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. With relatively little effort, compatibility with Python 2.6 could be restored.
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
The tests can then be run like this:
Or with tox (but then you will need to have binaries for all tested Python versions installed):
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.
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¶
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
[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.
CHANGES.rst(version number and list of changes)
Ensure you have no uncommitted changes in the working copy.
tox, ensuring all tests pass.
Tag the current commit with the version number (there must be a
git tag v0.1
Create a distribution (
.tar.gzfile). 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
python3 setup.py sdist
If necessary, pip install
twineand then upload the generated tar file to PyPI:
twine upload dist/cutadapt-0.1.tar.gz # adjust version number
Push the tag:
git push --tags
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
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.