def from_notebook_cell(self, cell, fh, idx = 0):
if not hasattr(cell, 'execution_count') or cell.execution_count is None or self.no_index:
fh.write('\n%cell {}\n'.format(cell.cell_type))
else:
idx += 1
fh.write('\n%cell {} {}\n'.format(cell.cell_type,
idx if self.reset_index else cell.execution_count))
if cell.cell_type == 'code':
if any(cell.source.startswith(x) for x in ('%run', '%restart', '%dict', '%get', '%use', '%with', '%set', '%paste', '%matplotlib', '%edit')):
if self.remove_magic:
cell.source = '\n'.join(cell.source.split('\n')[1:])
if self.add_header and not any([SOS_SECTION_HEADER.match(x) for x in cell.source.split('\n')]):
cell.source = '[{}]\n'.format(idx if self.reset_index else cell.execution_count) + cell.source
fh.write(cell.source.strip() + '\n')
elif cell.cell_type == "markdown":
fh.write('\n'.join('#! ' + x for x in cell.source.split('\n')) + '\n')
return idx
def from_notebook_cell(self, cell, fh, idx = 0):
if not hasattr(cell, 'execution_count') or cell.execution_count is None or self.no_index:
fh.write('\n%cell {}\n'.format(cell.cell_type))
else:
idx += 1
fh.write('\n%cell {} {}\n'.format(cell.cell_type,
idx if self.reset_index else cell.execution_count))
if cell.cell_type == 'code':
if any(cell.source.startswith(x) for x in ('%run', '%restart', '%dict', '%get', '%use', '%with', '%set', '%paste', '%matplotlib', '%edit')):
if self.remove_magic:
cell.source = '\n'.join(cell.source.split('\n')[1:])
if self.add_header and not any([SOS_SECTION_HEADER.match(x) for x in cell.source.split('\n')]):
cell.source = '[{}]\n'.format(idx if self.reset_index else cell.execution_count) + cell.source
fh.write(cell.source.strip() + '\n')
elif cell.cell_type == "markdown":
fh.write('\n'.join('#! ' + x for x in cell.source.split('\n')) + '\n')
return idx
def runfile(script=None, args='', wdir='.', code=None, **kwargs):
# this has something to do with Prefix matching rule of parse_known_args
#
# That is to say
#
# --rep 3
#
# would be parsed as
#
# args.workflow=3, unknown --rep
#
# instead of
#
# args.workflow=None, unknown --rep 3
#
# we then have to change the parse to disable args.workflow when
# there is no workflow option.
if isinstance(args, str):
args = shlex.split(args)
if (script is None and code is None) or '-h' in args:
parser = get_run_parser(interactive=True, with_workflow=True)
parser.print_help()
return
if args and args[0].lstrip().startswith('-'):
parser = get_run_parser(interactive=True, with_workflow=False)
parser.error = _parse_error
args, workflow_args = parser.parse_known_args(args)
args.workflow = None
else:
parser = get_run_parser(interactive=True, with_workflow=True)
parser.error = _parse_error
args, workflow_args = parser.parse_known_args(args)
# no multi-processing in interactive mode
env.max_jobs = 1
env.verbosity = args.verbosity
env.__task_engine__ = 'interactive'
#
env.sig_mode = args.__sigmode__
if args.__bin_dirs__:
import fasteners
for d in args.__bin_dirs__:
if d == '~/.sos/bin' and not os.path.isdir(os.path.expanduser(d)):
with fasteners.InterProcessLock('/tmp/sos_lock_bin'):
os.makedirs(os.path.expanduser(d))
elif not os.path.isdir(os.path.expanduser(d)):
raise ValueError('directory does not exist: {}'.format(d))
os.environ['PATH'] = os.pathsep.join([os.path.expanduser(x) for x in args.__bin_dirs__]) + os.pathsep + os.environ['PATH']
# clear __step_input__, __step_output__ etc because there is
# no concept of passing input/outputs across cells.
env.sos_dict.set('__step_output__', [])
for k in ['__step_input__', '__default_output__', 'input', 'output', \
'depends', '_input', '_output', '_depends']:
env.sos_dict.pop(k, None)
try:
if script is None:
if not code.strip():
return
# if there is no section header, add a header so that the block
# appears to be a SoS script with one section
if not any([SOS_SECTION_HEADER.match(line) for line in code.splitlines()]):
code = '[interactive_0]\n' + code
script = SoS_Script(content=code, global_sigil=get_default_global_sigil())
else:
script = SoS_Script(filename=script, global_sigil=get_default_global_sigil())
workflow = script.workflow(args.workflow)
executor = Interactive_Executor(workflow, args=workflow_args, config={
'config_file': args.__config__,
'output_dag': args.__dag__,
'report_output': args.__report__})
if args.__dryrun__:
return executor.dryrun(args.__targets__)
else:
return executor.run(args.__targets__)
except Exception:
if args.verbosity and args.verbosity > 2:
sys.stderr.write(get_traceback())
raise
finally:
env.sig_mode = 'default'
env.verbosity = 1