[Neuroimaging] Technical details managing Python versions and packages.

Yaroslav Halchenko lists at onerussian.com
Mon Aug 3 16:17:16 CEST 2015

On Mon, 03 Aug 2015, Matthew Brett wrote:

> > If you're interested to do that, let me know, I'll write up a summary
> > of what to do.  I guess you are on Debian / Ubuntu?

> Despite deafening silence, I did write up the summary:

> https://matthew-brett.github.io/pydagogue/installing_on_debian.html

my 1c with the NeuroDebian/Debian developer hat on.

If you are into neuroimaging, and just a researcher/user who wants to
have work done, I would recommend to stick to using
(Neuro)Debian-provided packages as long as they are provided from our
repositories:  that is the point of having a distribution like Debian,
that we are taking care about compatibility between versions of
various packages you use and which inter-depend among  themselves.
And then your python packages live coherently with the rest of the
system,  so you can manage python and non-python packages with the same
commands.  If you need more recent versions of neuroimaging (and
related) python packages -- that is where NeuroDebian repository comes
in.  If interested to try -- there is a virtualbox VM, and docker images

And only then, when I hit the situation that some package is not yet
available from (Neuro)Debian, I usually create a virtualenv which
complements system-wide collection (virtualenv --system-site-packages)
and use its pip to install additional packages ideally by specifying
them within requirements.txt (pip install -r requirements.txt) so I
could later reproduce the same virtualenv.

Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Research Scientist,            Psychological and Brain Sciences Dept.
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        

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