code stringlengths 51 2.34k | sequence stringlengths 186 3.94k | docstring stringlengths 11 171 |
|---|---|---|
def bar_(self, label=None, style=None, opts=None, options={}):
try:
return self._get_chart("bar", style=style, opts=opts, label=label,
options=options)
except Exception as e:
self.err(e, self.bar_, "Can not draw bar chart") | module function_definition identifier parameters identifier default_parameter identifier none default_parameter identifier none default_parameter identifier none default_parameter identifier dictionary block try_statement block return_statement call attribute identifier identifier argument_list string string_start stri... | Get a bar chart |
def getmodule(object):
if ismodule(object):
return object
if isclass(object):
return sys.modules.get(object.__module__)
try:
file = getabsfile(object)
except TypeError:
return None
if modulesbyfile.has_key(file):
return sys.modules[modulesbyfile[file]]
for... | module function_definition identifier parameters identifier block if_statement call identifier argument_list identifier block return_statement identifier if_statement call identifier argument_list identifier block return_statement call attribute attribute identifier identifier identifier argument_list attribute identif... | Return the module an object was defined in, or None if not found. |
def _readhex(self, length, start):
if length % 4:
raise InterpretError("Cannot convert to hex unambiguously - "
"not multiple of 4 bits.")
if not length:
return ''
s = self._slice(start, start + length).tobytes()
try:
... | module function_definition identifier parameters identifier identifier identifier block if_statement binary_operator identifier integer block raise_statement call identifier argument_list concatenated_string string string_start string_content string_end string string_start string_content string_end if_statement not_ope... | Read bits and interpret as a hex string. |
def getRelativePath(basepath, path):
basepath = splitpath(os.path.abspath(basepath))
path = splitpath(os.path.abspath(path))
afterCommon = False
for c in basepath:
if afterCommon or path[0] != c:
path.insert(0, os.path.pardir)
afterCommon = True
else:
... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call identifier argument_list call attribute attribute identifier identifier identifier argument_list identifier expression_statement assignment identifier call identifier argument_list call attribute... | Get a path that is relative to the given base path. |
def cli(ctx, config, quiet):
ctx.obj = {}
ctx.obj['config'] = load_config(config.read())
ctx.obj['quiet'] = quiet
log(ctx, ' * ' + rnd_scotty_quote() + ' * ') | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment attribute identifier identifier dictionary expression_statement assignment subscript attribute identifier identifier string string_start string_content string_end call identifier argument_list call at... | AWS ECS Docker Deployment Tool |
def _ReloadArtifacts(self):
self._artifacts = {}
self._LoadArtifactsFromFiles(self._sources.GetAllFiles())
self.ReloadDatastoreArtifacts() | module function_definition identifier parameters identifier block expression_statement assignment attribute identifier identifier dictionary expression_statement call attribute identifier identifier argument_list call attribute attribute identifier identifier identifier argument_list expression_statement call attribute... | Load artifacts from all sources. |
def unregister_transform(self, node_class, transform, predicate=None):
self.transforms[node_class].remove((transform, predicate)) | module function_definition identifier parameters identifier identifier identifier default_parameter identifier none block expression_statement call attribute subscript attribute identifier identifier identifier identifier argument_list tuple identifier identifier | Unregister the given transform. |
def symbol(currency, *, native=True):
currency = validate_currency(currency)
if native:
return _currencies[currency]['symbol_native']
return _currencies[currency]['symbol'] | module function_definition identifier parameters identifier keyword_separator default_parameter identifier true block expression_statement assignment identifier call identifier argument_list identifier if_statement identifier block return_statement subscript subscript identifier identifier string string_start string_co... | return symbol of currency |
def nice_true_ces(tc):
cause_list = []
next_list = []
cause = '<--'
effect = '-->'
for event in tc:
if event.direction == Direction.CAUSE:
cause_list.append(["{0:.4f}".format(round(event.alpha, 4)),
event.mechanism, cause, event.purview])
el... | module function_definition identifier parameters identifier block expression_statement assignment identifier list expression_statement assignment identifier list expression_statement assignment identifier string string_start string_content string_end expression_statement assignment identifier string string_start string... | Format a true |CauseEffectStructure|. |
def create_and_run_collector(document, options):
collector = None
if not options.report == 'off':
collector = Collector()
collector.store.configure(document)
Event.configure(collector_queue=collector.queue)
collector.start()
return collector | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier none if_statement not_operator comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment identifier call identifier argume... | Create and run collector process for report data. |
def _resolve_time(value):
if value is None or isinstance(value,(int,long)):
return value
if NUMBER_TIME.match(value):
return long(value)
simple = SIMPLE_TIME.match(value)
if SIMPLE_TIME.match(value):
multiplier = long( simple.groups()[0] )
constant = SIMPLE_TIMES[ simple.groups()[1] ]
return... | module function_definition identifier parameters identifier block if_statement boolean_operator comparison_operator identifier none call identifier argument_list identifier tuple identifier identifier block return_statement identifier if_statement call attribute identifier identifier argument_list identifier block retu... | Resolve the time in seconds of a configuration value. |
def fix_positions(self):
shift_x = 0
for m in self.__reactants:
max_x = self.__fix_positions(m, shift_x, 0)
shift_x = max_x + 1
arrow_min = shift_x
if self.__reagents:
for m in self.__reagents:
max_x = self.__fix_positions(m, shift_x, 1... | module function_definition identifier parameters identifier block expression_statement assignment identifier integer for_statement identifier attribute identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier identifier integer expression_state... | fix coordinates of molecules in reaction |
def begin(self):
self._device.writeList(HT16K33_SYSTEM_SETUP | HT16K33_OSCILLATOR, [])
self.set_blink(HT16K33_BLINK_OFF)
self.set_brightness(15) | module function_definition identifier parameters identifier block expression_statement call attribute attribute identifier identifier identifier argument_list binary_operator identifier identifier list expression_statement call attribute identifier identifier argument_list identifier expression_statement call attribute... | Initialize driver with LEDs enabled and all turned off. |
def save(self):
self.cells = list(self.renumber())
if not self.cells[-1].endswith('\n'):
self.cells[-1] += '\n'
with open(self.filename, 'w') as file_open:
file_open.write('\n\n'.join(self.cells)) | module function_definition identifier parameters identifier block expression_statement assignment attribute identifier identifier call identifier argument_list call attribute identifier identifier argument_list if_statement not_operator call attribute subscript attribute identifier identifier unary_operator integer ide... | Format and save cells. |
def dropIndex(cls, fields) :
"removes an index created with ensureIndex "
con = RabaConnection(cls._raba_namespace)
rlf, ff = cls._parseIndex(fields)
for name in rlf :
con.dropIndex(name, 'anchor_raba_id')
con.dropIndex(cls.__name__, ff)
con.commit() | module function_definition identifier parameters identifier identifier block expression_statement string string_start string_content string_end expression_statement assignment identifier call identifier argument_list attribute identifier identifier expression_statement assignment pattern_list identifier identifier call... | removes an index created with ensureIndex |
def head(self, item):
uri = "/%s/%s" % (self.uri_base, utils.get_id(item))
return self._head(uri) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier binary_operator string string_start string_content string_end tuple attribute identifier identifier call attribute identifier identifier argument_list identifier return_statement call attribute identi... | Makes a HEAD request on a specific item. |
def biopython_protein_scale(inseq, scale, custom_scale_dict=None, window=7):
if scale == 'kd_hydrophobicity':
scale_dict = kd_hydrophobicity_one
elif scale == 'bulkiness':
scale_dict = bulkiness_one
elif scale == 'custom':
scale_dict = custom_scale_dict
else:
raise ValueE... | module function_definition identifier parameters identifier identifier default_parameter identifier none default_parameter identifier integer block if_statement comparison_operator identifier string string_start string_content string_end block expression_statement assignment identifier identifier elif_clause comparison... | Use Biopython to calculate properties using a sliding window over a sequence given a specific scale to use. |
def _make_txn(signer, setting_key, payload):
serialized_payload = payload.SerializeToString()
header = TransactionHeader(
signer_public_key=signer.get_public_key().as_hex(),
family_name='sawtooth_settings',
family_version='1.0',
inputs=_config_inputs(setting_key),
outputs... | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment identifier call attribute call identifier argument_list keyword_argument identifier call attribute call at... | Creates and signs a sawtooth_settings transaction with with a payload. |
def _traverse_command(self, name, *args, **kwargs):
if not name in self.available_commands:
raise AttributeError("%s is not an available command for %s" %
(name, self.__class__.__name__))
attr = getattr(self.connection, "%s" % name)
key = self.key
... | module function_definition identifier parameters identifier identifier list_splat_pattern identifier dictionary_splat_pattern identifier block if_statement not_operator comparison_operator identifier attribute identifier identifier block raise_statement call identifier argument_list binary_operator string string_start ... | Add the key to the args and call the Redis command. |
def ensure_stacker_compat_config(config_filename):
try:
with open(config_filename, 'r') as stream:
yaml.safe_load(stream)
except yaml.constructor.ConstructorError as yaml_error:
if yaml_error.problem.startswith(
'could not determine a constructor for the tag \'!'):
... | module function_definition identifier parameters identifier block try_statement block with_statement with_clause with_item as_pattern call identifier argument_list identifier string string_start string_content string_end as_pattern_target identifier block expression_statement call attribute identifier identifier argume... | Ensure config file can be loaded by Stacker. |
def checksum_contracts(self) -> None:
checksums: Dict[str, str] = {}
for contracts_dir in self.contracts_source_dirs.values():
file: Path
for file in contracts_dir.glob('*.sol'):
checksums[file.name] = hashlib.sha256(file.read_bytes()).hexdigest()
self.ove... | module function_definition identifier parameters identifier type none block expression_statement assignment identifier type generic_type identifier type_parameter type identifier type identifier dictionary for_statement identifier call attribute attribute identifier identifier identifier argument_list block expression_... | Remember the checksum of each source, and the overall checksum. |
def _create_plain_field(self, attr, options):
method = self._get_field_method(attr.py_type) or self._create_other_field
klass, options = method(attr, options)
if attr.is_unique:
options['validators'].append(validators.UniqueEntityValidator(attr.entity))
return klass, options | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier boolean_operator call attribute identifier identifier argument_list attribute identifier identifier attribute identifier identifier expression_statement assignment pattern_list identifier i... | Creates the form element. |
def update(self, **kwargs):
for key, value in kwargs.items():
setattr(self, key, value) | module function_definition identifier parameters identifier dictionary_splat_pattern identifier block for_statement pattern_list identifier identifier call attribute identifier identifier argument_list block expression_statement call identifier argument_list identifier identifier identifier | Creates or updates a property for the instance for each parameter. |
def install_supervisor(self, update=False):
script = supervisor.Recipe(
self.buildout,
self.name,
{'user': self.options.get('user'),
'program': self.options.get('program'),
'command': templ_cmd.render(config=self.conf_filename, prefix=self.prefix),
... | module function_definition identifier parameters identifier default_parameter identifier false block expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifier identifier attribute identifier identifier dictionary pair string string_start string_content string_end... | install supervisor config for redis |
def _get_results_from_api(identifiers, endpoints, api_key, api_secret):
if api_key is not None and api_secret is not None:
client = housecanary.ApiClient(api_key, api_secret)
else:
client = housecanary.ApiClient()
wrapper = getattr(client, endpoints[0].split('/')[0])
if len(endpoints) > ... | module function_definition identifier parameters identifier identifier identifier identifier block if_statement boolean_operator comparison_operator identifier none comparison_operator identifier none block expression_statement assignment identifier call attribute identifier identifier argument_list identifier identifi... | Use the HouseCanary API Python Client to access the API |
def _dmi_cast(key, val, clean=True):
if clean and not _dmi_isclean(key, val):
return
elif not re.match(r'serial|part|asset|product', key, flags=re.IGNORECASE):
if ',' in val:
val = [el.strip() for el in val.split(',')]
else:
try:
val = int(val)
... | module function_definition identifier parameters identifier identifier default_parameter identifier true block if_statement boolean_operator identifier not_operator call identifier argument_list identifier identifier block return_statement elif_clause not_operator call attribute identifier identifier argument_list stri... | Simple caster thingy for trying to fish out at least ints & lists from strings |
def extract_pls_rsp(rsp_str):
try:
rsp = json.loads(rsp_str)
except ValueError:
traceback.print_exc()
err = sys.exc_info()[1]
err_str = ERROR_STR_PREFIX + str(err)
return RET_ERROR, err_str, None
error_code = int(rsp['retType'])
if error_code != 1:
error_s... | module function_definition identifier parameters identifier block try_statement block expression_statement assignment identifier call attribute identifier identifier argument_list identifier except_clause identifier block expression_statement call attribute identifier identifier argument_list expression_statement assig... | Extract the response of PLS |
def export_to_dom(self):
namespaces = 'xmlns="http://www.neuroml.org/lems/%s" ' + \
'xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" ' + \
'xsi:schemaLocation="http://www.neuroml.org/lems/%s %s"'
namespaces = namespaces%(self.target_lems_version,self.targe... | module function_definition identifier parameters identifier block expression_statement assignment identifier binary_operator binary_operator string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end expression_statement assignment identifie... | Exports this model to a DOM. |
def execute(self):
self.autocomplete()
if len(self.argv):
cmd = self.argv[0]
cmd_argv = self.get_argv_for_command()
self.run_command(cmd, cmd_argv)
else:
self.show_help() | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list if_statement call identifier argument_list attribute identifier identifier block expression_statement assignment identifier subscript attribute identifier identifier integer expressi... | Executes whole process of parsing and running command. |
def _handleSmsStatusReport(self, notificationLine):
self.log.debug('SMS status report received')
cdsiMatch = self.CDSI_REGEX.match(notificationLine)
if cdsiMatch:
msgMemory = cdsiMatch.group(1)
msgIndex = cdsiMatch.group(2)
report = self.readStoredSms(msgIndex... | module function_definition identifier parameters identifier identifier block expression_statement call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end expression_statement assignment identifier call attribute attribute identifier identifier identifier arg... | Handler for SMS status reports |
def flush(self):
self._check_open_file()
if self.allow_update and not self.is_stream:
contents = self._io.getvalue()
if self._append:
self._sync_io()
old_contents = (self.file_object.byte_contents
if is_byte_string(c... | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list if_statement boolean_operator attribute identifier identifier not_operator attribute identifier identifier block expression_statement assignment identifier call attribute attribute i... | Flush file contents to 'disk'. |
def dictionary_validator(key_type, value_type):
def _validate_dictionary(instance, attribute, value):
if not isinstance(value, dict):
raise TypeError('"{}" must be a dictionary'.format(attribute.name))
for key, data in value.items():
if not isinstance(key, key_type):
... | module function_definition identifier parameters identifier identifier block function_definition identifier parameters identifier identifier identifier block if_statement not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list call attribute string string_sta... | Validator for ``attrs`` that performs deep type checking of dictionaries. |
def _dispatch_event(self, event: LutronEvent, params: Dict):
for handler, context in self._subscribers:
handler(self, context, event, params) | module function_definition identifier parameters identifier typed_parameter identifier type identifier typed_parameter identifier type identifier block for_statement pattern_list identifier identifier attribute identifier identifier block expression_statement call identifier argument_list identifier identifier identifi... | Dispatches the specified event to all the subscribers. |
def _py_expand_short(subsequence, sequence, max_l_dist):
subseq_len = len(subsequence)
if subseq_len == 0:
return (0, 0)
scores = list(range(1, subseq_len + 1))
min_score = subseq_len
min_score_idx = -1
for seq_index, char in enumerate(sequence):
a = seq_index
c = a + 1
... | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call identifier argument_list identifier if_statement comparison_operator identifier integer block return_statement tuple integer integer expression_statement assignment identifier call ide... | Straightforward implementation of partial match expansion. |
def _to_dict(self):
physical_prop_names = find_PhysicalProperty(self)
physical_prop_vals = [getattr(self, prop) for prop in physical_prop_names]
return dict(zip(physical_prop_names, physical_prop_vals)) | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list identifier expression_statement assignment identifier list_comprehension call identifier argument_list identifier identifier for_in_clause identifier identifier return_statement cal... | Return a dictionary representation of the current object. |
def diffuse_template(self, **kwargs):
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.diffuse_template_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(... | module function_definition identifier parameters identifier dictionary_splat_pattern identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list expression_statement call attribute identifier identifier argument_list dictionary_splat identifier exp... | return the file name for other diffuse map templates |
def theme_static_with_version(ctx, filename, external=False):
if current_app.theme_manager.static_folder:
url = assets.cdn_for('_themes.static',
filename=current.identifier + '/' + filename,
_external=external)
else:
url = assets.cdn_for(... | module function_definition identifier parameters identifier identifier default_parameter identifier false block if_statement attribute attribute identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list string string_start string_content string_... | Override the default theme static to add cache burst |
def strip(notebook):
for cell in notebook.cells:
if cell.cell_type == 'code':
cell.outputs = []
cell.execution_count = None | module function_definition identifier parameters identifier block for_statement identifier attribute identifier identifier block if_statement comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment attribute identifier identifier list expre... | Remove outputs from a notebook. |
def _is_mobile(ntype):
return (ntype == PhoneNumberType.MOBILE or
ntype == PhoneNumberType.FIXED_LINE_OR_MOBILE or
ntype == PhoneNumberType.PAGER) | module function_definition identifier parameters identifier block return_statement parenthesized_expression boolean_operator boolean_operator comparison_operator identifier attribute identifier identifier comparison_operator identifier attribute identifier identifier comparison_operator identifier attribute identifier ... | Checks if the supplied number type supports carrier lookup |
def install():
tmp_weboob_dir = '/tmp/weboob'
while (os.path.exists(tmp_weboob_dir)):
tmp_weboob_dir += '1'
print 'Fetching sources in temporary dir {}'.format(tmp_weboob_dir)
result = cmd_exec('git clone {} {}'.format(WEBOOB_REPO, tmp_weboob_dir))
if (result['error']):
print result[... | module function_definition identifier parameters block expression_statement assignment identifier string string_start string_content string_end while_statement parenthesized_expression call attribute attribute identifier identifier identifier argument_list identifier block expression_statement augmented_assignment iden... | Install weboob system-wide |
def create(self, id):
resp = self.client.accounts.create(id=id)
self.display(resp) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute attribute attribute identifier identifier identifier identifier argument_list keyword_argument identifier identifier expression_statement call attribute identifier identifier argument_l... | Create a new tenant id |
def fromTFExample(bytestr):
example = tf.train.Example()
example.ParseFromString(bytestr)
return example | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list expression_statement call attribute identifier identifier argument_list identifier return_statement identifier | Deserializes a TFExample from a byte string |
def schema_map(schema):
mapper = {}
for name in getFieldNames(schema):
mapper[name] = name
return mapper | module function_definition identifier parameters identifier block expression_statement assignment identifier dictionary for_statement identifier call identifier argument_list identifier block expression_statement assignment subscript identifier identifier identifier return_statement identifier | Return a valid ICachedItemMapper.map for schema |
def _write_to_graph(self):
traces = []
for byte_code, trace_data in self.coverage.items():
traces += [list(trace_data.keys()), list(trace_data.values()), "r--"]
plt.plot(*traces)
plt.axis([0, self.end - self.begin, 0, 100])
plt.xlabel("Duration (seconds)")
plt... | module function_definition identifier parameters identifier block expression_statement assignment identifier list for_statement pattern_list identifier identifier call attribute attribute identifier identifier identifier argument_list block expression_statement augmented_assignment identifier list call identifier argum... | Write the coverage results to a graph |
def _clean_result(self, text):
text = re.sub('\s\s+', ' ', text)
text = re.sub('\.\.+', '.', text)
text = text.replace("'", "\\'")
return text | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list string string_start string_content string_end string string_start string_content string_end identifier expression_statement assignment identifier cal... | Remove double spaces, punctuation and escapes apostrophes. |
def _question_line(self, section):
token = self.tok.get(want_leading = True)
if not token.is_whitespace():
self.last_name = dns.name.from_text(token.value, None)
name = self.last_name
token = self.tok.get()
if not token.is_identifier():
raise dns.exception... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list keyword_argument identifier true if_statement not_operator call attribute identifier identifier argument_list block expression_s... | Process one line from the text format question section. |
def _decode_temp(byte_1, byte_2):
temp = (byte_1 << 8) + byte_2
if (temp > 32767):
temp = temp - 65536
temp = temp / 10
return temp | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier binary_operator parenthesized_expression binary_operator identifier integer identifier if_statement parenthesized_expression comparison_operator identifier integer block expression_statement assignmen... | Decode a signed short temperature as two bytes to a single number. |
def to_vararray(var_instance, bounds):
assert isinstance(var_instance, SymbolVAR)
from symbols import BOUNDLIST
from symbols import VARARRAY
assert isinstance(bounds, BOUNDLIST)
var_instance.__class__ = VARARRAY
var_instance.class_ = CLASS.array
var_instance.bound... | module function_definition identifier parameters identifier identifier block assert_statement call identifier argument_list identifier identifier import_from_statement dotted_name identifier dotted_name identifier import_from_statement dotted_name identifier dotted_name identifier assert_statement call identifier argum... | Converts a var_instance to a var array one |
def app_profile_path(cls, project, instance, app_profile):
return google.api_core.path_template.expand(
"projects/{project}/instances/{instance}/appProfiles/{app_profile}",
project=project,
instance=instance,
app_profile=app_profile,
) | module function_definition identifier parameters identifier identifier identifier identifier block return_statement call attribute attribute attribute identifier identifier identifier identifier argument_list string string_start string_content string_end keyword_argument identifier identifier keyword_argument identifie... | Return a fully-qualified app_profile string. |
def reloadGraphs(self) :
"reloads the graph list"
r = self.connection.session.get(self.graphsURL)
data = r.json()
if r.status_code == 200 :
self.graphs = {}
for graphData in data["graphs"] :
try :
self.graphs[graphData["_key"]] ... | module function_definition identifier parameters identifier block expression_statement string string_start string_content string_end expression_statement assignment identifier call attribute attribute attribute identifier identifier identifier identifier argument_list attribute identifier identifier expression_statemen... | reloads the graph list |
def find_api_id(self):
allapis = self.client.get_rest_apis()
api_name = self.trigger_settings['api_name']
api_id = None
for api in allapis['items']:
if api['name'] == api_name:
api_id = api['id']
self.log.info("Found API for: %s", api_name)
... | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list expression_statement assignment identifier subscript attribute identifier identifier string string_start string_content string_end expressi... | Given API name, find API ID. |
def catCSVs(folder, ouputFileName, removeDups = False) :
strCmd = r %(folder, ouputFileName)
os.system(strCmd)
if removeDups :
removeDuplicates(ouputFileName, ouputFileName) | module function_definition identifier parameters identifier identifier default_parameter identifier false block expression_statement assignment identifier binary_operator identifier tuple identifier identifier expression_statement call attribute identifier identifier argument_list identifier if_statement identifier blo... | Concatenates all csv in 'folder' and wites the results in 'ouputFileName'. My not work on non Unix systems |
def colordict(self):
d = {}
i=0
n = len(self.constraints)
for c in self.constraints:
d[c] = cm.jet(1.*i/n)
i+=1
return d | module function_definition identifier parameters identifier block expression_statement assignment identifier dictionary expression_statement assignment identifier integer expression_statement assignment identifier call identifier argument_list attribute identifier identifier for_statement identifier attribute identifie... | Dictionary holding colors that correspond to constraints. |
def energy(self):
e = 0
for i in range(len(self.state)):
e += self.distance_matrix[self.state[i-1]][self.state[i]]
return e | module function_definition identifier parameters identifier block expression_statement assignment identifier integer for_statement identifier call identifier argument_list call identifier argument_list attribute identifier identifier block expression_statement augmented_assignment identifier subscript subscript attribu... | Calculates the length of the route. |
def base_url(klass, space_id, resource_id=None, public=False, environment_id=None, **kwargs):
if public:
environment_slug = ""
if environment_id is not None:
environment_slug = "/environments/{0}".format(environment_id)
return "spaces/{0}{1}/public/content_typ... | module function_definition identifier parameters identifier identifier default_parameter identifier none default_parameter identifier false default_parameter identifier none dictionary_splat_pattern identifier block if_statement identifier block expression_statement assignment identifier string string_start string_end ... | Returns the URI for the content type. |
def _get_app_config(self, app_name):
matches = [app_config for app_config in apps.get_app_configs()
if app_config.name == app_name]
if not matches:
return
return matches[0] | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier list_comprehension identifier for_in_clause identifier call attribute identifier identifier argument_list if_clause comparison_operator attribute identifier identifier identifier if_statement not_oper... | Returns an app config for the given name, not by label. |
def urlencode(params):
if not isinstance(params, dict):
raise TypeError("Only dicts are supported.")
params = flatten(params)
url_params = OrderedDict()
for param in params:
value = param.pop()
name = parametrize(param)
if isinstance(value, (list, tuple)):
nam... | module function_definition identifier parameters identifier block if_statement not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list string string_start string_content string_end expression_statement assignment identifier call identifier argument_list ident... | Urlencode a multidimensional dict. |
def _get_s3_files(local_dir, file_info, params):
assert len(file_info) == 1
files = file_info.values()[0]
fnames = []
for k in ["1", "2"]:
if files[k] not in fnames:
fnames.append(files[k])
out = []
for fname in fnames:
bucket, key = fname.replace("s3://", "").split("... | module function_definition identifier parameters identifier identifier identifier block assert_statement comparison_operator call identifier argument_list identifier integer expression_statement assignment identifier subscript call attribute identifier identifier argument_list integer expression_statement assignment id... | Retrieve s3 files to local directory, handling STORMSeq inputs. |
def sqlvm_group_create(client, cmd, sql_virtual_machine_group_name, resource_group_name, location, sql_image_offer,
sql_image_sku, domain_fqdn, cluster_operator_account, sql_service_account,
storage_account_url, storage_account_key, cluster_bootstrap_account=None,
... | module function_definition identifier parameters identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier default_parameter identifier none default_parameter identifier none default_parameter identifier none default_parameter identifier none blo... | Creates a SQL virtual machine group. |
def home(request):
try:
DBSession.query(User).first()
except DBAPIError:
return Response(
conn_err_msg,
content_type="text/plain",
status_int=500,
)
return {"project": "pyramid_tut"} | module function_definition identifier parameters identifier block try_statement block expression_statement call attribute call attribute identifier identifier argument_list identifier identifier argument_list except_clause identifier block return_statement call identifier argument_list identifier keyword_argument ident... | Try to connect to database, and list available examples. |
def _read_depth_images(self, num_images):
depth_images = self._ros_read_images(self._depth_image_buffer, num_images, self.staleness_limit)
for i in range(0, num_images):
depth_images[i] = depth_images[i] * MM_TO_METERS
if self._flip_images:
depth_images[i] = np.fl... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifier identifier identifier attribute identifier identifier for_statement identifier call identifier argument_list integer identifier ... | Reads depth images from the device |
def load_yaml(fname):
yaml = YAML(typ="safe")
yaml.allow_duplicate_keys = True
HassSafeConstructor.name = fname
yaml.Constructor = HassSafeConstructor
with open(fname, encoding="utf-8") as conf_file:
return yaml.load(conf_file) or {} | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list keyword_argument identifier string string_start string_content string_end expression_statement assignment attribute identifier identifier true expression_statement assignment attrib... | Load a YAML file. |
def cli(sequencepath, report, refseq_database):
main(sequencepath, report, refseq_database, num_threads=multiprocessing.cpu_count()) | module function_definition identifier parameters identifier identifier identifier block expression_statement call identifier argument_list identifier identifier identifier keyword_argument identifier call attribute identifier identifier argument_list | Pass command line arguments to, and run the feature extraction functions |
def dynare_import(filename,full_output=False, debug=False):
import os
basename = os.path.basename(filename)
fname = re.compile('(.*)\.(.*)').match(basename).group(1)
f = open(filename)
txt = f.read()
model = parse_dynare_text(txt,full_output=full_output, debug=debug)
model.name = fname
r... | module function_definition identifier parameters identifier default_parameter identifier false default_parameter identifier false block import_statement dotted_name identifier expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list identifier expression_stateme... | Imports model defined in specified file |
def start(self, ccallbacks=None):
self.__manage_g = gevent.spawn(self.__manage_connections, ccallbacks)
self.__ready_ev.wait() | module function_definition identifier parameters identifier default_parameter identifier none block expression_statement assignment attribute identifier identifier call attribute identifier identifier argument_list attribute identifier identifier identifier expression_statement call attribute attribute identifier ident... | Establish and maintain connections. |
def busy_display():
sys.stdout.write("\033[?25l")
sys.stdout.flush()
for x in range(1800):
symb = ['\\', '|', '/', '-']
sys.stdout.write("\033[D{}".format(symb[x % 4]))
sys.stdout.flush()
gevent.sleep(0.1) | module function_definition identifier parameters block expression_statement call attribute attribute identifier identifier identifier argument_list string string_start string_content escape_sequence string_end expression_statement call attribute attribute identifier identifier identifier argument_list for_statement ide... | Display animation to show activity. |
def _try_import(module_name):
try:
mod = importlib.import_module(module_name)
return mod
except ImportError:
err_msg = ("Tried importing %s but failed. See setup.py extras_require. "
"The dataset you are trying to use may have additional "
"dependencies.")
utils.reraise... | module function_definition identifier parameters identifier block try_statement block expression_statement assignment identifier call attribute identifier identifier argument_list identifier return_statement identifier except_clause identifier block expression_statement assignment identifier parenthesized_expression co... | Try importing a module, with an informative error message on failure. |
def treeplot(self, qlist, credible_interval):
for y, _, label, values, color in self.iterator():
ntiles = np.percentile(values.flatten(), qlist)
ntiles[0], ntiles[-1] = hpd(values.flatten(), credible_interval)
yield y, label, ntiles, color | module function_definition identifier parameters identifier identifier identifier block for_statement pattern_list identifier identifier identifier identifier identifier call attribute identifier identifier argument_list block expression_statement assignment identifier call attribute identifier identifier argument_list... | Get data for each treeplot for the variable. |
def worker_loop_v1(dataset, key_queue, data_queue, batchify_fn):
while True:
idx, samples = key_queue.get()
if idx is None:
break
batch = batchify_fn([dataset[i] for i in samples])
data_queue.put((idx, batch)) | module function_definition identifier parameters identifier identifier identifier identifier block while_statement true block expression_statement assignment pattern_list identifier identifier call attribute identifier identifier argument_list if_statement comparison_operator identifier none block break_statement expre... | Worker loop for multiprocessing DataLoader. |
def restore(self):
if self.proxy_object is None:
if self.getter:
setattr(self.getter_class, self.attr_name, self.getter)
elif self.is_local:
setattr(self.orig_object, self.attr_name, self.orig_value)
else:
delattr(self.orig_obje... | module function_definition identifier parameters identifier block if_statement comparison_operator attribute identifier identifier none block if_statement attribute identifier identifier block expression_statement call identifier argument_list attribute identifier identifier attribute identifier identifier attribute id... | Restore the saved value for the attribute of the object. |
def _array2cstr(arr):
out = StringIO()
np.save(out, arr)
return b64encode(out.getvalue()) | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list expression_statement call attribute identifier identifier argument_list identifier identifier return_statement call identifier argument_list call attribute identifier identifier arg... | Serializes a numpy array to a compressed base64 string |
def search_fetch_force(request, id, redirect_to):
search = Search.objects.get(id=id)
search.fetch(force=True)
msg = _("Fetched tweets for %s" % search.criteria)
messages.success(request, msg, fail_silently=True)
return HttpResponseRedirect(redirect_to) | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list keyword_argument identifier identifier expression_statement call attribute identifier identifier argument_list keywor... | Forcibly fetch tweets for the search |
def listDatasetAccessTypes(self, dataset_access_type=""):
if isinstance(dataset_access_type, basestring):
try:
dataset_access_type = str(dataset_access_type)
except:
dbsExceptionHandler('dbsException-invalid-input', 'dataset_access_type given is not va... | module function_definition identifier parameters identifier default_parameter identifier string string_start string_end block if_statement call identifier argument_list identifier identifier block try_statement block expression_statement assignment identifier call identifier argument_list identifier except_clause block... | List dataset access types |
def json_wrap(function, *args, **kwargs):
try:
response = json.loads(function(*args, **kwargs).content)
if 'data' in response:
return response['data'] or True
else:
return response
except Exception as exc:
raise ClientException(exc) | module function_definition identifier parameters identifier list_splat_pattern identifier dictionary_splat_pattern identifier block try_statement block expression_statement assignment identifier call attribute identifier identifier argument_list attribute call identifier argument_list list_splat identifier dictionary_s... | Return the json content of a function that returns a request |
def max(cls):
max_recid = db.session.query(func.max(cls.recid)).scalar()
return max_recid if max_recid else 0 | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute call attribute attribute identifier identifier identifier argument_list call attribute identifier identifier argument_list attribute identifier identifier identifier argument_list return_statement... | Get max record identifier. |
def default_user_agent(name="python-requests"):
_implementation = platform.python_implementation()
if _implementation == 'CPython':
_implementation_version = platform.python_version()
elif _implementation == 'PyPy':
_implementation_version = '%s.%s.%s' % (sys.pypy_version_info.major,
... | module function_definition identifier parameters default_parameter identifier string string_start string_content string_end block expression_statement assignment identifier call attribute identifier identifier argument_list if_statement comparison_operator identifier string string_start string_content string_end block ... | Return a string representing the default user agent. |
def identity(ctx, variant_id):
if not variant_id:
LOG.warning("Please provide a variant id")
ctx.abort()
adapter = ctx.obj['adapter']
version = ctx.obj['version']
LOG.info("Search variants {0}".format(adapter))
result = adapter.get_clusters(variant_id)
if result.count() == 0:
... | module function_definition identifier parameters identifier identifier block if_statement not_operator identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end expression_statement call attribute identifier identifier argument_list expression... | Check how well SVs are working in the database |
def weighted_tanimoto(a, b, weights):
weighted = lambda s: map(lambda (x,y): float(x)*float(y), zip(s, weights))
return tanimoto_coefficient(weighted(a), weighted(b)) | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier lambda lambda_parameters identifier call identifier argument_list lambda lambda_parameters tuple_pattern identifier identifier binary_operator call identifier argument_list identifier call ... | Same as the Tanimoto coefficient, but wit weights for each dimension. |
def ssh_config(ssh_user, ssh_private_key_file):
try:
ssh_file = NamedTemporaryFile(delete=False, mode='w+')
ssh_file.write('Host *\n')
ssh_file.write(' IdentityFile %s\n' % ssh_private_key_file)
ssh_file.write(' User %s' % ssh_user)
ssh_file.close()
yield ssh_fi... | module function_definition identifier parameters identifier identifier block try_statement block expression_statement assignment identifier call identifier argument_list keyword_argument identifier false keyword_argument identifier string string_start string_content string_end expression_statement call attribute identi... | Create temporary ssh config file. |
def c_str(string):
if not isinstance(string, str):
string = string.decode('ascii')
return ctypes.c_char_p(string.encode('utf-8')) | module function_definition identifier parameters identifier block if_statement not_operator call identifier argument_list identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list string string_start string_content string_end return_statement call attribut... | Convert a python string to C string. |
def create_database_session(engine):
try:
Session = sessionmaker(bind=engine)
return Session()
except OperationalError as e:
raise DatabaseError(error=e.orig.args[1], code=e.orig.args[0]) | module function_definition identifier parameters identifier block try_statement block expression_statement assignment identifier call identifier argument_list keyword_argument identifier identifier return_statement call identifier argument_list except_clause as_pattern identifier as_pattern_target identifier block rais... | Connect to the database |
def __load_countries(self, db):
try:
countries = self.__read_countries_file()
except IOError as e:
raise LoadError(str(e))
try:
with db.connect() as session:
for country in countries:
session.add(country)
except Exce... | module function_definition identifier parameters identifier identifier block try_statement block expression_statement assignment identifier call attribute identifier identifier argument_list except_clause as_pattern identifier as_pattern_target identifier block raise_statement call identifier argument_list call identif... | Load the list of countries |
def select_locale_by_request(self, request, locales=()):
default_locale = locales and locales[0] or self.cfg.default_locale
if len(locales) == 1 or 'ACCEPT-LANGUAGE' not in request.headers:
return default_locale
ulocales = [
(q, locale_delim_re.split(v)[0])
fo... | module function_definition identifier parameters identifier identifier default_parameter identifier tuple block expression_statement assignment identifier boolean_operator boolean_operator identifier subscript identifier integer attribute attribute identifier identifier identifier if_statement boolean_operator comparis... | Choose an user's locales by request. |
def _load_rules(forcefield):
rules = dict()
for rule_name, smarts in forcefield.atomTypeDefinitions.items():
overrides = forcefield.atomTypeOverrides.get(rule_name)
if overrides is not None:
overrides = set(overrides)
else:
overrides = set()
rules[rule_nam... | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list for_statement pattern_list identifier identifier call attribute attribute identifier identifier identifier argument_list block expression_statement assignment identifier call attrib... | Load atomtyping rules from a forcefield into SMARTSGraphs. |
def load_data(self):
try:
df = self.live_quote_arg_func(self.tickers)
for index, ticker in enumerate(self.tickers):
ticker_info = df.loc[index]
self.ticker_dict[ticker].append(ticker_info['price'],
ticker_inf... | module function_definition identifier parameters identifier block try_statement block expression_statement assignment identifier call attribute identifier identifier argument_list attribute identifier identifier for_statement pattern_list identifier identifier call identifier argument_list attribute identifier identifi... | Overwrite this for new source data structures |
def resource(self):
if self._resource:
return self._resource
elif self.binding:
return self.binding.resource | module function_definition identifier parameters identifier block if_statement attribute identifier identifier block return_statement attribute identifier identifier elif_clause attribute identifier identifier block return_statement attribute attribute identifier identifier identifier | Resource associated with operation. |
def append_rally_point(self, p):
if (self.rally_count() > 9):
print("Can't have more than 10 rally points, not adding.")
return
self.rally_points.append(p)
self.reindex() | module function_definition identifier parameters identifier identifier block if_statement parenthesized_expression comparison_operator call attribute identifier identifier argument_list integer block expression_statement call identifier argument_list string string_start string_content string_end return_statement expres... | add rallypoint to end of list |
def to_dict(self):
if not self.url:
return None
return {
'url': self.url,
'width': self.width,
'height': self.height
} | module function_definition identifier parameters identifier block if_statement not_operator attribute identifier identifier block return_statement none return_statement dictionary pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attrib... | Convert Image into raw dictionary data. |
def fetch(index, tokens):
if len(tokens) == 0:
return set()
return set.intersection(*[set(index.get(token, [])) for token in tokens]) | module function_definition identifier parameters identifier identifier block if_statement comparison_operator call identifier argument_list identifier integer block return_statement call identifier argument_list return_statement call attribute identifier identifier argument_list list_splat list_comprehension call ident... | Fetch the codes from given tokens |
def read_header(self):
with fopen(self.vpk_path, 'rb') as f:
(self.signature,
self.version,
self.tree_length
) = struct.unpack("3I", f.read(3*4))
if self.signature != 0x55aa1234:
raise ValueError("File is not VPK (invalid magic)")
... | module function_definition identifier parameters identifier block with_statement with_clause with_item as_pattern call identifier argument_list attribute identifier identifier string string_start string_content string_end as_pattern_target identifier block expression_statement assignment tuple_pattern attribute identif... | Reads VPK file header from the file |
def _read_temp(data):
tout = StringIO()
tout.write(data)
tout.seek(0)
output = tout.readlines()
tout.close()
return output | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list expression_statement call attribute identifier identifier argument_list identifier expression_statement call attribute identifier identifier argument_list integer expression_stateme... | Return what would be written to disk |
def stop_jobs(self, job_ids=None):
self.lock()
jobs = self.get_jobs(job_ids)
for job in jobs:
if job.status in ('executing', 'queued', 'waiting') and job.queue_name == 'local':
logger.info("Reset job '%s' (%s) in the database", job.name, self._format_log(job.id))
job.submit()
self.... | module function_definition identifier parameters identifier default_parameter identifier none block expression_statement call attribute identifier identifier argument_list expression_statement assignment identifier call attribute identifier identifier argument_list identifier for_statement identifier identifier block i... | Resets the status of the job to 'submitted' when they are labeled as 'executing'. |
def cl_picard(self, command, options, memscale=None):
options = ["%s=%s" % (x, y) for x, y in options]
options.append("VALIDATION_STRINGENCY=SILENT")
return self._get_picard_cmd(command, memscale=memscale) + options | module function_definition identifier parameters identifier identifier identifier default_parameter identifier none block expression_statement assignment identifier list_comprehension binary_operator string string_start string_content string_end tuple identifier identifier for_in_clause pattern_list identifier identifi... | Prepare a Picard commandline. |
def strip( text ):
members = [attr for attr in Colors.__dict__.keys() if not attr.startswith( "__" ) and not attr == 'strip']
for c in members:
text = text.replace( vars( Colors )[c], '' )
return text | module function_definition identifier parameters identifier block expression_statement assignment identifier list_comprehension identifier for_in_clause identifier call attribute attribute identifier identifier identifier argument_list if_clause boolean_operator not_operator call attribute identifier identifier argumen... | Strips all color codes from a text. |
def DiffArrayObjects(self, oldObj, newObj, isElementLinks=False):
if oldObj == newObj:
return True
if not oldObj or not newObj:
return False
if len(oldObj) != len(newObj):
__Log__.debug('DiffArrayObjects: Array lengths do not match %d != %d'
% (len(oldObj), len(n... | module function_definition identifier parameters identifier identifier identifier default_parameter identifier false block if_statement comparison_operator identifier identifier block return_statement true if_statement boolean_operator not_operator identifier not_operator identifier block return_statement false if_stat... | Method which deligates the diffing of arrays based on the type |
def plot_gaps(plot, columns):
from plot_window import window_plot_convolve as plot_window
plot_window([[100 - i for i in columns]], len(columns)*.01, plot) | module function_definition identifier parameters identifier identifier block import_from_statement dotted_name identifier aliased_import dotted_name identifier identifier expression_statement call identifier argument_list list list_comprehension binary_operator integer identifier for_in_clause identifier identifier bin... | plot % of gaps at each position |
def getMouse(self):
self.mouse_x.value = -1
self.mouse_y.value = -1
while self.mouse_x.value == -1 and self.mouse_y.value == -1:
time.sleep(.1)
return (self.mouse_x.value, self.mouse_y.value) | module function_definition identifier parameters identifier block expression_statement assignment attribute attribute identifier identifier identifier unary_operator integer expression_statement assignment attribute attribute identifier identifier identifier unary_operator integer while_statement boolean_operator compa... | Waits for a mouse click. |
def _split_string_to_tokens(text):
if not text:
return []
ret = []
token_start = 0
is_alnum = [c in _ALPHANUMERIC_CHAR_SET for c in text]
for pos in xrange(1, len(text)):
if is_alnum[pos] != is_alnum[pos - 1]:
token = text[token_start:pos]
if token != u" " or token_start == 0:
ret.... | module function_definition identifier parameters identifier block if_statement not_operator identifier block return_statement list expression_statement assignment identifier list expression_statement assignment identifier integer expression_statement assignment identifier list_comprehension comparison_operator identifi... | Splits text to a list of string tokens. |
def handle_pubrel(self):
self.logger.info("PUBREL received")
ret, mid = self.in_packet.read_uint16()
if ret != NC.ERR_SUCCESS:
return ret
evt = event.EventPubrel(mid)
self.push_event(evt)
return NC.ERR_SUCCESS | module function_definition identifier parameters identifier block expression_statement call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end expression_statement assignment pattern_list identifier identifier call attribute attribute identifier identifier i... | Handle incoming PUBREL packet. |
def detach(self):
if not self._closed:
del self._as_parameter_
self._closed = True
self._ptr = None | module function_definition identifier parameters identifier block if_statement not_operator attribute identifier identifier block delete_statement attribute identifier identifier expression_statement assignment attribute identifier identifier true expression_statement assignment attribute identifier identifier none | Detach the underlying LLVM resource without disposing of it. |
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