CONTRIBUTING.rst

Contributions

Contributions are welcome in the form of pull requests.

Once the implementation of a piece of functionality is considered to be bug free and properly documented (both API docs and an example script), it can be incorporated into the master branch.

To help developing hnn-core, you will need a few adjustments to your installation as shown below.

If your contributions will make use of parallel backends for using more than one core, please see the additional installation steps for parallel_backends

Running tests

To run the tests using pytest, you need to have the git cloned hnn-core repository with an editable pip install:

$ git clone https://github.com/jonescompneurolab/hnn-core --depth 1
$ cd hnn-core
$ pip install -e .
$ python setup.py build_mod

Then, install the following python packages:

$ pip install flake8 pytest pytest-cov

If you update a mod file, you will have to rebuild them using the command:

$ python setup.py build_mod

MPI tests are skipped if the mpi4py module is not installed. This allows testing features not related to parallelization without installing the extra dependencies as described in parallel_backends.

Updating documentation

Update doc/api.rst and doc/whats_new.rst as appropriate.

Building the documentation

The documentation can be built using sphinx. For that, please additionally install the following:

$ pip install matplotlib sphinx numpydoc sphinx-gallery sphinx_bootstrap_theme pillow mpi4py joblib psutil

If you are using a newer version of pip, you may be prompted to use the flag --use-feature=2020-resolver. If this happens, please add it as recommended:

$ pip install --use-feature=2020-resolver matplotlib sphinx numpydoc sphinx-gallery sphinx_bootstrap_theme pillow mpi4py joblib psutil

You can build the documentation locally using the command:

$ cd doc/
$ make html

While MNE is not needed to install hnn-core, as a developer you will need to install it to run all the examples and tests successfully. Please find the installation instructions on the MNE website.

If you want to build the documentation locally without running all the examples, use the command:

$ make html-noplot

Continuous Integration

The repository is tested via continuous integration with Travis and Circle. The automated tests run on Travis while the documentation is built on Circle.