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merge branch python3 for python 3 support
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@robince
robince committed Oct 2, 2019
2 parents eae0fff + f7c2695 commit f76e073
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Showing 10 changed files with 6,966 additions and 3,804 deletions.
230 changes: 114 additions & 116 deletions gsl_dist/gsl_Extension.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,7 @@



from array_includes import array_include_dirs
from gsl_dist.array_includes import array_include_dirs


# steel --gsl-prefix from option list
Expand All @@ -30,9 +30,9 @@
if gsl_prefix_match:
gsl_prefix_option=gsl_prefix_match.group(1)
gsl_prefix_option.strip()
argv[pos:pos+1]=[]
break
pos+=1
argv[pos:pos+1]=[]
break
pos+=1

# Extension class adapted for gsl
class _gsl_Location:
Expand Down Expand Up @@ -68,8 +68,8 @@ def get_gsl_version(self):
return self.version

def _split_version(self, version):
if version[-1] == '+':
version = version[:-1]
if version[-1] == '+':
version = version[:-1]
return re.split('\.',version)

def get_swig(self):
Expand All @@ -93,7 +93,7 @@ def __init__(self):
self.prefix = self.get_gsl_info('--prefix').strip()
self.cflags = self.get_gsl_info('--cflags').strip()
self.libs = self.get_gsl_info('--libs').strip()
self.version = self._split_version(self.get_gsl_info('--version').strip())[:2]
self.version = self._split_version(self.get_gsl_info('--version').strip())[:2]

# I am running on swig. I suppose that swig is in the path
self.swig = "swig"
Expand All @@ -110,8 +110,8 @@ def get_gsl_info(self, 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
if not gsl_output:
raise DistutilsExecError("could not start %s"%self.gsl_config_tool)
return gsl_output


Expand All @@ -120,133 +120,131 @@ def __init__(self):
_gsl_Location.__init__(self)
try:
import gsl_site
except ImportError, des:
except ImportError as des:
msg = "I do not know how to run gsl-config \n"+\
"on this system. Therefore you must provide me with the information\n" +\
"where to find the GSL library. I could not import `gsl_site'.\n" +\
"Reason: %s. Copy gsl_site_example.py to gsl_site.py.\n"+\
"Edit the variables in that file to reflect your installation."
raise DistutilsExecError, msg % des
"on this system. Therefore you must provide me with the information\n" +\
"where to find the GSL library. I could not import `gsl_site'.\n" +\
"Reason: %s. Copy gsl_site_example.py to gsl_site.py.\n"+\
"Edit the variables in that file to reflect your installation."
raise DistutilsExecError(msg % des)

self.prefix = gsl_site.prefix
self.cflags = gsl_site.cflags
self.libs = gsl_site.libs
self.swig = gsl_site.swig
self.version = self._split_version(gsl_site.version)
self.libs = gsl_site.libs
self.swig = gsl_site.swig
self.version = self._split_version(gsl_site.version)

if os.name == 'posix':
gsl_Location = _gsl_Location_gsl_config()
gsl_Location = _gsl_Location_gsl_config()
else:
gsl_Location = _gsl_Location_file()
gsl_Location = _gsl_Location_file()


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
):


# 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[0:0]=[os.path.join(self.gsl_prefix,'include')]
include_dirs= include_dirs + array_include_dirs

# prepend library directory
if library_dirs is None: library_dirs=[]
library_dirs[0:0] = [os.path.join(self.gsl_prefix,'lib')]

# prepare lib list
# split optionlist and strip blanks from each option
gsl_lib_list=map(string.strip,self.get_gsl_libs().split())

# filter options with -l
not_lib_opt=lambda a:a[:2]=="-l"
gsl_lib_list=filter(not_lib_opt,gsl_lib_list)
# cut -l
only_lib_name=lambda a:a[2:]
gsl_lib_list=map(only_lib_name,gsl_lib_list)

if libraries is None: libraries=[]
#libraries.append('pygsl')
libraries.extend(gsl_lib_list)

# test if Numeric module is available
if define_macros is None:
define_macros=[]
try:
imp.find_module("Numeric")
define_macros = define_macros + [("NUMERIC",1),]
except ImportError:
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)
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),]

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
)
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):

# 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[0:0]=[os.path.join(self.gsl_prefix,'include')]
include_dirs= include_dirs + array_include_dirs

# prepend library directory
if library_dirs is None: library_dirs=[]
library_dirs[0:0] = [os.path.join(self.gsl_prefix,'lib')]

# prepare lib list
# split optionlist and strip blanks from each option
gsl_lib_list=map(str.strip,self.get_gsl_libs().split())

# filter options with -l
not_lib_opt=lambda a:a[:2]=="-l"
gsl_lib_list=filter(not_lib_opt,gsl_lib_list)
# cut -l
only_lib_name=lambda a:a[2:]
gsl_lib_list=map(only_lib_name,gsl_lib_list)

if libraries is None: libraries=[]
#libraries.append('pygsl')
libraries.extend(gsl_lib_list)

# test if Numeric module is available
if define_macros is None:
define_macros=[]
try:
imp.find_module("Numeric")
define_macros = define_macros + [("NUMERIC",1),]
except ImportError:
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)
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),]

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
)

def check_version(self, required_version, this_version):
min_length=min(len(required_version),len(this_version))
for pos in range(min_length):
this_type=type(required_version[pos])
if this_type== types.StringType:
if this_type== bytes:
if required_version[pos]>this_version[pos]: return 0
elif this_type == types.IntType:
elif this_type == int:
if required_version[pos]>int(this_version[pos]): 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
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


Expand All @@ -264,8 +262,8 @@ def get_gsl_info(self, 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
if not gsl_output:
raise DistutilsExecError("could not start %s"%self.gsl_config_tool)
return gsl_output

def get_gsl_prefix(self,):
Expand Down
4 changes: 2 additions & 2 deletions pyentropy/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,8 +26,8 @@
__author__ = 'Robin Ince'
__version__ = '0.5.0dev'

from systems import DiscreteSystem, SortedDiscreteSystem
from utils import (prob, decimalise, nsb_entropy, quantise,
from pyentropy.systems import DiscreteSystem, SortedDiscreteSystem
from pyentropy.utils import (prob, decimalise, nsb_entropy, quantise,
dec2base, base2dec, quantise_discrete)

from numpy.testing import Tester
Expand Down
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