New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Offscreen is False for test_slicer #767

Merged
merged 5 commits into from Nov 8, 2015

Conversation

Projects
None yet
3 participants
@Garyfallidis
Member

Garyfallidis commented Nov 6, 2015

Depending on the hardware/software version of the bot sometimes the snapshot cannot work in stealthmode. For now I am changing for this test to offscreen=False. Hopefully this will resolve the current fail in master and in the future we can figure out how to stabilize xvfb.

@arokem

This comment has been minimized.

Member

arokem commented Nov 6, 2015

Fingers crossed!

On Fri, Nov 6, 2015 at 11:38 AM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

Depending on the hardware/software version of the bot sometimes the
snapshot cannot work in stealthmode. For now I am changing for this test to
offscreen=False. Hopefully this will resolve the current fail in master and

in the future we can figure out how to stabilize xvfb.

You can view, comment on, or merge this pull request online at:

#767
Commit Summary

  • Offscreen is False for test_slicer

File Changes

Patch Links:


Reply to this email directly or view it on GitHub
#767.

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 6, 2015

Let see how it goes. I think a lot of these issues will be solved when move the bots to VTK 6.... Well, maybe...

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 7, 2015

@arokem this is now passing. I had to skip the slicer test in VTK 5.

@arokem

This comment has been minimized.

arokem commented on dipy/viz/tests/test_fvtk_actors.py in 2d5b04f Nov 7, 2015

This did work on version 5 on your machine, no? Maybe we only want to skip if it's version 5, and we are on Travis, or on darwin?

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 7, 2015

Good idea I can try to make it skip on Travis and vtk 5.

@arokem

This comment has been minimized.

Member

arokem commented Nov 7, 2015

Yeah - you'll know you're on travis with this check: https://github.com/nipy/dipy/blob/master/dipy/testing/decorators.py#L54

@arokem

This comment has been minimized.

arokem commented on dipy/viz/tests/test_fvtk_actors.py in 34cbeb9 Nov 8, 2015

Should probably be:

... and (os.environ.get('TEST_WITH_XVFB', False) or sys.platform=='darwin':

Because this was also failing on mac with VTK 5

This comment has been minimized.

arokem replied Nov 8, 2015

Of course import sys at the top, and don't have the typos I made :-)

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

Can you double check that this test still fails in darwin?

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

I have now offscreen=False so that should work on Darwin.

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

You're right! That one does actually pass. But this one is failing under vtk 5 on darwin:

======================================================================
FAIL: dipy.viz.tests.test_fvtk_widgets.test_text_widget
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/Users/arokem/anaconda/envs/py2/lib/python2.7/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/Users/arokem/anaconda/envs/py2/lib/python2.7/site-packages/nose/util.py", line 620, in newfunc
    return func(*arg, **kw)
  File "/Users/arokem/source/dipy/dipy/testing/decorators.py", line 63, in test_with_xvfb
    my_test()
  File "/Users/arokem/anaconda/envs/py2/lib/python2.7/site-packages/numpy/testing/decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "/Users/arokem/anaconda/envs/py2/lib/python2.7/site-packages/numpy/testing/decorators.py", line 146, in skipper_func
    return f(*args, **kwargs)
  File "/Users/arokem/source/dipy/dipy/viz/tests/test_fvtk_widgets.py", line 180, in test_text_widget
    npt.assert_equal(report.objects, 3)
  File "/Users/arokem/anaconda/envs/py2/lib/python2.7/site-packages/numpy/testing/utils.py", line 354, in assert_equal
    raise AssertionError(msg)
AssertionError: 
Items are not equal:
 ACTUAL: 492
 DESIRED: 3

Should we skip it on darwin?

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

No because it is fine with some darwin machines. But I can force it to go offscreen=False which may resolve the problem. You can try it too.

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

That actually worries me a bit. What's different about these machines? Are these other darwin machines on which this test passes also running vtk5 installed through conda?

We might not be able to get to the bottom of this, but it is a bit disturbing.

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

Yes, there were two darwin machines passing those tests.

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

Look what I understand right now is that with Darwin machines offscreen=True (in snapshot) is not working sometimes. And that is normal in VTK 5 as I said before the snapshot was made initially to run the visual tests in Linux machines for VTK 5 and hopefully support more OS's with VTK 6. Does this explanation help?

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

Where do I put the offscreen=False?

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

What's different about those two laptops?

I am running OS 10.11.1
Python 2.7.10 from Anaconda

vtk.vtkVersion.GetVTKMajorVersion(): 5
Version.GetVTKBuildVersion(): 1
vtk.vtkVersion.GetVTKMinorVersion(): 10
vtk.vtkVersion.GetVTKSourceVersion(): 'vtk version 5.10.1'
vtk.vtkVersion.GetVTKVersion(): '5.10.1'

np.version : '1.10.1'

Is it any different from the machines on which this does pass?

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

window.snapshot

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

It's set to be offscreen=True per default:

https://github.com/nipy/dipy/blob/master/dipy/viz/window.py#L661

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

So - I should set that to False?

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

It fails in the same way when I do that.

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

Same vtk different hardware. More recent hardware notebooks. @daducci what version is you macbook and what graphics card does it have?

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

Okay this is unexpected!

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

Ugh. Hardware differences.

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

Do you get the same issue with VTK 6?

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

Nope. VTK6 seems to fix it.

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

Let's take this conversation to gitter!

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

OKay so most likely this is a VTK 5 issue on some Mac machines.

@Garyfallidis

This comment has been minimized.

Member

Garyfallidis commented Nov 8, 2015

Can you try to run window.record and see if the PNG file comes out correctly?

arokem added a commit that referenced this pull request Nov 8, 2015

Merge pull request #767 from Garyfallidis/update_slicer_test
Offscreen is False for test_slicer

@arokem arokem merged commit f47a96f into nipy:master Nov 8, 2015

1 check passed

continuous-integration/travis-ci/pr The Travis CI build passed
Details
@daducci

This comment has been minimized.

daducci commented Nov 8, 2015

I recently upgraded to "El Capitan" (OSX 10.11)and the video card is listed as "Intel Iris 1536 MB". @Garyfallidis, do you need more info?

@arokem

This comment has been minimized.

Member

arokem commented Nov 8, 2015

Yeah - I have both of these as well (El-Capitan, and Intel Iris Graphics
6100 1536 MB)

@daducci: how did you install vtk on your mac? I installed with Anaconda.
Did you get yours through homebrew, or something like that?

On Sun, Nov 8, 2015 at 2:52 PM, Alessandro Daducci <notifications@github.com

wrote:

I recently upgraded to "El Capitan" (OSX 10.11)and the video card is
listed as "Intel Iris 1536 MB". @Garyfallidis
https://github.com/Garyfallidis, do you need more info?


Reply to this email directly or view it on GitHub
#767 (comment).

@daducci

This comment has been minimized.

daducci commented Nov 8, 2015

Hi @arokem ,
to be honest, I do not remember.. Is that a way to check it a posteriori? I guess it came with Anaconda as well.

@arokem

This comment has been minimized.

Member

arokem commented Nov 9, 2015

If you have anaconda it's likely it's from there.

You could check with:

import vtk
vtk.__file__

On my machine it looks like this:
'/Users/arokem/anaconda/envs/py2/lib/python2.7/site-packages/vtk/__init__.pyc'

On Sun, Nov 8, 2015 at 3:10 PM, Alessandro Daducci <notifications@github.com

wrote:

Hi @arokem https://github.com/arokem ,
to be honest, I do not remember.. Is that a way to check it a posteriori?
I guess it came with Anaconda as well.


Reply to this email directly or view it on GitHub
#767 (comment).

@daducci

This comment has been minimized.

daducci commented Nov 9, 2015

Yes, I confirm:
'/Users/ale/anaconda/lib/python2.7/site-packages/vtk/__init__.pyc'

@arokem

This comment has been minimized.

Member

arokem commented Nov 9, 2015

Could you please run pip freeze and paste the whole thing here?

Just confirming: tests all run without a hitch for you on current dipy
master?

On Sun, Nov 8, 2015 at 5:13 PM, Alessandro Daducci <notifications@github.com

wrote:

Yes, I confirm:
'/Users/ale/anaconda/lib/python2.7/site-packages/vtk/init.pyc'


Reply to this email directly or view it on GitHub
#767 (comment).

@daducci

This comment has been minimized.

daducci commented Nov 9, 2015

For the tests, you should ask @Garyfallidis: I had lent him my laptop and actually I don't know what he tested in detail. Btw, here is the output from pip freeze:

abstract-rendering==0.5.1
alabaster==0.7.6
amico==1.0
appnope==0.1.0
argcomplete==0.8.1
astropy==1.0.3
atom==0.3.9
autopep8==1.1.1
Babel==2.1.1
backports.ssl-match-hostname==3.4.0.2
beautifulsoup4==4.3.2
binstar==0.7.1
bitarray==0.8.1
blaze==0.6.3
blz==0.6.2
bokeh==0.6.1
boto==2.32.1
casuarius==1.1
cdecimal==2.3
certifi==14.5.14
cffi==0.8.6
chaco==4.4.1
colorama==0.3.1
commit==1.0
conda==3.18.3
conda-build==1.8.2
conda-env==2.4.4
configobj==5.0.6
cryptography==0.5.4
cycler==0.9.0
Cython==0.21
cytoolz==0.7.0
DataShape==0.3.0
decorator==4.0.4
docutils==0.12
enable==4.3.0
enaml==0.9.8
Flask==0.10.1
future==0.13.1
futures==2.1.6
gevent==1.0.1
gevent-websocket==0.9.3
glueviz==0.5.1
greenlet==0.4.4
grin==1.2.1
h5py==2.3.1
ipykernel==4.1.1
ipython==4.0.0
ipython-genutils==0.1.0
itsdangerous==0.24
jdcal==1.0
jedi==0.9.0
Jinja2==2.8
jsonschema==2.4.0
jupyter-client==4.1.1
jupyter-core==4.0.6
kiwisolver==0.1.3
llvmpy==0.12.7
lxml==3.4.0
MarkupSafe==0.23
matplotlib==1.4.0
mistune==0.7.1
mock==1.0.1
multipledispatch==0.4.7
nbconvert==4.0.0
nbformat==4.0.1
networkx==1.9.1
nibabel==2.0.0
nltk==3.0.0
nose==1.3.4
numba==0.14.0
numexpr==2.3.1
numpy==1.9.3
openpyxl==1.8.5
pandas==0.16.2
path.py==0.0.0
patsy==0.3.0
pep8==1.6.2
pexpect==3.3
pickleshare==0.5
PIL==1.1.7
Pillow==2.9.0
ply==3.4
psutil==3.2.2
ptyprocess==0.4
py==1.4.25
PyAudio==0.2.7
pycosat==0.6.1
pycparser==2.10
pycrypto==2.6.1
pycurl==7.19.5
pyface==4.4.0
pyflakes==1.0.0
Pygments==2.0.2
PyInstaller==3.0
pyOpenSSL==0.14
pyparsing==2.0.1
pytest==2.6.3
python-dateutil==2.4.1
pytz==2015.7
PyYAML==3.11
pyzmq==14.7.0
qtconsole==4.1.0
redis==2.9.1
requests==2.8.1
rope==0.9.4
runipy==0.1.1
scikit-image==0.11.3
scikit-learn==0.15.2
scipy==0.15.1
simplegeneric==0.8.1
six==1.10.0
snowballstemmer==1.2.0
sockjs-tornado==1.0.1
spams==2.5
Sphinx==1.3.1
sphinx-rtd-theme==0.1.7
spyder==2.3.7
SQLAlchemy==0.9.7
statsmodels==0.5.0
sympy==0.7.5
tables==3.1.1
terminado==0.5
toolz==0.7.0
tornado==4.2.1
tractconverter==0.7.5.dev0
traitlets==4.0.0
traits==4.4.0
traitsui==4.4.0
ujson==1.33
unicodecsv==0.9.4
VTK==5.10.1
Werkzeug==0.9.6
wheel==0.26.0
xlrd==0.9.3
XlsxWriter==0.5.7
xlwt==0.7.5
@arokem

This comment has been minimized.

Member

arokem commented Nov 10, 2015

Thanks. I am still not sure why this works on your machine, but not mine.

On Mon, Nov 9, 2015 at 10:25 AM, Alessandro Daducci <
notifications@github.com> wrote:

For the tests, you should ask @Garyfallidis
https://github.com/Garyfallidis: I had lent him my laptop and actually
I don't know what he tested in detail. Btw, here is the output from pip
freeze:

abstract-rendering==0.5.1
alabaster==0.7.6
amico==1.0
appnope==0.1.0
argcomplete==0.8.1
astropy==1.0.3
atom==0.3.9
autopep8==1.1.1
Babel==2.1.1
backports.ssl-match-hostname==3.4.0.2
beautifulsoup4==4.3.2
binstar==0.7.1
bitarray==0.8.1
blaze==0.6.3
blz==0.6.2
bokeh==0.6.1
boto==2.32.1
casuarius==1.1
cdecimal==2.3
certifi==14.5.14
cffi==0.8.6
chaco==4.4.1
colorama==0.3.1
commit==1.0
conda==3.18.3
conda-build==1.8.2
conda-env==2.4.4
configobj==5.0.6
cryptography==0.5.4
cycler==0.9.0
Cython==0.21
cytoolz==0.7.0
DataShape==0.3.0
decorator==4.0.4
docutils==0.12
enable==4.3.0
enaml==0.9.8
Flask==0.10.1
future==0.13.1
futures==2.1.6
gevent==1.0.1
gevent-websocket==0.9.3
glueviz==0.5.1
greenlet==0.4.4
grin==1.2.1
h5py==2.3.1
ipykernel==4.1.1
ipython==4.0.0
ipython-genutils==0.1.0
itsdangerous==0.24
jdcal==1.0
jedi==0.9.0
Jinja2==2.8
jsonschema==2.4.0
jupyter-client==4.1.1
jupyter-core==4.0.6
kiwisolver==0.1.3
llvmpy==0.12.7
lxml==3.4.0
MarkupSafe==0.23
matplotlib==1.4.0
mistune==0.7.1
mock==1.0.1
multipledispatch==0.4.7
nbconvert==4.0.0
nbformat==4.0.1
networkx==1.9.1
nibabel==2.0.0
nltk==3.0.0
nose==1.3.4
numba==0.14.0
numexpr==2.3.1
numpy==1.9.3
openpyxl==1.8.5
pandas==0.16.2
path.py==0.0.0
patsy==0.3.0
pep8==1.6.2
pexpect==3.3
pickleshare==0.5
PIL==1.1.7
Pillow==2.9.0
ply==3.4
psutil==3.2.2
ptyprocess==0.4
py==1.4.25
PyAudio==0.2.7
pycosat==0.6.1
pycparser==2.10
pycrypto==2.6.1
pycurl==7.19.5
pyface==4.4.0
pyflakes==1.0.0
Pygments==2.0.2
PyInstaller==3.0
pyOpenSSL==0.14
pyparsing==2.0.1
pytest==2.6.3
python-dateutil==2.4.1
pytz==2015.7
PyYAML==3.11
pyzmq==14.7.0
qtconsole==4.1.0
redis==2.9.1
requests==2.8.1
rope==0.9.4
runipy==0.1.1
scikit-image==0.11.3
scikit-learn==0.15.2
scipy==0.15.1
simplegeneric==0.8.1
six==1.10.0
snowballstemmer==1.2.0
sockjs-tornado==1.0.1
spams==2.5
Sphinx==1.3.1
sphinx-rtd-theme==0.1.7
spyder==2.3.7
SQLAlchemy==0.9.7
statsmodels==0.5.0
sympy==0.7.5
tables==3.1.1
terminado==0.5
toolz==0.7.0
tornado==4.2.1
tractconverter==0.7.5.dev0
traitlets==4.0.0
traits==4.4.0
traitsui==4.4.0
ujson==1.33
unicodecsv==0.9.4
VTK==5.10.1
Werkzeug==0.9.6
wheel==0.26.0
xlrd==0.9.3
XlsxWriter==0.5.7
xlwt==0.7.5


Reply to this email directly or view it on GitHub
#767 (comment).

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment