From 2c48088476eb5e19c7723a3e725607b019147cd1 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Thu, 15 Aug 2019 12:40:28 +0200 Subject: [PATCH 01/18] Add requirements --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index a03b536..c112ce1 100644 --- a/setup.py +++ b/setup.py @@ -221,7 +221,7 @@ setup(name='cosmotool', version='1.0.0a0', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, - setup_requires=['cython'], + setup_requires=['cython','cffi','numexpr'], ext_modules=[CosmoTool_extension], description='A small cosmotool box of useful functions', long_description=open("./README.md", 'r').read(), From 1bd685e9c5ebbe8487b566d311d62cd66fffc4a7 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Wed, 21 Aug 2019 11:19:03 +0300 Subject: [PATCH 02/18] Add more support for strings --- src/hdf5_array.hpp | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/src/hdf5_array.hpp b/src/hdf5_array.hpp index 711c0bc..11762bb 100644 --- a/src/hdf5_array.hpp +++ b/src/hdf5_array.hpp @@ -263,6 +263,35 @@ namespace CosmoTool { } }; + struct CosmoString { + char const * s; + operator char const *() { return s; } + char const *operator=(char const *s0) { + s = s0; + return s0; + } + }; + + class hdf5_CosmoStringType { + public: + H5::StrType type; + + hdf5_CosmoStringType() : type(H5::PredType::C_S1, H5T_VARIABLE) { + } + + static const hdf5_CosmoStringType *ctype() + { + static hdf5_CosmoStringType singleton; + return &singleton; + } + }; + + template<> struct get_hdf5_data_type { + static H5::DataType type() { + return hdf5_CosmoStringType::ctype()->type; + } + }; + template void hdf5_write_array(H5_CommonFileGroup& fg, const std::string& data_set_name, const ArrayType& data ) { From 71691956cc4a317127d4df54b98e4d18adce3eeb Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Mon, 11 Nov 2019 10:32:40 +0100 Subject: [PATCH 03/18] Some fixups --- python/_cosmo_bispectrum.cpp | 4 ++++ python/_cosmo_power.pyx | 12 ++++++++++++ python/_project.pyx | 10 ++++------ sample/simple3DFilter.cpp | 2 +- setup.py | 2 +- src/mykdtree.tcc | 4 ++-- 6 files changed, 24 insertions(+), 10 deletions(-) diff --git a/python/_cosmo_bispectrum.cpp b/python/_cosmo_bispectrum.cpp index db6a6e0..867dd71 100644 --- a/python/_cosmo_bispectrum.cpp +++ b/python/_cosmo_bispectrum.cpp @@ -171,6 +171,7 @@ void CosmoTool_compute_bispectrum( size_t *Ntriangles, double* B, double delta_k, size_t Nk ) { +#if 0 // First remap to multi_array for easy access size_t kNz = Nz/2+1; #ifdef _OPENMP @@ -246,6 +247,7 @@ void CosmoTool_compute_bispectrum( #else #warning Serial version not implemented #endif +#endif } @@ -255,6 +257,7 @@ void CosmoTool_compute_powerspectrum( size_t *Ncounts, double* P, double delta_k, size_t Nk ) { +#if 0 // First remap to multi_array for easy access size_t kNz = Nz/2+1; boost::multi_array_ref, 3> a_delta(reinterpret_cast*>(delta_hat), boost::extents[Nx][Ny][kNz]); @@ -275,4 +278,5 @@ void CosmoTool_compute_powerspectrum( a_Nc[q1] ++; a_P[q1] += std::norm(v1); } +#endif } diff --git a/python/_cosmo_power.pyx b/python/_cosmo_power.pyx index 47e7bab..2d01e72 100644 --- a/python/_cosmo_power.pyx +++ b/python/_cosmo_power.pyx @@ -65,18 +65,30 @@ cdef class CosmologyPower: cdef CosmoPower power def __init__(self,**cosmo): + """Constructor + + Keyword arguments: + * omega_B_0 + * omega_M_0 + * h + * ns + * T27 + """ self.power = CosmoPower() self.power.OMEGA_B = cosmo['omega_B_0'] self.power.OMEGA_C = cosmo['omega_M_0']-cosmo['omega_B_0'] self.power.h = cosmo['h'] if 'ns' in cosmo: self.power.n = cosmo['ns'] + if 'T27' in cosmo: + self.power.THETA_27 = cosmo['T27'] assert self.power.OMEGA_C > 0 self.power.updateCosmology() def setNormalization(self,A): + """Set manual normalization for A_S""" self.power.setNormalization(A) def normalize(self,s8,k_min=-1,k_max=-1): diff --git a/python/_project.pyx b/python/_project.pyx index 0974383..6ff1d5c 100644 --- a/python/_project.pyx +++ b/python/_project.pyx @@ -509,19 +509,17 @@ cdef void INTERNAL_project_cic_with_mass_periodic(DTYPE_t[:,:,:] g, cdef int b1[3] for i in range(x.shape[0]): - for j in range(3): a[j] = (x[i,j]+shifter)*delta_Box b[j] = int(floor(a[j])) - b1[j] = b[j]+1 - while b1[j] < 0: - b1[j] += Ngrid - while b1[j] >= Ngrid: - b1[j] -= Ngrid + b1[j] = (b[j]+1) % Ngrid a[j] -= b[j] c[j] = 1-a[j] + b[j] %= Ngrid + + m0 = mass[i] g[b[0],b[1],b[2]] += c[0]*c[1]*c[2]*m0 g[b1[0],b[1],b[2]] += a[0]*c[1]*c[2]*m0 diff --git a/sample/simple3DFilter.cpp b/sample/simple3DFilter.cpp index 0b8d7da..000c6b7 100644 --- a/sample/simple3DFilter.cpp +++ b/sample/simple3DFilter.cpp @@ -146,7 +146,7 @@ int main(int argc, char **argv) if (rx < 0 || rx >= Nres || ry < 0 || ry >= Nres || rz < 0 || rz >= Nres) continue; -#pragma omp atomic update +//#pragma omp atomic update bins[rx][ry][rz]++; } v1_data.resize(boost::extents[1][1]); diff --git a/setup.py b/setup.py index c112ce1..a3d1a58 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a0', + version='1.0.0a2', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, setup_requires=['cython','cffi','numexpr'], diff --git a/src/mykdtree.tcc b/src/mykdtree.tcc index d937b23..e3fbdc8 100644 --- a/src/mykdtree.tcc +++ b/src/mykdtree.tcc @@ -277,7 +277,7 @@ namespace CosmoTool { coords tmpBound; NodeIntType nodeId; -#pragma omp atomic capture +//#pragma omp atomic capture nodeId = (this->lastNode)++; node = &nodes[nodeId]; @@ -293,7 +293,7 @@ namespace CosmoTool { tmpBound[axis] = node->value->coord[axis]; depth++; -#pragma omp task private(tmpBound) +//#pragma omp task private(tmpBound) { node->children[0] = buildTree(cell0, mid, depth, minBound, tmpBound); } From cf90393c36172c6690d424d239972c36408df6bd Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Mon, 10 Feb 2020 08:40:17 +0100 Subject: [PATCH 04/18] Portability fixes --- CMakeLists.txt | 2 +- src/CMakeLists.txt | 2 +- src/loadRamses.cpp | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 0e21c7d..2690baf 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -55,7 +55,7 @@ IF(YORICK_SUPPORT) ENDIF(YORICK_SUPPORT) find_program(CYTHON cython3 cython) -find_library(ZLIB z) +find_library(ZLIB_LIBRARY z) find_library(DL_LIBRARY dl) find_library(MATH_LIBRARY m) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 196ed36..a4c81e8 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -79,7 +79,7 @@ if(YORICK_SUPPORT) endif(YORICK_SUPPORT) if (HDF5_FOUND) - set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB}) + set(CosmoTool_LIBS ${CosmoTool_LIBS} ${HDF5_CXX_LIBRARIES} ${HDF5_HL_LIBRARIES} ${HDF5_LIBRARIES} ${ZLIB_LIBRARY}) message(STATUS "CosmoTool_LIBS: ${CosmoTool_LIBS}") endif (HDF5_FOUND) diff --git a/src/loadRamses.cpp b/src/loadRamses.cpp index 0c628f8..3e841d5 100644 --- a/src/loadRamses.cpp +++ b/src/loadRamses.cpp @@ -34,7 +34,7 @@ knowledge of the CeCILL license and that you accept its terms. +*/ #include -#include "/usr/include/regex.h" +#include #include #include #include From bc2e126075a295d1dc9f5881b92ee731b7fd25c2 Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Fri, 6 Mar 2020 08:23:55 +0100 Subject: [PATCH 05/18] Add support for multiple attributes in CTPV --- python/cosmotool/ctpv.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/python/cosmotool/ctpv.py b/python/cosmotool/ctpv.py index 22a9d22..4d90f1a 100644 --- a/python/cosmotool/ctpv.py +++ b/python/cosmotool/ctpv.py @@ -87,7 +87,7 @@ class ProgrammableParticleHistoryLoad(object): class ProgrammableDensityLoad(object): @staticmethod - def main_script(source, density, extents=None, aname="default"): + def main_script(source, density, extents=None, aname="default", extra_arrays={}): import vtk from vtk.util import numpy_support @@ -116,6 +116,11 @@ class ProgrammableDensityLoad(object): arr = numpy_support.numpy_to_vtk(density.transpose().astype(np.float64).ravel(), deep=1) arr.SetName(aname) ido.GetPointData().AddArray(arr) + + for k in extra_arrays.keys(): + arr = numpy_support.numpy_to_vtk(extra_arrays[k].transpose().astype(np.float64).ravel(), deep=1) + arr.SetName(k) + ido.GetPointData().AddArray(arr) @staticmethod def request_information(source, density=None, dims=None): From a3f30b5d8fb8a596feb5f295d88a0915b9d27c37 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Fri, 3 Apr 2020 19:17:27 +0200 Subject: [PATCH 06/18] Fixes to support ninja --- external/external_build.cmake | 17 +++++++++-------- src/CMakeLists.txt | 2 ++ 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index c8fedcf..53037ed 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -56,19 +56,19 @@ if (ENABLE_SHARP) IF(NOT ENABLE_OPENMP) SET(SHARP_OPENMP --disable-openmp) ENDIF() - ExternalProject_Add(sharp - URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz - PREFIX ${BUILD_PREFIX}/sharp-prefix - BUILD_IN_SOURCE 1 - CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP} - BUILD_COMMAND ${CMAKE_MAKE_PROGRAM} - INSTALL_COMMAND echo "No install" - ) SET(CUTILS_LIBRARY ${DEP_BUILD}/lib/libc_utils.a) SET(FFTPACK_LIBRARY ${DEP_BUILD}/lib/libfftpack.a) SET(SHARP_LIBRARY ${DEP_BUILD}/lib/libsharp.a) SET(SHARP_LIBRARIES ${SHARP_LIBRARY} ${FFTPACK_LIBRARY} ${CUTILS_LIBRARY}) SET(SHARP_INCLUDE_PATH ${DEP_BUILD}/include) + ExternalProject_Add(sharp + URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz + PREFIX ${BUILD_PREFIX}/sharp-prefix + BUILD_IN_SOURCE 1 + CONFIGURE_COMMAND autoconf && ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP} + INSTALL_COMMAND echo "No install" + BUILD_BYPRODUCTS ${SHARP_LIBRARIES} + ) endif (ENABLE_SHARP) @@ -375,6 +375,7 @@ ExternalProject_Add(omptl BUILD_COMMAND echo "No build" PATCH_COMMAND patch -p1 -t -N < ${CMAKE_SOURCE_DIR}/external/patch-omptl INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${OMPTL_BUILD_DIR} ${EXT_INSTALL}/include/omptl + BUILD_BYPRODUCTS ${EXT_INSTALL}/include/omptl ) include_directories(${EXT_INSTALL}/include) ##include_directories(${OMPTL_BUILD_DIR}/src/) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index a4c81e8..2cc4b29 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -92,11 +92,13 @@ if (BUILD_SHARED_LIBS) add_library(CosmoTool_static STATIC ${CosmoTool_SRCS} $) target_link_libraries(CosmoTool_static) set_property(TARGET CosmoTool_static PROPERTY POSITION_INDEPENDENT_CODE ON) + add_dependencies(CosmoTool_static ${cosmotool_DEPS}) endif(BUILD_STATIC_LIBS) else (BUILD_SHARED_LIBS) add_library(CosmoTool STATIC ${CosmoTool_SRCS} $) target_link_libraries(CosmoTool) set_property(TARGET CosmoTool PROPERTY POSITION_INDEPENDENT_CODE ON) + add_dependencies(CosmoTool ${cosmotool_DEPS}) endif (BUILD_SHARED_LIBS) IF(NOT COSMOTOOL_PYTHON_PACKAGING) From e4924917b9ddc145f802a19c714df35e9fe96021 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Fri, 10 Apr 2020 18:02:18 +0200 Subject: [PATCH 07/18] Add some support for boost >= 1.70 --- external/external_build.cmake | 13 ++++++++----- src/CMakeLists.txt | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 53037ed..458b803 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -2,8 +2,8 @@ include(FindOpenMP) OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF) -SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE URL "URL to download FFTW from") -SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE URL "URL to download Eigen from") +SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from") +SET(EIGEN_URL "http://bitbucket.org/eigen/eigen/get/3.2.10.tar.gz" CACHE STRING "URL to download Eigen from") SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from") SET(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.18/src/hdf5-1.8.18.tar.bz2" CACHE STRING "URL to download HDF5 from") SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from") @@ -246,10 +246,13 @@ if (INTERNAL_BOOST) set(Boost_DEP boost) ELSE (INTERNAL_BOOST) - find_package(Boost 1.53 QUIET) - set(Boost_DEP) + find_package(Boost 1.69 QUIET) if (NOT Boost_FOUND) - cmessage(CWARNING "Boost >= 1.53 was not found") + cmessage(CWARNING "Boost >= 1.69 was not found") + endif() + if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) + set(Boost_DEP Boost::headers) + set(Boost_TARGET Boost::headers PARENT_SCOPE) endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 2cc4b29..3d6b1ff 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -72,7 +72,7 @@ SET(CosmoTool_SRCS ${CosmoTool_SRCS} include_directories(${GSL_INCLUDE_PATH} ${CMAKE_BINARY_DIR}/src) -set(CosmoTool_LIBS ${GSL_LIBRARIES}) +set(CosmoTool_LIBS ${GSL_LIBRARIES} ${Boost_TARGET}) if(YORICK_SUPPORT) set(CosmoTool_LIBS ${CosmoTool_LIBS} ${NETCDFCPP_LIBRARY} ${NETCDF_LIBRARY} ${GSL_LIBRARIES}) include_directories(${NETCDF_INCLUDE_PATH} ${NETCDFCPP_INCLUDE_PATH}) From 3773c1ab43af2b3b0f871436cdf84fa8568a0952 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 14 Apr 2020 17:46:14 +0200 Subject: [PATCH 08/18] Add support for newer boost --- external/external_build.cmake | 2 +- src/CMakeLists.txt | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 458b803..780dff6 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -252,7 +252,7 @@ ELSE (INTERNAL_BOOST) endif() if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) set(Boost_DEP Boost::headers) - set(Boost_TARGET Boost::headers PARENT_SCOPE) + set(Boost_TARGET Boost::headers) endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index 3d6b1ff..4f39695 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -96,7 +96,7 @@ if (BUILD_SHARED_LIBS) endif(BUILD_STATIC_LIBS) else (BUILD_SHARED_LIBS) add_library(CosmoTool STATIC ${CosmoTool_SRCS} $) - target_link_libraries(CosmoTool) + target_link_libraries(CosmoTool ${CosmoTool_LIBS}) set_property(TARGET CosmoTool PROPERTY POSITION_INDEPENDENT_CODE ON) add_dependencies(CosmoTool ${cosmotool_DEPS}) endif (BUILD_SHARED_LIBS) From 8d91ec20fabef7c0c18366340a31af8076f149ad Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Sun, 26 Apr 2020 09:36:40 +0200 Subject: [PATCH 09/18] Better test of boost --- external/external_build.cmake | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 780dff6..43e0021 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -249,10 +249,14 @@ ELSE (INTERNAL_BOOST) find_package(Boost 1.69 QUIET) if (NOT Boost_FOUND) cmessage(CWARNING "Boost >= 1.69 was not found") + else() + cmessage(STATUS "Boost has been found (version=${Boost_VERSION})") endif() - if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) - set(Boost_DEP Boost::headers) - set(Boost_TARGET Boost::headers) + if (Boost_VERSION) + if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) + set(Boost_DEP Boost::headers) + set(Boost_TARGET Boost::headers) + endif() endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) From 74a59cb21b4e7e4a5bdfa4f708db93d213f4bf96 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 14:12:36 +0200 Subject: [PATCH 10/18] Adjust linkage --- python/CMakeLists.txt | 8 ++++---- python/_cosmo_power.pyx | 2 +- setup.py | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/python/CMakeLists.txt b/python/CMakeLists.txt index 6045aca..90d3e6e 100644 --- a/python/CMakeLists.txt +++ b/python/CMakeLists.txt @@ -50,11 +50,11 @@ if(APPLE) set(CMAKE_MODULE_LINKER_FLAGS "-undefined dynamic_lookup") endif() -target_link_libraries(_cosmotool ${CosmoTool_local} ${GSL_LIBRARIES}) -target_link_libraries(_cosmo_power ${CosmoTool_local} ${GSL_LIBRARIES}) -target_link_libraries(_cosmo_cic ${CosmoTool_local} ${GSL_LIBRARIES}) +target_link_libraries(_cosmotool PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES}) +target_link_libraries(_cosmo_power PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES}) +target_link_libraries(_cosmo_cic PRIVATE ${CosmoTool_local} ${GSL_LIBRARIES}) target_link_libraries(_project ) -target_link_libraries(_fast_interp ${CosmoTool_local} ) +target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} ) SET(ct_TARGETS _cosmotool _project _cosmo_power _cosmo_cic _fast_interp ) diff --git a/python/_cosmo_power.pyx b/python/_cosmo_power.pyx index 2d01e72..bf4bd4b 100644 --- a/python/_cosmo_power.pyx +++ b/python/_cosmo_power.pyx @@ -81,7 +81,7 @@ cdef class CosmologyPower: if 'ns' in cosmo: self.power.n = cosmo['ns'] if 'T27' in cosmo: - self.power.THETA_27 = cosmo['T27'] + self.power.Theta_27 = cosmo['T27'] assert self.power.OMEGA_C > 0 diff --git a/setup.py b/setup.py index a3d1a58..74d4925 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a2', + version='1.0.0a3', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, setup_requires=['cython','cffi','numexpr'], From f35d0cc6944370175169456cb6ca81c77f9165c1 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 14:52:59 +0200 Subject: [PATCH 11/18] Add dummy source code --- python/dummy.c | 1 + setup.py | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) create mode 100644 python/dummy.c diff --git a/python/dummy.c b/python/dummy.c new file mode 100644 index 0000000..ad8787c --- /dev/null +++ b/python/dummy.c @@ -0,0 +1 @@ +static void dummyFunc() {} diff --git a/setup.py b/setup.py index 74d4925..f1cf6d6 100644 --- a/setup.py +++ b/setup.py @@ -21,7 +21,7 @@ class CMakeExtension(Extension): doesn't try to build your sources for you """ - def __init__(self, name, sources=[]): + def __init__(self, name, sources=["python/dummy.c"]): super().__init__(name = name, sources = sources) @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a3', + version='1.0.0a4', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, setup_requires=['cython','cffi','numexpr'], From 6bc0b80e3986deb2b7f4fabd78181b2a30f9e545 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 18:23:44 +0200 Subject: [PATCH 12/18] Add script and metadata to build binary packages. --- LICENCE.txt | 508 ++++++++++++++++++++++++++++++++++++++++ MANIFEST.in | 169 +++++++++++++ builder/build-wheels.sh | 27 +++ builder/start.sh | 12 + setup.py | 3 +- 5 files changed, 718 insertions(+), 1 deletion(-) create mode 100644 LICENCE.txt create mode 100644 MANIFEST.in create mode 100755 builder/build-wheels.sh create mode 100755 builder/start.sh diff --git a/LICENCE.txt b/LICENCE.txt new file mode 100644 index 0000000..acde39e --- /dev/null +++ b/LICENCE.txt @@ -0,0 +1,508 @@ +Copyright (C) 2009-2020 Guilhem Lavaux + + +CeCILL FREE SOFTWARE LICENSE AGREEMENT + + + Notice + +This Agreement is a Free Software license agreement that is the result +of discussions between its authors in order to ensure compliance with +the two main principles guiding its drafting: + + * firstly, compliance with the principles governing the distribution + of Free Software: access to source code, broad rights granted to + users, + * secondly, the election of a governing law, French law, with which + it is conformant, both as regards the law of torts and + intellectual property law, and the protection that it offers to + both authors and holders of the economic rights over software. + +The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre]) +license are: + +Commissariat à l'Energie Atomique - CEA, a public scientific, technical +and industrial research establishment, having its principal place of +business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France. + +Centre National de la Recherche Scientifique - CNRS, a public scientific +and technological establishment, having its principal place of business +at 3 rue Michel-Ange, 75794 Paris cedex 16, France. + +Institut National de Recherche en Informatique et en Automatique - +INRIA, a public scientific and technological establishment, having its +principal place of business at Domaine de Voluceau, Rocquencourt, BP +105, 78153 Le Chesnay cedex, France. + + + Preamble + +The purpose of this Free Software license agreement is to grant users +the right to modify and redistribute the software governed by this +license within the framework of an open source distribution model. + +The exercising of these rights is conditional upon certain obligations +for users so as to preserve this status for all subsequent redistributions. + +In consideration of access to the source code and the rights to copy, +modify and redistribute granted by the license, users are provided only +with a limited warranty and the software's author, the holder of the +economic rights, and the successive licensors only have limited liability. + +In this respect, the risks associated with loading, using, modifying +and/or developing or reproducing the software by the user are brought to +the user's attention, given its Free Software status, which may make it +complicated to use, with the result that its use is reserved for +developers and experienced professionals having in-depth computer +knowledge. Users are therefore encouraged to load and test the +suitability of the software as regards their requirements in conditions +enabling the security of their systems and/or data to be ensured and, +more generally, to use and operate it in the same conditions of +security. 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However, any +licenses that it may have granted prior to termination of the Agreement +shall remain valid subject to their having been granted in compliance +with the terms and conditions hereof. + + + Article 11 - MISCELLANEOUS + + + 11.1 EXCUSABLE EVENTS + +Neither Party shall be liable for any or all delay, or failure to +perform the Agreement, that may be attributable to an event of force +majeure, an act of God or an outside cause, such as defective +functioning or interruptions of the electricity or telecommunications +networks, network paralysis following a virus attack, intervention by +government authorities, natural disasters, water damage, earthquakes, +fire, explosions, strikes and labor unrest, war, etc. + +11.2 Any failure by either Party, on one or more occasions, to invoke +one or more of the provisions hereof, shall under no circumstances be +interpreted as being a waiver by the interested Party of its right to +invoke said provision(s) subsequently. + +11.3 The Agreement cancels and replaces any or all previous agreements, +whether written or oral, between the Parties and having the same +purpose, and constitutes the entirety of the agreement between said +Parties concerning said purpose. No supplement or modification to the +terms and conditions hereof shall be effective as between the Parties +unless it is made in writing and signed by their duly authorized +representatives. + +11.4 In the event that one or more of the provisions hereof were to +conflict with a current or future applicable act or legislative text, +said act or legislative text shall prevail, and the Parties shall make +the necessary amendments so as to comply with said act or legislative +text. All other provisions shall remain effective. Similarly, invalidity +of a provision of the Agreement, for any reason whatsoever, shall not +cause the Agreement as a whole to be invalid. + + + 11.5 LANGUAGE + +The Agreement is drafted in both French and English and both versions +are deemed authentic. + + + Article 12 - NEW VERSIONS OF THE AGREEMENT + +12.1 Any person is authorized to duplicate and distribute copies of this +Agreement. + +12.2 So as to ensure coherence, the wording of this Agreement is +protected and may only be modified by the authors of the License, who +reserve the right to periodically publish updates or new versions of the +Agreement, each with a separate number. These subsequent versions may +address new issues encountered by Free Software. + +12.3 Any Software distributed under a given version of the Agreement may +only be subsequently distributed under the same version of the Agreement +or a subsequent version, subject to the provisions of Article 5.3.4. + + + Article 13 - GOVERNING LAW AND JURISDICTION + +13.1 The Agreement is governed by French law. The Parties agree to +endeavor to seek an amicable solution to any disagreements or disputes +that may arise during the performance of the Agreement. + +13.2 Failing an amicable solution within two (2) months as from their +occurrence, and unless emergency proceedings are necessary, the +disagreements or disputes shall be referred to the Paris Courts having +jurisdiction, by the more diligent Party. + + +Version 2.0 dated 2006-09-05. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..8d92fca --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,169 @@ +include .gitignore +include CMakeLists.txt +include FindNumPy.cmake +include FindPyLibs.cmake +include GetGitRevisionDescription.cmake +include GetGitRevisionDescription.cmake.in +include LICENCE.txt +include LICENCE_CeCILL_V2 +include README.md +include build_tools/gather_sources.py +include color_msg.cmake +include doc/Makefile +include doc/make.bat +include doc/source/conf.py +include doc/source/cpplibrary.rst +include doc/source/index.rst +include doc/source/intro.rst +include doc/source/pythonmodule.rst +include external/external_build.cmake +include external/libsharp-6077806.tar.gz +include external/omptl-20120422.tar.bz2 +include external/patch-omptl +include python/CMakeLists.txt +include python/_cosmo_bispectrum.cpp +include python/_cosmo_cic.pyx +include python/_cosmo_power.pyx +include python/_cosmotool.pyx +include python/_fast_interp.pyx +include python/_project.pyx +include python/copy.pxd +include python/cosmotool/__init__.py +include python/cosmotool/bispectrum.py +include python/cosmotool/borg.py +include python/cosmotool/cic.py +include python/cosmotool/cl_cic.py +include python/cosmotool/config.py.in +include python/cosmotool/ctpv.py +include python/cosmotool/fftw.py +include python/cosmotool/grafic.py +include python/cosmotool/simu.py +include python/cosmotool/smooth.py +include python/cosmotool/timing.py +include python/cppHelper.hpp +include python/dummy.c +include python/project_tool.hpp +include python/safe_gadget.hpp +include python_sample/build_2lpt_ksz.py +include python_sample/build_2lpt_skymap.py +include python_sample/build_dipole_ksz_from_galaxies.py +include python_sample/build_nbody_ksz.py +include python_sample/build_nbody_ksz_from_galaxies.py +include python_sample/build_nbody_skymap.py +include python_sample/gen_2lpt_asmooth.py +include python_sample/gen_2lpt_density.py +include python_sample/icgen/__init__.py +include python_sample/icgen/borgadaptor.py +include python_sample/icgen/borgicgen.py +include python_sample/icgen/cosmogrowth.py +include python_sample/icgen/gen_ic_from_borg.py +include python_sample/icgen/test_ic_from_borg.py +include python_sample/icgen/test_whitify.py +include python_sample/ksz/__init__.py +include python_sample/ksz/constants.py +include python_sample/ksz/gal_prof.py +include python_sample/ramsesToArray.py +include python_sample/test_bispectrum.py +include python_sample/test_spheric_proj.py +include sample/CMakeLists.txt +include sample/Hartmann_Matrix.txt +include sample/gadgetToArray.cpp +include sample/gadgetToDensity.cpp +include sample/graficToDensity.cpp +include sample/simple3DFilter.cpp +include sample/simpleDistanceFilter.cpp +include sample/testAlgo.cpp +include sample/testBQueue.cpp +include sample/testBSP.cpp +include sample/testDelaunay.cpp +include sample/testEskow.cpp +include sample/testHDF5.cpp +include sample/testInterpolate.cpp +include sample/testNewton.cpp +include sample/testPool.cpp +include sample/testReadFlash.cpp +include sample/testSmooth.cpp +include sample/test_cosmopower.cpp +include sample/test_fft_calls.cpp +include sample/test_healpix_calls.cpp +include sample/testkd.cpp +include sample/testkd2.cpp +include sample/testkd3.cpp +include setup.py +include src/CMakeLists.txt +include src/algo.hpp +include src/bqueue.hpp +include src/bqueue.tcc +include src/bsp_simple.hpp +include src/bsp_simple.tcc +include src/cic.cpp +include src/cic.hpp +include src/config.hpp +include src/cosmopower.cpp +include src/cosmopower.hpp +include src/dinterpolate.hpp +include src/dinterpolate.tcc +include src/eskow.hpp +include src/field.hpp +include src/fixArray.hpp +include src/fortran.cpp +include src/fortran.hpp +include src/fourier/base_types.hpp +include src/fourier/details/euclidian_maps.hpp +include src/fourier/details/euclidian_spectrum_1d.hpp +include src/fourier/details/euclidian_spectrum_1d_bin.hpp +include src/fourier/details/euclidian_transform.hpp +include src/fourier/details/healpix_alms.hpp +include src/fourier/details/healpix_map.hpp +include src/fourier/details/healpix_spectrum.hpp +include src/fourier/details/healpix_transform.hpp +include src/fourier/details/healpix_utility.hpp +include src/fourier/euclidian.hpp +include src/fourier/fft/fftw_calls.hpp +include src/fourier/fft/fftw_calls_mpi.hpp +include src/fourier/fft/fftw_complex.hpp +include src/fourier/healpix.hpp +include src/growthFactor.cpp +include src/growthFactor.hpp +include src/h5_readFlash.cpp +include src/h5_readFlash.hpp +include src/hdf5_array.hpp +include src/hdf5_flash.h +include src/interpolate.cpp +include src/interpolate.hpp +include src/interpolate3d.hpp +include src/kdtree_leaf.hpp +include src/kdtree_leaf.tcc +include src/kdtree_splitters.hpp +include src/loadFlash.cpp +include src/loadFlash.hpp +include src/loadFlash_dummy.cpp +include src/loadGadget.cpp +include src/loadGadget.hpp +include src/loadRamses.cpp +include src/loadRamses.hpp +include src/loadSimu.hpp +include src/load_data.cpp +include src/load_data.hpp +include src/mach.hpp +include src/miniargs.cpp +include src/miniargs.hpp +include src/mykdtree.hpp +include src/mykdtree.tcc +include src/newton.hpp +include src/octTree.hpp +include src/octTree.tcc +include src/openmp.hpp +include src/pool.hpp +include src/powerSpectrum.cpp +include src/powerSpectrum.hpp +include src/replicateGenerator.hpp +include src/sparseGrid.hpp +include src/sparseGrid.tcc +include src/sphSmooth.hpp +include src/sphSmooth.tcc +include src/symbol_visible.hpp +include src/tf_fit.hpp +include src/yorick.hpp +include src/yorick_nc3.cpp +include src/yorick_nc4.cpp diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh new file mode 100755 index 0000000..32ecd8b --- /dev/null +++ b/builder/build-wheels.sh @@ -0,0 +1,27 @@ +#!/bin/bash +set -e -x + +# Install a system package required by our library +#yum install -y atlas-devel +yum install -y cmake3 + + +ALL_PYTHON=cp38-cp38 + +# Compile wheels +for pkg in $ALL_PYTHON; do + PYBIN=/opt/python/${pkg}/bin +# "${PYBIN}/pip" install -r /io/dev-requirements.txt + "${PYBIN}/pip" wheel -v /io/ -w wheelhouse/ +done + +# Bundle external shared libraries into the wheels +for whl in wheelhouse/*.whl; do + auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/ +done + +# Install packages and test +for pkg in $ALL_PYTHON; do + PYBIN=/opt/python/${pkg}/bin + "${PYBIN}/pip" install cosmotool --no-index -f /io/wheelhouse +done diff --git a/builder/start.sh b/builder/start.sh new file mode 100755 index 0000000..31f95f0 --- /dev/null +++ b/builder/start.sh @@ -0,0 +1,12 @@ +#!/bin/bash + +d=$(pwd) +if test x"$(basename $d)" = xbuilder; then + d=${d}/../ +fi +if ! [ -e ${d}/setup.py ] ; then + echo "Unknown directory. Please move to the root of cosmotool source tree." + exit 1 +fi + +podman run -ti --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2014_x86_64 /io/builder/build-wheels.sh diff --git a/setup.py b/setup.py index f1cf6d6..226be38 100644 --- a/setup.py +++ b/setup.py @@ -241,5 +241,6 @@ setup(name='cosmotool', 'build_ext': BuildCMakeExt, 'install_data': InstallCMakeLibsData, 'install_lib': InstallCMakeLibs, - } + }, + python_requires='>=3.6' ) From 9703cbfd70af34ab19dc908ed458976a39b25e2b Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 21:08:27 +0200 Subject: [PATCH 13/18] Improvement for Boost detection --- external/external_build.cmake | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/external/external_build.cmake b/external/external_build.cmake index 43e0021..6f00ec6 100644 --- a/external/external_build.cmake +++ b/external/external_build.cmake @@ -247,17 +247,23 @@ if (INTERNAL_BOOST) ELSE (INTERNAL_BOOST) find_package(Boost 1.69 QUIET) - if (NOT Boost_FOUND) - cmessage(CWARNING "Boost >= 1.69 was not found") - else() - cmessage(STATUS "Boost has been found (version=${Boost_VERSION})") - endif() if (Boost_VERSION) + if (${Boost_VERSION} VERSION_GREATER 1000) + math(EXPR TMP_MAJOR "${Boost_VERSION} / 100000") + math(EXPR TMP_MINOR "(${Boost_VERSION} - ${TMP_MAJOR} * 100000) / 100") + math(EXPR TMP_PATCHLEVEL "${Boost_VERSION} - ${TMP_MAJOR} * 100000 - ${TMP_MINOR} * 100") + set(Boost_VERSION ${TMP_MAJOR}.${TMP_MINOR}.${TMP_PATCHLEVEL}) + ENDIF() if (${Boost_VERSION} VERSION_GREATER_EQUAL 1.70.0) set(Boost_DEP Boost::headers) set(Boost_TARGET Boost::headers) endif() endif() + if (NOT Boost_FOUND) + cmessage(CWARNING "Boost >= 1.69 was not found") + else() + cmessage(STATUS "Boost has been found (version=${Boost_VERSION}), Boost_TARGET=${Boost_Target}") + endif() endif (INTERNAL_BOOST) mark_as_advanced(Boost_INCLUDE_DIRS Boost_LIBRARIES) From 772677590c83d40cc83886d33ba29c1d367aad8f Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 22:34:49 +0200 Subject: [PATCH 14/18] Automate building --- builder/build-wheels.sh | 9 ++++++--- setup.py | 5 +++-- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh index 32ecd8b..ffef437 100755 --- a/builder/build-wheels.sh +++ b/builder/build-wheels.sh @@ -3,16 +3,19 @@ set -e -x # Install a system package required by our library #yum install -y atlas-devel -yum install -y cmake3 +yum install -y cmake3 gsl-devel zlib-devel + +ln -fs /usr/bin/cmake3 /usr/bin/cmake -ALL_PYTHON=cp38-cp38 +ALL_PYTHON="cp37-cp37m cp38-cp38" # Compile wheels for pkg in $ALL_PYTHON; do PYBIN=/opt/python/${pkg}/bin # "${PYBIN}/pip" install -r /io/dev-requirements.txt - "${PYBIN}/pip" wheel -v /io/ -w wheelhouse/ + "${PYBIN}/pip" install -r /io/requirements.txt + "${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/ done # Bundle external shared libraries into the wheels diff --git a/setup.py b/setup.py index 226be38..90aa9d6 100644 --- a/setup.py +++ b/setup.py @@ -218,10 +218,11 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a4', + version='1.0.0a5', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, - setup_requires=['cython','cffi','numexpr'], + install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], + setup_requires=['cython','cffi','numpy','numexpr'], ext_modules=[CosmoTool_extension], description='A small cosmotool box of useful functions', long_description=open("./README.md", 'r').read(), From f6b99a084e5338174c3c9aa63bb10eeaaf633485 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Tue, 28 Apr 2020 22:35:26 +0200 Subject: [PATCH 15/18] Add python requirements --- requirements.txt | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 requirements.txt diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..ef3f5d4 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,5 @@ +numpy +cffi +numexpr +pyfftw +cython From 689cc70daa8006f4e4eeeda29d7bc460f37bf5a7 Mon Sep 17 00:00:00 2001 From: LAVAUX Guilhem Date: Wed, 29 Apr 2020 14:36:41 +0200 Subject: [PATCH 16/18] Fix some warnings --- src/algo.hpp | 2 +- src/config.hpp | 2 +- src/hdf5_array.hpp | 6 ++---- 3 files changed, 4 insertions(+), 6 deletions(-) diff --git a/src/algo.hpp b/src/algo.hpp index 5f896ef..9dcf1bc 100644 --- a/src/algo.hpp +++ b/src/algo.hpp @@ -93,6 +93,6 @@ namespace CosmoTool -}; +} #endif diff --git a/src/config.hpp b/src/config.hpp index 6fa7b63..940919b 100644 --- a/src/config.hpp +++ b/src/config.hpp @@ -165,6 +165,6 @@ namespace CosmoTool FilesystemFullException() : Exception() {} }; -}; +} #endif diff --git a/src/hdf5_array.hpp b/src/hdf5_array.hpp index 11762bb..4cab937 100644 --- a/src/hdf5_array.hpp +++ b/src/hdf5_array.hpp @@ -78,8 +78,6 @@ namespace CosmoTool { } }; - //, typename boost::enable_if >::type> \ - // #define HDF5_TYPE(tl, thdf5) \ template struct get_hdf5_data_type >::type > \ { static H5::DataType type() { return H5::PredType::thdf5; }; } @@ -122,7 +120,7 @@ namespace CosmoTool { template<> struct hdf5_extent_gen<0> { - static inline boost::multi_array_types::extent_gen build(hsize_t *d) + static inline boost::multi_array_types::extent_gen build(hsize_t *) { return boost::extents; } @@ -513,7 +511,7 @@ namespace CosmoTool { \ }; \ }; -}; +} #endif From 46831ba9abc1eb41d48732632c91daf54cdf4e5d Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 4 Aug 2020 10:43:45 +0200 Subject: [PATCH 17/18] Fixes for gadget IO --- builder/build-wheels.sh | 2 +- builder/start.sh | 2 +- python/_cosmotool.pyx | 3 ++- python/cosmotool/simu.py | 4 ++-- 4 files changed, 6 insertions(+), 5 deletions(-) diff --git a/builder/build-wheels.sh b/builder/build-wheels.sh index ffef437..e5c1b6f 100755 --- a/builder/build-wheels.sh +++ b/builder/build-wheels.sh @@ -8,7 +8,7 @@ yum install -y cmake3 gsl-devel zlib-devel ln -fs /usr/bin/cmake3 /usr/bin/cmake -ALL_PYTHON="cp37-cp37m cp38-cp38" +ALL_PYTHON="cp36-cp36m cp37-cp37m cp38-cp38" # Compile wheels for pkg in $ALL_PYTHON; do diff --git a/builder/start.sh b/builder/start.sh index 31f95f0..9fbc185 100755 --- a/builder/start.sh +++ b/builder/start.sh @@ -9,4 +9,4 @@ if ! [ -e ${d}/setup.py ] ; then exit 1 fi -podman run -ti --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2014_x86_64 /io/builder/build-wheels.sh +podman run -ti --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh diff --git a/python/_cosmotool.pyx b/python/_cosmotool.pyx index 61ba1a0..ed9195e 100644 --- a/python/_cosmotool.pyx +++ b/python/_cosmotool.pyx @@ -513,7 +513,8 @@ def writeGadget(str filename, object simulation): simdata.TotalNumPart = NumPart simdata.NumPart = NumPart - cxx_writeGadget(filename, &simdata) + filename_b = bytes(filename, 'utf-8') + cxx_writeGadget(filename_b, &simdata) def loadRamses(str basepath, int snapshot_id, int cpu_id, bool doublePrecision = False, bool loadPosition = True, bool loadVelocity = False, bool loadId = False, bool loadMass = False): """ loadRamses(basepath, snapshot_id, cpu_id, doublePrecision = False, loadPosition = True, loadVelocity = False) diff --git a/python/cosmotool/simu.py b/python/cosmotool/simu.py index 2389926..157e107 100644 --- a/python/cosmotool/simu.py +++ b/python/cosmotool/simu.py @@ -98,12 +98,12 @@ def simpleWriteGadget(filename, positions, boxsize=1.0, Hubble=100, Omega_M=0.30 s.positions = positions - if velocities: + if velocities is not None: s.velocities = velocities else: s.velocities = [np.zeros(positions[0].size,dtype=np.float32)]*3 - if identifiers: + if identifiers is not None: s.identifiers = identifiers else: s.identifiers = np.arange(positions[0].size, dtype=np.int64) From 11f732bd16fbd8565fa6426c69ec4c86f5c7c25a Mon Sep 17 00:00:00 2001 From: Guilhem Lavaux Date: Tue, 4 Aug 2020 11:51:05 +0200 Subject: [PATCH 18/18] Bump version --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 90aa9d6..9bdbd96 100644 --- a/setup.py +++ b/setup.py @@ -218,7 +218,7 @@ class BuildCMakeExt(build_ext): CosmoTool_extension = CMakeExtension(name="cosmotool") setup(name='cosmotool', - version='1.0.0a5', + version='1.0.0a6', packages=["cosmotool"], package_dir={'cosmotool': 'python/cosmotool'}, install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],