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Re: Enabling Python bindings for jellyfish

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Hi Guillaume,

On Thu, Dec 31, 2015 at 06:24:57PM -0500, Guillaume Marcais wrote:
> if I am attached to the name Jellyfish for the main software itself, the
> script bindings have seen little use (I believe) up to now. Renaming python
> module to dna_jellyfish, bio_jellyfish, or some other suggestion, would be
> OK with me.

Since you are the author would you mind fixing a name yourself.  The
rationale is that if we might choose a name for Debian other distributions
(or consumers of the code from source directly) might choose a different
one which might lead to a lot of confusion.  It would be great if you could
issue a new release with a proper name for the Python module.
 
> Regarding the module itself, it should work for both Python2 and Python3.
> If you have example where it does not, please let me know.

When trying to build the module I get:

...
running build_ext
building '_jellyfish' extension
creating build/temp.linux-x86_64-3.5
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c jellyfish_wrap.cxx -o build/temp.linux-x86_64-3.5/jellyfish_wrap.o -std=c++0x
cc1plus: warning: command line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No such file or directory
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1


since the includes are not properly set.

Kind regards

       Andreas.


-- 
http://fam-tille.de

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Thread

Enabling Python bindings for jellyfish Andreas Tille <andreas@an3as.eu> - 2015-12-29 00:40 +0100
  Re: Enabling Python bindings for jellyfish Scott Kitterman <debian@kitterman.com> - 2015-12-29 18:00 +0100
    Re: Enabling Python bindings for jellyfish Scott Kitterman <debian@kitterman.com> - 2015-12-29 18:10 +0100
      Re: Enabling Python bindings for jellyfish Paul Tagliamonte <paultag@ubuntu.com> - 2015-12-29 18:30 +0100
        Re: Enabling Python bindings for jellyfish Paul Tagliamonte <paultag@ubuntu.com> - 2015-12-29 19:00 +0100
          Re: Enabling Python bindings for jellyfish Scott Kitterman <debian@kitterman.com> - 2015-12-29 20:30 +0100
        Re: Enabling Python bindings for jellyfish Scott Kitterman <debian@kitterman.com> - 2015-12-29 19:00 +0100
          Re: Enabling Python bindings for jellyfish "Diego M. Rodriguez" <diego.plan9@gmail.com> - 2015-12-29 19:30 +0100
            Re: Enabling Python bindings for jellyfish Paul Tagliamonte <paultag@ubuntu.com> - 2015-12-29 20:10 +0100
              Re: Enabling Python bindings for jellyfish Andreas Tille <andreas@an3as.eu> - 2015-12-29 21:50 +0100
              Re: Enabling Python bindings for jellyfish "Diego M. Rodriguez" <diego.plan9@gmail.com> - 2015-12-31 18:40 +0100
                Re: Enabling Python bindings for jellyfish Scott Kitterman <debian@kitterman.com> - 2015-12-31 18:50 +0100
                Re: Enabling Python bindings for jellyfish "Diego M. Rodriguez" <diego.plan9@gmail.com> - 2015-12-31 20:30 +0100
                Re: Enabling Python bindings for jellyfish Andreas Tille <andreas@fam-tille.de> - 2015-12-31 21:40 +0100
                Re: Enabling Python bindings for jellyfish Guillaume Marcais <gmarcais@umd.edu> - 2016-01-01 00:50 +0100
                Re: Enabling Python bindings for jellyfish Andreas Tille <andreas@an3as.eu> - 2016-01-01 19:30 +0100

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