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DOC: Add development and testing section to introduce tox
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effigies committed May 4, 2024
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Expand Up @@ -25,14 +25,38 @@ If you want to live on the bleeding edge, you can install from master:

> pip install git+https://github.com/bids-standard/pybids.git
#### Dependencies
### Dependencies
PyBIDS has a number of dependencies. The core querying functionality requires only the `BIDS-Validator` package. However, most other modules require the core Python neuroimaging stack: `numpy`, `scipy`, `pandas`, and `nibabel`. The `reports` module additionally requires `num2words`. By default, all dependencies will be installed with pybids (if they aren't already available).

## Usage
Get started by checking out [the documentation](https://bids-standard.github.io/pybids)!

Or you can start at [our tutorial](https://bids-standard.github.io/pybids/examples/pybids_tutorial.html)! You can run it interactively without installing anything via [binder](https://mybinder.org/v2/gh/bids-standard/pybids/master). Click on the link and then navigate to `doc/examples/pybids_tutorial.md` to explore.

## Development and testing
PyBIDS uses [tox](https://tox.wiki/) to manage testing environments and ensure that the same
commands can easily be run locally and in CI.

Install tox with:

```
pip install tox
```

To run tests with standard, minimal, or pre-release dependencies, use:

```
tox run -e [full|min|pre]
```

To run with a specific version, also specify `py3X`:

```
tox run -e py311-full
```

See `tox` documentation for more detail.

## How to cite
To credit PyBIDS in your work, please cite both the [JOSS paper](https://joss.theoj.org/papers/10.21105/joss.01294) and the [Zenodo archive](https://zenodo.org/record/3363985). The former provides a high level description of the package, and the latter points to a permanent record of all PyBIDS versions (we encourage you to cite the specific version you used). Example citations (for PyBIDS 0.9.3):

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