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Merge pull request #133539 from yl3dy/gudhi

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Sandro 2021-08-20 23:40:49 +02:00 committed by GitHub
parent d229b90da3 8c01dd2ca0
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6
maintainers/maintainer-list.nix
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@ -11812,6 +11812,12 @@
githubId = 26011724;
name = "Burim Augustin Berisa";
};
yl3dy = {
email = "aleksandr.kiselyov@gmail.com";
github = "yl3dy";
githubId = 1311192;
name = "Alexander Kiselyov";
};
yochai = {
email = "yochai@titat.info";
github = "yochai";

64
pkgs/development/python-modules/gudhi/default.nix Normal file
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@ -0,0 +1,64 @@
{ lib
, fetchFromGitHub
, buildPythonPackage
, cmake
, boost
, eigen
, gmp
, cgal_5 # see https://github.com/NixOS/nixpkgs/pull/94875 about cgal
, mpfr
, tbb
, numpy
, cython
, pybind11
, matplotlib
, scipy
, pytest
, enableTBB ? false
}:
buildPythonPackage rec {
pname = "gudhi";
version = "3.4.1";
src = fetchFromGitHub {
owner = "GUDHI";
repo = "gudhi-devel";
rev = "tags/gudhi-release-${version}";
fetchSubmodules = true;
sha256 = "1m03qazzfraxn62l1cb11icjz4x8q2sg9c2k3syw5v0yv9ndgx1v";
};
patches = [ ./remove_explicit_PYTHONPATH.patch ];
nativeBuildInputs = [ cmake numpy cython pybind11 matplotlib ];
buildInputs = [ boost eigen gmp cgal_5 mpfr ]
++ lib.optionals enableTBB [ tbb ];
propagatedBuildInputs = [ numpy scipy ];
checkInputs = [ pytest ];
cmakeFlags = [
"-DCMAKE_BUILD_TYPE=Release"
"-DWITH_GUDHI_PYTHON=ON"
"-DPython_ADDITIONAL_VERSIONS=3"
];
preBuild = ''
cd src/python
'';
checkPhase = ''
rm -r gudhi
${cmake}/bin/ctest --output-on-failure
'';
pythonImportsCheck = [ "gudhi" "gudhi.hera" "gudhi.point_cloud" "gudhi.clustering" ];
meta = {
description = "Library for Computational Topology and Topological Data Analysis (TDA)";
homepage = "https://gudhi.inria.fr/python/latest/";
downloadPage = "https://github.com/GUDHI/gudhi-devel";
license = with lib.licenses; [ mit gpl3 ];
maintainers = with lib.maintainers; [ yl3dy ];
};
}

174
pkgs/development/python-modules/gudhi/remove_explicit_PYTHONPATH.patch Normal file
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@ -0,0 +1,174 @@
diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 5c1402a..48a1250 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -271,9 +271,6 @@ if(PYTHONINTERP_FOUND)
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMAND ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_BINARY_DIR}/setup.py" "build_ext" "--inplace")
- add_custom_target(python ALL DEPENDS gudhi.so
- COMMENT "Do not forget to add ${CMAKE_CURRENT_BINARY_DIR}/ to your PYTHONPATH before using examples or tests")
-
install(CODE "execute_process(COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py install)")
# Documentation generation is available through sphinx - requires all modules
@@ -295,14 +292,14 @@ if(PYTHONINTERP_FOUND)
# sphinx target requires gudhi.so, because conf.py reads gudhi version from it
add_custom_target(sphinx
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doc
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env
${SPHINX_PATH} -b html ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/sphinx
DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/gudhi.so"
COMMENT "${GUDHI_SPHINX_MESSAGE}" VERBATIM)
add_test(NAME sphinx_py_test
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env
${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
# Set missing or not modules
@@ -346,13 +343,13 @@ if(PYTHONINTERP_FOUND)
# Bottleneck and Alpha
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"
-f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
# Tangential
add_test(NAME tangential_complex_plain_homology_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/tangential_complex_plain_homology_from_off_file_example.py"
--no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
@@ -361,13 +358,13 @@ if(PYTHONINTERP_FOUND)
# Witness complex
add_test(NAME euclidean_strong_witness_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/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
add_test(NAME euclidean_witness_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/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
--no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
@@ -379,7 +376,7 @@ if(PYTHONINTERP_FOUND)
# Bottleneck
add_test(NAME bottleneck_basic_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/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"
-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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E 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 ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+ COMMAND ${CMAKE_COMMAND} -E env
${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/voronoi_graph_induced_complex.py"
-f human.off -n 700 -v)
@@ -422,11 +419,11 @@ if(PYTHONINTERP_FOUND)
# Alpha
add_test(NAME alpha_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/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
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@ -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
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@ -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 ];
};
}

6
pkgs/top-level/python-packages.nix
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@ -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 { };