GitHub stats for 2013/12/24 - 2014/12/26 (tag: 0.7.0) The following 19 authors contributed 1176 commits. Andrew Lawrence Ariel Rokem Bago Amirbekian Demian Wassermann Eleftherios Garyfallidis Gabriel Girard Gregory R. Lee Jean-Christophe Houde Kesshi jordan Marc-Alexandre Cote Matthew Brett Matthias Ekman Matthieu Dumont Mauro Zucchelli Maxime Descoteaux Michael Paquette Omar Ocegueda Samuel St-Jean Stefan van der Walt We closed a total of 388 issues, 155 pull requests and 233 regular issues;
this is the full list (generated with the script
Pull Requests (155): PR #544: Refactor propspeed - updated PR #543: MRG: update to plot_2d fixes and tests PR #537: NF: add requirements.txt file PR #534: BF: removed ftmp variable PR #536: Update Changelog PR #535: Happy New Year PR! PR #531: BF: extend pip timeout to reduce install failures PR #527: Remove npymath library from cython extensions PR #528: MRG: move conditional compiling to C PR #530: BF: work round ugly MSVC manifest bug PR #529: MRG: a couple of small cleanup fixes PR #526: Readme.rst and info.py update about the license PR #525: Added shore gpl warning in the readme PR #524: Replaced DiPy with DIPY in readme.rst and info.py PR #523: RF: copy includes list for extensions PR #522: DOC: Web-site release notes, and some updates on front page. PR #521: Life bots PR #520: Relaxing precision for win32 PR #519: Christmas PR! Correcting typos, linking and language for max odf tracking PR #513: BF + TST: Reinstated eig_from_lo_tri PR #508: Tests for reslicing PR #515: TST: Increasing testing on life. PR #516: TST: Reduce sensitivity on these tests. PR #495: NF - Deterministic Maximum Direction Getter PR #514: Website update PR #510: BF: another fvtk 5 to 6 incompatibility PR #509: DOC: Small fixes in documentation. PR #497: New sphere for ODF reconstruction PR #460: Sparse Fascicle Model PR #499: DOC: Warn about the GPL license of SHORE. PR #491: RF - Make peaks_from_model part of dipy.direction PR #501: TST: Test for both data with and w/0 b0. PR #507: BF - use different sort method to avoid mergsort for older numpy. PR #504: Bug fix float overflow in estimate_sigma PR #494: Fix round PR #503: Fixed compatibility issues between vtk 5 and 6 PR #498: DTI min_signal PR #471: Use importlib instead of __import__ PR #419: LiFE PR #489: Fix diffeomorphic registration test failures PR #484: Clear tabs from examples for website PR #490: DOC: corrected typos in the tracking PR PR #341: Traco Redesign PR #483: NF: Find the closest vertex on a sphere for an input vector. PR #488: BF: fix travis version setting PR #485: RF: deleted unused files PR #482: Skipping tests for different versions of Scipy for optimize.py PR #480: Enhance SLR to allow for series of registrations PR #479: Report on coverage for old scipy. PR #481: BF - make examples was confusing files with similar names, fixed PR #476: Fix optimize defaults for older scipy versions for L-BFGS-B PR #478: TST: Increase the timeout on the Travis pip install PR #477: MAINT+TST: update minimum nibabel dependency PR #474: RF: switch travis tests to use virtualenvs PR #473: TST: Make Travis provide verbose test outputs. PR #472: ENH: GradientTable now calculates qvalues PR #469: Fix evolution save win32 PR #463: DOC: update RESTORE tutorial to use new noise estimation technique PR #466: BF: cannot quote command for Windows PR #465: BF: increased SCIPY version definition flag to 0.12 PR #462: BF: fix writing history to file in Python 3 PR #433: Added local variance estimation PR #458: DOC: docstring fixes in dipy/align/crosscorr.pyx PR #448: BF: fix link to npy_math function PR #447: BF: supposed fix for the gh-439, but still unable to reproduce OP. PR #443: Fix buildbots errors introduced with the registration module PR #456: MRG: relax threshold for failing test + cleanup PR #454: DOC: fix docstring for compile-time checker PR #453: BF: refactor conditional compiling again PR #446: Streamline-based Linear Registration PR #445: NF: generate config.pxi file with Cython DEF vars PR #440: DOC - add info on how to change default tempdir (multiprocessing). PR #431: Change the writeable flag back to its original state when finished. PR #408: Symmetric diffeomorphic non-linear registration PR #438: Missing a blank line in examples/tracking_quick_start.py PR #405: fixed frozen windows executable issue PR #418: RF: move script running code into own module PR #437: Update Cython download URL PR #435: BF: replaced non-ascii character in dipy.reconst.dti line 956 PR #434: DOC: References for the DTI ODF calculation. PR #430: Revert “Support read-only numpy array.” PR #427: Support read-only numpy array. PR #421: Fix nans in gfa PR #422: BF: Use the short version to verify scipy version. PR #415: RF - move around some of the predict stuff PR #420: Rename README.txt to README.rst PR #413: Faster spherical harmonics PR #416: Removed memory_leak unittest in test_strealine.py PR #417: Fix streamlinespeed tests PR #411: Fix memory leak in cython functions length and set_number_of_points PR #409: minor corrections to pipe function PR #396: TST : this is not exactly equal on some platforms. PR #407: BF: fixed problem with NANs in odfdeconv PR #406: Revert “Merge pull request #346 from omarocegueda/syn_registration” PR #402: Fix AE test error in test_peak_directions_thorough PR #403: Added mask shape check in tenfit PR #346: Symmetric diffeomorphic non-linear registration PR #401: BF: fix skiptest invocation for missing mpl PR #340: CSD fit issue PR #397: BF: fix import statement for get_cmap PR #393: RF: update Cython dependency PR #382: Cythonized version of streamlines’ resample() and length() functions. PR #386: DOC: Small fix in the xval example. PR #335: Xval PR #352: Fix utils docs and affine PR #384: odf_sh_sharpening function fix and new test PR #374: MRG: bumpy numpy requirement to 1.5 / compat fixes PR #380: DOC: Update a few Dipy links to link to the correct repo PR #378: Fvtk cleanup PR #379: fixed typos in shm.py PR #339: FVTK small improvement: Arbitrary matplotlib colormaps can be used to color spherical functions PR #373: Fixed discrepancies between doc and code PR #371: RF: don’t use -fopenmp flag if it doesn’t work PR #372: BF: set integer type for crossplatform compilation PR #337: Piesno PR #370: Tone down the front page a bit. PR #364: Add the mode param for border management. PR #368: New banner for website PR #367: MRG: refactor API generation for sharing PR #363: RF: make cvxopt optional for tests PR #362: Changes to fix issue #361: matrix sizing in tracking.utils.connectivity_matrix PR #360: Added missing :math:` sign PR #355: DOC: Updated API change document to add target function change PR #357: Changed the logo to full black as the one that I sent as suggestion for HBM and ISMRM PR #356: Auto-generate API docs PR #349: Added api changes file to track breaks of backwards compatibility PR #348: Website update PR #347: DOC: Updating citations PR #345: TST: Make travis look at test coverage. PR #338: Add positivity constraint on the propagator PR #334: Fix vec2vec PR #324: Constrained optimisation for SHORE to set E(0)=1 when the CVXOPT package is available PR #320: Denoising images using non-local means PR #331: DOC: correct number of seeds in streamline_tools example PR #326: Fix brain extraction example PR #327: add small and big delta PR #323: Shore pdf grid speed improvement PR #319: DOC: Updated the highlights to promote the release and the upcoming paper PR #318: Corrected some rendering problems with the installation instructions PR #317: BF: more problems with path quoting in windows PR #316: MRG: more fixes for windows script tests PR #315: BF: EuDX odf_vertices param has no default value PR #305: DOC: Some more details in installation instructions. PR #314: BF - callable response does not work PR #311: Bf seeds from mask PR #309: MRG: Windows test fixes PR #308: typos + pep stuf PR #303: BF: try and fix nibabel setup requirement PR #304: Update README.txt PR #302: Time for 0.8.0.dev! PR #299: BF: Put back utils.length. PR #301: Updated info.py and copyright year PR #300: Bf fetcher bug on windows PR #298: TST - rework tests so that we do not need to download any data PR #290: DOC: Started generating 0.7 release notes. Issues (233): #544: Refactor propspeed - updated #540: MRG: refactor propspeed #542: TST: Testing regtools #543: MRG: update to plot_2d fixes and tests #541: BUG: plot_2d_diffeomorphic_map #439: ValueError in RESTORE #538: WIP: TEST: relaxed precision #449: local variable ‘ftmp’ referenced before assignment #537: NF: add requirements.txt file #534: BF: removed ftmp variable #536: Update Changelog #535: Happy New Year PR! #512: reconst.dti.eig_from_lo_tri #467: Optimize failure on Windows #464: Diffeomorphic registration test failures on PPC #531: BF: extend pip timeout to reduce install failures #527: Remove npymath library from cython extensions #528: MRG: move conditional compiling to C #530: BF: work round ugly MSVC manifest bug #529: MRG: a couple of small cleanup fixes #526: Readme.rst and info.py update about the license #525: Added shore gpl warning in the readme #524: Replaced DiPy with DIPY in readme.rst and info.py #523: RF: copy includes list for extensions #522: DOC: Web-site release notes, and some updates on front page. #521: Life bots #520: Relaxing precision for win32 #519: Christmas PR! Correcting typos, linking and language for max odf tracking #513: BF + TST: Reinstated eig_from_lo_tri #508: Tests for reslicing #515: TST: Increasing testing on life. #516: TST: Reduce sensitivity on these tests. #495: NF - Deterministic Maximum Direction Getter #514: Website update #510: BF: another fvtk 5 to 6 incompatibility #511: Error estimating tensors on hcp dataset #509: DOC: Small fixes in documentation. #497: New sphere for ODF reconstruction #460: Sparse Fascicle Model #499: DOC: Warn about the GPL license of SHORE. #491: RF - Make peaks_from_model part of dipy.direction #501: TST: Test for both data with and w/0 b0. #507: BF - use different sort method to avoid mergsort for older numpy. #505: stable/wheezy debian – ar.argsort(kind=’mergesort’) causes TypeError: requested sort not available for type ( #506: RF: Use integer datatype for unique_rows sorting. #504: Bug fix float overflow in estimate_sigma #399: Multiprocessing runtime error in Windows 64 bit #383: typo in multi tensor fit example #350: typo in SNR example #424: test more python versions with travis #493: BF - older C compilers do not have round in math.h, using dpy_math instead #494: Fix round #503: Fixed compatibility issues between vtk 5 and 6 #500: SHORE hyp2F1 #502: Fix record vtk6 #498: DTI min_signal #496: Revert “BF: supposed fix for the gh-439, but still unable to reproduce O… #492: TST - new DTI test to help develop min_signal handling #471: Use importlib instead of __import__ #419: LiFE #489: Fix diffeomorphic registration test failures #484: Clear tabs from examples for website #490: DOC: corrected typos in the tracking PR #341: Traco Redesign #410: Faster spherical harmonics implementation #483: NF: Find the closest vertex on a sphere for an input vector. #487: Travis Problem #488: BF: fix travis version setting #485: RF: deleted unused files #486: cvxopt is gpl licensed #482: Skipping tests for different versions of Scipy for optimize.py #480: Enhance SLR to allow for series of registrations #479: Report on coverage for old scipy. #481: BF - make examples was confusing files with similar names, fixed #428: WIP: refactor travis building #429: WIP: Refactor travising #476: Fix optimize defaults for older scipy versions for L-BFGS-B #478: TST: Increase the timeout on the Travis pip install #477: MAINT+TST: update minimum nibabel dependency #475: Does the optimizer still need tmp_files? #474: RF: switch travis tests to use virtualenvs #473: TST: Make Travis provide verbose test outputs. #470: Enhance SLR with applying series of transformations and fix optimize bug for parameter missing in old scipy versions #472: ENH: GradientTable now calculates qvalues #469: Fix evolution save win32 #463: DOC: update RESTORE tutorial to use new noise estimation technique #466: BF: cannot quote command for Windows #461: Buildbot failures with missing ‘nit’ key in dipy.core.optimize #465: BF: increased SCIPY version definition flag to 0.12 #462: BF: fix writing history to file in Python 3 #433: Added local variance estimation #432: auto estimate the standard deviation globally for nlmeans #451: Warning for DTI normalization #458: DOC: docstring fixes in dipy/align/crosscorr.pyx #448: BF: fix link to npy_math function #447: BF: supposed fix for the gh-439, but still unable to reproduce OP. #443: Fix buildbots errors introduced with the registration module #456: MRG: relax threshold for failing test + cleanup #455: Test failure on master #454: DOC: fix docstring for compile-time checker #450: Find if replacing matrix44 from streamlinear with compose_matrix from dipy.core.geometry is a good idea #453: BF: refactor conditional compiling again #446: Streamline-based Linear Registration #452: Replace raise by auto normalization when creating a gradient table with un-normalized bvecs. #398: assert AE < 2. failure in test_peak_directions_thorough #444: heads up - MKL error in parallel mode #445: NF: generate config.pxi file with Cython DEF vars #440: DOC - add info on how to change default tempdir (multiprocessing). #431: Change the writeable flag back to its original state when finished. #408: Symmetric diffeomorphic non-linear registration #333: Bundle alignment #438: Missing a blank line in examples/tracking_quick_start.py #426: nlmeans_3d breaks with mask=None #405: fixed frozen windows executable issue #418: RF: move script running code into own module #437: Update Cython download URL #435: BF: replaced non-ascii character in dipy.reconst.dti line 956 #434: DOC: References for the DTI ODF calculation. #425: NF added class to save streamlines in vtk format #430: Revert “Support read-only numpy array.” #427: Support read-only numpy array. #421: Fix nans in gfa #422: BF: Use the short version to verify scipy version. #415: RF - move around some of the predict stuff #420: Rename README.txt to README.rst #413: Faster spherical harmonics #416: Removed memory_leak unittest in test_strealine.py #417: Fix streamlinespeed tests #411: Fix memory leak in cython functions length and set_number_of_points #412: Use simple multiplication instead exponentiation and pow #409: minor corrections to pipe function #396: TST : this is not exactly equal on some platforms. #407: BF: fixed problem with NANs in odfdeconv #406: Revert “Merge pull request #346 from omarocegueda/syn_registration” #402: Fix AE test error in test_peak_directions_thorough #403: Added mask shape check in tenfit #346: Symmetric diffeomorphic non-linear registration #401: BF: fix skiptest invocation for missing mpl #340: CSD fit issue #397: BF: fix import statement for get_cmap #393: RF: update Cython dependency #391: memory usage: 16GB wasn’t sufficient #382: Cythonized version of streamlines’ resample() and length() functions. #386: DOC: Small fix in the xval example. #385: cross_validation example doesn’t render properly #335: Xval #352: Fix utils docs and affine #384: odf_sh_sharpening function fix and new test #374: MRG: bumpy numpy requirement to 1.5 / compat fixes #381: Bago fix utils docs and affine #380: DOC: Update a few Dipy links to link to the correct repo #378: Fvtk cleanup #379: fixed typos in shm.py #376: BF: Adjust the dimensionality of the peak_values, if provided. #377: Demianw fvtk colormap #339: FVTK small improvement: Arbitrary matplotlib colormaps can be used to color spherical functions #373: Fixed discrepancies between doc and code #371: RF: don’t use -fopenmp flag if it doesn’t work #372: BF: set integer type for crossplatform compilation #337: Piesno #370: Tone down the front page a bit. #364: Add the mode param for border management. #368: New banner for website #367: MRG: refactor API generation for sharing #359: cvxopt dependency #363: RF: make cvxopt optional for tests #361: Matrix size wrong for tracking.utils.connectivity_matrix #362: Changes to fix issue #361: matrix sizing in tracking.utils.connectivity_matrix #360: Added missing ` sign #358: typo in doc #355: DOC: Updated API change document to add target function change #357: Changed the logo to full black as the one that I sent as suggestion for HBM and ISMRM #356: Auto-generate API docs #349: Added api changes file to track breaks of backwards compatibility #348: Website update #347: DOC: Updating citations #345: TST: Make travis look at test coverage. #338: Add positivity constraint on the propagator #334: Fix vec2vec #343: Please Ignore this PR! #324: Constrained optimisation for SHORE to set E(0)=1 when the CVXOPT package is available #277: WIP: PIESNO framework for estimating the underlying std of the gaussian distribution #336: Demianw shore e0 constrained #235: WIP: Cross-validation #329: WIP: Fix vec2vec #320: Denoising images using non-local means #331: DOC: correct number of seeds in streamline_tools example #330: DOC: number of seeds per voxel, inconsistent documentation? #326: Fix brain extraction example #327: add small and big delta #323: Shore pdf grid speed improvement #319: DOC: Updated the highlights to promote the release and the upcoming paper #318: Corrected some rendering problems with the installation instructions #317: BF: more problems with path quoting in windows #316: MRG: more fixes for windows script tests #315: BF: EuDX odf_vertices param has no default value #312: Sphere and default used through the code #305: DOC: Some more details in installation instructions. #314: BF - callable response does not work #16: quickie: ‘from raw data to tractographies’ documentation implies dipy can’t do anything with nonisotropic voxel sizes #311: Bf seeds from mask #307: Streamline_tools example stops working when I change density from 1 to 2 #241: Wrong normalization in peaks_from_model #248: Clarify dsi example #220: Add ndindex to peaks_from_model #253: Parallel peaksFromModel timing out on buildbot #256: writing data to /tmp peaks_from_model #278: tenmodel.bvec, not existing anymore? #282: fvtk documentation is incomprehensible #228: buildbot error in mask.py #197: DOC: some docstrings are not rendered correctly #181: OPT: Change dipy.core.sphere_stats.random_uniform_on_sphere #177: Extension test in dipy_fit_tensor seems brittle #171: Fix auto_attrs #31: Plotting in test suite #42: RuntimeWarning in dti.py #43: Problems with edges and faces in create_half_unit_sphere #53: Is ravel_multi_index a new thing? #64: Fix examples that rely on old API and removed data-sets #67: viz.projections.sph_projection is broken #92: dti.fa division by 0 warning in tests #306: Tests fail after windows 32 bit installation and running import dipy; dipy.test() #310: Windows test failure for tracking test_rmi #309: MRG: Windows test fixes #308: typos + pep stuf #303: BF: try and fix nibabel setup requirement #304: Update README.txt #302: Time for 0.8.0.dev! #299: BF: Put back utils.length. #301: Updated info.py and copyright year #300: Bf fetcher bug on windows #298: TST - rework tests so that we do not need to download any data #290: DOC: Started generating 0.7 release notes.Release notes for DIPY version 0.8
tools/github_stats.py):