change to new cython version

[wkerzendorf]

@unoebauer, @scoder
version 0.28.4 should have the right fix in there.

cython/cython#2199

[wkerzendorf]

@unoebauer - should we merge?

[unoebauer]

I think we should - Travis is happy with both Linux and OSX builds, so I don't see a reason why we shouldn't. We might wait for @Heringer-Epson though to check whether this version works on his local installation.

[wkerzendorf]

@unoebauer - no I removed the OSX build for now.

[wkerzendorf]

I would merge and put a reminder in my phone to check in 3 months to reinclude the OSX build

[unoebauer]

Sorry, I missed that the OSX is deactivated. So on OSX the segfault is still triggered? And locally on your OSX build it works?

[wkerzendorf]

@unoebauer it doesn't segfault in the debugger even. I think, I will just disable it for now.

[Heringer-Epson]

Sorry for the delay. I will check this today.

[Heringer-Epson]

I tried to install the current tardis version with Cython 0.28.4. Still got a segmentation fault.

To be clear, I was having trouble checking out the PR 59e625f, so I simply modified the tardis_env27.yml file to uncomment Cython and have it the 0.28.4 version. When I tried to python setup.py install, I got the following error:

tardis/simulation/setup_package.py:2: RuntimeWarning: Parent module 'tardis.simulation' not found while handling absolute import
from setuptools import Extension
tardis/simulation/setup_package.py:3: RuntimeWarning: Parent module 'tardis.simulation' not found while handling absolute import
from astropy_helpers.setup_helpers import get_distutils_option
tardis/simulation/setup_package.py:4: RuntimeWarning: Parent module 'tardis.simulation' not found while handling absolute import
import numpy as np
tardis/plasma/setup_package.py:2: RuntimeWarning: Parent module 'tardis.plasma' not found while handling absolute import
from setuptools import Extension
tardis/plasma/setup_package.py:3: RuntimeWarning: Parent module 'tardis.plasma' not found while handling absolute import
from astropy_helpers.setup_helpers import get_distutils_option
tardis/plasma/setup_package.py:4: RuntimeWarning: Parent module 'tardis.plasma' not found while handling absolute import
import numpy as np
tardis/montecarlo/setup_package.py:2: RuntimeWarning: Parent module 'tardis.montecarlo' not found while handling absolute import
from setuptools import Extension
tardis/montecarlo/setup_package.py:3: RuntimeWarning: Parent module 'tardis.montecarlo' not found while handling absolute import
import numpy as np
tardis/montecarlo/setup_package.py:4: RuntimeWarning: Parent module 'tardis.montecarlo' not found while handling absolute import
import os
tardis/montecarlo/setup_package.py:5: RuntimeWarning: Parent module 'tardis.montecarlo' not found while handling absolute import
from astropy_helpers.setup_helpers import get_distutils_option
tardis/montecarlo/setup_package.py:6: RuntimeWarning: Parent module 'tardis.montecarlo' not found while handling absolute import
from Cython.Build import cythonize
tardis/montecarlo/setup_package.py:8: RuntimeWarning: Parent module 'tardis.montecarlo' not found while handling absolute import
from glob import glob
Freezing version number to tardis/version.py
Compiling tardis/montecarlo/montecarlo.pyx because it changed.
[1/1] Cythonizing tardis/montecarlo/montecarlo.pyx
Segmentation fault (core dumped)

[wkerzendorf]

@Heringer-Epson be sure to delete montecarlo.c (look at it - it will say generated with Cython VERSION_NUMBER then rerun the compilation.

[unoebauer]

We should merge after we hear back from @Heringer-Epson

[unoebauer]

Should we leave this in as a comment? This way, we'll know what to do when some strange cython error appears in the future.

[wkerzendorf]

That’s why I put it in

[unoebauer]

I was thinking of keeping the procedure of getting bleeding-edge cython via github and compiling it with custom flags as a comment block and providing some additional information.

[Heringer-Epson]

Yes, this worked upon trying to rerun the installation. Note, using the conda env suggestion in tardis_env27.yml triggers an error due to Pyqt not being installed (I believe it's required for the gui interface). Installing Pyqt=4.11 on the local env then caused a bunch of packages to be downgraded.

[wkerzendorf]

that's interesting. anyways. I'll merge once I add the manual cython installing instructions in.

[unoebauer]

Excellent, exactly what I had in mind