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Correcting the incorrect pointers on pygsl_lite_odeiv2_system
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Formatting the extension files.
Adding swig as a build requirement
Making the warning "incompatible-pointer-types" to an error
Adding basic unit tests on ODE (w. Jacobians)
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@raffienficiaud
raffienficiaud committed Aug 19, 2024
1 parent 8860506 commit 5b1169b
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Showing 8 changed files with 1,211 additions and 908 deletions.
370 changes: 194 additions & 176 deletions gsl_dist/gsl_Extension.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,191 +16,209 @@
import re
import string
import types
from sys import argv,version_info
from sys import argv, version_info

from gsl_Location import gsl_Location

try:
from array_includes import array_include_dirs
from array_includes import array_include_dirs
except ImportError:
from pygsl_lite.gsl_dist.array_includes import array_include_dirs
from pygsl_lite.gsl_dist.array_includes import array_include_dirs


#def check_dependencies(sources, depends):
# """Check if any of the dependencies is newer than the src
# def check_dependencies(sources, depends):
# """Check if any of the dependencies is newer than the src
#
# It assumes that the dependencies are in the same directory as the
# src file
#
# Returns:
# the deps if they are newer than the src file, None if not
# """
# is_old = True
# for src in sources:
# t_dir = os.path.dirname(src)
# check_deps = map(lambda x: os.path.join(t_dir, x), depends)
# is_old = newer_group(check_deps, src)
# print("src %s is old %s" % (src, is_old))
# if is_old == True:
# break
#
# if is_old == False:
# return None
# It assumes that the dependencies are in the same directory as the
# src file
#
# return depends
# Returns:
# the deps if they are newer than the src file, None if not
# """
# is_old = True
# for src in sources:
# t_dir = os.path.dirname(src)
# check_deps = map(lambda x: os.path.join(t_dir, x), depends)
# is_old = newer_group(check_deps, src)
# print("src %s is old %s" % (src, is_old))
# if is_old == True:
# break
#
# if is_old == False:
# return None
#
# return depends


class gsl_Extension(Extension):
"""
for gsl needs
"""
def __init__(self, name, sources,
include_dirs=None,
define_macros=None,
undef_macros=None,
library_dirs=None,
libraries=None,
runtime_library_dirs=None,
extra_objects=None,
extra_compile_args=None,
extra_link_args=None,
export_symbols=None,
gsl_prefix=None,
gsl_min_version=None,
python_min_version=None,
depends=None,
**kws
):


# get real prefix
self.gsl_prefix=self.get_gsl_prefix()

gsl_major_version, gsl_minor_version = self.get_gsl_version()
# check gsl version
if gsl_min_version is not None and \
not self.check_gsl_version(gsl_min_version):
raise DistutilsExecError("min gsl version %s required"%repr(gsl_min_version))

# check python version
if python_min_version is not None and \
not self.check_python_version(python_min_version):
raise DistutilsExecError("min python version %s required"%repr(python_min_version))

# prepend include directory
if include_dirs is None: include_dirs=[]
include_dirs.append('Include')
include_dirs.append('.')
include_dirs = gsl_Location.get_gsl_include_dirs() + include_dirs
include_dirs = include_dirs + array_include_dirs

# prepend library directory
if library_dirs is None: library_dirs=[]
library_dirs = library_dirs + gsl_Location.get_gsl_library_dirs()

# Testing linking to non standard location if standard location is available
#runtime_library_dirs = gsl_Location.get_gsl_library_dirs()
if libraries is None: libraries=[]
#libraries.append('pygsl_lite')
libraries.extend(gsl_Location.get_gsl_lib_list())

# test if Numeric module is available
if define_macros is None:
define_macros=[]
define_macros = define_macros + [("NUMERIC",0), ]
if undef_macros == None:
undef_macros = []
if 'NDEBUG' not in undef_macros:
undef_macros.append('NDEBUG')
tmp = map(lambda x: x[0], define_macros)

# Now config will test of GSL_MAJOR_VERSION and GSL_MINOR_VERSION is defined
#if "PYGSL_GSL_MAJOR_VERSION" not in tmp:
# define_macros = define_macros + [("PYGSL_GSL_MAJOR_VERSION", gsl_major_version),]


#if "PYGSL_GSL_MINOR_VERSION" not in tmp:
# #define_macros.append(("PYGSL_GSL_MINOR_VERSION", gsl_minor_version))
# define_macros = define_macros + [("PYGSL_GSL_MINOR_VERSION", gsl_minor_version),]

# dependes triggers always a recompile ...
# try to fix it
# if depends is not None:
# depends = check_dependencies(sources, depends)

Extension.__init__(self, name, sources,
include_dirs,
define_macros,
undef_macros,
library_dirs,
libraries,
runtime_library_dirs,
extra_objects,
extra_compile_args,
extra_link_args,
export_symbols,
depends = depends,
**kws
)

def check_version(self, required_version, this_version):
this_version = tuple(this_version)
#print("req '%s' this '%s'" %(required_version, this_version))
min_length=min(len(required_version),len(this_version))
for pos in range(min_length):
t_val = this_version[pos]
test_val = required_version[pos]
#print("\t %d: req '%s' this '%s'" %( pos, test_val, t_val))

this_type=type(t_val)
if this_type== type(" "):
t_val = int(t_val)

if type(test_val)== type(" "):
test_val = int(test_val)

if t_val > test_val:
# already larger
return 1
elif t_val == test_val:
continue
elif t_val < test_val:
return 0
else:
raise DistutilsExecError("incorrect version specification")
# problematic: 0.9 < 0.9.0, but assures that 0.9.1 > 0.9
if len(required_version)>len(this_version): return 0
return 1



def check_gsl_version(self, version_array):
return self.check_version(version_array,self.get_gsl_version())

def check_python_version(self, version_array):
return self.check_version(version_array,version_info)

# get gsl-prefix option
def get_gsl_info(self, arguments):
"""
executes gsl-config with given arguments
"""
gsl_command=os.popen(self.gsl_config_tool+' '+arguments)
gsl_output=gsl_command.readline()
gsl_command.close()
if not gsl_output:
raise DistutilsExecError("could not start %s"%self.gsl_config_tool)
return gsl_output

def get_gsl_prefix(self,):
return gsl_Location.get_gsl_prefix()

def get_gsl_cflags(self):
return gsl_Location.get_gsl_cflags()

def get_gsl_libs(self):
return gsl_Location.get_gsl_libs()

def get_gsl_version(self):
return gsl_Location.get_gsl_version()

"""
for gsl needs
"""

def __init__(
self,
name,
sources,
include_dirs=None,
define_macros=None,
undef_macros=None,
library_dirs=None,
libraries=None,
runtime_library_dirs=None,
extra_objects=None,
extra_compile_args=None,
extra_link_args=None,
export_symbols=None,
gsl_prefix=None,
gsl_min_version=None,
python_min_version=None,
depends=None,
**kws,
):

# get real prefix
self.gsl_prefix = self.get_gsl_prefix()

extra_compile_args = (extra_compile_args or []) + [
"-Werror=incompatible-pointer-types"
]

gsl_major_version, gsl_minor_version = self.get_gsl_version()
# check gsl version
if gsl_min_version is not None and not self.check_gsl_version(gsl_min_version):
raise DistutilsExecError(
"min gsl version %s required" % repr(gsl_min_version)
)

# check python version
if python_min_version is not None and not self.check_python_version(
python_min_version
):
raise DistutilsExecError(
"min python version %s required" % repr(python_min_version)
)

# prepend include directory
if include_dirs is None:
include_dirs = []
include_dirs.append("Include")
include_dirs.append(".")
include_dirs = gsl_Location.get_gsl_include_dirs() + include_dirs
include_dirs = include_dirs + array_include_dirs

# prepend library directory
if library_dirs is None:
library_dirs = []
library_dirs = library_dirs + gsl_Location.get_gsl_library_dirs()

# Testing linking to non standard location if standard location is available
# runtime_library_dirs = gsl_Location.get_gsl_library_dirs()
if libraries is None:
libraries = []
# libraries.append('pygsl_lite')
libraries.extend(gsl_Location.get_gsl_lib_list())

# test if Numeric module is available
if define_macros is None:
define_macros = []
define_macros = define_macros + [
("NUMERIC", 0),
]
if undef_macros == None:
undef_macros = []
if "NDEBUG" not in undef_macros:
undef_macros.append("NDEBUG")
tmp = map(lambda x: x[0], define_macros)

# Now config will test of GSL_MAJOR_VERSION and GSL_MINOR_VERSION is defined
# if "PYGSL_GSL_MAJOR_VERSION" not in tmp:
# define_macros = define_macros + [("PYGSL_GSL_MAJOR_VERSION", gsl_major_version),]

# if "PYGSL_GSL_MINOR_VERSION" not in tmp:
# #define_macros.append(("PYGSL_GSL_MINOR_VERSION", gsl_minor_version))
# define_macros = define_macros + [("PYGSL_GSL_MINOR_VERSION", gsl_minor_version),]

# dependes triggers always a recompile ...
# try to fix it
# if depends is not None:
# depends = check_dependencies(sources, depends)

Extension.__init__(
self,
name,
sources,
include_dirs,
define_macros,
undef_macros,
library_dirs,
libraries,
runtime_library_dirs,
extra_objects,
extra_compile_args,
extra_link_args,
export_symbols,
depends=depends,
**kws,
)

def check_version(self, required_version, this_version):
this_version = tuple(this_version)
# print("req '%s' this '%s'" %(required_version, this_version))
min_length = min(len(required_version), len(this_version))
for pos in range(min_length):
t_val = this_version[pos]
test_val = required_version[pos]
# print("\t %d: req '%s' this '%s'" %( pos, test_val, t_val))

this_type = type(t_val)
if this_type == type(" "):
t_val = int(t_val)

if type(test_val) == type(" "):
test_val = int(test_val)

if t_val > test_val:
# already larger
return 1
elif t_val == test_val:
continue
elif t_val < test_val:
return 0
else:
raise DistutilsExecError("incorrect version specification")
# problematic: 0.9 < 0.9.0, but assures that 0.9.1 > 0.9
if len(required_version) > len(this_version):
return 0
return 1

def check_gsl_version(self, version_array):
return self.check_version(version_array, self.get_gsl_version())

def check_python_version(self, version_array):
return self.check_version(version_array, version_info)

# get gsl-prefix option
def get_gsl_info(self, arguments):
"""
executes gsl-config with given arguments
"""
gsl_command = os.popen(self.gsl_config_tool + " " + arguments)
gsl_output = gsl_command.readline()
gsl_command.close()
if not gsl_output:
raise DistutilsExecError("could not start %s" % self.gsl_config_tool)
return gsl_output

def get_gsl_prefix(
self,
):
return gsl_Location.get_gsl_prefix()

def get_gsl_cflags(self):
return gsl_Location.get_gsl_cflags()

def get_gsl_libs(self):
return gsl_Location.get_gsl_libs()

def get_gsl_version(self):
return gsl_Location.get_gsl_version()
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