# Release notes for DIPY version 0.12

GitHub stats for 2016/02/21 - 2017/06/26 (tag: 0.11.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 48 authors contributed 1491 commits.

- Alexandre Gauvin

- Antonio Ossa

- Ariel Rokem

- Bago Amirbekian

- Bishakh Ghosh

- David Reagan

- Eleftherios Garyfallidis

- Etienne St-Onge

- Gabriel Girard

- Gregory R. Lee

- Jean-Christophe Houde

- Jon Haitz Legarreta

- Julio Villalon

- Kesshi Jordan

- Manu Tej Sharma

- Marc-Alexandre Côté

- Matthew Brett

- Matthieu Dumont

- Nil Goyette

- Omar Ocegueda Gonzalez

- Rafael Neto Henriques

- Ranveer Aggarwal

- Riddhish Bhalodia

- Rutger Fick

- Samuel St-Jean

- Serge Koudoro

- Shahnawaz Ahmed

- Sourav Singh

- Stephan Meesters

- Stonge Etienne

- Guillaume Theaud

- Tingyi Wanyan

- Tom Wright

- Vibhatha Abeykoon

- Yaroslav Halchenko

- Eric Peterson

- Sven Dorkenwald

- theaverageguy

We closed a total of 511 issues, 169 pull requests and 342 regular issues; this is the full list (generated with the script `tools/github_stats.py`):

Pull Requests (169):

- PR #1273: Release 0.12 doc fix

- PR #1272: small correction for debugging purpose on nlmeans

- PR #1269: Odf slicer

- PR #1271: Viz tut update

- PR #1268: Following up on #1243.

- PR #1223: local PCA using SVD

- PR #1270: Doc cleaning deprecation warning

- PR #1267: Adding a decorator for skipping test if openmp is not available

- PR #1090: Documentation for command line interfaces

- PR #1243: Better fvtk.viz error when no VTK installed

- PR #1263: Cast Streamline attrs to numpy ints, to avoid buffer mismatch.

- PR #1254: Automate script installation

- PR #1261: removing absolute path in tracking module

- PR #1255: Fix missing documentation content

- PR #1260: removing absolute path in reconst

- PR #1241: Csa and csd reconstruction workflow rebased

- PR #1250: DOC: Fix reconst_dki.py DKI example documentation typos.

- PR #1244: TEST: Decrease precision of tests for dki micro model prediction

- PR #1235: New hdf5 file format for saving PeaksAndMetrics objects

- PR #1231: TST: Reduce precision requirement for test of tortuosity estimation.

- PR #1233: Feature: Added environment override for dipy_home variable

- PR #1234: BUG: Fix non-ASCII characters in reconst_dki.py example.

- PR #1222: A lightweight UI for medical visualizations #5: 2D Circular Slider

- PR #1228: RF: Use cython imports instead of relying on extern

- PR #1227: BF: Use np.npy_intp instead of assuming long for ArraySequence attributes

- PR #1226: DKI Microstructural model

- PR #1229: RF: allow for scipy pre-release deprecations

- PR #1225: Add one more multi b-value data-set

- PR #1219: MRG:Data off dropbox

- PR #1221: NF: Check multi b-value

- PR #1212: Follow PEP8 in reconst (part 2)

- PR #1217: Use integer division in reconst_gqi.py

- PR #1205: A lightweight UI for medical visualizations #4: 2D Line Slider

- PR #1166: RF: Use the average sigma in the mask.

- PR #1216: Use integer division to avoid errors in indexing

- PR #1214: DOC: add a clarification note to simplify_warp_funcion_3d

- PR #1208: Follow PEP8 in reconst (part 1)

- PR #1206: Revert #1204, and add a filter to suppress warnings.

- PR #1196: MRG: Use dipy’s array comparisons for tests

- PR #1204: Suppress warnings regarding one-dimensional arrays changes in scipy 0.18

- PR #1199: A lightweight UI for medical visualizations #3: Changes to Event Handling

- PR #1202: Use integer division to avoid errors in indexing

- PR #1198: ENH: avoid log zero

- PR #1201: Fix out of bounds point not being classified OUTSIDEIMAGE (binary cla…

- PR #1115: Bayesian Tissue Classification

- PR #1052: Conda install

- PR #1183: A lightweight UI for medical visualizations #2: TextBox

- PR #1186: MRG: use newer wheelhouse for installs

- PR #1195: Make PeaksAndMetrics pickle-able

- PR #1194: Use assert_arrays_equal when needed.

- PR #1193: Deprecate the Accent colormap, in anticipation of changes in MPL 2.0

- PR #1140: A lightweight UI for medical visualizations #1: Button

- PR #1171: fix:dev: added numpy.int64 for my triangle array

- PR #1123: Add the mask workflow

- PR #1174: NF: added the repulsion 200 sphere.

- PR #1177: BF: fix interpolation call with Numpy 1.12

- PR #1162: Return S0 value for DTI fits

- PR #1147: add this fix for newer version of pytables.

- PR #1076: ENH: Add support for ArraySequence in length function

- PR #1050: ENH: expand OpenMP utilities and move from denspeed.pyx to dipy.utils

- PR #1082: Add documentation uploading script

- PR #1153: Athena mapmri

- PR #1159: TST - add tests for various affine matrices for local tracking

- PR #1157: Replace get_affine with affine and get_header with header.

- PR #1160: Add Shahnawaz to list of contributors.

- PR #1158: BF: closing matplotlib plots for each file while running the examples

- PR #1151: Define fmin() for Visual Studio

- PR #1149: Change DKI_signal to dki_signal

- PR #1137: Small fix to insure that fwDTI non-linear procedure does not crash

- PR #942: NF: Added support to colorize each line points individually

- PR #1141: Do not cover files related to benchmarks.

- PR #1098: Adding custom interactor for visualisation

- PR #1136: Update deprecated function.

- PR #1113: TST: Test for invariance of model_params to splitting of the data.

- PR #1134: Rebase of https://github.com/dipy/dipy/pull/993

- PR #1064: Faster dti odf

- PR #1114: flexible grid to streamline affine generation and pathlength function

- PR #1122: Add the reconst_dti workflow

- PR #1132: Update .travis.yml and README.md

- PR #1125: Intensity adjustment. Find a better upper bound for interpolating images.

- PR #1130: Minor corrections for showing surfaces

- PR #1092: Line-based target()

- PR #1129: Fix 1127

- PR #1034: Viz surfaces

- PR #1060: Fast computation of Cross Correlation metric

- PR #1124: Small fix in free water DTI model

- PR #1058: IVIM

- PR #1110: WIP : Ivim linear fitting

- PR #1120: Fix 1119

- PR #1075: Drop26

- PR #835: NF: Free water tensor model

- PR #1046: BF - peaks_from_model with nbr_processes <= 0

- PR #1049: MAINT: minor cython cleanup in align/vector_fields.pyx

- PR #1087: Base workflow enhancements + tests

- PR #1112: DOC: Math rendering issue in SFM gallery example.

- PR #1109: Changed default value of mni template

- PR #1106: Including MNI Template 2009c in Fetcher

- PR #1066: Adaptive Denoising

- PR #1091: Modifications for building docs with python3

- PR #1105: Import reload function from imp module explicitly for python3

- PR #1102: MRG: add pytables to travis-ci, Py35 full test run

- PR #1100: Fix for Python 3 in io.dpy

- PR #1094: Updates to FBC measures documentation

- PR #1059: Documentation to discourage misuse of GradientTable

- PR #1063: Fixes #1061 : Changed all S0 to 1.0

- PR #1089: BF: fix test error on Python 3

- PR #1079: Return a generator from orient_by_roi

- PR #1088: Restored the older implementation of nlmeans

- PR #1080: DOC: TensorModel.__init__ docstring.

- PR #828: Fiber to bundle coherence measures

- PR #1072: DOC: Added a coverage badge to README.rst

- PR #1025: PEP8: Fix pep8 in segment

- PR #1077: DOC: update fibernavigator link

- PR #1069: DOC: Small one – we need this additional line of white space to render.

- PR #1068: Renamed test_shore for consistency

- PR #1067: Generate b vectors using disperse_charges

- PR #1065: improve OMP parallelization with scheduling

- PR #1062: BF - fix CSD.predict to work with nd inputs.

- PR #1056: Remove tracking interfaces

- PR #1028: BF: Predict DKI with a volume of S0

- PR #1041: NF - Add PMF Threshold to Tractography

- PR #1039: Doc - fix definition of real_sph_harm functions

- PR #1019: MRG: fix heavy dependency check; no numpy for setup

- PR #1018: Fix: denspeed.pyx to give correct output for nlmeans

- PR #1035: Fix for fetcher files in Windows

- PR #974: Minor change in tools/github_stats.py

- PR #1021: Added warning for VTK not installed

- PR #1024: Documentation fix for reconst_dsid.py

- PR #981: Fixes #979 : No figures in DKI example - Add new line after figure

- PR #958: FIX: PEP8 in testing

- PR #1005: FIX: Use absolute imports in io

- PR #951: Contextual Enhancement update: fix SNR issue, fix reference

- PR #1015: Fix progressbar of fetcher

- PR #992: FIX: Update the import statements to use absolute import in core

- PR #1003: FIX: Change the import statements in direction

- PR #1004: FIX: Use absolute import in pkg_info

- PR #1006: FIX: Use absolute import in utils and scratch

- PR #1010: Absolute Imports in Viz

- PR #929: Fix PEP8 in data

- PR #941: BW: skimage.filter module name warning

- PR #976: Fix PEP8 in sims and remove unnecessary imports

- PR #956: FIX: PEP8 in reconst/test and reconst/benchmarks

- PR #955: FIX: PEP8 in external

- PR #952: FIX: PEP8 in tracking and tracking benchmarks/tests

- PR #982: FIX: relative imports in dipy/align

- PR #972: Fixes #901 : Added documentation for “step” in dti

- PR #971: Add progress bar feature to dipy.data.fetcher

- PR #989: copyright 2008-2016

- PR #977: Relative import fix in dipy/align

- PR #957: FIX: PEP8 in denoise

- PR #959: FIX: PEP8 in utils

- PR #967: Update index.rst correcting the date of release 0.11

- PR #954: FIX: PEP8 in direction

- PR #965: Fix typo

- PR #948: Fix PEP8 in boots

- PR #946: FIX: PEP8 for test_sumsqdiff and test_scalespace

- PR #964: FIX: PEP8 in test_imaffine

- PR #963: FIX: PEP8 in core

- PR #947: FIX: PEP8 for test files

- PR #897: PEP8

- PR #926: Fix PEP8 in fixes

- PR #937: BF : Clamping of the value of v in winding function

- PR #907: DOC: switch to using mathjax for maths

- PR #932: Fixes #931 : checks if nb_points=0

- PR #927: Fix PEP8 in io and remove duplicate definition in test_bvectxt.py

- PR #913: Fix pep8 in workflows

- PR #935: Setup: go on to version 0.12 development.

- PR #934: DOC: Update github stats for 0.11 as of today.

- PR #933: Updating release dates

Issues (342):

- #1273: Release 0.12 doc fix

- #1272: small correction for debugging purpose on nlmeans

- #1269: Odf slicer

- #1143: Slice through ODF fields

- #1271: Viz tut update

- #1246: WIP: Replace widget with ui components in example.

- #1268: Following up on #1243.

- #1223: local PCA using SVD

- #1265: Test failure on OSX in test_nlmeans_4d_3dsigma_and_threads

- #1270: Doc cleaning deprecation warning

- #1251: Slice through ODF fields - Rebased

- #1267: Adding a decorator for skipping test if openmp is not available

- #1090: Documentation for command line interfaces

- #1243: Better fvtk.viz error when no VTK installed

- #1238: Cryptic fvtk.viz error when no VTK installed

- #1242: DKI microstructure model tests still fail intermittenly

- #1252: Debug PR only - Odf slicer vtk tests (do not merge)

- #1263: Cast Streamline attrs to numpy ints, to avoid buffer mismatch.

- #1257: revamp piesno docstring

- #978: Use absolute import in align

- #1179: Automate workflow generation

- #1253: Automate script installation for workflows

- #1254: Automate script installation

- #1261: removing absolute path in tracking module

- #1001: Use absolute import in tracking

- #1255: Fix missing documentation content

- #1260: removing absolute path in reconst

- #999: Use absolute import in reconst

- #1258: Fix nlmeans indexing

- #369: Add TESTs for resample

- #1155: csa and csd reconstruction workflow

- #1000: Use absolute import in segment, testing and tests

- #1070: [Docs] Examples using deprecated function

- #711: Update api_changes.rst for interp_rbf

- #321: Median otsu figures in example don’t look good

- #994: Use absolute import in dipy/core

- #608: Customize at runtime the number of cores nlmeans is using

- #865: PEP8 in test_imwarp

- #591: Allow seed_from_mask to generate random seeds

- #518: TODO: aniso2iso module will be completely removed in version 0.10.

- #328: “incompatible” import of peaks_from_model in your recent publication

- #1241: Csa and csd reconstruction workflow rebased

- #1250: DOC: Fix reconst_dki.py DKI example documentation typos.

- #1244: TEST: Decrease precision of tests for dki micro model prediction

- #1235: New hdf5 file format for saving PeaksAndMetrics objects

- #1231: TST: Reduce precision requirement for test of tortuosity estimation.

- #1210: Switching branches in windows and pip install error

- #1209: Move data files out of dropbox => persistent URL

- #1233: Feature: Added environment override for dipy_home variable

- #1234: BUG: Fix non-ASCII characters in reconst_dki.py example.

- #1222: A lightweight UI for medical visualizations #5: 2D Circular Slider

- #1185: unable to use fvtk.show after ubuntu 16.10 install

- #1228: RF: Use cython imports instead of relying on extern

- #909: Inconsistent output for values_from_volume

- #1182: CSD vs CSA

- #1211: dipy.data.read_bundles_2_subjects doesn’t fetch data as expected

- #1227: BF: Use np.npy_intp instead of assuming long for ArraySequence attributes

- #1027: (DO NOT MERGE THIS PR) NF: DKI microstructural model

- #1226: DKI Microstructural model

- #1229: RF: allow for scipy pre-release deprecations

- #1225: Add one more multi b-value data-set

- #1219: MRG:Data off dropbox

- #1218: [Docs] Error while generating html

- #1221: NF: Check multi b-value

- #1212: Follow PEP8 in reconst (part 2)

- #1217: Use integer division in reconst_gqi.py

- #1205: A lightweight UI for medical visualizations #4: 2D Line Slider

- #1166: RF: Use the average sigma in the mask.

- #1216: Use integer division to avoid errors in indexing

- #1215: [Docs] Error while building examples: tracking_quick_start.py

- #1213: dipy.align.vector_fields.simplify_warp_function_3d: Wrong equation in docstring

- #1214: DOC: add a clarification note to simplify_warp_funcion_3d

- #1208: Follow PEP8 in reconst (part 1)

- #1206: Revert #1204, and add a filter to suppress warnings.

- #1196: MRG: Use dipy’s array comparisons for tests

- #1191: Test failures for cluster code with current numpy master

- #1207: Follow PEP8 in reconst

- #1204: Suppress warnings regarding one-dimensional arrays changes in scipy 0.18

- #1107: Dipy.align.reslice: either swallow the scipy warning or rework to avoid it

- #1199: A lightweight UI for medical visualizations #3: Changes to Event Handling

- #1200: [Docs] Error while generating docs

- #1202: Use integer division to avoid errors in indexing

- #1188: Colormap test errors for new matplotlib

- #1187: Negative integer powers error with numpy 1.12

- #1170: Importing vtk with dipy

- #1086: ENH: avoid calling log() on zero-valued elements in anisotropic_power

- #1198: ENH: avoid log zero

- #1201: Fix out of bounds point not being classified OUTSIDEIMAGE (binary cla…

- #1115: Bayesian Tissue Classification

- #1052: Conda install

- #1183: A lightweight UI for medical visualizations #2: TextBox

- #1173: TST: Test on Python 3.6

- #1186: MRG: use newer wheelhouse for installs

- #1190: Pickle error for Python 3.6 and test_peaksFromModelParallel

- #1195: Make PeaksAndMetrics pickle-able

- #1194: Use assert_arrays_equal when needed.

- #1193: Deprecate the Accent colormap, in anticipation of changes in MPL 2.0

- #1189: Np1.12

- #1140: A lightweight UI for medical visualizations #1: Button

- #1022: Fixes #720 : Auto generate ipython notebooks

- #1139: The shebang again! Python: bad interpreter: No such file or directory

- #1171: fix:dev: added numpy.int64 for my triangle array

- #1123: Add the mask workflow

- #1174: NF: added the repulsion 200 sphere.

- #1176: Dipy.tracking.local.interpolation.nearestneighbor_interpolate raises when used with Numpy 1.12

- #1177: BF: fix interpolation call with Numpy 1.12

- #1162: Return S0 value for DTI fits

- #1142: pytables version and streamlines_format.py example

- #1147: add this fix for newer version of pytables.

- #1076: ENH: Add support for ArraySequence in length function

- #1050: ENH: expand OpenMP utilities and move from denspeed.pyx to dipy.utils

- #1082: Add documentation uploading script

- #1153: Athena mapmri

- #1097: Added to quantize_evecs: multiprocessing and v

- #1159: TST - add tests for various affine matrices for local tracking

- #1163: WIP: Combined contour function with slicer to use affine

- #940: Drop python 2.6

- #1040: SFM example using deprecated code

- #1118: pip install dipy failing on my windows

- #1119: Buildbots failing with workflow merge

- #1127: Windows buildbot failures after ivim_linear merge

- #1128: Support for non linear denoise?

- #1138: A few broken builds

- #1148: Actual S0 for DTI data

- #1157: Replace get_affine with affine and get_header with header.

- #1160: Add Shahnawaz to list of contributors.

- #740: Improved mapmri implementation with laplacian regularization and new …

- #1045: Allow affine ‘shear’ tolerance in LocalTracking

- #1154: [Bug] connectivity matrix image in streamline_tools example

- #1158: BF: closing matplotlib plots for each file while running the examples

- #1151: Define fmin() for Visual Studio

- #1145: DKI_signal should be dki_signal in dipy.sims.voxel

- #1149: Change DKI_signal to dki_signal

- #1137: Small fix to insure that fwDTI non-linear procedure does not crash

- #827: Free Water Elimination DTI

- #942: NF: Added support to colorize each line points individually

- #1141: Do not cover files related to benchmarks.

- #1098: Adding custom interactor for visualisation

- #1136: Update deprecated function.

- #1113: TST: Test for invariance of model_params to splitting of the data.

- #1134: Rebase of https://github.com/dipy/dipy/pull/993

- #1064: Faster dti odf

- #1114: flexible grid to streamline affine generation and pathlength function

- #1122: Add the reconst_dti workflow

- #1132: Update .travis.yml and README.md

- #1051: ENH: use parallel processing in the cython code for CCMetric

- #993: FIX: Use absolute imports in testing,tests and segment files

- #673: WIP: Workflow for syn registration

- #859: [WIP] Suppress warnings in tests

- #983: PEP8 in sims #884

- #984: PEP8 in reconst #881

- #1009: Absolute Imports in Tracking

- #1036: Estimate S0 from data (DTI)

- #1125: Intensity adjustment. Find a better upper bound for interpolating images.

- #1130: Minor corrections for showing surfaces

- #1092: Line-based target()

- #1129: Fix 1127

- #1034: Viz surfaces

- #394: Update documentation for VTK and Anaconda

- #973: Minor change in tools/github_stats.py

- #1060: Fast computation of Cross Correlation metric

- #1124: Small fix in free water DTI model

- #1058: IVIM

- #1110: WIP : Ivim linear fitting

- #1120: Fix 1119

- #1121: Recons dti workflow

- #1083: nlmeans problem

- #1075: Drop26

- #835: NF: Free water tensor model

- #1046: BF - peaks_from_model with nbr_processes <= 0

- #1049: MAINT: minor cython cleanup in align/vector_fields.pyx

- #1087: Base workflow enhancements + tests

- #1112: DOC: Math rendering issue in SFM gallery example.

- #670: Tissue classification using MAP-MRF

- #332: A sample nipype interface for fit_tensor

- #1116: failing to build the docs: issue with io.BufferedIOBase

- #1109: Changed default value of mni template

- #1106: Including MNI Template 2009c in Fetcher

- #1066: Adaptive Denoising

- #351: Dipy.tracking.utils.target affine parameter is misleading

- #1091: Modifications for building docs with python3

- #912: Unable to build documentation with Python 3

- #1105: Import reload function from imp module explicitly for python3

- #1104: restore_dti.py example does not work in python3

- #1102: MRG: add pytables to travis-ci, Py35 full test run

- #1100: Fix for Python 3 in io.dpy

- #1103: BF: This raises a warning on line 367 otherwise.

- #1101: Test with optional dependencies (including pytables) on Python 3.

- #1094: Updates to FBC measures documentation

- #1059: Documentation to discourage misuse of GradientTable

- #1061: Inconsistency in specifying S0 values in multi_tensor and single_tensor

- #1063: Fixes #1061 : Changed all S0 to 1.0

- #1089: BF: fix test error on Python 3

- #1079: Return a generator from orient_by_roi

- #1088: Restored the older implementation of nlmeans

- #1080: DOC: TensorModel.__init__ docstring.

- #1085: Enhanced workflows

- #1081: mean_diffusivity from the reconst.dti module returns incorrect shape

- #1031: improvements for denoise/denspeed.pyx

- #828: Fiber to bundle coherence measures

- #1072: DOC: Added a coverage badge to README.rst

- #1071: report coverage and add a badge?

- #1038: BF: Should fix #1037

- #1078: Fetcher for ivim data, needs md5

- #953: FIX: PEP8 for segment

- #1025: PEP8: Fix pep8 in segment

- #883: PEP8 in segment

- #1077: DOC: update fibernavigator link

- #1069: DOC: Small one – we need this additional line of white space to render.

- #1068: Renamed test_shore for consistency

- #1067: Generate b vectors using disperse_charges

- #1011: Discrepancy with output of nlmeans.py

- #1055: WIP: Ivim implementation

- #1065: improve OMP parallelization with scheduling

- #1062: BF - fix CSD.predict to work with nd inputs.

- #1057: Workaround for https://github.com/dipy/dipy/issues/852

- #1037: tracking.interfaces imports SlowAdcOpdfModel, but it is not defined

- #1056: Remove tracking interfaces

- #813: Windows 64-bit error in segment.featurespeed.extract

- #1054: Remove tracking interfaces

- #1028: BF: Predict DKI with a volume of S0

- #1041: NF - Add PMF Threshold to Tractography

- #1039: Doc - fix definition of real_sph_harm functions

- #1019: MRG: fix heavy dependency check; no numpy for setup

- #1018: Fix: denspeed.pyx to give correct output for nlmeans

- #1043: DO NOT MERGE: Add a test of local tracking, using data from dipy.data.

- #899: SNR in contextual enhancement example

- #991: Documentation footer has 2008-2015 mentioned.

- #1008: [WIP] NF: Implementation of CHARMED model

- #1030: Fetcher files not found on Windows

- #1035: Fix for fetcher files in Windows

- #1016: viz.fvtk has no attribute ‘ren’

- #1033: Viz surfaces

- #1032: Merge pull request #1 from nipy/master

- #1029: Errors building Cython extensions on Python 3.5

- #974: Minor change in tools/github_stats.py

- #1002: Use absolute import in utils and scratch

- #1014: Progress bar works only for some data

- #1013: dipy.data.make_fetcher test fails with Python 3

- #1020: Documentation does not mention Scipy as a dependency for VTK widgets.

- #1023: display in dsi example is broken

- #1021: Added warning for VTK not installed

- #882: PEP8 in reconst tests/benchmarks

- #888: PEP8 in tracking benchmarks/tests

- #885: PEP8 in testing

- #902: fix typo

- #1024: Documentation fix for reconst_dsid.py

- #979: No figures in DKI example

- #981: Fixes #979 : No figures in DKI example - Add new line after figure

- #958: FIX: PEP8 in testing

- #1005: FIX: Use absolute imports in io

- #997: Use absolute import in io

- #675: Voxelwise stabilisation

- #951: Contextual Enhancement update: fix SNR issue, fix reference

- #1015: Fix progressbar of fetcher

- #1012: TST: install the dipy.data tests.

- #992: FIX: Update the import statements to use absolute import in core

- #1003: FIX: Change the import statements in direction

- #996: Use absolute import in dipy/direction

- #1004: FIX: Use absolute import in pkg_info

- #998: Use absolute import in dipy/pkg_info.py

- #1006: FIX: Use absolute import in utils and scratch

- #1010: Absolute Imports in Viz

- #1007: Use absolute import in viz

- #929: Fix PEP8 in data

- #874: PEP8 in data

- #980: Fix pep8 in reconst

- #1017: Fixes #1016 : Raises VTK not installed

- #877: PEP8 in external

- #887: PEP8 in tracking

- #941: BW: skimage.filter module name warning

- #976: Fix PEP8 in sims and remove unnecessary imports

- #884: PEP8 in sims

- #956: FIX: PEP8 in reconst/test and reconst/benchmarks

- #955: FIX: PEP8 in external

- #952: FIX: PEP8 in tracking and tracking benchmarks/tests

- #982: FIX: relative imports in dipy/align

- #972: Fixes #901 : Added documentation for “step” in dti

- #901: DTI step parameter not documented.

- #995: Use absolute import in dipy/data/__init__.py

- #344: Update citation page

- #971: Add progress bar feature to dipy.data.fetcher

- #970: Downloading data with dipy.data.fetcher does not show any progress bar

- #986: “pip3 install dipy” in Installation for python3

- #990: No figures in DKI example

- #989: copyright 2008-2016

- #988: doc/conf.py shows copyright 2008-2015. Should be 2016?

- #975: Use absolute import in imaffine, imwarp, metrics

- #517: TODO: Peaks to be removed from dipy.reconst in 0.10

- #977: Relative import fix in dipy/align

- #875: PEP8 in denoise

- #957: FIX: PEP8 in denoise

- #960: PEP8 in sims #884

- #961: PEP8 in reconst #880

- #962: PEP8 in reconst #881

- #889: PEP8 in utils

- #959: FIX: PEP8 in utils

- #866: PEP8 in test_metrics

- #867: PEP8 in test_parzenhist

- #868: PEP8 in test_scalespace

- #869: PEP8 in test_sumsqdiff

- #870: PEP8 in test_transforms

- #871: PEP8 in test_vector_fields

- #864: PEP8 in test_imaffine

- #967: Update index.rst correcting the date of release 0.11

- #862: PEP8 in test_crosscorr

- #873: PEP8 in core

- #831: ACT tracking example gives weird streamlines

- #876: PEP8 in direction

- #954: FIX: PEP8 in direction

- #965: Fix typo

- #968: Use relative instead of absolute import

- #948: Fix PEP8 in boots

- #872: PEP8 in boots

- #946: FIX: PEP8 for test_sumsqdiff and test_scalespace

- #964: FIX: PEP8 in test_imaffine

- #963: FIX: PEP8 in core

- #966: fix typo

- #947: FIX: PEP8 for test files

- #920: STYLE:PEP8 for test_imaffine

- #897: PEP8

- #950: PEP8 fixed in reconst/tests and reconst/benchmarks

- #949: Fixed Pep8 utils tracking testing denoise

- #926: Fix PEP8 in fixes

- #878: PEP8 in fixes

- #939: Fixed PEP8 in utils, denoise , tracking and testing

- #945: FIX: PEP8 in test_scalespace

- #937: BF : Clamping of the value of v in winding function

- #930: pep8 fix issue #896 - “continuation line over-indented for visual indent”

- #943: BF: Removed unused code in slicer

- #907: DOC: switch to using mathjax for maths

- #931: dipy/tracking/streamlinespeed set_number_of_points crash when nb_points=0

- #932: Fixes #931 : checks if nb_points=0

- #927: Fix PEP8 in io and remove duplicate definition in test_bvectxt.py

- #924: in dipy/io/tests/test_bvectxt.py function with same name is defined twice

- #879: PEP8 in io

- #913: Fix pep8 in workflows

- #891: PEP8 in workflows

- #938: PEP8 issues solved in utils, testing and denoise

- #935: Setup: go on to version 0.12 development.

- #934: DOC: Update github stats for 0.11 as of today.

- #933: Updating release dates