--- avogadro-1.0.0.orig/debian/compat +++ avogadro-1.0.0/debian/compat @@ -0,0 +1 @@ +5 --- avogadro-1.0.0.orig/debian/python-avogadro.install +++ avogadro-1.0.0/debian/python-avogadro.install @@ -0,0 +1,2 @@ +usr/lib/python*/*-packages +usr/share/libavogadro/engineScripts/wireframe.py --- avogadro-1.0.0.orig/debian/python-avogadro.dirs +++ avogadro-1.0.0/debian/python-avogadro.dirs @@ -0,0 +1,2 @@ +/usr/share/libavogadro/extensionScripts +/usr/share/libavogadro/engineScripts --- avogadro-1.0.0.orig/debian/avogadro.manpages +++ avogadro-1.0.0/debian/avogadro.manpages @@ -0,0 +1 @@ +debian/avogadro.1 --- avogadro-1.0.0.orig/debian/avogadro.xpm +++ avogadro-1.0.0/debian/avogadro.xpm @@ -0,0 +1,231 @@ +/* XPM */ +static char * avogadro_xpm[] = { +"32 32 196 2", +" c None", +". c #000000", +"+ c #EE2F00", +"@ c #EE3000", +"# c #F14205", +"$ c #FA8B19", +"% c #FEAA21", +"& c #FD9C1D", +"* c #F4590B", +"= c #F14706", +"- c #F24C08", +"; c #EF3401", +"> c #FD9B1D", +", c #FFAE22", +"' c #FFAC22", +") c #F24A07", +"! c #EF3802", +"~ c #F24907", +"{ c #EF3702", +"] c #FA8517", +"^ c #FFAC21", +"/ c #F24E08", +"( c #F77513", +"_ c #681500", +": c #F77413", +"< c #FC981C", +"[ c #FFAB21", +"} c #FEA41F", +"| c #F03E04", +"1 c #FD9E1E", +"2 c #FC951B", +"3 c #F14807", +"4 c #F77212", +"5 c #A02000", +"6 c #200600", +"7 c #0A0200", +"8 c #721600", +"9 c #F03B03", +"0 c #F66A10", +"a c #FC991C", +"b c #FA8A18", +"c c #F5640E", +"d c #EF3301", +"e c #EE3100", +"f c #F66D11", +"g c #F77011", +"h c #EE3101", +"i c #FB911A", +"j c #FEA921", +"k c #FA8918", +"l c #F0540A", +"m c #991F00", +"n c #250700", +"o c #0B0200", +"p c #6F1600", +"q c #DC3D05", +"r c #F87B14", +"s c #FC971C", +"t c #F6680F", +"u c #F77112", +"v c #FC9B1D", +"w c #EF3502", +"x c #F6670F", +"y c #EF3A03", +"z c #F87A14", +"A c #F24B07", +"B c #A62100", +"C c #DE3F05", +"D c #F87C14", +"E c #FB931B", +"F c #F0550A", +"G c #BF2600", +"H c #9B1F00", +"I c #DB3D05", +"J c #F98016", +"K c #FB8E1A", +"L c #BC2600", +"M c #F04105", +"N c #FEA620", +"O c #F24F08", +"P c #F14305", +"Q c #FDA01E", +"R c #F35209", +"S c #090200", +"T c #651400", +"U c #D53804", +"V c #FB8F1A", +"W c #F24D08", +"X c #F5670F", +"Y c #EC4F09", +"Z c #8E1C00", +"` c #F5610D", +" . c #FC9A1D", +".. c #F24F09", +"+. c #F3550A", +"@. c #FD9D1E", +"#. c #F25009", +"$. c #220700", +"%. c #AF2501", +"&. c #F45E0D", +"*. c #F98517", +"=. c #F98216", +"-. c #D83904", +";. c #4E0F00", +">. c #FFAD22", +",. c #FDA11F", +"'. c #F14406", +"). c #050100", +"!. c #EB4D08", +"~. c #F6690F", +"{. c #A82301", +"]. c #1B0500", +"^. c #F45C0C", +"/. c #F03D04", +"(. c #FB901A", +"_. c #F66B10", +":. c #C82800", +"<. c #2A0800", +"[. c #C02D02", +"}. c #FA8617", +"|. c #DF3B04", +"1. c #B62701", +"2. c #E44507", +"3. c #5D1200", +"4. c #F03C03", +"5. c #D75C0E", +"6. c #EB4E09", +"7. c #F25B0C", +"8. c #891B00", +"9. c #140400", +"0. c #531000", +"a. c #DD3E05", +"b. c #E93903", +"c. c #F76F11", +"d. c #F77312", +"e. c #D23603", +"f. c #3B0C00", +"g. c #150400", +"h. c #A32200", +"i. c #F66E11", +"j. c #FB8E19", +"k. c #9D2000", +"l. c #0E0300", +"m. c #601300", +"n. c #EA4C08", +"o. c #F3530A", +"p. c #F14907", +"q. c #EE530A", +"r. c #661400", +"s. c #80480D", +"t. c #83400A", +"u. c #2C0900", +"v. c #D13603", +"w. c #E64406", +"x. c #3D0C00", +"y. c #341704", +"z. c #4B3109", +"A. c #451201", +"B. c #440D00", +"C. c #4A2A07", +"D. c #382206", +"E. c #120400", +"F. c #DE3101", +"G. c #F87813", +"H. c #F3560A", +"I. c #480E00", +"J. c #EE3201", +"K. c #F98116", +"L. c #F97E15", +"M. c #FDA21F", +"N. c #F87613", +"O. c #F03C04", +"P. c #FEA31F", +"Q. c #F4580B", +"R. c #010000", +"S. c #211003", +"T. c #410E00", +"U. c #2F0900", +"V. c #180500", +"W. c #410D00", +"X. c #230901", +"Y. c #ED4305", +"Z. c #160400", +"`. c #971E00", +" + c #961E00", +".+ c #170400", +"++ c #ED4506", +"@+ c #F14606", +"#+ c #F87C15", +"$+ c #B57817", +"%+ c #B27316", +"&+ c #FB941B", +"*+ c #EF3903", +"=+ c #EF3602", +"-+ c #440E00", +";+ c #420D00", +" ", +" . . . . . . ", +" + @ + . . . . . . ", +" # $ % & * . . . . . . . . ", +" @ = - ; > , , , ' ) . . . . . . . . + ! ~ - { ", +"+ ] , ^ / , , , , , ( _ . . . . . . . . @ - : < [ [ , } | ", +"+ 1 2 { 3 , , , , , 4 5 6 . . . . . . 7 8 9 0 a b c = d e f , - ", +" g & h @ i , , , j 3 k l m n . . o p q r s t 9 + u v h ", +" w a x y z < k A B C D E F G H I J K l L + + M N O ", +" P Q R + . S T U r V W X Y Z 6 . ` .i ..+. ", +" 3 @.#. . . $.%.&.A *.=.-.;.. . 3 >., , ,.h ", +" '. .* . ).8 !.E ~.d + #.E 0 {.].. ^., , , , 9 ", +" /.(._.:.<.[.r }.|. 1._.i 2.3. 4.N , , V + ", +" ; z 5.6.2 7.8.9. . 0.a.V f b.c.# d._.! ", +" h ( $ e.f.. . g.h.i.V | ", +" /.j.f k.l.. ]. g.. . m.n.< o. ", +" p.a q.r.. . . s.#.+ /.t.. . . u.v.i t + ", +" o.v w.x.. . . . y.z.A.u.g.B.C.D.. . . . E.F.}.G.@ ", +" H.& # I.. . . . . . . . . . . . . . . . . . J.K.L.@ ", +" O M.'. . . . . . . . . . . . . . . . . . . . . J.b N.+ ", +" O.P.Q. . . . . . . . . . . . . . . . . . . . . y ,.^. ", +" r 2 + R.. . . . S.T.U.. . . . . . V.W.X.. . . . ). ~.P.w ", +"+ Q v - Y.Z.. . . . `. +. . . . .+++@+#+, / ", +" 4 [ , $+. . . . . . . . . . %+>., &+*+", +" d =+-+. . . . . . . . . . ;+d =++ ", +" . . . . . . . . . . ", +" . . . . . . . . . . ", +" . . . . . . . . . . . ", +" . . . . . . . ", +" ", +" ", +" "}; --- avogadro-1.0.0.orig/debian/libavogadro-dev.install +++ avogadro-1.0.0/debian/libavogadro-dev.install @@ -0,0 +1,5 @@ +usr/include +usr/lib/*.so +usr/lib/avogadro/*.cmake +usr/lib/avogadro/*/cmake +usr/lib/avogadro/*/*.cmake --- avogadro-1.0.0.orig/debian/rules +++ avogadro-1.0.0/debian/rules @@ -0,0 +1,29 @@ +#!/usr/bin/make -f + +include /usr/share/cdbs/1/rules/debhelper.mk +include /usr/share/cdbs/1/rules/utils.mk +include /usr/share/cdbs/1/class/cmake.mk +include /usr/share/cdbs/1/rules/simple-patchsys.mk + +LDFLAGS += -Wl,-z,defs +LDFLAGS += -Wl,--as-needed + +# Generate more tight versioned dependency? +# DEB_DH_MAKESHLIBS_ARGS_libavogadro1 = -V + +DEB_SHLIBDEPS_LIBRARY_avogadro = libavogadro1 +DEB_SHLIBDEPS_INCLUDE_avogadro = debian/libavogadro1/usr/lib +DEB_DH_INSTALL_SOURCEDIR = debian/tmp +DEB_CMAKE_EXTRA_FLAGS = -DENABLE_GLSL=ON -DENABLE_RPATH=OFF -DENABLE_UPDATE_CHECKER=OFF + +PYVER = $(shell pyversions -dv) +DEB_DH_GENCONTROL_ARGS_python-avogadro = -- -V'pyavo:Depends=python$(PYVER)-numpy, python-qt4' + +binary-install/python-avogadro:: + dh_sip + dh_pycentral -ppython-avogadro + +common-binary-post-install-arch:: list-missing + +clean:: + $(RM) conf.log conf.pri --- avogadro-1.0.0.orig/debian/watch +++ avogadro-1.0.0/debian/watch @@ -0,0 +1,4 @@ +# See uscan(1) for format + +version=3 +http://sf.net/avogadro/avogadro-([\d\.]+)\.tar.gz --- avogadro-1.0.0.orig/debian/avogadro.install +++ avogadro-1.0.0/debian/avogadro.install @@ -0,0 +1,6 @@ +usr/bin +usr/share/applications +usr/share/avogadro/i18n +usr/share/pixmaps + +../../debian/avogadro.xpm usr/share/pixmaps/ --- avogadro-1.0.0.orig/debian/avogadro.1 +++ avogadro-1.0.0/debian/avogadro.1 @@ -0,0 +1,29 @@ +.TH "AVOGADRO" "1" "22 January 2009" "" "User commands" + +.SH NAME +avogadro \- Molecular Graphics and Modelling System + +.SH SYNOPSIS +\fBavogadro\fR [\fBoptions\fR] [\fIfiles\fR] + +.SH DESCRIPTION +.PP +\fBavogadro\fR is a molecular graphics and modelling system targeted at molecules +and biomolecules. It can visualize properties like molecular orbitals or +electrostatic potentials and features an intuitive molecular builder. + +.SH OPTIONS +.PP +Listed below are the command line options for \fBavogadro\fR: +.TP +.B \-\-help, \-h +Show help options. +.TP +.B \-\-version, \-v +Show version information. + +.SH AUTHOR +.PP +This manual page was written by Jordan Mantha <\&laserjock@ubuntu.com\&>. +.PP +Released under the GNU General Public License, version 2 or later. --- avogadro-1.0.0.orig/debian/libavogadro1.install +++ avogadro-1.0.0/debian/libavogadro1.install @@ -0,0 +1,5 @@ +usr/lib/*.so.* +usr/lib/avogadro/*/extensions +usr/lib/avogadro/*/tools +usr/lib/avogadro/*/engines +usr/lib/avogadro/*/colors --- avogadro-1.0.0.orig/debian/control +++ avogadro-1.0.0/debian/control @@ -0,0 +1,96 @@ +Source: avogadro +Section: science +Priority: optional +Maintainer: Ubuntu MOTU Developers <ubuntu-motu@lists.ubuntu.com> +XSBC-Original-Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org> +Uploaders: Jordan Mantha <laserjock@ubuntu.com>, + Michael Banck <mbanck@debian.org>, + Daniel Leidert (dale) <daniel.leidert@wgdd.de> +Build-Depends: cdbs (>= 0.4.50), debhelper (>= 5.0.38), cmake (>= 2.6.0), + patchutils, pkg-config, libboost-python-dev, libeigen2-dev (>= 2.0~beta6), + libglew1.5-dev, libqt4-dev (>= 4.4.0), qt4-dev-tools, zlib1g-dev, + libqt4-opengl-dev, libopenbabel-dev (>= 2.2.0), python-dev, python-central, + python-numpy, python-sip4-dev, sip4 +Standards-Version: 3.8.3 +XS-Python-Version: current +Homepage: http://avogadro.sourceforge.net/ +Vcs-Browser: http://svn.debian.org/wsvn/debichem/ +Vcs-Svn: svn://svn.debian.org/svn/debichem/unstable/avogadro/ +DM-Upload-Allowed: yes + +Package: avogadro +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, libavogadro1 (= ${binary:Version}) +Recommends: avogadro-data (>= 1.0.0-2) +Description: Molecular Graphics and Modelling System + Avogadro is a molecular graphics and modelling system targetted at molecules + and biomolecules. It can visualize properties like molecular orbitals or + electrostatic potentials and features an intuitive molecular builder. + . + Features include: + * Molecular modeller with automatic force-field based geometry optimization + * Molecular Mechanics including constraints and conformer searches + * Visualization of molecular orbitals and general isosurfaces + * Visualization of vibrations and plotting of vibrational spectra + * Support for crystallographic unit cells + * Input generation for the Gaussian, GAMESS and MOLPRO quantum chemistry + packages + * Flexible plugin architecture and Python scripting + . + File formats Avogadro can read include PDB, XYZ, CML, CIF, Molden, as well as + Gaussian, GAMESS and MOLPRO output. + +Package: avogadro-data +Architecture: all +Depends: ${misc:Depends} +Conflicts: avogadro (<< 1.0.0-2), libavogadro0 (<< 1.0.0-2) +Replaces: avogadro (<< 1.0.0-2), libavogadro0 (<< 1.0.0-2) +Description: Molecular Graphics and Modelling System (Data Files) + Avogadro is a molecular graphics and modelling system targetted at molecules + and biomolecules. It can visualize properties like molecular orbitals or + electrostatic potentials and features an intuitive molecular builder. + . + This package contains data files like molecular builder fragments or + OpenGL shaders. + +Package: libavogadro1 +Conflicts: libavogadro0 +Replaces: libavogadro0 +Architecture: any +Section: libs +Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: python-avogadro, avogadro-data (>= 1.0.0-2) +Description: Molecular Graphics and Modelling System (library) + Avogadro is a molecular graphics and modelling system targetted at small + to medium molecules. It can visualize properties like molecular orbitals or + electrostatic potentials and features an intuitive molecular builder. + . + This package provides the shared library. + +Package: libavogadro-dev +Architecture: any +Section: libdevel +Priority: extra +Depends: ${misc:Depends}, libavogadro1 (= ${binary:Version}), libqt4-dev (>= 4.4.0), libeigen2-dev (>= 2.0~beta6), libopenbabel-dev (>= 2.2.0) +Description: Molecular Graphics and Modelling System (development files) + Avogadro is a molecular graphics and modelling system targetted at small + to medium molecules. It can visualize properties like molecular orbitals or + electrostatic potentials and features an intuitive molecular builder. + . + This package provides the development and header files. + +Package: python-avogadro +Architecture: any +Section: python +Priority: extra +Depends: ${misc:Depends}, ${python:Depends}, ${shlibs:Depends}, ${pyavo:Depends} +Replaces: libavogadro0 (<< 0.9.8) +Conflicts: libavogadro0 (<< 0.9.8) +Provides: ${python:Provides} +XB-Python-Version: ${python:Versions} +Description: Molecular Graphics and Modelling System (Python module) + Avogadro is a molecular graphics and modelling system targetted at small + to medium molecules. It can visualize properties like molecular orbitals or + electrostatic potentials and features an intuitive molecular builder. + . + This package provides the Python module. --- avogadro-1.0.0.orig/debian/pycompat +++ avogadro-1.0.0/debian/pycompat @@ -0,0 +1 @@ +2 --- avogadro-1.0.0.orig/debian/copyright +++ avogadro-1.0.0/debian/copyright @@ -0,0 +1,176 @@ +This package was debianized by Jordan Mantha <mantha@ubuntu.com> on +Sat, 10 Nov 2007 16:09:59 -0800 + +It was downloaded from: http://sourceforge.net/projects/avogadro/ + +Upstream Authors: + + Geoffrey Hutchison et al. + For the full list see /usr/share/doc/avogadro/AUTHORS. + +Copyright: + + Copyright (C) 2006-2009 The Avogadro Project. + Copyright (C) 2007 Shahzad Ali. + Copyright (C) 2008 Michael Banck. + Copyright (C) 2007 Ross Braithwaite. + Copyright (C) 2007 James Bunt. + Copyright (C) 2006-2008 Donald Ephraim Curtis. + Copyright (C) 2008 Albert De Fusco. + Copyright (C) 2007-2009 Marcus D. Hanwell. + Copyright (C) 2006-2009 Geoffrey R. Hutchison. + Copyright (C) 2006-2008 Benoit Jacob. + Copyright (C) 2008 Naomi Fox. + Copyright (C) 2007 Carsten. + Copyright (C) 2007-2009 Tim Vandermeersch. + Copyright (C) 1992-2008 Trolltech ASA. + + libavogadro/src/extensions/gamessinputdata.h: + Copyright (C) 2004 Iowa State University + + libavogadro/src/extensions/shaders/vmd.frag, + libavogadro/src/extensions/shaders/vmd.vert: + Copyright (C) 1995-2007 The Board of Trustees of the University of Illinois. + + libavogadro/src/extensions/shaders/plasma.vert, + libavogadro/src/extensions/shaders/gooch.frag, + libavogadro/src/extensions/shaders/plasma.frag, + libavogadro/src/extensions/shaders/gooch.vert: + Copyright (C) 2002-2004 3Dlabs Inc. Ltd. + + testfiles/*: + Copyright (C) 2006 Jerome Pansanel. + + avogadro/gl2ps/*: + Copyright (C) 1999-2006 Christophe Geuzaine. + + cmake/modules/MacroEnsureVersion.cmake + Copyright (C) 2006 David Faure <faure@kde.org>. + Copyright (C) 2007 Will Stephenson <wstephenson@kde.org>. + + cmake/modules/FindEigen2.cmake: + Copyright (C) 2006, 2007 Montel Laurent <montel@kde.org>. + + cmake/modules/FindOpenBabel2.cmake + Copyright (C) 2006, 2007 Carsten Niehaus <cniehaus@gmx.de>. + Copyright (C) 2008 Marcus D. Hanwell <marcus@cryos.org>. + + debian/*: + Copyright (C) 2007 Jordan Mantha <mantha@ubuntu.com>. + Copyright (C) 2008,2009 debichem team <debichem-devel@lists.alioth.debian.org> + +License: + +**/*: GPL2 (several files), GPL2+ + + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program; if not, write to the Free Software Foundation, + Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301, USA. + + On Debian systems, the complete text of the GNU General Public + License (latest version) can be found in `/usr/share/common-licenses/GPL'. + +avogadro/gl2ps/*, +libavogadro/src/extensions/basisset.cpp, +libavogadro/src/extensions/basisset.h, +libavogadro/src/extensions/gaussianfchk.cpp, +libavogadro/src/extensions/gaussianfchk.h, +libavogadro/src/extensions/mopacaux.cpp, +libavogadro/src/extensions/mopacaux.h, +libavogadro/src/extensions/slaterset.cpp, +libavogadro/src/extensions/slaterset.h, +libavogadro/src/extensions/supercelldialog.cpp, +libavogadro/src/extensions/supercelldialog.h, +libavogadro/src/extensions/vdwsurface.cpp, +libavogadro/src/extensions/vdwsurface.h, +libavogadro/src/meshgenerator.cpp, +libavogadro/src/meshgenerator.h, +libavogadro/src/periodictableview.cpp, +libavogadro/src/periodictableview.h: LGPL2.1+ + + This library is free software; you can redistribute it and/or modify + it under the terms of the GNU Library General Public License as + published by the Free Software Foundation; either version 2.1 of the + License, or (at your option) any later version. + + This library is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Lesser General Public License for more details. + + You should have received a copy of the GNU Lesser General Public + License along with this library; if not, write to the Free Software + Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + + On Debian systems, the complete text of the GNU Lesser General Public + License (latest version) can be found in `/usr/share/common-licenses/LGPL'. + +libavogadro/src/extensions/shaders/gooch.frag, +libavogadro/src/extensions/shaders/gooch.vert, +libavogadro/src/extensions/shaders/plasma.frag, +libavogadro/src/extensions/shaders/plasma.vert: BSD-C3 + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions + are met: + + Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + + Neither the name of 3Dlabs Inc. Ltd. nor the names of its + contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE + COPYRIGHT HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; + LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER + CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT + LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN + ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE + POSSIBILITY OF SUCH DAMAGE. + +cmake/*: BSD-C3 + + Redistribution and use in source and binary forms, with or without + modification, are permitted under the terms of the BSD License. + + THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND + ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE + IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE + ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE + FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS + OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) + HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT + LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY + OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF + SUCH DAMAGE. + + On Debian systems, the complete text of the 3-clause BSD license can be + found in `/usr/share/common-licenses/BSD'. + +============================================================================== + +The Debian packaging is Copyright (C) 2007-2009 by Jordan Mantha +<mantha@ubuntu.com> and Debichem Team <debichem-devel@lists.alioth.debian.org> +and is licensed under the GPL, see above. --- avogadro-1.0.0.orig/debian/avogadro.menu +++ avogadro-1.0.0/debian/avogadro.menu @@ -0,0 +1,7 @@ +?package(avogadro):\ + needs="X11"\ + section="Applications/Science/Chemistry"\ + title="Avogadro"\ + longtitle="3D Molecular Editor and Visualizer"\ + icon="/usr/share/pixmaps/avogadro.xpm"\ + command="/usr/bin/avogadro" --- avogadro-1.0.0.orig/debian/changelog +++ avogadro-1.0.0/debian/changelog @@ -0,0 +1,357 @@ +avogadro (1.0.0-2ubuntu3) lucid; urgency=low + + * Remove faulty depends for python2.6-qt4 and python2.6-sip4 in debian/rules + * Use dh_sip in debian/rules + + -- Jonathan Thomas <echidnaman@kubuntu.org> Thu, 22 Apr 2010 00:29:35 -0400 + +avogadro (1.0.0-2ubuntu2) lucid; urgency=low + + * Add sip_4.10_support.patch from upstream. Fixes FTBFS with new SIP + versions + + -- Jonathan Thomas <echidnaman@kubuntu.org> Tue, 20 Apr 2010 23:38:34 -0400 + +avogadro (1.0.0-2ubuntu1) lucid; urgency=low + + * Sync with Debian + * Edit python-avogadro.install for python 2.6 directories + + -- Jonathan Riddell <jriddell@ubuntu.com> Wed, 06 Jan 2010 14:36:13 +0000 + +avogadro (1.0.0-2) unstable; urgency=low + + [ Michael Banck ] + * debian/libavogadro0.install: Wildcard the API directory. + * debian/libavogadro-dev.install: Likewise. + * debian/libavogadro0.install: Renamed to ... + * debian/libavogadro1.install: ... this. + * debian/control (libavogadro0): Renamed package to libavogadro1. Update + all references. + * debian/rules: Likewise. + * debian/control (libavogadro1): Replace and Conflict with libavogadro0. + * debian/control (avogadro-data): New package. + * debian/control (avogadro): Recommend avogadro-data. + * debian/control (libavogadro1): Likewise. + * debian/libavogadro1.install: No longer ship /usr/share/libavogadro. + * debian/avogadro.install: Only ship i18n directory from + /usr/share/avogadro. + * debian/avogadro-data.install: New file. + * debian/python-avogadro.install: Install wireframe.py explicitely + ommitting example.py (closes: #555627). + * debian/libavogadro-dev.install: Ship AvogadroBuildSettings.cmake, + AvogadroLibraryDeps.cmake and AvogadroUse.cmake as well. + * debian/control (avogadro-date): Replace and Conflict with prior versions + of the avogadro and libavogadro0 packages. + * debian/python-avogadro.dirs: New file. + + [ Daniel Leidert ] + * debian/python-avogadro.files: Dropped. + * debian/python-avogadro.install: Install scripts from debian/tmp. + * debian/rules (binary-install/python-avogadro): Adjusted for changes above. + + -- Michael Banck <mbanck@debian.org> Fri, 13 Nov 2009 19:57:07 +0100 + +avogadro (1.0.0-1) unstable; urgency=low + + * New upstream release. + * debian/patches/sip_4.9_support.patch: Removed, applied upstream. + * debian/patches/fix_empty_second_window.patch: Likewise. + * debian/patches/fix_molpro_input_generator.patch: Likewise. + * debian/libavogadro0.install: Adjust for additional API directory. + * debian/libavogadro-dev.install: Likewise. + + -- Michael Banck <mbanck@debian.org> Fri, 23 Oct 2009 23:59:03 +0200 + +avogadro (0.9.9-1) unstable; urgency=low + + * New upstream release. + + Fixes german umlauts in the interface (closes: #538075). + + [ Michael Banck ] + * debian/patches/vibrations_ordering.patch: Removed, applied upstream. + * debian/patches/sip_4.9_support.patch: New patch, recognize new SIP + version, taken from upstream (closes: #551244). + * debian/rules (binary-fixup/python-avogadro): Removed rule, no longer + needed. + * debian/libavogadro0.install: Put extensions, engines and tools into + library package. + * debian/libavogadro-dev.install: Put cmake files into development package. + * debian/avogadro.install: No longer put /usr/lib/avogadro into application + package. + * debian/patches/fix_empty_second_window.patch: New patch, fixes opening an + empty second window when Avogadro gets opened with a molecule, taken from + upstream. + * debian/patches/fix_molpro_input_generator.patch: New patch, makes the + Molpro input generator work again, taken from upstream. + + [ Daniel Leidert ] + * debian/control: Added python-avogadro package (closes: #513441). + (Build-Depends): Added python-dev and python-central. Increase dh version + to >= 5.0.38 for the latter. + (Standrads-Version): Bumped to 3.8.3. + (Depends): Move Python (module) dependencies to python-avogadro. + (Recommends): Let libavogadro0 recommend python-avogadro. + * debian/rules: Added targets and rules to create new python-avogadro + package. Make sure we comply to the Python policy and depend on + pythonX.Y-foo for the moment. + * debian/libavogadro0.install: Don't install Python module. + * debian/pycomat: Added with compat leven 2. + * debian/python-avogadro.files: Added to move Python scripts over to + python-avogadro. + * debian/python-avogadro.install: Added to install Python module. + + -- Michael Banck <mbanck@debian.org> Thu, 22 Oct 2009 14:44:53 +0200 + +avogadro (0.9.7-1ubuntu2) karmic; urgency=low + + * Build with -DENABLE_PYTHON=OFF, Python bits do not build with Sip 4.9 + + -- Jonathan Riddell <jriddell@ubuntu.com> Wed, 14 Oct 2009 00:55:35 +0100 + +avogadro (0.9.7-1ubuntu1) karmic; urgency=low + + * Merge from debian unstable, Ubuntu remaining changes: + - debian/control: Replace dependency on python2.5 with python2.6. + - debian/libavogadro0.install: Install the Python 2.6 extension. + + -- Alessio Treglia <quadrispro@ubuntu.com> Mon, 20 Jul 2009 11:12:09 +0200 + +avogadro (0.9.7-1) unstable; urgency=low + + * New upstream release. + + [ Daniel Leidert ] + * debian/rules (binary-fixup/libavogadro0): Don't install + extensionScripts/example.py for the moment (closes: #536281). + + [ Michael Banck ] + * debian/patches/orbitalextension_link_zlib.patch: Removed, applied + upstream. + * debian/patches/sip_4.8_support.patch: Likewise. + * debian/control (Build-Depends): Removed libboost-python1.37-dev and + libboost-python1.38-dev, added qt4-dev-tools. + * debian/avogadro.examples: New file. + + -- Michael Banck <mbanck@debian.org> Sun, 19 Jul 2009 17:34:22 +0200 + +avogadro (0.9.6-1ubuntu1) karmic; urgency=low + + * Merge from debian unstable, Ubuntu remaining changes: + - debian/libavogadro0.install: Install the Python 2.6 extension. + - debian/control: Don't depend on python2.5, use python2.6 instead. + + -- Alessio Treglia <quadrispro@ubuntu.com> Mon, 29 Jun 2009 09:09:30 +0200 + +avogadro (0.9.6-1) unstable; urgency=low + + * New upstream release. + * debian/patches/ignore_f_orbitals.patch: Removed, applied upstream. + * debian/patches/ignore_missing_intensities.patch: Likewise. + * debian/patches/molpro_orbitals.patch: Likewise. + * debian/patches/install_desktop_on_kfreebsd.patch: Likewise. + * debian/libavogadro0.install: Wildcard python directory, the old + "Avogadro.so" no longer matches. + * debian/control (Build-Depends): Added zlib1g-dev. + * debian/patches/orbitalextension_link_zlib.patch: New patch, fixes build + failure due to a missing link to zlib, taken from upstream. + * debian/rules (DEB_CMAKE_EXTRA_FLAGS): Added -DENABLE_UPDATE_CHECKER=OFF. + * debian/patches/vibrations_ordering.patch: New patch, fixing sorting of + vibrations, taken from upstream. + * debian/patches/sip_4.8_support.patch: New patch, adding support for + python-sip4-4.8 (closes: #533939). + * debian/control (Build-Depends): Added sip4, needed by the build system to + detect the sip4 version. + + -- Michael Banck <mbanck@debian.org> Sun, 21 Jun 2009 19:01:36 +0200 + +avogadro (0.9.4-3) unstable; urgency=low + + * debian/avogadro.install: Include the .desktop file (closes: #528166). + * debian/patches/install_desktop_on_kfreebsd.patch: Added. + - avogadro/src/CMakeLists.txt: Install .desktop file and icon on kfreebsd + too to avoid an FTBFS. + + -- Daniel Leidert (dale) <daniel.leidert@wgdd.de> Thu, 14 May 2009 19:03:30 +0200 + +avogadro (0.9.4-2ubuntu1) karmic; urgency=low + + * Fix FTBFS due to change of phython default from 2.5 to 2.6 (LP: #372576) + * debian/libavogadro0.install: update to install the Avogadro.so python2.6 extension + * debian/control: update libavogadro0 dependency on python2.6 + + -- Manny Vindiola <mannyv@gmail.com> Wed, 06 May 2009 02:11:52 -0400 + +avogadro (0.9.4-2) unstable; urgency=low + + [ Daniel Leidert ] + * debian/avogadro.desktop: Dropped. Upstream installs a valid one now. + * debian/avogadro.install: Don't install self-written .desktop file over the + one installed by upstream and install missing icon. + * debian/control (Build-Depends): (Re-)Add Boost 1.37 as alternative to 1.38 + for Ubuntu. + * debian/rules: Removed hardcoded CC and CXX definitions. Set + LDFLAGS += -Wl,-z,defs -Wl,--as-needed. + (get-orig-source): Dropped (we don't need a special target for this). + * debian/copyright: Minor updates and cosmetics. + + [ Michael Banck ] + * debian/control (Description): Updated to reflect recent feature additions. + * debian/patches/ignore_missing_intensities.patch: New patch, takes into + account missing intensity information for vibrations so that Avogadro no + longer crashes, taken from upstream. + + -- Michael Banck <mbanck@debian.org> Tue, 05 May 2009 15:14:54 +0200 + +avogadro (0.9.4-1) unstable; urgency=low + + * New upstream release. + + [ Daniel Leidert ] + * debian/control (Build-Depends): Use Boost 1.38. + (Standards-Version): Bumped to 3.8.1 (no other changes). + (Vcs-Svn): Fixed vcs-field-uses-not-recommended-uri-format. + * debain/rules (DEB_CMAKE_EXTRA_FLAGS): Disable rpath support. + + [ Michael Banck ] + * debian/patches/molpro_orbitals.patch: Updated. + * debian/patches/ignore_f_orbitals.patch: New patch, tries to properly + ignore f-type orbitals when calculating molecular orbitals. + + -- Jordan Mantha <laserjock@ubuntu.com> Sun, 03 May 2009 19:52:02 -0700 + +avogadro (0.9.3-1) unstable; urgency=low + + * New upstream release. + + [ Daniel Leidert ] + * debian/control (Build-Depends): Build-depend on boost1.37. + (Priority): libavogadro-dev must be priority extra as libeigen2-dev is, + see Debian policy section 2.5. + + [ Jordan Mantha ] + * debian/libavogadro0.install: install the Avogadro.so python extension + * debian/control: add libavogadro0 dependency on python2.5 for extension + + [ Michael Banck ] + * debian/patches/molpro_orbitals.patch: New patch, adds support for MOLPRO + molecular orbitals. + + -- Michael Banck <mbanck@debian.org> Mon, 13 Apr 2009 16:11:30 +0200 + +avogadro (0.9.2-1) unstable; urgency=low + + * New upstream release 0.9.2. + + * debian/control (Uploaders): Added myself. + (Section): Fixed binary-control-field-duplicates-source. + (Build-Depends): Use boost 1.35. + * debian/copyright: Updated and completed. + * debian/rules: List missing (not-installed) files. + + -- Daniel Leidert (dale) <daniel.leidert@wgdd.de> Fri, 06 Mar 2009 16:06:16 +0100 + +avogadro (0.9.0-2) experimental; urgency=low + + * debian/control: added python-sip4-dev for complete python support + * debian/avogadro.1: (thanks Daniel Leidert) + - typo fix and a few nit-picking formatting changes + + -- Jordan Mantha <laserjock@ubuntu.com> Fri, 23 Jan 2009 21:01:16 -0800 + +avogadro (0.9.0-1) experimental; urgency=low + + * remove patches included upstream: + - 01_AddHydrogens.patch + - 10_QVarLengthArray.patch + - 11_ExportGraphics.patch + * debian/control - update dependencies: + - bump Qt version + - switch from eigen to eigen2 + - drop -1 from openbabel dependency + - add python-numpy for python support + - added libglew1.5-dev for GL shading support + * debian/rules - add cmake flag to turn on GL shadding support + * debian/control - fix lintian warnings: + - add ${misc:Depends} to libavogadro0 and libavogadro-dev + - s/python/Python/ in long description + - added manpage, avogadro.1 + + -- Jordan Mantha <laserjock@ubuntu.com> Thu, 22 Jan 2009 10:43:40 -0800 + +avogadro (0.8.1-5) unstable; urgency=low + + * add patches/11_ExportGraphics.patch + fixes graphics export, by Tim Vandermeersch (Closes: #507046) + * debian/control: Updated descriptions + * debian/control: Added VCS-* links. + + -- Michael Banck <mbanck@debian.org> Mon, 01 Dec 2008 01:42:41 +0100 + +avogadro (0.8.1-4) unstable; urgency=low + + * Upload to unstable + * debian/control: Bump cmake build dependency to 2.6.0 to work around + bug #479907 (Closes: #488990) + + -- Jordan Mantha <laserjock@ubuntu.com> Thu, 24 Jul 2008 12:15:32 -0700 + +avogadro (0.8.1-3) experimental; urgency=low + + * debian/control: + - bump standards version to 3.8.0 (no changes needed) + - bump openbabel dependency to >= 2.2.0-1 + + -- Jordan Mantha <laserjock@ubuntu.com> Mon, 14 Jul 2008 21:07:23 -0700 + +avogadro (0.8.1-2) experimental; urgency=low + + * add debian/patches/10_QVarLengthArray.patch + from upstream r1513. fixes Align/Measure tool crash + + -- Jordan Mantha <laserjock@ubuntu.com> Wed, 02 Jul 2008 15:18:55 -0700 + +avogadro (0.8.1-1) experimental; urgency=low + + * New upstream release + * add debian/avogadro.desktop + * debian/avogadro.install: + - install avogadro.desktop, avogadro.png, and avogadro.xpm + * add avogadro.menu + * debian/control: + - update minimum versions of qt (4.3.4) and cmake (2.4.7) and openbabel + (2.2.0~beta6~r2551-2) + - add build dependency on libboost-python-dev to enable python terminal + - remove unneeded python-dev build dependency + - add build dependency on patchutils for simple-patchsys + - add python-qt4 depdency for python console garbage collection + - strict dependency on libavogadro0 for avogadro (${binary:Version}) + - update libavogadro-dev dependencies + * debian/rules: + - include simple-patchsys CDBS rule + * debian/patches/: + - added 01_AddHydrogens.patch to fix openbabel/avogadro argument + mismatch + * debian/watch: update to use gzipped rather than b2ziped tarballs. + + -- Jordan Mantha <laserjock@ubuntu.com> Sat, 28 Jun 2008 15:12:07 -0700 + +avogadro (0.8.0-1) experimental; urgency=low + + * New upstream release + * debian/control: + - add build dependency on pkg-config, python-dev and libqt4-opengl-dev + + -- Jordan Mantha <mantha@ubuntu.com> Fri, 23 May 2008 18:49:09 -0700 + +avogadro (0.6.1-1) experimental; urgency=low + + * New upstream release + + -- Jordan Mantha <mantha@ubuntu.com> Sun, 09 Mar 2008 06:16:09 +0000 + +avogadro (0.6.0-1) experimental; urgency=low + + * Initial release. (Closes: #450814) + + -- Jordan Mantha <mantha@ubuntu.com> Mon, 03 Mar 2008 14:44:29 -0800 --- avogadro-1.0.0.orig/debian/avogadro.examples +++ avogadro-1.0.0/debian/avogadro.examples @@ -0,0 +1 @@ +testfiles/* --- avogadro-1.0.0.orig/debian/avogadro-data.install +++ avogadro-1.0.0/debian/avogadro-data.install @@ -0,0 +1,3 @@ +usr/share/avogadro/fragments +usr/share/avogadro/builder +usr/share/libavogadro/shaders --- avogadro-1.0.0.orig/debian/patches/sip_4.10_support.patch +++ avogadro-1.0.0/debian/patches/sip_4.10_support.patch @@ -0,0 +1,28 @@ +commit 6df73a72dcd6eaa1d8c58f73c05c93d13479bec6 +Author: Tim Vandermeersch <tim.vandermeersch@gmail.com> +Date: Sat Feb 20 21:42:00 2010 +0100 + + Make sure python support compiles with sip 4.10. + +diff --git a/cmake/modules/PythonDeps.cmake b/cmake/modules/PythonDeps.cmake +index c93925d..32a28e6 100644 +--- a/cmake/modules/PythonDeps.cmake ++++ b/cmake/modules/PythonDeps.cmake +@@ -59,14 +59,10 @@ else(Boost_PYTHON_FOUND AND PYTHONLIBS_FOUND AND NUMPY_FOUND) + if (EXISTS ${PYTHON_INCLUDE_PATH}/sip.h) + message(STATUS "Found sip.h header...") + execute_process(COMMAND sip -V OUTPUT_VARIABLE SIP_VERSION) +- if (${SIP_VERSION} MATCHES "4.8") +- message(STATUS "using sip version 4.8...") ++ if (${SIP_VERSION} VERSION_GREATER "4.8") ++ message(STATUS "using sip version 4.8 or above...") + add_definitions( -DSIP_4_8 ) +- endif (${SIP_VERSION} MATCHES "4.8") +- if (${SIP_VERSION} MATCHES "4.9") +- message(STATUS "using sip version 4.9...") +- add_definitions( -DSIP_4_8 ) +- endif (${SIP_VERSION} MATCHES "4.9") ++ endif (${SIP_VERSION} VERSION_GREATER "4.8") + else (EXISTS ${PYTHON_INCLUDE_PATH}/sip.h) + message(STATUS "sip.h header NOT found - Python support disabled") + # message(STATUS "debian/ubuntu: install the python-sip4-dev package.")