Contributors to MNE-BIDS-Pipeline are expected to follow our Code of Conduct.
First, you need to make sure you have MNE-Python installed and working on your system. See the installation instructions. Once this is done, you should be able to run this in a terminal:
$ python -c "import mne; mne.sys_info()"
You can then install the following additional package via pip. Note that
the URL points to the bleeding edge version of mne_bids:
$ pip install https://github.com/mne-tools/mne-bids/zipball/main
Now, get the pipeline through git:
$ git clone https://github.com/mne-tools/mne-bids-pipeline.git
If you do not know how to use git, download the pipeline as a zip file here.
Finally, for source analysis you'll also need FreeSurfer, follow the
instructions on their website.
The tests are run using pytest. You can run them by calling
pytest mne_bids_pipeline to run
all tests, or for example with pytest -k DATASET to run tests for a
specific dataset only, or pytest -m "not dataset_test" to run non-dataset
tests. To download data for a given dataset, use
pytest -k DATASET --download.
For every pull request or merge into the main branch of the
mne-bids-pipeline,
CircleCI
will run tests as defined in ./circleci/config.yml.
To run the test in debugging mode, just pass --pdb to the pytest call
as usual. This will place you in debugging mode on failure.
See the
pdb help
for more commands.
Nested in the tests directory is a configs directory, which contains
config files for specific test datasets. For example, the config_ds001810.py
file specifies parameters only for the ds001810 data, which should overwrite
the more general parameters in the main _config.py file.