Old engine for Continuous Time Bayesian Networks. Superseded by reCTBN. 🐍
https://github.com/madlabunimib/PyCTBN
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317 lines
10 KiB
317 lines
10 KiB
4 years ago
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"""
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exec_command
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Implements exec_command function that is (almost) equivalent to
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commands.getstatusoutput function but on NT, DOS systems the
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returned status is actually correct (though, the returned status
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values may be different by a factor). In addition, exec_command
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takes keyword arguments for (re-)defining environment variables.
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Provides functions:
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exec_command --- execute command in a specified directory and
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in the modified environment.
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find_executable --- locate a command using info from environment
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variable PATH. Equivalent to posix `which`
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command.
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Author: Pearu Peterson <pearu@cens.ioc.ee>
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Created: 11 January 2003
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Requires: Python 2.x
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Successfully tested on:
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======== ============ =================================================
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os.name sys.platform comments
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======== ============ =================================================
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posix linux2 Debian (sid) Linux, Python 2.1.3+, 2.2.3+, 2.3.3
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PyCrust 0.9.3, Idle 1.0.2
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posix linux2 Red Hat 9 Linux, Python 2.1.3, 2.2.2, 2.3.2
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posix sunos5 SunOS 5.9, Python 2.2, 2.3.2
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posix darwin Darwin 7.2.0, Python 2.3
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nt win32 Windows Me
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Python 2.3(EE), Idle 1.0, PyCrust 0.7.2
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Python 2.1.1 Idle 0.8
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nt win32 Windows 98, Python 2.1.1. Idle 0.8
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nt win32 Cygwin 98-4.10, Python 2.1.1(MSC) - echo tests
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fail i.e. redefining environment variables may
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not work. FIXED: don't use cygwin echo!
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Comment: also `cmd /c echo` will not work
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but redefining environment variables do work.
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posix cygwin Cygwin 98-4.10, Python 2.3.3(cygming special)
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nt win32 Windows XP, Python 2.3.3
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======== ============ =================================================
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Known bugs:
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* Tests, that send messages to stderr, fail when executed from MSYS prompt
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because the messages are lost at some point.
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"""
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__all__ = ['exec_command', 'find_executable']
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import os
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import sys
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import subprocess
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import locale
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import warnings
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from numpy.distutils.misc_util import is_sequence, make_temp_file
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from numpy.distutils import log
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def filepath_from_subprocess_output(output):
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"""
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Convert `bytes` in the encoding used by a subprocess into a filesystem-appropriate `str`.
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Inherited from `exec_command`, and possibly incorrect.
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"""
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mylocale = locale.getpreferredencoding(False)
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if mylocale is None:
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mylocale = 'ascii'
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output = output.decode(mylocale, errors='replace')
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output = output.replace('\r\n', '\n')
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# Another historical oddity
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if output[-1:] == '\n':
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output = output[:-1]
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return output
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def forward_bytes_to_stdout(val):
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"""
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Forward bytes from a subprocess call to the console, without attempting to
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decode them.
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The assumption is that the subprocess call already returned bytes in
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a suitable encoding.
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"""
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if hasattr(sys.stdout, 'buffer'):
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# use the underlying binary output if there is one
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sys.stdout.buffer.write(val)
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elif hasattr(sys.stdout, 'encoding'):
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# round-trip the encoding if necessary
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sys.stdout.write(val.decode(sys.stdout.encoding))
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else:
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# make a best-guess at the encoding
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sys.stdout.write(val.decode('utf8', errors='replace'))
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def temp_file_name():
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# 2019-01-30, 1.17
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warnings.warn('temp_file_name is deprecated since NumPy v1.17, use '
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'tempfile.mkstemp instead', DeprecationWarning, stacklevel=1)
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fo, name = make_temp_file()
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fo.close()
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return name
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def get_pythonexe():
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pythonexe = sys.executable
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if os.name in ['nt', 'dos']:
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fdir, fn = os.path.split(pythonexe)
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fn = fn.upper().replace('PYTHONW', 'PYTHON')
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pythonexe = os.path.join(fdir, fn)
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assert os.path.isfile(pythonexe), '%r is not a file' % (pythonexe,)
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return pythonexe
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def find_executable(exe, path=None, _cache={}):
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"""Return full path of a executable or None.
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Symbolic links are not followed.
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"""
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key = exe, path
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try:
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return _cache[key]
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except KeyError:
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pass
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log.debug('find_executable(%r)' % exe)
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orig_exe = exe
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if path is None:
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path = os.environ.get('PATH', os.defpath)
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if os.name=='posix':
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realpath = os.path.realpath
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else:
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realpath = lambda a:a
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if exe.startswith('"'):
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exe = exe[1:-1]
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suffixes = ['']
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if os.name in ['nt', 'dos', 'os2']:
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fn, ext = os.path.splitext(exe)
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extra_suffixes = ['.exe', '.com', '.bat']
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if ext.lower() not in extra_suffixes:
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suffixes = extra_suffixes
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if os.path.isabs(exe):
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paths = ['']
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else:
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paths = [ os.path.abspath(p) for p in path.split(os.pathsep) ]
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for path in paths:
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fn = os.path.join(path, exe)
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for s in suffixes:
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f_ext = fn+s
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if not os.path.islink(f_ext):
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f_ext = realpath(f_ext)
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if os.path.isfile(f_ext) and os.access(f_ext, os.X_OK):
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log.info('Found executable %s' % f_ext)
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_cache[key] = f_ext
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return f_ext
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log.warn('Could not locate executable %s' % orig_exe)
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return None
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############################################################
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def _preserve_environment( names ):
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log.debug('_preserve_environment(%r)' % (names))
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env = {name: os.environ.get(name) for name in names}
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return env
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def _update_environment( **env ):
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log.debug('_update_environment(...)')
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for name, value in env.items():
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os.environ[name] = value or ''
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def exec_command(command, execute_in='', use_shell=None, use_tee=None,
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_with_python = 1, **env ):
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"""
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Return (status,output) of executed command.
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.. deprecated:: 1.17
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Use subprocess.Popen instead
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Parameters
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----------
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command : str
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A concatenated string of executable and arguments.
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execute_in : str
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Before running command ``cd execute_in`` and after ``cd -``.
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use_shell : {bool, None}, optional
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If True, execute ``sh -c command``. Default None (True)
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use_tee : {bool, None}, optional
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If True use tee. Default None (True)
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Returns
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-------
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res : str
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Both stdout and stderr messages.
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Notes
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-----
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On NT, DOS systems the returned status is correct for external commands.
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Wild cards will not work for non-posix systems or when use_shell=0.
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"""
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# 2019-01-30, 1.17
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warnings.warn('exec_command is deprecated since NumPy v1.17, use '
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'subprocess.Popen instead', DeprecationWarning, stacklevel=1)
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log.debug('exec_command(%r,%s)' % (command,
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','.join(['%s=%r'%kv for kv in env.items()])))
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if use_tee is None:
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use_tee = os.name=='posix'
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if use_shell is None:
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use_shell = os.name=='posix'
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execute_in = os.path.abspath(execute_in)
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oldcwd = os.path.abspath(os.getcwd())
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if __name__[-12:] == 'exec_command':
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exec_dir = os.path.dirname(os.path.abspath(__file__))
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elif os.path.isfile('exec_command.py'):
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exec_dir = os.path.abspath('.')
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else:
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exec_dir = os.path.abspath(sys.argv[0])
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if os.path.isfile(exec_dir):
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exec_dir = os.path.dirname(exec_dir)
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if oldcwd!=execute_in:
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os.chdir(execute_in)
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log.debug('New cwd: %s' % execute_in)
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else:
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log.debug('Retaining cwd: %s' % oldcwd)
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oldenv = _preserve_environment( list(env.keys()) )
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_update_environment( **env )
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try:
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st = _exec_command(command,
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use_shell=use_shell,
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use_tee=use_tee,
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**env)
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finally:
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if oldcwd!=execute_in:
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os.chdir(oldcwd)
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log.debug('Restored cwd to %s' % oldcwd)
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_update_environment(**oldenv)
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return st
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def _exec_command(command, use_shell=None, use_tee = None, **env):
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"""
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Internal workhorse for exec_command().
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"""
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if use_shell is None:
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use_shell = os.name=='posix'
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if use_tee is None:
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use_tee = os.name=='posix'
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if os.name == 'posix' and use_shell:
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# On POSIX, subprocess always uses /bin/sh, override
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sh = os.environ.get('SHELL', '/bin/sh')
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if is_sequence(command):
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command = [sh, '-c', ' '.join(command)]
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else:
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command = [sh, '-c', command]
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use_shell = False
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elif os.name == 'nt' and is_sequence(command):
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# On Windows, join the string for CreateProcess() ourselves as
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# subprocess does it a bit differently
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command = ' '.join(_quote_arg(arg) for arg in command)
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# Inherit environment by default
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env = env or None
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try:
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# universal_newlines is set to False so that communicate()
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# will return bytes. We need to decode the output ourselves
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# so that Python will not raise a UnicodeDecodeError when
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# it encounters an invalid character; rather, we simply replace it
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proc = subprocess.Popen(command, shell=use_shell, env=env,
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stdout=subprocess.PIPE,
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stderr=subprocess.STDOUT,
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universal_newlines=False)
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except EnvironmentError:
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# Return 127, as os.spawn*() and /bin/sh do
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return 127, ''
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text, err = proc.communicate()
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mylocale = locale.getpreferredencoding(False)
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if mylocale is None:
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mylocale = 'ascii'
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text = text.decode(mylocale, errors='replace')
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text = text.replace('\r\n', '\n')
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# Another historical oddity
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if text[-1:] == '\n':
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text = text[:-1]
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if use_tee and text:
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print(text)
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return proc.returncode, text
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def _quote_arg(arg):
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"""
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Quote the argument for safe use in a shell command line.
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"""
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# If there is a quote in the string, assume relevants parts of the
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# string are already quoted (e.g. '-I"C:\\Program Files\\..."')
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if '"' not in arg and ' ' in arg:
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return '"%s"' % arg
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return arg
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############################################################
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