Getting started with khmer development

This document is for people who would like to contribute to khmer. It walks first-time contributors through making their own copy of khmer, building it, and submitting changes for review and merge into the master copy of khmer.

Start by making your own copy of khmer and setting yourself up for development; then, build khmer 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.

We've provided a quick guide to the khmer code base here: A quick guide to the khmer codebase.

One-time Preparation

  1. Install the dependencies.

    OS X users

    1. Install Xcode from the Mac App Store (requires root).
    2. Register as an Apple Developer.
    3. Install the Xcode command-line tools: Xcode -> preferences -> Downloads -> Command Line Tools (requires root).

    Linux users

    1. Install the python development environment, virtualenv, pip, gcc, and g++.

      On recent Debian and Ubuntu this can be done with:

      sudo apt-get install python2.7-dev python-virtualenv python-pip gcc \
      g++ git astyle gcovr cppcheck

      For RHEL6:

      sudo yum install -y python-devel python-pip git gcc gcc-c++ make
      sudo pip install virtualenv

    For Arch Linux:

    sudo pacman -S python2 python2-pip python2-virtualenv gcc make
  2. Get a GitHub account.

    (We use GitHub to manage khmer contributions.)

  3. Fork

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

    (This makes a copy of the khmer source code in your own GitHub account.)

  4. Clone your copy of khmer 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 khmer on your development machine.)

  5. Add a git reference to the khmer dib-lab repository:

    cd khmer
    git remote add dib
    cd ../

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

  6. Create a virtual Python environment within which to work with virtualenv:

    python2.7 -m virtualenv env

    This gives you a place to install packages necessary for running khmer.

    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

    Conda users on any platform should instead create a separate Conda environment:

    conda create -n khmer anaconda
  7. Activate the virtualenv and install a few packages:

    source env/bin/activate
    cd khmer
    make install-dependencies

    (This installs Sphinx and nose, packages we use for building the documentation and running the tests.)

    In Conda to activate the previously created environment and install dependencies:

    source activate khmer
    cd khmer
    make install-dependencies
  8. Cppcheck installation:

    Debian and Ubuntu Linux distro users can install cppcheck by executing from the command line:

    sudo apt-get install cppcheck

    Mac ports users on the OS X platform can install cppcheck by executing from the command line:

    sudo port install cppcheck

    Homebrew users on the OS X platform can install cppcheck by executing from the command line:

    sudo brew install cppcheck
  9. ccache installation:

    Debian and Ubuntu Linux distro users can install ccache to speed up their compile times:

    sudo apt-get install ccache
    echo 'export PATH="/usr/lib/ccache:$PATH" # enable ccache' >> ~/.bashrc
    export PATH="/usr/lib/ccache:$PATH"

Building khmer and running the tests

  1. Activate (or re-activate) the virtualenv:

    source ../env/bin/activate

    ... or for Conda users:

    source activate khmer

    You can run this many times without any ill effects.

    (This puts you in the development environment.)

  2. Build khmer:


    If this fails, we apologize -- please go create a new issue, paste in the failure message, and we'll try to help you work through it!

    (This takes the C++ source code and compiles it into something that Python can run.)

  3. Run the tests:

    make test

    You should see lots of output, with something like:

    Ran 633 tests in 47.446s

    at the end.

    (This will run all of the Python tests in the tests/ directory.)

Congratulations! You're ready to develop!

Claiming an issue and starting to develop

  1. Find an open issue and claim it.

    Go to the list of open khmer issues and find one you like; we suggest starting with the low-hanging fruit issues).

    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 khmer master branch:

    git checkout master
    git pull dib master

    (This pulls in all of the latest changes from whatever we've been doing on dib-lab.)

    It is possible that when you do a git pull 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. This frequently happens in the ChangeLog file.

    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 khmer.)

  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. 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.

    You should also visit and read Coding guidelines and code review checklist.

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

    git pull dib master

    (This pulls in all of the latest changes from whatever we've been doing on dib-lab - 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 pep8 diff-cover

    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" khmer.

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

    In a Web browser, go to your GitHub fork of khmer, 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 khmer 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 Coding guidelines and code review checklist 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. When you are ready to have the pull request reviewed, please mention @luizirber, @camillescott, @mr-c, or @ctb with a comment 'Ready for review!'

  13. The khmer team will now review your pull request and communicate with you through the pull request page. Please feel free to add 'ping!' and an @ in the comments if you are looking for feedback -- this will alert us that you are still on the line -- but we will automatically get notified of your pull request and any new comments, so use sparingly.

    If this is still your first issue, please don't take another issue until we've merged your first one - thanks!

  14. 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.

Here are a few suggestions:

  • If you're knowledgeable in C++ and/or Python and/or documentation and/or biology, we'd love to attract further contributions to khmer. Please visit the issues list and browse about and find something interesting looking.
  • One general thing we'd like to do is increase our test coverage. You can go find test coverage information on our continuous integration server by clicking down to individual files; or, ask us on for suggestions.
  • Ask us! Ask for suggestions on what to do next. We can suggest particularly ripe low-hanging fruit, or find some other issues that suit your interests and background.
  • You can also help other people out by watching for new issues or looking at pull requests. Remember to be nice and polite!

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.

Advanced merging with git-merge-changelog

Often one can get a merge conflict due to updates in the ChangeLog. To teach Git how to handle these on its own you can install a special merge driver.

On Debian & Ubuntu systems you'll need the git-merge-changelog package:

sudo apt-get install git-merge-changelog

Ubuntu 14.04 LTS users will need to add an external repository that contains a backport of the package first before installing:

sudo apt-add-repository ppa:misterc/gedlab
sudo apt-get update
sudo apt-get install git-merge-changelog

Everyone should then update their ~/.gitconfig file with the following:

[merge "merge-changelog"]
          name = GNU-style ChangeLog merge driver
          driver = /usr/bin/git-merge-changelog %O %A %B

Pull request cleanup (commit squashing)

Submitters are invited to reduce the numbers of commits in their pull requests either via git rebase -i dib/master or this recipe:

git pull # make sure the local is up to date
git pull dib master # get up to date
# fix any merge conflicts
git status # sanity check
git diff dib/master # does the diff look correct? (no merge markers)
git reset --soft dib/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
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