[Numpy-discussion] test for long double support
What is the recommended way to test for long double and clongdouble? Is it: #if NPY_SIZEOF_LONGDOUBLE == NPY_SIZEOF_DOUBLE ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Difference in astype() for scalars and arrays?
On Monday 13 September 2010 Pauli Virtanen wrote: Doesn't seem correct -- please file a bug ticket. I did that: http://projects.scipy.org/numpy/ticket/1611 Regards, Lorenz ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] test for long double support
Neal Becker wrote: What is the recommended way to test for long double and clongdouble? Is it: #if NPY_SIZEOF_LONGDOUBLE == NPY_SIZEOF_DOUBLE I guess I found it? #if HAVE_LONG_DOUBLE// defined in pyconfig.h ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] how to store variable length string in array and get single char by it's position?
On Tue, Sep 14, 2010 at 9:25 AM, kee chen keekychen.sha...@gmail.com wrote: Dear All, Suppose I have a list group some kind like DNA sequence: 1 ATGCATGCAATTGGCC 2 ATGCATGCAATTGGCCATCD 3 CATGCAATTGGC .. 10 CATGCAAATTGGC the string length of each item is not sure and may get change/update later, then how can I store above in a numpy array (include the ID) and easy to get the single value? for example 1. ATGCATGCAATTGGCC I want get the first T then I use something like array[1][1], means A[T]G.. and if I want to update the 3rd postion I can use array[1][2] = T to set the AT[G]C... to AT[T]C...? How about using a python list: array = ['ATGC', 'CATGA', 'A'] array[0][1] 'T' ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] how to store variable length string in array and get single char by it's position?
On 09/14/2010 11:33 AM, Keith Goodman wrote: On Tue, Sep 14, 2010 at 9:25 AM, kee chenkeekychen.sha...@gmail.com wrote: Dear All, Suppose I have a list group some kind like DNA sequence: 1 ATGCATGCAATTGGCC 2 ATGCATGCAATTGGCCATCD 3 CATGCAATTGGC .. 10 CATGCAAATTGGC the string length of each item is not sure and may get change/update later, then how can I store above in a numpy array (include the ID) and easy to get the single value? for example 1. ATGCATGCAATTGGCC I want get the first T then I use something like array[1][1], means A[T]G.. and if I want to update the 3rd postion I can use array[1][2] = T to set the AT[G]C... to AT[T]C...? How about using a python list: array = ['ATGC', 'CATGA', 'A'] array[0][1] 'T' ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion Variable length is incompatible with numpy: 'NumPy arrays have a fixed size at creation, unlike Python lists (which can grow dynamically).' http://docs.scipy.org/doc/numpy/user/whatisnumpy.html So you have to allocate the space for the largest sequence - although you can try using Scipy's sparse matrix (where nucleotides/amino acids are coded in numbers starting at 1 such that zeros code the empty areas. If lists (or dictionaries) don't work for you, you might want to explore bioinformatics packages like 'pygr' (http://code.google.com/p/pygr/) and Biopython (http://biopython.org/wiki/Main_Page) or try more general approaches such hdf5 and pytables. Bruce ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Can we freeze the subversion repository and move to github this week?
On Sep 13, 2010, at 3:46 PM, Charles R Harris wrote: On Mon, Sep 13, 2010 at 2:33 PM, Travis Oliphant oliph...@enthought.com wrote: Are we ready to do this yet? I know there were some outstanding questions. Are there major concerns remaining? Or, is it just picking a time to freeze subversion when someone like David or Pauli who know how to move the repository to github correctly a time to do it. I didn't see any problems, but I didn't use the test repository that much. Maybe we should just make the jump and iron out any little wrinkles as they show up. Losing small bits of history doesn't bother me much. I think you guys have a big chore ahead of you to merge the refactored stuff while keeping all the fixes that have gone in since the fork. Good Luck! I know. That's why I want to do it with git as much as possible... ;-) -Travis ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Can we freeze the subversion repository and move to github this week?
On Sep 13, 2010, at 6:20 PM, Pauli Virtanen wrote: Mon, 13 Sep 2010 21:41:18 +, Pauli Virtanen wrote: [clip] I can upload a final repository today/tomorrow. If it seems OK, we can freeze SVN trunk a few days after that. Or we can freeze the trunk sooner than that after the final repo is up, and patch up things manually, if something turns up (unlikely). Here we go: http://github.com/numpy/numpy http://github.com/numpy/vendor Thanks! This is really great work. So much thanks is due to Pauli and David for making this happen. I will get Aaron River to freeze the SVN trunk as well as work on trac integration. There may be some learning for using the git workflow, and but it sounds like there are some good tutorials for doing it. I've heard several people say that once they used git, they can't imagine going back to SVN. -Travis ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] test for long double support
On 14 September 2010 12:47, Neal Becker ndbeck...@gmail.com wrote: Neal Becker wrote: What is the recommended way to test for long double and clongdouble? Is it: #if NPY_SIZEOF_LONGDOUBLE == NPY_SIZEOF_DOUBLE I guess I found it? #if HAVE_LONG_DOUBLE // defined in pyconfig.h I think these two are different things. For example, MSVC do support 'long double', it is a different type than 'double', but sizeof(long double) == sizeof(double). Also look at CPython's objimpl.h, union _gc_head, you will see an unprotected usage of 'long double', so it seems that CPython requires that the C compiler to support 'long double'. -- Lisandro Dalcin --- CIMEC (INTEC/CONICET-UNL) Predio CONICET-Santa Fe Colectora RN 168 Km 472, Paraje El Pozo Tel: +54-342-4511594 (ext 1011) Tel/Fax: +54-342-4511169 ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Can we freeze the subversion repository and move to github this week?
On Tue, Sep 14, 2010 at 4:05 PM, Travis Oliphant oliph...@enthought.com wrote: Here we go: http://github.com/numpy/numpy http://github.com/numpy/vendor Thanks! This is really great work. So much thanks is due to Pauli and David for making this happen. I will get Aaron River to freeze the SVN trunk as well as work on trac integration. Ditto thanks! There may be some learning for using the git workflow, and but it sounds like there are some good tutorials for doing it. I keep a list of resources here in case someone finds them useful: http://fperez.org/py4science/git.html I've heard several people say that once they used git, they can't imagine going back to SVN. As you were writing this, Min RK and I were discussing on IRC: minrk1 there are so many people who provide patches on github, since the process is so easy fperez I couldn't think of going back from git to svn now. :) Cheers, f ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] [OT: MATLAB] Any way to globally make Matlab struct attributes Python-property-like
On Mon, Sep 13, 2010 at 10:24 PM, David Goldsmith d.l.goldsm...@gmail.com wrote: I.e., I'd, at minimum, like to globally replace get(Handel, 'Property') with object.Property and set(Handel, 'Property', value) with object.Property = value to an arbitrary level of composition. Both structures and objects of both handle and value types work exactly like you're asking for. You're probably talking about handle graphics objects (which are just opaque numeric values representing things related to the UI), which do still require the get/set functions. They're just doubles, after all. It should be feasible to write a class that wraps them for ease of use, but that wouldn't be a topic for here. If that intrigues you, try asking about it on StackOverflow. ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] sf.net export controls for numpy/scipy
Hello, I plan to update the export controls settings for both numpy and scipy to: This project does NOT incorporate, access, call upon, or otherwise use encryption of any kind, including, but not limited to, open source algorithms and/or calls to encryption in the operating system or underlying platform. Unless I hear from someone that I overlooked something, I will make the changes tomorrow. Best, Jarrod ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Buildbot errors and failures
Just thought I'd throw these out there, they've been showing for a while. Windows XP: === ERROR: test_fromfile_tofile_seeks (test_regression.TestRegression) -- Traceback (most recent call last): File C:\buildbot\numpy\b11\numpy-install25\Lib\site-packages\numpy\core\tests\test_regression.py, line 1384, in test_fromfile_tofile_seeks ret = np.fromfile(f, count=4, dtype='u1') IOError: first argument must be an open file BSD : = gmake test /usr/local/bin/python2.6 -c 'import numpy,sys;sys.exit(not numpy.test(full, verbose=10).wasSuccessful())' Traceback (most recent call last): File string, line 1, in module File /home/doconnor/numpy-buildbot/b12/numpy-install/lib/python2.6/site-packages/numpy/__init__.py, line 136, in module import add_newdocs File /home/doconnor/numpy-buildbot/b12/numpy-install/lib/python2.6/site-packages/numpy/add_newdocs.py, line 9, in module from numpy.lib import add_newdoc File /home/doconnor/numpy-buildbot/b12/numpy-install/lib/python2.6/site-packages/numpy/lib/__init__.py, line 13, in module from polynomial import * File /home/doconnor/numpy-buildbot/b12/numpy-install/lib/python2.6/site-packages/numpy/lib/polynomial.py, line 17, in module from numpy.linalg import eigvals, lstsq File /home/doconnor/numpy-buildbot/b12/numpy-install/lib/python2.6/site-packages/numpy/linalg/__init__.py, line 48, in module from linalg import * File /home/doconnor/numpy-buildbot/b12/numpy-install/lib/python2.6/site-packages/numpy/linalg/linalg.py, line 23, in module from numpy.linalg import lapack_lite ImportError: /usr/local/lib/liblapack.so.4: Undefined symbol _gfortran_st_write Chuck ___ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion
