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def _save_installed(self): import json from utility import json_serial, get_json fulldata = get_json(self.instpath, {}) fulldata["installed"] = self.installed with open(self.instpath, 'w') as f: json.dump(fulldata, f, default=json_serial)
Saves the list of installed repo XML settings files.
def add_metadata(track_file, track_data): mp3 = mutagen.mp3.MP3(track_file) mp3['TPE1'] = mutagen.id3.TPE1(encoding=3, text=track_data.user['username']) mp3['TIT2'] = mutagen.id3.TIT2(encoding=3, text=track_data.title) cover_bytes = requests.get(track_data.artwork_url, stream=True).raw.read() mp3.ta...
Adds artist and title from the track data, and downloads the cover and embeds it in the MP3 tags.
def ess(self): _, y_vals, values, colors = self.labels_ticks_and_vals() for y, value, color in zip(y_vals, values, colors): if value.ndim != 2 or value.shape[0] < 2: yield y, None, color else: yield y, _get_ess(value), color
Get effective n data for the variable.
def _handle_dot(self): self.printer = DotPrinter(self.todolist) try: arg = self.argument(1) todo = self.todolist.todo(arg) arg = self.argument(1) todos = set([self.todolist.todo(arg)]) todos |= set(self.todolist.children(todo)) todo...
Handles the dot subsubcommand.
def _previous(self): self.summaries.rotate() current_summary = self.summaries[0] self._update_summary(current_summary)
Get the previous summary and present it.
def write_text(filename: str, text: str) -> None: with open(filename, 'w') as f: print(text, file=f)
Writes text to a file.
def remove_pane(self, pane): assert isinstance(pane, Pane) if pane in self.panes: if pane == self.active_pane: if self.previous_active_pane: self.active_pane = self.previous_active_pane else: self.focus_next() ...
Remove pane from this Window.
def attrlist(self): 'Transform the KEY_MAP paramiter into an attrlist for ldap filters' keymap = self.config.get('KEY_MAP') if keymap: return [s.encode('utf-8') for s in keymap.values()] else: return None
Transform the KEY_MAP paramiter into an attrlist for ldap filters
def do_start_alerts(self, _): if self._alerter_thread.is_alive(): print("The alert thread is already started") else: self._stop_thread = False self._alerter_thread = threading.Thread(name='alerter', target=self._alerter_thread_func) self._alerter_thread.st...
Starts the alerter thread
def join_right_in(self, *objs): if not objs: return self.table.c[self.fielda]!=self.table.c[self.fielda] else: keys = get_objs_columns(objs, self.reference_fieldname) return (self.table.c[self.fieldb] == self.reference_class.c[self.reference_fieldname]) & (self.table....
Create a join condition, connect B and C
def _get_span(s, pattern): i, j = -1, -1 match = pattern.match(s) if not match: return i, j for group_name in pattern.groupindex: i, j = match.span(group_name) if (i, j) != (-1, -1): return i, j return i, j
Return the span of the first group that matches the pattern.
def _probe_positions(probe, group): positions = probe['channel_groups'][group]['geometry'] channels = _probe_channels(probe, group) return np.array([positions[channel] for channel in channels])
Return the positions of a probe channel group.
def OnEnterSelectionMode(self, event): self.grid.sel_mode_cursor = list(self.grid.actions.cursor) self.grid.EnableDragGridSize(False) self.grid.EnableEditing(False)
Event handler for entering selection mode, disables cell edits
def sc_cuts_alg(self, viewer, event, msg=True): if self.cancut: direction = self.get_direction(event.direction) self._cycle_cuts_alg(viewer, msg, direction=direction) return True
Adjust cuts algorithm interactively.
def _sanitize_title(self, title): title = re.sub(self.inside_brackets, "", title) title = re.sub(self.after_delimiter, "", title) return title.strip()
Remove redunant meta data from title and return it
def filepath(self) -> str: return os.path.join(self._dirpath, self.name + '.nc')
The NetCDF file path.
def create(name, packages=None, user=None): packages = packages or '' packages = packages.split(',') packages.append('pip') args = packages + ['--yes', '-q'] cmd = _create_conda_cmd('create', args=args, env=name, user=user) ret = _execcmd(cmd, user=user, return0=True) if ret['retcode'] == 0:...
Create a conda env
def on_epoch_end(self, last_metrics, **kwargs): "Set the final result in `last_metrics`." return add_metrics(last_metrics, self.val/self.count)
Set the final result in `last_metrics`.
def list_policies(self, scaling_group): uri = "/%s/%s/policies" % (self.uri_base, utils.get_id(scaling_group)) resp, resp_body = self.api.method_get(uri) return [AutoScalePolicy(self, data, scaling_group) for data in resp_body.get("policies", [])]
Returns a list of all policies defined for the specified scaling group.
def sha1sum_numpy(np_array): import hashlib return hashlib.sha1(np_array.view(np.uint8)).hexdigest()
Return the secure hash digest with sha1 algorithm for a numpy array
def log_metrics(metrics, summ_writer, log_prefix, step, history=None): rjust_len = max([len(name) for name in metrics]) for name, value in six.iteritems(metrics): step_log(step, "%s %s | % .8f" % ( log_prefix.ljust(5), name.rjust(rjust_len), value)) full_name = "metrics/" + name if history: ...
Log metrics to summary writer and history.
def as_ul(self, current_linkable=False, class_current="active_link", before_1="", after_1="", before_all="", after_all=""): return self.__do_menu("as_ul", current_linkable, class_current, before_1=before_1, after_1=after_1, before_all=before_all, after_all=after_all)
It returns menu as ul
def urls(order_by: Optional[str] = None): url_rules: List[Rule] = current_app.url_map._rules if order_by == 'view': url_rules = sorted(url_rules, key=lambda rule: _get_rule_view(rule)) elif order_by != 'priority': url_rules = sorted(url_rules, key=lambda rule: getattr(rule, order_by)) he...
List all URLs registered with the app.
def orthologize(self, ortho_species_id, belast): if ( self.orthologs and ortho_species_id in self.orthologs and ortho_species_id != self.species_id ): self.orthology_species = ortho_species_id self.canonical = self.orthologs[ortho_species_id]["...
Decanonical ortholog name used
def cont_c(self, percent=0.9, N=None): if not hasattr(self, 'G'): self.fs_c(N=self.rank) return apply_along_axis(lambda _: _/self.L[:N], 1, apply_along_axis(lambda _: _*self.c, 0, self.G[:, :N]**2))
Return the contribution of each column.
def print_todo(self, p_todo): todo_str = p_todo.source() for ppf in self.filters: todo_str = ppf.filter(todo_str, p_todo) return TopydoString(todo_str)
Given a todo item, pretty print it.
def _ProcessEntries(self, fd): p = config_file.KeyValueParser(kv_sep="{", term="}", sep=None) data = utils.ReadFileBytesAsUnicode(fd) entries = p.ParseEntries(data) for entry in entries: for section, cfg in iteritems(entry): if cfg: cfg = cfg[0].strip() else: cf...
Extract entries from the xinetd config files.
def skull_strip(dset,suffix='_ns',prefix=None,unifize=True): return available_method('skull_strip')(dset,suffix,prefix,unifize)
attempts to cleanly remove skull from ``dset``
def trend_coefficients(self, order=LINEAR): if not len(self.points): raise ArithmeticError('Cannot calculate the trend of an empty series') return LazyImport.numpy().polyfit(self.timestamps, self.values, order)
Calculate trend coefficients for the specified order.
def start(self): "start the pool's workers" for i in xrange(self.size): scheduler.schedule(self._runner) self._closing = False
start the pool's workers
def check_update(): r = requests.get("https://pypi.python.org/pypi/prof/json") data = r.json() if versiontuple(data['info']['version']) > versiontuple(__version__): return True return False
Return True if an update is available on pypi
def coinc(self, s0, s1, slide, step): loglr = - s0 - s1 threshes = [self.fits_by_tid[i]['thresh'] for i in self.ifos] loglr += sum([t**2. / 2. for t in threshes]) return (2. * loglr) ** 0.5
Calculate the final coinc ranking statistic
def proximal(self): if self.quadratic_coeff < 0: raise TypeError('`quadratic_coeff` {} must be non-negative' ''.format(self.quadratic_coeff)) return proximal_quadratic_perturbation( self.functional.proximal, a=self.quadratic_coeff, u=self.l...
Proximal factory of the quadratically perturbed functional.
def getCol(self, x): return [self.getCell(x, i) for i in self.__size_range]
return the x-th column, starting at 0
def rglob(dirname, pattern, dirs=False, sort=True): fns = [] path = str(dirname) if os.path.isdir(path): fns = glob(os.path.join(escape(path), pattern)) dns = [fn for fn in [os.path.join(path, fn) for fn in os.listdir(path)] if os...
recursive glob, gets all files that match the pattern within the directory tree
def spam(self, tag=None, fromdate=None, todate=None): return self.call("GET", "/stats/outbound/spam", tag=tag, fromdate=fromdate, todate=todate)
Gets a total count of recipients who have marked your email as spam.
def writefits(self, *args, **kwargs): old_wave = self.wave self.wave = self._wavetable try: super(UniformTransmission, self).writefits(*args, **kwargs) finally: self.wave = old_wave
Write to file using default waveset.
def cookies(self): return [line.strip() for line in self.conn.issue_command("GetCookies").split("\n") if line.strip()]
Returns a list of all cookies in cookie string format.
def add_date_facet(self, *args, **kwargs): self.facets.append(DateHistogramFacet(*args, **kwargs))
Add a date factory facet
def output(data, **kwargs): if isinstance(data, Exception): data = six.text_type(data) if 'output_indent' in __opts__ and __opts__['output_indent'] >= 0: return pprint.pformat(data, indent=__opts__['output_indent']) return pprint.pformat(data)
Print out via pretty print
def _get_classifier(self, prefix): with self.name_scope(): classifier = nn.Dense(2, prefix=prefix) return classifier
Construct a decoder for the next sentence prediction task
def getReferenceByName(self, name): if name not in self._referenceNameMap: raise exceptions.ReferenceNameNotFoundException(name) return self._referenceNameMap[name]
Returns the reference with the specified name.
def _request_raw_content(self, url, timeout): request = Request(url) if self.referer is not None: request.add_header('Referer', self.referer) raw_xml = self._call_geocoder( request, timeout=timeout, deserializer=None ) return raw_xm...
Send the request to get raw content.
def runGetReferenceSet(self, id_): referenceSet = self.getDataRepository().getReferenceSet(id_) return self.runGetRequest(referenceSet)
Runs a getReferenceSet request for the specified ID.
def verify_claims(self, claims): scopes = self.get_settings('OIDC_RP_SCOPES', 'openid email') if 'email' in scopes.split(): return 'email' in claims LOGGER.warning('Custom OIDC_RP_SCOPES defined. ' 'You need to override `verify_claims` for custom claims verific...
Verify the provided claims to decide if authentication should be allowed.
def add_option(self, *args, **kwargs): if self.parseTool == 'argparse': if args and args[0] == '': args = args[1:] return self.parser.add_argument(*args, **kwargs) else: return self.parser.add_option(*args, **kwargs)
Add optparse or argparse option depending on CmdHelper initialization.
def bbox_hflip(bbox, rows, cols): x_min, y_min, x_max, y_max = bbox return [1 - x_max, y_min, 1 - x_min, y_max]
Flip a bounding box horizontally around the y-axis.
def update(ctx, migrate=False): msg = 'Update all dependencies' if migrate: msg += ' and migrate data' header(msg) info('Updating Python dependencies') lrun('pip install -r requirements/develop.pip') lrun('pip install -e .') info('Updating JavaScript dependencies') lrun('npm inst...
Perform a development update
def init_group_read(self, dst_addr=1): self.init_group(dst_addr) self.tpci_apci = 0x00 self.data = [0]
Initialize the CEMI frame for a group read operation.
async def format(self, fstype, *, uuid=None): self._data = await self._handler.format( system_id=self.node.system_id, id=self.id, fstype=fstype, uuid=uuid)
Format this block device.
async def recv_multipart_expect(self, data: Tuple[bytes, ...]=(b'',)) -> None: expect_all(await self.recv_multipart(), data)
Waits for the next multipart message and asserts that it contains the given data.
def timeline(self): rev = int(self.db.get('site:rev')) if rev != self.revision: self.reload_site() return self._timeline
Get timeline, reloading the site if needed.
def process(self, sched, coro): super(AddCoro, self).process(sched, coro) self.result = sched.add(self.coro, self.args, self.kwargs, self.prio & priority.OP) if self.prio & priority.CORO: return self, coro else: sched.active.append( (None, coro))
Add the given coroutine in the scheduler.
def _raise_response_exceptions(response): if not response.ok and 'www-authenticate' in response.headers: msg = response.headers['www-authenticate'] if 'insufficient_scope' in msg: raise OAuthInsufficientScope('insufficient_scope', response.url) elif 'invalid_token' in msg: ...
Raise specific errors on some status codes.
def _get_service_state(service_id: str): LOG.debug('Getting state of service %s', service_id) services = get_service_id_list() service_ids = [s for s in services if service_id in s] if len(service_ids) != 1: return 'Service not found! services = {}'.format(str(services)) ...
Get the Service state object for the specified id.
def hmsStrToDeg(ra): hour, min, sec = ra.split(':') ra_deg = hmsToDeg(int(hour), int(min), float(sec)) return ra_deg
Convert a string representation of RA into a float in degrees.
def _flatten(self, field, items, transform = None): values = [item[field] for item in items] flattened = [] for value in values: flattened.extend([value] if isinstance(value, str) else value) return transform(flattened) if transform != None else flattened
Extracts the entry `field` from each item in the supplied iterable, flattening any nested lists
def _create_product_map(self): self._product_map = {} for dep in self._tile.dependencies: try: dep_tile = IOTile(os.path.join('build', 'deps', dep['unique_id'])) except (ArgumentError, EnvironmentError): raise BuildError("Could not find required de...
Create a map of all products produced by this or a dependency.
def delete_session_entity_type(project_id, session_id, entity_type_display_name): import dialogflow_v2 as dialogflow session_entity_types_client = dialogflow.SessionEntityTypesClient() session_entity_type_name = ( session_entity_types_client.session_entity_type_path( ...
Delete session entity type with the given entity type display name.
def step(self): u = self._u if u is None: raise ValueError("the levelset function is not set " "(use set_levelset)") data = self.data inside = (u > 0) outside = (u <= 0) c0 = data[outside].sum() / float(outside.sum()) c1 = ...
Perform a single step of the morphological Chan-Vese evolution.
def constant_image_value(image, crs='EPSG:32613', scale=1): return getinfo(ee.Image(image).reduceRegion( reducer=ee.Reducer.first(), scale=scale, geometry=ee.Geometry.Rectangle([0, 0, 10, 10], crs, False)))
Extract the output value from a calculation done with constant images
def close_threads(self, parent): logger.debug("Call ThreadManager's 'close_threads'") if parent is None: self.pending_threads = [] threadlist = [] for threads in list(self.started_threads.values()): threadlist += threads else: ...
Close threads associated to parent_id
def _config_win32_search(self, search): search = str(search) split_char = self._determine_split_char(search) search_list = search.split(split_char) for s in search_list: if not s in self.search: self.search.add(dns.name.from_text(s))
Configure a Search registry entry.
def add_listener(self, name, listener, priority=0): if name not in self.listeners: self.listeners[name] = [] self.listeners[name].append((listener, priority)) self.listeners[name].sort(key=lambda listener: listener[1], reverse=True)
Add a new listener to the dispatch
def inet_pton(address_family, ip_string): global __inet_pton if __inet_pton is None: if hasattr(socket, 'inet_pton'): __inet_pton = socket.inet_pton else: from ospd import win_socket __inet_pton = win_socket.inet_pton return __inet_pton(address_family, ip_...
A platform independent version of inet_pton
def coerce(self, value, **kwargs): result = [] for v in value: result.append(self._coercion.coerce(v, **kwargs)) return result
Coerces array items with proper coercion.
def _populate_and_save_user_profile(self): try: app_label, class_name = django.conf.settings.AUTH_PROFILE_MODULE.split('.') profile_model = apps.get_model(app_label, class_name) profile, created = profile_model.objects.get_or_create(user=self._user) save_profile =...
Populates a User profile object with fields from the LDAP directory.
def load_config(filename): try: with open(filename, 'r') as config_file: return json.loads(config_file.read()) except IOError: pass
Read contents of config file.
def _export_signatures(meta_graph): named_signatures = tf_v1.get_collection(_SIGNATURE_COLLECTION) if not named_signatures: raise ValueError("No signatures present. Please call hub.add_signature(...)" "at least once in the module_fn.") for key, signature in named_signatures: meta_grap...
Exports signatures from current graph into a MetaGraphDef.
def read_name(self): result = '' off = self.offset next = -1 first = off while 1: len = ord(self.data[off]) off += 1 if len == 0: break t = len & 0xC0 if t == 0x00: result = ''.join((resul...
Reads a domain name from the packet
def make_describe_attrs(self): lst = [] if self.all_groups: lst.append((NEWLINE, '\n')) lst.append((INDENT, '')) for group in self.all_groups: if group.name: lst.extend(self.tokens.make_describe_attr(group.kls_name)) return ...
Create tokens for setting is_noy_spec on describes
def make_id(self): if self.url_id is None: self.url_id = select([func.coalesce(func.max(self.__class__.url_id + 1), 1)], self.__class__.parent == self.parent)
Create a new URL id that is unique to the parent container
def _run_sequence(self, sequence): self._check_pause() self._pre_test() session_data = self.target.get_session_data() self._test_info() resp = None for edge in sequence: if edge.callback: edge.callback(self, edge, resp) session_data...
Run a single sequence
def from_callable_parameter(cls, parameter): if parameter.kind == parameter.KEYWORD_ONLY or \ parameter.kind == parameter.POSITIONAL_OR_KEYWORD and parameter.default is not parameter.empty: if parameter.annotation is not parameter.empty: constraint = parameter.annotat...
Produces a parameter from a function or method
def check_dataset(dataset, mode): names = [x['name'] for x in dataset.schema] types = [x['type'] for x in dataset.schema] if mode == 'train': if (set(['image_url', 'label']) != set(names) or any(t != 'STRING' for t in types)): raise ValueError('Invalid dataset. Expect only "image_url,label" STRING colum...
Validate we have a good dataset.
def install_key(self, key_data): logger.info(("importing repository signing key {0} " "{1}".format(self.key_info['fingerprint'], self.key_info['uids'][0]))) import_result = self.gpg.import_keys(key_data) logger.debug("import results: {0}".fo...
Install untrusted repo signing key
def to_csc(self): self._X_train = csc_matrix(self._X_train) self._X_test = csc_matrix(self._X_test)
Convert Dataset to scipy's Compressed Sparse Column matrix.
def _is_charge_balanced(struct): if sum([s.specie.oxi_state for s in struct.sites]) == 0.0: return True else: return False
checks if the structure object is charge balanced
def create_install_template_skin(self): ckan_extension_template(self.name, self.target) self.install_package_develop('ckanext-' + self.name + 'theme')
Create an example ckan extension for this environment and install it
def reverse_query(self): self.qry_start = self.qry_length - self.qry_start - 1 self.qry_end = self.qry_length - self.qry_end - 1
Changes the coordinates as if the query sequence has been reverse complemented
def serverdir(): path = join(ROOT_DIR, 'server') path = normpath(path) if sys.platform == 'cygwin': path = realpath(path) return path
Get the location of the server subpackage
def create_form_groupings(self, vocabularies, solr_response, element_group_dict, sort_order): element_list = [] for group_name, group_list in element_group_dict.items(): el...
Create a group object from groupings of element objects.
def _check_metrics_file(self, bam_name, metrics_ext): base, _ = os.path.splitext(bam_name) try: int(base[-1]) can_glob = False except ValueError: can_glob = True check_fname = "{base}{maybe_glob}.{ext}".format( base=base, maybe_glob="*" if ...
Check for an existing metrics file for the given BAM.
def __upload(self, resource, bytes): headers = { 'x-ton-expires': http_time(self.options.get('x-ton-expires', self._DEFAULT_EXPIRE)), 'content-length': str(self._file_size), 'content-type': self.content_type } return Request(self._client, 'post', resource, ...
Performs a single chunk upload.
def sync_release_files(self): release_files = [] for release in self.releases.values(): release_files.extend(release) downloaded_files = set() deferred_exception = None for release_file in release_files: try: downloaded_file = self.download...
Purge + download files returning files removed + added
def cb(option, value, parser): arguments = [value] for arg in parser.rargs: if arg[0] != "-": arguments.append(arg) else: del parser.rargs[:len(arguments)] break if getattr(parser.values, option.dest): arguments.extend(getattr(parser.values, option...
Callback function to handle variable number of arguments in optparse
def _create_session(team, auth): session = requests.Session() session.hooks.update(dict( response=partial(_handle_response, team) )) session.headers.update({ "Content-Type": "application/json", "Accept": "application/json", "User-Agent": "quilt-cli/%s (%s %s) %s/%s" % ( ...
Creates a session object to be used for `push`, `install`, etc.
def database_dsn(self): if not self._config.library.database: return 'sqlite:///{root}/library.db'.format(root=self._root) return self._config.library.database.format(root=self._root)
Substitute the root dir into the database DSN, for Sqlite
def _defaultErrorHandler(varBinds, **context): errors = context.get('errors') if errors: err = errors[-1] raise err['error']
Raise exception on any error if user callback is missing
def make_sa(): configuration = dict(config.items('coilmq')) engine = engine_from_config(configuration, 'qstore.sqlalchemy.') init_model(engine) store = SAQueue() return store
Factory to creates a SQLAlchemy queue store, pulling config values from the CoilMQ configuration.
def apply(cls, args, run): try: lvl = int(args) except ValueError: lvl = args run.root_logger.setLevel(lvl)
Adjust the loglevel of the root-logger of this run.
def ellipsize(o): r = repr(o) if len(r) < 800: return r r = r[:60] + ' ... ' + r[-15:] return r
Ellipsize the representation of the given object.
def buy_market_order(self, amount, base="btc", quote="usd"): data = {'amount': amount} url = self._construct_url("buy/market/", base, quote) return self._post(url, data=data, return_json=True, version=2)
Order to buy amount of bitcoins for market price.
def add_class_button_status(self): if self.class_form.text() and self.radius_form.value() >= 0: self.add_class_button.setEnabled(True) else: self.add_class_button.setEnabled(False)
Function to enable or disable add class button.
def create_tomodir(self, directory): pwd = os.getcwd() if not os.path.isdir(directory): os.makedirs(directory) os.chdir(directory) directories = ( 'config', 'exe', 'grid', 'mod', 'mod/pot', 'mod/sens', ...
Create a tomodir subdirectory structure in the given directory
def thread(self): log.info('@{}.thread starting'.format(self.__class__.__name__)) thread = threading.Thread(target=thread_wrapper(self.consume), args=()) thread.daemon = True thread.start()
Start a thread for this consumer.
def releasers(cls): return [ HookReleaser, VersionFileReleaser, PythonReleaser, CocoaPodsReleaser, NPMReleaser, CReleaser, ChangelogReleaser, GitHubReleaser, GitReleaser, ]
Returns all of the supported releasers.
def _plt_gogrouped(self, goids, go2color_usr, **kws): fout_img = self.get_outfile(kws['outfile'], goids) sections = read_sections(kws['sections'], exclude_ungrouped=True) grprobj_cur = self._get_grprobj(goids, sections) grpcolor = GrouperColors(grprobj_cur) grp_go2color = grpcolo...
Plot grouped GO IDs.
def parse_lines(log_parsers, fileinp): while 1: logentry = fileinp.readline() if not logentry: break elif not logentry.rstrip(): continue processed = False for lp in log_parsers: if lp.grok(logentry): processed = True ...
parse lines from the fileinput and send them to the log_parsers
def load_from_file(self, file_path, format=None): if format is None: base_name, file_extension = os.path.splitext(file_path) if file_extension in (".yaml", ".yml"): format = "yaml" elif file_extension in (".json"): format = "json" e...
Return dict from a file config