content
stringlengths
1
1.04M
input_ids
listlengths
1
774k
ratio_char_token
float64
0.38
22.9
token_count
int64
1
774k
import pytest from django.contrib.contenttypes.models import ContentType from constants import user_system from event_manager.event import Attribute, Event from event_manager.events import ( bookmark, build_job, chart_view, cluster, experiment, experiment_group, experiment_job, job, notebook, permission, project, repo, search, superuser, tensorboard, user ) from event_manager.events.experiment import ExperimentSucceededEvent from factories.factory_experiments import ExperimentFactory from libs.json_utils import loads from tests.utils import BaseTest @pytest.mark.events_mark
[ 11748, 12972, 9288, 198, 198, 6738, 42625, 14208, 13, 3642, 822, 13, 11299, 19199, 13, 27530, 1330, 14041, 6030, 198, 198, 6738, 38491, 1330, 2836, 62, 10057, 198, 6738, 1785, 62, 37153, 13, 15596, 1330, 3460, 4163, 11, 8558, 198, 6738,...
3.018605
215
from ldp import DirectContainer from pycdm import Collection as PcdmCollection from pycdm import Object as PcdmObject from pycdm import PcdmReader as PcdmReaderBase
[ 198, 6738, 300, 26059, 1330, 4128, 29869, 198, 6738, 12972, 10210, 76, 1330, 12251, 355, 350, 10210, 76, 36307, 198, 6738, 12972, 10210, 76, 1330, 9515, 355, 350, 10210, 76, 10267, 198, 6738, 12972, 10210, 76, 1330, 350, 10210, 76, 3363...
3.458333
48
#!/usr/bin/env python from miflora_server.srv import * from miflora_msgs.msg import * import rospkg import rospy import sys import subprocess import json sensor_pub = rospy.Publisher('/miflora', miflora, queue_size=10) sensor_msg = miflora() def callback_msg(msg): ''' Read sensor and return measurements ''' # Check to see is MAC has been set if msg.MAC == '00:00:00:00:00:00': rospy.logwarn("MAC address not set. Run $ rosrun miflora_server discover_devices.py") break # Run sensor driver. Requires python >=3.6 # HACK: Done this way to remove conflicts with ROS python version. path = rospkg.RosPack().get_path('miflora_server') miflora_out = subprocess.check_output(["python3.7", path+"/src/miflora_driver.py", msg.MAC]) try: miflora_data = json.loads(miflora_out.replace("'", '"')) response = read_mifloraResponse() response.sensor.header.stamp = rospy.Time.now() response.sensor.header.frame_id = msg.FrameID response.sensor.moisture = miflora_data['soil-moisture'] response.sensor.battery = miflora_data['battery'] response.sensor.illuminance = miflora_data['light'] response.sensor.temperature = miflora_data['soil-temperature'] response.sensor.conductivity = miflora_data['soil-ec'] # Publish reading to topic sensor_msg = response.sensor sensor_pub.publish(sensor_msg) # Return reading to service client return response except: # Return blank measurements on error. rospy.logerr(miflora_out) rospy.logwarn("Try resetting BLE: $ sudo hciconfig hci0 down && sudo hciconfig hci0 up") rospy.logwarn("Or add reset to crontab: $ sudo crontab -e ") rospy.logwarn("add to bottom: 1 * * * * hciconfig hci0 reset") return read_mifloraResponse() if __name__ == "__main__": service_server()
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 198, 198, 6738, 285, 361, 4685, 64, 62, 15388, 13, 27891, 85, 1330, 1635, 198, 6738, 285, 361, 4685, 64, 62, 907, 14542, 13, 19662, 1330, 1635, 220, 198, 11748, 686, 2777, 10025, 198, 117...
2.548252
715
from django.test import SimpleTestCase from django.urls import reverse, resolve from django.contrib.auth import views as auth_views from hospital.views import * ######### ######### ###### ###### ###### ###### ######## ####### ####### #######
[ 6738, 42625, 14208, 13, 9288, 1330, 17427, 14402, 20448, 198, 6738, 42625, 14208, 13, 6371, 82, 1330, 9575, 11, 10568, 198, 6738, 42625, 14208, 13, 3642, 822, 13, 18439, 1330, 5009, 355, 6284, 62, 33571, 198, 6738, 4436, 13, 33571, 1330...
2.484127
126
from .models import User, Vaccine, User_Vaccine, Agendamento, Estabelecimento, EstabelecimentoAtendimento, Uf, Municipio from rest_framework import serializers from rest_framework.validators import UniqueValidator
[ 6738, 764, 27530, 1330, 11787, 11, 31749, 500, 11, 11787, 62, 53, 4134, 500, 11, 2449, 437, 3263, 78, 11, 10062, 397, 11129, 66, 3681, 78, 11, 10062, 397, 11129, 66, 3681, 78, 2953, 437, 3681, 78, 11, 471, 69, 11, 27338, 952, 198,...
3.323077
65
__version__ = VERSION = '0.6.0'
[ 834, 9641, 834, 796, 44156, 2849, 796, 705, 15, 13, 21, 13, 15, 6, 198 ]
2.133333
15
"""retrieve dns addresses from router and write to local csv file""" import os.path import csv; from paramiko import SSHClient from scp import SCPClient router_ip = 'router.mvanvuren.local' ip_range = '192.168.0.' remote_hosts_file = '/tmp/etc/hosts.dnsmasq' local_hosts_file = './hosts.dnsmasq' remote_dnsmasq_file = '/tmp/etc/dnsmasq.conf' local_dnsmasq_file = './dnsmasq.conf' dns_file = './dns.csv' field_names = ['ip', 'mac', 'name', 'comments'] main()
[ 37811, 1186, 30227, 288, 5907, 9405, 422, 20264, 290, 3551, 284, 1957, 269, 21370, 2393, 37811, 198, 11748, 28686, 13, 6978, 198, 11748, 269, 21370, 26, 198, 6738, 5772, 12125, 1330, 33825, 11792, 198, 6738, 629, 79, 1330, 17527, 11792, ...
2.460733
191
from mWindowsSDK import *; from .fThrowLastError import fThrowLastError; from mRegistry import cRegistryValue; oSystemInfo = cSystemInfo();
[ 6738, 285, 11209, 10305, 42, 1330, 1635, 26, 198, 6738, 764, 69, 39431, 5956, 12331, 1330, 277, 39431, 5956, 12331, 26, 198, 6738, 285, 8081, 4592, 1330, 269, 8081, 4592, 11395, 26, 198, 198, 78, 11964, 12360, 796, 269, 11964, 12360, ...
3.333333
42
from typing import List, Union from pystratis.api import APIRequest, EndpointRegister, endpoint from pystratis.api.federationgateway.responsemodels import * from pystratis.api.federationgateway.requestmodels import * from pystratis.core import DestinationChain from pystratis.core.types import Address, Money, uint256 from pystratis.core.networks import StraxMain, StraxTest, StraxRegTest, CirrusMain, CirrusTest, CirrusRegTest, Ethereum class FederationGateway(APIRequest, metaclass=EndpointRegister): """Implements the federationgateway api endpoints.""" route = '/api/federationgateway' @endpoint(f'{route}/deposits') def deposits(self, block_height: int, **kwargs) -> List[MaturedBlockDepositsModel]: """Retrieves block deposits Args: block_height (int): The block height at which to obtain deposits. **kwargs: Extra keyword arguments. Returns: List[MaturedBlockDepositsModel]: A list of matured block deposits. Raises: APIError: Error thrown by node API. See message for details. """ request_model = DepositsRequest(block_height=block_height) data = self.get(request_model, **kwargs) serializable_result = SerializableResult(**data) matured_block_deposit_models = [] for item in serializable_result.value: data = {'deposits': [], 'blockInfo': item['blockInfo']} for deposit in item['deposits']: deposit['amount'] = Money.from_satoshi_units(deposit['amount']) if 'targetChain' in deposit: if deposit['targetChain'] == DestinationChain.ETH.value: deposit['targetAddress'] = Address(address=deposit['targetAddress'], network=Ethereum()) else: chain_name = DestinationChain(deposit['targetChain']).name raise RuntimeWarning(f'Validation for {chain_name} not implemented.') else: if self._network == StraxMain(): deposit['targetAddress'] = Address(address=deposit['targetAddress'], network=CirrusMain()) if self._network == CirrusMain(): deposit['targetAddress'] = Address(address=deposit['targetAddress'], network=StraxMain()) if self._network == StraxTest(): deposit['targetAddress'] = Address(address=deposit['targetAddress'], network=CirrusTest()) if self._network == CirrusTest(): deposit['targetAddress'] = Address(address=deposit['targetAddress'], network=StraxTest()) if self._network == StraxRegTest() or self._network == CirrusRegTest(): deposit['targetAddress'] = Address(address=deposit['targetAddress'], network=StraxRegTest()) if self._network == StraxRegTest() or self._network == CirrusRegTest(): deposit['targetAddress'] = Address(address=deposit['targetAddress'], network=StraxRegTest()) data['deposits'].append(deposit) matured_block_deposit_models.append(MaturedBlockDepositsModel(**data)) return matured_block_deposit_models @endpoint(f'{route}/transfer/pending') def pending_transfer(self, deposit_id: Union[str, uint256], transaction_id: Union[str, uint256], **kwargs) -> List[CrossChainTransferModel]: """Gets pending transfers. Args: deposit_id (uint256, str): The deposit id hash. transaction_id (uint256, str): The transaction id hash. **kwargs: Extra keyword arguments. Returns: List[CrossChainTransferModel]: A list of cross chain transfers. Raises: APIError: Error thrown by node API. See message for details. """ if isinstance(deposit_id, str): deposit_id = uint256(deposit_id) if isinstance(transaction_id, str): transaction_id = uint256(transaction_id) request_model = PendingTransferRequest(deposit_id=deposit_id, transaction_id=transaction_id) data = self.get(request_model, **kwargs) return [CrossChainTransferModel(**x) for x in data] @endpoint(f'{route}/transfer/fullysigned') def fullysigned_transfer(self, deposit_id: Union[str, uint256], transaction_id: Union[str, uint256], **kwargs) -> List[CrossChainTransferModel]: """Get fully signed transfers. Args: deposit_id (uint256, str): The deposit id hash. transaction_id (uint256, str): The transaction id hash. **kwargs: Extra keyword arguments. Returns: List[CrossChainTransferModel]: A list of cross chain transfers. Raises: APIError: Error thrown by node API. See message for details. """ if isinstance(deposit_id, str): deposit_id = uint256(deposit_id) if isinstance(transaction_id, str): transaction_id = uint256(transaction_id) request_model = FullySignedTransferRequest(deposit_id=deposit_id, transaction_id=transaction_id) data = self.get(request_model, **kwargs) return [CrossChainTransferModel(**x) for x in data] @endpoint(f'{route}/member/info') def member_info(self, **kwargs) -> FederationMemberInfoModel: """Gets info on the state of a multisig member. Args: **kwargs: Extra keyword arguments. Returns: FederationMemberInfoModel: Information on the current multisig member. Raises: APIError: Error thrown by node API. See message for details. """ data = self.get(**kwargs) return FederationMemberInfoModel(**data) @endpoint(f'{route}/info') def info(self, **kwargs) -> FederationGatewayInfoModel: """Gets info on the state of the federation. Args: **kwargs: Extra keyword arguments. Returns: FederationGatewayInfoModel: Information on the federation gateway. Raises: APIError: Error thrown by node API. See message for details. """ data = self.get(**kwargs) data['multisigAddress'] = Address(address=data['multisigAddress'], network=self._network) return FederationGatewayInfoModel(**data) @endpoint(f'{route}/member/ip/add') def ip_add(self, ipaddr: str, **kwargs) -> str: """Add a federation member's IP address to the federation IP list Args: ipaddr (str): The endpoint. **kwargs: Extra keyword arguments. Returns: str: Response to ip add request. Raises: APIError: Error thrown by node API. See message for details. """ request_model = MemberIPAddRequest(ipaddr=ipaddr) data = self.put(request_model, **kwargs) return data @endpoint(f'{route}/member/ip/remove') def ip_remove(self, ipaddr: str, **kwargs) -> str: """Remove a federation member's IP address to the federation IP list Args: ipaddr (str): The endpoint. **kwargs: Extra keyword arguments. Returns: str: response to ip remove request. Raises: APIError: Error thrown by node API. See message for details. """ request_model = MemberIPRemoveRequest(ipaddr=ipaddr) data = self.put(request_model, **kwargs) return data @endpoint(f'{route}/member/ip/replace') def ip_replace(self, ipaddrtouse: str, ipaddr: str, **kwargs) -> str: """Replace a federation member's IP from the federation IP list with another. Args: ipaddrtouse (str): The new endpoint. ipaddr (str): The endpoint being replaced. **kwargs: Extra keyword arguments. Returns: str: Response to ip replace request. Raises: APIError: Error thrown by node API. See message for details. """ request_model = MemberIPReplaceRequest(ipaddrtouse=ipaddrtouse, ipaddr=ipaddr) data = self.put(request_model, **kwargs) return data @endpoint(f'{route}/transfer/verify') def verify_transfer(self, deposit_id_transaction_id: Union[str, uint256], **kwargs) -> Union[str, ValidateTransactionResultModel]: """Validate a transfer transaction. Args: deposit_id_transaction_id (uint256, str): The transaction id containing the deposit with the deposit id. **kwargs: Extra keyword arguments. Returns: Union[str, ValidateTransactionResultModel]: A model describing the validity of the transfer. Raises: APIError: Error thrown by node API. See message for details. """ if isinstance(deposit_id_transaction_id, str): deposit_id_transaction_id = uint256(deposit_id_transaction_id) request_model = VerifyTransferRequest(deposit_id_transaction_id=deposit_id_transaction_id) data = self.get(request_model, **kwargs) if isinstance(data, str): return data return ValidateTransactionResultModel(**data) @endpoint(f'{route}/transfers/deletesuspended') def transfers_delete_suspended(self, **kwargs) -> str: """Delete a suspended transfer transaction. Args: **kwargs: Extra keyword arguments. Returns: str: A message about the deletion request. Raises: APIError: Error thrown by node API. See message for details. """ data = self.delete(**kwargs) return data @endpoint(f'{route}/transfer') def transfer(self, deposit_id: Union[str, uint256], **kwargs) -> CrossChainTransferModel: """Gets pending transfers. Args: deposit_id (uint256, str): The deposit id hash. **kwargs: Extra keyword arguments. Returns: CrossChainTransferModel: A cross chain transfer. Raises: APIError: Error thrown by node API. See message for details. """ if isinstance(deposit_id, str): deposit_id = uint256(deposit_id) request_model = TransferRequest(deposit_id=deposit_id) data = self.get(request_model, **kwargs) return CrossChainTransferModel(**data)
[ 6738, 19720, 1330, 7343, 11, 4479, 198, 6738, 12972, 2536, 37749, 13, 15042, 1330, 7824, 18453, 11, 5268, 4122, 38804, 11, 36123, 198, 6738, 12972, 2536, 37749, 13, 15042, 13, 69, 9748, 10494, 1014, 13, 26209, 27530, 1330, 1635, 198, 67...
2.344903
4,552
from json import loads from pathlib import PosixPath as Path from galaxy_swift.exceptions import InvalidPlugin from galaxy_swift.types import Manifest
[ 6738, 33918, 1330, 15989, 198, 6738, 3108, 8019, 1330, 18574, 844, 15235, 355, 10644, 198, 198, 6738, 16161, 62, 2032, 2135, 13, 1069, 11755, 1330, 17665, 37233, 198, 6738, 16161, 62, 2032, 2135, 13, 19199, 1330, 36757, 628 ]
4.026316
38
import pandas as pd import pytest from pandas.testing import assert_frame_equal from seaborn._core.groupby import GroupBy from seaborn._stats.aggregation import Agg
[ 198, 11748, 19798, 292, 355, 279, 67, 198, 198, 11748, 12972, 9288, 198, 6738, 19798, 292, 13, 33407, 1330, 6818, 62, 14535, 62, 40496, 198, 198, 6738, 384, 397, 1211, 13557, 7295, 13, 8094, 1525, 1330, 4912, 3886, 198, 6738, 384, 397...
3.313725
51
from django.db.models.signals import post_delete from django.dispatch import Signal, receiver from baserow.contrib.database.table.cache import ( invalidate_table_model_cache_and_related_models, ) from baserow.contrib.database.table.models import Table table_created = Signal() table_updated = Signal() table_deleted = Signal() tables_reordered = Signal() @receiver(post_delete, sender=Table)
[ 6738, 42625, 14208, 13, 9945, 13, 27530, 13, 12683, 874, 1330, 1281, 62, 33678, 198, 6738, 42625, 14208, 13, 6381, 17147, 1330, 26484, 11, 9733, 198, 198, 6738, 1615, 263, 322, 13, 3642, 822, 13, 48806, 13, 11487, 13, 23870, 1330, 357...
3.174603
126
import subprocess import sys member_list = [ "ZbT8sM1VLUA", "ZbT8sM1VLUA" ] #この辺りでvideokeyやタイトルをごにょごにょする。 def main(): """ main関数 """ for video_id in member_list: cmd = 'chat_downloader https://www.youtube.com/watch?v=' + video_id + ' --cookies ../cookie.txt --output "result_member/' + video_id + '.json" > result_member/' + video_id + '.txt' # 実行するコマンド print(cmd) for result in command(cmd): print(result) if __name__ == "__main__": main()
[ 11748, 850, 14681, 198, 11748, 25064, 198, 198, 19522, 62, 4868, 796, 685, 198, 220, 220, 220, 366, 57, 65, 51, 23, 82, 44, 16, 47468, 34970, 1600, 198, 220, 220, 220, 366, 57, 65, 51, 23, 82, 44, 16, 47468, 34970, 1, 198, 60, ...
1.98062
258
from django.db.models.signals import post_save from django.dispatch import receiver import short_url import logging from .models import Publication _log = logging.getLogger(__name__) @receiver(post_save, sender=Publication)
[ 6738, 42625, 14208, 13, 9945, 13, 27530, 13, 12683, 874, 1330, 1281, 62, 21928, 198, 6738, 42625, 14208, 13, 6381, 17147, 1330, 9733, 198, 11748, 1790, 62, 6371, 198, 11748, 18931, 198, 198, 6738, 764, 27530, 1330, 45065, 198, 198, 62, ...
3.304348
69
from ruamel import yaml from jinja2 import Environment, FileSystemLoader, Template import datetime import os # Edit ls output now = datetime.datetime.now() file = open('./config.yaml', 'r') config_data = yaml.load(file, Loader=yaml.Loader) # # List main server os.system('lftp -c "source conf/original.conf && find -l . && exit" > lists/original.txt') txt_editor("lists/original.txt", "lists/original_list.txt") # Verify mirrors diff and update config data mirrors = config_data['mirrors'] for mirror in mirrors: os.system('lftp -c "source conf/' + mirror + '.conf && find -l . && exit" > lists/' + mirror + '.txt') txt_editor("lists/" + mirror + ".txt", "lists/" + mirror + "_list.txt") os.system("diff -u lists/original_list.txt lists/" + mirror + "_list.txt > webpage/" + mirrors[mirror]['diffFile']) if os.stat(mirrors[mirror]['diffFile']).st_size==0: if mirrors[mirror]['updated'] == False: mirrors[mirror]['lastUpdate'] = now.strftime("%Y-%m-%d %H:%M") mirrors[mirror]['updated'] = True else: mirrors[mirror]['updated'] = False # Update time config_data['lastRun'] = now.strftime("%Y-%m-%d %H:%M") template_name = config_data['template'] # Save data file = open('./config.yaml', 'w') yaml.dump(config_data, file, Dumper=yaml.RoundTripDumper) # Load Jinja2 template env = Environment(loader = FileSystemLoader('./'), trim_blocks=True, lstrip_blocks=True) template = env.get_template('templates/' + template_name +'/template.j2') # Update template files in the webpage folder os.system('cp -r templates/' + template_name +'/* webpage/ ; rm webpage/template.j2') # Render the template with data and save in webpage/index.html file = open('webpage/index.html', 'w') file.write(template.render(config_data))
[ 6738, 7422, 17983, 1330, 331, 43695, 198, 6738, 474, 259, 6592, 17, 1330, 9344, 11, 9220, 11964, 17401, 11, 37350, 198, 11748, 4818, 8079, 198, 11748, 28686, 198, 198, 2, 5312, 43979, 5072, 628, 198, 2197, 796, 4818, 8079, 13, 19608, ...
2.789969
638
# # Copyright 2020 Jaroslav Chmurny # # This file is part of Library of Graph Algorithms for Python. # # Library of Graph Algorithms for Python is free software developed for # educational # and experimental purposes. It is licensed under the Apache # License, Version 2.0 # (the "License"); you may not use this file except # in compliance with the # License. You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # """Unit tests for the graphlib.util module. """ from pytest import raises from graphlib.util import QueueableItem, RepriorizablePriorityQueue, SimplePriorityQueue from graphlib.util import UnionFind class TestSimplePriorityQueue: # pylint: disable=R0201,C0116,C0121 """Collection of test methods exercising the class :class: graphlib.util.SimplePriorityQueue. """ class TestRepriorizablePriorityQueue: # pylint: disable=R0201,C0116,C0121 """Collection of test methods exercising the class :class: graphlib.util.RepriorizablePriorityQueue. """ class TestUnionFind: # pylint: disable=R0201,C0116,C0301,C0121 """Collection of test methods exercising the class :class: graphlib.util.UnionFind. """
[ 2, 201, 198, 2, 15069, 12131, 15374, 26388, 609, 76, 700, 88, 201, 198, 2, 201, 198, 2, 770, 2393, 318, 636, 286, 10074, 286, 29681, 978, 7727, 907, 329, 11361, 13, 201, 198, 2, 201, 198, 2, 10074, 286, 29681, 978, 7727, 907, 32...
3.186475
488
import locale class NumberUtil: """ Number Utility """ def toCurrency(n): """ Convert given number into currency format. Args: n (float): Number to convert. Returns: string """ if not isinstance(n, float): n = float(n) locale.setlocale(locale.LC_ALL, 'en_US.UTF-8') return locale.currency(n, grouping = True)
[ 11748, 36693, 198, 198, 4871, 7913, 18274, 346, 25, 198, 220, 220, 220, 220, 198, 220, 220, 220, 37227, 7913, 34030, 198, 220, 220, 220, 37227, 198, 220, 220, 220, 220, 198, 220, 220, 220, 825, 284, 34, 13382, 7, 77, 2599, 198, 22...
1.977778
225
# Copyright 2019 Splunk, Inc. # # Use of this source code is governed by a BSD-2-clause-style # license that can be found in the LICENSE-BSD2 file or at # https://opensource.org/licenses/BSD-2-Clause import random from jinja2 import Environment from .sendmessage import * from .splunkutils import * from .timeutils import * env = Environment() # <46>1 2021-12-08T21:07:19.100000Z sysloghost CylancePROTECT - - - Event Type: ExploitAttempt, Event Name: none, Device Name: DEVICENAME, IP Address: (), Action: None, Process ID: 72724, Process Name: C:\Program Files (x86)\Medcon\Medcon Common\Dicom2Avi_App.exe, User Name: tcsadmin, Violation Type: Stack Pivot, Zone Names: (Windows Server 2008), Device Id: a603a6e8-cac7-4d06-970c-24671e5af6cc, Policy Name: Servers Complete Policy
[ 2, 15069, 13130, 13341, 2954, 11, 3457, 13, 198, 2, 198, 2, 5765, 286, 428, 2723, 2438, 318, 21825, 416, 257, 347, 10305, 12, 17, 12, 565, 682, 12, 7635, 198, 2, 5964, 326, 460, 307, 1043, 287, 262, 38559, 24290, 12, 21800, 17, ...
2.962264
265
from django.contrib.gis.measure import D from django.contrib.gis.db.models.functions import Distance from froide.publicbody.models import PublicBody from .amenity import AmenityProvider class AmenityLocalProvider(AmenityProvider): ''' Like Amenity provider but tries to find the public body for the amenity at its location ''' NEARBY_RADIUS = 200
[ 6738, 42625, 14208, 13, 3642, 822, 13, 70, 271, 13, 1326, 5015, 1330, 360, 198, 6738, 42625, 14208, 13, 3642, 822, 13, 70, 271, 13, 9945, 13, 27530, 13, 12543, 2733, 1330, 34600, 198, 198, 6738, 8400, 485, 13, 11377, 2618, 13, 27530...
3.04918
122
#!/usr/bin/python import argparse import os import subprocess import tempfile from itertools import chain from scipy.sparse import csc_matrix, save_npz from CMash import MinHash as MH ## TODO: adjust for very large files by only loading portions of hdf5 database file at a time if __name__ == '__main__': parser = argparse.ArgumentParser( description="Forms the sensing matrix `A` when given a database of WGS genomes in FASTA format. Also" "runs KMC on a temporary FASTA file consisting of each kmer counted by CMash for intersection" "with sample FASTA files.", formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('-k', '--k_size', type=int, help="k-mer size to use (Default: 21)", default=21) parser.add_argument('-c', '--cmash_loc', type=str, help="Location of CMash for accessing MakeStreamingDNADatabase.py.", required=True) parser.add_argument('-i', '--input_file', type=str, help="Path to file containing absolute file names of training genomes", required=True) parser.add_argument('-o', '--output_file', type=str, help="Output file of sparse representation of sensing matrix `A` in .mat format.", default="TrainingDatabase", required=True) ## Read in the arguments args = parser.parse_args() k_size = args.k_size input_file_names = os.path.abspath(args.input_file) if not os.path.exists(input_file_names): raise Exception("Input file %s does not exist." % input_file_names) output_file_name = os.path.abspath(args.output_file) cmash_loc = args.cmash_loc ## Run CMash and load database print("Running CMash.") database_file_name = output_file_name + ".h5" to_run = f"python {os.path.join(cmash_loc, 'scripts/MakeStreamingDNADatabase.py')} -k {k_size} {input_file_names} {database_file_name}" res = subprocess.run(to_run, shell=True, stdout=subprocess.DEVNULL) if res.returncode != 0: raise Exception("Error running CMash (MakeStreamingDNADatabase.py)") print("Loading in database.") database = MH.import_multiple_from_single_hdf5(database_file_name) ## Extract list of kmers print("Gathering kmers.") # (convert to set for removing duplicates, sort for consistent ordering) kmers = sorted(set(chain.from_iterable(genome._kmers for genome in database))) ## Gather data for, create, and save csc_matrix, each column representing the counts of a particular genome's kmers print("Creating matrix.") data = [] indices = [] indptr = [0] for genome in database: column_indices = [kmers.index(kmer) for kmer in genome._kmers] # Find indices of a particular genome's kmers sorter = sorted(range(len(column_indices)), key=column_indices.__getitem__) # argsort the indices # Concatenate sorted indices and corresponding data (counts) for canonical csc_matrix format indices += [column_indices[i] for i in sorter] data += [genome._counts[i] for i in sorter] indptr.append(len(indices)) save_npz(output_file_name, csc_matrix((data, indices, indptr), shape=(len(kmers), len(database))), compressed=True) ## Run KMC on artificial FASTA file for future intersection with y vectors print("Creating FASTA and running KMC.") # Check if kmc is installed res = subprocess.run("kmc", shell=True, stdout=subprocess.DEVNULL) if res.returncode != 0: raise Exception( "It appears that kmc is not installed. Please consult the README, install kmc, and try again.") with tempfile.TemporaryDirectory() as temp_dir: with open("test.fasta", "w+") as training_out_file: to_write = "" iterator = 0 for kmer in kmers: to_write += ">seq%d\n" % iterator to_write += "%s\n" % kmer iterator += 1 training_out_file.write(to_write) # Run KMC on training fasta to_run = f"kmc -k{k_size} -sm -fm -ci0 -cs3 {training_out_file.name} {output_file_name} {temp_dir}" res = subprocess.run(to_run, shell=True, stdout=subprocess.PIPE, stderr=subprocess.DEVNULL) if res.returncode != 0: raise Exception("An unexpected error was encountered while running kmc.") print("Completed.")
[ 2, 48443, 14629, 14, 8800, 14, 29412, 198, 11748, 1822, 29572, 198, 11748, 28686, 198, 11748, 850, 14681, 198, 11748, 20218, 7753, 198, 6738, 340, 861, 10141, 1330, 6333, 198, 6738, 629, 541, 88, 13, 82, 29572, 1330, 269, 1416, 62, 67...
2.466739
1,849
#!/usr/bin/env python3 # Fabio Zanarello, Sanger Institute, 2019 # this script reads a table of precomputed score (space delimited, no header): # 2 103060300 intronic IL18RAP 0.03276616 0.3697275149820258 # and a results table from NCBoost and produce an output in which the NCBoost results # have four new columns to corresponding to: # precomp_region # precomp_closest_gene_name # precomp_NCBoost_Score # precomp_NCboost_chr_rank_perc # NA if the variant is not precomputed import os import sys import argparse from collections import defaultdict if __name__ == "__main__": main()
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 18, 198, 2, 14236, 952, 47022, 533, 18798, 11, 311, 2564, 5136, 11, 13130, 198, 198, 2, 428, 4226, 9743, 257, 3084, 286, 662, 785, 17128, 4776, 357, 13200, 46728, 863, 11, 645, 13639, 259...
3.115789
190
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from ...testing import assert_equal from ..utility import Select
[ 2, 47044, 46, 12, 35353, 1137, 11617, 416, 4899, 14, 42116, 431, 6359, 13, 9078, 532, 8410, 5626, 48483, 198, 6738, 2644, 33407, 1330, 6818, 62, 40496, 198, 6738, 11485, 315, 879, 1330, 9683, 628, 198 ]
3.361111
36
import streamlit as st import pandas as pd import numpy as np
[ 11748, 4269, 18250, 355, 336, 198, 198, 11748, 19798, 292, 355, 279, 67, 198, 11748, 299, 32152, 355, 45941 ]
3.263158
19
import pytest from s2v_similarity import S2vSimilarity @pytest.fixture @pytest.fixture
[ 11748, 12972, 9288, 198, 6738, 264, 17, 85, 62, 38610, 414, 1330, 311, 17, 85, 18925, 414, 198, 198, 31, 9078, 9288, 13, 69, 9602, 628, 198, 31, 9078, 9288, 13, 69, 9602, 628, 628, 198, 220, 220, 220, 220 ]
2.45
40
# https://leetcode.com/problems/unique-paths/ from math import comb
[ 2, 3740, 1378, 293, 316, 8189, 13, 785, 14, 1676, 22143, 14, 34642, 12, 6978, 82, 14, 198, 198, 6738, 10688, 1330, 1974, 628 ]
2.916667
24
# Copyright (c) 2018, Oracle and/or its affiliates. # This software is made available to you under the terms of the GPL 3.0 license or the Apache 2.0 license. # GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt) # Apache License v2.0 # See LICENSE.TXT for details. import pytest from nose.plugins.skip import SkipTest import logging from ansible.modules.cloud.oracle import oci_db_node from ansible.module_utils.oracle import oci_db_utils, oci_utils try: import oci from oci.util import to_dict from oci.database.models import DbNode from oci.exceptions import ServiceError, ClientError except ImportError: raise SkipTest("test_oci_db_node.py requires `oci` module") @pytest.fixture() @pytest.fixture() @pytest.fixture() @pytest.fixture()
[ 2, 15069, 357, 66, 8, 2864, 11, 18650, 290, 14, 273, 663, 29116, 13, 198, 2, 770, 3788, 318, 925, 1695, 284, 345, 739, 262, 2846, 286, 262, 38644, 513, 13, 15, 5964, 393, 262, 24843, 362, 13, 15, 5964, 13, 198, 2, 22961, 3611, ...
2.918149
281
import sys import pandas as pd import numpy as np import re import nltk from sqlalchemy import create_engine nltk.download(['punkt', 'wordnet']) from sklearn.ensemble import GradientBoostingClassifier from nltk.stem import WordNetLemmatizer from sklearn.linear_model import LogisticRegression from sqlalchemy import create_engine from nltk.tokenize import word_tokenize from nltk.corpus import stopwords from sklearn.pipeline import Pipeline, FeatureUnion from sklearn.feature_extraction.text import CountVectorizer, TfidfTransformer from sklearn.base import BaseEstimator, TransformerMixin from sklearn.multioutput import MultiOutputClassifier from sklearn.ensemble import RandomForestClassifier from sklearn.neighbors import KNeighborsClassifier from sklearn.model_selection import train_test_split, GridSearchCV from sklearn.metrics import confusion_matrix, accuracy_score, classification_report, f1_score,\ precision_score, recall_score, make_scorer import pickle if __name__ == '__main__': main()
[ 11748, 25064, 198, 11748, 19798, 292, 355, 279, 67, 198, 11748, 299, 32152, 355, 45941, 198, 11748, 302, 198, 11748, 299, 2528, 74, 198, 6738, 44161, 282, 26599, 1330, 2251, 62, 18392, 198, 77, 2528, 74, 13, 15002, 7, 17816, 30354, 83...
3.414141
297
import jax import jax.numpy as jnp import snow from collections import namedtuple import numpy as np Exploration = namedtuple("Exploration", ['type', 'param']) if __name__ == '__main__': import numpy as np k = 1.15 l = 2 dmin = 0.8 dmax = dmin * l ** 0.6 hierarchization_config = ( (5, dmin * l ** 2, dmax * l ** 2, 1 / k ** 0, 1 / k ** 0), (5, dmin * l ** 1, dmax * l ** 1, 1 / k ** 1, 1 / k ** 1), (5, dmin * l ** 0, dmax * l ** 0, 1 / k ** 2, 1 / k ** 2), ) N_ACTORS = int(np.prod(tuple(dim for dim, _, _, _, _ in hierarchization_config))) # recomputed_returns = np.random.uniform(size=(N_ACTORS,), high=12) recomputed_returns = np.linspace(1, 0, N_ACTORS) recomputed_returns = np.stack([np.linspace(1, 0, N_ACTORS)] * 2, axis=1) recomputed_actions = np.stack([np.random.uniform(size=(N_ACTORS, 7), low=-1, high=1)], axis=1) ps = get_actions_probabilities(recomputed_returns, hierarchization_config, upsilon=0.0) # print(f'{ps=}\n\n') key = jax.random.PRNGKey(3) actions = sample(recomputed_actions, ps, key)
[ 11748, 474, 897, 198, 11748, 474, 897, 13, 77, 32152, 355, 474, 37659, 198, 11748, 6729, 198, 6738, 17268, 1330, 3706, 83, 29291, 198, 11748, 299, 32152, 355, 45941, 628, 198, 18438, 6944, 796, 3706, 83, 29291, 7203, 18438, 6944, 1600, ...
2.241449
497
#_ __ # | |/ /___ ___ _ __ ___ _ _ ® # | ' </ -_) -_) '_ \/ -_) '_| # |_|\_\___\___| .__/\___|_| # |_| # # Keeper Commander # Copyright 2018 Keeper Security Inc. # Contact: ops@keepersecurity.com # import argparse import collections import logging import re import fnmatch import shutil import functools import os import json from collections import OrderedDict from .. import api, display from ..subfolder import BaseFolderNode, try_resolve_path, find_folders from ..record import Record from .base import user_choice, suppress_exit, raise_parse_exception, Command from ..params import LAST_SHARED_FOLDER_UID, LAST_FOLDER_UID from ..error import CommandError ls_parser = argparse.ArgumentParser(prog='ls', description='List folder contents.') ls_parser.add_argument('-l', '--list', dest='detail', action='store_true', help='show detailed list') ls_parser.add_argument('-f', '--folders', dest='folders', action='store_true', help='display folders') ls_parser.add_argument('-r', '--records', dest='records', action='store_true', help='display records') ls_parser.add_argument('-s', '--short', dest='short', action='store_true', help='Do not display record details.') ls_parser.add_argument('-v', '--verbose', dest='verbose', action='store_true', help='verbose output') ls_parser.add_argument('pattern', nargs='?', type=str, action='store', help='search pattern') ls_parser.error = raise_parse_exception ls_parser.exit = suppress_exit cd_parser = argparse.ArgumentParser(prog='cd', description='Change current folder.') cd_parser.add_argument('folder', nargs='?', type=str, action='store', help='folder path or UID') cd_parser.error = raise_parse_exception cd_parser.exit = suppress_exit tree_parser = argparse.ArgumentParser(prog='tree', description='Display the folder structure.') tree_parser.add_argument('folder', nargs='?', type=str, action='store', help='folder path or UID') tree_parser.error = raise_parse_exception tree_parser.exit = suppress_exit rmdir_parser = argparse.ArgumentParser(prog='rmdir', description='Remove a folder and its contents.') rmdir_parser.add_argument('-f', '--force', dest='force', action='store_true', help='remove folder without prompting') rmdir_parser.add_argument('-q', '--quiet', dest='quiet', action='store_true', help='remove folder without folder info') rmdir_parser.add_argument('pattern', nargs='*', type=str, action='store', help='folder path or UID') rmdir_parser.error = raise_parse_exception rmdir_parser.exit = suppress_exit mkdir_parser = argparse.ArgumentParser(prog='mkdir', description='Create a folder.') mkdir_parser.add_argument('-sf', '--shared-folder', dest='shared_folder', action='store_true', help='create shared folder') mkdir_parser.add_argument('-uf', '--user-folder', dest='user_folder', action='store_true', help='create user folder') mkdir_parser.add_argument('-a', '--all', dest='grant', action='store_true', help='anyone has all permissions by default') mkdir_parser.add_argument('-u', '--manage-users', dest='manage_users', action='store_true', help='anyone can manage users by default') mkdir_parser.add_argument('-r', '--manage-records', dest='manage_records', action='store_true', help='anyone can manage records by default') mkdir_parser.add_argument('-s', '--can-share', dest='can_share', action='store_true', help='anyone can share records by default') mkdir_parser.add_argument('-e', '--can-edit', dest='can_edit', action='store_true', help='anyone can edit records by default') mkdir_parser.add_argument('folder', nargs='?', type=str, action='store', help='folder path') mkdir_parser.error = raise_parse_exception mkdir_parser.exit = suppress_exit mv_parser = argparse.ArgumentParser(prog='mv', description='Move a record or folder to another folder.') mv_parser.add_argument('-f', '--force', dest='force', action='store_true', help='do not prompt') mv_parser.add_argument('-s', '--can-reshare', dest='can_reshare', action='store_true', help='anyone can reshare records') mv_parser.add_argument('-e', '--can-edit', dest='can_edit', action='store_true', help='anyone can edit records') mv_parser.add_argument('src', nargs='?', type=str, action='store', help='source path to folder/record or UID') mv_parser.add_argument('dst', nargs='?', type=str, action='store', help='destination folder or UID') mv_parser.error = raise_parse_exception mv_parser.exit = suppress_exit ln_parser = argparse.ArgumentParser(prog='ln', description='Create a link between a record and a folder.') ln_parser.add_argument('-f', '--force', dest='force', action='store_true', help='do not prompt') ln_parser.add_argument('-s', '--can-reshare', dest='can_reshare', action='store_true', help='anyone can reshare records') ln_parser.add_argument('-e', '--can-edit', dest='can_edit', action='store_true', help='anyone can edit records') ln_parser.add_argument('src', nargs='?', type=str, action='store', help='source path to folder/record or UID') ln_parser.add_argument('dst', nargs='?', type=str, action='store', help='destination folder or UID') ln_parser.error = raise_parse_exception ln_parser.exit = suppress_exit def get_shared_folder_delete_rq(params, sf_requests, uid): """Adds a delete request to given dictionary for specified shared folder uid""" if uid in params.shared_folder_cache and uid not in sf_requests: sf = params.shared_folder_cache[uid] rq = { 'command': 'shared_folder_update', 'operation': 'delete', 'shared_folder_uid': sf['shared_folder_uid'] } if 'shared_folder_key' not in sf: if 'teams' in sf: for team in sf['teams']: rq['from_team_uid'] = team['team_uid'] break sf_requests[uid] = rq def get_shared_subfolder_delete_rq(params, sf_requests, user_folder, user_folder_ids): """Recursively searches a user folder for shared folders to delete""" delete_rq_added = False user_folder_ids.add(user_folder.uid) for uid in user_folder.subfolders: subfolder = params.folder_cache[uid] if subfolder.type == BaseFolderNode.SharedFolderType: delete_rq_added = True get_shared_folder_delete_rq(params, sf_requests, uid) elif uid not in user_folder_ids: delete_rq_added = get_shared_subfolder_delete_rq(params, sf_requests, subfolder, user_folder_ids) return delete_rq_added
[ 2, 62, 220, 11593, 198, 2, 930, 930, 14, 1220, 17569, 46444, 4808, 11593, 220, 46444, 4808, 4808, 38852, 198, 2, 930, 705, 7359, 532, 62, 8, 532, 62, 8, 705, 62, 3467, 14, 532, 62, 8, 705, 62, 91, 198, 2, 930, 62, 91, 59, 62...
2.847922
2,262
import datetime import numpy as np from pyproj import CRS from RAiDER.models.ecmwf import ECMWF
[ 11748, 4818, 8079, 198, 198, 11748, 299, 32152, 355, 45941, 198, 6738, 12972, 1676, 73, 1330, 327, 6998, 198, 198, 6738, 17926, 72, 14418, 13, 27530, 13, 721, 76, 86, 69, 1330, 13182, 14326, 37, 628 ]
2.75
36
# Copyright 2019 The TensorTrade Authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License import os import pandas as pd import datetime import tensorflow as tf from tensortrade.environments.render import BaseRenderer from tensortrade.environments.utils.helpers import create_auto_file_name, check_path DEFAULT_LOG_FORMAT = '[%(asctime)-15s] %(message)s' DEFAULT_TIMESTAMP_FORMAT = '%Y-%m-%d %H:%M:%S'
[ 2, 15069, 13130, 383, 309, 22854, 35965, 46665, 13, 198, 2, 198, 2, 49962, 739, 262, 24843, 13789, 11, 10628, 362, 13, 15, 357, 1169, 366, 34156, 15341, 198, 2, 345, 743, 407, 779, 428, 2393, 2845, 287, 11846, 351, 262, 13789, 13, ...
3.340741
270
from django import forms from django.contrib.auth.forms import AuthenticationForm from .models import Group,Profile,Question,Choice class GroupForm(forms.ModelForm): ''' Class to create a form for an authenticated user to create Group ''' #************************************************************************************************************* class QuestionForm(forms.ModelForm): ''' Class to create a form for an authenticated user to post a poll ''' #************************************************** Enter A Choice ********************************************** class ChoiceForm(forms.ModelForm): ''' Class to create a form for an authenticated user to post a poll ''' #************************************* SET UP A PROFILE ********************************************************** class ProfileForm(forms.ModelForm): ''' Class to create a form for an authenticated user to update profile ''' #***********************************************************ACTUAL VOTING**************************************** class VoteForm(forms.ModelForm): ''' Class to create a form for an authenticated user to vote '''
[ 6738, 42625, 14208, 1330, 5107, 198, 6738, 42625, 14208, 13, 3642, 822, 13, 18439, 13, 23914, 1330, 48191, 8479, 198, 6738, 764, 27530, 1330, 4912, 11, 37046, 11, 24361, 11, 46770, 628, 198, 198, 4871, 4912, 8479, 7, 23914, 13, 17633, ...
4.310469
277
# -*- coding: utf-8 -*- # Copyright 2020 Google LLC # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # import proto # type: ignore from google.cloud.monitoring_dashboard_v1.types import metrics from google.protobuf import duration_pb2 # type: ignore __protobuf__ = proto.module( package="google.monitoring.dashboard.v1", manifest={"Scorecard",}, ) class Scorecard(proto.Message): r"""A widget showing the latest value of a metric, and how this value relates to one or more thresholds. Attributes: time_series_query (google.cloud.monitoring_dashboard_v1.types.TimeSeriesQuery): Required. Fields for querying time series data from the Stackdriver metrics API. gauge_view (google.cloud.monitoring_dashboard_v1.types.Scorecard.GaugeView): Will cause the scorecard to show a gauge chart. spark_chart_view (google.cloud.monitoring_dashboard_v1.types.Scorecard.SparkChartView): Will cause the scorecard to show a spark chart. thresholds (Sequence[google.cloud.monitoring_dashboard_v1.types.Threshold]): The thresholds used to determine the state of the scorecard given the time series' current value. For an actual value x, the scorecard is in a danger state if x is less than or equal to a danger threshold that triggers below, or greater than or equal to a danger threshold that triggers above. Similarly, if x is above/below a warning threshold that triggers above/below, then the scorecard is in a warning state - unless x also puts it in a danger state. (Danger trumps warning.) As an example, consider a scorecard with the following four thresholds: { value: 90, category: 'DANGER', trigger: 'ABOVE', }, { value: 70, category: 'WARNING', trigger: 'ABOVE', }, { value: 10, category: 'DANGER', trigger: 'BELOW', }, { value: 20, category: 'WARNING', trigger: 'BELOW', } Then: values less than or equal to 10 would put the scorecard in a DANGER state, values greater than 10 but less than or equal to 20 a WARNING state, values strictly between 20 and 70 an OK state, values greater than or equal to 70 but less than 90 a WARNING state, and values greater than or equal to 90 a DANGER state. """ class GaugeView(proto.Message): r"""A gauge chart shows where the current value sits within a pre-defined range. The upper and lower bounds should define the possible range of values for the scorecard's query (inclusive). Attributes: lower_bound (float): The lower bound for this gauge chart. The value of the chart should always be greater than or equal to this. upper_bound (float): The upper bound for this gauge chart. The value of the chart should always be less than or equal to this. """ lower_bound = proto.Field(proto.DOUBLE, number=1,) upper_bound = proto.Field(proto.DOUBLE, number=2,) class SparkChartView(proto.Message): r"""A sparkChart is a small chart suitable for inclusion in a table-cell or inline in text. This message contains the configuration for a sparkChart to show up on a Scorecard, showing recent trends of the scorecard's timeseries. Attributes: spark_chart_type (google.cloud.monitoring_dashboard_v1.types.SparkChartType): Required. The type of sparkchart to show in this chartView. min_alignment_period (google.protobuf.duration_pb2.Duration): The lower bound on data point frequency in the chart implemented by specifying the minimum alignment period to use in a time series query. For example, if the data is published once every 10 minutes it would not make sense to fetch and align data at one minute intervals. This field is optional and exists only as a hint. """ spark_chart_type = proto.Field( proto.ENUM, number=1, enum=metrics.SparkChartType, ) min_alignment_period = proto.Field( proto.MESSAGE, number=2, message=duration_pb2.Duration, ) time_series_query = proto.Field( proto.MESSAGE, number=1, message=metrics.TimeSeriesQuery, ) gauge_view = proto.Field( proto.MESSAGE, number=4, oneof="data_view", message=GaugeView, ) spark_chart_view = proto.Field( proto.MESSAGE, number=5, oneof="data_view", message=SparkChartView, ) thresholds = proto.RepeatedField( proto.MESSAGE, number=6, message=metrics.Threshold, ) __all__ = tuple(sorted(__protobuf__.manifest))
[ 2, 532, 9, 12, 19617, 25, 3384, 69, 12, 23, 532, 9, 12, 198, 2, 15069, 12131, 3012, 11419, 198, 2, 198, 2, 49962, 739, 262, 24843, 13789, 11, 10628, 362, 13, 15, 357, 1169, 366, 34156, 15341, 198, 2, 345, 743, 407, 779, 428, 2...
2.419124
2,374
# Generated by Django 2.2.10 on 2020-03-08 20:00 from django.db import migrations, models
[ 2, 2980, 515, 416, 37770, 362, 13, 17, 13, 940, 319, 12131, 12, 3070, 12, 2919, 1160, 25, 405, 198, 198, 6738, 42625, 14208, 13, 9945, 1330, 15720, 602, 11, 4981, 628 ]
2.875
32
import unittest from Statistics.Statistics import Statistics import pprint # def test_instantiate_calculator(self): # self.assertIsInstance(self.statistics, Statistics) if __name__ == '__main__': unittest.main()
[ 11748, 555, 715, 395, 198, 198, 6738, 14370, 13, 48346, 1330, 14370, 198, 11748, 279, 4798, 628, 198, 2, 220, 220, 220, 825, 1332, 62, 8625, 415, 9386, 62, 9948, 3129, 1352, 7, 944, 2599, 198, 2, 220, 220, 220, 220, 220, 220, 220,...
2.8875
80
import torch import torch.nn as nn if __name__ == '__main__': net = sphere(64) print(net)
[ 11748, 28034, 198, 11748, 28034, 13, 20471, 355, 299, 77, 628, 198, 198, 361, 11593, 3672, 834, 6624, 705, 834, 12417, 834, 10354, 198, 220, 220, 220, 2010, 796, 16558, 7, 2414, 8, 198, 220, 220, 220, 3601, 7, 3262, 8 ]
2.439024
41
from __future__ import unicode_literals from contextlib import closing import io import os.path from shutil import rmtree import sqlite3 from tempfile import mkdtemp import unittest from wsgiref.headers import Headers from wsgiref.util import FileWrapper, setup_testing_defaults from wsgiref.validate import validator import wsgir if __name__ == '__main__': unittest.main()
[ 6738, 11593, 37443, 834, 1330, 28000, 1098, 62, 17201, 874, 198, 198, 6738, 4732, 8019, 1330, 9605, 198, 11748, 33245, 198, 11748, 28686, 13, 6978, 198, 6738, 4423, 346, 1330, 374, 16762, 631, 198, 11748, 44161, 578, 18, 198, 6738, 2021...
3.121951
123
from django.conf.urls import patterns, include, url from store_search import views urlpatterns = ( url(r'^search$', views.search_page, name='store_search'), )
[ 6738, 42625, 14208, 13, 10414, 13, 6371, 82, 1330, 7572, 11, 2291, 11, 19016, 198, 6738, 3650, 62, 12947, 1330, 5009, 628, 198, 6371, 33279, 82, 796, 357, 198, 220, 220, 220, 19016, 7, 81, 6, 61, 12947, 3, 3256, 5009, 13, 12947, 6...
3
55
from __future__ import absolute_import # NOQA from .celery import app as celery_app # NOQA
[ 6738, 11593, 37443, 834, 1330, 4112, 62, 11748, 220, 1303, 8005, 48, 32, 198, 6738, 764, 7015, 88, 1330, 598, 355, 18725, 1924, 62, 1324, 220, 1303, 8005, 48, 32, 198 ]
3
31
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * class RXml(RPackage): """Tools for Parsing and Generating XML Within R and S-Plus Many approaches for both reading and creating XML (and HTML) documents (including DTDs), both local and accessible via HTTP or FTP. Also offers access to an 'XPath' "interpreter".""" homepage = "https://cloud.r-project.org/package=XML" url = "https://cloud.r-project.org/src/contrib/XML_3.98-1.9.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/XML" version('3.99-0.5', sha256='60529b7360f162eba07da455eeb9b94a732b2dd623c49e0f04328a2e97bd53a6') version('3.98-1.20', sha256='46af86376ea9a0fb1b440cf0acdf9b89178686a05c4b77728fcff1f023aa4858') version('3.98-1.19', sha256='81b1c4a2df24c5747fa8b8ec2d76b4e9c3649b56ca94f6c93fbd106c8a72beab') version('3.98-1.9', sha256='a3b70169cb2fbd8d61a41ff222d27922829864807e9ecad373f55ba0df6cf3c3') version('3.98-1.5', sha256='deaff082e4d37931d2dabea3a60c3d6916d565821043b22b3f9522ebf3918d35') version('3.98-1.4', sha256='9c0abc75312f66aac564266b6b79222259c678aedee9fc347462978354f11126') depends_on('r@2.13.0:', type=('build', 'run')) depends_on('r@4.0.0:', when='@3.99-0.5:', type=('build', 'run')) depends_on('libxml2@2.6.3:')
[ 2, 15069, 2211, 12, 1238, 2481, 13914, 45036, 3549, 2351, 4765, 11, 11419, 290, 584, 198, 2, 1338, 441, 4935, 34152, 13, 4091, 262, 1353, 12, 5715, 27975, 38162, 9947, 2393, 329, 3307, 13, 198, 2, 198, 2, 30628, 55, 12, 34156, 12, ...
2.177877
669
#!/usr/bin/python3 -u ## Copyright (C) 2012 - 2022 ENCRYPTED SUPPORT LP <adrelanos@whonix.org> ## See the file COPYING for copying conditions. # Since it will be useful to know something about the script, # for the later tests, the terms are defined here: # (A discussion of Python language structure is beyond # the scope of this document) # [1] http://en.wikipedia.org/wiki/Ipv4 # [2] http://en.wikipedia.org/wiki/Internet_Control_Message_Protocol # [3] http://en.wikipedia.org/wiki/IP_routing # [4] http://en.wikipedia.org/wiki/Ping # [5] http://en.wikipedia.org/wiki/Internet_Control_Message_Protocol#List_of_permitted_control_messages_.28incomplete_list.29 # [6] http://www.secdev.org/projects/scapy/doc/usage.html#send-and-receive-packets-sr # [7] http://www.secdev.org/projects/scapy/doc/usage.html#stacking-layers import sys from scapy.all import * # define the target gateway & data payload # IP HARDCODED but only needed during manual leak testing. target = "10.152.152.10" #target = "45.33.32.156" data = "testing" # define packets # These define two variables, that are set to the object types IP # and ICMP respectively. These objects in Scapy define the protocol # type for IP (default IPv4) [1] and ICMP [2] respectively. # And will send packets on the wire of these types when used. ip = IP() icmp = ICMP() # define packet parameters ip.dst = target # IP packets are used for routing [3] between networks on the Internet. # So, we assign the destination (dst) in the IP portion of the # packet we are going to assemble and send out. icmp.type = 8 icmp.code = 0 # Defines the type of ICMP message to send out. The ..8 type.. is # a type defined as ..echo request.., e.g. a simple ping [4]. # See a list here of various types of ICMP [5] messages here. # The sr1() [6] command will ..send and receive network traffic, # returning the 1st packet received... # The notation of ..ip/icmp/data.. is the notation for encapsulation # of various instances of networking protocols [7]. # Read it right to left: ..data encapsulated inside an ICMP message # and encapsulated inside an IP datagram... test_ping = sr1(ip/icmp/data) if isinstance(test_ping, types.NoneType): print("No response") else: # Prints a short report on the packet received (if any). test_ping.summary()
[ 2, 48443, 14629, 14, 8800, 14, 29412, 18, 532, 84, 198, 198, 2235, 15069, 357, 34, 8, 2321, 532, 33160, 412, 7792, 18276, 11571, 1961, 43333, 18470, 1279, 324, 2411, 40015, 31, 1929, 261, 844, 13, 2398, 29, 198, 2235, 4091, 262, 239...
3.150068
733
# -*- coding: utf-8 -*- import click import logging from pathlib import Path from dotenv import find_dotenv, load_dotenv import pandas as pd def make_dataset(input_csv_filepath, output_dirpath): """ Runs data processing scripts to transform raw data from (../raw) into cleaned and data-defacto view ready to be analyzed/feature-engineered/encoded (saved in ../interim). """ logger = logging.getLogger(__name__) logger.info(f'making cleaned dataset from {input_csv_filepath}') # Get data logger.info('getting data...') df = pd.read_csv(Path.cwd().joinpath(input_csv_filepath)) # Get Col Types continuous_cols = [x for x in df.columns if x in ['encounter_id', 'hospital_id', 'patient_id', 'icu_id', 'gcs_eyes_apache', 'gcs_motor_apache', 'gcs_verbal_apache', 'age', 'height', 'pre_icu_los_days', 'weight', 'albumin_apache', 'bilirubin_apache', 'bun_apache', 'creatinine_apache', 'fio2_apache', 'glucose_apache', 'heart_rate_apache', 'hematocrit_apache', 'map_apache', 'paco2_apache', 'paco2_for_ph_apache', 'pao2_apache', 'ph_apache', 'resprate_apache', 'sodium_apache', 'temp_apache', 'urineoutput_apache', 'wbc_apache', 'd1_diasbp_invasive_max', 'd1_diasbp_invasive_min', 'd1_diasbp_max', 'd1_diasbp_min', 'd1_diasbp_noninvasive_max', 'd1_diasbp_noninvasive_min', 'd1_heartrate_max', 'd1_heartrate_min', 'd1_mbp_invasive_max', 'd1_mbp_invasive_min', 'd1_mbp_max', 'd1_mbp_min', 'd1_mbp_noninvasive_max', 'd1_mbp_noninvasive_min', 'd1_resprate_max', 'd1_resprate_min', 'd1_spo2_max', 'd1_spo2_min', 'd1_sysbp_invasive_max', 'd1_sysbp_invasive_min', 'd1_sysbp_max', 'd1_sysbp_min', 'd1_sysbp_noninvasive_max', 'd1_sysbp_noninvasive_min', 'd1_temp_max', 'd1_temp_min', 'h1_diasbp_invasive_max', 'h1_diasbp_invasive_min', 'h1_diasbp_max', 'h1_diasbp_min', 'h1_diasbp_noninvasive_max', 'h1_diasbp_noninvasive_min', 'h1_heartrate_max', 'h1_heartrate_min', 'h1_mbp_invasive_max', 'h1_mbp_invasive_min', 'h1_mbp_max', 'h1_mbp_min', 'h1_mbp_noninvasive_max', 'h1_mbp_noninvasive_min', 'h1_resprate_max', 'h1_resprate_min', 'h1_spo2_max', 'h1_spo2_min', 'h1_sysbp_invasive_max', 'h1_sysbp_invasive_min', 'h1_sysbp_max', 'h1_sysbp_min', 'h1_sysbp_noninvasive_max', 'h1_sysbp_noninvasive_min', 'h1_temp_max', 'h1_temp_min', 'd1_albumin_max', 'd1_albumin_min', 'd1_bilirubin_max', 'd1_bilirubin_min', 'd1_bun_max', 'd1_bun_min', 'd1_calcium_max', 'd1_calcium_min', 'd1_creatinine_max', 'd1_creatinine_min', 'd1_glucose_max', 'd1_glucose_min', 'd1_hco3_max', 'd1_hco3_min', 'd1_hemaglobin_max', 'd1_hemaglobin_min', 'd1_hematocrit_max', 'd1_hematocrit_min', 'd1_inr_max', 'd1_inr_min', 'd1_lactate_max', 'd1_lactate_min', 'd1_platelets_max', 'd1_platelets_min', 'd1_potassium_max', 'd1_potassium_min', 'd1_sodium_max', 'd1_sodium_min', 'd1_wbc_max', 'd1_wbc_min', 'h1_albumin_max', 'h1_albumin_min', 'h1_bilirubin_max', 'h1_bilirubin_min', 'h1_bun_max', 'h1_bun_min', 'h1_calcium_max', 'h1_calcium_min', 'h1_creatinine_max', 'h1_creatinine_min', 'h1_glucose_max', 'h1_glucose_min', 'h1_hco3_max', 'h1_hco3_min', 'h1_hemaglobin_max', 'h1_hemaglobin_min', 'h1_hematocrit_max', 'h1_hematocrit_min', 'h1_inr_max', 'h1_inr_min', 'h1_lactate_max', 'h1_lactate_min', 'h1_platelets_max', 'h1_platelets_min', 'h1_potassium_max', 'h1_potassium_min', 'h1_sodium_max', 'h1_sodium_min', 'h1_wbc_max', 'h1_wbc_min', 'd1_arterial_pco2_max', 'd1_arterial_pco2_min', 'd1_arterial_ph_max', 'd1_arterial_ph_min', 'd1_arterial_po2_max', 'd1_arterial_po2_min', 'd1_pao2fio2ratio_max', 'd1_pao2fio2ratio_min', 'h1_arterial_pco2_max', 'h1_arterial_pco2_min', 'h1_arterial_ph_max', 'h1_arterial_ph_min', 'h1_arterial_po2_max', 'h1_arterial_po2_min', 'h1_pao2fio2ratio_max', 'h1_pao2fio2ratio_min', 'apache_4a_hospital_death_prob', 'apache_4a_icu_death_prob', 'bmi', 'apache_2_diagnosis', 'apache_3j_diagnosis']] # noqa categorical_cols = [x for x in df.columns if x in ['ethnicity', 'gender', 'hospital_admit_source', 'icu_admit_source', 'icu_stay_type', 'icu_type', 'apache_3j_bodysystem', 'apache_2_bodysystem']] # noqa binary_cols = [x for x in df.columns if x in ['elective_surgery', 'readmission_status', 'apache_post_operative', 'arf_apache', 'gcs_unable_apache', 'intubated_apache', 'ventilated_apache', 'aids', 'cirrhosis', 'diabetes_mellitus', 'hepatic_failure', 'immunosuppression', 'leukemia', 'lymphoma', 'solid_tumor_with_metastasis']] # noqa target_col = [x for x in df.columns if x in ['hospital_death']] logger.info(f'Target cols: {target_col}') logger.info(f'Continuous cols: {continuous_cols}') logger.info(f'Categorical cols: {categorical_cols}') logger.info(f'Binary cols: {binary_cols}') logger.info(f'Masking columns') df = df[target_col + continuous_cols + categorical_cols + binary_cols] logger.info(f'Dataframe has these cols {list(df.columns)}') # Typify logger.info('typifying...') if 0 < len(continuous_cols): df[continuous_cols] = df[continuous_cols].astype('float32') if 0 < len(categorical_cols): df[categorical_cols] = df[categorical_cols].astype('str').astype('category') if 0 < len(binary_cols): df[binary_cols] = df[binary_cols].astype('str').astype('category') if 0 < len(target_col): df[target_col] = df[target_col].astype('str').astype('category') # Export output_filename = Path.cwd().joinpath(input_csv_filepath).stem + '.feather' df.to_feather(Path.cwd().joinpath(output_dirpath).joinpath(output_filename)) @click.command() @click.argument('input_csv_filepath', type=click.Path(exists=True), default='data/raw/training_v2.csv') @click.argument('output_dirpath', type=click.Path(exists=True), default='data/interim/') if __name__ == '__main__': log_fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s' logging.basicConfig(level=logging.INFO, format=log_fmt) # not used in this stub but often useful for finding various files project_dir = Path(__file__).resolve().parents[2] # find .env automagically by walking up directories until it's found, then # load up the .env entries as environment variables load_dotenv(find_dotenv()) main()
[ 2, 532, 9, 12, 19617, 25, 3384, 69, 12, 23, 532, 9, 12, 198, 11748, 3904, 198, 11748, 18931, 198, 6738, 3108, 8019, 1330, 10644, 198, 6738, 16605, 24330, 1330, 1064, 62, 26518, 24330, 11, 3440, 62, 26518, 24330, 198, 11748, 19798, 2...
2.238545
2,750
#!/usr/bin/python # coding: utf8 import geocoder import requests_mock location = 'New York City' coordinates = [45.3, -75.4]
[ 2, 48443, 14629, 14, 8800, 14, 29412, 198, 2, 19617, 25, 3384, 69, 23, 198, 198, 11748, 4903, 420, 12342, 198, 11748, 7007, 62, 76, 735, 198, 198, 24886, 796, 705, 3791, 1971, 2254, 6, 198, 37652, 17540, 796, 685, 2231, 13, 18, 11...
2.529412
51
def print_bst_level(root): """Prints the tree in level order.""" if root is None: return print_bst_level(root.left) print(root.data, end=' ') print_bst_level(root.right) def print_levels_bst(root): """Prints the tree in level order.""" if root is None: return q = [] q.append(root) while len(q) > 0: node = q.pop(0) print(node.data, end=' ') if node.left is not None: q.append(node.left) if node.right is not None: q.append(node.right)
[ 198, 198, 4299, 3601, 62, 65, 301, 62, 5715, 7, 15763, 2599, 198, 220, 220, 220, 37227, 18557, 82, 262, 5509, 287, 1241, 1502, 526, 15931, 198, 220, 220, 220, 611, 6808, 318, 6045, 25, 198, 220, 220, 220, 220, 220, 220, 220, 1441,...
2.017857
280
#!/usr/bin/env python """Scikit-learn trainer package setup.""" import setuptools REQUIRED_PACKAGES = [ "scikit-learn==0.20.4", "pandas==0.24.2", "pandas-gbq==0.13.2", "cloudml-hypertune", "gensim==3.8.3", ] setuptools.setup( name="hashy", version="0.1.0", install_requires=REQUIRED_PACKAGES, packages=setuptools.find_packages(), include_package_data=True, description="Hashtag Suggestions", )
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 198, 198, 37811, 50, 979, 15813, 12, 35720, 21997, 5301, 9058, 526, 15931, 198, 198, 11748, 900, 37623, 10141, 628, 198, 2200, 10917, 37819, 62, 47, 8120, 25552, 796, 685, 198, 220, 220, 22...
2.20398
201
import collections import json import logging import sys import regex as re import requests import discord log = logging.getLogger(__name__)
[ 11748, 17268, 198, 11748, 33918, 198, 11748, 18931, 198, 11748, 25064, 198, 198, 11748, 40364, 355, 302, 198, 11748, 7007, 198, 11748, 36446, 198, 198, 6404, 796, 18931, 13, 1136, 11187, 1362, 7, 834, 3672, 834, 8, 628, 628, 628, 628, ...
3.581395
43
from time import time # Implementation using a decorator # to store least recently used cache from functools import lru_cache @lru_cache(maxsize=1000) start = time() (fibonacci_with_decorator(500)) end = time() runtime = end - start # runtime=0.0009982585906982422 # explicit implementation of fibonacci function # here a dict caches/stored the already calculated values of the fibonacci function # and uses them in the next calculation that would require the fibonacci of a stored number fibonacci_cached = {} fibonacci(900) # basic implementation num1, num2 = 0, 1 for _ in range(0, 10): print(num1) num1, num2 = num2, num1 + num2 # implementation using generator for number in fibonacci(10): print(number)
[ 6738, 640, 1330, 640, 198, 2, 46333, 1262, 257, 11705, 1352, 198, 2, 284, 3650, 1551, 2904, 973, 12940, 198, 198, 6738, 1257, 310, 10141, 1330, 300, 622, 62, 23870, 628, 198, 31, 75, 622, 62, 23870, 7, 9806, 7857, 28, 12825, 8, 62...
3.10084
238
import json import os import uuid import pytest from prefect.storage import Local from viadot.flows import SupermetricsToAzureSQLv3 CWD = os.getcwd() STORAGE = Local(path=CWD) @pytest.fixture(scope="session") uuid_4 = uuid.uuid4() file_name = f"test_file_{uuid_4}.csv" adls_path = f"raw/supermetrics/{file_name}"
[ 11748, 33918, 198, 11748, 28686, 198, 11748, 334, 27112, 198, 198, 11748, 12972, 9288, 198, 6738, 662, 2309, 13, 35350, 1330, 10714, 198, 198, 6738, 25357, 324, 313, 13, 44041, 1330, 3115, 4164, 10466, 2514, 26903, 495, 17861, 85, 18, 1...
2.507813
128
__author__ = "Stephen W. O'Neill Jr. soneill5045@gmail.com" from .calculate_smoothness import calculate_smoothness
[ 198, 198, 834, 9800, 834, 796, 366, 24920, 370, 13, 440, 6, 26538, 7504, 13, 264, 505, 359, 1120, 2231, 31, 14816, 13, 785, 1, 198, 198, 6738, 764, 9948, 3129, 378, 62, 5796, 5226, 1108, 1330, 15284, 62, 5796, 5226, 1108 ]
2.785714
42
#import json import numpy as np import os try: import ujson as json except ImportError: try: import simplejson as json except ImportError: import json class NumpyEncoder(json.JSONEncoder): """ Special json encoder for numpy types Original code from: https://github.com/mpld3/mpld3/issues/434#issuecomment-340255689 Then modified by: https://stackoverflow.com/a/49677241 """ def write_to_json(dic, target_dir): """ A function that saves JSON files. """ dumped = json.dumps(dic, cls=NumpyEncoder) file = open(target_dir, 'w') json.dump(dumped, file) file.close() def read_from_json(target_dir, use_dumps=False): """ A function that reads JSON files. """ f = open(target_dir, 'r') data = json.load(f) if use_dumps is True: data = json.dumps(data) data = json.loads(data) f.close() return data
[ 2, 11748, 33918, 198, 11748, 299, 32152, 355, 45941, 198, 11748, 28686, 628, 198, 28311, 25, 198, 220, 220, 220, 1330, 334, 17752, 355, 33918, 198, 16341, 17267, 12331, 25, 198, 220, 220, 220, 1949, 25, 198, 220, 220, 220, 220, 220, ...
2.454787
376
from sqlalchemy.ext.automap import automap_base from sqlalchemy import create_engine, MetaData from ..databuddy import SqlaQueryBuilder from flask import current_app from toolspy import merge, fetch_nested_key_from_dict
[ 6738, 44161, 282, 26599, 13, 2302, 13, 2306, 296, 499, 1330, 3557, 499, 62, 8692, 198, 6738, 44161, 282, 26599, 1330, 2251, 62, 18392, 11, 30277, 6601, 198, 6738, 11485, 19608, 397, 21584, 1330, 311, 80, 5031, 20746, 32875, 198, 6738, ...
3.358209
67
from django.conf import settings # define the minimal weight of a tag in the tagcloud TAGCLOUD_MIN = getattr(settings, 'TAGGIT_TAGCLOUD_MIN', 1.0) # define the maximum weight of a tag in the tagcloud TAGCLOUD_MAX = getattr(settings, 'TAGGIT_TAGCLOUD_MAX', 6.0)
[ 6738, 42625, 14208, 13, 10414, 1330, 6460, 198, 198, 2, 8160, 262, 10926, 3463, 286, 257, 7621, 287, 262, 7621, 17721, 198, 42197, 5097, 2606, 35, 62, 23678, 796, 651, 35226, 7, 33692, 11, 705, 42197, 38, 2043, 62, 42197, 5097, 2606, ...
2.778947
95
#!/usr/bin/env python __author__ = 'Stephen P. Henrie' from interface.services.coi.iobject_management_service import BaseObjectManagementService from pyon.util.containers import is_basic_identifier from pyon.core.exception import BadRequest, NotFound from pyon.core.interfaces.interface_util import is_yaml_string_valid class ObjectManagementService(BaseObjectManagementService): """ A service for defining and managing object types used as resource, messages, etc. """ def create_object_type(self, object_type=None): """ Should receive an ObjectType object """ # Return Value # ------------ # {object_type_id: ''} # if not is_basic_identifier(object_type.name): raise BadRequest("Invalid object_type name: %s" % object_type.name) if not is_yaml_string_valid(object_type.definition): raise BadRequest("Invalid YAML definition") object_type_id, version = self.clients.resource_registry.create(object_type) return object_type_id def update_object_type(self, object_type=None): """ Should receive an ObjectType object """ # Return Value # ------------ # {success: true} # if not is_basic_identifier(object_type.name): raise BadRequest("Invalid object_type name: %s" % object_type.name) if not is_yaml_string_valid(object_type.definition): raise BadRequest("Invalid YAML definition") object_id, version = self.clients.resource_registry.update(object_type) return object_id def read_object_type(self, object_type_id=''): """ Should return an ObjectType object """ # Return Value # ------------ # object_type: {} # if not object_type_id: raise BadRequest("The resource_type_id parameter is missing") return self.clients.resource_registry.read(object_type_id) def delete_object_type(self, object_type_id=''): """method docstring """ # Return Value # ------------ # {success: true} # if not object_type_id: raise BadRequest("The object_type_id parameter is missing") return self.clients.resource_registry.delete(object_type_id)
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 198, 198, 834, 9800, 834, 796, 705, 24920, 350, 13, 6752, 5034, 6, 628, 198, 6738, 7071, 13, 30416, 13, 1073, 72, 13, 72, 15252, 62, 27604, 62, 15271, 1330, 7308, 10267, 48032, 16177, 198...
2.491435
934
# -*- coding: utf-8 -*- import datetime from south.db import db from south.v2 import SchemaMigration from django.db import models
[ 2, 532, 9, 12, 19617, 25, 3384, 69, 12, 23, 532, 9, 12, 198, 11748, 4818, 8079, 198, 6738, 5366, 13, 9945, 1330, 20613, 198, 6738, 5366, 13, 85, 17, 1330, 10011, 2611, 44, 4254, 198, 6738, 42625, 14208, 13, 9945, 1330, 4981, 198 ]
2.954545
44
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other # Spack Project Developers. See the top-level COPYRIGHT file for details. # # SPDX-License-Identifier: (Apache-2.0 OR MIT) from spack import * class Brpc(CMakePackage): """An industrial-grade RPC framework used throughout Baidu, with 1,000,000+ instances(not counting clients) and thousands kinds of services, called "baidu-rpc" inside Baidu. Only C++ implementatioo on is opensourced right now.""" homepage = "https://github.com/apache/incubator-brpc" url = "https://github.com/apache/incubator-brpc/archive/0.9.7.tar.gz" version('0.9.7', sha256='722cd342baf3b05189ca78ecf6c56ea6ffec22e62fc2938335e4e5bab545a49c') version('0.9.6', sha256='b872ca844999e0ba768acd823b409761f126590fb34cb0183da915a595161446') version('0.9.5', sha256='11ca8942242a4c542c11345b7463a4aea33a11ca33e91d9a2f64f126df8c70e9') depends_on('gflags') depends_on('protobuf') depends_on('leveldb') depends_on('openssl') patch('narrow.patch', sha256='d7393029443853ddda6c09e3d2185ac2f60920a36a8b685eb83b6b80c1535539', when='@:0.9.7')
[ 2, 15069, 2211, 12, 1238, 1828, 13914, 45036, 3549, 2351, 4765, 11, 11419, 290, 584, 198, 2, 1338, 441, 4935, 34152, 13, 4091, 262, 1353, 12, 5715, 27975, 38162, 9947, 2393, 329, 3307, 13, 198, 2, 198, 2, 30628, 55, 12, 34156, 12, ...
2.344969
487
# Copyright 2017 AT&T Intellectual Property. All other rights reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """ A logging filter to prepend request scoped formatting to all logging records that use this filter. Request-based values will cause the log records to have correlation values that can be used to better trace logs. If no handler that supports a request scope is present, does not attempt to change the logs in any way Threads initiated using threading. Thread can be correlated to the request they came from by setting a kwarg of log_extra, containing a dictionary of values matching the VALID_ADDL_FIELDS below and any fields that are set as additional_fields by the setup_logging function. This mechanism assumes that the thread will maintain the correlation values for the life of the thread. """ import logging # Import uwsgi to determine if it has been provided to the application. # Only import the UwsgiLogFilter if uwsgi is present try: import uwsgi from shipyard_airflow.control.logging.uwsgi_filter import UwsgiLogFilter except ImportError: uwsgi = None # BASE_ADDL_FIELDS are fields that will be included in the request based # logging - these fields need not be set up independently as opposed to the # additional_fields parameter used below, which allows for more fields beyond # this default set. BASE_ADDL_FIELDS = ['req_id', 'external_ctx', 'user', 'user_id'] LOG = logging.getLogger(__name__) def set_logvar(key, value): """ Attempts to set the logvar in the request scope, or ignores it if not running in an environment that supports it. """ if value: if uwsgi: uwsgi.set_logvar(key, value) # If there were a different handler than uwsgi, here is where we'd # need to set the logvar value for its use. def assign_request_filter(handler, additional_fields=None): """Adds the request-scoped filter log filter to the passed handler :param handler: a logging handler, e.g. a ConsoleHandler :param additional_fields: fields that will be included in the logging records (if a matching logging format is used) """ handler_cls = handler.__class__.__name__ if uwsgi: if additional_fields is None: additional_fields = [] addl_fields = [*BASE_ADDL_FIELDS, *additional_fields] handler.addFilter(UwsgiLogFilter(uwsgi, addl_fields)) LOG.info("UWSGI present, added UWSGI log filter to handler %s", handler_cls) # if there are other handlers that would allow for request scoped logging # to be set up, we could include those options here. else: LOG.info("No request based logging filter in the current environment. " "No log filter added to handler %s", handler_cls)
[ 2, 15069, 2177, 5161, 5, 51, 42443, 14161, 13, 220, 1439, 584, 2489, 10395, 13, 198, 2, 198, 2, 49962, 739, 262, 24843, 13789, 11, 10628, 362, 13, 15, 357, 1169, 366, 34156, 15341, 198, 2, 345, 743, 407, 779, 428, 2393, 2845, 287,...
3.267857
1,008
# # Pyserini: Reproducible IR research with sparse and dense representations # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # import argparse import json import sys # We're going to explicitly use a local installation of Pyserini (as opposed to a pip-installed one). # Comment these lines out to use a pip-installed one instead. sys.path.insert(0, './') from pyserini.search.lucene import LuceneSearcher if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument('--qrels', type=str, help='qrels file', required=True) parser.add_argument('--index', type=str, help='index location', required=True) args = parser.parse_args() searcher = LuceneSearcher(args.index) with open(args.qrels, 'r') as reader: for line in reader.readlines(): arr = line.split('\t') doc = json.loads(searcher.doc(arr[2]).raw())['contents'] print(f'{arr[2]}\t{doc}')
[ 2, 198, 2, 350, 893, 263, 5362, 25, 36551, 37369, 14826, 2267, 351, 29877, 290, 15715, 24612, 198, 2, 198, 2, 49962, 739, 262, 24843, 13789, 11, 10628, 362, 13, 15, 357, 1169, 366, 34156, 15341, 198, 2, 345, 743, 407, 779, 428, 23...
3.062099
467
"""Code snippets vol-45-snippet-223 Subprocess return code. stevepython.wordpress.com Download all snippets so far: https://wp.me/Pa5TU8-1yg """ import subprocess # Change 'notepade.exe' to some other executable if you are no using Windows. result = subprocess.run(['notepad.exe'], stdout=subprocess.DEVNULL) print(result.returncode) if not result.returncode: print('Returned from process without error') # 0 is returned to indicate no error, else error.
[ 37811, 10669, 45114, 2322, 12, 2231, 12, 16184, 3974, 316, 12, 22047, 198, 7004, 14681, 1441, 2438, 13, 198, 198, 4169, 303, 29412, 13, 40346, 13, 785, 198, 10002, 477, 45114, 523, 1290, 25, 198, 5450, 1378, 24142, 13, 1326, 14, 28875...
3.14094
149
import winograd.o6x6k3x3 import block8x8 from common import _MM_SHUFFLE for post_operation in ["store", "stream"]: arg_d_pointer = Argument(ptr(const_float_), name="d_pointer") arg_wd_pointer = Argument(ptr(float_), name="wd_pointer") arg_d_stride = Argument(size_t, name="d_stride") arg_wd_stride = Argument(size_t, name="wd_stride") arg_row_count = Argument(uint32_t, name="row_count") arg_column_count = Argument(uint32_t, name="column_count") arg_row_offset = Argument(uint32_t, name="row_offset") arg_column_offset = Argument(uint32_t, name="column_offset") with Function("nnp_iwt8x8_3x3_and_{post_operation}__avx2".format(post_operation=post_operation), (arg_d_pointer, arg_wd_pointer, arg_d_stride, arg_wd_stride, arg_row_count, arg_column_count, arg_row_offset, arg_column_offset), target=uarch.default + isa.fma3 + isa.avx2): reg_d = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_d, arg_d_pointer) reg_wd = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_wd, arg_wd_pointer) reg_stride_d = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_stride_d, arg_d_stride) reg_stride_wd = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_stride_wd, arg_wd_stride) reg_row_cnt = GeneralPurposeRegister32() LOAD.ARGUMENT(reg_row_cnt, arg_row_count) reg_col_cnt = GeneralPurposeRegister32() LOAD.ARGUMENT(reg_col_cnt, arg_column_count) reg_row_off = GeneralPurposeRegister32() LOAD.ARGUMENT(reg_row_off, arg_row_offset) reg_col_off = GeneralPurposeRegister32() LOAD.ARGUMENT(reg_col_off, arg_column_offset) ymm_data = [YMMRegister() for _ in range(8)] block8x8.load_with_padding(ymm_data, reg_d, reg_stride_d, reg_row_off, reg_row_cnt, reg_col_off, reg_col_cnt) ymm_data = winograd.o6x6k3x3.input_transform(ymm_data) winograd.o6x6k3x3.transpose8x8(ymm_data) ymm_data = winograd.o6x6k3x3.input_transform(ymm_data) VSTOREPS = {"store": VMOVAPS, "stream": VMOVNTPS}[post_operation] for ymm_row in ymm_data: VSTOREPS([reg_wd], ymm_row) if ymm_row is not ymm_data[-1]: ADD(reg_wd, reg_stride_wd) RETURN() for reverse_kernel in [False, True]: for post_operation in ["store", "stream"]: arg_g_pointer = Argument(ptr(const_float_), name="d_pointer") arg_wg_pointer = Argument(ptr(float_), name="wd_pointer") arg_g_stride = Argument(size_t, name="d_stride") arg_wg_stride = Argument(size_t, name="wd_stride") arg_row_count = Argument(uint32_t, name="row_count") arg_column_count = Argument(uint32_t, name="column_count") arg_row_offset = Argument(uint32_t, name="row_offset") arg_column_offset = Argument(uint32_t, name="column_offset") kwt_arguments = (arg_g_pointer, arg_wg_pointer, arg_g_stride, arg_wg_stride, arg_row_count, arg_column_count, arg_row_offset, arg_column_offset) with Function("nnp_kwt8x8_3{reverse}x3{reverse}_and_{post_operation}__avx2".format( reverse="R" if reverse_kernel else "", post_operation=post_operation), kwt_arguments, target=uarch.default + isa.fma3 + isa.avx2): reg_g = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_g, arg_g_pointer) reg_wg = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_wg, arg_wg_pointer) reg_stride_g = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_stride_g, arg_g_stride) reg_stride_wg = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_stride_wg, arg_wg_stride) # stride is in elements; multiply by sizeof(float) to get stride in bytes SHL(reg_stride_g, 2) xmm_load_mask = XMMRegister() VMOVAPS(xmm_load_mask.as_ymm, Constant.float32x8(-0.0, -0.0, -0.0, +0.0, +0.0, +0.0, +0.0, +0.0)) xmm_g = [XMMRegister() for _ in range(3)] for xmm in xmm_g: VMASKMOVPS(xmm, xmm_load_mask, [reg_g]) if xmm is not xmm_g[-1]: ADD(reg_g, reg_stride_g) if reverse_kernel: xmm_g = xmm_g[::-1] ymm_wg_rows = winograd.o6x6k3x3.kernel_transform([xmm.as_ymm for xmm in xmm_g], rescale_coefficients=False) ymm_g_rows = winograd.o6x6k3x3.transpose8x3([ymm.as_xmm for ymm in ymm_wg_rows]) if reverse_kernel: ymm_g_rows = ymm_g_rows[::-1] ymm_wg_rows = winograd.o6x6k3x3.kernel_transform(ymm_g_rows, rescale_coefficients=False) rcp_9 = float.fromhex("0x1.C71C72p-4") rcp_81 = float.fromhex("0x1.948B10p-7") rcp_90 = float.fromhex("0x1.6C16C2p-7") rcp_180 = float.fromhex("0x1.6C16C2p-8") rcp_810 = float.fromhex("0x1.43A274p-10") rcp_1620 = float.fromhex("0x1.43A274p-11") rcp_8100 = float.fromhex("0x1.02E85Cp-13") rcp_16200 = float.fromhex("0x1.02E85Cp-14") rcp_32400 = float.fromhex("0x1.02E85Cp-15") ymm_edge_scale = YMMRegister() VMOVAPS(ymm_edge_scale, Constant.float32x8( 1.0, -2.0 * rcp_9, -2.0 * rcp_9, rcp_90, rcp_90, rcp_180, rcp_180, 1.0)) VMULPS(ymm_wg_rows[0], ymm_wg_rows[0], ymm_edge_scale) VMULPS(ymm_wg_rows[7], ymm_wg_rows[7], ymm_edge_scale) ymm_row12_scale = YMMRegister() VMOVAPS(ymm_row12_scale, Constant.float32x8(-2.0 * rcp_9, 4.0 * rcp_81, 4.0 * rcp_81, -2.0 * rcp_810, -2.0 * rcp_810, -2.0 * rcp_1620, -2.0 * rcp_1620, -2.0 * rcp_9)) VMULPS(ymm_wg_rows[1], ymm_wg_rows[1], ymm_row12_scale) VMULPS(ymm_wg_rows[2], ymm_wg_rows[2], ymm_row12_scale) ymm_row34_scale = YMMRegister() VMOVAPS(ymm_row34_scale, Constant.float32x8( rcp_90, -2.0 * rcp_810, -2.0 * rcp_810, rcp_8100, rcp_8100, rcp_16200, rcp_16200, rcp_90)) VMULPS(ymm_wg_rows[3], ymm_wg_rows[3], ymm_row34_scale) VMULPS(ymm_wg_rows[4], ymm_wg_rows[4], ymm_row34_scale) ymm_row56_scale = YMMRegister() VMOVAPS(ymm_row56_scale, Constant.float32x8( rcp_180, -2.0 * rcp_1620, -2.0 * rcp_1620, rcp_16200, rcp_16200, rcp_32400, rcp_32400, rcp_180)) VMULPS(ymm_wg_rows[5], ymm_wg_rows[5], ymm_row56_scale) VMULPS(ymm_wg_rows[6], ymm_wg_rows[6], ymm_row56_scale) # Write output with stride VSTOREPS = {"store": VMOVAPS, "stream": VMOVNTPS}[post_operation] for ymm_wg_row in ymm_wg_rows: VSTOREPS([reg_wg], ymm_wg_row) if ymm_wg_row is not ymm_wg_rows[-1]: ADD(reg_wg, reg_stride_wg) RETURN() arg_m_pointer = Argument(ptr(const_float_), name="m_pointer") arg_s_pointer = Argument(ptr(float_), name="s_pointer") arg_bias = Argument(ptr(const_float_), name="bias_pointer") arg_m_stride = Argument(size_t, name="m_stride") arg_s_stride = Argument(size_t, name="s_stride") arg_row_count = Argument(uint32_t, name="row_count") arg_column_count = Argument(uint32_t, name="column_count") arg_row_offset = Argument(uint32_t, name="row_offset") arg_column_offset = Argument(uint32_t, name="column_offset") for with_bias in [False, True]: for with_relu in [False, True]: if with_bias: owt8x8_arguments = (arg_m_pointer, arg_s_pointer, arg_bias, arg_m_stride, arg_s_stride, arg_row_count, arg_column_count) else: owt8x8_arguments = (arg_m_pointer, arg_s_pointer, arg_m_stride, arg_s_stride, arg_row_count, arg_column_count, arg_row_offset, arg_column_offset) with Function("nnp_owt8x8_3x3{with_bias}{with_relu}__avx2".format(with_bias="_with_bias" if with_bias else "", with_relu="_with_relu" if with_relu else ""), owt8x8_arguments, target=uarch.default + isa.fma3 + isa.avx2): reg_m = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_m, arg_m_pointer) reg_s = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_s, arg_s_pointer) if with_bias: reg_bias = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_bias, arg_bias) xmm_bias = XMMRegister() VINSERTPS(xmm_bias, xmm_bias, [reg_bias], 0b1101 | 1<<4) reg_m_stride = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_m_stride, arg_m_stride) reg_s_stride = GeneralPurposeRegister64() LOAD.ARGUMENT(reg_s_stride, arg_s_stride) reg_row_count = GeneralPurposeRegister32() LOAD.ARGUMENT(reg_row_count, arg_row_count) reg_column_count = GeneralPurposeRegister32() LOAD.ARGUMENT(reg_column_count, arg_column_count) ymm_m = [YMMRegister() for _ in range(8)] for ymm in ymm_m: if with_bias and ymm is ymm_m[1]: VADDPS(ymm, xmm_bias.as_ymm, [reg_m]) else: VMOVAPS(ymm, [reg_m]) if ymm is not ymm_m[-1]: ADD(reg_m, reg_m_stride) ymm_t = winograd.o6x6k3x3.output_transform(ymm_m) ymm_tt = winograd.o6x6k3x3.transpose6x8(ymm_t) ymm_s = winograd.o6x6k3x3.output_transform(ymm_tt) block8x8.store_packed(ymm_s, reg_s, reg_s_stride, reg_row_count, reg_column_count, None, None, with_relu) RETURN()
[ 11748, 1592, 519, 6335, 13, 78, 21, 87, 21, 74, 18, 87, 18, 198, 11748, 2512, 23, 87, 23, 198, 6738, 2219, 1330, 4808, 12038, 62, 9693, 47588, 2538, 628, 198, 1640, 1281, 62, 27184, 287, 14631, 8095, 1600, 366, 5532, 1, 5974, 198,...
1.867928
5,179
#!/usr/bin/env python # instance_editor_selection.py -- Example of an instance editor # with instance selection from traits.api \ import HasStrictTraits, Int, Instance, List, Regex, Str from traitsui.api \ import View, Item, InstanceEditor people = [ Person( name = 'Dave', age = 39, phone = '555-1212' ), Person( name = 'Mike', age = 28, phone = '555-3526' ), Person( name = 'Joe', age = 34, phone = '555-6943' ), Person( name = 'Tom', age = 22, phone = '555-7586' ), Person( name = 'Dick', age = 63, phone = '555-3895' ), Person( name = 'Harry', age = 46, phone = '555-3285' ), Person( name = 'Sally', age = 43, phone = '555-8797' ), Person( name = 'Fields', age = 31, phone = '555-3547' ) ] if __name__ == '__main__': Team( name = 'Vultures', captain = people[0], roster = people ).configure_traits()
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 220, 198, 198, 2, 4554, 62, 35352, 62, 49283, 13, 9078, 1377, 17934, 286, 281, 4554, 5464, 198, 2, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, ...
2.407407
378
""" Basic mixin for MongoEngine backed data models """ import logging from typing import Dict, List, Union, no_type_check import mongoengine as me from util.deco import classproperty logger = logging.getLogger(__name__)
[ 37811, 14392, 5022, 259, 329, 42591, 13798, 9763, 1366, 4981, 37227, 198, 198, 11748, 18931, 198, 6738, 19720, 1330, 360, 713, 11, 7343, 11, 4479, 11, 645, 62, 4906, 62, 9122, 198, 198, 11748, 285, 25162, 18392, 355, 502, 198, 198, 67...
3.461538
65
#!/usr/bin/env python import logging import flask import RPi.GPIO as GPIO PIN_GREEN = 16 PIN_BLUE = 20 PIN_RED = 21 pwms = None if __name__ == '__main__': import IPython import argparse parser = argparse.ArgumentParser() parser.add_argument('color', help='Color in RGB (0-1) or (0-255). E.g. 255 255 0') args = parser.parse_args() GPIO.setmode(GPIO.BCM) setup() color(*[float(i) for i in args.color.split(' ')]) IPython.embed() GPIO.cleanup()
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 198, 11748, 18931, 198, 198, 11748, 42903, 198, 11748, 25812, 72, 13, 16960, 9399, 355, 50143, 628, 198, 44032, 62, 43016, 796, 1467, 198, 44032, 62, 9148, 8924, 796, 1160, 198, 44032, 62, ...
2.438424
203
import torch from torch.nn import functional as fn def fixed_padding(inputs: torch.Tensor, kernel_size: int, dilation: int) -> torch.Tensor: """Computes the effective kernel size given the dilation (3x3 with dilation 2 is in fact a 5x5), then computes the start and end padding (e.g. for a 5x5: |xx|c|xx| => padding=2 left and right required), lastly it expands the input by the computed amount in all directions. :param inputs: input tensor not yet padded :type inputs: torch.Tensor :param kernel_size: nominal kernel size, not accounting for dilations :type kernel_size: int :param dilation: kernel dilation :type dilation: int :return: padded input, with the same shape, except height and width :rtype: torch.Tensor """ kernel_size_effective = kernel_size + (kernel_size - 1) * (dilation - 1) pad_total = kernel_size_effective - 1 pad_beg = pad_total // 2 pad_end = pad_total - pad_beg padded_inputs = fn.pad(inputs, (pad_beg, pad_end, pad_beg, pad_end)) return padded_inputs
[ 11748, 28034, 198, 6738, 28034, 13, 20471, 1330, 10345, 355, 24714, 628, 198, 4299, 5969, 62, 39231, 7, 15414, 82, 25, 28034, 13, 51, 22854, 11, 9720, 62, 7857, 25, 493, 11, 288, 10520, 25, 493, 8, 4613, 28034, 13, 51, 22854, 25, ...
2.903581
363
# Copyright 2019 The TensorNetwork Authors # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. from __future__ import absolute_import from __future__ import division from __future__ import print_function import tensornetwork import pytest import numpy as np import tensorflow as tf import torch import jax from jax.config import config import tensornetwork.config as config_file config.update("jax_enable_x64", True) tf.compat.v1.enable_v2_behavior() np_dtypes = [np.float32, np.float64, np.complex64, np.complex128, np.int32] tf_dtypes = [tf.float32, tf.float64, tf.complex64, tf.complex128, tf.int32] torch_dtypes = [torch.float32, torch.float64, torch.int32, torch.int64] jax_dtypes = [ jax.numpy.float32, jax.numpy.float64, jax.numpy.complex64, jax.numpy.complex128, jax.numpy.int32 ] @pytest.mark.parametrize("backend, dtype", [ *list(zip(['numpy'] * len(np_dtypes), np_dtypes)), *list(zip(['tensorflow'] * len(tf_dtypes), tf_dtypes)), *list(zip(['pytorch'] * len(torch_dtypes), torch_dtypes)), *list(zip(['jax'] * len(jax_dtypes), jax_dtypes)), ])
[ 2, 15069, 13130, 383, 309, 22854, 26245, 46665, 198, 2, 198, 2, 49962, 739, 262, 24843, 13789, 11, 10628, 362, 13, 15, 357, 1169, 366, 34156, 15341, 198, 2, 345, 743, 407, 779, 428, 2393, 2845, 287, 11846, 351, 262, 13789, 13, 198, ...
2.795262
591
#!/usr/bin/env python # -*- coding: utf-8 -*- import click from pyparallel import Downloader @click.command() @click.option('--url', required=True, help='Download URL') @click.option('--conns', required=True, help='Number of parts') @click.option('--filename', required=True, help='Output filename')
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 198, 2, 532, 9, 12, 19617, 25, 3384, 69, 12, 23, 532, 9, 12, 198, 11748, 3904, 198, 198, 6738, 12972, 1845, 29363, 1330, 10472, 263, 628, 198, 31, 12976, 13, 21812, 3419, 198, 31, 12976...
3.091837
98
# Python3 # Definition for singly-linked list: # class ListNode(object): # def __init__(self, x): # self.value = x # self.next = None #
[ 2, 11361, 18, 198, 198, 2, 30396, 329, 1702, 306, 12, 25614, 1351, 25, 198, 2, 1398, 7343, 19667, 7, 15252, 2599, 198, 2, 220, 220, 825, 11593, 15003, 834, 7, 944, 11, 2124, 2599, 198, 2, 220, 220, 220, 220, 2116, 13, 8367, 796,...
2.45
60
import yaml with open("analysis_config.yml", mode="r") as fptr: analysis_config = yaml.safe_load(fptr) # Read in the variable dictionary variable_dict = analysis_config["timeseries"] # Grab a list of variables variable_list = list(variable_dict.keys()) # Add the vertical transformations to the list of variables all_variables = variable_dict all_variables.update(analysis_config["coordinate_transformations"]) # Determine which variables need to converted # TODO rename - unit_conversion_var (include units somewhere in here) variables_to_convert = {} for variable in all_variables.keys(): if all_variables[variable]["units_out"]: variables_to_convert.update({variable: all_variables[variable]})
[ 11748, 331, 43695, 198, 198, 4480, 1280, 7203, 20930, 62, 11250, 13, 88, 4029, 1600, 4235, 2625, 81, 4943, 355, 277, 20692, 25, 198, 220, 220, 220, 3781, 62, 11250, 796, 331, 43695, 13, 21230, 62, 2220, 7, 69, 20692, 8, 198, 198, ...
3.293578
218
import logging _DEBUG = True if _DEBUG: logging.basicConfig(level=logging.DEBUG, format='%(levelname)s > %(asctime)s > %(message)s [in %(filename)s at %(lineno)d]', datefmt='%Y-%m-%d %H:%M:%S') else: logging.basicConfig(level=logging.INFO, format='%(levelname)s > %(asctime)s > %(message)s', datefmt='%Y-%m-%d %H:%M:%S')
[ 11748, 18931, 198, 198, 62, 30531, 796, 6407, 198, 198, 361, 4808, 30531, 25, 198, 220, 220, 220, 18931, 13, 35487, 16934, 7, 5715, 28, 6404, 2667, 13, 30531, 11, 198, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 220, 22...
1.714859
249
""" ——————————————————————— Python3 LC20_validParentheses.py ——————————————————————— 个人备注 2020-10-10 需要再次尝试 思路完全理解,利用进出栈及字典思路解题,代码还需熟悉 ——————————————————————— 题目出处 LC#20 有效的括号 简单 https://leetcode-cn.com/problems/valid-parentheses/ NC#52 括号序列 简单 栈 字符串 https://www.nowcoder.com/practice/37548e94a270412c8b9fb85643c8ccc2 ——————————————————————— 题目描述 给定一个只包括 '(',')','{','}','[',']' 的字符串,判断字符串是否有效。 有效字符串需满足: 1.左括号必须用相同类型的右括号闭合。 2.左括号必须以正确的顺序闭合。 注意空字符串可被认为是有效字符串。 ——————————————————————— """ testCases = ['{[[[(]])]}', '{([(())])}', '', ')(', '([{}'] class Solution: """ :type string: str :rtype: bool """ if __name__ == '__main__': main()
[ 37811, 198, 30542, 8184, 4500, 960, 198, 37906, 18, 220, 198, 5639, 1238, 62, 12102, 24546, 39815, 13, 9078, 198, 30542, 8184, 4500, 960, 198, 10310, 103, 21689, 13783, 229, 37345, 101, 198, 42334, 12, 940, 12, 940, 198, 165, 250, 222...
1.192982
570
import json from schema import And, Schema, Use # This is what you would see if you uses boto3 client.receive_messages() # This is what you would see as the input event for a lambda triggered by sqs # This is what you would see as the input event for a lambda triggered by sqs # via eventbridge
[ 11748, 33918, 198, 198, 6738, 32815, 1330, 843, 11, 10011, 2611, 11, 5765, 628, 198, 2, 770, 318, 644, 345, 561, 766, 611, 345, 3544, 275, 2069, 18, 5456, 13, 260, 15164, 62, 37348, 1095, 3419, 628, 198, 2, 770, 318, 644, 345, 561...
3.682927
82
import os import numpy as np import torch from torch.utils.data import Dataset
[ 11748, 28686, 198, 11748, 299, 32152, 355, 45941, 198, 198, 11748, 28034, 198, 6738, 28034, 13, 26791, 13, 7890, 1330, 16092, 292, 316, 628 ]
3.375
24
import json from decimal import Decimal from django.conf import settings from django.core.urlresolvers import reverse import commonware.log from rest_framework import response, serializers from tower import ungettext as ngettext import mkt from drf_compound_fields.fields import ListField from mkt.api.fields import (ESTranslationSerializerField, LargeTextField, ReverseChoiceField, SemiSerializerMethodField, TranslationSerializerField) from mkt.constants.applications import DEVICE_TYPES from mkt.constants.categories import CATEGORY_CHOICES from mkt.constants.features import FeatureProfile from mkt.constants.payments import PROVIDER_BANGO from mkt.prices.models import AddonPremium, Price from mkt.search.serializers import BaseESSerializer, es_to_datetime from mkt.site.helpers import absolutify from mkt.submit.forms import mark_for_rereview from mkt.submit.serializers import PreviewSerializer, SimplePreviewSerializer from mkt.tags.models import attach_tags from mkt.translations.utils import no_translation from mkt.versions.models import Version from mkt.webapps.models import (AddonUpsell, AppFeatures, Geodata, Preview, Webapp) from mkt.webapps.utils import dehydrate_content_rating log = commonware.log.getLogger('z.api') class ESAppFeedSerializer(BaseESAppFeedSerializer): """ App serializer targetted towards the Feed, Fireplace's homepage. Specifically for Feed Apps/Brands that feature the whole app tile and an install button rather than just an icon. """ class ESAppFeedCollectionSerializer(BaseESAppFeedSerializer): """ App serializer targetted towards the Feed, Fireplace's homepage. Specifically for Feed Apps, Collections, Shelves that only need app icons. """ class SimpleAppSerializer(AppSerializer): """ App serializer with fewer fields (and fewer db queries as a result). Used as a base for FireplaceAppSerializer and CollectionAppSerializer. """ previews = SimplePreviewSerializer(many=True, required=False, source='all_previews') class RocketbarESAppSerializer(serializers.Serializer): """Used by Firefox OS's Rocketbar apps viewer.""" name = ESTranslationSerializerField() @property class RocketbarESAppSerializerV2(AppSerializer, RocketbarESAppSerializer): """ Replaced `icon` key with `icons` for various pixel sizes: 128, 64, 48, 32. """
[ 11748, 33918, 198, 6738, 32465, 1330, 4280, 4402, 198, 198, 6738, 42625, 14208, 13, 10414, 1330, 6460, 198, 6738, 42625, 14208, 13, 7295, 13, 6371, 411, 349, 690, 1330, 9575, 198, 198, 11748, 2219, 1574, 13, 6404, 198, 6738, 1334, 62, ...
3.033939
825
from drf_yasg.utils import swagger_auto_schema from core.docs import dict_response_schema, param, list_response_schema shipping_items_response = { "uuid": "45563485-ca00-43e7-b573-7890fd4c3822", "tracking_number": "20220309-0003066198", "sku": "1234", "status": "CREATED", "shipping_batches_history": [ { "alias": "20220309-CqaaCZx", "completed": True, "shipping_transport__uuid": "ef7d79b3-5267-4f02-acde-593844fb02a0", "shipping_transport__distribution_center_code_source": "AFK", "shipping_transport__distribution_center_code_destination": "S01" }, { "alias": "20220309-xWK", "completed": False, "shipping_transport__uuid": None, "shipping_transport__distribution_center_code_source": None, "shipping_transport__distribution_center_code_destination": None } ], "current_distribution_center_code": "S01", "timestamp_created": "2022-03-01T22:03:00+09:00", "timestamp_completed": None } shipping_batch_response = { "uuid": "5dd9b051-9c42-417e-9287-71751b9442b2", "alias": "20220309-xWK", "completed": False, "shipping_transport": None, "timestamp_created": None, "timestamp_completed": None } shipping_transport_response = { "uuid": "ef7d79b3-5267-4f02-acde-593844fb02a0", "completed": False, "batch_count": 2, "distribution_center_source": { "uuid": "48574f05-a29e-4735-a817-839b228c3e82", "center_code": "AFK", "name": "AFK", "staff_names": "" }, "distribution_center_destination": None, "driver": None, "timestamp_created": "2022-03-09T22:20:15.418651+09:00", "timestamp_departed": "2022-03-12T16:15:35.224593+09:00", "timestamp_arrived": "2022-03-12T16:24:32.355557+09:00" } doc_transport_batches = swagger_auto_schema( operation_id='transport_batches', operation_description= 'Description: \n' ' - list batches in transport \n' ' - \n\n' 'Params: \n' '- ordering: timestamp_created, timestamp_completed\n' '- completed: 1, 0\n\n' 'Permission: ' ' - IsStaff | HasAPIKey\n\n' 'Link: <link for extra information>', operation_summary="list batches in transport", manual_parameters=[ param('ordering', 'timestamp_created, timestamp_completed, -timestamp_created, -timestamp_completed'), param('completed', '1, 0') ], tags=["shipping"], responses={ 200: dict_response_schema( list_response_schema( shipping_batch_response ) ), } ) doc_batch_items = swagger_auto_schema( operation_id='batch_items', operation_description= 'Description: \n' ' - list shipping items in a batch \n' ' - \n\n' 'Params: \n' '- status: \n' '- ordering: timestamp_created, timestamp_completed\n\n' 'Permission: ' ' - IsStaff | HasAPIKey\n\n' 'Link: <link for extra information>', operation_summary="list shipping items in a batch \n", manual_parameters=[ param('status', 'CREATED, MOVING, COMPLETED, DAMAGED, LOST'), param('completed', '1, 0') ], tags=["shipping"], responses={ 200: dict_response_schema( list_response_schema( shipping_items_response ) ) } )
[ 6738, 1553, 69, 62, 88, 292, 70, 13, 26791, 1330, 1509, 7928, 62, 23736, 62, 15952, 2611, 198, 6738, 4755, 13, 31628, 1330, 8633, 62, 26209, 62, 15952, 2611, 11, 5772, 11, 1351, 62, 26209, 62, 15952, 2611, 628, 198, 1477, 4501, 62, ...
2.156511
1,559
# Import the relevant libraries # Data manipulation import pandas as pd import numpy as np # Save files import pickle # Machine Learning models from xgboost import XGBClassifier from sklearn.experimental import enable_halving_search_cv from sklearn.model_selection import HalvingGridSearchCV # import x_train = pd.read_csv('data/x_train.csv') y_train = pd.read_csv('data/y_train.csv') columns_selected = ['Gender', 'Age', 'Region_Code', 'Previously_Insured', 'Vehicle_Damage', 'Annual_Premium', 'Policy_Sales_Channel', 'age_class', 'Vehicle_Age_0', 'Vehicle_Age_1', 'Vehicle_Age_2'] x_train_fs = x_train[columns_selected] # Model xgb_tuning = XGBClassifier(random_state=42) # Parameters parameters = { 'n_estimators': [300, 400, 500], 'eta': [0.5], 'max_depth': [10], 'subsample': [0.9], 'colsample_bytree': [0.6] } # Fit xgb_tuning = HalvingGridSearchCV(xgb_tuning, parameters, verbose=1, n_jobs=1, cv=3, scoring='roc_auc') xgb_tuning.fit(x_train_fs, y_train.values) print(xgb_tuning.best_params_)
[ 2, 17267, 262, 5981, 12782, 198, 2, 6060, 17512, 198, 11748, 19798, 292, 355, 279, 67, 198, 11748, 299, 32152, 355, 45941, 198, 198, 2, 12793, 3696, 198, 11748, 2298, 293, 198, 198, 2, 10850, 18252, 4981, 198, 6738, 2124, 70, 39521, ...
1.904011
698
# Push an element to stack # Pop an element from stack 1 and push it to stack two. if __name__ == '__main': stack = Stack() stack.push(3) stack.push(1) stack.push(6) stack.push(10) stack.pop() print(stack.display())
[ 198, 220, 220, 220, 220, 198, 220, 220, 220, 1303, 23691, 281, 5002, 284, 8931, 628, 220, 220, 220, 1303, 8099, 281, 5002, 422, 8931, 352, 290, 4574, 340, 284, 8931, 734, 13, 628, 198, 361, 11593, 3672, 834, 6624, 705, 834, 12417, ...
2.304348
115
# Copyright 2017 Rodrigo Pinheiro Marques de Araujo <fenrrir@gmail.com> # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation the # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell # copies of the Software, and to permit persons to whom the Software is furnished # to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included in all # copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, # EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS # OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN # AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH # THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. import abc import codecs import six @six.add_metaclass(abc.ABCMeta) @six.add_metaclass(abc.ABCMeta)
[ 2, 15069, 2177, 46198, 13727, 258, 7058, 1526, 13281, 390, 30574, 84, 7639, 1279, 41037, 21062, 343, 31, 14816, 13, 785, 29, 198, 2, 198, 2, 2448, 3411, 318, 29376, 7520, 11, 1479, 286, 3877, 11, 284, 597, 1048, 16727, 257, 198, 2, ...
3.638235
340
#!/usr/bin/env python # Licensed to Cloudera, Inc. under one # or more contributor license agreements. See the NOTICE file # distributed with this work for additional information # regarding copyright ownership. Cloudera, Inc. licenses this file # to you under the Apache License, Version 2.0 (the # "License"); you may not use this file except in compliance # with the License. You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. from __future__ import print_function import sys import threading from django.conf import settings from django.core.management.base import BaseCommand from django.test.signals import template_rendered from django_nose.runner import NoseTestSuiteRunner, translate_option from mako import runtime from mako.template import Template __all__ = ['HueTestRunner'] # Capturing the mako context is not thread safe, so we wrap rendering in a mutex. _MAKO_LOCK = threading.RLock() def _instrumented_test_render(self, *args, **data): """ An instrumented Template render method, providing a signal that can be intercepted by the test system Client """ with _MAKO_LOCK: if hasattr(self, 'original_callable_'): self.original_callable_.append(self.callable_) else: self.original_callable_ = [self.callable_] self.callable_ = mako_callable_ try: response = runtime._render(self, self.original_callable_[-1], args, data) finally: self.callable_ = self.original_callable_.pop() return response
[ 2, 48443, 14629, 14, 8800, 14, 24330, 21015, 198, 2, 49962, 284, 1012, 280, 1082, 64, 11, 3457, 13, 739, 530, 198, 2, 393, 517, 18920, 5964, 11704, 13, 220, 4091, 262, 28536, 2393, 198, 2, 9387, 351, 428, 670, 329, 3224, 1321, 198...
3.372477
545
# -*- coding: utf-8 -*- import os os_env = os.environ class ProdConfig(Config): """Production configuration. - aligned to openshift """ ENV = 'prod' DEBUG = False DEBUG_TB_ENABLED = False # Disable Debug toolbar class DevConfig(Config): """Development configuration.""" ENV = 'dev' DEBUG = True # Put the db file in project root #DB_NAME = 'dev.db' #DB_PATH = os.path.join(Config.PROJECT_ROOT, DB_NAME) #SQLALCHEMY_DATABASE_URI = 'sqlite:///{0}'.format(DB_PATH) DEBUG_TB_ENABLED = True ASSETS_DEBUG = True # Don't bundle/minify static assets CACHE_TYPE = 'simple' # Can be "memcached", "redis", etc.
[ 2, 532, 9, 12, 19617, 25, 3384, 69, 12, 23, 532, 9, 12, 198, 11748, 28686, 198, 198, 418, 62, 24330, 796, 28686, 13, 268, 2268, 628, 198, 4871, 1041, 67, 16934, 7, 16934, 2599, 198, 220, 220, 220, 37227, 35027, 8398, 13, 532, 22...
2.492537
268
import aspose.slides as slides
[ 11748, 355, 3455, 13, 6649, 1460, 355, 19392 ]
3.75
8
# -*- coding: utf-8 -*- """ :copyright: Copyright 2016-2020 Sphinx Confluence Builder Contributors (AUTHORS) :license: BSD-2-Clause (LICENSE) """ from collections import namedtuple from sphinxcontrib.confluencebuilder.translator import ConfluenceBaseTranslator from tests.lib import prepareConfiguration from tests.lib import prepareDirectories from tests.lib import prepareSphinx import os import unittest Reporter = namedtuple('Reporter', 'warning')
[ 2, 532, 9, 12, 19617, 25, 3384, 69, 12, 23, 532, 9, 12, 198, 37811, 198, 25, 22163, 4766, 25, 15069, 1584, 12, 42334, 45368, 28413, 7326, 23079, 35869, 25767, 669, 357, 32, 24318, 20673, 8, 198, 25, 43085, 25, 347, 10305, 12, 17, ...
3.413534
133
#pragma out import dylink_portability dylink_portability.run_unrestricted_repy_code("testchunklib_bigchunk_multisockets.py")
[ 2, 1050, 363, 2611, 503, 198, 11748, 288, 2645, 676, 62, 634, 1799, 198, 30360, 676, 62, 634, 1799, 13, 5143, 62, 403, 49343, 62, 7856, 88, 62, 8189, 7203, 9288, 354, 2954, 8019, 62, 14261, 354, 2954, 62, 16680, 271, 11603, 13, 90...
2.717391
46
# -*- coding: utf-8 -*- # Copyright (c) 2021 The Project GNOME Pomodoro Tracking Authors import os import argparse import configparser import sys from datetime import datetime, timedelta import logging import gnome_pomodoro_tracking.utils as utils
[ 2, 532, 9, 12, 19617, 25, 3384, 69, 12, 23, 532, 9, 12, 198, 2, 15069, 357, 66, 8, 33448, 383, 4935, 40339, 25505, 375, 16522, 37169, 46665, 198, 11748, 28686, 198, 11748, 1822, 29572, 198, 11748, 4566, 48610, 198, 11748, 25064, 198...
3.444444
72
import datetime import pytest import aiomysql.cursors BOB = {'name': 'bob', 'age': 21, 'DOB': datetime.datetime(1990, 2, 6, 23, 4, 56)} JIM = {'name': 'jim', 'age': 56, 'DOB': datetime.datetime(1955, 5, 9, 13, 12, 45)} FRED = {'name': 'fred', 'age': 100, 'DOB': datetime.datetime(1911, 9, 12, 1, 1, 1)} CURSOR_TYPE = aiomysql.cursors.DictCursor @pytest.mark.run_loop @pytest.mark.run_loop @pytest.mark.run_loop
[ 11748, 4818, 8079, 198, 198, 11748, 12972, 9288, 198, 198, 11748, 257, 29005, 893, 13976, 13, 66, 1834, 669, 628, 198, 8202, 33, 796, 1391, 6, 3672, 10354, 705, 65, 672, 3256, 705, 496, 10354, 2310, 11, 198, 220, 220, 220, 220, 220,...
2.050691
217
import pytest import sqlalchemy as sa from sqlalchemy_utils.observer import observes @pytest.fixture @pytest.fixture @pytest.fixture @pytest.fixture @pytest.fixture @pytest.fixture @pytest.mark.usefixtures('postgresql_dsn')
[ 11748, 12972, 9288, 198, 11748, 44161, 282, 26599, 355, 473, 198, 198, 6738, 44161, 282, 26599, 62, 26791, 13, 672, 15388, 1330, 34526, 628, 198, 31, 9078, 9288, 13, 69, 9602, 628, 198, 31, 9078, 9288, 13, 69, 9602, 628, 198, 31, 90...
2.626374
91
#!c:\users\patrick\documents\github\ojomebeta\ojomebeta\scripts\python.exe from django.core import management if __name__ == "__main__": management.execute_from_command_line()
[ 2, 0, 66, 7479, 18417, 59, 29615, 59, 15390, 2886, 59, 12567, 59, 13210, 462, 31361, 59, 13210, 462, 31361, 59, 46521, 59, 29412, 13, 13499, 198, 6738, 42625, 14208, 13, 7295, 1330, 4542, 198, 198, 361, 11593, 3672, 834, 6624, 366, ...
2.967213
61
# [LICENSE] # Copyright (c) 2020, Alliance for Sustainable Energy. # All rights reserved. # # Redistribution and use in source and binary forms, # with or without modification, are permitted provided # that the following conditions are met: # # 1. Redistributions of source code must retain the above # copyright notice, this list of conditions and the # following disclaimer. # # 2. Redistributions in binary form must reproduce the # above copyright notice, this list of conditions and the # following disclaimer in the documentation and/or other # materials provided with the distribution. # # 3. Neither the name of the copyright holder nor the # names of its contributors may be used to endorse or # promote products derived from this software without # specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND # CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF # MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR # CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, # BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR # SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) # HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE # OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS # SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # [/LICENSE] import pytest @pytest.fixture(scope="session",autouse=True)
[ 2, 685, 43, 2149, 24290, 60, 198, 2, 15069, 357, 66, 8, 12131, 11, 10302, 329, 45276, 6682, 13, 198, 2, 1439, 2489, 10395, 13, 198, 2, 220, 198, 2, 2297, 396, 3890, 290, 779, 287, 2723, 290, 13934, 5107, 11, 220, 198, 2, 351, ...
3.366
500
import numpy as np import argparse from utils import data_utils from utils import ml_utils import pickle if __name__ == "__main__": main()
[ 11748, 299, 32152, 355, 45941, 198, 11748, 1822, 29572, 198, 198, 6738, 3384, 4487, 1330, 1366, 62, 26791, 198, 6738, 3384, 4487, 1330, 25962, 62, 26791, 198, 11748, 2298, 293, 628, 628, 198, 198, 361, 11593, 3672, 834, 6624, 366, 834, ...
2.921569
51
# Generated by Django 3.0.7 on 2020-06-18 18:57 from django.db import migrations, models
[ 2, 2980, 515, 416, 37770, 513, 13, 15, 13, 22, 319, 12131, 12, 3312, 12, 1507, 1248, 25, 3553, 198, 198, 6738, 42625, 14208, 13, 9945, 1330, 15720, 602, 11, 4981, 628 ]
2.84375
32
from pymol import cmd from pymol import util from luna.wrappers.cgo_arrow import cgo_arrow from luna.util.exceptions import PymolSessionNotInitialized, IllegalArgumentError from luna.util.default_values import PYMOL_INTERACTION_COLOR, INTERACTION_SHORT_NAMES from luna.util.file import get_filename, get_file_format from Bio.Data.SCOPData import protein_letters_3to1 import logging logger = logging.getLogger() NUCLEOPHILE_INTERS = ["Orthogonal multipolar", "Parallel multipolar", "Antiparallel multipolar", "Tilted multipolar", "Multipolar", "Cation-nucleophile", "Unfavorable anion-nucleophile", "Unfavorable nucleophile-nucleophile"] ELECTROPHILE_INTERS = ["Orthogonal multipolar", "Parallel multipolar", "Antiparallel multipolar", "Tilted multipolar", "Multipolar", "Anion-electrophile", "Unfavorable cation-electrophile", "Unfavorable electrophile-electrophile"] UNFAVORABLE_INTERS = ["Repulsive", "Unfavorable anion-nucleophile", "Unfavorable cation-electrophile", "Unfavorable nucleophile-nucleophile", "Unfavorable electrophile-electrophile"] class PymolWrapper: """This class provides functions to provide easy access to common functions from Pymol.""" def get_cmd(self): """Expose the Pymol ``cmd`` object, so that one can call Pymol functions directly.""" return cmd def load(self, input_file, obj_name=None): """Load a molecular file (e.g., PDB files). Parameters ---------- input_file : str The pathname of the molecular file to be loaded. obj_name : str, optional Pymol object to store the loaded structure. If not provided, the filename will be used instead. """ self.input_file = input_file if not obj_name: obj_name = get_filename(input_file) cmd.load(input_file, obj_name) def show(self, tuples): """Display atom and bond representations for certain selections. Parameters ---------- tuples : iterable of tuple Each tuple should contain a Pymol representation (e.g., 'sticks') and a selection (e.g., 'hetatm'). """ for representation, selection in tuples: cmd.show(representation, selection) def hide(self, tuples): """Hide atom and bond representations for certain selections. Parameters ---------- tuples : iterable of tuple Each tuple should contain a Pymol representation (e.g., 'sticks') and a selection (e.g., 'hetatm'). """ for representation, selection in tuples: cmd.hide(representation, selection) def hide_all(self): """Hide all representations.""" self.hide([('everything', '')]) def center(self, selection): """Translate the window, the clipping slab, and the origin to a point centered within the selection.""" cmd.center(selection) def label(self, tuples): """Draw text labels for PyMOL objects. Parameters ---------- tuples : iterable of tuple Each tuple should contain a selection (e.g., 'hetatm') and some string to label the given selection. """ for selection, expression in tuples: cmd.label(selection, expression) def add_pseudoatom(self, name, opts=None): """Create a molecular object with a pseudoatom or add a pseudoatom to a molecular object if the specified object already exists. Parameters ---------- name : str The object name to create or modify. opts : dict A set of options to create the pseudoatom. Check `Pymol <https://pymolwiki.org/index.php/Pseudoatom>`_ to discover which options are available. """ opts = opts or {} cmd.pseudoatom(name, **opts) def select(self, selection, name="sele", enable=0): """Create a named selection from an atom selection. Parameters ---------- selection : str The expression to select atoms. name : str The selection name, which by default is 'sele'. enable : {0, 1} If ``1``, activate the selection, i.e., show selection indicators. The default value is 0, which implies the selection indicators won't be shown. """ cmd.select(name, selection, enable=enable) def get_names(self, obj_type): """Get names of objects, grouped objects, or selections. Parameters ---------- obj_type : {'objects', 'selections', 'all', 'public_objects', 'public_selections', 'public_nongroup_objects', 'public_group_objects', 'nongroup_objects', 'group_objects'} The target object type. Returns ------- : list of str """ return cmd.get_names(obj_type) def sel_exists(self, name): """Check if a selection exists given by its name ``name``.""" return name in cmd.get_names("selections") def obj_exists(self, name): """Check if an object exists given by its name ``name``.""" return name in cmd.get_names("objects") def group_exists(self, name): """Check if a group of objects exists given by its name ``name``.""" return name in cmd.get_names("group_objects") def get_coords(self, selection): """Get atomic coordinates for a given atom selection. Parameters ---------- selection : str The expression to select atoms. Returns ------- : array_like of float (size 3) Atomic coordinates (x, y, z) of each atom selected. """ return cmd.get_coords(selection) def distance(self, name, sel1, sel2): """Create a new distance object between two atoms given by their selection-expressions. Parameters ---------- name : str Name of the distance object to create. sel1 : str The expression to select the first atom. sel2 : str The expression to select the second atom. """ cmd.distance(name, sel1, sel2) def arrow(self, name, atm_sel1, atm_sel2, opts=None): """Draw an arrow object between two atoms given by their selection-expressions. Parameters ---------- name : str Name of the arrow object to create. sel1 : str The expression to select the first atom. sel2 : str The expression to select the second atom. opts : dict A set of options to create the arrow. Check `Pymol <https://pymolwiki.org/index.php/Cgo_arrow>`_ to discover which options are available. """ opts = opts or {} cgo_arrow(atm_sel1, atm_sel2, name=name, **opts) def save_png(self, output_file, width=1200, height=1200, dpi=100, ray=1): """Save the current Pymol session as a PNG format image file. Parameters ---------- output_file : str The output image pathname. width : int The width in pixels. The default value is 1,200. height : int or str The height in pixels. The default value is 1,200. dpi : float Dots-per-inch. The default value is 100. ray : {0, 1} If ``1`` (the default), run ray first to make high-resolution photos. """ cmd.png(output_file, width, height, dpi, ray) def save_session(self, output_file): """Save the current PyMOL state to a PSE format file to later use. Parameters ---------- output_file : str The output pathname. """ if get_file_format(output_file) != 'pse': output_file += '.pse' cmd.save(output_file) def color(self, tuples): """Color objects and atoms. Parameters ---------- tuples : iterable of tuple Each tuple should contain a color (e.g., 'red') and a selection (e.g., 'hetatm'). """ for color, selection in tuples: cmd.color(color, selection) def color_by_element(self, selections, c_color="green"): """Color atoms by their default element color (e.g., oxygen in red). Parameters ---------- selections : iterable of str A sequence of selections to define which atoms will be colored by element. c_color : {'green', 'cyan', 'light magenta', 'yellow', 'salmon', 'white', 'slate', 'bright orange', 'purple', 'pink'} The carbon color. The default value is 'green'. """ valid_colors = ['green', 'cyan', 'light magenta', 'yellow', 'salmon', 'white', 'slate', 'bright orange', 'purple', 'pink'] if c_color.lower() not in valid_colors: raise IllegalArgumentError("Invalid color '%s'. The accepted colors are: %s." % (c_color, ", ".join(valid_colors))) c_color = c_color.lower() for selection in selections: if c_color == 'green': util.cbag(selection) elif c_color == 'cyan': util.cbac(selection) elif c_color == 'light magenta': util.cbam(selection) elif c_color == 'yellow': util.cbay(selection) elif c_color == 'salmon': util.cbas(selection) elif c_color == 'white': util.cbaw(selection) elif c_color == 'slate': util.cbab(selection) elif c_color == 'bright orange': util.cbao(selection) elif c_color == 'purple': util.cbap(selection) elif c_color == 'pink': util.cbak(selection) def group(self, name, members, action=None): """Create or update a group object. Parameters ---------- name : str The group name to create or update. members : iterable of str The objects to include in the group. action : {'add', 'remove', 'open', 'close', 'toggle', 'auto', 'empty', 'purge', 'excise'}, optional An action to take. If not provided, the default value 'auto' will be used instead. The description of the actions are described below (source: Pymol documentation): * add: add members to group. * remove: remove members from group (members will be ungrouped). * empty: remove all members from group. * purge: remove all members from group and delete them. * excise: remove all members from group and delete group. * open: expand group display in object menu panel. * close: collapse group display in object menu panel. * toggle: toggle group display in object menu panel. * auto: add or toggle. """ for member in members: if action: cmd.group(name, member, action) else: cmd.group(name, member) def create(self, name, selection): """Create a new molecular object from a selection. Note that the selected atoms won't be extracted from the original object. Instead, a copy of them will be created in the new object. Parameters ---------- name : str The object name to be created. selection : str The expression to select atoms. """ cmd.create(name, selection) def alter(self, selection, expression): """Modify atomic properties. Parameters ---------- selection : str The expression to select atoms. expression : str Expression in Python language to define which properties should be modified. This can be used, for instance, to rename an atom or chain. Examples -------- Alter the name of a ligand carbon from 'C1' to 'CA'. >>> pw_obj.alter("hetatm and name C1", "name='CA'") Alter the chain A name to 'Z'. >>> pw_obj.alter("chain A", "chain='Z'") """ cmd.alter(selection, expression) def set(self, name, value, opts=None): """Modify global, object, object-state, or per-atom settings. Parameters ---------- name : str The setting name to modify. value : str The new setting value. opts : dict A set of options. Check `Pymol <https://pymolwiki.org/index.php/Pseudoatom>`_ to discover which options are available. """ opts = opts or {} cmd.set(name, value, **opts) def align(self, mobile, target, opts=None): """Align the structure ``mobile`` to the ``target`` structure. Parameters ---------- mobile : str The structure to be aligned given by an atomic selection. target : str The target structure given by an atomic selection. opts : dict Alignment options. Check `Pymol <https://pymolwiki.org/index.php/Align>`_ to discover which options are available. """ opts = opts or {} cmd.align(mobile, target, **opts) def delete(self, selections): """Delete the provided selections. Parameters ---------- selections : iterable of str A sequence of selections to be deleted. Wildcards can be used to define object or selection names. """ for selection in selections: cmd.delete(selection) def remove(self, selections): """Remove a selection of atoms from models. Parameters ---------- selections : iterable of str A sequence of selections to define which atoms will be removed. """ for selection in selections: cmd.remove(selection) def extract(self, tuples): """Perform multiple extractions, i.e., extract atoms from an object to another object. Parameters ---------- tuples : iterable of tuple Each tuple should contain the object name to where atoms will be added and the selection itself that defines which atoms will be extracted (e.g., 'hetatm'). """ for name, selection in tuples: cmd.extract(name, selection) def load_mol_from_pdb_block(self, pdb_block, obj_name): """Load a molecular file from a PDB block string. Parameters ---------- pdb_block :str The PDB block string. obj_name : str Pymol object to store the loaded structure. """ cmd.read_pdbstr(pdb_block, obj_name, state=1) def reinitialize(self): """Clear all objects and resets all parameters to default.""" cmd.reinitialize('everything') self.input_file = None def quit(self): """Terminate Pymol.""" cmd.quit() def run(self, func_name, opts): """Run a Pymol command ``func_name`` with parameters ``opts``. Parameters ---------- func_name : str The Pymol command name. opts : dict Parameters to pass to the command. """ return getattr(cmd, func_name)(**opts) def run_cmds(self, commands): """Run a set of Pymol commands. Parameters ---------- commands : iterable of tuple Each tuple should contain a Pymol command and its parameters. See :meth:`run` to more details. """ for func_name, opts in commands: getattr(cmd, func_name)(**opts) class PymolSessionManager: """Class to start, manage, and save Pymol sessions. This class provides useful built-in functions to load PDB/Mol files and show interactions. .. note:: This class is not intended to be used directly because :meth:`set_view` is not implemented by default. Instead, you should use a class that inherits from `PymolSessionManager` and implements :meth:`set_view`. An example is the class :class:`~luna.interaction.view.InteractionViewer` that implements a custom :meth:`set_view` to show interactions. Therefore, you should define your own logic beyond :meth:`set_view` to save a Pymol session that meets your goals. Parameters ---------- show_cartoon : bool If True, show the protein structure as cartoons. bg_color : str The background color. The default value is "white". Check `Pymol <https://pymolwiki.org/index.php/Color_Values>`_ to discover which colors are available. add_directional_arrows : bool If True, show arrows for directional interactions (e.g., hydrogen bonds and multipolar interactions). show_res_labels : bool If True (the default), show residue labels. inter_color : :class:`~luna.util.ColorPallete` A Pymol-compatible color scheme for interactions. The default value is :const:`~luna.util.default_values.PYMOL_INTERACTION_COLOR`. pse_export_version : str Define a legacy format for saving Pymol sessions (PSE files). The default value os '1.8'. """ def new_session(self, data, output_file): """Start a new session, which includes the following steps: * Start a new Pymol session (:meth:`start_session`); * Set the view (:meth:`set_view`); * Save the Pymol session to ``output_file``; * Finish the Pymol session. Parameters ---------- data : iterable Data to be processed by :meth:`set_view`. output_file : str The pathname to where the Pymol session will be saved. """ self.start_session() self.set_view(data) self.save_session(output_file) self.finish_session() def start_session(self): """Start a new session and set Pymol settings, including the background color and the PSE export version. """ self.wrapper = PymolWrapper() self.wrapper.set("pse_export_version", self.pse_export_version) self.wrapper.set("transparency_mode", 3) self.wrapper.set("group_auto_mode", 2) self.wrapper.run_cmds([("bg_color", {"color": self.bg_color})]) self.wrapper.set("internal_gui_width", 370) def set_view(self, data): """Set the session view. However, this method is not implemented by default. Instead, you should use a class that inherits from `PymolSessionManager` and implements :meth:`set_view`. An example is the class :class:`~luna.interaction.view.InteractionViewer` that implements a custom :meth:`set_view` to show interactions. Therefore, you should define your own logic beyond :meth:`set_view` to save a Pymol session that meets your goals. Parameters ---------- data : iterable The data that will be used to set the Pymol view. """ raise NotImplementedError("Use a class that implements this method.") def load_pdb(self, pdb_file, pdb_obj, mol_block=None, is_ftmap_output=False): """Load molecules from PDB files to the current Pymol session. Optionally, ligands can also be loaded from a separate molecular string block. This is especially useful when working with docked molecules in which the protein structure is in a PDB file and ligands are in a separate molecular file. Parameters ---------- pdb_file : str The pathname of the PDB file to be loaded. pdb_obj : str Pymol object to store the loaded structure. mol_block : str, optional A molecular string block to load together with the PDB file. is_ftmap_output : bool If the PDB file is an FTMap output. If so, an additional processing step is performed to standardize the loaded Pymol objects. """ prot_obj = "%s.prot" % pdb_obj self.wrapper.load(pdb_file, prot_obj) if is_ftmap_output: objs = self.wrapper.get_names("objects") to_merge = [] for obj in objs: if obj == "protein": to_merge.append(obj) sel = "protein and not resn %s" % " and not resn ".join(protein_letters_3to1.keys()) self.wrapper.alter(sel, "type='HETATM'") elif obj.endswith(".pdb"): to_merge.append(obj) self.wrapper.alter(obj, "type='HETATM'") self.wrapper.create(prot_obj, " | ".join(to_merge)) self.wrapper.delete(objs) self.wrapper.extract([("%s.hets" % pdb_obj, "hetatm and %s" % prot_obj)]) if mol_block is not None: self.wrapper.load_mol_from_pdb_block(mol_block, "%s.hets" % pdb_obj) self.wrapper.color_by_element([pdb_obj]) self.wrapper.hide([("everything", pdb_obj)]) if self.show_cartoon: self.wrapper.show([("cartoon", pdb_obj)]) def set_interactions_view(self, interactions, main_grp, secondary_grp=None): """Display molecular interactions. Parameters ---------- interactions : iterable of :class:`~luna.interaction.type.InteractionType` A sequence of interactions to show. main_grp : str Main Pymol object to store atom groups. secondary_grp : str, optional Secondary Pymol object to store interactions. If not provided, ``main_grp`` will be used instead. """ residue_selections = set() secondary_grp = secondary_grp or main_grp for i, inter in enumerate(interactions): # # Centroid 1 # obj1_name = "%s.centroids.%s" % (main_grp, hash(tuple(sorted(inter.src_interacting_atms)))) centroid_obj1 = inter.src_centroid centroid_obj1_visible = True # Define the centroid in a nucleophile with two atoms as the position of its more electronegative atom. # Remember that the position in the interaction object matters. We have defined that the first group is always # the nucleophile for both dipole-dipole and ion-dipole interactions. if inter.type in NUCLEOPHILE_INTERS and len(inter.src_grp.atoms) == 2: dipole_atm = inter.src_grp.atoms[0] if (inter.src_grp.atoms[0].electronegativity > inter.src_grp.atoms[1].electronegativity) else inter.src_grp.atoms[1] obj1_name += "_%s" % hash(dipole_atm.name) centroid_obj1 = dipole_atm.coord centroid_obj1_visible = False # For unfavorable multipolar interactions, it may happen that the first atom group is an electrophile as well. elif inter.type == "Unfavorable electrophile-electrophile" and len(inter.src_grp.atoms) == 2: dipole_atm = inter.src_grp.atoms[0] if (inter.src_grp.atoms[0].electronegativity < inter.src_grp.atoms[1].electronegativity) else inter.src_grp.atoms[1] obj1_name += "_%s" % hash(dipole_atm.name) centroid_obj1 = dipole_atm.coord centroid_obj1_visible = False # # Centroid 2 # obj2_name = "%s.centroids.%s" % (main_grp, hash(tuple(sorted(inter.trgt_interacting_atms)))) centroid_obj2 = inter.trgt_centroid centroid_obj2_visible = True # Define the centroid in an electrophile with two atoms as the position of its less electronegative atom. # Remember that the position in the interaction object matters. We have defined that the second group is always # the electrophile for both dipole-dipole and ion-dipole interactions. if inter.type in ELECTROPHILE_INTERS and len(inter.trgt_grp.atoms) == 2: dipole_atm = inter.trgt_grp.atoms[0] if (inter.trgt_grp.atoms[0].electronegativity < inter.trgt_grp.atoms[1].electronegativity) else inter.trgt_grp.atoms[1] obj2_name += "_%s" % hash(dipole_atm.name) centroid_obj2 = dipole_atm.coord centroid_obj2_visible = False # For unfavorable multipolar interactions, it may happen that the second atom group is a nucleophile as well. elif inter.type == "Unfavorable nucleophile-nucleophile" and len(inter.trgt_grp.atoms) == 2: dipole_atm = inter.trgt_grp.atoms[0] if (inter.trgt_grp.atoms[0].electronegativity > inter.trgt_grp.atoms[1].electronegativity) else inter.trgt_grp.atoms[1] obj2_name += "_%s" % hash(dipole_atm.name) centroid_obj2 = dipole_atm.coord centroid_obj2_visible = False # Add pseudoatoms if not self.wrapper.obj_exists(obj1_name): self.wrapper.add_pseudoatom(obj1_name, {"vdw": 1, "pos": list(centroid_obj1)}) if not self.wrapper.obj_exists(obj2_name): self.wrapper.add_pseudoatom(obj2_name, {"vdw": 1, "pos": list(centroid_obj2)}) # Set the representation for each compound in the groups involved in the interaction. for compound in inter.src_grp.compounds.union(inter.trgt_grp.compounds): if compound.is_water(): comp_repr = "sphere" elif compound.is_hetatm(): if len(compound.child_list) == 1 or len([atm for atm in compound.child_list if atm.element != "H"]) == 1: comp_repr = "sphere" else: comp_repr = "sticks" else: comp_repr = "sticks" comp_sel = "%s and %s" % (main_grp, mybio_to_pymol_selection(compound)) self.wrapper.show([(comp_repr, comp_sel)]) carb_color = "green" if compound.is_target() else "gray" self.wrapper.color([(carb_color, comp_sel + " AND elem C")]) if compound.is_residue(): residue_selections.add(comp_sel) # Show residue label if required. if self.show_res_labels: self.wrapper.label([("%s AND name CA" % comp_sel, '"%s-%s" % (resn, resi)')]) # Check if the interaction involves the same compound: intramolecular interactions. inter_grp = "intra" if inter.is_intramol_interaction() else "inter" src_grp_name = "+".join(["%s-%s-%d%s" % (c.parent.id, c.resname, c.id[1], c.id[2].strip()) for c in sorted(inter.src_grp.compounds)]) trgt_grp_name = "+".join(["%s-%s-%d%s" % (c.parent.id, c.resname, c.id[1], c.id[2].strip()) for c in sorted(inter.trgt_grp.compounds)]) inter_name = "%s.all_inters.%s.%s.i%d_%s_and_%s.line" % (secondary_grp, inter_grp, INTERACTION_SHORT_NAMES[inter.type], i, src_grp_name, trgt_grp_name) self.wrapper.distance(inter_name, obj1_name, obj2_name) self.wrapper.hide([("label", inter_name)]) # Set styles to the interactions. self.wrapper.color([(self.inter_color.get_color(inter.type), inter_name)]) if self.add_directional_arrows: if inter.type in UNFAVORABLE_INTERS: arrow_name1 = "%s.all_inters.%s.%s.inter%d.arrow1" % (secondary_grp, inter_grp, INTERACTION_SHORT_NAMES[inter.type], i) arrow_name2 = "%s.all_inters.%s.%s.inter%d.arrow2" % (secondary_grp, inter_grp, INTERACTION_SHORT_NAMES[inter.type], i) square_name = "%s.all_inters.%s.%s.inter%d.block" % (secondary_grp, inter_grp, INTERACTION_SHORT_NAMES[inter.type], i) arrow_opts = {"radius": 0.03, "gap": 0.9, "hlength": 0.5, "hradius": 0.2, "color": self.inter_color.get_color(inter.type)} square_opts = {"radius": 0.3, "gap": 1.5, "hlength": 0, "hradius": 0, "color": self.inter_color.get_color(inter.type)} # Two arrows in different directions self.wrapper.arrow(arrow_name1, obj1_name, obj2_name, arrow_opts) if not inter.is_directional(): self.wrapper.arrow(arrow_name2, obj2_name, obj1_name, arrow_opts) # Add a square-like object self.wrapper.arrow(square_name, obj1_name, obj2_name, square_opts) # Add arrows over the interaction lines to represent directional interactions elif inter.is_directional(): arrow_name = "%s.all_inters.%s.%s.inter%d.arrow" % (secondary_grp, inter_grp, INTERACTION_SHORT_NAMES[inter.type], i) arrow_opts = {"radius": 0.03, "gap": 0.9, "hlength": 0.5, "hradius": 0.2, "color": self.inter_color.get_color(inter.type)} self.wrapper.arrow(arrow_name, obj1_name, obj2_name, arrow_opts) # If a group object contains more than one atom. if inter.src_grp.size > 1 and centroid_obj1_visible: # Add the centroids to the group "centroids" and append them to the main group self._set_centroid_style(obj1_name) # Otherwise, just remove the centroid as it will not add any new information (the atom represented # by the centroid is already the atom itself). else: self.wrapper.delete([obj1_name]) # If a group object contains more than one atom. if inter.trgt_grp.size > 1 and centroid_obj2_visible: # Add the centroids to the group "centroids" and append them to the main group self._set_centroid_style(obj2_name) # Otherwise, just remove the centroid as it will not add any new information (the atom represented # by the centroid is already been displayed). else: self.wrapper.delete([obj2_name]) return residue_selections def set_last_details_to_view(self): """This method can be called to apply final modifications to the Pymol session. In its default version, the following modifications are applied: * Dash radius for interactions is set to 0.08; * Labels are set to bold and their size is set to 20; * Atomic spheres' scale is set to 0.3; * Hydrogen atoms are hidden; * The view is centered within the visible objects. """ self.wrapper.set("dash_radius", 0.08) self.wrapper.set("label_font_id", "13") self.wrapper.set("label_size", "20") self.wrapper.set("sphere_scale", "0.3", {"selection": "visible and not name PS*"}) self.wrapper.hide([("everything", "elem H+D")]) self.wrapper.center("visible") def save_session(self, output_file): """Save the Pymol session as a PSE file of name ``output_file``.""" if not isinstance(self.wrapper, PymolWrapper): raise PymolSessionNotInitialized("No session was initialized.") self.wrapper.save_session(output_file) def finish_session(self): """Clear all objects and resets all parameters to default.""" if not isinstance(self.wrapper, PymolWrapper): raise PymolSessionNotInitialized("No session was initialized.") self.wrapper.reinitialize() self.wrapper = None def mybio_to_pymol_selection(entity): """Transform an :class:`~luna.MyBio.PDB.Entity.Entity` instance into a Pymol selection-expression, which can then be used to select atoms in a Pymol session. Parameters ---------- entity : :class:`~luna.MyBio.PDB.Entity.Entity` An entity to be transformed into a Pymol selection-expression. Returns ------- : str The Pymol selection-expression. Examples -------- First, let's parse a PDB file to work with. >>> from luna.util.default_values import LUNA_PATH >>> from luna.MyBio.PDB.PDBParser import PDBParser >>> pdb_parser = PDBParser(PERMISSIVE=True, QUIET=True) >>> structure = pdb_parser.get_structure("Protein", f"{LUNA_PATH}/tutorial/inputs/3QQK.pdb") Now, let's get the Pymol selection-expression for the chain A. >>> from luna.wrappers.pymol import mybio_to_pymol_selection >>> print(mybio_to_pymol_selection(structure[0]['A'])) chain A Finally, we can get the Pymol selection-expression for the ligand X02. >>> from luna.wrappers.pymol import mybio_to_pymol_selection >>> print(mybio_to_pymol_selection(structure[0]["A"][('H_X02', 497, ' ')])) resn X02 AND res 497 AND chain A """ params = {} if entity.level == 'S' or entity.level == 'M': params[''] = 'all' elif entity.level == 'C': params['chain'] = entity.id elif entity.level == 'R': params['resn'] = entity.resname params['res'] = str(entity.id[1]) + entity.id[2].strip() params['chain'] = entity.get_parent().id elif entity.level == 'A': residue = entity.get_parent() params['id'] = entity.serial_number params['name'] = entity.name params['resn'] = residue.resname params['res'] = str(residue.id[1]) + residue.id[2].strip() params['chain'] = residue.get_parent().id else: return {} if "resn" in params: # Escape characters that can generate problems with Pymol params['resn'] = params['resn'].replace("+", "\\+") params['resn'] = params['resn'].replace("-", "\\-") return (' AND ').join(['%s %s' % (k, str(v)) for k, v in params.items()])
[ 6738, 279, 4948, 349, 1330, 23991, 198, 6738, 279, 4948, 349, 1330, 7736, 628, 198, 6738, 300, 9613, 13, 29988, 11799, 13, 66, 2188, 62, 6018, 1330, 269, 2188, 62, 6018, 198, 6738, 300, 9613, 13, 22602, 13, 1069, 11755, 1330, 350, 4...
2.274031
15,137
import os import sib_api_v3_sdk from sib_api_v3_sdk.rest import ApiException from uuid import UUID from app.api.models.namespaces import NamespacePrimaryKeyTransferEmailInfo, NamespacePrimaryKeyEmailInfo, NamespaceSchemaProjectNameEmailInfo from app.api.models.projects import ProjectPrimaryKeyName configuration = sib_api_v3_sdk.Configuration() configuration.api_key['api-key'] = os.getenv("SENDINBLUE_API_KEY") api_instance = sib_api_v3_sdk.TransactionalEmailsApi(sib_api_v3_sdk.ApiClient(configuration))
[ 11748, 28686, 198, 11748, 264, 571, 62, 15042, 62, 85, 18, 62, 21282, 74, 198, 6738, 264, 571, 62, 15042, 62, 85, 18, 62, 21282, 74, 13, 2118, 1330, 5949, 72, 16922, 198, 6738, 334, 27112, 1330, 471, 27586, 198, 198, 6738, 598, 13...
2.870787
178
"""Control local mopidy.""" import requests import json class MopidyError(Exception): """Mopidy control error.""" def mopidy_is_playing(): """Check if currently playing.""" json_data = { "method": "core.playback.get_state", "jsonrpc": "2.0", "prams": {}, "id": 1, } payload = json.dumps(json_data) try: ret = requests.post( "http://127.0.0.1:6680/mopidy/rpc", headers={"Content-Type": "application/json"}, data=payload, ) except requests.exceptions.ConnectionError: raise MopidyError("request failed") except Exception: raise MopidyError("unknown error") if ret.status_code != 200: raise MopidyError("request failed") return ret.json()["result"] == "playing" def mopidy_pause(): """Play.""" json_data = { "method": "core.playback.pause", "jsonrpc": "2.0", "prams": {}, "id": 1, } payload = json.dumps(json_data) try: ret = requests.post( "http://127.0.0.1:6680/mopidy/rpc", headers={"Content-Type": "application/json"}, data=payload, ) except requests.exceptions.ConnectionError: raise MopidyError("request failed") except Exception: raise MopidyError("unknown error") if ret.status_code != 200: raise MopidyError("request failed") def mopidy_play(): """Play.""" json_data = { "method": "core.playback.play", "jsonrpc": "2.0", "prams": {"tl_track": None, "tlid": None}, "id": 1, } payload = json.dumps(json_data) try: ret = requests.post( "http://127.0.0.1:6680/mopidy/rpc", headers={"Content-Type": "application/json"}, data=payload, ) except requests.exceptions.ConnectionError: raise MopidyError("request failed") except Exception: raise MopidyError("unknown error") if ret.status_code != 200: raise MopidyError("request failed")
[ 37811, 15988, 1957, 285, 404, 19325, 526, 15931, 198, 198, 11748, 7007, 198, 11748, 33918, 628, 198, 4871, 337, 404, 19325, 12331, 7, 16922, 2599, 198, 220, 220, 220, 37227, 44, 404, 19325, 1630, 4049, 526, 15931, 628, 198, 4299, 285, ...
2.166667
960
import unittest from redblacktree.redblacktree import Node, RedBlackTree, RED, BLACK if __name__ == '__main__': unittest.main()
[ 11748, 555, 715, 395, 198, 6738, 2266, 13424, 21048, 13, 445, 13424, 21048, 1330, 19081, 11, 2297, 9915, 27660, 11, 23848, 11, 31963, 628, 198, 198, 361, 11593, 3672, 834, 6624, 705, 834, 12417, 834, 10354, 198, 220, 220, 220, 555, 71...
2.87234
47
import os, sys, platform __SUPPORT_ANSI__ = False
[ 11748, 28686, 11, 25064, 11, 3859, 198, 198, 834, 40331, 15490, 62, 1565, 11584, 834, 796, 10352, 198, 220, 220, 220, 220, 220, 220, 220, 220, 198 ]
2.222222
27
# (C) 2012, Michael DeHaan, <michael.dehaan@gmail.com> # (c) 2017 Ansible Project # GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt) from __future__ import (absolute_import, division, print_function) __metaclass__ = type DOCUMENTATION = ''' callback: context_demo type: aggregate short_description: demo callback that adds play/task context description: - Displays some play and task context along with normal output - This is mostly for demo purposes version_added: "2.1" requirements: - whitelist in configuration ''' from ansible.plugins.callback import CallbackBase class CallbackModule(CallbackBase): """ This is a very trivial example of how any callback function can get at play and task objects. play will be 'None' for runner invocations, and task will be None for 'setup' invocations. """ CALLBACK_VERSION = 2.0 CALLBACK_TYPE = 'aggregate' CALLBACK_NAME = 'context_demo' CALLBACK_NEEDS_WHITELIST = True
[ 2, 357, 34, 8, 2321, 11, 3899, 1024, 23303, 272, 11, 1279, 76, 40302, 13, 2934, 3099, 272, 31, 14816, 13, 785, 29, 198, 2, 357, 66, 8, 2177, 28038, 856, 4935, 198, 2, 22961, 3611, 5094, 13789, 410, 18, 13, 15, 10, 357, 3826, 2...
2.979827
347
from django.conf.urls import url from rest_framework import routers from talentmap_api.common.urls import get_retrieve, post_create from talentmap_api.feature_flags.views import featureflags as views router = routers.SimpleRouter() urlpatterns = [ url(r'^$', views.FeatureFlagsView.as_view({**get_retrieve, 'post': 'perform_create'}), name='featureflags'), ] urlpatterns += router.urls
[ 6738, 42625, 14208, 13, 10414, 13, 6371, 82, 1330, 19016, 198, 6738, 1334, 62, 30604, 1330, 41144, 198, 6738, 7401, 8899, 62, 15042, 13, 11321, 13, 6371, 82, 1330, 651, 62, 1186, 30227, 11, 1281, 62, 17953, 198, 198, 6738, 7401, 8899,...
3.086614
127
# Generated from JSON.g4 by ANTLR 4.7.2 # encoding: utf-8 from antlr4 import * from io import StringIO from typing.io import TextIO import sys
[ 2, 2980, 515, 422, 19449, 13, 70, 19, 416, 3537, 14990, 49, 604, 13, 22, 13, 17, 198, 2, 21004, 25, 3384, 69, 12, 23, 198, 6738, 1885, 14050, 19, 1330, 1635, 198, 6738, 33245, 1330, 10903, 9399, 198, 6738, 19720, 13, 952, 1330, ...
2.830189
53
#new home for the weaponry lists, they shouldn't be in the core file #hopefully in 1.4 the entire purpose of this file dissolves and these lists go away. #
[ 2, 3605, 1363, 329, 262, 28479, 8341, 11, 484, 6584, 470, 307, 287, 262, 4755, 2393, 198, 2, 8548, 7549, 287, 352, 13, 19, 262, 2104, 4007, 286, 428, 2393, 6249, 9010, 290, 777, 8341, 467, 1497, 13, 198, 198, 2, 628 ]
3.761905
42
profile1 = { "name": "testing", "codeforces": "aaradhya0707", "codechef": "aaradhya0707", "atcoder": "aaradhya0707", "uva_handle": "aaradhya0707", "spoj": "aaradhya777", "uva_id": "1143870" } profile2 = { "name": "testinguser", "codeforces": "shivamsinghal1012", "codechef": "shivam1012" }
[ 13317, 16, 796, 1391, 198, 220, 220, 220, 366, 3672, 1298, 366, 33407, 1600, 198, 220, 220, 220, 366, 19815, 891, 273, 728, 1298, 366, 64, 283, 24411, 3972, 15, 24038, 1600, 198, 220, 220, 220, 366, 19815, 721, 258, 69, 1298, 366, ...
1.913295
173
[n,m] = list(map(int,input().split())) ai = list(map(int,input().split())) aux = [[]for i in range(m)] dp = [aux for i in range(n)] #def grundy(): for i in range(n): for j in range(m):
[ 58, 77, 11, 76, 60, 796, 1351, 7, 8899, 7, 600, 11, 15414, 22446, 35312, 3419, 4008, 198, 198, 1872, 796, 1351, 7, 8899, 7, 600, 11, 15414, 22446, 35312, 3419, 4008, 198, 198, 14644, 796, 16410, 60, 1640, 1312, 287, 2837, 7, 76, ...
2.136842
95
# Importing the Kratos Library import KratosMultiphysics import KratosMultiphysics.FluidDynamicsApplication as KratosFluid ## Import base class file from KratosMultiphysics.FluidDynamicsApplication.fluid_solver import FluidSolver from KratosMultiphysics.FluidDynamicsApplication import check_and_prepare_model_process_fluid
[ 2, 17267, 278, 262, 509, 10366, 418, 10074, 198, 11748, 509, 10366, 418, 15205, 13323, 23154, 198, 11748, 509, 10366, 418, 15205, 13323, 23154, 13, 37, 2290, 312, 35, 4989, 873, 23416, 355, 509, 10366, 418, 37, 2290, 312, 198, 198, 22...
3.125
104