Forums

Octave recently added support for mex files, and because of that
support, I decided to test out the CVS libsbml with the current version
of Octave (2.9.7, http://www.octave.org/). Everything works fine. I
don't know how to setup autconf for this, but if you do the following
the binding build will work:

* Make an executable file in your path called mex that is:

mkoctfile --mex $*

* Put any executable file in the path with the name matlab (autoconf
checks for matlab, probably to do tests).

If you want to run the tests, you can change to the
src/bindings/matlab/test directory and run

octave --path .. --eval testBinding

which will result in:

GNU Octave, version 2.9.7 (i486-pc-linux-gnu).
Copyright (C) 2006 John W. Eaton.
This is free software; see the source code for copying conditions.
There is ABSOLUTELY NO WARRANTY; not even for MERCHANTIBILITY or
FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'.

Additional information about Octave is available at http://www.octave.org.

Please contribute if you find this software useful.
For more information, visit http://www.octave.org/help-wanted.html

Report bugs to <bug@octave.org> (but first, please read
http://www.octave.org/bugs.html to learn how to write a helpful report).

Testing readFromFile1:
Number tests: 69
Number fails: 0
Pass rate: 100%

Testing readFromFile2:
Number tests: 81
Number fails: 0
Pass rate: 100%

Testing readFromFile3:
Number tests: 73
Number fails: 0
Pass rate: 100%

Testing readFromFile4:
Number tests: 21
Number fails: 0
Pass rate: 100%

Testing readFromFile5:
Number tests: 64
Number fails: 0
Pass rate: 100%

Testing readFromFile6:
Number tests: 25
Number fails: 0
Pass rate: 100%

Testing readFromFile7:
Number tests: 33
Number fails: 0
Pass rate: 100%

Overall tests:
Number tests: 7
Number fails: 0
Pass rate: 100%

Matlab binding successfull

There was one problem that I had, readFromFile6.m had a capitalization
issue (it will cause problems on any case-sensitive platform) that can
be fixed with the patch below (or renaming cSymbolTime-reaction-l2.xml
to csymbolTime-reaction-l2.xml).

Have a good day,

Bill

cvs diff: Diffing .
Index: testReadFromFile6.m
===================================================================
RCS file:
/cvsroot/sbml/libsbml/src/bindings/matlab/test/testReadFromFile6.m,v
retrieving revision 1.1
diff -u -r1.1 testReadFromFile6.m
--- testReadFromFile6.m 2 Dec 2005 10:56:11 -0000 1.1
+++ testReadFromFile6.m 18 Aug 2006 23:49:34 -0000
@@ -1,6 +1,6 @@
function y = testReadFromFile6

-filename = fullfile(pwd,'test-data', 'cSymbolTime-reaction-l2.xml');
+filename = fullfile(pwd,'test-data', 'csymbolTime-reaction-l2.xml');

m = TranslateSBML(filename);

@@ -105,4 +105,4 @@
else
y = 0;
end;
-
\ No newline at end of file
+
cvs diff: Diffing test-data

I guess I'll view my octave binding we worked on as a learning process
because it'll be a lot better for all involved if there is only one
toolbox between the two.

Bill

On Sat, 19 Aug 2006, Sarah Keating wrote:

> This is really cool Bill!
>
> But what about all the work you did on the octave binding :-)
>
> Sarah
>
>
> ----- Original Message ----- From: "Bill Denney" <denney@seas.upenn.edu>
> To: <libsbml-discuss@caltech.edu>
> Sent: Saturday, August 19, 2006 12:54 AM
> Subject: [libsbml-discuss] Using Matlab Bindings with Octave
>
>
>> Octave recently added support for mex files, and because of that support, I
>> decided to test out the CVS libsbml with the current version of Octave
>> (2.9.7, http://www.octave.org/). Everything works fine. I don't know how
>> to setup autconf for this, but if you do the following the binding build
>> will work:
>>
>> * Make an executable file in your path called mex that is:
>>
>> mkoctfile --mex $*
>>
>> * Put any executable file in the path with the name matlab (autoconf checks
>> for matlab, probably to do tests).
>>
>> If you want to run the tests, you can change to the
>> src/bindings/matlab/test directory and run
>>
>> octave --path .. --eval testBinding
>>
>> which will result in:
>>
>> GNU Octave, version 2.9.7 (i486-pc-linux-gnu).
>> Copyright (C) 2006 John W. Eaton.
>> This is free software; see the source code for copying conditions.
>> There is ABSOLUTELY NO WARRANTY; not even for MERCHANTIBILITY or
>> FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'.
>>
>> Additional information about Octave is available at http://www.octave.org.
>>
>> Please contribute if you find this software useful.
>> For more information, visit http://www.octave.org/help-wanted.html
>>
>> Report bugs to <bug@octave.org> (but first, please read
>> http://www.octave.org/bugs.html to learn how to write a helpful report).
>>
>> Testing readFromFile1:
>> Number tests: 69
>> Number fails: 0
>> Pass rate: 100%
>>
>> Testing readFromFile2:
>> Number tests: 81
>> Number fails: 0
>> Pass rate: 100%
>>
>> Testing readFromFile3:
>> Number tests: 73
>> Number fails: 0
>> Pass rate: 100%
>>
>> Testing readFromFile4:
>> Number tests: 21
>> Number fails: 0
>> Pass rate: 100%
>>
>> Testing readFromFile5:
>> Number tests: 64
>> Number fails: 0
>> Pass rate: 100%
>>
>> Testing readFromFile6:
>> Number tests: 25
>> Number fails: 0
>> Pass rate: 100%
>>
>> Testing readFromFile7:
>> Number tests: 33
>> Number fails: 0
>> Pass rate: 100%
>>
>> Overall tests:
>> Number tests: 7
>> Number fails: 0
>> Pass rate: 100%
>>
>> Matlab binding successfull
>>
>> There was one problem that I had, readFromFile6.m had a capitalization
>> issue (it will cause problems on any case-sensitive platform) that can be
>> fixed with the patch below (or renaming cSymbolTime-reaction-l2.xml to
>> csymbolTime-reaction-l2.xml).
>>
>> Have a good day,
>>
>> Bill
>>
>> cvs diff: Diffing .
>> Index: testReadFromFile6.m
>> ===================================================================
>> RCS file:
>> /cvsroot/sbml/libsbml/src/bindings/matlab/test/testReadFromFile6.m,v
>> retrieving revision 1.1
>> diff -u -r1.1 testReadFromFile6.m
>> --- testReadFromFile6.m 2 Dec 2005 10:56:11 -0000 1.1
>> +++ testReadFromFile6.m 18 Aug 2006 23:49:34 -0000
>> @@ -1,6 +1,6 @@
>> function y = testReadFromFile6
>>
>> -filename = fullfile(pwd,'test-data', 'cSymbolTime-reaction-l2.xml');
>> +filename = fullfile(pwd,'test-data', 'csymbolTime-reaction-l2.xml');
>>
>> m = TranslateSBML(filename);
>>
>> @@ -105,4 +105,4 @@
>> else
>> y = 0;
>> end;
>> -
>> \ No newline at end of file
>> +
>> cvs diff: Diffing test-data
>>
>>
>>
>
>
>

--
"Some people think they are worth a lot of money just because they have
it."
-- Fannie Hurst