Hey Nathan,

My setup / compilers / etc. are a software bundle maintained by STScI for the staff here (that's the ssb thing you can see in my paths). They do run as a virtual machine. I do not use Xcode. Both machines are on OSX 10.9.5. Any ideas as to what's wrong with the build environment? I'd really not like to have to install and maintain everything independently, especially since the build I have "just works" for every other application I have. If I can get the HDF5 problem diagnosed well then there's a chance they will be able to fix it here. 

Re. cython:
molly% cython -V
Cython version 0.22.1
And __file__ does confirm that it is installed as part of the virtual env ('/usr/stsci/ssb/python/lib/python2.7/site-packages/Cython-0.21.1-py2.7-macosx-10.6-x86_64.egg/cython.py')

--Molly


On Fri, Jul 31, 2015 at 11:29 AM, Nathan Goldbaum <nathan12343@gmail.com> wrote:


On Friday, July 31, 2015, Molly Peeples <molly@stsci.edu> wrote:
Hi folks,

I'm trying to install the dev branch of yt and I'm hitting some stumbling blocks. (For those of you who I talked to about this in May, the short version is that I've managed to recreate the same issues I had on my laptop but now on my desktop.)

The first thing I tried was the http://bitbucket.org/yt_analysis/yt/raw/yt/doc/install_script.sh script, which fails at installing HDF5 (http://pastebin.com/QSnKqHtW). The same thing happens for the stable branch install script, and when I try this on a different machine (laptop vs desktop, but similar setups and python installations). 

There is something wrong with your build environment. How did you set up your compilers? Using the Xcode command line tools or did you get your compilers from a third-party source?
 

I can install the stable branch no problem just doing pip install yt. But I'd still like the dev branch and / or source code. When I do hg clone https://bitbucket.org/yt_analysis/yt and then python setup.py develop, I get a:
[oak:~/yt] molly% python setup.py develop
Cython is a build-time requirement for the source tree of yt.
Please either install yt from a provided, release tarball,
or install Cython (version 0.22 or higher).
You may be able to accomplish this by typing:
     pip install -U Cython
Which, naturally, I did, and it says it's successfully installed, but I get the same error when I then rerun the setup.py. (I think this is the same line we went through when trying to get it working on my laptop which is why we eventually used conda to get the stable version + source on my laptop.) FWIW, I seem to not be able to uninstall cython, though it's somewhat unclear on why:
[oak:~/yt] molly% pip uninstall cython
Not uninstalling Cython at /usr/stsci/ssb/python/lib/python2.7/site-packages/Cython-0.21.1-py2.7-macosx-10.6-x86_64.egg, outside environment /Users/molly/ssbvirt/ssb-OS X




Soo...suggestions? It looks like I can get the binary no problem but if I want the source + dev branch, there are issues.
 

 

Does cython import successfully? If so, what's the output of cython.__file__? cython.__version?

I think this message about not uninstalling cython is related to virtualenvs. Do you use virtualenvs?

How did you set up your Python environment? You mentioned anaconda Python, what happens if you install cython using conda?

Finally, OSX 10.6 is getting a bit long in the tooth (for example, conda no longer supports it), maybe that's part of the issue?


 

 

--Molly

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