Closed GoogleCodeExporter closed 8 years ago
Hi Laurent,
thanks. I think it is related to this:
http://bugs.python.org/issue15610
Apparently, some default value of an import call changed and the original
default not causes this error. The problem is that the .c files packaged with
pysam are generated for python 2.7. For python 3 they need to be generated. I
have previously been advised to include the .c files in the package.
What I will now do is for python 3:
1. check for cython presence
2. if present, remove the .c files so that they will be recompiled.
Hopefully that will fix the problem. As a side-effect, the .c will
always be regenerated and recomputed even if the .pyx file has not changed.
Best wishes,
Andreas
Original comment by andreas....@gmail.com
on 27 Jun 2013 at 3:10
The side-effect seems mostly wanted, I think: should cython change/improve the
C code it generates, the user would benefit from it without you having to make
a new release.
Check whether the recommendation to ship C translations is still holding. It
might just be better to make the package `pysam` depend on cython and translate
.pyx at build time.
Original comment by lgaut...@gmail.com
on 27 Jun 2013 at 7:10
Hi Laurent,
I fully agree with you, yet cython says this:
http://docs.cython.org/src/userguide/source_files_and_compilation.html
"""
It is strongly recommended that you distribute the generated .c files as well
as your Cython sources, so that users can install your module without needing
to have Cython available.
It is also recommended that Cython compilation not be enabled by default in the
version you distribute. Even if the user has Cython installed, he probably
doesn’t want to use it just to install your module. Also, the version he has
may not be the same one you used, and may not compile your sources correctly.
"""
For the time being I will have this dual option - bundle .c, but re-cythonize
under python 3.
Best wishes,
Andreas
Original comment by andreas....@gmail.com
on 18 Sep 2013 at 7:10
Original issue reported on code.google.com by
lgaut...@gmail.com
on 10 Jun 2013 at 12:30