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CONTRIBUTING.md

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Contributions

Contributions are welcome in the form of pull requests which will be reviewed by core developers.

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

Running tests

Install development version of pd-parser

First, you should fork the pd-parser repository. Then, clone the fork and install it in "editable" mode.

$ git clone https://github.com/<your-GitHub-username>/pd-parser
$ pip install -e ./pd-parser

Install Python packages required to run tests

Install the following requirements for testing purposes to ensure you will be able to run all tests.

$ pip install -r requirements

Install the BIDS validator

Finally, it is necessary to install the BIDS validator. The outputs are run through the BIDS validator to check if the conversion worked properly and produced datasets that conforms to the BIDS specifications.

You will need the command line version of the validator.

Global (system-wide) installation

  • First, install Node.js.
  • For installing the stable version of bids-validator, please follow the instructions as detailed in the README of the bids-validator repository.
  • For installing the development version of bids-validator, see here.

Test your installation by running:

$ bids-validator --version

Local (per-user) development installation

Install Node.js. If you're use conda, you can install the nodejs package from conda-forge by running conda install -c conda-forge nodejs.

Then, retrieve the validator and install all its dependencies via npm.

$ git clone git@github.com:bids-standard bids-validator.git
$ cd bids-validator/bids-validator
$ npm i

Test your installation by running:

$ ./bin/bids-validator --version

Invoke pytest

Now you can finally run the tests by running pytest in the pd-parser directory.

$ cd pd-parser
$ pytest

If you have installed the bids-validator on a per-user basis, set the environment variable VALIDATOR_EXECUTABLE to point to the path of the bids-validator before invoking pytest:

$ VALIDATOR_EXECUTABLE=../bids-validator/bids-validator/bin/bids-validator pytest

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

To build the documentation locally, one can run:

$ cd docsrc/
$ make html

This makes plots in the doc/dev directory that you can then open in a webbrowser.