Getting started with Empirical development

This document is intended to help those just getting started with Empirical development. It details the initial one-time dependency installs and any similar routines necessary to get started with development.

Start by making your own copy of Empirical and setting yourself up for development; then, build Empirical and run the tests; and finally, claim an issue and start developing!

If you’re unfamiliar with git and branching in particular, check out the git-scm book.

One-time Preparation

  1. Get a GitHub account.

    (We use GitHub to manage Empirical contributions.)

  2. Fork

    Visit that page, and then click on the ‘fork’ button (upper right).

    This makes a copy of the Empirical source code in your own GitHub account. If you have contributor permissions to the main Empirical library, this step is optional (you can instead develop on a branch within the main repo).

  3. Clone your copy of Empirical to your local development environment.

    Your clone URL should look something like this:

    and the UNIX shell command should be:

    git clone

    (This makes a local copy of Empirical on your development machine.)

  4. Add a git reference to the Empirical repository:

    cd Empirical
    git remote add upstream
    cd ../

    (This makes it easy for you to pull down the latest changes in the main repository.)

  5. Install the development dependencies.

    Unix users

    a. Install the python virtualenv, pip, gcc, and g++, cmake, bison, flex

    On recent Debian and Ubuntu this can be done with:
        sudo apt-get install python-virtualenv python-pip gcc g++ git gcovr cmake bison flex
    OS X users and others may need to download virtualenv first:
    curl -O
    tar xzf virtualenv* cd virtualenv-*; python2.7
    ../env; cd ..

    Mac ports users on the OS X platform can

    : install pip by execution from the command line:

        sudo port install py27-pip

    Homebrew users on the OS X platform will have pip already installed

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b. Run the install-dependencies maketarget:

    make install-dependencies

This will create a virtual python environment to use for Empirical
development. In this environment it will install:
[Breathe](, and
[doxygen](, packages we use to
generate the documentation for Empirical

Building Empirical and running the tests

  1. Activate (or re-activate) the virtualenv (necessary only for building documentation):

    source third-party/env/bin/activate

    You can run this many times without any ill effects.

    (This puts you in the development environment.)

  2. Run the tests:

    make test

Congratulations! You’re ready to develop!

Claiming an issue and starting to develop

  1. Find an open issue and claim it.

    Once you’ve found an issue you like, make sure that no one has been assigned to it (see “assignee”, bottom right near “notifications”). Then, add a comment “I am working on this issue.” You’ve staked your claim!

    (We’re trying to avoid having multiple people working on the same issue.)

  2. In your local copy of the source code, update your master branch from the main Empirical master branch:

    git checkout master
    git pull upstream master

    (This pulls in all of the latest changes from whatever we’ve been doing on Empirical.)

    It is possible that when you do a [git pull]{.title-ref} you will get a “merge conflict” – This is what happens when something changed in the branch you’re pulling in in the same place you made a change in your local copy.

    Git will complain loudly about merges and tell you specifically in which files they occurred. If you open the file, you’ll see something vaguely like this in the place where the merge occurred:

    <<<<<<< HEAD
    Changes made on the branch that is being merged into. In most cases,
    this is the branch that you have currently checked out
    Changes made on the branch that is being merged in, almost certainly
    >>>>>>> abcde1234

    Though there are a variety of tools to assist with resolving merge conflicts they can be quite complicated at first glance and it is usually easy enough to manually resolve the conflict.

    To resolve the conflict you simply have to manually ‘meld’ the changes together and remove the merge markers.

    After this you’ll have to add and commit the merge just like any other set of changes. It’s also recommended that you run tests.

  3. Create a new branch and link it to your fork on GitHub:

    git checkout -b fix/brief_issue_description
    git push -u origin fix/brief_issue_description

    where you replace “brief_issue_description” with 2-3 words, separated by underscores, describing the issue.

    (This is the set of changes you’re going to ask to be merged into Empirical.)

  4. Make some changes and commit them.

    Though this will largely be issue-dependent the basics of committing are simple. After you’ve made a cohesive set of changes, run the command [git status]{.title-ref}. This will display a list of all the files git has noticed you changed. A file in the ‘untracked’ section are files that haven’t existed previously in the repository but git has noticed.

    To commit changes you have to ‘stage’ them–this is done by issuing the following command:

    git add path/to/file

    If you have a large quantity of changes and you don’t want to add each file manually you can do git add --patch which will display each set of changes to you before staging them for commit.

    Once you have staged your changes, it’s time to make a commit:

    git commit

    Git will then open your default console text editor to write a commit message – this is a short (typically 1-3 sentence) description of the changes you’ve made. Please make your commit message informative but concise – these messages become part of the ‘official’ history of the project.

    Once your changes have been committed, push them up to the remote branch:

    git push

    If this is your first commit on a new branch git will error out, telling you the remote branch doesn’t exist – This is fine, as it will also provide the command to create the branch. Copy/paste/run and you should be set.

  5. Periodically update your branch from the main Empirical master branch:

    git pull upstream master

    (This pulls in all of the latest changes from whatever we’ve been doing on the upstream branch- important especially during periods of fast change or for long-running pull requests.)

  6. Run the tests and/or build the docs before pushing to GitHub:

    make doc test

    Make sure they all pass!

  7. Push your branch to your own GitHub fork:

    git push origin

    (This pushes all of your changes to your own fork.)

  8. Repeat until you’re ready to merge your changes into “official” Empirical.

  9. Set up a Pull Request asking to merge things into the central Empirical repository.

    In a Web browser, go to your GitHub fork of Empirical, e.g.:

    and you will see a list of “recently pushed branches” just above the source code listing. On the right side of that should be a “Compare & pull request” green button. Click on it!


    • add a descriptive title (“updated tests for XXX”)

    • put the issue number in the comment (“fixes issue #532”)

    then click “Create pull request.”

    (This creates a new issue where we can all discuss your proposed changes; the Empirical team will be automatically notified and you will receive e-mail notifications as we add comments. See GitHub flow for more info.)

  10. Paste in the committer checklist from contribution-guidelines-and-review{.interpreted-text role=”doc”} and, after its pasted in, check off as many of the boxes as you can.

  11. As you add new commits to address bugs or formatting issues, you can keep pushing your changes to the pull request by doing:

    git push origin
  12. If we request changes, return to the step “Make some changes and commit them” and go from there. Any additional commits you make and push to your branch will automatically be added to the pull request (which is pretty dang cool.)

After your first issue is successfully merged…

You’re now an experienced GitHub user! Go ahead and take some more tasks; you can broaden out beyond the low hanging fruit if you like.

Your second contribution…

Here are a few pointers on getting started on your second (or third, or fourth, or nth contribution).

So, assuming you’ve found an issue you’d like to work on there are a couple things to do to make sure your local copy of the repository is ready for a new issue–specifically, we need to make sure it’s in sync with the remote repository so you aren’t working on a old copy. So:

git checkout master
git fetch --all
git pull

This puts you on the latest master branch and pulls down updates from GitHub with any changes that may have been made since your last contribution (usually including the merge of your last contribution). Then we merge those changes into your local copy of the master branch.

Now, you can go back to Claiming an issue and starting to develop.

Pull request cleanup (commit squashing)

Submitters are invited to reduce the numbers of commits in their pull requests either via [git rebase -i upstream/master]{.title-ref} or this recipe:

git pull ## make sure the local is up to date
git pull upstream master ## get up to date
## fix any merge conflicts
git status ## sanity check
git diff upstream/master ## does the diff look correct? (no merge markers)
git reset --soft upstream/master ## un-commit the differences from dib/master
git status ## sanity check
git commit --all ## package all differences in one commit
git status ## sanity check
git push ## should fail
git push --force ## override what's in GitHub's copy of the branch/pull request