[moose-generic] packaging questions

[Alexander K. <ak...@na...>]

Thought I could deposit this discussion here. There is a false 
broken link alarm down there but also few bits that could be 
helpful.

Thanks to the Moose' team for support!
/Alex.



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>From ak...@na... Wed Nov  7 09:22:42 2012
Date: Wed, 7 Nov 2012 09:22:42 +0100 (MET)
From: Alexander Kozlov <ak...@na...>
To: Niraj Dudani <ni...@nc...>
Subject: Re: parallel moose?

Hi Niraj,

Best congrats with new release!! This is awesome!

I wonder if any kind of Moose Users Group will be organized? Moose-generic
mailing list seems dead (or can I register and post questions there?)

Before I did, please fix moosegui link in the distribution! It refers to
absolute path to MooseGUI.py on a host machine in the source Makefile, ie
it's broken in binary distribution (amd64 deb, for example).

I build from sources now and plan to test and read up syntax soon so I have
lot of confusion ahead. Excited anyway!

Cheers,
Alex.



>From ad...@nc... Wed Nov  7 10:51:42 2012
Date: Wed, 7 Nov 2012 15:21:08 +0530
From: Aditya Gilra <ad...@nc...>
To: Alexander Kozlov <ak...@na...>
Cc: Niraj Dudani <ni...@nc...>
Subject: Re: parallel moose?

Dear Alex,
Could you give further details below about the broken amd64 package:

1) Did you use python2.6 or python2.7 version of the amd64 packge
that you mention i.e.
moose2.0.0_amd64_python2.6.deb ormoose2.0.0_amd64_python2.7.deb?

2) Are you installing on Ubuntu? Which version? If not, which linux
and which version?

3) Did you install using apt-get / Ubuntu software center or synaptic
or something else?

3) If you type moosegui on a terminal, can you tell me what the error
is (copy and paste the error) ....
On machines that I tested, moosegui links to
/usr/share/moose/gui/MooseGUI.py , so it should have worked.

4) On Ubuntu/Debian, you should also be able to run moosegui from the
mainmenu->Science/Education, or on the latest Ubuntu-s (Unity
interface 11.10 onwards) by typing moose in the dash, and clicking on
the icon for moosegui that appears.

I'd tested all 4 deb packages on their respective systems, so am
surprised by this bug....

Many thanks for the bug-report and for testing MOOSE.

Best,
Aditya.

On Wed, Nov 7, 2012 at 2:58 PM, Niraj Dudani <ni...@nc...>
wrote:
       Hello, Alex, and thanks for your mail and enthusiasm :)

       Feel free to send your questions to the moose-generic
       mailing list! :)
       Yes, it has had no activity, but it has a few subscribers
       already, and all
       of us are already on it. We have mentioned it on the
       MOOSE website, but we
       should really advertise it in the announcement emails as
       well. I'll
       consider sending an email to the comp-neuro mailing list
       announcing that
       this mailing list is functional, and can be used to
       discuss MOOSE issues.
       Thanks for bringing this up.

       Also thanks for the bug report!!! I'm CC'ing it to Aditya
       who has done the
       packaging.

       Regarding getting started with MOOSE syntax, you should
       look at the User
       Documentation section on the MOOSE website:
        http://moose.ncbs.res.in/content/view/5/6/

       You should also look at the 'Demos' directory for more
       examples, and the
       'Demos/snippets' directory for short examples showing
       usage for some basic
       things.

       Best wishes,
       Niraj


>From ak...@na... Wed Nov  7 11:17:39 2012
Date: Wed, 7 Nov 2012 11:17:39 +0100 (MET)
From: Alexander Kozlov <ak...@na...>
To: Aditya Gilra <ad...@nc...>
Cc: Niraj Dudani <ni...@nc...>
Subject: Re: parallel moose?

Hello!

Thank you for your reply.

> 1) Did you use python2.6 or python2.7 version of the amd64 packge that you
> mention i.e.
> moose2.0.0_amd64_python2.6.deb or moose2.0.0_amd64_python2.7.deb?

In the latter file (moose_2.0.0_amd64_python2.7.deb) I got from
http://moose.ncbs.res.in/content/view/35/70/, /usr/bin/moosegui links to
/home/user/moose_src/debian/moose/usr/share/moose/gui/MooseGUI.py

In the source Makefile, moosegui is installed by

ln -s $(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py \
   $(DESTDIR)$(install_prefix)/bin/moosegui

which is plain wrong, I think; particularly, if one makes a stage build for
further packaging. It should be relative instead:

ln -s ../share/moose/gui/MooseGUI.py \
   $(DESTDIR)$(install_prefix)/bin/moosegui

I build Moose from sources so I didn't try binary distribution.
I can do, if you like, I also run Debian on x86 and x86_64 machines.

Thank you again,
Alex.



>From ad...@nc... Wed Nov  7 11:49:18 2012
Date: Wed, 7 Nov 2012 16:18:37 +0530
From: Aditya Gilra <ad...@nc...>
To: Alexander Kozlov <ak...@na...>
Cc: Niraj Dudani <ni...@nc...>
Subject: Re: parallel moose?

Hi Alex,
Thanks for the prompt clarifications.

1) I note that you haven't actually installed the .deb package.
If you do go ahead and install, you'll find that the postinst script
creates a new /usr/bin/moosegui link that overwrites the previous one
and points to the correct location.

Thus, there is no functional bug as I explain in point 2 below, but
your method is simpler... It will eliminate the need for the above
extra link line in the postinst script, since the path is relative.

2) The Makefile line:

ln -s$(DESTDIR)$(install_prefix)/share/moose/gui/MooseGUI.py$(DESTDIR)$(install
_prefix)/bin/moosegui

is common for
(a) a person doing a source install 'sudo make install', in which
case $(DESTDIR) is blank and $(install_prefix) is /usr . Things go
fine here.

and

(b) for making the debian package, dh_install sets $(DESTDIR) to be a
local subdirectory where it wants all installed files for further
packaging. Later it strips away the local subdirectory path from all
the installed files, but it cannot strip away a soft linked path.
Hence I have put an overriding command to re-link in the postinst
script.

Thus, for both cases things work fine. You can install the deb file
and it should work fine.

Best,
Aditya.



>From ak...@na... Wed Nov  7 13:19:55 2012
Date: Wed, 7 Nov 2012 13:19:54 +0100 (MET)
From: Alexander Kozlov <ak...@na...>
To: Aditya Gilra <ad...@nc...>
Cc: Niraj Dudani <ni...@nc...>
Subject: Re: parallel moose?

OK, I see, deb package is fine then.

(Few more notes-- minor things, not bugs.)

1. Nevertheless, the Makefile instructions are misleading. Non-debian
packagers (Slackware, ARCH-Linux, CRUX, etc) will have to patch it or avoid
the whole 'install:' section.

2. Also, 'install:' introduces unnecessary dependencies on rsync and gtk+
(update-icon-caches) which are not listed in README.

3. Build depends on numpy headers installed or linked to

    /usr/include/python${PYTHON_VERSION}/numpy

This is Debian specific and not general. Default path for numpy headers is

    /usr/lib/python2.7/site-packages/numpy/core/include

To fix the build, I had to add extra path to CXXFLAGS:

    sed -i 's/pymoose: CXX.*/& -I$(shell python -c "import numpy;print
numpy.get_include()")/' Makefile

4. Not mentioned in README, make needs SVN=0 to build the package

    make SVN=0 BUILD=release

or

    make SVN=0

Would be nice to have it disabled by default in release.
In the rest it builds fine on my machine.

5. To run Demos/snippets, one needs matplotlib, python-dateutil and
setuptools to be installed. These should be mentioned in README too, I
think.

With best regards,
Alexander.




>From ad...@nc... Wed Nov  7 14:06:33 2012
Date: Wed, 7 Nov 2012 18:35:57 +0530
From: Aditya Gilra <ad...@nc...>
To: Alexander Kozlov <ak...@na...>
Cc: Niraj Dudani <ni...@nc...>, Subhasis Ray <sub...@nc...>
Subject: Re: parallel moose?

Many thanks Alex! Will incorporate these changes soon... Subha,
perhaps you could look into the build stuff.
Perhaps we should move such discussions to the moose-devel list, so
that discussions are publicly archived? What do people say?

Best,
Aditya.



>From sub...@nc... Thu Nov  8 07:40:53 2012
Date: Thu, 8 Nov 2012 12:10:40 +0530
From: Subhasis Ray <sub...@nc...>
To: Aditya Gilra <ad...@nc...>
Cc: Alexander Kozlov <ak...@na...>, Niraj Dudani <ni...@nc...>
Subject: Re: parallel moose?


On Wed, Nov 7, 2012 at 6:35 PM, Aditya Gilra <ad...@nc...>
wrote:

       Perhaps we should move such discussions to the
       moose-devel list, so that discussions are publicly
       archived? What do people say?


I agree.

       On Wed, Nov 7, 2012 at 5:49 PM, Alexander Kozlov
       <ak...@na...> wrote:
             OK, I see, deb package is fine then.

             (Few more notes-- minor things, not bugs.)

             1. Nevertheless, the Makefile instructions
             are misleading. Non-debian packagers
             (Slackware, ARCH-Linux, CRUX, etc) will have
             to patch it or avoid the whole 'install:'
             section.

             2. Also, 'install:' introduces unnecessary
             dependencies on rsync and gtk+
             (update-icon-caches) which are not listed in
             README.

             3. Build depends on numpy headers installed
             or linked to

              /usr/include/python${PYTHON_VERSION}/numpy

             This is Debian specific and not general.
             Default path for numpy headers is

             
             /usr/lib/python2.7/site-packages/numpy/core/include

             To fix the build, I had to add extra path to
             CXXFLAGS:

              sed -i 's/pymoose: CXX.*/& -I$(shell
             python -c "import numpy;print
             numpy.get_include()")/' Makefile


Thanks, this is useful. At some point we aim to switch to python
distutils or some other advanced build management system. Hopefully
detecting paths will be much simpler then.


             4. Not mentioned in README, make needs SVN=0
             to build the package

              make SVN=0 BUILD=release

             or

              make SVN=0

             Would be nice to have it disabled by default
             in release.
             In the rest it builds fine on my machine.


Good point. It is a developer feature to incorporate svn revision
number for runtime queries. We should have set it to 0 in the
release.


             5. To run Demos/snippets, one needs
             matplotlib, python-dateutil and setuptools to
             be installed. These should be mentioned in
             README too, I think.


matplotlib is required anyways for the gui. I am not aware of
python-dateutil or setuptools being used in the Demos/snippets. Can
you specify the suspect scripts?
Best,
Subha



>From ak...@na... Thu Nov  8 09:24:25 2012
Date: Thu, 8 Nov 2012 09:24:25 +0100 (MET)
From: Alexander Kozlov <ak...@na...>
To: Subhasis Ray <sub...@nc...>
Cc: Aditya Gilra <ad...@nc...>, Niraj Dudani <ni...@nc...>
Subject: Re: parallel moose?

> > > 5. To run Demos/snippets, one needs matplotlib, python-dateutil and
> > > setuptools to be installed. These should be mentioned in README too, I
> > > think.
> > > 
> > > 
> matplotlib is required anyways for the gui. I am not aware of
> python-dateutil or setuptools being used in the Demos/snippets. Can you
> specify the suspect scripts?

Actually, README is correct listing matplotlib only as a requirement so I
should withdraw my objection.

matplotlib (run time dep: python-dateutil (build dep: setuptools))

All included, and should be installed as package dependencies.

Thanks for your comments and sorry for noise,
Alex.