Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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556 lines
20 KiB
556 lines
20 KiB
import re
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import os
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import sys
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import warnings
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import platform
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import tempfile
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import hashlib
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import base64
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import subprocess
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from subprocess import Popen, PIPE, STDOUT
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from numpy.distutils.exec_command import filepath_from_subprocess_output
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from numpy.distutils.fcompiler import FCompiler
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from distutils.version import LooseVersion
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compilers = ['GnuFCompiler', 'Gnu95FCompiler']
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TARGET_R = re.compile(r"Target: ([a-zA-Z0-9_\-]*)")
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# XXX: handle cross compilation
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def is_win64():
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return sys.platform == "win32" and platform.architecture()[0] == "64bit"
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if is_win64():
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#_EXTRAFLAGS = ["-fno-leading-underscore"]
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_EXTRAFLAGS = []
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else:
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_EXTRAFLAGS = []
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class GnuFCompiler(FCompiler):
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compiler_type = 'gnu'
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compiler_aliases = ('g77', )
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description = 'GNU Fortran 77 compiler'
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def gnu_version_match(self, version_string):
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"""Handle the different versions of GNU fortran compilers"""
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# Strip warning(s) that may be emitted by gfortran
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while version_string.startswith('gfortran: warning'):
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version_string = version_string[version_string.find('\n') + 1:]
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# Gfortran versions from after 2010 will output a simple string
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# (usually "x.y", "x.y.z" or "x.y.z-q") for ``-dumpversion``; older
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# gfortrans may still return long version strings (``-dumpversion`` was
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# an alias for ``--version``)
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if len(version_string) <= 20:
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# Try to find a valid version string
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m = re.search(r'([0-9.]+)', version_string)
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if m:
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# g77 provides a longer version string that starts with GNU
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# Fortran
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if version_string.startswith('GNU Fortran'):
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return ('g77', m.group(1))
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# gfortran only outputs a version string such as #.#.#, so check
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# if the match is at the start of the string
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elif m.start() == 0:
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return ('gfortran', m.group(1))
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else:
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# Output probably from --version, try harder:
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m = re.search(r'GNU Fortran\s+95.*?([0-9-.]+)', version_string)
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if m:
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return ('gfortran', m.group(1))
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m = re.search(
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r'GNU Fortran.*?\-?([0-9-.]+\.[0-9-.]+)', version_string)
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if m:
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v = m.group(1)
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if v.startswith('0') or v.startswith('2') or v.startswith('3'):
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# the '0' is for early g77's
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return ('g77', v)
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else:
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# at some point in the 4.x series, the ' 95' was dropped
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# from the version string
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return ('gfortran', v)
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# If still nothing, raise an error to make the problem easy to find.
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err = 'A valid Fortran version was not found in this string:\n'
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raise ValueError(err + version_string)
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def version_match(self, version_string):
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v = self.gnu_version_match(version_string)
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if not v or v[0] != 'g77':
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return None
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return v[1]
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possible_executables = ['g77', 'f77']
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executables = {
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'version_cmd' : [None, "-dumpversion"],
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'compiler_f77' : [None, "-g", "-Wall", "-fno-second-underscore"],
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'compiler_f90' : None, # Use --fcompiler=gnu95 for f90 codes
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'compiler_fix' : None,
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'linker_so' : [None, "-g", "-Wall"],
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'archiver' : ["ar", "-cr"],
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'ranlib' : ["ranlib"],
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'linker_exe' : [None, "-g", "-Wall"]
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}
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module_dir_switch = None
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module_include_switch = None
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# Cygwin: f771: warning: -fPIC ignored for target (all code is
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# position independent)
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if os.name != 'nt' and sys.platform != 'cygwin':
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pic_flags = ['-fPIC']
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# use -mno-cygwin for g77 when Python is not Cygwin-Python
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if sys.platform == 'win32':
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for key in ['version_cmd', 'compiler_f77', 'linker_so', 'linker_exe']:
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executables[key].append('-mno-cygwin')
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g2c = 'g2c'
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suggested_f90_compiler = 'gnu95'
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def get_flags_linker_so(self):
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opt = self.linker_so[1:]
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if sys.platform == 'darwin':
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target = os.environ.get('MACOSX_DEPLOYMENT_TARGET', None)
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# If MACOSX_DEPLOYMENT_TARGET is set, we simply trust the value
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# and leave it alone. But, distutils will complain if the
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# environment's value is different from the one in the Python
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# Makefile used to build Python. We let disutils handle this
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# error checking.
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if not target:
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# If MACOSX_DEPLOYMENT_TARGET is not set in the environment,
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# we try to get it first from sysconfig and then
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# fall back to setting it to 10.9 This is a reasonable default
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# even when using the official Python dist and those derived
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# from it.
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import sysconfig
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target = sysconfig.get_config_var('MACOSX_DEPLOYMENT_TARGET')
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if not target:
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target = '10.9'
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s = f'Env. variable MACOSX_DEPLOYMENT_TARGET set to {target}'
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warnings.warn(s, stacklevel=2)
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os.environ['MACOSX_DEPLOYMENT_TARGET'] = target
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opt.extend(['-undefined', 'dynamic_lookup', '-bundle'])
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else:
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opt.append("-shared")
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if sys.platform.startswith('sunos'):
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# SunOS often has dynamically loaded symbols defined in the
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# static library libg2c.a The linker doesn't like this. To
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# ignore the problem, use the -mimpure-text flag. It isn't
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# the safest thing, but seems to work. 'man gcc' says:
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# ".. Instead of using -mimpure-text, you should compile all
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# source code with -fpic or -fPIC."
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opt.append('-mimpure-text')
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return opt
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def get_libgcc_dir(self):
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try:
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output = subprocess.check_output(self.compiler_f77 +
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['-print-libgcc-file-name'])
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except (OSError, subprocess.CalledProcessError):
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pass
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else:
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output = filepath_from_subprocess_output(output)
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return os.path.dirname(output)
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return None
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def get_libgfortran_dir(self):
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if sys.platform[:5] == 'linux':
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libgfortran_name = 'libgfortran.so'
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elif sys.platform == 'darwin':
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libgfortran_name = 'libgfortran.dylib'
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else:
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libgfortran_name = None
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libgfortran_dir = None
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if libgfortran_name:
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find_lib_arg = ['-print-file-name={0}'.format(libgfortran_name)]
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try:
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output = subprocess.check_output(
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self.compiler_f77 + find_lib_arg)
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except (OSError, subprocess.CalledProcessError):
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pass
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else:
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output = filepath_from_subprocess_output(output)
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libgfortran_dir = os.path.dirname(output)
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return libgfortran_dir
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def get_library_dirs(self):
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opt = []
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if sys.platform[:5] != 'linux':
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d = self.get_libgcc_dir()
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if d:
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# if windows and not cygwin, libg2c lies in a different folder
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if sys.platform == 'win32' and not d.startswith('/usr/lib'):
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d = os.path.normpath(d)
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path = os.path.join(d, "lib%s.a" % self.g2c)
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if not os.path.exists(path):
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root = os.path.join(d, *((os.pardir, ) * 4))
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d2 = os.path.abspath(os.path.join(root, 'lib'))
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path = os.path.join(d2, "lib%s.a" % self.g2c)
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if os.path.exists(path):
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opt.append(d2)
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opt.append(d)
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# For Macports / Linux, libgfortran and libgcc are not co-located
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lib_gfortran_dir = self.get_libgfortran_dir()
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if lib_gfortran_dir:
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opt.append(lib_gfortran_dir)
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return opt
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def get_libraries(self):
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opt = []
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d = self.get_libgcc_dir()
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if d is not None:
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g2c = self.g2c + '-pic'
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f = self.static_lib_format % (g2c, self.static_lib_extension)
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if not os.path.isfile(os.path.join(d, f)):
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g2c = self.g2c
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else:
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g2c = self.g2c
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if g2c is not None:
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opt.append(g2c)
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c_compiler = self.c_compiler
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if sys.platform == 'win32' and c_compiler and \
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c_compiler.compiler_type == 'msvc':
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opt.append('gcc')
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if sys.platform == 'darwin':
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opt.append('cc_dynamic')
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return opt
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def get_flags_debug(self):
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return ['-g']
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def get_flags_opt(self):
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v = self.get_version()
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if v and v <= '3.3.3':
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# With this compiler version building Fortran BLAS/LAPACK
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# with -O3 caused failures in lib.lapack heevr,syevr tests.
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opt = ['-O2']
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else:
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opt = ['-O3']
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opt.append('-funroll-loops')
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return opt
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def _c_arch_flags(self):
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""" Return detected arch flags from CFLAGS """
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from distutils import sysconfig
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try:
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cflags = sysconfig.get_config_vars()['CFLAGS']
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except KeyError:
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return []
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arch_re = re.compile(r"-arch\s+(\w+)")
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arch_flags = []
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for arch in arch_re.findall(cflags):
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arch_flags += ['-arch', arch]
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return arch_flags
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def get_flags_arch(self):
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return []
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def runtime_library_dir_option(self, dir):
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if sys.platform == 'win32':
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# Linux/Solaris/Unix support RPATH, Windows does not
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raise NotImplementedError
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# TODO: could use -Xlinker here, if it's supported
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assert "," not in dir
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if sys.platform == 'darwin':
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return f'-Wl,-rpath,{dir}'
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elif sys.platform[:3] == 'aix':
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# AIX RPATH is called LIBPATH
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return f'-Wl,-blibpath:{dir}'
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else:
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return f'-Wl,-rpath={dir}'
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class Gnu95FCompiler(GnuFCompiler):
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compiler_type = 'gnu95'
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compiler_aliases = ('gfortran', )
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description = 'GNU Fortran 95 compiler'
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def version_match(self, version_string):
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v = self.gnu_version_match(version_string)
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if not v or v[0] != 'gfortran':
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return None
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v = v[1]
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if LooseVersion(v) >= "4":
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# gcc-4 series releases do not support -mno-cygwin option
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pass
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else:
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# use -mno-cygwin flag for gfortran when Python is not
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# Cygwin-Python
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if sys.platform == 'win32':
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for key in [
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'version_cmd', 'compiler_f77', 'compiler_f90',
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'compiler_fix', 'linker_so', 'linker_exe'
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]:
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self.executables[key].append('-mno-cygwin')
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return v
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possible_executables = ['gfortran', 'f95']
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executables = {
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'version_cmd' : ["<F90>", "-dumpversion"],
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'compiler_f77' : [None, "-Wall", "-g", "-ffixed-form",
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"-fno-second-underscore"] + _EXTRAFLAGS,
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'compiler_f90' : [None, "-Wall", "-g",
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"-fno-second-underscore"] + _EXTRAFLAGS,
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'compiler_fix' : [None, "-Wall", "-g","-ffixed-form",
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"-fno-second-underscore"] + _EXTRAFLAGS,
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'linker_so' : ["<F90>", "-Wall", "-g"],
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'archiver' : ["ar", "-cr"],
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'ranlib' : ["ranlib"],
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'linker_exe' : [None, "-Wall"]
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}
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module_dir_switch = '-J'
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module_include_switch = '-I'
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if sys.platform[:3] == 'aix':
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executables['linker_so'].append('-lpthread')
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if platform.architecture()[0][:2] == '64':
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for key in ['compiler_f77', 'compiler_f90','compiler_fix','linker_so', 'linker_exe']:
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executables[key].append('-maix64')
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g2c = 'gfortran'
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def _universal_flags(self, cmd):
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"""Return a list of -arch flags for every supported architecture."""
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if not sys.platform == 'darwin':
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return []
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arch_flags = []
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# get arches the C compiler gets.
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c_archs = self._c_arch_flags()
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if "i386" in c_archs:
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c_archs[c_archs.index("i386")] = "i686"
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# check the arches the Fortran compiler supports, and compare with
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# arch flags from C compiler
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for arch in ["ppc", "i686", "x86_64", "ppc64"]:
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if _can_target(cmd, arch) and arch in c_archs:
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arch_flags.extend(["-arch", arch])
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return arch_flags
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def get_flags(self):
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flags = GnuFCompiler.get_flags(self)
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arch_flags = self._universal_flags(self.compiler_f90)
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if arch_flags:
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flags[:0] = arch_flags
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return flags
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def get_flags_linker_so(self):
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flags = GnuFCompiler.get_flags_linker_so(self)
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arch_flags = self._universal_flags(self.linker_so)
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if arch_flags:
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flags[:0] = arch_flags
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return flags
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def get_library_dirs(self):
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opt = GnuFCompiler.get_library_dirs(self)
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if sys.platform == 'win32':
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c_compiler = self.c_compiler
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if c_compiler and c_compiler.compiler_type == "msvc":
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target = self.get_target()
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if target:
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d = os.path.normpath(self.get_libgcc_dir())
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root = os.path.join(d, *((os.pardir, ) * 4))
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path = os.path.join(root, "lib")
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mingwdir = os.path.normpath(path)
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if os.path.exists(os.path.join(mingwdir, "libmingwex.a")):
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opt.append(mingwdir)
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# For Macports / Linux, libgfortran and libgcc are not co-located
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lib_gfortran_dir = self.get_libgfortran_dir()
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if lib_gfortran_dir:
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opt.append(lib_gfortran_dir)
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return opt
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def get_libraries(self):
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opt = GnuFCompiler.get_libraries(self)
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if sys.platform == 'darwin':
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opt.remove('cc_dynamic')
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if sys.platform == 'win32':
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c_compiler = self.c_compiler
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if c_compiler and c_compiler.compiler_type == "msvc":
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if "gcc" in opt:
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i = opt.index("gcc")
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opt.insert(i + 1, "mingwex")
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opt.insert(i + 1, "mingw32")
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c_compiler = self.c_compiler
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if c_compiler and c_compiler.compiler_type == "msvc":
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return []
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else:
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pass
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return opt
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def get_target(self):
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try:
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output = subprocess.check_output(self.compiler_f77 + ['-v'])
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except (OSError, subprocess.CalledProcessError):
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pass
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else:
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output = filepath_from_subprocess_output(output)
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m = TARGET_R.search(output)
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if m:
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return m.group(1)
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return ""
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def _hash_files(self, filenames):
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h = hashlib.sha1()
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for fn in filenames:
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with open(fn, 'rb') as f:
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while True:
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block = f.read(131072)
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if not block:
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break
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h.update(block)
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text = base64.b32encode(h.digest())
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text = text.decode('ascii')
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return text.rstrip('=')
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def _link_wrapper_lib(self, objects, output_dir, extra_dll_dir,
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chained_dlls, is_archive):
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"""Create a wrapper shared library for the given objects
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Return an MSVC-compatible lib
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"""
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c_compiler = self.c_compiler
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if c_compiler.compiler_type != "msvc":
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raise ValueError("This method only supports MSVC")
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object_hash = self._hash_files(list(objects) + list(chained_dlls))
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if is_win64():
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tag = 'win_amd64'
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else:
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tag = 'win32'
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basename = 'lib' + os.path.splitext(
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os.path.basename(objects[0]))[0][:8]
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root_name = basename + '.' + object_hash + '.gfortran-' + tag
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dll_name = root_name + '.dll'
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def_name = root_name + '.def'
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lib_name = root_name + '.lib'
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dll_path = os.path.join(extra_dll_dir, dll_name)
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def_path = os.path.join(output_dir, def_name)
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lib_path = os.path.join(output_dir, lib_name)
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if os.path.isfile(lib_path):
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# Nothing to do
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return lib_path, dll_path
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if is_archive:
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objects = (["-Wl,--whole-archive"] + list(objects) +
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["-Wl,--no-whole-archive"])
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self.link_shared_object(
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objects,
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dll_name,
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output_dir=extra_dll_dir,
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extra_postargs=list(chained_dlls) + [
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'-Wl,--allow-multiple-definition',
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'-Wl,--output-def,' + def_path,
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'-Wl,--export-all-symbols',
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'-Wl,--enable-auto-import',
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'-static',
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'-mlong-double-64',
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])
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# No PowerPC!
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if is_win64():
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specifier = '/MACHINE:X64'
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else:
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specifier = '/MACHINE:X86'
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# MSVC specific code
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lib_args = ['/def:' + def_path, '/OUT:' + lib_path, specifier]
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if not c_compiler.initialized:
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c_compiler.initialize()
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c_compiler.spawn([c_compiler.lib] + lib_args)
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|
|
return lib_path, dll_path
|
|
|
|
def can_ccompiler_link(self, compiler):
|
|
# MSVC cannot link objects compiled by GNU fortran
|
|
return compiler.compiler_type not in ("msvc", )
|
|
|
|
def wrap_unlinkable_objects(self, objects, output_dir, extra_dll_dir):
|
|
"""
|
|
Convert a set of object files that are not compatible with the default
|
|
linker, to a file that is compatible.
|
|
"""
|
|
if self.c_compiler.compiler_type == "msvc":
|
|
# Compile a DLL and return the lib for the DLL as
|
|
# the object. Also keep track of previous DLLs that
|
|
# we have compiled so that we can link against them.
|
|
|
|
# If there are .a archives, assume they are self-contained
|
|
# static libraries, and build separate DLLs for each
|
|
archives = []
|
|
plain_objects = []
|
|
for obj in objects:
|
|
if obj.lower().endswith('.a'):
|
|
archives.append(obj)
|
|
else:
|
|
plain_objects.append(obj)
|
|
|
|
chained_libs = []
|
|
chained_dlls = []
|
|
for archive in archives[::-1]:
|
|
lib, dll = self._link_wrapper_lib(
|
|
[archive],
|
|
output_dir,
|
|
extra_dll_dir,
|
|
chained_dlls=chained_dlls,
|
|
is_archive=True)
|
|
chained_libs.insert(0, lib)
|
|
chained_dlls.insert(0, dll)
|
|
|
|
if not plain_objects:
|
|
return chained_libs
|
|
|
|
lib, dll = self._link_wrapper_lib(
|
|
plain_objects,
|
|
output_dir,
|
|
extra_dll_dir,
|
|
chained_dlls=chained_dlls,
|
|
is_archive=False)
|
|
return [lib] + chained_libs
|
|
else:
|
|
raise ValueError("Unsupported C compiler")
|
|
|
|
|
|
def _can_target(cmd, arch):
|
|
"""Return true if the architecture supports the -arch flag"""
|
|
newcmd = cmd[:]
|
|
fid, filename = tempfile.mkstemp(suffix=".f")
|
|
os.close(fid)
|
|
try:
|
|
d = os.path.dirname(filename)
|
|
output = os.path.splitext(filename)[0] + ".o"
|
|
try:
|
|
newcmd.extend(["-arch", arch, "-c", filename])
|
|
p = Popen(newcmd, stderr=STDOUT, stdout=PIPE, cwd=d)
|
|
p.communicate()
|
|
return p.returncode == 0
|
|
finally:
|
|
if os.path.exists(output):
|
|
os.remove(output)
|
|
finally:
|
|
os.remove(filename)
|
|
return False
|
|
|
|
|
|
if __name__ == '__main__':
|
|
from distutils import log
|
|
from numpy.distutils import customized_fcompiler
|
|
log.set_verbosity(2)
|
|
|
|
print(customized_fcompiler('gnu').get_version())
|
|
try:
|
|
print(customized_fcompiler('g95').get_version())
|
|
except Exception as e:
|
|
print(e)
|
|
|