Os Command shorcuts

Collection of function related to os and sys operations.

os_command_py.os_command.check_directory_exist(directory)

Check is a directory exist.

Parameters:directory (str) – directory path Returns:if the file exist Return type:bool Example:

>>> test_exist = check_directory_exist(TEST_PATH)
>>> print("Directory {} exist: {}".format(TEST_PATH, test_exist))    #doctest: +ELLIPSIS
Directory ...input exist: True
>>> test_exist = check_directory_exist(os.path.join(TEST_PATH,'no_way'))
>>> print("Directory {} exist: {}".format(
... TEST_PATH+'/no_way', test_exist)) #doctest: +ELLIPSIS
Directory ...no_way exist: False

os_command_py.os_command.check_file_and_create_path(file)

Check if file exist and create path if not available

Parameters:file (str) – file path Returns:File existance Return type:bool

os_command_py.os_command.check_file_exist(file)

Check is a file exist.

Parameters:file (str) – file path Returns:if the file exist Return type:bool Example:

>>> test_exist = check_file_exist(os.path.join(TEST_PATH, "1y0m.pdb"))
>>> print("1y0m.pdb exist: {}".format(test_exist))
1y0m.pdb exist: True

os_command_py.os_command.create_and_go_dir(dir_name)

Create the path to a directory and change path in it.

Parameters:dir_name – directorie name Example:

>>> TEST_OUT = str(getfixture('tmpdir'))
>>> start_dir = os.getcwd()
>>> create_and_go_dir(os.path.join(TEST_OUT, "tmp"))
>>> print("Path: {}".format(os.getcwd())) #doctest: +ELLIPSIS
Path: ...tmp
>>> os.chdir(start_dir)

os_command_py.os_command.create_dir(dir_name)

Create the path to a directory.

Parameters:dir_name – directorie name

os_command_py.os_command.delete_directory(directory)

Delete a file.

Parameters:directory (str) – directory path Returns:operation sucess Return type:bool

os_command_py.os_command.delete_file(file)

Delete a file.

Parameters:file (str) – file path Returns:operation sucess Return type:bool

os_command_py.os_command.full_path_and_check(file)

Return the full path of a file

Parameters:file (str) – file path Returns:File path Return type:str

os_command_py.os_command.get_directory(file)

Return the path of a file directory

Parameters:file (str) – file path Returns:File path Return type:str

os_command_py.os_command.get_gmx_version()

Get gromacs version of mdrun.

Example:

print('Version is {}'.format(get_gmx_version()))
Version is 2016.4

os_command_py.os_command.is_exe(fpath)

Check is a file path exist and if user has access to it

Parameters:fpath (str) – file path Returns:if the file is an executable Return type:bool Example:

>>> ls_path = which('ls')
>>> print(is_exe(ls_path))
True

os_command_py.os_command.which(*program_list)

find and return the first path of a program if find. Look for all combination within the $PATH env variable

Parameters:program_list (list of str) – list of program name Returns:path of the program Return type:str Example:

>>> ls_path = which('dontexist', 'ls')
>>> print(ls_path.find('ls') != -1) #doctest: +ELLIPSIS
True

..note:

Consider using shutil.which(program) for windows.