Thank you very much for your answer, and sorry for such a long delay in
answering.
In the end I am trying to build a binary package using pyinstaller, because
I need to reach a broad audience if possible.
Do you have any suggestions about building binaries using igraph? I need to
prepare at least some packages for Linux and Mac systems.
I can successfully build my script using pyinstaller, but then when I run
the executable it complains that can't find the '_igraph' module.
$: ./dist/vcf2network
Traceback (most recent call last):
File "<string>", line 8, in <module>
File
"/usr/local/lib/python2.7/dist-packages/PyInstaller/loader/pyi_importers.py",
line 270, in load_module
exec(bytecode, module.__dict__)
File
"/home/gioby/workspace/vcf2networks/build/vcf2network/out00-PYZ.pyz/binary_to_network",
line 11, in <module>
File
"/usr/local/lib/python2.7/dist-packages/PyInstaller/loader/pyi_importers.py",
line 270, in load_module
exec(bytecode, module.__dict__)
File
"/home/gioby/workspace/vcf2networks/build/vcf2network/out00-PYZ.pyz/GenotypeNetwork",
line 9, in <module>
File
"/usr/local/lib/python2.7/dist-packages/PyInstaller/loader/pyi_importers.py",
line 270, in load_module
exec(bytecode, module.__dict__)
File
"/home/gioby/workspace/vcf2networks/build/vcf2network/out00-PYZ.pyz/igraph",
line 34, in <module>
ImportError: No module named _igraph
I suspect that it doesn't find the igraph C headers, but I am not sure how
I can tell him where to find them.
On Fri, Nov 1, 2013 at 11:05 PM, Tamás Nepusz <[email protected]> wrote:
> Hello,
>
> > The main problem is that one of the requirements of my suite is igraph
> 0.6, which is based on the igraph 0.6 C library. This C library must be
> installed manually, and I don't know how to define the dependency in the
> setup.py script.
> There is no way to define that because you can depend only on other Python
> packages within your setup.py script.
>
> > With the previous 0.5.4 version, the C code was included in the igraph
> .egg package
>
> Are you sure about that? As far as I remember, I stopped shipping the
> source code of the C library with the Python interface starting from igraph
> 0.5.
>
> > However, in the newer 0.6 version, the C library is not included anymore
> in the igraph package on PyPI. What is the recommended procedure to
> distribute a python package based on igraph 0.6?
> Well, it depends on your target audience. For instance, will they have a C
> compiler on their machine so they can compile the C core of igraph if
> needed? Will they use a 32-bit or a 64-bit machine? What operating system
> will they use? What Python version?
>
> If your package is targeting developers who should at least know what a C
> compiler and a C library is, then it should not be too complicated for them
> to install or compile the C core of igraph on their own, so I think it
> would be enough to declare a dependency on python-igraph in your setup.py
> and then add a README which states that the C core of igraph must be
> installed beforehand, either to a standard location or to a location where
> pkg-config is able to find it.
>
> However, if you want your package to be easy to use by everyone, including
> people who have never seen a C compiler at all, then your best bet is
> probably to prepare a completely self-contained installer that installs a
> basic Python runtime and all the dependencies. Creating such an installer
> is outside the scope of a simple setup.py script, but it can be done with
> cx_Freeze or PyInstaller. The installer would then contain a pre-compiled
> version of igraph that you compiled on your machine. Chances are that you
> would need several virtual machines to do this for all the platforms you
> want to support. To be honest, it’s not an easy task at all.
>
> In the meanwhile, I am working on making python-igraph more
> “easy_install”-friendly. Ideally, I want python-igraph to be installable
> simply by invoking “easy_install python-igraph” or “pip install
> python-igraph”, in which case python-igraph should check whether the C core
> is available and download (and compile and install) it as well if needed.
> Due to lack of time on my side, I don’t think it’s gonna happen any time
> soon, though.
>
> All the best,
> Tamas
>
>
--
Giovanni Marco Dall'Olio, PhD
IBE, Institut de Biologia Evolutiva, CEXS-UPF (Barcelona, Spain)
My blog on bioinformatics: http://bioinfoblog.it
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