def _check_stata_output(output):
""".. Check Stata output"""
regex = "end of do-file[\s]*r\([0-9]*\);"
if re.search(regex, output):
error_message = 'Stata program executed with errors.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, 'See makelog for more detail.'),
None)
def run_module(root, module, build_script='make.py', osname=None):
""".. Run module.
Runs script `build_script` in module directory `module` relative to root of repository `root`.
Parameters
----------
root : str
Directory of root.
module: str
Name of module.
build_script : str
Name of build script. Defaults to ``make.py``.
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
Returns
-------
None
Example
-------
The following code runs the script ``root/module/make.py``.
.. code-block:: python
run_module(root = 'root', module = 'module')
"""
osname = osname if osname else os.name # https://github.com/sphinx-doc/sphinx/issues/759
try:
module_dir = os.path.join(root, module)
os.chdir(module_dir)
build_script = norm_path(build_script)
if not os.path.isfile(build_script):
raise CritError(messages.crit_error_no_file % build_script)
message = 'Running module `%s`' % module
message = format_message(message)
message = colored(message, attrs=['bold'])
print('\n' + message)
status = os.system(
'%s %s' %
(metadata.default_executables[osname]['python'], build_script))
if status != 0:
raise ProgramError()
except ProgramError:
sys.exit()
except:
error_message = 'Error with `run_module`. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def execute_command(paths, command, **kwargs):
""".. Run system command.
Runs system command `command` with shell execution boolean ``shell``.
Outputs are appended to file ``makelog`` and written to system command log file ``log``.
Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
command : str
System command to run.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of system command log. System command log is only written if specified.
Defaults to ``''`` (i.e., not written).
Path Keys
---------
makelog : str
Path of makelog.
Note
----
We recommend leaving all other parameters to their defaults.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to check if OS is supported. Defaults to ``os.name``.
Returns
-------
None
Example
-------
The following code executes the ``ls`` command,
writes outputs to system command log file ``'file'``,
and appends outputs and/or status messages to ``paths['makelog']``.
.. code-block:: python
execute_command(paths, 'ls', log = 'file')
"""
try:
makelog = get_path(paths, 'makelog')
direct = Directive(makelog=makelog, **kwargs)
# Execute
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'Command executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
except ProgramError:
raise
except:
error_message = 'Error with `execute_command`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_lyx(paths, program, doctype='', **kwargs):
""".. Run LyX script using system command.
Compiles document ``program`` using system command, with document specified
in the form of ``script.lyx``. Status messages are appended to file ``makelog``.
PDF outputs are written in directory ``output_dir``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
doctype : str, optional
Type of LyX document. Takes either ``'handout'`` and ``'comments'``.
All other strings will default to standard document type.
Defaults to ``''`` (i.e., standard document type).
Path Keys
---------
makelog : str
Path of makelog.
output_dir : str
Directory to write PDFs.
Note
----
We recommend leaving all other parameters to their defaults.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_lyx(paths, program = 'script.lyx')
"""
try:
makelog = get_path(paths, 'makelog')
output_dir = get_path(paths, 'output_dir')
direct = LyXDirective(output_dir=output_dir,
doctype=doctype,
application='lyx',
program=program,
makelog=makelog,
**kwargs)
# Make handout/comments LyX file
if direct.doctype:
temp_name = os.path.join(direct.program_name + '_' +
direct.doctype)
temp_program = os.path.join(direct.program_dir, temp_name + '.lyx')
beamer = False
shutil.copy2(direct.program, temp_program)
for line in fileinput.input(temp_program,
inplace=True,
backup='.bak'):
if r'\textclass beamer' in line:
beamer = True
if direct.doctype == 'handout' and beamer and (r'\options'
in line):
line = line.rstrip('\n') + ', handout\n'
elif direct.doctype == 'comments' and (
r'\begin_inset Note Note' in line):
line = line.replace('Note Note', 'Note Greyedout')
print(line)
else:
temp_name = direct.program_name
temp_program = direct.program
# Execute
command = metadata.commands[direct.osname][direct.application] % (
direct.executable, direct.option, temp_program)
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'LyX program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
# Move PDF output
temp_pdf = os.path.join(direct.program_dir, temp_name + '.pdf')
output_pdf = os.path.join(direct.output_dir,
direct.program_name + '.pdf')
if temp_pdf != output_pdf:
shutil.copy2(temp_pdf, output_pdf)
os.remove(temp_pdf)
# Remove handout/comments LyX file
if direct.doctype:
os.remove(temp_program)
except ProgramError:
raise
except:
error_message = 'Error with `run_lyx`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_stata(paths, program, **kwargs):
""".. Run Stata script using system command.
Runs script ``program`` using system command, with script specified
in the form of ``script.do``. Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
Path Keys
---------
makelog : str
Path of makelog.
Note
----
We recommend leaving all other parameters to their defaults.
Note
----
When a do-file contains a space in its name, different version of Stata save the
corresponding log file with different names. Some versions of Stata truncate the
name to everything before the first space of the do-file name.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_stata(paths, program = 'script.do')
"""
try:
makelog = get_path(paths, 'makelog')
direct = ProgramDirective(application='stata',
program=program,
makelog=makelog,
**kwargs)
# Get program output (partial)
program_name = direct.program.split(" ")[0]
program_name = os.path.split(program_name)[-1]
program_name = os.path.splitext(program_name)[0]
program_log_partial = os.path.join(os.getcwd(), program_name + '.log')
# Get program output (full)
program_log_full = os.path.join(os.getcwd(),
direct.program_name + '.log')
# Sanitize program
if direct.osname == "posix":
direct.program = re.escape(direct.program)
# Execute
command = metadata.commands[direct.osname]['stata'] % (
direct.executable, direct.option, direct.program)
exit_code, stderr = direct.execute_command(command)
if exit_code != 0:
error_message = 'Stata program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
try:
output = direct.move_program_output(program_log_partial,
direct.log)
except:
output = direct.move_program_output(program_log_full, direct.log)
_check_stata_output(output)
except ProgramError:
raise
except:
error_message = 'Error with `run_stata`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_stat_transfer(paths, program, **kwargs):
""".. Run StatTransfer script using system command.
Runs script ``program`` using system command, with script specified
in the form of ``script.stc`` or ``script.stcmd``.
Status messages are appended to file ``makelog``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
Path Keys
---------
makelog : str
Path of makelog.
Note
----
We recommend leaving all other parameters to their defaults.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_stat_transfer(paths, program = 'script.stc')
"""
try:
makelog = get_path(paths, 'makelog')
direct = ProgramDirective(application='st',
program=program,
makelog=makelog,
**kwargs)
# Execute
command = metadata.commands[direct.osname][direct.application] % (
direct.executable, direct.program)
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'StatTransfer program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
except ProgramError:
raise
except:
error_message = 'Error with `run_stat_transfer`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
def run_latex(paths, program, **kwargs):
""".. Run LaTeX script using system command.
Compiles document ``program`` using system command, with document specified
in the form of ``script.tex``. Status messages are appended to file ``makelog``.
PDF outputs are written in directory ``output_dir``.
Parameters
----------
paths : dict
Dictionary of paths. Dictionary should contain values for all keys listed below.
program : str
Path of script to run.
Path Keys
---------
makelog : str
Path of makelog.
output_dir : str
Directory to write PDFs.
Note
----
We recommend leaving all other parameters to their defaults.
Note
----
This function creates and removes a directory named ``latex_auxiliary_dir``.
Other Parameters
----------------
osname : str, optional
Name of OS. Used to determine syntax of system command. Defaults to ``os.name``.
shell : `bool`, optional
See `here <https://docs.python.org/3/library/subprocess.html#frequently-used-arguments>`_.
Defaults to ``True``.
log : str, optional
Path of program log. Program log is only written if specified.
Defaults to ``''`` (i.e., not written).
executable : str, optional
Executable to use for system command.
Defaults to executable specified in :ref:`default settings<default settings>`.
option : str, optional
Options for system command. Defaults to options specified in :ref:`default settings<default settings>`.
args : str, optional
Not applicable.
Returns
-------
None
Example
-------
.. code-block:: python
run_latex(paths, program = 'script.tex')
"""
try:
makelog = get_path(paths, 'makelog')
output_dir = get_path(paths, 'output_dir')
direct = LyXDirective(output_dir=output_dir,
application='latex',
program=program,
makelog=makelog,
**kwargs)
temp_name = direct.program_name
temp_program = direct.program
# Generate folder for auxiliary files
os.mkdir('latex_auxiliary_dir')
# Execute
command = metadata.commands[direct.osname][direct.application] % (
direct.executable, direct.option, temp_program)
exit_code, stderr = direct.execute_command(command)
direct.write_log()
if exit_code != 0:
error_message = 'LaTeX program executed with errors. Traceback can be found below.'
error_message = format_message(error_message)
raise_from(ProgramError(error_message, stderr), None)
# Move PDF output
temp_pdf = os.path.join('latex_auxiliary_dir', temp_name + '.pdf')
output_pdf = os.path.join(direct.output_dir,
direct.program_name + '.pdf')
if temp_pdf != output_pdf:
shutil.copy2(temp_pdf, output_pdf)
shutil.rmtree('latex_auxiliary_dir')
# Remove auxiliary files
except ProgramError:
raise
except:
error_message = 'Error with `run_latex`. Traceback can be found below.'
error_message = format_message(error_message)
write_to_makelog(paths,
error_message + '\n\n' + traceback.format_exc())
raise_from(ColoredError(error_message, traceback.format_exc()), None)
