debian/0000775000000000000000000000000012313267377007203 5ustar debian/patches/0000775000000000000000000000000012276653176010636 5ustar debian/patches/boost148.patch0000664000000000000000000000317512276653176013250 0ustar Description: Work around moc limitations Some parts of Boost, introduced in Boost 1.48 are not understood by the limited C++ parser of moc. This patch defines header guards that prevent the troublesome boost headers from being processed. Bug-Debian: http://bugs.debian.org/653625 Author: Tobias Frost Reviewed-By: Steve Robbins --- a/libavogadro/src/extensions/pythonterminal.h +++ b/libavogadro/src/extensions/pythonterminal.h @@ -23,6 +23,10 @@ #ifndef PYTHONTERMINAL_H #define PYTHONTERMINAL_H +#ifdef Q_MOC_RUN +#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED +#endif + #include #include #include --- a/libavogadro/src/pythonengine_p.h +++ b/libavogadro/src/pythonengine_p.h @@ -25,6 +25,10 @@ #ifndef PYTHONENGINE_H #define PYTHONENGINE_H +#ifdef Q_MOC_RUN +#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED +#endif + #include #include #include --- a/libavogadro/src/pythonextension_p.h +++ b/libavogadro/src/pythonextension_p.h @@ -26,6 +26,10 @@ #ifndef PYTHONEXTENSION_H #define PYTHONEXTENSION_H +#ifdef Q_MOC_RUN +#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED +#endif + #include #include #include --- a/libavogadro/src/pythontool_p.h +++ b/libavogadro/src/pythontool_p.h @@ -25,6 +25,10 @@ #ifndef PYTHONTOOL_H #define PYTHONTOOL_H +#ifdef Q_MOC_RUN +#define BOOST_TT_HAS_OPERATOR_HPP_INCLUDED +#endif + #include #include #include debian/patches/series0000664000000000000000000000004612276653176012053 0ustar link_to_libgl2ps.patch boost148.patch debian/patches/link_to_libgl2ps.patch0000664000000000000000000000163012276653176015114 0ustar Description: Link to libgl2ps.so instead of compiling the internally shipped copy. Fix the 'embedded-library: gl2ps' lintian error. Author: Daniel Leidert Forwarded: not-needed Last-Update: 2013-05-13 --- a/libavogadro/src/extensions/CMakeLists.txt +++ b/libavogadro/src/extensions/CMakeLists.txt @@ -4,9 +4,7 @@ set(DESTINATION_DIR ${Avogadro_PLUGIN_INSTALL_DIR}/extensions) -include_directories(${CMAKE_CURRENT_BINARY_DIR} - "${CMAKE_CURRENT_SOURCE_DIR}/gl2ps" -) +include_directories(${CMAKE_CURRENT_BINARY_DIR}) set(LINK_LIBS avogadro) set(PLUGIN_LABEL extensions) @@ -113,8 +111,8 @@ target_link_libraries(networkfetchextension ${QT_QTNETWORK_LIBRARY}) # GL2PS -avogadro_plugin(gl2psextension - "gl2psextension.cpp;gl2ps/gl2ps.c") +avogadro_plugin(gl2psextension gl2psextension.cpp) +target_link_libraries(gl2psextension gl2ps) # Subdirs add_subdirectory(crystallography) debian/patches/use_python_include_dirs.patch0000664000000000000000000002357612276653176016615 0ustar Author: Philip Muškovac Reviwed-By: Daniel Leidert Description: Add support for multiarch python. Use PYTHON_INCLUDE_DIRS instead of PYTHON_INCLUDE_PATH and drop shipped FindPythonLibs.cmake in favour of the system one. Origin: http://patches.ubuntu.com/a/avogadro/avogadro_1.0.3-5ubuntu5.patch --- a/cmake/modules/FindPythonLibs.cmake +++ /dev/null @@ -1,196 +0,0 @@ -# - Find python libraries -# This module finds if Python is installed and determines where the -# include files and libraries are. It also determines what the name of -# the library is. This code sets the following variables: -# -# PYTHONLIBS_FOUND - have the Python libs been found -# PYTHON_LIBRARIES - path to the python library -# PYTHON_INCLUDE_PATH - path to where Python.h is found (deprecated) -# PYTHON_INCLUDE_DIRS - path to where Python.h is found -# PYTHON_DEBUG_LIBRARIES - path to the debug library -# Python_ADDITIONAL_VERSIONS - list of additional Python versions to search for - -#============================================================================= -# Copyright 2001-2009 Kitware, Inc. -# -# Distributed under the OSI-approved BSD License (the "License"); -# see accompanying file Copyright.txt for details. -# -# This software is distributed WITHOUT ANY WARRANTY; without even the -# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the License for more information. -#============================================================================= -# (To distribute this file outside of CMake, substitute the full -# License text for the above reference.) - -INCLUDE(CMakeFindFrameworks) -# Search for the python framework on Apple. -CMAKE_FIND_FRAMEWORKS(Python) - -# Set up the versions we know about, in the order we will search. Always add -# the user supplied additional versions to the front. -set(_Python_VERSIONS - ${Python_ADDITIONAL_VERSIONS} - 2.7 2.6 2.5 2.4 2.3 2.2 2.1 2.0 1.6 1.5) - -FOREACH(_CURRENT_VERSION ${_Python_VERSIONS}) - STRING(REPLACE "." "" _CURRENT_VERSION_NO_DOTS ${_CURRENT_VERSION}) - IF(WIN32) - FIND_LIBRARY(PYTHON_DEBUG_LIBRARY - NAMES python${_CURRENT_VERSION_NO_DOTS}_d python - PATHS - [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs/Debug - [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs ) - ENDIF(WIN32) - - FIND_LIBRARY(PYTHON_LIBRARY - NAMES python${_CURRENT_VERSION_NO_DOTS} python${_CURRENT_VERSION} - PATHS - [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/libs - # Avoid finding the .dll in the PATH. We want the .lib. - NO_SYSTEM_ENVIRONMENT_PATH - ) - # Look for the static library in the Python config directory - FIND_LIBRARY(PYTHON_LIBRARY - NAMES python${_CURRENT_VERSION_NO_DOTS} python${_CURRENT_VERSION} - # Avoid finding the .dll in the PATH. We want the .lib. - NO_SYSTEM_ENVIRONMENT_PATH - # This is where the static library is usually located - PATH_SUFFIXES python${_CURRENT_VERSION}/config - ) - - # For backward compatibility, honour value of PYTHON_INCLUDE_PATH, if - # PYTHON_INCLUDE_DIR is not set. - IF(DEFINED PYTHON_INCLUDE_PATH AND NOT DEFINED PYTHON_INCLUDE_DIR) - SET(PYTHON_INCLUDE_DIR "${PYTHON_INCLUDE_PATH}" CACHE PATH - "Path to where Python.h is found" FORCE) - ENDIF(DEFINED PYTHON_INCLUDE_PATH AND NOT DEFINED PYTHON_INCLUDE_DIR) - - SET(PYTHON_FRAMEWORK_INCLUDES) - IF(Python_FRAMEWORKS AND NOT PYTHON_INCLUDE_DIR) - FOREACH(dir ${Python_FRAMEWORKS}) - SET(PYTHON_FRAMEWORK_INCLUDES ${PYTHON_FRAMEWORK_INCLUDES} - ${dir}/Versions/${_CURRENT_VERSION}/include/python${_CURRENT_VERSION}) - ENDFOREACH(dir) - ENDIF(Python_FRAMEWORKS AND NOT PYTHON_INCLUDE_DIR) - - FIND_PATH(PYTHON_INCLUDE_DIR - NAMES Python.h - PATHS - ${PYTHON_FRAMEWORK_INCLUDES} - [HKEY_LOCAL_MACHINE\\SOFTWARE\\Python\\PythonCore\\${_CURRENT_VERSION}\\InstallPath]/include - PATH_SUFFIXES - python${_CURRENT_VERSION} - ) - - # For backward compatibility, set PYTHON_INCLUDE_PATH, but make it internal. - SET(PYTHON_INCLUDE_PATH "${PYTHON_INCLUDE_DIR}" CACHE INTERNAL - "Path to where Python.h is found (deprecated)") - -ENDFOREACH(_CURRENT_VERSION) - -MARK_AS_ADVANCED( - PYTHON_DEBUG_LIBRARY - PYTHON_LIBRARY - PYTHON_INCLUDE_DIR -) - -# We use PYTHON_INCLUDE_DIR, PYTHON_LIBRARY and PYTHON_DEBUG_LIBRARY for the -# cache entries because they are meant to specify the location of a single -# library. We now set the variables listed by the documentation for this -# module. -SET(PYTHON_INCLUDE_DIRS "${PYTHON_INCLUDE_DIR}") -SET(PYTHON_LIBRARIES "${PYTHON_LIBRARY}") -SET(PYTHON_DEBUG_LIBRARIES "${PYTHON_DEBUG_LIBRARY}") - - -INCLUDE(FindPackageHandleStandardArgs) -FIND_PACKAGE_HANDLE_STANDARD_ARGS(PythonLibs DEFAULT_MSG PYTHON_LIBRARIES PYTHON_INCLUDE_DIRS) - - -# PYTHON_ADD_MODULE( src1 src2 ... srcN) is used to build modules for python. -# PYTHON_WRITE_MODULES_HEADER() writes a header file you can include -# in your sources to initialize the static python modules -FUNCTION(PYTHON_ADD_MODULE _NAME ) - GET_PROPERTY(_TARGET_SUPPORTS_SHARED_LIBS - GLOBAL PROPERTY TARGET_SUPPORTS_SHARED_LIBS) - OPTION(PYTHON_ENABLE_MODULE_${_NAME} "Add module ${_NAME}" TRUE) - OPTION(PYTHON_MODULE_${_NAME}_BUILD_SHARED - "Add module ${_NAME} shared" ${_TARGET_SUPPORTS_SHARED_LIBS}) - - # Mark these options as advanced - MARK_AS_ADVANCED(PYTHON_ENABLE_MODULE_${_NAME} - PYTHON_MODULE_${_NAME}_BUILD_SHARED) - - IF(PYTHON_ENABLE_MODULE_${_NAME}) - IF(PYTHON_MODULE_${_NAME}_BUILD_SHARED) - SET(PY_MODULE_TYPE MODULE) - ELSE(PYTHON_MODULE_${_NAME}_BUILD_SHARED) - SET(PY_MODULE_TYPE STATIC) - SET_PROPERTY(GLOBAL APPEND PROPERTY PY_STATIC_MODULES_LIST ${_NAME}) - ENDIF(PYTHON_MODULE_${_NAME}_BUILD_SHARED) - - SET_PROPERTY(GLOBAL APPEND PROPERTY PY_MODULES_LIST ${_NAME}) - ADD_LIBRARY(${_NAME} ${PY_MODULE_TYPE} ${ARGN}) -# TARGET_LINK_LIBRARIES(${_NAME} ${PYTHON_LIBRARIES}) - - IF(PYTHON_MODULE_${_NAME}_BUILD_SHARED) - SET_TARGET_PROPERTIES(${_NAME} PROPERTIES PREFIX "${PYTHON_MODULE_PREFIX}") - IF(WIN32 AND NOT CYGWIN) - SET_TARGET_PROPERTIES(${_NAME} PROPERTIES SUFFIX ".pyd") - ENDIF(WIN32 AND NOT CYGWIN) - ENDIF(PYTHON_MODULE_${_NAME}_BUILD_SHARED) - - ENDIF(PYTHON_ENABLE_MODULE_${_NAME}) -ENDFUNCTION(PYTHON_ADD_MODULE) - -FUNCTION(PYTHON_WRITE_MODULES_HEADER _filename) - - GET_PROPERTY(PY_STATIC_MODULES_LIST GLOBAL PROPERTY PY_STATIC_MODULES_LIST) - - GET_FILENAME_COMPONENT(_name "${_filename}" NAME) - STRING(REPLACE "." "_" _name "${_name}") - STRING(TOUPPER ${_name} _nameUpper) - SET(_filename ${CMAKE_CURRENT_BINARY_DIR}/${_filename}) - - SET(_filenameTmp "${_filename}.in") - FILE(WRITE ${_filenameTmp} "/*Created by cmake, do not edit, changes will be lost*/\n") - FILE(APPEND ${_filenameTmp} -"#ifndef ${_nameUpper} -#define ${_nameUpper} - -#include - -#ifdef __cplusplus -extern \"C\" { -#endif /* __cplusplus */ - -") - - FOREACH(_currentModule ${PY_STATIC_MODULES_LIST}) - FILE(APPEND ${_filenameTmp} "extern void init${PYTHON_MODULE_PREFIX}${_currentModule}(void);\n\n") - ENDFOREACH(_currentModule ${PY_STATIC_MODULES_LIST}) - - FILE(APPEND ${_filenameTmp} -"#ifdef __cplusplus -} -#endif /* __cplusplus */ - -") - - - FOREACH(_currentModule ${PY_STATIC_MODULES_LIST}) - FILE(APPEND ${_filenameTmp} "int ${_name}_${_currentModule}(void) \n{\n static char name[]=\"${PYTHON_MODULE_PREFIX}${_currentModule}\"; return PyImport_AppendInittab(name, init${PYTHON_MODULE_PREFIX}${_currentModule});\n}\n\n") - ENDFOREACH(_currentModule ${PY_STATIC_MODULES_LIST}) - - FILE(APPEND ${_filenameTmp} "void ${_name}_LoadAllPythonModules(void)\n{\n") - FOREACH(_currentModule ${PY_STATIC_MODULES_LIST}) - FILE(APPEND ${_filenameTmp} " ${_name}_${_currentModule}();\n") - ENDFOREACH(_currentModule ${PY_STATIC_MODULES_LIST}) - FILE(APPEND ${_filenameTmp} "}\n\n") - FILE(APPEND ${_filenameTmp} "#ifndef EXCLUDE_LOAD_ALL_FUNCTION\nvoid CMakeLoadAllPythonModules(void)\n{\n ${_name}_LoadAllPythonModules();\n}\n#endif\n\n#endif\n") - -# with CONFIGURE_FILE() cmake complains that you may not use a file created using FILE(WRITE) as input file for CONFIGURE_FILE() - EXECUTE_PROCESS(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${_filenameTmp}" "${_filename}" OUTPUT_QUIET ERROR_QUIET) - -ENDFUNCTION(PYTHON_WRITE_MODULES_HEADER) --- a/libavogadro/src/CMakeLists.txt +++ b/libavogadro/src/CMakeLists.txt @@ -182,7 +182,7 @@ message(STATUS "Setting new boost python libraries") include_directories( ${Boost_INCLUDE_DIRS} - ${PYTHON_INCLUDE_PATH}) + ${PYTHON_INCLUDE_DIRS}) qt4_add_resources(pythontool_RC_SRCS pythontool.qrc) list(APPEND AVO_LINK_LIBRARIES ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}) list(APPEND libavogadro_HDRS --- a/libavogadro/src/python/CMakeLists.txt +++ b/libavogadro/src/python/CMakeLists.txt @@ -3,7 +3,7 @@ ${CMAKE_CURRENT_BINARY_DIR} ${OPENBABEL2_INCLUDE_DIR} ${BOOST_PYTHON_INCLUDES} - ${PYTHON_INCLUDE_PATH} + ${PYTHON_INCLUDE_DIRS} ${NUMPY_INCLUDE_DIR} ${SIP_INCLUDE_DIR} ) --- a/libavogadro/tests/CMakeLists.txt +++ b/libavogadro/tests/CMakeLists.txt @@ -16,7 +16,7 @@ ${EIGEN2_INCLUDE_DIR} ${OPENBABEL2_INCLUDE_DIR} ${BOOST_PYTHON_INCLUDES} - ${PYTHON_INCLUDE_PATH} + ${PYTHON_INCLUDE_DIRS} ) link_directories( --- a/cmake/modules/FindSIP.cmake +++ b/cmake/modules/FindSIP.cmake @@ -22,9 +22,9 @@ # search for sip.h if(SIP_INCLUDE_DIR) set(SIP_FOUND TRUE) - elseif(EXISTS ${PYTHON_INCLUDE_PATH}/sip.h) + elseif(EXISTS ${PYTHON_INCLUDE_DIR}/sip.h) # The SIP headers are often packaged in the Python include directory - set(SIP_INCLUDE_DIR ${PYTHON_INCLUDE_PATH}) + set(SIP_INCLUDE_DIR ${PYTHON_INCLUDE_DIR}) else() # Attempt to find the SIP headers in the normal system path find_path(SIP_INCLUDE_DIR NAMES sip.h debian/avogadro.examples0000664000000000000000000000001412276653176012544 0ustar testfiles/* debian/libavogadro-dev.install0000664000000000000000000000024312276653176013643 0ustar usr/features/*prf /usr/share/qt4/mkspecs/ usr/include usr/lib/*.so usr/lib/avogadro/*.cmake usr/lib/avogadro/*/*.cmake usr/lib/avogadro/*/cmake usr/lib/pkgconfig debian/python-avogadro.install0000664000000000000000000000011512276653176013715 0ustar usr/lib/python*/*-packages usr/share/libavogadro/engineScripts/wireframe.py debian/control0000664000000000000000000001203512276653176010613 0ustar Source: avogadro Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debichem Team Uploaders: Michael Banck Build-Depends: cmake (>> 2.6.0), debhelper (>> 7.0.50~), libboost-python-dev, libeigen2-dev (>> 2.0~beta6), libgl2ps-dev, libglew-dev, libopenbabel-dev (>> 2.2.0), libqt4-dev (>> 4.5.0), libqt4-opengl-dev, pkg-config, python (>> 2.6.6-3~), python-dev, python-numpy (>> 1:1.4.1-4~), python-sip-dev, qt4-dev-tools, zlib1g-dev Standards-Version: 3.9.4 X-Python-Version: current Homepage: http://avogadro.sourceforge.net/ Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/experimental/avogadro/ Vcs-Svn: svn://anonscm.debian.org/debichem/experimental/avogadro/ Package: avogadro Architecture: any Depends: libavogadro1 (= ${binary:Version}), ${misc:Depends}, ${shlibs:Depends} Recommends: avogadro-data (>= 1.0.0-2) Description: Molecular Graphics and Modelling System Avogadro 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. . 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} Breaks: 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 targeted 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: ${misc:Depends}, ${shlibs:Depends} Recommends: avogadro-data (>= 1.0.0-2), python-avogadro Description: Molecular Graphics and Modelling System (library) Avogadro is a molecular graphics and modelling system targeted 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: libavogadro1 (= ${binary:Version}), libeigen2-dev (>= 2.0~beta6), libglew-dev, libopenbabel-dev (>= 2.2.0), libqt4-dev (>= 4.4.0), libpython2.7-dev, libboost-python-dev, ${misc:Depends} Description: Molecular Graphics and Modelling System (development files) Avogadro is a molecular graphics and modelling system targeted 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 XB-Python-Version: ${python:Versions} Depends: python-numpy, python-qt4, python-sip, ${misc:Depends}, ${python:Depends}, ${shlibs:Depends}, ${sip:Depends} Replaces: libavogadro0 (<< 0.9.8) Breaks: libavogadro0 (<< 0.9.8) Provides: ${python:Provides} Description: Molecular Graphics and Modelling System (Python module) Avogadro is a molecular graphics and modelling system targeted 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. Package: avogadro-dbg Architecture: any Section: debug Priority: extra Depends: avogadro (= ${binary:Version}), libavogadro1 (= ${binary:Version}), ${misc:Depends} Description: Molecular Graphics and Modelling System (debugging symbols) Avogadro is a molecular graphics and modelling system targeted 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 debugging symbols for the library, the application and modules. debian/upstream0000664000000000000000000000153512276653176010776 0ustar Name: Avogadro Homepage: http://avogadro.openmolecules.net Bug-Database: http://sourceforge.net/tracker/?atid=835077&group_id=165310&func=browse Reference: - Author: Marcus D Hanwell and Donald E Curtis and David C Lonie and Tim Vandermeersch and Eva Zurek and Geoffrey R Hutchison Title: "Avogadro: An advanced semantic chemical editor, visualization, and analysis platform" Journal: J. Cheminf. Year: 2012 Volume: 4 Pages: 17 DOI: 10.1186/1758-2946-4-17 URL: http://www.jcheminf.com/content/4/1/17 Cite-As: "Avogadro: an open-source molecular builder and visualization tool. Version 1.XX. http://avogadro.openmolecules.net/" Contact: avogadro-devel@lists.sourceforge.net Repository: git://github.com/cryos/avogadro.git Repository-Browse: https://github.com/cryos/avogadro/ Screenshots: http://avogadro.openmolecules.net/wiki/Screencasts debian/copyright0000664000000000000000000002003212276653176011137 0ustar This package was debianized by Jordan Mantha 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 . Copyright (C) 2007 Will Stephenson . cmake/modules/FindEigen2.cmake: Copyright (C) 2006, 2007 Montel Laurent . cmake/modules/FindOpenBabel2.cmake Copyright (C) 2006, 2007 Carsten Niehaus . Copyright (C) 2008 Marcus D. Hanwell . debian/*: Copyright (C) 2007 Jordan Mantha . Copyright (C) 2008,2009 debichem team 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 provided that the following conditions are met: 1. Redistributions of source code must retain the copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``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 AUTHOR 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. testfiles/*: Some files in the testfiles directory include license and use restriction hints and copyright notices of some commercial and non-disclosure software. To our understanding (see http://bugs.debian.org/643921) these texts refer to the non-free software programs (like Gaussian) that produced this output but not to the file format nor any output file. ============================================================================== The Debian packaging is Copyright (C) 2007-2009 Jordan Mantha and Copyright (C) 2007-2013 Debichem Team and is licensed under the GPL, see above. debian/changelog0000664000000000000000000006023612313267377011064 0ustar avogadro (1.1.1-0ubuntu2) trusty; urgency=medium * No-change rebuild against sip 4.15.5. -- Dmitry Shachnev Sat, 22 Mar 2014 15:07:23 +0400 avogadro (1.1.1-0ubuntu1) trusty; urgency=medium * New upstream release -- Jonathan Riddell Wed, 12 Feb 2014 11:10:29 +0000 avogadro (1.1.0-4ubuntu2) trusty; urgency=medium * No change rebuild against glew 1.10. -- Dimitri John Ledkov Thu, 02 Jan 2014 13:20:09 +0000 avogadro (1.1.0-4ubuntu1) trusty; urgency=low * Merge from debian, remaining changes - Add libpython2.7-dev libboost-python-dev to libavogadro-dev -- Rohan Garg Thu, 28 Nov 2013 17:50:48 +0100 avogadro (1.1.0-4) experimental; urgency=low [ Daniel Leidert ] * debian/rules (override_dh_auto_configure): Drop setting of -DPYTHON_INCLUDE_DIRS and fix the FTBFS too (really closes: #710703). * debian/patches/use_python_include_dirs.patch: Reverted to 1.1.0-2. * debian/patches/series: Don't use the use_python_include_dirs.patch patch. -- Debichem Team Sun, 02 Jun 2013 21:39:03 +0200 avogadro (1.1.0-3) experimental; urgency=low [ Daniel Leidert ] * debian/control (Vcs-Browser, Vcs-Svn): Fixed vcs-field-not-canonical. * debian/rules: Try to fix an FTBFS if several Python versions are installed (closes: Bug#710703) and don't FTBFS if there is no multi-arch Python. -- Debichem Team Sat, 01 Jun 2013 23:50:49 +0200 avogadro (1.1.0-2) experimental; urgency=low [ Daniel Leidert ] * debian/rules (CPPFLAGS, LDFLAGS): Added -fPIC to fix FTBFS. * debian/patches/use_python_include_dirs.patch: Minor fix to FindSIP.cmake to fix FTBFS. -- Debichem Team Thu, 30 May 2013 00:09:24 +0200 avogadro (1.1.0-1) experimental; urgency=low * New upstream release (LP: #1155529). [ Daniel Leidert ] * debian/avogadro-data.install: Added crystals directory. * debian/control: Added a package for debugging symbols. (Vcs-Browser, Vcs-Svn): Fixed location. * debian/libavogadro-dev.install: Added pkg-config file. * debian/rules: Enable debug package and remove python specific stuff. * debian/watch: Catch experimental releases. * debian/patches/hurd_ftbfs.patch: Removed (not applicable). * debian/patches/nwchem_input_ccsd.patch: Dropped (applied upstream). * debian/patches/boost148.patch: Updated. * debian/patches/link_to_libgl2ps.patch: Updated. * debian/patches/use_python_include_dirs.diff: Renamed to debian/patches/use_python_include_dirs.patch, updated and enabled. * debian/patches/series: Updated. -- Debichem Team Mon, 13 May 2013 23:06:32 +0200 avogadro (1.0.3-6) unstable; urgency=low [ Daniel Leidert ] * debian/control: Dropped DM-Upload-Allowed field. (Uploaders): Removed myself. (Standards-Version): Bumped to 3.9.4. (Depends): Added non-versioned dependencies to python-numpy, python-qt4 and python-sip (see #679819). * debian/copyright: Added a hint about the text found in some files in the testfile directory (closes: #643921). * debian/rules: Removed code to generate versioned dependencies to python-numpy, python-qt4 and python-sip. Enable hardening. * debian/watch: Minor update to catch bzip2 compressed tarballs and ignore experimental releases. * debian/patches/use_python_include_dirs.diff: Added based on the patch by Ubuntu. [ Michael Banck ] * debian/upstream: Added reference. -- Debichem Team Sun, 12 May 2013 21:30:52 +0200 avogadro (1.0.3-5ubuntu10) trusty; urgency=low * No change rebuild for Boost 1.54 transition. -- Dmitrijs Ledkovs Tue, 22 Oct 2013 18:08:37 +0100 avogadro (1.0.3-5ubuntu9) saucy; urgency=low * Do the same with libboost-python-dev -- Philip Muškovac Sat, 17 Aug 2013 16:57:02 +0200 avogadro (1.0.3-5ubuntu8) saucy; urgency=low * Add dependency on libpython2.7-dev to libavogadro-dev as cmake expects it to be there -- Philip Muškovac Sat, 17 Aug 2013 15:35:14 +0200 avogadro (1.0.3-5ubuntu7) saucy; urgency=low * Make avogadro look for python-py27 boost library, fixing FTBFS. * Force using python2.7 via Python_ADDITIONAL_VERSIONS -- Dmitrijs Ledkovs Fri, 09 Aug 2013 13:13:44 +0100 avogadro (1.0.3-5ubuntu6) saucy; urgency=low * Rebuild against sip-api-10 -- Scott Kitterman Thu, 20 Jun 2013 11:16:36 -0400 avogadro (1.0.3-5ubuntu5) saucy; urgency=low * No change rebuild for Boost 1.53 transition. -- Dmitrijs Ledkovs Fri, 26 Apr 2013 19:18:39 +0100 avogadro (1.0.3-5ubuntu4) raring; urgency=low * Add support for multiarch python: - add use_python_include_dirs.diff to use PYTHON_INCLUDE_DIRS instead of PYTHON_INCLUDE_PATH and drop shipped FindPythonLibs.cmake in favour of the system one. - don't specify the python library and include path by hand in rules -- Philip Muškovac Thu, 20 Dec 2012 10:07:35 +0100 avogadro (1.0.3-5ubuntu3) raring; urgency=low * Rebuild against sip-api-9.0. -- Colin Watson Wed, 07 Nov 2012 09:29:53 +0000 avogadro (1.0.3-5ubuntu2) quantal; urgency=low * No change rebuild with the new glew -- Sebastien Bacher Fri, 10 Aug 2012 17:29:15 +0200 avogadro (1.0.3-5ubuntu1) quantal; urgency=low * Apply patch from Debian bug #679819: Drop semi-obsolete use of version specify python packages to restore installability (python-qt4 stopped providing one of the required packages). -- Stéphane Graber Wed, 04 Jul 2012 16:21:22 -0400 avogadro (1.0.3-5) unstable; urgency=low * debian/control (Uploaders): Removed Jordan Mantha. Thanks for your work. (Build-Depends): Use libglew-dev. (Depends): Let libavogadro-dev depend on libglew-dev. -- Daniel Leidert (dale) Wed, 06 Jun 2012 22:54:58 +0200 avogadro (1.0.3-4) unstable; urgency=low [ Michael Banck ] * Acknowledge NMU. * debian/patches/hurd_ftbfs.patch: New patch, fixing build on hurd-i386, thanks to Pino Toscano. [ Daniel Leidert ] * debian/control (Standards-Version): Bumped to 3.9.3. (Build-Depends): Added versioned dependency on python-numpy. * debian/rules (override_dh_python2): Added call to dh_numpy to fix lintian error. * debian/upstream: Added. -- Daniel Leidert (dale) Mon, 04 Jun 2012 21:55:51 +0200 avogadro (1.0.3-3.1) unstable; urgency=low * Non-Maintainer Upload. * patches/boost148.patch: New. Work around moc limitation. Closes: #653625. -- Steve M. Robbins Sat, 28 Jan 2012 05:36:13 -0600 avogadro (1.0.3-3) unstable; urgency=low * debian/control (Build-Depends): Added libgl2ps-dev. * debian/patches/link_to_libgl2ps.patch: Added. - Link with -lgl2ps instead of compiling and linking the internal copy. * debian/patches/series: Adjusted. -- Daniel Leidert (dale) Mon, 05 Dec 2011 22:20:31 +0100 avogadro (1.0.3-2) unstable; urgency=low [ Michael Banck ] * debian/copyright: Explicitly state the 3-clause BSD license for the cmake module files. * debian/rules, debian/control: Convert to dh_python2, thanks to Barry Warsaw (Closes: #616742) * debian/patches/nwchem_input_ccsd.patch: New patch, fixes NWChem input extension input file generation for the CCSD method. [ Daniel Leidert ] * debian/avogadro.install: Install missing avopkg tool. * debian/compat: Increased dh compatibility level. * debian/control: Set X-Python-Version to 'current'. Use wrap-and-sort for *Depends* and Uploaders. (Build-Depends): Removed cdbs and patchutils. Increased required debhelper version. (Standards-Version): Bumped to 3.9.2. (Vcs-Browser): Point to real location. (Description): Fixed a typo reported by lintian. (Conflicts): Changed conflicts-with-version warning into Breaks. * debian/copyright: Minor update. * debian/pycompat: Dropped obsolete file. * debian/rules: Rewritten for debhelper 7. * debian/patches/nwchem_input_ccsd.patch: Added patch documentation. * debian/patches/series: Added. -- Daniel Leidert (dale) Sun, 04 Dec 2011 23:59:34 +0100 avogadro (1.0.3-1) unstable; urgency=low * New upstream release. * debian/patches/install_translations.patch: Removed, applied upstream. * debian/source/format: New file, switching to 3.0/quilt. -- Michael Banck Mon, 25 Apr 2011 19:26:20 +0200 avogadro (1.0.2-1) unstable; urgency=low * New upstream release. + Fixes crash on Undo after erasing of any atom with attached Hs (Closes: #602388). * debian/avogadro.install: Explicitly install /usr/bin/avogadro, avoiding avopkg. * debian/libavogadro-dev.install: Move avogadro.prf from /usr/features to /usr/share/qt4/mkspecs. * debian/patches/install_translations.patch: New file, fix installation of translations, taken from upstream. * debian/control (Build-Depends): Removed sip4. * debian/control (Standards-Version): Bumped to 3.9.1. -- Michael Banck Sun, 24 Apr 2011 01:00:16 +0200 avogadro (1.0.1-3) unstable; urgency=low [ Daniel Leidert ] * debian/avogadro.install: Install manual pages from upstream. * debian/avogadro.manpages, debian/avogadro.1: Dropped in favour of upstream manual pages. * debian/libavogadro-dev.install: Install .prf file for QMake projects. [ Michael Banck ] * debian/rules (DEB_DH_GENCONTROL_ARGS_python-avogadro): Replace python$(PYVER)-sip4 by python$(PYVER)-sip (Closes: #581972). * debian/rules (binary-install/python-avogadro): Added dh_sip. * debian/control (python-avogadro/Depends): Added ${sip:Depends}. * debian/control (Build-Depends): Replaced python-sip4-dev by python-sip-dev. -- Michael Banck Wed, 19 May 2010 18:35:43 +0200 avogadro (1.0.1-2) unstable; urgency=low * debian/rules (DEB_CMAKE_EXTRA_FLAGS): Define PYTHON_EXECUTABLE, PYTHON_LIBRARY and PYTHON_INCLUDE_DIR in order to make sure the correct version of python is used in case several are co-installed, thanks to Jakub Wilk (Closes: #577439). -- Michael Banck Fri, 07 May 2010 15:05:07 +0200 avogadro (1.0.1-1) unstable; urgency=low * New upstream release. + Fixes crash when importing PDB files via network (Closes: #570230). * debian/patches/sip_4.10_support.patch: Removed, applied upstream. * debian/control (Build-Depends): Bump required libqt4-dev version to 4.5.0, as per CMakeLists.txt. -- Michael Banck Wed, 05 May 2010 17:57:59 +0200 avogadro (1.0.0-3) unstable; urgency=low [ Jordan Mantha ] * debian/python-avogadro.install: use wildcard to catch both site-packages and dist-packages python directories. [ Michael Banck ] * debian/patches/sip_4.10_support.patch: New patch, recognize new SIP version, taken from upstream (closes: #569438). -- Michael Banck Sat, 20 Feb 2010 23:33:54 +0100 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 explicitly 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 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 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 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 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 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 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 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 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) 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 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 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 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 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) 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 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 ${misc:Depends} to libavogadro0 and libavogadro-dev - s/python/Python/ in long description - added manpage, avogadro.1 -- Jordan Mantha Thu, 22 Jan 2009 10:43:40 -0800 avogadro (0.8.1-5) unstable; urgency=low * add patches/11_ExportGraphics.patch fixes graphics export, by Tim Vandermeersch (Closes: #507046) * debian/control: Updated descriptions * debian/control: Added VCS-* links. -- Michael Banck Mon, 01 Dec 2008 01:42:41 +0100 avogadro (0.8.1-4) unstable; urgency=low * Upload to unstable * debian/control: Bump cmake build dependency to 2.6.0 to work around bug #479907 (Closes: #488990) -- Jordan Mantha Thu, 24 Jul 2008 12:15:32 -0700 avogadro (0.8.1-3) experimental; urgency=low * debian/control: - bump standards version to 3.8.0 (no changes needed) - bump openbabel dependency to >= 2.2.0-1 -- Jordan Mantha Mon, 14 Jul 2008 21:07:23 -0700 avogadro (0.8.1-2) experimental; urgency=low * add debian/patches/10_QVarLengthArray.patch from upstream r1513. fixes Align/Measure tool crash -- Jordan Mantha Wed, 02 Jul 2008 15:18:55 -0700 avogadro (0.8.1-1) experimental; urgency=low * New upstream release * add debian/avogadro.desktop * debian/avogadro.install: - install avogadro.desktop, avogadro.png, and avogadro.xpm * add avogadro.menu * debian/control: - update minimum versions of qt (4.3.4) and cmake (2.4.7) and openbabel (2.2.0~beta6~r2551-2) - add build dependency on libboost-python-dev to enable python terminal - remove unneeded python-dev build dependency - add build dependency on patchutils for simple-patchsys - add python-qt4 depdency for python console garbage collection - strict dependency on libavogadro0 for avogadro (${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 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 Fri, 23 May 2008 18:49:09 -0700 avogadro (0.6.1-1) experimental; urgency=low * New upstream release -- Jordan Mantha Sun, 09 Mar 2008 06:16:09 +0000 avogadro (0.6.0-1) experimental; urgency=low * Initial release. (Closes: #450814) -- Jordan Mantha Mon, 03 Mar 2008 14:44:29 -0800 debian/avogadro.install0000664000000000000000000000020512276653176012376 0ustar usr/bin usr/share/applications usr/share/avogadro/i18n usr/share/man usr/share/pixmaps ../../debian/avogadro.xpm usr/share/pixmaps/ debian/rules0000775000000000000000000000232712276653176010273 0ustar #!/usr/bin/make -f #export DH_VERBOSE=1 export CPPFLAGS := $(shell dpkg-buildflags --get CPPFLAGS) -fPIC export CFLAGS := $(CPPFLAGS) $(shell dpkg-buildflags --get CFLAGS) export CXXFLAGS := $(CPPFLAGS) $(shell dpkg-buildflags --get CXXFLAGS) export LDFLAGS := -fPIC $(shell dpkg-buildflags --get LDFLAGS) -Wl,-z,defs -Wl,--as-needed DEB_HOST_MULTIARCH := $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) PYTHON_VERSION := $(shell pyversions -dv) ifneq ($(wildcard /usr/lib/$(DEB_HOST_MULTIARCH)/libpython$(PYTHON_VERSION).so),) PYTHON_LIBRARY=/usr/lib/$(DEB_HOST_MULTIARCH)/libpython$(PYTHON_VERSION).so else PYTHON_LIBRARY=/usr/lib/libpython$(PYTHON_VERSION).so endif %: dh $@ --with python2 --parallel override_dh_auto_configure: dh_auto_configure -- \ -DENABLE_GLSL=ON \ -DENABLE_RPATH=OFF \ -DENABLE_UPDATE_CHECKER=OFF \ -DPYTHON_EXECUTABLE=/usr/bin/python$(PYTHON_VERSION) \ -DPYTHON_LIBRARY=$(PYTHON_LIBRARY) \ -DPYTHON_INCLUDE_DIR=/usr/include/python$(PYTHON_VERSION)/ override_dh_install: dh_install --list-missing override_dh_clean: dh_clean conf.log conf.pri override_dh_python2: dh_python2 -ppython-avogadro dh_numpy -ppython-avogadro dh_sip override_dh_strip: dh_strip --dbg-package=avogadro-dbg debian/libavogadro1.install0000664000000000000000000000017312276653176013152 0ustar usr/lib/*.so.* usr/lib/avogadro/*/colors usr/lib/avogadro/*/engines usr/lib/avogadro/*/extensions usr/lib/avogadro/*/tools debian/source/0000775000000000000000000000000012276653176010507 5ustar debian/source/format0000664000000000000000000000001412276653176011715 0ustar 3.0 (quilt) debian/avogadro.menu0000664000000000000000000000033612276653176011701 0ustar ?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" debian/avogadro.xpm0000664000000000000000000001237012276653176011542 0ustar /* 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", "! 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