repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens listlengths 20 707 | docstring stringlengths 3 17.3k | docstring_tokens listlengths 3 222 | sha stringlengths 40 40 | url stringlengths 87 242 | partition stringclasses 1
value | idx int64 0 252k |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
maykinmedia/django-timeline-logger | timeline_logger/management/commands/report_mailing.py | Command.get_recipients | def get_recipients(self, **options):
"""
Figures out the recipients
"""
if options['recipients_from_setting']:
return settings.TIMELINE_DIGEST_EMAIL_RECIPIENTS
users = get_user_model()._default_manager.all()
if options['staff']:
users = users.filt... | python | def get_recipients(self, **options):
"""
Figures out the recipients
"""
if options['recipients_from_setting']:
return settings.TIMELINE_DIGEST_EMAIL_RECIPIENTS
users = get_user_model()._default_manager.all()
if options['staff']:
users = users.filt... | [
"def",
"get_recipients",
"(",
"self",
",",
"*",
"*",
"options",
")",
":",
"if",
"options",
"[",
"'recipients_from_setting'",
"]",
":",
"return",
"settings",
".",
"TIMELINE_DIGEST_EMAIL_RECIPIENTS",
"users",
"=",
"get_user_model",
"(",
")",
".",
"_default_manager",... | Figures out the recipients | [
"Figures",
"out",
"the",
"recipients"
] | 1bc67b6283eb94c84e0936e3a882e1b63cfb5ed3 | https://github.com/maykinmedia/django-timeline-logger/blob/1bc67b6283eb94c84e0936e3a882e1b63cfb5ed3/timeline_logger/management/commands/report_mailing.py#L63-L75 | train | 65,100 |
bouncer-app/bouncer | bouncer/models.py | Ability.expand_actions | def expand_actions(self, actions):
"""Accepts an array of actions and returns an array of actions which match.
This should be called before "matches?" and other checking methods since they
rely on the actions to be expanded."""
results = list()
for action in actions:
... | python | def expand_actions(self, actions):
"""Accepts an array of actions and returns an array of actions which match.
This should be called before "matches?" and other checking methods since they
rely on the actions to be expanded."""
results = list()
for action in actions:
... | [
"def",
"expand_actions",
"(",
"self",
",",
"actions",
")",
":",
"results",
"=",
"list",
"(",
")",
"for",
"action",
"in",
"actions",
":",
"if",
"action",
"in",
"self",
".",
"aliased_actions",
":",
"results",
".",
"append",
"(",
"action",
")",
"for",
"it... | Accepts an array of actions and returns an array of actions which match.
This should be called before "matches?" and other checking methods since they
rely on the actions to be expanded. | [
"Accepts",
"an",
"array",
"of",
"actions",
"and",
"returns",
"an",
"array",
"of",
"actions",
"which",
"match",
".",
"This",
"should",
"be",
"called",
"before",
"matches?",
"and",
"other",
"checking",
"methods",
"since",
"they",
"rely",
"on",
"the",
"actions"... | 2d645dce18e3849d338d21380529abf8db5eeb9d | https://github.com/bouncer-app/bouncer/blob/2d645dce18e3849d338d21380529abf8db5eeb9d/bouncer/models.py#L190-L204 | train | 65,101 |
cytomine/Cytomine-python-client | cytomine/cytomine_job.py | _software_params_to_argparse | def _software_params_to_argparse(parameters):
"""
Converts a SoftwareParameterCollection into an ArgumentParser object.
Parameters
----------
parameters: SoftwareParameterCollection
The software parameters
Returns
-------
argparse: ArgumentParser
An initialized argument ... | python | def _software_params_to_argparse(parameters):
"""
Converts a SoftwareParameterCollection into an ArgumentParser object.
Parameters
----------
parameters: SoftwareParameterCollection
The software parameters
Returns
-------
argparse: ArgumentParser
An initialized argument ... | [
"def",
"_software_params_to_argparse",
"(",
"parameters",
")",
":",
"# Check software parameters",
"argparse",
"=",
"ArgumentParser",
"(",
")",
"boolean_defaults",
"=",
"{",
"}",
"for",
"parameter",
"in",
"parameters",
":",
"arg_desc",
"=",
"{",
"\"dest\"",
":",
"... | Converts a SoftwareParameterCollection into an ArgumentParser object.
Parameters
----------
parameters: SoftwareParameterCollection
The software parameters
Returns
-------
argparse: ArgumentParser
An initialized argument parser | [
"Converts",
"a",
"SoftwareParameterCollection",
"into",
"an",
"ArgumentParser",
"object",
"."
] | bac19722b900dd32c6cfd6bdb9354fc784d33bc4 | https://github.com/cytomine/Cytomine-python-client/blob/bac19722b900dd32c6cfd6bdb9354fc784d33bc4/cytomine/cytomine_job.py#L80-L108 | train | 65,102 |
cytomine/Cytomine-python-client | cytomine/cytomine_job.py | CytomineJob.start | def start(self):
"""
Connect to the Cytomine server and switch to job connection
Incurs dataflows
"""
run_by_ui = False
if not self.current_user.algo:
# If user connects as a human (CLI execution)
self._job = Job(self._project.id, self._software.i... | python | def start(self):
"""
Connect to the Cytomine server and switch to job connection
Incurs dataflows
"""
run_by_ui = False
if not self.current_user.algo:
# If user connects as a human (CLI execution)
self._job = Job(self._project.id, self._software.i... | [
"def",
"start",
"(",
"self",
")",
":",
"run_by_ui",
"=",
"False",
"if",
"not",
"self",
".",
"current_user",
".",
"algo",
":",
"# If user connects as a human (CLI execution)",
"self",
".",
"_job",
"=",
"Job",
"(",
"self",
".",
"_project",
".",
"id",
",",
"s... | Connect to the Cytomine server and switch to job connection
Incurs dataflows | [
"Connect",
"to",
"the",
"Cytomine",
"server",
"and",
"switch",
"to",
"job",
"connection",
"Incurs",
"dataflows"
] | bac19722b900dd32c6cfd6bdb9354fc784d33bc4 | https://github.com/cytomine/Cytomine-python-client/blob/bac19722b900dd32c6cfd6bdb9354fc784d33bc4/cytomine/cytomine_job.py#L257-L288 | train | 65,103 |
cytomine/Cytomine-python-client | cytomine/cytomine_job.py | CytomineJob.close | def close(self, value):
"""
Notify the Cytomine server of the job's end
Incurs a dataflows
"""
if value is None:
status = Job.TERMINATED
status_comment = "Job successfully terminated"
else:
status = Job.FAILED
status_comment... | python | def close(self, value):
"""
Notify the Cytomine server of the job's end
Incurs a dataflows
"""
if value is None:
status = Job.TERMINATED
status_comment = "Job successfully terminated"
else:
status = Job.FAILED
status_comment... | [
"def",
"close",
"(",
"self",
",",
"value",
")",
":",
"if",
"value",
"is",
"None",
":",
"status",
"=",
"Job",
".",
"TERMINATED",
"status_comment",
"=",
"\"Job successfully terminated\"",
"else",
":",
"status",
"=",
"Job",
".",
"FAILED",
"status_comment",
"=",... | Notify the Cytomine server of the job's end
Incurs a dataflows | [
"Notify",
"the",
"Cytomine",
"server",
"of",
"the",
"job",
"s",
"end",
"Incurs",
"a",
"dataflows"
] | bac19722b900dd32c6cfd6bdb9354fc784d33bc4 | https://github.com/cytomine/Cytomine-python-client/blob/bac19722b900dd32c6cfd6bdb9354fc784d33bc4/cytomine/cytomine_job.py#L290-L304 | train | 65,104 |
pyecore/pyecoregen | pyecoregen/cli.py | generate_from_cli | def generate_from_cli(args):
"""CLI entry point."""
parser = argparse.ArgumentParser(description="Generate Python classes from an Ecore model.")
parser.add_argument(
'--ecore-model',
'-e',
help="Path to Ecore XMI file.",
required=True
)
parser.add_argument(
'-... | python | def generate_from_cli(args):
"""CLI entry point."""
parser = argparse.ArgumentParser(description="Generate Python classes from an Ecore model.")
parser.add_argument(
'--ecore-model',
'-e',
help="Path to Ecore XMI file.",
required=True
)
parser.add_argument(
'-... | [
"def",
"generate_from_cli",
"(",
"args",
")",
":",
"parser",
"=",
"argparse",
".",
"ArgumentParser",
"(",
"description",
"=",
"\"Generate Python classes from an Ecore model.\"",
")",
"parser",
".",
"add_argument",
"(",
"'--ecore-model'",
",",
"'-e'",
",",
"help",
"=... | CLI entry point. | [
"CLI",
"entry",
"point",
"."
] | 8c7a792f46d7d94e5d13e00e2967dd237351a4cf | https://github.com/pyecore/pyecoregen/blob/8c7a792f46d7d94e5d13e00e2967dd237351a4cf/pyecoregen/cli.py#L18-L62 | train | 65,105 |
pyecore/pyecoregen | pyecoregen/cli.py | select_uri_implementation | def select_uri_implementation(ecore_model_path):
"""Select the right URI implementation regarding the Ecore model path schema."""
if URL_PATTERN.match(ecore_model_path):
return pyecore.resources.resource.HttpURI
return pyecore.resources.URI | python | def select_uri_implementation(ecore_model_path):
"""Select the right URI implementation regarding the Ecore model path schema."""
if URL_PATTERN.match(ecore_model_path):
return pyecore.resources.resource.HttpURI
return pyecore.resources.URI | [
"def",
"select_uri_implementation",
"(",
"ecore_model_path",
")",
":",
"if",
"URL_PATTERN",
".",
"match",
"(",
"ecore_model_path",
")",
":",
"return",
"pyecore",
".",
"resources",
".",
"resource",
".",
"HttpURI",
"return",
"pyecore",
".",
"resources",
".",
"URI"... | Select the right URI implementation regarding the Ecore model path schema. | [
"Select",
"the",
"right",
"URI",
"implementation",
"regarding",
"the",
"Ecore",
"model",
"path",
"schema",
"."
] | 8c7a792f46d7d94e5d13e00e2967dd237351a4cf | https://github.com/pyecore/pyecoregen/blob/8c7a792f46d7d94e5d13e00e2967dd237351a4cf/pyecoregen/cli.py#L77-L81 | train | 65,106 |
pyecore/pyecoregen | pyecoregen/cli.py | load_model | def load_model(ecore_model_path):
"""Load a single Ecore model and return the root package."""
rset = pyecore.resources.ResourceSet()
uri_implementation = select_uri_implementation(ecore_model_path)
resource = rset.get_resource(uri_implementation(ecore_model_path))
return resource.contents[0] | python | def load_model(ecore_model_path):
"""Load a single Ecore model and return the root package."""
rset = pyecore.resources.ResourceSet()
uri_implementation = select_uri_implementation(ecore_model_path)
resource = rset.get_resource(uri_implementation(ecore_model_path))
return resource.contents[0] | [
"def",
"load_model",
"(",
"ecore_model_path",
")",
":",
"rset",
"=",
"pyecore",
".",
"resources",
".",
"ResourceSet",
"(",
")",
"uri_implementation",
"=",
"select_uri_implementation",
"(",
"ecore_model_path",
")",
"resource",
"=",
"rset",
".",
"get_resource",
"(",... | Load a single Ecore model and return the root package. | [
"Load",
"a",
"single",
"Ecore",
"model",
"and",
"return",
"the",
"root",
"package",
"."
] | 8c7a792f46d7d94e5d13e00e2967dd237351a4cf | https://github.com/pyecore/pyecoregen/blob/8c7a792f46d7d94e5d13e00e2967dd237351a4cf/pyecoregen/cli.py#L84-L89 | train | 65,107 |
galaxy-genome-annotation/python-apollo | apollo/client.py | Client.post | def post(self, client_method, data, post_params=None, is_json=True):
"""Make a POST request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
if post_params is None:
post_params = {}
headers = {
'Content-Type': 'application/json'
}
... | python | def post(self, client_method, data, post_params=None, is_json=True):
"""Make a POST request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
if post_params is None:
post_params = {}
headers = {
'Content-Type': 'application/json'
}
... | [
"def",
"post",
"(",
"self",
",",
"client_method",
",",
"data",
",",
"post_params",
"=",
"None",
",",
"is_json",
"=",
"True",
")",
":",
"url",
"=",
"self",
".",
"_wa",
".",
"apollo_url",
"+",
"self",
".",
"CLIENT_BASE",
"+",
"client_method",
"if",
"post... | Make a POST request | [
"Make",
"a",
"POST",
"request"
] | 2bc9991302abe4402ec2885dcaac35915475b387 | https://github.com/galaxy-genome-annotation/python-apollo/blob/2bc9991302abe4402ec2885dcaac35915475b387/apollo/client.py#L29-L65 | train | 65,108 |
galaxy-genome-annotation/python-apollo | apollo/client.py | Client.get | def get(self, client_method, get_params, is_json=True):
"""Make a GET request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
headers = {}
response = requests.get(url, headers=headers,
verify=self.__verify, params=get_params,
... | python | def get(self, client_method, get_params, is_json=True):
"""Make a GET request"""
url = self._wa.apollo_url + self.CLIENT_BASE + client_method
headers = {}
response = requests.get(url, headers=headers,
verify=self.__verify, params=get_params,
... | [
"def",
"get",
"(",
"self",
",",
"client_method",
",",
"get_params",
",",
"is_json",
"=",
"True",
")",
":",
"url",
"=",
"self",
".",
"_wa",
".",
"apollo_url",
"+",
"self",
".",
"CLIENT_BASE",
"+",
"client_method",
"headers",
"=",
"{",
"}",
"response",
"... | Make a GET request | [
"Make",
"a",
"GET",
"request"
] | 2bc9991302abe4402ec2885dcaac35915475b387 | https://github.com/galaxy-genome-annotation/python-apollo/blob/2bc9991302abe4402ec2885dcaac35915475b387/apollo/client.py#L67-L83 | train | 65,109 |
bouncer-app/bouncer | bouncer/__init__.py | can | def can(user, action, subject):
"""Checks if a given user has the ability to perform the action on a subject
:param user: A user object
:param action: an action string, typically 'read', 'edit', 'manage'. Use bouncer.constants for readability
:param subject: the resource in question. Either a Class o... | python | def can(user, action, subject):
"""Checks if a given user has the ability to perform the action on a subject
:param user: A user object
:param action: an action string, typically 'read', 'edit', 'manage'. Use bouncer.constants for readability
:param subject: the resource in question. Either a Class o... | [
"def",
"can",
"(",
"user",
",",
"action",
",",
"subject",
")",
":",
"ability",
"=",
"Ability",
"(",
"user",
",",
"get_authorization_method",
"(",
")",
")",
"return",
"ability",
".",
"can",
"(",
"action",
",",
"subject",
")"
] | Checks if a given user has the ability to perform the action on a subject
:param user: A user object
:param action: an action string, typically 'read', 'edit', 'manage'. Use bouncer.constants for readability
:param subject: the resource in question. Either a Class or an instance of a class. Pass the cla... | [
"Checks",
"if",
"a",
"given",
"user",
"has",
"the",
"ability",
"to",
"perform",
"the",
"action",
"on",
"a",
"subject"
] | 2d645dce18e3849d338d21380529abf8db5eeb9d | https://github.com/bouncer-app/bouncer/blob/2d645dce18e3849d338d21380529abf8db5eeb9d/bouncer/__init__.py#L16-L28 | train | 65,110 |
bouncer-app/bouncer | bouncer/__init__.py | cannot | def cannot(user, action, subject):
"""inverse of ``can``"""
ability = Ability(user, get_authorization_method())
return ability.cannot(action, subject) | python | def cannot(user, action, subject):
"""inverse of ``can``"""
ability = Ability(user, get_authorization_method())
return ability.cannot(action, subject) | [
"def",
"cannot",
"(",
"user",
",",
"action",
",",
"subject",
")",
":",
"ability",
"=",
"Ability",
"(",
"user",
",",
"get_authorization_method",
"(",
")",
")",
"return",
"ability",
".",
"cannot",
"(",
"action",
",",
"subject",
")"
] | inverse of ``can`` | [
"inverse",
"of",
"can"
] | 2d645dce18e3849d338d21380529abf8db5eeb9d | https://github.com/bouncer-app/bouncer/blob/2d645dce18e3849d338d21380529abf8db5eeb9d/bouncer/__init__.py#L31-L34 | train | 65,111 |
bouncer-app/bouncer | bouncer/__init__.py | ensure | def ensure(user, action, subject):
""" Similar to ``can`` but will raise a AccessDenied Exception if does not have access"""
ability = Ability(user, get_authorization_method())
if ability.cannot(action, subject):
raise AccessDenied() | python | def ensure(user, action, subject):
""" Similar to ``can`` but will raise a AccessDenied Exception if does not have access"""
ability = Ability(user, get_authorization_method())
if ability.cannot(action, subject):
raise AccessDenied() | [
"def",
"ensure",
"(",
"user",
",",
"action",
",",
"subject",
")",
":",
"ability",
"=",
"Ability",
"(",
"user",
",",
"get_authorization_method",
"(",
")",
")",
"if",
"ability",
".",
"cannot",
"(",
"action",
",",
"subject",
")",
":",
"raise",
"AccessDenied... | Similar to ``can`` but will raise a AccessDenied Exception if does not have access | [
"Similar",
"to",
"can",
"but",
"will",
"raise",
"a",
"AccessDenied",
"Exception",
"if",
"does",
"not",
"have",
"access"
] | 2d645dce18e3849d338d21380529abf8db5eeb9d | https://github.com/bouncer-app/bouncer/blob/2d645dce18e3849d338d21380529abf8db5eeb9d/bouncer/__init__.py#L37-L41 | train | 65,112 |
cytomine/Cytomine-python-client | cytomine/models/annotation.py | Annotation.dump | def dump(self, dest_pattern="{id}.jpg", override=True, mask=False, alpha=False, bits=8,
zoom=None, max_size=None, increase_area=None, contrast=None, gamma=None, colormap=None, inverse=None):
"""
Download the annotation crop, with optional image modifications.
Parameters
---... | python | def dump(self, dest_pattern="{id}.jpg", override=True, mask=False, alpha=False, bits=8,
zoom=None, max_size=None, increase_area=None, contrast=None, gamma=None, colormap=None, inverse=None):
"""
Download the annotation crop, with optional image modifications.
Parameters
---... | [
"def",
"dump",
"(",
"self",
",",
"dest_pattern",
"=",
"\"{id}.jpg\"",
",",
"override",
"=",
"True",
",",
"mask",
"=",
"False",
",",
"alpha",
"=",
"False",
",",
"bits",
"=",
"8",
",",
"zoom",
"=",
"None",
",",
"max_size",
"=",
"None",
",",
"increase_a... | Download the annotation crop, with optional image modifications.
Parameters
----------
dest_pattern : str, optional
Destination path for the downloaded image. "{X}" patterns are replaced by the value of X attribute
if it exists.
override : bool, optional
... | [
"Download",
"the",
"annotation",
"crop",
"with",
"optional",
"image",
"modifications",
"."
] | bac19722b900dd32c6cfd6bdb9354fc784d33bc4 | https://github.com/cytomine/Cytomine-python-client/blob/bac19722b900dd32c6cfd6bdb9354fc784d33bc4/cytomine/models/annotation.py#L62-L144 | train | 65,113 |
galaxy-genome-annotation/python-apollo | arrow/commands/annotations/set_sequence.py | cli | def cli(ctx, organism, sequence):
"""Set the sequence for subsequent requests. Mostly used in client scripts to avoid passing the sequence and organism on every function call.
Output:
None
"""
return ctx.gi.annotations.set_sequence(organism, sequence) | python | def cli(ctx, organism, sequence):
"""Set the sequence for subsequent requests. Mostly used in client scripts to avoid passing the sequence and organism on every function call.
Output:
None
"""
return ctx.gi.annotations.set_sequence(organism, sequence) | [
"def",
"cli",
"(",
"ctx",
",",
"organism",
",",
"sequence",
")",
":",
"return",
"ctx",
".",
"gi",
".",
"annotations",
".",
"set_sequence",
"(",
"organism",
",",
"sequence",
")"
] | Set the sequence for subsequent requests. Mostly used in client scripts to avoid passing the sequence and organism on every function call.
Output:
None | [
"Set",
"the",
"sequence",
"for",
"subsequent",
"requests",
".",
"Mostly",
"used",
"in",
"client",
"scripts",
"to",
"avoid",
"passing",
"the",
"sequence",
"and",
"organism",
"on",
"every",
"function",
"call",
"."
] | 2bc9991302abe4402ec2885dcaac35915475b387 | https://github.com/galaxy-genome-annotation/python-apollo/blob/2bc9991302abe4402ec2885dcaac35915475b387/arrow/commands/annotations/set_sequence.py#L12-L19 | train | 65,114 |
hearsaycorp/normalize | normalize/selector.py | MultiFieldSelector.path | def path(self):
"""The path attribute returns a stringified, concise representation of
the MultiFieldSelector. It can be reversed by the ``from_path``
constructor.
"""
if len(self.heads) == 1:
return _fmt_mfs_path(self.heads.keys()[0], self.heads.values()[0])
... | python | def path(self):
"""The path attribute returns a stringified, concise representation of
the MultiFieldSelector. It can be reversed by the ``from_path``
constructor.
"""
if len(self.heads) == 1:
return _fmt_mfs_path(self.heads.keys()[0], self.heads.values()[0])
... | [
"def",
"path",
"(",
"self",
")",
":",
"if",
"len",
"(",
"self",
".",
"heads",
")",
"==",
"1",
":",
"return",
"_fmt_mfs_path",
"(",
"self",
".",
"heads",
".",
"keys",
"(",
")",
"[",
"0",
"]",
",",
"self",
".",
"heads",
".",
"values",
"(",
")",
... | The path attribute returns a stringified, concise representation of
the MultiFieldSelector. It can be reversed by the ``from_path``
constructor. | [
"The",
"path",
"attribute",
"returns",
"a",
"stringified",
"concise",
"representation",
"of",
"the",
"MultiFieldSelector",
".",
"It",
"can",
"be",
"reversed",
"by",
"the",
"from_path",
"constructor",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/selector.py#L626-L636 | train | 65,115 |
hearsaycorp/normalize | normalize/selector.py | MultiFieldSelector.get | def get(self, obj):
"""Creates a copy of the passed object which only contains the parts
which are pointed to by one of the FieldSelectors that were used to
construct the MultiFieldSelector. Can be used to produce 'filtered'
versions of objects.
"""
ctor = type(obj)
... | python | def get(self, obj):
"""Creates a copy of the passed object which only contains the parts
which are pointed to by one of the FieldSelectors that were used to
construct the MultiFieldSelector. Can be used to produce 'filtered'
versions of objects.
"""
ctor = type(obj)
... | [
"def",
"get",
"(",
"self",
",",
"obj",
")",
":",
"ctor",
"=",
"type",
"(",
"obj",
")",
"if",
"isinstance",
"(",
"obj",
",",
"(",
"list",
",",
"ListCollection",
")",
")",
":",
"if",
"self",
".",
"has_string",
":",
"raise",
"TypeError",
"(",
"\"Multi... | Creates a copy of the passed object which only contains the parts
which are pointed to by one of the FieldSelectors that were used to
construct the MultiFieldSelector. Can be used to produce 'filtered'
versions of objects. | [
"Creates",
"a",
"copy",
"of",
"the",
"passed",
"object",
"which",
"only",
"contains",
"the",
"parts",
"which",
"are",
"pointed",
"to",
"by",
"one",
"of",
"the",
"FieldSelectors",
"that",
"were",
"used",
"to",
"construct",
"the",
"MultiFieldSelector",
".",
"C... | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/selector.py#L785-L835 | train | 65,116 |
hearsaycorp/normalize | normalize/selector.py | MultiFieldSelector.delete | def delete(self, obj, force=False):
"""Deletes all of the fields at the specified locations.
args:
``obj=``\ *OBJECT*
the object to remove the fields from
``force=``\ *BOOL*
if True, missing attributes do not raise errors. Otherwise,
... | python | def delete(self, obj, force=False):
"""Deletes all of the fields at the specified locations.
args:
``obj=``\ *OBJECT*
the object to remove the fields from
``force=``\ *BOOL*
if True, missing attributes do not raise errors. Otherwise,
... | [
"def",
"delete",
"(",
"self",
",",
"obj",
",",
"force",
"=",
"False",
")",
":",
"# TODO: this could be a whole lot more efficient!",
"if",
"not",
"force",
":",
"for",
"fs",
"in",
"self",
":",
"try",
":",
"fs",
".",
"get",
"(",
"obj",
")",
"except",
"Fiel... | Deletes all of the fields at the specified locations.
args:
``obj=``\ *OBJECT*
the object to remove the fields from
``force=``\ *BOOL*
if True, missing attributes do not raise errors. Otherwise,
the first failure raises an exception wit... | [
"Deletes",
"all",
"of",
"the",
"fields",
"at",
"the",
"specified",
"locations",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/selector.py#L837-L862 | train | 65,117 |
merll/docker-fabric | dockerfabric/tasks.py | reset_socat | def reset_socat(use_sudo=False):
"""
Finds and closes all processes of `socat`.
:param use_sudo: Use `sudo` command. As Docker-Fabric does not run `socat` with `sudo`, this is by default set to
``False``. Setting it to ``True`` could unintentionally remove instances from other users.
:type use_su... | python | def reset_socat(use_sudo=False):
"""
Finds and closes all processes of `socat`.
:param use_sudo: Use `sudo` command. As Docker-Fabric does not run `socat` with `sudo`, this is by default set to
``False``. Setting it to ``True`` could unintentionally remove instances from other users.
:type use_su... | [
"def",
"reset_socat",
"(",
"use_sudo",
"=",
"False",
")",
":",
"output",
"=",
"stdout_result",
"(",
"'ps -o pid -C socat'",
",",
"quiet",
"=",
"True",
")",
"pids",
"=",
"output",
".",
"split",
"(",
"'\\n'",
")",
"[",
"1",
":",
"]",
"puts",
"(",
"\"Remo... | Finds and closes all processes of `socat`.
:param use_sudo: Use `sudo` command. As Docker-Fabric does not run `socat` with `sudo`, this is by default set to
``False``. Setting it to ``True`` could unintentionally remove instances from other users.
:type use_sudo: bool | [
"Finds",
"and",
"closes",
"all",
"processes",
"of",
"socat",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L63-L75 | train | 65,118 |
merll/docker-fabric | dockerfabric/tasks.py | version | def version():
"""
Shows version information of the remote Docker service, similar to ``docker version``.
"""
output = docker_fabric().version()
col_len = max(map(len, output.keys())) + 1
puts('')
for k, v in six.iteritems(output):
fastprint('{0:{1}} {2}'.format(''.join((k, ':')), co... | python | def version():
"""
Shows version information of the remote Docker service, similar to ``docker version``.
"""
output = docker_fabric().version()
col_len = max(map(len, output.keys())) + 1
puts('')
for k, v in six.iteritems(output):
fastprint('{0:{1}} {2}'.format(''.join((k, ':')), co... | [
"def",
"version",
"(",
")",
":",
"output",
"=",
"docker_fabric",
"(",
")",
".",
"version",
"(",
")",
"col_len",
"=",
"max",
"(",
"map",
"(",
"len",
",",
"output",
".",
"keys",
"(",
")",
")",
")",
"+",
"1",
"puts",
"(",
"''",
")",
"for",
"k",
... | Shows version information of the remote Docker service, similar to ``docker version``. | [
"Shows",
"version",
"information",
"of",
"the",
"remote",
"Docker",
"service",
"similar",
"to",
"docker",
"version",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L79-L88 | train | 65,119 |
merll/docker-fabric | dockerfabric/tasks.py | list_images | def list_images(list_all=False, full_ids=False):
"""
Lists images on the Docker remote host, similar to ``docker images``.
:param list_all: Lists all images (e.g. dependencies). Default is ``False``, only shows named images.
:type list_all: bool
:param full_ids: Shows the full ids. When ``False`` (... | python | def list_images(list_all=False, full_ids=False):
"""
Lists images on the Docker remote host, similar to ``docker images``.
:param list_all: Lists all images (e.g. dependencies). Default is ``False``, only shows named images.
:type list_all: bool
:param full_ids: Shows the full ids. When ``False`` (... | [
"def",
"list_images",
"(",
"list_all",
"=",
"False",
",",
"full_ids",
"=",
"False",
")",
":",
"images",
"=",
"docker_fabric",
"(",
")",
".",
"images",
"(",
"all",
"=",
"list_all",
")",
"_format_output_table",
"(",
"images",
",",
"IMAGE_COLUMNS",
",",
"full... | Lists images on the Docker remote host, similar to ``docker images``.
:param list_all: Lists all images (e.g. dependencies). Default is ``False``, only shows named images.
:type list_all: bool
:param full_ids: Shows the full ids. When ``False`` (default) only shows the first 12 characters.
:type full_i... | [
"Lists",
"images",
"on",
"the",
"Docker",
"remote",
"host",
"similar",
"to",
"docker",
"images",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L116-L126 | train | 65,120 |
merll/docker-fabric | dockerfabric/tasks.py | list_containers | def list_containers(list_all=True, short_image=True, full_ids=False, full_cmd=False):
"""
Lists containers on the Docker remote host, similar to ``docker ps``.
:param list_all: Shows all containers. Default is ``False``, which omits exited containers.
:type list_all: bool
:param short_image: Hides ... | python | def list_containers(list_all=True, short_image=True, full_ids=False, full_cmd=False):
"""
Lists containers on the Docker remote host, similar to ``docker ps``.
:param list_all: Shows all containers. Default is ``False``, which omits exited containers.
:type list_all: bool
:param short_image: Hides ... | [
"def",
"list_containers",
"(",
"list_all",
"=",
"True",
",",
"short_image",
"=",
"True",
",",
"full_ids",
"=",
"False",
",",
"full_cmd",
"=",
"False",
")",
":",
"containers",
"=",
"docker_fabric",
"(",
")",
".",
"containers",
"(",
"all",
"=",
"list_all",
... | Lists containers on the Docker remote host, similar to ``docker ps``.
:param list_all: Shows all containers. Default is ``False``, which omits exited containers.
:type list_all: bool
:param short_image: Hides the repository prefix for preserving space. Default is ``True``.
:type short_image: bool
:... | [
"Lists",
"containers",
"on",
"the",
"Docker",
"remote",
"host",
"similar",
"to",
"docker",
"ps",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L130-L144 | train | 65,121 |
merll/docker-fabric | dockerfabric/tasks.py | list_networks | def list_networks(full_ids=False):
"""
Lists networks on the Docker remote host, similar to ``docker network ls``.
:param full_ids: Shows the full network ids. When ``False`` (default) only shows the first 12 characters.
:type full_ids: bool
"""
networks = docker_fabric().networks()
_format... | python | def list_networks(full_ids=False):
"""
Lists networks on the Docker remote host, similar to ``docker network ls``.
:param full_ids: Shows the full network ids. When ``False`` (default) only shows the first 12 characters.
:type full_ids: bool
"""
networks = docker_fabric().networks()
_format... | [
"def",
"list_networks",
"(",
"full_ids",
"=",
"False",
")",
":",
"networks",
"=",
"docker_fabric",
"(",
")",
".",
"networks",
"(",
")",
"_format_output_table",
"(",
"networks",
",",
"NETWORK_COLUMNS",
",",
"full_ids",
")"
] | Lists networks on the Docker remote host, similar to ``docker network ls``.
:param full_ids: Shows the full network ids. When ``False`` (default) only shows the first 12 characters.
:type full_ids: bool | [
"Lists",
"networks",
"on",
"the",
"Docker",
"remote",
"host",
"similar",
"to",
"docker",
"network",
"ls",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L148-L156 | train | 65,122 |
merll/docker-fabric | dockerfabric/tasks.py | cleanup_containers | def cleanup_containers(**kwargs):
"""
Removes all containers that have finished running. Similar to the ``prune`` functionality in newer Docker versions.
"""
containers = docker_fabric().cleanup_containers(**kwargs)
if kwargs.get('list_only'):
puts('Existing containers:')
for c_id, c... | python | def cleanup_containers(**kwargs):
"""
Removes all containers that have finished running. Similar to the ``prune`` functionality in newer Docker versions.
"""
containers = docker_fabric().cleanup_containers(**kwargs)
if kwargs.get('list_only'):
puts('Existing containers:')
for c_id, c... | [
"def",
"cleanup_containers",
"(",
"*",
"*",
"kwargs",
")",
":",
"containers",
"=",
"docker_fabric",
"(",
")",
".",
"cleanup_containers",
"(",
"*",
"*",
"kwargs",
")",
"if",
"kwargs",
".",
"get",
"(",
"'list_only'",
")",
":",
"puts",
"(",
"'Existing contain... | Removes all containers that have finished running. Similar to the ``prune`` functionality in newer Docker versions. | [
"Removes",
"all",
"containers",
"that",
"have",
"finished",
"running",
".",
"Similar",
"to",
"the",
"prune",
"functionality",
"in",
"newer",
"Docker",
"versions",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L169-L177 | train | 65,123 |
merll/docker-fabric | dockerfabric/tasks.py | cleanup_images | def cleanup_images(remove_old=False, **kwargs):
"""
Removes all images that have no name, and that are not references as dependency by any other named image. Similar
to the ``prune`` functionality in newer Docker versions, but supports more filters.
:param remove_old: Also remove images that do have a ... | python | def cleanup_images(remove_old=False, **kwargs):
"""
Removes all images that have no name, and that are not references as dependency by any other named image. Similar
to the ``prune`` functionality in newer Docker versions, but supports more filters.
:param remove_old: Also remove images that do have a ... | [
"def",
"cleanup_images",
"(",
"remove_old",
"=",
"False",
",",
"*",
"*",
"kwargs",
")",
":",
"keep_tags",
"=",
"env",
".",
"get",
"(",
"'docker_keep_tags'",
")",
"if",
"keep_tags",
"is",
"not",
"None",
":",
"kwargs",
".",
"setdefault",
"(",
"'keep_tags'",
... | Removes all images that have no name, and that are not references as dependency by any other named image. Similar
to the ``prune`` functionality in newer Docker versions, but supports more filters.
:param remove_old: Also remove images that do have a name, but no `latest` tag.
:type remove_old: bool | [
"Removes",
"all",
"images",
"that",
"have",
"no",
"name",
"and",
"that",
"are",
"not",
"references",
"as",
"dependency",
"by",
"any",
"other",
"named",
"image",
".",
"Similar",
"to",
"the",
"prune",
"functionality",
"in",
"newer",
"Docker",
"versions",
"but"... | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L181-L196 | train | 65,124 |
merll/docker-fabric | dockerfabric/tasks.py | save_image | def save_image(image, filename=None):
"""
Saves a Docker image from the remote to a local files. For performance reasons, uses the Docker command line client
on the host, generates a gzip-tarball and downloads that.
:param image: Image name or id.
:type image: unicode
:param filename: File name... | python | def save_image(image, filename=None):
"""
Saves a Docker image from the remote to a local files. For performance reasons, uses the Docker command line client
on the host, generates a gzip-tarball and downloads that.
:param image: Image name or id.
:type image: unicode
:param filename: File name... | [
"def",
"save_image",
"(",
"image",
",",
"filename",
"=",
"None",
")",
":",
"local_name",
"=",
"filename",
"or",
"'{0}.tar.gz'",
".",
"format",
"(",
"image",
")",
"cli",
".",
"save_image",
"(",
"image",
",",
"local_name",
")"
] | Saves a Docker image from the remote to a local files. For performance reasons, uses the Docker command line client
on the host, generates a gzip-tarball and downloads that.
:param image: Image name or id.
:type image: unicode
:param filename: File name to store the local file. If not provided, will us... | [
"Saves",
"a",
"Docker",
"image",
"from",
"the",
"remote",
"to",
"a",
"local",
"files",
".",
"For",
"performance",
"reasons",
"uses",
"the",
"Docker",
"command",
"line",
"client",
"on",
"the",
"host",
"generates",
"a",
"gzip",
"-",
"tarball",
"and",
"downlo... | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L214-L226 | train | 65,125 |
merll/docker-fabric | dockerfabric/tasks.py | load_image | def load_image(filename, timeout=120):
"""
Uploads an image from a local file to a Docker remote. Note that this temporarily has to extend the service timeout
period.
:param filename: Local file name.
:type filename: unicode
:param timeout: Timeout in seconds to set temporarily for the upload.
... | python | def load_image(filename, timeout=120):
"""
Uploads an image from a local file to a Docker remote. Note that this temporarily has to extend the service timeout
period.
:param filename: Local file name.
:type filename: unicode
:param timeout: Timeout in seconds to set temporarily for the upload.
... | [
"def",
"load_image",
"(",
"filename",
",",
"timeout",
"=",
"120",
")",
":",
"c",
"=",
"docker_fabric",
"(",
")",
"with",
"open",
"(",
"expand_path",
"(",
"filename",
")",
",",
"'r'",
")",
"as",
"f",
":",
"_timeout",
"=",
"c",
".",
"_timeout",
"c",
... | Uploads an image from a local file to a Docker remote. Note that this temporarily has to extend the service timeout
period.
:param filename: Local file name.
:type filename: unicode
:param timeout: Timeout in seconds to set temporarily for the upload.
:type timeout: int | [
"Uploads",
"an",
"image",
"from",
"a",
"local",
"file",
"to",
"a",
"Docker",
"remote",
".",
"Note",
"that",
"this",
"temporarily",
"has",
"to",
"extend",
"the",
"service",
"timeout",
"period",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/tasks.py#L230-L247 | train | 65,126 |
hearsaycorp/normalize | normalize/record/__init__.py | Record.diff_iter | def diff_iter(self, other, **kwargs):
"""Generator method which returns the differences from the invocant to
the argument.
args:
``other=``\ *Record*\ \|\ *Anything*
The thing to compare against; the types must match, unless
``duck_type=True`` is p... | python | def diff_iter(self, other, **kwargs):
"""Generator method which returns the differences from the invocant to
the argument.
args:
``other=``\ *Record*\ \|\ *Anything*
The thing to compare against; the types must match, unless
``duck_type=True`` is p... | [
"def",
"diff_iter",
"(",
"self",
",",
"other",
",",
"*",
"*",
"kwargs",
")",
":",
"from",
"normalize",
".",
"diff",
"import",
"diff_iter",
"return",
"diff_iter",
"(",
"self",
",",
"other",
",",
"*",
"*",
"kwargs",
")"
] | Generator method which returns the differences from the invocant to
the argument.
args:
``other=``\ *Record*\ \|\ *Anything*
The thing to compare against; the types must match, unless
``duck_type=True`` is passed.
*diff_option*\ =\ *value*
... | [
"Generator",
"method",
"which",
"returns",
"the",
"differences",
"from",
"the",
"invocant",
"to",
"the",
"argument",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/record/__init__.py#L153-L168 | train | 65,127 |
zhanglab/psamm | psamm/commands/primarypairs.py | _parse_weights | def _parse_weights(weight_args, default_weight=0.6):
"""Parse list of weight assignments."""
weights_dict = {}
r_group_weight = default_weight
for weight_arg in weight_args:
for weight_assignment in weight_arg.split(','):
if '=' not in weight_assignment:
raise ValueEr... | python | def _parse_weights(weight_args, default_weight=0.6):
"""Parse list of weight assignments."""
weights_dict = {}
r_group_weight = default_weight
for weight_arg in weight_args:
for weight_assignment in weight_arg.split(','):
if '=' not in weight_assignment:
raise ValueEr... | [
"def",
"_parse_weights",
"(",
"weight_args",
",",
"default_weight",
"=",
"0.6",
")",
":",
"weights_dict",
"=",
"{",
"}",
"r_group_weight",
"=",
"default_weight",
"for",
"weight_arg",
"in",
"weight_args",
":",
"for",
"weight_assignment",
"in",
"weight_arg",
".",
... | Parse list of weight assignments. | [
"Parse",
"list",
"of",
"weight",
"assignments",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/commands/primarypairs.py#L215-L236 | train | 65,128 |
zhanglab/psamm | psamm/commands/primarypairs.py | PrimaryPairsCommand._combine_transfers | def _combine_transfers(self, result):
"""Combine multiple pair transfers into one."""
transfers = {}
for reaction_id, c1, c2, form in result:
key = reaction_id, c1, c2
combined_form = transfers.setdefault(key, Formula())
transfers[key] = combined_form | form
... | python | def _combine_transfers(self, result):
"""Combine multiple pair transfers into one."""
transfers = {}
for reaction_id, c1, c2, form in result:
key = reaction_id, c1, c2
combined_form = transfers.setdefault(key, Formula())
transfers[key] = combined_form | form
... | [
"def",
"_combine_transfers",
"(",
"self",
",",
"result",
")",
":",
"transfers",
"=",
"{",
"}",
"for",
"reaction_id",
",",
"c1",
",",
"c2",
",",
"form",
"in",
"result",
":",
"key",
"=",
"reaction_id",
",",
"c1",
",",
"c2",
"combined_form",
"=",
"transfe... | Combine multiple pair transfers into one. | [
"Combine",
"multiple",
"pair",
"transfers",
"into",
"one",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/commands/primarypairs.py#L162-L171 | train | 65,129 |
merll/docker-fabric | dockerfabric/cli.py | copy_resource | def copy_resource(container, resource, local_filename, contents_only=True):
"""
Copies a resource from a container to a compressed tarball and downloads it.
:param container: Container name or id.
:type container: unicode
:param resource: Name of resource to copy.
:type resource: unicode
:p... | python | def copy_resource(container, resource, local_filename, contents_only=True):
"""
Copies a resource from a container to a compressed tarball and downloads it.
:param container: Container name or id.
:type container: unicode
:param resource: Name of resource to copy.
:type resource: unicode
:p... | [
"def",
"copy_resource",
"(",
"container",
",",
"resource",
",",
"local_filename",
",",
"contents_only",
"=",
"True",
")",
":",
"with",
"temp_dir",
"(",
")",
"as",
"remote_tmp",
":",
"base_name",
"=",
"os",
".",
"path",
".",
"basename",
"(",
"resource",
")"... | Copies a resource from a container to a compressed tarball and downloads it.
:param container: Container name or id.
:type container: unicode
:param resource: Name of resource to copy.
:type resource: unicode
:param local_filename: Path to store the tarball locally.
:type local_filename: unicod... | [
"Copies",
"a",
"resource",
"from",
"a",
"container",
"to",
"a",
"compressed",
"tarball",
"and",
"downloads",
"it",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/cli.py#L290-L320 | train | 65,130 |
merll/docker-fabric | dockerfabric/cli.py | save_image | def save_image(image, local_filename):
"""
Saves a Docker image as a compressed tarball. This command line client method is a suitable alternative, if the
Remove API method is too slow.
:param image: Image id or tag.
:type image: unicode
:param local_filename: Local file name to store the image... | python | def save_image(image, local_filename):
"""
Saves a Docker image as a compressed tarball. This command line client method is a suitable alternative, if the
Remove API method is too slow.
:param image: Image id or tag.
:type image: unicode
:param local_filename: Local file name to store the image... | [
"def",
"save_image",
"(",
"image",
",",
"local_filename",
")",
":",
"r_name",
",",
"__",
",",
"i_name",
"=",
"image",
".",
"rpartition",
"(",
"'/'",
")",
"i_name",
",",
"__",
",",
"__",
"=",
"i_name",
".",
"partition",
"(",
"':'",
")",
"with",
"temp_... | Saves a Docker image as a compressed tarball. This command line client method is a suitable alternative, if the
Remove API method is too slow.
:param image: Image id or tag.
:type image: unicode
:param local_filename: Local file name to store the image into. If this is a directory, the image will be st... | [
"Saves",
"a",
"Docker",
"image",
"as",
"a",
"compressed",
"tarball",
".",
"This",
"command",
"line",
"client",
"method",
"is",
"a",
"suitable",
"alternative",
"if",
"the",
"Remove",
"API",
"method",
"is",
"too",
"slow",
"."
] | 785d84e40e17265b667d8b11a6e30d8e6b2bf8d4 | https://github.com/merll/docker-fabric/blob/785d84e40e17265b667d8b11a6e30d8e6b2bf8d4/dockerfabric/cli.py#L410-L425 | train | 65,131 |
zhanglab/psamm | psamm/datasource/modelseed.py | decode_name | def decode_name(s):
"""Decode names in ModelSEED files"""
# Some names contain XML-like entity codes
return re.sub(r'&#(\d+);', lambda x: chr(int(x.group(1))), s) | python | def decode_name(s):
"""Decode names in ModelSEED files"""
# Some names contain XML-like entity codes
return re.sub(r'&#(\d+);', lambda x: chr(int(x.group(1))), s) | [
"def",
"decode_name",
"(",
"s",
")",
":",
"# Some names contain XML-like entity codes",
"return",
"re",
".",
"sub",
"(",
"r'&#(\\d+);'",
",",
"lambda",
"x",
":",
"chr",
"(",
"int",
"(",
"x",
".",
"group",
"(",
"1",
")",
")",
")",
",",
"s",
")"
] | Decode names in ModelSEED files | [
"Decode",
"names",
"in",
"ModelSEED",
"files"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/modelseed.py#L31-L34 | train | 65,132 |
zhanglab/psamm | psamm/datasource/modelseed.py | parse_compound_file | def parse_compound_file(f, context=None):
"""Iterate over the compound entries in the given file"""
f.readline() # Skip header
for lineno, row in enumerate(csv.reader(f, delimiter='\t')):
compound_id, names, formula = row[:3]
names = (decode_name(name) for name in names.split(',<br>'))
... | python | def parse_compound_file(f, context=None):
"""Iterate over the compound entries in the given file"""
f.readline() # Skip header
for lineno, row in enumerate(csv.reader(f, delimiter='\t')):
compound_id, names, formula = row[:3]
names = (decode_name(name) for name in names.split(',<br>'))
... | [
"def",
"parse_compound_file",
"(",
"f",
",",
"context",
"=",
"None",
")",
":",
"f",
".",
"readline",
"(",
")",
"# Skip header",
"for",
"lineno",
",",
"row",
"in",
"enumerate",
"(",
"csv",
".",
"reader",
"(",
"f",
",",
"delimiter",
"=",
"'\\t'",
")",
... | Iterate over the compound entries in the given file | [
"Iterate",
"over",
"the",
"compound",
"entries",
"in",
"the",
"given",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/modelseed.py#L88-L111 | train | 65,133 |
zhanglab/psamm | psamm/commands/search.py | SearchCommand.init_parser | def init_parser(cls, parser):
"""Initialize argument parser"""
subparsers = parser.add_subparsers(title='Search domain')
# Compound subcommand
parser_compound = subparsers.add_parser(
'compound', help='Search in compounds')
parser_compound.set_defaults(which='compoun... | python | def init_parser(cls, parser):
"""Initialize argument parser"""
subparsers = parser.add_subparsers(title='Search domain')
# Compound subcommand
parser_compound = subparsers.add_parser(
'compound', help='Search in compounds')
parser_compound.set_defaults(which='compoun... | [
"def",
"init_parser",
"(",
"cls",
",",
"parser",
")",
":",
"subparsers",
"=",
"parser",
".",
"add_subparsers",
"(",
"title",
"=",
"'Search domain'",
")",
"# Compound subcommand",
"parser_compound",
"=",
"subparsers",
".",
"add_parser",
"(",
"'compound'",
",",
"h... | Initialize argument parser | [
"Initialize",
"argument",
"parser"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/commands/search.py#L36-L64 | train | 65,134 |
zhanglab/psamm | psamm/commands/search.py | SearchCommand.run | def run(self):
"""Run search command."""
which_command = self._args.which
if which_command == 'compound':
self._search_compound()
elif which_command == 'reaction':
self._search_reaction() | python | def run(self):
"""Run search command."""
which_command = self._args.which
if which_command == 'compound':
self._search_compound()
elif which_command == 'reaction':
self._search_reaction() | [
"def",
"run",
"(",
"self",
")",
":",
"which_command",
"=",
"self",
".",
"_args",
".",
"which",
"if",
"which_command",
"==",
"'compound'",
":",
"self",
".",
"_search_compound",
"(",
")",
"elif",
"which_command",
"==",
"'reaction'",
":",
"self",
".",
"_searc... | Run search command. | [
"Run",
"search",
"command",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/commands/search.py#L66-L73 | train | 65,135 |
hearsaycorp/normalize | normalize/property/json.py | JsonProperty.to_json | def to_json(self, propval, extraneous=False, to_json_func=None):
"""This function calls the ``json_out`` function, if it was specified,
otherwise continues with JSON conversion of the value in the slot by
calling ``to_json_func`` on it.
"""
if self.json_out:
return se... | python | def to_json(self, propval, extraneous=False, to_json_func=None):
"""This function calls the ``json_out`` function, if it was specified,
otherwise continues with JSON conversion of the value in the slot by
calling ``to_json_func`` on it.
"""
if self.json_out:
return se... | [
"def",
"to_json",
"(",
"self",
",",
"propval",
",",
"extraneous",
"=",
"False",
",",
"to_json_func",
"=",
"None",
")",
":",
"if",
"self",
".",
"json_out",
":",
"return",
"self",
".",
"json_out",
"(",
"propval",
")",
"else",
":",
"if",
"not",
"to_json_f... | This function calls the ``json_out`` function, if it was specified,
otherwise continues with JSON conversion of the value in the slot by
calling ``to_json_func`` on it. | [
"This",
"function",
"calls",
"the",
"json_out",
"function",
"if",
"it",
"was",
"specified",
"otherwise",
"continues",
"with",
"JSON",
"conversion",
"of",
"the",
"value",
"in",
"the",
"slot",
"by",
"calling",
"to_json_func",
"on",
"it",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/property/json.py#L78-L89 | train | 65,136 |
zhanglab/psamm | psamm/datasource/reaction.py | parse_compound | def parse_compound(s, global_compartment=None):
"""Parse a compound specification.
If no compartment is specified in the string, the global compartment
will be used.
"""
m = re.match(r'^\|(.*)\|$', s)
if m:
s = m.group(1)
m = re.match(r'^(.+)\[(\S+)\]$', s)
if m:
compou... | python | def parse_compound(s, global_compartment=None):
"""Parse a compound specification.
If no compartment is specified in the string, the global compartment
will be used.
"""
m = re.match(r'^\|(.*)\|$', s)
if m:
s = m.group(1)
m = re.match(r'^(.+)\[(\S+)\]$', s)
if m:
compou... | [
"def",
"parse_compound",
"(",
"s",
",",
"global_compartment",
"=",
"None",
")",
":",
"m",
"=",
"re",
".",
"match",
"(",
"r'^\\|(.*)\\|$'",
",",
"s",
")",
"if",
"m",
":",
"s",
"=",
"m",
".",
"group",
"(",
"1",
")",
"m",
"=",
"re",
".",
"match",
... | Parse a compound specification.
If no compartment is specified in the string, the global compartment
will be used. | [
"Parse",
"a",
"compound",
"specification",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/reaction.py#L226-L244 | train | 65,137 |
zhanglab/psamm | psamm/randomsparse.py | random_sparse | def random_sparse(strategy, prob, obj_reaction, flux_threshold):
"""Find a random minimal network of model reactions.
Given a reaction to optimize and a threshold, delete entities randomly
until the flux of the reaction to optimize falls under the threshold.
Keep deleting until no more entities can be ... | python | def random_sparse(strategy, prob, obj_reaction, flux_threshold):
"""Find a random minimal network of model reactions.
Given a reaction to optimize and a threshold, delete entities randomly
until the flux of the reaction to optimize falls under the threshold.
Keep deleting until no more entities can be ... | [
"def",
"random_sparse",
"(",
"strategy",
",",
"prob",
",",
"obj_reaction",
",",
"flux_threshold",
")",
":",
"essential",
"=",
"set",
"(",
")",
"deleted",
"=",
"set",
"(",
")",
"for",
"entity",
",",
"deleted_reactions",
"in",
"strategy",
".",
"iter_tests",
... | Find a random minimal network of model reactions.
Given a reaction to optimize and a threshold, delete entities randomly
until the flux of the reaction to optimize falls under the threshold.
Keep deleting until no more entities can be deleted. It works
with two strategies: deleting reactions or deletin... | [
"Find",
"a",
"random",
"minimal",
"network",
"of",
"model",
"reactions",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/randomsparse.py#L152-L224 | train | 65,138 |
zhanglab/psamm | psamm/commands/gapcheck.py | GapCheckCommand.run_sink_check | def run_sink_check(self, model, solver, threshold, implicit_sinks=True):
"""Run sink production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
for reaction_id in model.reactions:
lower, upper = model.limits[reaction_id]
... | python | def run_sink_check(self, model, solver, threshold, implicit_sinks=True):
"""Run sink production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
for reaction_id in model.reactions:
lower, upper = model.limits[reaction_id]
... | [
"def",
"run_sink_check",
"(",
"self",
",",
"model",
",",
"solver",
",",
"threshold",
",",
"implicit_sinks",
"=",
"True",
")",
":",
"prob",
"=",
"solver",
".",
"create_problem",
"(",
")",
"# Create flux variables",
"v",
"=",
"prob",
".",
"namespace",
"(",
"... | Run sink production check method. | [
"Run",
"sink",
"production",
"check",
"method",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/commands/gapcheck.py#L112-L157 | train | 65,139 |
zhanglab/psamm | psamm/commands/gapcheck.py | GapCheckCommand.run_reaction_production_check | def run_reaction_production_check(self, model, solver, threshold,
implicit_sinks=True):
"""Run reaction production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
for reaction_id in model.reaction... | python | def run_reaction_production_check(self, model, solver, threshold,
implicit_sinks=True):
"""Run reaction production check method."""
prob = solver.create_problem()
# Create flux variables
v = prob.namespace()
for reaction_id in model.reaction... | [
"def",
"run_reaction_production_check",
"(",
"self",
",",
"model",
",",
"solver",
",",
"threshold",
",",
"implicit_sinks",
"=",
"True",
")",
":",
"prob",
"=",
"solver",
".",
"create_problem",
"(",
")",
"# Create flux variables",
"v",
"=",
"prob",
".",
"namespa... | Run reaction production check method. | [
"Run",
"reaction",
"production",
"check",
"method",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/commands/gapcheck.py#L159-L217 | train | 65,140 |
zhanglab/psamm | psamm/lpsolver/cplex.py | Problem.add_linear_constraints | def add_linear_constraints(self, *relations):
"""Add constraints to the problem
Each constraint is represented by a Relation, and the
expression in that relation can be a set expression.
"""
constraints = []
for relation in relations:
if self._check_relation... | python | def add_linear_constraints(self, *relations):
"""Add constraints to the problem
Each constraint is represented by a Relation, and the
expression in that relation can be a set expression.
"""
constraints = []
for relation in relations:
if self._check_relation... | [
"def",
"add_linear_constraints",
"(",
"self",
",",
"*",
"relations",
")",
":",
"constraints",
"=",
"[",
"]",
"for",
"relation",
"in",
"relations",
":",
"if",
"self",
".",
"_check_relation",
"(",
"relation",
")",
":",
"constraints",
".",
"append",
"(",
"Con... | Add constraints to the problem
Each constraint is represented by a Relation, and the
expression in that relation can be a set expression. | [
"Add",
"constraints",
"to",
"the",
"problem"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/lpsolver/cplex.py#L206-L221 | train | 65,141 |
zhanglab/psamm | psamm/lpsolver/cplex.py | Problem.set_objective | def set_objective(self, expression):
"""Set objective expression of the problem."""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression(offset=expression)
linear = [... | python | def set_objective(self, expression):
"""Set objective expression of the problem."""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression(offset=expression)
linear = [... | [
"def",
"set_objective",
"(",
"self",
",",
"expression",
")",
":",
"if",
"isinstance",
"(",
"expression",
",",
"numbers",
".",
"Number",
")",
":",
"# Allow expressions with no variables as objective,",
"# represented as a number",
"expression",
"=",
"Expression",
"(",
... | Set objective expression of the problem. | [
"Set",
"objective",
"expression",
"of",
"the",
"problem",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/lpsolver/cplex.py#L223-L270 | train | 65,142 |
zhanglab/psamm | psamm/lpsolver/cplex.py | Problem._reset_problem_type | def _reset_problem_type(self):
"""Reset problem type to whatever is appropriate."""
# Only need to reset the type after the first solve. This also works
# around a bug in Cplex where get_num_binary() is some rare cases
# causes a segfault.
if self._solve_count > 0:
i... | python | def _reset_problem_type(self):
"""Reset problem type to whatever is appropriate."""
# Only need to reset the type after the first solve. This also works
# around a bug in Cplex where get_num_binary() is some rare cases
# causes a segfault.
if self._solve_count > 0:
i... | [
"def",
"_reset_problem_type",
"(",
"self",
")",
":",
"# Only need to reset the type after the first solve. This also works",
"# around a bug in Cplex where get_num_binary() is some rare cases",
"# causes a segfault.",
"if",
"self",
".",
"_solve_count",
">",
"0",
":",
"integer_count",... | Reset problem type to whatever is appropriate. | [
"Reset",
"problem",
"type",
"to",
"whatever",
"is",
"appropriate",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/lpsolver/cplex.py#L288-L341 | train | 65,143 |
zhanglab/psamm | psamm/lpsolver/cplex.py | Result.get_value | def get_value(self, expression):
"""Return value of expression."""
self._check_valid()
return super(Result, self).get_value(expression) | python | def get_value(self, expression):
"""Return value of expression."""
self._check_valid()
return super(Result, self).get_value(expression) | [
"def",
"get_value",
"(",
"self",
",",
"expression",
")",
":",
"self",
".",
"_check_valid",
"(",
")",
"return",
"super",
"(",
"Result",
",",
"self",
")",
".",
"get_value",
"(",
"expression",
")"
] | Return value of expression. | [
"Return",
"value",
"of",
"expression",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/lpsolver/cplex.py#L468-L471 | train | 65,144 |
zhanglab/psamm | psamm/formula.py | _parse_formula | def _parse_formula(s):
"""Parse formula string."""
scanner = re.compile(r'''
(\s+) | # whitespace
(\(|\)) | # group
([A-Z][a-z]*) | # element
(\d+) | # number
([a-z]) | # variable
(\Z) | # end
(.) # error
... | python | def _parse_formula(s):
"""Parse formula string."""
scanner = re.compile(r'''
(\s+) | # whitespace
(\(|\)) | # group
([A-Z][a-z]*) | # element
(\d+) | # number
([a-z]) | # variable
(\Z) | # end
(.) # error
... | [
"def",
"_parse_formula",
"(",
"s",
")",
":",
"scanner",
"=",
"re",
".",
"compile",
"(",
"r'''\n (\\s+) | # whitespace\n (\\(|\\)) | # group\n ([A-Z][a-z]*) | # element\n (\\d+) | # number\n ([a-z]) | # variable\n (\\Z) | ... | Parse formula string. | [
"Parse",
"formula",
"string",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/formula.py#L425-L510 | train | 65,145 |
hearsaycorp/normalize | normalize/visitor.py | Visitor.copy | def copy(self):
"""Be sure to implement this method when sub-classing, otherwise you
will lose any specialization context."""
doppel = type(self)(
self.unpack, self.apply, self.collect, self.reduce,
apply_empty_slots=self.apply_empty_slots,
extraneous=self.ext... | python | def copy(self):
"""Be sure to implement this method when sub-classing, otherwise you
will lose any specialization context."""
doppel = type(self)(
self.unpack, self.apply, self.collect, self.reduce,
apply_empty_slots=self.apply_empty_slots,
extraneous=self.ext... | [
"def",
"copy",
"(",
"self",
")",
":",
"doppel",
"=",
"type",
"(",
"self",
")",
"(",
"self",
".",
"unpack",
",",
"self",
".",
"apply",
",",
"self",
".",
"collect",
",",
"self",
".",
"reduce",
",",
"apply_empty_slots",
"=",
"self",
".",
"apply_empty_sl... | Be sure to implement this method when sub-classing, otherwise you
will lose any specialization context. | [
"Be",
"sure",
"to",
"implement",
"this",
"method",
"when",
"sub",
"-",
"classing",
"otherwise",
"you",
"will",
"lose",
"any",
"specialization",
"context",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/visitor.py#L105-L119 | train | 65,146 |
hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.unpack | def unpack(cls, value, value_type, visitor):
"""Unpack a value during a 'visit'
args:
``value=``\ *object*
The instance being visited
``value_type=``\ *RecordType*
The expected type of the instance
``visitor=``\ *Visitor*
... | python | def unpack(cls, value, value_type, visitor):
"""Unpack a value during a 'visit'
args:
``value=``\ *object*
The instance being visited
``value_type=``\ *RecordType*
The expected type of the instance
``visitor=``\ *Visitor*
... | [
"def",
"unpack",
"(",
"cls",
",",
"value",
",",
"value_type",
",",
"visitor",
")",
":",
"if",
"issubclass",
"(",
"value_type",
",",
"Collection",
")",
":",
"try",
":",
"generator",
"=",
"value",
".",
"itertuples",
"(",
")",
"except",
"AttributeError",
":... | Unpack a value during a 'visit'
args:
``value=``\ *object*
The instance being visited
``value_type=``\ *RecordType*
The expected type of the instance
``visitor=``\ *Visitor*
The context/options
returns a tuple with ... | [
"Unpack",
"a",
"value",
"during",
"a",
"visit"
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/visitor.py#L196-L247 | train | 65,147 |
hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.apply | def apply(cls, value, prop, visitor):
"""'apply' is a general place to put a function which is called on
every extant record slot. This is usually the most important function
to implement when sub-classing.
The default implementation passes through the slot value as-is, but
exp... | python | def apply(cls, value, prop, visitor):
"""'apply' is a general place to put a function which is called on
every extant record slot. This is usually the most important function
to implement when sub-classing.
The default implementation passes through the slot value as-is, but
exp... | [
"def",
"apply",
"(",
"cls",
",",
"value",
",",
"prop",
",",
"visitor",
")",
":",
"return",
"(",
"None",
"if",
"isinstance",
"(",
"value",
",",
"(",
"AttributeError",
",",
"KeyError",
")",
")",
"else",
"value",
")"
] | apply' is a general place to put a function which is called on
every extant record slot. This is usually the most important function
to implement when sub-classing.
The default implementation passes through the slot value as-is, but
expected exceptions are converted to ``None``.
... | [
"apply",
"is",
"a",
"general",
"place",
"to",
"put",
"a",
"function",
"which",
"is",
"called",
"on",
"every",
"extant",
"record",
"slot",
".",
"This",
"is",
"usually",
"the",
"most",
"important",
"function",
"to",
"implement",
"when",
"sub",
"-",
"classing... | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/visitor.py#L250-L284 | train | 65,148 |
hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.aggregate | def aggregate(self, mapped_coll_generator, coll_type, visitor):
"""Hook called for each normalize.coll.Collection, after mapping over
each of the items in the collection.
The default implementation calls
:py:meth:`normalize.coll.Collection.tuples_to_coll` with
``coerce=False``, ... | python | def aggregate(self, mapped_coll_generator, coll_type, visitor):
"""Hook called for each normalize.coll.Collection, after mapping over
each of the items in the collection.
The default implementation calls
:py:meth:`normalize.coll.Collection.tuples_to_coll` with
``coerce=False``, ... | [
"def",
"aggregate",
"(",
"self",
",",
"mapped_coll_generator",
",",
"coll_type",
",",
"visitor",
")",
":",
"return",
"coll_type",
".",
"tuples_to_coll",
"(",
"mapped_coll_generator",
",",
"coerce",
"=",
"False",
")"
] | Hook called for each normalize.coll.Collection, after mapping over
each of the items in the collection.
The default implementation calls
:py:meth:`normalize.coll.Collection.tuples_to_coll` with
``coerce=False``, which just re-assembles the collection into a native
python collect... | [
"Hook",
"called",
"for",
"each",
"normalize",
".",
"coll",
".",
"Collection",
"after",
"mapping",
"over",
"each",
"of",
"the",
"items",
"in",
"the",
"collection",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/visitor.py#L287-L309 | train | 65,149 |
hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.reduce | def reduce(self, mapped_props, aggregated, value_type, visitor):
"""This reduction is called to combine the mapped slot and collection
item values into a single value for return.
The default implementation tries to behave naturally; you'll almost
always get a dict back when mapping over... | python | def reduce(self, mapped_props, aggregated, value_type, visitor):
"""This reduction is called to combine the mapped slot and collection
item values into a single value for return.
The default implementation tries to behave naturally; you'll almost
always get a dict back when mapping over... | [
"def",
"reduce",
"(",
"self",
",",
"mapped_props",
",",
"aggregated",
",",
"value_type",
",",
"visitor",
")",
":",
"reduced",
"=",
"None",
"if",
"mapped_props",
":",
"reduced",
"=",
"dict",
"(",
"(",
"k",
".",
"name",
",",
"v",
")",
"for",
"k",
",",
... | This reduction is called to combine the mapped slot and collection
item values into a single value for return.
The default implementation tries to behave naturally; you'll almost
always get a dict back when mapping over a record, and list or some
other collection when mapping over colle... | [
"This",
"reduction",
"is",
"called",
"to",
"combine",
"the",
"mapped",
"slot",
"and",
"collection",
"item",
"values",
"into",
"a",
"single",
"value",
"for",
"return",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/visitor.py#L312-L359 | train | 65,150 |
hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.reflect | def reflect(cls, X, **kwargs):
"""Reflect is for visitors where you are exposing some information
about the types reachable from a starting type to an external system.
For example, a front-end, a REST URL router and documentation
framework, an avro schema definition, etc.
X can ... | python | def reflect(cls, X, **kwargs):
"""Reflect is for visitors where you are exposing some information
about the types reachable from a starting type to an external system.
For example, a front-end, a REST URL router and documentation
framework, an avro schema definition, etc.
X can ... | [
"def",
"reflect",
"(",
"cls",
",",
"X",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"isinstance",
"(",
"X",
",",
"type",
")",
":",
"value",
"=",
"None",
"value_type",
"=",
"X",
"else",
":",
"value",
"=",
"X",
"value_type",
"=",
"type",
"(",
"X",
"... | Reflect is for visitors where you are exposing some information
about the types reachable from a starting type to an external system.
For example, a front-end, a REST URL router and documentation
framework, an avro schema definition, etc.
X can be a type or an instance.
This AP... | [
"Reflect",
"is",
"for",
"visitors",
"where",
"you",
"are",
"exposing",
"some",
"information",
"about",
"the",
"types",
"reachable",
"from",
"a",
"starting",
"type",
"to",
"an",
"external",
"system",
".",
"For",
"example",
"a",
"front",
"-",
"end",
"a",
"RE... | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/visitor.py#L482-L506 | train | 65,151 |
hearsaycorp/normalize | normalize/visitor.py | VisitorPattern.map | def map(cls, visitor, value, value_type):
"""The common visitor API used by all three visitor implementations.
args:
``visitor=``\ *Visitor*
Visitor options instance: contains the callbacks to use to
implement the visiting, as well as traversal & filtering
... | python | def map(cls, visitor, value, value_type):
"""The common visitor API used by all three visitor implementations.
args:
``visitor=``\ *Visitor*
Visitor options instance: contains the callbacks to use to
implement the visiting, as well as traversal & filtering
... | [
"def",
"map",
"(",
"cls",
",",
"visitor",
",",
"value",
",",
"value_type",
")",
":",
"unpacked",
"=",
"visitor",
".",
"unpack",
"(",
"value",
",",
"value_type",
",",
"visitor",
")",
"if",
"unpacked",
"==",
"cls",
".",
"StopVisiting",
"or",
"isinstance",
... | The common visitor API used by all three visitor implementations.
args:
``visitor=``\ *Visitor*
Visitor options instance: contains the callbacks to use to
implement the visiting, as well as traversal & filtering
options.
``value=``\ *Obj... | [
"The",
"common",
"visitor",
"API",
"used",
"by",
"all",
"three",
"visitor",
"implementations",
"."
] | 8b36522ddca6d41b434580bd848f3bdaa7a999c8 | https://github.com/hearsaycorp/normalize/blob/8b36522ddca6d41b434580bd848f3bdaa7a999c8/normalize/visitor.py#L591-L639 | train | 65,152 |
zhanglab/psamm | psamm/fluxanalysis.py | _get_fba_problem | def _get_fba_problem(model, tfba, solver):
"""Convenience function for returning the right FBA problem instance"""
p = FluxBalanceProblem(model, solver)
if tfba:
p.add_thermodynamic()
return p | python | def _get_fba_problem(model, tfba, solver):
"""Convenience function for returning the right FBA problem instance"""
p = FluxBalanceProblem(model, solver)
if tfba:
p.add_thermodynamic()
return p | [
"def",
"_get_fba_problem",
"(",
"model",
",",
"tfba",
",",
"solver",
")",
":",
"p",
"=",
"FluxBalanceProblem",
"(",
"model",
",",
"solver",
")",
"if",
"tfba",
":",
"p",
".",
"add_thermodynamic",
"(",
")",
"return",
"p"
] | Convenience function for returning the right FBA problem instance | [
"Convenience",
"function",
"for",
"returning",
"the",
"right",
"FBA",
"problem",
"instance"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L35-L40 | train | 65,153 |
zhanglab/psamm | psamm/fluxanalysis.py | flux_balance | def flux_balance(model, reaction, tfba, solver):
"""Run flux balance analysis on the given model.
Yields the reaction id and flux value for each reaction in the model.
This is a convenience function for sertting up and running the
FluxBalanceProblem. If the FBA is solved for more than one parameter
... | python | def flux_balance(model, reaction, tfba, solver):
"""Run flux balance analysis on the given model.
Yields the reaction id and flux value for each reaction in the model.
This is a convenience function for sertting up and running the
FluxBalanceProblem. If the FBA is solved for more than one parameter
... | [
"def",
"flux_balance",
"(",
"model",
",",
"reaction",
",",
"tfba",
",",
"solver",
")",
":",
"fba",
"=",
"_get_fba_problem",
"(",
"model",
",",
"tfba",
",",
"solver",
")",
"fba",
".",
"maximize",
"(",
"reaction",
")",
"for",
"reaction",
"in",
"model",
"... | Run flux balance analysis on the given model.
Yields the reaction id and flux value for each reaction in the model.
This is a convenience function for sertting up and running the
FluxBalanceProblem. If the FBA is solved for more than one parameter
it is recommended to setup and reuse the FluxBalancePr... | [
"Run",
"flux",
"balance",
"analysis",
"on",
"the",
"given",
"model",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L293-L320 | train | 65,154 |
zhanglab/psamm | psamm/fluxanalysis.py | flux_variability | def flux_variability(model, reactions, fixed, tfba, solver):
"""Find the variability of each reaction while fixing certain fluxes.
Yields the reaction id, and a tuple of minimum and maximum value for each
of the given reactions. The fixed reactions are given in a dictionary as
a reaction id to value ma... | python | def flux_variability(model, reactions, fixed, tfba, solver):
"""Find the variability of each reaction while fixing certain fluxes.
Yields the reaction id, and a tuple of minimum and maximum value for each
of the given reactions. The fixed reactions are given in a dictionary as
a reaction id to value ma... | [
"def",
"flux_variability",
"(",
"model",
",",
"reactions",
",",
"fixed",
",",
"tfba",
",",
"solver",
")",
":",
"fba",
"=",
"_get_fba_problem",
"(",
"model",
",",
"tfba",
",",
"solver",
")",
"for",
"reaction_id",
",",
"value",
"in",
"iteritems",
"(",
"fix... | Find the variability of each reaction while fixing certain fluxes.
Yields the reaction id, and a tuple of minimum and maximum value for each
of the given reactions. The fixed reactions are given in a dictionary as
a reaction id to value mapping.
This is an implementation of flux variability analysis (... | [
"Find",
"the",
"variability",
"of",
"each",
"reaction",
"while",
"fixing",
"certain",
"fluxes",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L323-L357 | train | 65,155 |
zhanglab/psamm | psamm/fluxanalysis.py | flux_minimization | def flux_minimization(model, fixed, solver, weights={}):
"""Minimize flux of all reactions while keeping certain fluxes fixed.
The fixed reactions are given in a dictionary as reaction id
to value mapping. The weighted L1-norm of the fluxes is minimized.
Args:
model: MetabolicModel to solve.
... | python | def flux_minimization(model, fixed, solver, weights={}):
"""Minimize flux of all reactions while keeping certain fluxes fixed.
The fixed reactions are given in a dictionary as reaction id
to value mapping. The weighted L1-norm of the fluxes is minimized.
Args:
model: MetabolicModel to solve.
... | [
"def",
"flux_minimization",
"(",
"model",
",",
"fixed",
",",
"solver",
",",
"weights",
"=",
"{",
"}",
")",
":",
"fba",
"=",
"FluxBalanceProblem",
"(",
"model",
",",
"solver",
")",
"for",
"reaction_id",
",",
"value",
"in",
"iteritems",
"(",
"fixed",
")",
... | Minimize flux of all reactions while keeping certain fluxes fixed.
The fixed reactions are given in a dictionary as reaction id
to value mapping. The weighted L1-norm of the fluxes is minimized.
Args:
model: MetabolicModel to solve.
fixed: dict of additional lower bounds on reaction fluxes... | [
"Minimize",
"flux",
"of",
"all",
"reactions",
"while",
"keeping",
"certain",
"fluxes",
"fixed",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L360-L385 | train | 65,156 |
zhanglab/psamm | psamm/fluxanalysis.py | flux_randomization | def flux_randomization(model, threshold, tfba, solver):
"""Find a random flux solution on the boundary of the solution space.
The reactions in the threshold dictionary are constrained with the
associated lower bound.
Args:
model: MetabolicModel to solve.
threshold: dict of additional l... | python | def flux_randomization(model, threshold, tfba, solver):
"""Find a random flux solution on the boundary of the solution space.
The reactions in the threshold dictionary are constrained with the
associated lower bound.
Args:
model: MetabolicModel to solve.
threshold: dict of additional l... | [
"def",
"flux_randomization",
"(",
"model",
",",
"threshold",
",",
"tfba",
",",
"solver",
")",
":",
"optimize",
"=",
"{",
"}",
"for",
"reaction_id",
"in",
"model",
".",
"reactions",
":",
"if",
"model",
".",
"is_reversible",
"(",
"reaction_id",
")",
":",
"... | Find a random flux solution on the boundary of the solution space.
The reactions in the threshold dictionary are constrained with the
associated lower bound.
Args:
model: MetabolicModel to solve.
threshold: dict of additional lower bounds on reaction fluxes.
tfba: If True enable th... | [
"Find",
"a",
"random",
"flux",
"solution",
"on",
"the",
"boundary",
"of",
"the",
"solution",
"space",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L388-L417 | train | 65,157 |
zhanglab/psamm | psamm/fluxanalysis.py | consistency_check | def consistency_check(model, subset, epsilon, tfba, solver):
"""Check that reaction subset of model is consistent using FBA.
Yields all reactions that are *not* flux consistent. A reaction is
consistent if there is at least one flux solution to the model that both
respects the model constraints and als... | python | def consistency_check(model, subset, epsilon, tfba, solver):
"""Check that reaction subset of model is consistent using FBA.
Yields all reactions that are *not* flux consistent. A reaction is
consistent if there is at least one flux solution to the model that both
respects the model constraints and als... | [
"def",
"consistency_check",
"(",
"model",
",",
"subset",
",",
"epsilon",
",",
"tfba",
",",
"solver",
")",
":",
"fba",
"=",
"_get_fba_problem",
"(",
"model",
",",
"tfba",
",",
"solver",
")",
"subset",
"=",
"set",
"(",
"subset",
")",
"while",
"len",
"(",... | Check that reaction subset of model is consistent using FBA.
Yields all reactions that are *not* flux consistent. A reaction is
consistent if there is at least one flux solution to the model that both
respects the model constraints and also allows the reaction in question to
have non-zero flux.
Th... | [
"Check",
"that",
"reaction",
"subset",
"of",
"model",
"is",
"consistent",
"using",
"FBA",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L420-L470 | train | 65,158 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.add_thermodynamic | def add_thermodynamic(self, em=1000):
"""Apply thermodynamic constraints to the model.
Adding these constraints restricts the solution space to only
contain solutions that have no internal loops [Schilling00]_. This is
solved as a MILP problem as described in [Muller13]_. The time to so... | python | def add_thermodynamic(self, em=1000):
"""Apply thermodynamic constraints to the model.
Adding these constraints restricts the solution space to only
contain solutions that have no internal loops [Schilling00]_. This is
solved as a MILP problem as described in [Muller13]_. The time to so... | [
"def",
"add_thermodynamic",
"(",
"self",
",",
"em",
"=",
"1000",
")",
":",
"internal",
"=",
"set",
"(",
"r",
"for",
"r",
"in",
"self",
".",
"_model",
".",
"reactions",
"if",
"not",
"self",
".",
"_model",
".",
"is_exchange",
"(",
"r",
")",
")",
"# R... | Apply thermodynamic constraints to the model.
Adding these constraints restricts the solution space to only
contain solutions that have no internal loops [Schilling00]_. This is
solved as a MILP problem as described in [Muller13]_. The time to solve
a problem with thermodynamic constrai... | [
"Apply",
"thermodynamic",
"constraints",
"to",
"the",
"model",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L110-L168 | train | 65,159 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.maximize | def maximize(self, reaction):
"""Solve the model by maximizing the given reaction.
If reaction is a dictionary object, each entry is interpreted as a
weight on the objective for that reaction (non-existent reaction will
have zero weight).
"""
self._prob.set_objective(se... | python | def maximize(self, reaction):
"""Solve the model by maximizing the given reaction.
If reaction is a dictionary object, each entry is interpreted as a
weight on the objective for that reaction (non-existent reaction will
have zero weight).
"""
self._prob.set_objective(se... | [
"def",
"maximize",
"(",
"self",
",",
"reaction",
")",
":",
"self",
".",
"_prob",
".",
"set_objective",
"(",
"self",
".",
"flux_expr",
"(",
"reaction",
")",
")",
"self",
".",
"_solve",
"(",
")"
] | Solve the model by maximizing the given reaction.
If reaction is a dictionary object, each entry is interpreted as a
weight on the objective for that reaction (non-existent reaction will
have zero weight). | [
"Solve",
"the",
"model",
"by",
"maximizing",
"the",
"given",
"reaction",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L170-L179 | train | 65,160 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.flux_bound | def flux_bound(self, reaction, direction):
"""Return the flux bound of the reaction.
Direction must be a positive number to obtain the upper bound or a
negative number to obtain the lower bound. A value of inf or -inf is
returned if the problem is unbounded.
"""
try:
... | python | def flux_bound(self, reaction, direction):
"""Return the flux bound of the reaction.
Direction must be a positive number to obtain the upper bound or a
negative number to obtain the lower bound. A value of inf or -inf is
returned if the problem is unbounded.
"""
try:
... | [
"def",
"flux_bound",
"(",
"self",
",",
"reaction",
",",
"direction",
")",
":",
"try",
":",
"self",
".",
"maximize",
"(",
"{",
"reaction",
":",
"direction",
"}",
")",
"except",
"FluxBalanceError",
"as",
"e",
":",
"if",
"not",
"e",
".",
"result",
".",
... | Return the flux bound of the reaction.
Direction must be a positive number to obtain the upper bound or a
negative number to obtain the lower bound. A value of inf or -inf is
returned if the problem is unbounded. | [
"Return",
"the",
"flux",
"bound",
"of",
"the",
"reaction",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L181-L195 | train | 65,161 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem._add_minimization_vars | def _add_minimization_vars(self):
"""Add variables and constraints for L1 norm minimization."""
self._z = self._prob.namespace(self._model.reactions, lower=0)
# Define constraints
v = self._v.set(self._model.reactions)
z = self._z.set(self._model.reactions)
self._prob.... | python | def _add_minimization_vars(self):
"""Add variables and constraints for L1 norm minimization."""
self._z = self._prob.namespace(self._model.reactions, lower=0)
# Define constraints
v = self._v.set(self._model.reactions)
z = self._z.set(self._model.reactions)
self._prob.... | [
"def",
"_add_minimization_vars",
"(",
"self",
")",
":",
"self",
".",
"_z",
"=",
"self",
".",
"_prob",
".",
"namespace",
"(",
"self",
".",
"_model",
".",
"reactions",
",",
"lower",
"=",
"0",
")",
"# Define constraints",
"v",
"=",
"self",
".",
"_v",
".",... | Add variables and constraints for L1 norm minimization. | [
"Add",
"variables",
"and",
"constraints",
"for",
"L1",
"norm",
"minimization",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L197-L206 | train | 65,162 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.minimize_l1 | def minimize_l1(self, weights={}):
"""Solve the model by minimizing the L1 norm of the fluxes.
If the weights dictionary is given, the weighted L1 norm if minimized
instead. The dictionary contains the weights of each reaction
(default 1).
"""
if self._z is None:
... | python | def minimize_l1(self, weights={}):
"""Solve the model by minimizing the L1 norm of the fluxes.
If the weights dictionary is given, the weighted L1 norm if minimized
instead. The dictionary contains the weights of each reaction
(default 1).
"""
if self._z is None:
... | [
"def",
"minimize_l1",
"(",
"self",
",",
"weights",
"=",
"{",
"}",
")",
":",
"if",
"self",
".",
"_z",
"is",
"None",
":",
"self",
".",
"_add_minimization_vars",
"(",
")",
"objective",
"=",
"self",
".",
"_z",
".",
"expr",
"(",
"(",
"reaction_id",
",",
... | Solve the model by minimizing the L1 norm of the fluxes.
If the weights dictionary is given, the weighted L1 norm if minimized
instead. The dictionary contains the weights of each reaction
(default 1). | [
"Solve",
"the",
"model",
"by",
"minimizing",
"the",
"L1",
"norm",
"of",
"the",
"fluxes",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L208-L224 | train | 65,163 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.max_min_l1 | def max_min_l1(self, reaction, weights={}):
"""Maximize flux of reaction then minimize the L1 norm.
During minimization the given reaction will be fixed at the maximum
obtained from the first solution. If reaction is a dictionary object,
each entry is interpreted as a weight on the obje... | python | def max_min_l1(self, reaction, weights={}):
"""Maximize flux of reaction then minimize the L1 norm.
During minimization the given reaction will be fixed at the maximum
obtained from the first solution. If reaction is a dictionary object,
each entry is interpreted as a weight on the obje... | [
"def",
"max_min_l1",
"(",
"self",
",",
"reaction",
",",
"weights",
"=",
"{",
"}",
")",
":",
"self",
".",
"maximize",
"(",
"reaction",
")",
"if",
"isinstance",
"(",
"reaction",
",",
"dict",
")",
":",
"reactions",
"=",
"list",
"(",
"reaction",
")",
"el... | Maximize flux of reaction then minimize the L1 norm.
During minimization the given reaction will be fixed at the maximum
obtained from the first solution. If reaction is a dictionary object,
each entry is interpreted as a weight on the objective for that
reaction (non-existent reaction ... | [
"Maximize",
"flux",
"of",
"reaction",
"then",
"minimize",
"the",
"L1",
"norm",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L226-L251 | train | 65,164 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem._solve | def _solve(self):
"""Solve the problem with the current objective."""
# Remove temporary constraints
while len(self._remove_constr) > 0:
self._remove_constr.pop().delete()
try:
self._prob.solve(lp.ObjectiveSense.Maximize)
except lp.SolverError as e:
... | python | def _solve(self):
"""Solve the problem with the current objective."""
# Remove temporary constraints
while len(self._remove_constr) > 0:
self._remove_constr.pop().delete()
try:
self._prob.solve(lp.ObjectiveSense.Maximize)
except lp.SolverError as e:
... | [
"def",
"_solve",
"(",
"self",
")",
":",
"# Remove temporary constraints",
"while",
"len",
"(",
"self",
".",
"_remove_constr",
")",
">",
"0",
":",
"self",
".",
"_remove_constr",
".",
"pop",
"(",
")",
".",
"delete",
"(",
")",
"try",
":",
"self",
".",
"_p... | Solve the problem with the current objective. | [
"Solve",
"the",
"problem",
"with",
"the",
"current",
"objective",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L261-L276 | train | 65,165 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.flux_expr | def flux_expr(self, reaction):
"""Get LP expression representing the reaction flux."""
if isinstance(reaction, dict):
return self._v.expr(iteritems(reaction))
return self._v(reaction) | python | def flux_expr(self, reaction):
"""Get LP expression representing the reaction flux."""
if isinstance(reaction, dict):
return self._v.expr(iteritems(reaction))
return self._v(reaction) | [
"def",
"flux_expr",
"(",
"self",
",",
"reaction",
")",
":",
"if",
"isinstance",
"(",
"reaction",
",",
"dict",
")",
":",
"return",
"self",
".",
"_v",
".",
"expr",
"(",
"iteritems",
"(",
"reaction",
")",
")",
"return",
"self",
".",
"_v",
"(",
"reaction... | Get LP expression representing the reaction flux. | [
"Get",
"LP",
"expression",
"representing",
"the",
"reaction",
"flux",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L282-L286 | train | 65,166 |
zhanglab/psamm | psamm/fluxanalysis.py | FluxBalanceProblem.get_flux | def get_flux(self, reaction):
"""Get resulting flux value for reaction."""
return self._prob.result.get_value(self._v(reaction)) | python | def get_flux(self, reaction):
"""Get resulting flux value for reaction."""
return self._prob.result.get_value(self._v(reaction)) | [
"def",
"get_flux",
"(",
"self",
",",
"reaction",
")",
":",
"return",
"self",
".",
"_prob",
".",
"result",
".",
"get_value",
"(",
"self",
".",
"_v",
"(",
"reaction",
")",
")"
] | Get resulting flux value for reaction. | [
"Get",
"resulting",
"flux",
"value",
"for",
"reaction",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/fluxanalysis.py#L288-L290 | train | 65,167 |
zhanglab/psamm | psamm/lpsolver/qsoptex.py | Problem.set_objective | def set_objective(self, expression):
"""Set linear objective of problem"""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression()
self._p.set_linear_objective(
... | python | def set_objective(self, expression):
"""Set linear objective of problem"""
if isinstance(expression, numbers.Number):
# Allow expressions with no variables as objective,
# represented as a number
expression = Expression()
self._p.set_linear_objective(
... | [
"def",
"set_objective",
"(",
"self",
",",
"expression",
")",
":",
"if",
"isinstance",
"(",
"expression",
",",
"numbers",
".",
"Number",
")",
":",
"# Allow expressions with no variables as objective,",
"# represented as a number",
"expression",
"=",
"Expression",
"(",
... | Set linear objective of problem | [
"Set",
"linear",
"objective",
"of",
"problem"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/lpsolver/qsoptex.py#L150-L160 | train | 65,168 |
zhanglab/psamm | psamm/lpsolver/qsoptex.py | Result.unbounded | def unbounded(self):
"""Whether the solution is unbounded"""
self._check_valid()
return (self._problem._p.get_status() ==
qsoptex.SolutionStatus.UNBOUNDED) | python | def unbounded(self):
"""Whether the solution is unbounded"""
self._check_valid()
return (self._problem._p.get_status() ==
qsoptex.SolutionStatus.UNBOUNDED) | [
"def",
"unbounded",
"(",
"self",
")",
":",
"self",
".",
"_check_valid",
"(",
")",
"return",
"(",
"self",
".",
"_problem",
".",
"_p",
".",
"get_status",
"(",
")",
"==",
"qsoptex",
".",
"SolutionStatus",
".",
"UNBOUNDED",
")"
] | Whether the solution is unbounded | [
"Whether",
"the",
"solution",
"is",
"unbounded"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/lpsolver/qsoptex.py#L245-L249 | train | 65,169 |
smartfile/python-librsync | librsync/__init__.py | _execute | def _execute(job, f, o=None):
"""
Executes a librsync "job" by reading bytes from `f` and writing results to
`o` if provided. If `o` is omitted, the output is ignored.
"""
# Re-use the same buffer for output, we will read from it after each
# iteration.
out = ctypes.create_string_buffer(RS_J... | python | def _execute(job, f, o=None):
"""
Executes a librsync "job" by reading bytes from `f` and writing results to
`o` if provided. If `o` is omitted, the output is ignored.
"""
# Re-use the same buffer for output, we will read from it after each
# iteration.
out = ctypes.create_string_buffer(RS_J... | [
"def",
"_execute",
"(",
"job",
",",
"f",
",",
"o",
"=",
"None",
")",
":",
"# Re-use the same buffer for output, we will read from it after each",
"# iteration.",
"out",
"=",
"ctypes",
".",
"create_string_buffer",
"(",
"RS_JOB_BLOCKSIZE",
")",
"while",
"True",
":",
"... | Executes a librsync "job" by reading bytes from `f` and writing results to
`o` if provided. If `o` is omitted, the output is ignored. | [
"Executes",
"a",
"librsync",
"job",
"by",
"reading",
"bytes",
"from",
"f",
"and",
"writing",
"results",
"to",
"o",
"if",
"provided",
".",
"If",
"o",
"is",
"omitted",
"the",
"output",
"is",
"ignored",
"."
] | 1859a5f44317dce3e0997c740ac0f8675d77c4e3 | https://github.com/smartfile/python-librsync/blob/1859a5f44317dce3e0997c740ac0f8675d77c4e3/librsync/__init__.py#L118-L152 | train | 65,170 |
smartfile/python-librsync | librsync/__init__.py | signature | def signature(f, s=None, block_size=RS_DEFAULT_BLOCK_LEN):
"""
Generate a signature for the file `f`. The signature will be written to `s`.
If `s` is omitted, a temporary file will be used. This function returns the
signature file `s`. You can specify the size of the blocks using the
optional `block... | python | def signature(f, s=None, block_size=RS_DEFAULT_BLOCK_LEN):
"""
Generate a signature for the file `f`. The signature will be written to `s`.
If `s` is omitted, a temporary file will be used. This function returns the
signature file `s`. You can specify the size of the blocks using the
optional `block... | [
"def",
"signature",
"(",
"f",
",",
"s",
"=",
"None",
",",
"block_size",
"=",
"RS_DEFAULT_BLOCK_LEN",
")",
":",
"if",
"s",
"is",
"None",
":",
"s",
"=",
"tempfile",
".",
"SpooledTemporaryFile",
"(",
"max_size",
"=",
"MAX_SPOOL",
",",
"mode",
"=",
"'wb+'",
... | Generate a signature for the file `f`. The signature will be written to `s`.
If `s` is omitted, a temporary file will be used. This function returns the
signature file `s`. You can specify the size of the blocks using the
optional `block_size` parameter. | [
"Generate",
"a",
"signature",
"for",
"the",
"file",
"f",
".",
"The",
"signature",
"will",
"be",
"written",
"to",
"s",
".",
"If",
"s",
"is",
"omitted",
"a",
"temporary",
"file",
"will",
"be",
"used",
".",
"This",
"function",
"returns",
"the",
"signature",... | 1859a5f44317dce3e0997c740ac0f8675d77c4e3 | https://github.com/smartfile/python-librsync/blob/1859a5f44317dce3e0997c740ac0f8675d77c4e3/librsync/__init__.py#L161-L175 | train | 65,171 |
smartfile/python-librsync | librsync/__init__.py | delta | def delta(f, s, d=None):
"""
Create a delta for the file `f` using the signature read from `s`. The delta
will be written to `d`. If `d` is omitted, a temporary file will be used.
This function returns the delta file `d`. All parameters must be file-like
objects.
"""
if d is None:
d ... | python | def delta(f, s, d=None):
"""
Create a delta for the file `f` using the signature read from `s`. The delta
will be written to `d`. If `d` is omitted, a temporary file will be used.
This function returns the delta file `d`. All parameters must be file-like
objects.
"""
if d is None:
d ... | [
"def",
"delta",
"(",
"f",
",",
"s",
",",
"d",
"=",
"None",
")",
":",
"if",
"d",
"is",
"None",
":",
"d",
"=",
"tempfile",
".",
"SpooledTemporaryFile",
"(",
"max_size",
"=",
"MAX_SPOOL",
",",
"mode",
"=",
"'wb+'",
")",
"sig",
"=",
"ctypes",
".",
"c... | Create a delta for the file `f` using the signature read from `s`. The delta
will be written to `d`. If `d` is omitted, a temporary file will be used.
This function returns the delta file `d`. All parameters must be file-like
objects. | [
"Create",
"a",
"delta",
"for",
"the",
"file",
"f",
"using",
"the",
"signature",
"read",
"from",
"s",
".",
"The",
"delta",
"will",
"be",
"written",
"to",
"d",
".",
"If",
"d",
"is",
"omitted",
"a",
"temporary",
"file",
"will",
"be",
"used",
".",
"This"... | 1859a5f44317dce3e0997c740ac0f8675d77c4e3 | https://github.com/smartfile/python-librsync/blob/1859a5f44317dce3e0997c740ac0f8675d77c4e3/librsync/__init__.py#L179-L205 | train | 65,172 |
smartfile/python-librsync | librsync/__init__.py | patch | def patch(f, d, o=None):
"""
Patch the file `f` using the delta `d`. The patched file will be written to
`o`. If `o` is omitted, a temporary file will be used. This function returns
the be patched file `o`. All parameters should be file-like objects. `f` is
required to be seekable.
"""
if o ... | python | def patch(f, d, o=None):
"""
Patch the file `f` using the delta `d`. The patched file will be written to
`o`. If `o` is omitted, a temporary file will be used. This function returns
the be patched file `o`. All parameters should be file-like objects. `f` is
required to be seekable.
"""
if o ... | [
"def",
"patch",
"(",
"f",
",",
"d",
",",
"o",
"=",
"None",
")",
":",
"if",
"o",
"is",
"None",
":",
"o",
"=",
"tempfile",
".",
"SpooledTemporaryFile",
"(",
"max_size",
"=",
"MAX_SPOOL",
",",
"mode",
"=",
"'wb+'",
")",
"@",
"patch_callback",
"def",
"... | Patch the file `f` using the delta `d`. The patched file will be written to
`o`. If `o` is omitted, a temporary file will be used. This function returns
the be patched file `o`. All parameters should be file-like objects. `f` is
required to be seekable. | [
"Patch",
"the",
"file",
"f",
"using",
"the",
"delta",
"d",
".",
"The",
"patched",
"file",
"will",
"be",
"written",
"to",
"o",
".",
"If",
"o",
"is",
"omitted",
"a",
"temporary",
"file",
"will",
"be",
"used",
".",
"This",
"function",
"returns",
"the",
... | 1859a5f44317dce3e0997c740ac0f8675d77c4e3 | https://github.com/smartfile/python-librsync/blob/1859a5f44317dce3e0997c740ac0f8675d77c4e3/librsync/__init__.py#L209-L235 | train | 65,173 |
zhanglab/psamm | psamm/gapfill.py | _find_integer_tolerance | def _find_integer_tolerance(epsilon, v_max, min_tol):
"""Find appropriate integer tolerance for gap-filling problems."""
int_tol = min(epsilon / (10 * v_max), 0.1)
min_tol = max(1e-10, min_tol)
if int_tol < min_tol:
eps_lower = min_tol * 10 * v_max
logger.warning(
'When the m... | python | def _find_integer_tolerance(epsilon, v_max, min_tol):
"""Find appropriate integer tolerance for gap-filling problems."""
int_tol = min(epsilon / (10 * v_max), 0.1)
min_tol = max(1e-10, min_tol)
if int_tol < min_tol:
eps_lower = min_tol * 10 * v_max
logger.warning(
'When the m... | [
"def",
"_find_integer_tolerance",
"(",
"epsilon",
",",
"v_max",
",",
"min_tol",
")",
":",
"int_tol",
"=",
"min",
"(",
"epsilon",
"/",
"(",
"10",
"*",
"v_max",
")",
",",
"0.1",
")",
"min_tol",
"=",
"max",
"(",
"1e-10",
",",
"min_tol",
")",
"if",
"int_... | Find appropriate integer tolerance for gap-filling problems. | [
"Find",
"appropriate",
"integer",
"tolerance",
"for",
"gap",
"-",
"filling",
"problems",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/gapfill.py#L36-L49 | train | 65,174 |
zhanglab/psamm | psamm/gapfill.py | gapfind | def gapfind(model, solver, epsilon=0.001, v_max=1000, implicit_sinks=True):
"""Identify compounds in the model that cannot be produced.
Yields all compounds that cannot be produced. This method
assumes implicit sinks for all compounds in the model so
the only factor that influences whether a compound c... | python | def gapfind(model, solver, epsilon=0.001, v_max=1000, implicit_sinks=True):
"""Identify compounds in the model that cannot be produced.
Yields all compounds that cannot be produced. This method
assumes implicit sinks for all compounds in the model so
the only factor that influences whether a compound c... | [
"def",
"gapfind",
"(",
"model",
",",
"solver",
",",
"epsilon",
"=",
"0.001",
",",
"v_max",
"=",
"1000",
",",
"implicit_sinks",
"=",
"True",
")",
":",
"prob",
"=",
"solver",
".",
"create_problem",
"(",
")",
"# Set integrality tolerance such that w constraints are... | Identify compounds in the model that cannot be produced.
Yields all compounds that cannot be produced. This method
assumes implicit sinks for all compounds in the model so
the only factor that influences whether a compound can be
produced is the presence of the compounds needed to produce it.
Epsi... | [
"Identify",
"compounds",
"in",
"the",
"model",
"that",
"cannot",
"be",
"produced",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/gapfill.py#L52-L140 | train | 65,175 |
zhanglab/psamm | psamm/datasource/native.py | float_constructor | def float_constructor(loader, node):
"""Construct Decimal from YAML float encoding."""
s = loader.construct_scalar(node)
if s == '.inf':
return Decimal('Infinity')
elif s == '-.inf':
return -Decimal('Infinity')
elif s == '.nan':
return Decimal('NaN')
return Decimal(s) | python | def float_constructor(loader, node):
"""Construct Decimal from YAML float encoding."""
s = loader.construct_scalar(node)
if s == '.inf':
return Decimal('Infinity')
elif s == '-.inf':
return -Decimal('Infinity')
elif s == '.nan':
return Decimal('NaN')
return Decimal(s) | [
"def",
"float_constructor",
"(",
"loader",
",",
"node",
")",
":",
"s",
"=",
"loader",
".",
"construct_scalar",
"(",
"node",
")",
"if",
"s",
"==",
"'.inf'",
":",
"return",
"Decimal",
"(",
"'Infinity'",
")",
"elif",
"s",
"==",
"'-.inf'",
":",
"return",
"... | Construct Decimal from YAML float encoding. | [
"Construct",
"Decimal",
"from",
"YAML",
"float",
"encoding",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L64-L73 | train | 65,176 |
zhanglab/psamm | psamm/datasource/native.py | yaml_load | def yaml_load(stream):
"""Load YAML file using safe loader."""
# Surprisingly, the CSafeLoader does not seem to be used by default.
# Check whether the CSafeLoader is available and provide a log message
# if it is not available.
global _HAS_YAML_LIBRARY
if _HAS_YAML_LIBRARY is None:
_HA... | python | def yaml_load(stream):
"""Load YAML file using safe loader."""
# Surprisingly, the CSafeLoader does not seem to be used by default.
# Check whether the CSafeLoader is available and provide a log message
# if it is not available.
global _HAS_YAML_LIBRARY
if _HAS_YAML_LIBRARY is None:
_HA... | [
"def",
"yaml_load",
"(",
"stream",
")",
":",
"# Surprisingly, the CSafeLoader does not seem to be used by default.",
"# Check whether the CSafeLoader is available and provide a log message",
"# if it is not available.",
"global",
"_HAS_YAML_LIBRARY",
"if",
"_HAS_YAML_LIBRARY",
"is",
"Non... | Load YAML file using safe loader. | [
"Load",
"YAML",
"file",
"using",
"safe",
"loader",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L76-L94 | train | 65,177 |
zhanglab/psamm | psamm/datasource/native.py | _check_id | def _check_id(entity, entity_type):
"""Check whether the ID is valid.
First check if the ID is missing, and then check if it is a qualified
string type, finally check if the string is empty. For all checks, it
would raise a ParseError with the corresponding message.
Args:
entity: a string ... | python | def _check_id(entity, entity_type):
"""Check whether the ID is valid.
First check if the ID is missing, and then check if it is a qualified
string type, finally check if the string is empty. For all checks, it
would raise a ParseError with the corresponding message.
Args:
entity: a string ... | [
"def",
"_check_id",
"(",
"entity",
",",
"entity_type",
")",
":",
"if",
"entity",
"is",
"None",
":",
"raise",
"ParseError",
"(",
"'{} ID missing'",
".",
"format",
"(",
"entity_type",
")",
")",
"elif",
"not",
"isinstance",
"(",
"entity",
",",
"string_types",
... | Check whether the ID is valid.
First check if the ID is missing, and then check if it is a qualified
string type, finally check if the string is empty. For all checks, it
would raise a ParseError with the corresponding message.
Args:
entity: a string type object to be checked.
entity_t... | [
"Check",
"whether",
"the",
"ID",
"is",
"valid",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L620-L644 | train | 65,178 |
zhanglab/psamm | psamm/datasource/native.py | parse_compound | def parse_compound(compound_def, context=None):
"""Parse a structured compound definition as obtained from a YAML file
Returns a CompoundEntry."""
compound_id = compound_def.get('id')
_check_id(compound_id, 'Compound')
mark = FileMark(context, None, None)
return CompoundEntry(compound_def, ma... | python | def parse_compound(compound_def, context=None):
"""Parse a structured compound definition as obtained from a YAML file
Returns a CompoundEntry."""
compound_id = compound_def.get('id')
_check_id(compound_id, 'Compound')
mark = FileMark(context, None, None)
return CompoundEntry(compound_def, ma... | [
"def",
"parse_compound",
"(",
"compound_def",
",",
"context",
"=",
"None",
")",
":",
"compound_id",
"=",
"compound_def",
".",
"get",
"(",
"'id'",
")",
"_check_id",
"(",
"compound_id",
",",
"'Compound'",
")",
"mark",
"=",
"FileMark",
"(",
"context",
",",
"N... | Parse a structured compound definition as obtained from a YAML file
Returns a CompoundEntry. | [
"Parse",
"a",
"structured",
"compound",
"definition",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L647-L656 | train | 65,179 |
zhanglab/psamm | psamm/datasource/native.py | parse_compound_list | def parse_compound_list(path, compounds):
"""Parse a structured list of compounds as obtained from a YAML file
Yields CompoundEntries. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for compound_def in compounds:
if 'include' in compound_def:
f... | python | def parse_compound_list(path, compounds):
"""Parse a structured list of compounds as obtained from a YAML file
Yields CompoundEntries. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for compound_def in compounds:
if 'include' in compound_def:
f... | [
"def",
"parse_compound_list",
"(",
"path",
",",
"compounds",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"compound_def",
"in",
"compounds",
":",
"if",
"'include'",
"in",
"compound_def",
":",
"file_format",
"=",
"compound_def",
".",
"g... | Parse a structured list of compounds as obtained from a YAML file
Yields CompoundEntries. Path can be given as a string or a context. | [
"Parse",
"a",
"structured",
"list",
"of",
"compounds",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L659-L674 | train | 65,180 |
zhanglab/psamm | psamm/datasource/native.py | parse_compound_table_file | def parse_compound_table_file(path, f):
"""Parse a tab-separated file containing compound IDs and properties
The compound properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
for i, row in enumerate(csv.D... | python | def parse_compound_table_file(path, f):
"""Parse a tab-separated file containing compound IDs and properties
The compound properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
for i, row in enumerate(csv.D... | [
"def",
"parse_compound_table_file",
"(",
"path",
",",
"f",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"i",
",",
"row",
"in",
"enumerate",
"(",
"csv",
".",
"DictReader",
"(",
"f",
",",
"delimiter",
"=",
"str",
"(",
"'\\t'",
")... | Parse a tab-separated file containing compound IDs and properties
The compound properties are parsed according to the header which specifies
which property is contained in each column. | [
"Parse",
"a",
"tab",
"-",
"separated",
"file",
"containing",
"compound",
"IDs",
"and",
"properties"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L677-L696 | train | 65,181 |
zhanglab/psamm | psamm/datasource/native.py | parse_compound_file | def parse_compound_file(path, format):
"""Open and parse reaction file based on file extension or given format
Path can be given as a string or a context.
"""
context = FilePathContext(path)
# YAML files do not need to explicitly specify format
format = resolve_format(format, context.filepath... | python | def parse_compound_file(path, format):
"""Open and parse reaction file based on file extension or given format
Path can be given as a string or a context.
"""
context = FilePathContext(path)
# YAML files do not need to explicitly specify format
format = resolve_format(format, context.filepath... | [
"def",
"parse_compound_file",
"(",
"path",
",",
"format",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"# YAML files do not need to explicitly specify format",
"format",
"=",
"resolve_format",
"(",
"format",
",",
"context",
".",
"filepath",
")",
"i... | Open and parse reaction file based on file extension or given format
Path can be given as a string or a context. | [
"Open",
"and",
"parse",
"reaction",
"file",
"based",
"on",
"file",
"extension",
"or",
"given",
"format"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L720-L750 | train | 65,182 |
zhanglab/psamm | psamm/datasource/native.py | parse_reaction_equation_string | def parse_reaction_equation_string(equation, default_compartment):
"""Parse a string representation of a reaction equation.
Converts undefined compartments to the default compartment.
"""
def _translate_compartments(reaction, compartment):
"""Translate compound with missing compartments.
... | python | def parse_reaction_equation_string(equation, default_compartment):
"""Parse a string representation of a reaction equation.
Converts undefined compartments to the default compartment.
"""
def _translate_compartments(reaction, compartment):
"""Translate compound with missing compartments.
... | [
"def",
"parse_reaction_equation_string",
"(",
"equation",
",",
"default_compartment",
")",
":",
"def",
"_translate_compartments",
"(",
"reaction",
",",
"compartment",
")",
":",
"\"\"\"Translate compound with missing compartments.\n\n These compounds will have the specified com... | Parse a string representation of a reaction equation.
Converts undefined compartments to the default compartment. | [
"Parse",
"a",
"string",
"representation",
"of",
"a",
"reaction",
"equation",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L753-L772 | train | 65,183 |
zhanglab/psamm | psamm/datasource/native.py | parse_reaction_equation | def parse_reaction_equation(equation_def, default_compartment):
"""Parse a structured reaction equation as obtained from a YAML file
Returns a Reaction.
"""
def parse_compound_list(l, compartment):
"""Parse a list of reactants or metabolites"""
for compound_def in l:
compou... | python | def parse_reaction_equation(equation_def, default_compartment):
"""Parse a structured reaction equation as obtained from a YAML file
Returns a Reaction.
"""
def parse_compound_list(l, compartment):
"""Parse a list of reactants or metabolites"""
for compound_def in l:
compou... | [
"def",
"parse_reaction_equation",
"(",
"equation_def",
",",
"default_compartment",
")",
":",
"def",
"parse_compound_list",
"(",
"l",
",",
"compartment",
")",
":",
"\"\"\"Parse a list of reactants or metabolites\"\"\"",
"for",
"compound_def",
"in",
"l",
":",
"compound_id",... | Parse a structured reaction equation as obtained from a YAML file
Returns a Reaction. | [
"Parse",
"a",
"structured",
"reaction",
"equation",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L775-L812 | train | 65,184 |
zhanglab/psamm | psamm/datasource/native.py | parse_reaction | def parse_reaction(reaction_def, default_compartment, context=None):
"""Parse a structured reaction definition as obtained from a YAML file
Returns a ReactionEntry.
"""
reaction_id = reaction_def.get('id')
_check_id(reaction_id, 'Reaction')
reaction_props = dict(reaction_def)
# Parse rea... | python | def parse_reaction(reaction_def, default_compartment, context=None):
"""Parse a structured reaction definition as obtained from a YAML file
Returns a ReactionEntry.
"""
reaction_id = reaction_def.get('id')
_check_id(reaction_id, 'Reaction')
reaction_props = dict(reaction_def)
# Parse rea... | [
"def",
"parse_reaction",
"(",
"reaction_def",
",",
"default_compartment",
",",
"context",
"=",
"None",
")",
":",
"reaction_id",
"=",
"reaction_def",
".",
"get",
"(",
"'id'",
")",
"_check_id",
"(",
"reaction_id",
",",
"'Reaction'",
")",
"reaction_props",
"=",
"... | Parse a structured reaction definition as obtained from a YAML file
Returns a ReactionEntry. | [
"Parse",
"a",
"structured",
"reaction",
"definition",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L815-L832 | train | 65,185 |
zhanglab/psamm | psamm/datasource/native.py | parse_reaction_list | def parse_reaction_list(path, reactions, default_compartment=None):
"""Parse a structured list of reactions as obtained from a YAML file
Yields tuples of reaction ID and reaction object. Path can be given as a
string or a context.
"""
context = FilePathContext(path)
for reaction_def in reacti... | python | def parse_reaction_list(path, reactions, default_compartment=None):
"""Parse a structured list of reactions as obtained from a YAML file
Yields tuples of reaction ID and reaction object. Path can be given as a
string or a context.
"""
context = FilePathContext(path)
for reaction_def in reacti... | [
"def",
"parse_reaction_list",
"(",
"path",
",",
"reactions",
",",
"default_compartment",
"=",
"None",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"reaction_def",
"in",
"reactions",
":",
"if",
"'include'",
"in",
"reaction_def",
":",
"i... | Parse a structured list of reactions as obtained from a YAML file
Yields tuples of reaction ID and reaction object. Path can be given as a
string or a context. | [
"Parse",
"a",
"structured",
"list",
"of",
"reactions",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L835-L851 | train | 65,186 |
zhanglab/psamm | psamm/datasource/native.py | parse_reaction_table_file | def parse_reaction_table_file(path, f, default_compartment):
"""Parse a tab-separated file containing reaction IDs and properties
The reaction properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
for line... | python | def parse_reaction_table_file(path, f, default_compartment):
"""Parse a tab-separated file containing reaction IDs and properties
The reaction properties are parsed according to the header which specifies
which property is contained in each column.
"""
context = FilePathContext(path)
for line... | [
"def",
"parse_reaction_table_file",
"(",
"path",
",",
"f",
",",
"default_compartment",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"lineno",
",",
"row",
"in",
"enumerate",
"(",
"csv",
".",
"DictReader",
"(",
"f",
",",
"delimiter",
... | Parse a tab-separated file containing reaction IDs and properties
The reaction properties are parsed according to the header which specifies
which property is contained in each column. | [
"Parse",
"a",
"tab",
"-",
"separated",
"file",
"containing",
"reaction",
"IDs",
"and",
"properties"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L863-L883 | train | 65,187 |
zhanglab/psamm | psamm/datasource/native.py | parse_reaction_file | def parse_reaction_file(path, default_compartment=None):
"""Open and parse reaction file based on file extension
Path can be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
if format == 'tsv':
logger.debug('Parsing re... | python | def parse_reaction_file(path, default_compartment=None):
"""Open and parse reaction file based on file extension
Path can be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
if format == 'tsv':
logger.debug('Parsing re... | [
"def",
"parse_reaction_file",
"(",
"path",
",",
"default_compartment",
"=",
"None",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"format",
"=",
"resolve_format",
"(",
"None",
",",
"context",
".",
"filepath",
")",
"if",
"format",
"==",
"'tsv... | Open and parse reaction file based on file extension
Path can be given as a string or a context. | [
"Open",
"and",
"parse",
"reaction",
"file",
"based",
"on",
"file",
"extension"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L886-L911 | train | 65,188 |
zhanglab/psamm | psamm/datasource/native.py | parse_exchange | def parse_exchange(exchange_def, default_compartment):
"""Parse a structured exchange definition as obtained from a YAML file.
Returns in iterator of compound, reaction, lower and upper bounds.
"""
default_compartment = exchange_def.get('compartment', default_compartment)
for compound_def in exch... | python | def parse_exchange(exchange_def, default_compartment):
"""Parse a structured exchange definition as obtained from a YAML file.
Returns in iterator of compound, reaction, lower and upper bounds.
"""
default_compartment = exchange_def.get('compartment', default_compartment)
for compound_def in exch... | [
"def",
"parse_exchange",
"(",
"exchange_def",
",",
"default_compartment",
")",
":",
"default_compartment",
"=",
"exchange_def",
".",
"get",
"(",
"'compartment'",
",",
"default_compartment",
")",
"for",
"compound_def",
"in",
"exchange_def",
".",
"get",
"(",
"'compoun... | Parse a structured exchange definition as obtained from a YAML file.
Returns in iterator of compound, reaction, lower and upper bounds. | [
"Parse",
"a",
"structured",
"exchange",
"definition",
"as",
"obtained",
"from",
"a",
"YAML",
"file",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L929-L942 | train | 65,189 |
zhanglab/psamm | psamm/datasource/native.py | parse_exchange_list | def parse_exchange_list(path, exchange, default_compartment):
"""Parse a structured exchange list as obtained from a YAML file.
Yields tuples of compound, reaction ID, lower and upper flux bounds. Path
can be given as a string or a context.
"""
context = FilePathContext(path)
for exchange_def... | python | def parse_exchange_list(path, exchange, default_compartment):
"""Parse a structured exchange list as obtained from a YAML file.
Yields tuples of compound, reaction ID, lower and upper flux bounds. Path
can be given as a string or a context.
"""
context = FilePathContext(path)
for exchange_def... | [
"def",
"parse_exchange_list",
"(",
"path",
",",
"exchange",
",",
"default_compartment",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"exchange_def",
"in",
"exchange",
":",
"if",
"'include'",
"in",
"exchange_def",
":",
"include_context",
... | Parse a structured exchange list as obtained from a YAML file.
Yields tuples of compound, reaction ID, lower and upper flux bounds. Path
can be given as a string or a context. | [
"Parse",
"a",
"structured",
"exchange",
"list",
"as",
"obtained",
"from",
"a",
"YAML",
"file",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L953-L971 | train | 65,190 |
zhanglab/psamm | psamm/datasource/native.py | parse_exchange_table_file | def parse_exchange_table_file(f):
"""Parse a space-separated file containing exchange compound flux limits.
The first two columns contain compound IDs and compartment while the
third column contains the lower flux limits. The fourth column is
optional and contains the upper flux limit.
"""
for... | python | def parse_exchange_table_file(f):
"""Parse a space-separated file containing exchange compound flux limits.
The first two columns contain compound IDs and compartment while the
third column contains the lower flux limits. The fourth column is
optional and contains the upper flux limit.
"""
for... | [
"def",
"parse_exchange_table_file",
"(",
"f",
")",
":",
"for",
"line",
"in",
"f",
":",
"line",
",",
"_",
",",
"comment",
"=",
"line",
".",
"partition",
"(",
"'#'",
")",
"line",
"=",
"line",
".",
"strip",
"(",
")",
"if",
"line",
"==",
"''",
":",
"... | Parse a space-separated file containing exchange compound flux limits.
The first two columns contain compound IDs and compartment while the
third column contains the lower flux limits. The fourth column is
optional and contains the upper flux limit. | [
"Parse",
"a",
"space",
"-",
"separated",
"file",
"containing",
"exchange",
"compound",
"flux",
"limits",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L999-L1027 | train | 65,191 |
zhanglab/psamm | psamm/datasource/native.py | parse_exchange_file | def parse_exchange_file(path, default_compartment):
"""Parse a file as a list of exchange compounds with flux limits.
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, c... | python | def parse_exchange_file(path, default_compartment):
"""Parse a file as a list of exchange compounds with flux limits.
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, c... | [
"def",
"parse_exchange_file",
"(",
"path",
",",
"default_compartment",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"format",
"=",
"resolve_format",
"(",
"None",
",",
"context",
".",
"filepath",
")",
"if",
"format",
"==",
"'tsv'",
":",
"log... | Parse a file as a list of exchange compounds with flux limits.
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context. | [
"Parse",
"a",
"file",
"as",
"a",
"list",
"of",
"exchange",
"compounds",
"with",
"flux",
"limits",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1038-L1063 | train | 65,192 |
zhanglab/psamm | psamm/datasource/native.py | parse_limit | def parse_limit(limit_def):
"""Parse a structured flux limit definition as obtained from a YAML file
Returns a tuple of reaction, lower and upper bound.
"""
lower, upper = get_limits(limit_def)
reaction = limit_def.get('reaction')
return reaction, lower, upper | python | def parse_limit(limit_def):
"""Parse a structured flux limit definition as obtained from a YAML file
Returns a tuple of reaction, lower and upper bound.
"""
lower, upper = get_limits(limit_def)
reaction = limit_def.get('reaction')
return reaction, lower, upper | [
"def",
"parse_limit",
"(",
"limit_def",
")",
":",
"lower",
",",
"upper",
"=",
"get_limits",
"(",
"limit_def",
")",
"reaction",
"=",
"limit_def",
".",
"get",
"(",
"'reaction'",
")",
"return",
"reaction",
",",
"lower",
",",
"upper"
] | Parse a structured flux limit definition as obtained from a YAML file
Returns a tuple of reaction, lower and upper bound. | [
"Parse",
"a",
"structured",
"flux",
"limit",
"definition",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1074-L1083 | train | 65,193 |
zhanglab/psamm | psamm/datasource/native.py | parse_limits_list | def parse_limits_list(path, limits):
"""Parse a structured list of flux limits as obtained from a YAML file
Yields tuples of reaction ID, lower and upper flux bounds. Path can be
given as a string or a context.
"""
context = FilePathContext(path)
for limit_def in limits:
if 'include' ... | python | def parse_limits_list(path, limits):
"""Parse a structured list of flux limits as obtained from a YAML file
Yields tuples of reaction ID, lower and upper flux bounds. Path can be
given as a string or a context.
"""
context = FilePathContext(path)
for limit_def in limits:
if 'include' ... | [
"def",
"parse_limits_list",
"(",
"path",
",",
"limits",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"limit_def",
"in",
"limits",
":",
"if",
"'include'",
"in",
"limit_def",
":",
"include_context",
"=",
"context",
".",
"resolve",
"(",... | Parse a structured list of flux limits as obtained from a YAML file
Yields tuples of reaction ID, lower and upper flux bounds. Path can be
given as a string or a context. | [
"Parse",
"a",
"structured",
"list",
"of",
"flux",
"limits",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1086-L1101 | train | 65,194 |
zhanglab/psamm | psamm/datasource/native.py | parse_limits_table_file | def parse_limits_table_file(f):
"""Parse a space-separated file containing reaction flux limits
The first column contains reaction IDs while the second column contains
the lower flux limits. The third column is optional and contains the
upper flux limit.
"""
for line in f:
line, _, com... | python | def parse_limits_table_file(f):
"""Parse a space-separated file containing reaction flux limits
The first column contains reaction IDs while the second column contains
the lower flux limits. The third column is optional and contains the
upper flux limit.
"""
for line in f:
line, _, com... | [
"def",
"parse_limits_table_file",
"(",
"f",
")",
":",
"for",
"line",
"in",
"f",
":",
"line",
",",
"_",
",",
"comment",
"=",
"line",
".",
"partition",
"(",
"'#'",
")",
"line",
"=",
"line",
".",
"strip",
"(",
")",
"if",
"line",
"==",
"''",
":",
"co... | Parse a space-separated file containing reaction flux limits
The first column contains reaction IDs while the second column contains
the lower flux limits. The third column is optional and contains the
upper flux limit. | [
"Parse",
"a",
"space",
"-",
"separated",
"file",
"containing",
"reaction",
"flux",
"limits"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1104-L1131 | train | 65,195 |
zhanglab/psamm | psamm/datasource/native.py | parse_limits_file | def parse_limits_file(path):
"""Parse a file as a list of reaction flux limits
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
if format == 'tsv'... | python | def parse_limits_file(path):
"""Parse a file as a list of reaction flux limits
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context.
"""
context = FilePathContext(path)
format = resolve_format(None, context.filepath)
if format == 'tsv'... | [
"def",
"parse_limits_file",
"(",
"path",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"format",
"=",
"resolve_format",
"(",
"None",
",",
"context",
".",
"filepath",
")",
"if",
"format",
"==",
"'tsv'",
":",
"logger",
".",
"debug",
"(",
"... | Parse a file as a list of reaction flux limits
The file format is detected and the file is parsed accordingly. Path can
be given as a string or a context. | [
"Parse",
"a",
"file",
"as",
"a",
"list",
"of",
"reaction",
"flux",
"limits"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1143-L1167 | train | 65,196 |
zhanglab/psamm | psamm/datasource/native.py | parse_model_group | def parse_model_group(path, group):
"""Parse a structured model group as obtained from a YAML file
Path can be given as a string or a context.
"""
context = FilePathContext(path)
for reaction_id in group.get('reactions', []):
yield reaction_id
# Parse subgroups
for reaction_id in... | python | def parse_model_group(path, group):
"""Parse a structured model group as obtained from a YAML file
Path can be given as a string or a context.
"""
context = FilePathContext(path)
for reaction_id in group.get('reactions', []):
yield reaction_id
# Parse subgroups
for reaction_id in... | [
"def",
"parse_model_group",
"(",
"path",
",",
"group",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"reaction_id",
"in",
"group",
".",
"get",
"(",
"'reactions'",
",",
"[",
"]",
")",
":",
"yield",
"reaction_id",
"# Parse subgroups",
... | Parse a structured model group as obtained from a YAML file
Path can be given as a string or a context. | [
"Parse",
"a",
"structured",
"model",
"group",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1170-L1184 | train | 65,197 |
zhanglab/psamm | psamm/datasource/native.py | parse_model_group_list | def parse_model_group_list(path, groups):
"""Parse a structured list of model groups as obtained from a YAML file
Yields reaction IDs. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for model_group in groups:
if 'include' in model_group:
include... | python | def parse_model_group_list(path, groups):
"""Parse a structured list of model groups as obtained from a YAML file
Yields reaction IDs. Path can be given as a string or a context.
"""
context = FilePathContext(path)
for model_group in groups:
if 'include' in model_group:
include... | [
"def",
"parse_model_group_list",
"(",
"path",
",",
"groups",
")",
":",
"context",
"=",
"FilePathContext",
"(",
"path",
")",
"for",
"model_group",
"in",
"groups",
":",
"if",
"'include'",
"in",
"model_group",
":",
"include_context",
"=",
"context",
".",
"resolve... | Parse a structured list of model groups as obtained from a YAML file
Yields reaction IDs. Path can be given as a string or a context. | [
"Parse",
"a",
"structured",
"list",
"of",
"model",
"groups",
"as",
"obtained",
"from",
"a",
"YAML",
"file"
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1187-L1201 | train | 65,198 |
zhanglab/psamm | psamm/datasource/native.py | _reaction_representer | def _reaction_representer(dumper, data):
"""Generate a parsable reaction representation to the YAML parser.
Check the number of compounds in the reaction, if it is larger than 10,
then transform the reaction data into a list of directories with all
attributes in the reaction; otherwise, just return the... | python | def _reaction_representer(dumper, data):
"""Generate a parsable reaction representation to the YAML parser.
Check the number of compounds in the reaction, if it is larger than 10,
then transform the reaction data into a list of directories with all
attributes in the reaction; otherwise, just return the... | [
"def",
"_reaction_representer",
"(",
"dumper",
",",
"data",
")",
":",
"if",
"len",
"(",
"data",
".",
"compounds",
")",
">",
"_MAX_REACTION_LENGTH",
":",
"def",
"dict_make",
"(",
"compounds",
")",
":",
"for",
"compound",
",",
"value",
"in",
"compounds",
":"... | Generate a parsable reaction representation to the YAML parser.
Check the number of compounds in the reaction, if it is larger than 10,
then transform the reaction data into a list of directories with all
attributes in the reaction; otherwise, just return the text_type format
of the reaction data. | [
"Generate",
"a",
"parsable",
"reaction",
"representation",
"to",
"the",
"YAML",
"parser",
"."
] | dc427848c4f9d109ca590f0afa024c63b685b3f4 | https://github.com/zhanglab/psamm/blob/dc427848c4f9d109ca590f0afa024c63b685b3f4/psamm/datasource/native.py#L1278-L1310 | train | 65,199 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.