Add ZLIB package

CMakeLists.txt

@@ -42,6 +42,7 @@ 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)
@@ -82,7 +83,7 @@ SET(CPACK_PACKAGE_VERSION_MINOR "3")
 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

@@ -206,6 +206,7 @@ if (INTERNAL_NETCDF)
     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

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(

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)

setup.py

@@ -237,10 +237,10 @@ class BuildCMakeExt(build_ext):
 CosmoTool_extension = CMakeExtension(name="cosmotool")
 
 setup(name='cosmotool',
-      version='1.3.5',
+      version='1.3.6',
       packages=["cosmotool"],
       package_dir={'cosmotool': 'python/cosmotool'},
-      install_requires=['numpy','cffi','numexpr','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/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