Building and Testing

All our package has been built for you! However, if you wish to join the development or build from source, you will find all the dependencies and the steps to build, test, and install! Our dependencies are quite standard for packages developed by our team, as we mainly use the same tools.

Unit Testing

For contributions and new changes, we would like to ensure that all our tests pass. Or if necessary, we need to add new tests so that we can ensure code quality! To do this, we use pytest internally, and our testing codes rely on it for mocking and parametrization.

Dependencies

You will need to install the following packages:

• pytest

• pytest-cov

• pytest-mock

• coverage

Running Tests

To run the tests, we recommend installing the package in develop mode first by running the following codes:

python setup.py develop #Only need to run once
pytest . --cov

Note that this approach allows you to run the tests as a package instead of from local files, which is advantagous. The --cov option gives you a coverage report of our tests.

If you don’t want to do the installation, you can run the following:

python -m pytest --cov PyCytoData

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Documentation

Our documentation is automatically built by ReadTheDocs. However, if you’re so inclined to build locally or contribute to our docs, you’re more than welcomed to do so!

Dependencies

You will need the following packages:

• sphinx

• sphinx-rtd-theme

• sphinx-git

• sphinxcontrib-autoprogram

Note

sphinx-git is available on PyPI only. If you use a conda environment, use pip to install.

Build Documentation

You can simply run the following codes to build the documentation locally:

cd docs
make html

The resulting HTML will be in the build folder, and click on index.html and you’re all set to view the documentation. We don’t have unit tests to test the documentation.