BEAST Development

Basic Workflow

You are encouraged to help maintain and improve the beast. Before doing so, please familiarize yourself with basic version control and Git workflow concepts. A good description of the standard fork-branch-pull workflow can be found here:

Some other useful guides are:

In short, the fork-branch-pull workflow for contributing to the beast project is:

  • Create your own ‘fork’ of the official beast repository
  • Create purpose-specific ‘branches’ off your ‘fork’
  • Make changes or additions within the branches
  • Contribute your modified codes to the beast project or share them with your collaborators via ‘pull requests’
  • Keep your fork updated to benefit from continued development of the official version and to minimize version conflicts
  • Resolve version conflicts as much as possible before sending pull requests

Development Install

It is much easier to perform development if any changes you make to the code are immediately reflected in how the beast runs (in contrast to needed to perform a new install each team). This can be achieved by using a development install.

This is most easily achieved via a pip development install. Navigate to the directory in your your beast repository that contains, and run:

$ mv beast beast-official
$ git clone
$ mv beast beast-YourName
$ mv beast-official beast
  • Set the value of the fork’s ‘upstream’ to the official distribution so you can incorporate changes made by others to your development fork. In the clone of your fork, run the following:

    $ git remote add upstream

Adding Branches

  • Make sure you are in the directory for your fork of the beast. You will be on branch ‘master’ by default.

  • Create and switch to a branch (here named ‘beast-dev1’; generally it’s good practice to give branches names related to their purpose)

    $ git checkout -b beast-dev1
  • Instead, if you want to create first a branch and then switch to it:

    $ git branch beast-dev1
    $ git checkout beast-dev1
  • To see a list of all branches of the fork, with ‘*’ indicating which branch you are currently working on:

    $ git branch
  • To ‘upload’ this branch to your fork:

    $ git push origin beast-dev1
  • To revert back to your fork’s master branch:

    $ git checkout master

Development Install

To perform development, and see your changes reflected immediately in your installed copy of the BEAST, you can perform a development install. This can either be performed via a pip development install, by navigating to the directory that contains and running:

$ pip install -e .

Alternatively, you can perform a development install directly though Python with:

$ python develop

Making Changes

It is recommended that branches have a single purpose; for example, if you are working on adding a test suite, on improving the fitting algorithm and on speeding up some task, those should be in separate branches (e.g.) add-test-suite, improve-fitting-algorithm and beast-dev1.

  • Anywhere below ‘beast-YourName’, switch to the branch you wish to work off of:

    $ git checkout beast-dev1
  • Make changes to the existing files as you wish and/or create new files.

  • To see what changes have been made at any time:

    $ git status
  • To stage any new or edited file (e.g., ‘’) in preparation for committing:

    $ git add
  • To add all edited files (not recommended unless you are sure of all your changes):

    $ git add -A
  • To ‘commit’ all changes after adding desired files:

    $ git commit -m 'brief comments describing changes'
  • Commit messages should be short but descriptive.

  • To see the status of or commit changes of a single file:

    $ git status PathToFile/filename
    $ git commit PathToFile/filename
  • To undo all changes made to a file since last commit:

    $ git checkout PathToFile/filename
  • To sync changes made to the branch locally with your GitHub repo:

    $ git push origin beast-dev1

Test Changes

It is a good idea to test that your changes have not caused problems. In the base beast directory the following commands may be run to do this.

Run existing tests, including a regression test against a full beast model run. Once the command below has finished, the coverage of the tests can be viewed in a web browser by pointing to files in the htmlconv subdirectory (which gets produced when the tests are run).

$ python test --remote-data --coverage

Make sure the documentation can be created.

$ python build_docs

The resulting HTML files are placed in docs/_build/html subdirectory, and can be viewed in a web browser.

Collaborating and Contributing

BEAST on Slack

There is a beast space on Slack. Email for an invite.

Visualizing Repository Commits

The commits to the beast repository can be visualized using gource. This creates a movie showing the time evolution of the code and who make the changes.

Version created 22 Jan 2018: <>

Command to create it:

$ gource -s .06 -1280x720 --auto-skip-seconds .1 --multi-sampling  --stop-at-end --key --highlight-users --hide mouse,progress --file-idle-time 0 --max-files 0  --background-colour 000000 --font-size 22 --title "This is beast" --output-ppm-stream - --output-framerate 30 | avconv -y -r 30 -f image2pipe -vcodec ppm -i - -b 65536K beast_repo.mp4