Software Process

Continuous Integration

HDMF is tested against Ubuntu, macOS, and Windows operating systems. The project has both unit and integration tests. Tests run on GitHub Actions.

Each time a PR is created or updated, the project is built, packaged, and tested on all supported operating systems and python distributions. That way, as a contributor, you know if you introduced regressions or coding style inconsistencies.

There are badges in the README file which shows the current condition of the dev branch.


Code coverage is computed and reported using the coverage tool. There are two coverage-related badges in the README file. One shows the status of the GitHub Action workflow which runs the coverage tool and uploads the report to codecov, and the other badge shows the percentage coverage reported from codecov. A detailed report can be found on codecov, which shows line by line which lines are covered by the tests.

Installation Requirements

pyproject.toml contains a list of package dependencies and their version ranges allowed for running HDMF. As a library, upper bound version constraints create more harm than good in the long term (see this blog post) so we avoid setting upper bounds on requirements.

If some of the packages are outdated, see How to Update Requirements Files.

Testing Requirements

There are several kinds of requirements files used for testing PyNWB.

The first one is requirements-min.txt, which lists the package dependencies and their minimum versions for installing HDMF.

The second one is requirements.txt, which lists the pinned (concrete) dependencies to reproduce an entire development environment to use HDMF.

The third one is requirements-dev.txt, which list the pinned (concrete) dependencies to reproduce an entire development environment to use HDMF, run HDMF tests, check code style, compute coverage, and create test environments.

The fourth one is requirements-opt.txt, which lists the pinned (concrete) optional dependencies to use all available features in HDMF.

The final one is environment-ros3.yml, which lists the dependencies used to test ROS3 streaming in HDMF.

Documentation Requirements

requirements-doc.txt lists the dependencies to generate the documentation for HDMF. Both this file and requirements.txt are used by ReadTheDocs to initialize the local environment for Sphinx to run.

Versioning and Releasing

HDMF uses setuptools_scm for versioning source and wheel distributions. setuptools_scm creates a semi-unique release name for the wheels that are created based on git tags. After all the tests pass, the “Deploy release” GitHub Actions workflow creates both a wheel (\*.whl) and source distribution (\*.tar.gz) for Python 3 and uploads them back to GitHub as a release.

It is important to note that GitHub automatically generates source code archives in .zip and .tar.gz formats and attaches those files to all releases as an asset. These files currently do not contain the submodules within HDMF and thus do not serve as a complete installation. For a complete source code archive, use the source distribution generated by GitHub Actions, typically named hdmf-{version}.tar.gz.