gromacs/core.py
def Popen(self, *args, **kwargs):
        """Returns a special Popen instance (:class:`PopenWithInput`).

        The instance has its input pre-set so that calls to
        :meth:`~PopenWithInput.communicate` will not need to supply
        input. This is necessary if one wants to chain the output from
        one command to an input from another.

        :TODO:
          Write example.
        """
        stderr = kwargs.pop('stderr', None)     # default: print to stderr (if STDOUT then merge)
        if stderr is False:                     # False: capture it
            stderr = PIPE
        elif stderr is True:
            stderr = None                       # use stderr

        stdout = kwargs.pop('stdout', None)     # either set to PIPE for capturing output
        if stdout is False:                     # ... or to False
            stdout = PIPE
        elif stdout is True:
            stdout = None                       # for consistency, make True write to screen

        stdin = kwargs.pop('stdin', None)
        input = kwargs.pop('input', None)

        use_shell = kwargs.pop('use_shell', False)
        if input:
            stdin = PIPE
            if isinstance(input, six.string_types) and not input.endswith('\n'):
                # make sure that input is a simple string with \n line endings
                input = six.text_type(input) + '\n'
            else:
                try:
                    # make sure that input is a simple string with \n line endings
                    input = '\n'.join(map(six.text_type, input)) + '\n'
                except TypeError:
                    # so maybe we are a file or something ... and hope for the best
                    pass

        cmd = self._commandline(*args, **kwargs)   # lots of magic happening here
                                                   # (cannot move out of method because filtering of stdin etc)
        try:
            p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout,
                               universal_newlines=True, input=input, shell=use_shell)
        except OSError as err:
            logger.error(" ".join(cmd))            # log command line
            if err.errno == errno.ENOENT:
                errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name)
                logger.fatal(errmsg)
                raise OSError(errmsg)
            else:
                logger.exception("Setting up Gromacs command {0!r} raised an exception.".format(self.command_name))
                raise
        logger.debug(p.command_string)
        return p
def Popen(self, *args, **kwargs):
        """Returns a special Popen instance (:class:`PopenWithInput`).

        The instance has its input pre-set so that calls to
        :meth:`~PopenWithInput.communicate` will not need to supply
        input. This is necessary if one wants to chain the output from
        one command to an input from another.

        :TODO:
          Write example.
        """
        stderr = kwargs.pop('stderr', None)     # default: print to stderr (if STDOUT then merge)
        if stderr is False:                     # False: capture it
            stderr = PIPE
        elif stderr is True:
            stderr = None                       # use stderr

        stdout = kwargs.pop('stdout', None)     # either set to PIPE for capturing output
        if stdout is False:                     # ... or to False
            stdout = PIPE
        elif stdout is True:
            stdout = None                       # for consistency, make True write to screen

        stdin = kwargs.pop('stdin', None)
        input = kwargs.pop('input', None)

        use_shell = kwargs.pop('use_shell', False)
        if input:
            stdin = PIPE
            if isinstance(input, six.string_types) and not input.endswith('\n'):
                # make sure that input is a simple string with \n line endings
                input = six.text_type(input) + '\n'
            else:
                try:
                    # make sure that input is a simple string with \n line endings
                    input = '\n'.join(map(six.text_type, input)) + '\n'
                except TypeError:
                    # so maybe we are a file or something ... and hope for the best
                    pass

        cmd = self._commandline(*args, **kwargs)   # lots of magic happening here
                                                   # (cannot move out of method because filtering of stdin etc)
        try:
            p = PopenWithInput(cmd, stdin=stdin, stderr=stderr, stdout=stdout,
                               universal_newlines=True, input=input, shell=use_shell)
        except OSError as err:
            logger.error(" ".join(cmd))            # log command line
            if err.errno == errno.ENOENT:
                errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?".format(self.command_name)
                logger.fatal(errmsg)
                raise OSError(errmsg)
            else:
                logger.exception("Setting up Gromacs command {0!r} raised an exception.".format(self.command_name))
                raise
        logger.debug(p.command_string)
        return p
def Popen ( self , * args , * * kwargs ) : stderr = kwargs . pop ( 'stderr' , None ) # default: print to stderr (if STDOUT then merge) if stderr is False : # False: capture it stderr = PIPE elif stderr is True : stderr = None # use stderr stdout = kwargs . pop ( 'stdout' , None ) # either set to PIPE for capturing output if stdout is False : # ... or to False stdout = PIPE elif stdout is True : stdout = None # for consistency, make True write to screen stdin = kwargs . pop ( 'stdin' , None ) input = kwargs . pop ( 'input' , None ) use_shell = kwargs . pop ( 'use_shell' , False ) if input : stdin = PIPE if isinstance ( input , six . string_types ) and not input . endswith ( '\n' ) : # make sure that input is a simple string with \n line endings input = six . text_type ( input ) + '\n' else : try : # make sure that input is a simple string with \n line endings input = '\n' . join ( map ( six . text_type , input ) ) + '\n' except TypeError : # so maybe we are a file or something ... and hope for the best pass cmd = self . _commandline ( * args , * * kwargs ) # lots of magic happening here # (cannot move out of method because filtering of stdin etc) try : p = PopenWithInput ( cmd , stdin = stdin , stderr = stderr , stdout = stdout , universal_newlines = True , input = input , shell = use_shell ) except OSError as err : logger . error ( " " . join ( cmd ) ) # log command line if err . errno == errno . ENOENT : errmsg = "Failed to find Gromacs command {0!r}, maybe its not on PATH or GMXRC must be sourced?" . format ( self . command_name ) logger . fatal ( errmsg ) raise OSError ( errmsg ) else : logger . exception ( "Setting up Gromacs command {0!r} raised an exception." . format ( self . command_name ) ) raise logger . debug ( p . command_string ) return p
Returns a special Popen instance (:class:`PopenWithInput`).

        The instance has its input pre-set so that calls to
        :meth:`~PopenWithInput.communicate` will not need to supply
        input. This is necessary if one wants to chain the output from
        one command to an input from another.

        :TODO:
          Write example.
Returns a special Popen instance ( : class : PopenWithInput ) .