diff --git a/README.rst b/README.rst index 3378e751c2..45856f6795 100644 --- a/README.rst +++ b/README.rst @@ -1,110 +1,149 @@ .. -*- rest -*- .. vim:syntax=rst -.. image:: https://codecov.io/gh/nipy/nibabel/branch/master/graph/badge.svg - :target: https://codecov.io/gh/nipy/nibabel - -.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.591597.svg - :target: https://doi.org/10.5281/zenodo.591597 - -.. image:: https://repology.org/badge/version-for-repo/aur/python:nibabel.svg?header=Arch%20%28%41%55%52%29 - :target: https://repology.org/project/python:nibabel/versions - :alt: Arch (AUR) - -.. image:: https://repology.org/badge/version-for-repo/debian_unstable/nibabel.svg?header=Debian%20Unstable - :target: https://repology.org/project/nibabel/versions - :alt: Debian Unstable package - -.. image:: https://repology.org/badge/version-for-repo/gentoo_ovl_science/nibabel.svg?header=Gentoo%20%28%3A%3Ascience%29 - :target: https://repology.org/project/nibabel/versions - :alt: Gentoo (::science) - -.. image:: https://repology.org/badge/version-for-repo/nix_unstable/python:nibabel.svg?header=nixpkgs%20unstable - :target: https://repology.org/project/python:nibabel/versions - :alt: nixpkgs unstable - -.. Following contents should be from LONG_DESCRIPTION in nibabel/info.py - - -======= -NiBabel -======= - -Read / write access to some common neuroimaging file formats - -This package provides read +/- write access to some common medical and -neuroimaging file formats, including: ANALYZE_ (plain, SPM99, SPM2 and later), -GIFTI_, NIfTI1_, NIfTI2_, `CIFTI-2`_, MINC1_, MINC2_, `AFNI BRIK/HEAD`_, MGH_ and -ECAT_ as well as Philips PAR/REC. We can read and write FreeSurfer_ geometry, -annotation and morphometry files. There is some very limited support for -DICOM_. NiBabel is the successor of PyNIfTI_. - -.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm +.. image:: doc/pics/logo.png + :target: https://nipy.org/nibabel + :alt: NiBabel logo + +.. list-table:: + :widths: 20 80 + :header-rows: 0 + + * - Code + - + .. image:: https://img.shields.io/pypi/pyversions/nibabel.svg + :target: https://pypi.python.org/pypi/nibabel/ + :alt: PyPI - Python Version + .. image:: https://img.shields.io/badge/code%20style-blue-blue.svg + :target: https://blue.readthedocs.io/en/latest/ + :alt: code style: blue + .. image:: https://img.shields.io/badge/imports-isort-1674b1 + :target: https://pycqa.github.io/isort/ + :alt: imports: isort + .. image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white + :target: https://github.com/pre-commit/pre-commit + :alt: pre-commit + + * - Tests + - + .. image:: https://github.com/nipy/NiBabel/actions/workflows/stable.yml/badge.svg + :target: https://github.com/nipy/NiBabel/actions/workflows/stable.yml + :alt: stable tests + .. image:: https://codecov.io/gh/nipy/NiBabel/branch/master/graph/badge.svg + :target: https://codecov.io/gh/nipy/NiBabel + :alt: codecov badge + + * - PyPI + - + .. image:: https://img.shields.io/pypi/v/nibabel.svg + :target: https://pypi.python.org/pypi/nibabel/ + :alt: PyPI version + .. image:: https://img.shields.io/pypi/dm/nibabel.svg + :target: https://pypistats.org/packages/nibabel + :alt: PyPI - Downloads + + * - Packages + - + .. image:: https://img.shields.io/conda/vn/conda-forge/nibabel + :target: https://anaconda.org/conda-forge/nibabel + :alt: Conda package + .. image:: https://repology.org/badge/version-for-repo/debian_unstable/nibabel.svg?header=Debian%20Unstable + :target: https://repology.org/project/nibabel/versions + :alt: Debian Unstable package + .. image:: https://repology.org/badge/version-for-repo/aur/python:nibabel.svg?header=Arch%20%28%41%55%52%29 + :target: https://repology.org/project/python:nibabel/versions + :alt: Arch (AUR) + .. image:: https://repology.org/badge/version-for-repo/gentoo_ovl_science/nibabel.svg?header=Gentoo%20%28%3A%3Ascience%29 + :target: https://repology.org/project/nibabel/versions + :alt: Gentoo (::science) + .. image:: https://repology.org/badge/version-for-repo/nix_unstable/python:nibabel.svg?header=nixpkgs%20unstable + :target: https://repology.org/project/python:nibabel/versions + :alt: nixpkgs unstable + + * - License & DOI + - + .. image:: https://img.shields.io/pypi/l/nibabel.svg + :target: https://github.com/nipy/nibabel/blob/master/COPYING + :alt: License + .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.591597.svg + :target: https://doi.org/10.5281/zenodo.591597 + :alt: Zenodo DOI + +.. Following contents should be copied from LONG_DESCRIPTION in nibabel/info.py + + +Read and write access to common neuroimaging file formats, including: +ANALYZE_ (plain, SPM99, SPM2 and later), GIFTI_, NIfTI1_, NIfTI2_, `CIFTI-2`_, +MINC1_, MINC2_, `AFNI BRIK/HEAD`_, ECAT_ and Philips PAR/REC. +In addition, NiBabel also supports FreeSurfer_'s MGH_, geometry, annotation and +morphometry files, and provides some limited support for DICOM_. + +NiBabel's API gives full or selective access to header information (metadata), +and image data is made available via NumPy arrays. For more information, see +NiBabel's `documentation site`_ and `API reference`_. + +.. _API reference: https://nipy.org/nibabel/api.html .. _AFNI BRIK/HEAD: https://afni.nimh.nih.gov/pub/dist/src/README.attributes -.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/ -.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/ +.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm .. _CIFTI-2: https://www.nitrc.org/projects/cifti/ +.. _DICOM: http://medical.nema.org/ +.. _documentation site: http://nipy.org/nibabel +.. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat +.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu +.. _GIFTI: https://www.nitrc.org/projects/gifti +.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat .. _MINC1: https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference .. _MINC2: https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference -.. _PyNIfTI: http://niftilib.sourceforge.net/pynifti/ -.. _GIFTI: https://www.nitrc.org/projects/gifti -.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat -.. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat -.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu -.. _DICOM: http://medical.nema.org/ +.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/ +.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/ -The various image format classes give full or selective access to header -(meta) information and access to the image data is made available via NumPy -arrays. +Installation +============ -Website -======= +To install NiBabel's `current release`_ with ``pip``, run:: -Current documentation on nibabel can always be found at the `NIPY nibabel -website `_. + pip install nibabel -Mailing Lists -============= +To install the latest development version, run:: -Please send any questions or suggestions to the `neuroimaging mailing list -`_. + pip install git+https://github.com/nipy/nibabel -Code -==== +When working on NiBabel itself, it may be useful to install in "editable" mode:: -Install nibabel with:: + git clone https://github.com/nipy/nibabel.git + pip install -e ./nibabel - pip install nibabel +For more information on previous releases, see the `release archive`_ or +`development changelog`_. -You may also be interested in: +.. _current release: https://pypi.python.org/pypi/NiBabel +.. _release archive: https://github.com/nipy/NiBabel/releases +.. _development changelog: https://nipy.org/nibabel/changelog.html -* the `nibabel code repository`_ on Github; -* documentation_ for all releases and current development tree; -* download the `current release`_ from pypi; -* download `current development version`_ as a zip file; -* downloads of all `available releases`_. +Mailing List +============ -.. _nibabel code repository: https://github.com/nipy/nibabel -.. _Documentation: http://nipy.org/nibabel -.. _current release: https://pypi.python.org/pypi/nibabel -.. _current development version: https://github.com/nipy/nibabel/archive/master.zip -.. _available releases: https://github.com/nipy/nibabel/releases +Please send any questions or suggestions to the `neuroimaging mailing list +`_. License ======= -Nibabel is licensed under the terms of the MIT license. Some code included -with nibabel is licensed under the BSD license. Please see the COPYING file -in the nibabel distribution. +NiBabel is licensed under the terms of the `MIT license +`__. +Some code included with NiBabel is licensed under the `BSD license`_. +For more information, please see the COPYING_ file. -Citing nibabel -============== +.. _BSD license: https://opensource.org/licenses/BSD-3-Clause +.. _COPYING: https://github.com/nipy/nibabel/blob/master/COPYING -Please see the `available releases`_ for the release of nibabel that you are -using. Recent releases have a Zenodo_ `Digital Object Identifier`_ badge at -the top of the release notes. Click on the badge for more information. +Citation +======== + +NiBabel releases have a Zenodo_ `Digital Object Identifier`_ (DOI) badge at +the top of the release notes. Click on the badge for more information. -.. _zenodo: https://zenodo.org .. _Digital Object Identifier: https://en.wikipedia.org/wiki/Digital_object_identifier +.. _zenodo: https://zenodo.org diff --git a/doc/pics/logo.png b/doc/pics/logo.png new file mode 100644 index 0000000000..570d38f476 Binary files /dev/null and b/doc/pics/logo.png differ diff --git a/doc/source/index.rst b/doc/source/index.rst index 8eb8a9c7d5..701de01362 100644 --- a/doc/source/index.rst +++ b/doc/source/index.rst @@ -7,6 +7,10 @@ # ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### +======= +NiBabel +======= + .. include:: _long_description.inc Documentation diff --git a/nibabel/info.py b/nibabel/info.py index 96031ac954..063978444c 100644 --- a/nibabel/info.py +++ b/nibabel/info.py @@ -1,7 +1,7 @@ -"""Define distribution parameters for nibabel, including package version +"""Define static nibabel metadata for nibabel -The long description parameter is used to fill settings in setup.py, the -nibabel top-level docstring, and in building the docs. +The long description parameter is used in the nibabel top-level docstring, +and in building the docs. We exec this file in several places, so it cannot import nibabel or use relative imports. """ @@ -12,86 +12,79 @@ # We also include this text in the docs by ``..include::`` in # ``docs/source/index.rst``. long_description = """ -======= -NiBabel -======= +Read and write access to common neuroimaging file formats, including: +ANALYZE_ (plain, SPM99, SPM2 and later), GIFTI_, NIfTI1_, NIfTI2_, `CIFTI-2`_, +MINC1_, MINC2_, `AFNI BRIK/HEAD`_, ECAT_ and Philips PAR/REC. +In addition, NiBabel also supports FreeSurfer_'s MGH_, geometry, annotation and +morphometry files, and provides some limited support for DICOM_. -Read / write access to some common neuroimaging file formats +NiBabel's API gives full or selective access to header information (metadata), +and image data is made available via NumPy arrays. For more information, see +NiBabel's `documentation site`_ and `API reference`_. -This package provides read +/- write access to some common medical and -neuroimaging file formats, including: ANALYZE_ (plain, SPM99, SPM2 and later), -GIFTI_, NIfTI1_, NIfTI2_, `CIFTI-2`_, MINC1_, MINC2_, `AFNI BRIK/HEAD`_, MGH_ and -ECAT_ as well as Philips PAR/REC. We can read and write FreeSurfer_ geometry, -annotation and morphometry files. There is some very limited support for -DICOM_. NiBabel is the successor of PyNIfTI_. - -.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm +.. _API reference: https://nipy.org/nibabel/api.html .. _AFNI BRIK/HEAD: https://afni.nimh.nih.gov/pub/dist/src/README.attributes -.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/ -.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/ +.. _ANALYZE: http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm .. _CIFTI-2: https://www.nitrc.org/projects/cifti/ +.. _DICOM: http://medical.nema.org/ +.. _documentation site: http://nipy.org/nibabel +.. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat +.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu +.. _GIFTI: https://www.nitrc.org/projects/gifti +.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat .. _MINC1: https://en.wikibooks.org/wiki/MINC/Reference/MINC1_File_Format_Reference .. _MINC2: https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference -.. _PyNIfTI: http://niftilib.sourceforge.net/pynifti/ -.. _GIFTI: https://www.nitrc.org/projects/gifti -.. _MGH: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat -.. _ECAT: http://xmedcon.sourceforge.net/Docs/Ecat -.. _Freesurfer: https://surfer.nmr.mgh.harvard.edu -.. _DICOM: http://medical.nema.org/ +.. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/ +.. _NIfTI2: http://nifti.nimh.nih.gov/nifti-2/ -The various image format classes give full or selective access to header -(meta) information and access to the image data is made available via NumPy -arrays. +Installation +============ -Website -======= +To install NiBabel's `current release`_ with ``pip``, run:: -Current documentation on nibabel can always be found at the `NIPY nibabel -website `_. + pip install nibabel -Mailing Lists -============= +To install the latest development version, run:: -Please send any questions or suggestions to the `neuroimaging mailing list -`_. + pip install git+https://github.com/nipy/nibabel -Code -==== +When working on NiBabel itself, it may be useful to install in "editable" mode:: -Install nibabel with:: + git clone https://github.com/nipy/nibabel.git + pip install -e ./nibabel - pip install nibabel +For more information on previous releases, see the `release archive`_ or +`development changelog`_. -You may also be interested in: +.. _current release: https://pypi.python.org/pypi/NiBabel +.. _release archive: https://github.com/nipy/NiBabel/releases +.. _development changelog: https://nipy.org/nibabel/changelog.html -* the `nibabel code repository`_ on Github; -* documentation_ for all releases and current development tree; -* download the `current release`_ from pypi; -* download `current development version`_ as a zip file; -* downloads of all `available releases`_. +Mailing List +============ -.. _nibabel code repository: https://github.com/nipy/nibabel -.. _Documentation: http://nipy.org/nibabel -.. _current release: https://pypi.python.org/pypi/nibabel -.. _current development version: https://github.com/nipy/nibabel/archive/master.zip -.. _available releases: https://github.com/nipy/nibabel/releases +Please send any questions or suggestions to the `neuroimaging mailing list +`_. License ======= -Nibabel is licensed under the terms of the MIT license. Some code included -with nibabel is licensed under the BSD license. Please see the COPYING file -in the nibabel distribution. +NiBabel is licensed under the terms of the `MIT license +`__. +Some code included with NiBabel is licensed under the `BSD license`_. +For more information, please see the COPYING_ file. -Citing nibabel -============== +.. _BSD license: https://opensource.org/licenses/BSD-3-Clause +.. _COPYING: https://github.com/nipy/nibabel/blob/master/COPYING -Please see the `available releases`_ for the release of nibabel that you are -using. Recent releases have a Zenodo_ `Digital Object Identifier`_ badge at -the top of the release notes. Click on the badge for more information. +Citation +======== + +NiBabel releases have a Zenodo_ `Digital Object Identifier`_ (DOI) badge at +the top of the release notes. Click on the badge for more information. -.. _zenodo: https://zenodo.org .. _Digital Object Identifier: https://en.wikipedia.org/wiki/Digital_object_identifier -""" +.. _zenodo: https://zenodo.org +""" # noqa: E501