Mailman 3 December 2002 - SciPy-Dev

PYTHONINCLUDE and sitecustomize.py
by Pearu Peterson 30 Dec '02

30 Dec '02

On Thu, 19 Dec 2002 eric(a)localhost.localdomain wrote: > Modified Files: > build_clib.py build_ext.py Actually, build_clib.py does not need the PYTHONINCLUDE feature. I'd remove it. > Log Message: > made changes to use a PYTHONINCLUDE environment variable to search for > include files during extension building. > > (1) include directories. > Distutils knows to include files from /usr/include/python2.2 (or > wherever it is installed) whenever building extension modules. > Numeric installs its header files inside this directory when installed > as root. However, when I install Numeric in /home/eric/linux, the > header files are installed in /home/eric/linux/python2.2. Distutils > doesn't know to look in hear for headers. To solve this, I'd have to > hack all the setup.py files for modules that rely on Numeric to use my > include_dirs. This isn't so nice. > > To rectify the problem, scipy_distutils now searches for an > environment variable called PYTHONINCLUDE that uses the same syntax as > PYTHONPATH and PATH. If PYTHONINCLUDE is found, the directories > listed in it are added to the include path during compilation of C/C++ > files by build_ext.py and build_clib.py. On my machine, I specify > > export PYTHONINCLUDE=$OSDIR/include/python2.2 > > and all setup.py files work unaltered. I think this is a reasonable > solution. There is one gotcha with the implementation of this solution. Consider the following situation: Numeric is installed as root. An user installs another version of Numeric using, say, --prefix=$HOME. As a result Numeric header files are installed to $HOME/include/python2.2. Now, when building an extension module that uses Numeric and defining PYTHONINCLUDE=$HOME/include/python2.2, then the compiler argument will contain -I/usr/include/python2.2 -I$HOME/include/python2.2 As a result, wrong Numeric header files (from /usr/include/python2.2/Numeric) are being used when compiling extension modules. Obviously, $HOME/include/python2.2 should appear before /usr/include/python2.2 and that can be easily accomplished by inserting PYTHONINCLUDE directory(-ies) just before the '/usr/include/python2.2' item in self.include_dirs list. It appears from distutils code that '/usr/include/python2.2' is always the last item in the list and that makes the fix easier. However, IMHO distutils should take care of inserting <prefix>/include/python2.2 to the list include_dirs whenever --prefix=<prefix> is used. And if this will be fixed in distutils, then PYTHONINCLUDE feature becomes YAGNI. So, I would avoid introducing PYTHONINCLUDE feature because the original issue can be resolved using sitecustomize.py alone (after all that is the "standard" way to customize Python). Moreover, the other issue of adding <prefix>/lib/python<version>/site-packages (and .pth extensions) to sys.path can be resolved in sitecustomize.py as well as Perry already indicated (and users would not need to modify their PYTHONPATH). A version of sitecustomize.py is attached to this message and I'd like to propose adding this script to scipy directory. The attached sitecustomize.py script contains also a fix to distutils.util.get_platform function that is broken for Mac OSX system. This script might be useful also for back-porting other Python fixes/features to older Python versions that SciPy is supposed to support. What do you think? Pearu

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[Off-topic] Subversion.
by Prabhu Ramachandran 22 Dec '02

22 Dec '02

hi, I thought you folks might be interested in Subversion which is a replacement for CVS thats currently under development. http://subversion.tigris.org/ There is also an ONLamp article on it: http://www.onlamp.com/pub/a/onlamp/2002/10/31/subversion.html cheers, prabhu

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issues with installing Numeric in a user directory
by eric jones 20 Dec '02

20 Dec '02

I have been building/installing 3rd party python (numeric/scipy/etc.) as a user instead of as root lately. This means the packages are installed in a non-standard place (like /home/eric/linux or /home/eric/sunos). I do this using: python setup.py install --prefix=$OSDIR where OSDIR is an environment variable set to specify a platform dependent path (my home directory is shared between about 6 different architectures). The user (instead of root) installed locations have caused several annoyances, one with include directories and one with .pth files. They have both manifested themselves when dealing with Numeric. (1) include directories. Distutils knows to include files from /usr/include/python2.2 (or wherever it is installed) whenever building extension modules. Numeric installs its header files inside this directory when installed as root. However, when I install Numeric in /home/eric/linux, the header files are installed in /home/eric/linux/python2.2. Distutils doesn't know to look in hear for headers. To solve this, I'd have to hack all the setup.py files for modules that rely on Numeric to use my include_dirs. This isn't so nice. To rectify the problem, scipy_distutils now searches for an environment variable called PYTHONINCLUDE that uses the same syntax as PYTHONPATH and PATH. If PYTHONINCLUDE is found, the directories listed in it are added to the include path during compilation of C/C++ files by build_ext.py and build_clib.py. On my machine, I specify export PYTHONINCLUDE=$OSDIR/include/python2.2 and all setup.py files work unaltered. I think this is a reasonable solution. Has anyone solved this problem with an alternative method that might be better. (2) .pth files Numeric is a "package" that doesn't really behave as a package. It dumps all of its files in site-packages/Numeric, but it doesn't define a __init__.py file. Instead, it also puts a Numeric.pth file in site-packages that tells python to also search site-packages/Numeric for modules. This works fine when Numeric is installed as root, but it doesn't work when it is installed in non-standard places. This is because .pth files are only expaneded when they exist in the "system" locations. They are ignored anywhere else in the search path. As a result, after installing Numeric with "python setup.py install --prefix=$OSDIR", importing Numeric fails even if PYTHONPATH=$OSDIR/lib/python2.2/site-packages The fix is easy for someone who understands what is going on -- add $OSDIR/lib/python2.2/site-packages/Numeric to the PYTHONPATH. However, the uninitiated may flail around a long time trying to figure out why installing a package to there standard location doesn't work -- especially if it has worked for every other package they have installed. I haven't figured out a nice work around here, other than actually making Numeric a real package which I doubt is even close to an option. Does anyone else have a better solution? Thanks, eric ---------------------------------------------- eric jones 515 Congress Ave www.enthought.com Suite 1614 512 536-1057 Austin, Tx 78701

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RE:HELLO
by EKI OLUWA 19 Dec '02

19 Dec '02

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Restructuring of Chaco/Kiva/FreeType into SciPy
by David C. Morrill 19 Dec '02

19 Dec '02

We are looking at restructuring the Chaco/Kiva projects so that they are contained within the overall SciPy source hierarchy. In particular, the changes being considered are: - Move Chaco from the top level of CVS to SciPy - Move Kiva from the top level of CVS to SciPy - Move FreeType from inside of Kiva to SciPy There will also be corresponding changes made to various 'setup.py' and 'setup_xxx.py' scripts to support building Chaco/Kiva as part of SciPy, and also to allow them to be built stand-alone, apart from the rest of SciPy. I'm hoping that any CVS wizards out there can suggest the best way to do this, without creating any more CVS gunk (Attic files, etc.) than necessary. For example, could we simply move directories around? What are the pros and cons of doing that versus a large number of add/delete operations? Thanks in advance for any guidance... Dave Morrill

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PCF-ONLINE.COM
by The Portal 17 Dec '02

17 Dec '02

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problems with weave
by m.prosperi＠libero.it 16 Dec '02

16 Dec '02

hello, I've installed the binary distrib of weave on my winNT system with mingw32 2.95.2 compiler. When I run the tests I get complains because the file cl.exe is missing. Can you give me some help? regards, Marco Prosperi

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Other scipy problems on OS X
by Tim Lahey 16 Dec '02

16 Dec '02

Hi, Thanks to Eric, I've managed to get scipy to compile. After installing it, I now get the following error upon import. I start a new terminal window, start python, and then the following happens. Note that there is a cephes.so in the special directory under site-packages. Is there a PATH setting I need to fix ? Thanks, Tim Lahey Python 2.2 (#1, 07/14/02, 23:25:09) [GCC Apple cpp-precomp 6.14] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import scipy Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/lib/python2.2/site-packages/scipy/__init__.py", line 49, in ? import special, io, linalg, stats, fftpack File "/usr/lib/python2.2/site-packages/scipy/special/__init__.py", line 326, in ? from special import * File "/usr/lib/python2.2/site-packages/scipy/special/special.py", line 5, in ? from cephes import * ImportError: Failure linking new module

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Possible FreeBSD workaround
by Robert Kern 16 Dec '02

16 Dec '02

If I understand the problem correctly, we need a way to replace 'cc' with 'c++' or something similar on some systems. I propose checking for the environment variable 'CXX' and using its contents to replace the linker when it's defined. To compile on systems where gcc can't be autodetected, simply define CXX appropriately in your shell. A better solution might be to check .pydistutils.cfg for a [weave] section or similar, but that's a little more involved. Attached is a patch to build_tools.py . Please let me know if this works. I don't have a FreeBSD machine to test on. -- Robert Kern Ruddock House President kern(a)caltech.edu "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter

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Error in compiling on OS X
by Tim Lahey 15 Dec '02

15 Dec '02

Hi, I'm trying to build scipy from CVS and I get a number of errors during the compile. The compile dies upon the following compile (which I think is the first). I think the problem lies in the space in the build directory name "build/temp.darwin-6.2-Power Macintosh-2.2" which I think is also a problem earlier in the build process. Any ideas for how to fix this ? g77 -Wall -fno-second-underscore -fPIC -O3 -funroll-loops -c /Users/tjlahey/devel/scipy/special/mach/d1mach.f -o build/temp.darwin-6.2-Power Macintosh-2.2/d1mach.o g77: cannot specify -o with -c or -S and multiple compilations error: failure during compile (exit status = 256) Thanks, Tim Lahey

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