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PyBIDS\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.01294/status.svg)](https://doi.org/10.21105/joss.01294)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2537312.svg)](https://doi.org/10.5281/zenodo.2537312)\n\n[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/bids-standard/pybids/master)\n[![PyPI version](https://badge.fury.io/py/pybids.svg)](https://badge.fury.io/py/pybids)\n[![Conda version](https://img.shields.io/conda/vn/conda-forge/pybids)](https://anaconda.org/conda-forge/pybids)\n\nPyBIDS is a Python library to centralize interactions with datasets conforming\nBIDS (Brain Imaging Data Structure) format.  For more information about BIDS\nvisit https://bids.neuroimaging.io.\n\nPyBIDS currently supports Python 3 on POSIX operating systems (including Mac OS).  Windows is not officially supported, though most PyBIDS functionality will probably work fine.\n\n## Installation\nPyBIDS is most easily installed from pip. To install the latest official release:\n\n\u003e pip install pybids\n\nOr, alternatively via conda:\n\n\u003e conda install -c conda-forge pybids\n\nIf you want to live on the bleeding edge, you can install from master:\n\n\u003e pip install git+https://github.com/bids-standard/pybids.git\n\n### Dependencies\nPyBIDS 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).\n\n## Usage\nGet started by checking out [the documentation](https://bids-standard.github.io/pybids)!\n\nOr 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.\n\n## Development and testing\nPyBIDS uses [tox](https://tox.wiki/) to manage testing environments and ensure that the same\ncommands can easily be run locally and in CI.\n\nInstall tox with:\n\n```\npip install tox\n```\n\nTo run tests with standard, minimal, or pre-release dependencies, use:\n\n```\ntox run -e [full|min|pre]\n```\n\nTo run with a specific version, also specify `py3X`:\n\n```\ntox run -e py311-full\n```\n\nSee `tox` documentation for more detail.\n\n## How to cite\nTo 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):\n\nYarkoni et al., (2019). PyBIDS: Python tools for BIDS datasets. Journal of Open Source Software, 4(40), 1294, https://doi.org/10.21105/joss.01294\n\nYarkoni, Tal, Markiewicz, Christopher J., de la Vega, Alejandro, Gorgolewski, Krzysztof J., Halchenko, Yaroslav O., Salo, Taylor, … Blair, Ross. (2019, August 8). bids-standard/pybids: 0.9.3 (Version 0.9.3). Zenodo. https://doi.org/10.5281/zenodo.3363985\n\n## Community guidelines\nBug reports, feedback, and other contributions to PyBIDS are welcome. To report a bug, request a feature, or raise a technical (non-usage-related) question for discussion, please [open an issue on GitHub](https://github.com/bids-standard/pybids/issues). Requests for support and questions about usage (where no bug is suspected) should be posted on the [NeuroStars](https://neurostars.org) forum. For questions about the [BIDS specification](https://github.com/bids-standard/bids-specification) or [BIDS-Validator](https://github.com/bids-standard/bids-validator), please see the corresponding repositories. For general BIDS-related discussion, see the [bids-discussion](https://groups.google.com/forum/#!forum/bids-discussion) mailing list.\n\nPull requests are always welcome. If you have any doubts about the suitability of a PR, or want to discuss implementation-related issues, feel free to open an issue for discussion.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-standard%2Fpybids","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbids-standard%2Fpybids","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbids-standard%2Fpybids/lists"}