BEAST Development

You are encouraged to help maintain and improve the BEAST. Before doing so, please familiarize yourself with basic version control and Git workflow concepts using one or more of these guides:

Here is the recommended work-flow for contributing to the BEAST project. Details follow.

  • Create your own ‘fork’ of the official BEAST release
  • 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

BEAST on Slack

There is a BEAST space on slack. Email for an invite.

Fork the BEAST distro

  • The main BEAST repository lives at <>. The master branch of this repository is the version that is distributed.

  • Log in to your github account, and on the top right corner of the BEAST repository page click on the ‘Fork’ button. This will create a copy of the repository in your github accout.

  • Clone a copy of your fork to your local computer. If you have a copy of the official BEAST distro, you may need to rename it; cloning will automatically name the folder ‘beast’.

  • Example of cloning your fork into ‘beast-YourName’ while keeping the official distribution in ‘beast’:

    $ 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:

.. code-block:: console
$ 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 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.

$ python test --remote-data --coverage

Make sure the documentation can be created. The resulting files can be viewed in a web browser by point to files in the docs/docs/_build/html subdirectory.

$ python build_docs

Collaborating and Contributing

Once you have changes that you’d like to contribute back to the project or share with collaborators, you can open a pull request. It is a good idea to check with the projects or your collaborators which branch of their BEAST repo you should send the pull requests.

Note: Generally in git-lingo, ‘Pull’ is to ‘download’ what ‘Push’ is to ‘upload’. When you are making a ‘pull request’, you are requesting that your contributions are ‘pulled’ from the other side. So you are not pushing it, but the other party is pulling it :-)

  • Use ‘git add’, ‘git commit’ and ‘git push’ as summarized earlier to sync your local edits with your github repo
  • From the github page of your fork of BEAST, e.g., click on ‘Branches’. Next to the name of the branch on which you commited/pushed the changes, click on ‘New pull request’. Verify that names of the target repo (‘base fork’) and branch (‘master’) to which you want to send the pull request, and those of your repo (‘head fork’) and your branch (‘compare’) from which you are sending the pull request match what you intend to do.
  • In the comments section briefly describe the changes/additions you made and submit the pull request.
  • It is at the other party’s (project, collaborator etc.) discretion to accept the changes and merge them with their repo.

Staying up-to-date

The BEAST project’s official repository will be updated from time to time to accommodate bug fixes, improvements and new features. You may keep your fork’s master repo up to date with the following steps.

It is highly recommended that you do this if you intend to contribute changes back to the project. Creating new branches off of an up-to-date fork-master minimizes the chances of conflicting contributions, duplicative efforts and other complications.

  • Switch to your fork’s master branch:

    $ git checkout master
  • Fetch the project’s up-to-date distribution:

    $ git fetch upstream
  • Merge the project-master (upstream) with your fork’s master (master):

    $ git merge upstream/master
  • Sync this change with your GitHub repo:

    $ git push origin master
  • Any branch created off of the fork’s master now will start from the correct BEAST distro and not contain any changes made to any prior branch, unless those changes have been incorporated into the official distro via an accepted pull request and merge

Managing Conflicts

Let’s consider a situation where a fork’s master has been updated. A local branch (e.g., beast-dev1) was created before the update and it has changes that hadn’t been contributed back to the project. As a results, there may be conflicting versions of some files. The following steps can resolve this.

  • Merge your fork’s master with upstream/master, and push the master

    $ git checkout master
    $ git fetch upstream
    $ git merge upstream/master
    $ git push origin master
  • Create a new branch from the updated fork-master, and push the new branch

    $ git checkout -b beast-dev2
    $ git push origin beast-dev2
  • Switch to the branch where your made changes, make a backup and push it

    $ git checkout beast-dev1
    $ git branch beast-dev1-backup beast-dev1
    $ git push origin beast-dev1-backup
  • Check the differences between the two branches and merge the two branches. (Edit files on the newer branch to resolve differences manually if needed.)

    $ git diff beast-dev1 beast-dev2
    $ git checkout beast-dev2
    $ git merge beast-dev1
  • Finally, push the updated new branch into your gitHub repo (Note: an error free push confirms that all conflicts have been resolved both locally and on the gitHub repo.)

    $ git push origin beast-dev2
  • If later you wish to restore the backup:

    $ git reset --hard beast-dev1-backup
  • Once all conflicts have been resolved and the re-base goes through, you can delete the backup branch:

    $ git branch -D beast-dev1-backup

Managing Conflicts via Re-basing

In some unusual situations, conflicts may seem unresolvable or version conflicts between branches/master/upstream may get messy. One last ditch solution can be re-basing, but this not recommended and certainly is not the preferred way to resolve conflicts. Here are the general steps to do this.

  • Merge your fork’s master with upstream/master, and push the master

  • Switch to and backup the branch with conflicts, and push the backup

  • Re-base the branch on upstream/master, and push it

  • Example:

    • Do the preparatory steps

      $ git checkout master
      $ git fetch upstream
      $ git merge upstream/master
      $ git push origin master
      $ git checkout beast-dev1
      $ git branch beast-dev1-backup beast-dev1
      $ git push origin beast-dev1-backup
    • Now re-base the branch:

      $ git rebase upstream/master
    • Once all conflicts have been resolved and the re-base goes through without any error message, push the changes to your gitHub repo:

      $ git push origin beast-dev1
    • If something goes wrong during re-base, you can start over:

      $ git rebase --abort
    • If you wish to restore the backup:

      $ git reset --hard beast-dev1-backup

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