Metadata-Version: 2.1
Name: pybids
Version: 0.15.6
Summary: bids: interface with datasets conforming to BIDS
Author-email: PyBIDS Developers <bids-discussion@googlegroups.com>
License: The MIT License (MIT)
        
        Copyright (c) 2015-2016, Ariel Rokem, The University of Washington eScience Institute.
        Copyright (c) 2016--, PyBIDS developers, Planet Earth
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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Project-URL: Homepage, http://github.com/bids-standard/pybids
Project-URL: Bug Tracker, http://github.com/bids-standard/pybids/issues
Keywords: BIDS,neuroimaging
Platform: OS Independent
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.7
Description-Content-Type: text/markdown
Provides-Extra: doc
Provides-Extra: plotting
Provides-Extra: test
Provides-Extra: tutorial
Provides-Extra: ci_tests
Provides-Extra: docs
Provides-Extra: tests
Provides-Extra: dev
License-File: LICENSE

# PyBIDS
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01294/status.svg)](https://doi.org/10.21105/joss.01294)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2537312.svg)](https://doi.org/10.5281/zenodo.2537312)

[![Build Status (Linux and OS X)](https://travis-ci.org/bids-standard/pybids.svg?branch=master)](https://travis-ci.org/bids-standard/pybids)<!---[![Build Status (Windows)](https://ci.appveyor.com/api/projects/status/5aa4c6e3m15ew4v7?svg=true)](https://ci.appveyor.com/project/chrisfilo/pybids-ilb80)-->
[![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/bids-standard/pybids/master)
[![PyPI version](https://badge.fury.io/py/pybids.svg)](https://badge.fury.io/py/pybids)
[![Conda version](https://img.shields.io/conda/vn/conda-forge/pybids)](https://anaconda.org/conda-forge/pybids)

PyBIDS is a Python library to centralize interactions with datasets conforming
BIDS (Brain Imaging Data Structure) format.  For more information about BIDS
visit http://bids.neuroimaging.io.

PyBIDS currently supports Python 3 on POSIX operating systems (including Mac OS).  Windows is not officially supported, though most PyBIDS functionality will probably work fine.

## Installation
PyBIDS is most easily installed from pip. To install the latest official release:

> pip install pybids

Or, alternatively via conda:

> conda install -c conda-forge pybids

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
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.

## 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):

Yarkoni et al., (2019). PyBIDS: Python tools for BIDS datasets. Journal of Open Source Software, 4(40), 1294, https://doi.org/10.21105/joss.01294

Yarkoni, 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. http://doi.org/10.5281/zenodo.3363985

## Community guidelines
Bug 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.

Pull 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.
