Merge pull request #475 from matthew-brett/release-preparations

MRG: updating docs for upcoming 2.1 release

Update documentation ready for release.

Rewrite Changelog format with sections.

Author: matthew-brett

.mailmap

@@ -31,3 +31,7 @@ Ben Cipollini <ben.cipollini@gmail.com> Ben Cipollini <bcipolli@ucsd.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@bu.edu>
 Chris Markiewicz <effigies@gmail.com> Christopher J. Markiewicz <effigies@gmail.com>
 Chris Markiewicz <effigies@gmail.com> Chris Johnson <effigies@bu.edu>
+Jaakko Leppäkangas <jaeilepp@student.jyu.fi> jaeilepp <jaeilepp@student.jyu.fi>
+Ariel Rokem <arokem@gmail.com> arokem <arokem@gmail.com>
+Oliver P. Hinds <ohinds@gmail.com> ohinds <ohinds@gmail.com>
+Marc-Alexandre Côté <marc.cote.19@gmail.com> Marc-Alexandre Cote <marc.cote.19@gmail.com>

AUTHOR

@@ -1,3 +1,7 @@
 Matthew Brett <matthew.brett@gmail.com>
 Michael Hanke <michael.hanke@gmail.com>
+Ben Cipollini <ben.cipollini@gmail.com>
+Marc-Alexandre Côté <marc.cote.19@gmail.com>
+Chris Markiewicz <effigies@gmail.com>
 Stephan Gerhard <connectome@unidesign.ch>
+Eric Larson <larson.eric.d@gmail.com>

Changelog

@@ -16,9 +16,9 @@ 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_, MINC1_, MINC2_, MGH_ and ECAT_ as well as Philips
-PAR/REC.  We can read and write Freesurfer_ geometry, and read Freesurfer
-morphometry and annotation files.  There is some very limited support for
-DICOM_.  NiBabel is the successor of PyNIfTI_.
+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
 .. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/
@@ -34,8 +34,9 @@ DICOM_.  NiBabel is the successor of PyNIfTI_.
 .. _Freesurfer: https://surfer.nmr.mgh.harvard.edu
 .. _DICOM: http://medical.nema.org/
 
-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.
+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.
 
 Website
 =======
@@ -52,15 +53,19 @@ Please send any questions or suggestions to the `neuroimaging mailing list
 Code
 ====
 
-You can find our sources and single-click downloads:
+Install nibabel with::
 
-* `Main 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`_.
+    pip install nibabel
 
-.. _main repository: https://github.com/nipy/nibabel
+You may also be interested in:
+
+* 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`_.
+
+.. _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
@@ -69,6 +74,6 @@ You can find our sources and single-click downloads:
 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.  Please see the COPYING file
+in the nibabel distribution.

README.rst

@@ -83,7 +83,7 @@
 
 # General information about the project.
 project = u'NiBabel'
-copyright = u'2006-2015, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
+copyright = u'2006-2016, %(MAINTAINER)s <%(AUTHOR_EMAIL)s>' % rel
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the

doc/source/conf.py

@@ -44,9 +44,15 @@ Release checklist
   notes are as complete as possible and that every contributor was recognized.
 
 * Look at ``doc/source/index.rst`` and add any authors not yet acknowledged.
+  You might want to use the following to list authors by the date of their
+  contributions::
 
-* Update new authors and add thansk in ``doc/source/index.rst`` and consider
-  any updates to the ``AUTHOR`` file.
+    git log --format="%aN <%aE>" --reverse | perl -e 'my %dedupe; while (<STDIN>) { print unless $dedupe{$_}++}'
+
+  (From:
+  http://stackoverflow.com/questions/6482436/list-of-authors-in-git-since-a-given-commit#6482473)
+
+  Consider any updates to the ``AUTHOR`` file.
 
 * Use the opportunity to update the ``.mailmap`` file if there are any
   duplicate authors listed from ``git shortlog -nse``.
@@ -63,9 +69,10 @@ Release checklist
   because this will be the output used by pypi_
 
 * Check the dependencies listed in ``nibabel/info.py`` (e.g.
-  ``NUMPY_MIN_VERSION``) and in ``doc/source/installation.rst``.  They should
-  at least match. Do they still hold?  Make sure `nibabel on travis`_ is
-  testing the minimum dependencies specifically.
+  ``NUMPY_MIN_VERSION``) and in ``doc/source/installation.rst`` and in
+  ``requirements.txt`` and ``.travis.yml``.  They should at least match. Do
+  they still hold?  Make sure `nibabel on travis`_ is testing the minimum
+  dependencies specifically.
 
 * Do a final check on the `nipy buildbot`_.  Use the ``try_branch.py``
   scheduler available in nibotmi_ to test particular schedulers.

doc/source/devel/make_release.rst

@@ -27,42 +27,49 @@ discussions, release procedure and more.
 Authors and Contributors
 ========================
 
-The main authors of NiBabel are `Matthew Brett`_, `Michael Hanke`_ and `Stephan
-Gerhard`_.  The authors are grateful to the following people who have
+The main authors of NiBabel are `Matthew Brett`_, `Michael Hanke`_, `Ben
+Cipollini`_, `Marc-Alexandre Côté`_, Chris Markiewicz, `Stephan Gerhard`_ and
+`Eric Larson`_.  The authors are grateful to the following people who have
 contributed code and discussion (in rough order of appearance):
 
 * `Yaroslav O. Halchenko`_
 * Chris Burns
 * `Gaël Varoquaux`_
 * Ian Nimmo-Smith
-* Jarrod Millman
-* Bertrand Thirion
+* `Jarrod Millman`_
+* `Bertrand Thirion`_
 * Thomas Ballinger
 * Cindee Madison
 * Valentin Haenel
-* Alexandre Gramfort
+* `Alexandre Gramfort`_
 * Christian Haselgrove
 * Krish Subramaniam
 * Yannick Schwartz
 * Bago Amirbekian
 * Brendan Moloney
 * Félix C. Morency
-* Chris Markiewicz
 * JB Poline
-* Nolan Nichols
-* Nguyen, Ly
 * Basile Pinsard
-* Kevin S. Hahn
-* Eric Larson
-* Nikolaas N. Oosterhof
-* ohinds
-* Michiel Cottaar
-* Satrajit Ghosh
-* Demian Wassermann
+* `Satrajit Ghosh`_
+* `Nolan Nichols`_
+* Nguyen, Ly
 * Philippe Gervais
+* Demian Wassermann
 * Justin Lecher
-* `Ben Cipollini`_
+* Oliver P. Hinds
+* Nikolaas N. Oosterhof
+* Kevin S. Hahn
+* Michiel Cottaar
+* Erik Kastman
+* Github user ``freec84``
+* Peter Fischer
 * Clemens C. C. Bauer
+* Samuel St-Jean
+* Gregory R. Lee
+* Eric M. Baker
+* `Ariel Rokem`_
+* Eleftherios Garyfallidis
+* Jaakko Leppäkangas
 
 License reprise
 ===============

doc/source/index.rst

@@ -234,6 +234,14 @@
 .. _Gaël Varoquaux: http://gael-varoquaux.info/
 .. _Stephan Gerhard: http://www.unidesign.ch
 .. _Ben Cipollini: http://bcipolli.github.io/
+.. _Eric Larson: https://staff.washington.edu/larsoner
+.. _Marc-Alexandre Côté: https://marccote.github.io
+.. _Jarrod Millman: http://www.jarrodmillman.com/
+.. _Alexandre Gramfort: http://alexandre.gramfort.net
+.. _Ariel Rokem: http://arokem.org
+.. _Bertrand Thirion: https://team.inria.fr/parietal/bertrand-thirions-page
+.. _Nolan Nichols: http://www.nolan-nichols.com
+.. _Satrajit Ghosh: http://satra.cogitatum.org
 
 .. Substitutions
 .. |emdash| unicode:: U+02014

doc/source/links_names.txt

@@ -109,9 +109,9 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 This package provides read +/- write access to some common medical and
 neuroimaging file formats, including: ANALYZE_ (plain, SPM99, SPM2 and later),
 GIFTI_, NIfTI1_, NIfTI2_, MINC1_, MINC2_, MGH_ and ECAT_ as well as Philips
-PAR/REC.  We can read and write Freesurfer_ geometry, and read Freesurfer
-morphometry and annotation files.  There is some very limited support for
-DICOM_.  NiBabel is the successor of PyNIfTI_.
+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
 .. _NIfTI1: http://nifti.nimh.nih.gov/nifti-1/
@@ -127,8 +127,9 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 .. _Freesurfer: https://surfer.nmr.mgh.harvard.edu
 .. _DICOM: http://medical.nema.org/
 
-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.
+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.
 
 Website
 =======
@@ -145,15 +146,19 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 Code
 ====
 
-You can find our sources and single-click downloads:
+Install nibabel with::
 
-* `Main 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`_.
+    pip install nibabel
 
-.. _main repository: https://github.com/nipy/nibabel
+You may also be interested in:
+
+* 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`_.
+
+.. _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
@@ -162,9 +167,9 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 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.  Please see the COPYING file
+in the nibabel distribution.
 """
 
 # versions for dependencies. Check these against:
@@ -184,7 +189,7 @@ def cmp_pkg_version(version_str, pkg_version_str=__version__):
 DOWNLOAD_URL = "https://github.com/nipy/nibabel"
 LICENSE = "MIT license"
 CLASSIFIERS = CLASSIFIERS
-AUTHOR = "Matthew Brett, Michael Hanke, Stephan Gerhard"
+AUTHOR = "nibabel developers"
 AUTHOR_EMAIL = "neuroimaging@python.org"
 PLATFORMS = "OS Independent"
 MAJOR = _version_major