MRG: Release candidate 2.0.2 #377

effigies · 2015-11-06T03:19:28Z

This is a cherry-picked branch off of maint/2.0.x of the bug-fix pull-requests since 2.0.1. The only PR that needed a little massaging was #363.

There are a number of little DOC and TST fixes that could probably also fit in, if people think it makes sense.

Closes #373

Omar pointed out the integer overflow in calculating the image size of an image of size > 4GB, on a 32-bit platform.

Windows .bat file shadow of Python script fails for paths with spaces. Thanks to P. Renner for the fix - see matthew-brett/myscripter#2

Always returned `False`.

Numpy 1.10 cannot broadcast a strided array that is set as writeable

matthew-brett · 2015-11-06T03:27:43Z

Changelog

@@ -24,6 +24,23 @@ and Stephan Gerhard (SG).

 References like "pr/298" refer to github pull request numbers.

+* Upcoming
+
+  * Trackvis reader will now allow final streamline to have fewer points that


Trackvis changes not included in fact.

Would you rather pull in the changes or drop the changelog entry?

Just drop the changelog entry I guess, it is a minor API change.

Make TripWireError subclass AttributeError. This prevents the Python 3.5 doctest machinery triggering a TripWireError when inspecting the module containing a TripWire instance during doctest initialization.

The doctest string markup was for allowing doctests running on Python 3 and Python < 2.6. We haven't used it for a few years. This commit removes that code in the hope that no-one else is using it.

effigies · 2015-11-06T14:09:06Z

Removed the changelog entries.

@yarikoptic @ignatenkobrain Any extra commits in Debian/Fedora packages that you'd like to see in this release?

yarikoptic · 2015-11-06T14:19:59Z

On Fri, 06 Nov 2015, Chris Markiewicz wrote:

Removed the changelog entries.

[1]@yarikoptic [2]@ignatenkobrain Any extra commits in Debian/Fedora packages
that you'd like to see in this release?

I don't think I have any patches BUT I would appreciate if you give me
one day -- I will test 2.0.1-148-gdd4e725 regarding different
debian/ubuntu releases and possibly breaking dependents

Yaroslav O. Halchenko
Center for Open Neuroscience http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419
WWW: http://www.linkedin.com/in/yarik

effigies · 2015-11-06T14:21:51Z

Sounds good. I don't think we're in a rush, so just ping this thread when you're ready to go.

ignatenkobrain · 2015-11-06T14:26:31Z

I don't see new problems, but would be great if you will fix import for pydicom. Because we need to do import pydicom instead of import dicom.

ignatenkobrain · 2015-11-06T14:28:29Z

https://github.com/darcymason/pydicom/blob/master/setup.py#L11-L15

effigies · 2015-11-06T14:35:58Z

That means something like #351. I may have a few minutes to give that a try, but we'll need to test.

@matthew-brett Is it easy to make a new Travis test that would test against pydicom 1.0?

yarikoptic · 2015-11-06T20:34:49Z

FWIW -- everything looked splendid across debians for me with 2.0.1-148-gdd4e725

effigies · 2015-11-06T23:52:31Z

@yarikoptic Not sure quite how to interpret the string 2.0.1-148-gdd4e725. I'm guessing that means applying this branch to your last debian release?

yarikoptic · 2015-11-07T00:23:56Z

On Fri, 06 Nov 2015, Chris Markiewicz wrote:

[1]@yarikoptic Not sure quite how to interpret the string 2.0.1-148-gdd4e725.
I'm guessing that means applying this branch to your last debian release?

$> git show 2.0.1-148-gdd4e725 
commit dd4e725156206661aa218db9b3be9c2f02246ecf
Author: Matthew Brett <matthew.brett@gmail.com>
Date:   Thu Nov 5 18:24:45 2015 -0800

    DOC: remove trailing sentence

    Fixes gh-374.

that was the output of git describe on master at that point, e.g. as

$> git describe dd4e725156206661aa218db9b3be9c2f02246ecf
2.0.1-148-gdd4e725

effigies · 2015-11-07T00:43:13Z

Oh, I see. Just FYI this PR is just cherry-picked bug fixes on top of the maint/2.0.x branch, not everything that's gone into master.

If people would rather just package master into a new release, that's fine, too. These were almost clean cherry-picks, so I've sunk very little work into this branch.

ignatenkobrain · 2015-11-07T18:42:16Z

@effigies can you also backport pydicom's patch to this PR? It's required oneline massaging only.

matthew-brett · 2015-11-07T18:44:17Z

Chris - any interest in being the release manager for this one? Instructions here : https://github.com/nipy/nibabel/blob/master/doc/source/devel/make_release.rst - but I am sure they could be improved.

TST: Use consistent import style in tests Conflicts: nibabel/nicom/dicomwrappers.py Backport retains BinOpener

effigies · 2015-11-18T22:58:45Z

@bcipolli @surchs Would you mind testing this branch with the NIPY_EXTRA_TESTS=slow environment variable set, as well? I added a commit that's just #383 squashed and backported.

bcipolli · 2015-11-18T23:12:00Z

Worked like a champ!

effigies · 2015-11-18T23:14:32Z

Cool. Thanks for the validation.

Otherwise it won't be copied across to the sdist.

NB: This does not resolve the underlying issue (see conda/conda#1824), but incidentally prevents nibabel from triggering the bug during testing. -CJM

Squashed for 2.0.2 release. See nipygh-383 for full history. BF: Use buffered gzip read in Py3.5.0, specifically TST: Add high-memory usage test for large nifti1 files Conflicts: nibabel/testing/__init__.py

effigies · 2015-11-20T20:41:41Z

Okay. I think code-wise, this is ready to go. @matthew-brett could you walk me through the build-bots? I'm not quite sure how to go about this. (Also ssh buildbot@nipy.bic.berkeley.edu echo doesn't work, so I don't think my key is in yet.)

And should I merge --ff into maint/2.0.x or use this PR? Any preference?

Edit: To clarify, I've done everything on the checklist up to python -m compileall ., except sdist and virtualenv tests, since they're on Travis.

matthew-brett · 2015-11-22T02:56:40Z

Chris - I updated the instructions here : #386 - does that doc make sense to you?

matthew-brett · 2015-11-22T03:04:09Z

For merging, my preference is always to do non-ff merge unless there's a good reason - to keep the set of commits as an identifiable set of work.

effigies · 2015-11-23T17:01:10Z

Those instructions look good. I've been able to force builds (from the buildbot machine, not via the web interface), but haven't figured out pushing the NIPY_EXTRA_TESTS environment variable.

matthew-brett · 2015-11-23T18:40:39Z

Did you manage to get the web interface working in the end? It's less useful as you have to push something to the main repo before you can build it - for example you can build a tag once it's pushed, but you usually want to try building stuff before it's pushed.

There's no easy way to push an environment variable, but in any case, the smaller Windows machine probably can't run the big test - the larger 64-bit machine probably can. I'll try enabling that by default on the larger Windows machine.

matthew-brett · 2015-11-23T19:17:20Z

See for example env vars defined here : http://nipy.bic.berkeley.edu/builders/nibabel-bdist64-27/builds/43/steps/shell/logs/stdio

matthew-brett · 2015-11-23T19:18:03Z

I had to do this by logging into the machine remotely and setting the enviroment variable in the users profile. Can give you access to this machine if you need it.

matthew-brett · 2015-11-23T19:38:09Z

Oops - even for the 6GB windows machine it was too much:

http://nipy.bic.berkeley.edu/builders/nibabel-bdist64-27/builds/43/steps/shell_6/logs/stdio

======================================================================
ERROR: nibabel.tests.test_nifti1.test_large_nifti1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "c:\buildslaves\mike-win7-64\nibabel-bdist64-27\build\venv\lib\site-packages\nose\case.py", line 197, in runTest
    self.test(*self.arg)
  File "c:\Python27\lib\site-packages\numpy\testing\decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "c:\buildslaves\mike-win7-64\nibabel-bdist64-27\build\venv\lib\site-packages\nibabel-2.1.0.dev0-py2.7-win-amd64.egg\nibabel\tests\test_nifti1.py", line 1257, in test_large_nifti1
    data = load('test.nii.gz').get_data()
  File "c:\buildslaves\mike-win7-64\nibabel-bdist64-27\build\venv\lib\site-packages\nibabel-2.1.0.dev0-py2.7-win-amd64.egg\nibabel\spatialimages.py", line 572, in get_data
    data = np.asanyarray(self._dataobj)
  File "c:\Python27\lib\site-packages\numpy\core\numeric.py", line 287, in asanyarray
    return array(a, dtype, copy=False, order=order, subok=True)
  File "c:\buildslaves\mike-win7-64\nibabel-bdist64-27\build\venv\lib\site-packages\nibabel-2.1.0.dev0-py2.7-win-amd64.egg\nibabel\arrayproxy.py", line 145, in __array__
    raw_data = self.get_unscaled()
  File "c:\buildslaves\mike-win7-64\nibabel-bdist64-27\build\venv\lib\site-packages\nibabel-2.1.0.dev0-py2.7-win-amd64.egg\nibabel\arrayproxy.py", line 140, in get_unscaled
    mmap=self._mmap)
  File "c:\buildslaves\mike-win7-64\nibabel-bdist64-27\build\venv\lib\site-packages\nibabel-2.1.0.dev0-py2.7-win-amd64.egg\nibabel\volumeutils.py", line 518, in array_from_file
    n_read = infile.readinto(data_bytes)
  File "c:\Python27\Lib\gzip.py", line 256, in read
    self._read(readsize)
  File "c:\Python27\Lib\gzip.py", line 308, in _read
    self._add_read_data( uncompress )
  File "c:\Python27\Lib\gzip.py", line 326, in _add_read_data
    self.extrabuf = self.extrabuf[offset:] + data
MemoryError

effigies · 2015-11-23T19:42:30Z

Yeah. I can run the test on a 24GB machine but not an 8GB machine. Maybe if we just have one of the build slaves set to always run with NIPY_EXTRA_TESTS=slow,bigmem, and we make sure to run against that one before releases, that will be enough?

Also, I set up a pypi user cjmarkie, in case you need to add upload permissions.

matthew-brett · 2015-11-23T19:57:20Z

OK - done for pypi.

I enabled slow,bigmem test for the big Mac buildslave:

nipy/nibotmi@2322a76

(I had to log on and update the relevant file on that machine, then restart the buildbot slave).

I updated the release instructions adding the suggestion to run on this machine first:

https://github.com/nipy/nibabel/pull/386/files#diff-d13ddc96596291d914cd84c6165cc10bR130

effigies · 2015-11-23T19:58:37Z

Great. Build successful.

I think I should be good to go. I'll let you know if I run into any more issues.

REL: Bugfix release 2.0.2

effigies · 2015-11-23T22:13:16Z

@matthew-brett Release pushed. Hopefully I didn't somehow miss anything too egregious. Will make notes on #386.

@ignatenkobrain 2.0.2 is released. Source is also on pypi

matthew-brett and others added 11 commits November 5, 2015 22:02

BUG: work round int overflow in size calculation

731d711

Omar pointed out the integer overflow in calculating the image size of an image of size > 4GB, on a 32-bit platform.

DOC: fix ReST markup error in get_data docstring

0cd05be

BF: FreeSurfer nifti surfaces can have >3 dimensions

b4e7ca7

BF: Fix benchmark range bounds

a2e8399

BF: fix bug for Windows bat-file install

223b636

Windows .bat file shadow of Python script fails for paths with spaces. Thanks to P. Renner for the fix - see matthew-brett/myscripter#2

TEST/BF: Test cases skipped; STY: PEP8

665f65a

TEST: Update out_tup to what is expected

208412c

TEST: Clarify test_qform_sform test

ecec4f3

BF: Misplaced parenthesis

2584053

Always returned `False`.

TST: Verify pixdim check for non-negative values

262b33f

BF: Set strided_scalar as not writeable

627d12a

Numpy 1.10 cannot broadcast a strided array that is set as writeable

matthew-brett reviewed Nov 6, 2015
View reviewed changes

matthew-brett added 3 commits November 6, 2015 09:05

RF+API: TripWireError subclasses AttributeError

3689b46

Make TripWireError subclass AttributeError. This prevents the Python 3.5 doctest machinery triggering a TripWireError when inspecting the module containing a TripWire instance during doctest initialization.

TST: enable Python 3.5 tests

6b7b7dd

RF: remove doctest string markup

b27c954

The doctest string markup was for allowing doctests running on Python 3 and Python < 2.6. We haven't used it for a few years. This commit removes that code in the hope that no-one else is using it.

effigies force-pushed the candidate2.0.2 branch from b40d11c to b27c954 Compare November 6, 2015 14:05

effigies added 2 commits November 8, 2015 08:57

BF: Prepare for pydicom 1.0

7468ce3

TST: Use consistent import style in tests Conflicts: nibabel/nicom/dicomwrappers.py Backport retains BinOpener

TST: Travis with pydicom > 0.9.9 git commit

e3f8c28

effigies and others added 2 commits November 18, 2015 18:23

TST: Add sdist, wheel & requirements INSTALL_TYPEs

eedd8de

BF: add requirements.txt to MANIFEST.in

b9d1461

Otherwise it won't be copied across to the sdist.

effigies force-pushed the candidate2.0.2 branch 2 times, most recently from 56e3e9b to 587f4a1 Compare November 19, 2015 16:27

TST: debugging round trip error

c9bd3d8

NB: This does not resolve the underlying issue (see conda/conda#1824), but incidentally prevents nibabel from triggering the bug during testing. -CJM

effigies force-pushed the candidate2.0.2 branch from 587f4a1 to 7926c98 Compare November 20, 2015 16:45

BF: Gzip workaround for Python 3.5.0

b7a98a6

Squashed for 2.0.2 release. See nipygh-383 for full history. BF: Use buffered gzip read in Py3.5.0, specifically TST: Add high-memory usage test for large nifti1 files Conflicts: nibabel/testing/__init__.py

effigies force-pushed the candidate2.0.2 branch from 7926c98 to 487a432 Compare November 20, 2015 20:20

effigies added 3 commits November 23, 2015 15:59

DOC: Update Changelog, contributors

1bc3d43

DOC: Force sphinx on Python 2, for now

fb581bb

REL: update info for 2.0.2 release

1eca265

effigies force-pushed the candidate2.0.2 branch from 487a432 to 1eca265 Compare November 23, 2015 21:01

effigies added a commit that referenced this pull request Nov 23, 2015

Merge pull request #377 from effigies/candidate2.0.2

8522d9d

REL: Bugfix release 2.0.2

effigies merged commit 8522d9d into nipy:maint/2.0.x Nov 23, 2015

effigies deleted the candidate2.0.2 branch November 23, 2015 21:31

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MRG: Release candidate 2.0.2 #377

MRG: Release candidate 2.0.2 #377

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MRG: Release candidate 2.0.2 #377

MRG: Release candidate 2.0.2 #377

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