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9,500 | 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.'''
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)]) | [
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9,501 | 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[
'SOS_DEBUG']:
env.log_to_file(
... | python | 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[
'SOS_DEBUG']:
env.log_to_file(
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9,502 | 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():
# if k.isupper():
# self._check_readonly(k, v)
if env.verbosity > 2:
self._log(k, v) | [
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9,503 | 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
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global_def,
global_vars,
task='',
task_params='',
proc_vars={},
shared_vars=[],
config={}):
'''Execute a substep with specific input etc
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9,504 | 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"'
)
return [(x[0], eval(x[1])) for x in cur.... | [
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9,505 | 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')
for node in self.nodes():
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9,506 | 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 = []
if env.config['trace_existing']:
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9,507 | 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')
# first, find all nodes with targets
subnodes = []
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9,508 | 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):
'''Connect nodes according to status of targets'''
# right now we do not worry about status of nodes
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9,509 | 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]
# we only monitor ru... | python | 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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9,510 | 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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9,511 | 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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9,512 | 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)
return 0 if leading is None else len(leading.group(2)) | [
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9,513 | 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():
if not self.values:
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9,514 | 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
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... | [
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9,515 | 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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9,516 | 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]
else:
self.values.append(line)
if self... | python | 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]
else:
self.values.append(line)
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9,517 | 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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9,518 | 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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9,519 | 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
# executed after the previous one.
if not workflow.sect... | [
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9,520 | 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
# parameter: --> use last comm... | [
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9,521 | 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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9,522 | 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(
' [workflow_name | -t ... | [
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9,523 | 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.
"""
pattern = os.path... | [
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9,524 | 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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9,525 | 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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9,526 | 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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9,527 | 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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9,528 | 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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9,529 | 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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9,530 | 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
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'''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
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9,531 | 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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9,532 | 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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9,533 | vatlab/SoS | src/sos/actions.py | script | def script(script, interpreter='', suffix='', args='', **kwargs):
'''Execute specified script using specified interpreter. 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 prepend... | python | def script(script, interpreter='', suffix='', args='', **kwargs):
'''Execute specified script using specified interpreter. This action accepts common
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9,534 | 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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9,535 | 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
destination. If `filename.md5` files are downloaded, they are used to
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9,536 | 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
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... | [
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9,537 | 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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9,538 | 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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9,539 | 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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9,540 | 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()
& accessed_vars(strip_param_defs(se... | [
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9,541 | 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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9,542 | vatlab/SoS | src/sos/section_analyzer.py | get_step_output | def get_step_output(section, default_output):
'''determine step output'''
step_output: sos_targets = sos_targets()
#
if 'provides' in section.options and default_output:
step_output = default_output
# look for input statement.
output_idx = find_statement(section, 'output')
if output... | python | def get_step_output(section, default_output):
'''determine step output'''
step_output: sos_targets = sos_targets()
#
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step_output = default_output
# look for input statement.
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9,543 | vatlab/SoS | src/sos/section_analyzer.py | analyze_section | def analyze_section(section: SoS_Step,
default_input: Optional[sos_targets] = None,
default_output: Optional[sos_targets] = None,
context={},
vars_and_output_only: bool = False) -> Dict[str, Any]:
'''Analyze a section for how it uses in... | python | def analyze_section(section: SoS_Step,
default_input: Optional[sos_targets] = None,
default_output: Optional[sos_targets] = None,
context={},
vars_and_output_only: bool = False) -> Dict[str, Any]:
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9,544 | vatlab/SoS | src/sos/converter.py | extract_workflow | def extract_workflow(notebook):
'''Extract workflow from a notebook file or notebook JSON instance'''
if isinstance(notebook, str):
nb = nbformat.read(notebook, nbformat.NO_CONVERT)
else:
nb = notebook
cells = nb.cells
content = '#!/usr/bin/env sos-runner\n#fileformat=SOS1.0\n\n'
... | python | def extract_workflow(notebook):
'''Extract workflow from a notebook file or notebook JSON instance'''
if isinstance(notebook, str):
nb = nbformat.read(notebook, nbformat.NO_CONVERT)
else:
nb = notebook
cells = nb.cells
content = '#!/usr/bin/env sos-runner\n#fileformat=SOS1.0\n\n'
... | [
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9,545 | vatlab/SoS | misc/vim-ipython/vim_ipython.py | vim_ipython_is_open | def vim_ipython_is_open():
"""
Helper function to let us know if the vim-ipython shell is currently
visible
"""
for w in vim.windows:
if w.buffer.name is not None and w.buffer.name.endswith("vim-ipython"):
return True
return False | python | def vim_ipython_is_open():
"""
Helper function to let us know if the vim-ipython shell is currently
visible
"""
for w in vim.windows:
if w.buffer.name is not None and w.buffer.name.endswith("vim-ipython"):
return True
return False | [
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9,546 | vatlab/SoS | misc/vim-ipython/vim_ipython.py | with_subchannel | def with_subchannel(f,*args):
"conditionally monitor subchannel"
def f_with_update(*args):
try:
f(*args)
if monitor_subchannel:
update_subchannel_msgs(force=True)
except AttributeError: #if kc is None
echo("not connected to IPython", 'Error')
... | python | def with_subchannel(f,*args):
"conditionally monitor subchannel"
def f_with_update(*args):
try:
f(*args)
if monitor_subchannel:
update_subchannel_msgs(force=True)
except AttributeError: #if kc is None
echo("not connected to IPython", 'Error')
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9,547 | vatlab/SoS | misc/vim-ipython/vim_ipython.py | set_pid | def set_pid():
"""
Explicitly ask the ipython kernel for its pid
"""
global pid
lines = '\n'.join(['import os', '_pid = os.getpid()'])
try:
msg_id = send(lines, silent=True, user_variables=['_pid'])
except TypeError: # change in IPython 3.0+
msg_id = send(lines, silent=True,... | python | def set_pid():
"""
Explicitly ask the ipython kernel for its pid
"""
global pid
lines = '\n'.join(['import os', '_pid = os.getpid()'])
try:
msg_id = send(lines, silent=True, user_variables=['_pid'])
except TypeError: # change in IPython 3.0+
msg_id = send(lines, silent=True,... | [
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9,548 | BradRuderman/pyhs2 | pyhs2/cursor.py | Cursor.fetchmany | def fetchmany(self,size=-1):
""" return a sequential set of records. This is guaranteed by locking,
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this has the side effect that other threads may have to wait for
an arbitrary long time for the completion of the curre... | python | def fetchmany(self,size=-1):
""" return a sequential set of records. This is guaranteed by locking,
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9,549 | kashifrazzaqui/json-streamer | jsonstreamer/jsonstreamer.py | JSONStreamer.on_number | def on_number(self, ctx, value):
''' Since this is defined both integer and double callbacks are useless '''
value = int(value) if value.isdigit() else float(value)
top = self._stack[-1]
if top is JSONCompositeType.OBJECT:
self.fire(JSONStreamer.VALUE_EVENT, value)
el... | python | def on_number(self, ctx, value):
''' Since this is defined both integer and double callbacks are useless '''
value = int(value) if value.isdigit() else float(value)
top = self._stack[-1]
if top is JSONCompositeType.OBJECT:
self.fire(JSONStreamer.VALUE_EVENT, value)
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9,550 | kashifrazzaqui/json-streamer | jsonstreamer/jsonstreamer.py | JSONStreamer.close | def close(self):
"""Closes the streamer which causes a `DOC_END_EVENT` to be fired and frees up memory used by yajl"""
self.fire(JSONStreamer.DOC_END_EVENT)
self._stack = None
self._parser.close() | python | def close(self):
"""Closes the streamer which causes a `DOC_END_EVENT` to be fired and frees up memory used by yajl"""
self.fire(JSONStreamer.DOC_END_EVENT)
self._stack = None
self._parser.close() | [
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9,551 | paolodragone/pymzn | pymzn/mzn/aio/minizinc.py | minizinc | async def minizinc(
mzn, *dzn_files, args=None, data=None, include=None, stdlib_dir=None,
globals_dir=None, declare_enums=True, allow_multiple_assignments=False,
keep=False, output_vars=None, output_base=None, output_mode='dict',
solver=None, timeout=None, two_pass=None, pre_passes=None,
output_obje... | python | async def minizinc(
mzn, *dzn_files, args=None, data=None, include=None, stdlib_dir=None,
globals_dir=None, declare_enums=True, allow_multiple_assignments=False,
keep=False, output_vars=None, output_base=None, output_mode='dict',
solver=None, timeout=None, two_pass=None, pre_passes=None,
output_obje... | [
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Parameters
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max_queue_size : int
Maximum number of solutions in the queue between the solution parser and
the returned solution stream. When the queue is full, the solver
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9,552 | paolodragone/pymzn | pymzn/dzn/parse.py | parse_value | def parse_value(val, var_type=None, enums=None, rebase_arrays=True):
"""Parses the value of a dzn statement.
Parameters
----------
val : str
A value in dzn format.
var_type : dict
The dictionary of variable type as returned by the command ``minizinc
--model-types-only``. Def... | python | def parse_value(val, var_type=None, enums=None, rebase_arrays=True):
"""Parses the value of a dzn statement.
Parameters
----------
val : str
A value in dzn format.
var_type : dict
The dictionary of variable type as returned by the command ``minizinc
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9,553 | paolodragone/pymzn | pymzn/dzn/parse.py | dzn2dict | def dzn2dict(dzn, *, rebase_arrays=True, types=None, return_enums=False):
"""Parses a dzn string or file into a dictionary of variable assignments.
Parameters
----------
dzn : str
A dzn content string or a path to a dzn file.
rebase_arrays : bool
Whether to return arrays as zero-bas... | python | def dzn2dict(dzn, *, rebase_arrays=True, types=None, return_enums=False):
"""Parses a dzn string or file into a dictionary of variable assignments.
Parameters
----------
dzn : str
A dzn content string or a path to a dzn file.
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Whether to return arrays as zero-bas... | [
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9,554 | paolodragone/pymzn | pymzn/mzn/solvers.py | Solver.args | def args(
self, all_solutions=False, num_solutions=None, free_search=False,
parallel=None, seed=None, **kwargs
):
"""Returns a list of command line arguments for the specified options.
If the solver parser is able to parse statistics, this function should
always add options ... | python | def args(
self, all_solutions=False, num_solutions=None, free_search=False,
parallel=None, seed=None, **kwargs
):
"""Returns a list of command line arguments for the specified options.
If the solver parser is able to parse statistics, this function should
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9,555 | paolodragone/pymzn | pymzn/log.py | debug | def debug(dbg=True):
"""Enables or disables debugging messages on the standard output."""
global _debug_handler
if dbg and _debug_handler is None:
_debug_handler = logging.StreamHandler()
logger.addHandler(_debug_handler)
logger.setLevel(logging.DEBUG)
elif not dbg and _debug_han... | python | def debug(dbg=True):
"""Enables or disables debugging messages on the standard output."""
global _debug_handler
if dbg and _debug_handler is None:
_debug_handler = logging.StreamHandler()
logger.addHandler(_debug_handler)
logger.setLevel(logging.DEBUG)
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9,556 | paolodragone/pymzn | pymzn/mzn/minizinc.py | minizinc_version | def minizinc_version():
"""Returns the version of the found minizinc executable."""
vs = _run_minizinc('--version')
m = re.findall('version ([\d\.]+)', vs)
if not m:
raise RuntimeError('MiniZinc executable not found.')
return m[0] | python | def minizinc_version():
"""Returns the version of the found minizinc executable."""
vs = _run_minizinc('--version')
m = re.findall('version ([\d\.]+)', vs)
if not m:
raise RuntimeError('MiniZinc executable not found.')
return m[0] | [
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9,557 | paolodragone/pymzn | pymzn/mzn/minizinc.py | preprocess_model | def preprocess_model(model, rewrap=True, **kwargs):
"""Preprocess a MiniZinc model.
This function takes care of preprocessing the model by resolving the
template using the arguments passed as keyword arguments to this function.
Optionally, this function can also "rewrap" the model, deleting spaces at
... | python | def preprocess_model(model, rewrap=True, **kwargs):
"""Preprocess a MiniZinc model.
This function takes care of preprocessing the model by resolving the
template using the arguments passed as keyword arguments to this function.
Optionally, this function can also "rewrap" the model, deleting spaces at
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9,558 | paolodragone/pymzn | pymzn/mzn/minizinc.py | save_model | def save_model(model, output_file=None, output_dir=None, output_prefix='pymzn'):
"""Save a model to file.
Parameters
----------
model : str
The minizinc model (i.e. the content of a ``.mzn`` file).
output_file : str
The path to the output file. If this parameter is ``None`` (default... | python | def save_model(model, output_file=None, output_dir=None, output_prefix='pymzn'):
"""Save a model to file.
Parameters
----------
model : str
The minizinc model (i.e. the content of a ``.mzn`` file).
output_file : str
The path to the output file. If this parameter is ``None`` (default... | [
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9,559 | paolodragone/pymzn | pymzn/mzn/minizinc.py | check_instance | def check_instance(
mzn, *dzn_files, data=None, include=None, stdlib_dir=None, globals_dir=None,
allow_multiple_assignments=False
):
"""Perform instance checking on a model + data.
This function calls the command ``minizinc --instance-check-only`` to check
for consistency of the given model + data.... | python | def check_instance(
mzn, *dzn_files, data=None, include=None, stdlib_dir=None, globals_dir=None,
allow_multiple_assignments=False
):
"""Perform instance checking on a model + data.
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for consistency of the given model + data.
Parameters
----------
mzn : str
The minizinc model. This can be either the path to the ``.mzn`` file or
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9,560 | paolodragone/pymzn | pymzn/mzn/minizinc.py | check_model | def check_model(
mzn, *, include=None, stdlib_dir=None, globals_dir=None
):
"""Perform model checking on a given model.
This function calls the command ``minizinc --model-check-only`` to check
for consistency of the given model.
Parameters
----------
mzn : str
The minizinc model. T... | python | def check_model(
mzn, *, include=None, stdlib_dir=None, globals_dir=None
):
"""Perform model checking on a given model.
This function calls the command ``minizinc --model-check-only`` to check
for consistency of the given model.
Parameters
----------
mzn : str
The minizinc model. T... | [
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9,561 | paolodragone/pymzn | pymzn/mzn/minizinc.py | minizinc | def minizinc(
mzn, *dzn_files, args=None, data=None, include=None, stdlib_dir=None,
globals_dir=None, declare_enums=True, allow_multiple_assignments=False,
keep=False, output_vars=None, output_base=None, output_mode='dict',
solver=None, timeout=None, two_pass=None, pre_passes=None,
output_objective=... | python | def minizinc(
mzn, *dzn_files, args=None, data=None, include=None, stdlib_dir=None,
globals_dir=None, declare_enums=True, allow_multiple_assignments=False,
keep=False, output_vars=None, output_base=None, output_mode='dict',
solver=None, timeout=None, two_pass=None, pre_passes=None,
output_objective=... | [
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*dzn_files
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9,562 | paolodragone/pymzn | pymzn/mzn/minizinc.py | solve | def solve(
solver, mzn, *dzn_files, data=None, include=None, stdlib_dir=None,
globals_dir=None, allow_multiple_assignments=False, output_mode='item',
timeout=None, two_pass=None, pre_passes=None, output_objective=False,
non_unique=False, all_solutions=False, num_solutions=None,
free_search=False, pa... | python | def solve(
solver, mzn, *dzn_files, data=None, include=None, stdlib_dir=None,
globals_dir=None, allow_multiple_assignments=False, output_mode='item',
timeout=None, two_pass=None, pre_passes=None, output_objective=False,
non_unique=False, all_solutions=False, num_solutions=None,
free_search=False, pa... | [
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solver : Solver
The ``Solver`` instance to use.
mzn : str
The path to the minizinc model file.
*dzn_files
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9,563 | paolodragone/pymzn | pymzn/mzn/minizinc.py | mzn2fzn | def mzn2fzn(
mzn, *dzn_files, args=None, data=None, include=None, stdlib_dir=None,
globals_dir=None, declare_enums=True, allow_multiple_assignments=False,
keep=False, output_vars=None, output_base=None, output_mode='item',
no_ozn=False
):
"""Flatten a MiniZinc model into a FlatZinc one.
This fu... | python | def mzn2fzn(
mzn, *dzn_files, args=None, data=None, include=None, stdlib_dir=None,
globals_dir=None, declare_enums=True, allow_multiple_assignments=False,
keep=False, output_vars=None, output_base=None, output_mode='item',
no_ozn=False
):
"""Flatten a MiniZinc model into a FlatZinc one.
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This function is equivalent to the command ``minizinc --compile``.
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mzn : str
The minizinc model. This can be either the path to the ``.mzn`` file or
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9,564 | paolodragone/pymzn | pymzn/mzn/output.py | Solutions.print | def print(self, output_file=sys.stdout, log=False):
"""Print the solution stream"""
for soln in iter(self):
print(soln, file=output_file)
print(SOLN_SEP, file=output_file)
if self.status == 0:
print(SEARCH_COMPLETE, file=output_file)
if (self.status... | python | def print(self, output_file=sys.stdout, log=False):
"""Print the solution stream"""
for soln in iter(self):
print(soln, file=output_file)
print(SOLN_SEP, file=output_file)
if self.status == 0:
print(SEARCH_COMPLETE, file=output_file)
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9,565 | paolodragone/pymzn | pymzn/config.py | Config.dump | def dump(self):
"""Writes the changes to the configuration file."""
try:
import yaml
cfg_file = self._cfg_file()
cfg_dir, __ = os.path.split(cfg_file)
os.makedirs(cfg_dir, exist_ok=True)
with open(cfg_file, 'w') as f:
yaml.dump(... | python | def dump(self):
"""Writes the changes to the configuration file."""
try:
import yaml
cfg_file = self._cfg_file()
cfg_dir, __ = os.path.split(cfg_file)
os.makedirs(cfg_dir, exist_ok=True)
with open(cfg_file, 'w') as f:
yaml.dump(... | [
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9,566 | paolodragone/pymzn | pymzn/mzn/templates.py | discretize | def discretize(value, factor=100):
"""Discretize the given value, pre-multiplying by the given factor"""
if not isinstance(value, Iterable):
return int(value * factor)
int_value = list(deepcopy(value))
for i in range(len(int_value)):
int_value[i] = int(int_value[i] * factor)
return i... | python | def discretize(value, factor=100):
"""Discretize the given value, pre-multiplying by the given factor"""
if not isinstance(value, Iterable):
return int(value * factor)
int_value = list(deepcopy(value))
for i in range(len(int_value)):
int_value[i] = int(int_value[i] * factor)
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9,567 | paolodragone/pymzn | pymzn/mzn/templates.py | from_string | def from_string(source, args=None):
"""Renders a template string"""
if _has_jinja:
logger.info('Precompiling model with arguments: {}'.format(args))
return _jenv.from_string(source).render(args or {})
if args:
raise RuntimeError(_except_text)
return source | python | def from_string(source, args=None):
"""Renders a template string"""
if _has_jinja:
logger.info('Precompiling model with arguments: {}'.format(args))
return _jenv.from_string(source).render(args or {})
if args:
raise RuntimeError(_except_text)
return source | [
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9,568 | paolodragone/pymzn | pymzn/mzn/templates.py | add_package | def add_package(package_name, package_path='templates', encoding='utf-8'):
"""Adds the given package to the template search routine"""
if not _has_jinja:
raise RuntimeError(_except_text)
_jload.add_loader(PackageLoader(package_name, package_path, encoding)) | python | def add_package(package_name, package_path='templates', encoding='utf-8'):
"""Adds the given package to the template search routine"""
if not _has_jinja:
raise RuntimeError(_except_text)
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9,569 | paolodragone/pymzn | pymzn/mzn/templates.py | add_path | def add_path(searchpath, encoding='utf-8', followlinks=False):
"""Adds the given path to the template search routine"""
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raise RuntimeError(_except_text)
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"""Adds the given path to the template search routine"""
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raise RuntimeError(_except_text)
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9,570 | paolodragone/pymzn | pymzn/dzn/marsh.py | val2dzn | def val2dzn(val, wrap=True):
"""Serializes a value into its dzn representation.
The supported types are ``bool``, ``int``, ``float``, ``set``, ``array``.
Parameters
----------
val
The value to serialize
wrap : bool
Whether to wrap the serialized value.
Returns
-------
... | python | def val2dzn(val, wrap=True):
"""Serializes a value into its dzn representation.
The supported types are ``bool``, ``int``, ``float``, ``set``, ``array``.
Parameters
----------
val
The value to serialize
wrap : bool
Whether to wrap the serialized value.
Returns
-------
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9,571 | paolodragone/pymzn | pymzn/dzn/marsh.py | stmt2dzn | def stmt2dzn(name, val, declare=True, assign=True, wrap=True):
"""Returns a dzn statement declaring and assigning the given value.
Parameters
----------
val
The value to serialize.
declare : bool
Whether to include the declaration of the variable in the statement or
just the... | python | def stmt2dzn(name, val, declare=True, assign=True, wrap=True):
"""Returns a dzn statement declaring and assigning the given value.
Parameters
----------
val
The value to serialize.
declare : bool
Whether to include the declaration of the variable in the statement or
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9,572 | paolodragone/pymzn | pymzn/dzn/marsh.py | stmt2enum | def stmt2enum(enum_type, declare=True, assign=True, wrap=True):
"""Returns a dzn enum declaration from an enum type.
Parameters
----------
enum_type : Enum
The enum to serialize.
declare : bool
Whether to include the ``enum`` declatation keyword in the statement or
just the ... | python | def stmt2enum(enum_type, declare=True, assign=True, wrap=True):
"""Returns a dzn enum declaration from an enum type.
Parameters
----------
enum_type : Enum
The enum to serialize.
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Whether to include the ``enum`` declatation keyword in the statement or
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9,573 | paolodragone/pymzn | pymzn/dzn/marsh.py | dict2dzn | def dict2dzn(
objs, declare=False, assign=True, declare_enums=True, wrap=True, fout=None
):
"""Serializes the objects in input and produces a list of strings encoding
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Supported types of objects include: ``str``, ``int``, ``float``... | python | def dict2dzn(
objs, declare=False, assign=True, declare_enums=True, wrap=True, fout=None
):
"""Serializes the objects in input and produces a list of strings encoding
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Supported types of objects include: ``str``, ``int``, ``float``, ``set``,
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9,574 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.async_or_eager | def async_or_eager(self, **options):
"""
Attempt to call self.apply_async, or if that fails because of a problem
with the broker, run the task eagerly and return an EagerResult.
"""
args = options.pop("args", None)
kwargs = options.pop("kwargs", None)
possible_bro... | python | def async_or_eager(self, **options):
"""
Attempt to call self.apply_async, or if that fails because of a problem
with the broker, run the task eagerly and return an EagerResult.
"""
args = options.pop("args", None)
kwargs = options.pop("kwargs", None)
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9,575 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.async_or_fail | def async_or_fail(self, **options):
"""
Attempt to call self.apply_async, but if that fails with an exception,
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allows us to seamlessly handle errors on task creation the same way we
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"""
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9,576 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.delay_or_eager | def delay_or_eager(self, *args, **kwargs):
"""
Wrap async_or_eager with a convenience signiture like delay
"""
return self.async_or_eager(args=args, kwargs=kwargs) | python | def delay_or_eager(self, *args, **kwargs):
"""
Wrap async_or_eager with a convenience signiture like delay
"""
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9,577 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.delay_or_run | def delay_or_run(self, *args, **kwargs):
"""
Attempt to call self.delay, or if that fails, call self.run.
Returns a tuple, (result, required_fallback). ``result`` is the result
of calling delay or run. ``required_fallback`` is True if the broker
failed we had to resort to `self.... | python | def delay_or_run(self, *args, **kwargs):
"""
Attempt to call self.delay, or if that fails, call self.run.
Returns a tuple, (result, required_fallback). ``result`` is the result
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9,578 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.delay_or_fail | def delay_or_fail(self, *args, **kwargs):
"""
Wrap async_or_fail with a convenience signiture like delay
"""
return self.async_or_fail(args=args, kwargs=kwargs) | python | def delay_or_fail(self, *args, **kwargs):
"""
Wrap async_or_fail with a convenience signiture like delay
"""
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9,579 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.simulate_async_error | def simulate_async_error(self, exception):
"""
Take this exception and store it as an error in the result backend.
This unifies the handling of broker-connection errors with any other
type of error that might occur when running the task. So the same
error-handling that might retr... | python | def simulate_async_error(self, exception):
"""
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9,580 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.calc_progress | def calc_progress(self, completed_count, total_count):
"""
Calculate the percentage progress and estimated remaining time based on
the current number of items completed of the total.
Returns a tuple of ``(percentage_complete, seconds_remaining)``.
"""
self.logger.debug(
... | python | def calc_progress(self, completed_count, total_count):
"""
Calculate the percentage progress and estimated remaining time based on
the current number of items completed of the total.
Returns a tuple of ``(percentage_complete, seconds_remaining)``.
"""
self.logger.debug(
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9,581 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.update_progress | def update_progress(
self,
completed_count,
total_count,
update_frequency=1,
):
"""
Update the task backend with both an estimated percentage complete and
number of seconds remaining until completion.
``completed_count`` Number of task "units" that ha... | python | def update_progress(
self,
completed_count,
total_count,
update_frequency=1,
):
"""
Update the task backend with both an estimated percentage complete and
number of seconds remaining until completion.
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9,582 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask._validate_required_class_vars | def _validate_required_class_vars(self):
"""
Ensure that this subclass has defined all of the required class
variables.
"""
required_members = (
'significant_kwargs',
'herd_avoidance_timeout',
)
for required_member in required_members:
... | python | def _validate_required_class_vars(self):
"""
Ensure that this subclass has defined all of the required class
variables.
"""
required_members = (
'significant_kwargs',
'herd_avoidance_timeout',
)
for required_member in required_members:
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9,583 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask.on_success | def on_success(self, retval, task_id, args, kwargs):
"""
Store results in the backend even if we're always eager. This ensures
the `delay_or_run` calls always at least have results.
"""
if self.request.is_eager:
# Store the result because celery wouldn't otherwise
... | python | def on_success(self, retval, task_id, args, kwargs):
"""
Store results in the backend even if we're always eager. This ensures
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"""
if self.request.is_eager:
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9,584 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask._get_cache | def _get_cache(self):
"""
Return the cache to use for thundering herd protection, etc.
"""
if not self._cache:
self._cache = get_cache(self.app)
return self._cache | python | def _get_cache(self):
"""
Return the cache to use for thundering herd protection, etc.
"""
if not self._cache:
self._cache = get_cache(self.app)
return self._cache | [
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9,585 | PolicyStat/jobtastic | jobtastic/task.py | JobtasticTask._get_cache_key | def _get_cache_key(self, **kwargs):
"""
Take this task's configured ``significant_kwargs`` and build a hash
that all equivalent task calls will match.
Takes in kwargs and returns a string.
To change the way the cache key is generated or do more in-depth
processing, over... | python | def _get_cache_key(self, **kwargs):
"""
Take this task's configured ``significant_kwargs`` and build a hash
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Takes in kwargs and returns a string.
To change the way the cache key is generated or do more in-depth
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9,586 | PolicyStat/jobtastic | jobtastic/cache/__init__.py | get_cache | def get_cache(app):
"""
Attempt to find a valid cache from the Celery configuration
If the setting is a valid cache, just use it.
Otherwise, if Django is installed, then:
If the setting is a valid Django cache entry, then use that.
If the setting is empty use the default cache
Other... | python | def get_cache(app):
"""
Attempt to find a valid cache from the Celery configuration
If the setting is a valid cache, just use it.
Otherwise, if Django is installed, then:
If the setting is a valid Django cache entry, then use that.
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9,587 | dodger487/dplython | dplython/dplython.py | select | def select(*args):
"""Select specific columns from DataFrame.
Output will be DplyFrame type. Order of columns will be the same as input into
select.
>>> diamonds >> select(X.color, X.carat) >> head(3)
Out:
color carat
0 E 0.23
1 E 0.21
2 E 0.23
Grouping variables are implied... | python | def select(*args):
"""Select specific columns from DataFrame.
Output will be DplyFrame type. Order of columns will be the same as input into
select.
>>> diamonds >> select(X.color, X.carat) >> head(3)
Out:
color carat
0 E 0.23
1 E 0.21
2 E 0.23
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9,588 | dodger487/dplython | dplython/dplython.py | arrange | def arrange(*args):
"""Sort DataFrame by the input column arguments.
>>> diamonds >> sample_n(5) >> arrange(X.price) >> select(X.depth, X.price)
Out:
depth price
28547 61.0 675
35132 59.1 889
42526 61.3 1323
3468 61.6 3392
23829 62.0 11903
"""
names = [column._name f... | python | def arrange(*args):
"""Sort DataFrame by the input column arguments.
>>> diamonds >> sample_n(5) >> arrange(X.price) >> select(X.depth, X.price)
Out:
depth price
28547 61.0 675
35132 59.1 889
42526 61.3 1323
3468 61.6 3392
23829 62.0 11903
"""
names = [column._name f... | [
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>>> diamonds >> sample_n(5) >> arrange(X.price) >> select(X.depth, X.price)
Out:
depth price
28547 61.0 675
35132 59.1 889
42526 61.3 1323
3468 61.6 3392
23829 62.0 11903 | [
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9,589 | dodger487/dplython | dplython/dplython.py | rename | def rename(**kwargs):
"""Rename one or more columns, leaving other columns unchanged
Example usage:
diamonds >> rename(new_name=old_name)
"""
def rename_columns(df):
column_assignments = {old_name_later._name: new_name
for new_name, old_name_later in kwargs.items()}
return... | python | def rename(**kwargs):
"""Rename one or more columns, leaving other columns unchanged
Example usage:
diamonds >> rename(new_name=old_name)
"""
def rename_columns(df):
column_assignments = {old_name_later._name: new_name
for new_name, old_name_later in kwargs.items()}
return... | [
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9,590 | dodger487/dplython | dplython/dplython.py | transmute | def transmute(*args, **kwargs):
""" Similar to `select` but allows mutation in column definitions.
In : (diamonds >>
head(3) >>
transmute(new_price=X.price * 2, x_plus_y=X.x + X.y))
Out:
new_price x_plus_y
0 652 7.93
1 652 7.73
2 654 8.... | python | def transmute(*args, **kwargs):
""" Similar to `select` but allows mutation in column definitions.
In : (diamonds >>
head(3) >>
transmute(new_price=X.price * 2, x_plus_y=X.x + X.y))
Out:
new_price x_plus_y
0 652 7.93
1 652 7.73
2 654 8.... | [
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Out:
new_price x_plus_y
0 652 7.93
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9,591 | dodger487/dplython | dplython/dplython.py | get_join_cols | def get_join_cols(by_entry):
""" helper function used for joins
builds left and right join list for join function
"""
left_cols = []
right_cols = []
for col in by_entry:
if isinstance(col, str):
left_cols.append(col)
right_cols.append(col)
else:
left_cols.append(col[0])
right... | python | def get_join_cols(by_entry):
""" helper function used for joins
builds left and right join list for join function
"""
left_cols = []
right_cols = []
for col in by_entry:
if isinstance(col, str):
left_cols.append(col)
right_cols.append(col)
else:
left_cols.append(col[0])
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9,592 | dodger487/dplython | dplython/dplython.py | mutating_join | def mutating_join(*args, **kwargs):
""" generic function for mutating dplyr-style joins
"""
# candidate for improvement
left = args[0]
right = args[1]
if 'by' in kwargs:
left_cols, right_cols = get_join_cols(kwargs['by'])
else:
left_cols, right_cols = None, None
if 'suffixes' in kwargs:
dsuf... | python | def mutating_join(*args, **kwargs):
""" generic function for mutating dplyr-style joins
"""
# candidate for improvement
left = args[0]
right = args[1]
if 'by' in kwargs:
left_cols, right_cols = get_join_cols(kwargs['by'])
else:
left_cols, right_cols = None, None
if 'suffixes' in kwargs:
dsuf... | [
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9,593 | mher/chartkick.py | chartkick/ext.py | ChartExtension._chart_support | def _chart_support(self, name, data, caller, **kwargs):
"template chart support function"
id = 'chart-%s' % next(self.id)
name = self._chart_class_name(name)
options = dict(self.environment.options)
options.update(name=name, id=id)
# jinja2 prepends 'l_' or 'l_{{ n }}'(v... | python | def _chart_support(self, name, data, caller, **kwargs):
"template chart support function"
id = 'chart-%s' % next(self.id)
name = self._chart_class_name(name)
options = dict(self.environment.options)
options.update(name=name, id=id)
# jinja2 prepends 'l_' or 'l_{{ n }}'(v... | [
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9,594 | mher/chartkick.py | chartkick/ext.py | ChartExtension.load_library | def load_library(self):
"loads configuration options"
try:
filename = self.environment.get_template('chartkick.json').filename
except TemplateNotFound:
return {}
else:
options = Options()
options.load(filename)
return options | python | def load_library(self):
"loads configuration options"
try:
filename = self.environment.get_template('chartkick.json').filename
except TemplateNotFound:
return {}
else:
options = Options()
options.load(filename)
return options | [
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9,595 | mher/chartkick.py | chartkick/__init__.py | js | def js():
"returns home directory of js"
return os.path.join(os.path.dirname(os.path.abspath(__file__)), 'js') | python | def js():
"returns home directory of js"
return os.path.join(os.path.dirname(os.path.abspath(__file__)), 'js') | [
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9,596 | mher/chartkick.py | chartkick/templatetags/chartkick.py | parse_options | def parse_options(source):
"""parses chart tag options"""
options = {}
tokens = [t.strip() for t in source.split('=')]
name = tokens[0]
for token in tokens[1:-1]:
value, next_name = token.rsplit(' ', 1)
options[name.strip()] = value
name = next_name
options[name.strip()]... | python | def parse_options(source):
"""parses chart tag options"""
options = {}
tokens = [t.strip() for t in source.split('=')]
name = tokens[0]
for token in tokens[1:-1]:
value, next_name = token.rsplit(' ', 1)
options[name.strip()] = value
name = next_name
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9,597 | BerkeleyAutomation/autolab_core | autolab_core/rigid_transformations.py | RigidTransform.copy | def copy(self):
"""Returns a copy of the RigidTransform.
Returns
-------
:obj:`RigidTransform`
A deep copy of the RigidTransform.
"""
return RigidTransform(np.copy(self.rotation), np.copy(self.translation), self.from_frame, self.to_frame) | python | def copy(self):
"""Returns a copy of the RigidTransform.
Returns
-------
:obj:`RigidTransform`
A deep copy of the RigidTransform.
"""
return RigidTransform(np.copy(self.rotation), np.copy(self.translation), self.from_frame, self.to_frame) | [
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9,598 | BerkeleyAutomation/autolab_core | autolab_core/rigid_transformations.py | RigidTransform._check_valid_rotation | def _check_valid_rotation(self, rotation):
"""Checks that the given rotation matrix is valid.
"""
if not isinstance(rotation, np.ndarray) or not np.issubdtype(rotation.dtype, np.number):
raise ValueError('Rotation must be specified as numeric numpy array')
if len(rotation.sh... | python | def _check_valid_rotation(self, rotation):
"""Checks that the given rotation matrix is valid.
"""
if not isinstance(rotation, np.ndarray) or not np.issubdtype(rotation.dtype, np.number):
raise ValueError('Rotation must be specified as numeric numpy array')
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9,599 | BerkeleyAutomation/autolab_core | autolab_core/rigid_transformations.py | RigidTransform._check_valid_translation | def _check_valid_translation(self, translation):
"""Checks that the translation vector is valid.
"""
if not isinstance(translation, np.ndarray) or not np.issubdtype(translation.dtype, np.number):
raise ValueError('Translation must be specified as numeric numpy array')
t = tr... | python | def _check_valid_translation(self, translation):
"""Checks that the translation vector is valid.
"""
if not isinstance(translation, np.ndarray) or not np.issubdtype(translation.dtype, np.number):
raise ValueError('Translation must be specified as numeric numpy array')
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