| Name | pybids JSON |
| Version |
0.16.4
JSON |
| download |
| home_page | |
| Summary | bids: interface with datasets conforming to BIDS |
| upload_time | 2023-11-30 19:26:29 |
| maintainer | |
| docs_url | None |
| author | |
| requires_python | >=3.8 |
| 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 copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
bids
neuroimaging
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
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| coveralls test coverage |
No coveralls.
|
# PyBIDS
[](https://doi.org/10.21105/joss.01294)
[](https://doi.org/10.5281/zenodo.2537312)
[](https://mybinder.org/v2/gh/bids-standard/pybids/master)
[](https://badge.fury.io/py/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 https://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. https://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.
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"description": "# PyBIDS\n[](https://doi.org/10.21105/joss.01294)\n[](https://doi.org/10.5281/zenodo.2537312)\n\n[](https://mybinder.org/v2/gh/bids-standard/pybids/master)\n[](https://badge.fury.io/py/pybids)\n[](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> pip install pybids\n\nOr, alternatively via conda:\n\n> conda install -c conda-forge pybids\n\nIf you want to live on the bleeding edge, you can install from master:\n\n> 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## 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, \u2026 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",
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