Re: Packaging gwamar for Debian
Hi Michal, On Mon, Dec 14, 2015 at 10:09:48AM +0100, Michał Woźniak wrote: > I have already fixed the 2to3 issue as well as versioning names. Fine. I have adapted the packaging to version 1.15.2. > I keep working on clarifying the messages and making sure the parameters > are easy to specify. I gave the new version a try and noticed the following: $ gwamar -a p -w 4 -d mtu173 p0_save_strains_ordered.py: saves strains in the order consistent with the phylogenetic tree. Start. File /usr/share/gwamar/datasets/mtu173/input//strains_ordered.txt already exists. First remove it. p0_save_strains_ordered.py. Finished. p1_prepare_experiments.py: prepares folders to store results. Start. h Traceback (most recent call last): File "/usr/share/gwamar/src/drsoft/prepare/p1_prepare_experiments.py", line 35, in output_fh = open(output_dir + "res_profiles.txt", "w") FileNotFoundError: [Errno 2] No such file or directory: '/usr/share/gwamar/datasets/mtu173//exP/res_profiles.txt' If you are at it: If people install gwamar via the Debian package the datasets are *currently* in a readonly dir. This might be a wrong decision taken by me since it was not clear to me what purpose these files are serving. Please let me know which files are considere as readonly inputs and which one are rather shared databases where users need write access or even only results for single user consumption. > Will be back to you once done. Thanks for keeping me up to date Andreas. > 2015-12-08 16:56 GMT+01:00 Andreas Tille : > > > 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 : > > > > > > > > > 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 th
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 : > > > > > 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 > > > 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 > > > > > >
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 : > > > 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 > > 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
Re: Packaging gwamar for Debian
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. 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) 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. 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. Best regards, Michal 2015-11-21 18:53 GMT+01:00 Andreas Tille : > 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 > 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 >
Re: Packaging gwamar for Debian
Hi Michał, thanks for your very quick reply. I'm perfectly fine with your schedule. Thanks for your cooperation Andreas. On Sat, Nov 21, 2015 at 08:10:58PM +0100, Michał Woźniak wrote: > Hi Andreas, >I'm delighted to hear that! > > Thanks for all the comments too, here are my short answers: > > 0. sure I will change the approach > 1. The intended license is GPL v3. If there is no explicite statement > I will add it as part of point 2. > 2. I will put some effort in the next couple of days and will try to > fix the build quickly both on Python 2 and 3. > 3. I will investigate the possible approaches and will do it better > 4. I will investigate this as part of point point 2. > > I estimate this will take me about a week or two is that fine? > > Best wishes, > Michal > > 2015-11-21 18:53 GMT+01:00 Andreas Tille : > > 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 > > 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
Re: Packaging gwamar for Debian
Hi Andreas, I'm delighted to hear that! Thanks for all the comments too, here are my short answers: 0. sure I will change the approach 1. The intended license is GPL v3. If there is no explicite statement I will add it as part of point 2. 2. I will put some effort in the next couple of days and will try to fix the build quickly both on Python 2 and 3. 3. I will investigate the possible approaches and will do it better 4. I will investigate this as part of point point 2. I estimate this will take me about a week or two is that fine? Best wishes, Michal 2015-11-21 18:53 GMT+01:00 Andreas Tille : > 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 > 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
Packaging gwamar for Debian
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 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
