Re: [Pytables-users] git strategy to move forward with

[Antonio V. <ant...@ti...>]

Hi Chris,

Il giorno 20/ago/2011, alle ore 03.57, Chris Kees ha scritto:

> Hi,
> 
> We use pytables and numexpr, and I'd like to add them as submodules to
> our project so that I can easily keep updated with pytables
> improvements and pass changes back up stream if I can be of any help
> (we do a lot of HPC work with pytables). Is there a plan to add 2.3 as
> a release branch fairly soon or some other stable point in the git
> repository that I could point my submodule to? I could also stick with
> 2.2 for the time being but noticed below that 2.3beta had been used in
> EPD so I thought there must be a branch or fork somewhere that is

The master branch should be beta quality at the moment. We plan to pack a beta release soon.
If you look at 

https://github.com/PyTables/PyTables/issues?milestone=2&state=open

there are still a few bugs to close and they are mainly related to the setup process which seems to be your problem too.



> relatively stable.  I would just go with the head of the master
> branch, but compiling with Cython 0.15 and numpy 1.6.1 gave me the
> error below.
> 
> Thanks,
> Chris

Chris, I'm setting up a virtual environment  to reproduce your issue.
Can you confirm that the cython executable is in your path?

Looking at the error message below it seems that the setup script is unable to find the HDF5 runtime:

".. WARNING:: Could not find the HDF5 runtime."

Can you please post more detail on your system setup and the exact command line you used?


> * Found numpy 1.6.2.dev-f21011a package installed.
> * Found numexpr 1.5.dev package installed.
> * Found Cython 0.15 package installed.
> * Found HDF5 headers at
> ``/Users/cekees/src/proteus-git/darwin/include``, library at
> ``/Users/cekees/src/proteus-git/darwin/lib``.
> .. WARNING:: Could not find the HDF5 runtime.
>  The HDF5 shared library was *not* found in the default library
>  paths. In case of runtime problems, please remember to install it.
> * Could not find LZO 2 headers and library; disabling support for it.
> * Could not find LZO 1 headers and library; disabling support for it.
> * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``.
> cythoning tables/utilsExtension.pyx to tables/utilsExtension.c
> Traceback (most recent call last):
> File "setup.py", line 464, in <module>
>   cython_extfiles = get_cython_extfiles(cython_extnames)
> File "setup.py", line 455, in get_cython_extfiles
>   retcode = subprocess.call(["cython", extpfile])
> File "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 493, in call
>   return Popen(*popenargs, **kwargs).wait()
> File "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 679, in __init__
>   errread, errwrite)
> File "/Users/cekees/src/proteus-git/darwin/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/subprocess.py",
> line 1228, in _execute_child
>   raise child_exception

regards

--
Antonio Valentino