Add ZLIB package

CMakeLists.txt

@@ -42,6 +42,18 @@ ENDIF(BUILD_PYTHON)
 
 MESSAGE(STATUS "Using the target ${CosmoTool_local} to build python module")
 
+find_package(ZLIB)
+find_library(ZLIB_LIBRARY z)
+find_library(DL_LIBRARY dl)
+find_library(RT_LIBRARY rt)
+if (RT_LIBRARY)
+  SET(RT_DEP rt)
+  message(STATUS "RT found, linking against it")
+else()
+  SET(RT_DEP)
+endif()
+find_library(MATH_LIBRARY m)
+
 include(${CMAKE_SOURCE_DIR}/external/external_build.cmake)
 
 IF(YORICK_SUPPORT)
@@ -55,9 +67,6 @@ IF(YORICK_SUPPORT)
 ENDIF(YORICK_SUPPORT)
 
 find_program(CYTHON NAMES cython3 cython)
-find_library(ZLIB_LIBRARY z)
-find_library(DL_LIBRARY dl)
-find_library(MATH_LIBRARY m)
 
 set(NETCDF_FIND_REQUIRED ${YORICK_SUPPORT})
 set(GSL_FIND_REQUIRED TRUE)
@@ -71,10 +80,10 @@ SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
 SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "1${EXTRA_VERSION}")
+SET(CPACK_PACKAGE_VERSION_PATCH "4${EXTRA_VERSION}")
 SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
 SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
-SET(CPACK_SOURCE_IGNORE_FILES 
+SET(CPACK_SOURCE_IGNORE_FILES
 "/CVS/;/\\\\.git/;/\\\\.svn/;\\\\.swp$;\\\\.#;/#;.*~;cscope.*;/CMakeFiles/;.*\\\\.cmake;Makefile")
 
 add_subdirectory(src)

MANIFEST.in

@@ -1,4 +1,5 @@
 include  .gitignore
+include  pyproject.toml
 include  CMakeLists.txt
 include  FindNumPy.cmake
 include  FindPyLibs.cmake
@@ -16,14 +17,17 @@ include  doc/source/cpplibrary.rst
 include  doc/source/index.rst
 include  doc/source/intro.rst
 include  doc/source/pythonmodule.rst
+include  external/config.guess
+include  external/config.sub
 include  external/external_build.cmake
-include  external/libsharp-6077806.tar.gz
+include  external/libsharp-8d51946.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/_cosmomath.pyx
 include  python/_cosmotool.pyx
 include  python/_fast_interp.pyx
 include  python/_project.pyx
@@ -93,6 +97,7 @@ include  sample/testkd3.cpp
 include  setup.py
 include  src/CMakeLists.txt
 include  src/algo.hpp
+include  src/numpy_adaptors.hpp
 include  src/bqueue.hpp
 include  src/bqueue.tcc
 include  src/bsp_simple.hpp

builder/build-wheels.sh

@@ -16,7 +16,7 @@ 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="cp39-cp39 cp310-cp310"
 
 # Compile wheels
 for pkg in $ALL_PYTHON; do
@@ -24,11 +24,11 @@ for pkg in $ALL_PYTHON; do
 #    "${PYBIN}/pip" install -r /io/dev-requirements.txt
     "${PYBIN}/pip" install setuptools wheel Cython 
     "${PYBIN}/pip" install -r /io/requirements.txt
-    "${PYBIN}/pip" wheel -vvv /io/ -w wheelhouse/
+    "${PYBIN}/pip" wheel -vvv /io/ -w /io/wheelhouse/
 done
 
 # Bundle external shared libraries into the wheels
-for whl in /io/wheelhouse/cosmotool*.whl; do
+for whl in /io/wheelhouse/cosmotool*linux*.whl; do
     auditwheel repair "$whl" --plat $PLAT -w /io/wheelhouse/fix
 done
 

builder/start.sh

@@ -9,4 +9,4 @@ if ! [ -e ${d}/setup.py ] ; then
   exit 1
 fi
 
-podman run -ti  --rm -e PLAT=manylinux2010_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2010_x86_64 /io/builder/build-wheels.sh
+podman run -ti  --rm -e PLAT=manylinux2014_x86_64 -v ${d}:/io:Z quay.io/pypa/manylinux2014_x86_64 /io/builder/build-wheels.sh

external/external_build.cmake

@@ -2,6 +2,7 @@ include(FindOpenMP)
 
 OPTION(ENABLE_OPENMP "Set to Yes if Healpix and/or you need openMP" OFF)
 
+SET(SOURCE_PREFIX ${CMAKE_SOURCE_DIR})
 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(GENGETOPT_URL "ftp://ftp.gnu.org/gnu/gengetopt/gengetopt-2.22.5.tar.gz" CACHE STRING "URL to download gengetopt from")
@@ -12,6 +13,8 @@ SET(BOOST_URL "https://boostorg.jfrog.io/artifactory/main/release/1.82.0/source/
 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)
 
+file(MAKE_DIRECTORY ${SOURCE_PREFIX}/downloads)
+
 SET(all_deps)
 
 MACRO(CHECK_CHANGE_STATE VAR) 
@@ -36,12 +39,13 @@ CHECK_CHANGE_STATE(INTERNAL_DLIB DLIB_INCLUDE_DIR DLIB_LIBRARIES)
 
 IF(ENABLE_OPENMP)
   IF (NOT OPENMP_FOUND)
-    MESSAGE(ERROR "No known compiler option for enabling OpenMP")
+    MESSAGE(NOTICE "No known compiler option for enabling OpenMP")
+  ELSE()
+    SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+    SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}")
   ENDIF(NOT OPENMP_FOUND)
 
-  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-  SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS}")
 ENDIF(ENABLE_OPENMP)
 
 
@@ -55,21 +59,25 @@ if (ENABLE_SHARP)
   SET(DEP_BUILD ${BUILD_PREFIX}/sharp-prefix/src/sharp/auto)
   IF(NOT ENABLE_OPENMP)
     SET(SHARP_OPENMP --disable-openmp)
+  ELSE()
+    SET(SHARP_OPENMP)
   ENDIF()
   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)
+  message(STATUS "Flags: ${CMAKE_C_FLAGS}")
   ExternalProject_Add(sharp
-    URL ${CMAKE_SOURCE_DIR}/external/libsharp-6077806.tar.gz
+    URL ${CMAKE_SOURCE_DIR}/external/libsharp-8d51946.tar.gz
     PREFIX ${BUILD_PREFIX}/sharp-prefix
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     BUILD_IN_SOURCE 1 
     CONFIGURE_COMMAND
           cp -f ${CMAKE_SOURCE_DIR}/external/config.guess . &&
           cp -f ${CMAKE_SOURCE_DIR}/external/config.sub . &&
           autoconf &&
-          ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
+          ./configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" "CFLAGS=${CMAKE_C_FLAGS}" "LDFLAGS=${CMAKE_EXE_LINKER_FLAGS}" --prefix=${DEP_BUILD} ${SHARP_OPENMP}
     INSTALL_COMMAND echo "No install"
     BUILD_BYPRODUCTS ${SHARP_LIBRARIES}
   )
@@ -87,22 +95,17 @@ if (INTERNAL_HDF5)
     PREFIX ${BUILD_PREFIX}/hdf5-prefix
     URL ${HDF5_URL}
     URL_HASH MD5=30172c75e436d7f2180e274071a4ca97
-    CMAKE_ARGS
-       -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
-       -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-       -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
-       -DHDF5_BUILD_CPP_LIB=ON
-       -DHDF5_BUILD_TOOLS=ON
-       -DHDF5_BUILD_HL_LIB=ON
-       -DBUILD_SHARED_LIBS=OFF
-       -DHDF5_ENABLE_Z_LIB_SUPPORT=ON
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
+    CONFIGURE_COMMAND
+        ${HDF5_SOURCE_DIR}/configure "CC=${CMAKE_C_COMPILER}" "CXX=${CMAKE_CXX_COMPILER}" "CFLAGS=${CMAKE_C_FLAGS}" "LDFLAGS=${CMAKE_EXE_LINKER_FLAGS}" --prefix=${HDF5_BIN_DIR} --disable-shared  --enable-cxx --enable-hl --enable-tools --with-pic
+    INSTALL_COMMAND make install
   )
   SET(cosmotool_DEPS ${cosmotool_DEPS} hdf5)
   SET(hdf5_built hdf5)
   SET(ENV{HDF5_ROOT} ${HDF5_BIN_DIR})
   SET(HDF5_ROOTDIR ${HDF5_BIN_DIR})
   SET(CONFIGURE_LDFLAGS "${CONFIGURE_LDFLAGS} -L${HDF5_BIN_DIR}/lib")
-  SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl")
+  SET(CONFIGURE_LIBS "${CONFIGURE_LIBS} -ldl ${RT_LIBRARY}")
   set(HDF5_C_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5.a)
   set(HDF5_HL_STATIC_LIBRARY ${HDF5_BIN_DIR}/lib/libhdf5_hl.a)
   set(HDF5_LIBRARIES ${HDF5_BIN_DIR}/lib/libhdf5.a CACHE STRING "HDF5 lib" FORCE)
@@ -172,37 +175,45 @@ if (INTERNAL_NETCDF)
   string(REPLACE ";" "|" CMAKE_PREFIX_PATH_ALT_SEP "${CMAKE_PREFIX_PATH}")
   ExternalProject_Add(netcdf
     DEPENDS ${hdf5_built}
+    URL_HASH MD5=f48ee01534365006934f0c63d4055ea0
     PREFIX ${BUILD_PREFIX}/netcdf-prefix
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     URL ${NETCDF_URL}
-  LIST_SEPARATOR |
-	CMAKE_ARGS
+    LIST_SEPARATOR |
+    CMAKE_ARGS
 		-DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH_ALT_SEP}
 		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
 		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                -DNC_EXTRA_DEPS=${RT_DEP}
 		-DBUILD_SHARED_LIBS=OFF
 		-DBUILD_TESTING=OFF
 		-DCMAKE_BUILD_TYPE=Release
 		-DENABLE_NETCDF4=ON
                 -DENABLE_BYTERANGE=FALSE
-    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
-    -DENABLE_DAP=OFF
+		-DCMAKE_POSITION_INDEPENDENT_CODE=ON
+		-DENABLE_DAP=OFF
 		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
                 -DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY}
                 -DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY}
                 -DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS}
-    -DCMAKE_INSTALL_LIBDIR=lib
+		-DCMAKE_INSTALL_LIBDIR=lib
   )
   
   SET(NETCDFCXX_SOURCE_DIR ${BUILD_PREFIX}/netcdf-c++-prefix/src/netcdf-c++)
   ExternalProject_Add(netcdf-c++
     DEPENDS ${hdf5_built} netcdf
     PREFIX ${BUILD_PREFIX}/netcdf-c++-prefix
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     URL ${NETCDFCXX_URL}
 	CMAKE_ARGS
+		-DCMAKE_PREFIX_PATH=${CMAKE_PREFIX_PATH_ALT_SEP}
 		-DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
 		-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
 		-DBUILD_SHARED_LIBS=OFF
-    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
+                -DCMAKE_POSITION_INDEPENDENT_CODE=ON
+                -DHDF5_C_LIBRARY=${HDF5_C_STATIC_LIBRARY}
+                -DHDF5_HL_LIBRARY=${HDF5_HL_STATIC_LIBRARY}
+                -DHDF5_INCLUDE_DIR=${HDF5_INCLUDE_DIRS}
 		-DBUILD_TESTING=OFF
 		-DCMAKE_BUILD_TYPE=Release
 		-DCMAKE_INSTALL_PREFIX=${NETCDF_BIN_DIR}
@@ -240,6 +251,7 @@ if (INTERNAL_BOOST)
   ExternalProject_Add(boost
     URL ${BOOST_URL}
     PREFIX ${BUILD_PREFIX}/boost-prefix
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     URL_HASH MD5=f7050f554a65f6a42ece221eaeec1660
     CONFIGURE_COMMAND 
            ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost
@@ -283,6 +295,7 @@ IF(INTERNAL_GSL)
   ExternalProject_Add(gsl
     URL ${GSL_URL}
     PREFIX ${BUILD_PREFIX}/gsl-prefix
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
     CONFIGURE_COMMAND ${GSL_SOURCE_DIR}/configure
            --prefix=${EXT_INSTALL} --disable-shared
            --with-pic
@@ -335,6 +348,7 @@ IF(INTERNAL_FFTW)
   ExternalProject_Add(fftw
      URL ${FFTW_URL}
      PREFIX ${BUILD_PREFIX}/fftw-prefix
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
      CONFIGURE_COMMAND 
            ${FFTW_SOURCE}/configure
                  --prefix=${EXT_INSTALL}
@@ -364,6 +378,7 @@ IF (INTERNAL_EIGEN)
   ExternalProject_Add(eigen
      URL ${EIGEN_URL}
      URL_HASH MD5=b9e98a200d2455f06db9c661c5610496
+    DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
      PREFIX ${BUILD_PREFIX}/eigen-prefix
      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${EXT_INSTALL}
        -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@@ -396,6 +411,7 @@ SET(cosmotool_DEPS ${cosmotool_DEPS} omptl)
 SET(OMPTL_BUILD_DIR ${BUILD_PREFIX}/omptl-prefix/src/omptl)
 ExternalProject_Add(omptl
   PREFIX ${BUILD_PREFIX}/omptl-prefix
+  DOWNLOAD_DIR ${SOURCE_PREFIX}/downloads
   URL ${CMAKE_SOURCE_DIR}/external/omptl-20120422.tar.bz2
   CONFIGURE_COMMAND echo "No configure"
   BUILD_COMMAND echo "No build"

pyproject.toml

@@ -0,0 +1,8 @@
+[build-system]
+requires = ["setuptools","wheel","cython"]
+build-backend = "setuptools.build_meta"
+
+
+[tool.towncrier]
+directory = "changes"
+

python/CMakeLists.txt

@@ -2,7 +2,7 @@ set(CMAKE_SHARED_MODULE_PREFIX)
 
 
 set(PYTHON_INCLUDES ${NUMPY_INCLUDE_DIRS} ${PYTHON_INCLUDE_PATH} ${CMAKE_SOURCE_DIR}/python)
-include_directories(${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src)
+include_directories(${CMAKE_SOURCE_DIR}/python ${CMAKE_SOURCE_DIR}/src ${CMAKE_BINARY_DIR}/src)
 
 IF(CYTHON)
   add_custom_command(
@@ -69,13 +69,10 @@ target_link_libraries(_fast_interp PRIVATE ${CosmoTool_local} )
 SET(ct_TARGETS   _cosmotool _project _cosmo_power _cosmo_cic _fast_interp _cosmomath)
 
 if (Boost_FOUND)
-  message(STATUS "Building bispectrum support (path = ${Boost_INCLUDE_DIRS})")
+  message(STATUS "Building bispectrum support")
   include_directories(${Boost_INCLUDE_DIRS})
   add_library(_cosmo_bispectrum MODULE _cosmo_bispectrum.cpp)
   target_link_libraries(_cosmo_bispectrum ${MATH_LIBRARY})
-  if(ENABLE_OPENMP)
-    set_target_properties(_cosmo_bispectrum PROPERTIES COMPILE_FLAGS "${OpenMP_CXX_FLAGS}" LINK_FLAGS "${OpenMP_CXX_FLAGS}")
-  endif()
   if (Boost_DEP)
     add_dependencies(_cosmo_bispectrum ${Boost_DEP})
   endif()

python/_cosmomath.pyx

@@ -12,7 +12,7 @@ cdef extern from "numpy/npy_common.h":
    ctypedef npy_intp
 
 cdef extern from "special_math.hpp" namespace "CosmoTool":
-   T log_modified_bessel_first_kind[T](T v, T z) nogil except +
+   T log_modified_bessel_first_kind[T](T v, T z) except + nogil
 
 cdef extern from "numpy_adaptors.hpp" namespace "CosmoTool":
    void parallel_ufunc_dd_d[T,IT](char **args, IT* dimensions, IT* steps, void *func)

python/_cosmotool.pyx

@@ -39,7 +39,7 @@ cdef extern from "loadSimu.hpp" namespace "CosmoTool":
 
 cdef extern from "loadGadget.hpp" namespace "CosmoTool":
 
-  SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) nogil except +
+  SimuData *loadGadgetMulti(const char *fname, int id, int flags, int gformat) except + nogil
   void cxx_writeGadget "CosmoTool::writeGadget" (const char * s, SimuData *data) except +
 
 cdef extern from "safe_gadget.hpp":
@@ -313,6 +313,13 @@ tries to get an array from the object."""
 references to the object are gone. """
         pass
 
+
+cdef extern from "numpy/arrayobject.h":
+    # a little bit awkward: the reference to obj will be stolen
+    # using PyObject*  to signal that Cython cannot handle it automatically
+    int PyArray_SetBaseObject(np.ndarray arr, PyObject *obj) except -1 # -1 means there was an error
+
+
 cdef object wrap_array(void *p, np.uint64_t s, int typ):
     cdef np.ndarray ndarray
     cdef ArrayWrapper wrapper
@@ -320,7 +327,8 @@ cdef object wrap_array(void *p, np.uint64_t s, int typ):
     wrapper = ArrayWrapper()
     wrapper.set_data(s, typ, p)
     ndarray = np.array(wrapper, copy=False)
-    ndarray.base = <PyObject*> wrapper
+    #ndarray.base = <PyObject*> wrapper
+    PyArray_SetBaseObject(ndarray, <PyObject*> wrapper)
     Py_INCREF(wrapper)
 
     return ndarray

python/_project.pyx

@@ -727,7 +727,7 @@ cdef DTYPE_t C_line_of_sight_projection(DTYPE_t[:,:,:] density,
     cdef int iu0[3]
     cdef int i
     cdef int N = density.shape[0]
-    cdef int half_N = density.shape[0]/2
+    cdef int half_N = density.shape[0]//2
     cdef int completed
     cdef DTYPE_t I0, d, dist2, delta, s, max_distance2
     cdef int jumper[1]

requirements.txt

@@ -1,5 +1,4 @@
 numpy<1.22
 cffi
 numexpr
-pyfftw
-cython
+cython<3

sample/CMakeLists.txt

@@ -1,4 +1,8 @@
 SET(tolink  ${CosmoTool_local} ${CosmoTool_LIBS} ${GSL_LIBRARIES} ${DL_LIBRARY})
+if (RT_LIBRARY)
+  SET(tolink ${tolink} ${RT_LIBRARY})
+endif()
+
 include_directories(${CMAKE_SOURCE_DIR}/src)
 include_directories(${FFTW3_INCLUDE_DIRS} ${EIGEN3_INCLUDE_DIRS} ${GSL_INCLUDE_PATH})
 if(YORICK_SUPPORT)

sample/simple3DFilter.cpp

@@ -84,6 +84,7 @@ int main(int argc, char **argv) {
   char *fname1, *outFile;
   double rLimit, boxsize, rLimit2, cx, cy, cz;
   int Nres;
+  int periodic;
 
   MiniArgDesc args[] = {{"INPUT DATA1", &fname1, MINIARG_STRING},
                         {"RADIUS LIMIT", &rLimit, MINIARG_DOUBLE},
@@ -93,6 +94,7 @@ int main(int argc, char **argv) {
                         {"CY", &cy, MINIARG_DOUBLE},
                         {"CZ", &cz, MINIARG_DOUBLE},
                         {"OUTPUT FILE", &outFile, MINIARG_STRING},
+                        {"PERIODIC", &periodic, MINIARG_INT},
                         {0, 0, MINIARG_NULL}};
 
   if (!parseMiniArgs(argc, argv, args))
@@ -148,6 +150,7 @@ int main(int argc, char **argv) {
 
   cout << "Building trees..." << endl;
   MyTree tree1(allCells_1, N1_points);
+  tree1.setPeriodic(periodic != 0, boxsize);
 
   cout << "Creating smoothing filter..." << endl;
 

setup.py

@@ -2,6 +2,7 @@ import stat
 import os
 import sys
 import shutil
+from sysconfig import get_config_var
 from distutils.command.install_data import install_data
 import pathlib
 from setuptools import find_packages, setup, Extension
@@ -76,9 +77,9 @@ class InstallCMakeLibs(install_lib):
 #        # your files are moved to the appropriate location when the installation
 #        # is run
 #
-#        libs = [os.path.join(bin_dir, _lib) for _lib in 
-#                os.listdir(bin_dir) if 
-#                os.path.isfile(os.path.join(bin_dir, _lib)) and 
+#        libs = [os.path.join(bin_dir, _lib) for _lib in
+#                os.listdir(bin_dir) if
+#                os.path.isfile(os.path.join(bin_dir, _lib)) and
 #                os.path.splitext(_lib)[1] in [".dll", ".so"]
 #                and not (_lib.startswith("python") or _lib.startswith(PACKAGE_NAME))]
 #
@@ -87,16 +88,16 @@ class InstallCMakeLibs(install_lib):
 #            shutil.move(lib, os.path.join(self.build_dir,
 #                                          os.path.basename(lib)))
 #
-#        # Mark the libs for installation, adding them to 
-#        # distribution.data_files seems to ensure that setuptools' record 
+#        # Mark the libs for installation, adding them to
+#        # distribution.data_files seems to ensure that setuptools' record
 #        # writer appends them to installed-files.txt in the package's egg-info
 #        #
-#        # Also tried adding the libraries to the distribution.libraries list, 
-#        # 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 
-#        # into eager_resources in the call to setup(), which I think puts them 
-#        # in data_files anyways. 
-#        # 
+#        # Also tried adding the libraries to the distribution.libraries list,
+#        # 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
+#        # into eager_resources in the call to setup(), which I think puts them
+#        # in data_files anyways.
+#        #
 #        # What is the best way?
 #
 #        # These are the additional installation files that should be
@@ -104,7 +105,7 @@ class InstallCMakeLibs(install_lib):
 #        # step; depending on the files that are generated from your cmake
 #        # 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))
 #                                        for lib in libs]
 #        print(self.distribution.data_files)
@@ -167,17 +168,24 @@ class BuildCMakeExt(build_ext):
         # Change your cmake arguments below as necessary
         # Below is just an example set of arguments for building Blender as a Python module
 
+        c_compiler=os.environ.get('CC', get_config_var("CC"))
+        cxx_compiler=os.environ.get('CXX', get_config_var("CXX"))
+
         compilers=[]
         fill_up_settings=[
-              ("CMAKE_C_COMPILER", "CC"),
-              ("CMAKE_CXX_COMPILER", "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]}")
+              ("CMAKE_C_COMPILER", "CC", get_config_var("CC")),
+              ("CMAKE_CXX_COMPILER", "CXX", get_config_var("CXX")),
+              ("CMAKE_C_FLAGS", "CFLAGS", None),
+              ("CMAKE_CXX_FLAGS", "CXXFLAGS", None),
+              ("CMAKE_EXE_LINKER_FLAGS_INIT", "LDFLAGS", None),
+              ("CMAKE_SHARED_LINKER_FLAGS_INIT", "LDFLAGS", None),
+              ("CMAKE_MODULE_LINKER_FLAGS_INIT", "LDFLAGS", None)]
+        for cmake_flag, os_flag, default_flag in fill_up_settings:
+          if os_flag in os.environ or default_flag is not None:
+             c = os.environ.get(os_flag, default_flag)
+             if not c is None:
+               compilers.append(f"-D{cmake_flag}={c}")
+        print(compilers)
 
         self.spawn(['cmake', '-H'+SOURCE_DIR, '-B'+self.build_temp,
                     '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON',
@@ -213,7 +221,7 @@ class BuildCMakeExt(build_ext):
                if  _pyd_top[0].startswith(PACKAGE_NAME):
                    if os.path.splitext(_pyd)[1] in [".pyd", ".so"] or _pyd_top[-1] == 'config.py':
                      pyd_path.append((_pyd_top,_pyd))
-               
+
 
         for top,p in pyd_path:
            _,n = os.path.split(p)
@@ -229,10 +237,10 @@ class BuildCMakeExt(build_ext):
 CosmoTool_extension = CMakeExtension(name="cosmotool")
 
 setup(name='cosmotool',
-      version='1.3.2',
+      version='1.3.6',
       packages=["cosmotool"],
       package_dir={'cosmotool': 'python/cosmotool'},
-      install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],
+      install_requires=['cython','numpy','cffi','numexpr','h5py'],
       setup_requires=['cython','cffi','numpy','numexpr'],
       ext_modules=[CosmoTool_extension],
       description='A small cosmotool box of useful functions',

src/hdf5_array.hpp

@@ -426,7 +426,7 @@ namespace CosmoTool {
 #define CTOOL_HDF5_INSERT_ELEMENT(r, STRUCT, element) \
      { \
        ::CosmoTool::get_hdf5_data_type<BOOST_PP_TUPLE_ELEM(2, 0, element)> t; \
-       long position = HOFFSET(STRUCT, BOOST_PP_TUPLE_ELEM(2, 1, element)); \
+       long position = offsetof(STRUCT, 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()); \
      } 

src/interpolate.cpp

@@ -157,6 +157,7 @@ const Interpolate& Interpolate::operator=(const Interpolate& a)
   gsl_spline_init(spline, a.spline->x, a.spline->y, a.spline->size);
   logx = a.logx;
   logy = a.logy;
+  return *this;
 }
 
 double Interpolate::getMaxX() const

src/sphSmooth.hpp

@@ -72,7 +72,9 @@ namespace CosmoTool {
     void
     fetchNeighbours(const typename SPHTree::coords &c, SPHState *state = 0);
 
-    void fetchNeighbours(const typename SPHTree::coords &c, uint32_t newNsph);
+    void fetchNeighbours(
+        const typename SPHTree::coords &c, uint32_t newNsph,
+        SPHState *state = 0);
     void fetchNeighboursOnVolume(
         const typename SPHTree::coords &c, ComputePrecision radius);
     const typename SPHTree::coords &getCurrentCenter() const {

src/sphSmooth.tcc

@@ -35,32 +35,38 @@ namespace CosmoTool {
 
   template <typename ValType, int Ndims>
   void SPHSmooth<ValType, Ndims>::fetchNeighbours(
-      const typename SPHTree::coords &c, uint32_t newNngb) {
+      const typename SPHTree::coords &c, uint32_t newNngb, SPHState *state) {
     ComputePrecision d2, max_dist = 0;
     uint32_t requested = newNngb;
 
-    if (requested > maxNgb) {
-      maxNgb = requested;
-      internal.ngb = boost::shared_ptr<P_SPHCell[]>(new P_SPHCell[maxNgb]);
-      internal.distances =
-          boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
+    if (state != 0) {
+      state->distances = boost::shared_ptr<CoordType[]>(new CoordType[newNngb]);
+      state->ngb = boost::shared_ptr<SPHCell *[]>(new SPHCell *[newNngb]);
+    } else {
+      state = &internal;
+      if (requested > maxNgb) {
+        maxNgb = requested;
+        internal.ngb = boost::shared_ptr<P_SPHCell[]>(new P_SPHCell[maxNgb]);
+        internal.distances =
+            boost::shared_ptr<CoordType[]>(new CoordType[maxNgb]);
+      }
     }
 
-    memcpy(internal.currentCenter, c, sizeof(c));
+    memcpy(state->currentCenter, c, sizeof(c));
     tree->getNearestNeighbours(
-        c, requested, (SPHCell **)internal.ngb.get(),
-        (CoordType *)internal.distances.get());
+        c, requested, (SPHCell **)state->ngb.get(),
+        (CoordType *)state->distances.get());
 
-    internal.currentNgb = 0;
-    for (uint32_t i = 0; i < requested && (internal.ngb)[i] != 0;
-         i++, internal.currentNgb++) {
-      internal.distances[i] = sqrt(internal.distances[i]);
-      d2 = internal.distances[i];
+    state->currentNgb = 0;
+    for (uint32_t i = 0; i < requested && (state->ngb)[i] != 0;
+         i++, state->currentNgb++) {
+      state->distances[i] = sqrt(state->distances[i]);
+      d2 = state->distances[i];
       if (d2 > max_dist)
         max_dist = d2;
     }
 
-    internal.smoothRadius = max_dist / 2;
+    state->smoothRadius = max_dist / 2;
   }
 
   template <typename ValType, int Ndims>
@@ -206,7 +212,7 @@ namespace CosmoTool {
       ComputePrecision d = state->distances[i];
       SPHCell &cell = *(state->ngb[i]);
       double kernel_value = getKernel(d / state->smoothRadius) / r3;
-#pragma omp atomic
+#pragma omp atomic update
       cell.val.weight += kernel_value;
     }
   }
@@ -241,5 +247,4 @@ namespace CosmoTool {
       const SPHSmooth<ValType2, Ndims> &s2) {
     return (s1.getSmoothingLen() < s2.getSmoothingLen());
   }
-
 }; // namespace CosmoTool