partition stringclasses 3
values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
|---|---|---|---|---|---|---|---|---|---|---|---|
test | SRegistryMessage.useColor | useColor will determine if color should be added
to a print. Will check if being run in a terminal, and
if has support for asci | sregistry/logger/message.py | def useColor(self):
'''useColor will determine if color should be added
to a print. Will check if being run in a terminal, and
if has support for asci'''
COLORIZE = get_user_color_preference()
if COLORIZE is not None:
return COLORIZE
streams = [self.errorStrea... | def useColor(self):
'''useColor will determine if color should be added
to a print. Will check if being run in a terminal, and
if has support for asci'''
COLORIZE = get_user_color_preference()
if COLORIZE is not None:
return COLORIZE
streams = [self.errorStrea... | [
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"if",
"being",
"run",
"in",
"a",
"terminal",
"and",
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] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/logger/message.py#L59-L72 | [
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"for... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | SRegistryMessage.addColor | addColor to the prompt (usually prefix) if terminal
supports, and specified to do so | sregistry/logger/message.py | def addColor(self, level, text):
'''addColor to the prompt (usually prefix) if terminal
supports, and specified to do so'''
if self.colorize:
if level in self.colors:
text = "%s%s%s" % (self.colors[level],
text,
... | def addColor(self, level, text):
'''addColor to the prompt (usually prefix) if terminal
supports, and specified to do so'''
if self.colorize:
if level in self.colors:
text = "%s%s%s" % (self.colors[level],
text,
... | [
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] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/logger/message.py#L74-L82 | [
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... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | SRegistryMessage.emitError | determine if a level should print to
stderr, includes all levels but INFO and QUIET | sregistry/logger/message.py | def emitError(self, level):
'''determine if a level should print to
stderr, includes all levels but INFO and QUIET'''
if level in [ABORT,
ERROR,
WARNING,
VERBOSE,
VERBOSE1,
VERBOSE2,
... | def emitError(self, level):
'''determine if a level should print to
stderr, includes all levels but INFO and QUIET'''
if level in [ABORT,
ERROR,
WARNING,
VERBOSE,
VERBOSE1,
VERBOSE2,
... | [
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"print",
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"stderr",
"includes",
"all",
"levels",
"but",
"INFO",
"and",
"QUIET"
] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/logger/message.py#L84-L96 | [
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"]",
":",
"return",
"True",
"return",
"False"
] | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | SRegistryMessage.emit | emit is the main function to print the message
optionally with a prefix
:param level: the level of the message
:param message: the message to print
:param prefix: a prefix for the message | sregistry/logger/message.py | def emit(self, level, message, prefix=None, color=None):
'''emit is the main function to print the message
optionally with a prefix
:param level: the level of the message
:param message: the message to print
:param prefix: a prefix for the message
'''
if color is ... | def emit(self, level, message, prefix=None, color=None):
'''emit is the main function to print the message
optionally with a prefix
:param level: the level of the message
:param message: the message to print
:param prefix: a prefix for the message
'''
if color is ... | [
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"... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | SRegistryMessage.write | write will write a message to a stream,
first checking the encoding | sregistry/logger/message.py | def write(self, stream, message):
'''write will write a message to a stream,
first checking the encoding
'''
if isinstance(message, bytes):
message = message.decode('utf-8')
stream.write(message) | def write(self, stream, message):
'''write will write a message to a stream,
first checking the encoding
'''
if isinstance(message, bytes):
message = message.decode('utf-8')
stream.write(message) | [
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] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/logger/message.py#L149-L155 | [
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] | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | SRegistryMessage.get_logs | get_logs will return the complete history, joined by newline
(default) or as is. | sregistry/logger/message.py | def get_logs(self, join_newline=True):
''''get_logs will return the complete history, joined by newline
(default) or as is.
'''
if join_newline:
return '\n'.join(self.history)
return self.history | def get_logs(self, join_newline=True):
''''get_logs will return the complete history, joined by newline
(default) or as is.
'''
if join_newline:
return '\n'.join(self.history)
return self.history | [
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test | SRegistryMessage.show_progress | create a terminal progress bar, default bar shows for verbose+
Parameters
==========
iteration: current iteration (Int)
total: total iterations (Int)
length: character length of bar (Int) | sregistry/logger/message.py | def show_progress(self,
iteration,
total,
length=40,
min_level=0,
prefix=None,
carriage_return=True,
suffix=None,
symbol=None):
'''creat... | def show_progress(self,
iteration,
total,
length=40,
min_level=0,
prefix=None,
carriage_return=True,
suffix=None,
symbol=None):
'''creat... | [
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"... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | SRegistryMessage.table | table will print a table of entries. If the rows is
a dictionary, the keys are interpreted as column names. if
not, a numbered list is used. | sregistry/logger/message.py | def table(self, rows, col_width=2):
'''table will print a table of entries. If the rows is
a dictionary, the keys are interpreted as column names. if
not, a numbered list is used.
'''
labels = [str(x) for x in range(1,len(rows)+1)]
if isinstance(rows, dict):
... | def table(self, rows, col_width=2):
'''table will print a table of entries. If the rows is
a dictionary, the keys are interpreted as column names. if
not, a numbered list is used.
'''
labels = [str(x) for x in range(1,len(rows)+1)]
if isinstance(rows, dict):
... | [
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... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | push | push an image to Singularity Registry
path: should correspond to an absolte image path (or derive it)
name: should be the complete uri that the user has requested to push.
tag: should correspond with an image tag. This is provided to mirror Docker | sregistry/main/__template__/push.py | def push(self, path, name, tag=None):
'''push an image to Singularity Registry
path: should correspond to an absolte image path (or derive it)
name: should be the complete uri that the user has requested to push.
tag: should correspond with an image tag. This is provided to mirror Docker
'''
... | def push(self, path, name, tag=None):
'''push an image to Singularity Registry
path: should correspond to an absolte image path (or derive it)
name: should be the complete uri that the user has requested to push.
tag: should correspond with an image tag. This is provided to mirror Docker
'''
... | [
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"path"... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | push | push an image to Globus endpoint. In this case, the name is the
globus endpoint id and path.
--name <endpointid>:/path/for/image | sregistry/main/globus/push.py | def push(self, path, name, tag=None):
'''push an image to Globus endpoint. In this case, the name is the
globus endpoint id and path.
--name <endpointid>:/path/for/image
'''
# Split the name into endpoint and rest
endpoint, remote = self._parse_endpoint_name(name)
path = os.path.a... | def push(self, path, name, tag=None):
'''push an image to Globus endpoint. In this case, the name is the
globus endpoint id and path.
--name <endpointid>:/path/for/image
'''
# Split the name into endpoint and rest
endpoint, remote = self._parse_endpoint_name(name)
path = os.path.a... | [
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... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | get_template | return a default template for some function in sregistry
If there is no template, None is returned.
Parameters
==========
name: the name of the template to retrieve | sregistry/utils/templates.py | def get_template(name):
'''return a default template for some function in sregistry
If there is no template, None is returned.
Parameters
==========
name: the name of the template to retrieve
'''
name = name.lower()
templates = dict()
templates['tarinfo'] = {"gid": 0,
... | def get_template(name):
'''return a default template for some function in sregistry
If there is no template, None is returned.
Parameters
==========
name: the name of the template to retrieve
'''
name = name.lower()
templates = dict()
templates['tarinfo'] = {"gid": 0,
... | [
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test | update_token | update_token uses HTTP basic authentication to get a token for
Docker registry API V2 operations. We get here if a 401 is
returned for a request.
Parameters
==========
response: the http request response to parse for the challenge.
https://docs.docker.com/registry/spec/auth/token/ | sregistry/main/aws/api.py | def update_token(self):
'''update_token uses HTTP basic authentication to get a token for
Docker registry API V2 operations. We get here if a 401 is
returned for a request.
Parameters
==========
response: the http request response to parse for the challenge.
https://docs.docker.com/reg... | def update_token(self):
'''update_token uses HTTP basic authentication to get a token for
Docker registry API V2 operations. We get here if a 401 is
returned for a request.
Parameters
==========
response: the http request response to parse for the challenge.
https://docs.docker.com/reg... | [
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... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | download_layers | download layers is a wrapper to do the following for a client loaded
with a manifest for an image:
1. use the manifests to retrieve list of digests (get_digests)
2. atomically download the list to destination (get_layers)
This function uses the MultiProcess client to download lay... | sregistry/main/aws/api.py | def download_layers(self, repo_name, digest=None, destination=None):
''' download layers is a wrapper to do the following for a client loaded
with a manifest for an image:
1. use the manifests to retrieve list of digests (get_digests)
2. atomically download the list to destination (ge... | def download_layers(self, repo_name, digest=None, destination=None):
''' download layers is a wrapper to do the following for a client loaded
with a manifest for an image:
1. use the manifests to retrieve list of digests (get_digests)
2. atomically download the list to destination (ge... | [
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test | get_manifest | return the image manifest via the aws client, saved in self.manifest | sregistry/main/aws/api.py | def get_manifest(self, repo_name, tag):
'''return the image manifest via the aws client, saved in self.manifest
'''
image = None
repo = self.aws.describe_images(repositoryName=repo_name)
if 'imageDetails' in repo:
for contender in repo.get('imageDetails'):
if tag in contender['i... | def get_manifest(self, repo_name, tag):
'''return the image manifest via the aws client, saved in self.manifest
'''
image = None
repo = self.aws.describe_images(repositoryName=repo_name)
if 'imageDetails' in repo:
for contender in repo.get('imageDetails'):
if tag in contender['i... | [
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"the",
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"manifest",
"via",
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"client",
"saved",
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] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/main/aws/api.py#L98-L120 | [
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"co... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | get_digests | return a list of layers from a manifest.
The function is intended to work with both version
1 and 2 of the schema. All layers (including redundant)
are returned. By default, we try version 2 first,
then fall back to version 1.
For version 1 manifests: extraction is reversed
P... | sregistry/main/aws/api.py | def get_digests(self, repo_name, tag):
'''
return a list of layers from a manifest.
The function is intended to work with both version
1 and 2 of the schema. All layers (including redundant)
are returned. By default, we try version 2 first,
then fall back to version 1.
For... | def get_digests(self, repo_name, tag):
'''
return a list of layers from a manifest.
The function is intended to work with both version
1 and 2 of the schema. All layers (including redundant)
are returned. By default, we try version 2 first,
then fall back to version 1.
For... | [
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... | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/main/aws/api.py#L123-L143 | [
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")",
"sys",
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"exit",
"(",
"1",
")"... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | prepare_metadata | prepare a key/value list of metadata for the request. The metadata
object that comes in is only parsed one level. | sregistry/main/google_storage/utils.py | def prepare_metadata(metadata):
'''prepare a key/value list of metadata for the request. The metadata
object that comes in is only parsed one level.
'''
pairs = {
'metadata': {
'items': [{
'key': 'client',
'value': 'sregistry'
}
... | def prepare_metadata(metadata):
'''prepare a key/value list of metadata for the request. The metadata
object that comes in is only parsed one level.
'''
pairs = {
'metadata': {
'items': [{
'key': 'client',
'value': 'sregistry'
}
... | [
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"that",
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"is",
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"parsed",
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] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/main/google_storage/utils.py#L16-L37 | [
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",",
"val",
"in",
"metadata",
"... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | get_build_template | get a particular build template, by default we return templates
that are based on package managers.
Parameters
==========
name: the full path of the template file to use.
manager: the package manager to use in the template (yum or apt) | sregistry/main/google_storage/utils.py | def get_build_template(name=None, manager='apt'):
'''get a particular build template, by default we return templates
that are based on package managers.
Parameters
==========
name: the full path of the template file to use.
manager: the package manager to use in the template (yum... | def get_build_template(name=None, manager='apt'):
'''get a particular build template, by default we return templates
that are based on package managers.
Parameters
==========
name: the full path of the template file to use.
manager: the package manager to use in the template (yum... | [
"get",
"a",
"particular",
"build",
"template",
"by",
"default",
"we",
"return",
"templates",
"that",
"are",
"based",
"on",
"package",
"managers",
"."
] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/main/google_storage/utils.py#L40-L59 | [
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"name",
"=",
"\"%s/main/templates/build/singularity-builder-%s.sh\"",
"%",
"(",
"base",
","... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | get_metadata | extract metadata using Singularity inspect, if the executable is found.
If not, return a reasonable default (the parsed image name)
Parameters
==========
image_file: the full path to a Singularity image
names: optional, an extracted or otherwise created dictionary of
va... | sregistry/main/base/inspect.py | def get_metadata(self, image_file, names={}):
'''extract metadata using Singularity inspect, if the executable is found.
If not, return a reasonable default (the parsed image name)
Parameters
==========
image_file: the full path to a Singularity image
names: optional, an extracte... | def get_metadata(self, image_file, names={}):
'''extract metadata using Singularity inspect, if the executable is found.
If not, return a reasonable default (the parsed image name)
Parameters
==========
image_file: the full path to a Singularity image
names: optional, an extracte... | [
"extract",
"metadata",
"using",
"Singularity",
"inspect",
"if",
"the",
"executable",
"is",
"found",
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"If",
"not",
"return",
"a",
"reasonable",
"default",
"(",
"the",
"parsed",
"image",
"name",
")"
] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/main/base/inspect.py#L27-L74 | [
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"if",
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"None",
":",
"if",
"not",
"os",
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"... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | _pull | pull an image from a docker hub. This is a (less than ideal) workaround
that actually does the following:
- creates a sandbox folder
- adds docker layers, metadata folder, and custom metadata to it
- converts to a squashfs image with build
the docker manifests are stored with registry ... | sregistry/main/docker/pull.py | def _pull(self,
file_name,
names,
save=True,
force=False,
uri="docker://",
**kwargs):
'''pull an image from a docker hub. This is a (less than ideal) workaround
that actually does the following:
- creates a sandbox folder
- add... | def _pull(self,
file_name,
names,
save=True,
force=False,
uri="docker://",
**kwargs):
'''pull an image from a docker hub. This is a (less than ideal) workaround
that actually does the following:
- creates a sandbox folder
- add... | [
"pull",
"an",
"image",
"from",
"a",
"docker",
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".",
"This",
"is",
"a",
"(",
"less",
"than",
"ideal",
")",
"workaround",
"that",
"actually",
"does",
"the",
"following",
":"
] | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/main/docker/pull.py#L84-L185 | [
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"kwargs",
")",
":",
"# Use Singularity to build the image, based on user preference",
"if",
"fil... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | Client._update_secrets | update secrets will take a secrets credential file
either located at .sregistry or the environment variable
SREGISTRY_CLIENT_SECRETS and update the current client
secrets as well as the associated API base. This is where you
should do any customization of the secrets flie, o... | sregistry/main/__template__/__init__.py | def _update_secrets(self):
'''update secrets will take a secrets credential file
either located at .sregistry or the environment variable
SREGISTRY_CLIENT_SECRETS and update the current client
secrets as well as the associated API base. This is where you
should do an... | def _update_secrets(self):
'''update secrets will take a secrets credential file
either located at .sregistry or the environment variable
SREGISTRY_CLIENT_SECRETS and update the current client
secrets as well as the associated API base. This is where you
should do an... | [
"update",
"secrets",
"will",
"take",
"a",
"secrets",
"credential",
"file",
"either",
"located",
"at",
".",
"sregistry",
"or",
"the",
"environment",
"variable",
"SREGISTRY_CLIENT_SECRETS",
"and",
"update",
"the",
"current",
"client",
"secrets",
"as",
"well",
"as",
... | singularityhub/sregistry-cli | python | https://github.com/singularityhub/sregistry-cli/blob/abc96140a1d15b5e96d83432e1e0e1f4f8f36331/sregistry/main/__template__/__init__.py#L38-L65 | [
"def",
"_update_secrets",
"(",
"self",
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"# Get a setting for client myclient and some variable name VAR. ",
"# returns None if not set",
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"'SREGISTRY_MYCLIENT_VAR'",
")",
"# Get (and if found in environment (1) settings (2) up... | abc96140a1d15b5e96d83432e1e0e1f4f8f36331 |
test | _make_repr | Generate a repr string.
Positional arguments should be the positional arguments used to
construct the class. Keyword arguments should consist of tuples of
the attribute value and default. If the value is the default, then
it won't be rendered in the output.
Here's an example::
def __repr_... | fs_s3fs/_s3fs.py | def _make_repr(class_name, *args, **kwargs):
"""
Generate a repr string.
Positional arguments should be the positional arguments used to
construct the class. Keyword arguments should consist of tuples of
the attribute value and default. If the value is the default, then
it won't be rendered in ... | def _make_repr(class_name, *args, **kwargs):
"""
Generate a repr string.
Positional arguments should be the positional arguments used to
construct the class. Keyword arguments should consist of tuples of
the attribute value and default. If the value is the default, then
it won't be rendered in ... | [
"Generate",
"a",
"repr",
"string",
"."
] | PyFilesystem/s3fs | python | https://github.com/PyFilesystem/s3fs/blob/1c5e3a1b6abbb9dff91ea7fc4cec7353798cd536/fs_s3fs/_s3fs.py#L34-L58 | [
"def",
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"\"{}={!r}\"",
".",
"format",
"(",
"name",
... | 1c5e3a1b6abbb9dff91ea7fc4cec7353798cd536 |
test | s3errors | Translate S3 errors to FSErrors. | fs_s3fs/_s3fs.py | def s3errors(path):
"""Translate S3 errors to FSErrors."""
try:
yield
except ClientError as error:
_error = error.response.get("Error", {})
error_code = _error.get("Code", None)
response_meta = error.response.get("ResponseMetadata", {})
http_status = response_meta.get... | def s3errors(path):
"""Translate S3 errors to FSErrors."""
try:
yield
except ClientError as error:
_error = error.response.get("Error", {})
error_code = _error.get("Code", None)
response_meta = error.response.get("ResponseMetadata", {})
http_status = response_meta.get... | [
"Translate",
"S3",
"errors",
"to",
"FSErrors",
"."
] | PyFilesystem/s3fs | python | https://github.com/PyFilesystem/s3fs/blob/1c5e3a1b6abbb9dff91ea7fc4cec7353798cd536/fs_s3fs/_s3fs.py#L171-L192 | [
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"=",
"_error",
".",
"get",
"(",
"\"Co... | 1c5e3a1b6abbb9dff91ea7fc4cec7353798cd536 |
test | S3File.factory | Create a S3File backed with a temporary file. | fs_s3fs/_s3fs.py | def factory(cls, filename, mode, on_close):
"""Create a S3File backed with a temporary file."""
_temp_file = tempfile.TemporaryFile()
proxy = cls(_temp_file, filename, mode, on_close=on_close)
return proxy | def factory(cls, filename, mode, on_close):
"""Create a S3File backed with a temporary file."""
_temp_file = tempfile.TemporaryFile()
proxy = cls(_temp_file, filename, mode, on_close=on_close)
return proxy | [
"Create",
"a",
"S3File",
"backed",
"with",
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"temporary",
"file",
"."
] | PyFilesystem/s3fs | python | https://github.com/PyFilesystem/s3fs/blob/1c5e3a1b6abbb9dff91ea7fc4cec7353798cd536/fs_s3fs/_s3fs.py#L65-L69 | [
"def",
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",",
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",",
"on_close",
"=",
"on_close",
... | 1c5e3a1b6abbb9dff91ea7fc4cec7353798cd536 |
test | gravatar_url | Builds a gravatar url from an user or email | django_gravatar/templatetags/gravatar.py | def gravatar_url(user_or_email, size=GRAVATAR_DEFAULT_SIZE):
""" Builds a gravatar url from an user or email """
if hasattr(user_or_email, 'email'):
email = user_or_email.email
else:
email = user_or_email
try:
return escape(get_gravatar_url(email=email, size=size))
except:
... | def gravatar_url(user_or_email, size=GRAVATAR_DEFAULT_SIZE):
""" Builds a gravatar url from an user or email """
if hasattr(user_or_email, 'email'):
email = user_or_email.email
else:
email = user_or_email
try:
return escape(get_gravatar_url(email=email, size=size))
except:
... | [
"Builds",
"a",
"gravatar",
"url",
"from",
"an",
"user",
"or",
"email"
] | twaddington/django-gravatar | python | https://github.com/twaddington/django-gravatar/blob/c4849d93ed43b419eceff0ff2de83d4265597629/django_gravatar/templatetags/gravatar.py#L11-L21 | [
"def",
"gravatar_url",
"(",
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"GRAVATAR_DEFAULT_SIZE",
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"email",
"else",
":",
"email",
"=",
"user_or_email",
"try",
... | c4849d93ed43b419eceff0ff2de83d4265597629 |
test | gravatar | Builds an gravatar <img> tag from an user or email | django_gravatar/templatetags/gravatar.py | def gravatar(user_or_email, size=GRAVATAR_DEFAULT_SIZE, alt_text='', css_class='gravatar'):
""" Builds an gravatar <img> tag from an user or email """
if hasattr(user_or_email, 'email'):
email = user_or_email.email
else:
email = user_or_email
try:
url = escape(get_gravatar_url(e... | def gravatar(user_or_email, size=GRAVATAR_DEFAULT_SIZE, alt_text='', css_class='gravatar'):
""" Builds an gravatar <img> tag from an user or email """
if hasattr(user_or_email, 'email'):
email = user_or_email.email
else:
email = user_or_email
try:
url = escape(get_gravatar_url(e... | [
"Builds",
"an",
"gravatar",
"<img",
">",
"tag",
"from",
"an",
"user",
"or",
"email"
] | twaddington/django-gravatar | python | https://github.com/twaddington/django-gravatar/blob/c4849d93ed43b419eceff0ff2de83d4265597629/django_gravatar/templatetags/gravatar.py#L24-L41 | [
"def",
"gravatar",
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"user_or_email",
",",
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"GRAVATAR_DEFAULT_SIZE",
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"alt_text",
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"user_or_email",
",",
"'email'",
")",
":",
"email",
"=",
"user_or_email",
"."... | c4849d93ed43b419eceff0ff2de83d4265597629 |
test | get_gravatar_url | Builds a url to a gravatar from an email address.
:param email: The email to fetch the gravatar for
:param size: The size (in pixels) of the gravatar to fetch
:param default: What type of default image to use if the gravatar does not exist
:param rating: Used to filter the allowed gravatar ratings
... | django_gravatar/helpers.py | def get_gravatar_url(email, size=GRAVATAR_DEFAULT_SIZE, default=GRAVATAR_DEFAULT_IMAGE,
rating=GRAVATAR_DEFAULT_RATING, secure=GRAVATAR_DEFAULT_SECURE):
"""
Builds a url to a gravatar from an email address.
:param email: The email to fetch the gravatar for
:param size: The size (in pixels) of t... | def get_gravatar_url(email, size=GRAVATAR_DEFAULT_SIZE, default=GRAVATAR_DEFAULT_IMAGE,
rating=GRAVATAR_DEFAULT_RATING, secure=GRAVATAR_DEFAULT_SECURE):
"""
Builds a url to a gravatar from an email address.
:param email: The email to fetch the gravatar for
:param size: The size (in pixels) of t... | [
"Builds",
"a",
"url",
"to",
"a",
"gravatar",
"from",
"an",
"email",
"address",
"."
] | twaddington/django-gravatar | python | https://github.com/twaddington/django-gravatar/blob/c4849d93ed43b419eceff0ff2de83d4265597629/django_gravatar/helpers.py#L41-L71 | [
"def",
"get_gravatar_url",
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",",
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")",
":",
"if",
"secure",
":",
"url_base"... | c4849d93ed43b419eceff0ff2de83d4265597629 |
test | has_gravatar | Returns True if the user has a gravatar, False if otherwise | django_gravatar/helpers.py | def has_gravatar(email):
"""
Returns True if the user has a gravatar, False if otherwise
"""
# Request a 404 response if the gravatar does not exist
url = get_gravatar_url(email, default=GRAVATAR_DEFAULT_IMAGE_404)
# Verify an OK response was received
try:
request = Request(url)
... | def has_gravatar(email):
"""
Returns True if the user has a gravatar, False if otherwise
"""
# Request a 404 response if the gravatar does not exist
url = get_gravatar_url(email, default=GRAVATAR_DEFAULT_IMAGE_404)
# Verify an OK response was received
try:
request = Request(url)
... | [
"Returns",
"True",
"if",
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"user",
"has",
"a",
"gravatar",
"False",
"if",
"otherwise"
] | twaddington/django-gravatar | python | https://github.com/twaddington/django-gravatar/blob/c4849d93ed43b419eceff0ff2de83d4265597629/django_gravatar/helpers.py#L74-L87 | [
"def",
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"# Verify an OK response was received",
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"="... | c4849d93ed43b419eceff0ff2de83d4265597629 |
test | get_gravatar_profile_url | Builds a url to a gravatar profile from an email address.
:param email: The email to fetch the gravatar for
:param secure: If True use https, otherwise plain http | django_gravatar/helpers.py | def get_gravatar_profile_url(email, secure=GRAVATAR_DEFAULT_SECURE):
"""
Builds a url to a gravatar profile from an email address.
:param email: The email to fetch the gravatar for
:param secure: If True use https, otherwise plain http
"""
if secure:
url_base = GRAVATAR_SECURE_URL
e... | def get_gravatar_profile_url(email, secure=GRAVATAR_DEFAULT_SECURE):
"""
Builds a url to a gravatar profile from an email address.
:param email: The email to fetch the gravatar for
:param secure: If True use https, otherwise plain http
"""
if secure:
url_base = GRAVATAR_SECURE_URL
e... | [
"Builds",
"a",
"url",
"to",
"a",
"gravatar",
"profile",
"from",
"an",
"email",
"address",
"."
] | twaddington/django-gravatar | python | https://github.com/twaddington/django-gravatar/blob/c4849d93ed43b419eceff0ff2de83d4265597629/django_gravatar/helpers.py#L90-L108 | [
"def",
"get_gravatar_profile_url",
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"email",
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":",
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"else",
":",
"url_base",
"=",
"GRAVATAR_URL",
"# Calculate the email hash",
"email_hash",
"=",
"calcu... | c4849d93ed43b419eceff0ff2de83d4265597629 |
test | graph_coloring_qubo | the QUBO for k-coloring a graph A is as follows:
variables:
x_{v,c} = 1 if vertex v of A gets color c; x_{v,c} = 0 otherwise
constraints:
1) each v in A gets exactly one color.
This constraint is enforced by including the term (\sum_c x_{v,c} - 1)^2 in the QUBO,
which is minimized when ... | examples/fourcolor.py | def graph_coloring_qubo(graph, k):
"""
the QUBO for k-coloring a graph A is as follows:
variables:
x_{v,c} = 1 if vertex v of A gets color c; x_{v,c} = 0 otherwise
constraints:
1) each v in A gets exactly one color.
This constraint is enforced by including the term (\sum_c x_{v,c} - 1)... | def graph_coloring_qubo(graph, k):
"""
the QUBO for k-coloring a graph A is as follows:
variables:
x_{v,c} = 1 if vertex v of A gets color c; x_{v,c} = 0 otherwise
constraints:
1) each v in A gets exactly one color.
This constraint is enforced by including the term (\sum_c x_{v,c} - 1)... | [
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"QUBO",
"for",
"k",
"-",
"coloring",
"a",
"graph",
"A",
"is",
"as",
"follows",
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] | dwavesystems/minorminer | python | https://github.com/dwavesystems/minorminer/blob/05cac6db180adf8223a613dff808248e3048b07d/examples/fourcolor.py#L43-L70 | [
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"=",
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... | 05cac6db180adf8223a613dff808248e3048b07d |
test | chimera_blocks | Generator for blocks for a chimera block quotient | examples/fourcolor.py | def chimera_blocks(M=16, N=16, L=4):
"""
Generator for blocks for a chimera block quotient
"""
for x in xrange(M):
for y in xrange(N):
for u in (0, 1):
yield tuple((x, y, u, k) for k in xrange(L)) | def chimera_blocks(M=16, N=16, L=4):
"""
Generator for blocks for a chimera block quotient
"""
for x in xrange(M):
for y in xrange(N):
for u in (0, 1):
yield tuple((x, y, u, k) for k in xrange(L)) | [
"Generator",
"for",
"blocks",
"for",
"a",
"chimera",
"block",
"quotient"
] | dwavesystems/minorminer | python | https://github.com/dwavesystems/minorminer/blob/05cac6db180adf8223a613dff808248e3048b07d/examples/fourcolor.py#L73-L80 | [
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"(",
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")",
... | 05cac6db180adf8223a613dff808248e3048b07d |
test | chimera_block_quotient | Extract the blocks from a graph, and returns a
block-quotient graph according to the acceptability
functions block_good and eblock_good
Inputs:
G: a networkx graph
blocks: a tuple of tuples | examples/fourcolor.py | def chimera_block_quotient(G, blocks):
"""
Extract the blocks from a graph, and returns a
block-quotient graph according to the acceptability
functions block_good and eblock_good
Inputs:
G: a networkx graph
blocks: a tuple of tuples
"""
from networkx import Graph
from i... | def chimera_block_quotient(G, blocks):
"""
Extract the blocks from a graph, and returns a
block-quotient graph according to the acceptability
functions block_good and eblock_good
Inputs:
G: a networkx graph
blocks: a tuple of tuples
"""
from networkx import Graph
from i... | [
"Extract",
"the",
"blocks",
"from",
"a",
"graph",
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"returns",
"a",
"block",
"-",
"quotient",
"graph",
"according",
"to",
"the",
"acceptability",
"functions",
"block_good",
"and",
"eblock_good"
] | dwavesystems/minorminer | python | https://github.com/dwavesystems/minorminer/blob/05cac6db180adf8223a613dff808248e3048b07d/examples/fourcolor.py#L83-L126 | [
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"... | 05cac6db180adf8223a613dff808248e3048b07d |
test | embed_with_quotient | Produce an embedding in target_graph suitable to
check if source_graph is 4-colorable. More generally,
if target_graph is a (M,N,L) Chimera subgraph, the
test is for L-colorability. This depends heavily upon
the Chimera structure
Inputs:
source_graph, target_graph: networkx graphs
... | examples/fourcolor.py | def embed_with_quotient(source_graph, target_graph, M=16, N=16, L=4, **args):
"""
Produce an embedding in target_graph suitable to
check if source_graph is 4-colorable. More generally,
if target_graph is a (M,N,L) Chimera subgraph, the
test is for L-colorability. This depends heavily upon
the ... | def embed_with_quotient(source_graph, target_graph, M=16, N=16, L=4, **args):
"""
Produce an embedding in target_graph suitable to
check if source_graph is 4-colorable. More generally,
if target_graph is a (M,N,L) Chimera subgraph, the
test is for L-colorability. This depends heavily upon
the ... | [
"Produce",
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"embedding",
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"suitable",
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"check",
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"-",
"colorable",
".",
"More",
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"is",
"a",
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"M",
"N",
"L",
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"Chimera",
"subgraph",
"the",
"test",
"is"... | dwavesystems/minorminer | python | https://github.com/dwavesystems/minorminer/blob/05cac6db180adf8223a613dff808248e3048b07d/examples/fourcolor.py#L129-L202 | [
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"=",
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"chimera_blocks",
... | 05cac6db180adf8223a613dff808248e3048b07d |
test | enumerate_resonance_smiles | Return a set of resonance forms as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible resonance form.
:rtype: set of strings. | molvs/resonance.py | def enumerate_resonance_smiles(smiles):
"""Return a set of resonance forms as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible resonance form.
:rtype: set of strings.
"""
mol = Chem.MolFromSmiles(smiles)
#Che... | def enumerate_resonance_smiles(smiles):
"""Return a set of resonance forms as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible resonance form.
:rtype: set of strings.
"""
mol = Chem.MolFromSmiles(smiles)
#Che... | [
"Return",
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"set",
"of",
"resonance",
"forms",
"as",
"SMILES",
"strings",
"given",
"a",
"SMILES",
"string",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/resonance.py#L81-L91 | [
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"ResonanceEnumerator",
"(",
")",
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"enumerate",
"(",
"mol"... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | ResonanceEnumerator.enumerate | Enumerate all possible resonance forms and return them as a list.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: A list of all possible resonance forms of the molecule.
:rtype: list of rdkit.Chem.rdchem.Mol | molvs/resonance.py | def enumerate(self, mol):
"""Enumerate all possible resonance forms and return them as a list.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: A list of all possible resonance forms of the molecule.
:rtype: list of rdkit.Chem.rdchem.Mol
"""
... | def enumerate(self, mol):
"""Enumerate all possible resonance forms and return them as a list.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: A list of all possible resonance forms of the molecule.
:rtype: list of rdkit.Chem.rdchem.Mol
"""
... | [
"Enumerate",
"all",
"possible",
"resonance",
"forms",
"and",
"return",
"them",
"as",
"a",
"list",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/resonance.py#L52-L76 | [
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"KEKULE_ALL",
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"allow_incomplete_octets",
":",
"flags",
"=",
"flags",
"|",
"Chem"... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | Normalizer.normalize | Apply a series of Normalization transforms to correct functional groups and recombine charges.
A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
until no further changes occur. If any changes occurred, we go back and start from the first Nor... | molvs/normalize.py | def normalize(self, mol):
"""Apply a series of Normalization transforms to correct functional groups and recombine charges.
A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
until no further changes occur. If any changes occurred, we... | def normalize(self, mol):
"""Apply a series of Normalization transforms to correct functional groups and recombine charges.
A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
until no further changes occur. If any changes occurred, we... | [
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"of",
"Normalization",
"transforms",
"to",
"correct",
"functional",
"groups",
"and",
"recombine",
"charges",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/normalize.py#L114-L137 | [
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"fragments",
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"for",
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".",
"GetMolF... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | Normalizer._apply_transform | Repeatedly apply normalization transform to molecule until no changes occur.
It is possible for multiple products to be produced when a rule is applied. The rule is applied repeatedly to
each of the products, until no further changes occur or after 20 attempts. If there are multiple unique products
... | molvs/normalize.py | def _apply_transform(self, mol, rule):
"""Repeatedly apply normalization transform to molecule until no changes occur.
It is possible for multiple products to be produced when a rule is applied. The rule is applied repeatedly to
each of the products, until no further changes occur or after 20 a... | def _apply_transform(self, mol, rule):
"""Repeatedly apply normalization transform to molecule until no changes occur.
It is possible for multiple products to be produced when a rule is applied. The rule is applied repeatedly to
each of the products, until no further changes occur or after 20 a... | [
"Repeatedly",
"apply",
"normalization",
"transform",
"to",
"molecule",
"until",
"no",
"changes",
"occur",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/normalize.py#L156-L174 | [
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"for"... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | TautomerCanonicalizer.canonicalize | Return a canonical tautomer by enumerating and scoring all possible tautomers.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: The canonical tautomer.
:rtype: rdkit.Chem.rdchem.Mol | molvs/tautomer.py | def canonicalize(self, mol):
"""Return a canonical tautomer by enumerating and scoring all possible tautomers.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: The canonical tautomer.
:rtype: rdkit.Chem.rdchem.Mol
"""
# TODO: Overload the... | def canonicalize(self, mol):
"""Return a canonical tautomer by enumerating and scoring all possible tautomers.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: The canonical tautomer.
:rtype: rdkit.Chem.rdchem.Mol
"""
# TODO: Overload the... | [
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"a",
"canonical",
"tautomer",
"by",
"enumerating",
"and",
"scoring",
"all",
"possible",
"tautomers",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/tautomer.py#L170-L215 | [
"def",
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"re... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | TautomerEnumerator.enumerate | Enumerate all possible tautomers and return them as a list.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: A list of all possible tautomers of the molecule.
:rtype: list of rdkit.Chem.rdchem.Mol | molvs/tautomer.py | def enumerate(self, mol):
"""Enumerate all possible tautomers and return them as a list.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: A list of all possible tautomers of the molecule.
:rtype: list of rdkit.Chem.rdchem.Mol
"""
smiles =... | def enumerate(self, mol):
"""Enumerate all possible tautomers and return them as a list.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: A list of all possible tautomers of the molecule.
:rtype: list of rdkit.Chem.rdchem.Mol
"""
smiles =... | [
"Enumerate",
"all",
"possible",
"tautomers",
"and",
"return",
"them",
"as",
"a",
"list",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/tautomer.py#L240-L327 | [
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"# Create a keku... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | validate_smiles | Return log messages for a given SMILES string using the default validations.
Note: This is a convenience function for quickly validating a single SMILES string. It is more efficient to use
the :class:`~molvs.validate.Validator` class directly when working with many molecules or when custom options
are need... | molvs/validate.py | def validate_smiles(smiles):
"""Return log messages for a given SMILES string using the default validations.
Note: This is a convenience function for quickly validating a single SMILES string. It is more efficient to use
the :class:`~molvs.validate.Validator` class directly when working with many molecules... | def validate_smiles(smiles):
"""Return log messages for a given SMILES string using the default validations.
Note: This is a convenience function for quickly validating a single SMILES string. It is more efficient to use
the :class:`~molvs.validate.Validator` class directly when working with many molecules... | [
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"log",
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"for",
"a",
"given",
"SMILES",
"string",
"using",
"the",
"default",
"validations",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/validate.py#L105-L119 | [
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] | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | MetalDisconnector.disconnect | Break covalent bonds between metals and organic atoms under certain conditions.
The algorithm works as follows:
- Disconnect N, O, F from any metal.
- Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge, In, Sn, As, Tl, Pb, Bi, Po).
- For every bond broken, adju... | molvs/metal.py | def disconnect(self, mol):
"""Break covalent bonds between metals and organic atoms under certain conditions.
The algorithm works as follows:
- Disconnect N, O, F from any metal.
- Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge, In, Sn, As, Tl, Pb, Bi, Po).... | def disconnect(self, mol):
"""Break covalent bonds between metals and organic atoms under certain conditions.
The algorithm works as follows:
- Disconnect N, O, F from any metal.
- Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge, In, Sn, As, Tl, Pb, Bi, Po).... | [
"Break",
"covalent",
"bonds",
"between",
"metals",
"and",
"organic",
"atoms",
"under",
"certain",
"conditions",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/metal.py#L38-L72 | [
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"_metal_non",
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... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | standardize_smiles | Return a standardized canonical SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing a single SMILES string. It is more efficient to use
the :class:`~molvs.standardize.Standardizer` class directly when working with many molecules or when custom options
are nee... | molvs/standardize.py | def standardize_smiles(smiles):
"""Return a standardized canonical SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing a single SMILES string. It is more efficient to use
the :class:`~molvs.standardize.Standardizer` class directly when working with many molec... | def standardize_smiles(smiles):
"""Return a standardized canonical SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing a single SMILES string. It is more efficient to use
the :class:`~molvs.standardize.Standardizer` class directly when working with many molec... | [
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"standardized",
"canonical",
"SMILES",
"string",
"given",
"a",
"SMILES",
"string",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L289-L303 | [
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test | enumerate_tautomers_smiles | Return a set of tautomers as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible tautomer.
:rtype: set of strings. | molvs/standardize.py | def enumerate_tautomers_smiles(smiles):
"""Return a set of tautomers as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible tautomer.
:rtype: set of strings.
"""
# Skip sanitize as standardize does this anyway
m... | def enumerate_tautomers_smiles(smiles):
"""Return a set of tautomers as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible tautomer.
:rtype: set of strings.
"""
# Skip sanitize as standardize does this anyway
m... | [
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] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L306-L317 | [
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... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | canonicalize_tautomer_smiles | Return a standardized canonical tautomer SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing and finding the canonical tautomer for a single
SMILES string. It is more efficient to use the :class:`~molvs.standardize.Standardizer` class directly when working
wi... | molvs/standardize.py | def canonicalize_tautomer_smiles(smiles):
"""Return a standardized canonical tautomer SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing and finding the canonical tautomer for a single
SMILES string. It is more efficient to use the :class:`~molvs.standardize... | def canonicalize_tautomer_smiles(smiles):
"""Return a standardized canonical tautomer SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing and finding the canonical tautomer for a single
SMILES string. It is more efficient to use the :class:`~molvs.standardize... | [
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] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L320-L335 | [
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... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | Standardizer.standardize | Return a standardized version the given molecule.
The standardization process consists of the following stages: RDKit
:py:func:`~rdkit.Chem.rdmolops.RemoveHs`, RDKit :py:func:`~rdkit.Chem.rdmolops.SanitizeMol`,
:class:`~molvs.metal.MetalDisconnector`, :class:`~molvs.normalize.Normalizer`,
... | molvs/standardize.py | def standardize(self, mol):
"""Return a standardized version the given molecule.
The standardization process consists of the following stages: RDKit
:py:func:`~rdkit.Chem.rdmolops.RemoveHs`, RDKit :py:func:`~rdkit.Chem.rdmolops.SanitizeMol`,
:class:`~molvs.metal.MetalDisconnector`, :cla... | def standardize(self, mol):
"""Return a standardized version the given molecule.
The standardization process consists of the following stages: RDKit
:py:func:`~rdkit.Chem.rdmolops.RemoveHs`, RDKit :py:func:`~rdkit.Chem.rdmolops.SanitizeMol`,
:class:`~molvs.metal.MetalDisconnector`, :cla... | [
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"standardized",
"version",
"the",
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"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L78-L99 | [
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"disconnect_m... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | Standardizer.tautomer_parent | Return the tautomer parent of a given molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been standardized.
:returns: The tautomer parent molecule.
:rtype: rdkit.Chem.rdchem.Mol | molvs/standardize.py | def tautomer_parent(self, mol, skip_standardize=False):
"""Return the tautomer parent of a given molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been standardized.
:returns: The tautomer pare... | def tautomer_parent(self, mol, skip_standardize=False):
"""Return the tautomer parent of a given molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been standardized.
:returns: The tautomer pare... | [
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"of",
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"molecule",
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] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L101-L114 | [
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test | Standardizer.fragment_parent | Return the fragment parent of a given molecule.
The fragment parent is the largest organic covalent unit in the molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been standardized.
:returns: T... | molvs/standardize.py | def fragment_parent(self, mol, skip_standardize=False):
"""Return the fragment parent of a given molecule.
The fragment parent is the largest organic covalent unit in the molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Se... | def fragment_parent(self, mol, skip_standardize=False):
"""Return the fragment parent of a given molecule.
The fragment parent is the largest organic covalent unit in the molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Se... | [
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] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L116-L131 | [
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"# TODO: Consider applying FragmentRemover first to remove salts, solvent... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | Standardizer.stereo_parent | Return the stereo parent of a given molecule.
The stereo parent has all stereochemistry information removed from tetrahedral centers and double bonds.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been stan... | molvs/standardize.py | def stereo_parent(self, mol, skip_standardize=False):
"""Return the stereo parent of a given molecule.
The stereo parent has all stereochemistry information removed from tetrahedral centers and double bonds.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:para... | def stereo_parent(self, mol, skip_standardize=False):
"""Return the stereo parent of a given molecule.
The stereo parent has all stereochemistry information removed from tetrahedral centers and double bonds.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:para... | [
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"stereo",
"parent",
"of",
"a",
"given",
"molecule",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L133-L149 | [
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test | Standardizer.isotope_parent | Return the isotope parent of a given molecule.
The isotope parent has all atoms replaced with the most abundant isotope for that element.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been standardized.
... | molvs/standardize.py | def isotope_parent(self, mol, skip_standardize=False):
"""Return the isotope parent of a given molecule.
The isotope parent has all atoms replaced with the most abundant isotope for that element.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_... | def isotope_parent(self, mol, skip_standardize=False):
"""Return the isotope parent of a given molecule.
The isotope parent has all atoms replaced with the most abundant isotope for that element.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_... | [
"Return",
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"isotope",
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"of",
"a",
"given",
"molecule",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L151-L169 | [
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"mo... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | Standardizer.charge_parent | Return the charge parent of a given molecule.
The charge parent is the uncharged version of the fragment parent.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been standardized.
:returns: The charge... | molvs/standardize.py | def charge_parent(self, mol, skip_standardize=False):
"""Return the charge parent of a given molecule.
The charge parent is the uncharged version of the fragment parent.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True i... | def charge_parent(self, mol, skip_standardize=False):
"""Return the charge parent of a given molecule.
The charge parent is the uncharged version of the fragment parent.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True i... | [
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"charge",
"parent",
"of",
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"given",
"molecule",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L171-L190 | [
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test | Standardizer.super_parent | Return the super parent of a given molecule.
THe super parent is fragment, charge, isotope, stereochemistry and tautomer insensitive. From the input
molecule, the largest fragment is taken. This is uncharged and then isotope and stereochemistry information is
discarded. Finally, the canonical t... | molvs/standardize.py | def super_parent(self, mol, skip_standardize=False):
"""Return the super parent of a given molecule.
THe super parent is fragment, charge, isotope, stereochemistry and tautomer insensitive. From the input
molecule, the largest fragment is taken. This is uncharged and then isotope and stereochem... | def super_parent(self, mol, skip_standardize=False):
"""Return the super parent of a given molecule.
THe super parent is fragment, charge, isotope, stereochemistry and tautomer insensitive. From the input
molecule, the largest fragment is taken. This is uncharged and then isotope and stereochem... | [
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"the",
"super",
"parent",
"of",
"a",
"given",
"molecule",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/standardize.py#L192-L213 | [
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test | Standardizer.canonicalize_tautomer | :returns: A callable :class:`~molvs.tautomer.TautomerCanonicalizer` instance. | molvs/standardize.py | def canonicalize_tautomer(self):
"""
:returns: A callable :class:`~molvs.tautomer.TautomerCanonicalizer` instance.
"""
return TautomerCanonicalizer(transforms=self.tautomer_transforms, scores=self.tautomer_scores,
max_tautomers=self.max_tautomers) | def canonicalize_tautomer(self):
"""
:returns: A callable :class:`~molvs.tautomer.TautomerCanonicalizer` instance.
"""
return TautomerCanonicalizer(transforms=self.tautomer_transforms, scores=self.tautomer_scores,
max_tautomers=self.max_tautomers) | [
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test | main | Main function for molvs command line interface. | molvs/cli.py | def main():
"""Main function for molvs command line interface."""
# Root options
parser = MolvsParser(epilog='use "molvs <command> -h" to show help for a specific command')
subparsers = parser.add_subparsers(title='Available commands')
# Options common to all commands
common_parser = MolvsPar... | def main():
"""Main function for molvs command line interface."""
# Root options
parser = MolvsParser(epilog='use "molvs <command> -h" to show help for a specific command')
subparsers = parser.add_subparsers(title='Available commands')
# Options common to all commands
common_parser = MolvsPar... | [
"Main",
"function",
"for",
"molvs",
"command",
"line",
"interface",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/cli.py#L35-L65 | [
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test | Reionizer.reionize | Enforce charges on certain atoms, then perform competitive reionization.
First, charge corrections are applied to ensure, for example, that free metals are correctly ionized. Then, if
a molecule with multiple acid groups is partially ionized, ensure the strongest acids ionize first.
The algori... | molvs/charge.py | def reionize(self, mol):
"""Enforce charges on certain atoms, then perform competitive reionization.
First, charge corrections are applied to ensure, for example, that free metals are correctly ionized. Then, if
a molecule with multiple acid groups is partially ionized, ensure the strongest aci... | def reionize(self, mol):
"""Enforce charges on certain atoms, then perform competitive reionization.
First, charge corrections are applied to ensure, for example, that free metals are correctly ionized. Then, if
a molecule with multiple acid groups is partially ionized, ensure the strongest aci... | [
"Enforce",
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"on",
"certain",
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"then",
"perform",
"competitive",
"reionization",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/charge.py#L154-L241 | [
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"for",
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"charge_corre... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | Uncharger.uncharge | Neutralize molecule by adding/removing hydrogens.
:param mol: The molecule to uncharge.
:type mol: rdkit.Chem.rdchem.Mol
:return: The uncharged molecule.
:rtype: rdkit.Chem.rdchem.Mol | molvs/charge.py | def uncharge(self, mol):
"""Neutralize molecule by adding/removing hydrogens.
:param mol: The molecule to uncharge.
:type mol: rdkit.Chem.rdchem.Mol
:return: The uncharged molecule.
:rtype: rdkit.Chem.rdchem.Mol
"""
log.debug('Running Uncharger')
mol = co... | def uncharge(self, mol):
"""Neutralize molecule by adding/removing hydrogens.
:param mol: The molecule to uncharge.
:type mol: rdkit.Chem.rdchem.Mol
:return: The uncharged molecule.
:rtype: rdkit.Chem.rdchem.Mol
"""
log.debug('Running Uncharger')
mol = co... | [
"Neutralize",
"molecule",
"by",
"adding",
"/",
"removing",
"hydrogens",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/charge.py#L272-L314 | [
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test | Uncharger._get_neg_skip | Get negatively charged atoms to skip (up to pos_count). | molvs/charge.py | def _get_neg_skip(self, mol, pos_count):
"""Get negatively charged atoms to skip (up to pos_count)."""
neg_skip = set()
if pos_count:
# Get negative oxygens in charge-separated nitro groups TODO: Any other special cases to skip?
for occurrence in mol.GetSubstructMatches(s... | def _get_neg_skip(self, mol, pos_count):
"""Get negatively charged atoms to skip (up to pos_count)."""
neg_skip = set()
if pos_count:
# Get negative oxygens in charge-separated nitro groups TODO: Any other special cases to skip?
for occurrence in mol.GetSubstructMatches(s... | [
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] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/charge.py#L316-L331 | [
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"."... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | FragmentRemover.remove | Return the molecule with specified fragments removed.
:param mol: The molecule to remove fragments from.
:type mol: rdkit.Chem.rdchem.Mol
:return: The molecule with fragments removed.
:rtype: rdkit.Chem.rdchem.Mol | molvs/fragment.py | def remove(self, mol):
"""Return the molecule with specified fragments removed.
:param mol: The molecule to remove fragments from.
:type mol: rdkit.Chem.rdchem.Mol
:return: The molecule with fragments removed.
:rtype: rdkit.Chem.rdchem.Mol
"""
log.debug('Running ... | def remove(self, mol):
"""Return the molecule with specified fragments removed.
:param mol: The molecule to remove fragments from.
:type mol: rdkit.Chem.rdchem.Mol
:return: The molecule with fragments removed.
:rtype: rdkit.Chem.rdchem.Mol
"""
log.debug('Running ... | [
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"# If nothing is left or leave_last and only one... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | LargestFragmentChooser.choose | Return the largest covalent unit.
The largest fragment is determined by number of atoms (including hydrogens). Ties are broken by taking the
fragment with the higher molecular weight, and then by taking the first alphabetically by SMILES if needed.
:param mol: The molecule to choose the larges... | molvs/fragment.py | def choose(self, mol):
"""Return the largest covalent unit.
The largest fragment is determined by number of atoms (including hydrogens). Ties are broken by taking the
fragment with the higher molecular weight, and then by taking the first alphabetically by SMILES if needed.
:param mol:... | def choose(self, mol):
"""Return the largest covalent unit.
The largest fragment is determined by number of atoms (including hydrogens). Ties are broken by taking the
fragment with the higher molecular weight, and then by taking the first alphabetically by SMILES if needed.
:param mol:... | [
"Return",
"the",
"largest",
"covalent",
"unit",
"."
] | mcs07/MolVS | python | https://github.com/mcs07/MolVS/blob/d815fe52d160abcecbcbf117e6437bf727dbd8ad/molvs/fragment.py#L200-L243 | [
"def",
"choose",
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")",
"# TODO: Alternatively allow a list of fragments to be passed as the mol parameter",
"fragments",
"=",
"Chem",
".",
"GetMolFrags",
"(",
"mol",
",",
"as... | d815fe52d160abcecbcbf117e6437bf727dbd8ad |
test | integrate_ivp | Example program integrating an IVP problem of van der Pol oscillator | examples/van_der_pol.py | def integrate_ivp(u0=1.0, v0=0.0, mu=1.0, tend=10.0, dt0=1e-8, nt=0,
nsteps=600, t0=0.0, atol=1e-8, rtol=1e-8, plot=False,
savefig='None', method='bdf', dpi=100, verbose=False):
"""
Example program integrating an IVP problem of van der Pol oscillator
"""
f, j = get_f_... | def integrate_ivp(u0=1.0, v0=0.0, mu=1.0, tend=10.0, dt0=1e-8, nt=0,
nsteps=600, t0=0.0, atol=1e-8, rtol=1e-8, plot=False,
savefig='None', method='bdf', dpi=100, verbose=False):
"""
Example program integrating an IVP problem of van der Pol oscillator
"""
f, j = get_f_... | [
"Example",
"program",
"integrating",
"an",
"IVP",
"problem",
"of",
"van",
"der",
"Pol",
"oscillator"
] | bjodah/pycvodes | python | https://github.com/bjodah/pycvodes/blob/00637a682d363319bc5c7c73a78f033556fde8a5/examples/van_der_pol.py#L25-L50 | [
"def",
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"dt0",
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"nsteps",
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"t0",
"=",
"0.0",
",",
"atol",
"=",
"1e-8",
... | 00637a682d363319bc5c7c73a78f033556fde8a5 |
test | integrate_adaptive | Integrates a system of ordinary differential equations.
Solves the initial value problem (IVP) defined by the user supplied
arguments. The solver chooses at what values of the independent variable
results should be reported.
Parameters
----------
rhs : callable
Function with signature ... | pycvodes/__init__.py | def integrate_adaptive(rhs, jac, y0, x0, xend, atol, rtol, dx0=.0,
dx_min=.0, dx_max=.0, nsteps=500, method=None, nderiv=0,
roots=None, nroots=0, return_on_root=False,
check_callable=False, check_indexing=False,
**kwargs):
"... | def integrate_adaptive(rhs, jac, y0, x0, xend, atol, rtol, dx0=.0,
dx_min=.0, dx_max=.0, nsteps=500, method=None, nderiv=0,
roots=None, nroots=0, return_on_root=False,
check_callable=False, check_indexing=False,
**kwargs):
"... | [
"Integrates",
"a",
"system",
"of",
"ordinary",
"differential",
"equations",
"."
] | bjodah/pycvodes | python | https://github.com/bjodah/pycvodes/blob/00637a682d363319bc5c7c73a78f033556fde8a5/pycvodes/__init__.py#L21-L147 | [
"def",
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"dx_max",
"=",
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"nsteps",
"=",
"500",
",",
"method",
"=",
"None",
... | 00637a682d363319bc5c7c73a78f033556fde8a5 |
test | integrate_predefined | Integrates a system of ordinary differential equations.
Solves the initial value problem (IVP) defined by the user supplied
arguments. The user chooses at what values of the independent variable
results should be reported.
Parameters
----------
rhs : callable
Function with signature f(... | pycvodes/__init__.py | def integrate_predefined(rhs, jac, y0, xout, atol, rtol, jac_type="dense",
dx0=.0, dx_min=.0, dx_max=.0, nsteps=500, method=None,
nderiv=0, roots=None, nroots=0, check_callable=False,
check_indexing=False, **kwargs):
""" Integrates a system ... | def integrate_predefined(rhs, jac, y0, xout, atol, rtol, jac_type="dense",
dx0=.0, dx_min=.0, dx_max=.0, nsteps=500, method=None,
nderiv=0, roots=None, nroots=0, check_callable=False,
check_indexing=False, **kwargs):
""" Integrates a system ... | [
"Integrates",
"a",
"system",
"of",
"ordinary",
"differential",
"equations",
"."
] | bjodah/pycvodes | python | https://github.com/bjodah/pycvodes/blob/00637a682d363319bc5c7c73a78f033556fde8a5/pycvodes/__init__.py#L150-L275 | [
"def",
"integrate_predefined",
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"dx_min",
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"dx_max",
"=",
".0",
",",
"nsteps",
"=",
"500",
",",
... | 00637a682d363319bc5c7c73a78f033556fde8a5 |
test | GitHub_LLNL_Stats.get_stats | Retrieves the statistics from the given organization with the given
credentials. Will not retreive data if file exists and force hasn't been
set to True. This is to save GH API requests. | scripts/github_stats.py | def get_stats(self, username='', password='', organization='llnl',
force=True, repo_type='public'):
"""
Retrieves the statistics from the given organization with the given
credentials. Will not retreive data if file exists and force hasn't been
set to True. This is to save GH API... | def get_stats(self, username='', password='', organization='llnl',
force=True, repo_type='public'):
"""
Retrieves the statistics from the given organization with the given
credentials. Will not retreive data if file exists and force hasn't been
set to True. This is to save GH API... | [
"Retrieves",
"the",
"statistics",
"from",
"the",
"given",
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"with",
"the",
"given",
"credentials",
".",
"Will",
"not",
"retreive",
"data",
"if",
"file",
"exists",
"and",
"force",
"hasn",
"t",
"been",
"set",
"to",
"True",
".",
"This",
"is",
"t... | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L38-L86 | [
"def",
"get_stats",
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"username",
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"repo_type",
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"'public'",
")",
":",
"date",
"=",
"str",
"(",
"datetime",
".",
"date",
"."... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_mems_of_org | Retrieves the number of members of the organization. | scripts/github_stats.py | def get_mems_of_org(self):
"""
Retrieves the number of members of the organization.
"""
print 'Getting members.'
counter = 0
for member in self.org_retrieved.iter_members():
self.members_json[member.id] = member.to_json()
counter += 1
retur... | def get_mems_of_org(self):
"""
Retrieves the number of members of the organization.
"""
print 'Getting members.'
counter = 0
for member in self.org_retrieved.iter_members():
self.members_json[member.id] = member.to_json()
counter += 1
retur... | [
"Retrieves",
"the",
"number",
"of",
"members",
"of",
"the",
"organization",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L147-L156 | [
"def",
"get_mems_of_org",
"(",
"self",
")",
":",
"print",
"'Getting members.'",
"counter",
"=",
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"for",
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"in",
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"org_retrieved",
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"iter_members",
"(",
")",
":",
"self",
".",
"members_json",
"[",
"member",
".",
"id",
"]",
"=",
... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_teams_of_org | Retrieves the number of teams of the organization. | scripts/github_stats.py | def get_teams_of_org(self):
"""
Retrieves the number of teams of the organization.
"""
print 'Getting teams.'
counter = 0
for team in self.org_retrieved.iter_teams():
self.teams_json[team.id] = team.to_json()
counter += 1
return counter | def get_teams_of_org(self):
"""
Retrieves the number of teams of the organization.
"""
print 'Getting teams.'
counter = 0
for team in self.org_retrieved.iter_teams():
self.teams_json[team.id] = team.to_json()
counter += 1
return counter | [
"Retrieves",
"the",
"number",
"of",
"teams",
"of",
"the",
"organization",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L158-L167 | [
"def",
"get_teams_of_org",
"(",
"self",
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":",
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"'Getting teams.'",
"counter",
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"org_retrieved",
".",
"iter_teams",
"(",
")",
":",
"self",
".",
"teams_json",
"[",
"team",
".",
"id",
"]",
"=",
"team",
... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.repos | Retrieves info about the repos of the current organization. | scripts/github_stats.py | def repos(self, repo_type='public', organization='llnl'):
"""
Retrieves info about the repos of the current organization.
"""
print 'Getting repos.'
for repo in self.org_retrieved.iter_repos(type=repo_type):
#JSON
json = repo.to_json()
self.rep... | def repos(self, repo_type='public', organization='llnl'):
"""
Retrieves info about the repos of the current organization.
"""
print 'Getting repos.'
for repo in self.org_retrieved.iter_repos(type=repo_type):
#JSON
json = repo.to_json()
self.rep... | [
"Retrieves",
"info",
"about",
"the",
"repos",
"of",
"the",
"current",
"organization",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L169-L207 | [
"def",
"repos",
"(",
"self",
",",
"repo_type",
"=",
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"=",
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"print",
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"for",
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"self",
".",
"org_retrieved",
".",
"iter_repos",
"(",
"type",
"=",
"repo_type",
")",
":",
"#JSON... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_total_contributors | Retrieves the number of contributors to a repo in the organization.
Also adds to unique contributor list. | scripts/github_stats.py | def get_total_contributors(self, repo):
"""
Retrieves the number of contributors to a repo in the organization.
Also adds to unique contributor list.
"""
repo_contributors = 0
for contributor in repo.iter_contributors():
repo_contributors += 1
self... | def get_total_contributors(self, repo):
"""
Retrieves the number of contributors to a repo in the organization.
Also adds to unique contributor list.
"""
repo_contributors = 0
for contributor in repo.iter_contributors():
repo_contributors += 1
self... | [
"Retrieves",
"the",
"number",
"of",
"contributors",
"to",
"a",
"repo",
"in",
"the",
"organization",
".",
"Also",
"adds",
"to",
"unique",
"contributor",
"list",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L209-L219 | [
"def",
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"iter_contributors",
"(",
")",
":",
"repo_contributors",
"+=",
"1",
"self",
".",
"unique_contributors",
"[",
"contributor... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_pull_reqs | Retrieves the number of pull requests on a repo in the organization. | scripts/github_stats.py | def get_pull_reqs(self, repo):
"""
Retrieves the number of pull requests on a repo in the organization.
"""
pull_reqs_open = 0
pull_reqs_closed = 0
for pull_request in repo.iter_pulls(state='all'):
self.pull_requests_json[repo.name].append(pull_request.to_json... | def get_pull_reqs(self, repo):
"""
Retrieves the number of pull requests on a repo in the organization.
"""
pull_reqs_open = 0
pull_reqs_closed = 0
for pull_request in repo.iter_pulls(state='all'):
self.pull_requests_json[repo.name].append(pull_request.to_json... | [
"Retrieves",
"the",
"number",
"of",
"pull",
"requests",
"on",
"a",
"repo",
"in",
"the",
"organization",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L221-L233 | [
"def",
"get_pull_reqs",
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"iter_pulls",
"(",
"state",
"=",
"'all'",
")",
":",
"self",
".",
"pull_requests_json",
"[",
"rep... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_issues | Retrieves the number of closed issues. | scripts/github_stats.py | def get_issues(self, repo, organization='llnl'):
"""
Retrieves the number of closed issues.
"""
#JSON
path = ('../github-data/' + organization + '/' + repo.name + '/issues')
is_only_today = False
if not os.path.exists(path): #no previous path, get all issues
... | def get_issues(self, repo, organization='llnl'):
"""
Retrieves the number of closed issues.
"""
#JSON
path = ('../github-data/' + organization + '/' + repo.name + '/issues')
is_only_today = False
if not os.path.exists(path): #no previous path, get all issues
... | [
"Retrieves",
"the",
"number",
"of",
"closed",
"issues",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L235-L265 | [
"def",
"get_issues",
"(",
"self",
",",
"repo",
",",
"organization",
"=",
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"path",
"=",
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"'../github-data/'",
"+",
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"+",
"'/'",
"+",
"repo",
".",
"name",
"+",
"'/issues'",
")",
"is_only_today",
"=",
"False",
... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_languages | Retrieves the languages used in the repo and increments the respective
counts of those languages. Only increments languages that have names.
Anything else is not incremented (i.e. numbers). | scripts/github_stats.py | def get_languages(self, repo, temp_repo):
"""
Retrieves the languages used in the repo and increments the respective
counts of those languages. Only increments languages that have names.
Anything else is not incremented (i.e. numbers).
"""
try:
self.languages[... | def get_languages(self, repo, temp_repo):
"""
Retrieves the languages used in the repo and increments the respective
counts of those languages. Only increments languages that have names.
Anything else is not incremented (i.e. numbers).
"""
try:
self.languages[... | [
"Retrieves",
"the",
"languages",
"used",
"in",
"the",
"repo",
"and",
"increments",
"the",
"respective",
"counts",
"of",
"those",
"languages",
".",
"Only",
"increments",
"languages",
"that",
"have",
"names",
".",
"Anything",
"else",
"is",
"not",
"incremented",
... | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L267-L289 | [
"def",
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"KeyError",
":",
"count",
"=",
"self",
".",
"languages",
"[",
"repo",
".",
"la... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_readme | Checks to see if the given repo has a ReadMe. MD means it has a correct
Readme recognized by GitHub. | scripts/github_stats.py | def get_readme(self, repo):
"""
Checks to see if the given repo has a ReadMe. MD means it has a correct
Readme recognized by GitHub.
"""
readme_contents = repo.readme()
if readme_contents is not None:
self.total_readmes += 1
return 'MD'
if ... | def get_readme(self, repo):
"""
Checks to see if the given repo has a ReadMe. MD means it has a correct
Readme recognized by GitHub.
"""
readme_contents = repo.readme()
if readme_contents is not None:
self.total_readmes += 1
return 'MD'
if ... | [
"Checks",
"to",
"see",
"if",
"the",
"given",
"repo",
"has",
"a",
"ReadMe",
".",
"MD",
"means",
"it",
"has",
"a",
"correct",
"Readme",
"recognized",
"by",
"GitHub",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L291-L315 | [
"def",
"get_readme",
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",",
"repo",
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"readme_contents",
"=",
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")",
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"readme_contents",
"is",
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"None",
":",
"self",
".",
"total_readmes",
"+=",
"1",
"return",
"'MD'",
"if",
"self",
".",
"search_lim... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_license | Checks to see if the given repo has a top level LICENSE file. | scripts/github_stats.py | def get_license(self, repo):
"""
Checks to see if the given repo has a top level LICENSE file.
"""
if self.search_limit >= 28:
print 'Hit search limit. Sleeping for 60 sec.'
time.sleep(60)
self.search_limit = 0
self.search_limit += 1
se... | def get_license(self, repo):
"""
Checks to see if the given repo has a top level LICENSE file.
"""
if self.search_limit >= 28:
print 'Hit search limit. Sleeping for 60 sec.'
time.sleep(60)
self.search_limit = 0
self.search_limit += 1
se... | [
"Checks",
"to",
"see",
"if",
"the",
"given",
"repo",
"has",
"a",
"top",
"level",
"LICENSE",
"file",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L317-L336 | [
"def",
"get_license",
"(",
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",",
"repo",
")",
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"if",
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"'Hit search limit. Sleeping for 60 sec.'",
"time",
".",
"sleep",
"(",
"60",
")",
"self",
".",
"search_limit",
"=",
"0",
"self",
".",
"se... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.get_commits | Retrieves the number of commits to a repo in the organization. If it is
the first time getting commits for a repo, it will get all commits and
save them to JSON. If there are previous commits saved, it will only get
commits that have not been saved to disk since the last date of commits. | scripts/github_stats.py | def get_commits(self, repo, organization='llnl'):
"""
Retrieves the number of commits to a repo in the organization. If it is
the first time getting commits for a repo, it will get all commits and
save them to JSON. If there are previous commits saved, it will only get
commits th... | def get_commits(self, repo, organization='llnl'):
"""
Retrieves the number of commits to a repo in the organization. If it is
the first time getting commits for a repo, it will get all commits and
save them to JSON. If there are previous commits saved, it will only get
commits th... | [
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test | GitHub_LLNL_Stats.write_org_json | Writes stats from the organization to JSON. | scripts/github_stats.py | def write_org_json(self, date=(datetime.date.today()),
organization='llnl',dict_to_write={}, path_ending_type='',
is_list=False):
"""
Writes stats from the organization to JSON.
"""
path = ('../github-data/' + organization + '-org/'
+ path_ending_type + '/' + ... | def write_org_json(self, date=(datetime.date.today()),
organization='llnl',dict_to_write={}, path_ending_type='',
is_list=False):
"""
Writes stats from the organization to JSON.
"""
path = ('../github-data/' + organization + '-org/'
+ path_ending_type + '/' + ... | [
"Writes",
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"from",
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"to",
"JSON",
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] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L372-L393 | [
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test | GitHub_LLNL_Stats.write_repo_json | #Writes repo specific data to JSON. | scripts/github_stats.py | def write_repo_json(self, date=(datetime.date.today()),
organization='llnl', dict_to_write={}, path_ending_type='',
is_list=False, is_dict=False):
"""
#Writes repo specific data to JSON.
"""
for repo in dict_to_write:
path = ('../github-data/' + organization +... | def write_repo_json(self, date=(datetime.date.today()),
organization='llnl', dict_to_write={}, path_ending_type='',
is_list=False, is_dict=False):
"""
#Writes repo specific data to JSON.
"""
for repo in dict_to_write:
path = ('../github-data/' + organization +... | [
"#Writes",
"repo",
"specific",
"data",
"to",
"JSON",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L395-L422 | [
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test | GitHub_LLNL_Stats.write_to_file | Writes the current organization information to file (csv). | scripts/github_stats.py | def write_to_file(self, file_path='', date=str(datetime.date.today()),
organization='N/A', members=0, teams=0):
"""
Writes the current organization information to file (csv).
"""
self.checkDir(file_path)
with open(file_path, 'w+') as output:
output.write('date... | def write_to_file(self, file_path='', date=str(datetime.date.today()),
organization='N/A', members=0, teams=0):
"""
Writes the current organization information to file (csv).
"""
self.checkDir(file_path)
with open(file_path, 'w+') as output:
output.write('date... | [
"Writes",
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"current",
"organization",
"information",
"to",
"file",
"(",
"csv",
")",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L424-L462 | [
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"... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.write_totals | Updates the total.csv file with current data. | scripts/github_stats.py | def write_totals(self, file_path='', date=str(datetime.date.today()),
organization='N/A', members=0, teams=0):
"""
Updates the total.csv file with current data.
"""
total_exists = os.path.isfile(file_path)
with open(file_path, 'a') as out_total:
if not total_... | def write_totals(self, file_path='', date=str(datetime.date.today()),
organization='N/A', members=0, teams=0):
"""
Updates the total.csv file with current data.
"""
total_exists = os.path.isfile(file_path)
with open(file_path, 'a') as out_total:
if not total_... | [
"Updates",
"the",
"total",
".",
"csv",
"file",
"with",
"current",
"data",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L464-L496 | [
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"t... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.write_languages | Updates languages.csv file with current data. | scripts/github_stats.py | def write_languages(self, file_path='',date=str(datetime.date.today())):
"""
Updates languages.csv file with current data.
"""
self.remove_date(file_path=file_path, date=date)
languages_exists = os.path.isfile(file_path)
with open(file_path, 'a') as out_languages:
... | def write_languages(self, file_path='',date=str(datetime.date.today())):
"""
Updates languages.csv file with current data.
"""
self.remove_date(file_path=file_path, date=date)
languages_exists = os.path.isfile(file_path)
with open(file_path, 'a') as out_languages:
... | [
"Updates",
"languages",
".",
"csv",
"file",
"with",
"current",
"data",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L498-L521 | [
"def",
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"=",
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",",
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"=",
"date"... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.checkDir | Checks if a directory exists. If not, it creates one with the specified
file_path. | scripts/github_stats.py | def checkDir(self, file_path=''):
"""
Checks if a directory exists. If not, it creates one with the specified
file_path.
"""
if not os.path.exists(os.path.dirname(file_path)):
try:
os.makedirs(os.path.dirname(file_path))
except OSError as e... | def checkDir(self, file_path=''):
"""
Checks if a directory exists. If not, it creates one with the specified
file_path.
"""
if not os.path.exists(os.path.dirname(file_path)):
try:
os.makedirs(os.path.dirname(file_path))
except OSError as e... | [
"Checks",
"if",
"a",
"directory",
"exists",
".",
"If",
"not",
"it",
"creates",
"one",
"with",
"the",
"specified",
"file_path",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L523-L533 | [
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"p... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.remove_date | Removes all rows of the associated date from the given csv file.
Defaults to today. | scripts/github_stats.py | def remove_date(self, file_path='', date=str(datetime.date.today())):
"""
Removes all rows of the associated date from the given csv file.
Defaults to today.
"""
languages_exists = os.path.isfile(file_path)
if languages_exists:
with open(file_path, 'rb') as in... | def remove_date(self, file_path='', date=str(datetime.date.today())):
"""
Removes all rows of the associated date from the given csv file.
Defaults to today.
"""
languages_exists = os.path.isfile(file_path)
if languages_exists:
with open(file_path, 'rb') as in... | [
"Removes",
"all",
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"the",
"associated",
"date",
"from",
"the",
"given",
"csv",
"file",
".",
"Defaults",
"to",
"today",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L535-L550 | [
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"isfile",
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"file_path",
")",
"if",
"l... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_LLNL_Stats.delete_last_line | The following code was modified from
http://stackoverflow.com/a/10289740 &
http://stackoverflow.com/a/17309010
It essentially will check if the total for the current date already
exists in total.csv. If it does, it just removes the last line.
This is so the script could be run mo... | scripts/github_stats.py | def delete_last_line(self, file_path='', date=str(datetime.date.today())):
"""
The following code was modified from
http://stackoverflow.com/a/10289740 &
http://stackoverflow.com/a/17309010
It essentially will check if the total for the current date already
exists in tota... | def delete_last_line(self, file_path='', date=str(datetime.date.today())):
"""
The following code was modified from
http://stackoverflow.com/a/10289740 &
http://stackoverflow.com/a/17309010
It essentially will check if the total for the current date already
exists in tota... | [
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... | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/github_stats.py#L552-L579 | [
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"file_path",... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | gov_orgs | Returns a list of the names of US Government GitHub organizations
Based on: https://government.github.com/community/
Exmample return:
{'llnl', '18f', 'gsa', 'dhs-ncats', 'spack', ...} | scraper/github/__init__.py | def gov_orgs():
"""
Returns a list of the names of US Government GitHub organizations
Based on: https://government.github.com/community/
Exmample return:
{'llnl', '18f', 'gsa', 'dhs-ncats', 'spack', ...}
"""
us_gov_github_orgs = set()
gov_orgs = requests.get('https://government.gi... | def gov_orgs():
"""
Returns a list of the names of US Government GitHub organizations
Based on: https://government.github.com/community/
Exmample return:
{'llnl', '18f', 'gsa', 'dhs-ncats', 'spack', ...}
"""
us_gov_github_orgs = set()
gov_orgs = requests.get('https://government.gi... | [
"Returns",
"a",
"list",
"of",
"the",
"names",
"of",
"US",
"Government",
"GitHub",
"organizations"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/github/__init__.py#L14-L31 | [
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"[... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | create_session | Create a github3.py session connected to GitHub.com
If token is not provided, will attempt to use the GITHUB_API_TOKEN
environment variable if present. | scraper/github/__init__.py | def create_session(token=None):
"""
Create a github3.py session connected to GitHub.com
If token is not provided, will attempt to use the GITHUB_API_TOKEN
environment variable if present.
"""
if token is None:
token = os.environ.get('GITHUB_API_TOKEN', None)
gh_session = github3.lo... | def create_session(token=None):
"""
Create a github3.py session connected to GitHub.com
If token is not provided, will attempt to use the GITHUB_API_TOKEN
environment variable if present.
"""
if token is None:
token = os.environ.get('GITHUB_API_TOKEN', None)
gh_session = github3.lo... | [
"Create",
"a",
"github3",
".",
"py",
"session",
"connected",
"to",
"GitHub",
".",
"com"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/github/__init__.py#L34-L49 | [
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... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | create_enterprise_session | Create a github3.py session for a GitHub Enterprise instance
If token is not provided, will attempt to use the GITHUB_API_TOKEN
environment variable if present. | scraper/github/__init__.py | def create_enterprise_session(url, token=None):
"""
Create a github3.py session for a GitHub Enterprise instance
If token is not provided, will attempt to use the GITHUB_API_TOKEN
environment variable if present.
"""
gh_session = github3.enterprise_login(url=url, token=token)
if gh_sessio... | def create_enterprise_session(url, token=None):
"""
Create a github3.py session for a GitHub Enterprise instance
If token is not provided, will attempt to use the GITHUB_API_TOKEN
environment variable if present.
"""
gh_session = github3.enterprise_login(url=url, token=token)
if gh_sessio... | [
"Create",
"a",
"github3",
".",
"py",
"session",
"for",
"a",
"GitHub",
"Enterprise",
"instance"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/github/__init__.py#L52-L66 | [
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test | _check_api_limits | Simplified check for API limits
If necessary, spin in place waiting for API to reset before returning.
See: https://developer.github.com/v3/#rate-limiting | scraper/github/__init__.py | def _check_api_limits(gh_session, api_required=250, sleep_time=15):
"""
Simplified check for API limits
If necessary, spin in place waiting for API to reset before returning.
See: https://developer.github.com/v3/#rate-limiting
"""
api_rates = gh_session.rate_limit()
api_remaining = api_ra... | def _check_api_limits(gh_session, api_required=250, sleep_time=15):
"""
Simplified check for API limits
If necessary, spin in place waiting for API to reset before returning.
See: https://developer.github.com/v3/#rate-limiting
"""
api_rates = gh_session.rate_limit()
api_remaining = api_ra... | [
"Simplified",
"check",
"for",
"API",
"limits"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/github/__init__.py#L76-L101 | [
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"]... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | connect | Create a GitHub session for making requests | scraper/github/__init__.py | def connect(url='https://github.com', token=None):
"""
Create a GitHub session for making requests
"""
gh_session = None
if url == 'https://github.com':
gh_session = create_session(token)
else:
gh_session = create_enterprise_session(url, token)
if gh_session is None:
... | def connect(url='https://github.com', token=None):
"""
Create a GitHub session for making requests
"""
gh_session = None
if url == 'https://github.com':
gh_session = create_session(token)
else:
gh_session = create_enterprise_session(url, token)
if gh_session is None:
... | [
"Create",
"a",
"GitHub",
"session",
"for",
"making",
"requests"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/github/__init__.py#L104-L121 | [
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test | query_repos | Yields GitHub3.py repo objects for provided orgs and repo names
If orgs and repos are BOTH empty, execute special mode of getting ALL
repositories from the GitHub Server.
If public_only is True, will return only those repos that are marked as
public. Set this to false to return all organizations that ... | scraper/github/__init__.py | def query_repos(gh_session, orgs=None, repos=None, public_only=True):
"""
Yields GitHub3.py repo objects for provided orgs and repo names
If orgs and repos are BOTH empty, execute special mode of getting ALL
repositories from the GitHub Server.
If public_only is True, will return only those repos ... | def query_repos(gh_session, orgs=None, repos=None, public_only=True):
"""
Yields GitHub3.py repo objects for provided orgs and repo names
If orgs and repos are BOTH empty, execute special mode of getting ALL
repositories from the GitHub Server.
If public_only is True, will return only those repos ... | [
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] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/github/__init__.py#L124-L164 | [
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test | GitHub_Stargazers.get_stats | Retrieves the traffic for the users of the given organization.
Requires organization admin credentials token to access the data. | scripts/get_stargazers.py | def get_stats(self, username='', password='', organization='llnl', force=True):
"""
Retrieves the traffic for the users of the given organization.
Requires organization admin credentials token to access the data.
"""
date = str(datetime.date.today())
stargazers_file_path ... | def get_stats(self, username='', password='', organization='llnl', force=True):
"""
Retrieves the traffic for the users of the given organization.
Requires organization admin credentials token to access the data.
"""
date = str(datetime.date.today())
stargazers_file_path ... | [
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] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/get_stargazers.py#L11-L29 | [
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test | GitHub_Stargazers.get_org | Retrieves an organization via given org name. If given
empty string, prompts user for an org name. | scripts/get_stargazers.py | def get_org(self, organization_name=''):
"""
Retrieves an organization via given org name. If given
empty string, prompts user for an org name.
"""
self.organization_name = organization_name
if(organization_name == ''):
self.organization_name = raw_input('Orga... | def get_org(self, organization_name=''):
"""
Retrieves an organization via given org name. If given
empty string, prompts user for an org name.
"""
self.organization_name = organization_name
if(organization_name == ''):
self.organization_name = raw_input('Orga... | [
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"user",
"for",
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"name",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/get_stargazers.py#L80-L89 | [
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"'Organizat... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_Stargazers.get_repos | Gets the repos for the organization and builds the URL/headers for
getting timestamps of stargazers. | scripts/get_stargazers.py | def get_repos(self):
"""
Gets the repos for the organization and builds the URL/headers for
getting timestamps of stargazers.
"""
print 'Getting repos.'
#Uses the developer API. Note this could change.
headers = {'Accept': 'application/vnd.github.v3.star+json', '... | def get_repos(self):
"""
Gets the repos for the organization and builds the URL/headers for
getting timestamps of stargazers.
"""
print 'Getting repos.'
#Uses the developer API. Note this could change.
headers = {'Accept': 'application/vnd.github.v3.star+json', '... | [
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] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/get_stargazers.py#L91-L107 | [
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":",
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... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_Stargazers.get_stargazers | Return a list of the stargazers of a GitHub repo
Includes both the 'starred_at' and 'user' data.
param: url
url is the 'stargazers_url' of the form:
https://api.github.com/repos/LLNL/spack/stargazers | scripts/get_stargazers.py | def get_stargazers(self, url, headers={}):
"""
Return a list of the stargazers of a GitHub repo
Includes both the 'starred_at' and 'user' data.
param: url
url is the 'stargazers_url' of the form:
https://api.github.com/repos/LLNL/spack/stargazers
"""... | def get_stargazers(self, url, headers={}):
"""
Return a list of the stargazers of a GitHub repo
Includes both the 'starred_at' and 'user' data.
param: url
url is the 'stargazers_url' of the form:
https://api.github.com/repos/LLNL/spack/stargazers
"""... | [
"Return",
"a",
"list",
"of",
"the",
"stargazers",
"of",
"a",
"GitHub",
"repo"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/get_stargazers.py#L109-L128 | [
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"%... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_Stargazers.write_to_file | Writes stargazers data to file. | scripts/get_stargazers.py | def write_to_file(self, file_path='', date=(datetime.date.today()),
organization='llnl'):
"""
Writes stargazers data to file.
"""
with open(file_path, 'w+') as out:
out.write('date,organization,stargazers\n')
sorted_stargazers = sorted(self.stargazers)#sor... | def write_to_file(self, file_path='', date=(datetime.date.today()),
organization='llnl'):
"""
Writes stargazers data to file.
"""
with open(file_path, 'w+') as out:
out.write('date,organization,stargazers\n')
sorted_stargazers = sorted(self.stargazers)#sor... | [
"Writes",
"stargazers",
"data",
"to",
"file",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/get_stargazers.py#L147-L157 | [
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"... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | Project.from_github3 | Create CodeGovProject object from github3 Repository object | scraper/code_gov/models.py | def from_github3(klass, repository, labor_hours=True):
"""
Create CodeGovProject object from github3 Repository object
"""
if not isinstance(repository, github3.repos.repo._Repository):
raise TypeError('Repository must be a github3 Repository object')
logger.info('Pr... | def from_github3(klass, repository, labor_hours=True):
"""
Create CodeGovProject object from github3 Repository object
"""
if not isinstance(repository, github3.repos.repo._Repository):
raise TypeError('Repository must be a github3 Repository object')
logger.info('Pr... | [
"Create",
"CodeGovProject",
"object",
"from",
"github3",
"Repository",
"object"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/code_gov/models.py#L178-L283 | [
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"'Repositor... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | Project.from_gitlab | Create CodeGovProject object from GitLab Repository | scraper/code_gov/models.py | def from_gitlab(klass, repository, labor_hours=True):
"""
Create CodeGovProject object from GitLab Repository
"""
if not isinstance(repository, gitlab.v4.objects.Project):
raise TypeError('Repository must be a gitlab Repository object')
project = klass()
log... | def from_gitlab(klass, repository, labor_hours=True):
"""
Create CodeGovProject object from GitLab Repository
"""
if not isinstance(repository, gitlab.v4.objects.Project):
raise TypeError('Repository must be a gitlab Repository object')
project = klass()
log... | [
"Create",
"CodeGovProject",
"object",
"from",
"GitLab",
"Repository"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/code_gov/models.py#L286-L360 | [
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"'Repository must... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | Project.from_stashy | Handles crafting Code.gov Project for Bitbucket Server repositories | scraper/code_gov/models.py | def from_stashy(klass, repository, labor_hours=True):
"""
Handles crafting Code.gov Project for Bitbucket Server repositories
"""
# if not isinstance(repository, stashy.repos.Repository):
# raise TypeError('Repository must be a stashy Repository object')
if not isinst... | def from_stashy(klass, repository, labor_hours=True):
"""
Handles crafting Code.gov Project for Bitbucket Server repositories
"""
# if not isinstance(repository, stashy.repos.Repository):
# raise TypeError('Repository must be a stashy Repository object')
if not isinst... | [
"Handles",
"crafting",
"Code",
".",
"gov",
"Project",
"for",
"Bitbucket",
"Server",
"repositories"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/code_gov/models.py#L363-L447 | [
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"# raise TypeError('Repository must be a stashy Repository object')",
"if",
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... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | Project.from_doecode | Create CodeGovProject object from DOE CODE record
Handles crafting Code.gov Project | scraper/code_gov/models.py | def from_doecode(klass, record):
"""
Create CodeGovProject object from DOE CODE record
Handles crafting Code.gov Project
"""
if not isinstance(record, dict):
raise TypeError('`record` must be a dict')
project = klass()
# -- REQUIRED FIELDS --
... | def from_doecode(klass, record):
"""
Create CodeGovProject object from DOE CODE record
Handles crafting Code.gov Project
"""
if not isinstance(record, dict):
raise TypeError('`record` must be a dict')
project = klass()
# -- REQUIRED FIELDS --
... | [
"Create",
"CodeGovProject",
"object",
"from",
"DOE",
"CODE",
"record"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/code_gov/models.py#L450-L573 | [
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"# -- REQUIRED FIELDS --",
"project",... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | Project.from_tfs | Creates CodeGovProject object from TFS/VSTS/AzureDevOps Instance | scraper/code_gov/models.py | def from_tfs(klass, tfs_project, labor_hours=True):
"""
Creates CodeGovProject object from TFS/VSTS/AzureDevOps Instance
"""
project = klass()
project_web_url = ''
# -- REQUIRED FIELDS --
project['name'] = tfs_project.projectInfo.name
if 'web' in tfs_pro... | def from_tfs(klass, tfs_project, labor_hours=True):
"""
Creates CodeGovProject object from TFS/VSTS/AzureDevOps Instance
"""
project = klass()
project_web_url = ''
# -- REQUIRED FIELDS --
project['name'] = tfs_project.projectInfo.name
if 'web' in tfs_pro... | [
"Creates",
"CodeGovProject",
"object",
"from",
"TFS",
"/",
"VSTS",
"/",
"AzureDevOps",
"Instance"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/code_gov/models.py#L576-L628 | [
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... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | process_config | Master function to process a Scraper config file
Returns a Code.gov Metadata file | scraper/code_gov/__init__.py | def process_config(config):
"""
Master function to process a Scraper config file
Returns a Code.gov Metadata file
"""
agency = config.get('agency', 'UNKNOWN')
logger.debug('Agency: %s', agency)
method = config.get('method', 'other')
logger.debug('Inventory Method: %s', method)
co... | def process_config(config):
"""
Master function to process a Scraper config file
Returns a Code.gov Metadata file
"""
agency = config.get('agency', 'UNKNOWN')
logger.debug('Agency: %s', agency)
method = config.get('method', 'other')
logger.debug('Inventory Method: %s', method)
co... | [
"Master",
"function",
"to",
"process",
"a",
"Scraper",
"config",
"file"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/code_gov/__init__.py#L13-L128 | [
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"... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | force_attributes | Forces certain fields in the Code.gov Metadata json | scraper/code_gov/__init__.py | def force_attributes(metadata, config):
"""
Forces certain fields in the Code.gov Metadata json
"""
organization = config.get('organization', '')
logger.debug('Organization: %s', organization)
contact_email = config.get('contact_email')
logger.debug('Contact Email: %s', contact_email)
... | def force_attributes(metadata, config):
"""
Forces certain fields in the Code.gov Metadata json
"""
organization = config.get('organization', '')
logger.debug('Organization: %s', organization)
contact_email = config.get('contact_email')
logger.debug('Contact Email: %s', contact_email)
... | [
"Forces",
"certain",
"fields",
"in",
"the",
"Code",
".",
"gov",
"Metadata",
"json"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/code_gov/__init__.py#L131-L172 | [
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... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | _license_obj | A helper function to look up license object information
Use names from: https://api.github.com/licenses | scraper/github/util.py | def _license_obj(license):
"""
A helper function to look up license object information
Use names from: https://api.github.com/licenses
"""
obj = None
if license in ('MIT', 'MIT License'):
obj = {
'URL': 'https://api.github.com/licenses/mit',
'name': 'MIT'
... | def _license_obj(license):
"""
A helper function to look up license object information
Use names from: https://api.github.com/licenses
"""
obj = None
if license in ('MIT', 'MIT License'):
obj = {
'URL': 'https://api.github.com/licenses/mit',
'name': 'MIT'
... | [
"A",
"helper",
"function",
"to",
"look",
"up",
"license",
"object",
"information"
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scraper/github/util.py#L6-L89 | [
"def",
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"elif",
"lic... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_Traffic.get_stats | Retrieves the traffic for the users of the given organization.
Requires organization admin credentials token to access the data. | scripts/get_traffic.py | def get_stats(self, username='', password='', organization='llnl', force=True):
"""
Retrieves the traffic for the users of the given organization.
Requires organization admin credentials token to access the data.
"""
date = str(datetime.date.today())
referrers_file_path =... | def get_stats(self, username='', password='', organization='llnl', force=True):
"""
Retrieves the traffic for the users of the given organization.
Requires organization admin credentials token to access the data.
"""
date = str(datetime.date.today())
referrers_file_path =... | [
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")",
")",
"referr... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
test | GitHub_Traffic.get_traffic | Retrieves the traffic for the repositories of the given organization. | scripts/get_traffic.py | def get_traffic(self):
"""
Retrieves the traffic for the repositories of the given organization.
"""
print 'Getting traffic.'
#Uses the developer API. Note this could change.
headers = {'Accept': 'application/vnd.github.spiderman-preview', 'Authorization': 'token ' + self... | def get_traffic(self):
"""
Retrieves the traffic for the repositories of the given organization.
"""
print 'Getting traffic.'
#Uses the developer API. Note this could change.
headers = {'Accept': 'application/vnd.github.spiderman-preview', 'Authorization': 'token ' + self... | [
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"organization",
"."
] | LLNL/scraper | python | https://github.com/LLNL/scraper/blob/881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea/scripts/get_traffic.py#L115-L132 | [
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"... | 881a316e4c04dfa5a9cf491b7c7f9f997a7c56ea |
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