Chimera 2 Revision Control

We will use git and git flow for revision control to manage Chimera 2 source code. Development will follow the ​Vincent Driessen's branching model where the master branch is the release branch and the develop branch is the daily build branch. A team repository is the repository that is used to create release and daily builds, i.e., changes committed in developer repositories but not pushed to the team repository will not appear in either release or daily builds.

The remainder of this document describes some common tasks using git.

Cloning a Developer Repository

To make changes to the source code, a developer must have a working repository. The repository may be on the same host as the team repository, or it may be on a separate host.

The following example shows the steps for creating a repository in the same directory, /usr/local/projects/chimera/git, as the team repository. Developer repositories do not need to be the the same directory as the team repository. The last argument to git clone specifies the location where the developer repository will be created and it may be a full path. However, the web server on the cluster is configured to simplify accessing files below /usr/local/projects/chimera/git (see NotYetWritten), for example, for viewing changes to HTML files; so it may be more convenient to have developer repositories there than elsewhere.

After cloning the repository, it is necessary to initialize it for git flow, the tool for managing branches. The -d flag specifies that the default branch names for development and feature branches be used. Even if there is no plan to use git flow operations, executing this command is useful since it checks out the develop branch rather than leaving the repository on the master branch, which should only be modified during releases.

franklin:~ conrad$ cd /usr/local/projects/chimera2/git
franklin:git conrad$ git clone chimera2.git myrepo
Initialized empty Git repository in /usr/local/projects/chimera2/git/myrepo/.git/
franklin:git conrad$ cd myrepo
/usr/local/projects/chimera2/git/myrepo
franklin:myrepo conrad$ git flow init -d
Using default branch names.

Which branch should be used for bringing forth production releases?
   - master
Branch name for production releases: [master]
Branch name for "next release" development: [develop]

How to name your supporting branch prefixes?
Feature branches? [feature/]
Release branches? [release/]
Hotfix branches? [hotfix/]
Support branches? [support/]
Version tag prefix? []
franklin:myrepo conrad$ ls -l
total 36
drwxrwxr-x  4 conrad ferrin 3864 May  3 11:01 docs/
-rw-rw-r--  1 conrad ferrin  183 May  3 11:01 index.html
-rw-rw-r--  1 conrad ferrin  657 May  3 11:01 Makefile
drwxrwxr-x  2 conrad ferrin 3864 May  3 11:01 mk/
drwxrwxr-x 28 conrad ferrin 3864 May  3 11:01 prereqs/
-rw-rw-r--  1 conrad ferrin 1262 May  3 11:01 README.rst
drwxrwxr-x  7 conrad ferrin 3864 May  3 11:01 src/
-rwxrwxr-x  1 conrad ferrin 3589 May  3 11:01 vsvars.sh*
drwxrwxr-x  3 conrad ferrin 3864 May  3 11:01 webdemo/

Alternatively, a developer may use a repository on his own workstation rather than the cluster. Below is an example of creating a clone on the remote host, <b>loft</b>, running Cygwin on Windows 7. The <b>ssh</b> agent has already been initialized, so no passwords are required. The steps after git clone are effective the same as the example above.

[loft - /e]$ git clone \
  ssh://conrad@plato.cgl.ucsf.edu/usr/local/projects/chimera2/git/chimera2.git \
  chimera2
Cloning into 'chimera2'...
remote: Counting objects: 556, done.
remote: Compressing objects: 100% (533/533), done.
remote: Total 556 (delta 170), reused 275 (delta 16)
Receiving objects: 100% (556/556), 311.17 MiB | 621 KiB/s, done.
Resolving deltas: 100% (170/170), done.
[loft - /e]$ cd chimera2
/e/chimera2
[loft - /e/chimera2]$ git flow init -d
Using default branch names.

Which branch should be used for bringing forth production releases?
   - master
Branch name for production releases: [master]
Branch name for "next release" development: [develop]

How to name your supporting branch prefixes?
Feature branches? [feature/]
Release branches? [release/]
Hotfix branches? [hotfix/]
Support branches? [support/]
Version tag prefix? []
[loft - /e/chimera2]$ ls -l
total 26
-rw-r--r--+ 1 conrad None  657 May  3 10:51 Makefile
-rw-r--r--+ 1 conrad None 1262 May  3 10:51 README.rst
drwxr-xr-x+ 1 conrad None    0 May  3 10:51 docs/
-rw-r--r--+ 1 conrad None  183 May  3 10:51 index.html
drwxr-xr-x+ 1 conrad None    0 May  3 10:51 mk/
drwxr-xr-x+ 1 conrad None    0 May  3 10:51 prereqs/
drwxr-xr-x+ 1 conrad None    0 May  3 10:51 src/
-rwxr-xr-x+ 1 conrad None 3589 May  3 10:51 vsvars.sh*
drwxr-xr-x+ 1 conrad None    0 May  3 10:51 webdemo/

Use develop Branch Directly for Development

Use Feature Branch for Development

Stash Modified Files before Switching Branches

Use plato Repository to Coordinate Development on Multiple Hosts

Create Team Repository

In this section, examples refer to /var/tmp/conrad/example since the actual path /usr/local/projects/chimera2/git is already in use. Examples in other sections of this document refer to the correct path.

Create the bare git repository that will serve as the team repository for Chimera 2 source code. Note that the repository is created for sharing within a group. The chgrp command defines which group will have cloning and update privileges. The access permissions such as the setgid bit of directories (meaning files created will inherit the group of the parent directory) in the repository is maintained by git and should not require manual intervention.

franklin:example conrad$ cd /var/tmp/conrad/example
franklin:example conrad$ git init --bare --shared=group chimera2.git
Initialized empty shared Git repository in /var/tmp/conrad/example/chimera2.git/
franklin:example conrad$ chgrp -R chimdev chimera2.git
franklin:example conrad$ ls -l
total 4
drwxrwsr-x 7 conrad chimdev 3864 May  1 09:34 chimera2.git/

Create a bootstrap repository so that we can set up the initial configuration for the project. The reason this repository is temporary is that the push/pull linkage between local and remote branches need to be set up when the branches are created, but are handled automatically during cloning after they have been created. Since we will only use master and develop branches in the team repository, we can set them up now and developers who clone later will not have to worry about configuring the push/pull targets.

franklin:example conrad$ git clone --shared chimera2.git bootstrap
Initialized empty Git repository in /var/tmp/conrad/example/bootstrap/.git/
warning: You appear to have cloned an empty repository.
franklin:example conrad$ cd bootstrap
/var/tmp/conrad/example/bootstrap
franklin:bootstrap conrad$ ls -la
total 12
drwxr-xr-x 3 conrad ferrin 3864 May  1 10:32 ./
drwxrwxr-x 5 conrad ferrin 3864 May  1 10:32 ../
drwxrwxr-x 7 conrad ferrin 3864 May  1 10:32 .git/

Use git flow to set up the branches in the bootstrap repository. After initialization, we are on the develop branch where we add our initial files; xyzzy is our only file in this example. The add -A command adds all modified and untracked files to the staging area; the commit command commits files in the staging area to the local repository; the push command pushes the state of the current branch from the local repository, bootstrap, to the remote team repository, origin, which represents the repository from which we are cloned (chimera2.git in this case).

franklin:bootstrap conrad$ git flow init -d
Using default branch names.
No branches exist yet. Base branches must be created now.
Branch name for production releases: [master]
Branch name for "next release" development: [develop]

How to name your supporting branch prefixes?
Feature branches? [feature/]
Release branches? [release/]
Hotfix branches? [hotfix/]
Support branches? [support/]
Version tag prefix? []
franklin:bootstrap conrad$ git status
# On branch develop
nothing to commit (working directory clean)
franklin:bootstrap conrad$ echo hello > xyzzy
franklin:bootstrap conrad$ git add -A
franklin:bootstrap conrad$ git status
# On branch develop
# Changes to be committed:
#   (use "git reset HEAD <file>..." to unstage)
#
#       new file:   xyzzy
#
franklin:bootstrap conrad$ git commit -m "initial setup"
[develop ff9b042] initial setup
 1 files changed, 1 insertions(+), 0 deletions(-)
 create mode 100644 xyzzy
franklin:bootstrap conrad$ git push origin develop
Counting objects: 5, done.
Delta compression using up to 64 threads.
Compressing objects: 100% (2/2), done.
Writing objects: 100% (5/5), 384 bytes, done.
Total 5 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (5/5), done.
To /var/tmp/conrad/example/chimera2.git
 * [new branch]      develop -> develop

Make the master branch match the develop branch. The checkout command is used to switch from one branch to another; note that this command only uses the local repository and does not require access to the team repository.

franklin:bootstrap conrad$ git checkout master
Switched to branch 'master'
You have new mail in /var/spool/mail/conrad
franklin:bootstrap conrad$ git merge develop
Updating 76fd917..ff9b042
Fast-forward
 xyzzy |    1 +
 1 files changed, 1 insertions(+), 0 deletions(-)
 create mode 100644 xyzzy
franklin:bootstrap conrad$ git push origin master
Total 0 (delta 0), reused 0 (delta 0)
To /var/tmp/conrad/example/chimera2.git
 * [new branch]      master -> master

At this point, the team repository set up is complete. All the files are under revision control and the bootstrap repository may be safely deleted. The team repository, chimera2.git, with master and develop branches, is ready for by developers. Note that developers still have to set up and use git flow after cloning in order to follow the ​Vincent Driessen's branching model conveniently.

franklin:bootstrap conrad$ cd ..
franklin:example conrad$ ls -l
total 12
drwxr-xr-x 3 conrad ferrin  3864 May  1 11:19 bootstrap/
drwxrwsr-x 7 conrad chimdev 3864 May  1 09:34 chimera2.git/
franklin:example conrad$ rm -rf bootstrap