Contribute to AskOmics

Issues

If you have an idea for a feature to add or an approach for a bugfix, it is best to communicate with developers early. The most common venues for this are GitHub issues.

Pull requests

All changes to AskOmics should be made through pull requests to this repository.

For the askomics repository to your account. To keep your copy up to date, you need to frequently sync your fork:

git remote add upstream https://github.com/askomics/askomics
git fetch upstream
git checkout master
git merge upstream/master

Then, create a new branch for your new feature

git checkout -b my_new_feature

Commit and push your modification to your fork. If your changes modify code, please ensure that is conform to AskOmics style

Write tests for your changes, and make sure that they passes.

cd askomics
source venv/bin/activate
nosetests

Open a pull request against the master branch of askomics. The message of your pull request should describe your modifications (why and how).

The pull request should pass all the continuous integration tests which are automatically run by Github using Travis CI. The coverage must be at least remain the same (but it’s better if it increases)

Tests

AskOmics use nosetests for Python tests. To run the tests, activate the Python virtual environment and run nosetests.

source venv/bin/activate
nosetests

Tests needs a Virtuoso instance and a Galaxy instance. You can use docker images.

To skip the Galaxy tests, run

nosetests -a '!galaxy'

To target a single file test

nosetests --tests askomics/test/askView_test.py

# Virtuoso
docker pull askomics/virtuoso
docker run -d -p :8890:8890 -e DBA_PASSWORD=dba -e SPARQL_UPDATE=true -e DEFAULT_GRAPH=http://localhost:8890/DAV --net="host" -t tenforce/virtuoso
# Galaxy
docker pull bgruening/galaxy-stable
docker run -d -p 8080:80 bgruening/galaxy-stable

The testing configuration is set in the askomics/config/test.virtuoso.ini INI file. You can see that the Galaxy account API key is admin. The docker image bgruening/galaxy-stable have a default admin account with this API key. If you use another galaxy instance, change the url and API key.

Coding style guidelines

General

Ensure all user-enterable strings are unicode capable. Use only English language for everything (code, documentation, logs, comments, …)

Python

We follow PEP-8, with particular emphasis on the parts about knowing when to be inconsistent, and readability being the ultimate goal.

  • Whitespace around operators and inside parentheses
  • 4 spaces per indent, spaces, not tabs
  • Include docstrings on your modules, class and methods
  • Avoid from module import *. It can cause name collisions that are tedious to track down.
  • Class should be in CamelCase, methods and variables in lowercase_with_underscore