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Daniel Lütgehetmann
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First public version.
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‎.clang-format

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BasedOnStyle: LLVM
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IndentWidth: 4
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TabWidth: 4
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ColumnLimit: 120
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AccessModifierOffset: -4
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AllowShortIfStatementsOnASingleLine: true
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AllowShortLoopsOnASingleLine: true
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AllowShortBlocksOnASingleLine: true
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AllowShortFunctionsOnASingleLine: true
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DerivePointerAlignment: false
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PointerAlignment: Left
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UseTab: ForIndentation

‎.gitignore

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DerivedData
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ripser
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ripser-coeff
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er
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flagser
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flagser-debug
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flagser-memory
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flagser-count
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flagser-coefficients
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flagser-coefficients-memory
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pathhom
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pathhom-count
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*.dSYM
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*.flag
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*.homology
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*.h5
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*.png
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*.mat
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test/tmp
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include/algorithms.h
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*.vscode
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.install-consent
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.cache
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build/

‎CMakeLists.txt

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cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
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project(flagser)
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enable_language(CXX)
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set(CMAKE_CXX_STANDARD 14)
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set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated-declarations -Ofast -D NDEBUG")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_POSITION_INDEPENDANT}")
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find_package(HDF5)
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IF(HDF5_FOUND)
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include_directories(${HDF5_INCLUDE_DIR})
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DWITH_HDF5")
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ENDIF()
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FIND_PACKAGE(OpenMP)
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IF(OPENMP_FOUND)
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set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
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set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS} -DOPENMP_SUPPORT")
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ENDIF()
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# Also add the time of the file + output file into consideration
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# Add the include dir to the watch list
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add_custom_command(
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COMMAND ../build_custom_algorithms.sh
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DEPENDS parser/math_parser.py algorithms.math
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OUTPUT include/algorithms.h
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COMMENT "Check for custom algorithms"
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)
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add_custom_target(generate_custom_algorithms DEPENDS include/algorithms.h)
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add_executable(flagser src/flagser.cpp include/algorithms.h)
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add_dependencies(flagser generate_custom_algorithms)
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add_executable(flagser-coefficients src/flagser.cpp)
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add_dependencies(flagser-coefficients generate_custom_algorithms)
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target_compile_definitions(flagser-coefficients PRIVATE USE_COEFFICIENTS=1)
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add_executable(flagser-memory src/flagser.cpp include/algorithms.h)
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target_compile_definitions(flagser-memory PRIVATE KEEP_FLAG_COMPLEX_IN_MEMORY=1)
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add_dependencies(flagser-memory generate_custom_algorithms)
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add_executable(flagser-coefficients-memory src/flagser.cpp include/algorithms.h)
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target_compile_definitions(flagser-coefficients-memory PRIVATE USE_COEFFICIENTS=1 KEEP_FLAG_COMPLEX_IN_MEMORY=1)
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add_dependencies(flagser-coefficients-memory generate_custom_algorithms)
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add_executable(flagser-count src/flagser-count.cpp)
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add_executable(er src/er.cpp)
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message("")
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message("** CMAKE_CXX_FLAGS: \t\t\t${CMAKE_CXX_FLAGS}")
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message("** CMAKE_CXX_LINK_FLAGS: \t\t${CMAKE_CXX_LINK_FLAGS}")
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message("")
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TARGET_LINK_LIBRARIES(flagser ${HDF5_LIBRARIES})
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TARGET_LINK_LIBRARIES(flagser-coefficients ${HDF5_LIBRARIES})
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TARGET_LINK_LIBRARIES(flagser-memory ${HDF5_LIBRARIES})
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TARGET_LINK_LIBRARIES(flagser-coefficients-memory ${HDF5_LIBRARIES})
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TARGET_LINK_LIBRARIES(flagser-count ${HDF5_LIBRARIES})
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TARGET_LINK_LIBRARIES(er ${HDF5_LIBRARIES})
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install(TARGETS flagser flagser-coefficients flagser-memory flagser-coefficients-memory flagser-count RUNTIME DESTINATION bin)
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add_custom_command(
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TARGET flagser POST_BUILD
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COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/flagser ${CMAKE_SOURCE_DIR})
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add_custom_command(
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TARGET flagser-coefficients POST_BUILD
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COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/flagser-coefficients ${CMAKE_SOURCE_DIR})
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add_custom_command(
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TARGET flagser-memory POST_BUILD
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COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/flagser-memory ${CMAKE_SOURCE_DIR})
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add_custom_command(
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TARGET flagser-coefficients-memory POST_BUILD
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COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/flagser-coefficients-memory ${CMAKE_SOURCE_DIR})
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add_custom_command(
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TARGET flagser-count POST_BUILD
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COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/flagser-count ${CMAKE_SOURCE_DIR})
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add_custom_command(
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TARGET er POST_BUILD
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COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/er ${CMAKE_SOURCE_DIR}/tools)

‎COPYING.LESSER.txt

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GNU LESSER GENERAL PUBLIC LICENSE
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Version 3, 29 June 2007
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Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
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Everyone is permitted to copy and distribute verbatim copies
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of this license document, but changing it is not allowed.
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This version of the GNU Lesser General Public License incorporates
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the terms and conditions of version 3 of the GNU General Public
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License, supplemented by the additional permissions listed below.
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0. Additional Definitions.
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As used herein, "this License" refers to version 3 of the GNU Lesser
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General Public License, and the "GNU GPL" refers to version 3 of the GNU
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General Public License.
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"The Library" refers to a covered work governed by this License,
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other than an Application or a Combined Work as defined below.
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An "Application" is any work that makes use of an interface provided
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by the Library, but which is not otherwise based on the Library.
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Defining a subclass of a class defined by the Library is deemed a mode
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of using an interface provided by the Library.
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A "Combined Work" is a work produced by combining or linking an
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Application with the Library. The particular version of the Library
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with which the Combined Work was made is also called the "Linked
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Version".
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The "Minimal Corresponding Source" for a Combined Work means the
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Corresponding Source for the Combined Work, excluding any source code
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for portions of the Combined Work that, considered in isolation, are
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based on the Application, and not on the Linked Version.
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The "Corresponding Application Code" for a Combined Work means the
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object code and/or source code for the Application, including any data
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and utility programs needed for reproducing the Combined Work from the
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Application, but excluding the System Libraries of the Combined Work.
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1. Exception to Section 3 of the GNU GPL.
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You may convey a covered work under sections 3 and 4 of this License
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without being bound by section 3 of the GNU GPL.
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2. Conveying Modified Versions.
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If you modify a copy of the Library, and, in your modifications, a
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facility refers to a function or data to be supplied by an Application
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that uses the facility (other than as an argument passed when the
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facility is invoked), then you may convey a copy of the modified
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version:
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a) under this License, provided that you make a good faith effort to
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ensure that, in the event an Application does not supply the
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function or data, the facility still operates, and performs
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whatever part of its purpose remains meaningful, or
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b) under the GNU GPL, with none of the additional permissions of
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this License applicable to that copy.
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3. Object Code Incorporating Material from Library Header Files.
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The object code form of an Application may incorporate material from
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a header file that is part of the Library. You may convey such object
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code under terms of your choice, provided that, if the incorporated
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material is not limited to numerical parameters, data structure
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layouts and accessors, or small macros, inline functions and templates
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Library is used in it and that the Library and its use are
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b) Accompany the object code with a copy of the GNU GPL and this license
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document.
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4. Combined Works.
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You may convey a Combined Work under terms of your choice that,
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taken together, effectively do not restrict modification of the
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portions of the Library contained in the Combined Work and reverse
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engineering for debugging such modifications, if you also do each of
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a) Give prominent notice with each copy of the Combined Work that
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the Library is used in it and that the Library and its use are
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covered by this License.
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b) Accompany the Combined Work with a copy of the GNU GPL and this license
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c) For a Combined Work that displays copyright notices during
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copies of the GNU GPL and this license document.
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d) Do one of the following:
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0) Convey the Minimal Corresponding Source under the terms of this
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License, and the Corresponding Application Code in a form
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suitable for, and under terms that permit, the user to
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recombine or relink the Application with a modified version of
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the Linked Version to produce a modified Combined Work, in the
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manner specified by section 6 of the GNU GPL for conveying
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Corresponding Source.
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1) Use a suitable shared library mechanism for linking with the
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a copy of the Library already present on the user's computer
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of the Library that is interface-compatible with the Linked
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Version.
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e) Provide Installation Information, but only if you would otherwise
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be required to provide such information under section 6 of the
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GNU GPL, and only to the extent that such information is
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necessary to install and execute a modified version of the
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Combined Work produced by recombining or relinking the
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Application with a modified version of the Linked Version. (If
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you use option 4d0, the Installation Information must accompany
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the Minimal Corresponding Source and Corresponding Application
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Information in the manner specified by section 6 of the GNU GPL
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5. Combined Libraries.
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You may place library facilities that are a work based on the
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Library side by side in a single library together with other library
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facilities that are not Applications and are not covered by this
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License, and convey such a combined library under terms of your
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choice, if you do both of the following:
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a) Accompany the combined library with a copy of the same work based
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on the Library, uncombined with any other library facilities,
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conveyed under the terms of this License.
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b) Give prominent notice with the combined library that part of it
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is a work based on the Library, and explaining where to find the
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accompanying uncombined form of the same work.
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6. Revised Versions of the GNU Lesser General Public License.
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The Free Software Foundation may publish revised and/or new versions
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of the GNU Lesser General Public License from time to time. Such new
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versions will be similar in spirit to the present version, but may
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differ in detail to address new problems or concerns.
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applies to it, you have the option of following the terms and
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