[Neurodebian-devel] Neurodebian tasks (and Debian Science)

[Yaroslav Halchenko]

On Tue, 05 Apr 2016, Ole Streicher wrote:
> Dear Yaroslav, and all,

> I am currently looking on how we get the Debian Blends into the
> installer for the next release. This is connected to Bug #758116 [1]

> One of the points there is the inclusion of NeuroDebian, which does not
> follow the usual Pure Blends scheme. Since you gave a "+100" in the bug,
> I however suspect that there is some interest in having NeuroDebian
> visible in the installer.

Thank you for thinking about us! ;)   Sorry for a long "quick" reply.

still +100 although... I am wondering now how valuable would be to have
those large meta-packages installed as part of debian installer -- in
many (if not majority or all) of the cases any of those are valuable
primarily as pointers to what packages they point to, so users could go
and select particular packages (e.g. in aptitude) from those among
Recommended and Suggested.  

Would any user ever want that particular selection of Recommended
packages?   may be, but I see that most often users would want a
particular selection from those pointed by Suggests and Recommends.  Are
you aiming to provide that level of granularity within debian installer?
if so -- that would be cool.  But unlikely, at least at current stage I
guess.  Don't take it as discouragement, just merely as my expression of
an opinion/concern.

> Looking into your repository content [2], the "by field" selection is
> quite close to a number of Debian Science tasks:

>  * Packages for Electrophysiology
>     --> science-electrophysiology
>  * Packages for Modeling of neural systems
>     --> science-neuroscience-modelling
>  * Packages for Neuroscience Datasets
>     --> science-neuroscience-datasets
>  * Packages for Psychophysics
>     --> science-psychophysics

> Some Fields in neurodebian seem not to have 1:1 tasks in debian-science:

>  * Packages for Distributed Computing
>     --> science-distributedcomputing (your selection is a bit smaller?)
>  * Packages for Magnetic Reasonance Imaging
>  * Packages for Neuroscience Education

> The debian-science task "science-neuroscience-congnitive" has no
> corresponding "field" in neurodebian, but seems to belong there.

Let me leave it for Michael Hanke to reply since he is the master guru
beyond neurodebian web site "engine".

> The Debian-Science blend is quite filled with tasks: there are currently
> 47 tasks in it. Wouldn't it make sense to move out the specific tasks
> (science-electrophysiology. science-neuroscience-modelling,
> science-neuroscience-datasets, science-psychophysics, and
> science-neuroscience-congnitive) into the "neurodebian" package (and
> remove it from debian-science)?

Do you consider neuroscience not a science? ;)  Or is debian-science
blend is solely to collect all other sciences which haven't
found/established their own blends? and as soon as they do, new
naming/packages arrive etc...

moreover many of those are not neuro- specific, and some times even
though used in neuro-, they might be used in other sciences (e.g.
consider electrophysiology -- it is not just neuroelectrophysiology)

that somewhat points to our "concern" with current approach on blends --
pretty much attempt to impose separate hierarchies wherever structure is
more of a tag cloud (single software/task could be a part of multiple
blends).  That is why we somewhat tried to avoid creating our own
neuro- blend and just contributed where we thought neuroscience related
tasks/software was  most appropriate -- to debian-science and/or -med.
That is why at some point I came up with (now unused)
http://anonscm.debian.org/cgit/pkg-exppsy/neurodebian.git/tree/tools/blends-inject
to ease 'injection' of entries of task files for multiple blends.

Sorry if it is all non-constructive and more of a whining ;)

> We then would just need a metapackage that includes (recommends) all
> neurodebian tasks that should be installed on a default NeuroDebian
> blend. 

I am not sure what such a default blend should carry really... how
could I decide for a lab to use e.g. AFNI vs FSL vs HCP vs  some other
processing toolkit, or psychtoolbox vs psychopy vs visionegg vs ...  --
or why to install all of them (unless they are like me ;) )

> A "neurodebian-tasks" package would be useful as well so that
> people could use tasksel to install additonal NeuroDebian tasks (or to
> remove them if not needed).

I guess we could indeed establish a neurodebian-tasks package which
could may be provide some pre-canned tasks and also one of which would
include neurodebian package  itself.  But I don't think that those tasks
would be the tasks as the blends composes them.  I see pretty much tasks
which would be nearly a single package tasks pointing to most common
neuro- toolkits so a new user could immediately recognize
familiar/necessary tools to be installed.  That would IMHO be indeed
practically useful.  I do see thought some possible larger tasks, e.g.
"Neuroimaging in Python", which would install a bit wider collection
than a single toolkit, and helper tools (ipython{,-notebook}, pudb,
spyder, ..) to equip box with typical collection for such a case.

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik