Re: Packaging gwamar for Debian
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.
> 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
> 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.
> 2015-11-21 18:53 GMT+01:00 Andreas Tille <firstname.lastname@example.org>:
> > 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 and started the packaging in Debian Git.
> > When doing so I stumbled upons some issues in the download archive:
> > 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 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. 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.
> >  http://bioputer.mimuw.edu.pl/gwamar/
> >  git://anonscm.debian.org/debian-med/gwamar.git
> >  http://bioputer.mimuw.edu.pl/gwamar/software/gwamar_v1.14/gwamar.zip
> >  https://bitbucket.org/mimowo/gwamar
> > 
> > https://anonscm.debian.org/cgit/debian-med/gwamar.git/tree/debian/patches/adapt_debian_locations_of_binaries.patch
> > --
> > http://fam-tille.de