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REL: 2.3.1#667

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Oct 16, 2018

Commits

Commits on Nov 3, 2017

• RF: moved all the functionality from nib-ls under nibabel.cmdline

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• ENH: added a skeleton for nib-diff command

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Commits on Nov 6, 2017

• TODO1 attempt 1: processed data type, data shape, and data offset of two different headers

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Commits on Nov 16, 2017

• tweaked to remove AnalyzeHeader but currently still has problems

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Commits on Nov 17, 2017

• added nib-diff to setup.py

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• first attempt at nib-diff that doesnt work

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• removed incorrectly committed changes

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• BK: stab at the test_dict_diff

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Commits on Nov 28, 2017

• first attempt at diff_dicts method and diff testing file

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• Merge branch 'nf-nib-diff' of https://github.com/yarikoptic/nibabel into nf-nib-diff

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Commits on Nov 30, 2017

• tried something else with header fields

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• latest attempt: restructured diff_dicts() method, troubleshooting ensuing errors

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Commits on Dec 1, 2017

• corrected misplacement of cmdline files and latest attempt at diff_dicts method

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• progress! tweaked bugs, corrected rookie mistakes like cmdline placement, implemented yarik suggestions

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Commits on Dec 2, 2017

• got rid of proc file and function works at a basic level

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Commits on Dec 3, 2017

• tweaked diff_dicts to be compatible with tests

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Commits on Dec 9, 2017

• got rid of None, troubleshot tests

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Commits on Dec 15, 2017

• introduced hypothesis to use for testing with pretty sexy results

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Commits on Dec 16, 2017

• noted hypothesis need for tests, refactored diff_dicts name

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Commits on Dec 18, 2017

• attempt at TODO#2: allowing specification of header fields

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Commits on Dec 21, 2017

• now functional for several header files.

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Commits on Dec 23, 2017

• tweak to make hypothesis work with a list, but problem above has not been addressed

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Commits on Dec 24, 2017

• tweaked names and code as suggested!

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Commits on Dec 27, 2017

• bug fix

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Commits on Jan 5, 2018

• cosmetic tweaks

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Commits on Jan 7, 2018

• cleaned up code

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Commits on Jan 13, 2018

• promoted generic programming and got test to work again

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• tried to clean code but couldnt get comprehension going

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Commits on Jan 15, 2018

• comment and docstring

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Commits on Jan 21, 2018

• added options for text, json, yaml but still have to implement

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Commits on Feb 3, 2018

• work in progress with all outputs

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Commits on Mar 14, 2018

• simplified code but now bizarrely doesnt run with two files

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Commits on Mar 16, 2018

• beautified text output, next up json and yaml

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Commits on Mar 17, 2018

• modified the tests for the new diff_values

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Commits on Mar 18, 2018

• commenting out json and yaml, cosmetic mod to ls.py

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Commits on Mar 26, 2018

• BF: all those flags are just boolean flags and no need to repeat their identical names in dest

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Commits on Mar 29, 2018

• progress towards table formatting

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• table now works and looks p good

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• slight tweak to table formatting

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Commits on Apr 4, 2018

• very inefficient but successfully removed dtype when its identical

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Commits on Apr 5, 2018

• removed extra blank line lol

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• boosting coverage

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• Merge remote-tracking branch 'nibabel/master' into nf-nib-diff

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Commits on Apr 12, 2018

• data comparison function added

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Commits on Apr 24, 2018

• implemented test-nib-diff

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Commits on Apr 25, 2018

• added another test

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• changed travis appveyor utils per test errors

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Commits on Apr 26, 2018

• test files

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• wasnt included in last commit by accident

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• maybe this will work instead

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• maybe this will work instead

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Commits on May 5, 2018

• test fixed

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• Merge branch 'nf-nib-diff' of https://github.com/yarikoptic/nibabel into nf-nib-diff

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Commits on May 6, 2018

• fixed to be more generic

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Commits on May 24, 2018

• fixed file name issue in nib diff

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• fixed changes as yarik requested

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Commits on May 31, 2018

• fixed problems noted by Travis CI

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• building in difflib to see whats going on

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Commits on Jun 3, 2018

• Merge branch 'master' into nf-nib-diff

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Commits on Jun 12, 2018

• MAINT: 2.4.0-dev

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• Merge branch 'maint/2.3.x' into HEAD

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• DOC: Update changelog with release date

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Commits on Jun 26, 2018

• latest attempt at compliance changes dict to list

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• Merge branch 'nf-nib-diff' of https://github.com/yarikoptic/nibabel into nf-nib-diff

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Commits on Jun 27, 2018

• Remove unrelated to PR difference

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• RF+BF: report that diff if any header of data differs, return dict of diffs

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Commits on Jun 28, 2018

• combined into one line

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Commits on Jul 4, 2018

• new structure, names, tests

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Commits on Jul 5, 2018

• hypothesis: all my problems were due to that one test

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• whoops missed this

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Commits on Jul 9, 2018

• Fix in coordinate_systems tutorial

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• Merge pull request #646 from nipy/coordinate_systems_blooper

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Commits on Jul 11, 2018

• i think im going to cry. code cleaned and made more pythonic

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• added and fixed tests

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• fixing up appveyor and travis problems

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Commits on Jul 12, 2018

• fixed a fringe use case

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• style tweak for travis

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• BF: deterministic order of slice_time deduction, warning if multiple match

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• DOC: minor typo

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Commits on Jul 13, 2018

• ENH(TST): basic test for consistent choice of slice_code in case of multiple available

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Commits on Jul 16, 2018

• removed duplication, made things more generic

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Commits on Jul 17, 2018

• moved functionality outside to test and increase coverage

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Commits on Jul 18, 2018

• RF+NF: Use OrderedDict and OrderedSet in Recoder

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• ENH(TST): test that we issue a warning upon multiple matches

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Commits on Jul 19, 2018

• TEST: Ensure warning isn't suppressed

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Commits on Jul 23, 2018

• Merge pull request #647 from yarikoptic/bf-sliceorder

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Commits on Jul 24, 2018

• boosting coverage by testing main

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Commits on Jul 27, 2018

• main test corrected for max coverage

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• FIX: Allow tr=0 in mghformat

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• FIX: Better messages

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• imported StringIO from six instead of io

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• added a test for cmdline function

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• Merge pull request #653 from larsoner/tr

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Commits on Jul 28, 2018

• changes per Yariks comments!

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Commits on Aug 1, 2018

• Replace genfromtxt with loadtxt

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Commits on Aug 2, 2018

• Merge pull request #617 from yarikoptic/nf-nib-diff

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Commits on Aug 7, 2018

• Merge pull request #655 from MichielCottaar/opt_genfromtxt

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Commits on Aug 17, 2018

• BF: allow for PPC64 little endian long doubles

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Commits on Aug 23, 2018

• RF: remove redundant line

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• BF: fix missing width variable

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Commits on Aug 24, 2018

• Merge pull request #658 from matthew-brett/ppc64le-fixes

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Commits on Sep 14, 2018

• RF+ENH: nib-diff - allow to specify absolute and/or relative maximal differences to tolerate

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• ENH: nib-diff Field/File not just Field in the header

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Commits on Sep 21, 2018

• changed as commented out in the pull request

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• changes as commented

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Commits on Sep 25, 2018

• RF: anticipated files of different shapes, fixed table display, corrected tests

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Commits on Sep 26, 2018

• CI: Test on Python 3.7 on Travis

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• CI: Use dist xenial

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• CI: Use matrix include for Python 3.7

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• CI: Use Python 3.7-dev

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• DOCTEST: FutureWarning repr changed in 3.7

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• CI: Use 3.7 proper, move trusty+3.4 to matrix

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• TEST: Catch warnings in clear_and_catch tests

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• CI: Add Python 3.7 to AppVeyor matrix

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Commits on Sep 27, 2018

• FIX: Annotation labels are RGB, no alpha

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• TEST: Update tests to use RGB only

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• elaborated docstring, modified get_data_diff to allow direct array input, added tests for coverage

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Commits on Sep 28, 2018

• DOC: Update ctab documentation, comments

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• CI: Drop extraneous 2.7 build on Travis

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• added to diff documentation, undid executable change, took out debugging script in test_scripts

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• Merge pull request #651 from nipy/ci/travis_py37

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• undid permission snafu on test_scripts

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Commits on Oct 1, 2018

• Merge pull request #666 from effigies/fix/annot_labels

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• Merge remote-tracking branch 'upstream/master' into rel/2.3.1

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• DOC: Update Changelog

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• MNT: .mailmap

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• MAINT: Drop -dev

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• MNT: Update YOH, CC initials

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Commits on Oct 2, 2018

• TST: Require hypothesis>=3.7

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• docstring and function name clarification, change get_data to get_fdata()

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• corrected styles per Travis, limited fdata to float32

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Commits on Oct 3, 2018

• STY: Break overly-long line

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• ENH: Add ndim to ArrayProxy protocol

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• TEST: Validate expected ndim behavior

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• prepared for future PR to allow modification of dtype used in diff comparison

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• Merge branch 'enh-diff' of https://github.com/yarikoptic/nibabel into enh-diff

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• added cmdline functionality for modifying datatype used for file data comparisons

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Commits on Oct 4, 2018

• ENH: Pass ndim through to DataobjImage

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• TEST: Validate DataobjImage.ndim

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• added testing for dtype at cmdline, assuming cmdline functionality. changed value output in data_diff function to allow for validation of data type

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Commits on Oct 6, 2018

• RF: do not use hypothesis

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• BF: properly compare NaNs and test for >2 arguments given to are_values_different

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Commits on Oct 8, 2018

• RF: long -> large, NaN -> nan

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• BF: reintroduce try/except guarding around initial np.isnan

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• BF: exception string matching for not implemented in numpy 1.7.1

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• BF: another workaround for elderly numpy 1.7.1

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Commits on Oct 9, 2018

• BF(DOC): fixed damn trailing whitespaces in a docsting

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Commits on Oct 10, 2018

• storing changes for main testing

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• Merge branch 'no-hypothesis' of https://github.com/yarikoptic/nibabel into no-hypothesis

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Commits on Oct 11, 2018

• added tests to fix coverage problem

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• cmdline test added for dtype access

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• Merge pull request #678 from yarikoptic/no-hypothesis

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• ENH: adjusted some strings etc to fit the width and avoid duplicate spaces

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• Merge branch 'master' into enh-diff-dtype

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Commits on Oct 12, 2018

• Merge pull request #672 from chrispycheng/enh-diff-dtype

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• Revert "TST: Require hypothesis>=3.7"

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• Merge remote-tracking branch 'upstream/master' into rel/2.3.1

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• Merge pull request #674 from effigies/enh/arrayproxy_ndim

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• DOC: Update changelog

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• TEST,BK: Update arrayproxy tests to test expected behaviour more thoroughly

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• TEST: Refactor keep_file_open tests to be more comprehensive

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• BF,RF: Fix behaviour of keep_file_open flag. Now two internal flags are used,

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• TEST: Avoid file close errors on windows

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• TEST: Remove debug

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• Merge pull request #679 from pauldmccarthy/bf/fix_keep_file_open

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• Update changelog

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