Re: Packaging gwamar for Debian
Hi again,
I would like to report that I found another Python2 to Python3 issue
which I fixed by the help of 2to3. You can download and review the
patch here:
https://anonscm.debian.org/cgit/debian-med/gwamar.git/tree/debian/patches/2to3.patch
I have two further hints:
1. The download contains several __pycache__ and *.pyc files.
I'd recommend to remove these and I think if you add these
to your .gitignore file these will not be propagated to your
remote Git dir.
2. In the help message you are refering to a manual.pdf. This
is a broken link on your web site. BTW, it would be good if
you could add the (LaTeX-?)source of the manual to the download
archive.
Apropos help: A simple usage hint when specifying
gwamar -h
would be quite helpful for your users.
Kind regards
Andreas.
On Mon, Dec 07, 2015 at 10:59:12AM +0100, Andreas Tille wrote:
> 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
>
>
--
http://fam-tille.de
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