[ITP] libSBML-5.12.0-core and moose-3.0.2

[ITP] libSBML-5.12.0-core and moose-3.0.2

[Subhasis Ray]

Hi,
  I am willing to maintain cygwin packaging of the MOOSE simulation
environment (http://moose.ncbs.res.in) and its dependency libSBML-core
(http://sbml.org/Software/libSBML). MOOSE is GPL3 and libSBML is LGPL.
I created working cygport files for both:

-----------8<----------------------libSBML------------------------>8--------
inherit cmake
# package name
NAME="libsbml-core"
VERSION=5.12.0
SRC_DIR="libsbml-core-${VERSION}"
# setup.hint generation
CATEGORY="Science Libs"
SUMMARY="The Systems Biology Markup Language (SBML) is an XML-based
description language for representing computational models in systems
biology."
DESCRIPTION="LibSBML is a free, open-source programming library to
help you read, write, manipulate, translate, and validate SBML files
and data streams. It's not an application itself (though it does come
with example programs), but rather a library you embed in your own
applications.

LibSBML is available for free under LGPL terms in both source-code
form and precompiled binaries for Windows, Mac OS X, and Linux.

Visit http://sbml.org for more information."
# source and patch files
SRC_URI="https://sourceforge.net/projects/sbml/files/libsbml/5.12.0/stable/libSBML-5.12.0-core-src.tar.gz"
SRC_DIR="libsbml-${VERSION}"
# use the standard src_compile, src_install and src_test
-----------8<----------------------libSBML till here
------------------------>8--------



-----------8<----------------------MOOSE------------------------>8--------
inherit python-distutils
# package name
NAME="moose"
VERSION=3.0.2
RELEASE=2
SRC_DIR="moose-${VERSION}"
# setup.hint generation
CATEGORY="Science Python"
SUMMARY="Simulation environment for systems biology"
DESCRIPTION="the Multiscale Object-Oriented Simulation Environment.
It is designed to simulate neural systems ranging from subcellular
components and biochemical reactions to complex models of single
neurons, circuits, and large networks. MOOSE can operate at many
levels of detail, from stochastic chemical computations, to
multicompartment single-neuron models, to spiking neuron network
models.

MOOSE is a simulation environment, not just a numerical engine. It
provides the essentials by way of object-oriented representations of
model concepts and fast numerical solvers, but its scope is much
broader.
It has a scripting interface with Python, graphical displays with
Matplotlib, PyQt, and OpenGL, and support for many model formats.

MOOSE can read kinetic models in SBML and GENESIS kkit formats, from
BioModels.net and DOQCS. MOOSE also supports electrical models
specified in NeuroML and Genesis .p formats, and can load over 30,000
morphology files from NeuroMorpho.org (.swc format). "
# source and patch files
SRC_URI="https://github.com/BhallaLab/moose-core/archive/cygwin.tar.gz"
SRC_DIR="moose-core-cygwin"

# use the standard src_compile, src_install and src_test
-----------8<----------------------MOOSE till
here------------------------>8--------

This is my first time with cygwin packaging and it is not clear to me
from the package contributors' guide if I should already upload the
package files or do so after I get a green signal from the forum.

Looking forward to your comments,
- Subhasis Ray

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Marco Atzeri]

On 03/03/2016 17:32, Subhasis Ray wrote:
> Hi,

Hi Ray

>    I am willing to maintain cygwin packaging of the MOOSE simulation
> environment (http://moose.ncbs.res.in) and its dependency libSBML-core
> (http://sbml.org/Software/libSBML). MOOSE is GPL3 and libSBML is LGPL.
> I created working cygport files for both:
>
[cut]

as attachment was better

>
> This is my first time with cygwin packaging and it is not clear to me
> from the package contributors' guide if I should already upload the
> package files or do so after I get a green signal from the forum.
>
> Looking forward to your comments,
> - Subhasis Ray
>

you should provide access to your packages for peer review.

libSBML-core is in debian, so it is fine for general acceptance

But I am not sure about Moose, can you provide data about any Linux
main distribution already packaging it ?
I see a Moose perl framework that I assume is not the same.

Any reason why there is a specific source package for cygwin ?
https://github.com/BhallaLab/moose-core/archive/cygwin.tar.gz

It is a bit unusual.

Regards
Marco

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Achim Gratz]

Marco Atzeri writes:
> I see a Moose perl framework that I assume is not the same.

Yes, Moose for Perl is a totally different thing.


Regards,
Achim.
-- 
+<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+

Factory and User Sound Singles for Waldorf Q+, Q and microQ:
http://Synth.Stromeko.net/Downloads.html#WaldorfSounds

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Subhasis Ray]

Hi Marco, Achim,
  Thanks for your quick feedback.

On Thu, Mar 3, 2016 at 11:51 AM, Marco Atzeri <marco.atzeri@gmail.com> wrote:
> On 03/03/2016 17:32, Subhasis Ray wrote:
>>
>> I created working cygport files for both:
>>
> [cut]
>
> as attachment was better
>
The contributors guide explicitly says setup.hint should be part of
the text rather than attachment in the mail. I guess the instructions
are outdated.


>
> you should provide access to your packages for peer review.
>

Am I expected to upload only the files in the dist directory generated
by cygport? I uploaded them here:
https://sourceforge.net/projects/moose/files/cygwin/libSBML/libSBML-core-5.12.0/
I am not sure if these are the correct files. In particular the
libSBML-libSBML-libSBML.tar.xz filename seems odd, though its contents
seem correct. Is this expected?

> libSBML-core is in debian, so it is fine for general acceptance
>
> But I am not sure about Moose, can you provide data about any Linux
> main distribution already packaging it ?
> I see a Moose perl framework that I assume is not the same.
>

Yes, this is different and is not part of any linux distribution yet.

> Any reason why there is a specific source package for cygwin ?
> https://github.com/BhallaLab/moose-core/archive/cygwin.tar.gz
>
> It is a bit unusual.

The reason is the main package builds with Make/CMake and I could not
get that to work on cygwin, possibly due to includes and libs path
issues, where setup.py works. I had created this branch specifically
for cygwin, but things have been merged since. So I just changed the
url to point to master.

The files generated in dist directory by cygport are here:
https://sourceforge.net/projects/moose/files/cygwin/moose/moose-3.0.2/




Thanks for your help,
  Subhasis

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Marco Atzeri]

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On 03/03/2016 22:19, Subhasis Ray wrote:
> Hi Marco, Achim,
>    Thanks for your quick feedback.
>
> On Thu, Mar 3, 2016 at 11:51 AM, Marco Atzeri <marco.atzeri@gmail.com> wrote:
>> On 03/03/2016 17:32, Subhasis Ray wrote:
>>>
>>> I created working cygport files for both:
>>>
>> [cut]
>>
>> as attachment was better
>>
> The contributors guide explicitly says setup.hint should be part of
> the text rather than attachment in the mail. I guess the instructions
> are outdated.
>>
>> you should provide access to your packages for peer review.
>>
>
> Am I expected to upload only the files in the dist directory generated
> by cygport? I uploaded them here:
> https://sourceforge.net/projects/moose/files/cygwin/libSBML/libSBML-core-5.12.0/
> I am not sure if these are the correct files. In particular the
> libSBML-libSBML-libSBML.tar.xz filename seems odd, though its contents
> seem correct. Is this expected?

attached a modified version that solve that issue
and split the package in shared lib and development

libSBML should be fine with with it.

Moose is another matter anyway; as it is not in any Linux distribution
you need to obtain 5 positive votes from the maintainers before its 
inclusion.


> Thanks for your help,
>    Subhasis

Regards
Marco

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inherit cmake
# package name
NAME="libsbml-core"
VERSION="5.12.0"
RELEASE=1
# setup.hint generation
CATEGORY="Science Libs"
SUMMARY="The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology."
DESCRIPTION="LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It's not an application itself (though it does come with example programs), but rather a library you embed in your own applications.

LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux.

Visit http://sbml.org for more information."
# source and patch files
SRC_URI="https://sourceforge.net/projects/sbml/files/libsbml/5.12.0/stable/libSBML-5.12.0-core-src.tar.gz"
SRC_DIR="libsbml-${VERSION}"
# use the standard src_compile, src_install and src_test

PKG_NAMES="libSBML5 libSBML-devel"

libSBML5_CONTENTS="usr/bin"
libSBML5_SUMMARY="Systems Biology Markup Language (SBML) - runtime"

libSBML_devel_CONTENTS="usr/include usr/lib usr/share"
libSBML_devel_SUMMARY="Systems Biology Markup Language (SBML) - headers"

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Corinna Vinschen]

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On Mar  4 21:03, Marco Atzeri wrote:
> On 03/03/2016 22:19, Subhasis Ray wrote:
> >Hi Marco, Achim,
> >   Thanks for your quick feedback.
> >
> >On Thu, Mar 3, 2016 at 11:51 AM, Marco Atzeri <marco.atzeri@gmail.com> wrote:
> >>On 03/03/2016 17:32, Subhasis Ray wrote:
> >>>
> >>>I created working cygport files for both:
> >>>
> >>[cut]
> >>
> >>as attachment was better
> >>
> >The contributors guide explicitly says setup.hint should be part of
> >the text rather than attachment in the mail. I guess the instructions
> >are outdated.
> >>
> >>you should provide access to your packages for peer review.
> >>
> >
> >Am I expected to upload only the files in the dist directory generated
> >by cygport? I uploaded them here:
> >https://sourceforge.net/projects/moose/files/cygwin/libSBML/libSBML-core-5.12.0/
> >I am not sure if these are the correct files. In particular the
> >libSBML-libSBML-libSBML.tar.xz filename seems odd, though its contents
> >seem correct. Is this expected?
> 
> attached a modified version that solve that issue
> and split the package in shared lib and development
> 
> libSBML should be fine with with it.
> 
> Moose is another matter anyway; as it is not in any Linux distribution
> you need to obtain 5 positive votes from the maintainers before its
> inclusion.

I wonder if we should change that (back) to three votes.  Five votes is
kind of hard to get to.

More important to me is that the maintainer-to-be subscribes to the
cygwin user mailing list as well as the cygwin-apps maintainer mailing
list and promises to scna the list for user problems with his/her
package.


Corinna

-- 
Corinna Vinschen                  Please, send mails regarding Cygwin to
Cygwin Maintainer                 cygwin AT cygwin DOT com
Red Hat

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Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Achim Gratz]

Corinna Vinschen writes:
> More important to me is that the maintainer-to-be subscribes to the
> cygwin user mailing list as well as the cygwin-apps maintainer mailing
> list and promises to scna the list for user problems with his/her
> package.

s/scna/scan/ I suppose?

Regards,
Achim.
-- 
+<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+

SD adaptations for Waldorf Q V3.00R3 and Q+ V3.54R2:
http://Synth.Stromeko.net/Downloads.html#WaldorfSDada

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Subhasis Ray]

Hi,
  Thanks for all the feedback. I feel that it is better to get moose
included in debian first since the primary development and usage
platform for it is Unix/Linux anyway.
   For libsbml, I am not sure how to separate the include headers and
the  dll into two packages with cygport. Any pointer to existing
documentation will be appreciated.
Regards,
   Subhasis


On Sat, Mar 5, 2016 at 8:22 AM, Achim Gratz <Stromeko@nexgo.de> wrote:
> Corinna Vinschen writes:
>> More important to me is that the maintainer-to-be subscribes to the
>> cygwin user mailing list as well as the cygwin-apps maintainer mailing
>> list and promises to scna the list for user problems with his/her
>> package.
>
> s/scna/scan/ I suppose?
>
> Regards,
> Achim.
> --
> +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+
>
> SD adaptations for Waldorf Q V3.00R3 and Q+ V3.54R2:
> http://Synth.Stromeko.net/Downloads.html#WaldorfSDada

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Subhasis Ray]

My bad. Marco had already sent the corrected cygport file.
Best,
- Subhasis


On Sat, Mar 5, 2016 at 2:18 PM, Subhasis Ray <ray.subhasis@gmail.com> wrote:
> Hi,
>   Thanks for all the feedback. I feel that it is better to get moose
> included in debian first since the primary development and usage
> platform for it is Unix/Linux anyway.
>    For libsbml, I am not sure how to separate the include headers and
> the  dll into two packages with cygport. Any pointer to existing
> documentation will be appreciated.
> Regards,
>    Subhasis
>
>
> On Sat, Mar 5, 2016 at 8:22 AM, Achim Gratz <Stromeko@nexgo.de> wrote:
>> Corinna Vinschen writes:
>>> More important to me is that the maintainer-to-be subscribes to the
>>> cygwin user mailing list as well as the cygwin-apps maintainer mailing
>>> list and promises to scna the list for user problems with his/her
>>> package.
>>
>> s/scna/scan/ I suppose?
>>
>> Regards,
>> Achim.
>> --
>> +<[Q+ Matrix-12 WAVE#46+305 Neuron microQkb Andromeda XTk Blofeld]>+
>>
>> SD adaptations for Waldorf Q V3.00R3 and Q+ V3.54R2:
>> http://Synth.Stromeko.net/Downloads.html#WaldorfSDada

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Subhasis Ray]

Hi all,

On Fri, Mar 4, 2016 at 3:03 PM, Marco Atzeri <marco.atzeri@gmail.com> wrote:

>
> attached a modified version that solve that issue
> and split the package in shared lib and development
>
> libSBML should be fine with with it.
>

Many thanks to Marco for fixing the cygport file. I used it to redo
the packaging and uploaded the two components here:
https://sourceforge.net/projects/moose/files/cygwin/libSBML/libSBML5/
and here: https://sourceforge.net/projects/moose/files/cygwin/libSBML/libSBML-devel/.
Please review and let me know.

As Corinna suggested, I also subscribed to the main cygwin mailing
list (seems to be the cygwin user mailing list).

Thanks and regards,
   Subhasis

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Warren Young]

On Mar 5, 2016, at 6:22 AM, Achim Gratz <Stromeko@nexgo.de> wrote:
> 
> Corinna Vinschen writes:
>> More important to me is that the maintainer-to-be subscribes to the
>> cygwin user mailing list as well as the cygwin-apps maintainer mailing
>> list and promises to scna the list for user problems with his/her
>> package.
> 
> s/scna/scan/ I suppose?

No, it’s a new Cygwin acronym entry: seriously consider not abdicating.

Re: [ITP] libSBML-5.12.0-core and moose-3.0.2

[Corinna Vinschen]

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On Mar  7 12:44, Warren Young wrote:
> On Mar 5, 2016, at 6:22 AM, Achim Gratz <Stromeko@nexgo.de> wrote:
> > 
> > Corinna Vinschen writes:
> >> More important to me is that the maintainer-to-be subscribes to the
> >> cygwin user mailing list as well as the cygwin-apps maintainer mailing
> >> list and promises to scna the list for user problems with his/her
> >> package.
> > 
> > s/scna/scan/ I suppose?
> 
> No, it’s a new Cygwin acronym entry: seriously consider not abdicating.

Hmm, so far I was pretty sure it was just a typo...


Corinna

-- 
Corinna Vinschen                  Please, send mails regarding Cygwin to
Cygwin Maintainer                 cygwin AT cygwin DOT com
Red Hat

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