Merge pull request #133539 from yl3dy/gudhi
This commit is contained in:
Sandro
GitHub
commit
851722fafb
@ -11812,6 +11812,12 @@
|
||||
githubId = 26011724;
|
||||
name = "Burim Augustin Berisa";
|
||||
};
|
||||
yl3dy = {
|
||||
email = "aleksandr.kiselyov@gmail.com";
|
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github = "yl3dy";
|
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githubId = 1311192;
|
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name = "Alexander Kiselyov";
|
||||
};
|
||||
yochai = {
|
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email = "yochai@titat.info";
|
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github = "yochai";
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||||
|
||||
64
pkgs/development/python-modules/gudhi/default.nix
Normal file
64
pkgs/development/python-modules/gudhi/default.nix
Normal file
@ -0,0 +1,64 @@
|
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{ lib
|
||||
, fetchFromGitHub
|
||||
, buildPythonPackage
|
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, cmake
|
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, boost
|
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, eigen
|
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, gmp
|
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, cgal_5 # see https://github.com/NixOS/nixpkgs/pull/94875 about cgal
|
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, mpfr
|
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, tbb
|
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, numpy
|
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, cython
|
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, pybind11
|
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, matplotlib
|
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, scipy
|
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, pytest
|
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, enableTBB ? false
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}:
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|
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buildPythonPackage rec {
|
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pname = "gudhi";
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version = "3.4.1";
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||||
|
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src = fetchFromGitHub {
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owner = "GUDHI";
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repo = "gudhi-devel";
|
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rev = "tags/gudhi-release-${version}";
|
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fetchSubmodules = true;
|
||||
sha256 = "1m03qazzfraxn62l1cb11icjz4x8q2sg9c2k3syw5v0yv9ndgx1v";
|
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};
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|
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patches = [ ./remove_explicit_PYTHONPATH.patch ];
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|
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nativeBuildInputs = [ cmake numpy cython pybind11 matplotlib ];
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buildInputs = [ boost eigen gmp cgal_5 mpfr ]
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++ lib.optionals enableTBB [ tbb ];
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propagatedBuildInputs = [ numpy scipy ];
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checkInputs = [ pytest ];
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cmakeFlags = [
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"-DCMAKE_BUILD_TYPE=Release"
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"-DWITH_GUDHI_PYTHON=ON"
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"-DPython_ADDITIONAL_VERSIONS=3"
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];
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|
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preBuild = ''
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cd src/python
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'';
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|
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checkPhase = ''
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rm -r gudhi
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${cmake}/bin/ctest --output-on-failure
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'';
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|
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pythonImportsCheck = [ "gudhi" "gudhi.hera" "gudhi.point_cloud" "gudhi.clustering" ];
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|
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meta = {
|
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description = "Library for Computational Topology and Topological Data Analysis (TDA)";
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homepage = "https://gudhi.inria.fr/python/latest/";
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downloadPage = "https://github.com/GUDHI/gudhi-devel";
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license = with lib.licenses; [ mit gpl3 ];
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maintainers = with lib.maintainers; [ yl3dy ];
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};
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}
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@ -0,0 +1,174 @@
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diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
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index 5c1402a..48a1250 100644
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--- a/src/python/CMakeLists.txt
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+++ b/src/python/CMakeLists.txt
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@@ -271,9 +271,6 @@ if(PYTHONINTERP_FOUND)
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
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|
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- add_custom_target(python ALL DEPENDS gudhi.so
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- COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
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-
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install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
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|
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# Documentation generation is available through sphinx - requires all modules
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@@ -295,14 +292,14 @@ if(PYTHONINTERP_FOUND)
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# sphinx target requires gudhi.so, because conf.py reads gudhi version from it
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add_custom_target(sphinx
|
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WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
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${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
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DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
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COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
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|
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add_test(NAME sphinx_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
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${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
|
||||
|
||||
# Set missing or not modules
|
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@@ -346,13 +343,13 @@ if(PYTHONINTERP_FOUND)
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# Bottleneck and Alpha
|
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add_test(NAME alpha_rips_persistence_bottleneck_distance_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
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-f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
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# Tangential
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add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
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- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
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--no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
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|
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@@ -361,13 +358,13 @@ if(PYTHONINTERP_FOUND)
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# Witness complex
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add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
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- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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+ COMMAND ${CMAKE_COMMAND} -E env
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
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--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
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add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
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- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
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+ COMMAND ${CMAKE_COMMAND} -E env
|
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${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
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--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
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|
||||
@@ -379,7 +376,7 @@ if(PYTHONINTERP_FOUND)
|
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# Bottleneck
|
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add_test(NAME bottleneck_basic_example_py_test
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||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/bottleneck_basic_example.py")
|
||||
|
||||
if (PYBIND11_FOUND)
|
||||
@@ -392,26 +389,26 @@ if(PYTHONINTERP_FOUND)
|
||||
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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/nerve_of_a_covering.py"
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-f human.off -c 2 -r 10 -g 0.3)
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|
||||
add_test(NAME cover_complex_coordinate_gic_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/coordinate_graph_induced_complex.py"
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-f human.off -c 0 -v)
|
||||
|
||||
add_test(NAME cover_complex_functional_gic_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/functional_graph_induced_complex.py"
|
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-o lucky_cat.off
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-f lucky_cat_PCA1 -v)
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|
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add_test(NAME cover_complex_voronoi_gic_example_py_test
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
|
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-f human.off -n 700 -v)
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|
||||
@@ -422,11 +419,11 @@ if(PYTHONINTERP_FOUND)
|
||||
# Alpha
|
||||
add_test(NAME alpha_complex_from_points_example_py_test
|
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WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
|
||||
add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
|
||||
--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
|
||||
add_gudhi_py_test(test_alpha_complex)
|
||||
@@ -441,13 +438,13 @@ if(PYTHONINTERP_FOUND)
|
||||
# Cubical
|
||||
add_test(NAME periodic_cubical_complex_barcode_persistence_from_perseus_file_example_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
|
||||
--no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
|
||||
|
||||
add_test(NAME random_cubical_complex_persistence_example_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
|
||||
10 10 10)
|
||||
|
||||
@@ -456,19 +453,19 @@ if(PYTHONINTERP_FOUND)
|
||||
# Rips
|
||||
add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
|
||||
--no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
|
||||
|
||||
add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
|
||||
--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -e 0.25 -d 3)
|
||||
|
||||
add_test(NAME rips_complex_from_points_example_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_from_points_example.py)
|
||||
|
||||
add_gudhi_py_test(test_rips_complex)
|
||||
@@ -476,7 +473,7 @@ if(PYTHONINTERP_FOUND)
|
||||
# Simplex tree
|
||||
add_test(NAME simplex_tree_example_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/simplex_tree_example.py)
|
||||
|
||||
add_gudhi_py_test(test_simplex_tree)
|
||||
@@ -485,7 +482,7 @@ if(PYTHONINTERP_FOUND)
|
||||
# Witness
|
||||
add_test(NAME witness_complex_from_nearest_landmark_table_py_test
|
||||
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
|
||||
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
|
||||
+ COMMAND ${CMAKE_COMMAND} -E env
|
||||
${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/witness_complex_from_nearest_landmark_table.py)
|
||||
|
||||
add_gudhi_py_test(test_witness_complex)
|
||||
55
pkgs/development/python-modules/pot/default.nix
Normal file
55
pkgs/development/python-modules/pot/default.nix
Normal file
@ -0,0 +1,55 @@
|
||||
{ lib
|
||||
, fetchPypi
|
||||
, buildPythonPackage
|
||||
, numpy
|
||||
, scipy
|
||||
, cython
|
||||
, matplotlib
|
||||
, scikit-learn
|
||||
, cupy
|
||||
, pymanopt
|
||||
, autograd
|
||||
, pytestCheckHook
|
||||
, enableDimensionalityReduction ? false
|
||||
, enableGPU ? false
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "pot";
|
||||
version = "0.7.0";
|
||||
|
||||
src = fetchPypi {
|
||||
pname = "POT";
|
||||
inherit version;
|
||||
sha256 = "01mdsiv8rlgqzvm3bds9aj49khnn33i523c2cqqrl10zg742pb6l";
|
||||
};
|
||||
|
||||
postPatch = ''
|
||||
substituteInPlace setup.cfg \
|
||||
--replace "--cov-report= --cov=ot" ""
|
||||
'';
|
||||
|
||||
nativeBuildInputs = [ numpy cython ];
|
||||
propagatedBuildInputs = [ numpy scipy ]
|
||||
++ lib.optionals enableGPU [ cupy ]
|
||||
++ lib.optionals enableDimensionalityReduction [ pymanopt autograd ];
|
||||
checkInputs = [ matplotlib scikit-learn pytestCheckHook ];
|
||||
|
||||
# To prevent importing of an incomplete package from the build directory
|
||||
# instead of nix store (`ot` is the top-level package name).
|
||||
preCheck = ''
|
||||
rm -r ot
|
||||
'';
|
||||
|
||||
# GPU tests are always skipped because of sandboxing
|
||||
disabledTests = [ "warnings" ];
|
||||
|
||||
pythonImportsCheck = [ "ot" "ot.lp" ];
|
||||
|
||||
meta = {
|
||||
description = "Python Optimal Transport Library";
|
||||
homepage = "https://pythonot.github.io/";
|
||||
license = lib.licenses.mit;
|
||||
maintainers = with lib.maintainers; [ yl3dy ];
|
||||
};
|
||||
}
|
||||
39
pkgs/development/python-modules/pymanopt/default.nix
Normal file
39
pkgs/development/python-modules/pymanopt/default.nix
Normal file
@ -0,0 +1,39 @@
|
||||
{ lib
|
||||
, fetchFromGitHub
|
||||
, buildPythonPackage
|
||||
, numpy
|
||||
, scipy
|
||||
, autograd
|
||||
, nose2
|
||||
}:
|
||||
|
||||
buildPythonPackage rec {
|
||||
pname = "pymanopt";
|
||||
version = "0.2.5";
|
||||
|
||||
src = fetchFromGitHub {
|
||||
owner = pname;
|
||||
repo = pname;
|
||||
rev = version;
|
||||
sha256 = "0zk775v281375sangc5qkwrkb8yc9wx1g8b1917s4s8wszzkp8k6";
|
||||
};
|
||||
|
||||
propagatedBuildInputs = [ numpy scipy ];
|
||||
checkInputs = [ nose2 autograd ];
|
||||
|
||||
checkPhase = ''
|
||||
# nose2 doesn't properly support excludes
|
||||
rm tests/test_{problem,tensorflow,theano}.py
|
||||
|
||||
nose2 tests -v
|
||||
'';
|
||||
|
||||
pythonImportsCheck = [ "pymanopt" ];
|
||||
|
||||
meta = {
|
||||
description = "Python toolbox for optimization on Riemannian manifolds with support for automatic differentiation";
|
||||
homepage = "https://www.pymanopt.org/";
|
||||
license = lib.licenses.bsd3;
|
||||
maintainers = with lib.maintainers; [ yl3dy ];
|
||||
};
|
||||
}
|
||||
@ -3208,6 +3208,8 @@ in {
|
||||
|
||||
guestfs = callPackage ../development/python-modules/guestfs { };
|
||||
|
||||
gudhi = callPackage ../development/python-modules/gudhi { };
|
||||
|
||||
gumath = callPackage ../development/python-modules/gumath { };
|
||||
|
||||
gunicorn = callPackage ../development/python-modules/gunicorn { };
|
||||
@ -5573,6 +5575,8 @@ in {
|
||||
|
||||
postorius = callPackage ../servers/mail/mailman/postorius.nix { };
|
||||
|
||||
pot = callPackage ../development/python-modules/pot { };
|
||||
|
||||
potr = callPackage ../development/python-modules/potr { };
|
||||
|
||||
power = callPackage ../development/python-modules/power { };
|
||||
@ -6273,6 +6277,8 @@ in {
|
||||
|
||||
pymaging_png = callPackage ../development/python-modules/pymaging_png { };
|
||||
|
||||
pymanopt = callPackage ../development/python-modules/pymanopt { };
|
||||
|
||||
pymata-express = callPackage ../development/python-modules/pymata-express { };
|
||||
|
||||
pymatgen = callPackage ../development/python-modules/pymatgen { };
|
||||
|
||||
Loading…
Reference in New Issue
Block a user