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tensorflow/skflow | scripts/docs/docs.py | Library.write_other_members | def write_other_members(self, f, catch_all=False):
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f: File to write to.
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/multiprocess.py | MultiprocessPrometheusMetrics.start_http_server | def start_http_server(self, port, host='0.0.0.0', endpoint=None):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.init_app | def init_app(self, app):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.register_endpoint | def register_endpoint(self, path, app=None):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.start_http_server | def start_http_server(self, port, host='0.0.0.0', endpoint='/metrics'):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.histogram | def histogram(self, name, description, labels=None, **kwargs):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.summary | def summary(self, name, description, labels=None, **kwargs):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.gauge | def gauge(self, name, description, labels=None, **kwargs):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.counter | def counter(self, name, description, labels=None, **kwargs):
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics._track | def _track(metric_type, metric_call, metric_kwargs, name, description, labels,
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"""
Internal method decorator logic.
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.do_not_track | def do_not_track():
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rycus86/prometheus_flask_exporter | prometheus_flask_exporter/__init__.py | PrometheusMetrics.info | def info(self, name, description, labelnames=None, labelvalues=None, **labels):
"""
Report any information as a Prometheus metric.
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berdario/pew | pew/pew.py | inve | def inve(env, command, *args, **kwargs):
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berdario/pew | pew/pew.py | ls_cmd | def ls_cmd(argv):
"""List available environments."""
parser = argparse.ArgumentParser()
p_group = parser.add_mutually_exclusive_group()
p_group.add_argument('-b', '--brief', action='store_false')
p_group.add_argument('-l', '--long', action='store_true')
args = parser.parse_args(argv)
lsvirtu... | python | def ls_cmd(argv):
"""List available environments."""
parser = argparse.ArgumentParser()
p_group = parser.add_mutually_exclusive_group()
p_group.add_argument('-b', '--brief', action='store_false')
p_group.add_argument('-l', '--long', action='store_true')
args = parser.parse_args(argv)
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berdario/pew | pew/pew.py | workon_cmd | def workon_cmd(argv):
"""List or change working virtual environments."""
parser = argparse.ArgumentParser(prog='pew workon')
parser.add_argument('envname', nargs='?')
parser.add_argument(
'-n', '--no-cd', action='store_true',
help=('Do not change working directory to project directory af... | python | def workon_cmd(argv):
"""List or change working virtual environments."""
parser = argparse.ArgumentParser(prog='pew workon')
parser.add_argument('envname', nargs='?')
parser.add_argument(
'-n', '--no-cd', action='store_true',
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berdario/pew | pew/pew.py | add_cmd | def add_cmd(argv):
"""Add the specified directories to the Python path for the currently active virtualenv.
This will be done by placing the directory names in a path file named
"virtualenv_path_extensions.pth" inside the virtualenv's site-packages
directory; if this file does not exists, it will be created first.... | python | def add_cmd(argv):
"""Add the specified directories to the Python path for the currently active virtualenv.
This will be done by placing the directory names in a path file named
"virtualenv_path_extensions.pth" inside the virtualenv's site-packages
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berdario/pew | pew/pew.py | lssitepackages_cmd | def lssitepackages_cmd(argv):
"""Show the content of the site-packages directory of the current virtualenv."""
site = sitepackages_dir()
print(*sorted(site.iterdir()), sep=os.linesep)
extra_paths = site / '_virtualenv_path_extensions.pth'
if extra_paths.exists():
print('from _virtualenv_path... | python | def lssitepackages_cmd(argv):
"""Show the content of the site-packages directory of the current virtualenv."""
site = sitepackages_dir()
print(*sorted(site.iterdir()), sep=os.linesep)
extra_paths = site / '_virtualenv_path_extensions.pth'
if extra_paths.exists():
print('from _virtualenv_path... | [
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berdario/pew | pew/pew.py | toggleglobalsitepackages_cmd | def toggleglobalsitepackages_cmd(argv):
"""Toggle the current virtualenv between having and not having access to the global site-packages."""
quiet = argv == ['-q']
site = sitepackages_dir()
ngsp_file = site.parent / 'no-global-site-packages.txt'
if ngsp_file.exists():
ngsp_file.unlink()
... | python | def toggleglobalsitepackages_cmd(argv):
"""Toggle the current virtualenv between having and not having access to the global site-packages."""
quiet = argv == ['-q']
site = sitepackages_dir()
ngsp_file = site.parent / 'no-global-site-packages.txt'
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berdario/pew | pew/pew.py | cp_cmd | def cp_cmd(argv):
"""Duplicate the named virtualenv to make a new one."""
parser = argparse.ArgumentParser()
parser.add_argument('source')
parser.add_argument('target', nargs='?')
parser.add_argument('-d', '--dont-activate', action='store_false',
default=True, dest='activate'... | python | def cp_cmd(argv):
"""Duplicate the named virtualenv to make a new one."""
parser = argparse.ArgumentParser()
parser.add_argument('source')
parser.add_argument('target', nargs='?')
parser.add_argument('-d', '--dont-activate', action='store_false',
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berdario/pew | pew/pew.py | rename_cmd | def rename_cmd(argv):
"""Rename a virtualenv"""
parser = argparse.ArgumentParser()
parser.add_argument('source')
parser.add_argument('target')
pargs = parser.parse_args(argv)
copy_virtualenv_project(pargs.source, pargs.target)
return rmvirtualenvs([pargs.source]) | python | def rename_cmd(argv):
"""Rename a virtualenv"""
parser = argparse.ArgumentParser()
parser.add_argument('source')
parser.add_argument('target')
pargs = parser.parse_args(argv)
copy_virtualenv_project(pargs.source, pargs.target)
return rmvirtualenvs([pargs.source]) | [
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berdario/pew | pew/pew.py | setproject_cmd | def setproject_cmd(argv):
"""Given a virtualenv directory and a project directory, set the \
virtualenv up to be associated with the project."""
args = dict(enumerate(argv))
project = os.path.abspath(args.get(1, '.'))
env = args.get(0, os.environ.get('VIRTUAL_ENV'))
if not env:
sys.exit(... | python | def setproject_cmd(argv):
"""Given a virtualenv directory and a project directory, set the \
virtualenv up to be associated with the project."""
args = dict(enumerate(argv))
project = os.path.abspath(args.get(1, '.'))
env = args.get(0, os.environ.get('VIRTUAL_ENV'))
if not env:
sys.exit(... | [
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berdario/pew | pew/pew.py | getproject_cmd | def getproject_cmd(argv):
"""Print a virtualenv's project directory, if set.
If called without providing a virtualenv name as argument, print the
current virtualenv's project directory.
"""
# Parse command line arguments
parser = argparse.ArgumentParser(
description="Print an environmen... | python | def getproject_cmd(argv):
"""Print a virtualenv's project directory, if set.
If called without providing a virtualenv name as argument, print the
current virtualenv's project directory.
"""
# Parse command line arguments
parser = argparse.ArgumentParser(
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berdario/pew | pew/pew.py | mkproject_cmd | def mkproject_cmd(argv):
"""Create a new project directory and its associated virtualenv."""
if '-l' in argv or '--list' in argv:
templates = [t.name[9:] for t in workon_home.glob("template_*")]
print("Available project templates:", *templates, sep='\n')
return
parser = mkvirtualenv... | python | def mkproject_cmd(argv):
"""Create a new project directory and its associated virtualenv."""
if '-l' in argv or '--list' in argv:
templates = [t.name[9:] for t in workon_home.glob("template_*")]
print("Available project templates:", *templates, sep='\n')
return
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berdario/pew | pew/pew.py | mktmpenv_cmd | def mktmpenv_cmd(argv):
"""Create a temporary virtualenv."""
parser = mkvirtualenv_argparser()
env = '.'
while (workon_home / env).exists():
env = hex(random.getrandbits(64))[2:-1]
args, rest = parser.parse_known_args(argv)
mkvirtualenv(env, args.python, args.packages, requirements=arg... | python | def mktmpenv_cmd(argv):
"""Create a temporary virtualenv."""
parser = mkvirtualenv_argparser()
env = '.'
while (workon_home / env).exists():
env = hex(random.getrandbits(64))[2:-1]
args, rest = parser.parse_known_args(argv)
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berdario/pew | pew/pew.py | inall_cmd | def inall_cmd(argv):
"""Run a command in each virtualenv."""
envs = lsenvs()
errors = False
for env in envs:
print("\n%s:" % env)
try:
inve(env, *argv)
except CalledProcessError as e:
errors = True
err(e)
sys.exit(errors) | python | def inall_cmd(argv):
"""Run a command in each virtualenv."""
envs = lsenvs()
errors = False
for env in envs:
print("\n%s:" % env)
try:
inve(env, *argv)
except CalledProcessError as e:
errors = True
err(e)
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berdario/pew | pew/pew.py | in_cmd | def in_cmd(argv):
"""Run a command in the given virtualenv."""
if len(argv) == 1:
return workon_cmd(argv)
parse_envname(argv, lambda : sys.exit('You must provide a valid virtualenv to target'))
return inve(*argv) | python | def in_cmd(argv):
"""Run a command in the given virtualenv."""
if len(argv) == 1:
return workon_cmd(argv)
parse_envname(argv, lambda : sys.exit('You must provide a valid virtualenv to target'))
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berdario/pew | pew/pew.py | restore_cmd | def restore_cmd(argv):
"""Try to restore a broken virtualenv by reinstalling the same python version on top of it"""
if len(argv) < 1:
sys.exit('You must provide a valid virtualenv to target')
env = argv[0]
path = workon_home / env
py = path / env_bin_dir / ('python.exe' if windows else 'p... | python | def restore_cmd(argv):
"""Try to restore a broken virtualenv by reinstalling the same python version on top of it"""
if len(argv) < 1:
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berdario/pew | pew/pew.py | dir_cmd | def dir_cmd(argv):
"""Print the path for the virtualenv directory"""
env = parse_envname(argv, lambda : sys.exit('You must provide a valid virtualenv to target'))
print(workon_home / env) | python | def dir_cmd(argv):
"""Print the path for the virtualenv directory"""
env = parse_envname(argv, lambda : sys.exit('You must provide a valid virtualenv to target'))
print(workon_home / env) | [
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berdario/pew | pew/pew.py | install_cmd | def install_cmd(argv):
'''Use Pythonz to download and build the specified Python version'''
installer = InstallCommand()
options, versions = installer.parser.parse_args(argv)
if len(versions) != 1:
installer.parser.print_help()
sys.exit(1)
else:
try:
actual_instal... | python | def install_cmd(argv):
'''Use Pythonz to download and build the specified Python version'''
installer = InstallCommand()
options, versions = installer.parser.parse_args(argv)
if len(versions) != 1:
installer.parser.print_help()
sys.exit(1)
else:
try:
actual_instal... | [
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berdario/pew | pew/pew.py | version_cmd | def version_cmd(argv):
"""Prints current pew version"""
import pkg_resources
try:
__version__ = pkg_resources.get_distribution('pew').version
except pkg_resources.DistributionNotFound:
__version__ = 'unknown'
print('Setuptools has some issues here, failed to get our own package.... | python | def version_cmd(argv):
"""Prints current pew version"""
import pkg_resources
try:
__version__ = pkg_resources.get_distribution('pew').version
except pkg_resources.DistributionNotFound:
__version__ = 'unknown'
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peterbe/premailer | premailer/merge_style.py | csstext_to_pairs | def csstext_to_pairs(csstext):
"""
csstext_to_pairs takes css text and make it to list of
tuple of key,value.
"""
# The lock is required to avoid ``cssutils`` concurrency
# issues documented in issue #65
with csstext_to_pairs._lock:
return sorted(
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(prop.... | python | def csstext_to_pairs(csstext):
"""
csstext_to_pairs takes css text and make it to list of
tuple of key,value.
"""
# The lock is required to avoid ``cssutils`` concurrency
# issues documented in issue #65
with csstext_to_pairs._lock:
return sorted(
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peterbe/premailer | premailer/merge_style.py | merge_styles | def merge_styles(inline_style, new_styles, classes, remove_unset_properties=False):
"""
This will merge all new styles where the order is important
The last one will override the first
When that is done it will apply old inline style again
The old inline style is always important and... | python | def merge_styles(inline_style, new_styles, classes, remove_unset_properties=False):
"""
This will merge all new styles where the order is important
The last one will override the first
When that is done it will apply old inline style again
The old inline style is always important and... | [
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peterbe/premailer | premailer/premailer.py | make_important | def make_important(bulk):
"""makes every property in a string !important.
"""
return ";".join(
"%s !important" % p if not p.endswith("!important") else p
for p in bulk.split(";")
) | python | def make_important(bulk):
"""makes every property in a string !important.
"""
return ";".join(
"%s !important" % p if not p.endswith("!important") else p
for p in bulk.split(";")
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peterbe/premailer | premailer/premailer.py | capitalize_float_margin | def capitalize_float_margin(css_body):
"""Capitalize float and margin CSS property names
"""
def _capitalize_property(match):
return "{0}:{1}{2}".format(
match.group("property").capitalize(),
match.group("value"),
match.group("terminator"),
)
return ... | python | def capitalize_float_margin(css_body):
"""Capitalize float and margin CSS property names
"""
def _capitalize_property(match):
return "{0}:{1}{2}".format(
match.group("property").capitalize(),
match.group("value"),
match.group("terminator"),
)
return ... | [
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peterbe/premailer | premailer/premailer.py | Premailer._load_external | def _load_external(self, url):
"""loads an external stylesheet from a remote url or local path
"""
if url.startswith("//"):
# then we have to rely on the base_url
if self.base_url and "https://" in self.base_url:
url = "https:" + url
else:
... | python | def _load_external(self, url):
"""loads an external stylesheet from a remote url or local path
"""
if url.startswith("//"):
# then we have to rely on the base_url
if self.base_url and "https://" in self.base_url:
url = "https:" + url
else:
... | [
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peterbe/premailer | premailer/premailer.py | Premailer._css_rules_to_string | def _css_rules_to_string(self, rules):
"""given a list of css rules returns a css string
"""
lines = []
for item in rules:
if isinstance(item, tuple):
k, v = item
lines.append("%s {%s}" % (k, make_important(v)))
# media rule
... | python | def _css_rules_to_string(self, rules):
"""given a list of css rules returns a css string
"""
lines = []
for item in rules:
if isinstance(item, tuple):
k, v = item
lines.append("%s {%s}" % (k, make_important(v)))
# media rule
... | [
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vatlab/SoS | src/sos/workers.py | WorkerManager.check_workers | def check_workers(self):
'''Kill workers that have been pending for a while and check if all workers
are alive. '''
if time.time() - self._worker_alive_time > 5:
self._worker_alive_time = time.time()
# join processes if they are now gone, it should not do anything bad
... | python | def check_workers(self):
'''Kill workers that have been pending for a while and check if all workers
are alive. '''
if time.time() - self._worker_alive_time > 5:
self._worker_alive_time = time.time()
# join processes if they are now gone, it should not do anything bad
... | [
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vatlab/SoS | src/sos/workers.py | WorkerManager.kill_all | def kill_all(self):
'''Kill all workers'''
while self._num_workers > 0 and self._worker_backend_socket.poll(1000):
msg = self._worker_backend_socket.recv_pyobj()
self._worker_backend_socket.send_pyobj(None)
self._num_workers -= 1
self.report(f'Kill {msg[1:... | python | def kill_all(self):
'''Kill all workers'''
while self._num_workers > 0 and self._worker_backend_socket.poll(1000):
msg = self._worker_backend_socket.recv_pyobj()
self._worker_backend_socket.send_pyobj(None)
self._num_workers -= 1
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vatlab/SoS | src/sos/targets_python.py | Py_Module._install | def _install(self, name, autoinstall):
'''Check existence of Python module and install it using command
pip install if necessary.'''
import importlib
import pkg_resources
spam_spec = importlib.util.find_spec(name)
reinstall = False
if spam_spec is not None:
... | python | def _install(self, name, autoinstall):
'''Check existence of Python module and install it using command
pip install if necessary.'''
import importlib
import pkg_resources
spam_spec = importlib.util.find_spec(name)
reinstall = False
if spam_spec is not None:
... | [
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vatlab/SoS | src/sos/task_executor.py | execute_task | def execute_task(task_id,
verbosity=None,
runmode='run',
sigmode=None,
monitor_interval=5,
resource_monitor_interval=60):
'''Execute single or master task, return a dictionary'''
tf = TaskFile(task_id)
# this will automati... | python | def execute_task(task_id,
verbosity=None,
runmode='run',
sigmode=None,
monitor_interval=5,
resource_monitor_interval=60):
'''Execute single or master task, return a dictionary'''
tf = TaskFile(task_id)
# this will automati... | [
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vatlab/SoS | src/sos/targets.py | textMD5 | def textMD5(text):
'''Get md5 of a piece of text'''
m = hash_md5()
if isinstance(text, str):
m.update(text.encode())
else:
m.update(text)
return m.hexdigest() | python | def textMD5(text):
'''Get md5 of a piece of text'''
m = hash_md5()
if isinstance(text, str):
m.update(text.encode())
else:
m.update(text)
return m.hexdigest() | [
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vatlab/SoS | src/sos/targets.py | objectMD5 | def objectMD5(obj):
'''Get md5 of an object'''
if hasattr(obj, 'target_name'):
return obj.target_name()
try:
return textMD5(pickle.dumps(obj))
except:
return '' | python | def objectMD5(obj):
'''Get md5 of an object'''
if hasattr(obj, 'target_name'):
return obj.target_name()
try:
return textMD5(pickle.dumps(obj))
except:
return '' | [
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vatlab/SoS | src/sos/targets.py | fileMD5 | def fileMD5(filename, partial=True):
'''Calculate partial MD5, basically the first and last 8M
of the file for large files. This should signicicantly reduce
the time spent on the creation and comparison of file signature
when dealing with large bioinformat ics datasets. '''
filesize = os.path.getsiz... | python | def fileMD5(filename, partial=True):
'''Calculate partial MD5, basically the first and last 8M
of the file for large files. This should signicicantly reduce
the time spent on the creation and comparison of file signature
when dealing with large bioinformat ics datasets. '''
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vatlab/SoS | src/sos/targets.py | file_target.target_signature | def target_signature(self):
'''Return file signature'''
if self.exists():
if not self._md5:
self._md5 = fileMD5(self)
return (os.path.getmtime(self), os.path.getsize(self), self._md5)
elif (self + '.zapped').is_file():
with open(self + '.zapped... | python | def target_signature(self):
'''Return file signature'''
if self.exists():
if not self._md5:
self._md5 = fileMD5(self)
return (os.path.getmtime(self), os.path.getsize(self), self._md5)
elif (self + '.zapped').is_file():
with open(self + '.zapped... | [
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vatlab/SoS | src/sos/targets.py | file_target.validate | def validate(self, sig=None):
'''Check if file matches its signature'''
if sig is not None:
sig_mtime, sig_size, sig_md5 = sig
else:
try:
with open(self.sig_file()) as sig:
sig_mtime, sig_size, sig_md5 = sig.read().strip().split()
... | python | def validate(self, sig=None):
'''Check if file matches its signature'''
if sig is not None:
sig_mtime, sig_size, sig_md5 = sig
else:
try:
with open(self.sig_file()) as sig:
sig_mtime, sig_size, sig_md5 = sig.read().strip().split()
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vatlab/SoS | src/sos/targets.py | file_target.write_sig | def write_sig(self):
'''Write signature to sig store'''
if not self._md5:
self._md5 = fileMD5(self)
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sig.write(
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'''Write signature to sig store'''
if not self._md5:
self._md5 = fileMD5(self)
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sig.write(
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vatlab/SoS | src/sos/targets.py | sos_targets.remove_targets | def remove_targets(self, type, kept=None):
'''Remove targets of certain type'''
if kept is None:
kept = [
i for i, x in enumerate(self._targets)
if not isinstance(x, type)
]
if len(kept) == len(self._targets):
return self
... | python | def remove_targets(self, type, kept=None):
'''Remove targets of certain type'''
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kept = [
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if not isinstance(x, type)
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if len(kept) == len(self._targets):
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vatlab/SoS | src/sos/targets.py | sos_targets.resolve_remote | def resolve_remote(self):
'''If target is of remote type, resolve it'''
for idx, target in enumerate(self._targets):
if isinstance(target, remote):
resolved = target.resolve()
if isinstance(resolved, str):
resolved = interpolate(resolved, e... | python | def resolve_remote(self):
'''If target is of remote type, resolve it'''
for idx, target in enumerate(self._targets):
if isinstance(target, remote):
resolved = target.resolve()
if isinstance(resolved, str):
resolved = interpolate(resolved, e... | [
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vatlab/SoS | src/sos/targets.py | sos_targets._handle_paired_with | def _handle_paired_with(self, paired_with):
'''Handle input option paired_with'''
if paired_with is None or not paired_with:
var_name = []
var_value = []
elif isinstance(paired_with, str):
var_name = ['_' + paired_with]
if paired_with not in env.so... | python | def _handle_paired_with(self, paired_with):
'''Handle input option paired_with'''
if paired_with is None or not paired_with:
var_name = []
var_value = []
elif isinstance(paired_with, str):
var_name = ['_' + paired_with]
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vatlab/SoS | src/sos/targets.py | sos_targets._handle_group_with | def _handle_group_with(self, group_with):
'''Handle input option group_with'''
if group_with is None or not group_with:
var_name = []
var_value = []
elif isinstance(group_with, str):
var_name = ['_' + group_with]
if group_with not in env.sos_dict:
... | python | def _handle_group_with(self, group_with):
'''Handle input option group_with'''
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var_name = []
var_value = []
elif isinstance(group_with, str):
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vatlab/SoS | src/sos/targets.py | sos_targets._handle_extract_pattern | def _handle_extract_pattern(self, pattern):
'''Handle input option pattern'''
if pattern is None or not pattern:
patterns = []
elif isinstance(pattern, str):
patterns = [pattern]
elif isinstance(pattern, Iterable):
patterns = pattern
else:
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'''Handle input option pattern'''
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patterns = [pattern]
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vatlab/SoS | src/sos/targets.py | RuntimeInfo.write | def write(self):
'''Write signature file with signature of script, input, output and dependent files.
Because local input and output files can only be determined after the execution
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'''
if not self.output_files.valid():
... | python | def write(self):
'''Write signature file with signature of script, input, output and dependent files.
Because local input and output files can only be determined after the execution
of workflow. They are not part of the construction.
'''
if not self.output_files.valid():
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vatlab/SoS | src/sos/executor_utils.py | clear_output | def clear_output(output=None):
'''
Remove file targets in `_output` when a step fails to complete
'''
for target in env.sos_dict['_output'] if output is None else output:
if isinstance(target, file_target) and target.exists():
try:
target.unlink()
except E... | python | def clear_output(output=None):
'''
Remove file targets in `_output` when a step fails to complete
'''
for target in env.sos_dict['_output'] if output is None else output:
if isinstance(target, file_target) and target.exists():
try:
target.unlink()
except E... | [
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vatlab/SoS | src/sos/workflow_executor.py | Base_Executor.add_forward_workflow | def add_forward_workflow(self, dag, sections, satisfies=None):
'''Add a forward-workflow, return number of nodes added
'''
dag.new_forward_workflow()
if 'DAG' in env.config['SOS_DEBUG'] or 'ALL' in env.config['SOS_DEBUG']:
env.log_to_file(
'DAG', f'Adding min... | python | def add_forward_workflow(self, dag, sections, satisfies=None):
'''Add a forward-workflow, return number of nodes added
'''
dag.new_forward_workflow()
if 'DAG' in env.config['SOS_DEBUG'] or 'ALL' in env.config['SOS_DEBUG']:
env.log_to_file(
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vatlab/SoS | src/sos/workflow_executor.py | Base_Executor.initialize_dag | def initialize_dag(self,
targets: Optional[List[str]] = [],
nested: bool = False) -> SoS_DAG:
'''Create a DAG by analyzing sections statically.'''
self.reset_dict()
dag = SoS_DAG(name=self.md5)
targets = sos_targets(targets)
self.ad... | python | def initialize_dag(self,
targets: Optional[List[str]] = [],
nested: bool = False) -> SoS_DAG:
'''Create a DAG by analyzing sections statically.'''
self.reset_dict()
dag = SoS_DAG(name=self.md5)
targets = sos_targets(targets)
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vatlab/SoS | src/sos/utils.py | short_repr | def short_repr(obj, noneAsNA=False):
'''Return a short representation of obj for clarity.'''
if obj is None:
return 'unspecified' if noneAsNA else 'None'
elif isinstance(obj, str) and len(obj) > 80:
return '{}...{}'.format(obj[:60].replace('\n', '\\n'),
obj[-2... | python | def short_repr(obj, noneAsNA=False):
'''Return a short representation of obj for clarity.'''
if obj is None:
return 'unspecified' if noneAsNA else 'None'
elif isinstance(obj, str) and len(obj) > 80:
return '{}...{}'.format(obj[:60].replace('\n', '\\n'),
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vatlab/SoS | src/sos/utils.py | tail_of_file | def tail_of_file(filename, n, ansi2html=False):
"""Reads a n lines from f with an offset of offset lines. """
avg_line_length = 74
to_read = n
with open(filename) as f:
while 1:
try:
f.seek(-(avg_line_length * to_read), 2)
except IOError:
... | python | def tail_of_file(filename, n, ansi2html=False):
"""Reads a n lines from f with an offset of offset lines. """
avg_line_length = 74
to_read = n
with open(filename) as f:
while 1:
try:
f.seek(-(avg_line_length * to_read), 2)
except IOError:
... | [
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vatlab/SoS | src/sos/utils.py | sample_lines | def sample_lines(lines, n):
'''Draw a sample of n lines from filename, largely evenly.'''
if len(lines) <= n:
return ''.join(lines)
else:
m = len(lines)
return ''.join([lines[x * m // n + m // (2 * n)] for x in range(n)]) | python | def sample_lines(lines, n):
'''Draw a sample of n lines from filename, largely evenly.'''
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m = len(lines)
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vatlab/SoS | src/sos/utils.py | WorkflowDict.set | def set(self, key, value):
'''A short cut to set value to key without triggering any logging
or warning message.'''
if hasattr(value, 'labels'):
if 'VARIABLE' in env.config['SOS_DEBUG'] or 'ALL' in env.config[
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env.log_to_file(
... | python | def set(self, key, value):
'''A short cut to set value to key without triggering any logging
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if hasattr(value, 'labels'):
if 'VARIABLE' in env.config['SOS_DEBUG'] or 'ALL' in env.config[
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vatlab/SoS | src/sos/utils.py | WorkflowDict.update | def update(self, obj):
'''Redefine update to trigger logging message'''
self._dict.update(obj)
for k, v in obj.items():
# if k.isupper():
# self._check_readonly(k, v)
if env.verbosity > 2:
self._log(k, v) | python | def update(self, obj):
'''Redefine update to trigger logging message'''
self._dict.update(obj)
for k, v in obj.items():
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# self._check_readonly(k, v)
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vatlab/SoS | src/sos/substep_executor.py | execute_substep | def execute_substep(stmt,
global_def,
global_vars,
task='',
task_params='',
proc_vars={},
shared_vars=[],
config={}):
'''Execute a substep with specific input etc
Substep ... | python | def execute_substep(stmt,
global_def,
global_vars,
task='',
task_params='',
proc_vars={},
shared_vars=[],
config={}):
'''Execute a substep with specific input etc
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vatlab/SoS | src/sos/signatures.py | WorkflowSignatures.files | def files(self):
'''Listing files related to workflows related to current directory'''
try:
cur = self.conn.cursor()
cur.execute(
'SELECT id, item FROM workflows WHERE entry_type = "tracked_files"'
)
return [(x[0], eval(x[1])) for x in cur.... | python | def files(self):
'''Listing files related to workflows related to current directory'''
try:
cur = self.conn.cursor()
cur.execute(
'SELECT id, item FROM workflows WHERE entry_type = "tracked_files"'
)
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vatlab/SoS | src/sos/dag.py | SoS_DAG.find_executable | def find_executable(self):
'''Find an executable node, which means nodes that has not been completed
and has no input dependency.'''
if 'DAG' in env.config['SOS_DEBUG'] or 'ALL' in env.config['SOS_DEBUG']:
env.log_to_file('DAG', 'find_executable')
for node in self.nodes():
... | python | def find_executable(self):
'''Find an executable node, which means nodes that has not been completed
and has no input dependency.'''
if 'DAG' in env.config['SOS_DEBUG'] or 'ALL' in env.config['SOS_DEBUG']:
env.log_to_file('DAG', 'find_executable')
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vatlab/SoS | src/sos/dag.py | SoS_DAG.dangling | def dangling(self, targets: sos_targets):
'''returns
1. missing targets, which are missing from the DAG or from the provided targets
2. existing targets of provided target list, not in DAG
'''
existing = []
missing = []
if env.config['trace_existing']:
... | python | def dangling(self, targets: sos_targets):
'''returns
1. missing targets, which are missing from the DAG or from the provided targets
2. existing targets of provided target list, not in DAG
'''
existing = []
missing = []
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vatlab/SoS | src/sos/dag.py | SoS_DAG.subgraph_from | def subgraph_from(self, targets: sos_targets):
'''Trim DAG to keep only nodes that produce targets'''
if 'DAG' in env.config['SOS_DEBUG'] or 'ALL' in env.config['SOS_DEBUG']:
env.log_to_file('DAG', 'create subgraph')
# first, find all nodes with targets
subnodes = []
... | python | def subgraph_from(self, targets: sos_targets):
'''Trim DAG to keep only nodes that produce targets'''
if 'DAG' in env.config['SOS_DEBUG'] or 'ALL' in env.config['SOS_DEBUG']:
env.log_to_file('DAG', 'create subgraph')
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vatlab/SoS | src/sos/dag.py | SoS_DAG.build | def build(self):
'''Connect nodes according to status of targets'''
# right now we do not worry about status of nodes
# connecting the output to the input of other nodes
#
# NOTE: This is implemented in the least efficient way just for
# testing. It has to be re-implement... | python | def build(self):
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# right now we do not worry about status of nodes
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vatlab/SoS | src/sos/task_engines.py | TaskEngine.monitor_tasks | def monitor_tasks(self, tasks=None, status=None, age=None):
'''Start monitoring specified or all tasks'''
self.engine_ready.wait()
if not tasks:
tasks = self.task_status.keys()
else:
tasks = [x for x in tasks if x in self.task_status]
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'''Start monitoring specified or all tasks'''
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vatlab/SoS | src/sos/task_engines.py | BackgroundProcess_TaskEngine._submit_task_with_template | def _submit_task_with_template(self, task_ids):
'''Submit tasks by interpolating a shell script defined in job_template'''
runtime = self.config
runtime.update({
'workdir': os.getcwd(),
'cur_dir': os.getcwd(), # for backward compatibility
'verbosity': env.ver... | python | def _submit_task_with_template(self, task_ids):
'''Submit tasks by interpolating a shell script defined in job_template'''
runtime = self.config
runtime.update({
'workdir': os.getcwd(),
'cur_dir': os.getcwd(), # for backward compatibility
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vatlab/SoS | src/sos/parser.py | is_type_hint | def is_type_hint(stmt: str) -> bool:
'''Try to differentiate
var: type = value
with
action: input = whatever
'''
if stmt.count('=') > 1:
return False
if ':' not in stmt:
return False
#
# action:
if not stmt.split(':')[1].strip():
return False
#
... | python | def is_type_hint(stmt: str) -> bool:
'''Try to differentiate
var: type = value
with
action: input = whatever
'''
if stmt.count('=') > 1:
return False
if ':' not in stmt:
return False
#
# action:
if not stmt.split(':')[1].strip():
return False
#
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vatlab/SoS | src/sos/parser.py | SoS_Step.indented_script | def indented_script(self) -> bool:
''' check self._script and see if it is indented '''
# get all leading space, tab and newline
leading = INDENTED.match(self._script)
return 0 if leading is None else len(leading.group(2)) | python | def indented_script(self) -> bool:
''' check self._script and see if it is indented '''
# get all leading space, tab and newline
leading = INDENTED.match(self._script)
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vatlab/SoS | src/sos/parser.py | SoS_Step.category | def category(self) -> Optional[str]:
'''Determine the category of existing statement'''
if self.statements:
if self.statements[-1][0] == ':':
# a hack. ... to avoid calling isValid recursively
def validDirective():
if not self.values:
... | python | def category(self) -> Optional[str]:
'''Determine the category of existing statement'''
if self.statements:
if self.statements[-1][0] == ':':
# a hack. ... to avoid calling isValid recursively
def validDirective():
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vatlab/SoS | src/sos/parser.py | SoS_Step.isValid | def isValid(self) -> bool:
'''Determine if the statement, expression or directive is valid. Otherwise
the parser will continue until a valid multi-line expression or statement
can be found.'''
if not self.values:
return True
try:
if self.category() == 'dir... | python | def isValid(self) -> bool:
'''Determine if the statement, expression or directive is valid. Otherwise
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if not self.values:
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vatlab/SoS | src/sos/parser.py | SoS_Step.extend | def extend(self, line: str) -> None:
'''Extend the current directive, expression or script'''
if self.category() == 'directive':
self.add_directive(None, line)
elif self.category() == 'script':
self._script += line
else:
self.add_statement(line) | python | def extend(self, line: str) -> None:
'''Extend the current directive, expression or script'''
if self.category() == 'directive':
self.add_directive(None, line)
elif self.category() == 'script':
self._script += line
else:
self.add_statement(line) | [
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vatlab/SoS | src/sos/parser.py | SoS_Step.add_statement | def add_statement(self, line: str, lineno: Optional[int] = None) -> None:
'''statements are regular python statements'''
# there can be only one statement block
if self.category() != 'statements':
self.values = [line]
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self.values.append(line)
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vatlab/SoS | src/sos/parser.py | SoS_Step.get_tokens | def get_tokens(self) -> str:
'''Get tokens after input statement'''
def _get_tokens(statement):
return [
x[1]
for x in generate_tokens(StringIO(statement).readline)
if x[1] not in ('', '\n')
]
tokens: List = []
for... | python | def get_tokens(self) -> str:
'''Get tokens after input statement'''
def _get_tokens(statement):
return [
x[1]
for x in generate_tokens(StringIO(statement).readline)
if x[1] not in ('', '\n')
]
tokens: List = []
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vatlab/SoS | src/sos/parser.py | SoS_Step.show | def show(self):
'''Output for command sos show'''
textWidth = max(60, shutil.get_terminal_size((80, 20)).columns)
text = f' {self.step_name() + ":":<21} ' + self.comment
print('\n'.join(
textwrap.wrap(
text,
width=textWidth,
in... | python | def show(self):
'''Output for command sos show'''
textWidth = max(60, shutil.get_terminal_size((80, 20)).columns)
text = f' {self.step_name() + ":":<21} ' + self.comment
print('\n'.join(
textwrap.wrap(
text,
width=textWidth,
in... | [
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vatlab/SoS | src/sos/parser.py | SoS_Workflow.extend | def extend(self, workflow: 'SoS_Workflow') -> None:
'''Append another workflow to existing one to created a combined workflow'''
# all sections are simply appended ...
# but we will need to make sure that the new workflow is
# executed after the previous one.
if not workflow.sect... | python | def extend(self, workflow: 'SoS_Workflow') -> None:
'''Append another workflow to existing one to created a combined workflow'''
# all sections are simply appended ...
# but we will need to make sure that the new workflow is
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vatlab/SoS | src/sos/parser.py | SoS_Script.add_comment | def add_comment(self, line: str) -> None:
'''Keeping track of "last comment" for section and parameter '''
# the rule is like
#
# # comment line --> add to last comment
# blank line --> clears last comment
# [ ] --> use last comment
# parameter: --> use last comm... | python | def add_comment(self, line: str) -> None:
'''Keeping track of "last comment" for section and parameter '''
# the rule is like
#
# # comment line --> add to last comment
# blank line --> clears last comment
# [ ] --> use last comment
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vatlab/SoS | src/sos/parser.py | SoS_Script.workflow | def workflow(self,
workflow_name: Optional[str] = None,
use_default: bool = True) -> SoS_Workflow:
'''Return a workflow with name_step+name_step specified in wf_name
This function might be called recursively because of nested
workflow.'''
if workflow_nam... | python | def workflow(self,
workflow_name: Optional[str] = None,
use_default: bool = True) -> SoS_Workflow:
'''Return a workflow with name_step+name_step specified in wf_name
This function might be called recursively because of nested
workflow.'''
if workflow_nam... | [
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vatlab/SoS | src/sos/parser.py | SoS_Script.print_help | def print_help(self, script_name: str):
'''print a help message from the script'''
textWidth = max(60, shutil.get_terminal_size((80, 20)).columns)
if len(script_name) > 20:
print(f'usage: sos run {script_name}')
print(
' [workflow_name | -t ... | python | def print_help(self, script_name: str):
'''print a help message from the script'''
textWidth = max(60, shutil.get_terminal_size((80, 20)).columns)
if len(script_name) > 20:
print(f'usage: sos run {script_name}')
print(
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vatlab/SoS | src/sos/pattern.py | glob_wildcards | def glob_wildcards(pattern: str, files: Optional[List[str]] = None
) -> Dict[str, Union[List[Any], List[str]]]:
"""
Glob the values of the wildcards by matching the given pattern to the filesystem.
Returns a named tuple with a list of values for each wildcard.
"""
pattern = os.path... | python | def glob_wildcards(pattern: str, files: Optional[List[str]] = None
) -> Dict[str, Union[List[Any], List[str]]]:
"""
Glob the values of the wildcards by matching the given pattern to the filesystem.
Returns a named tuple with a list of values for each wildcard.
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vatlab/SoS | src/sos/pattern.py | extract_pattern | def extract_pattern(pattern: str, ifiles: List[str]) -> Dict[str, any]:
'''This function match pattern to a list of input files, extract and return
pieces of filenames as a list of variables with keys defined by pattern.'''
res = glob_wildcards(pattern, [])
for ifile in ifiles:
matched = glob_wi... | python | def extract_pattern(pattern: str, ifiles: List[str]) -> Dict[str, any]:
'''This function match pattern to a list of input files, extract and return
pieces of filenames as a list of variables with keys defined by pattern.'''
res = glob_wildcards(pattern, [])
for ifile in ifiles:
matched = glob_wi... | [
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vatlab/SoS | src/sos/pattern.py | expand_pattern | def expand_pattern(pattern: str) -> List[str]:
'''This function expand patterns against the current namespace
and return a list of filenames'''
ofiles = []
sz = None
res = glob_wildcards(pattern, [])
sz = None
wildcard = [{}]
for key in res.keys():
if key not in env.sos_dict:
... | python | def expand_pattern(pattern: str) -> List[str]:
'''This function expand patterns against the current namespace
and return a list of filenames'''
ofiles = []
sz = None
res = glob_wildcards(pattern, [])
sz = None
wildcard = [{}]
for key in res.keys():
if key not in env.sos_dict:
... | [
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vatlab/SoS | src/sos/eval.py | interpolate | def interpolate(text, global_dict=None, local_dict=None):
'''Evaluate expressions in `text` '''
# step 1, make it a f-string (add quotation marks and f
# step 2, evaluate as a string
try:
return eval(as_fstring(text), global_dict, local_dict)
except Exception as e:
raise ValueError(f... | python | def interpolate(text, global_dict=None, local_dict=None):
'''Evaluate expressions in `text` '''
# step 1, make it a f-string (add quotation marks and f
# step 2, evaluate as a string
try:
return eval(as_fstring(text), global_dict, local_dict)
except Exception as e:
raise ValueError(f... | [
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vatlab/SoS | src/sos/eval.py | SoS_eval | def SoS_eval(expr: str, extra_dict: dict = {}) -> Any:
'''Evaluate an expression with sos dict.'''
return eval(expr, env.sos_dict.dict(), extra_dict) | python | def SoS_eval(expr: str, extra_dict: dict = {}) -> Any:
'''Evaluate an expression with sos dict.'''
return eval(expr, env.sos_dict.dict(), extra_dict) | [
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vatlab/SoS | src/sos/eval.py | SoS_exec | def SoS_exec(script: str, _dict: dict = None,
return_result: bool = True) -> None:
'''Execute a statement.'''
if _dict is None:
_dict = env.sos_dict.dict()
if not return_result:
exec(
compile(script, filename=stmtHash.hash(script), mode='exec'), _dict)
retur... | python | def SoS_exec(script: str, _dict: dict = None,
return_result: bool = True) -> None:
'''Execute a statement.'''
if _dict is None:
_dict = env.sos_dict.dict()
if not return_result:
exec(
compile(script, filename=stmtHash.hash(script), mode='exec'), _dict)
retur... | [
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vatlab/SoS | src/sos/step_executor.py | expand_depends_files | def expand_depends_files(*args, **kwargs):
'''handle directive depends'''
args = [x.resolve() if isinstance(x, dynamic) else x for x in args]
kwargs = {
x: (y.resolve() if isinstance(y, dynamic) else y)
for x, y in kwargs.items()
}
return sos_targets(
*args,
**kwargs,... | python | def expand_depends_files(*args, **kwargs):
'''handle directive depends'''
args = [x.resolve() if isinstance(x, dynamic) else x for x in args]
kwargs = {
x: (y.resolve() if isinstance(y, dynamic) else y)
for x, y in kwargs.items()
}
return sos_targets(
*args,
**kwargs,... | [
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vatlab/SoS | src/sos/step_executor.py | Step_Executor.wait_for_subworkflows | def wait_for_subworkflows(self, workflow_results):
'''Wait for results from subworkflows'''
wf_ids = sum([x['pending_workflows'] for x in workflow_results], [])
for wf_id in wf_ids:
# here we did not check if workflow ids match
yield self.socket
res = self.soc... | python | def wait_for_subworkflows(self, workflow_results):
'''Wait for results from subworkflows'''
wf_ids = sum([x['pending_workflows'] for x in workflow_results], [])
for wf_id in wf_ids:
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vatlab/SoS | src/sos/actions_r.py | Rmarkdown | def Rmarkdown(script=None,
input=None,
output=None,
args='{input:r}, output_file={output:ar}',
**kwargs):
'''Convert input file to output using Rmarkdown
The input can be specified in three ways:
1. instant script, which is assumed to be in md format... | python | def Rmarkdown(script=None,
input=None,
output=None,
args='{input:r}, output_file={output:ar}',
**kwargs):
'''Convert input file to output using Rmarkdown
The input can be specified in three ways:
1. instant script, which is assumed to be in md format... | [
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vatlab/SoS | src/sos/docker/client.py | SoS_DockerClient.total_memory | def total_memory(self, image='ubuntu'):
'''Get the available ram fo the docker machine in Kb'''
try:
ret = subprocess.check_output(
f'''docker run -t {image} cat /proc/meminfo | grep MemTotal''',
shell=True,
stdin=subprocess.DEVNULL)
... | python | def total_memory(self, image='ubuntu'):
'''Get the available ram fo the docker machine in Kb'''
try:
ret = subprocess.check_output(
f'''docker run -t {image} cat /proc/meminfo | grep MemTotal''',
shell=True,
stdin=subprocess.DEVNULL)
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vatlab/SoS | src/sos/actions.py | script | def script(script, interpreter='', suffix='', args='', **kwargs):
'''Execute specified script using specified interpreter. This action accepts common
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content of one or more files specified by option input would be prepend... | python | def script(script, interpreter='', suffix='', args='', **kwargs):
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vatlab/SoS | src/sos/actions.py | stop_if | def stop_if(expr, msg='', no_output=False):
'''Abort the execution of the current step or loop and yield
an warning message `msg` if `expr` is False '''
if expr:
raise StopInputGroup(msg=msg, keep_output=not no_output)
return 0 | python | def stop_if(expr, msg='', no_output=False):
'''Abort the execution of the current step or loop and yield
an warning message `msg` if `expr` is False '''
if expr:
raise StopInputGroup(msg=msg, keep_output=not no_output)
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vatlab/SoS | src/sos/actions.py | download | def download(URLs, dest_dir='.', dest_file=None, decompress=False, max_jobs=5):
'''Download files from specified URL, which should be space, tab or
newline separated URLs. The files will be downloaded to specified
destination. If `filename.md5` files are downloaded, they are used to
validate downloaded ... | python | def download(URLs, dest_dir='.', dest_file=None, decompress=False, max_jobs=5):
'''Download files from specified URL, which should be space, tab or
newline separated URLs. The files will be downloaded to specified
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vatlab/SoS | src/sos/actions.py | run | def run(script, args='', **kwargs):
'''Execute specified script using bash. This action accepts common action arguments such as
input, active, workdir, docker_image and args. In particular, content of one or more files
specified by option input would be prepended before the specified script.'''
if sys.p... | python | def run(script, args='', **kwargs):
'''Execute specified script using bash. This action accepts common action arguments such as
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vatlab/SoS | src/sos/actions.py | pandoc | def pandoc(script=None,
input=None,
output=None,
args='{input:q} --output {output:q}',
**kwargs):
'''Convert input file to output using pandoc
The input can be specified in three ways:
1. instant script, which is assumed to be in md format
pandoc: output=... | python | def pandoc(script=None,
input=None,
output=None,
args='{input:q} --output {output:q}',
**kwargs):
'''Convert input file to output using pandoc
The input can be specified in three ways:
1. instant script, which is assumed to be in md format
pandoc: output=... | [
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vatlab/SoS | src/sos/section_analyzer.py | get_changed_vars | def get_changed_vars(section: SoS_Step):
'''changed vars are variables that are "shared" and therefore "provides"
to others '''
if 'shared' not in section.options:
return set()
changed_vars = set()
svars = section.options['shared']
if isinstance(svars, str):
changed_vars.add(sva... | python | def get_changed_vars(section: SoS_Step):
'''changed vars are variables that are "shared" and therefore "provides"
to others '''
if 'shared' not in section.options:
return set()
changed_vars = set()
svars = section.options['shared']
if isinstance(svars, str):
changed_vars.add(sva... | [
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vatlab/SoS | src/sos/section_analyzer.py | get_all_used_vars | def get_all_used_vars(section):
'''Get variables which are variables used by input statement and statements before it'''
all_used_vars = set()
for statement in section.statements:
if statement[0] == '=':
all_used_vars |= accessed_vars('='.join(statement[1:3]))
elif statement[0] =... | python | def get_all_used_vars(section):
'''Get variables which are variables used by input statement and statements before it'''
all_used_vars = set()
for statement in section.statements:
if statement[0] == '=':
all_used_vars |= accessed_vars('='.join(statement[1:3]))
elif statement[0] =... | [
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vatlab/SoS | src/sos/section_analyzer.py | get_signature_vars | def get_signature_vars(section):
'''Get signature variables which are variables that will be
saved with step signatures'''
# signature vars should contain parameters defined in global section
# #1155
signature_vars = set(
section.parameters.keys()
& accessed_vars(strip_param_defs(se... | python | def get_signature_vars(section):
'''Get signature variables which are variables that will be
saved with step signatures'''
# signature vars should contain parameters defined in global section
# #1155
signature_vars = set(
section.parameters.keys()
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vatlab/SoS | src/sos/section_analyzer.py | get_step_input | def get_step_input(section, default_input):
'''Find step input
'''
step_input: sos_targets = sos_targets()
dynamic_input = True
# look for input statement.
input_idx = find_statement(section, 'input')
if input_idx is None:
return step_input, dynamic_input
# input statement
... | python | def get_step_input(section, default_input):
'''Find step input
'''
step_input: sos_targets = sos_targets()
dynamic_input = True
# look for input statement.
input_idx = find_statement(section, 'input')
if input_idx is None:
return step_input, dynamic_input
# input statement
... | [
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