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Re: Packaging gwamar for Debian



Hi,

On Sun, Dec 06, 2015 at 02:33:56PM +0100, Michał Woźniak wrote:
> Hi Andreas,
> I have resolved all the issues listed in your mail. Still, if possible I
> would prefer to have a week more time to clean up console messages to be
> more clear and less confusing.

You have whatever time you need. ;-)

> Please find my answers to your comments one by one:
> 
>  0. fixed, I attach version number to each zip file when building (the
> current version is 1.15.1)

While verison 1.15.1 is fine I think you have a typo in all other files
which are named g_m_amar*.zip.
 
>   1. I have attached Apache License 2 in LICENSE file.

Fine.

>   2. Indeed I've searched "print " and found some results which  resolved.
> I've tested it on Python3.

I'll check later and will report if I might find some remainings.

>   3. indeed, this was ugly, I've moved all external tools configuration to
> a separate config_tools.txt, and change accordingly to your proposal

Thanks.

>   4. I've improved the information on what happens when no parameters are
> provided to the program. The error you were getting was caused because the
> default action "-a" parameter to set to a method which assumed some
> preprocessing. Now, I require the parameter to be explicitly set in console.

Thanks for your support and I'll keep you updated about issues I might
find in 1.15.1.  I will not upload anything befor I'll get your final
confirmation that you cleaned up everything.

Kind regards

      Andreas.

> 2015-11-21 18:53 GMT+01:00 Andreas Tille <andreas@an3as.eu>:
> 
> > Hello,
> >
> > I'm writing you on behalf of the Debian Med team that has the objective
> > to package all free software that is relevant in Biology and Medicine
> > for official Debian.
> >
> > I came across GWAMAR[1] and started the packaging in Debian Git[2].
> > When doing so I stumbled upons some issues in the download archive[3]:
> >
> >   0. Just a comment:  It would be more convenient to find versioned
> >      download archives rather than versioned directories.  The
> >      rationale behind this is that you have files with the same name
> >      but different content.
> >
> >   1. I did not found any explicite license statement neither at the
> >      website nor inside the code.  Could you be so kind to clarify
> >      this?
> >
> >   2. At Bitbucket[4] you write:
> >        This software is written in Python, thus Python 2 or 3 is
> >        required to run GWAMAR.
> >      When trying to build with Python3 I've git some errors
> >      (basically in print statements with Python2 syntax.  Please
> >      let me know if you are interested in patches fixing this.
> >
> >   3. I noticed that the default config file in the download archive
> >      contains several private PATH settings.  I patched these to
> >      the Debian locations in the packaging git[5].  It would be
> >      great if you could change the default config file to a more
> >      neutral setting.
> >
> >   4. Finally I endet up by an error message
> >
> >        File "a1_save_details_scores_all.py", line 161, in <module>
> >          input_fh = open(input_fn)
> >        IOError: [Errno 2] No such file or directory:
> > 'datasets/mtu173/exP//res_profiles.txt'
> >
> >      I have no idea how to deal with this since this file is
> >      neither in the download tarball nor can I see it in the
> >      repository at Bitbucket.
> >
> > I hope you like the intend to package GWAMAR for Debian and can
> > help with these issues.
> >
> > Kind regards
> >
> >       Andreas.
> >
> > [1] http://bioputer.mimuw.edu.pl/gwamar/
> > [2] git://anonscm.debian.org/debian-med/gwamar.git
> > [3] http://bioputer.mimuw.edu.pl/gwamar/software/gwamar_v1.14/gwamar.zip
> > [4] https://bitbucket.org/mimowo/gwamar
> > [5]
> > https://anonscm.debian.org/cgit/debian-med/gwamar.git/tree/debian/patches/adapt_debian_locations_of_binaries.patch
> >
> > --
> > http://fam-tille.de
> >

-- 
http://fam-tille.de


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