Merge branch 'master' of bitbucket.org:glavaux/cosmotool

CMakeLists.txt

@@ -70,8 +70,8 @@ SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "A toolbox for impatient cosmologists")
 SET(CPACK_PACKAGE_VENDOR "Guilhem Lavaux")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_CURRENT_SOURCE_DIR}/LICENCE_CeCILL_V2")
 SET(CPACK_PACKAGE_VERSION_MAJOR "1")
-SET(CPACK_PACKAGE_VERSION_MINOR "2")
+SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "2${EXTRA_VERSION}")
+SET(CPACK_PACKAGE_VERSION_PATCH "0${EXTRA_VERSION}")
 SET(CPACK_PACKAGE_INSTALL_DIRECTORY "CosmoToolbox-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
 SET(CPACK_STRIP_FILES "lib/libCosmoTool.so")
 SET(CPACK_SOURCE_IGNORE_FILES 

MANIFEST.in

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

conda/conda_build_config.yaml

@@ -1,8 +1,10 @@
 python:
-  - 3.7
-  - 3.8
   - 3.9
+  - 3.8
+  - 3.7
 
 numpy:
-  - 1.11
   - 1.19
+
+gsl:
+  - 2.4

conda/meta.yaml

@@ -1,48 +1,50 @@
 package:
   name: cosmotool
-  version: "1.2.2"
+  version: "1.3.0"
 
 source:
-  git_rev: 03033b6
+  git_rev: a86c9a8
   git_url: https://bitbucket.org/glavaux/cosmotool
 
 requirements:
   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('cxx') }}
-    - python
+    - llvm-openmp                            # [osx]
-    - setuptools
+    - libgomp                                # [linux]
-    - cython
-    - healpy
-    - numexpr
-    - cffi
-    - pyfftw
-    - gsl
-    - h5py
 
   host:
     - python
+    - pip
+    - numpy
+    - pkgconfig
     - numexpr
     - cython
     - healpy
     - cffi
     - pyfftw
-    - gsl
+    - gsl {{ gsl }}
     - h5py
-
   run:
-    - numpy
     - python
+    - {{ pin_compatible('numpy') }}
     - healpy
     - numexpr
     - cffi
     - pyfftw
     - h5py
+    - {{ pin_compatible('gsl') }}
+    - llvm-openmp
 
 test:
   imports:
     - cosmotool
+  requires:
+    - pip
 
 about:
   home: https://bitbucket.org/glavaux/cosmotool

external/external_build.cmake

@@ -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(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(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 ")
 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
     URL ${BOOST_URL}
     PREFIX ${BUILD_PREFIX}/boost-prefix
+    URL_HASH MD5=da07ca30dd1c0d1fdedbd487efee01bd
     CONFIGURE_COMMAND 
            ${BOOST_SOURCE_DIR}/bootstrap.sh --prefix=${CMAKE_BINARY_DIR}/ext_build/boost
     BUILD_IN_SOURCE 1

external/patch-omptl

@@ -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 @@
  #define OMPTL_ALGORITHM 1
  
@@ -22,9 +22,9 @@ diff -ur omptl.orig/omptl_algorithm omptl/omptl_algorithm
  #endif
  
  #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 @@
  #include <cmath>
  #include <cstdlib>
@@ -36,9 +36,18 @@ diff -ur omptl.orig/omptl_algorithm_par.h omptl/omptl_algorithm_par.h
  
  #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 @@
  #define OMPTL_NUMERIC 1
  
@@ -63,9 +72,9 @@ diff -ur omptl.orig/omptl_numeric omptl/omptl_numeric
 +#include "omptl_numeric_extensions.h"
  
  #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 @@
  } // namespace
  
@@ -78,9 +87,9 @@ diff -ur omptl.orig/omptl_numeric_extensions.h omptl/omptl_numeric_extensions.h
  #endif
  
  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 @@
  #include <functional>
  #include <iterator>
@@ -92,15 +101,15 @@ diff -ur omptl.orig/omptl_numeric_par.h omptl/omptl_numeric_par.h
  
  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)
- 	{

python/CMakeLists.txt

@@ -116,8 +116,17 @@ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cosmotool/config.py.in ${CMAKE_CURREN
 
 INSTALL(TARGETS
   ${ct_TARGETS}
+  COMPONENT python
   LIBRARY DESTINATION ${PYTHON_SITE_PACKAGES}/cosmotool
 )
 
-INSTALL(DIRECTORY cosmotool ${CMAKE_CURRENT_BINARY_DIR}/cosmotool DESTINATION ${PYTHON_SITE_PACKAGES} 
+INSTALL(DIRECTORY cosmotool ${CMAKE_CURRENT_BINARY_DIR}/cosmotool
+        COMPONENT python DESTINATION ${PYTHON_SITE_PACKAGES}
         FILES_MATCHING PATTERN "*.py")
+
+add_custom_target(
+    python-install
+    DEPENDS ${ct_TARGETS}
+    COMMAND "${CMAKE_COMMAND}" -DCMAKE_INSTALL_COMPONENT=python -P
+            "${CMAKE_BINARY_DIR}/cmake_install.cmake")
+

python/_cosmotool.pyx

@@ -247,6 +247,9 @@ class PySimulationAdaptor(PySimulationBase):
   def __init__(self,sim):
     self.simu = sim
 
+  def getNumParticles(self):
+    return self.simu.numParticles
+
   def getBoxsize(self):
     return self.simu.BoxSize
 

python/_project.pyx

@@ -533,12 +533,13 @@ cdef void INTERNAL_project_cic_with_mass_periodic(DTYPE_t[:,:,:] g,
 
 
 def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, ndim=1] mass, int Ngrid,
-                double Lbox, bool periodic = False, centered=True):
+                double Lbox, bool periodic = False, centered=True, output=None):
     """
-    project_cic(x array (N,3), mass (may be None), Ngrid, Lbox, periodict, centered=True)
+    project_cic(x array (N,3), mass (may be None), Ngrid, Lbox, periodict, centered=True, output=None)
 
     This function does a Cloud-In-Cell projection of a 3d unstructured dataset. First argument is a Nx3 array of coordinates.
     Second argument is an optinal mass. Ngrid is the size output grid and Lbox is the physical size of the grid.
+    if output is not None, it must be a numpy array with dimension NgridxNgridxNgrid. The result will be accumulated in that array.
     """
     cdef npx.ndarray[DTYPE_t, ndim=3] g
     cdef double shifter
@@ -558,7 +559,13 @@ def project_cic(npx.ndarray[DTYPE_t, ndim=2] x not None, npx.ndarray[DTYPE_t, nd
     if mass is not None and mass.shape[0] != x.shape[0]:
         raise ValueError("Mass array and coordinate array must have the same number of elements")
 
-    g = np.zeros((Ngrid,Ngrid,Ngrid),dtype=DTYPE)
+    if output is None:
+        g = np.zeros((Ngrid,Ngrid,Ngrid),dtype=DTYPE)
+    else:
+        if type(output) != np.ndarray:
+            raise ValueError("Invalid array type")
+        g = output
+
     cdef DTYPE_t[:,:,:] d_g = g
     cdef DTYPE_t[:,:] d_x = x
 

requirements.txt

@@ -1,4 +1,4 @@
-numpy
+numpy<1.19
 cffi
 numexpr
 pyfftw

setup.py

@@ -168,10 +168,16 @@ class BuildCMakeExt(build_ext):
         # Below is just an example set of arguments for building Blender as a Python module
 
         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,
                     '-DENABLE_OPENMP=ON','-DINTERNAL_BOOST=ON','-DINTERNAL_EIGEN=ON',
@@ -223,7 +229,7 @@ class BuildCMakeExt(build_ext):
 CosmoTool_extension = CMakeExtension(name="cosmotool")
 
 setup(name='cosmotool',
-      version='1.2.2',
+      version='1.3.0',
       packages=["cosmotool"],
       package_dir={'cosmotool': 'python/cosmotool'},
       install_requires=['numpy','cffi','numexpr','pyfftw','h5py'],

src/CMakeLists.txt

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

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; \
-       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)); \
        type.insertMember(field_name,  position, t.type()); \
      } 
@@ -439,7 +439,6 @@ namespace CosmoTool { \
   \
       TNAME() : type(sizeof(STRUCT)) \
       {  \
-        long position; \
         BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ELEMENT, STRUCT, ATTRIBUTES) \
       }  \
       \
@@ -471,7 +470,6 @@ namespace CosmoTool { \
   \
       TNAME() : type(sizeof(STRUCT)) \
       {  \
-        long position; \
         BOOST_PP_SEQ_FOR_EACH(CTOOL_HDF5_INSERT_ENUM_ELEMENT, STRUCT, ATTRIBUTES) \
       }  \
       \

src/yorick.hpp

@@ -222,8 +222,7 @@ namespace CosmoTool
 
   template<typename T>
   void loadArray(const std::string& fname,
-		 T*& array, uint32_t *& dimList, uint32_t& rank)
+		 T*& array, uint32_t *& dimList, uint32_t& rank);
-    throw (NoSuchFileException);
 
   ProgressiveDoubleOutput saveDoubleArrayProgressive(const char *fname, uint32_t *dimList, uint32_t rank);
 };

src/yorick_nc4.cpp

@@ -224,7 +224,6 @@ namespace CosmoTool {
   template<typename T>
   void loadArray(const std::string& fname,
 		 T*&array, uint32_t *&dimList, uint32_t& rank)
-	throw (NoSuchFileException)
   {
     NcFile f(fname.c_str(), NcFile::read);