Developing

The Cutadapt source code is on GitHub. Cutadapt is written in Python with some extension modules that are written in Cython. Cutadapt uses a single code base that is compatible with both Python 2 and 3. Python 2.7 is the minimum supported Python version.

Development installation

For development, make sure that you install Cython and tox. We also recommend using a virtualenv. This sequence of commands should work:

git clone https://github.com/marcelm/cutadapt.git  # or clone your own fork
cd cutadapt
virtualenv -p python3 venv  # or omit the "-p python3" for Python 2
venv/bin/pip3 install Cython pytest nose tox  # pip3 becomes just pip for Python 2
venv/bin/pip3 install -e .

Then you can run Cutadapt like this (or activate the virtualenv and omit the venv/bin part):

venv/bin/cutadapt --help

The tests can then be run like this:

venv/bin/pytest

Or with tox (but then you will need to have binaries for all tested Python versions installed):

venv/bin/tox

Development installation (without virtualenv)

Alternatively, if you do not want to use virtualenv, running the following may work from within the cloned repository:

python3 setup.py build_ext -i  # omit the "3" for Python 2
pytest

This requires Cython and pytest to be installed. Avoid this method and use a virtualenv instead if you can.

Code style

Cutadapt tries to follow PEP8, with some exceptions:

  • Indentation is made with tabs, not with spaces

  • The maximum line length for code 100 characters, not 80, but try to wrap comments at 80 characters for readability.

Yes, there are inconsistencies in the current code base since it’s a few years old already.

Making a release

Since version 1.17, Travis CI is used to automatically deploy a new Cutadapt release (both as an sdist and as wheels) whenever a new tag is pushed to the Git repository.

Cutadapt uses versioneer to automatically manage version numbers. This means that the version is not stored in the source code but derived from the most recent Git tag. The following procedure can be used to bump the version and make a new release.

  1. Update CHANGES.rst (version number and list of changes)

  2. Ensure you have no uncommitted changes in the working copy.

  3. Run a git pull.

  4. Run tox, ensuring all tests pass.

  5. Tag the current commit with the version number (there must be a v prefix):

    git tag v0.1

    To release a development version, use a dev version number such as v1.17.dev1. Users will not automatically get these unless they use pip install --pre.

  6. Push the tag:

    git push --tags

  7. Wait for Travis to finish and to deploy to PyPI.

  8. Update the bioconda recipe. It is probly easiest to edit the recipe via the web interface and send in a pull request. Ensure that the list of dependencies (the requirements: section in the recipe) is in sync with the setup.py file.

    Since this is just a version bump, the pull request does not need a review by other bioconda developers. As soon as the tests pass and if you have the proper permissions, it can be merged directly.

Releases to bioconda still need to be made manually.

Making a release manually

If this is the first time you attempt to upload a distribution to PyPI, create a configuration file named .pypirc in your home directory with the following contents:

[distutils]
index-servers =
    pypi

[pypi]
username=my-user-name
password=my-password

See also this blog post about getting started with PyPI. In particular, note that a % in your password needs to be doubled and that the password must not be put between quotation marks even if it contains spaces.

Cutadapt uses versioneer to automatically manage version numbers. This means that the version is not stored in the source code but derived from the most recent Git tag. The following procedure can be used to bump the version and make a new release.

  1. Update CHANGES.rst (version number and list of changes)

  2. Ensure you have no uncommitted changes in the working copy.

  3. Run a git pull.

  4. Run tox, ensuring all tests pass.

  5. Tag the current commit with the version number (there must be a v prefix):

    git tag v0.1

  6. Create a distribution (.tar.gz file). Double-check that the auto-generated version number in the tarball is as you expect it by looking at the name of the generated file in dist/:

    python3 setup.py sdist

  7. If necessary, pip install twine and then upload the generated tar file to PyPI:

    twine upload dist/cutadapt-0.1.tar.gz  # adjust version number

  8. Push the tag:

    git push --tags

  9. Update the bioconda recipe. It is probly easiest to edit the recipe via the web interface and send in a pull request. Ensure that the list of dependencies (the requirements: section in the recipe) is in sync with the setup.py file.

    Since this is just a version bump, the pull request does not need a review by other bioconda developers. As soon as the tests pass and if you have the proper permissions, it can be merged directly.

If something went wrong after you uploaded a tarball, fix the problem and follow the above instructions again, but with an incremented revision in the version number. That is, go from version x.y to x.y.1. Do not change a version that has already been uploaded.