Developer guide

Development Installation

These are development setup. If you are a contributor to bioc, it might a be a good idea to follow these guidelines as well.

Compile from source

bioc is actively developed on GitHub repository. The other way to install bioc is to clone its GitHub repository.

# Checkout repository
$ git clone https://github.com/bionlplab/bioc.git
$ cd bioc

# Set up Python environment
$ python -m venv venv
$ source venv/bin/activate

# Install dependencies
$ python -m pip install --upgrade pip
$ pip install -r requirements.txt

Test the code

$ pytest --cov html tests

Create this documentation

We use Sphinx and MyST to generate documentation.

$ pip install sphinx sphinx_rtd_theme myst-parser
$ cd docs
$ make html

Publish BioC to PyPI and TestPyPI

First, you need a PyPI user account. You can create an account using the form on the PyPI/TestPyPI website.

Now you’ll create a PyPI/TestPyPI API token so you will be able to securely upload your project.

Go to https://pypi.org/manage/account/#api-tokens and create a new API token; don’t limit its scope to a particular project, since you are creating a new project.

$ pip install build twine
$ python -m build

Using local package with pip

$ pip install --force-reinstall dist/PACKAGE.whl

Using TestPyPI with pip

$ twine upload --repository testpypi dist/*
$ pip install --index-url https://test.pypi.org/simple/ bioc