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CONTRIBUTING.md

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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 seek, you will need a few adjustments to your installation as shown below.

Running tests

(Optional) Install Docker

To run workflows, it is recommended to use Docker. Install Docker at: https://docs.docker.com/get-docker/.

Install development version of seek

First, you should fork the seek repository. Then, clone the fork and install it in.

TODO insert how to install and setup, or link to instructions.

Install Python packages required to run tests

Install the following packages for testing purposes, plus all optonal MNE-BIDS dependencies to ensure you will be able to run all tests.

$ pip install flake8 pytest pytest-cov

Running code linter:

Building the documentation

TODO: @Christopher Coogan, can you help fill this in?

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

$ pip install matplotlib nilearn sphinx numpydoc sphinx-gallery sphinx_bootstrap_theme pillow

To build the documentation locally, one can run:

$ cd doc/
$ make html

or

$ make html-noplot

if you don't want to run the examples to build the documentation. This will result in a faster build but produce no plots in the examples.

Creating a DAG for each workflow

Snakemake has the nice property of implicitly building a directed acyclic graph (DAG) of your anatomical analysis. To visualize this DAG for your subjects, one can make use of the snakemake command:

$ snakemake --snakefile ./workflow/recon_workflow/Snakefile --forceall --dag | dot -Tpdf > ./recon_workflow.pdf;

We package all these DAG creation commands into a Makefile recipe, which can be ran as:

$ make create_dags

BIDS-Validation

To robustly apply seek workflows and reconstruction visualiztion, we rely on the BIDS specification for storing data. One can use the bids-validator to verify that a dataset is BIDS-compliant.

Install the BIDS validator

Finally, it is necessary to install the BIDS validator. The outputs of MNE-BIDS 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 [email protected]:bids-standard bids-validator.git
$ cd bids-validator/bids-validator
$ npm i

Test your installation by running:

$ ./bin/bids-validator --version