Package: release.debian.org Severity: normal User: release.debian....@packages.debian.org Usertags: unblock Please unblock meta-package debichem which updates a couple of packages from debichem, as per http://lists.debian.org/debian-release/2012/06/msg00323.html
It also removes some of the publication data which has since been included in debian/upstream files, and fixes the Vcs-Browser URL/bumps Standards-Version (the latter two were added a while ago in subversion). If you prefer to just have the package additions for easier review, I could upload a revised package instead. unblock debichem/0.0.3 Cheers, Michael
diff -Nru debichem-0.0.2/debian/changelog debichem-0.0.3/debian/changelog --- debichem-0.0.2/debian/changelog 2011-11-01 23:53:01.000000000 +0100 +++ debichem-0.0.3/debian/changelog 2013-02-24 17:46:12.000000000 +0100 @@ -1,3 +1,24 @@ +debichem (0.0.3) unstable; urgency=low + + [ Michael Banck ] + * tasks/visualisation: Added jmol and qutemol. + * tasks/visualisation: Added cclib. + * tasks/semiempirical: Added cp2k. + * tasks/cheminformatics: Added python-indigo. + * tasks/visualization: Added shelxle, xcrysden and drawxtl. + * tasks/cheminformatics: Added python-fmcs, python-chemfp and libopsin-java. + * tasks/visualization: Added gamgi. + * tasks/molmech, tasks/visualization, tasks/cheminformatics: Removed some + citation data which is already present in the respective debian/upstream + files. + * tasks/visualization: Added ballview, raster3d and kalzium. + + [ Daniel Leidert ] + * debian/control.stub (Standards-Version): Bumped to 3.9.3. + (Vcs-Browser): Adjusted. + + -- Michael Banck <mba...@debian.org> Sun, 24 Feb 2013 16:30:10 +0100 + debichem (0.0.2) unstable; urgency=low [ Andreas Tille ] diff -Nru debichem-0.0.2/debian/control debichem-0.0.3/debian/control --- debichem-0.0.2/debian/control 2011-11-01 22:11:26.000000000 +0100 +++ debichem-0.0.3/debian/control 2013-02-24 17:46:30.000000000 +0100 @@ -5,9 +5,9 @@ Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Uploaders: Michael Banck <mba...@debian.org>, Andreas Tille <ti...@debian.org> Build-Depends-Indep: blends-dev (>= 0.6.13) -Standards-Version: 3.9.0 +Standards-Version: 3.9.3 Homepage: http://alioth.debian.org/projects/debichem -Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/?rev=0&sc=0 +Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/ Vcs-Svn: svn://svn.debian.org/blends/projects/debichem/trunk/debichem/ Package: debichem-tasks @@ -30,9 +30,9 @@ Package: debichem-cheminformatics Architecture: all Depends: debichem-tasks (= ${binary:Version}) -Recommends: libcdk-java, openbabel, python-cinfony, python-openbabel, python-rdkit +Recommends: libcdk-java, libopsin-java, openbabel, python-chemfp, python-cinfony, python-fmcs, python-indigo, python-openbabel, python-rdkit Description: DebiChem Cheminformatics - This metapackage will install cheminformatics packages + This metapackage will install cheminformatics packages useful for chemists. Package: debichem-modelling @@ -48,6 +48,7 @@ Architecture: all Depends: debichem-tasks (= ${binary:Version}) Recommends: adun.app, avogadro, ghemical, gromacs +Suggests: vmd Description: DebiChem Molecular Mechanics This metapackage will install Molecular Mechanics which might be useful for chemists. @@ -64,7 +65,7 @@ Package: debichem-semiempirical Architecture: all Depends: debichem-tasks (= ${binary:Version}) -Recommends: mopac7-bin +Recommends: cp2k, mopac7-bin Description: DebiChem Semi Empirical This metapackage will install Semi Empirical which might be useful for chemists. @@ -81,7 +82,7 @@ Package: debichem-visualisation Architecture: all Depends: debichem-tasks (= ${binary:Version}) -Recommends: adun.app, avogadro, gabedit, garlic, gausssum, gcrystal, gdis, gdpc, rasmol, v-sim, viewmol, xbs, xmakemol +Recommends: adun.app, avogadro, ballview, cclib, drawxtl, gabedit, garlic, gausssum, gcrystal, gdis, gdpc, jmol, kalzium, qutemol, rasmol, raster3d, shelxle, v-sim, viewmol, xbs, xcrysden, xmakemol Description: DebiChem 3D Viewers and Calculation Output Visualization This metapackage will install 3D Viewers and Calculation Output Visualization which might be useful for chemists. diff -Nru debichem-0.0.2/debian/control.stub debichem-0.0.3/debian/control.stub --- debichem-0.0.2/debian/control.stub 2010-07-19 23:08:28.000000000 +0200 +++ debichem-0.0.3/debian/control.stub 2013-02-22 12:44:15.000000000 +0100 @@ -4,9 +4,9 @@ Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Uploaders: Michael Banck <mba...@debian.org>, Andreas Tille <ti...@debian.org> Build-Depends-Indep: blends-dev (>= 0.6.13) -Standards-Version: 3.9.0 +Standards-Version: 3.9.3 Homepage: http://alioth.debian.org/projects/debichem -Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/?rev=0&sc=0 +Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/debichem/trunk/debichem/ Vcs-Svn: svn://svn.debian.org/blends/projects/debichem/trunk/debichem/ Package: debichem-tasks diff -Nru debichem-0.0.2/debichem-tasks.desc debichem-0.0.3/debichem-tasks.desc --- debichem-0.0.2/debichem-tasks.desc 2011-11-01 23:54:35.000000000 +0100 +++ debichem-0.0.3/debichem-tasks.desc 2013-02-24 17:46:23.000000000 +0100 @@ -13,12 +13,13 @@ openmx nwchem aces3 + cp2k quantum-espresso Task: debichem-cheminformatics Section: debichem Description: DebiChem Cheminformatics - This metapackage will install cheminformatics packages + This metapackage will install cheminformatics packages useful for chemists. Relevance: 10 Key: @@ -28,6 +29,11 @@ python-openbabel libcdk-java python-rdkit + python-indigo + python-cinfony + python-fmcs + python-chemfp + libopsin-java Task: debichem-modelling Section: debichem @@ -80,6 +86,7 @@ debichem-semiempirical Packages: list mopac7-bin + cp2k Task: debichem-view-edit-2d Section: debichem @@ -106,16 +113,25 @@ debichem-visualisation Packages: list adun.app - gabedit - gausssum - gdpc - viewmol avogadro + cclib + gabedit garlic + gausssum gcrystal gdis + gdpc + jmol + qutemol rasmol v-sim + viewmol xbs xmakemol + shelxle + xcrysden + drawxtl + ballview + raster3d + kalzium diff -Nru debichem-0.0.2/tasks/abinitio debichem-0.0.3/tasks/abinitio --- debichem-0.0.2/tasks/abinitio 2011-11-01 22:09:35.000000000 +0100 +++ debichem-0.0.3/tasks/abinitio 2013-02-22 12:44:15.000000000 +0100 @@ -4,7 +4,9 @@ might be useful for chemists. Depends: mpqc - +Published-Title: http://www.mpqc.org +Published-Authors: The Massively Parallel Quantum Chemistry Program (MPQC), Version 3.0.0 Prerelease, C. L. Janssen, I. B. Nielsen, M. L. Leininger, E. F. Valeev, J. P. Kenny, E. T. Seidl +Published-URL: http://www.mpqc.org Depends: psi3 Published-Title: PSI3: an open-source Ab Initio electronic structure package diff -Nru debichem-0.0.2/tasks/cheminformatics debichem-0.0.3/tasks/cheminformatics --- debichem-0.0.2/tasks/cheminformatics 2011-11-01 22:10:36.000000000 +0100 +++ debichem-0.0.3/tasks/cheminformatics 2013-02-23 18:32:52.000000000 +0100 @@ -1,23 +1,11 @@ Task: Cheminformatics Description: DebiChem Cheminformatics - This metapackage will install cheminformatics packages + This metapackage will install cheminformatics packages useful for chemists. Depends: openbabel -Published-Title: Open Babel: An open chemical toolbox -Published-Authors: N. M. O'Boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch, and G. R. Hutchison -Published-In: J. Cheminf. 3:33 -Published-Year: 2011 -Published-URL: http://www.jcheminf.com/content/3/1/33 -Published-DOI: 10.1186/1758-2946-3-33 Depends: python-openbabel -Published-Title: Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit -Published-Authors: N. M. O'Boyle, C. Morley and G. R. Hutchison -Published-In: Chem. Cent. J. 2:5 -Published-Year: 2008 -Published-URL: http://journal.chemistrycentral.com/content/2/1/5 -Published-DOI: 10.1186/1752-153X-2-5 Depends: libcdk-java Published-Title: The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics @@ -29,10 +17,13 @@ Depends: python-rdkit +Depends: python-indigo + Depends: python-cinfony -Published-Title: Cinfony - combining Open Source cheminformatics toolkits behind a common interface -Published-Authors: N. M. O'Boyle and G. R. Hutchison Published-In: Chem. Cent. J. 2:24 -Published-Year: 2008 -Published-URL: http://journal.chemistrycentral.com/content/2/1/24 -Published-DOI: 10.1186/1752-153X-2-24 + +Depends: python-fmcs + +Depends: python-chemfp + +Depends: libopsin-java diff -Nru debichem-0.0.2/tasks/molmech debichem-0.0.3/tasks/molmech --- debichem-0.0.2/tasks/molmech 2011-11-01 22:09:35.000000000 +0100 +++ debichem-0.0.3/tasks/molmech 2013-02-22 17:05:45.000000000 +0100 @@ -16,11 +16,23 @@ Depends: ghemical Depends: gromacs -Published-Title: GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation -Published-Authors: B. Hess, C. Kutzner, D. van der Spoel and E. Lindahl -Published-In: J. Chem. Theory Comput. 4(3):435-447 -Published-Year: 2008 -Published-URL: http://pubs.acs.org/doi/abs/10.1021/ct700301q -Published-DOI: 10.1021/ct700301q -X-Published-Other: Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis. J. Mol. Model. 2001;7(8):306.17 -X-Published-Other: Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. GROMACS: Fast, Flexible, and Free. J Comput. Chem. 2005;26(16):1701.18 + +Depends: vmd +License: non-free +Homepage: http://www.ks.uiuc.edu/Research/vmd/ +Vcs-Browser: http://svn.debian.org/wsvn/debichem/wnpp/vmd/ +Vcs-Svn: svn://svn.debian.org/svn/debichem/wnpp/vmd/ +Responsible: Michael Banck <mba...@debian.org>, Steffen Moeller <moel...@debian.org> +Pkg-Description: presentation of traces of molecular dynamics runs + VMD stands for Visual Molecular Dynamics. While text books + and even structure databases because of technical problems only + present static pictures of proteins or DNA, for the understanding + of the properties of those molecules their vibration or their + movement in general is important. + . + The movements itself are calculated by molecular dynamics programs, + such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The + latter two are already in the distribution. VMD has a series of + nice features, from displaying through animation to analysing. + It can be scripted, clustered, and runs on all common OS.. + diff -Nru debichem-0.0.2/tasks/polymer debichem-0.0.3/tasks/polymer --- debichem-0.0.2/tasks/polymer 2011-11-01 22:09:35.000000000 +0100 +++ debichem-0.0.3/tasks/polymer 2013-02-23 18:32:52.000000000 +0100 @@ -5,20 +5,15 @@ view mass spectra. -Depends: massxpert +Depends: massxpert Published-Title: massXpert 2: a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data Published-Authors: F. Rusconi Published-In: Bioinformatics 25(20):2741-2742 -Published-Year: 2009 Published-URL: http://bioinformatics.oxfordjournals.org/content/25/20/2741 -Published-DOI: 10.1093/bioinformatics/btp504 Depends: mmass Published-Title: mMass 3: A Cross-Platform Software Environment for Precise Analysis of Mass Spectrometric Data Published-Authors: M. Strohalm, D. Kavan, P. Novak, M. Volny and V. Havlicek Published-In: Anal. Chem. 82(11):4648-4651 -Published-Year: 2010 -Published-URL: http://pubs.acs.org/doi/abs/10.1021/ac100818g -Published-DOI: 10.1021/ac100818g Depends: lutefisk diff -Nru debichem-0.0.2/tasks/semiempirical debichem-0.0.3/tasks/semiempirical --- debichem-0.0.2/tasks/semiempirical 2009-07-29 19:49:34.000000000 +0200 +++ debichem-0.0.3/tasks/semiempirical 2013-02-23 18:32:52.000000000 +0100 @@ -4,3 +4,5 @@ which might be useful for chemists. Depends: mopac7-bin + +Depends: cp2k diff -Nru debichem-0.0.2/tasks/visualisation debichem-0.0.3/tasks/visualisation --- debichem-0.0.2/tasks/visualisation 2011-11-01 22:09:35.000000000 +0100 +++ debichem-0.0.3/tasks/visualisation 2013-02-23 18:32:52.000000000 +0100 @@ -4,46 +4,49 @@ which might be useful for chemists. Depends: adun.app -Published-Title: Framework Based Design of a New All-Purpose Molecular Simulation Application: The Adun Simulator -Published-Authors: M.A. Johnston, I.F. Galván and J. Vill�| -Freixa -Published-In: J. Comput. Chem. 26(15):1647-1659 -Published-Year: 2005 -Published-URL: http://www3.interscience.wiley.com/cgi-bin/abstract/112094040/ABSTRACT -Published-DOI: 10.1002/jcc.20312 -Depends: gabedit -Published-Title: Gabedit - A graphical user interface for computational chemistry softwares -Published-Authors: A.-R. Allouche -Published-In: J. Comput. Chem. 32(1):174-182 -Published-Year: 2011 -Published-URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.21600/abstract -Published-DOI: 10.1002/jcc.21600 - -Depends: gausssum - -Depends: gdpc +Depends: avogadro -Depends: viewmol +Depends: cclib +Published-Title: cclib: a library for package-independent computational chemistry algorithms +Published-Authors: N. M. O'Boyle, A. L. Tenderholt, K. M. Langner +Published-In: J. Comput. Chem. 29(5):839-845 -Depends: avogadro +Depends: gabedit Depends: garlic +Depends: gausssum + Depends: gcrystal Depends: gdis +Depends: gdpc + +Depends: jmol + +Depends: qutemol + Depends: rasmol Registration: http://www.rasmol.org/register.shtml -Published-Title: RasMol: Biomolecular graphics for all -Published-Authors: R. A. Sayle and E.-J. Milner-White -Published-In: Trends Biochem. Sci. 20(9):374 -Published-Year: 1995 -Published-URL: http://www.sciencedirect.com/science/article/pii/S0968000400890805 -Published-DOI: 10.1016/S0968-0004(00)89080-5 Depends: v-sim +Depends: viewmol + Depends: xbs Depends: xmakemol + +Depends: shelxle + +Depends: xcrysden + +Depends: drawxtl + +Depends: ballview + +Depends: raster3d + +Depends: kalzium diff -Nru debichem-0.0.2/TODO debichem-0.0.3/TODO --- debichem-0.0.2/TODO 1970-01-01 01:00:00.000000000 +0100 +++ debichem-0.0.3/TODO 2013-02-22 12:44:15.000000000 +0100 @@ -0,0 +1,18 @@ +Reinstate revision 3133 and parts of revision 3419: + + * tasks/abinitio: Split up to ... + * tasks/molecular-abinitio: ... this and ... + * tasks/periodic-abinitio: ... this. + * tasks/molmech: Renamed to ... + * tasks/molecular-dynamics: ... this. + * tasks/molecular-dynamics: Removed ghemical and avogadro, added cp2k and + nwchem. + * tasks/modelling: Moved nmoldyn to ... + * tasks/molecular-dynamics: ... this. + * tasks/visualisation: Added cclib. + * tasks/crystallography: New task, including shelxle and xcrysden (ITP'd). + * tasks/visualisation: Moved gcrystal to ... + * tasks/crystallography: ... this. + + [ Daniel Leidert ] + * tasks/crystallography: Added drawxtl.