[Numpy-discussion] Error building numpy documentation
I just dowloads the latest numpy's svn version and tried to build its documentation with $ make latex on the doc subdirectory, and got the following error message: writing... Sphinx error: too many nesting section levels for LaTeX, at heading: numpy.ma.MaskedArray.__lt__ make: *** [latex] Error 1 Machine: 64 bit gentoo linux running texlive2007 Any ideas? Nadav ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy 1.3 release date ?
Wed, 04 Feb 2009 11:04:25 +0900, David Cournapeau wrote: [clip] Talking about the things I have worked on for 1.3, I did not have the time to finish everything. The things which I would like to be done before a 1.3.0 release are: - fix formatting issues that Pauli and me worked on (for locale independence and all): I believe it is mostly a matter of merging the changes in the trunk, and testing. Pauli, do you agree ? Agree, I think it should be OK, and IIRC tests passed also on Windows (well, Wine to be accurate). I don't recall anything more that would be required to do. It might be nice also to address this wart: http://scipy.org/scipy/numpy/ticket/883 for Numpy 1.3. But it's a separate issue from the locale and formatting problems. Pauli ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Few minor issues with numscons
Brian Granger wrote: The releases are on Pypi for quite some time. I converted the repo to git and put it on github, but I have not really worked on numscons for several months now for lack of time ( and because numscons it mostly done and the main limitations of numscons are not fixable without fixing some fairly major scons limitations). Basically, the repo on github is only the convertion from bzr, without any new features. Do you have plans to continue to maintain it though? I can't say for sure; I am still quite interested in working on build/distributions problems in numpy and more generally python. But in my mind, this work only really makes sense if it becomes integrated to numpy.distutils and even can be used by arbitrary python extension as some point. And that's just not realistic at this point because of some fundamental scons limitations (I would like scons to be callable from a pure python scripts, as a library). So I spent quite some time on scons itself (and more recently waf, which started as a scons fork). There is also the fundamental time problem, but we all are in the same boat on this one :) One other things I forgot to mention. I first tried the head of your git repo and numpy complained that the version of numscons (0.10) was too *old*. It wanted the version to be greater than somehting like 0.9.1, and clearly it was, so it looks like there is a bug in the numscons version parsing in numpy.distutils. Can be a stupid bug in the version check. It should be ok with numpy trunk, though. David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Error building numpy documentation
2009/2/4 Nadav Horesh nad...@visionsense.com: I just dowloads the latest numpy's svn version and tried to build its documentation with $ make latex on the doc subdirectory, and got the following error message: writing... Sphinx error: too many nesting section levels for LaTeX, at heading: numpy.ma.MaskedArray.__lt__ make: *** [latex] Error 1 Machine: 64 bit gentoo linux running texlive2007 Any ideas? No ideas, but this has been reported before: http://projects.scipy.org/pipermail/numpy-discussion/2009-January/039917.html I've filed a ticket: http://scipy.org/scipy/numpy/ticket/998 Cheers, Scott ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy 1.3 release date ?
Scott Sinclair wrote: There are a bunch of documentation patches that should to be reviewed and applied to SVN before the release (especially those marked 'Needs review' or better). http://docs.scipy.org/numpy/patch/ In my mind, documentations fixes are much less important than code, not because documentation matters less, but because it can be handled at the last moment much more easily - there is little chance that a doc change breaks on windows only, for example. David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] poly1d left versus right multiplication with np numbers
On Feb 4, 2009, at 11:00 AM, josef.p...@gmail.com wrote: I just had a hard to find bug in my program. poly1d treats numpy scalars differently than python numbers when left or right multiplication is used. Essentially, if the first term is the numpy scalar, multiplied by a polynomial, then the result is an np.array. If the order is reversed, then the result is an instance of np.poly1d. The return types are also the same for numpy arrays, which is at least understandable, although a warning would be good) When using plain (python) numbers, then both left and right multiplication of the number with the polynomial returns a polynomial. Is this a bug or a feature? I didn't see it mentioned in the docs. Looks like yet another example of ticket #826: http://scipy.org/scipy/numpy/ticket/826 This one is getting quite a problem, and I have no idea how to fix it... ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Resolver One -- .NET spreadsheet with NumPy -- beta testers?
Hi all We're about to release the first public beta of Resolver One, our Pythonic spreadsheet, with (rather basic) NumPy integration. It requires 32-bit Windows and .NET 2.0SP1 to run, so it may not be appropriate for everyone, but -- if anyone is interested in playing with it -- it would be really useful to have some real live NumPy users telling us what we could improve. If anyone here would like to try it out, please let me know, and I'll arrange beta access. Cheers William http://resolversystems.com/ ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] poly1d left versus right multiplication with np numbers
On Wed, Feb 4, 2009 at 11:19 AM, Pierre GM pgmdevl...@gmail.com wrote: On Feb 4, 2009, at 11:00 AM, josef.p...@gmail.com wrote: I just had a hard to find bug in my program. poly1d treats numpy scalars differently than python numbers when left or right multiplication is used. Essentially, if the first term is the numpy scalar, multiplied by a polynomial, then the result is an np.array. If the order is reversed, then the result is an instance of np.poly1d. The return types are also the same for numpy arrays, which is at least understandable, although a warning would be good) When using plain (python) numbers, then both left and right multiplication of the number with the polynomial returns a polynomial. Is this a bug or a feature? I didn't see it mentioned in the docs. Looks like yet another example of ticket #826: http://scipy.org/scipy/numpy/ticket/826 This one is getting quite a problem, and I have no idea how to fix it... Thanks, yes it looks exactly like this ticket. At least, once I know about it, it is not too difficult to work around, but it costs a lot of debugging time to figure this out. Josef ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy 1.3 release date ?
Scott Sinclair scott.sinclair...@gmail.com wrote: 2009/2/4 David Cournapeau courn...@gmail.com: On Tue, Feb 3, 2009 at 11:49 PM, Pierre GM pgmdevl...@gmail.com wrote: All, When can we expect numpy 1.3 to be released ? I think official 2.6 support (with binaries for the platforms where we support binaries), x64 support and everything which has been done already would be enough to make a release. I'd like to see a self-consistent and reasonably recent numpy/scipy make the Ubuntu 9.04 FeatureFreeze deadline of 19 February. Is this possible? One of the reasons we had discussed doing more frequent releases was to get consistent and recent packages in the mainstream Linuxes, and Ubuntu is very popular in our community. There are a bunch of documentation patches that should to be reviewed and applied to SVN before the release (especially those marked 'Needs review' or better). http://docs.scipy.org/numpy/patch/ At this point, we're focussing on getting semi-decent drafts of as many docstrings as possible rather than on polishing the ones we have as drafts, on the basis of something is always better than nothing as long as it's not wrong. So, please don't hold up a release for review, just get as many drafts in as possible. Also, it has become clear that we need separate technical and writing reviews, as a number of pages marked as reviewed are deficient in one or the other area, probably the one that wasn't the strength of the reviewer. That entails discussion and revamping of the site, which can happen once we have a larger percentage of the docstrings in draft form. (Any discussion on the merits of this should take place on scipy-dev, which is the home of doc discussions.) --jh-- ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy 1.3 release date ?
2009/2/4 David Cournapeau da...@ar.media.kyoto-u.ac.jp: Scott Sinclair wrote: There are a bunch of documentation patches that should to be reviewed and applied to SVN before the release (especially those marked 'Needs review' or better). http://docs.scipy.org/numpy/patch/ In my mind, documentations fixes are much less important than code, not because documentation matters less, but because it can be handled at the last moment much more easily - there is little chance that a doc change breaks on windows only, for example. Sure. Just trying to encourage a few more reviews and documentation contributions. Cheers, Scott ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] porting NumPy to Python 3
Hi Ondrej, To get 2to3 to run without warnings, the following files require minor changes: - numpy/distutils/fcompiler/intel.py - numpy/distutils/misc_util.py - numpy/distutils/command/build_src.py - numpy/f2py/crackfortran.py - numpy/lib/function_base.py - numpy/linalg/lapack_lite/make_lite.py There are also other (possibly many, still working on this) files that require syntactic changes to run post 2to3. Is there anywhere specific I should upload these changes? Is this list appropriate? Is there a developer I can send these and future patches to? James. Date: Tue, 3 Feb 2009 01:03:15 -0800 From: Ondrej Certik ond...@certik.cz Subject: Re: [Numpy-discussion] porting NumPy to Python 3 To: Discussion of Numerical Python numpy-discussion@scipy.org Message-ID: 85b5c3130902030103w69180a6bm4143050b4b82b...@mail.gmail.com Content-Type: text/plain; charset=UTF-8 Hi James, On Thu, Jan 29, 2009 at 2:11 AM, James Watson watson@gmail.com wrote: Hi, I am interested in contributing to the port of NumPy to Python 3. Who I should coordinate effort with? I have started at the Python end of the problem (as opposed to http://www.scipy.org/Python3k), e.g. I have several patches to get 2to3 to work on NumPy's Python source code. I am sorry that noone has replied to your email. Could you please upload your patches somewhere? Ondrej ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] genfromtxt view with object dtype
hi, i am using genfromtxt, with a dtype like this:
[('seqid', '|S24'), ('source', '|S16'), ('type', '|S16'), ('start',
'i4'), ('end', 'i4'), ('score', 'f8'), ('strand', '|S1'), ('phase',
'i4'), ('attrs', '|O4')]
where i'm having problems with the attrs column which i'd like to be a
dict. i can specify a convertor to parse a string into a dict, and it
is correctly converted to a dict,
but then in io.py it tries to take a view() of that dtype and it gives
the error:
A = np.genfromtxt(fname, **kwargs)
File /usr/lib/python2.5/site-packages/numpy/lib/io.py, line 922,
in genfromtxt
output = rows.view(dtype)
TypeError: Cannot change data-type for object array.
is there anyway around this or must that col be kept as a string?
it seems like genfromtxt expects you to specify either a dtype _or_ a
convertor, not both.
thanks,
-brent
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Re: [Numpy-discussion] porting NumPy to Python 3
On Wed, Feb 4, 2009 at 10:02 AM, James Watson watson@gmail.com wrote: Hi Ondrej, To get 2to3 to run without warnings, the following files require minor changes: - numpy/distutils/fcompiler/intel.py - numpy/distutils/misc_util.py - numpy/distutils/command/build_src.py - numpy/f2py/crackfortran.py - numpy/lib/function_base.py - numpy/linalg/lapack_lite/make_lite.py There are also other (possibly many, still working on this) files that require syntactic changes to run post 2to3. Is there anywhere specific I should upload these changes? Is this list appropriate? Is there a developer I can send these and future patches to? Maybe we could add a python 3 milestone so folks could post tickets for these sorts of things. For the time being you could just post to the list here with the patches and something in the subject line that identifies it as a patch for python 3. I think we could make any small changes as long as they are compatible with python 2.4. Chuck ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Numpy 1.3 release date ?
On Wed, Feb 4, 2009 at 10:01 AM, j...@physics.ucf.edu wrote: Scott Sinclair scott.sinclair...@gmail.com wrote: 2009/2/4 David Cournapeau courn...@gmail.com: On Tue, Feb 3, 2009 at 11:49 PM, Pierre GM pgmdevl...@gmail.com wrote: All, When can we expect numpy 1.3 to be released ? I think official 2.6 support (with binaries for the platforms where we support binaries), x64 support and everything which has been done already would be enough to make a release. I'd like to see a self-consistent and reasonably recent numpy/scipy make the Ubuntu 9.04 FeatureFreeze deadline of 19 February. Is this possible? One of the reasons we had discussed doing more frequent releases was to get consistent and recent packages in the mainstream Linuxes, and Ubuntu is very popular in our community. That deadline is pretty close ;) There has been a dearth of developer time these last few months, what with work, holidays, and dissertations, and I don't know when that is going to get better. Chuck ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] porting NumPy to Python 3
Charles R Harris wrote: On Wed, Feb 4, 2009 at 10:02 AM, James Watson watson@gmail.com mailto:watson@gmail.com wrote: Hi Ondrej, To get 2to3 to run without warnings, the following files require minor changes: - numpy/distutils/fcompiler/intel.py - numpy/distutils/misc_util.py - numpy/distutils/command/build_src.py - numpy/f2py/crackfortran.py - numpy/lib/function_base.py - numpy/linalg/lapack_lite/make_lite.py There are also other (possibly many, still working on this) files that require syntactic changes to run post 2to3. Is there anywhere specific I should upload these changes? Is this list appropriate? Is there a developer I can send these and future patches to? Maybe we could add a python 3 milestone so folks could post tickets for these sorts of things. For the time being you could just post to the list here with the patches and something in the subject line that identifies it as a patch for python 3. I think we could make any small changes as long as they are compatible with python 2.4. Chuck ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion If you follow Guido's recommendation (at the bottom of http://docs.python.org/dev/3.0/whatsnew/3.0.html), then we should first be compatible with Python 2.6 (about the current stage) . Then compatible using Python 2.3 with the -3 flag (warn about Python 3.x incompatibilities) and fix warnings like: numpy/core/__init__.py:11: DeprecationWarning: the cPickle module has been removed in Python 3.0 (Of course you lose speed of cPickle if you blindly change it to use the old Pickle in Python 2.x) Finally use the 2to3 tool to get a Python 3 version. Bruce ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] ImportError: No module named dateutil.parser
Hi, I just updated to the latest SVN but I get a failure when running the tests due to missing dateutil.parser. Should this module exist in Numpy or just a inappropriate test? Bruce numpy.test() Running unit tests for numpy NumPy version 1.3.0.dev6338 NumPy is installed in /usr/lib64/python2.5/site-packages/numpy Python version 2.5.2 (r252:60911, Sep 30 2008, 15:42:03) [GCC 4.3.2 20080917 (Red Hat 4.3.2-4)] nose version 0.10.3 .....K.E.. .. == ERROR: Tests updatemapper -- Traceback (most recent call last): File /usr/lib64/python2.5/site-packages/numpy/lib/tests/test__iotools.py, line 133, in test_upgrademapper import dateutil.parser ImportError: No module named dateutil.parser -- Ran 1888 tests in 6.084s FAILED (KNOWNFAIL=9, errors=1) nose.result.TextTestResult run=1888 errors=1 failures=0 ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] ImportError: No module named dateutil.parser
On Wed, Feb 4, 2009 at 14:40, Bruce Southey bsout...@gmail.com wrote: Hi, I just updated to the latest SVN but I get a failure when running the tests due to missing dateutil.parser. Should this module exist in Numpy or just a inappropriate test? It's a bad test. -- Robert Kern I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth. -- Umberto Eco ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] ImportError: No module named dateutil.parser
On Wed, Feb 4, 2009 at 14:54, Pierre GM pgmdevl...@gmail.com wrote: On Feb 4, 2009, at 3:40 PM, Bruce Southey wrote: Hi, I just updated to the latest SVN but I get a failure when running the tests due to missing dateutil.parser. Should this module exist in Numpy or just a inappropriate test? I put the corresponding tests in a try/except ImportError block (r6339), that should fix it. No, rewrite the test to not use external libraries, please. Test the functionality without needing dateutils. -- Robert Kern I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth. -- Umberto Eco ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Multiplying a matrix by a vector
Bit of a newb question I suspect... I have a matrix and a vector which has the same number of elements as the matrix has rows. I want to multiply each element in a row in the matrix by the corresponding element in the vector. I can obviously do this with a loop, but am guessing there is a more elegant (and faster?) solution. Just for clarity... Matrix [X1, X2, X3] [Y1, Y2, Y3] Vector [A, B] Desired result [X1*A, X2*A, X3*A] [Y1*B, Y2*B, Y3*B] -- View this message in context: http://www.nabble.com/Multiplying-a-matrix-by-a-vector-tp21839828p21839828.html Sent from the Numpy-discussion mailing list archive at Nabble.com. ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Array dtype problems
Hello,
I'm having an issue with 'array' dtypes; if I do this:
mydtype = numpy.dtype(('i', (4,)))
arr = numpy.empty((100,), dtype=mydtype)
then the array datatype shape is absorbed into the shape of the
array. This simplifies indexing, but is really annoying as it means
that the dtype doesn't round trip; I can't even use use astype as it
complains about a shape mismatch. How can I create an array in a
manner that preserves the dtype array information? Or is there a way
to take an existing array of the correct shape and re-cast it to use
an array dtype?
Thanks,
Andrew Collette
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Re: [Numpy-discussion] ImportError: No module named dateutil.parser
On Feb 4, 2009, at 3:56 PM, Robert Kern wrote: No, rewrite the test to not use external libraries, please. Test the functionality without needing dateutils. OK then, should be fixed in r6340. ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] ImportError: No module named dateutil.parser
On Wed, Feb 4, 2009 at 16:12, Pierre GM pgmdevl...@gmail.com wrote: On Feb 4, 2009, at 3:56 PM, Robert Kern wrote: No, rewrite the test to not use external libraries, please. Test the functionality without needing dateutils. OK then, should be fixed in r6340. Thank you! -- Robert Kern I have come to believe that the whole world is an enigma, a harmless enigma that is made terrible by our own mad attempt to interpret it as though it had an underlying truth. -- Umberto Eco ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] Multiplying a matrix by a vector
Simon Palmer wrote: I have a matrix and a vector which has the same number of elements as the matrix has rows. I want to multiply each element in a row in the matrix by the corresponding element in the vector. M = np.arange(6).reshape((2,3)) M array([[0, 1, 2], [3, 4, 5]]) v = np.array((4,5)).reshape((-1,1)) # make it a column vector v array([[4], [5]]) M * v array([[ 0, 4, 8], [15, 20, 25]]) you can also do it with np.newaxis: v = np.array((4,5)) M * v[:,np.newaxis] array([[ 0, 4, 8], [15, 20, 25]]) http://www.scipy.org/EricsBroadcastingDoc If you are really working with a matrix, rather than a 2-d array, you may want to look at the np.matrix object. -Chris -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/ORR(206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception chris.bar...@noaa.gov ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
[Numpy-discussion] Renaming a field of an object array
All,
I'm a tad puzzled by the following behavior (I'm trying to correct a
bug in genfromtxt):
I'm creating an empty structured ndarray, using np.object as dtype.
a = np.empty(1,dtype=[('',np.object)])
array([(None,)],
dtype=[('f0', '|O4')])
Now, I'd like to rename the field:
a.view([('NAME',np.object)])
TypeError: Cannot change data-type for object array.
I understand why I can't change the *type* of the field, but not why I
can't change its name that way. What would be an option that wouldn't
involve creating a new array ?
Thx in advance.
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Re: [Numpy-discussion] Renaming a field of an object array
On Wed, Feb 4, 2009 at 2:50 PM, Pierre GM pgmdevl...@gmail.com wrote:
All,
I'm a tad puzzled by the following behavior (I'm trying to correct a
bug in genfromtxt):
I'm creating an empty structured ndarray, using np.object as dtype.
a = np.empty(1,dtype=[('',np.object)])
array([(None,)],
dtype=[('f0', '|O4')])
Now, I'd like to rename the field:
a.view([('NAME',np.object)])
TypeError: Cannot change data-type for object array.
I understand why I can't change the *type* of the field, but not why I
can't change its name that way. What would be an option that wouldn't
involve creating a new array ?
Thx in advance.
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hi, i was looking at this as well. the code in arrayobject.c doesnt
match the error string. i changed the code to do what the error string
says and seems thing to work.
i think the if-block below it should also use xor (not changed in this
patch), but i'm not a c programmer so i may be missing something
obvious.
svn diff numpy/core/src/arrayobject.c
Index: numpy/core/src/arrayobject.c
===
--- numpy/core/src/arrayobject.c(revision 6338)
+++ numpy/core/src/arrayobject.c(working copy)
@@ -6506,9 +6506,16 @@
PyErr_SetString(PyExc_TypeError, invalid data-type for array);
return -1;
}
-if (PyDataType_FLAGCHK(newtype, NPY_ITEM_HASOBJECT) ||
-PyDataType_FLAGCHK(newtype, NPY_ITEM_IS_POINTER) ||
-PyDataType_FLAGCHK(self-descr, NPY_ITEM_HASOBJECT) ||
+if (PyDataType_FLAGCHK(newtype, NPY_ITEM_HASOBJECT) ^
+PyDataType_FLAGCHK(self-descr, NPY_ITEM_HASOBJECT)) {
+PyErr_SetString(PyExc_TypeError, \
+Cannot change data-type for object \
+array.);
+Py_DECREF(newtype);
+return -1;
+}
+
+if (PyDataType_FLAGCHK(newtype, NPY_ITEM_IS_POINTER) ||
PyDataType_FLAGCHK(self-descr, NPY_ITEM_IS_POINTER)) {
PyErr_SetString(PyExc_TypeError, \
Cannot change data-type for object \
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Re: [Numpy-discussion] Numpy 1.3 release date ?
On Thu, Feb 5, 2009 at 2:48 AM, Charles R Harris charlesr.har...@gmail.com wrote: On Wed, Feb 4, 2009 at 10:01 AM, j...@physics.ucf.edu wrote: Scott Sinclair scott.sinclair...@gmail.com wrote: 2009/2/4 David Cournapeau courn...@gmail.com: On Tue, Feb 3, 2009 at 11:49 PM, Pierre GM pgmdevl...@gmail.com wrote: All, When can we expect numpy 1.3 to be released ? I think official 2.6 support (with binaries for the platforms where we support binaries), x64 support and everything which has been done already would be enough to make a release. I'd like to see a self-consistent and reasonably recent numpy/scipy make the Ubuntu 9.04 FeatureFreeze deadline of 19 February. Is this possible? One of the reasons we had discussed doing more frequent releases was to get consistent and recent packages in the mainstream Linuxes, and Ubuntu is very popular in our community. That deadline is pretty close ;) I think it is safe to say it will not be possible to release numpy for that date. Concerning Ubuntu, it sounds more realistic to make sure it is updated to 1.2.1, and if possible to release 0.7.0. David ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] genfromtxt view with object dtype
OK, Brent, try r6341.
I fixed genfromtxt for cases like yours (explicit dtype involving a
np.object).
Note that the fix won't work if the dtype is nested and involves
np.objects (as we would hit the pb of renaming fields we observed...).
Let me know how it goes.
P.
On Feb 4, 2009, at 4:03 PM, Brent Pedersen wrote:
On Wed, Feb 4, 2009 at 9:36 AM, Pierre GM pgmdevl...@gmail.com
wrote:
On Feb 4, 2009, at 12:09 PM, Brent Pedersen wrote:
hi, i am using genfromtxt, with a dtype like this:
[('seqid', '|S24'), ('source', '|S16'), ('type', '|S16'), ('start',
'i4'), ('end', 'i4'), ('score', 'f8'), ('strand', '|S1'),
('phase',
'i4'), ('attrs', '|O4')]
Brent,
Please post a simple, self-contained example with a few lines of the
file you want to load.
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hi pierre, here is an example.
thanks,
-brent
##
import numpy as np
from cStringIO import StringIO
gffstr = \
##gff-version 3
1\tucb\tgene\t2234602\t2234702\t.\t-\t.
\tID
=
grape_1_2234602_2234702
;match
=
EVM_prediction_supercontig_1.248,EVM_prediction_supercontig_1.248.mRNA
1\tucb\tgene\t2300292\t2302123\t.\t+\t.
\tID=grape_1_2300292_2302123;match=EVM_prediction_supercontig_244.8
1\tucb\tgene\t2303615\t2303967\t.\t+\t.
\tID=grape_1_2303615_2303967;match=EVM_prediction_supercontig_244.8
1\tucb\tgene\t2303616\t2303966\t.\t+\t.
\tParent=grape_1_2303615_2303967
1\tucb\tgene\t3596400\t3596503\t.\t-\t.
\tID=grape_1_3596400_3596503;match=evm.TU.supercontig_167.27
1\tucb\tgene\t3600651\t3600977\t.\t-\t.
\tmatch=evm.model.supercontig_1217.1,evm.model.supercontig_1217.1.mRNA
dtype = {'names' :
('seqid', 'source', 'type', 'start', 'end',
'score', 'strand', 'phase', 'attrs') ,
'formats':
['S24', 'S16', 'S16', 'i4', 'i4', 'f8',
'S1', 'i4', 'S128']}
#OK with S128 for attrs
print np.genfromtxt(StringIO(gffstr), dtype = dtype)
def _attr(kvstr):
pairs = [kv.split(=) for kv in kvstr.split(;)]
return dict(pairs)
# change S128 to object to have col attrs as dictionary
dtype['formats'][-1] = 'O'
converters = {8: _attr }
#NOT OK
print np.genfromtxt(StringIO(gffstr), dtype = dtype,
converters=converters)
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Re: [Numpy-discussion] genfromtxt view with object dtype
On Wed, Feb 4, 2009 at 8:51 PM, Pierre GM pgmdevl...@gmail.com wrote:
OK, Brent, try r6341.
I fixed genfromtxt for cases like yours (explicit dtype involving a
np.object).
Note that the fix won't work if the dtype is nested and involves
np.objects (as we would hit the pb of renaming fields we observed...).
Let me know how it goes.
P.
that fixes it. thanks again pierre!
-b
On Feb 4, 2009, at 4:03 PM, Brent Pedersen wrote:
On Wed, Feb 4, 2009 at 9:36 AM, Pierre GM pgmdevl...@gmail.com
wrote:
On Feb 4, 2009, at 12:09 PM, Brent Pedersen wrote:
hi, i am using genfromtxt, with a dtype like this:
[('seqid', '|S24'), ('source', '|S16'), ('type', '|S16'), ('start',
'i4'), ('end', 'i4'), ('score', 'f8'), ('strand', '|S1'),
('phase',
'i4'), ('attrs', '|O4')]
Brent,
Please post a simple, self-contained example with a few lines of the
file you want to load.
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hi pierre, here is an example.
thanks,
-brent
##
import numpy as np
from cStringIO import StringIO
gffstr = \
##gff-version 3
1\tucb\tgene\t2234602\t2234702\t.\t-\t.
\tID
=
grape_1_2234602_2234702
;match
=
EVM_prediction_supercontig_1.248,EVM_prediction_supercontig_1.248.mRNA
1\tucb\tgene\t2300292\t2302123\t.\t+\t.
\tID=grape_1_2300292_2302123;match=EVM_prediction_supercontig_244.8
1\tucb\tgene\t2303615\t2303967\t.\t+\t.
\tID=grape_1_2303615_2303967;match=EVM_prediction_supercontig_244.8
1\tucb\tgene\t2303616\t2303966\t.\t+\t.
\tParent=grape_1_2303615_2303967
1\tucb\tgene\t3596400\t3596503\t.\t-\t.
\tID=grape_1_3596400_3596503;match=evm.TU.supercontig_167.27
1\tucb\tgene\t3600651\t3600977\t.\t-\t.
\tmatch=evm.model.supercontig_1217.1,evm.model.supercontig_1217.1.mRNA
dtype = {'names' :
('seqid', 'source', 'type', 'start', 'end',
'score', 'strand', 'phase', 'attrs') ,
'formats':
['S24', 'S16', 'S16', 'i4', 'i4', 'f8',
'S1', 'i4', 'S128']}
#OK with S128 for attrs
print np.genfromtxt(StringIO(gffstr), dtype = dtype)
def _attr(kvstr):
pairs = [kv.split(=) for kv in kvstr.split(;)]
return dict(pairs)
# change S128 to object to have col attrs as dictionary
dtype['formats'][-1] = 'O'
converters = {8: _attr }
#NOT OK
print np.genfromtxt(StringIO(gffstr), dtype = dtype,
converters=converters)
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