REL: 2.3.2 #708
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REL: 2.3.2 #708
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Fix small typos in the help of the parrec cmdline tool
MNT: Remove deprecated numpy.asscalar
…vecs For example, post-processed ADC maps will be marked as diffusion scans but only have 3D data. The b-values and vectors from the original scan are not available in the header in this case.
…ion coefficient map
FIX: Read .PAR files corresponding to ADC maps
STY: Flake8 3.6+ cleanup
Siemens CSA Reader: Increase maximum number of items
Add a toggle for crosshairs with ctrl+x
This reverts commit 0a1ea75.
``` /Users/arokem/.virtualenvs/afq/lib/python3.7/site-packages/nibabel/streamlines/trk.py:562: DeprecationWarning: The binary mode of fromstring is deprecated, as it behaves surprisingly on unicode inputs. Use frombuffer instead header_rec = np.fromstring(string=header_str, dtype=header_2_dtype) ```
This is because newer numpy doesn't allow to change the writeable flag.
Hyperlink DOI to preferred resolver
ENH: Add crosshair toggling to OrthoSlicer3D
Fix future warning on use of `np.issubdtype`. Fixes: ``` /home/travis/build/nipy/dipy/venv/lib/python3.4/site-packages/nibabel/streamlines/array_sequence.py:23: FutureWarning: Conversion of the second argument of issubdtype from `bool` to `np.generic` is deprecated. In future, it will be treated as `np.bool_ == np.dtype(bool).type`. ``` observed in projects using Nibabel, e.g. DIPY: https://travis-ci.org/nipy/dipy/jobs/471947136 More information about the issue and the fix at: numpy/numpy#2334 numpy/numpy#9505
…reWarningDeprecation BUG: Fix future warning on use of `np.issubdtype`.
FIX: Numpy pre-release accommodations
To provide consistent linear flow and output of git describe * tag '2.3.1': REL: 2.3.1
Merge 2.3.1 release tag into rel/2.3.2
Codecov Report
@@ Coverage Diff @@
## maint/2.3.x #708 +/- ##
===============================================
- Coverage 88.87% 88.83% -0.04%
===============================================
Files 93 93
Lines 11447 11460 +13
Branches 1891 1896 +5
===============================================
+ Hits 10174 10181 +7
- Misses 933 937 +4
- Partials 340 342 +2
Continue to review full report at Codecov.
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Reset the head to The status on the buildbots is deteriorating. It's a little unclear whether they are still necessary. Considering moving Windows/OSX builds to Azure pipelines, which would hopefully also avoid the AppVeyor issues. |
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FWIW I did a build across Debian/Ubuntus and seems to be ok (even uploaded to Debian unstable so to resolve a critical bug) |
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Looks like numpy's pre-release builds are causing test failures downstream, so might as well start the release process. This will be a bug-fix release, so I'm not going to make an active attempt to squeeze in other PRs (nothing looks immediately ready).
Please make some noise if there are any must-have fixes that I'm ignoring.
Targeting release tomorrow, also pending objection. I know it's a holiday, so can push off another day or two, but would rather not release on a Friday.
Leaving the base at
masterfor review, but will merge intomaint/2.3.xfor release.cc @yarikoptic for any Debian-related tests that need doing.
cc @matthew-brett for any process concerns.
Open issues/PRs that could go in quickly
Pre-release checklist
doc/source/index.rstand add any authors not yet acknowledged..mailmap fileif there are any duplicate authors listed fromgit shortlog -nse.LONG_DESCRIPTIONininfo.pyby runningmake refresh-readme.nibabel/info.py(e.g.NUMPY_MIN_VERSION) and indoc/source/installation.rstand inrequirements.txtand.travis.yml. They should at least match. Do they still hold? Make sure nibabel on travis is testing the minimum dependencies specifically.nosetests --with-doctest nibabelnibabel/info.pyto set_version_extrato''; commitpip install bz2filefailureAdapted from http://nipy.org/nibabel/devel/make_release.html#release-checklist