[Biopython-dev] Build & Test

[Dragoslav Zaric]

I am sorry Peter, but you are right. It is too ambitious for me.

I can not do it. I am sorry if I wasted your time.

Good luck and all best.

On Thu, Oct 28, 2010 at 8:36 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Oct 28, 2010 at 5:24 PM, Dragoslav Zaric
> <zaricdragoslav at gmail.com> wrote:
>> Hi Peter,
>>
>> To bring me up to speed for build&test process, can I ask you how
>> exactly this process should go.
>>
>> For example if I put this in setup.py file:
>>
>> class build_ext_biopython(build_ext):
>>    def run(self):
>>        if not check_dependencies_once():
>>            return
>>        if is_Numpy_installed():
>>            import numpy
>>            numpy_include_dir = numpy.get_include()
>>            self.extensions.append(
>>                Extension('Bio.Motif._pwm',
>>                          ["Bio/Motif/_pwm.c"],
>>                          include_dirs=[numpy_include_dir],
>>                          ))
>>        build_ext.run(self)
>>
>> what command I should run from command line to build and test:
>>
>> python3.1 setup.py build
>> or/and
>> python3.1 setup.py install
>>
>> After this I will have folder build/lib/Bio, so should I go to folder build/lib
>> and start python3.1 to test this, or after python3.1 setup.py install it is
>> copied to root folder.
>
> You can do this:
>
> python3.1 setup,py build
> python3.1 setup.py test
>
> and it should use the compiled C code from the build folder.
> This is equivalent to:
>
> python3.1 setup,py build
> cd Tests
> python3.1 run_tests.py
>
> The advantage of calling run_tests.py directly is you can test particular
> bits of Biopython rather than all of it, e.g.
>
> python3.1 setup,py build
> cd Tests
> python3.1 run_tests.py test_Motif.py
>
> If you try and run a test directly (e.g. python3.31 test_Motif.py) then
> in will use the installed version of Biopython (and it will fail if you
> haven't installed Biopython).
>
>> Also after building I will have -pwm.so file, is this final file that
>> is imported from python code ?
>>
>> Currently i can import Seq and Motif but when I run
>>
>> m.scanPWM(Seq.Seq("ACGTGTGCGTAGTGCGT",m.alphabet))
>>
>> I get:
>>
>> Traceback (most recent call last):
>>  File "<stdin>", line 1, in <module>
>>  File "Bio/Motif/_Motif.py", line 778, in scanPWM
>>    import _pwm
>> ImportError: No module named _pwm
>>
>
> On Python 2.6 (on my Mac) I have these files:
>
> $ ls build/lib.macosx-10.6-universal-2.6/Bio/Motif/
> Applications   Thresholds.py  _Motif.py      __init__.py    _pwm.so
> Parsers        Thresholds.pyc _Motif.pyc     __init__.pyc
>
> Trying to import _pwm will load the _pwm.so file.
>
> It sounds like you were able to compile _pwm.so under
> Python 3, but it doesn't import. Is your _pwm.c file still
> using Py_InitModule4 or have you changed it to something
> Python 3 compatible yet like PyModule_Create?
>
> [It may not have been clear to you earlier, but porting
> Python C extensions from Python 2 to Python 3 requires
> quite a lot of background knowledge about Python, C,
> compiling, and so on. I hope this wasn't too ambitious.]
>
> Regards,
>
> Peter
>



-- 
Dragoslav Zaric

Professional Programmer
MSc Astrophysics