On Feb 2, 10:31 pm, Robert Bradshaw <[email protected]> wrote: > On Feb 2, 2010, at 7:20 PM, M. Yurko wrote: > > > The small example that I posted used pyximport. The extension module > > that made me originally see the issue was built with a setup.py > > distutils script. I have the same issue with both of them. They work > > on a normal python distribution, but fail if there is not a system- > > wide install of numpy. The issue happens if the setup.py script uses > > either the original .pyx files or the generated .c files. > > Can you post a setup.py for your simple example along with the > commands you used to compile it? It sounds like it's not getting > numpy_include_dirs correctly. > > - Robert > > > On Feb 2, 9:33 pm, Robert Bradshaw <[email protected]> > > wrote: > >> On Feb 2, 2010, at 4:11 PM, M. Yurko wrote: > > >>> On Feb 2, 6:44 pm, "Georg S. Weber" <[email protected]> > >>> wrote: > >>>> On 2 Feb., 21:26, Michael Yurko <[email protected]> wrote: > > >>>>> Hello All, > > >>>>> I've recently been building an extension module using both cython > >>>>> and numpy. > >>>>> It works fine with my system-wide install of python with numpy and > >>>>> cython as > >>>>> well as my install of sage. However, when I try to run it from > >>>>> sage on a > >>>>> system that doesn't have a system wide install of cython and > >>>>> numpy, it fails > >>>>> with: > >>>>> /home/myurko/.pyxbld/temp.linux-x86_64-2.6/pyrex/numpy_test.c: > >>>>> 144:31: error: > >>>>> numpy/arrayobject.h: No such file or > >>>>> directory > >>>>> /home/myurko/.pyxbld/temp.linux-x86_64-2.6/pyrex/numpy_test.c: > >>>>> 145:31: error: > >>>>> numpy/ufuncobject.h: No such file or directory > > >>>>> and then pages of issues relating to the failure to include > >>>>> arrayobject.h > >>>>> and ufuncobect.h . This issue is simply illustrated by the two > >>>>> short > >>>>> files:http://modular.math.washington.edu/home/myurko/misc/npt_wrapper.pyand > >>>>> .... Before > >>>>> I open a ticket, I just wanted to make sure that there already > >>>>> isn't one > >>>>> open, or there is not some other issue at play. > > >>>>> Thanks, > >>>>> Mike Yurko > > >>>> Try adding the line (yes, it's a *comment*) > > >>>> #cinclude $SAGE_ROOT/local/lib/python/site-packages/numpy/core/ > >>>> include > > >>>> to your *.pyx file. I don't remember right now where this stuff > >>>> (#cinclude, #clib, ...) for .pyx modules in conjunction with Sage > >>>> is > >>>> documented. But it's not a bug, it's a feature ... > > >>>> Cheers, > >>>> Georg > > >>> Hmm. That doesn't seem to work either in my trivial example, or my > >>> original extension module. I did find mention on #cinclude in the > >>> documentation (http://www.sagemath.org/doc/developer/ > >>> coding_in_other.html). > > >> That's only for using %cython in the notebook. > > >>> However, I probably should have been more > >>> specific. For now, I'm just trying to use sage as a python install > >>> that has both cython and numpy. I've been running the script with > >>> "sage -python ..." It seems odd to me that the behavior of the > >>> included python would be modified. > > >> How did you build your .pyx modules? Did you make a setup.py and run > >> "sage -python setup.py"? > > >> - Robert > > > -- > > To post to this group, send an email to [email protected] > > To unsubscribe from this group, send an email to > > [email protected] > > For more options, visit this group > > athttp://groups.google.com/group/sage-devel > > URL:http://www.sagemath.org
For the simple example I just used pyximport. For the extension module I used a setup.py script. The start of the extension module is at http://modular.math.washington.edu/home/myurko/qap/qap/ . I haven't set any of the numpy include directories in the setup.py script. Is it nessecary? It builds fine on my system with numpy installed. -- Mike Yurko -- To post to this group, send an email to [email protected] To unsubscribe from this group, send an email to [email protected] For more options, visit this group at http://groups.google.com/group/sage-devel URL: http://www.sagemath.org
