To develop IGB, we use the Forking Workflow described in https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow, but with one difference - we issue pull requests to the development branch, not the master branch.
The following sections describe how to use this workflow to develop IGB.
To contribute a change to the IGB code base, create your own fork of the IGB repository.
To create your own fork:
Next, you'll see a form that let's you give your fork a name and description. Here's an example:
Fill in the fields and click Fork repository.
After a moment, the Overview page for your forked repository will appear. Click Settings and change the main branch to the IGB development branch.
See Atlassian documentation Forking a Repository.
Clone a copy of your forked IGB repository onto your computer. You will make changes to your local clone, commit them to your local repository, and then ultimately push your changes to your fork hosted on Bitbucket.
To clone your fork, use git clone with the address of your remote fork. (Copy the address from your fork's Overview page at Bitbucket.)
For example, if your fork is named my-igb-fork, you would execute
git clone <ADDRESS> |
where ADDRESS is the address of your fork on Bitbucket. To get the address of your fork, look at the top the top right of your fork's home page on Bitbucket.
Before you start making changes to your local clone, you should first create a new branch for the changes you intend to make. This will allow you to issue focused, low risk pull requests that can be easily merged with other branches of development.
To make a branch:
git checkout igb_8_3 |
git branch -b <BRANCH> |
where BRANCH is the name of the branch, e.g., IGBF-203, the name of a story in the IGB JIRA issue-tracking system.
Now, all commits will be associated with the branch you've just created. Commit your changes to your local repo and then push them to your fork hosted on bitbucket.
To request that your edits be incorporated into the main line of development:
A Pull request form will appear. Fill in the fields:
Bitbucket has utilities to help you pull in the latest code when you are working in their web application (see https://blog.bitbucket.org/2013/02/04/syncing-and-merging-come-to-bitbucket/). However, you will likely want to use the command line to keep your branch in sync with the remote branch you are tracking. The details about how this works are outside the scope of this article; however, we provide a simple example for your reference.
The following example assumes we followed the workflow above and are working on a development branch named igb_8_3.
To bring our remote fork up to date:
git remote add upstream git@bitbucket.org:lorainelab/integrated-genome-browser.git |
Fetch and merge changes from upstream for the development branch named igb_8_3.
git pull upstream igb_8_3 |
git pull --rebase upstream igb_8_3 |