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 <andr...@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