guilhem_lavaux/cosmotool
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'origin/master'

Browse Source
This commit is contained in:
guilhem.lavaux@iap.fr 2023-12-03 20:30:25 +01:00
commit d2cd6bb650
3 changed files with 34 additions and 29 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

7
builder/build-wheels.sh
View File

@ -13,6 +13,9 @@ yum install -y cmake3 gsl-devel zlib-devel fftw3-devel libffi-devel hdf5 hdf5-de
ln -fs /usr/bin/cmake3 /usr/bin/cmake ln -fs /usr/bin/cmake3 /usr/bin/cmake
test -d /io/wheelhouse || mkdir /io/wheelhouse
test -d /io/wheelhouse/fix || mkdir /io/wheelhouse/fix
ALL_PYTHON="cp37-cp37m cp38-cp38 cp39-cp39 cp310-cp310" ALL_PYTHON="cp37-cp37m cp38-cp38 cp39-cp39 cp310-cp310"
# Compile wheels # Compile wheels
@ -25,8 +28,8 @@ for pkg in $ALL_PYTHON; do
done done
# Bundle external shared libraries into the wheels # Bundle external shared libraries into the wheels
for whl in wheelhouse/cosmotool*.whl; do for whl in /io/wheelhouse/cosmotool*.whl; do
auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/ auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/fix
done done
# Install packages and test # Install packages and test

28
external/external_build.cmake vendored
View File

@ -5,11 +5,11 @@ 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 STRING "URL to download FFTW from") SET(FFTW_URL "http://www.fftw.org/fftw-3.3.3.tar.gz" CACHE STRING "URL to download FFTW from")
SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" CACHE STRING "URL to download Eigen from") SET(EIGEN_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" 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(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(HDF5_URL "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2.tar.gz" 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 "https://downloads.unidata.ucar.edu/netcdf-c/4.9.2/netcdf-c-4.9.2.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/v4.3.1.tar.gz" CACHE STRING "URL to download NetCDF-C++ 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(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/boost_1_82_0.tar.gz" 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 "https://ftpmirror.gnu.org/gsl/gsl-2.7.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)
SET(all_deps) SET(all_deps)
@ -90,7 +90,7 @@ if (INTERNAL_HDF5)
ExternalProject_Add(hdf5 ExternalProject_Add(hdf5
PREFIX ${BUILD_PREFIX}/hdf5-prefix PREFIX ${BUILD_PREFIX}/hdf5-prefix
URL ${HDF5_URL} URL ${HDF5_URL}
URL_HASH MD5=29117bf488887f89888f9304c8ebea0b URL_HASH MD5=30172c75e436d7f2180e274071a4ca97
CMAKE_ARGS CMAKE_ARGS
-DCMAKE_INSTALL_PREFIX=${EXT_INSTALL} -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@ -99,6 +99,7 @@ if (INTERNAL_HDF5)
-DHDF5_BUILD_TOOLS=ON -DHDF5_BUILD_TOOLS=ON
-DHDF5_BUILD_HL_LIB=ON -DHDF5_BUILD_HL_LIB=ON
-DBUILD_SHARED_LIBS=OFF -DBUILD_SHARED_LIBS=OFF
-DHDF5_ENABLE_Z_LIB_SUPPORT=ON
) )
SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5) SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5)
SET(hdf5_built hdf5) SET(hdf5_built hdf5)
@ -106,11 +107,11 @@ if (INTERNAL_HDF5)
SET(HDF5_ROOTDIR ${HDF5_BIN_DIR}) SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib") SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl") SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl")
set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5-static.a) set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a)
set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a) set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a)
set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5-static.a CACHE STRING "HDF5 lib" FORCE) set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl-static.a CACHE STRING "HDF5 HL lib" FORCE) set(HDF5_HL_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_hl.a CACHE STRING "HDF5 HL lib" FORCE)
set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp-static.a CACHE STRING "HDF5 C++ lib" FORCE) set(HDF5_CXX_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5_cpp.a CACHE STRING "HDF5 C++ lib" FORCE)
SET(HDF5_INCLUDE_DIRS ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE) SET(HDF5_INCLUDE_DIRS ${HDF5_BIN_DIR}/include CACHE STRING "HDF5 include path" FORCE)
mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS) mark_as_advanced(HDF5_LIBRARIES HDF5_CXX_LIBRARIES HDF5_INCLUDE_DIRS)
@ -168,7 +169,7 @@ if (INTERNAL_NETCDF)
SET(NETCDF_CONFIG_COMMAND ${NETCDF_SOURCE_DIR}/configure SET(NETCDF_CONFIG_COMMAND ${NETCDF_SOURCE_DIR}/configure
--prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib --prefix=${NETCDF_BIN_DIR} --libdir=${NETCDF_BIN_DIR}/lib
--enable-netcdf-4 --with-pic --disable-shared --disable-dap --enable-netcdf-4 --with-pic --disable-shared --disable-dap
--disable-cdmremote --disable-rpc --enable-cxx-4 --disable-byterange --disable-cdmremote --disable-rpc --enable-cxx-4
--disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER} --disable-examples ${EXTRA_NC_FLAGS} CC=${CMAKE_C_COMPILER}
CXX=${CMAKE_CXX_COMPILER}) CXX=${CMAKE_CXX_COMPILER})
list(INSERT CMAKE_PREFIX_PATH 0 ${EXT_INSTALL}) list(INSERT CMAKE_PREFIX_PATH 0 ${EXT_INSTALL})
@ -186,6 +187,7 @@ if (INTERNAL_NETCDF)
-DBUILD_TESTING=OFF -DBUILD_TESTING=OFF
-DCMAKE_BUILD_TYPE=Release -DCMAKE_BUILD_TYPE=Release
-DENABLE_NETCDF4=ON -DENABLE_NETCDF4=ON
-DENABLE_BYTERANGE=FALSE
-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_POSITION_INDEPENDENT_CODE=ON
-DENABLE_DAP=OFF -DENABLE_DAP=OFF
-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR} -DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
@ -242,7 +244,7 @@ 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 URL_HASH MD5=f7050f554a65f6a42ece221eaeec1660
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

28
setup.py
View File

@ -76,9 +76,9 @@ class InstallCMakeLibs(install_lib):
# # your files are moved to the appropriate location when the installation # # your files are moved to the appropriate location when the installation
# # is run # # is run
# #
# libs = [os.path.join(bin_dir, _lib) for _lib in # libs = [os.path.join(bin_dir, _lib) for _lib in
# os.listdir(bin_dir) if # os.listdir(bin_dir) if
# os.path.isfile(os.path.join(bin_dir, _lib)) and # os.path.isfile(os.path.join(bin_dir, _lib)) and
# os.path.splitext(_lib)[1] in [".dll", ".so"] # os.path.splitext(_lib)[1] in [".dll", ".so"]
# and not (_lib.startswith("python") or _lib.startswith(PACKAGE_NAME))] # and not (_lib.startswith("python") or _lib.startswith(PACKAGE_NAME))]
# #
@ -87,16 +87,16 @@ class InstallCMakeLibs(install_lib):
# shutil.move(lib, os.path.join(self.build_dir, # shutil.move(lib, os.path.join(self.build_dir,
# os.path.basename(lib))) # os.path.basename(lib)))
# #
# # Mark the libs for installation, adding them to # # Mark the libs for installation, adding them to
# # distribution.data_files seems to ensure that setuptools' record # # distribution.data_files seems to ensure that setuptools' record
# # writer appends them to installed-files.txt in the package's egg-info # # writer appends them to installed-files.txt in the package's egg-info
# # # #
# # Also tried adding the libraries to the distribution.libraries list, # # Also tried adding the libraries to the distribution.libraries list,
# # but that never seemed to add them to the installed-files.txt in the # # but that never seemed to add them to the installed-files.txt in the
# # egg-info, and the online recommendation seems to be adding libraries # # egg-info, and the online recommendation seems to be adding libraries
# # into eager_resources in the call to setup(), which I think puts them # # into eager_resources in the call to setup(), which I think puts them
# # in data_files anyways. # # in data_files anyways.
# # # #
# # What is the best way? # # What is the best way?
# #
# # These are the additional installation files that should be # # These are the additional installation files that should be
@ -104,7 +104,7 @@ class InstallCMakeLibs(install_lib):
# # step; depending on the files that are generated from your cmake # # step; depending on the files that are generated from your cmake
# # build chain, you may need to modify the below code # # build chain, you may need to modify the below code
# #
# self.distribution.data_files = [os.path.join(self.install_dir, # self.distribution.data_files = [os.path.join(self.install_dir,
# os.path.basename(lib)) # os.path.basename(lib))
# for lib in libs] # for lib in libs]
# print(self.distribution.data_files) # print(self.distribution.data_files)
@ -213,7 +213,7 @@ class BuildCMakeExt(build_ext):
if _pyd_top[0].startswith(PACKAGE_NAME): if _pyd_top[0].startswith(PACKAGE_NAME):
if os.path.splitext(_pyd)[1] in [".pyd", ".so"] or _pyd_top[-1] == 'config.py': if os.path.splitext(_pyd)[1] in [".pyd", ".so"] or _pyd_top[-1] == 'config.py':
pyd_path.append((_pyd_top,_pyd)) pyd_path.append((_pyd_top,_pyd))
for top,p in pyd_path: for top,p in pyd_path:
_,n = os.path.split(p) _,n = os.path.split(p)
@ -229,7 +229,7 @@ class BuildCMakeExt(build_ext):
CosmoTool_extension = CMakeExtension(name="cosmotool") CosmoTool_extension = CMakeExtension(name="cosmotool")
setup(name='cosmotool', setup(name='cosmotool',
version='1.3.2', version='1.3.3',
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'],