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def _get_signature(self, entry): if self._sha1_sigs: if not os.path.exists(entry.filename): return None try: with open(entry.filename, "r") as f: data = f.read() return hashlib.sha1(data.encode("utf-8")).digest() ...
Return the signature of the file stored in entry.
def length(self): return sum([shot.length for shot in self.shots if not shot.is_splay])
Total surveyed cave length, not including splays.
def close_connection (self): if self.url_connection is not None: try: self.url_connection.quit() except Exception: pass self.url_connection = None
Release the open connection from the connection pool.
def run_actor(self, actor): set_actor(actor) if not actor.mailbox.address: address = ('127.0.0.1', 0) actor._loop.create_task( actor.mailbox.start_serving(address=address) ) actor._loop.run_forever()
Start running the ``actor``.
def as_dict(self): "Get the WorkResult as a dict." return { 'output': self.output, 'test_outcome': self.test_outcome, 'worker_outcome': self.worker_outcome, 'diff': self.diff, }
Get the WorkResult as a dict.
def encode(value, encoding='utf-8', encoding_errors='strict'): if isinstance(value, bytes): return value if not isinstance(value, basestring): value = str(value) if isinstance(value, unicode): value = value.encode(encoding, encoding_errors) return value
Return a bytestring representation of the value.
def function_end(self): self.newline_label(self.shared.function_name + "_exit", True, True) self.move("%14", "%15") self.pop("%14") self.newline_text("RET", True)
Inserts an exit label and function return instructions
def param_dict_to_list(dict,skeys=None): RV = SP.concatenate([dict[key].flatten() for key in skeys]) return RV pass
convert from param dictionary to list
def render_registration(self): surface = self.get_surface() if self.canvas is None or self.df_canvas_corners.shape[0] == 0: return surface corners = self.df_canvas_corners.copy() corners['w'] = 1 transform = self.canvas.shapes_to_canvas_transform canvas_corner...
Render pinned points on video frame as red rectangle.
def fileserver(opts, backends): return LazyLoader(_module_dirs(opts, 'fileserver'), opts, tag='fileserver', whitelist=backends, pack={'__utils__': utils(opts)})
Returns the file server modules
def on_batch_begin(self, train, **kwargs:Any)->None: "Record learning rate and momentum at beginning of batch." if train: self.lrs.append(self.opt.lr) self.moms.append(self.opt.mom)
Record learning rate and momentum at beginning of batch.
def precheck(): cfg_path = local_config['PROJECT']['CONFIG_PATH'] logging = set_logging(local_config) if os.path.exists(cfg_path): logger.info('%s: config_path parameter: %s' % (inspect.stack()[0][3], cfg_path)) logger.info( '%s: Existing configuration file found. precheck pass.'...
Verify project runtime dependencies
def add_dependency(self, value): if value.name in self.dependencies: self.dependencies[value.name.lower()].append(value) else: self.dependencies[value.name.lower()] = [ value ]
Adds the specified executable dependency to the list for this executable.
def NoCache(self, *targets): tlist = [] for t in targets: tlist.extend(self.arg2nodes(t, self.fs.Entry)) for t in tlist: t.set_nocache() return tlist
Tags a target so that it will not be cached
def parse_field(source, loc, tokens): name = tokens[0].lower() value = normalize_value(tokens[2]) if name == 'author' and ' and ' in value: value = [field.strip() for field in value.split(' and ')] return (name, value)
Returns the tokens of a field as key-value pair.
def writeln(self, text, fg='black', bg='white'): if not isinstance(text, str): text = str(text) self.write(text + '\n', fg=fg, bg=bg)
write to the console with linefeed
def send_keys(self, keyserver, *keyids): result = self._result_map['list'](self) log.debug('send_keys: %r', keyids) data = _util._make_binary_stream("", self._encoding) args = ['--keyserver', keyserver, '--send-keys'] args.extend(keyids) self._handle_io(args, data, result...
Send keys to a keyserver.
def to_det_id(self, det_id_or_det_oid): try: int(det_id_or_det_oid) except ValueError: return self.get_det_id(det_id_or_det_oid) else: return det_id_or_det_oid
Convert det ID or OID to det ID
def pack_value(self, val): if isinstance(val, bytes): val = list(iterbytes(val)) slen = len(val) if self.pad: pad = b'\0\0' * (slen % 2) else: pad = b'' return struct.pack('>' + 'H' * slen, *val) + pad, slen, None
Convert 8-byte string into 16-byte list
def builds(self, confs): self._named_builds = {} self._builds = [] for values in confs: if len(values) == 2: self._builds.append(BuildConf(values[0], values[1], {}, {}, self.reference)) elif len(values) == 4: self._builds.append(BuildConf(v...
For retro compatibility directly assigning builds
def _svg_path(self, pathcodes, data): def gen_path_elements(pathcodes, data): counts = {'M': 1, 'L': 1, 'C': 3, 'Z': 0} it = iter(data) for code in pathcodes: yield code for _ in range(counts[code]): p = next(it) ...
Return the SVG path's 'd' element.
def getStats(jobStore): def aggregateStats(fileHandle,aggregateObject): try: stats = json.load(fileHandle, object_hook=Expando) for key in list(stats.keys()): if key in aggregateObject: aggregateObject[key].append(stats[key]) else: ...
Collect and return the stats and config data.
def _register_data_plane_account_arguments(self, command_name): from azure.cli.core.commands.parameters import get_resource_name_completion_list from ._validators import validate_client_parameters command = self.command_loader.command_table.get(command_name, None) if not command: ...
Add parameters required to create a storage client
def _new_sample(self, sink): if self.running: buf = sink.emit('pull-sample').get_buffer() mem = buf.get_all_memory() success, info = mem.map(Gst.MapFlags.READ) if success: data = info.data mem.unmap(info) self.queue....
The callback for appsink's "new-sample" signal.
def pid_from_context(_, context): pid = (context or {}).get('pid') return pid.pid_value if pid else missing
Get PID from marshmallow context.
def path(self): if (self.source_file.startswith('a/') and self.target_file.startswith('b/')): filepath = self.source_file[2:] elif (self.source_file.startswith('a/') and self.target_file == '/dev/null'): filepath = self.source_file[2:] elif (...
Return the file path abstracted from VCS.
def DualDBFlow(cls): if issubclass(cls, flow.GRRFlow): raise ValueError("Mixin class shouldn't inherit from GRRFlow.") if cls.__name__[-5:] != "Mixin": raise ValueError("Flow mixin should have a name that ends in 'Mixin'.") flow_name = cls.__name__[:-5] aff4_cls = type(flow_name, (cls, flow.GRRFlow), {}...
Decorator that creates AFF4 and RELDB flows from a given mixin.
def _get_ratings_page(self): self._build_url() soup = get_soup(self.url) if soup: return soup self._build_url(shorten=False) soup = get_soup(self.url) if soup: return soup return SearchDaily(self.category, date=self.date).fetch_result()
Do a limited search for the correct url.
def save(cls, filename, config): mode = os.O_WRONLY | os.O_TRUNC | os.O_CREAT with os.fdopen(os.open(filename, mode, 0o600), 'w') as fname: yaml.safe_dump(config, fname, indent=4, default_flow_style=False)
Save configuration to yaml file.
def read_calibration( detx=None, det_id=None, from_file=False, det_id_table=None ): from km3pipe.calib import Calibration if not (detx or det_id or from_file): return None if detx is not None: return Calibration(filename=detx) if from_file: det_ids = np.unique(det_id_tabl...
Retrive calibration from file, the DB.
def resolve(self,size, distribution): if not self.variablesize(): raise Exception("Can only resize patterns with * wildcards") nrofwildcards = 0 for x in self.sequence: if x == '*': nrofwildcards += 1 assert (len(distribution) == nrofwildcards) ...
Resolve a variable sized pattern to all patterns of a certain fixed size
def calculate_quality_metrics(metrics, designs, verbose=False): for metric in metrics: if metric.progress_update: print metric.progress_update metric.load(designs, verbose)
Have each metric calculate all the information it needs.
def make_compound_ctype(self, varname): compoundname = self.get_var_type(varname) nfields = self.inq_compound(compoundname) fields = [] for i in range(nfields): (fieldname, fieldtype, fieldrank, fieldshape) = self.inq_compound_field(compoundname, i) a...
Create a ctypes type that corresponds to a compound type in memory.
def _fetch_metric(self, metric_name): request = { 'Namespace': self.CLOUDWATCH_NAMESPACE, 'MetricName': metric_name, 'Dimensions': [ { 'Name': 'TrainingJobName', 'Value': self.name } ], ...
Fetch all the values of a named metric, and add them to _data
def token(self): if AUTH_TOKEN_HEADER in self.request.headers: return self.request.headers[AUTH_TOKEN_HEADER] else: return self.get_cookie(AUTH_COOKIE_NAME)
The token used for the request
def simplify_recursive(typ): if isinstance(typ, UnionType): return combine_types(typ.items) elif isinstance(typ, ClassType): simplified = ClassType(typ.name, [simplify_recursive(arg) for arg in typ.args]) args = simplified.args if (simplified.name == 'Dict' and len(args) == 2 ...
Simplify all components of a type.
def _remove_deprecated_options(self, old_version): old_defaults = self._load_old_defaults(old_version) for section in old_defaults.sections(): for option, _ in old_defaults.items(section, raw=self.raw): if self.get_default(section, option) is NoDefault: ...
Remove options which are present in the .ini file but not in defaults
def _lab_to_rgb(labs): labs, n_dim = _check_color_dim(labs) y = (labs[:, 0] + 16.) / 116. x = (labs[:, 1] / 500.) + y z = y - (labs[:, 2] / 200.) xyz = np.concatenate(([x], [y], [z])) over = xyz > 0.2068966 xyz[over] = xyz[over] ** 3. xyz[~over] = (xyz[~over] - 0.13793103448275862) / 7.7...
Convert Nx3 or Nx4 lab to rgb
def __init_yaml(): global _yaml_initialized if not _yaml_initialized: _yaml_initialized = True yaml.add_constructor(u'tag:yaml.org,2002:Frame', _frame_constructor) yaml.add_constructor(u'tag:yaml.org,2002:Signal', _signal_constructor) yaml.add_representer(canmatrix.Frame, _frame_...
Lazy init yaml because canmatrix might not be fully loaded when loading this format.
def copy_from(self, other_state): for prop in self.properties().values(): setattr(self, prop.name, getattr(other_state, prop.name))
Copy data from another shard state entity to self.
def _get_config(self, rel_path, view, api_version=1): self._require_min_api_version(api_version) params = view and dict(view=view) or None resp = self._get_resource_root().get(self._path() + '/' + rel_path, params=params) return json_to_config(resp, view == 'full')
Retrieves an ApiConfig list from the given relative path.
def _convert_value(value): try: return restore(ast.literal_eval(value)) except (ValueError, SyntaxError): if SETTINGS.COMMAND_LINE.STRICT_PARSING: raise return value
Parse string as python literal if possible and fallback to string.
def isRealmUser(self, realmname, username, environ): try: course = self.course_factory.get_course(realmname) ok = self.user_manager.has_admin_rights_on_course(course, username=username) return ok except: return False
Returns True if this username is valid for the realm, False otherwise.
def gen_procfile(ctx, wsgi, dev): if wsgi is None: if os.path.exists("wsgi.py"): wsgi = "wsgi.py" elif os.path.exists("app.py"): wsgi = "app.py" else: wsgi = "app.py" ctx.invoke(gen_apppy) def write_procfile(filename, server_process, debug)...
Generates Procfiles which can be used with honcho or foreman.
def indexables(self): if self._indexables is None: d = self.description self._indexables = [GenericIndexCol(name='index', axis=0)] for i, n in enumerate(d._v_names): dc = GenericDataIndexableCol( name=n, pos=i, values=[n], version=self.vers...
create the indexables from the table description
def textbetween(variable, firstnum=None, secondnum=None, locationoftext='regular'): if locationoftext == 'regular': return variable[firstnum:secondnum] elif locationoftext == 'toend': return variable[firstnum:] elif locationoftext == 'tostart':...
Get The Text Between Two Parts
def complex_out_dtype(self): if self.__complex_out_dtype is None: raise AttributeError( 'no complex variant of output dtype {} defined' ''.format(dtype_repr(self.scalar_out_dtype))) else: return self.__complex_out_dtype
The complex dtype corresponding to this space's `out_dtype`.
def date(ctx, year, month, day): return _date(conversions.to_integer(year, ctx), conversions.to_integer(month, ctx), conversions.to_integer(day, ctx))
Defines a date value
def npd_to_pmf(nodal_plane_dist, use_default=False): if isinstance(nodal_plane_dist, PMF): return nodal_plane_dist else: if use_default: return PMF([(1.0, NodalPlane(0.0, 90.0, 0.0))]) else: raise ValueError('Nodal Plane distribution not defined')
Returns the nodal plane distribution as an instance of the PMF class
def _from_dict(cls, _dict): args = {} if 'grammars' in _dict: args['grammars'] = [ Grammar._from_dict(x) for x in (_dict.get('grammars')) ] else: raise ValueError( 'Required property \'grammars\' not present in Grammars JSON') ...
Initialize a Grammars object from a json dictionary.
def run(self): for msg in self.messages: col = getattr(msg, 'col', 0) yield msg.lineno, col, (msg.tpl % msg.message_args), msg.__class__
Yield the error messages.
def kdists(matrix, k=7, ix=None): ix = ix or kindex(matrix, k) return matrix[ix][np.newaxis].T
Returns the k-th nearest distances, row-wise, as a column vector
def use_plenary_composition_view(self): self._object_views['composition'] = PLENARY for session in self._get_provider_sessions(): try: session.use_plenary_composition_view() except AttributeError: pass
Pass through to provider CompositionLookupSession.use_plenary_composition_view
def _get_opts_seaborn(self, opts, style): if opts is None: if self.chart_opts is None: opts = {} else: opts = self.chart_opts if style is None: if self.chart_style is None: style = self.chart_style else: ...
Initialialize for chart rendering
def main(): actions = [] try: options, arguments = getopt.getopt(sys.argv[1:], 'cdh', [ 'convert', 'to-html', 'demo', 'help', ]) for option, value in options: if option in ('-c', '--convert', '--to-html'): actions.append(functools.partial(convert_c...
Command line interface for the ``coloredlogs`` program.
def page_prev(self): window_start = (self.parent.value('window_start') - self.parent.value('window_length')) if window_start < 0: return self.parent.overview.update_position(window_start)
Go to the previous page.
def close(self): for channel in self._listening_to: self.toredis.unsubscribe(channel) self.toredis.unsubscribe(self.group_pubsub)
Unsubscribe the group and all jobs being listened too
def stop(self): if self._thread is not None and self._thread.isAlive(): self._done.set()
Stop the running task
def _setup_http_session(self): headers = {"Content-type": "application/json"} if (self._id_token): headers.update({"authorization": "Bearer {}".format( self._id_token)}) self._session.headers.update(headers) self._session.verify = False
Sets up the common HTTP session parameters used by requests.
def field_from_json(self, key_and_type, json_value): assert ':' in key_and_type key, type_code = key_and_type.split(':', 1) from_json = self.field_function(type_code, 'from_json') value = from_json(json_value) return key, value
Convert a JSON-serializable representation back to a field.
def convert_table(app, docname, source): num_tables = 0 for i,j in enumerate(source): table = [] output = '' in_table = False for l in j.split('\n'): r = l.strip() if r.startswith('|'): table.append(r) in_table = True ...
Find tables in a markdown and then convert them into the rst format
def distance(a, b): R = 3963 lat1, lon1 = math.radians(a[0]), math.radians(a[1]) lat2, lon2 = math.radians(b[0]), math.radians(b[1]) return math.acos(math.sin(lat1) * math.sin(lat2) + math.cos(lat1) * math.cos(lat2) * math.cos(lon1 - lon2)) * R
Calculates distance between two latitude-longitude coordinates.
def create_cookie(name, value, domain, httponly=None, **kwargs): if domain == 'localhost': domain = '' config = dict( name=name, value=value, version=0, port=None, domain=domain, path='/', secure=False, expires=None, discard=True, ...
Creates `cookielib.Cookie` instance
def must_contain(self, value, q, strict=False): if value is not None: if value.find(q) != -1: return self.shout('Value %r does not contain %r', strict, value, q)
if value must contain q
def _raise_on_error(data: Union[str, dict]) -> None: if isinstance(data, str): raise_error(data) elif 'status' in data and data['status'] != 'success': raise_error(data['data']['message'])
Raise the appropriate exception on error.
def d(msg, *args, **kwargs): return logging.log(DEBUG, msg, *args, **kwargs)
log a message at debug level;
def _serialize(self, include_run_logs=False, strict_json=False): result = {'command': self.command, 'name': self.name, 'started_at': self.started_at, 'completed_at': self.completed_at, 'success': self.successful, 'soft_tim...
Serialize a representation of this Task to a Python dict.
def _build_graph(self): if not self.colors: self.palette = self.env.get_template('palette.js') self.template_vars.update({'palette': self.palette.render()}) self.colors = {x['name']: 'palette.color()' for x in self.json_data} template_vars = [] for index, data...
Build Rickshaw graph syntax with all data
def exclude(self, d, item): try: md = d.__metadata__ pmd = getattr(md, '__print__', None) if pmd is None: return False excludes = getattr(pmd, 'excludes', []) return ( item[0] in excludes ) except: pass retu...
check metadata for excluded items
def munge_source(v): lines = v.split('\n') if not lines: return tuple(), '' firstline = lines[0].lstrip() while firstline == '' or firstline[0] == '@': del lines[0] firstline = lines[0].lstrip() if not lines: return tuple(), '' params = tuple( parm.strip()...
Take Python source code, return a pair of its parameters and the rest of it dedented
def rm(venv_name): inenv = InenvManager() venv = inenv.get_venv(venv_name) click.confirm("Delete dir {}".format(venv.path)) shutil.rmtree(venv.path)
Removes the venv by name
def bool_str(string): if string not in BOOL_STRS: raise ValueError('Invalid boolean string: "{}"'.format(string)) return True if string == 'true' else False
Returns a boolean from a string imput of 'true' or 'false
def describe(self): description = { 'description': self._description, 'type': self.name, } description.update(self.extra_params) return description
Provide a dictionary with information describing itself.
def initialize(self): if self._pooler is None: params = { "inputWidth": self.inputWidth, "lateralInputWidths": [self.cellCount] * self.numOtherCorticalColumns, "cellCount": self.cellCount, "sdrSize": self.sdrSize, "onlineLearning": self.onlineLearning, "maxSdrSi...
Initialize the internal objects.
def read_ncstream_err(fobj): err = read_proto_object(fobj, stream.Error) raise RuntimeError(err.message)
Handle reading an NcStream error from a file-like object and raise as error.
def makeref2namesdct(name2refdct): ref2namesdct = {} for key, values in name2refdct.items(): for value in values: ref2namesdct.setdefault(value, set()).add(key) return ref2namesdct
make the ref2namesdct in the idd_index
def _rank_qr(self, choices): from bernard.platforms.facebook import layers as fbl try: qr = self.request.get_layer(fbl.QuickReply) self.chosen = choices[qr.slug] self.slug = qr.slug if self.when is None or self.when == qr.slug: return 1.0 ...
Look for the QuickReply layer's slug into available choices.
def sortable_title(instance): title = plone_sortable_title(instance) if safe_callable(title): title = title() return title.lower()
Uses the default Plone sortable_text index lower-case
def dnd_endSnooze(self, **kwargs) -> SlackResponse: self._validate_xoxp_token() return self.api_call("dnd.endSnooze", json=kwargs)
Ends the current user's snooze mode immediately.
def data_filler_customer(self, number_of_rows, pipe): try: for i in range(number_of_rows): pipe.hmset('customer:%s' % i, { 'id': rnd_id_generator(self), 'name': self.faker.first_name(), 'lastname': self.faker.last_name(), ...
creates keys with customer data
def _split_str(s, n): length = len(s) return [s[i:i + n] for i in range(0, length, n)]
split string into list of strings by specified number.
def refresh_all_state_machines(self): self.refresh_state_machines(list(self.model.state_machine_manager.state_machines.keys()))
Refreshes all state machine tabs
def _update_staticmethod(self, oldsm, newsm): self._update(None, None, oldsm.__get__(0), newsm.__get__(0))
Update a staticmethod update.
def remove(self): self._multivol.deallocate(self.id) ARRAY_CACHE.pop(self.id, None) PIXEL_CACHE.pop(self.id, None)
Remove the layer artist for good
def pick_summary_data(key, summary_df, selected_summaries): selected_summaries_dict = create_selected_summaries_dict(selected_summaries) value = selected_summaries_dict[key] return summary_df.iloc[:, summary_df.columns.get_level_values(1) == value]
picks the selected pandas.DataFrame
def wandb_pty(resize=True): master_fd, slave_fd = pty.openpty() try: tty.setraw(master_fd) except termios.error: pass if resize: if SIGWINCH_HANDLER is not None: SIGWINCH_HANDLER.add_fd(master_fd) return master_fd, slave_fd
Get a PTY set to raw mode and registered to hear about window size changes.
def _sign(self,params): for k, v in params.iteritems(): if type(v) == int: v = str(v) elif type(v) == float: v = '%.2f'%v elif type(v) in (list, set): v = ','.join([str(i) for i in v]) elif type(v) == bool: v = 'true' if v else 'false' ...
Generate API sign code
def _save_to(self, im, path, format=None): format = format or im.format if not format: _, format = splitext(path) format = format[1:] im.format = format.lower() im.save(filename=path)
Save the image for testing.
def _wf_to_dict(wf): inputs, outputs = _get_wf_inout(wf) out = {"name": _id_to_name(wf.tool["id"]).replace("-", "_"), "inputs": inputs, "outputs": outputs, "steps": [], "subworkflows": [], "requirements": []} for step in wf.steps: inputs, outputs = _get_step_inout(step) ...
Parse a workflow into cwl2wdl style dictionary.
def send_root_file(self, filename): cache_timeout = self.get_send_file_max_age(filename) return send_from_directory(self.config['ROOT_FOLDER'], filename, cache_timeout=cache_timeout)
Function used to send static files from the root of the domain.
def quantile(image, q, nonzero=True): img_arr = image.numpy() if isinstance(q, (list,tuple)): q = [qq*100. if qq <= 1. else qq for qq in q] if nonzero: img_arr = img_arr[img_arr>0] vals = [np.percentile(img_arr, qq) for qq in q] return tuple(vals) elif isinstance(...
Get the quantile values from an ANTsImage
def _affine_inv_mult(c, m): "Applies the inverse affine transform described in `m` to `c`." size = c.flow.size() h,w = c.size m[0,1] *= h/w m[1,0] *= w/h c.flow = c.flow.view(-1,2) a = torch.inverse(m[:2,:2].t()) c.flow = torch.mm(c.flow - m[:2,2], a).view(size) return c
Applies the inverse affine transform described in `m` to `c`.
def extern_store_f64(self, context_handle, f64): c = self._ffi.from_handle(context_handle) return c.to_value(f64)
Given a context and double, return a new Handle to represent the double.
def lastChild(self): ret = libxml2mod.xmlGetLastChild(self._o) if ret is None:raise treeError('xmlGetLastChild() failed') __tmp = xmlNode(_obj=ret) return __tmp
Search the last child of a node.
def duration(self): self._duration = self.lib.iperf_get_test_duration(self._test) return self._duration
The test duration in seconds.
def generate_url(self, suffix): url_base_path = os.path.dirname(self.path) netloc = "{}:{}".format(*self.server.server_address) return urlunparse(( "http", netloc, url_base_path + "/" + suffix, "", "", ""))
Return URL by combining server details with a path suffix.
def _solve(self): while len(self._remove_constr) > 0: self._remove_constr.pop().delete() try: self._prob.solve(lp.ObjectiveSense.Maximize) except lp.SolverError as e: raise_from(FluxBalanceError('Failed to solve: {}'.format( e), result=self._pr...
Solve the problem with the current objective.
def delete_token(): username = get_admin()[0] admins = get_couchdb_admins() if username in admins: print 'I delete {} CouchDB user'.format(username) delete_couchdb_admin(username) if os.path.isfile(LOGIN_FILENAME): print 'I delete {} token file'.format(LOGIN_FILENAME) os....
Delete current token, file & CouchDB admin user
def plotnoise(noisepkl, mergepkl, plot_width=950, plot_height=400): d = pickle.load(open(mergepkl)) ndist, imstd, flagfrac = plotnoisedist(noisepkl, plot_width=plot_width/2, plot_height=plot_height) fluxscale = calcfluxscale(d, imstd, flagfrac) logger.info('Median image noise is {0:.3} Jy.'.format(fluxs...
Make two panel plot to summary noise analysis with estimated flux scale
def _Members(self, group): group.members = set(group.members).union(self.gids.get(group.gid, [])) return group
Unify members of a group and accounts with the group as primary gid.