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ulupoammedmarammedmarreds-heiggtauzin
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Create giotto-tda v0.2.2 (#414)
* Fix issue with docstring example and document reshaping of 1D outputs (#396) * Toc (#394) * Update P landscapes Signed-off-by: ammedmar <[email protected]> * Add distances, inner products and kernels glossary entry Signed-off-by: ammedmar <[email protected]> * Remake vectorization changes Signed-off-by: ammedmar <[email protected]> * Change [] for \lbrack \rbrack Signed-off-by: ammedmar <[email protected]> * Update after W's comments Signed-off-by: ammedmar <[email protected]> * Update after W's comments Signed-off-by: ammedmar <[email protected]> * Update afte W's second comments Signed-off-by: ammedmar <[email protected]> * Update after Umbe's comments Signed-off-by: ammedmar <[email protected]> * Update after Umbe's second comments Signed-off-by: ammedmar <[email protected]> * Update after Umbe's third comments Signed-off-by: ammedmar <[email protected]> * Update after Umbe's 4th comments Signed-off-by: ammedmar <[email protected]> * Remove concept k-skeleton Signed-off-by: ammedmar <[email protected]> * Add table of content Signed-off-by: ammedmar <[email protected]> * Add Lp & lp. Update landscape Signed-off-by: ammedmar <[email protected]> * Update TOC indentation Signed-off-by: ammedmar <[email protected]> * Add heat vectorizations entry Signed-off-by: ammedmar <[email protected]> * Update indentation of TOC Signed-off-by: ammedmar <[email protected]> * Fix extra spacing in bibliography Signed-off-by: ammedmar <[email protected]> * Update bibliography hack for caps Signed-off-by: ammedmar <[email protected]> * After Umbe's Comments Signed-off-by: ammedmar <[email protected]> * Update after issue #398 Signed-off-by: ammedmar <[email protected]> * Update after Umbe's comments Signed-off-by: ammedmar <[email protected]> * Update after Umbe's 2nd comments Signed-off-by: ammedmar <[email protected]> Co-authored-by: ammedmar <[email protected]> * Speedup windows pipeline (#402) * Improve boost location for azure pipeline on windows The boost version installed in the pipeline is now used Signed-off-by: julian <[email protected]> Co-authored-by: Umberto Lupo <[email protected]> * Make bindings public (#395) * Make bindings public Signed-off-by: Guillaume Tauzin <[email protected]> * Fix pipeline on Mac (#407) * Refresh ccache * Enforce CXX standard to 14 on each module * Change variable name to comply with E741 Signed-off-by: julian <[email protected]> Co-authored-by: Umberto Lupo <[email protected]> * Mapper visualisation refactor: fix bugs, add summary statistics in hovertext, improve opacity, remove matplotlib dependency, add node_scale kwarg, add clone_pipeline kwarg to interactive plots,restructure/rename plotly_kwargs, improve code (#406) * Refactor of `mapper/visualisation.py` and `mapper/utils/visualisation.py` - Removal of color scaling - More modularity - Variable and function name changes - Remove matplotlib functions used for hoverlabel background color - Remove cmin and cmax - Change return signature of some functions * Add test-output.xml to .gitignore * Replace "text" key in plot_options["node_trace"] with "hovertext" * Improve width and opacity of nodes and edges * Display summary statistics in hovertext with significant figure rounding via new n_sig_figs kwarg * Rename plotly_kwargs to plotly_params * Remove matplotlib installation requirement * Fix mapper notebook * Add small comment on use of matplotlib in voids_on_the_plane * Place matplotlib in examples requirement in setup.py * Improve docstring of make_mapper_pipeline * Improve examples for make_mapper_pipeline and create one for plot_static_mapper_graph * Hide set_node_sizeref, add node_scale kwarg, add clone_pipeline kwarg to plot_interactive_mapper_graph - Update docstrings - Update quickstart notebook * Add helper function for colorscale-based interpolations, improve use of plotly_params Static and interactive plots display the expect hoverlabel colors in 3D, or white if things go wrong. Thanks to @lewtun for pointing out that this was needed. * Improve docstrings * Hide visualization module in mapper/utils * Add pip install matplotlib to notebook tests in manylinux job (#410) * Fix mapper docstring issues following #406 (#411) * Fix issues with mapper docs following #406 * Create giotto-tda version 0.2.2 (#413) * Turn CODE_OWNERS and CODE_AUTHORS into an rst file * Bump version number to 0.2.2 * Add release notes for v0.2.2 Co-authored-by: Anibal M. Medina-Mardones <[email protected]> Co-authored-by: ammedmar <[email protected]> Co-authored-by: REDS institute <[email protected]> Co-authored-by: Guillaume Tauzin <[email protected]>
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‎.azure-ci/install_boost.py

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‎.gitignore

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.pytest_cache/
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.hypothesis/
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# Pytest output files
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test-output.xml
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# Latex
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*.aux
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*.bbl
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*.log
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*.pdf
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*.synctex.gz
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*.toc
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doc/theory/glossary_backup
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# development
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tda/mapper/scratch/

‎CMakeLists.txt

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#######################################################################
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pybind11_add_module(gtda_ripser "${BINDINGS_DIR}/ripser_bindings.cpp")
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set_property(TARGET gtda_ripser PROPERTY CXX_STANDARD 14)
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if(OpenMP_FOUND)
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target_link_libraries(gtda_ripser PRIVATE OpenMP::OpenMP_CXX)
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endif()
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target_compile_definitions(gtda_ripser PRIVATE ASSEMBLE_REDUCTION_MATRIX=1)
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target_compile_definitions(gtda_ripser PRIVATE ASSEMBLE_REDUCTION_MATRIX=1)
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target_include_directories(gtda_ripser PRIVATE "${RIPSER_SRC_DIR}/ripser")
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if(MSVC)
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#######################################################################
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pybind11_add_module(gtda_ripser_coeff "${BINDINGS_DIR}/ripser_bindings.cpp")
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set_property(TARGET gtda_ripser_coeff PROPERTY CXX_STANDARD 14)
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if(OpenMP_FOUND)
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target_link_libraries(gtda_ripser_coeff PRIVATE OpenMP::OpenMP_CXX)
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endif()
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target_compile_definitions(gtda_ripser_coeff PRIVATE USE_COEFFICIENTS=1 ASSEMBLE_REDUCTION_MATRIX=1)
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target_compile_definitions(gtda_ripser_coeff PRIVATE USE_COEFFICIENTS=1 ASSEMBLE_REDUCTION_MATRIX=1)
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target_include_directories(gtda_ripser_coeff PRIVATE "${RIPSER_SRC_DIR}/ripser")
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if(MSVC)
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#######################################################################
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pybind11_add_module(gtda_wasserstein ${BINDINGS_DIR}/wasserstein_bindings.cpp)
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set_property(TARGET gtda_wasserstein PROPERTY CXX_STANDARD 14)
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target_link_libraries(gtda_wasserstein LINK_PUBLIC ${Boost_LIBRARIES})
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target_compile_definitions(gtda_wasserstein PRIVATE BOOST_RESULT_OF_USE_DECLTYPE=1 BOOST_ALL_NO_LIB=1 BOOST_SYSTEM_NO_DEPRECATED=1)
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#######################################################################
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pybind11_add_module(gtda_bottleneck "${BINDINGS_DIR}/bottleneck_bindings.cpp")
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set_property(TARGET gtda_bottleneck PROPERTY CXX_STANDARD 14)
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target_link_libraries(gtda_bottleneck LINK_PUBLIC ${Boost_LIBRARIES})
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target_compile_definitions(gtda_bottleneck PRIVATE BOOST_RESULT_OF_USE_DECLTYPE=1 BOOST_ALL_NO_LIB=1 BOOST_SYSTEM_NO_DEPRECATED=1)
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#######################################################################
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pybind11_add_module(gtda_cubical_complex "${BINDINGS_DIR}/cubical_complex_bindings.cpp")
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set_property(TARGET gtda_cubical_complex PROPERTY CXX_STANDARD 14)
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if(OpenMP_FOUND)
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target_link_libraries(gtda_cubical_complex PRIVATE OpenMP::OpenMP_CXX)
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#######################################################################
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pybind11_add_module(gtda_persistent_cohomology "${BINDINGS_DIR}/persistent_cohomology_bindings.cpp")
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set_property(TARGET gtda_persistent_cohomology PROPERTY CXX_STANDARD 14)
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if(OpenMP_FOUND)
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target_link_libraries(gtda_persistent_cohomology PRIVATE OpenMP::OpenMP_CXX)
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pybind11_add_module(gtda_simplex_tree "${BINDINGS_DIR}/simplex_tree_bindings.cpp")
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set_property(TARGET gtda_simplex_tree PROPERTY CXX_STANDARD 14)
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if(OpenMP_FOUND)
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target_link_libraries(gtda_simplex_tree PRIVATE OpenMP::OpenMP_CXX)
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pybind11_add_module(gtda_periodic_cubical_complex "${BINDINGS_DIR}/periodic_cubical_complex_bindings.cpp")
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set_property(TARGET gtda_periodic_cubical_complex PROPERTY CXX_STANDARD 14)
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target_link_libraries(gtda_periodic_cubical_complex PRIVATE OpenMP::OpenMP_CXX)
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pybind11_add_module(gtda_witness_complex "${BINDINGS_DIR}/witness_complex_bindings.cpp")
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set_property(TARGET gtda_witness_complex PROPERTY CXX_STANDARD 14)
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target_link_libraries(gtda_witness_complex PRIVATE OpenMP::OpenMP_CXX)
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pybind11_add_module(gtda_strong_witness_complex "${BINDINGS_DIR}/strong_witness_complex_bindings.cpp")
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set_property(TARGET gtda_strong_witness_complex PROPERTY CXX_STANDARD 14)
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target_link_libraries(gtda_strong_witness_complex PRIVATE OpenMP::OpenMP_CXX)
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pybind11_add_module(gtda_sparse_rips_complex "${BINDINGS_DIR}/rips_complex_bindings.cpp")
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set_property(TARGET gtda_sparse_rips_complex PROPERTY CXX_STANDARD 14)
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target_link_libraries(gtda_sparse_rips_complex PRIVATE OpenMP::OpenMP_CXX)
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pybind11_add_module(gtda_cech_complex "${BINDINGS_DIR}/cech_complex_bindings.cpp")
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set_property(TARGET gtda_cech_complex PROPERTY CXX_STANDARD 14)
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if(OpenMP_FOUND)
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target_link_libraries(gtda_cech_complex PRIVATE OpenMP::OpenMP_CXX)

‎CODE_AUTHORS

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‎CODE_AUTHORS.rst

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The following is the list of code authors of the ``giotto-tda`` python package.
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Where component authors are known, add them here.
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| Guillaume Tauzin, [email protected]
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| Umberto Lupo, [email protected]
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| Lewis Tunstall, [email protected]
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| Matteo Caorsi, [email protected]
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| Philippe Nguyen, [email protected]
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| Julian Burella Pérez, [email protected]
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| Alessio Ghiraldello, [email protected]
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| Adélie Garin, [email protected]
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| Anibal Medina-Mardones, [email protected]
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| Wojciech Reise, [email protected]
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| Roman Yurchak, [email protected]

‎CODE_OWNERS

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‎CODE_OWNERS.rst

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The following is the list of code owners of the ``giotto-tda`` Python package:
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- L2F SA
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- EPFL - Ecole Polytechnique Fédérale de Lausanne
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- REDS Institute of the Haut Ecole d'Ingénierie et Gestion du canton Vaud

‎README.rst

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- joblib (>= 0.13)
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- scikit-learn (>= 0.22.0)
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- python-igraph (>= 0.7.1.post6)
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- matplotlib (>= 3.0.3)
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- plotly (>= 4.4.1)
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- ipywidgets (>= 7.5.1)
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‎azure-pipelines.yml

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- task: Cache@2
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key: '"ccache-wheels-v2020.04.07" | $(Agent.OS) | "$(python.version)"'
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key: '"ccache-wheels-v2020.05.12" | $(Agent.OS) | "$(python.version)"'
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pip install pandas openml
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pip install pandas openml matplotlib
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key: '"ccache-v2020.04.07" | $(Agent.OS) | "$(python.version)"'
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key: '"ccache-v2020.05.12" | $(Agent.OS) | "$(python.version)"'
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# Set BOOST_ROOT_PIPELINE to the version used in the pipeline
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# See https://github.com/actions/virtual-environments/issues/687#issuecomment-616345933
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echo "##vso[task.setvariable variable=BOOST_ROOT_PIPELINE]%BOOST_ROOT_1_72_0%"
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displayName: 'Set env variable for boost version'
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‎cmake/HelperBoost.cmake

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list(APPEND BOOST_ROOT "") # Add custom path to your boost installation
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# Changes introduced in latest version of the giotto-tda Azure pipelines produce
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# compilation errors because CMake cannot find boost header files.
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# After discussing in https://github.com/actions/virtual-environments/issues/687
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# this solution is used due to custom paths in the Azure setup.
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message(STATUS "BOOST_ROOT_PIPELINE: $ENV{BOOST_ROOT_PIPELINE}")
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if(DEFINED ENV{BOOST_ROOT_PIPELINE})
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file(TO_CMAKE_PATH $ENV{BOOST_ROOT_PIPELINE} CMAKE_BOOST_ROOT)
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list(APPEND BOOST_ROOT "${CMAKE_BOOST_ROOT}")
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list(APPEND BOOST_INCLUDEDIR "${CMAKE_BOOST_ROOT}/boost/include")
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list(APPEND BOOST_LIBRARYDIR "${CMAKE_BOOST_ROOT}/lib")
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endif()
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find_package(Boost 1.56 REQUIRED)

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