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Contributing

Style guide

We follow PEP8 standards with the following exceptions:

  • Use tabs instead of spaces - this allows all individuals to have visual depth of indentation they prefer, without changing the source code at all, and it is simply smaller

Testing

Easiest way to run tests is by running the command tox from the terminal. The default Python environments for testing with are py27 and py34, but you can specify your own by running e.g. tox -e py35.

Branching / Release

We currently use the gitflow workflow. Feature branches are created from and merged back to the dev branch, and the master branch stores snapshots/releases of the dev branch.

See also the much simpler github flow here

Versioning

For the sake of reproducibility, always be sure to work with a release when doing the analysis!

We use semantic versioning (http://semver.org), and the current version of ExpAn is: v0.4.0.

The version is maintained in setup.cfg, and propagated from there to various files by the bumpversion program. The most important propagation destination is in version.py where it is held in the string __version__ with the form:

'{major}.{minor}.{patch}'

The __version__ string and a version() function is imported by core.__init__ and so is accessible to imported functions in expan.

The version(format_str) function generates version strings of any form. It can use git's commit count and revision number to generate a long version string which may be useful for pip versioning? Examples: NB: caution using this... it won't work if not in the original git repository.

>>> import core.binning
>>> core.version()
'v0.4.0'
>>> core.version('{major}.{minor}..{commits}')
'0.0..176'
>>> core.version('{commit}')
'a24730a42a4b5ae01bbdb05f6556dedd453c1767'

See: StackExchange 151558

Bumping Version

Can use bumpversion to maintain the __version__ in version.py:

$ bumpversion patch

or

$ bumpversion minor

This will update the version number, create a new tag in git, and commit the changes with a standard commit message.

When you have done this, you must push the commit and new tag to the repository with:

$ git push --tags

Travis CI and PyPI deployment

We use Travis CI for testing builds and deploying our PyPI package.

A build and test is triggered when a commit is pushed to either

  • dev,
  • master
  • or a pull request branch to dev or master.

If you want to deploy to PyPI, then follow these steps:

  • assuming you have a dev branch that is up to date, create a pull request from dev to master (a travis job will be started for the pull request)
  • once the pull request is approved, merge it (another travis job will be started because a push to master happened)
  • checkout master
  • push tags to master (a third travis job will be started, but this time it will also push to PyPI because tags were pushed)

If you wish to skip triggering a CI task (for example when you change documentation), please include [ci skip] in your commit message.

The flow would then look like follows:

  1. git fetch
  2. git checkout dev
  3. git pull
  4. bumpversion (patch|minor)
  5. make docs
  6. git push --tags
  7. git push
  8. create pull request from dev to master
  9. merge pull request

TODOs

  • parallelization, eg. for the bootstrapping code
  • Bayesian updating/early stopping
  • multiple comparison correction, definitely relevant for delta and SGA, have to think about how to correct for time dependency in the trend analysis
  • implement from_json and to_json methods in the Binning class, in order to convert the Python object to a json format for persisting in the Results metadata and reloading from a script