Merge pull request dipy#1688 from skoudoro/release_0.15_information_u…

…pdate

Update information for release 0.15.0

.mailmap

@@ -34,6 +34,7 @@ Shahnawaz Ahmed <shahnawaz.ahmed95@gmail.com> Your Name <shahnawaz.ahmed95@gmail
 Sylvain Merlet <merlet.sylvain@gmail.com> smerlet <merlet.sylvain@gmail.com>
 Mauro Zucchelli <mauro.zucchelli88@gmail.com> Mauro <mauro@Mauro.(none)>
 Mauro Zucchelli <mauro.zucchelli88@gmail.com> maurozucchelli <mauro.zucchelli@gmail.com>
+Mauro Zucchelli <mauro.zucchelli88@gmail.com> maurozucchelli <mauro.zucchelli88@gmail.com>
 Andrew Lawrence <lawrenceajl@gmail.com> AndrewLawrence <AndrewLawrence@users.noreply.github.com>
 Samuel St-Jean <Samuel.St-Jean@usherbrooke.ca> samuelstjean <samuel.st-jean@usherbrooke.ca>
 Samuel St-Jean <Samuel.St-Jean@usherbrooke.ca> samuelstjean <stjeansam@gmail.com>
@@ -65,6 +66,7 @@ Alexandre Gauvin <gauvinalexandre@gmail.com> Alexandre Gauvin <alexandre.gauvin@
 Nil Goyette <nil.goyette@imeka.ca> Nil Goyette <nil.goyette@gmail.com>
 Eric Peterson <globshim@gmail.com> etpeterson <globshim@gmail.com>
 Rutger Fick <rutger.fick@inria.fr> Rutger Fick <fick.rutger@gmail.com>
+Rutger Fick <rutger.fick@inria.fr> Rutger Fick <rutger361988@gmail.com>
 Demian Wassermann <demian.wassermann@inria.fr> Demian Wassermann <demianw@users.noreply.github.com>
 Sourav Singh <souravsingh@users.noreply.github.com> Sourav <ssouravsingh12@gmail.com>
 Sven Dorkenwald <sven.dorkenwald@mpimf-heidelberg.mpg.de>
@@ -75,3 +77,13 @@ Matthieu Dumont <matthieu.dumont@usherbrooke.ca>  unknown <mdumont@Dinf-2900-01H
 Guillaume Theaud <guillaume.theaud@gmail.com>
 Adam Rybinski <adam.rybinski@outlook.com>
 Bennet Fauber <justbennet@users.noreply.github.com>
+Aman Arya <aman.arya524@gmail.com>
+Ricci Woo <ricciwoo@gmail.com> RicciWoo <ricciwoo@gmail.com>
+Francois Rheault <francois.m.rheault@usherbrooke>
+David Hunt <davhunt@indiana.edu> David <davhunt@indiana.edu>
+David Hunt <davhunt@indiana.edu> davhunt <davhunt@indiana.edu>
+Parichit Sharma <parichitsharma08@gmail.com> Parichit Sharma <schmuck@149-161-162-17.dhcp-bl.indiana.edu>
+Chandan Gangwar <chandan.gangwar0411@gmail.com>
+Naveen Kumarmarri <naveenkumarmarri6014@gmail.com>
+Jacob Wasserthal <j.wasserthal@dkfz.de>
+Shreyas Fadnavis <shreyasfadnavis@gmail.com>

AUTHOR

@@ -1,33 +1,92 @@
 Eleftherios Garyfallidis <garyfallidis@gmail.com>
-Ian Nimmo-Smith <iannimmosmith@gmail.com>
+Ariel Rokem <arokem@gmail.com>
 Matthew Brett <matthew.brett@gmail.com>
 Bago Amirbekian <mrbago@gmail.com>
-Stefan Van der Walt <sjvdwalt@gmail.com>
-Ariel Rokem <arokem@gmail.com>
-Christopher Nguyen <christopher.t.nguyen@gmail.com>
-Yaroslav Halchenko <debian@onerussian.com>
-Emanuele Olivetti <emanuele@relativita.com>
-Mauro Zucchelli <mauro.zucchelli88@gmail.com>
-Samuel St-Jean <samuel.st-jean@usherbrooke.ca>
-Maxime Descoteaux <m.descoteaux@usherbrooke.ca>
+Omar Ocegueda <jomaroceguedag@gmail.com>
+Rafael Neto Henriques <rafaelnh21@gmail.com>
+Serge Koudoro <skab12@gmail.com>
+Samuel St-Jean <Samuel.St-Jean@usherbrooke.ca>
 Gabriel Girard <girard.gabriel@gmail.com>
+Marc-Alexandre Côté <marc.cote.19@gmail.com>
+Rutger Fick <rutger.fick@inria.fr>
+Shahnawaz Ahmed <shahnawaz.ahmed95@gmail.com>
+Ian Nimmo-Smith <iannimmosmith@gmail.com>
+Mauro Zucchelli <mauro.zucchelli88@gmail.com>
 Matthieu Dumont <matthieu.dumont@usherbrooke.ca>
-Kimberly Chan <kimberlylchan@gmail.com>
-Erik Ziegler <erik.ziegler@ulg.ac.be>
-Emmanuel Caruyer <caruyer@gmail.com>
-Matthias Ekman <matthias.ekman@gmail.com>
+Stefan van der Walt <sjvdwalt@gmail.com>
+Kesshi Jordan <kesshi.jordan@gmail.com>
+Ranveer Aggarwal <ranveeraggarwal@gmail.com>
+Maxime Descoteaux <m.descoteaux@usherbrooke.ca>
+Riddhish Bhalodia <riddhishb@gmail.com>
+Bramsh Qamar <bramshq@gmail.com>
+Karandeep <karan.jkps@gmail.com>
+Bishakh Ghosh <ghoshbishakh@gmail.com>
+Christopher Nguyen <christopher.t.nguyen@gmail.com>
+Stephan Meesters <s.p.l.meesters@tue.nl>
+Ricci Woo <ricciwoo@gmail.com>
+Eric Peterson <globshim@gmail.com>
+Manu Tej Sharma <a.manutej@gmail.com>
+Sourav Singh <souravsingh@users.noreply.github.com>
+Julio Villalon <neurobarranquilla@hotmail.com>
 Jean-Christophe Houde <jean.christophe.houde@gmail.com>
-Michael Paquette <jotha885@gmail.com>
-Sylvain Merlet <merlet.sylvain@gmail.com>
-Omar Ocegueda <jomaroceguedag@gmail.com>
-Marc-Alexandre Cote <marc.cote.19@gmail.com>
+Jon Haitz Legarreta Gorroño <jhlegarreta@vicomtech.org>
+Kumar Ashutosh <kumarashutosh.ee@gmail.com>
+Shreyas Fadnavis <shreyasfadnavis@gmail.com>
+David Reagan <dmreagan@iu.edu>
+Parichit Sharma <parichitsharma08@gmail.com>
+Guillaume Theaud <guillaume.theaud@gmail.com>
+Aman Arya <aman.arya524@gmail.com>
+Dimitris Rozakis <dimrozakis@gmail.com>
+Gregory R. Lee <gregory.lee@cchmc.org>
+Saber Sheybani <sheybani.saber@gmail.com>
+ChantalTax <chantaltax88@gmail.com>
+Nil Goyette <nil.goyette@imeka.ca>
+Rohan Prinja <rohan.prinja@gmail.com>
+Antonio Ossa <aaossa@uc.cl>
 Demian Wassermann <demian.wassermann@inria.fr>
+Michael Paquette <jotha885@gmail.com>
+Tingyi Wanyan <tiwanyan@iu.edu>
+Jiri Borovec <jiri.borovec@fel.cvut.cz>
+Yaroslav Halchenko <debian@onerussian.com>
+Conor Corbin <ccorbin@usc.edu>
+Kimberly Chan <kimberlylchan@gmail.com>
+ArjitJ <32598699+ArjitJ@users.noreply.github.com>
+Enes Albay <albayenes@gmail.com>
+Etienne St-Onge <etienne.st-onge@usherbrooke.ca>
+Erik Ziegler <erik.ziegler@ulg.ac.be>
+David Qixiang Chen <qixiang.chen@gmail.com>
+Francois Rheault <francois.m.rheault@usherbrooke>
+Emanuele Olivetti <olivetti@fbk.eu>
+David Hunt <davhunt@indiana.edu>
+Alexandre Gauvin <gauvinalexandre@gmail.com>
+Pradeep Reddy Raamana <praamana@research.baycrest.org>
+theaverageguy <yash14123@iiitd.ac.in>
+Julio Villalon <villalonreina@users.noreply.github.com>
 endolith <endolith@gmail.com>
+Matthias Ekman <matthias.ekman@gmail.com>
+Oscar Esteban <code@oscaresteban.es>
+Emmanuel Caruyer <caruyer@gmail.com>
+Tom Wright <tom@maladmin.com>
+Jon Haitz Legarreta Gorroño <jon.haitz.legarreta@gmail.com>
 Andrew Lawrence <lawrenceajl@gmail.com>
-Gregory R. Lee <gregory.lee@cchmc.org>
+Naveen Kumarmarri <naveenkumarmarri6014@gmail.com>
+Chandan Gangwar <chandan.gangwar0411@gmail.com>
+Pradeep Reddy Raamana <raamana@gmail.com>
+Bennet Fauber <bennet@umich.edu>
+Matt Cieslak <mattcieslak@gmail.com>
+Sylvain Merlet <merlet.sylvain@gmail.com>
+Gonzalo Sanguinetti <gsangui@gmail.com>
+Vatsala Swaroop <smarshy@users.noreply.github.com>
+Vibhatha Abeykoon <Vibhatha Abeykoon>
+Adam Rybinski <adam.rybinski@outlook.com>
 Maria Luisa Mandelli <mmandelli@sampras.radiology.ucsf.edu>
-Kesshi jordan <Kesshi.Jordan@ucsf.edu>
-Chantal Tax <chantaltax88@gmail.com>
-Qiyuan Tian <qytian@stanford.edu>
-Shahnawaz Ahmed <shahnawaz.ahmed95@gmail.com>
-Eric Peterson <globshim@gmail.com>
+Sven Dorkenwald <sven.dorkenwald@mpimf-heidelberg.mpg.de>
+Qiyuan Tian <fdqiyuantian@gmail.com>
+Chris Filo Gorgolewski <krzysztof.gorgolewski@gmail.com>
+Bennet Fauber <justbennet@users.noreply.github.com>
+Daniel Enrico Cahall <danielenricocahall@gmail.com>
+Jon Mendoza <mrfox321@gmail.com>
+Sagun Pai <sagung.pai@gmail.com>
+Javier Guaje <guaje@users.noreply.github.com>
+Jacob Wasserthal <j.wasserthal@dkfz.de>
+Himanshu Mishra <himanshu2014iit@gmail.com>

Changelog

@@ -24,6 +24,19 @@ Dipy
 
 The code found in Dipy was created by the people found in the AUTHOR file.
 
+* 0.15 (Wednesday, 12 December 2018)
+
+- Updated RecoBundles for automatic anatomical bundle segmentation.
+- New Reconstruction Model: qtau-dMRI.
+- New command line interfaces (e.g. dipy_slr).
+- New continuous integration with AppVeyor CI.
+- Nibabel Streamlines API now used almost everywhere for better memory management.
+- Compatibility with Python 3.7.
+- Many tutorials added or updated (5 New).
+- Large documentation update.
+- Moved visualization module to a new library: FURY.
+- Closed 287 issues and merged 93 pull requests.   
+
 * 0.14 (Tuesday, 1 May 2018)
 
 - RecoBundles: anatomically relevant segmentation of bundles

LICENSE

@@ -1,7 +1,7 @@
 Unless otherwise specified by LICENSE.txt files in individual
 directories, or within individual files or functions, all code is:
 
-Copyright (c) 2008-2016, dipy developers
+Copyright (c) 2008-2019, dipy developers
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

dipy/info.py

@@ -72,9 +72,7 @@
 Please see the LICENSE file in the dipy distribution.
 
 DIPY uses other libraries also licensed under the BSD or the
-MIT licenses, with the only exception of the SHORE module which
-optionally uses the cvxopt library. Cvxopt is licensed
-under the GPL license.
+MIT licenses.
 """
 
 # versions for dependencies

doc/api_changes.rst

@@ -5,6 +5,29 @@ API changes
 Here we provide information about functions or classes that have been removed,
 renamed or are deprecated (not recommended) during different release circles.
 
+DIPY 0.15 Changes
+-----------------
+
+**IO**
+
+``load_tck`` and ``save_tck`` from ``dipy.io.streamline`` has been added. They are highly recommended for managing streamlines.
+
+**Gradient Table**
+
+The default value of ``b0_thresold`` has been changed(from 0 to 50). This change can impact your algorithm.
+If you want to assure that your code runs in exactly the same manner as before, please initialize your gradient table with the keyword argument ``b0_threshold`` set to 0.
+
+**Visualization**
+
+``dipy.viz.fvtk`` module has been removed. Use ``dipy.viz.*`` instead. This implies the following important changes:
+- Use ``from dipy.viz import window, actor`` instead of ``from dipy.viz import fvtk`.
+- Use ``window.Renderer()`` instead of ``fvtk.ren()``.
+- All available actors are in ``dipy.viz.actor`` instead of ``dipy.fvtk.actor``.
+- UI elements are available in ``dipy.viz.ui``.
+
+``dipy.viz`` depends on FURY package. To get more informations about FURY, go to https://fury.gl
+
+
 DIPY 0.14 Changes
 -----------------
 

doc/conf.py

@@ -66,7 +66,7 @@
 
 # General information about the project.
 project = u'dipy'
-copyright = u'2008-2018, %(AUTHOR)s <%(AUTHOR_EMAIL)s>' % rel
+copyright = u'2008-2019, %(AUTHOR)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/index.rst

@@ -13,18 +13,18 @@ visualization, and statistical analysis of MRI data.
 Highlights
 **********
 
-**DIPY 0.14.0** is now available. New features include:
-
-- RecoBundles: anatomically relevant segmentation of bundles
-- New super fast clustering algorithm: QuickBundlesX
-- New tracking algorithm: Particle Filtering Tracking.
-- New tracking algorithm: Probabilistic Residual Bootstrap Tracking.
-- Integration of the Streamlines API for reading, saving and processing tractograms.
-- Fiber ORientation Estimated using Continuous Axially Symmetric Tensors (Forecast).
-- New command line interfaces.
-- Deprecated fvtk (old visualization framework).
-- A range of new visualization improvements.
+**DIPY 0.15.0** is now available. New features include:
+
+- Updated RecoBundles for automatic anatomical bundle segmentation.
+- New Reconstruction Model: qtau-dMRI.
+- New command line interfaces (e.g. dipy_slr).
+- New continuous integration with AppVeyor CI.
+- Nibabel Streamlines API now used almost everywhere for better memory management.
+- Compatibility with Python 3.7.
+- Many tutorials added or updated (5 New).
 - Large documentation update.
+- Moved visualization module to a new library: FURY.
+- Closed 287 issues and merged 93 pull requests. 
 
 See :ref:`Older Highlights <old_highlights>`.
 
@@ -33,6 +33,7 @@ See :ref:`Older Highlights <old_highlights>`.
 Announcements
 *************
 
+- :ref:`DIPY 0.15 <release0.15>` released December 12, 2018.
 - :ref:`DIPY 0.14 <release0.14>` released May 1, 2018.
 - :ref:`DIPY 0.13 <release0.13>` released October 24, 2017.
 - :ref:`DIPY 0.12 <release0.12>` released June 26, 2017.