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GenomeBaser Developer HOWTO

In addition to what is described here, this document by Jeff Forcier and this talk from Carl Meyer provide wonderful footings for developing on/in open source projects.

Maintaining a consistent development environment

1) Ensure all development in performed within a virtualenv. A good way too bootstrap this is via virtualenv-burrito.

Execute the installation using:

$ curl -sL https://raw.githubusercontent.com/brainsik/virtualenv-burrito/master/virtualenv-burrito.sh | $SHELL

2) Make a virtualenv called GenomeBaser:

$ mkvirtualenv GenomeBaser

3) Install autoenv:

$ git clone git://github.com/kennethreitz/autoenv.git ~/.autoenv
$ echo 'source ~/.autoenv/activate.sh' >> ~/.bashrc

Get the current code from GitHub

Something like this:

$ cd $PATH_WHERE_I_KEEP_MY_REPOS
$ git clone https://github.com/mscook/GenomeBaser.git

Install dependencies

Something like this:

$ cd GenomeBaser
$ # Assuming you installed autoenv -
$ # You'll want to say 'y' as this will activate the virtualenv each time you enter the code directory
$ # Otherwise -
$ # workon GenomeBaser 
$ pip install -r requirements.txt
$ pip install -r requirements-dev.txt

Development workflow

Use GitHub. You will have already cloned the GenomeBaser repo (if you followed instructions above). To make things easier, please fork (https://github.com/mscook/GenomeBaser/fork) and update your local copy to point to your fork.

Something like this:

$ # Assuming your fork is like this
$ # https://github.com/$YOUR_USERNAME/GenomeBaser/
$ vi .git/config
$ # Replace:
$ # url = git@github.com:mscook/GenomeBaser.git
$ #  with:
$ # url = git@github.com:$YOUR_USERNAME/GenomeBaser.git

With this setup you will be able to push development changes to your fork and submit Pull Requests to the core GenomeBaser repo when you're happy.

Important Note: Upstream changes will not be synced to your fork by default. Please, before submitting a pull request please sync your fork with any upstream changes (specifically handle any merge conflicts). Info on syncing a fork can be found here.

Code style/testing/Continuous Integration

We try to make joining and/or modifying the GenomeBaser project simple.

General:
  • As close to PEP8 as possible but I ain't no Saint. Just a long as it's clean and readable,
  • Using standard lib UnitTest. There are convenience functions check_coverage.sh & tests/run_tests.sh respectively. We would prefer SMART test vs 100 % coverage.
In the master GitHub repository we use hooks that call:
  • landscape.io (code QC)
  • drone.io (continuous integration)
  • ReadTheDocs (documentation building)