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From: Andrea R. <ari...@pi...> - 2002-12-11 11:03:01
|
Hi, I've two question about PyArray_As2D function: 1) Looking at the source code I realized that the prototype given in the manual is different from that of the source: PyArray_As2D(PyObject *op, char **ptr, int *m, int *n, int type) (from manual) PyArray_As2D(PyObject **op, char ***ptr, int *d1, int *d2, int typecode) (from source) As far as I can understand the source version is correct while the manual's one is not. Am I wrong? 2) Next in the source code I've found the following memory allocation: data = (char **)malloc(n*sizeof(char *)); without checking if malloc return NULL or not. As far as I know it's not safe, even if it's very unlikely that this malloc would fail. Anyway in that case the following: ... data[i] = ap->data + i*ap->strides[0]; ... would cause the function to abort. Again am I wrong? Thanks in advance, Andrea. --- Andrea Riciputi <mailto:and...@li...> "Science is like sex: sometimes something useful comes out, but that is not the reason we are doing it" -- (Richard Feynman) |
From: Pearu P. <pe...@ce...> - 2002-12-11 10:48:02
|
On Wed, 11 Dec 2002, Andrea Riciputi wrote: > Hi there, > I'm playing with Numeric and even if I've not so much experience with > it I'm trying to write a C extention to Python that can use Numeric > arrays. The basic idea consists in handling C (dynamically allocated) > array as Numeric array (if Numeric is installed) or as simple Python > lists if not. > > How can I detect at compile time if Numeric is installed or not?? I've > thought something like: > > #ifdef NUMERIC_IS_HERE > #include "Numeric/arrayobject.h" > #endif > > But I've not found any hints in Numeric manual. Can anyone suggest a > solution to me? If you are using distutils for building extension modules then you can test if Numeric is available in setup.py file and define, say, HAVE_NUMPY macro, if Numeric is available. For example, #------- have_numpy = 0 try: import Numeric have_numpy = 1 except ImportError: pass define_macros = [] if have_numpy: define_macros.append(('HAVE_NUMPY', None)) if __name__ == "__main__": from distutils.core import setup setup(name = ..., ext_modules = [...], define_macros = define_macros ) #--------- and in extension source files use #ifdef HAVE_NUMPY ... #endif HTH, Pearu |
From: Konrad H. <hi...@cn...> - 2002-12-11 10:37:23
|
Andrea Riciputi <ari...@pi...> writes: > How can I detect at compile time if Numeric is installed or not?? I've > thought something like: > > #ifdef NUMERIC_IS_HERE > #include "Numeric/arrayobject.h" > #endif Supposing that you will use distutils for compilation and installation of your extension module, the solution is easy: your distutils script can test for Numeric and then add the compiler flag. For example: defines = [] try: import Numeric defines.append('NUMERIC_IS_HERE') except ImportError: pass ... Extension("foo", ["foo.c"], define_macros = defines) Konrad. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hi...@cn... Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- |
From: Andrea R. <ari...@pi...> - 2002-12-11 10:09:04
|
Hi there, I'm playing with Numeric and even if I've not so much experience with it I'm trying to write a C extention to Python that can use Numeric arrays. The basic idea consists in handling C (dynamically allocated) array as Numeric array (if Numeric is installed) or as simple Python lists if not. How can I detect at compile time if Numeric is installed or not?? I've thought something like: #ifdef NUMERIC_IS_HERE #include "Numeric/arrayobject.h" #endif But I've not found any hints in Numeric manual. Can anyone suggest a solution to me? Thanks in advance, Andrea. --- Andrea Riciputi <mailto:and...@li...> "Science is like sex: sometimes something useful comes out, but that is not the reason we are doing it" -- (Richard Feynman) |
From: Robert K. <ke...@ca...> - 2002-12-10 00:47:47
|
On Mon, Dec 09, 2002 at 09:06:43AM -0700, Tim Hochberg wrote: [snip] > This seems like a good plan. I'm not enthralled by the name though: > array_equal seems equally likely to describethe behaviour of the unfunc > equal as it does the behaviour above. Maybe array_identical or array_same or > equal_arrays or some such (although none of those are great). I'd put in my vote for array_equiv, equiv, or equivalent since I think "equivalence" best expresses the relationship tested here, not "equality." > -tim -- Robert Kern Ruddock House President ke...@ca... "In the fields of hell where the grass grows high Are the graves of dreams allowed to die." -- Richard Harter |
From: Dave B. <ba...@co...> - 2002-12-09 19:09:21
|
I just installed numpy on my RH 7.3 system under python 2.2.2. I get the following messages when I import Numeric. Could someone enlighten me as to what this means and what I should do about it? Thanks, Dave Bazell Python 2.2.2 (#1, Oct 21 2002, 12:22:55) [GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-110)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import Numeric Traceback (most recent call last): File "<stdin>", line 1, in ? File "/usr/local/lib/python2.2/site-packages/Numeric/Numeric.py", line 93, in ? from Precision import * File "/usr/local/lib/python2.2/site-packages/Numeric/Precision.py", line 26, in ? _code_table = _fill_table(typecodes) File "/usr/local/lib/python2.2/site-packages/Numeric/Precision.py", line 23, in _fill_table table[key] = _get_precisions(value) File "/usr/local/lib/python2.2/site-packages/Numeric/Precision.py", line 18, in _get_precisions lst.append( (zeros( (1,), t ).itemsize()*8, t) ) ValueError: Invalid type for array >>> import Numeric >>> |
From: Konrad H. <hi...@cn...> - 2002-12-09 17:08:44
|
"Perry Greenfield" <pe...@st...> writes: > Finally, the default reduction operation (i.e., add.reduce) could > be given the behavior described above. We are inclined to leave it > as is, i.e., to return scalars when reducing 1-d arrays and provide Please do! There is no point in breaking code without any gain in return. Konrad. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hi...@cn... Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- |
From: Konrad H. <hi...@cn...> - 2002-12-09 17:06:13
|
"Perry Greenfield" <pe...@st...> writes: > Instead we propose a function whose purpose is to determine > if two arrays are shape consistent (i.e., can be broadcast > against each other) and have all values equal to each other. So there would be that operation, plus one that checks identity of shape and all elements? That should cover all needs I can think of. Konrad. |
From: Perry G. <pe...@st...> - 2002-12-09 16:29:35
|
Tim Hochberg write: > > What is the argument against allowing __eq__ to continue to work, while > disallowing __lt__ and friends. The former is well defined. I > know comparing > floating point number for equality is a bit of a suckers game, but were > allowing it for floats and it's sometimes useful. > > On second thought, maybe I'm just misinterpreting you here since __eq__ > works fine for complex scalars. > > -tim I wasn't clear on this. What I was arguing was that less, less_equal, greater, greater_equal would not work, but that equal and not_equal Primarily because that is what Python does. It does allow one to test for equality (or non equality), but doesn't allow for >,<,>=,<=, which is sensible in my view. Perry |
From: Perry G. <pe...@st...> - 2002-12-09 16:24:16
|
Pearu Peterson write: > On Mon, 9 Dec 2002, Perry Greenfield wrote: > > > >>> array_equal(array([[1,2,3],[1,2,3]]), array([1,2,3])) > > 1 > > Hmm, I would have expected 0. > What's the rationale for 1? > Because the arrays can be broadcast into a consistent array. In other words equals(array([[1,2,3],[1,2,3]]), array([1,2,3]) returns array([[1,1,1],[1,1,1]]) But I take your meaning. There may be those that wish to ensure that two arrays are really identical in shape and have all equal values. Should these be two different functions? One function with different options. By the way, I'm open to better function names as Tim Hochberg suggests. > May be you meant > > >>> array_equal(array([[1,2,3]]), array([1,2,3])) > 1 > > which I would agree. Also > > >>> array_equal(array([[1],[2],[3]]), array([1,2,3])) > 1 > > but I am not sure about > > >>> array_equal(array([[1,2,3],[1,2,3]]), array([1,2,3,1,2,3])) > 1 > > Pearu Perry |
From: Tim H. <tim...@ie...> - 2002-12-09 16:14:44
|
> The questions just keep coming... > > We need to decide whether or not complex comparisons work. > They do not work for Python scalars. Consistency would argue > for them not working for numarray arrays. However some argue: > > 1) not allowing them defeats more generic programming. We agreed > until we found that IDL doesn't support them either, and we never > noticed. We are skeptical of this claim and would like to see > real-life examples. > > 2) it is useful to allow comparisons since that would result in > repeatable, sorting of values (e.g., to find duplicate values) > for ordering purposes. Cannot this just be handled by the sort > routines themselves? Why must this result in comparison operators > working? > > In the absence of good examples for 1) or good arguments for 2) > we propose to make complex comparisons generate exceptions. What is the argument against allowing __eq__ to continue to work, while disallowing __lt__ and friends. The former is well defined. I know comparing floating point number for equality is a bit of a suckers game, but were allowing it for floats and it's sometimes useful. On second thought, maybe I'm just misinterpreting you here since __eq__ works fine for complex scalars. -tim |
From: Pearu P. <pe...@ce...> - 2002-12-09 16:12:38
|
On Mon, 9 Dec 2002, Perry Greenfield wrote: > >>> array_equal(array([[1,2,3],[1,2,3]]), array([1,2,3])) > 1 Hmm, I would have expected 0. What's the rationale for 1? May be you meant >>> array_equal(array([[1,2,3]]), array([1,2,3])) 1 which I would agree. Also >>> array_equal(array([[1],[2],[3]]), array([1,2,3])) 1 but I am not sure about >>> array_equal(array([[1,2,3],[1,2,3]]), array([1,2,3,1,2,3])) 1 Pearu |
From: Perry G. <pe...@st...> - 2002-12-09 15:40:32
|
A little while ago we tackled the issue of whether indexing numarray arrays should return Python scalars or rank-0 arrays. For reasons gone into at great length previously on this list we decided to always return Python scalars when no precision is lost by conversion to Python scalars (Float128 may be an exception to this rule, but we'll deal with that later). We consider this issue closed. But there are some loose ends. There was an opinion that reduction operations (e.g., add.reduce) should always return arrays. However, some desired that the rank-0 arrays returned when reducing a rank-1 array should be indexable and have a length. In particular: >>> x = arange(10) >>> v = add.reduce(x) >>> print v 55 >>> v array(55) >>> len(v) 1 >>> v[0] 55 The great majority objected to len(rank-0) being allowed as well as rank-0[0] working. We agree. We propose that at least one version of the reduction operations always return arrays, but that the array "end-point" always be a rank-1 len-1 array instead of a rank-0 array. This is because a rank-1 len-1 array 1) has a len() = 1 2) can be indexed. 3) because of broadcasting, behaves like a scalar in expressions with arrays (i.e., as was intended for rank-0 arrays) Thus, if one repeatedly reduces an N-dimensional array, one eventually gets a rank-1 len-1 array, and reducing a rank-1 len-1 array simply generates a new rank-1 len-1 array with the same value. >>> x = arange(10) >>> v = add.areduce(x) >>> v array([55]) >>> add.areduce(v) array([55]) Is there any reason why this behavior would not serve the purposes of those that wanted rank-0 arrays returned from reduction operations? Likewise, we could provide a function to wrap scalars as rank-1 len-1 arrays (much like array(5) produces a rank-0 array) for the purposes of more generic functions and routines so that checks for scalars do not need to be made. This function would convert scalars to arrays, but simply return the arrays themselves if passed as arguments. One possibility is that we eliminate rank-0 arrays and use rank-1 len-1 arrays in their place (e.g., array(5) returns a rank-1 len-1 array). The problem is that there may be some who already dependon rank-0 properties and this probably will break existing code. Any opinions? Finally, the default reduction operation (i.e., add.reduce) could be given the behavior described above. We are inclined to leave it as is, i.e., to return scalars when reducing 1-d arrays and provide a different operator method (areduce) to always return arrays. Any disagreements? Perry Greenfield |
From: Perry G. <pe...@st...> - 2002-12-09 15:40:14
|
The questions just keep coming... We need to decide whether or not complex comparisons work. They do not work for Python scalars. Consistency would argue for them not working for numarray arrays. However some argue: 1) not allowing them defeats more generic programming. We agreed until we found that IDL doesn't support them either, and we never noticed. We are skeptical of this claim and would like to see real-life examples. 2) it is useful to allow comparisons since that would result in repeatable, sorting of values (e.g., to find duplicate values) for ordering purposes. Cannot this just be handled by the sort routines themselves? Why must this result in comparison operators working? In the absence of good examples for 1) or good arguments for 2) we propose to make complex comparisons generate exceptions. Perry Greenfield |
From: Perry G. <pe...@st...> - 2002-12-09 15:39:52
|
This is a Numeric/numarray compatibility question. Numeric currently allows the equals ufunc to compare arrays of unequal sizes and returns a scalar 0 in such cases. When arrays have consistent shapes, an array of ints is returned. We argue that this is inconsistent with normal ufunc behavior and that it should generate an exception as do all non-equality ufuncs. (numarray currently does not allow comparison of shape-inconsistent arrays including for equality). Instead we propose a function whose purpose is to determine if two arrays are shape consistent (i.e., can be broadcast against each other) and have all values equal to each other. >>> array_equal(arange(2), arange(4)) 0 >>> array_equal(array([1,2,3]), array([1,2,0])) 0 >>> array_equal( arange(2), None ) 0 >>> array_equal( arange(2), not_an_ndarray_instance) 0 >>> array_equal(array([[1,2,3],[1,2,3]]), array([1,2,3])) 1 Comments? Perry Greenfield |
From: Pearu P. <pe...@ce...> - 2002-12-08 17:23:07
|
F2PY - Fortran to Python Interface Generator, Version 2.32.225 --------------------------------------------------------------- I am pleased to announce the sixth public release of F2PY. The purpose of the F2PY project is to provide a connection between Python and Fortran programming languages. For more information, see http://cens.ioc.ee/projects/f2py2e/ Download source: http://cens.ioc.ee/projects/f2py2e/2.x/F2PY-2-latest.tar.gz What's new? ------------ It has been almost a year from the previous release of F2PY. This release comes with a number of improvements, most important ones are listed as follows: - The issue with a Fortran and C multi-dimensional array storage ordering is finally resolved. F2PY generated wrappers automatically carry out all necessary transformations, trying hard to minimize any performance hits. As a result, the end users of F2PY generated wrappers need not to worry about this issue anymore, multi-dimensional arrays in Python and Fortran have now exactly the same signatures. - Improved wrapping C functions with F2PY. - F2PY Users Guide has been throughly revised to describe and illustrate all latest F2PY features such as wrapping Fortran 77 COMMON blocks, Fortran 90 module data, including Fortran 90 module ALLOCATABLE arrays, etc. The F2PY Users Guide is composed using the Python Docutils tool and is available here: http://cens.ioc.ee/projects/f2py2e/usersguide/ - F2PY has new site for unit testing. - F2PY uses scipy_distutils from SciPy (www.scipy.org) project for compiling Fortran sources and building extension modules. Currently, the following Fortran 77/90 compilers are described by scipy_distutils: Absoft Sun SGI Intel Itanium NAG Compaq Digital Gnu VAST - Finally, F2PY has been extensively used/tested for wrapping large Fortran/C libraries, such as, LAPACK, BLAS, ATLAS, FFTW, FFTPACK, etc. (see SciPy project for more information). This experience has been a very important source for ideas how to make binding Fortran/C codes to Python easier and more robust. Enjoy, Pearu Peterson --------------- <P><A HREF="http://cens.ioc.ee/projects/f2py2e/">F2PY 2.32.225</A> - The Fortran to Python Interface Generator (08-Dec-02) |
From: Rob <ro...@py...> - 2002-12-07 16:39:54
|
Rob wrote: > > It should be in the educational corner. I've beefed up the intro to the > site. Will be interesting to see if I get many new hits. Rob. > -- > ----------------------------- > The Numeric Python EM Project > > www.pythonemproject.com > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > Numpy-discussion mailing list > Num...@li... > https://lists.sourceforge.net/lists/listinfo/numpy-discussion It was supposed to be in A & P magazine all the way back in June, but the editors goofed up, and profusely apologized :) Rob. -- ----------------------------- The Numeric Python EM Project www.pythonemproject.com |
From: Rob <ro...@py...> - 2002-12-06 23:14:23
|
It should be in the educational corner. I've beefed up the intro to the site. Will be interesting to see if I get many new hits. Rob. -- ----------------------------- The Numeric Python EM Project www.pythonemproject.com |
From: Chris B. <Chr...@no...> - 2002-12-06 18:09:30
|
José Fonseca wrote: > to say that the manipulation of numeric > arrays is only of interest to scientific programmers is the same of when > in the early computing days engineers saing that computers would only be > good for crunching numbers, and that the concept of personal computers > was just non-sense... I absolutely concur. > For a non-scientic usage of Numeric see the examples in > http://www.pygame.org/pcr/repository.php, but I can imagine the > usefullness of Numeric in many more non-scientific applications: > imaging, sound visualization plugins, 3D graphics, and probably much > more. It goes MUCH farther than this. All these examples are what I would call serious number crunching. Perhaps not strictly scientific, but certainly the realm of numeric programming, and all places where the "kinds" concept would be useful. However, there is a great deal of usefulness in Numeric for applications that are not doing a lot of number crunching. Performance is only one reason to use Numeric. The other reason is much cleaner and easier syntax for manipulating arrays of numbers, especially ones of more than one dimension. Being able to slice across multiple dimensions, array oriented arithmetic, overloaded comparisons, etc. I use Numeric for virtually every program I write, whether performance is an issue or not. Not having to write all those ugly, confusing and error prone loops is a godsend. All that being said, the "kinds" concept is probably mostly of concern to the Number crunching community. However, it is also sort of a low level concept, and having it part of core language makes sense, just like it makes sense to have complex number and long integers in the core language. -Chris -- Christopher Barker, Ph.D. Oceanographer NOAA/OR&R/HAZMAT (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chr...@no... |
From: Michael M. <mc...@ni...> - 2002-12-06 16:39:07
|
On Friday 06 December 2002 02:12 am, Brett Cannon wrote: > [Paul F Dubois] > > > We had put off consideration of PEP 242 Numeric kinds until June 2002 > > when a meeting of some interested parties was to occur but the meeting > > didn't occur. [...] > I just want to be able to add up a bunch of money values and not have a > few pennies disappear in the end; usually I am the one who has to eat the > loss and I am an poor college graduate who can't afford the rounding. =) Does the kinds implementation work with binary floats and decimal numbers? From a quick scan of the PEP it looks like it is only binary floats. If it only applies to binary numbers then the kinds capability will not eliminate decimal number rounding errors. That problem will require extending Python to include a decimal number type. The abstract mentions a clarification of decimal literals, but I suspect Paul was not suggesting that the numbers defined by kinds will use decimal arithmetic instead of binary arithmetic. |
From: Brett C. <ba...@OC...> - 2002-12-06 07:12:56
|
[Paul F Dubois] > We had put off consideration of PEP 242 Numeric kinds until June 2002 > when a meeting of some interested parties was to occur but the meeting > didn't occur. I have a draft implementation and users of it but my > feeling is that although correct and useful the PEP is not useful enough > to put it in the standard library. Since it really only interests > scientific programmers I propose simply making it a separate deliverable > on the Numeric site and withdrawing the PEP. > I say add it. If there are already users out there then that demonstrates as least some form of a demand. Besides, if rationals can get into the library (that module was finally accepted to be added to the library, right?) then a module to help do consistent decimal math should at least be included at least until the Python core can move to C99 (if I am remembering a comment from Tim saying that C99 adds more explicit numeric types, e.g., exactly 2 byte float). I just want to be able to add up a bunch of money values and not have a few pennies disappear in the end; usually I am the one who has to eat the loss and I am an poor college graduate who can't afford the rounding. =) -Brett |
From: Raymond H. <py...@rc...> - 2002-12-06 06:56:42
|
> I have a draft implementation and users of it but my > feeling is that although correct and useful the PEP is not useful enough > to put it in the standard library. Since it really only interests > scientific programmers I propose simply making it a separate deliverable > on the Numeric site and withdrawing the PEP. As the PEP author, your feeling is probably the most accurate. And, it is true that Kinds will, in general, appeal to the same crowd as Numeric. OTOH, "import kinds" is entirely unobtrusive and general purpose. The interface is simple; and may help some code become less platform sensitive (in the way the Metafont writes its own portable routines to create consistent lettering); and it has some educational value (making it easy to demonstrate the effects of truncation and floating point round-off). Also, I think accounting applications can benefit from having some positive assurance that multi-billion dollar calculations don't lose their pennies and that the books will still balance. So, the only downside is having an additional block of code to maintain. My vote is for adding it to the standard library. Control over precision is more of a core capability than it is an extension, but, as the PEP author and principal user, you probably know best. 'nuff said, Raymond Hettinger ################################################################# ################################################################# ################################################################# ##### ##### ##### ################################################################# ################################################################# ################################################################# |
From: F. <j_r...@ya...> - 2002-12-06 02:37:46
|
On Thu, Dec 05, 2002 at 05:02:26PM -0800, Paul F Dubois wrote: > Since it really only interests > scientific programmers I propose simply making it a separate deliverable > on the Numeric site and withdrawing the PEP. I'm not fully aware about the advantages/implications of puting Numeric in Python standard library, but to say that the manipulation of numeric arrays is only of interest to scientific programmers is the same of when in the early computing days engineers saing that computers would only be good for crunching numbers, and that the concept of personal computers was just non-sense... For a non-scientic usage of Numeric see the examples in http://www.pygame.org/pcr/repository.php, but I can imagine the usefullness of Numeric in many more non-scientific applications: imaging, sound visualization plugins, 3D graphics, and probably much more. The use of Numeric can speed up alot of algorithms which would be otherwise very slow in pure Python, and therefore forcing one to write C extensions. That's why IMHO something with the Numeric functionality should exist in the Python standard library. Note that this is not the same that saying that Numeric should be included as is - perhaps it's better to have it seperately to let it mature more, perhaps not - but still, there is much more than a niche interest around it. José Fonseca __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com |
From: Paul F D. <pa...@pf...> - 2002-12-06 01:02:42
|
We had put off consideration of PEP 242 Numeric kinds until June 2002 when a meeting of some interested parties was to occur but the meeting didn't occur. I have a draft implementation and users of it but my feeling is that although correct and useful the PEP is not useful enough to put it in the standard library. Since it really only interests scientific programmers I propose simply making it a separate deliverable on the Numeric site and withdrawing the PEP. |
From: Sebastian H. <ha...@ms...> - 2002-12-03 23:13:42
|
> On Tue, Dec 03, 2002 at 02:34:06PM -0800, Sebastian Haase wrote: > > Hi all, > > I downloaded numarray 0.4 about 5 minutes after I got the announce but > > my naive 'python2.2 ./setup.py build' gives this > > > > haase@baboon:~/numarray-0.4: python2.2 ./setup.py build > > running build > > running build_py > > not copying Lib/ndarray.py (output up-to-date) > [...] > > not copying Lib/memmap.py (output up-to-date) > > running build_ext > > building '_conv' extension > > error: file 'Src/_convmodule.c' does not exist > > > > What am I missing? I'm running Linux (debian woody) on i386. > > Looks like you have to run 'python2.2 ./setup.py install' instead. Looking at > setup.py, something special is done when the target is 'install'. > > [I think this is a bad idea, as I like to build stuff as my user, and > install as root. This requires me to build it as root.] I just tried it (actually as user not root!!) and it runs through up to a "cannot create directory..." error. That's probably fine with me (for now) and I'm just setting PYTHONPATH ... Thanks again, Sebastian. |