Package: release.debian.org
Severity: normal
User: release.debian....@packages.debian.org
Usertags: unblock
Please unblock package debichem
This is a post-freeze update of the debichem task metapackages for
jessie. I have attached a debdiff excluding the auto-generated changes,
prepared by "debdiff debichem_0.0.{3,4}.dsc | filterdiff -x
'*/debian/control' -x '*/debichem-tasks.desc' -x '*.json'"
unblock debichem/0.0.4
-- System Information:
Debian Release: jessie/sid
APT prefers testing-updates
APT policy: (500, 'testing-updates'), (500, 'testing')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 3.16-2-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_US.utf8, LC_CTYPE=en_US.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
diff -Nru debichem-0.0.3/debian/changelog debichem-0.0.4/debian/changelog
--- debichem-0.0.3/debian/changelog 2013-02-24 17:46:12.000000000 +0100
+++ debichem-0.0.4/debian/changelog 2014-12-05 16:45:46.000000000 +0100
@@ -1,3 +1,31 @@
+debichem (0.0.4) unstable; urgency=medium
+
+ [ Michael Banck ]
+ * tasks/abinitio: Added psi4.
+ * tasks/crystallography: New task, including shelxle and xcrysden.
+ * tasks/visualisation: Moved gcrystal to ...
+ * tasks/crystallography: ... this.
+ * tasks/crystallography: Added python-fabio.
+ * tasks/molmech: Added lammps.
+ * tasks/semiempirical: Added molds.
+ * tasks/abinitio: Added elk-lapw.
+ * tasks/abinitio: Added ergo.
+ * tasks/visualisation, tasks/crystallography: Added gamgi.
+ * tasks/visualisation: Added p4vasp.
+ * tasks/visualisation: Added travis.
+ * tasks/molmech: Added votca-csg.
+ * tasks/polymer: Changed r-cran-mixtools and r-other-amsmercury Suggests to
+ Depends.
+ * tasks/polymer: Added r-other-iwrlars.
+
+ [ Daniel Leidert ]
+ * tasks/crystallography: Added drawxtl.
+
+ [ Andreas Tille ]
+ * d/source/format: 3.0 (native)
+
+ -- Michael Banck <mba...@debian.org> Fri, 05 Dec 2014 16:45:37 +0100
+
debichem (0.0.3) unstable; urgency=low
[ Michael Banck ]
diff -Nru debichem-0.0.3/debian/control debichem-0.0.4/debian/control
diff -Nru debichem-0.0.3/debian/source/format
debichem-0.0.4/debian/source/format
--- debichem-0.0.3/debian/source/format 1970-01-01 01:00:00.000000000 +0100
+++ debichem-0.0.4/debian/source/format 2014-12-05 16:06:21.000000000 +0100
@@ -0,0 +1 @@
+3.0 (native)
diff -Nru debichem-0.0.3/debichem-tasks.desc debichem-0.0.4/debichem-tasks.desc
diff -Nru debichem-0.0.3/dependency_data/debichem_0.0.1.json
debichem-0.0.4/dependency_data/debichem_0.0.1.json
diff -Nru debichem-0.0.3/dependency_data/debichem_0.0.3.json
debichem-0.0.4/dependency_data/debichem_0.0.3.json
diff -Nru debichem-0.0.3/dependency_data/debichem_0.0.4.json
debichem-0.0.4/dependency_data/debichem_0.0.4.json
diff -Nru debichem-0.0.3/tasks/abinitio debichem-0.0.4/tasks/abinitio
--- debichem-0.0.3/tasks/abinitio 2013-02-22 12:44:15.000000000 +0100
+++ debichem-0.0.4/tasks/abinitio 2014-12-05 16:17:24.000000000 +0100
@@ -9,46 +9,22 @@
Published-URL: http://www.mpqc.org
Depends: psi3
-Published-Title: PSI3: an open-source Ab Initio electronic structure package
-Published-Authors: T. Daniel Crawford, C. David Sherrill, Edward F. Valeev,
Justin T. Fermann, Rollin A. King, Matthew L. Leininger, Shawn T. Brown, Curtis
L. Janssen, Edward T. Seidl, Joseph P. Kenny and Wesley D. Allen
-Published-In: J. Comput. Chem. 28(9):1610-1616
-Published-Year: 2007
-Published-URL: http://onlinelibrary.wiley.com/doi/10.1002/jcc.20573/abstract
-Published-DOI: 10.1002/jcc.20573
Depends: abinit
-Published-Title: ABINIT: First-principles approach to material and nanosystem
properties
-Published-Authors: X. Gonze, B. Amadon, P.-M. Anglade, J.-M. Beuken, F.
Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. C�t�, T. Deutsch,
L. Genovese, Ph. Ghosez, M. Giantomassi, S. Goedecker, D.R. Hamann, P. Hermet,
F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M. J. T. Oliveira, G.
Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M.
Torrent, M. J. Verstraete, G. Zerah and J. W. Zwanziger
-Published-In: Comput. Phys. Commun. 180(12):2582-2615
-Published-Year: 2009
-Published-URL:
http://www.sciencedirect.com/science/article/pii/S0010465509002276
-Published-DOI: 10.1016/j.cpc.2009.07.007
Depends: openmx
Depends: nwchem
-Published-Title: NWChem: a comprehensive and scalable open-source solution for
large scale molecular simulations
-Published-Authors: M. Valiev, E.J. Bylaska, N. Govind, K. Kowalski, T.P.
Straatsma, H.J.J. van Dam, D. Wang, J. Nieplocha, E. Apra, T.L. Windus and W.A.
de Jong
-Published-In: Comput. Phys. Commun. 181(9):1477-1489
-Published-Year: 2010
-Published-URL:
http://www.sciencedirect.com/science/article/pii/S0010465510001438
-Published-DOI: 10.1016/j.cpc.2010.04.018
Depends: aces3
-Published-Title: Parallel Implementation of Electronic Structure Energy,
Gradient and Hessian Calculations
-Published-Authors: V. Lotrich, N. Flocke, M. Ponton, A. Yau, A. Perera, E.
Deumens and R. J. Bartlett
-Published-In: J. Chem. Phys. 128:194104
-Published-Year: 2008
-Published-URL: http://jcp.aip.org/resource/1/jcpsa6/v128/i19/p194104_s1
-Published-DOI: 10.1063/1.2920482
Registration: http://www.qtp.ufl.edu/ACES/register.html
Depends: cp2k
Depends: quantum-espresso
-Published-Title: QUANTUM ESPRESSO: a modular and open-source software project
for quantum simulations of materials
-Published-Authors: P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C.
Cavazzoni, D. Ceresoli, G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso,
S. Fabris, G. Fratesi, S. de Gironcoli, R. Gebauer, U. Gerstmann, C.
Gougoussis, A. Kokalj, M. Lazzeri, L. Martin-Samos, N. Marzari, F. Mauri, R.
Mazzarello, S. Paolini, A. Pasquarello, L. Paulatto, C. Sbraccia, S. Scandolo,
G. Sclauzero, A. P. Seitsonen, A. Smogunov, P. Umari and R. M. Wentzcovitch
-Published-In: J. Phys. Condens. Matter 21:395502
-Published-Year: 2009
-Published-URL: http://iopscience.iop.org/0953-8984/21/39/395502
-Published-DOI: 10.1088/0953-8984/21/39/395502
+
+Depends: psi4
+
+Depends: elk-lapw
+
+Depends: ergo
diff -Nru debichem-0.0.3/tasks/crystallography
debichem-0.0.4/tasks/crystallography
--- debichem-0.0.3/tasks/crystallography 1970-01-01 01:00:00.000000000
+0100
+++ debichem-0.0.4/tasks/crystallography 2014-12-05 16:19:31.000000000
+0100
@@ -0,0 +1,16 @@
+Task: Crystallography
+Description: DebiChem crystallography
+ This metapackage will install packages for crystallography which might be
+ useful for chemists.
+
+Depends: drawxtl
+
+Depends: gcrystal
+
+Depends: python-fabio
+
+Depends: shelxle
+
+Depends: xcrysden
+
+Depends: gamgi
diff -Nru debichem-0.0.3/tasks/modelling debichem-0.0.4/tasks/modelling
--- debichem-0.0.3/tasks/modelling 2013-02-23 18:32:52.000000000 +0100
+++ debichem-0.0.4/tasks/modelling 2014-12-05 16:06:21.000000000 +0100
@@ -10,19 +10,6 @@
Depends: pymol
Depends: python-mmtk
-Homepage: http://dirac.cnrs-orleans.fr/MMTK/
-License: CeCILL-C
-Language: C, Python
-WNPP: 642586
-Responsible: Picca Frédéric-Emmanuel <pi...@synchrotron-soleil.fr>
-Pkg-Description: The molecular modeling toolkit
- The Molecular Modeling Toolkit (MMTK) is a library for molecular
- simulation applications. It provides the most common methods in
- molecular simulations (molecular dynamics, energy minimization,
- normal mode analysis) and several force fields used for biomolecules
- (Amber 94, Amber 99, several elastic network models). MMTK also
- serves as a code basis that can be easily extended and modified to
- deal with non-standard situations in molecular simulations.
Depends: nmoldyn
Homepage: http://dirac.cnrs-orleans.fr/plone/software/nmoldyn/
diff -Nru debichem-0.0.3/tasks/molmech debichem-0.0.4/tasks/molmech
--- debichem-0.0.3/tasks/molmech 2013-02-22 17:05:45.000000000 +0100
+++ debichem-0.0.4/tasks/molmech 2014-12-05 16:34:03.000000000 +0100
@@ -4,12 +4,6 @@
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: avogadro
@@ -17,22 +11,8 @@
Depends: gromacs
+Depends: lammps
+
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..
+Depends: votca-csg
diff -Nru debichem-0.0.3/tasks/polymer debichem-0.0.4/tasks/polymer
--- debichem-0.0.3/tasks/polymer 2013-02-23 18:32:52.000000000 +0100
+++ debichem-0.0.4/tasks/polymer 2014-12-05 16:40:02.000000000 +0100
@@ -1,19 +1,48 @@
Task: Polymer editors and mass spectrometry
-Description: DebiChem polymer sequence editors and mass spectrometry
- This metapackage will install packages which enable you to edit
- polymer sequences so as to perform mass spectrometry simulations and
- view mass spectra.
-
+Description: DebiChem Analytical BioChemistry
+ This metapackage will install packages which enable you to:
+ .
+ - load and convert mass spectrometric data files;
+ - edit biopolymer sequences;
+ - elaborate complex mass spectrometry workflows;
+ - perform protein database searches using tandem-ms data;
+ - view and mine mass spectrometric data;
+ .
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-URL: http://bioinformatics.oxfordjournals.org/content/25/20/2741
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
Depends: lutefisk
+
+Depends: openms
+
+Depends: libpwiz-tools
+
+Suggests: libpwiz-dev
+
+Depends: python-mzml
+
+Depends: libmstoolkit
+
+Depends: tandem-mass
+
+Depends: r-cran-maldiquant
+
+Depends: r-cran-maldiquantforeign
+
+Depends: r-cran-readbrukerflexdata
+
+Depends: r-cran-readmzxmldata
+
+Depends: biceps
+
+Depends: r-other-curvefdp
+
+Depends: r-other-nitpick
+
+Depends: r-cran-mixtools
+
+Depends: r-other-amsmercury
+
+Depends: r-other-iwrlars
diff -Nru debichem-0.0.3/tasks/semiempirical debichem-0.0.4/tasks/semiempirical
--- debichem-0.0.3/tasks/semiempirical 2013-02-23 18:32:52.000000000 +0100
+++ debichem-0.0.4/tasks/semiempirical 2014-12-05 16:06:21.000000000 +0100
@@ -6,3 +6,5 @@
Depends: mopac7-bin
Depends: cp2k
+
+Depends: molds
diff -Nru debichem-0.0.3/tasks/view-edit-2d debichem-0.0.4/tasks/view-edit-2d
--- debichem-0.0.3/tasks/view-edit-2d 2013-02-23 18:32:52.000000000 +0100
+++ debichem-0.0.4/tasks/view-edit-2d 2014-12-05 16:06:21.000000000 +0100
@@ -14,23 +14,5 @@
Depends: xdrawchem
Depends: osra
-Homepage: http://cactus.nci.nih.gov/osra/
-License: Creative Commons
-Pkg-Description: Optical Structure Recognition Application
- OSRA is a utility designed to convert graphical representations of
- chemical structures, as they appear in journal articles, patent
- documents, textbooks, trade magazines etc., into SMILES (Simplified
- Molecular Input Line Entry Specification - see
- http://en.wikipedia.org/wiki/SMILES) or SD files - a computer
- recognizable molecular structure format. OSRA can read a document in any
- of the over 90 graphical formats parseable by ImageMagick - including
- GIF, JPEG, PNG, TIFF, PDF, PS etc., and generate the SMILES or SDF
- representation of the molecular structure images encountered within that
- document.
- .
- Note that any software designed for optical recognition is unlikely to
- be perfect, and the output produced might, and probably will, contain
- errors, so curation by a human knowledgeable in chemical structures is
- highly recommended.
Remark: Packaging was discussed at
http://lists.alioth.debian.org/pipermail/debichem-devel/2009-November/002236.html
diff -Nru debichem-0.0.3/tasks/visualisation debichem-0.0.4/tasks/visualisation
--- debichem-0.0.3/tasks/visualisation 2013-02-23 18:32:52.000000000 +0100
+++ debichem-0.0.4/tasks/visualisation 2014-12-05 16:31:34.000000000 +0100
@@ -8,9 +8,6 @@
Depends: avogadro
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: gabedit
@@ -18,8 +15,6 @@
Depends: gausssum
-Depends: gcrystal
-
Depends: gdis
Depends: gdpc
@@ -50,3 +45,9 @@
Depends: raster3d
Depends: kalzium
+
+Depends: gamgi
+
+Depends: p4vasp
+
+Depends: travis
diff -Nru debichem-0.0.3/TODO debichem-0.0.4/TODO
--- debichem-0.0.3/TODO 2013-02-22 12:44:15.000000000 +0100
+++ debichem-0.0.4/TODO 2014-12-05 16:06:21.000000000 +0100
@@ -9,10 +9,3 @@
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.
