Re: Status of rsat?

[Andreas Tille <andreas@fam-tille.de>]

Hi Jacques,

On Thu, Nov 21, 2019 at 10:24:48PM +0100, Jacques van Helden wrote:
> Hi Andreas
> 
> Thanks a lot for your enthusiasm and constant help !

You are welcome.
 
> I think the reason why I still use pip is historical: initially I had a single script to install the python libraries on Mac OS X and Unix. 
> 
> However, I imagine that currently the best is to use as much as possible the OS-dependent package managers (apt-get, brew), so I will be pleased to replace this by apt-get and brew packages (in separate files).
> 
> Would this be OK ? 

I fully agree that prefering apt-get (I don't know brew but if it has a
similarly large software pool for sure) over pip.  The advantage is that
you get a more stable installation since if you install on Debian /
Ubuntu *stable* you have always the same (tested and security fixed)
versions instead of what version might be available via pip.
 
Kind regards

       Andreas.
 
> > On 21 Nov 2019, at 18:37, Andreas Tille <andreas@an3as.eu> wrote:
> > 
> > Hi Jacques,
> > 
> > On Thu, Nov 21, 2019 at 05:13:15PM +0100, Jacques van Helden wrote:
> >> https://github.com/RSAT-doc/installing-RSAT <https://github.com/RSAT-doc/installing-RSAT>
> >> 
> >> Ubuntu procedure
> >> 	https://rsat-doc.github.io/installing-RSAT/installing_RSAT_procedure.html <https://rsat-doc.github.io/installing-RSAT/installing_RSAT_procedure.html>
> >> 
> >> 
> >> The bash file sin the installer folder contain the lists of dependencies. 
> > 
> > I had a **quick** look at the script
> > 
> >   bash_install_scripts/installer/02_python_packages.bash
> > 
> > which is doing:
> > 
> > sudo pip install numpy
> > sudo pip install scipy
> > sudo pip install matplotlib
> > sudo pip install suds
> > sudo pip install soappy
> > sudo pip install fisher
> > sudo pip install httplib2
> > ## pip install pygraphviz ## OSError: Error locating graphviz.
> > 
> > 
> > With the exception of soappy (which is currently only available for
> > Python2 - see #938180) and fisher (which really needs to be packaged)
> > the first chunk of manually installed packages could be taken from the
> > Debian package pool.  Before I start to tackle things like fisher (or
> > help fixing bug #938180) could you explain your motivation why these are
> > installed via pip instead of apt?
> > 
> > Even python3-pygraphviz is available (and has no bug that would indicate
> > any loading problem).
> > 
> > Kind regards
> > 
> >      Andreas.
> > 
> > -- 
> > http://fam-tille.de
> 

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