Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
I think the documentation http://debian-med.alioth.debian.org/docs/policy.html was not so clear about how to handle a new upstream release. Anyway when I also found http://wiki.debian.org/Games/VCS/git#Adding_a_new_upstream_release I came to the conclusion that I needed to run git import-orig --pristine-tar again. erik@linux:~$ wget --quiet http://prime.sbc.su.se/download/prime-phylo-1.0.11.tar.gz erik@linux:~$ cd prime-phylo erik@linux:~/prime-phylo$ git branch * master pristine-tar upstream erik@linux:~/prime-phylo$ git import-orig --pristine-tar ../prime-phylo-1.0.11.tar.gz What is the upstream version? [1.0.11] gbp:info: Importing '../prime-phylo-1.0.11.tar.gz' to branch 'upstream'... gbp:info: Source package is prime-phylo gbp:info: Upstream version is 1.0.11 pristine-tar: committed prime-phylo_1.0.11.orig.tar.gz.delta to branch pristine-tar gbp:info: Merging to 'master' Merge made by the 'recursive' strategy. gbp:info: Successfully imported version 1.0.11 of ../prime-phylo-1.0.11.tar.gz erik@linux:~/prime-phylo$ git push --all Enter passphrase for key '/home/erik/.ssh/id_rsa': Counting objects: 25, done. Delta compression using up to 6 threads. Compressing objects: 100% (14/14), done. Writing objects: 100% (15/15), 19.70 KiB, done. Total 15 (delta 7), reused 0 (delta 0) To git+ssh://git.debian.org/git/debian-med/prime-phylo.git 9785bae..1f18d28 master - master 3e85ea5..8183c10 pristine-tar - pristine-tar d895eb7..0ad54f6 upstream - upstream erik@linux:~/prime-phylo$ git push --tags Enter passphrase for key '/home/erik/.ssh/id_rsa': Counting objects: 1, done. Writing objects: 100% (1/1), 184 bytes, done. Total 1 (delta 0), reused 0 (delta 0) cheers, Erik On Mon, Dec 17, 2012 at 5:26 PM, Andreas Tille andr...@an3as.eu wrote: On Mon, Dec 17, 2012 at 05:24:00PM +0100, Erik Sjölund wrote: How do I upload the new source code release into git.debian.org? http://debian-med.alioth.debian.org/docs/policy.html Seek for pristine-tar. -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cab+1q0s6prx3o6weqlbzj9yzmvaazi3eznkhnygvymuvrth...@mail.gmail.com
Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, On Tue, Dec 18, 2012 at 10:06:15AM +0100, Erik Sjölund wrote: I think the documentation http://debian-med.alioth.debian.org/docs/policy.html was not so clear about how to handle a new upstream release. Anyway when I also found http://wiki.debian.org/Games/VCS/git#Adding_a_new_upstream_release I came to the conclusion that I needed to run git import-orig --pristine-tar again. Yes, in dead. We would be happy about any patch to the Debian Med policy that might5 make this more clear. Sometimes it is hard to describe things which are clear to the people who are comfortable with the procedure to describe it for newcomers - so any hint is welcome. ... erik@linux:~/prime-phylo$ git push --tags Enter passphrase for key '/home/erik/.ssh/id_rsa': Counting objects: 1, done. Writing objects: 100% (1/1), 184 bytes, done. Total 1 (delta 0), reused 0 (delta 0) This worked for me. So the package is in principle ready for uploading with the one minor exception that the ITP bug is closed in some previous version and not the latest to be uploaded one. If you ask me I would simply strip the changelog to prime-phylo (1.0.11-1) unstable; urgency=low * Initial release (Closes: #684039) -- Erik Sjolund erik.sjol...@gmail.com Mon, 17 Dec 2012 14:11:13 +0100 by simply droping the detailed pre-Debian upload history which is not relevant for the *debian/*changelog. Usually ftpmasters are a bit disturbed about longish and for them uninteresting history and finally we do have the data inside Git repository anyway. In case you insist in keeping the longish changelog (which would be fine for me if you might have your personal preference) I would move the Closes statement just up to the latest changelog entry. However, in this case we should change the target distribution from unstable to UNRELEASED to make pretty clear that these versions never have hit the Debian mirrors. Please either change it in the way of your choice or tell me what you prefer and I'll do the change and upload. Thanks for preparing the package Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121218133053.ga19...@an3as.eu
Bug#694632: Bug#684039: Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
On Tue, Dec 18, 2012 at 2:30 PM, Andreas Tille andr...@an3as.eu wrote: Sometimes it is hard to describe things which are clear to the people who are comfortable with the procedure to describe it for newcomers - so any hint is welcome. I understand. I'll think about it... If you ask me I would simply strip the changelog to prime-phylo (1.0.11-1) unstable; urgency=low * Initial release (Closes: #684039) -- Erik Sjolund erik.sjol...@gmail.com Mon, 17 Dec 2012 14:11:13 +0100 I followed your suggestion (i.e. stripping the changelog). cheers, Erik -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAB+1q0TJ5-Mge17wM=uuh40o9d55uc2+hgsqydeb6gtsunc...@mail.gmail.com
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik On Tue, Dec 18, 2012 at 04:18:26PM +0100, Erik Sjölund wrote: On Tue, Dec 18, 2012 at 2:30 PM, Andreas Tille andr...@an3as.eu wrote: Sometimes it is hard to describe things which are clear to the people who are comfortable with the procedure to describe it for newcomers - so any hint is welcome. I understand. I'll think about it... This would be great. prime-phylo (1.0.11-1) unstable; urgency=low * Initial release (Closes: #684039) -- Erik Sjolund erik.sjol...@gmail.com Mon, 17 Dec 2012 14:11:13 +0100 I followed your suggestion (i.e. stripping the changelog). Thanks and uploaded. BTW, in the Debian Med team we did not formalised the sponsering process via filing RFS bugs (for no specific reason - it just worked without this.) I'm just not comfortable with the procedure and do not know where and when to close this RFS bug. If it should have been done in the changelog as well I just missed this. If its done by the sponsee please do so - if the sponsor is expected to close it just tell me to do so. Kind regards and thanks for your work on the package Andreas. PS: Please let us know whether you are subscribed to the list - I would stop CCing you in this case (and you can definitely remove me from CCs and rather use list-reply.) -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121218155314.ge19...@an3as.eu
Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
On Tue, Dec 18, 2012 at 4:53 PM, Andreas Tille andr...@an3as.eu wrote: Thanks and uploaded. Thanks a lot. BTW, in the Debian Med team we did not formalised the sponsering process via filing RFS bugs (for no specific reason - it just worked without this.) Good to know. PS: Please let us know whether you are subscribed to the list - I would stop CCing you in this case (and you can definitely remove me from CCs and rather use list-reply.) I am now subscribed to debian-...@lists.debian.org cheers, Erik -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cab+1q0tg2aemokn7wy2pquy4asqt-9uriwc7lecojaqhjt4...@mail.gmail.com
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
I have now created: http://anonscm.debian.org/gitweb/?p=debian-med/prime-phylo.git In the debian sub directory I also created the file upstream where I provided information about the scientific paper Simultaneous Bayesian gene tree reconstruction and reconciliation analysis I used utf-8 encoding to be able to write the name Åkerborg, Ö. Maybe utf-8 is not allowed for debian/upstream? cheers, Erik -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cab+1q0qcpy+rlgevwmmccwbaytcxml3i1nyep_rugovzr7x...@mail.gmail.com
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, thanks for your work on prime-phylo. On Mon, Dec 17, 2012 at 11:06:28AM +0100, Erik Sjölund wrote: I have now created: http://anonscm.debian.org/gitweb/?p=debian-med/prime-phylo.git Looks good so far with one exception I've found: Please check the copyright by using $ cme fix dpkg-copyright Fixing from Dpkg::Copyright... Configuration item 'Files:src/cxx/libraries/prime/beep2blas.hh License short_name' has a wrong value: value 'Software License for MTL' does not match grammar: ... The syntax is not really DEP5 conformant. I would have changed this simply to License: MTL but when I checked the License paragraph I detected some additional copyright statements which is somehow confusing. Does this mean the license is also copyrighted and has some authors? Could you please clarify this a bit? Besides this I'd regard the package ready for upload and I'd go for this once debian/copyright is passing cme. In the debian sub directory I also created the file upstream where I provided information about the scientific paper Simultaneous Bayesian gene tree reconstruction and reconciliation analysis I used utf-8 encoding to be able to write the name Åkerborg, Ö. Maybe utf-8 is not allowed for debian/upstream? debian/upstream file should be UTF-8 - so all is fine here. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121217110106.gb3...@an3as.eu
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
I followed your suggestion and changed the license short name to MTL. Regarding the file src/cxx/libraries/prime/beep2blas.hh when I started packaging Prime I tried to investigate where the file content came from. In the file the following text could be read: /* Basic Linear Algebra Subprograms for C/C++ Version 1.0 Matthew E. Gaston May 6, 1998 --*/ I searched google for that text and saw that the file had its origin from the file $ wget --quiet http://osl.iu.edu/download/research/mtl/mtl-2.1.2-22.tar.gz $ tar tvfz mtl-2.1.2-22.tar.gz | grep mtl/blas_interface.h -rw-r--r-- pgottsch/research 3534 2005-07-05 17:11 mtl-2.1.2-22/mtl/blas_interface.h I added the license text from the file $ tar tvfz mtl-2.1.2-22.tar.gz | grep -i license -rw-r--r-- pgottsch/research 3096 2005-06-02 19:01 mtl-2.1.2-22/license.mtl.txt to the files debian/copyright src/cxx/libraries/prime/beep2blas.hh Maybe I shouldn't have copied the license text? cheers, Erik -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAB+1q0RghK0W60tntx0Z8D=x_01-racbbrpoqun2va--wxg...@mail.gmail.com
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, On Mon, Dec 17, 2012 at 02:37:30PM +0100, Erik Sjölund wrote: I followed your suggestion and changed the license short name to MTL. OK. Regarding the file src/cxx/libraries/prime/beep2blas.hh when I started packaging Prime I tried to investigate where the file content came from. In the file the following text could be read: /* Basic Linear Algebra Subprograms for C/C++ Version 1.0 Matthew E. Gaston May 6, 1998 --*/ I searched google for that text and saw that the file had its origin from the file $ wget --quiet http://osl.iu.edu/download/research/mtl/mtl-2.1.2-22.tar.gz $ tar tvfz mtl-2.1.2-22.tar.gz | grep mtl/blas_interface.h -rw-r--r-- pgottsch/research 3534 2005-07-05 17:11 mtl-2.1.2-22/mtl/blas_interface.h I added the license text from the file $ tar tvfz mtl-2.1.2-22.tar.gz | grep -i license -rw-r--r-- pgottsch/research 3096 2005-06-02 19:01 mtl-2.1.2-22/license.mtl.txt to the files debian/copyright src/cxx/libraries/prime/beep2blas.hh Maybe I shouldn't have copied the license text? Copying the license text is correct. However, your debian/copyright says: Files: src/cxx/libraries/prime/beep2blas.hh Copyright: 2002 - 2007 The Maxtrix Template Library authors 2007 - 2012 Bengt Sennbladbengt.sennb...@ki.se License: MTL ... License: MTL Copyright (c) 2001-2005 The Trustees of Indiana University. All rights reserved. Copyright (c) 1998-2001 University of Notre Dame. All rights reserved. Authors: Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee . This file is part of the Matrix Template Library . According to DEP5 the Copyright field should be attached to the Files and here you give some additional and even conflicting information as free text in the license paragraph. The relation between The Maxtrix Template Library authors and Bengt Sennbladbengt.sennb...@ki.se and The Trustees of Indiana Universityand University of Notre Dame as well as Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee remains unclear. My reading of the copyright would be: Files: src/cxx/libraries/prime/beep2blas.hh Copyright: 2001-2005 The Trustees of Indiana University. All rights reserved. 1998-2001 University of Notre Dame. All rights reserved Andrew Lumsdaine, Jeremy G. Siek, Lie-Quan Lee 2007-2012 Bengt Sennblad bengt.sennb...@ki.se License: MTL which specifies former authors and the later changes done by Bengt Sennblad. The specification of the License: MTL paragraph should come without the extra Copyright information in the beginning - all else is fine. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121217140154.gd3...@an3as.eu
Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
I made a new upstream release http://prime.sbc.su.se/download/prime-phylo-1.0.11.tar.gz where I added the extra copyright statement // Copyright: Modifications to the original file by Bengt Sennblad bengt.sennb...@ki.se 2007-2012 to the file src/cxx/libraries/prime/beep2blas.hh I also modified the debian git http://anonscm.debian.org/gitweb/?p=debian-med/prime-phylo.git;a=commitdiff;h=9785baea0e5efe3f80f1970183e3ec109bb40e51 as you suggested. How do I upload the new source code release into git.debian.org? Maybe I will figure it out by myself ... cheers, Erik -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cab+1q0rggenyvmauczzdyq4m7zys0tmmtn2qfyrso+y-dsa...@mail.gmail.com
Bug#694632: Bug#684039: Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
On Mon, Dec 17, 2012 at 05:24:00PM +0100, Erik Sjölund wrote: I made a new upstream release http://prime.sbc.su.se/download/prime-phylo-1.0.11.tar.gz where I added the extra copyright statement // Copyright: Modifications to the original file by Bengt Sennblad bengt.sennb...@ki.se 2007-2012 to the file src/cxx/libraries/prime/beep2blas.hh I also modified the debian git http://anonscm.debian.org/gitweb/?p=debian-med/prime-phylo.git;a=commitdiff;h=9785baea0e5efe3f80f1970183e3ec109bb40e51 as you suggested. OK. How do I upload the new source code release into git.debian.org? Maybe I will figure it out by myself ... http://debian-med.alioth.debian.org/docs/policy.html Seek for pristine-tar. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121217162608.gf3...@an3as.eu
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Andreas, I've now created the account eriksjolund-guest at alioth.debian.org I would prefer to use git for the repository. If I understand you correctly, the next step will be that you now upload the debian packaging sub directory from prime-phylo into the Vcs? If you have any suggestions regarding the packaging you are most welcome to perform changes in the packaging code. cheers, Erik On Thu, Dec 6, 2012 at 4:16 PM, Andreas Tille andr...@an3as.eu wrote: Hi Erik, could you please confirm that you are interested in finding a sponsor for your work? As I said the Debian Med team is really interested. In case you have some time constraints or whatever I'd volunteer to commit your work to our Vcs (please specify whether you prefer Git or SVN) and will check whether it is ready for upload. Kind regards and thanks so far for your work Andreas. -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CAB+1q0R==gS3+28ZoB740qTyvr913no7JVLN=ao4vbzk6pu...@mail.gmail.com
Bug#694632: Bug#684039: ITP: prime-phylo -- Bayesian estimation of gene trees taking the species tree into account
Hi Erik, On Tue, Dec 11, 2012 at 03:37:28PM +0100, Erik Sjölund wrote: Hi Andreas, I've now created the account eriksjolund-guest at alioth.debian.org Fine I've just added you to the Debian Med team. I would prefer to use git for the repository. OK. If I understand you correctly, the next step will be that you now upload the debian packaging sub directory from prime-phylo into the Vcs? If you have any suggestions regarding the packaging you are most welcome to perform changes in the packaging code. I'd prefer if you would try to follow http://debian-med.alioth.debian.org/docs/policy.html to create the Git repository yourself and once you did so I would have a look. For sure I could do this as well but I'd regard this as a reasonable exercise for you to become comfortable with the Debian Med team work. For sure you will get all our support if something might not work as smooth as expected. For the very beginning to test you ssh login make sure you read the ssh tips paragraph specifically the link to the Debian wiki in the end of the paragraph. Just let us know in case of any trouble. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-mentors-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121211220816.ga20...@an3as.eu
