Contents

GenomeHubs

Travis-CI Build Status Coverage Status Documentation Status Code Style Black PyPI Package latest release Install with Conda Commits since latest release MIT License

Installation

conda install -c tolkit genomehubs

or

pip install genomehubs

You can also install the in-development version with:

pip install https://github.com/genomehubs/genomehubs/archive/main.zip

Documentation

https://genomehubs.readthedocs.io/

Development

To run all tests run:

tox

Installation

At the command line:

pip install genomehubs

Usage

To use genomehubs in a project:

import genomehubs

Reference

init

parse

index

fill

Contributing

Bug reports

When reporting a bug please include:

  • Your operating system name and version.

  • Any details about your local setup that might be helpful in troubleshooting.

  • Detailed steps to reproduce the bug.

Documentation improvements

Contributions to the official genomehubs docs and internal docstrings are always welcome.

Feature requests and feedback

The best way to send feedback is to file an issue at https://github.com/genomehubs/genomehubs/issues.

If you are proposing a feature:

  • Explain in detail how it would work.

  • Keep the scope as narrow as possible, to make it easier to implement.

  • Remember that code contributions are welcome

Development

To install the development version of genomehubs:

  1. Clone the genomehubs repository:

    git clone https://github.com/genomehubs/genomehubs

  2. Install the dependencies using pip:

    cd genomehubs
pip install -r requirements.txt

  3. Build and install the genomehubs package:

    python3 setup.py sdist bdist_wheel \
&& echo y | pip uninstall genomehubs \
&& pip install dist/genomehubs-2.0.0-py3-none-any.whl

To set up genomehubs for local development:

  1. Fork genomehubs <https://github.com/genomehubs/genomehubs> - (look for the “Fork” button).

  2. Clone your fork locally:

    git clone git@github.com:USERNAME/genomehubs.git

  3. Create a branch for local development:

    git checkout -b name-of-your-bugfix-or-feature

    Now you can make your changes locally.

  4. When you’re done making changes run all the checks and docs builder with tox one command:

    tox

  5. Commit your changes and push your branch to GitHub:

    git add .
git commit -m "Your detailed description of your changes."
git push origin name-of-your-bugfix-or-feature

  6. Submit a pull request through the GitHub website.

Pull Request Guidelines

If you need some code review or feedback while you’re developing the code just make the pull request.

For merging, you should:

  1. Include passing tests (run tox) 1.

  2. Update documentation when there’s new API, functionality etc.

  3. Add a note to CHANGELOG.rst about the changes.

  4. Add yourself to AUTHORS.rst.

1

If you don’t have all the necessary python versions available locally you can rely on Travis - it will run the tests for each change you add in the pull request.

It will be slower though …

Tips

To run a subset of tests:

tox -e envname -- pytest -k test_myfeature

To run all the test environments in parallel:

tox -p

Authors

Changelog

2.0.0 (2020-07-02)

  • First release on PyPI.

Indices and tables