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Merge tag '0.15.0' into debian
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Release 0.15

* tag '0.15.0': (570 commits)
  bump version to 0.15.0
  typo
  adress ariel comment
  highlight update
  update copyright date
  update changelog
  update description
  update 1 author
  update information
  remove default
  update affine
  fix tests
  use load_nifiti
  normalize snr workflow
  normalize positional args name
  pep8
  typo + pep8
  replace Nifti1Image by save_nifti
  replace Nifti1Image by save_nifti
  fix typo
  ...
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yarikoptic committed Dec 23, 2018
2 parents af2aef8 + 98fa5b8 commit f51d359
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29 changes: 29 additions & 0 deletions .codecov.yml
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@@ -0,0 +1,29 @@
comment:
layout: "reach, diff, files"
behavior: default
require_changes: false # if true: only post the comment if coverage changes
require_base: no # [yes :: must have a base report to post]
require_head: yes # [yes :: must have a head report to post]
branches: null

ignore:
- "*/benchmarks/*"
- "setup.py"
- "*/setup.py"
- "*/tests/*"
- "*/fixes/*"
- "*/external/*"

coverage:
status:
project:
default:
# Drops on the order 0.01% are typical even when no change occurs
# Having this threshold set a little higher (0.1%) than that makes it
# a little more tolerant to fluctuations
target: auto
threshold: 0.1%
patch:
default:
target: auto
threshold: 0.1%
3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -32,4 +32,5 @@ __config__.py
.buildbot.patch
.eggs/
dipy/.idea/
.idea/
.idea
.vscode
12 changes: 12 additions & 0 deletions .mailmap
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Expand Up @@ -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>
Expand Down Expand Up @@ -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>
Expand All @@ -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>
24 changes: 24 additions & 0 deletions .pep8speaks.yml
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@@ -0,0 +1,24 @@
# File : .pep8speaks.yml

message: # Customize the comment made by the bot
opened: # Messages when a new PR is submitted
header: "Hello @{name}, Thank you for submitting the Pull Request !"
# The keyword {name} is converted into the author's username
footer: "Do see the [DIPY coding Style guideline](https://github.com/nipy/dipy/blob/master/doc/devel/coding_style_guideline.rst)"
# The messages can be written as they would over GitHub
updated: # Messages when new commits are added to the PR
header: "Hello @{name}, Thank you for updating !"
footer: "" # Why to comment the link to the style guide everytime? :)
no_errors: "Cheers ! There are no PEP8 issues in this Pull Request. :beers: "

scanner:
diff_only: True # If True, errors caused by only the patch are shown

pycodestyle:
max-line-length: 80 # Default is 79 in PEP8
# ignore: # Errors and warnings to ignore
# - W391
# - E203

only_mention_files_with_errors: True # If False, a separate status comment for each file is made.
descending_issues_order: False # If True, PEP8 issues in message will be displayed in descending order of line numbers in the file
14 changes: 12 additions & 2 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -27,15 +27,20 @@ python:
- 3.4
- 3.5
- 3.6
# - "3.7" # TODO: Re-enable after https://github.com/travis-ci/travis-ci/issues/9815 is fixed

matrix:
include:
# TODO: Disable the local workaround
- python: 3.7
dist: xenial
sudo: true
- python: 2.7
# To test minimum dependencies
- python: 2.7
env:
# Check these values against requirements.txt and dipy/info.py
- DEPENDS="cython==0.25.1 numpy==1.7.1 scipy==0.9.0 nibabel==2.1.0 h5py==2.4.0"
- DEPENDS="cython==0.25.1 numpy==1.7.1 scipy==0.9.0 nibabel==2.3.0 h5py==2.4.0"
- python: 2.7
env:
- DEPENDS="$DEPENDS scikit_learn"
Expand All @@ -53,7 +58,7 @@ matrix:
- LIBGL_ALWAYS_INDIRECT=y
- VENV_ARGS="--system-site-packages --python=/usr/bin/python2.7"
- TEST_WITH_XVFB=true
- DEPENDS="$DEPENDS scikit_learn"
- DEPENDS="$DEPENDS scikit_learn fury"

- python: 2.7
env:
Expand All @@ -74,6 +79,10 @@ matrix:
# Check against latest available pre-release version of all packages
env:
- USE_PRE=1
allow_failures:
- python: 3.5
env:
- USE_PRE=1

before_install:
- PIPI="pip install $EXTRA_PIP_FLAGS"
Expand Down Expand Up @@ -125,6 +134,7 @@ script:
- 'echo "backend : agg" > matplotlibrc'
- if [ "${COVERAGE}" == "1" ]; then
cp ../.coveragerc .;
cp ../.codecov.yml .;
COVER_ARGS="--with-coverage --cover-package dipy";
fi
- nosetests --with-doctest --verbose $COVER_ARGS dipy
Expand Down
105 changes: 82 additions & 23 deletions AUTHOR
Original file line number Diff line number Diff line change
@@ -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>
13 changes: 13 additions & 0 deletions Changelog
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 2 additions & 2 deletions ISSUE_TEMPLATE.md
Original file line number Diff line number Diff line change
Expand Up @@ -12,10 +12,10 @@
- [ ] Operating system and version (run `python -c "import platform; print(platform.platform())"`)
- [ ] Python version (run `python -c "import sys; print("Python", sys.version)"`)
- [ ] dipy version (run `python -c "import dipy; print(dipy.__version__)"`)
- [ ] dependency version (numpy, scipy, nibabel, h5py, cvxpy, vtk)
- [ ] dependency version (numpy, scipy, nibabel, h5py, cvxpy, fury)
* import numpy; print("NumPy", numpy.__version__)
* import scipy; print("SciPy", scipy.__version__)
* import nibabel; print("Nibabel", nibabel.__version__)
* import h5py; print("H5py", h5py.__version__)
* import cvxpy; print("Cvxpy", cvxpy.__version__)
* import vtk; print(vtk.vtkVersion.GetVTKSourceVersion())
* import fury; print("fury", fury.__version__)
2 changes: 1 addition & 1 deletion LICENSE
Original file line number Diff line number Diff line change
@@ -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
Expand Down
19 changes: 15 additions & 4 deletions README.rst
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Expand Up @@ -23,7 +23,10 @@
.. image:: https://img.shields.io/badge/License-BSD%203--Clause-blue.svg
:target: https://github.com/nipy/dipy/blob/master/LICENSE

DIPY is a python toolbox for analysis of MR diffusion imaging.
.. image:: https://ci.appveyor.com/api/projects/status/github/nipy/dipy?branch=master&svg=true
:target: https://ci.appveyor.com/project/nipy/dipy

DIPY [DIPYREF]_ is a python library for analysis of MR diffusion imaging.

DIPY is for research only; please do not use results from DIPY for
clinical decisions.
Expand All @@ -40,7 +43,7 @@ Please see the developers' list at
https://mail.python.org/mailman/listinfo/neuroimaging

Please see the users' forum at
https://neurostars.org
https://neurostars.org/tags/dipy

Please join the gitter chatroom `here <https://gitter.im/nipy/dipy>`_.

Expand All @@ -67,10 +70,10 @@ DIPY can be installed using `pip`::

or using `conda`::

conda install -c conda-forge dipy vtk
conda install -c conda-forge dipy

For detailed installation instructions, including instructions for installing
from source, please read our `documentation <http://nipy.org/dipy/installation.html>`_.
from source, please read our `installation documentation <http://nipy.org/dipy/installation.html>`_.


License
Expand All @@ -83,3 +86,11 @@ Contributing
============

We welcome contributions from the community. Please read our `Contributing guidelines <https://github.com/nipy/dipy/blob/master/CONTRIBUTING.md>`_.

Reference
=========

.. [DIPYREF] E. Garyfallidis, M. Brett, B. Amirbekian, A. Rokem,
S. Van Der Walt, M. Descoteaux, I. Nimmo-Smith and DIPY contributors,
"DIPY, a library for the analysis of diffusion MRI data",
Frontiers in Neuroinformatics, vol. 8, p. 8, Frontiers, 2014.
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