This page explains how you can contribute to the development of scikit-survival.
There are a lot of ways you can contribute:
Writing new code, e.g. implementations of new algorithms, or examples.
Reviewing open pull requests.
scikit-survival is developed on GitHub using the Git version control system.
The preferred way to contribute to scikit-survival is to fork
the main repository on GitHub, then submit a pull request (PR).
These are the steps you need to take to create a copy of the scikit-survival repository
on your computer.
Create an account on
GitHub if you do not already have one.
the scikit-survival repository.
Clone your fork of the scikit-survival repository from your GitHub account to your local disk.
You have to execute from the command line:
git clone --recurse-submodules email@example.com:YourLogin/scikit-survival.git
After you created a copy of our main repository on GitHub, your need
to setup a local development environment.
We strongly recommend to use conda to
create a separate virtual environment containing all dependencies.
These are the steps you need to take.
Install conda for your operating system if you haven’t already.
Create a new environment, named sksurv:
python ci/list-requirements.py requirements/dev.txt > dev-requirements.txt
conda create -n sksurv -c sebp python=3 --file dev-requirements.txt
Activate the newly created environment:
conda activate sksurv
Compile the C/C++ extensions and install scikit-survival in development mode:
pip install --no-build-isolation -e .
For a pull request to be accepted, your changes must meet the below requirements.
All changes related to one feature must belong to one branch.
Each branch must be self-contained, with a single new feature or bugfix.
Create a new feature branch
git checkout -b my-new-feature
All code must follow the standard Python guidelines for code style,
To check that your code conforms to PEP8, you can install
tox and run:
tox -e py38-flake8
Each function, class, method, and attribute needs to be documented using docstrings.
scikit-survival conforms to the
numpy docstring standard.
Code submissions must always include unit tests.
We are using pytest.
All tests must be part of the tests directory.
You can run the test suite locally by executing:
Tests will also be executed automatically once you submit a pull request.
The contributed code will be licensed under the
GNU General Public License v3.0.
If you did not write the code yourself, you must ensure the existing license
is compatible and include the license information in the contributed files,
or obtain a permission from the original author to relicense the contributed code.
When you are done coding in your feature branch,
add changed or new files:
git add path/to/modified_file
Create a commit
message describing what you changed. Commit messages should be clear and concise.
The first line should contain the subject of the commit and not exceed 80 characters
in length. If necessary, add a blank line after the subject followed by a commit message body
with more details:
Push the changes to GitHub:
git push -u origin my_feature
Create a pull request.
The documentation resides in the doc/ folder and is written in
reStructuredText. HTML files of the documentation can be generated using Sphinx.
The easiest way to build the documentation is to install tox and run:
tox -e py38-docs
Generated files will be located in doc/_build/html. To open the main page
of the documentation, run: