Re: Status of rsat?
Hi again,
I forgot to ask explicitly: Since it seems you agreed that using
apt is sensible: I guess you would welcome if I would package
https://pypi.org/project/fisher/
One further remark: If you want to install those new packages on
Debian stable, please ask us for a backport. If you want to install
it on an older Ubuntu version it makes probably sense to maintain
some PPA providing the backports (I'm not sure whether there is some
comparable mechanism to Debian backports in Ubuntu).
Kind regards
Andreas.
On Thu, Nov 21, 2019 at 10:54:27PM +0100, Andreas Tille wrote:
> 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
> >
>
> --
> http://fam-tille.de
>
>
--
http://fam-tille.de
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