diff --git a/CMakeLists.txt b/CMakeLists.txt
index f9ca15fbfcf6ef1bd736edd42cd7825de03a10a4..3589391f0ea50eb2ac5308f62886a9ed04683355 100755
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -33,7 +33,7 @@ option(DOUBLEPREC "set precision for real numbers to double precision when this
option(USE_MPI "compile and link HySoP with mpi when this mode is enable. Default = on." ON)
option(WITH_TESTS "Enable testing. Default = off" ON)
option(BUILD_SHARED_LIBS "Enable dynamic library build, default = ON." ON)
-option(WITH_LIB_CXX "Generate libhysop from fortran files in src, wrapped into hysop.cpp2hysop module. Default = ON." ON)
+option(USE_CXX "Expand hysop with some new functions from a generated c++ to python interface, wrapped into hysop.cpp2hysop module. Default = ON." ON)
option(WITH_SCALES "compile/create scales lib and link it with HySoP. Default = ON." ON)
option(WITH_FFTW "Link with fftw library (required for some HySoP solvers), default = ON" ON)
option(WITH_EXTRAS "Link with some extra fortran libraries (like arnoldi solver), default = OFF" OFF)
@@ -74,26 +74,16 @@ endif()
if(NOT USE_MPI)
message(FATAL_ERROR "No-mpi version of hysop is broken, please enable mpi.")
endif()
-
+set(USE_FORTRAN "ON")
if(WITH_FFTW OR WITH_SCALES OR WITH_EXTRAS)
set(USE_FORTRAN "ON")
endif()
-if(NOT WITH_LIB_CXX)
+if(NOT USE_CXX)
set(WITH_MAIN_CXX "OFF")
set(WITH_GOOGLE_TESTS "OFF")
endif()
-# true if hysop used Fortran and/or c++ sources
-# We can not run scales or fftw without mpi ...
-if(USE_FORTRAN OR WITH_LIB_CXX)
- set(WITH_COMPILED_LIB "ON")
- #set(WITH_FFTW "ON")
-else()
- set(WITH_COMPILED_LIB "OFF")
- #set(WITH_FFTW "OFF")
-endif()
-
# Force a default build type if not provided by user
# CMAKE_BUILD_TYPE = empty, Debug, Release, RelWithDebInfo or MinSizeRel.
if(NOT CMAKE_BUILD_TYPE)
@@ -117,12 +107,14 @@ set(PROJECT_LIBRARY_NAME ${PROJECT_NAME})
# Note that because of OutOfSourceBuild, binary_dir and source_dir must be different.
set(LANGLIST)
-if(WITH_LIB_CXX)
+if(USE_CXX)
set(LANGLIST ${LANGLIST} C CXX)
endif()
+
if(USE_FORTRAN)
set(LANGLIST ${LANGLIST} Fortran)
endif()
+
include(HysopVersion)
project(${PROJECT_NAME} ${LANGLIST})
@@ -154,7 +146,7 @@ if(USE_MPI)
endif()
# --- Wheel, required for a proper build/install process ---
find_python_module(wheel REQUIRED)
-if(WITH_LIB_CXX)
+if(USE_CXX)
find_package(SWIG 3.0.2 REQUIRED)
# WARNING FP : for cmake < 3.0 UseSWIG.cmake
# does not work properly (bug for swig outdir)
@@ -165,7 +157,7 @@ if(WITH_LIB_CXX)
endif()
# Find python build dir name --> needed for tests and doc
-if(WITH_COMPILED_LIB)
+if(USE_CXX OR USE_FORTRAN)
execute_process(
COMMAND ${PYTHON_EXECUTABLE} -c "import distutils.util as ut ; import distutils.sysconfig as sy; print 'lib.'+ut.get_platform()+'-'+sy.get_python_version()"
OUTPUT_VARIABLE ${PROJECT_NAME}_PYTHON_BUILD_DIR)
@@ -255,6 +247,7 @@ set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES ${CMAKE_BINARY_D
set(PYTHON_SETUP "${CMAKE_CURRENT_BINARY_DIR}/setup.py")
if(USE_FORTRAN)
+ # if fortran is enabled, explicit setup of the compiler is required.
add_custom_target(wheel ALL
COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/setup.py bdist_wheel build config_fc --f90exec=${CMAKE_Fortran_COMPILER}#-d ${CMAKE_BINARY_DIR}/wheel/
COMMENT "create wheel file for ${PACKAGE_NAME} package"
@@ -280,15 +273,17 @@ include(HySoPInstallSetup)
# set precision for real numbers
# used to generate precision.f95 file/module and constant.py
if(DOUBLEPREC)
- set(WORKING_PRECISION DP)
+ set(WORKING_PRECISION dp)
set(MPI_PRECISION MPI_DOUBLE_PRECISION)
set(PYTHON_PREC np.float64)
set(MPI_PYTHON_PREC MPI.DOUBLE)
+ set(f2pymap_for_real double)
else()
- set(WORKING_PRECISION SP)
+ set(WORKING_PRECISION sp)
set(MPI_PRECISION MPI_FLOAT)
set(PYTHON_PREC np.float32)
set(MPI_PYTHON_PREC MPI.FLOAT)
+ set(f2pymap_for_real float)
endif()
# set data layout ('fortran' order or 'C' order)
@@ -304,29 +299,34 @@ if(EXISTS ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/constants.py.in)
configure_file(${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/constants.py.in
${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/constants.py)
endif()
-if(EXISTS ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/.f2py_f2cmap)
- message(STATUS "Generate f2py map file ...")
- configure_file(${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/.f2py_f2cmap
- ${CMAKE_BINARY_DIR}/.f2py_f2cmap)
-endif()
-if(EXISTS ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/f2hysop.pyf.in)
- message(STATUS "Generate f2hysop.pyf (f2py main signature file) ...")
- configure_file(${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/f2hysop.pyf.in
- ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/f2hysop.pyf)
-endif()
if(USE_FORTRAN)
- if(EXISTS ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/.f2py_f2cmap)
+
+ # Path to fortran-related generated files (.pyf, precision ...)
+ set(GENERATED_FORTRAN_FILES_DIR ${CMAKE_BINARY_DIR}/generated_fortran/)
+
+
+ # --- copy sort_f90 file to build ---
+ # Required for setup.py to handle fortran files dependencies
+ configure_file(${CMAKE_SOURCE_DIR}/sort_f90.py ${CMAKE_BINARY_DIR}/sort_f90.py)
+
+ # --- Generate f2py_f2cmap file ---
+ if(EXISTS ${CMAKE_SOURCE_DIR}/f2py_f2cmap.in)
message(STATUS "Generate f2py map file ...")
- configure_file(${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/.f2py_f2cmap
+ configure_file(${CMAKE_SOURCE_DIR}/f2py_f2cmap.in
${CMAKE_BINARY_DIR}/.f2py_f2cmap)
endif()
+
+ # --- Create top-level pyf file ---
+ # -> depends on cmake config. This file
+ # includes the other required pyf files.
+ # For example, if WITH_FFTW is ON, then
+ # add a line 'include fftw2py.py'
include(fortran_utils)
- # Create f2hysop.pyf file
write_main_pyf_file(f2hysop)
- # ====== Create non-python (fortran) libraries (fftw and scales interfaces), if required =====
+ # --- fortran libraries setup ---
# Set module files directory (i.e. where .mod will be created)
set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/Modules)
@@ -346,22 +346,22 @@ if(USE_FORTRAN)
set(Fortran_FLAGS ${CMAKE_Fortran_FLAGS})
append_flags(Fortran_FLAGS ${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}})
-
- if(EXISTS ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/precision.conf.in)
+ # --- Generate precision.f95 file ---
+ if(EXISTS ${CMAKE_SOURCE_DIR}/precision.conf.in)
message(STATUS "Generate precision.f95 file ...")
- configure_file(${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/precision.conf.in
- ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/utils_f/precision.f95)
+ configure_file(${CMAKE_SOURCE_DIR}/precision.conf.in
+ ${GENERATED_FORTRAN_FILES_DIR}/precision.f95)
endif()
endif()
-if(WITH_COMPILED_LIB)
- add_subdirectory(src)
+if(USE_CXX OR USE_FORTRAN)
+ #add_subdirectory(src)
#get_directory_property(FORTRAN_INCLUDE_DIRS
#DIRECTORY ${CMAKE_SOURCE_DIR}/src
#DEFINITION FORTRAN_INCLUDE_DIRS)
endif()
-if(WITH_LIB_CXX)
+if(USE_CXX)
#C++ variables used by setup.py.in for swig
if(DEV_MODE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -W -Wall -Wextra -Wno-unused-variable -Wno-unused-but-set-variable -Wno-unused-parameter")
@@ -405,7 +405,7 @@ endif()
# Hysop C++ library is generated in setup.py by swig
# --- C++ main and tests ---
-if(WITH_LIB_CXX)
+if(USE_CXX)
get_filename_component(CXX_DIR "${CMAKE_SOURCE_DIR}/src/hysop++" ABSOLUTE)
get_filename_component(CXX_MAIN_DIR "${CXX_DIR}/main" ABSOLUTE)
@@ -554,12 +554,12 @@ if(VERBOSE_MODE)
if(USE_FORTRAN)
message(STATUS " Fortran compiler : ${CMAKE_Fortran_COMPILER}")
else()
- message(WARNING "You deactivate libhysop (fortran) generation. This will disable the fortran interface, including fftw and scales fonctionnalities.")
+ message(WARNING "You deactivate fortran to python interface generation. This will disable the fortran interface, including fftw and scales fonctionnalities.")
endif()
- if(WITH_LIB_CXX)
+ if(USE_CXX)
message(STATUS " CXX compiler : ${CMAKE_CXX_COMPILER}")
else()
- message(WARNING "You deactivate libhysop (cxx) generation. This will disable the Aitken-Schwarz Poisson solver.")
+ message(WARNING "You deactivate c++ to python interface generation. This will disable the Aitken-Schwarz Poisson solver.")
endif()
message(STATUS " Sources are in : ${CMAKE_SOURCE_DIR}")
message(STATUS " Project uses MPI : ${USE_MPI}")
diff --git a/ci/config.sh b/ci/config.sh
index 5605ed2e1e0b4f2a9be0d1554af8140a9cdc3095..fd983559c56973578bda07dfe710dd198f8b9fdd 100644
--- a/ci/config.sh
+++ b/ci/config.sh
@@ -2,4 +2,4 @@
mkdir build
cd build
export FC=mpif90 CC=mpicc CXX=mpic++ F77=mpif90
-cmake -DCMAKE_BUILD_TYPE=Debug -DWITH_LIB_CXX=OFF ..
+cmake -DCMAKE_BUILD_TYPE=Debug -DUSE_CXX=OFF ..
diff --git a/ci/run_tests.sh b/ci/run_tests.sh
index f60cd72261aafdb06567fca7e78a79cdee041964..fc5e1a792093993de07e64f5c5a8e850416e487e 100644
--- a/ci/run_tests.sh
+++ b/ci/run_tests.sh
@@ -2,6 +2,6 @@
mkdir build
cd build
export FC=mpif90 CC=mpicc CXX=mpic++
-cmake -D CMAKE_BUILD_TYPE=Debug -DWITH_LIB_CXX=OFF ..
+cmake -D CMAKE_BUILD_TYPE=Debug -DUSE_CXX=OFF ..
make
make test
diff --git a/cmake/fortran_utils.cmake b/cmake/fortran_utils.cmake
index 8f56794452975c5e23ad0aed1de74d937fb21be4..96c2f7ddb46cf1127e66efe2c5d8d01f7c9f41fa 100644
--- a/cmake/fortran_utils.cmake
+++ b/cmake/fortran_utils.cmake
@@ -15,7 +15,10 @@
# --> create f2hysop.pyf that will be used to generate hysop.f2hysop module.
#
function(write_main_pyf_file filename)
- set(_file ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/${filename}.pyf.in)
+
+ # First writes filename.pyf.in, according to cmake current config
+ # and then generate filename.pyf.
+ set(_file ${GENERATED_FORTRAN_FILES_DIR}/${filename}.pyf.in)
file(WRITE ${_file}
"! -*- f90 -*-\n
! Generated file - Do not edit.\n
@@ -24,12 +27,12 @@ python module f2hysop ! in\n
interface\n")
file(APPEND ${_file}
" ! Example
- include '@CMAKE_SOURCE_DIR@/hysop/fortran/template.pyf'\n")
+ include '@CMAKE_SOURCE_DIR@/hysop/common_f/template.pyf'\n")
file(APPEND ${_file}
" ! precision
- include '@CMAKE_SOURCE_DIR@/hysop/f2py/parameters.pyf'\n")
- if(WITH_FFTW)
- file(APPEND ${_file}
+ !! include '@CMAKE_SOURCE_DIR@/hysop/f2py/parameters.pyf'\n")
+ if(WITH_FFTW)
+ file(APPEND ${_file}
" ! fftw
include '@CMAKE_SOURCE_DIR@/hysop/f2py/fftw2py.pyf'\n")
endif()
@@ -46,7 +49,7 @@ python module f2hysop ! in\n
file(APPEND ${_file} " end interface\n
end python module f2hysop")
-message(STATUS "Generate pyf file ...")
-configure_file(${_file} ${CMAKE_SOURCE_DIR}/${PACKAGE_NAME}/${filename}.pyf @ONLY)
+message(STATUS "Generate f2hysop.pyf file ...")
+configure_file(${_file} ${GENERATED_FORTRAN_FILES_DIR}/${filename}.pyf @ONLY)
endfunction()
diff --git a/f2py_f2cmap.in b/f2py_f2cmap.in
new file mode 100644
index 0000000000000000000000000000000000000000..906a2f6f9c2d4208ee5eca277eb3079376035797
--- /dev/null
+++ b/f2py_f2cmap.in
@@ -0,0 +1,3 @@
+{'integer':{'c_int':'int'}, 'real':{'real64':'double', 'real32':'float', 'wp':'@f2pymap_for_real@'}}
+
+
diff --git a/hysop/.f2py_f2cmap b/hysop/.f2py_f2cmap
deleted file mode 100644
index 99f5f3517caf6260a22a9851a15f66443a1045d4..0000000000000000000000000000000000000000
--- a/hysop/.f2py_f2cmap
+++ /dev/null
@@ -1,3 +0,0 @@
-{'integer':{'c_int':'int'}, 'real':{'real64':'double', 'wp':'double'}}
-
-
diff --git a/hysop/f2hysop.pyf.in b/hysop/f2hysop.pyf.in
deleted file mode 100644
index a11194e7df7e5f7f02bb55b202ff01bf3faa85e9..0000000000000000000000000000000000000000
--- a/hysop/f2hysop.pyf.in
+++ /dev/null
@@ -1,20 +0,0 @@
-! -*- f90 -*-
-
-! Generated file - Do not edit.
-
-! Note: the context of this file is case sensitive.
-
-python module f2hysop ! in
-
- interface
- ! Example
- include '@CMAKE_SOURCE_DIR@/hysop/fortran/template.pyf'
- ! precision
- include '@CMAKE_SOURCE_DIR@/hysop/f2py/parameters.pyf'
- ! fftw
- include '@CMAKE_SOURCE_DIR@/hysop/f2py/fftw2py.pyf'
- ! scales
- include '@CMAKE_SOURCE_DIR@/hysop/f2py/scales2py.pyf'
- end interface
-
-end python module f2hysop
\ No newline at end of file
diff --git a/hysop/fakef2py/__init__.py b/hysop/fakef2py/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/hysop/fakef2py/fftw2py/__init__.py b/hysop/fakef2py/fftw2py/__init__.py
deleted file mode 100644
index 95df2255c1722b1a16cd39a6452fe5d94a7385cb..0000000000000000000000000000000000000000
--- a/hysop/fakef2py/fftw2py/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-msg = " ==== Import f2py.fftw2py warning ==== \n"
-msg += "The package is empty since you disable "
-msg += "fftw when installing HySoP. \n"
-msg += "Whatever you'll do with this will probably failed."
-print (msg)
diff --git a/hysop/fakef2py/scales2py/__init__.py b/hysop/fakef2py/scales2py/__init__.py
deleted file mode 100644
index 58ba76d2f7aceb911bb77628ceefced262357ce7..0000000000000000000000000000000000000000
--- a/hysop/fakef2py/scales2py/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-msg = " ==== Import f2py.scales2py warning ==== \n"
-msg += "The package is empty since you disable "
-msg += "scales when installing HySoP. \n"
-msg += "Whatever you'll do with this will probably failed."
-print (msg)
diff --git a/hysop/operator/discrete/multiresolution_filter.py b/hysop/operator/discrete/multiresolution_filter.py
index 157dbbb10319b251af114e3a76d474a0ac7f7a2b..0539971c36aab79f9e445a5556f7def2e82acb46 100644
--- a/hysop/operator/discrete/multiresolution_filter.py
+++ b/hysop/operator/discrete/multiresolution_filter.py
@@ -6,16 +6,14 @@ from hysop.operator.discrete.discrete import DiscreteOperator
from hysop.tools.profiler import profile
import hysop.tools.numpywrappers as npw
from hysop.methods_keys import Remesh
-from hysop.methods import Rmsh_Linear, L2_1
-from hysop.numerics.remeshing import RemeshFormula
+from hysop.numerics.remeshing import RemeshFormula, Linear, L2_1
class FilterFineToCoarse(DiscreteOperator):
- """
- Discretized operator for filtering from fine to coarse grid.
+ """Discretized operator for filtering from fine to coarse grid.
"""
- authorized_methods = [Linear, L21]
+ authorized_methods = [Linear, L2_1]
def __init__(self, field_in, field_out, **kwds):
"""
diff --git a/hysop/operator/multiresolution_filter.py b/hysop/operator/multiresolution_filter.py
index 01cc7d0a6b06c7e073ba8d709203e366761cc948..5be1a8d249c36822a714dacab7d97cb1f98a955b 100644
--- a/hysop/operator/multiresolution_filter.py
+++ b/hysop/operator/multiresolution_filter.py
@@ -25,7 +25,7 @@ class MultiresolutionFilter(Computational):
"""
if 'method' not in kwds:
- kwds['method'] = default.MULTIRESOLUTION_FILER
+ kwds['method'] = default.MULTIRESOLUTION_FILTER
super(MultiresolutionFilter, self).__init__(**kwds)
self.d_in, self.d_out = d_in, d_out
self.input = self.variables
diff --git a/hysop/operator/tests/test_multiresolution_filter.py b/hysop/operator/tests/test_multiresolution_filter.py
index 198d8ce4a2a4c9cb2c640dbcd0b5c98ba0948288..a66c59b0a5d39450c01a901ab63109205ce27aca 100755
--- a/hysop/operator/tests/test_multiresolution_filter.py
+++ b/hysop/operator/tests/test_multiresolution_filter.py
@@ -116,8 +116,9 @@ def test_L21_X():
b, e, err = filter(d_coarse=Discretization([n_middle, 5, 5],
ghosts=[2, 2, 2]),
d_fine=Discretization([n_large, 5, 5]),
- method={Remesh: L21, },
+ method={Remesh: L2_1, },
func=func_periodic_X)
+ print b, e, err
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
@@ -125,7 +126,7 @@ def test_L21_Y():
b, e, err = filter(d_coarse=Discretization([5, n_middle, 5],
ghosts=[2, 2, 2]),
d_fine=Discretization([5, n_large, 5]),
- method={Remesh: L21, },
+ method={Remesh: L2_1, },
func=func_periodic_X)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
@@ -134,7 +135,7 @@ def test_L21_Z():
b, e, err = filter(d_coarse=Discretization([5, 5, n_middle],
ghosts=[2, 2, 2]),
d_fine=Discretization([5, 5, n_large]),
- method={Remesh: L21, },
+ method={Remesh: L2_1, },
func=func_periodic_X)
assert b, "max(|error|)=" + str(e) + " <= " + str(err)
@@ -181,7 +182,7 @@ def test_filter_linear():
op.setup()
topo_coarse = op.discreteFields[f].topology
topo_fine = [t for t in f.discreteFields.keys()
- if not t is topo_coarse][0]
+ if t is not topo_coarse][0]
f.initialize(topo=topo_fine)
f_out = f.discreteFields[topo_coarse]
op.apply(simu)
@@ -207,7 +208,7 @@ def test_filter_l2_1():
op.setup()
topo_coarse = op.discreteFields[f].topology
topo_fine = [t for t in f.discreteFields.keys()
- if not t is topo_coarse][0]
+ if t is not topo_coarse][0]
f.initialize(topo=topo_fine)
f_out = f.discreteFields[topo_coarse]
op.apply(simu)
diff --git a/setup.py.in b/setup.py.in
index e92172482a497b8cc2e1b82ab574cc54a6fedd44..1676f83c012e8972431cdf026b424be01beb8cff 100644
--- a/setup.py.in
+++ b/setup.py.in
@@ -1,7 +1,6 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
-"""
-setup.py file for @PYPACKAGE_NAME@
+"""setup.py file for @PYPACKAGE_NAME@
"""
from setuptools import find_packages
@@ -16,26 +15,48 @@ import fnmatch
# tools to deal with fortran dependencies.
import sys
-sys.path.append('@CMAKE_SOURCE_DIR@/')
+sys.path.append('@CMAKE_BINARY_DIR@/')
import sort_f90
-enable_cpp = "@WITH_LIB_CXX@"
+# --- Check if c++ interface is enabled ---
+enable_cpp = "@USE_CXX@"
if enable_cpp:
swig_executable = find_executable("@SWIG_EXECUTABLE@")
def parseCMakeVar(var):
+ """post-process cmake list-like variable
+
+ Example::
+
+ a = parseCMakeVar("var1;var2;var3;")
+ # --> a = ['var', 'var2', 'var3']
+ """
if var != "":
- return var.split(';')
+ res = list(set(var.split(';')))
+ # list/set stuff to avoid duplicates
+ # remove empty strings to avoid '-I -I' things leading to bugs
+ if res.count(''):
+ res.remove('')
+ return res
else:
return []
+
def parseCMakeDefines(var):
+ """post-process cmake variables, corresponding
+ to pre-processor definitions.
+
+ Example::
+
+ res = parseCMakeDefines("-DVAR=VAL1:-DVAR2=VAL2:-DVAR3=VAL3")
+ # --> res = [('VAR', 'VAL1'), ('VAR2', 'VAL2'), ('VAR3', 'VAL3')]
+ """
defines = parseCMakeVar(var)
- if defines == None:
+ if defines is None:
return None
-
- # regex to match compiler defines like -DMACRO_NAME or -DMACRO_NAME = MACRO_VALUE
+ # regex to match compiler defines like -DMACRO_NAME or
+ # -DMACRO_NAME = MACRO_VALUE
p = re.compile('\s*(?:-D)?\s*(\w+)(?:\s*=\s*(\w+))?\s*')
res = list()
@@ -44,26 +65,56 @@ def parseCMakeDefines(var):
if m:
res.append(m.group(1,2))
else:
- print "\tWarning: Could extract cmake define from '",d,"'."
+ print "\tWarning: Could extract cmake define from '", d, "'."
return res
-
+# --- external libraries to be linked with ---
hysop_link_libraries = parseCMakeVar("@HYSOP_LINK_LIBRARIES@")
-hysop_link_libraries_names = set([])
-hysop_link_libraries_dirs = set([])
+#hysop_link_libraries_names = set([])
+#hysop_link_libraries_dirs = set([])
# use set to avoid dupl.
-link_list = ""
-for lib in hysop_link_libraries:
- hysop_link_libraries_names.add(os.path.basename(lib))
- hysop_link_libraries_dirs.add(os.path.dirname(lib))
- link_list += lib + " "
-hysop_link_libraries_names = list(hysop_link_libraries_names)
-hysop_link_libraries_dirs = list(hysop_link_libraries_dirs)
+#link_list = ""
+# for lib in hysop_link_libraries:
+# hysop_link_libraries_names.add(os.path.basename(lib))
+# hysop_link_libraries_dirs.add(os.path.dirname(lib))
+# link_list += lib + " "
+# hysop_link_libraries_names = list(hysop_link_libraries_names)
+# hysop_link_libraries_dirs = list(hysop_link_libraries_dirs)
+
def create_fortran_extension(name, pyf_file=None, src_dirs=None, sources=None,
libdir=None, libs=None, debug_mode=0):
"""Create a new f2py module from fortran files
+
+ Parameters
+ ----------
+ name: string
+ python module name
+ pyf_file: string, optional
+ f2py interface file (absolute path)
+ src_dirs: list, optional
+ all directories containing fortran sources (absolute path)
+ that must be taken into account. Warning: dir. scan is not
+ recursive.
+ sources: list, optional
+ all fortran files that must be taken into account
+ libs: list of strings, optional
+ names of all libraries to be linked with to build f2py module
+ --> for -l option
+ libdir: list of strings, optional
+ list of directories, absolute path to libraries listed in libs
+ --> for -L... option
+ debug_mode: boolean, optional
+ if true enable f2py debug mode, default=False
+
+ Notes
+ -----
+ * either sources or src_dirs is required but both
+ can be used simultaneously.
+ * only .f90 and .f95 files are taken into account.
"""
+
+ # --- Collect list of fortran files ---
if sources is None:
sources = []
assert src_dirs is not None
@@ -71,29 +122,29 @@ def create_fortran_extension(name, pyf_file=None, src_dirs=None, sources=None,
for sdir in src_dirs:
sources += glob.glob(os.path.join(sdir, '*.f95'))
sources += glob.glob(os.path.join(sdir, '*.f90'))
- f2py_options = ['--no-lower', '--no-wrap-functions']
- options = []
# Reorder source list with fortran modules
# dependencies. It seems that this is not taken into
# account in f2py or distutils.
if pyf_file is not None:
sources.append(pyf_file)
sources = sort_f90.sort(sources)
- if debug_mode > 0:
+ # --- set f2py options ---
+ f2py_options = ['--no-lower', '--no-wrap-functions']
+ options = []
+ if debug_mode == 0:
options.append(('F2PY_REPORT_ON_ARRAY_COPY', '1'))
if os.uname()[0] == 'Linux':
options.append(('F2PY_REPORT_ATEXIT', '1'))
- inc_dir = '@MPI_Fortran_INCLUDE_PATH@'.split(';')
- # To avoid -I -I in compiler call, which results in a bug:
- while inc_dir.count('') > 0:
- inc_dir.remove('')
- inc_dir.append('@CMAKE_BINARY_DIR@/Modules')
+
+ # --- set include dir ---
+ inc_dir = parseCMakeVar("@MPI_Fortran_INCLUDE_PATH@")
+ inc_dir.append('@CMAKE_Fortran_MODULE_DIRECTORY@')
+ # --- set compilation flags ---
fortran_flags = ['@Fortran_FLAGS@']
-
#includes = parseCMakeVar("@FORTRAN_INCLUDE_DIRS@")
#if(includes != None):
- #for exti in includes:
- #inc_dir.append(exti)
+ # for exti in includes:
+ #i nc_dir.append(exti)
#libs += hysop_link_libraries_names
#libdir += hysop_link_libraries_dirs
# we trust cmake for external libraries and
@@ -114,37 +165,58 @@ def create_fortran_extension(name, pyf_file=None, src_dirs=None, sources=None,
def create_swig_extension(name, inc_dirs, src_dirs=None, sources=None):
"""Create a python module from C++ files, using swig
+
+ Parameters
+ ----------
+ name: string
+ module name
+ inc_dirs: list
+ list of directories for includes (-I ...), absolute path
+ containing headers (.hpp) and swig files (.i)
+ sources: list, optional
+ all c++ files that must be taken into account
+ src_dirs: list, optional
+ all directories containing fortran sources (absolute path)
+ that must be taken into account. Warning: no recursive scan
+ in src_dirs.
+
+ Notes
+ -----
+ * either sources, src_dirs or inc_dirs is required but all
+ can be used simultaneously.
+ * only .cpp files are taken into account.
+ * main config file for swig is assumed to be
+ name.i in CMAKE_SOURCE_DIR/swig/
+
"""
- swig_dir = os.path.join('@CMAKE_SOURCE_DIR@', 'swig')
- swig_config_file = os.path.join(swig_dir, name+'.i')
+ swig_dir = os.path.join('@CMAKE_SOURCE_DIR@', 'swig')
+ swig_config_file = os.path.join(swig_dir, name + '.i')
include_dirs = set(inc_dirs)
if sources is None:
sources = []
- if(src_dirs == None):
- assert(inc_dirs != None)
- for idir in inc_dirs:
- #sources += glob.glob(os.path.join(idir, '**/*.cpp'), recursive=True)
- for root, dirnames, filenames in os.walk(idir):
- for filename in fnmatch.filter(filenames, '*.cpp'):
- sources.append(os.path.join(root, filename))
- else:
- for sdir in src_dirs:
- sources += glob.glob(os.path.join(sdir, '*.cpp'))
- #else:
- #for f in sources:
- #include_dirs.add(os.path.dirname(f))
+ assert src_dirs is not None or inc_dirs is not None
+ if(src_dirs is None):
+ assert(inc_dirs is not None)
+ for idir in inc_dirs:
+ #sources += glob.glob(os.path.join(idir, '**/*.cpp'), recursive=True)
+ for root, dirnames, filenames in os.walk(idir):
+ for filename in fnmatch.filter(filenames, '*.cpp'):
+ sources.append(os.path.join(root, filename))
+ else:
+ for sdir in src_dirs:
+ sources += glob.glob(os.path.join(sdir, '*.cpp'))
- sources.insert(0,swig_config_file)
+ sources.insert(0, swig_config_file)
include_dirs = list(include_dirs)
name = 'hysop._' + name
swig_opts = ['-I' + swig_dir,
'-O', '-Wextra', '-Werror',
'-c++', '-extranative', '-safecstrings']
-
+
extern_includes = parseCMakeVar("@CXX_EXT_INCLUDES@")
- if(extern_includes != None):
+ if(extern_includes is not None):
for exti in extern_includes:
include_dirs.append(exti)
@@ -170,33 +242,10 @@ def create_swig_extension(name, inc_dirs, src_dirs=None, sources=None):
# List of modules (directories) to be included
with_test = "@WITH_TESTS@" is "ON"
if with_test:
- packages = find_packages(exclude=["*fakef2py*", "*gpu*"],where="@CMAKE_SOURCE_DIR@")
+ packages = find_packages(exclude=["*gpu*"], where="@CMAKE_SOURCE_DIR@")
else:
- packages = find_packages(exclude=["*tests*","*fakef2py*", "*gpu*"],where="@CMAKE_SOURCE_DIR@")
-
-# packages = ['hysop',
-# 'hysop.domain',
-# 'hysop.fields',
-# 'hysop.operator',
-# 'hysop.operator.discrete',
-# 'hysop.problem',
-# 'hysop.tools',
-# 'hysop.numerics',
-# 'hysop.numerics.integrators',
-# ]
-
-# packages_for_tests = ['hysop.domain.tests',
-# 'hysop.fields.tests',
-# 'hysop.operator.tests',
-# 'hysop.numerics.tests',
-# 'hysop.tools.tests',
-# 'hysop.problem.tests',
-# 'hysop.numerics.tests',
-# ]
-
-# if "@USE_MPI@" is "ON":
-# packages.append('hysop.mpi')
-# packages_for_tests.append('hysop.mpi.tests')
+ packages = find_packages(exclude=["*tests*", "*gpu*"],
+ where="@CMAKE_SOURCE_DIR@")
if "@WITH_GPU@" is "ON":
packages.append('hysop.gpu')
@@ -217,11 +266,12 @@ ext = {}
if enable_fortran is "ON":
fortran_root = \
'@CMAKE_SOURCE_DIR@/hysop'
- hysop_libdir = ['@CMAKE_BINARY_DIR@/src']
- hysoplib = ['@HYSOP_LIBRARY_NAME@']
+ hysop_libdir = [] ##### ['@CMAKE_BINARY_DIR@/src']
+ #####hysoplib = ['@HYSOP_LIBRARY_NAME@']
f2py_options = ['--no-lower']
fortran_src = set([])
- fortran_src.add('f2py/parameters.f90')
+
+ ####fortran_src.add('f2py/parameters.f90')
# -- fftw fortran sources --
withfftw = "@WITH_FFTW@"
if withfftw is "ON":
@@ -230,16 +280,12 @@ if enable_fortran is "ON":
#hysoplib.append('fftw3')
#hysoplib.append('fftw3_mpi')
hysop_libdir.append(fftwdir)
- else:
- packages.append('hysop.fakef2py')
- packages.append('hysop.fakef2py.fftw2py')
+
# -- scales sources --
withscales = '@WITH_SCALES@'
if withscales is "ON":
fortran_src.add('f2py/scales2py.f90')
- else:
- packages.append('hysop.fakef2py')
- packages.append('hysop.fakef2py.scales2py')
+
# -- set full path to fortran sources --
fortran_src = list(fortran_src)
for i in xrange(len(fortran_src)):
@@ -247,14 +293,15 @@ if enable_fortran is "ON":
# === Draft for future implementation of fortran interface ===
# -- f2py signature file --
- pyf_file = os.path.join(fortran_root, 'f2hysop.pyf')
+ pyf_file = os.path.join('@GENERATED_FORTRAN_FILES_DIR@', 'f2hysop.pyf')
# -- list of directories which contains fortran sources --
- # those dirs must be in hysop package directory
- subdirs = ['fortran',]
+ # path must be relative to hysop package directory
+ subdirs = ['common_f', ]
num_dirs = []
for sd in subdirs:
num_dirs.append(os.path.join(fortran_root, sd))
+ num_dirs.append('@GENERATED_FORTRAN_FILES_DIR@')
# create python interface to fortran sources
# For the moment, it includes the 'old' interface
# to scales and fftw (in sources) and the new
@@ -262,8 +309,8 @@ if enable_fortran is "ON":
ext['f2hysop'] = create_fortran_extension(
name='hysop.f2hysop',
sources=fortran_src,
- libdir=hysop_libdir,
- libs=hysoplib,
+ #libdir=hysop_libdir,
+ #libs=hysoplib,
pyf_file=pyf_file,
src_dirs=num_dirs)
@@ -283,12 +330,13 @@ if enable_cpp is "ON":
swig_include_dirs = [os.path.join('@CMAKE_SOURCE_DIR@','swig')]
cpp_include_dirs = ['src/fftw','src/hysop++/src']
- for id in cpp_include_dirs:
- swig_include_dirs.append(os.path.join('@CMAKE_SOURCE_DIR@', id))
+ for d in cpp_include_dirs:
+ swig_include_dirs.append(os.path.join('@CMAKE_SOURCE_DIR@', d))
ext = {}
cpp2hysop = "@CPP_2_HYSOP@"
- ext[cpp2hysop] = create_swig_extension(name=cpp2hysop, inc_dirs=swig_include_dirs)
+ ext[cpp2hysop] = create_swig_extension(name=cpp2hysop,
+ inc_dirs=swig_include_dirs)
for ex in ext:
ext_modules.append(ext[ex])
diff --git a/sort_f90.py b/sort_f90.py
index fb1f6a93cdb947c1fc9361561c05f842ab9bcc21..86257d4cfdbc396d6cc93c1fe1b6aefcfc9fad7a 100644
--- a/sort_f90.py
+++ b/sort_f90.py
@@ -1,61 +1,58 @@
"""
-Dependency scanner for F90/95 modules.
+Dependency scanner for F90/95 modules.
-The sort function provided below sorts fortran source files in order of
-increasing dependency. That is, the sorting order makes sure that modules are
-compiled before they are USE'd.
+The sort function provided below sorts fortran source files in order of
+increasing dependency. That is, the sorting order makes sure that modules are
+compiled before they are USE'd.
See:
http://scipy.org/scipy/numpy/ticket/752
-The regular expressions are modified versions from the SCons.Scanner.Fortran
+The regular expressions are modified versions from the SCons.Scanner.Fortran
module. The copyright notice for Scons is included below.
:Author: David Huard, Pearu Peterson
:Date: May, 2008
-"""
-"""
-Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons Foundation
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be included
-in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY
-KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
-WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
-LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
-OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+Copyright (c) 2001, 2002, 2003, 2004, 2005,
+ 2006, 2007, 2008 The SCons Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be included
+in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY
+KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
"""
-import re, copy, os
-import warnings
+import re
-__all__ = ['FortranFileSorter', 'sort']
+__all__ = ['FortranFileSorter', 'sort']
"""
Regular expression for a module name
------------------------------------
An alphanumeric word not beginning with a numeric character.
-
+
[a-z_] : a letter or an underscore
\w* : any number of alphanumeric characters
"""
modulename = """[a-z_]\w*"""
-
"""
Regular expression for a USE statement
--------------------------------------
@@ -95,8 +92,8 @@ Here is a breakdown of the regex:
(modulename_regex) : match the module name that is being USE'd, see above.
"""
use_regex = \
-"(?i)(?:^|;)\s*USE(?:\s+|(?:(?:\s*,\s*(?:NON_)?INTRINSIC)?\s*::))\s*(%s)"%\
-modulename
+ "(?i)(?:^|;)\s*USE(?:\s+|(?:(?:\s*,\s*(?:NON_)?INTRINSIC)?\s*::))\s*(%s)" %\
+ modulename
"""
@@ -123,7 +120,7 @@ Here is a breakdown of the regex:
that make up the defined module name and
save it in a group
"""
-def_regex = """(?i)^\s*MODULE\s+(?!PROCEDURE)(%s)"""%modulename
+def_regex = """(?i)^\s*MODULE\s+(?!PROCEDURE)(%s)""" % modulename
"""
@@ -203,18 +200,20 @@ remove all the comments.
.*$ : ignore the rest of the line
"""
comment_regex = r'(^.*)!?.*$'
-
+
+
class FortranFileSorter:
"""Given a list of fortran 90/95 files, return a file list sorted by module
dependency. If a file depends on a parent through a USE MODULE statement,
this parent file will occur earlier in the list.
-
+
Parameters
----------
files : sequence
The sequence of file names to be sorted.
-
+
"""
+
def __init__(self, files):
self.files = files
self.use_regex = re.compile(use_regex, re.MULTILINE)
@@ -239,11 +238,11 @@ class FortranFileSorter:
def match_defined(self, code):
"""Return the set of defined module in a code string."""
return set(map(str.lower, self.def_regex.findall(code)))
-
+
def match_included(self, code):
"""Return the set of included files in a code string."""
return set(self.include_regex.findall(code))
-
+
def externals(self):
"""Return the modules that are used but not defined in the list of
files."""
@@ -252,7 +251,7 @@ class FortranFileSorter:
all_used = reduce(set.union, self.mod_used.values())
all_defined = reduce(set.union, self.mod_defined.values())
return all_used.difference(all_defined)
-
+
def scan(self):
"""For each file, identify the set of modules that are
defined, used but not defined in the same file, and the set of
@@ -263,28 +262,28 @@ class FortranFileSorter:
self.included = {}
for f in self.files:
code = self.read_code(f)
- code = self.uncomment(code)
+ code = self.uncomment(code)
self.mod_defined[f] = self.match_defined(code)
self.mod_used[f] = self.match_used(code)
self.included[f] = self.match_included(code)
-
- # Remove from used the modules defined internally.
- # That is, keep elements in used but not in defined.
- self.mod_used[f].difference_update(self.mod_defined[f])
-
- # TODO : Deal with include (do we have too?)
+
+ # Remove from used the modules defined internally.
+ # That is, keep elements in used but not in defined.
+ self.mod_used[f].difference_update(self.mod_defined[f])
+
+ # TODO : Deal with include (do we have too?)
def sort(self):
"""Sort the files in order of dependency.
- """
+ """
ordered_list = []
-
+
# Take care of modules not defined anywhere in the files. eg.
- # an intrinsic module by assuming them known from the
+ # an intrinsic module by assuming them known from the
# start.
defined = self.externals()
-
- # This cycles through the files, and appends those whose dependencies
- # are already satisfied by the files in the ordered list.
+
+ # This cycles through the files, and appends those whose dependencies
+ # are already satisfied by the files in the ordered list.
remaining = set(self.files)
goon = True
while goon:
@@ -292,21 +291,20 @@ class FortranFileSorter:
for f in remaining:
dependencies_satisfied = self.mod_used[f].issubset(defined)
if dependencies_satisfied:
- ordered_list.append(f)
+ ordered_list.append(f)
defined.update(self.mod_defined[f])
goon = True
remaining.difference_update(set(ordered_list))
ordered_list.extend(list(remaining))
return ordered_list
-
-
-
+
+
def sort(files):
"""Given a list of fortran 90/95 files, return a file list sorted by module
dependency. If a file depends on a parent through a USE MODULE statement,
this parent file will occur earlier in the list.
-
+
Parameters
----------
files : sequence
@@ -314,13 +312,10 @@ def sort(files):
"""
FS = FortranFileSorter(files)
FS.scan()
- return FS.sort()
+ return FS.sort()
import sys
if __name__ == "__main__":
print sys.argv[1:]
sort(sys.argv[1:])
-
-
-
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 5eea76945fb822e3da511063aaf27f35d84576f3..a66936986a42225f07626ad70dc525877387296c 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -15,7 +15,7 @@ if(WITH_FFTW)
list(APPEND ${HYSOP_LIBRARY_NAME}_SRCDIRS fftw)
endif()
-if(WITH_LIB_CXX)
+if(USE_CXX)
list(APPEND ${HYSOP_LIBRARY_NAME}_SRCDIRS hysop++/src)
endif()
@@ -102,4 +102,4 @@ if(WITH_FORTRAN_TESTS)
target_link_libraries(${EXE_NAME} ${HYSOP_LIBRARY_NAME})
target_link_libraries(${EXE_NAME} ${HYSOP_LINK_LIBRARIES})
endif()
-endif()
\ No newline at end of file
+endif()