Mailman 3 December 2011 - NumPy-Discussion

test code for user defined types in numpy
by Geoffrey Irving Dec. 21, 2011

Dec. 21, 2011

Hello, As a followup to the prior thread on bugs in user defined types in numpy, I converted my rational number class from C++ to C and switched to 32 bits to remove the need for unportable 128 bit numbers. It should be usable as a fairly thorough test case for user defined types now. It does rather more than a minimal test case would need to do, but that isn't a problem unless you're concerned about code size. Let me know if any further changes are needed before it's suitable for inclusion in numpy as a test case. The repository is here: https://github.com/girving/rational The tests run under either py.test or nose. For completeness, my branch fixing all but one of the bugs I found in numpy user defined types is here: https://github.com/girving/numpy/tree/fixuserloops The remaining bug is that numpy incorrectly releases the GIL during casts even though NPY_NEEDS_API is set. The resulting crash goes away if the line defining ACQUIRE_GIL is uncommented. With the necessary locks in place, all my tests pass with my branch of numpy. I haven't tracked this one down and fixed it yet, but it shouldn't be hard to do so. Geoffrey

5 8

Getting non-normalized eigenvectors from generalized eigenvalue solution?
by Fahreddın Basegmez Dec. 21, 2011

Dec. 21, 2011

Howdy, Is it possible to get non-normalized eigenvectors from scipy.linalg.eig(a, b)? Preferably just by using numpy. BTW, Matlab/Octave provides this with its eig(a, b) function but I would like to use numpy for obvious reasons. Regards, Fahri

4 16

numpy1.6.1 install fortran compiler error
by Jack Bryan Dec. 21, 2011

Dec. 21, 2011

Hi, In order to install scipy, I am trying to install numpy 1.6.1. on GNU/linux redhat 2.6.18. But, I got error about fortran compiler. I have gfortran. I do not have f77/f90/g77/g90. I run :python setup.py build --fcompiler=gfortran It woks well and tells me that customize Gnu95FCompilerFound executable /usr/bin/gfortran But, i run: building library "npymath" sourcescustomize GnuFCompilerCould not locate executable g77Could not locate executable f77customize IntelFCompilerCould not locate executable ifortCould not locate executable ifccustomize LaheyFCompilerCould not locate executable lf95customize PGroupFCompilerCould not locate executable pgf90Could not locate executable pgf77customize AbsoftFCompilerCould not locate executable f90customize NAGFCompilerFound executable /usr/bin/f95customize Gnu95FCompilercustomize Gnu95FCompiler using configC compiler: gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC Do I have to install f77/f90/g77/g90 ? thanks

4 6

import_array weird behavior
by Marc POINOT Dec. 20, 2011

Dec. 20, 2011

Hi all, I've just changed to cython and old numpy module with a raw C API. The C module init is removed, and I've put the import_array in the 'pure-cython' part of the module init. Usual tutorial examples have these lines: import numpy as NPY cimport numpy as NPY NPY.import_array() But this fails (first numpy API call core dump) in my module, if I put back the import_array() in the C part of the module everything turns ok again. Now if I remove again this C API import_array and I write: import numpy as NPY cimport numpy as CNPY CNPY.import_array() all is ok. Do I miss something? It sounds good to me to have to separate scopes but I wonder if it's a common practice with potential side-effects or if it is the right way to use numpy with cython. And then, what about my core dump? cython 1.15.1 python 2.7.2 numpy 1.6.1 scons 2.1.0 linux x86 64 with gcc 4.3.4 -MP- ----------------------------------------------------------------------- Marc POINOT [ONERA/DSNA] Tel:+33.1.46.73.42.84 Fax:+33.1.46.73.41.66 Avertissement/disclaimer http://www.onera.fr/onera-en/emails-terms

2 1

Would it be possible to enhance np.unique(.) with a keyword kind
by eat Dec. 20, 2011

Dec. 20, 2011

Hi, Especially when the keyword return_index of np.unique(.) is specified to be True, would it in general also be reasonable to be able to specify the sorting algorithm of the underlying np.argsort(.)? The rationale is that (for at least some of my cases) higher level algorithms seems to be too over complicated unless I'm not able to request a stable sorting order from np.unique(.) (like np.unique(., return_index= True, kind= 'mergesort'). (FWIW, I apparently do have a working local hack for this kind of functionality, but without extensive testing of 'all' corner cases). Thanks, eat

2 4

[ANN] IPython 0.12 is out!
by Fernando Perez Dec. 19, 2011

Dec. 19, 2011

Hi all, on behalf of the IPython development team, I'm thrilled to announce, after an intense 4 1/2 months of work, the official release of IPython 0.12. This is a very important release for IPython, for several reasons. First and foremost, we have a major new feature, our interactive web-based notebook, that has been in our sights for a very long time. We tried to build one years ago (with WX) as a Google SoC project in 2005, had other prototypes later on, but things never quite worked. Finally the refactoring effort started two years ago, the communications architecture we built in 2010, and the advances of modern browsers, gave us all the necessary pieces. With this foundation in place, while part of the team worked on the 0.11 release, Brian Granger had already started quietly building the web notebook, which we demoed in early-alpha mode at the SciPy 2011 conference (http://www.archive.org/details/Wednesday-203-6-IpythonANewArchitectureForIn…). By the EuroScipy conference in August we had merged Brian's amazing effort into our master branch, and after that multiple people (old and new) jumped in to make all kinds of improvements, leaving us today with something that is an excellent foundation. It's still the first release of the notebook, and as such we know it has a number of rough edges, but several of us have been using it as a daily research tool for the last few months. Do not hesitate to file issues for any problems you encounter with it, and we even have an 'open issue' for general discussion of ideas and features for the notebook at: https://github.com/ipython/ipython/issues/977. Furthermore, it is clear that our big refactoring work, combined with the amazing facilities at Github, are paying off. The 0.11 series was a major amount of work, with 511 issues closed over almost two years. But that pales in comparison to this cycle: in only 4 1/2 months we closed 515 issues, with 50% being Pull Requests. And very importantly, our list of contributors includes many new faces (see the credits section in our release notes for full details), which is the best thing that can happen to an open source project. We hope you will find the new features (the notebook isn't the only one! see below) compelling, and that many more will not only use IPython but will join the project; there's plenty to do and now there are tasks for many different skill sets (web, javascript, gui work, low-level networking, parallel machinery, console apps, etc). *Downloads* Download links and instructions are at: http://ipython.org/download.html And IPython is also on PyPI: http://pypi.python.org/pypi/ipython Those contain a built version of the HTML docs; if you want pure source downloads with no docs, those are available on github: Tarball: https://github.com/ipython/ipython/tarball/rel-0.12 Zipball: https://github.com/ipython/ipython/zipball/rel-0.12 * Features * Here is a quick listing of the major new features: - An interactive browser-based Notebook with rich media support - Two-process terminal console - Tabbed QtConsole - Full Python 3 compatibility - Standalone Kernel - PyPy support And many more... We closed over 500 tickets, merged over 200 pull requests, and more than 45 people contributed commits for the final release. Please see our release notes for the full details on everything about this release: http://ipython.org/ipython-doc/stable/whatsnew/version0.12.html * IPython tutorial at PyCon 2012 * Those of you attending (or planning on it) PyCon 2012 in Santa Clara, CA, may be interested in attending a hands-on tutorial we will be presenting on the many faces of IPython. See https://us.pycon.org/2012/schedule/presentation/121/ for full details. * Errata * This was caught by Matthias Bussionnier's (one of our great new contributors) sharp eyes while I was writing these release notes: In the example notebook called display_protocol, the first cell starts with: from IPython.lib.pylabtools import print_figure which should instead be: from IPython.core.pylabtools import print_figure This has already been fixed on master, but since the final 0.12 files have been uploaded to github and PyPI, we'll let them be. As usual, if you find any other problem, please file a ticket --or even better, a pull request fixing it-- on our github issues site (https://github.com/ipython/ipython/issues/). Many thanks to all who contributed! Fernando, on behalf of the IPython development team. http://ipython.org

1 0

Re: [Numpy-discussion] Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2
by McNicol, Adam Dec. 18, 2011

Dec. 18, 2011

Hi, Definitely have the sdk installed. In the Developer/SDKs directory I have one for 10.6 and another for 10.7 - no idea where a second 10.6 would be coming from =( Adam. -----Original Message----- From: numpy-discussion-request(a)scipy.org [mailto:numpy-discussion-request@scipy.org] Sent: Sun 12/18/2011 9:52 PM To: numpy-discussion(a)scipy.org Subject: NumPy-Discussion Digest, Vol 63, Issue 55 Send NumPy-Discussion mailing list submissions to numpy-discussion(a)scipy.org To subscribe or unsubscribe via the World Wide Web, visit http://mail.scipy.org/mailman/listinfo/numpy-discussion or, via email, send a message with subject or body 'help' to numpy-discussion-request(a)scipy.org You can reach the person managing the list at numpy-discussion-owner(a)scipy.org When replying, please edit your Subject line so it is more specific than "Re: Contents of NumPy-Discussion digest..." Today's Topics: 1. Re: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 (McNicol, Adam) 2. Re: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 (Ralf Gommers) ---------------------------------------------------------------------- Message: 1 Date: Sun, 18 Dec 2011 18:48:47 -0000 From: "McNicol, Adam" <amcnicol(a)longroad.ac.uk> Subject: Re: [Numpy-discussion] Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 To: <numpy-discussion(a)scipy.org> Message-ID: <fd29dc5c77c7ee4f0f0622b3459e91a5d77badc3@localhost> Content-Type: text/plain; charset="iso-8859-1" Hi Ralf, Thanks for the response. I tried reinstalling Xcode 4.2.1 and the GCC/Fortran installer from http://r.research.att.com/tools/ (gcc-42-5666.3-darwin11.pkg) before installing the distribute package that you suggested. I then reran the numpy installer being sure to enter the three export lines as suggested on the numpy installation guide for Lion. Still no success. I guess I'll just have to wait for more official support for my configuration. I have included the output from terminal just in case it is useful as there were a few lines in red that suggest something isn't quite right with something. I have placed ** before the lines that appear in red. I appreciate the suggestions, Thanks again, Adam. running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building py_modules sources creating build creating build/src.macosx-10.6-intel-3.2 creating build/src.macosx-10.6-intel-3.2/numpy creating build/src.macosx-10.6-intel-3.2/numpy/distutils building library "npymath" sources customize NAGFCompiler **Could not locate executable f95 customize AbsoftFCompiler **Could not locate executable f90 **Could not locate executable f77 customize IBMFCompiler **Could not locate executable xlf90 **Could not locate executable xlf customize IntelFCompiler **Could not locate executable fort **Could not locate executable ifc customize GnuFCompiler **Could not locate executable g77 customize Gnu95FCompiler **Could not locate executable gfortran customize G95FCompiler **Could not locate executable g95 customize PGroupFCompiler **Could not locate executable pgf90 **Could not locate executable pgf77 **don't know how to compile Fortran code on platform 'posix' C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c' gcc-4.2: _configtest.c gcc-4.2 _configtest.o -o _configtest success! removing: _configtest.c _configtest.o _configtest customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c' gcc-4.2: _configtest.c _configtest.c:1: warning: conflicting types for built-in function ?exp? _configtest.c:1: warning: conflicting types for built-in function ?exp? gcc-4.2 _configtest.o -o _configtest success! removing: _configtest.c _configtest.o _configtest creating build/src.macosx-10.6-intel-3.2/numpy/core creating build/src.macosx-10.6-intel-3.2/numpy/core/src creating build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/npy_math.c conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/ieee754.c conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/npy_math_complex.c building extension "numpy.core._sort" sources Generating build/src.macosx-10.6-intel-3.2/numpy/core/include/numpy/config.h customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c' gcc-4.2: _configtest.c In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory lipo: can't figure out the architecture type of: /var/folders/_c/z033hf1s1cgfcxtxfnpg0lsm0000gn/T//ccKv548x.out In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory lipo: can't figure out the architecture type of: /var/folders/_c/z033hf1s1cgfcxtxfnpg0lsm0000gn/T//ccKv548x.out failure. removing: _configtest.c _configtest.o Running from numpy source directory.Traceback (most recent call last): File "setup.py", line 196, in <module> setup_package() File "setup.py", line 189, in setup_package configuration=configuration ) File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/core.py", line 148, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 917, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command cmd_obj.run() File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build.py", line 37, in run old_build.run(self) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/command/build.py", line 126, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command cmd_obj.run() File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 169, in build_sources self.build_extension_sources(ext) File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 328, in build_extension_sources sources = self.generate_sources(sources, ext) File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 410, in generate_config_h moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir) File "numpy/core/setup.py", line 41, in check_types out = check_types(*a, **kw) File "numpy/core/setup.py", line 271, in check_types "Cannot compile 'Python.h'. Perhaps you need to "\ SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. Message: 3 Date: Sun, 18 Dec 2011 09:49:00 +0100 From: Ralf Gommers <ralf.gommers(a)googlemail.com> Subject: Re: [Numpy-discussion] Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 To: Discussion of Numerical Python <numpy-discussion(a)scipy.org> Message-ID: <CABL7CQh-+t+6p5z_S_JVycRCB-FWK0Q3wiAWjazgmDp8AJkKqw(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" On Sat, Dec 17, 2011 at 12:59 PM, McNicol, Adam <amcnicol(a)longroad.ac.uk>wrote: > ** > > Hi There, > > Thanks for the responses. > > At this point I would settle from just being able to install matplotlib. > Even if some of the functionality isn't present currently that is fine. > > I'm afraid my knowledge of Python falls down about here as well. I > installed Python 3.2.2 via the installer from Python.org so I have no idea > whether Python.h is present or where indeed I would find it or how I would > add it to the search path. > > Do I have to install from source or something like that? > No, your Python install should be fine if you just got the dmg installer from python.org. I recommend you install the OS X SDKs and distribute ( http://pypi.python.org/pypi/distribute), as I said before, and try again to compile numpy. Unfortunately you have chosen a difficult combination of OS and Python version, so we don't have binary installers you can use (yet). Ralf > Thanks again, > > > Adam. > > > -----Original Message----- > From: McNicol, Adam > Sent: Fri 12/16/2011 11:07 PM > To: numpy-discussion(a)scipy.org > Subject: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 > > Hi There, > > I am very new to numpy and have really only started investigating it as > one of my students needs some functionality from matplotlib. I have managed > to install everything under Windows for work in class but I use a Mac at > home and have been struggling all night to get it to build and install. > > I should mention that I am using Python 3.2.2 both in school and at home > and it isn't an option to use Python 2.7 as all of the rest of my class is > taught in Python 3. I also have the most recent version of Xcode installed. > > I have installed the correct build of gcc-4.2 with Fortran (gcc-4.2 (Apple > build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)) from > http://r.research.att.com/tools/ > > I then followed the install instructions but the build fails with the > following message: > > File "numpy/core/setup.py", line 271, in check_types > "Cannot compile 'Python.h'. Perhaps you need to "\ > SystemError: Cannot compile 'Python.h'. Perhaps you need to install > python-dev|python-devel. > > I have got no idea what to do with this error message. Any help would be > much appreciated. > > Kind Regards, > > > Adam. > > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion(a)scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > >

1 0

Re: [Numpy-discussion] Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2
by McNicol, Adam Dec. 18, 2011

Dec. 18, 2011

Hi Ralf, Thanks for the response. I tried reinstalling Xcode 4.2.1 and the GCC/Fortran installer from http://r.research.att.com/tools/ (gcc-42-5666.3-darwin11.pkg) before installing the distribute package that you suggested. I then reran the numpy installer being sure to enter the three export lines as suggested on the numpy installation guide for Lion. Still no success. I guess I'll just have to wait for more official support for my configuration. I have included the output from terminal just in case it is useful as there were a few lines in red that suggest something isn't quite right with something. I have placed ** before the lines that appear in red. I appreciate the suggestions, Thanks again, Adam. running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building py_modules sources creating build creating build/src.macosx-10.6-intel-3.2 creating build/src.macosx-10.6-intel-3.2/numpy creating build/src.macosx-10.6-intel-3.2/numpy/distutils building library "npymath" sources customize NAGFCompiler **Could not locate executable f95 customize AbsoftFCompiler **Could not locate executable f90 **Could not locate executable f77 customize IBMFCompiler **Could not locate executable xlf90 **Could not locate executable xlf customize IntelFCompiler **Could not locate executable fort **Could not locate executable ifc customize GnuFCompiler **Could not locate executable g77 customize Gnu95FCompiler **Could not locate executable gfortran customize G95FCompiler **Could not locate executable g95 customize PGroupFCompiler **Could not locate executable pgf90 **Could not locate executable pgf77 **don't know how to compile Fortran code on platform 'posix' C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c' gcc-4.2: _configtest.c gcc-4.2 _configtest.o -o _configtest success! removing: _configtest.c _configtest.o _configtest customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c' gcc-4.2: _configtest.c _configtest.c:1: warning: conflicting types for built-in function exp _configtest.c:1: warning: conflicting types for built-in function exp gcc-4.2 _configtest.o -o _configtest success! removing: _configtest.c _configtest.o _configtest creating build/src.macosx-10.6-intel-3.2/numpy/core creating build/src.macosx-10.6-intel-3.2/numpy/core/src creating build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/npy_math.c conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/ieee754.c conv_template:> build/src.macosx-10.6-intel-3.2/numpy/core/src/npymath/npy_math_complex.c building extension "numpy.core._sort" sources Generating build/src.macosx-10.6-intel-3.2/numpy/core/include/numpy/config.h customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' customize NAGFCompiler customize AbsoftFCompiler customize IBMFCompiler customize IntelFCompiler customize GnuFCompiler customize Gnu95FCompiler customize G95FCompiler customize PGroupFCompiler **don't know how to compile Fortran code on platform 'posix' C compiler: gcc-4.2 -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -O3 -isysroot /Developer/SDKs/MacOSX10.6.sdk -arch i386 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m -c' gcc-4.2: _configtest.c In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory lipo: can't figure out the architecture type of: /var/folders/_c/z033hf1s1cgfcxtxfnpg0lsm0000gn/T//ccKv548x.out In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory In file included from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/bytearrayobject.h:9, from /Library/Frameworks/Python.framework/Versions/3.2/include/python3.2m/Python.h:73, from _configtest.c:1: /Developer/SDKs/MacOSX10.6.sdk/usr/include/stdarg.h:4:25: error: stdarg.h: No such file or directory lipo: can't figure out the architecture type of: /var/folders/_c/z033hf1s1cgfcxtxfnpg0lsm0000gn/T//ccKv548x.out failure. removing: _configtest.c _configtest.o Running from numpy source directory.Traceback (most recent call last): File "setup.py", line 196, in <module> setup_package() File "setup.py", line 189, in setup_package configuration=configuration ) File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/core.py", line 148, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 917, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command cmd_obj.run() File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build.py", line 37, in run old_build.run(self) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/command/build.py", line 126, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/cmd.py", line 313, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/3.2/lib/python3.2/distutils/dist.py", line 936, in run_command cmd_obj.run() File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 169, in build_sources self.build_extension_sources(ext) File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 328, in build_extension_sources sources = self.generate_sources(sources, ext) File "/Users/adammcnicol/Desktop/numpy-1.6.1/build/py3k/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 410, in generate_config_h moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir) File "numpy/core/setup.py", line 41, in check_types out = check_types(*a, **kw) File "numpy/core/setup.py", line 271, in check_types "Cannot compile 'Python.h'. Perhaps you need to "\ SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. Message: 3 Date: Sun, 18 Dec 2011 09:49:00 +0100 From: Ralf Gommers <ralf.gommers(a)googlemail.com> Subject: Re: [Numpy-discussion] Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 To: Discussion of Numerical Python <numpy-discussion(a)scipy.org> Message-ID: <CABL7CQh-+t+6p5z_S_JVycRCB-FWK0Q3wiAWjazgmDp8AJkKqw(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" On Sat, Dec 17, 2011 at 12:59 PM, McNicol, Adam <amcnicol(a)longroad.ac.uk>wrote: > ** > > Hi There, > > Thanks for the responses. > > At this point I would settle from just being able to install matplotlib. > Even if some of the functionality isn't present currently that is fine. > > I'm afraid my knowledge of Python falls down about here as well. I > installed Python 3.2.2 via the installer from Python.org so I have no idea > whether Python.h is present or where indeed I would find it or how I would > add it to the search path. > > Do I have to install from source or something like that? > No, your Python install should be fine if you just got the dmg installer from python.org. I recommend you install the OS X SDKs and distribute ( http://pypi.python.org/pypi/distribute), as I said before, and try again to compile numpy. Unfortunately you have chosen a difficult combination of OS and Python version, so we don't have binary installers you can use (yet). Ralf > Thanks again, > > > Adam. > > > -----Original Message----- > From: McNicol, Adam > Sent: Fri 12/16/2011 11:07 PM > To: numpy-discussion(a)scipy.org > Subject: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 > > Hi There, > > I am very new to numpy and have really only started investigating it as > one of my students needs some functionality from matplotlib. I have managed > to install everything under Windows for work in class but I use a Mac at > home and have been struggling all night to get it to build and install. > > I should mention that I am using Python 3.2.2 both in school and at home > and it isn't an option to use Python 2.7 as all of the rest of my class is > taught in Python 3. I also have the most recent version of Xcode installed. > > I have installed the correct build of gcc-4.2 with Fortran (gcc-4.2 (Apple > build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)) from > http://r.research.att.com/tools/ > > I then followed the install instructions but the build fails with the > following message: > > File "numpy/core/setup.py", line 271, in check_types > "Cannot compile 'Python.h'. Perhaps you need to "\ > SystemError: Cannot compile 'Python.h'. Perhaps you need to install > python-dev|python-devel. > > I have got no idea what to do with this error message. Any help would be > much appreciated. > > Kind Regards, > > > Adam. > > > _______________________________________________ > NumPy-Discussion mailing list > NumPy-Discussion(a)scipy.org > http://mail.scipy.org/mailman/listinfo/numpy-discussion > >

2 1

Re: [Numpy-discussion] Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2
by McNicol, Adam Dec. 18, 2011

Dec. 18, 2011

Hi There, Thanks for the responses. At this point I would settle from just being able to install matplotlib. Even if some of the functionality isn't present currently that is fine. I'm afraid my knowledge of Python falls down about here as well. I installed Python 3.2.2 via the installer from Python.org so I have no idea whether Python.h is present or where indeed I would find it or how I would add it to the search path. Do I have to install from source or something like that? Thanks again, Adam. -----Original Message----- From: McNicol, Adam Sent: Fri 12/16/2011 11:07 PM To: numpy-discussion(a)scipy.org Subject: Problem installing NumPy with Python 3.2.2/MacOS X 10.7.2 Hi There, I am very new to numpy and have really only started investigating it as one of my students needs some functionality from matplotlib. I have managed to install everything under Windows for work in class but I use a Mac at home and have been struggling all night to get it to build and install. I should mention that I am using Python 3.2.2 both in school and at home and it isn't an option to use Python 2.7 as all of the rest of my class is taught in Python 3. I also have the most recent version of Xcode installed. I have installed the correct build of gcc-4.2 with Fortran (gcc-4.2 (Apple build 5666.3) with GNU Fortran 4.2.4 for Mac OS X 10.7 (Lion)) from http://r.research.att.com/tools/ I then followed the install instructions but the build fails with the following message: File "numpy/core/setup.py", line 271, in check_types "Cannot compile 'Python.h'. Perhaps you need to "\ SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel. I have got no idea what to do with this error message. Any help would be much appreciated. Kind Regards, Adam.

2 1

Testing the python buffer protocol (bf_getbuffer / tp_as_buffer)
by Soeren Sonnenburg Dec. 18, 2011

Dec. 18, 2011

Hi, I've implemented the buffer protocol (http://www.python.org/dev/peps/pep-3118/) for some matrix class and when I manually call PyObject_GetBuffer on that object I see that I get the right matrix. Now I'd like to see numpy use the buffer protocol of my class. Does anyone know how to test that? What do I need to write, just x=MyMatrix([1,2,3]) y=numpy.array(x) (that doesn't call the buffer function though - so it must be sth else)? Any ideas? Soeren -- For the one fact about the future of which we can be certain is that it will be utterly fantastic. -- Arthur C. Clarke, 1962

4 6