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Enabling Python bindings for jellyfish

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  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

#8012 — Enabling Python bindings for jellyfish

Hi,

I realised that for jellyfish[1] Python bindings can be activated.  I
tried to do so and configuring and building works fine - but I have no
idea how to sensibly install the files into the python-jellyfish
package.  Any idea how to call swig/python/setup.py or do something else
to install the files into the right location.

Any help?

Kind regards

        Andreas.

[1] git://anonscm.debian.org/debian-med/jellyfish.git

-- 
http://fam-tille.de

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#8014

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On Tuesday, December 29, 2015 12:30:14 AM Andreas Tille wrote:
> Hi,
> 
> I realised that for jellyfish[1] Python bindings can be activated.  I
> tried to do so and configuring and building works fine - but I have no
> idea how to sensibly install the files into the python-jellyfish
> package.  Any idea how to call swig/python/setup.py or do something else
> to install the files into the right location.
> 
> Any help?
> 
> Kind regards
> 
>         Andreas.
> 
> [1] git://anonscm.debian.org/debian-med/jellyfish.git

I haven't been able to actually test this since when I try to build it, I get 
this error:

jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No such file or 
directory

I think it should ~work.  Note that these bindings are for python3, not 
python.  I've adjusted things accordingly.  The configure changes I made (so 
that configure wouldn't fail) mean perl bindings don't get built either.  I 
didn't check if that was working before.

Scott K

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#8015

On Tuesday, December 29, 2015 11:52:07 AM Scott Kitterman wrote:
> On Tuesday, December 29, 2015 12:30:14 AM Andreas Tille wrote:
> > Hi,
> > 
> > I realised that for jellyfish[1] Python bindings can be activated.  I
> > tried to do so and configuring and building works fine - but I have no
> > idea how to sensibly install the files into the python-jellyfish
> > package.  Any idea how to call swig/python/setup.py or do something else
> > to install the files into the right location.
> > 
> > Any help?
> > 
> > Kind regards
> > 
> >         Andreas.
> > 
> > [1] git://anonscm.debian.org/debian-med/jellyfish.git
> 
> I haven't been able to actually test this since when I try to build it, I
> get this error:
> 
> jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No such file
> or directory
> 
> I think it should ~work.  Note that these bindings are for python3, not
> python.  I've adjusted things accordingly.  The configure changes I made (so
> that configure wouldn't fail) mean perl bindings don't get built either.  I
> didn't check if that was working before.
> 
> Scott K

Correction: It's not in the diff, but I had to remove the auto-configure 
override to get through configure.

Scott K

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#8016

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Just FYI - there's a Python module called Jellyfish about to be uploaded;
can we resolve the name collision early?

https://pypi.python.org/pypi/jellyfish

Paul

On Tue, Dec 29, 2015 at 12:06 PM, Scott Kitterman <debian@kitterman.com>
wrote:

> On Tuesday, December 29, 2015 11:52:07 AM Scott Kitterman wrote:
> > On Tuesday, December 29, 2015 12:30:14 AM Andreas Tille wrote:
> > > Hi,
> > >
> > > I realised that for jellyfish[1] Python bindings can be activated.  I
> > > tried to do so and configuring and building works fine - but I have no
> > > idea how to sensibly install the files into the python-jellyfish
> > > package.  Any idea how to call swig/python/setup.py or do something
> else
> > > to install the files into the right location.
> > >
> > > Any help?
> > >
> > > Kind regards
> > >
> > >         Andreas.
> > >
> > > [1] git://anonscm.debian.org/debian-med/jellyfish.git
> >
> > I haven't been able to actually test this since when I try to build it, I
> > get this error:
> >
> > jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No such
> file
> > or directory
> >
> > I think it should ~work.  Note that these bindings are for python3, not
> > python.  I've adjusted things accordingly.  The configure changes I made
> (so
> > that configure wouldn't fail) mean perl bindings don't get built
> either.  I
> > didn't check if that was working before.
> >
> > Scott K
>
> Correction: It's not in the diff, but I had to remove the auto-configure
> override to get through configure.
>
> Scott K
>
>


-- 
All programmers are playwrights, and all computers are lousy actors.

#define sizeof(x) rand()
:wq

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#8017

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In the meantime, I suggest we both avoid uploading any python*-jellyfish
packages

  Paul

On Tue, Dec 29, 2015 at 12:56 PM, Scott Kitterman <debian@kitterman.com>
wrote:

> I think the respective maintainers should talk and then discuss with their
> upstreams as the collision potential isn't just in Debian.
>
> Scott K
>
> On Tuesday, December 29, 2015 12:27:37 PM Paul Tagliamonte wrote:
> > Just FYI - there's a Python module called Jellyfish about to be uploaded;
> > can we resolve the name collision early?
> >
> > https://pypi.python.org/pypi/jellyfish
> >
> > Paul
> >
> > On Tue, Dec 29, 2015 at 12:06 PM, Scott Kitterman <debian@kitterman.com>
> >
> > wrote:
> > > On Tuesday, December 29, 2015 11:52:07 AM Scott Kitterman wrote:
> > > > On Tuesday, December 29, 2015 12:30:14 AM Andreas Tille wrote:
> > > > > Hi,
> > > > >
> > > > > I realised that for jellyfish[1] Python bindings can be
> activated.  I
> > > > > tried to do so and configuring and building works fine - but I
> have no
> > > > > idea how to sensibly install the files into the python-jellyfish
> > > > > package.  Any idea how to call swig/python/setup.py or do something
> > >
> > > else
> > >
> > > > > to install the files into the right location.
> > > > >
> > > > > Any help?
> > > > >
> > > > > Kind regards
> > > > >
> > > > >         Andreas.
> > > > >
> > > > > [1] git://anonscm.debian.org/debian-med/jellyfish.git
> > > >
> > > > I haven't been able to actually test this since when I try to build
> it,
> > > > I
> > > > get this error:
> > > >
> > > > jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No
> such
> > >
> > > file
> > >
> > > > or directory
> > > >
> > > > I think it should ~work.  Note that these bindings are for python3,
> not
> > > > python.  I've adjusted things accordingly.  The configure changes I
> made
> > >
> > > (so
> > >
> > > > that configure wouldn't fail) mean perl bindings don't get built
> > >
> > > either.  I
> > >
> > > > didn't check if that was working before.
> > > >
> > > > Scott K
> > >
> > > Correction: It's not in the diff, but I had to remove the
> auto-configure
> > > override to get through configure.
> > >
> > > Scott K
>
>


-- 
All programmers are playwrights, and all computers are lousy actors.

#define sizeof(x) rand()
:wq

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#8021

Agreed.  I'll leave it to the maintainer/ITP owner to sort things out.

Scott K

On Tuesday, December 29, 2015 12:59:17 PM Paul Tagliamonte wrote:
> In the meantime, I suggest we both avoid uploading any python*-jellyfish
> packages
> 
>   Paul
> 
> On Tue, Dec 29, 2015 at 12:56 PM, Scott Kitterman <debian@kitterman.com>
> 
> wrote:
> > I think the respective maintainers should talk and then discuss with their
> > upstreams as the collision potential isn't just in Debian.
> > 
> > Scott K
> > 
> > On Tuesday, December 29, 2015 12:27:37 PM Paul Tagliamonte wrote:
> > > Just FYI - there's a Python module called Jellyfish about to be
> > > uploaded;
> > > can we resolve the name collision early?
> > > 
> > > https://pypi.python.org/pypi/jellyfish
> > > 
> > > Paul
> > > 
> > > On Tue, Dec 29, 2015 at 12:06 PM, Scott Kitterman <debian@kitterman.com>
> > > 
> > > wrote:
> > > > On Tuesday, December 29, 2015 11:52:07 AM Scott Kitterman wrote:
> > > > > On Tuesday, December 29, 2015 12:30:14 AM Andreas Tille wrote:
> > > > > > Hi,
> > > > > > 
> > > > > > I realised that for jellyfish[1] Python bindings can be
> > 
> > activated.  I
> > 
> > > > > > tried to do so and configuring and building works fine - but I
> > 
> > have no
> > 
> > > > > > idea how to sensibly install the files into the python-jellyfish
> > > > > > package.  Any idea how to call swig/python/setup.py or do
> > > > > > something
> > > > 
> > > > else
> > > > 
> > > > > > to install the files into the right location.
> > > > > > 
> > > > > > Any help?
> > > > > > 
> > > > > > Kind regards
> > > > > > 
> > > > > >         Andreas.
> > > > > > 
> > > > > > [1] git://anonscm.debian.org/debian-med/jellyfish.git
> > > > > 
> > > > > I haven't been able to actually test this since when I try to build
> > 
> > it,
> > 
> > > > > I
> > > > > get this error:
> > > > > 
> > > > > jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No
> > 
> > such
> > 
> > > > file
> > > > 
> > > > > or directory
> > > > > 
> > > > > I think it should ~work.  Note that these bindings are for python3,
> > 
> > not
> > 
> > > > > python.  I've adjusted things accordingly.  The configure changes I
> > 
> > made
> > 
> > > > (so
> > > > 
> > > > > that configure wouldn't fail) mean perl bindings don't get built
> > > > 
> > > > either.  I
> > > > 
> > > > > didn't check if that was working before.
> > > > > 
> > > > > Scott K
> > > > 
> > > > Correction: It's not in the diff, but I had to remove the
> > 
> > auto-configure
> > 
> > > > override to get through configure.
> > > > 
> > > > Scott K

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#8018

I think the respective maintainers should talk and then discuss with their 
upstreams as the collision potential isn't just in Debian.

Scott K

On Tuesday, December 29, 2015 12:27:37 PM Paul Tagliamonte wrote:
> Just FYI - there's a Python module called Jellyfish about to be uploaded;
> can we resolve the name collision early?
> 
> https://pypi.python.org/pypi/jellyfish
> 
> Paul
> 
> On Tue, Dec 29, 2015 at 12:06 PM, Scott Kitterman <debian@kitterman.com>
> 
> wrote:
> > On Tuesday, December 29, 2015 11:52:07 AM Scott Kitterman wrote:
> > > On Tuesday, December 29, 2015 12:30:14 AM Andreas Tille wrote:
> > > > Hi,
> > > > 
> > > > I realised that for jellyfish[1] Python bindings can be activated.  I
> > > > tried to do so and configuring and building works fine - but I have no
> > > > idea how to sensibly install the files into the python-jellyfish
> > > > package.  Any idea how to call swig/python/setup.py or do something
> > 
> > else
> > 
> > > > to install the files into the right location.
> > > > 
> > > > Any help?
> > > > 
> > > > Kind regards
> > > > 
> > > >         Andreas.
> > > > 
> > > > [1] git://anonscm.debian.org/debian-med/jellyfish.git
> > > 
> > > I haven't been able to actually test this since when I try to build it,
> > > I
> > > get this error:
> > > 
> > > jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No such
> > 
> > file
> > 
> > > or directory
> > > 
> > > I think it should ~work.  Note that these bindings are for python3, not
> > > python.  I've adjusted things accordingly.  The configure changes I made
> > 
> > (so
> > 
> > > that configure wouldn't fail) mean perl bindings don't get built
> > 
> > either.  I
> > 
> > > didn't check if that was working before.
> > > 
> > > Scott K
> > 
> > Correction: It's not in the diff, but I had to remove the auto-configure
> > override to get through configure.
> > 
> > Scott K

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#8019

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On Tue, Dec 29, 2015 at 12:56:20PM -0500, Scott Kitterman wrote:
> I think the respective maintainers should talk and then discuss with their 
> upstreams as the collision potential isn't just in Debian.

I'm chiming in as the (prospective) maintainer of the ITP python-jellyfish
package, just to note that I have discussed it with Andreas [1] and fully
agreed to rename "my" package. The choice of name was due to not being aware
of the Python bindings on the existing DNA-jelyfish package (and in part also
due to my inexperience on these matters), and I have contacted upstream
earlier today in the hopes of coming up with a good alternative name.

I'd be happy to follow up on the discussion with upstream once I get a reply,
in order to find out if he would be open to solving the conflict at a "higher"
level.

Best regards,

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716#42
-- 
Diego M. Rodriguez
36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232

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#8020

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That won't solve the problem, since both will provide the python module
jellyfish

On Tue, Dec 29, 2015 at 1:24 PM, Diego M. Rodriguez <diego.plan9@gmail.com>
wrote:

> On Tue, Dec 29, 2015 at 12:56:20PM -0500, Scott Kitterman wrote:
> > I think the respective maintainers should talk and then discuss with
> their
> > upstreams as the collision potential isn't just in Debian.
>
> I'm chiming in as the (prospective) maintainer of the ITP python-jellyfish
> package, just to note that I have discussed it with Andreas [1] and fully
> agreed to rename "my" package. The choice of name was due to not being
> aware
> of the Python bindings on the existing DNA-jelyfish package (and in part
> also
> due to my inexperience on these matters), and I have contacted upstream
> earlier today in the hopes of coming up with a good alternative name.
>
> I'd be happy to follow up on the discussion with upstream once I get a
> reply,
> in order to find out if he would be open to solving the conflict at a
> "higher"
> level.
>
> Best regards,
>
> [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716#42
> --
> Diego M. Rodriguez
> 36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232
>
>


-- 
All programmers are playwrights, and all computers are lousy actors.

#define sizeof(x) rand()
:wq

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#8022

On Tue, Dec 29, 2015 at 02:07:05PM -0500, Paul Tagliamonte wrote:
> That won't solve the problem, since both will provide the python module
> jellyfish

I agree.  BTW, I just became aware about the Python bindings of the DNA
Jellyfish by discussing with Diego. :-)

I'm not in a hurry with uploading the Python3 bindings for the existing
Jellyfish.

Kind regards

         Andreas.

-- 
http://fam-tille.de

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#8034

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On Tue, Dec 29, 2015 at 02:07:05PM -0500, Paul Tagliamonte wrote:
> That won't solve the problem, since both will provide the python module
> jellyfish

Fair point indeed, and I fully agree that ideally the problem should be solved
at the python module level.

I'm wondering if you or other senior, more experienced developers could
suggest what would be the recommended solution for the namespace conflict,
taking into account:

a) DNA-jellyfish is an stablished Debian package since 2011 [1]
b) STR-jellyfish is on PyPI [2] since 2010 (version 0.1)
c) both packages started their Github repos around the same time (summer 2010)
d) both packages seem to be a bit "niche" (popcon stats for "jellyfish" [3] and
"beets" [4], the package that would depend on STR-jellyfish, seem to hint that
they are both modestly used within Debian and cater to specific groups of
users)
e) other considerations I'm probably missing!

I would personally place a bit more weight on the fact that STR-jellyfish is
already on PyPI (based on the rationale that it is arguably the "de facto"
repository for Python packaging); but, again, I am relatively new to
Debian practices and arguing for keeping consistency within the Debian
repository seems reasonable to me as well.

Best regards,

[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644925
[2] https://pypi.python.org/pypi/jellyfish
[3] https://qa.debian.org/popcon.php?package=jellyfish
[4] https://qa.debian.org/popcon.php?package=beets

> 
> On Tue, Dec 29, 2015 at 1:24 PM, Diego M. Rodriguez <diego.plan9@gmail.com>
> wrote:
> 
> > On Tue, Dec 29, 2015 at 12:56:20PM -0500, Scott Kitterman wrote:
> > > I think the respective maintainers should talk and then discuss with
> > their
> > > upstreams as the collision potential isn't just in Debian.
> >
> > I'm chiming in as the (prospective) maintainer of the ITP python-jellyfish
> > package, just to note that I have discussed it with Andreas [1] and fully
> > agreed to rename "my" package. The choice of name was due to not being
> > aware
> > of the Python bindings on the existing DNA-jelyfish package (and in part
> > also
> > due to my inexperience on these matters), and I have contacted upstream
> > earlier today in the hopes of coming up with a good alternative name.
> >
> > I'd be happy to follow up on the discussion with upstream once I get a
> > reply,
> > in order to find out if he would be open to solving the conflict at a
> > "higher"
> > level.
> >
> > Best regards,
> >
> > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716#42
> > --
> > Diego M. Rodriguez
> > 36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232
> >
> >
> 
> 
> -- 
> All programmers are playwrights, and all computers are lousy actors.
> 
> #define sizeof(x) rand()
> :wq

-- 
Diego M. Rodriguez
36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232

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#8035

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On Thursday, December 31, 2015 06:32:43 PM Diego M. Rodriguez wrote:
> On Tue, Dec 29, 2015 at 02:07:05PM -0500, Paul Tagliamonte wrote:
> > On Tue, Dec 29, 2015 at 1:24 PM, Diego M. Rodriguez
> > <diego.plan9@gmail.com>
> > wrote:
> > > On Tue, Dec 29, 2015 at 12:56:20PM -0500, Scott Kitterman wrote:
> > > > I think the respective maintainers should talk and then discuss with
> > > their upstreams as the collision potential isn't just in Debian.
> > > 
> > > I'm chiming in as the (prospective) maintainer of the ITP
> > > python-jellyfish
> > > package, just to note that I have discussed it with Andreas [1] and
> > > fully
> > > agreed to rename "my" package. The choice of name was due to not being
> > > aware
> > > of the Python bindings on the existing DNA-jelyfish package (and in part
> > > also
> > > due to my inexperience on these matters), and I have contacted upstream
> > > earlier today in the hopes of coming up with a good alternative name.
> > > 
> > > I'd be happy to follow up on the discussion with upstream once I get a
> > > reply,
> > > in order to find out if he would be open to solving the conflict at a
> > > "higher"
> > > level.
> > > 
> > > Best regards,
> > > 
> > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716#42
> > > --
> > > Diego M. Rodriguez
> > > 36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232

> > > > > That won't solve the problem, since both will provide the python 
> > module jellyfish
> 
> Fair point indeed, and I fully agree that ideally the problem should be
> solved at the python module level.
> 
> I'm wondering if you or other senior, more experienced developers could
> suggest what would be the recommended solution for the namespace conflict,
> taking into account:
> 
> a) DNA-jellyfish is an stablished Debian package since 2011 [1]
> b) STR-jellyfish is on PyPI [2] since 2010 (version 0.1)
> c) both packages started their Github repos around the same time (summer
> 2010) d) both packages seem to be a bit "niche" (popcon stats for
> "jellyfish" [3] and "beets" [4], the package that would depend on
> STR-jellyfish, seem to hint that they are both modestly used within Debian
> and cater to specific groups of users)
> e) other considerations I'm probably missing!
> 
> I would personally place a bit more weight on the fact that STR-jellyfish is
> already on PyPI (based on the rationale that it is arguably the "de facto"
> repository for Python packaging); but, again, I am relatively new to Debian
> practices and arguing for keeping consistency within the Debian repository
> seems reasonable to me as well.
> 
> Best regards,
> 
> [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644925
> [2] https://pypi.python.org/pypi/jellyfish
> [3] https://qa.debian.org/popcon.php?package=jellyfish
> [4] https://qa.debian.org/popcon.php?package=beets

Here's what Debian Policy has to say on the matter:

10.1. Binaries
--------------

     Two different packages must not install programs with different
     functionality but with the same filenames.  (The case of two programs
     having the same functionality but different implementations is handled
     via "alternatives" or the "Conflicts" mechanism.  See Section 3.9,
     `Maintainer Scripts' and Section 7.4, `Conflicting binary packages -
     `Conflicts'' respectively.) If this case happens, one of the programs
     must be renamed.  The maintainers should report this to the
     `debian-devel' mailing list and try to find a consensus about which
     program will have to be renamed.  If a consensus cannot be reached,
     _both_ programs must be renamed.


That bit of policy doesn't officially kick in yet since these aren't both in the 
archive yet.  The policy is about consensus finding and not winning and losing.  
That's why I recommended discussing with the upstreams (and hopefully getting 
them in direct communication).

Scott K

P.S.  Fixed top posting

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#8037

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> That bit of policy doesn't officially kick in yet since these aren't both in the 
> archive yet.  The policy is about consensus finding and not winning and losing.  
> That's why I recommended discussing with the upstreams (and hopefully getting 
> them in direct communication).

Thanks for the pointer to the relevant Debian Policy chapter, Scott. My
previous message was indeed intented to hopefully serve as a common ground
towards reaching a consensus and as an aid when taking the discussion upstream,
rather than force or impose a decision - my apologies if it came too strong!

-- 
Diego M. Rodriguez
36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232

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#8039

Hi Guillaume,

when Diego intended to package python-jellyfish a discussion about the
duplicate name came up.  I even became aware that your jellyfish code
provides Python bindings and I intend to provide these as Debian package
as well.  This would lead to a conflict to the completely unrelated
multimedia jellyfish project.

Diego has layed out the problem on his posting to the Debian Python
mailing list
(https://lists.debian.org/debian-python/2015/12/msg00101.html) where
you can read the full thread about the problem.  Please let us know
what you think about the naming issue.

Kind regards

         Andreas.

On Thu, Dec 31, 2015 at 06:32:43PM +0100, Diego M. Rodriguez wrote:
> On Tue, Dec 29, 2015 at 02:07:05PM -0500, Paul Tagliamonte wrote:
> > That won't solve the problem, since both will provide the python module
> > jellyfish
> 
> Fair point indeed, and I fully agree that ideally the problem should be solved
> at the python module level.
> 
> I'm wondering if you or other senior, more experienced developers could
> suggest what would be the recommended solution for the namespace conflict,
> taking into account:
> 
> a) DNA-jellyfish is an stablished Debian package since 2011 [1]
> b) STR-jellyfish is on PyPI [2] since 2010 (version 0.1)
> c) both packages started their Github repos around the same time (summer 2010)
> d) both packages seem to be a bit "niche" (popcon stats for "jellyfish" [3] and
> "beets" [4], the package that would depend on STR-jellyfish, seem to hint that
> they are both modestly used within Debian and cater to specific groups of
> users)
> e) other considerations I'm probably missing!
> 
> I would personally place a bit more weight on the fact that STR-jellyfish is
> already on PyPI (based on the rationale that it is arguably the "de facto"
> repository for Python packaging); but, again, I am relatively new to
> Debian practices and arguing for keeping consistency within the Debian
> repository seems reasonable to me as well.
> 
> Best regards,
> 
> [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644925
> [2] https://pypi.python.org/pypi/jellyfish
> [3] https://qa.debian.org/popcon.php?package=jellyfish
> [4] https://qa.debian.org/popcon.php?package=beets
> 
> > 
> > On Tue, Dec 29, 2015 at 1:24 PM, Diego M. Rodriguez <diego.plan9@gmail.com>
> > wrote:
> > 
> > > On Tue, Dec 29, 2015 at 12:56:20PM -0500, Scott Kitterman wrote:
> > > > I think the respective maintainers should talk and then discuss with
> > > their
> > > > upstreams as the collision potential isn't just in Debian.
> > >
> > > I'm chiming in as the (prospective) maintainer of the ITP python-jellyfish
> > > package, just to note that I have discussed it with Andreas [1] and fully
> > > agreed to rename "my" package. The choice of name was due to not being
> > > aware
> > > of the Python bindings on the existing DNA-jelyfish package (and in part
> > > also
> > > due to my inexperience on these matters), and I have contacted upstream
> > > earlier today in the hopes of coming up with a good alternative name.
> > >
> > > I'd be happy to follow up on the discussion with upstream once I get a
> > > reply,
> > > in order to find out if he would be open to solving the conflict at a
> > > "higher"
> > > level.
> > >
> > > Best regards,
> > >
> > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716#42
> > > --
> > > Diego M. Rodriguez
> > > 36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232
> > >
> > >
> > 
> > 
> > -- 
> > All programmers are playwrights, and all computers are lousy actors.
> > 
> > #define sizeof(x) rand()
> > :wq
> 
> -- 
> Diego M. Rodriguez
> 36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232
> 



-- 
http://fam-tille.de

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#8040

[Multipart message — attachments visible in raw view] — view raw

On Thu, Dec 31, 2015 at 3:23 PM, Andreas Tille <andreas@fam-tille.de> wrote:

> Hi Guillaume,
>
> when Diego intended to package python-jellyfish a discussion about the
> duplicate name came up.  I even became aware that your jellyfish code
> provides Python bindings and I intend to provide these as Debian package
> as well.  This would lead to a conflict to the completely unrelated
> multimedia jellyfish project.
>
> Diego has layed out the problem on his posting to the Debian Python
> mailing list
> (https://lists.debian.org/debian-python/2015/12/msg00101.html) where
> you can read the full thread about the problem.  Please let us know
> what you think about the naming issue.
>

Hi all,

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.

Regarding the module itself, it should work for both Python2 and Python3.
If you have example where it does not, please let me know.

Guillaume.


> Kind regards
>
>          Andreas.
>
> On Thu, Dec 31, 2015 at 06:32:43PM +0100, Diego M. Rodriguez wrote:
> > On Tue, Dec 29, 2015 at 02:07:05PM -0500, Paul Tagliamonte wrote:
> > > That won't solve the problem, since both will provide the python module
> > > jellyfish
> >
> > Fair point indeed, and I fully agree that ideally the problem should be
> solved
> > at the python module level.
> >
> > I'm wondering if you or other senior, more experienced developers could
> > suggest what would be the recommended solution for the namespace
> conflict,
> > taking into account:
> >
> > a) DNA-jellyfish is an stablished Debian package since 2011 [1]
> > b) STR-jellyfish is on PyPI [2] since 2010 (version 0.1)
> > c) both packages started their Github repos around the same time (summer
> 2010)
> > d) both packages seem to be a bit "niche" (popcon stats for "jellyfish"
> [3] and
> > "beets" [4], the package that would depend on STR-jellyfish, seem to
> hint that
> > they are both modestly used within Debian and cater to specific groups of
> > users)
> > e) other considerations I'm probably missing!
> >
> > I would personally place a bit more weight on the fact that
> STR-jellyfish is
> > already on PyPI (based on the rationale that it is arguably the "de
> facto"
> > repository for Python packaging); but, again, I am relatively new to
> > Debian practices and arguing for keeping consistency within the Debian
> > repository seems reasonable to me as well.
> >
> > Best regards,
> >
> > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644925
> > [2] https://pypi.python.org/pypi/jellyfish
> > [3] https://qa.debian.org/popcon.php?package=jellyfish
> > [4] https://qa.debian.org/popcon.php?package=beets
> >
> > >
> > > On Tue, Dec 29, 2015 at 1:24 PM, Diego M. Rodriguez <
> diego.plan9@gmail.com>
> > > wrote:
> > >
> > > > On Tue, Dec 29, 2015 at 12:56:20PM -0500, Scott Kitterman wrote:
> > > > > I think the respective maintainers should talk and then discuss
> with
> > > > their
> > > > > upstreams as the collision potential isn't just in Debian.
> > > >
> > > > I'm chiming in as the (prospective) maintainer of the ITP
> python-jellyfish
> > > > package, just to note that I have discussed it with Andreas [1] and
> fully
> > > > agreed to rename "my" package. The choice of name was due to not
> being
> > > > aware
> > > > of the Python bindings on the existing DNA-jelyfish package (and in
> part
> > > > also
> > > > due to my inexperience on these matters), and I have contacted
> upstream
> > > > earlier today in the hopes of coming up with a good alternative name.
> > > >
> > > > I'd be happy to follow up on the discussion with upstream once I get
> a
> > > > reply,
> > > > in order to find out if he would be open to solving the conflict at a
> > > > "higher"
> > > > level.
> > > >
> > > > Best regards,
> > > >
> > > > [1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=806716#42
> > > > --
> > > > Diego M. Rodriguez
> > > > 36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232
> > > >
> > > >
> > >
> > >
> > > --
> > > All programmers are playwrights, and all computers are lousy actors.
> > >
> > > #define sizeof(x) rand()
> > > :wq
> >
> > --
> > Diego M. Rodriguez
> > 36B3 42A9 9F2F 2CFB F79B  FF9B B6C4 B901 06BC E232
> >
>
>
>
> --
> http://fam-tille.de
>

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#8042

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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