CONTRIBUTING.rst

Development Notes

Python style conventions

The plugin follows the same conventions as the main THAPBI PICT tool, PEP8 and black style enforced via pre-commit. Install these tools using:

$ pip install pre-commit
$ pre-commit install  # within the q2-thapbi-pict main directory

The checks will then run automatically when you make a git commit. You can also run the checks directly using:

$ pre-commit run -a

If your editor can be configured to run flake8 and/or ruff automatically, even better. These checks are done as part of the continuous integration when changes are made on GitHub.

Continuous Integration

Pending.

Installing from source

First, download the code from GitHub and decompress it if required. The best way to do this if you are likely to contribute any changes is at the command line with git. Then run the pip install command in developer mode:

$ git clone https://github.com/peterjc/q2-thapbi-pict.git
$ cd q2-thapbi-pict
$ pip install -e .  # assuming qiime2 conda env is active!

If you change the plugin's interface to Qiime2, you need to run this:

$ qiime dev refresh-cache

Otherwise changes to the plugin code take effect next time it is used.

Release process

The Qiime2 plugin is released on PyPI (as is THAPBI PICT itself):

rm -rf build/
python -m build
git tag vX.Y.Z
git push origin main --tags
twine upload dist/q2_thapbi_pict-X.Y.Z*

However, we do not package the Qiime2 plugin in BioConda as we'd need to depend on the Qiime2 conda channel.