampleTeam'...
remote: Counting objects: 4, done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 4 (delta 0), reused 0 (delta 0)
Receiving objects: 100% (4/4), done.
Checking connectivity... done.
$ ls
ExampleTeam
$ ls -a ExampleTeam/
.          ..         .DS_Store  .git       .gitignore README.md

$ cd ExampleTeam
$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
nothing to commit, working directory clean

Lets edit the README.md file to include team member names and email addresses.

$ cat README.md
Example
=======

Example repo
$ nano README.md
$ cat README.md
ExampleTeam Repo
=======

## Team Members

* Colin Rundel - rundel@gmail.com

$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   README.md

no changes added to commit (use "git add" and/or "git commit -a")

$ echo -e "* Add other team member's info\n* Fix formatting\n" > TODO
$ cat TODO
* Add other team member's info
* Fix formatting

$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

    modified:   README.md

Untracked files:
  (use "git add <file>..." to include in what will be committed)

    TODO

no changes added to commit (use "git add" and/or "git commit -a")

• One file README.md is tracked and modified (repo is already has this file but our current version differs from the previously saved version)

• The other file TODO is untracked (this file does not exist in the repo)

Our next step is the same for both files - we want to stage our local changes using git add.

$ git add README.md
$ git add TODO

$ git status
On branch master
Your branch is up-to-date with 'origin/master'.
Changes to be committed:
  (use "git reset HEAD <file>..." to unstage)

    modified:   README.md
    new file:   TODO

By using git add we have made git aware of the current version of both files, but we have not actually saved the changes yet.

To save the changes (locally) we need to commit them using git commit, since this change will be saved it is customary to add a message about the nature of the changes being made (for future reference).

git commit -m "Added Colin's information to README; Added TODO file."
[master f9c548c] Added Colin's information to README; Added TODO file.
 2 files changed, 7 insertions(+), 2 deletions(-)
 create mode 100644 TODO

$ git status
On branch master
Your branch is ahead of 'origin/master' by 1 commit.
  (use "git push" to publish your local commits)
nothing to commit, working directory clean

We've saved our changes but we're now out of sync with the repository on github.

What if at the same time I was making these edits my teammate John Doe was making changes to README.md on github?

We can attempt to send our changes back to github by using git push

$ git push
To git@github.com:Sta523-Fa14/ExampleTeam.git
 ! [rejected]        master -> master (fetch first)
error: failed to push some refs to 'git@github.com:Sta523-Fa14/ExampleTeam.git'
hint: Updates were rejected because the remote contains work that you do
hint: not have locally. This is usually caused by another repository pushing
hint: to the same ref. You may want to first integrate the remote changes
hint: (e.g., 'git pull ...') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.

$ git pull
remote: Counting objects: 3, done.
remote: Compressing objects: 100% (3/3), done.
remote: Total 3 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (3/3), done.
From github.com:Sta523-Fa14/ExampleTeam
   6b79df7..804e091  master     -> origin/master
Auto-merging README.md
CONFLICT (content): Merge conflict in README.md
Automatic merge failed; fix conflicts and then commit the result.

$ git status
On branch master
Your branch and 'origin/master' have diverged,
and have 1 and 1 different commit each, respectively.
  (use "git pull" to merge the remote branch into yours)
You have unmerged paths.
  (fix conflicts and run "git commit")

Unmerged paths:
  (use "git add <file>..." to mark resolution)

    both modified:   README.md

no changes added to commit (use "git add" and/or "git commit -a")

$ cat README.md 
ExampleTeam Repo
=======

## Team Members

<<<<<<< HEAD
* Colin Rundel - rundel@gmail.com
=======
* John Doe - j.doe@gmail.com
>>>>>>> 804e09178910383c128035ce67a58c9c1df3f558

• <<<<<<< - Indicates the start of the merge conflict.
• ======= - Indicates the break point used for comparison.
• >>>>>>> - Indicates the end of the lines that had a merge conflict.

Edit the merged file to reflect the changes you actually want.

$ nano README.md
$ cat README.md
ExampleTeam Repo
=======

## Team Members

* Colin Rundel - rundel@gmail.com
* John Doe - j.doe@gmail.com

$ git add README.md 
retBook-2:ExampleTeam rundel$ git status
On branch master
Your branch and 'origin/master' have diverged,
and have 1 and 1 different commit each, respectively.
  (use "git pull" to merge the remote branch into yours)
All conflicts fixed but you are still merging.
  (use "git commit" to conclude merge)

Changes to be committed:

    modified:   README.md

$ git commit -m "Merge changes"

$ git status
On branch master
Your branch is ahead of 'origin/master' by 2 commits.
  (use "git push" to publish your local commits)
nothing to commit, working directory clean
$ git push
Counting objects: 7, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (7/7), 791 bytes | 0 bytes/s, done.
Total 7 (delta 1), reused 0 (delta 0)
To git@github.com:Sta523-Fa14/ExampleTeam.git
   804e091..9c4a5e7  master -> master

• Make sure that your ssh public key encryption is working

  $ ssh -T git@github.com
  Hi rundel! You've successfully authenticated, but GitHub does not provide shell access.

• Everyone in your team should create a local copy of the team repo using git pull with the appropriate url.

• Individually update the local README.md file

  • Pick a new team name
  • Each team member should add their name and email address to their local repo copy
  • Stage and commit any local changes you make
  • Pick an order and one at a time, push your changes back to github
    • Handle any merge conflicts that arise

Above materials are derived in part from the following sources:

• Karl Broman - Wisc's Tools4RR
• Software Carpentry Project