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.
