def run_catch_fail(self, function, *args, autotries=2, failedon=None):
"""
This function will run the function provided, and catch unexpected error codes. It will automatically try the
function again for the number of provided autotries, then wait for the user to respond.
"""
while True:
try:
stdout = function(*args)
if self.verbose:
print(stdout)
break
except ProcessExecutionError as e:
if autotries != 0:
autotries -= 1
time.sleep(60)
continue
if failedon is not None:
print('Failed on: ' + failedon)
print('STDOUT: ', e.stdout)
with colors.red:
print('STDERR: ', e.stderr)
print('ERRNO: ', e.errno)
if terminal.ask('Try again'):
continue
if terminal.ask('Skip?'):
break
print('Exiting...')
exit(-1)
def test_ask(self):
with captured_stdout("\n") as stream:
self.assertTrue(ask("Do you like cats?", default = True))
self.assertEqual(stream.getvalue(), "Do you like cats? [Y/n] ")
with captured_stdout("\nyes") as stream:
self.assertTrue(ask("Do you like cats?"))
self.assertEqual(stream.getvalue(), "Do you like cats? (y/n) Invalid response, please try again\nDo you like cats? (y/n) ")
def test_ask(self, capsys):
with send_stdin("\n"):
assert ask("Do you like cats?", default = True)
assert capsys.readouterr()[0] == "Do you like cats? [Y/n] "
with send_stdin("\nyes"):
assert ask("Do you like cats?")
assert capsys.readouterr()[0] == "Do you like cats? (y/n) Invalid response, please try again\nDo you like cats? (y/n) "
def test_ask(self, capsys):
with send_stdin("\n"):
assert ask("Do you like cats?", default=True)
assert capsys.readouterr()[0] == "Do you like cats? [Y/n] "
with send_stdin("\nyes"):
assert ask("Do you like cats?")
assert capsys.readouterr(
)[0] == "Do you like cats? (y/n) Invalid response, please try again\nDo you like cats? (y/n) "
def ask_for_data():
"""This function asks the user the values of parameters, number of integration steps,
initial conditions and simulation_ID. Then creates a '.temp_for_create_infiles.txt' file to store them.
This file will be used by other functions to read the data"""
while (True):
in_data = terminal.prompt(
"Type the data in the form 'mu k N_steps x1_0 x2_0 y1_0 simulation_identifier"
)
split_values = in_data.split()
if (len(split_values) != 7):
print(colors.yellow | "You did not give 7 values. Try again.")
continue
try:
mu = float(in_data.split()[0])
k = float(in_data.split()[1])
N_steps = int(in_data.split()[2])
if (N_steps < 20000):
print(
colors.yellow |
"The number of integration steps may be too small. Convergence of Lyapunov exponents is not granted."
)
x1_0 = float(in_data.split()[3])
x2_0 = float(in_data.split()[4])
y1_0 = float(in_data.split()[5])
simulation_ID = in_data.split()[6]
except ValueError:
print(
colors.yellow |
"Some of the parameter values you gave are not numbers. Please try again."
)
continue
if (0 < mu < 10**2 and 1e-2 < k < 1e+2):
pass
else:
go_on1 = terminal.ask(
colors.yellow |
"""The values of mu or k you choose may cause overflow issues.
It is recommended that 0< mu< 10^2 and 10^-2< k < 10^2.
Continue anyway?""")
if (go_on1):
break
else:
continue
if ('.' not in simulation_ID):
break
else:
go_on2 = terminal.ask(
colors.yellow |
"""The presence of '.' character in simulation ID may cause issues when saving images. Continue anyway?"""
)
if (go_on2):
break
outfile = open(".temp_for_create_infiles.txt", 'w+')
outfile.write(in_data)
outfile.close()
def there_is_infile(self):
"""Asks the user if she wants to replace currently existing 'input_values.txt' file."""
answer = terminal.ask(
"Do you want to create a new 'input_values.txt' file?")
if (answer):
answer2 = terminal.ask(
colors.yellow |
"This process will overwrite DEFINITEVELY 'input_values.txt'. Do you still want to proceed?"
)
if (answer2):
self.create_infile()
def _generate_dev_docker_compose_file(self):
for service in TEMPLATE_SERVICE:
generate = ask("Do you want to generate docker-compose.yml "
"automatically for %s" % service,
default=True)
if generate:
return GenerateComposeFile(service).generate()
def _solve_render_conflict(self, dst_relpath: Path):
"""Properly solve render conflicts.
It can ask the user if running in interactive mode.
"""
assert not dst_relpath.is_absolute()
printf(
"conflict",
dst_relpath,
style=Style.DANGER,
quiet=self.quiet,
file_=sys.stderr,
)
if self.match_skip(dst_relpath):
printf(
"skip",
dst_relpath,
style=Style.OK,
quiet=self.quiet,
file_=sys.stderr,
)
return False
if self.overwrite or dst_relpath == self.answers_relpath:
printf(
"overwrite",
dst_relpath,
style=Style.WARNING,
quiet=self.quiet,
file_=sys.stderr,
)
return True
return bool(ask(f" Overwrite {dst_relpath}?", default=True))
def _init_env(self, *args, **kwargs):
self.env = self.parent.force_env or self.parent.env
config_path = '.'.join([self.env, DOCKER_COMPOSE_PATH])
if self.env == 'dev':
self.config_path = config_path
elif local.path(config_path).is_file():
self.config_path = config_path
elif local.path(DOCKER_COMPOSE_PATH).is_file():
self.config_path = DOCKER_COMPOSE_PATH
else:
raise_error(
"There is not %s.%s or %s file, please add one"
% (self.env, DOCKER_COMPOSE_PATH, DOCKER_COMPOSE_PATH))
self.main_service = self._get_main_service()
if self.env == 'dev':
if not local.path(self.config_path).isfile():
generate = ask(
"There is not dev.docker-compose.yml file.\n"
"Do you want to generate one automatically",
default=True)
if generate:
self.run_hook(GenerateDevComposeFile)
else:
raise_error("No dev.docker-compose.yml file, abort!")
self.compose = compose['-f', self.config_path]
def main(self, *search_terms):
try:
results = search(search_terms, adult=self.adult)
except KeyboardInterrupt:
results = None
if not results:
raise NoResults
with suppress(CommandNotFound):
print(
f"{local['df']('-h', '-P', '.').splitlines()[-1].split()[3]} available"
| yellow)
uri = choose_result(results)
if not uri:
return
try:
clip(uri)
except CommandNotFound:
print(uri | blue)
else:
print("Magnet URI copied to clipboard" | green)
show_connection()
try:
aria2c = local['aria2c']
except CommandNotFound:
print(
"If I'd found the 'aria2c' command, I'd have offered to launch it for you."
| yellow)
else:
if ask("Begin download with aria2" | magenta, True):
# try:
aria2c['--seed-time=0', uri] & FG
def overwrite_file(conf: ConfigData, dst_path: Path, rel_path: Path) -> bool:
printf("conflict", rel_path, style=Style.DANGER, quiet=conf.quiet)
if conf.force:
return True
if conf.skip:
return False
return bool(ask(f" Overwrite {dst_path}?", default=True))
def __init__(self, *args, **kwargs):
super(VoodooSub, self).__init__(*args, **kwargs)
if args and args[0] == 'voodoo new':
return
config_path = '.'.join([self.parent.env, DOCKER_COMPOSE_PATH])
if self.parent.env == 'dev':
self.config_path = config_path
elif local.path(config_path).is_file():
self.config_path = config_path
elif local.path(DOCKER_COMPOSE_PATH).is_file():
self.config_path = DOCKER_COMPOSE_PATH
else:
raise_error(
"There is not %s.%s or %s file, please add one"
% (self.parent.env, DOCKER_COMPOSE_PATH, DOCKER_COMPOSE_PATH))
self.main_service = self._get_main_service()
if self.parent.env == 'dev':
if not local.path(self.config_path).isfile():
generate = ask(
"There is not dev.docker-compose.yml file.\n"
"Do you want to generate one automatically",
default=True)
if generate:
self.run_hook(GenerateDevComposeFile)
else:
raise_error("No dev.docker-compose.yml file, abort!")
self.compose = compose['-f', self.config_path]
def _generate_dev_docker_compose_file(self):
print("There is not dev.docker-compose.yml file.\n")
for service in TEMPLATE_SERVICE:
generate = ask(
"Do you want to generate one automatically for %s" % service,
default=True)
if generate:
return GenerateComposeFile(service).generate()
raise_error("No dev.docker-compose.yml file, abort!")
def _generate_dev_docker_compose_file(self):
generate = ask(
"There is not dev.docker-compose.yml file.\n"
"Do you want to generate one automatically",
default=True)
if generate:
GenerateComposeFile(self.service).generate()
else:
raise_error("No dev.docker-compose.yml file, abort!")
def query_user_data(
questions_data: AnyByStrDict,
answers_data: AnyByStrDict,
ask_user: bool,
envops: EnvOps,
) -> AnyByStrDict:
"""Query the user for questions given in the config file."""
type_maps: Dict[str, Callable] = {
"bool": bool,
"float": float,
"int": int,
"json": json.loads,
"str": str,
"yaml": parse_yaml_string,
}
env = get_jinja_env(envops=envops)
result = DEFAULT_DATA.copy()
_render_value = partial(render_value, env=env, context=result)
_render_choices = partial(render_choices, env=env, context=result)
for question, details in questions_data.items():
# Get default answer
answer = default = answers_data.get(
question, _render_value(details.get("default")))
# Get question type; by default let YAML decide it
type_name = _render_value(details.get("type", "yaml"))
try:
type_fn = type_maps[type_name]
except KeyError:
raise InvalidTypeError()
if ask_user:
# Generate message to ask the user
emoji = "🕵️" if details.get("secret", False) else "🎤"
message = f"\n{bold | question}? Format: {type_name}\n{emoji} "
if details.get("help"):
message = (
f"\n{info & italics | _render_value(details['help'])}{message}"
)
# Use the right method to ask
if type_fn is bool:
answer = ask(message, default)
elif details.get("choices"):
choices = _render_choices(details["choices"])
answer = choose(message, choices, default)
else:
answer = prompt(message, type_fn, default)
result[question] = cast_answer_type(answer, type_fn)
for key in DEFAULT_DATA:
del result[key]
return result
def _ask_optional_service(self):
"""Container can be set as optional by adding the key
"optional" and "description". This method will ask the user to
use or not this optional container"""
for name, config in self.config['services'].items():
if config.get('optional'):
install = ask("%s. Do you want to install it" %
config['description'],
default=False)
if install:
# remove useless dockercompose key
del self.config['services'][name]['description']
del self.config['services'][name]['optional']
self.config['services']['odoo']['links'].append(name)
else:
del self.config['services'][name]
def overwrite_file(conf: ConfigData, dst_path: Path, rel_path: Path) -> bool:
"""Handle the case when there's an update conflict.
Arguments:
conf: Configuration obtained with [`make_config`][copier.config.factory.make_config].
dst_path: The destination file.
rel_path: The new file.
Returns:
True if the overwrite was forced or the user answered yes,
False if skipped by configuration or if the user answered no.
"""
printf("conflict", rel_path, style=Style.DANGER, quiet=conf.quiet)
if conf.force:
return True
if conf.skip:
return False
return bool(ask(f" Overwrite {dst_path}?", default=True))
def _ask_optional_service(self):
"""Container can be set as optional by adding the key
"optional" and "description". This method will ask the user to
use or not this optional container"""
answer = {}
for name, config in self.config['services'].copy().items():
if config.get('optional'):
option = config['optional']
if not option in answer:
answer[option] = ask("%s. Do you want to install it" %
option,
default=False)
if answer[option]:
# remove useless docker compose key
del self.config['services'][name]['optional']
if not 'links' in self.config['services'][self.service]:
self.config['services'][self.service]['links'] = []
self.config['services'][self.service]['links'].append(name)
else:
del self.config['services'][name]
def main(self):
"""This function leads the exectution of the program."""
if 'input_values.txt' in os.listdir(self.save_dir):
self.there_is_infile()
else:
self.there_is_not_infile()
if not self.dont_perform_integration:
self.integration_completed = integrator.generate_data(
self.save_dir, self.dt)
if not self.dont_calculate_lyapunov:
self.lyap_exp_calculated = lyapunov.lyapunov(self.save_dir)
if not self.dont_generate_images:
self.images_created = image_creator.image_creator(self.save_dir)
if (self.integration_completed and self.images_created
and self.verbose):
print(colors.green | "Process completed.")
if (self.verbose):
print(colors.green | "These processes have been performed:")
print(colors.green | "INTEGRATION:", self.integration_completed)
print(colors.green | "LYAPUNOV EPONENT:", self.lyapunov)
print(colors.green | "IMAGE GENERATION:", self.images_created)
if (self.alert):
"""Alert script. If you wish to modify the alert act here.
Change duration and/or frequency as you wish
Or change directly the command os.system receives a sinput."""
duration = 1 # seconds
freq = 441 # Hz
os.system('play -nq -t alsa synth {} sine {}'.format(
duration, freq))
if (terminal.ask("Run another simulation?")):
print(
"Please rename/save elsewhere the present 'input_values.txt' if you want to change it for this simulation."
)
self.main()
else:
sys.exit([0])
#!/usr/bin/env python3
import sys
from requests import get
from plumbum import local, ProcessExecutionError
from plumbum.cli.terminal import ask
from plumbum.cmd import peerflix, xclip, mpv
vpn = local['~/Code/vpn.py']
uris = sys.argv[1:] or xclip('-sel', 'clip', '-o').splitlines()
for uri in uris:
if uri.startswith('magnet:?xt=urn:btih:') or uri.endswith('.torrent'):
r = get('https://api.duckduckgo.com', {'q': 'ip', 'format': 'json'})
location = r.json()['Answer'].split('>')[1].split('<')[0]
if ask(f"Your IP address indicates you're in {location}. Connect to VPN?", True):
vpn['up', 'us'].run_fg()
try:
peerflix['-kdf', local.path('~/Downloads/peerflix'), uri, '--', '--no-resume-playback'].run_fg()
except (ProcessExecutionError, KeyboardInterrupt) as e:
print(e, file=sys.stderr)
if ask(f"Disconnect from VPN?", True):
vpn['down'].run_fg()
else:
mpv[uri].run_fg()
def _generate_env(self):
generate = ask("Do you want to generate .env file ?", default=True)
if generate:
return GenerateEnvFile().generate()
def main(self):
self.dest_dir = local.path(self.dest_dir)
self.meg_dir = local.path(self.meg_dir)
self.meg_conf = local.path(self.meg_conf)
# Run some checks on the provided arguments
if not self.meg_dir.is_file():
print("Provided MEG source directory:")
with colors.red:
print(self.meg_dir)
print("Does not exist")
if not self.meg_conf.is_file():
print("Provided config file:")
with colors.red:
print(self.meg_dir)
print("Does not exist")
if not self.dest_dir.is_dir():
if terminal.ask(
"Destination directory: %s does not exist, create" %
str(self.dest_dir), True):
self.dest_dir.mkdir()
else:
return -1
if self.verbose:
print("Verbose mode")
print("Raw MEG found at:", self.meg_dir)
print("Using config file: ", self.meg_conf)
with colors.green:
print("Outputting to: ", self.dest_dir)
self.completed_subjects = find_completed(self.dest_dir).keys()
print("Completed subjects: ", str(self.completed_subjects))
if self.update:
with colors.yellow:
print('WARNING: Overwriting existing data for subjects')
if self.only_acoustic:
print('Extracting acoustic data')
if self.all_subjects or self.remaining_subjects:
# determine remaining
# FIXME hardcoded path is stupid
toplevel = local.path(
'/media/demetres/My Book/LizPang2015/Children')
if not toplevel.exists():
print('No subjects available.')
return
pattern = re.compile("^CC[0-9]+(-[0-9]+)?")
self.subjects = []
self.subjects += [
subject.name for subject in toplevel
if pattern.fullmatch(subject.name) is not None
]
if self.remaining_subjects and self.update:
print(
'Warning: Remaining and update specified, going through all...'
)
if self.all_subjects and not self.update:
# easiest way to ensure that all get processed
self.update = True
if not self.update:
self.subjects = [
x for x in self.subjects if x not in self.completed_subjects
]
if self.verbose:
print('Subjects to process:', self.subjects)
subjectsprogress = progress.ProgressAuto(self.subjects, body=True)
subjectsprogress.start()
# Go through each subject remaining
for subject in self.subjects:
with colors.green:
print('Subject: ', subject)
# First extract the data for opensmile processing, if not already done
if preproc_csvs_dir.is_dir() and (len(preproc_csvs_dir.list()) > 0) and \
terminal.ask('Previously pre-processed data found, would you like to proceed ' +
'presuming it is for subject ' + str(subject) +
' (%d tests found)' % len(preproc_csvs_dir.list())):
pass
else:
print(
'Preprocessing raw MEG for opensmile feature extraction...'
)
stdout = preprocess(subject, audioonly=self.only_acoustic)
if self.verbose:
print(stdout[1])
with colors.red:
if stdout[0] != 0 or 'FAILED' in stdout[
1] or 'Complete.' not in stdout[1]:
print('Failed to extract data for subject:', subject)
print('Skipping...')
continue
with colors.green:
print("Completed outputting preprocessed csv files.")
# Run extractions on all the preprocessed data
for test in preproc_csvs_dir:
# Ignore the absolute path for just the last directory title
test_label = test.name.split('/')[-1]
if self.verbose:
print("Test: ", test_label)
directory = '/'.join([self.dest_dir, subject, test_label, ''])
if not self.only_acoustic:
dest_meg_dir = directory + 'MEG/'
mkdir(dest_meg_dir)
temp_meg_dir = test.glob('MEG').pop()
else:
temp_meg_dir = None
if not self.only_meg or not self.only_wavelets:
dest_acoustic_dir = directory + 'Acoustic/'
mkdir(dest_acoustic_dir)
temp_acoustic_dir = test.glob('Acoustic').pop()
else:
temp_acoustic_dir = None
temp_location = local.path(preproc_csvs_dir + '/temp.csv')
# MEG processing
if temp_meg_dir is not None and temp_meg_dir.is_dir() and \
not (self.only_acoustic or self.only_wavelets):
print('Extracting MEG features...')
for epoch in progress.Progress(temp_meg_dir,
has_output=True):
if self.verbose:
print(time.strftime('%X %x %Z'))
# Check if the epoch has already been processed
if not self.update:
if epoch.name.split('.')[0] in [
x.name.split('.')[0]
for x in local.path(dest_meg_dir)
]:
print("Already exists, skipping...")
continue
ProcessMEG.run_catch_fail(self,
opensmile_extract_features,
self.meg_conf,
epoch,
temp_location,
failedon=epoch)
ProcessMEG.run_catch_fail(
self,
mat_compress,
temp_location,
dest_meg_dir + epoch.name.split('.')[0] + '.mat',
failedon=epoch)
temp_location.delete()
# Acoustic Processing
if temp_acoustic_dir is not None and temp_acoustic_dir.is_dir() and \
not (self.only_meg or self.only_wavelets):
print('Extracting Audio features...')
for epoch in progress.Progress(temp_acoustic_dir,
has_output=True):
if self.verbose:
print(time.strftime('%X %x %Z'))
# Check if the epoch has already been processed
if not self.update:
if epoch.name.split('.')[0] in \
[x.name.split('.')[0] for x in local.path(dest_acoustic_dir)]:
print("Already exists, skipping...")
continue
ProcessMEG.run_catch_fail(self,
opensmile_extract_features,
self.acoustic_conf,
epoch,
temp_location,
failedon=epoch)
ProcessMEG.run_catch_fail(self,
mat_compress,
temp_location,
dest_acoustic_dir +
epoch.name.split('.')[0] +
'.mat',
failedon=epoch)
temp_location.delete()
# Wavelet Processing
if temp_meg_dir is not None and temp_meg_dir.is_dir() and \
not (self.only_acoustic or self.only_meg):
print("Extracting wavelet coefficients...")
for epoch in progress.Progress(temp_meg_dir,
has_output=True):
if self.verbose:
print(time.strftime('%X %x %Z'))
outname = epoch.name.split('.')[0] + '_wavelets'
# Check if the epoch has already been processed
if not self.update:
if outname in [
x.name.split('.')[0]
for x in local.path(dest_meg_dir)
]:
print("Already exists, skipping...")
continue
ProcessMEG.run_catch_fail(self,
extractwaveletcoef,
epoch,
dest_meg_dir + outname,
failedon=epoch)
test.delete()
# Increment
with colors.green & colors.bold:
subjectsprogress.increment()
subjectsprogress.done()
