Good VCS systems tag changes with authors who make them.
.. figure:: _static/repo_single.png
:scale: 50 %
Files are `added` from the `working directory`, which always holds the
current version of your files, to the `staging area`. `Staged` files will be stored into the repository in the next `commit`.
The repository itself contains all previous versions of all files ever committed.
.. figure:: _static/repo_distributed.png
Distributed Workflow using a centralized repository. Here, three local copies of one central repository allow you,
Jon and Matt to work on the same files and sync files between each other using the central server.
git at a Glance
***************
===============
git commands
------------
The git tool has many subcommands that can be invoked like `git <subcommand>` for instance `git status` to get the status of a repository.
...
...
@@ -68,12 +57,25 @@ you can read more about each command by invoking the help: ::
git help commit
git concepts
------------
commit
^^^^^^
A commit is a recorded set of changes in your project's file(s).
Try to group *logical* sets of changes together into one commit -- don't mix changes which are unrelated.
repository
^^^^^^^^^^
A repository is the history of all your project's commits.
git Settings
************
============
setting your identity
=====================
---------------------
Before we start, we should set the user name and e-mail address.
This is important because every git commit uses this information
...
...
@@ -111,6 +113,19 @@ You can use the `git config --list` command to list all your settings: ::
A Typical git Workflow
**********************
.. figure:: _static/repo_single.png
:scale: 50 %
Files are `added` from the `working directory`, which always holds the
current version of your files, to the `staging area`. `Staged` files will be stored into the repository in the next `commit`.
The repository itself contains all previous versions of all files ever committed.
.. figure:: _static/repo_distributed.png
Distributed Workflow using a centralized repository. Here, three local copies of one central repository allow you,
Jon and Matt to work on the same files and sync files between each other using the central server.
Creating a git Repository
=========================
...
...
@@ -280,47 +295,13 @@ Basically what this does is create a repository which all the files from the `.g
This also means that you should never add/edit/delete files in this directory. Rather clone this directory in another folder/computer,
edit files there and commit/push (see below)...
EMBL git server
***************
As part of the Bio-IT initiative, EMBL provides a central git server which can be used as a centralized resource to share and exchange data/code with collaborators:
http://git.embl.de/
The following rules apply:
- Repositories on the EMBL Git server are only granted to EMBL staff members.
- External users can be added as cooperators on a project, but the projects themselves have to be lead by someone with an active EMBL contract.
- Should the project leader leave EMBL, then the project has to be transferred to someone else or the complete repository will be removed.
- Repositories are always installed as sub-repositories of the project leader/repository responsible.
- By default, repositories are installed with only basic access permissions for the repository owner. He/she is then in charge of setting appropriate access permissions as
described on the `Howto <http://git.embl.de/howto.html>`_ page.
github
******
Basically, to use this server, you need to provide your full name, your EMBL
email address and username, the name and a short description of the
repository/project, along with your SSH public key to the admin and he will set
things up so you are able to access your repository: ::
.. note:: It's important to mention that the username for accessing the git.embl.de server is always **git**, not **your** username!
An SSH key can be generated using the command `ssh-keygen` (Windows users might want to use `putty <http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe>`_) like so: ::
ssh-keygen
Generating public/private rsa key pair.
Enter file in which to save the key (/home/username/.ssh/id_rsa):
Created directory '/home/username/.ssh'.
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /home/username/.ssh/id_rsa.
Your public key has been saved in /home/username/.ssh/id_rsa.pub.
The key fingerprint is: 2d:14:f5:d8:... username@hostname
This creates two files, in this case `/home/username/.ssh/id_rsa` and
`/home/username/.ssh/id_rsa.pub`. The former is your **private** key and should
**never** be handed out to anybody, while the latter one (ending in `.pub`)
should be distributed to any server on which you intend to use it...
