diff options
| -rw-r--r-- | .circleci/config.yml | 73 | ||||
| -rw-r--r-- | .github/how_to_use_github_to_contribute_to_gudhi.md | 15 | ||||
| -rw-r--r-- | src/Nerve_GIC/example/CMakeLists.txt | 34 | ||||
| -rw-r--r-- | src/Nerve_GIC/include/gudhi/GIC.h | 18 | ||||
| -rw-r--r-- | src/Nerve_GIC/test/CMakeLists.txt | 17 | ||||
| -rw-r--r-- | src/Nerve_GIC/utilities/CMakeLists.txt | 36 | ||||
| -rw-r--r-- | src/cmake/modules/GUDHI_submodules.cmake | 2 | ||||
| -rw-r--r-- | src/python/CMakeLists.txt | 64 | ||||
| -rw-r--r-- | src/python/setup.py.in | 2 | ||||
| -rw-r--r-- | src/python/test/test_persistence_graphical_tools.py | 5 |
10 files changed, 164 insertions, 102 deletions
diff --git a/.circleci/config.yml b/.circleci/config.yml index e2df5c87..c8c0b70b 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -10,6 +10,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test examples command: | mkdir build @@ -24,6 +29,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test unitary tests command: | mkdir build @@ -38,6 +48,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test utilities command: | mkdir build @@ -52,10 +67,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test python module. Generates and tests the python documentation command: | - git submodule init - git submodule update mkdir build cd build cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version .. @@ -83,10 +101,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Generates the C++ documentation with doxygen command: | - git submodule init - git submodule update mkdir build cd build cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version .. @@ -114,6 +135,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test examples without cgal and eigen command: | mkdir build @@ -128,6 +154,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test unitary tests without cgal and eigen command: | mkdir build @@ -142,6 +173,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test utilities without cgal and eigen command: | mkdir build @@ -156,10 +192,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test python module without cgal and eigen command: | - git submodule init - git submodule update mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .. @@ -176,6 +215,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test examples without cgal command: | mkdir build @@ -190,6 +234,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test unitary tests without cgal command: | mkdir build @@ -204,6 +253,11 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test utilities without cgal command: | mkdir build @@ -218,10 +272,13 @@ jobs: steps: - checkout - run: + name: Checkout submodules + command: | + git submodule sync + git submodule update --init + - run: name: Build and test python module without cgal command: | - git submodule init - git submodule update mkdir build cd build cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 .. diff --git a/.github/how_to_use_github_to_contribute_to_gudhi.md b/.github/how_to_use_github_to_contribute_to_gudhi.md index 738c1ce9..f72bb9d6 100644 --- a/.github/how_to_use_github_to_contribute_to_gudhi.md +++ b/.github/how_to_use_github_to_contribute_to_gudhi.md @@ -17,7 +17,7 @@ You can see your fork at https://github.com/LOGIN/gudhi-devel ## Create a local clone on your computer ```bash -git clone https://github.com/LOGIN/gudhi-devel.git +git clone --recurse-submodules https://github.com/LOGIN/gudhi-devel.git ``` This creates a directory gudhi-devel, which you are free to move around or rename. For the following, change to that directory: @@ -25,16 +25,14 @@ This creates a directory gudhi-devel, which you are free to move around or renam cd gudhi-devel ``` -When you clone the repository, you also need to download the *submodules*. - ## Submodules -Hera, used for Wasserstein distance, is available on an external git repository. To download it: +When you clone the repository, you also need to download the *submodules*. This is done automatically thanks to `--recurse-submodules`. +If you forgot this option, you can still download them with ```bash git submodule update --init ``` -[gudhi-deploy](https://github.com/GUDHI/gudhi-deploy) is used for Continuous Integration python -requirements and will also be downloaded by the above command. +The submodules appear in the `ext/` subdirectory. There are currently 2, [Hera](https://github.com/anigmetov/hera) for distances between persistence diagrams, and [gudhi-deploy](https://github.com/GUDHI/gudhi-deploy) for Continuous Integration. ## Configuring a remote for a fork ```bash @@ -68,6 +66,11 @@ It is safe, it will not mess with your files. git submodule sync git submodule update --init ``` +You can configure `git` to do this automatically with +```bash +git config submodule.recurse true +``` +(add `--global` if you want it to apply to other projects as well) ## Create a branch, based on the current master ```bash diff --git a/src/Nerve_GIC/example/CMakeLists.txt b/src/Nerve_GIC/example/CMakeLists.txt index 4b0f4677..9faf1f3b 100644 --- a/src/Nerve_GIC/example/CMakeLists.txt +++ b/src/Nerve_GIC/example/CMakeLists.txt @@ -1,25 +1,21 @@ project(Nerve_GIC_examples) -if (NOT CGAL_VERSION VERSION_LESS 4.11.0) +add_executable ( CoordGIC CoordGIC.cpp ) +add_executable ( FuncGIC FuncGIC.cpp ) - add_executable ( CoordGIC CoordGIC.cpp ) - add_executable ( FuncGIC FuncGIC.cpp ) +if (TBB_FOUND) + target_link_libraries(CoordGIC ${TBB_LIBRARIES}) + target_link_libraries(FuncGIC ${TBB_LIBRARIES}) +endif() - if (TBB_FOUND) - target_link_libraries(CoordGIC ${TBB_LIBRARIES}) - target_link_libraries(FuncGIC ${TBB_LIBRARIES}) - endif() +# Copy files for not to pollute sources when testing +file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - # Copy files for not to pollute sources when testing - file(COPY "${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY "${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC> + "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") - add_test(NAME Nerve_GIC_example_CoordGIC COMMAND $<TARGET_FILE:CoordGIC> - "${CMAKE_CURRENT_BINARY_DIR}/tore3D_1307.off" "0") - - add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> - "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" - "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") - -endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) +add_test(NAME Nerve_GIC_example_FuncGIC COMMAND $<TARGET_FILE:FuncGIC> + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat.off" + "${CMAKE_CURRENT_BINARY_DIR}/lucky_cat_PCA1") diff --git a/src/Nerve_GIC/include/gudhi/GIC.h b/src/Nerve_GIC/include/gudhi/GIC.h index 1b1f9323..047fba61 100644 --- a/src/Nerve_GIC/include/gudhi/GIC.h +++ b/src/Nerve_GIC/include/gudhi/GIC.h @@ -17,6 +17,14 @@ #include <mutex> #endif +#if __has_include(<CGAL/version.h>) +# define GUDHI_GIC_USE_CGAL 1 +# include <gudhi/Bottleneck.h> +#elif __has_include(<hera/bottleneck.h>) +# define GUDHI_GIC_USE_HERA 1 +# include <hera/bottleneck.h> +#endif + #include <gudhi/Debug_utils.h> #include <gudhi/graph_simplicial_complex.h> #include <gudhi/reader_utils.h> @@ -25,7 +33,6 @@ #include <gudhi/Points_off_io.h> #include <gudhi/distance_functions.h> #include <gudhi/Persistent_cohomology.h> -#include <gudhi/Bottleneck.h> #include <boost/config.hpp> #include <boost/graph/graph_traits.hpp> @@ -35,8 +42,6 @@ #include <boost/graph/subgraph.hpp> #include <boost/graph/graph_utility.hpp> -#include <CGAL/version.h> // for CGAL_VERSION_NR - #include <iostream> #include <vector> #include <map> @@ -1228,7 +1233,14 @@ class Cover_complex { Cboot.set_cover_from_function(); Cboot.find_simplices(); Cboot.compute_PD(); +#ifdef GUDHI_GIC_USE_CGAL double db = Gudhi::persistence_diagram::bottleneck_distance(this->PD, Cboot.PD); +#elif defined GUDHI_GIC_USE_HERA + double db = hera::bottleneckDistExact(this->PD, Cboot.PD); +#else + double db; + throw std::logic_error("This function requires CGAL or Hera for the bottleneck distance."); +#endif if (verbose) std::clog << db << std::endl; distribution.push_back(db); } diff --git a/src/Nerve_GIC/test/CMakeLists.txt b/src/Nerve_GIC/test/CMakeLists.txt index 567bf43f..e012a178 100644 --- a/src/Nerve_GIC/test/CMakeLists.txt +++ b/src/Nerve_GIC/test/CMakeLists.txt @@ -1,15 +1,12 @@ project(Graph_induced_complex_tests) -if (NOT CGAL_VERSION VERSION_LESS 4.11.0) - include(GUDHI_boost_test) +include(GUDHI_boost_test) - add_executable ( Nerve_GIC_test_unit test_GIC.cpp ) - if (TBB_FOUND) - target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES}) - endif() +add_executable ( Nerve_GIC_test_unit test_GIC.cpp ) +if (TBB_FOUND) + target_link_libraries(Nerve_GIC_test_unit ${TBB_LIBRARIES}) +endif() - file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +file(COPY data DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - gudhi_add_boost_test(Nerve_GIC_test_unit) - -endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) +gudhi_add_boost_test(Nerve_GIC_test_unit) diff --git a/src/Nerve_GIC/utilities/CMakeLists.txt b/src/Nerve_GIC/utilities/CMakeLists.txt index 65a08d9a..4521a992 100644 --- a/src/Nerve_GIC/utilities/CMakeLists.txt +++ b/src/Nerve_GIC/utilities/CMakeLists.txt @@ -1,27 +1,23 @@ project(Nerve_GIC_examples) -if (NOT CGAL_VERSION VERSION_LESS 4.11.0) +add_executable ( Nerve Nerve.cpp ) +add_executable ( VoronoiGIC VoronoiGIC.cpp ) - add_executable ( Nerve Nerve.cpp ) - add_executable ( VoronoiGIC VoronoiGIC.cpp ) +if (TBB_FOUND) + target_link_libraries(Nerve ${TBB_LIBRARIES}) + target_link_libraries(VoronoiGIC ${TBB_LIBRARIES}) +endif() - if (TBB_FOUND) - target_link_libraries(Nerve ${TBB_LIBRARIES}) - target_link_libraries(VoronoiGIC ${TBB_LIBRARIES}) - endif() +file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +# Copy files for not to pollute sources when testing +file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY KeplerMapperVisuFromTxtFile.py km.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - # Copy files for not to pollute sources when testing - file(COPY "${CMAKE_SOURCE_DIR}/data/points/human.off" DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) +add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve> + "human.off" "2" "10" "0.3") - add_test(NAME Nerve_GIC_utilities_nerve COMMAND $<TARGET_FILE:Nerve> - "human.off" "2" "10" "0.3") +add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> + "human.off" "100") - add_test(NAME Nerve_GIC_utilities_VoronoiGIC COMMAND $<TARGET_FILE:VoronoiGIC> - "human.off" "100") - - install(TARGETS Nerve DESTINATION bin) - install(TARGETS VoronoiGIC DESTINATION bin) - install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin) - -endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) +install(TARGETS Nerve DESTINATION bin) +install(TARGETS VoronoiGIC DESTINATION bin) +install(FILES KeplerMapperVisuFromTxtFile.py km.py km.py.COPYRIGHT DESTINATION bin) diff --git a/src/cmake/modules/GUDHI_submodules.cmake b/src/cmake/modules/GUDHI_submodules.cmake index c844386d..9ede852d 100644 --- a/src/cmake/modules/GUDHI_submodules.cmake +++ b/src/cmake/modules/GUDHI_submodules.cmake @@ -1,3 +1,5 @@ # For those who dislike bundled dependencies, this indicates where to find a preinstalled Hera. set(HERA_INTERNAL_INCLUDE_DIR ${CMAKE_SOURCE_DIR}/ext/hera/include) set(HERA_INCLUDE_DIR ${HERA_INTERNAL_INCLUDE_DIR} CACHE PATH "Directory where one can find hera/{wasserstein.h,bottleneck.h}") +# since everything is cleanly under include/hera/, there is no harm always including it +include_directories(${HERA_INCLUDE_DIR}) diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt index 32ec13bd..39e2acd4 100644 --- a/src/python/CMakeLists.txt +++ b/src/python/CMakeLists.txt @@ -44,7 +44,7 @@ function( add_gudhi_debug_info DEBUG_INFO ) endfunction( add_gudhi_debug_info ) if(PYTHONINTERP_FOUND) - if(PYBIND11_FOUND AND CYTHON_FOUND) + if(NUMPY_FOUND AND PYBIND11_FOUND AND CYTHON_FOUND) add_gudhi_debug_info("Pybind11 version ${PYBIND11_VERSION}") # PyBind11 modules set(GUDHI_PYTHON_MODULES "${GUDHI_PYTHON_MODULES}'bottleneck', ") @@ -163,10 +163,10 @@ if(PYTHONINTERP_FOUND) set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'clustering/_tomato', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/wasserstein', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'hera/bottleneck', ") + set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ") if (NOT CGAL_VERSION VERSION_LESS 4.11.0) set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'datasets/generators/_points', ") set(GUDHI_PYBIND11_MODULES "${GUDHI_PYBIND11_MODULES}'bottleneck', ") - set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'nerve_gic', ") endif () if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0) set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}'subsampling', ") @@ -432,38 +432,38 @@ if(PYTHONINTERP_FOUND) ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py") add_gudhi_py_test(test_bottleneck_distance) + endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) - # Cover complex - file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) - add_test(NAME cover_complex_nerve_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py" - -f human.off -c 2 -r 10 -g 0.3) + # Cover complex + file(COPY ${CMAKE_SOURCE_DIR}/data/points/human.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat.off DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + file(COPY ${CMAKE_SOURCE_DIR}/data/points/COIL_database/lucky_cat_PCA1 DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/) + add_test(NAME cover_complex_nerve_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py" + -f human.off -c 2 -r 10 -g 0.3) - add_test(NAME cover_complex_coordinate_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py" - -f human.off -c 0 -v) + add_test(NAME cover_complex_coordinate_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py" + -f human.off -c 0 -v) - add_test(NAME cover_complex_functional_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py" - -o lucky_cat.off - -f lucky_cat_PCA1 -v) + add_test(NAME cover_complex_functional_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py" + -o lucky_cat.off + -f lucky_cat_PCA1 -v) - add_test(NAME cover_complex_voronoi_gic_example_py_test - WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} - COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" - ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" - -f human.off -n 700 -v) + add_test(NAME cover_complex_voronoi_gic_example_py_test + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMAND ${CMAKE_COMMAND} -E env "${GUDHI_PYTHON_PATH_ENV}" + ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py" + -f human.off -n 700 -v) - add_gudhi_py_test(test_cover_complex) - endif (NOT CGAL_VERSION VERSION_LESS 4.11.0) + add_gudhi_py_test(test_cover_complex) if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0) # Alpha @@ -623,10 +623,10 @@ if(PYTHONINTERP_FOUND) # Set missing or not modules set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES") - else(PYBIND11_FOUND AND CYTHON_FOUND) - message("++ Python module will not be compiled because cython and/or pybind11 was/were not found") + else(NUMPY_FOUND AND PYBIND11_FOUND AND CYTHON_FOUND) + message("++ Python module will not be compiled because numpy and/or cython and/or pybind11 was/were not found") set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES") - endif(PYBIND11_FOUND AND CYTHON_FOUND) + endif(NUMPY_FOUND AND PYBIND11_FOUND AND CYTHON_FOUND) else(PYTHONINTERP_FOUND) message("++ Python module will not be compiled because no Python interpreter was found") set(GUDHI_MISSING_MODULES ${GUDHI_MISSING_MODULES} "python" CACHE INTERNAL "GUDHI_MISSING_MODULES") diff --git a/src/python/setup.py.in b/src/python/setup.py.in index 1ecbe985..6eb0db42 100644 --- a/src/python/setup.py.in +++ b/src/python/setup.py.in @@ -48,8 +48,6 @@ ext_modules = cythonize(ext_modules, compiler_directives={'language_level': '3'} for module in pybind11_modules: my_include_dirs = include_dirs + [pybind11.get_include(False), pybind11.get_include(True)] - if module.startswith('hera/'): - my_include_dirs = ['@HERA_INCLUDE_DIR@'] + my_include_dirs ext_modules.append(Extension( 'gudhi.' + module.replace('/', '.'), sources = [source_dir + module + '.cc'], diff --git a/src/python/test/test_persistence_graphical_tools.py b/src/python/test/test_persistence_graphical_tools.py index c19836b7..0e2ac3f8 100644 --- a/src/python/test/test_persistence_graphical_tools.py +++ b/src/python/test/test_persistence_graphical_tools.py @@ -12,6 +12,7 @@ import gudhi as gd import numpy as np import matplotlib as plt import pytest +import warnings def test_array_handler(): @@ -71,13 +72,13 @@ def test_limit_to_max_intervals(): (0, (0.0, 0.106382)), ] # check no warnings if max_intervals equals to the diagrams number - with pytest.warns(None) as record: + with warnings.catch_warnings(): + warnings.simplefilter("error") truncated_diags = gd.persistence_graphical_tools._limit_to_max_intervals( diags, 10, key=lambda life_time: life_time[1][1] - life_time[1][0] ) # check diagrams are not sorted assert truncated_diags == diags - assert len(record) == 0 # check warning if max_intervals lower than the diagrams number with pytest.warns(UserWarning) as record: |