def _call_process(self, method, *args, **kwargs):
"""Run the given git command with the specified arguments and return
the result as a String
:param method:
is the command. Contained "_" characters will be converted to dashes,
such as in 'ls_files' to call 'ls-files'.
:param args:
is the list of arguments. If None is included, it will be pruned.
This allows your commands to call git more conveniently as None
is realized as non-existent
:param kwargs:
is a dict of keyword arguments.
This function accepts the same optional keyword arguments
as execute().
``Examples``::
git.rev_list('master', max_count=10, header=True)
:return: Same as ``execute``"""
# Handle optional arguments prior to calling transform_kwargs
# otherwise these'll end up in args, which is bad.
_kwargs = {k: v for k, v in kwargs.items() if k in execute_kwargs}
kwargs = {k: v for k, v in kwargs.items() if k not in execute_kwargs}
insert_after_this_arg = kwargs.pop('insert_kwargs_after', None)
# Prepare the argument list
opt_args = self.transform_kwargs(**kwargs)
ext_args = self.__unpack_args([a for a in args if a is not None])
if insert_after_this_arg is None:
args = opt_args + ext_args
else:
try:
index = ext_args.index(insert_after_this_arg)
except ValueError:
raise ValueError(
"Couldn't find argument '%s' in args %s to insert kwargs after"
% (insert_after_this_arg, str(ext_args)))
# end handle error
args = ext_args[:index + 1] + opt_args + ext_args[index + 1:]
# end handle kwargs
call = [self.GIT_PYTHON_GIT_EXECUTABLE]
# add persistent git options
call.extend(self._persistent_git_options)
# add the git options, then reset to empty
# to avoid side_effects
call.extend(self._git_options)
self._git_options = ()
call.append(dashify(method))
call.extend(args)
return self.execute(call, **_kwargs)
def _call_process(self, method, *args, **kwargs):
"""Run the given git command with the specified arguments and return
the result as a String
:param method:
is the command. Contained "_" characters will be converted to dashes,
such as in 'ls_files' to call 'ls-files'.
:param args:
is the list of arguments. If None is included, it will be pruned.
This allows your commands to call git more conveniently as None
is realized as non-existent
:param kwargs:
is a dict of keyword arguments.
This function accepts the same optional keyword arguments
as execute().
``Examples``::
git.rev_list('master', max_count=10, header=True)
:return: Same as ``execute``"""
# Handle optional arguments prior to calling transform_kwargs
# otherwise these'll end up in args, which is bad.
_kwargs = {k: v for k, v in kwargs.items() if k in execute_kwargs}
kwargs = {k: v for k, v in kwargs.items() if k not in execute_kwargs}
insert_after_this_arg = kwargs.pop('insert_kwargs_after', None)
# Prepare the argument list
opt_args = self.transform_kwargs(**kwargs)
ext_args = self.__unpack_args([a for a in args if a is not None])
if insert_after_this_arg is None:
args = opt_args + ext_args
else:
try:
index = ext_args.index(insert_after_this_arg)
except ValueError:
raise ValueError("Couldn't find argument '%s' in args %s to insert kwargs after"
% (insert_after_this_arg, str(ext_args)))
# end handle error
args = ext_args[:index + 1] + opt_args + ext_args[index + 1:]
# end handle kwargs
call = [self.GIT_PYTHON_GIT_EXECUTABLE]
# add persistent git options
call.extend(self._persistent_git_options)
# add the git options, then reset to empty
# to avoid side_effects
call.extend(self._git_options)
self._git_options = ()
call.append(dashify(method))
call.extend(args)
return self.execute(call, **_kwargs)
def build_call(*args): # *.foo ellipsis
"""
returns the arguments as flattened list
"""
call = []
for arg in args:
if type(arg) is list:
for element in arg:
call.append(element)
else:
call.append(arg)
if debug:
print_debug("flattened call: "+str(call))
return call
def compile_call():
global Output_File
if Output_File is None or Output_File == "":
Output_File = path.splitext(Filename)[0] + "_" + "Output"
call = [
"clang++-" + str(ClangVer)[0], Filename,
"-o" + str(Optimisation_Level), "-o", Output_File
]
for dir in include_dirs:
if dir == "":
continue
else:
arg = "--include-directory="
arg = arg + dir
call.append(arg)
for dir in library_dirs:
if dir == "":
continue
else:
arg = "--library-directory="
arg = arg + dir
call.append(arg)
if Verbose:
call.append("--verbose")
return call
def sbatch(ex_script, jobname=None, sys_arg=None):
"""
Summary
-------
Python interface to slurm sbatch cmd line function
Args
----
ex_script: executable file (e.g. .sh) to pass to sbacth
jobname: string to pass as a job name
sys_arg: dict of named arguments to pass to the program being run
Returns
-------
JOBID (class Jid)
"""
call = []
if jobname is not None:
call.append("--job-name=" + jobname)
if sys_arg is not None:
args_list = [i for i in sys_arg.items()]
arg_name = args_list[0][0]
arg_val = args_list[0][1]
call.append("--export=" + str(arg_name) + "=" + str(arg_val))
call.append(ex_script)
if sys_arg is not None:
call.append(str(arg_val))
make_call = subprocess.run(["sbatch"] + call,
stdout=subprocess.PIPE).stdout.decode('utf-8')
jid = str(str.split(make_call.replace('\n', ''), ' ')[3])
scontrol = subprocess.run(['scontrol', 'show', 'job', jid],
stdout=subprocess.PIPE).stdout.decode('utf-8')
if len(scontrol):
scontrol = scontrol.split('\n')
stdout = []
for i in scontrol:
if (re.search('StdOut', i)):
stdout.append(i)
tofilepath = re.sub(r'|'.join((r'StdOut=', r' ')), '', stdout[0])
return (Jid(jid, tofilepath))
def _call_process(self, method, *args, **kwargs):
"""Run the given git command with the specified arguments and return
the result as a String
:param method:
is the command. Contained "_" characters will be converted to dashes,
such as in 'ls_files' to call 'ls-files'.
:param args:
is the list of arguments. If None is included, it will be pruned.
This allows your commands to call git more conveniently as None
is realized as non-existent
:param kwargs:
It contains key-values for the following:
- the :meth:`execute()` kwds, as listed in :var:`execute_kwargs`;
- "command options" to be converted by :meth:`transform_kwargs()`;
- the `'insert_kwargs_after'` key which its value must match one of ``*args``,
and any cmd-options will be appended after the matched arg.
Examples::
git.rev_list('master', max_count=10, header=True)
turns into::
git rev-list max-count 10 --header master
:return: Same as ``execute``"""
# Handle optional arguments prior to calling transform_kwargs
# otherwise these'll end up in args, which is bad.
exec_kwargs = dict(
(k, v) for k, v in kwargs.items() if k in execute_kwargs)
opts_kwargs = dict(
(k, v) for k, v in kwargs.items() if k not in execute_kwargs)
insert_after_this_arg = opts_kwargs.pop('insert_kwargs_after', None)
# Prepare the argument list
opt_args = self.transform_kwargs(**opts_kwargs)
ext_args = self.__unpack_args([a for a in args if a is not None])
if insert_after_this_arg is None:
args = opt_args + ext_args
else:
try:
index = ext_args.index(insert_after_this_arg)
except ValueError:
raise ValueError(
"Couldn't find argument '%s' in args %s to insert cmd options after"
% (insert_after_this_arg, str(ext_args)))
# end handle error
args = ext_args[:index + 1] + opt_args + ext_args[index + 1:]
# end handle opts_kwargs
call = [self.GIT_PYTHON_GIT_EXECUTABLE]
# add persistent git options
call.extend(self._persistent_git_options)
# add the git options, then reset to empty
# to avoid side_effects
call.extend(self._git_options)
self._git_options = ()
call.append(dashify(method))
call.extend(args)
return self.execute(call, **exec_kwargs)
def _call_process(self, method, *args, **kwargs):
"""Run the given git command with the specified arguments and return
the result as a String
:param method:
is the command. Contained "_" characters will be converted to dashes,
such as in 'ls_files' to call 'ls-files'.
:param args:
is the list of arguments. If None is included, it will be pruned.
This allows your commands to call git more conveniently as None
is realized as non-existent
:param kwargs:
It contains key-values for the following:
- the :meth:`execute()` kwds, as listed in :var:`execute_kwargs`;
- "command options" to be converted by :meth:`transform_kwargs()`;
- the `'insert_kwargs_after'` key which its value must match one of ``*args``,
and any cmd-options will be appended after the matched arg.
Examples::
git.rev_list('master', max_count=10, header=True)
turns into::
git rev-list max-count 10 --header master
:return: Same as ``execute``"""
# Handle optional arguments prior to calling transform_kwargs
# otherwise these'll end up in args, which is bad.
exec_kwargs = dict((k, v) for k, v in kwargs.items() if k in execute_kwargs)
opts_kwargs = dict((k, v) for k, v in kwargs.items() if k not in execute_kwargs)
insert_after_this_arg = opts_kwargs.pop('insert_kwargs_after', None)
# Prepare the argument list
opt_args = self.transform_kwargs(**opts_kwargs)
ext_args = self.__unpack_args([a for a in args if a is not None])
if insert_after_this_arg is None:
args = opt_args + ext_args
else:
try:
index = ext_args.index(insert_after_this_arg)
except ValueError:
raise ValueError("Couldn't find argument '%s' in args %s to insert cmd options after"
% (insert_after_this_arg, str(ext_args)))
# end handle error
args = ext_args[:index + 1] + opt_args + ext_args[index + 1:]
# end handle opts_kwargs
call = [self.GIT_PYTHON_GIT_EXECUTABLE]
# add persistent git options
call.extend(self._persistent_git_options)
# add the git options, then reset to empty
# to avoid side_effects
call.extend(self._git_options)
self._git_options = ()
call.append(dashify(method))
call.extend(args)
return self.execute(call, **exec_kwargs)
def getPandocCall(inputfile, outputfile, template=""):
call = ["pandoc"]
# Output file
call.append("-o")
call.append(outputfile)
# Standalone file
call.append("-s")
if (template != ""):
call.append("--template")
call.append(template)
# Do not parse html blocks
call.append("-R")
# Use listings package for code blocks
call.append("--listings")
# Input file
call.append(inputfile)
return(call)