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Merge remote-tracking branch 'origin/master'

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This commit is contained in:
Guilhem Lavaux 2021-08-05 08:54:26 +03:00
commit 2d0f34fbc0
10 changed files with 75 additions and 54 deletions
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2
CMakeLists.txt
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@ -71,7 +71,7 @@ SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2") SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
SET(CPACK_PACKAGE_VERSION_MAJOR "1") SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "2") SET(CPACK_PACKAGE_VERSION_MINOR "2")
SET(CPACK_PACKAGE_VERSION_PATCH "2${EXTRA_VERSION}") SET(CPACK_PACKAGE_VERSION_PATCH "3${EXTRA_VERSION}")
SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}") SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
SET(CPACK_STRIP_FILES "lib/libCosmoTool.so") SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
SET(CPACK_SOURCE_IGNORE_FILES SET(CPACK_SOURCE_IGNORE_FILES

2
MANIFEST.in
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@ -86,6 +86,7 @@ include sample/testSmooth.cpp
include sample/test_cosmopower.cpp include sample/test_cosmopower.cpp
include sample/test_fft_calls.cpp include sample/test_fft_calls.cpp
include sample/test_healpix_calls.cpp include sample/test_healpix_calls.cpp
include sample/test_special.cpp
include sample/testkd.cpp include sample/testkd.cpp
include sample/testkd2.cpp include sample/testkd2.cpp
include sample/testkd3.cpp include sample/testkd3.cpp
@ -167,3 +168,4 @@ include src/tf_fit.hpp
include src/yorick.hpp include src/yorick.hpp
include src/yorick_nc3.cpp include src/yorick_nc3.cpp
include src/yorick_nc4.cpp include src/yorick_nc4.cpp
include src/special_math.hpp

8
conda/conda_build_config.yaml
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@ -1,8 +1,10 @@
python: python:
- 3.7
- 3.8
- 3.9 - 3.9
- 3.8
- 3.7
numpy: numpy:
- 1.11
- 1.19 - 1.19
gsl:
- 2.4

32
conda/meta.yaml
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@ -1,48 +1,50 @@
package: package:
name: cosmotool name: cosmotool
version: "1.2.2" version: "1.2.3"
source: source:
git_rev: 03033b6 git_rev: a86c9a8
git_url: https://bitbucket.org/glavaux/cosmotool git_url: https://bitbucket.org/glavaux/cosmotool
requirements: requirements:
build: build:
- numpy >=1.11 - python # [build_platform != target_platform]
- cross-python_{{ target_platform }} # [build_platform != target_platform]
- cython # [build_platform != target_platform]
- numpy # [build_platform != target_platform]
- {{ compiler('c') }} - {{ compiler('c') }}
- {{ compiler('cxx') }} - {{ compiler('cxx') }}
- python - llvm-openmp # [osx]
- setuptools - libgomp # [linux]
- cython
- healpy
- numexpr
- cffi
- pyfftw
- gsl
- h5py
host: host:
- python - python
- pip
- numpy
- pkgconfig
- numexpr - numexpr
- cython - cython
- healpy - healpy
- cffi - cffi
- pyfftw - pyfftw
- gsl - gsl {{ gsl }}
- h5py - h5py
run: run:
- numpy
- python - python
- {{ pin_compatible('numpy') }}
- healpy - healpy
- numexpr - numexpr
- cffi - cffi
- pyfftw - pyfftw
- h5py - h5py
- {{ pin_compatible('gsl') }}
- llvm-openmp
test: test:
imports: imports:
- cosmotool - cosmotool
requires:
- pip
about: about:
home: https://bitbucket.org/glavaux/cosmotool home: https://bitbucket.org/glavaux/cosmotool

3
external/external_build.cmake vendored
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@ -8,7 +8,7 @@ SET(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACH
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(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") SET(NETCDF_URL "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.5.0.tar.gz" CACHE STRING "URL to download NetCDF from")
SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ from") SET(NETCDFCXX_URL "https://github.com/Unidata/netcdf-cxx4/archive/v4.3.0.tar.gz" CACHE STRING "URL to download NetCDF-C++ from")
SET(BOOST_URL "http://sourceforge.net/projects/boost/files/boost/1.61.0/boost_1_61_0.tar.gz/download" CACHE STRING "URL to download Boost from") SET(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.74.0/source/boost_1_74_0.tar.bz2" CACHE STRING "URL to download Boost from")
SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ") SET(GSL_URL "ftp://ftp.gnu.org/gnu/gsl/gsl-1.15.tar.gz" CACHE STRING "URL to download GSL from ")
mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL) mark_as_advanced(FFTW_URL EIGEN_URL HDF5_URL NETCDF_URL BOOST_URL GSL_URL)
@ -234,6 +234,7 @@ if (INTERNAL_BOOST)
ExternalProject_Add(boost ExternalProject_Add(boost
URL ${BOOST_URL} URL ${BOOST_URL}
PREFIX ${BUILD_PREFIX}/boost-prefix PREFIX ${BUILD_PREFIX}/boost-prefix
URL_HASH MD5=da07ca30dd1c0d1fdedbd487efee01bd
CONFIGURE_COMMAND CONFIGURE_COMMAND
${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost
BUILD_IN_SOURCE 1 BUILD_IN_SOURCE 1

57
external/patch-omptl vendored
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@ -1,6 +1,6 @@
diff -ur omptl.orig/omptl_algorithm omptl/omptl_algorithm diff -ur omptl.old/omptl_algorithm omptl/omptl_algorithm
--- omptl.orig/omptl_algorithm 2017-01-16 14:58:37.996690639 +0100 --- omptl.old/omptl_algorithm 2012-04-22 16:29:41.000000000 +0200
+++ omptl/omptl_algorithm 2017-01-16 15:00:26.678641720 +0100 +++ omptl/omptl_algorithm 2021-06-20 15:40:29.000000000 +0200
@@ -20,7 +20,7 @@ @@ -20,7 +20,7 @@
#define OMPTL_ALGORITHM 1 #define OMPTL_ALGORITHM 1
@ -22,9 +22,9 @@ diff -ur omptl.orig/omptl_algorithm omptl/omptl_algorithm
#endif #endif
#endif /* OMPTL_ALGORITHM */ #endif /* OMPTL_ALGORITHM */
diff -ur omptl.orig/omptl_algorithm_par.h omptl/omptl_algorithm_par.h diff -ur omptl.old/omptl_algorithm_par.h omptl/omptl_algorithm_par.h
--- omptl.orig/omptl_algorithm_par.h 2017-01-16 14:58:37.996690639 +0100 --- omptl.old/omptl_algorithm_par.h 2012-04-22 16:29:41.000000000 +0200
+++ omptl/omptl_algorithm_par.h 2017-01-16 14:59:57.974126410 +0100 +++ omptl/omptl_algorithm_par.h 2021-06-20 15:40:50.000000000 +0200
@@ -21,8 +21,8 @@ @@ -21,8 +21,8 @@
#include <cmath> #include <cmath>
#include <cstdlib> #include <cstdlib>
@ -36,9 +36,18 @@ diff -ur omptl.orig/omptl_algorithm_par.h omptl/omptl_algorithm_par.h
#include <iterator> #include <iterator>
diff -ur omptl.orig/omptl_numeric omptl/omptl_numeric @@ -1700,7 +1700,7 @@
--- omptl.orig/omptl_numeric 2017-01-16 14:58:37.996690639 +0100
+++ omptl/omptl_numeric 2017-01-16 15:00:57.051186974 +0100 std::vector<char> pivot_used(pivots.size(), false); // can't be bool due to parallel write
- const unsigned max_depth = std::floor(std::tr1::log2(P));
+ const unsigned max_depth = unsigned(std::floor(std::log2(P)));
assert(1u << max_depth <= P);
for (unsigned i = 0; i < max_depth; ++i)
{
diff -ur omptl.old/omptl_numeric omptl/omptl_numeric
--- omptl.old/omptl_numeric 2012-04-22 16:29:41.000000000 +0200
+++ omptl/omptl_numeric 2021-06-20 15:40:29.000000000 +0200
@@ -19,7 +19,7 @@ @@ -19,7 +19,7 @@
#define OMPTL_NUMERIC 1 #define OMPTL_NUMERIC 1
@ -63,9 +72,9 @@ diff -ur omptl.orig/omptl_numeric omptl/omptl_numeric
+#include "omptl_numeric_extensions.h" +#include "omptl_numeric_extensions.h"
#endif /* OMPTL_NUMERIC */ #endif /* OMPTL_NUMERIC */
diff -ur omptl.orig/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h diff -ur omptl.old/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h
--- omptl.orig/omptl_numeric_extensions.h 2017-01-16 14:58:37.996690639 +0100 --- omptl.old/omptl_numeric_extensions.h 2012-04-22 16:29:41.000000000 +0200
+++ omptl/omptl_numeric_extensions.h 2017-01-16 14:59:21.549472508 +0100 +++ omptl/omptl_numeric_extensions.h 2021-06-20 15:40:29.000000000 +0200
@@ -51,9 +51,9 @@ @@ -51,9 +51,9 @@
} // namespace } // namespace
@ -78,9 +87,9 @@ diff -ur omptl.orig/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h
#endif #endif
namespace omptl namespace omptl
diff -ur omptl.orig/omptl_numeric_par.h omptl/omptl_numeric_par.h diff -ur omptl.old/omptl_numeric_par.h omptl/omptl_numeric_par.h
--- omptl.orig/omptl_numeric_par.h 2017-01-16 14:58:37.996690639 +0100 --- omptl.old/omptl_numeric_par.h 2012-04-22 16:29:41.000000000 +0200
+++ omptl/omptl_numeric_par.h 2017-01-16 14:59:36.397739066 +0100 +++ omptl/omptl_numeric_par.h 2021-06-20 15:40:29.000000000 +0200
@@ -23,8 +23,8 @@ @@ -23,8 +23,8 @@
#include <functional> #include <functional>
#include <iterator> #include <iterator>
@ -92,15 +101,15 @@ diff -ur omptl.orig/omptl_numeric_par.h omptl/omptl_numeric_par.h
namespace omptl namespace omptl
{ {
diff -ur omptl.orig/omptl_algorithm_par.h omptl/omptl_algorithm_par.h diff -ur omptl.old/omptl_tools.h omptl/omptl_tools.h
--- omptl.orig/omptl_algorithm_par.h 2021-05-09 14:26:47.227632829 +0300 --- omptl.old/omptl_tools.h 2012-04-22 16:29:41.000000000 +0200
+++ omptl/omptl_algorithm_par.h 2021-05-09 14:27:02.815744567 +0300 +++ omptl/omptl_tools.h 2021-06-20 15:40:42.000000000 +0200
@@ -1700,7 +1700,7 @@ @@ -25,7 +25,7 @@
#include <climits>
#include <iterator>
std::vector<char> pivot_used(pivots.size(), false); // can't be bool due to parallel write -#include <tr1/cmath>
+#include <cmath>
- const unsigned max_depth = std::floor(std::tr1::log2(P)); namespace omptl
+ const unsigned max_depth = unsigned(std::floor(std::tr1::log2(P)));
assert(1u << max_depth <= P);
for (unsigned i = 0; i < max_depth; ++i)
{ {

2
requirements.txt
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@ -1,4 +1,4 @@
numpy numpy<1.19
cffi cffi
numexpr numexpr
pyfftw pyfftw

16
setup.py
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@ -168,10 +168,16 @@ class BuildCMakeExt(build_ext):
# Below is just an example set of arguments for building Blender as a Python module # Below is just an example set of arguments for building Blender as a Python module
compilers=[] compilers=[]
if "CC" in os.environ: fill_up_settings=[
compilers.append('-DCMAKE_C_COMPILER=' + os.environ["CC"]) ("CMAKE_C_COMPILER", "CC"),
if "CXX" in os.environ: ("CMAKE_CXX_COMPILER", "CXX"),
compilers.append("-DCMAKE_CXX_COMPILER=" + os.environ["CXX"]) ("CMAKE_C_FLAGS", "CFLAGS"),
("CMAKE_EXE_LINKER_FLAGS_INIT", "LDFLAGS"),
("CMAKE_SHARED_LINKER_FLAGS_INIT", "LDFLAGS"),
("CMAKE_MODULE_LINKER_FLAGS_INIT", "LDFLAGS")]
for cmake_flag, os_flag in fill_up_settings:
if os_flag in os.environ:
compilers.append(f"-D{cmake_flag}={os.environ[os_flag]}")
self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp, self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp,
'-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON', '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON',
@ -223,7 +229,7 @@ class BuildCMakeExt(build_ext):
CosmoTool_extension = CMakeExtension(name="cosmotool") CosmoTool_extension = CMakeExtension(name="cosmotool")
setup(name='cosmotool', setup(name='cosmotool',
version='1.2.2', version='1.2.3',
packages=["cosmotool"], packages=["cosmotool"],
package_dir={'cosmotool': 'python/cosmotool'}, package_dir={'cosmotool': 'python/cosmotool'},
install_requires=['numpy','cffi','numexpr','pyfftw','h5py'], install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],

1
src/CMakeLists.txt
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@ -38,6 +38,7 @@ if (HDF5_FOUND)
h5_readFlash.cpp h5_readFlash.cpp
loadFlash.cpp loadFlash.cpp
) )
add_dependencies(CosmoHDF5 ${cosmotool_DEPS})
set_property(TARGET CosmoHDF5 PROPERTY POSITION_INDEPENDENT_CODE ${BUILD_SHARED_LIBS}) set_property(TARGET CosmoHDF5 PROPERTY POSITION_INDEPENDENT_CODE ${BUILD_SHARED_LIBS})
target_include_directories(CosmoHDF5 BEFORE PRIVATE ${HDF5_INCLUDE_DIR}) target_include_directories(CosmoHDF5 BEFORE PRIVATE ${HDF5_INCLUDE_DIR})
else(HDF5_FOUND) else(HDF5_FOUND)

4
src/hdf5_array.hpp
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@ -426,7 +426,7 @@ namespace CosmoTool {
#define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \ #define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \
{ \ { \
::CosmoTool::get_hdf5_data_type<BOOST_PP_TUPLE_ELEM(2, 0, element)> t; \ ::CosmoTool::get_hdf5_data_type<BOOST_PP_TUPLE_ELEM(2, 0, element)> t; \
position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \ long position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \
const char *field_name = BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, element)); \ const char *field_name = BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2, 1, element)); \
type.insertMember(field_name, position, t.type()); \ type.insertMember(field_name, position, t.type()); \
} }
@ -439,7 +439,6 @@ namespace CosmoTool { \
\ \
TNAME() : type(sizeof(STRUCT)) \ TNAME() : type(sizeof(STRUCT)) \
{ \ { \
long position; \
BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ELEMENT, STRUCT, ATTRIBUTES) \ BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ELEMENT, STRUCT, ATTRIBUTES) \
} \ } \
\ \
@ -471,7 +470,6 @@ namespace CosmoTool { \
\ \
TNAME() : type(sizeof(STRUCT)) \ TNAME() : type(sizeof(STRUCT)) \
{ \ { \
long position; \
BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ENUM_ELEMENT, STRUCT, ATTRIBUTES) \ BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ENUM_ELEMENT, STRUCT, ATTRIBUTES) \
} \ } \
\ \