code stringlengths 51 2.34k | sequence stringlengths 186 3.94k | docstring stringlengths 11 171 |
|---|---|---|
def execute(self, fetchcommand, sql, params=None):
cur = self.conn.cursor()
if params:
if not type(params).__name__ == 'tuple':
raise ValueError('the params argument needs to be a tuple')
return None
cur.execute(sql, params)
else:
cur.execute(sql)
self.conn.commit()
if not fetchcommand or fet... | module function_definition identifier parameters identifier identifier identifier default_parameter identifier none block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list if_statement identifier block if_statement not_operator comparison_operator attribu... | where 'fetchcommand' is either 'fetchone' or 'fetchall' |
def update():
with settings(warn_only=True):
print(cyan('\nInstalling/Updating required packages...'))
pip = local('venv/bin/pip install -U --allow-all-external --src libs -r requirements.txt', capture=True)
if pip.failed:
print(red(pip))
abort("pip exited with return... | module function_definition identifier parameters block with_statement with_clause with_item call identifier argument_list keyword_argument identifier true block expression_statement call identifier argument_list call identifier argument_list string string_start string_content escape_sequence string_end expression_state... | Update virtual env with requirements packages. |
def new(self, request):
form = (self.form or generate_form(self.model))()
return self._render(
request = request,
template = 'new',
context = {
'form': form
},
status = 200
) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call parenthesized_expression boolean_operator attribute identifier identifier call identifier argument_list attribute identifier identifier argument_list return_statement call attribute identifier id... | Render a form to create a new object. |
def fetch_url(url, dest, parent_to_remove_before_fetch):
logger.debug('Downloading file {} from {}', dest, url)
try:
shutil.rmtree(parent_to_remove_before_fetch)
except FileNotFoundError:
pass
os.makedirs(parent_to_remove_before_fetch)
resp = requests.get(url, stream=True)
with o... | module function_definition identifier parameters identifier identifier identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end identifier identifier try_statement block expression_statement call attribute identifier identifier argument_list ... | Helper function to fetch a file from a URL. |
def build(self):
monomers = [HelicalHelix(major_pitch=self.major_pitches[i],
major_radius=self.major_radii[i],
major_handedness=self.major_handedness[i],
aa=self.aas[i],
minor_heli... | module function_definition identifier parameters identifier block expression_statement assignment identifier list_comprehension call identifier argument_list keyword_argument identifier subscript attribute identifier identifier identifier keyword_argument identifier subscript attribute identifier identifier identifier ... | Builds a model of a coiled coil protein using input parameters. |
def _optimize_providers(self, providers):
new_providers = {}
provider_by_driver = {}
for alias, driver in six.iteritems(providers):
for name, data in six.iteritems(driver):
if name not in provider_by_driver:
provider_by_driver[name] = {}
... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier dictionary expression_statement assignment identifier dictionary for_statement pattern_list identifier identifier call attribute identifier identifier argument_list identifier block for_statement patt... | Return an optimized mapping of available providers |
def upload():
build = g.build
utils.jsonify_assert(len(request.files) == 1,
'Need exactly one uploaded file')
file_storage = request.files.values()[0]
data = file_storage.read()
content_type, _ = mimetypes.guess_type(file_storage.filename)
artifact = _save_artifact(build... | module function_definition identifier parameters block expression_statement assignment identifier attribute identifier identifier expression_statement call attribute identifier identifier argument_list comparison_operator call identifier argument_list attribute identifier identifier integer string string_start string_c... | Uploads an artifact referenced by a run. |
def vip_create_event(self, vip_info):
vip_data = vip_info.get('vip')
port_id = vip_data.get('port_id')
vip_id = vip_data.get('id')
self.add_lbaas_port(port_id, vip_id) | 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 expression_statement assignment identifier call attribute identifier identifier argument_list string st... | Process vip create event. |
def _import_class(self, module2cls):
d = module2cls.rfind(".")
classname = module2cls[d + 1: len(module2cls)]
m = __import__(module2cls[0:d], globals(), locals(), [classname])
return getattr(m, classname) | 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 expression_statement assignment identifier subscript identifier slice binary_operator identifier intege... | Import class by module dot split string |
def createNetcon(self, thresh=10):
nc = h.NetCon(self.soma(0.5)._ref_v, None, sec = self.soma)
nc.threshold = thresh
return nc | module function_definition identifier parameters identifier default_parameter identifier integer block expression_statement assignment identifier call attribute identifier identifier argument_list attribute call attribute identifier identifier argument_list float identifier none keyword_argument identifier attribute id... | created netcon to record spikes |
def cart2spher(x, y, z):
hxy = np.hypot(x, y)
r = np.hypot(hxy, z)
theta = np.arctan2(z, hxy)
phi = np.arctan2(y, x)
return r, theta, phi | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier identifier expression_statement assignment identifier call attribute identifier identifier argument_list identifier identifier ... | Cartesian to Spherical coordinate conversion. |
def iterkeys(obj):
"Get key iterator from dictionary for Python 2 and 3"
return iter(obj.keys()) if sys.version_info.major == 3 else obj.iterkeys() | module function_definition identifier parameters identifier block expression_statement string string_start string_content string_end return_statement conditional_expression call identifier argument_list call attribute identifier identifier argument_list comparison_operator attribute attribute identifier identifier iden... | Get key iterator from dictionary for Python 2 and 3 |
def invert_delete_row(self, key, value):
self.rows = filter(lambda x: x.get(key) == value, self.rows) | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment attribute identifier identifier call identifier argument_list lambda lambda_parameters identifier comparison_operator call attribute identifier identifier argument_list identifier identifier attribute... | Inverts delete_row and returns the rows where key = value |
def excursion(directory):
old_dir = os.getcwd()
try:
os.chdir(directory)
yield
finally:
os.chdir(old_dir) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list try_statement block expression_statement call attribute identifier identifier argument_list identifier expression_statement yield finally_clause block expressio... | Context-manager that temporarily changes to a new working directory. |
def countWordOverlapFrequencies(filename="goodOverlapPairs.pkl"):
with open(filename,"rb") as f:
goodOverlapPairs = pickle.load(f)
with open("word_bitmaps_40_bits_minimum.pkl","rb") as f:
bitmaps = pickle.load(f)
wordFrequencies = {}
for w1, w2, overlap in goodOverlapPairs:
wordFrequencies[w1] = wor... | module function_definition identifier parameters default_parameter identifier string string_start string_content string_end 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... | Count how many high overlaps each word has, and print it out |
def parse_iso8601_date(string):
match = _RE_ISO8601_DATE.search(string)
if not match:
raise ValueError('Expected ISO 8601 date')
year = int(match.group('year'))
month = int(match.group('month'))
day = int(match.group('day'))
return date(year, month, day) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier if_statement not_operator identifier block raise_statement call identifier argument_list string string_start string_content string_end expression_sta... | Parse an ISO 8601 date string |
def management(self):
endpoint = self._instance.get_endpoint_for_service_type(
"management",
region_name=self._instance._region_name,
)
token = self._instance.auth.get_token(self._instance.session)
self._management = tuskar_client.get_client(
2, os_aut... | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end keyword_argument identifier attribute attribute identifier identifier identifier expression_s... | Returns an management service client |
def example_lab_to_xyz():
print("=== Simple Example: Lab->XYZ ===")
lab = LabColor(0.903, 16.296, -2.22)
print(lab)
xyz = convert_color(lab, XYZColor)
print(xyz)
print("=== End Example ===\n") | module function_definition identifier parameters block expression_statement call identifier argument_list string string_start string_content string_end expression_statement assignment identifier call identifier argument_list float float unary_operator float expression_statement call identifier argument_list identifier ... | This function shows a simple conversion of an Lab color to an XYZ color. |
def path_to_reference(path):
path = str(path)
if '.' not in path:
try:
return globals()["__builtins__"][path]
except KeyError:
try:
return getattr(globals()["__builtins__"], path)
except AttributeError:
pass
try:
... | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list identifier if_statement comparison_operator string string_start string_content string_end identifier block try_statement block return_statement subscript subscript call identifier a... | Convert an object path reference to a reference. |
def _check_prob_and_prob_vector(predictions):
from .._deps import numpy
ptype = predictions.dtype
import array
if ptype not in [float, numpy.ndarray, array.array, int]:
err_msg = "Input `predictions` must be of numeric type (for binary "
err_msg += "classification) or array (of probabil... | module function_definition identifier parameters identifier block import_from_statement relative_import import_prefix dotted_name identifier dotted_name identifier expression_statement assignment identifier attribute identifier identifier import_statement dotted_name identifier if_statement comparison_operator identifi... | Check that the predictionsa are either probabilities of prob-vectors. |
def _get_mosaik_nn_args(out_file):
base_nn_url = "https://raw.github.com/wanpinglee/MOSAIK/master/src/networkFile/"
out = []
for arg, fname in [("-annse", "2.1.26.se.100.005.ann"),
("-annpe", "2.1.26.pe.100.0065.ann")]:
arg_fname = os.path.join(os.path.dirname(out_file), fname... | module function_definition identifier parameters identifier block expression_statement assignment identifier string string_start string_content string_end expression_statement assignment identifier list for_statement pattern_list identifier identifier list tuple string string_start string_content string_end string stri... | Retrieve default neural network files from GitHub to pass to Mosaik. |
def _handle_ping(client, topic, dct):
if dct['type'] == 'request':
resp = {
'type': 'answer',
'name': client.name,
'source': dct
}
client.publish('ping', resp) | module function_definition identifier parameters identifier identifier identifier block if_statement comparison_operator subscript identifier string string_start string_content string_end string string_start string_content string_end block expression_statement assignment identifier dictionary pair string string_start s... | Internal method that will be called when receiving ping message. |
def rand_pad(padding:int, size:int, mode:str='reflection'):
"Fixed `mode` `padding` and random crop of `size`"
return [pad(padding=padding,mode=mode),
crop(size=size, **rand_pos)] | module function_definition identifier parameters typed_parameter identifier type identifier typed_parameter identifier type identifier typed_default_parameter identifier type identifier string string_start string_content string_end block expression_statement string string_start string_content string_end return_statemen... | Fixed `mode` `padding` and random crop of `size` |
def upload_data(job, master_ip, inputs, hdfs_name, upload_name, spark_on_toil):
if mock_mode():
truncate_file(master_ip, hdfs_name, spark_on_toil)
log.info("Uploading output BAM %s to %s.", hdfs_name, upload_name)
call_conductor(job, master_ip, hdfs_name, upload_name, memory=inputs.memory)
remov... | module function_definition identifier parameters identifier identifier identifier identifier identifier identifier block if_statement call identifier argument_list block expression_statement call identifier argument_list identifier identifier identifier expression_statement call attribute identifier identifier argument... | Upload file hdfsName from hdfs to s3 |
def object(self):
proxy = self._proxy
return ObjectProxy(proxy.get_connection(),
proxy.get_name(),
proxy.get_object_path()) | module function_definition identifier parameters identifier block expression_statement assignment identifier attribute identifier identifier return_statement call identifier argument_list call attribute identifier identifier argument_list call attribute identifier identifier argument_list call attribute identifier iden... | Get an ObjectProxy instanec for the underlying object. |
def append(self, item: TransItem):
self.data[item.key].append(item) | module function_definition identifier parameters identifier typed_parameter identifier type identifier block expression_statement call attribute subscript attribute identifier identifier attribute identifier identifier identifier argument_list identifier | Append an item to the internal dictionary. |
def calculate_dimensions(image, long_side, short_side):
if image.width >= image.height:
return '{0}x{1}'.format(long_side, short_side)
return '{0}x{1}'.format(short_side, long_side) | module function_definition identifier parameters identifier identifier identifier block if_statement comparison_operator attribute identifier identifier attribute identifier identifier block return_statement call attribute string string_start string_content string_end identifier argument_list identifier identifier retu... | Returns the thumbnail dimensions depending on the images format. |
def createCenterPointMarker(self):
self.axes.add_patch(patches.Rectangle((-0.75,-self.thick),0.5,2.0*self.thick,facecolor='orange',zorder=3))
self.axes.add_patch(patches.Rectangle((0.25,-self.thick),0.5,2.0*self.thick,facecolor='orange',zorder=3))
self.axes.add_patch(patches.Circle((0,0),radius=... | module function_definition identifier parameters identifier block expression_statement call attribute attribute identifier identifier identifier argument_list call attribute identifier identifier argument_list tuple unary_operator float unary_operator attribute identifier identifier float binary_operator float attribut... | Creates the center pointer in the middle of the screen. |
def cublasDsymm(handle, side, uplo, m, n, alpha, A, lda, B, ldb, beta, C, ldc):
status = _libcublas.cublasDsymm_v2(handle,
_CUBLAS_SIDE_MODE[side],
_CUBLAS_FILL_MODE[uplo],
m, n, ctypes.byref(ctypes... | module function_definition identifier parameters identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier subscript identif... | Matrix-matrix product for real symmetric matrix. |
def setup_options_button(self):
if not self.options_button:
self.options_button = create_toolbutton(
self, text=_('Options'), icon=ima.icon('tooloptions'))
actions = self.actions + [MENU_SEPARATOR] + self.plugin_actions
self.options_menu = QMenu(self)
... | module function_definition identifier parameters identifier block if_statement not_operator attribute identifier identifier block expression_statement assignment attribute identifier identifier call identifier argument_list identifier keyword_argument identifier call identifier argument_list string string_start string_... | Add the cog menu button to the toolbar. |
def parseFile(self, filename):
modname = self.filenameToModname(filename)
module = Module(modname, filename)
self.modules[modname] = module
if self.trackUnusedNames:
module.imported_names, module.unused_names = \
find_imports_and_track_names(filename,
... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call identifier argument_list identifier identifier expression_statement assignment subscript a... | Parse a single file. |
def getUmis(self, n):
if n < (self.random_fill_size - self.random_ix):
barcodes = self.random_umis[self.random_ix: self.random_ix+n]
else:
if n > self.random_fill_size:
self.random_fill_size = n * 2
self.refill_random()
barcodes = self.rand... | module function_definition identifier parameters identifier identifier block if_statement comparison_operator identifier parenthesized_expression binary_operator attribute identifier identifier attribute identifier identifier block expression_statement assignment identifier subscript attribute identifier identifier sli... | return n umis from the random_umis atr. |
def schema_exists(cls, cur, schema_name):
cur.execute("SELECT EXISTS (SELECT schema_name FROM information_schema.schemata WHERE schema_name = '{0}');"
.format(schema_name))
return cur.fetchone()[0] | module function_definition identifier parameters identifier identifier identifier block expression_statement call attribute identifier identifier argument_list call attribute string string_start string_content string_end identifier argument_list identifier return_statement subscript call attribute identifier identifier... | Check if schema exists |
def generate_nonce_timestamp():
global count
rng = botan.rng().get(30)
uuid4 = uuid.uuid4().bytes
tmpnonce = (bytes(str(count).encode('utf-8'))) + uuid4 + rng
nonce = tmpnonce[:41]
count += 1
return nonce | module function_definition identifier parameters block global_statement identifier expression_statement assignment identifier call attribute call attribute identifier identifier argument_list identifier argument_list integer expression_statement assignment identifier attribute call attribute identifier identifier argum... | Generate unique nonce with counter, uuid and rng. |
def _load_data(batch, targets, major_axis):
if isinstance(batch, list):
new_batch = []
for i in range(len(targets)):
new_batch.append([b.data[i] for b in batch])
new_targets = [[dst for _, dst in d_target] for d_target in targets]
_load_general(new_batch, new_targets, maj... | module function_definition identifier parameters identifier identifier identifier block if_statement call identifier argument_list identifier identifier block expression_statement assignment identifier list for_statement identifier call identifier argument_list call identifier argument_list identifier block expression_... | Load data into sliced arrays. |
def create_filehandlers(self, filenames, fh_kwargs=None):
filenames = list(OrderedDict.fromkeys(filenames))
logger.debug("Assigning to %s: %s", self.info['name'], filenames)
self.info.setdefault('filenames', []).extend(filenames)
filename_set = set(filenames)
created_fhs = {}
... | module function_definition identifier parameters identifier identifier default_parameter identifier none block expression_statement assignment identifier call identifier argument_list call attribute identifier identifier argument_list identifier expression_statement call attribute identifier identifier argument_list st... | Organize the filenames into file types and create file handlers. |
def proj_units_to_meters(proj_str):
proj_parts = proj_str.split()
new_parts = []
for itm in proj_parts:
key, val = itm.split('=')
key = key.strip('+')
if key in ['a', 'b', 'h']:
val = float(val)
if val < 6e6:
val *= 1000.
val = ... | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment identifier list for_statement identifier identifier block expression_statement assignment pattern_list identifier identifier cal... | Convert projection units from kilometers to meters. |
def sphinx_class(self):
classdoc = self.prop.sphinx_class().replace(
':class:`', '{info} of :class:`'
)
return classdoc.format(info=self.class_info) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute call attribute attribute identifier identifier identifier argument_list identifier argument_list string string_start string_content string_end string string_start string_content string_end return_... | Redefine sphinx class to point to prop class |
def _get_first_assessment_section(self):
if ('sections' not in self._my_map or not self._my_map['sections']):
assessment_id = self.get_assessment_offered().get_assessment().get_id()
first_part_id = get_first_part_id_for_assessment(assessment_id, runtime=self._runtime, proxy=self._proxy)
... | module function_definition identifier parameters identifier block if_statement parenthesized_expression boolean_operator comparison_operator string string_start string_content string_end attribute identifier identifier not_operator subscript attribute identifier identifier string string_start string_content string_end ... | Gets the first section for this Taken's Assessment. |
def _project_eigenvectors(self):
self._p_eigenvectors = []
for vecs_q in self._eigenvectors:
p_vecs_q = []
for vecs in vecs_q.T:
p_vecs_q.append(np.dot(vecs.reshape(-1, 3),
self._projection_direction))
self._p_eig... | module function_definition identifier parameters identifier block expression_statement assignment attribute identifier identifier list for_statement identifier attribute identifier identifier block expression_statement assignment identifier list for_statement identifier attribute identifier identifier block expression_... | Eigenvectors are projected along Cartesian direction |
def _assert_git_repo(target):
hooks_dir = os.path.abspath(os.path.join(target, HOOKS_DIR_PATH))
if not os.path.isdir(hooks_dir):
raise GitHookInstallerError(u"{0} is not a git repository.".format(target)) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list call attribute attribute identifier identifier identifier argument_list identifier identifier if_statement not_operator call attribute attr... | Asserts that a given target directory is a git repository |
def register_phonon_task(self, *args, **kwargs):
kwargs["task_class"] = PhononTask
return self.register_task(*args, **kwargs) | module function_definition identifier parameters identifier list_splat_pattern identifier dictionary_splat_pattern identifier block expression_statement assignment subscript identifier string string_start string_content string_end identifier return_statement call attribute identifier identifier argument_list list_splat... | Register a phonon task. |
def common_options(func):
def parse_preset(ctx, param, value):
return PRESETS.get(value, (None, None))
def parse_private(ctx, param, value):
return hex_from_b64(value) if value else None
func = click.option('--private', default=None, help='Private.', callback=parse_private)(func)
func = ... | module function_definition identifier parameters identifier block function_definition identifier parameters identifier identifier identifier block return_statement call attribute identifier identifier argument_list identifier tuple none none function_definition identifier parameters identifier identifier identifier blo... | Commonly used command options. |
def register_laser_hooks(self, hook_type: str, hook: Callable):
if hook_type == "add_world_state":
self._add_world_state_hooks.append(hook)
elif hook_type == "execute_state":
self._execute_state_hooks.append(hook)
elif hook_type == "start_sym_exec":
self._star... | module function_definition identifier parameters identifier typed_parameter identifier type identifier typed_parameter identifier type identifier block if_statement comparison_operator identifier string string_start string_content string_end block expression_statement call attribute attribute identifier identifier iden... | registers the hook with this Laser VM |
def extensions():
import numpy
from Cython.Build import cythonize
ext = [
Extension('phydmslib.numutils', ['phydmslib/numutils.pyx'],
include_dirs=[numpy.get_include()],
extra_compile_args=['-Wno-unused-function']),
]
return cythonize(e... | module function_definition identifier parameters block import_statement dotted_name identifier import_from_statement dotted_name identifier identifier dotted_name identifier expression_statement assignment identifier list call identifier argument_list string string_start string_content string_end list string string_sta... | Returns list of `cython` extensions for `lazy_cythonize`. |
def ingest_containers(self, containers=None):
containers = containers or self.stream or {}
output_containers = []
for container_name, definition in containers.items():
container = definition.copy()
container['name'] = container_name
output_containers.append(co... | module function_definition identifier parameters identifier default_parameter identifier none block expression_statement assignment identifier boolean_operator boolean_operator identifier attribute identifier identifier dictionary expression_statement assignment identifier list for_statement pattern_list identifier ide... | Transform the YAML into a dict with normalized keys |
def shovel_help(shovel, *names):
if not len(names):
return heirarchical_help(shovel, '')
else:
for name in names:
task = shovel[name]
if isinstance(task, Shovel):
return heirarchical_help(task, name)
else:
return task.help() | module function_definition identifier parameters identifier list_splat_pattern identifier block if_statement not_operator call identifier argument_list identifier block return_statement call identifier argument_list identifier string string_start string_end else_clause block for_statement identifier identifier block ex... | Return a string about help with the tasks, or lists tasks available |
def flash_errors(form, category='warning'):
for (field, errors) in form.errors.items():
for error in errors:
flash('{0} - {1}'.format(getattr(form, field).label.text, error),
category) | module function_definition identifier parameters identifier default_parameter identifier string string_start string_content string_end block for_statement tuple_pattern identifier identifier call attribute attribute identifier identifier identifier argument_list block for_statement identifier identifier block expressio... | Flash all form error messages |
def compute_radius(wcs):
ra, dec = wcs.wcs.crval
img_center = SkyCoord(ra=ra * u.degree, dec=dec * u.degree)
wcs_foot = wcs.calc_footprint()
img_corners = SkyCoord(ra=wcs_foot[:, 0] * u.degree,
dec=wcs_foot[:, 1] * u.degree)
radius = img_center.separation(img_corners).max(... | module function_definition identifier parameters identifier block expression_statement assignment pattern_list identifier identifier attribute attribute identifier identifier identifier expression_statement assignment identifier call identifier argument_list keyword_argument identifier binary_operator identifier attrib... | Compute the radius from the center to the furthest edge of the WCS. |
def _get_ssh_client(self):
return ipa_utils.get_ssh_client(
self.instance_ip,
self.ssh_private_key_file,
self.ssh_user,
timeout=self.timeout
) | module function_definition identifier parameters identifier block return_statement call attribute identifier identifier argument_list attribute identifier identifier attribute identifier identifier attribute identifier identifier keyword_argument identifier attribute identifier identifier | Return a new or existing SSH client for given ip. |
def measure_cost(repeat, scipy_trans_lhs, scipy_dns_lhs, func_name, *args, **kwargs):
mx.nd.waitall()
args_list = []
for arg in args:
args_list.append(arg)
start = time.time()
if scipy_trans_lhs:
args_list[0] = np.transpose(args_list[0]) if scipy_dns_lhs else sp.spmatrix.transpose(ar... | module function_definition identifier parameters identifier identifier identifier identifier list_splat_pattern identifier dictionary_splat_pattern identifier block expression_statement call attribute attribute identifier identifier identifier argument_list expression_statement assignment identifier list for_statement ... | Measure time cost of running a function |
def build(mnemonic, oprnd1, oprnd2, oprnd3):
ins = ReilInstruction()
ins.mnemonic = mnemonic
ins.operands = [oprnd1, oprnd2, oprnd3]
return ins | module function_definition identifier parameters identifier identifier identifier identifier block expression_statement assignment identifier call identifier argument_list expression_statement assignment attribute identifier identifier identifier expression_statement assignment attribute identifier identifier list iden... | Return the specified instruction. |
def _parse_region(self, rec, line_iter):
had_info = False
keyvals, section = self._parse_keyvals(line_iter)
if keyvals:
rec.metadata = keyvals[0]
while section and section[0] != "STUDY":
had_info = True
keyvals, next_section = self._parse_keyvals(line_... | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier false expression_statement assignment pattern_list identifier identifier call attribute identifier identifier argument_list identifier if_statement identifier block expression_statement ass... | Parse a section of an ISA-Tab, assigning information to a supplied record. |
def _get_collection_for_user(self, collection_id, user):
collection_query = Collection.objects.filter(pk=collection_id)
if not collection_query.exists():
raise exceptions.ValidationError('Collection id does not exist')
collection = collection_query.first()
if not user.has_per... | 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 if_statement not_operator call attribute identifier identifier argument_list b... | Check that collection exists and user has `add` permission. |
def scale_edges(self, multiplier):
if not isinstance(multiplier,int) and not isinstance(multiplier,float):
raise TypeError("multiplier must be an int or float")
for node in self.traverse_preorder():
if node.edge_length is not None:
node.edge_length *= multiplier | module function_definition identifier parameters identifier identifier block if_statement boolean_operator not_operator call identifier argument_list identifier identifier not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list string string_start string_cont... | Multiply all edges in this ``Tree`` by ``multiplier`` |
def lower_coerce_type_blocks(ir_blocks):
new_ir_blocks = []
for block in ir_blocks:
new_block = block
if isinstance(block, CoerceType):
predicate = BinaryComposition(
u'contains', Literal(list(block.target_class)), LocalField('@class'))
new_block = Filter(... | module function_definition identifier parameters identifier block expression_statement assignment identifier list for_statement identifier identifier block expression_statement assignment identifier identifier if_statement call identifier argument_list identifier identifier block expression_statement assignment identif... | Lower CoerceType blocks into Filter blocks with a type-check predicate. |
def _draw_outline(o:Patch, lw:int):
"Outline bounding box onto image `Patch`."
o.set_path_effects([patheffects.Stroke(
linewidth=lw, foreground='black'), patheffects.Normal()]) | module function_definition identifier parameters typed_parameter identifier type identifier typed_parameter identifier type identifier block expression_statement string string_start string_content string_end expression_statement call attribute identifier identifier argument_list list call attribute identifier identifie... | Outline bounding box onto image `Patch`. |
def _construct_mongos(self, logpath, port, configdb):
extra = ''
auth_param = ''
if self.args['auth']:
key_path = os.path.abspath(os.path.join(self.dir, 'keyfile'))
auth_param = '--keyFile %s' % key_path
if self.unknown_args:
extra = self._filter_valid... | module function_definition identifier parameters identifier identifier identifier identifier block expression_statement assignment identifier string string_start string_end expression_statement assignment identifier string string_start string_end if_statement subscript attribute identifier identifier string string_star... | Construct command line strings for a mongos process. |
def probes_used_extract_scores(full_scores, same_probes):
if full_scores.shape[1] != same_probes.shape[0]: raise "Size mismatch"
import numpy as np
model_scores = np.ndarray((full_scores.shape[0],np.sum(same_probes)), 'float64')
c=0
for i in range(0,full_scores.shape[1]):
if same_probes[i]:
for j in... | module function_definition identifier parameters identifier identifier block if_statement comparison_operator subscript attribute identifier identifier integer subscript attribute identifier identifier integer block raise_statement string string_start string_content string_end import_statement aliased_import dotted_nam... | Extracts a matrix of scores for a model, given a probes_used row vector of boolean |
def count(self, query):
if self.manual:
return self.total
if isinstance(query, Select):
q = query.with_only_columns([func.count()]).order_by(None).limit(None).offset(None)
return do_(q).scalar()
return query.count() | module function_definition identifier parameters identifier identifier block if_statement attribute identifier identifier block return_statement attribute identifier identifier if_statement call identifier argument_list identifier identifier block expression_statement assignment identifier call attribute call attribute... | If query is Select object, this function will try to get count of select |
def format_sms_payload(self, message, to, sender='elkme', options=[]):
self.validate_number(to)
if not isinstance(message, str):
message = " ".join(message)
message = message.rstrip()
sms = {
'from': sender,
'to': to,
'message': message
... | module function_definition identifier parameters identifier identifier identifier default_parameter identifier string string_start string_content string_end default_parameter identifier list block expression_statement call attribute identifier identifier argument_list identifier if_statement not_operator call identifie... | Helper function to create a SMS payload with little effort |
def run_cli():
"Command line interface to hiwenet."
features_path, groups_path, weight_method, num_bins, edge_range, \
trim_outliers, trim_percentile, return_networkx_graph, out_weights_path = parse_args()
features, groups = read_features_and_groups(features_path, groups_path)
extract(features, grou... | module function_definition identifier parameters block expression_statement string string_start string_content string_end expression_statement assignment pattern_list identifier identifier identifier identifier identifier line_continuation identifier identifier identifier identifier call identifier argument_list expres... | Command line interface to hiwenet. |
def _onArgument(self, name, annotation):
self.objectsStack[-1].arguments.append(Argument(name, annotation)) | module function_definition identifier parameters identifier identifier identifier block expression_statement call attribute attribute subscript attribute identifier identifier unary_operator integer identifier identifier argument_list call identifier argument_list identifier identifier | Memorizes a function argument |
def validate_path(ctx, param, value):
client = ctx.obj
if value is None:
from renku.models.provenance import ProcessRun
activity = client.process_commit()
if not isinstance(activity, ProcessRun):
raise click.BadParameter('No tool was found.')
return activity.path
... | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier attribute identifier identifier if_statement comparison_operator identifier none block import_from_statement dotted_name identifier identifier identifier dotted_name identifier expression_s... | Detect a workflow path if it is not passed. |
def community_colors(n):
if (n > 0):
colors = cl.scales['12']['qual']['Paired']
shuffle(colors)
return colors[:n]
else:
return choice(cl.scales['12']['qual']['Paired']) | module function_definition identifier parameters identifier block if_statement parenthesized_expression comparison_operator identifier integer block expression_statement assignment identifier subscript subscript subscript attribute identifier identifier string string_start string_content string_end string string_start ... | Returns a list of visually separable colors according to total communities |
def _op_msg_uncompressed(flags, command, identifier, docs, check_keys, opts):
data, total_size, max_bson_size = _op_msg_no_header(
flags, command, identifier, docs, check_keys, opts)
request_id, op_message = __pack_message(2013, data)
return request_id, op_message, total_size, max_bson_size | module function_definition identifier parameters identifier identifier identifier identifier identifier identifier block expression_statement assignment pattern_list identifier identifier identifier call identifier argument_list identifier identifier identifier identifier identifier identifier expression_statement assi... | Internal compressed OP_MSG message helper. |
def distribute_javaclasses(self, javaclass_dir, dest_dir="src"):
info('Copying java files')
ensure_dir(dest_dir)
for filename in glob.glob(javaclass_dir):
shprint(sh.cp, '-a', filename, dest_dir) | module function_definition identifier parameters identifier identifier default_parameter identifier string string_start string_content string_end block expression_statement call identifier argument_list string string_start string_content string_end expression_statement call identifier argument_list identifier for_state... | Copy existing javaclasses from build dir to current dist dir. |
def extract_cab (archive, compression, cmd, verbosity, interactive, outdir):
cmdlist = [cmd, '-d', outdir]
if verbosity > 0:
cmdlist.append('-v')
cmdlist.append(archive)
return cmdlist | module function_definition identifier parameters identifier identifier identifier identifier identifier identifier block expression_statement assignment identifier list identifier string string_start string_content string_end identifier if_statement comparison_operator identifier integer block expression_statement call... | Extract a CAB archive. |
def com_google_fonts_check_name_line_breaks(ttFont):
failed = False
for name in ttFont["name"].names:
string = name.string.decode(name.getEncoding())
if "\n" in string:
failed = True
yield FAIL, ("Name entry {} on platform {} contains"
" a line-break.").format(NameID(name.name... | module function_definition identifier parameters identifier block expression_statement assignment identifier false for_statement identifier attribute subscript identifier string string_start string_content string_end identifier block expression_statement assignment identifier call attribute attribute identifier identif... | Name table entries should not contain line-breaks. |
def _authenticate_client(self, client):
if self.login and not self.restart_required:
try:
db = client[self.auth_source]
if self.x509_extra_user:
db.authenticate(
DEFAULT_SUBJECT,
mechanism='MONGODB-X5... | module function_definition identifier parameters identifier identifier block if_statement boolean_operator attribute identifier identifier not_operator attribute identifier identifier block try_statement block expression_statement assignment identifier subscript identifier attribute identifier identifier if_statement a... | Authenticate the client if necessary. |
def _sig_handler(self, signum, stack):
log_debug("Got SIGINT.")
if signum == signal.SIGINT:
LLNetReal.running = False
if self._pktqueue.qsize() == 0:
self._pktqueue.put( (None,None,None) ) | module function_definition identifier parameters identifier identifier identifier block expression_statement call identifier argument_list string string_start string_content string_end if_statement comparison_operator identifier attribute identifier identifier block expression_statement assignment attribute identifier ... | Handle process INT signal. |
def to_browser_mode(self):
for message_no in range(len(self.messages)):
self.__to_browser(message_no) | module function_definition identifier parameters identifier block for_statement identifier call identifier argument_list call identifier argument_list attribute identifier identifier block expression_statement call attribute identifier identifier argument_list identifier | Write all the messages to files and open them in the browser |
def input_validate_aead(aead, name='aead', expected_len=None, max_aead_len = pyhsm.defines.YSM_AEAD_MAX_SIZE):
if isinstance(aead, pyhsm.aead_cmd.YHSM_GeneratedAEAD):
aead = aead.data
if expected_len != None:
return input_validate_str(aead, name, exact_len = expected_len)
else:
retur... | module function_definition identifier parameters identifier default_parameter identifier string string_start string_content string_end default_parameter identifier none default_parameter identifier attribute attribute identifier identifier identifier block if_statement call identifier argument_list identifier attribute... | Input validation for YHSM_GeneratedAEAD or string. |
def build(
c,
clean=False,
browse=False,
nitpick=False,
opts=None,
source=None,
target=None,
):
if clean:
_clean(c)
if opts is None:
opts = ""
if nitpick:
opts += " -n -W -T"
cmd = "sphinx-build{0} {1} {2}".format(
(" " + opts) if opts else "",... | module function_definition identifier parameters identifier default_parameter identifier false default_parameter identifier false default_parameter identifier false default_parameter identifier none default_parameter identifier none default_parameter identifier none block if_statement identifier block expression_statem... | Build the project's Sphinx docs. |
def _assign_as_root(self, id_):
rfc = self._ras.get_relationship_form_for_create(self._phantom_root_id, id_, [])
rfc.set_display_name('Implicit Root to ' + str(id_) + ' Parent-Child Relationship')
rfc.set_description(self._relationship_type.get_display_name().get_text() + ' relationship for impl... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list attribute identifier identifier identifier list expression_statement call attribute identifier identifier argument_list binary_o... | Assign an id_ a root object in the hierarchy |
def value_to_sql_str(v):
if v is None:
return 'null'
if type(v) in (types.IntType, types.FloatType, types.LongType):
return str(v)
if type(v) in (types.StringType, types.UnicodeType):
return "'%s'" %(v.replace(u"'", u"\\'"))
if isinstance(v, datetime):
return "'%s'" %(v.s... | module function_definition identifier parameters identifier block if_statement comparison_operator identifier none block return_statement string string_start string_content string_end if_statement comparison_operator call identifier argument_list identifier tuple attribute identifier identifier attribute identifier ide... | transform a python variable to the appropriate representation in SQL |
def create_prefix_dir(nb_file, fmt):
if 'prefix' in fmt:
nb_dir = os.path.dirname(nb_file) + os.path.sep
if not os.path.isdir(nb_dir):
logging.log(logging.WARNING, "[jupytext] creating missing directory %s", nb_dir)
os.makedirs(nb_dir) | module function_definition identifier parameters identifier identifier block if_statement comparison_operator string string_start string_content string_end identifier block expression_statement assignment identifier binary_operator call attribute attribute identifier identifier identifier argument_list identifier attri... | Create directory if fmt has a prefix |
def _make_walker(self, *args, **kwargs):
walker = self.walker_class(*args, **kwargs)
return walker | module function_definition identifier parameters identifier list_splat_pattern identifier dictionary_splat_pattern identifier block expression_statement assignment identifier call attribute identifier identifier argument_list list_splat identifier dictionary_splat identifier return_statement identifier | Create a walker instance. |
def show(self, y:Image=None, ax:plt.Axes=None, figsize:tuple=(3,3), title:Optional[str]=None, hide_axis:bool=True,
color:str='white', **kwargs):
"Show the `ImageBBox` on `ax`."
if ax is None: _,ax = plt.subplots(figsize=figsize)
bboxes, lbls = self._compute_boxes()
h,w = self.flo... | module function_definition identifier parameters identifier typed_default_parameter identifier type identifier none typed_default_parameter identifier type attribute identifier identifier none typed_default_parameter identifier type identifier tuple integer integer typed_default_parameter identifier type generic_type i... | Show the `ImageBBox` on `ax`. |
def render_description_meta_tag(context, is_og=False):
request = context['request']
content = ''
if context.get('object'):
try:
content = context['object'].get_meta_description()
except AttributeError:
pass
elif context.get('meta_tagger'):
content = contex... | module function_definition identifier parameters identifier default_parameter identifier false block expression_statement assignment identifier subscript identifier string string_start string_content string_end expression_statement assignment identifier string string_start string_end if_statement call attribute identif... | Returns the description as meta or open graph tag. |
def _make_graph(self, max_insert):
if len(self.partial_links) != 0:
raise Error('Error in _make_graph(). Cannot continue because there are partial links')
self.contig_links = {}
for key in self.links:
for l in self.links[key]:
insert_size = l.insert_size()... | module function_definition identifier parameters identifier identifier block if_statement comparison_operator call identifier argument_list attribute identifier identifier integer block raise_statement call identifier argument_list string string_start string_content string_end expression_statement assignment attribute ... | helper function to construct graph from current state of object |
def tags(self):
tag_list = self.spec.get('tag', [])
if isinstance(tag_list, (list, set, tuple)):
return list(tag_list)
return [tag_list] | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end list if_statement call identifier argument_list identifier tuple identifier identifier identi... | Returns a list of all the tags applied to this view |
def _sync_reminders(self, reminders_json):
for reminder_json in reminders_json:
reminder_id = reminder_json['id']
task_id = reminder_json['item_id']
if task_id not in self.tasks:
continue
task = self.tasks[task_id]
self.reminders[remind... | module function_definition identifier parameters identifier identifier block for_statement identifier identifier block expression_statement assignment identifier subscript identifier string string_start string_content string_end expression_statement assignment identifier subscript identifier string string_start string_... | Populate the user's reminders from a JSON encoded list. |
def build_available_time_string(availabilities):
prefix = 'We have availabilities at '
if len(availabilities) > 3:
prefix = 'We have plenty of availability, including '
prefix += build_time_output_string(availabilities[0])
if len(availabilities) == 2:
return '{} and {}'.format(prefix, bu... | module function_definition identifier parameters identifier block expression_statement assignment identifier string string_start string_content string_end if_statement comparison_operator call identifier argument_list identifier integer block expression_statement assignment identifier string string_start string_content... | Build a string eliciting for a possible time slot among at least two availabilities. |
def galprop_gasmap(self, **kwargs):
kwargs_copy = self.base_dict.copy()
kwargs_copy.update(**kwargs)
self._replace_none(kwargs_copy)
localpath = NameFactory.galprop_gasmap_format.format(**kwargs_copy)
if kwargs.get('fullpath', False):
return self.fullpath(loca... | 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 Galprop input gasmaps |
def main():
if len(argv) < 2:
print 'Usage: %s fst_file [optional: save_file]' % argv[0]
return
flex_a = Flexparser()
mma = flex_a.yyparse(argv[1])
mma.minimize()
print mma
if len(argv) == 3:
mma.save(argv[2]) | module function_definition identifier parameters block if_statement comparison_operator call identifier argument_list identifier integer block print_statement binary_operator string string_start string_content string_end subscript identifier integer return_statement expression_statement assignment identifier call ident... | Testing function for Flex Regular Expressions to FST DFA |
def process_exception(self, request, e):
if isinstance(e, RedirectException):
response = e.get_response()
self.process_response(request, response) | module function_definition identifier parameters identifier identifier identifier block if_statement call identifier argument_list identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement call attribute identifier identifier argument_... | Still process session data when specially Exception |
def update_time_reset_passwd(user_name, the_time):
entry = TabMember.update(
time_reset_passwd=the_time,
).where(TabMember.user_name == user_name)
try:
entry.execute()
return True
except:
return False | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute call attribute identifier identifier argument_list keyword_argument identifier identifier identifier argument_list comparison_operator attribute identifier identifier identifier try_sta... | Update the time when user reset passwd. |
def save(self, fname=''):
if fname is '':
self.case.save()
else:
self.case.SaveAs(self.path+os.sep+fname) | module function_definition identifier parameters identifier default_parameter identifier string string_start string_end block if_statement comparison_operator identifier string string_start string_end block expression_statement call attribute attribute identifier identifier identifier argument_list else_clause block ex... | Save the current case |
def mask_roi_unique(self):
A = np.vstack([self.mask_1.mask_roi_sparse,self.mask_2.mask_roi_sparse]).T
B = A[np.lexsort(A.T[::-1])]
return B[np.concatenate(([True],np.any(B[1:]!=B[:-1],axis=1)))] | module function_definition identifier parameters identifier block expression_statement assignment identifier attribute call attribute identifier identifier argument_list list attribute attribute identifier identifier identifier attribute attribute identifier identifier identifier identifier expression_statement assignm... | Assemble a set of unique magnitude tuples for the ROI |
def InterfaceMatcher(clazz, subclass, protocol):
interface = (clazz, subclass, protocol)
def Matcher(device):
for setting in device.iterSettings():
if GetInterface(setting) == interface:
return setting
return Matcher | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier tuple identifier identifier identifier function_definition identifier parameters identifier block for_statement identifier call attribute identifier identifier argument_list block if_statem... | Returns a matcher that returns the setting with the given interface. |
def _get_previous_open_tag(self, obj):
prev_instance = self.get_previous_instance(obj)
if prev_instance and prev_instance.plugin_type == self.__class__.__name__:
return prev_instance.glossary.get('open_tag') | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier if_statement boolean_operator identifier comparison_operator attribute identifier identifier attribute attribute identifier identifier ide... | Return the open tag of the previous sibling |
def uid(self, p_todo):
try:
return self._todo_id_map[p_todo]
except KeyError as ex:
raise InvalidTodoException from ex | module function_definition identifier parameters identifier identifier block try_statement block return_statement subscript attribute identifier identifier identifier except_clause as_pattern identifier as_pattern_target identifier block raise_statement identifier identifier | Returns the unique text-based ID for a todo item. |
def erase(ctx):
if os.path.exists(ctx.obj['report']):
os.remove(ctx.obj['report']) | module function_definition identifier parameters identifier block if_statement call attribute attribute identifier identifier identifier argument_list subscript attribute identifier identifier string string_start string_content string_end block expression_statement call attribute identifier identifier argument_list sub... | Erase the existing smother report. |
def require_content_type(self, content_type):
if self.request.headers.get('content-type', '') != content_type:
self.halt(400, 'Content type must be ' + content_type) | module function_definition identifier parameters identifier identifier block if_statement comparison_operator call attribute attribute attribute identifier identifier identifier identifier argument_list string string_start string_content string_end string string_start string_end identifier block expression_statement ca... | Raises a 400 if request content type is not as specified. |
def tax_for_order(self, order_deets):
request = self._post('taxes', order_deets)
return self.responder(request) | 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 identifier return_statement call attribute identifier identifier argument_list identifier | Shows the sales tax that should be collected for a given order. |
def _allow_custom_expire(self, load):
expire_override = self.opts.get('token_expire_user_override', False)
if expire_override is True:
return True
if isinstance(expire_override, collections.Mapping):
expire_whitelist = expire_override.get(load['eauth'], [])
if... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end false if_statement comparison_operator identifier true block return_statement true... | Return bool if requesting user is allowed to set custom expire |
def handle_pre_response(self, item_session: ItemSession) -> Actions:
action = self.consult_pre_response_hook(item_session)
if action == Actions.RETRY:
item_session.set_status(Status.skipped)
elif action == Actions.FINISH:
item_session.set_status(Status.done)
elif ... | module function_definition identifier parameters identifier typed_parameter identifier type identifier type identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier if_statement comparison_operator identifier attribute identifier identifier block expressi... | Process a response that is starting. |
def key(self):
prefix = type(self).cls_key()
return '{}:{}:obj'.format(prefix, self.id) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute call identifier argument_list identifier identifier argument_list return_statement call attribute string string_start string_content string_end identifier argument_list identifier attribute identi... | Returns the redis key to access this object's values |
def convert_to_annotation(file, output):
resource = parse_bel_resource(file)
write_annotation(
keyword=resource['Namespace']['Keyword'],
values={k: '' for k in resource['Values']},
citation_name=resource['Citation']['NameString'],
description=resource['Namespace']['DescriptionStr... | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call identifier argument_list identifier expression_statement call identifier argument_list keyword_argument identifier subscript subscript identifier string string_start string_content string_end str... | Convert a namespace file to an annotation file. |
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