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import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import seaborn as sns
import pandas as pd
import numpy as np
import os
import math
import scipy.optimize as opt
from scipy.optimize import curve_fit
def __sst(y_no_fitting):
"""
计算SST(total sum of squar... |
from __future__ import division
from yolov3.models import *
from utils.utils import *
from utils.datasets import *
from utils.parse_config import *
from my_models import Network, define_yolo, init_yolo
import os
import time
import datetime
import argparse
import tqdm
import numpy as np
import matplotlib.pyplot as plt... |
import random
from dataclasses import dataclass
from enum import IntEnum
from defaultlist import defaultlist
from PIL import Image, ImageDraw
with open('input.txt') as f:
inp = [int(x) for x in f.read().split(',')]
class Colors(IntEnum):
BLACK = 0
WHITE = 1
class Direction(IntEnum):
LEFT = 0
... |
from abc import ABC, abstractmethod
from copy import deepcopy
B_TAG_PREFIX = 'b-'
I_TAG_PREFIX = 'i-'
SCOPE_ATTRIB_SEP = '-'
LEVEL_ATTRIB_SEP = '_'
SIMPLE_TAG_ATTRIB_NAME = 'tag'
def merge_token_tag(
merged_structured_document, merged_token,
other_structured_document, other_token,
source_sc... |
from typing import TYPE_CHECKING
import graphene_django_optimizer as gql_optimizer
from django.db.models import Sum
from graphql import GraphQLError
from graphql_relay import from_global_id
from ...order import OrderStatus
from ...product import models
from ...search.backends import picker
from ..core.enums import Or... |
# Copyright 2018 RethinkDB
#
# 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, so... |
# _*_ coding: utf-8 _*_
import wda
import numpy as np
import cv2
import webbrowser
from urllib import parse
import requests
import datetime
import time
def cvBytes_to_numpyNdarray(imgBytes):
# cutBytesImg = np.ndarray.tobytes(cutImg)
img = np.asarray(bytearray(imgBytes), np.uint8)
img = cv2.imdecode(img,... |
# Copyright 2017 The TensorFlow Authors. All 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 applica... |
# Copyright (c) Microsoft Corporation.
# Licensed under the MIT license.
"""
FILE: sample_satellite_download.py
DESCRIPTION:
This sample demonstrates:
- Creating a Farmer and a Boundary
- Queuing a satellite data ingestion job, and waiting for its completion
- Dowloading the data synchronously/sequent... |
# -*- coding: utf-8 -*-
"""
Methods to generate geospatial points to sample data.
@author: <NAME> <<EMAIL>>
"""
import numpy as np
import geopandas as gpd
from numba import njit
from shapely.geometry import Point, Polygon, MultiPolygon
from shapely.errors import TopologicalError
from typing import Optional, Union
fr... |
"""mkdocs-categories-plugin
An MkDocs plugin allowing for categorization of pages in your wiki.
"""
import logging
import re
import shutil
import unicodedata
from logging import Logger, getLogger
from pathlib import Path
from mkdocs.config import config_options
from mkdocs.plugins import BasePlugin
from mkdocs.struc... |
# Copyright (c) 2016 <NAME>
# =======================================================================
# Distributed under the MIT License.
# (See accompanying file LICENSE or copy at
# http://opensource.org/licenses/MIT)
"""extract the groups from the iddfile"""
from __future__ import absolute_import
from __future_... |
import click
import os
import elasticsearch
import sys
import csv
import re
import sh
import json
import importlib_resources
from dotenv import load_dotenv, find_dotenv
from loguru import logger
from datetime import datetime
from dateutil import tz
from profanity_power_index.collect_tweets import collect_tweets
from ... |
import torch
from torch import nn
# from original centernet paper
def neg_loss(pred, gt):
''' Modified focal loss. Exactly the same as CornerNet.
Runs faster and costs a little bit more memory
Arguments:
pred (batch x c x h x w)
gt_regr (batch x c x h x w)
'''
pred = pred.unsqueeze(1)... |
##Text extractor.
##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 OTH... |
import torch
import math
def Diou_loss(preds, bbox, eps=1e-7, reduction='mean'):
'''
preds:[[x1,y1,x2,y2], [x1,y1,x2,y2],,,]
bbox:[[x1,y1,x2,y2], [x1,y1,x2,y2],,,]
eps: eps to avoid divide 0
reduction: mean or sum
return: diou-loss
'''
ix1 = torch.max(preds[:, 0], bbox[:, 0])... |
#
# Copyright (c) 2019, Neptune Labs Sp. z o.o.
#
# 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 agr... |
import sys
import numpy as np
import os
import logging
import torch
import torch.nn as nn
import torch.nn.functional as F
import torchvision
from absl import app, flags
from easydict import EasyDict
import resnet.models.resnet as resnet
from cleverhans.future.torch.attacks import fast_gradient_method, projected_gradi... |
#encoding: UTF-8
# Copyright (C) 2016 <NAME>
# This file is distributed under the terms of the # MIT License.
# See the file `License' in the root directory of the present distribution.
"""
A collection of wrappers for the *matplotlib* functions.
.. Note::
All functions return a *matplotlib* which can be modified... |
# -*- coding: utf-8 -*-
"""
Created on Sun Mar 1 18:17:35 2020
@author: yadav
"""
import argparse
import math
import time
import os
import io
import nntools
import torch
import torch.nn as nn
from models import LSTNetAttConvDirect
import numpy as np;
import importlib
import matplotlib.pyplot as plt
from plot_uti... |
#coding=utf-8
from functools import reduce
from werkzeug.security import generate_password_hash, check_password_hash
__author__ = 'archer'
from flask import current_app
from flask_sqlalchemy import BaseQuery
from itsdangerous import JSONWebSignatureSerializer
from . import db, login_manager
from flask_login im... |
"""
python contact_details.py 'Municipal contact detail - 28 April 2016.xlsx' 'muni.csv' 'persons.csv'
python -m pdb muni_contacts.py 'Municipal contact detail - 28 April 2016.xlsx' 'muni.csv' 'persons.csv'
"""
import csv
import string
import sys
import xlrd
from urllib.parse import urlparse
expected_headings = [
... |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from math import pi
from compas.utilities import pairwise
from compas.geometry import angle_vectors
from compas.geometry import is_ccw_xy
__all__ = [
'network_find_cycles',
]
PI2 = 2.0 * pi
def netwo... |
print('EXERCITIUL 1')
# 1.Take two int values from user and print greatest among them
def greatest_num(a,b):
if a>b:
print(a, "is the greatest value")
elif b>a:
print(b, "is the greatest value")
else:
print("the two numbers are equal")
a = int(input("da primul numar: "))
b = int(inp... |
#!/usr/bin/env python
import os
import re
import pygal
import json
import requests
from bson import json_util
import logging
from pymongo import MongoClient
from datetime import datetime
from datetime import timedelta
logging.basicConfig(filename='{0}weather.log'.format(os.environ['OPENSHIFT_PYTHON_LOG_DIR']),
... |
import matplotlib.pyplot as plt
import numpy as np
import math
from shapely import geometry
import os
# TODO : write to file in xppaut style rather than like this.. or open weak coupling solution
c = ['#511845', '#900c3f', '#c70039', '#ff5733']
s = ['-', '--']
flatten = lambda t: [item for sublist in contour1.collec... |
from typing import List
from typing import Union
from lexer import Token
from parseTree import *
class SFunction:
'''Subduce function
'''
def __init__(self, scopeStack: 'ScopeStack', func: Union[function, FunctionDefinition]):
self.func = func
class SList:
'''Subduce list
'''
def __ini... |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# ----------------------------------------------------------------------
# Copyright 2017-2019 Airinnova AB and the PyTornado authors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# Y... |
'''可以被 TensorFlow，MXNet，PyTorch 同时使用
'''
import time
from IPython import display
import numpy as np
from matplotlib import pyplot as plt
plt.rcParams['font.sans-serif'] = ['SimHei'] # 用来正常显示中文标签
plt.rcParams['axes.unicode_minus'] = False # 用来正常显示负号
def use_svg_display():
"""Use the svg format to display a pl... |
import pandas as pd
import numpy as np
import scipy.stats as ss
import statsmodels.api as sm
import matplotlib.pyplot as plt
from tkinter.filedialog import askopenfilename, asksaveasfilename
import re
import multiprocessing as mp
from labtools.plot import plot_calibration_line
import random
global data
data = {}
de... |
import os.path
import sys
from warnings import warn
try:
_console = sys._jy_console
_reader = _console.reader
except AttributeError:
raise ImportError("Cannot access JLine2 setup")
try:
# jarjar-ed version
from org.python.jline.console.history import MemoryHistory
except ImportError:
# dev ver... |
import pageattributes
import htmlhandler
import random
import yarachecker
import scoringchecker
from yarachecker import rulesInterpretation
supportedAlgorithms = ('static heuristics', 'scoring mechanism', 'yara rules')
class UnsupportedCheckingAlgorithmException(Exception):
pass
class YaraRulesPathNotSetExcepti... |
'''
DNS-related code
'''
import time
import logging
import urllib
import ipaddress
import cachetools
import aiohttp
import aiodns
from . import stats
from . import config
from . import memory
LOGGER = logging.getLogger(__name__)
async def prefetch(url, resolver):
with stats.coroutine_state('DNS prefetch'):
... |
# Copyright (c) Microsoft Corporation.
# Licensed under the MIT license.
"""
Input：raw files of T_Rex dataset
output："T_REx_example.json"
example：
{'docid': 'Q3343462',
'token': ['Nora','Zaïdi','(','Nora','Mebrak','-','Zaïdi','),','born','on','July','6',',','1965','in','Bethoncourt','(','French','département','of',
... |
import numpy as np
import pytest
from simple_neural_network.evolution import Evolution
# init random number generator
rg = np.random.default_rng()
params = Evolution.allowed_hyperparameters
def test_init_obj():
generations, pop_size = 5, 10
evo = Evolution(generations=generations, population_size=pop_size)... |
# -*- coding: utf-8 -*-
"""
Functions for fetching annotations (from the internet, if necessary)
"""
from collections import defaultdict
from pathlib import Path
import re
import shutil
from nilearn.datasets.utils import _fetch_file
from neuromaps.datasets.utils import (get_data_dir, get_dataset_info,
... |
'''
Created on 2013-11-27
@author: Nich
'''
from collections import defaultdict
from Systems.NetworkMessageSystem import NetworkMessage
from description.description import ObjectDescriber
import description.description_planner as dp
from pynlg.lexicon import XMLLexicon
import os
def walk_tree_bf(starting_node):
... |
import re
import os
import pandas as pd
import numpy as np
import gc
import nltk
#nltk.download('stopwords')
#nltk.download('punkt')
from nltk.corpus import stopwords
from nltk.stem import PorterStemmer
from nltk.tokenize import sent_tokenize, word_tokenize
from mpids.utils.PandasUtils import get_pandas_version
D... |
#!/usr/bin/env python
# cardinal_pythonlib/sqlalchemy/insert_on_duplicate.py
"""
===============================================================================
Original code copyright (C) 2009-2021 <NAME> (<EMAIL>).
This file is part of cardinal_pythonlib.
Licensed under the Apache License, Version 2.0... |
from enum import Enum
import json
import logging_util
import requests
# reference beepscore Remy / TVService.swift
# https://github.com/beepscore/Remy/blob/master/Remy/TVService.swift
# instantiate at module level, not class level
# https://stackoverflow.com/questions/22807972/python-best-practice-in-terms-of-logging... |
import numpy as np
import pandas as pd
import argparse
import math
import csv
from collections import OrderedDict
def get_args():
parser = argparse.ArgumentParser(description='Call peaks over CRISPRi screen windows.')
parser.add_argument('guide_data',help='Input flow-fish guide count data.')
parser.add... |
import os
from datetime import datetime, timedelta
import pytz
from flask import current_app, url_for
from sqlalchemy import func
from notifications_utils.template import SMSMessageTemplate, WithSubjectTemplate, get_html_email_body
local_timezone = pytz.timezone(os.getenv("TIMEZONE", "America/Toronto"))
def pagina... |
import re
import torch
import torch.nn as nn
def decompose_bnn_lstm(encoder):
state_dict = encoder.state_dict()
input_size = encoder.input_size
hidden_size = encoder.hidden_size
num_layer = encoder.num_layers
bidirectional = encoder.bidirectional
model_list = []
for layer_index in ran... |
import multiprocessing
import datetime
import time
import websocket
from pprint import pprint
import loghandler
import configparser
import csv
import sys
import cbpro
from google.protobuf.json_format import MessageToDict
from pymongo import MongoClient
logger = loghandler.LogHandler().create_logger("sidebyside")
co... |
import traceback
from abc import ABC
from copy import deepcopy
from itertools import chain
from inspect import getmembers, isroutine
from functools import wraps
import pyarrow as pa
def feature(pyarrow_type=None, is_helper=False, exceptions=None, **type_args):
exceptions = exceptions or tuple()
exceptions = ... |
#!/usr/bin/env python
#
# Copyright (c) 2016, The OpenThread Authors.
# 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
# notic... |
#####################################################################
#
# wavegen.py
#
# Copyright (c) 2015, <NAME>
#
# Released under the MIT License (http://opensource.org/licenses/MIT)
#
#####################################################################
import numpy as np
import wave
from audio import *
# now,... |
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# --------------------------------------------------------------------... |
# Tencent is pleased to support the open source community by making GNES available.
#
# Copyright (C) 2019 THL A29 Limited, a Tencent company. All 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... |
"""
### **Data Stores**
You will need to store artifacts and intermediate results. You cannot
simply write these artifacts to the local filesystem, because each
command runs in a container with its own filesystem that disappears
when the container exits. And, in cloud mode, containers run on different
machines, so ther... |
# -----------------------------------
# import
# -----------------------------------
from .basebox import Box
from heifpy.file import BinaryFileReader
# -----------------------------------
# define
# -----------------------------------
# -----------------------------------
# function
# -----------------... |
import numpy as np
import os
import torch
import matplotlib.pyplot as plt
import matplotlib.colors as mcolors
def plot_training_loss(minibatch_losses, num_epochs, averaging_iterations=100, custom_label=''):
iter_per_epoch = len(minibatch_losses) // num_epochs
plt.figure()
ax1 = plt.subplot(1, 1, 1)
... |
import warnings
from sqlalchemy import Column, Table, exc
from sqlalchemy.orm import column_property
from sqlalchemy.orm.interfaces import AttributeExtension
from sqlalchemy.sql.expression import Alias
from sqlalchemy.sql import expression
from sqlalchemy.ext.compiler import compiles
from sqlalchemy.dialects.postgresq... |
# -*- coding:utf8 -*-
"""Backlog v2 API
"""
import re
import os
import shutil
import requests
import yaml
from urllib import unquote
import time
class Api(object):
"""docstring for BacklogApi"""
def __init__(self, space_id, api_key=None):
self.space_id = space_id
self.api_key = api_key
... |
import pickle
import math
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
from tqdm.notebook import tqdm
import scipy
import sklearn
sns.set(color_codes=True)
import torch
import torch.nn as nn
from torch.utils.data import Dataset, DataLoader, Subset
import torch.optim as... |
from typing import List
import pandas as pd
import panel as pn
import param
import plotly.express as px
import plotly.graph_objects as go
import tensorflow_model_analysis as tfma
from zenml.core.pipelines.training_pipeline import TrainingPipeline
from zenml.core.repo.repo import Repository
from zenml.utils.enums impo... |
###############################################################################
# WaterTAP Copyright (c) 2021, The Regents of the University of California,
# through Lawrence Berkeley National Laboratory, Oak Ridge National
# Laboratory, National Renewable Energy Laboratory, and National Energy
# Technology Laboratory ... |
from sklearn.model_selection import train_test_split
from imutils import face_utils
import matplotlib.pyplot as plt
import numpy as np
import cv2
import dlib
def facial_landmark(image):
detector = dlib.get_frontal_face_detector()
predictor = dlib.shape_predictor("shape_predictor_68_face_landmarks.dat")
r... |
import itertools
import re
from copy import deepcopy
from rangeslicetools import *
groupsRx = re.compile(r"([bl])(\d+)")
inf = float("inf")
def isPowerOf2(n: int):
return not (n & (n - 1))
class Level:
__slots__ = ("size", "big")
def __init__(self, size: int, big: bool):
self.size = size
self.big = big
... |
import glob
import os
import time
import unittest
import elasticsearch
import nose.tools as nt
from elasticsearch.exceptions import ConnectionError
from nose.plugins.skip import SkipTest
from topik.fileio import TopikProject
from topik.fileio.tests import test_data_path
# make logging quiet during testing, to keep T... |
from types import NoneType
import PySimpleGUI as sg
import funcoes
import webbrowser
from classes import acessoSAP
# Classe principal da criação do programa
class ProgramPainel:
def __init__(self):
font_str = 'Arial, 12'
size_Input = (6,1)
sg.change_look_and_feel('DarkGrey4')
# Layo... |
from sqlalchemy import Column
from sqlalchemy import exc
from sqlalchemy import Integer
from sqlalchemy import MetaData
from sqlalchemy import select
from sqlalchemy import Table
from sqlalchemy import text
from sqlalchemy.schema import DDL
from sqlalchemy.schema import Sequence
from sqlalchemy.sql import ClauseElement... |
"""
Implementations of IDependenciesPrinter
"""
from dataclasses import asdict, dataclass
from enum import Enum
from pathlib import Path
from subprocess import check_output
from sys import stdin, stdout
from typing import Dict, Iterable, Iterator, List, Optional, Tuple
import yaml
from jinja2 import Template
from dep... |
# Copyright 2021, <NAME>, mailto:<EMAIL>
#
# Part of "Nuitka", an optimizing Python compiler that is compatible and
# integrates with CPython, but also works on its own.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the Lice... |
#%%
#Problem one
nums = [2,7,11,15]
target = 9
def twoSum(arr, target):
values = {}
for ind, val in enumerate(arr):
if val in values:
values[val].append(ind)
else:
values[val] = [ind]
output = None
for key, val in zip(values.keys(), values.values()):
if a... |
"""
@author: <NAME>
@ email: <EMAIL>
@ Date: 17.05.2020
"""
import torch
from torch.autograd import Variable as V
import torchvision.models as models
import skimage.io
from torchvision import transforms as trn
from torch.nn import functional as F
import os
import numpy as np
import cv2
# function to load exif of image... |
#!/usr/bin/env python3
'''AMQ List Downloader
This Python 3 module downloads songs from all availble shows on a user's list from Anime Music Quiz's Expand Library.
Python dependencies:
pyyaml
selenium
Other dependencies:
geckodriver
Firefox
ffmpeg
'''
import argparse
import json
import os
import re
imp... |
import logging
from django.db import IntegrityError
from django import forms
from django.utils.translation import ugettext as _
from django.contrib.auth import authenticate
from dreamauthbackend.opinsys.models import OpinsysAuthProvider, OpinsysAssociation
LOG = logging.getLogger(__name__)
class PuavoAuthenticati... |
"""
Unit tests of the mongoengine interface to MongoDB
Does not use portal or fractal server interfaces.
"""
import pytest
import qcfractal.interface as portal
from qcfractal.storage_sockets.models import Molecule, Result, Options, \
Procedure, OptimizationProcedure, TorsiondriveProcedur... |
"""
Simple Parallel Model Selection
===============================
In this example, we'll demonstrate how to quickly write a hyperparameter
tuning script that evaluates a set of hyperparameters in parallel.
This script will demonstrate how to use two important parts of the Ray API:
using ``ray.remote`` to define rem... |
import json
import csv
import codecs
from collections import Counter, namedtuple
import numpy as np
from correlations import Correlations
#from analyzer import SortedThetas
SortedThetas = namedtuple('SortedThetas', 'thetas labels histogram correlations')
class ComplexDecoder(object):
'''Decodes json complex array... |
# Copyright (C) 2016 <NAME> <<EMAIL>>
# All rights reserved.
# This file is part of the Python Automatic Forecasting (PyAF) library and is made available under
# the terms of the 3 Clause BSD license
import pandas as pd
import numpy as np
from enum import IntEnum
from . import Utils as tsutil
class eDatePart(IntEnu... |
import magma as m
from magma.testing import check_files_equal
import logging
import pytest
import coreir
class And2(m.Circuit):
name = "And2"
io = m.IO(I0=m.In(m.Bit), I1=m.In(m.Bit), O=m.Out(m.Bit))
@pytest.mark.parametrize("target,suffix",
[("verilog", "v"), ("coreir", "json")])
d... |
"""
train_classifier.py
--------------------------------------------------
This script takes the cleaned data and creates a machine learning model for later use.
"""
# Importing necessary libraries
import re
import ssl
import sys
import nltk
import pandas as pd
from sqlalchemy import create_engine
# running nltk.dow... |
import math
import numpy as np
import paddle.v2 as paddle
import paddle.v2.dataset.conll05 as conll05
import paddle.v2.fluid as fluid
word_dict, verb_dict, label_dict = conll05.get_dict()
word_dict_len = len(word_dict)
label_dict_len = len(label_dict)
pred_len = len(verb_dict)
mark_dict_len = 2
word_dim = 32
mark_di... |
import os
import json
import numpy as np
import matplotlib.pyplot as plt
def compute_iou(box_1, box_2):
'''
This function takes a pair of bounding boxes and returns intersection-over-
union (IoU) of two bounding boxes.
'''
yA = max(box_1[0], box_2[0])
xA = max(box_1[1], box_2[1])
yB = min(b... |
"""
ORM for Brick
"""
from collections import defaultdict
from . import namespaces as ns
from sqlalchemy import Column, String, ForeignKey, create_engine
from sqlalchemy.orm import relationship, sessionmaker
from sqlalchemy.ext.declarative import declarative_base
Base = declarative_base()
# TODO: brick:feeds (many-to-... |
import einops
import keras
import keras.layers
import keras.metrics
import numpy as np
import tensorflow as tf
from attrdict import AttrDict
import models.eval_metrics
import models.model_trainer
import models.util
import tfu
import tfu3d
from options import FLAGS
class Metro(keras.Model):
def __init__(self, bac... |
from .interpolator import RaveTrajectoryWrapper, SplineInterpolator
from .constraint import (
JointAccelerationConstraint,
JointVelocityConstraint,
DiscretizationType,
SecondOrderConstraint,
)
from .algorithm import TOPPRA
import numpy as np
import logging
import time
logger = logging.getLogger(__name_... |
import pycuda.autoinit
import pycuda.driver as drv
from pycuda.compiler import SourceModule
import numpy as np
from wave_2d_fd_perf_gpu.propagators import Propagator
class VPycuda(Propagator):
"""PyCUDA implementations."""
def __init__(self, jitfunc1, jitfunc2, fd_d, model, batch_size, pad, dx,
... |
"""
Quickstart
1. Pip-install the following dependencies:
- sqlalchemy
- psycopg2
- -e git+https://github.com/kids-first/kf-lib-data-ingest#egg=kf-lib-data-ingest
2. Export the following environmental variables:
- KF_WAREHOUSE_DB_URL=
- FHIR_USER=
- FHIR_PASS=
3. Tunnel to Bastion dev and run.
For the detailed ex... |
from django.shortcuts import render
from django.views.decorators.http import require_http_methods
from django.http import HttpResponseNotFound, JsonResponse
from django.views.decorators.http import require_http_methods
from django.views.decorators.csrf import csrf_exempt
import bcrypt
from project1.api.models import... |
# KBaseMetagenomes.AnnotatedMetagenomeAssembly indexer
from src.index_runner.es_indexers.indexer_utils import mean, handle_id_to_file
from src.utils.config import config
import tempfile
import json
import gzip
import shutil
import os
def _index_ama(features_file_gz_path, data, ama_id, ver_ama_id, tmp_dir, conf):
... |
import sys
import pymemcache
from pymemcache.client.base import Client
from pymemcache.exceptions import MemcacheClientError
from pymemcache.exceptions import MemcacheIllegalInputError
from pymemcache.exceptions import MemcacheServerError
from pymemcache.exceptions import MemcacheUnknownCommandError
from pymemcache.ex... |
import unittest
import sys
from pyspark.ml import Pipeline
from pyspark.ml.classification import LogisticRegression
from pyspark.ml.feature import StringIndexer, OneHotEncoderEstimator, VectorAssembler
from onnxmltools import convert_sparkml
from onnxmltools.convert.sparkml import buildInitialTypesSimple, build... |
import os
from pathlib import Path
from typing import Dict, List, Optional, Tuple, Union
import numpy as np
import torch
from pytorch_lightning import LightningDataModule
from torch.utils.data import DataLoader
from .dataset import InferenceDataset, InferenceDicomDataset, InferencePngDataset, XRayAnomalyDataset, \
... |
import argparse
from sys import stdin, stdout, stderr
import csv
import base64
import os
import os.path
import datetime
import ijson
def prepare_args():
parser = argparse.ArgumentParser(
description="Tool export PNG files and detection data to CSV.",
usage="./credo-user-mapping.py -j export_0_152... |
import numpy as np
from randnn.topologies.utils import get_connected_components
from randnn.topologies.scale_free import get_degree_seq, degree_seq_to_edges, power_law_dist
def test_power_law_dist():
min_degree = 1
max_degree = 3
alpha1 = 0.5
alpha2 = 1.5
alpha3 = 2.5
alpha4 = 3.5
assert... |
#!/usr/bin/env python3
# Copyright © 2012-13 Qtrac Ltd. All rights reserved.
# This program or module is free software: you can redistribute it
# and/or modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option)... |
import signal
import sys
import textwrap
import os
from typing import List
from gooey.python_bindings.constants import Events
from gooey.python_bindings import constants
from gooey.gui.util.freeze import getResourcePath
from gooey.python_bindings.types import GooeyParams
from gooey.util.functional import merge
def... |
import numpy as np
import sys
import os
import fnmatch
import argparse
try:
import cv2 as cv
except ImportError:
raise ImportError('Can\'t find OpenCV Python module. If you\'ve built it from sources without installation, '
'configure environment variable PYTHONPATH to "opencv_bu... |
"""NFSP agents trained on simplified risk."""
from absl import app
from absl import flags
from absl import logging
import tensorflow.compat.v1 as tf
import numpy as np
import igraph as ig
import cairocffi
import random
import pyspiel
from open_spiel.python import policy
from open_spiel.python import rl_environment
fr... |
import numpy as np
import ray
ray.shutdown()
ray.init()
# A : Action Space
# S : State Space
@ray.remote
class VI_worker(object):
def __init__(self, list_of_actions, tran_dict, reward_dict, beta, backup_states, true_action_prob=0.8,
unknown_value=0):
self.backup_states = backup_states
... |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import re
from astropy.table import Table
import Quaternion
from parse_cm import read_backstop, read_or_list
from Chandra.Time import DateTime
import hopper
def check_characteristics_date(ofls_characteristics_file, ref_date=None):
# de_bytetring the... |
import unittest
from recordclass import litelist
import gc
import pickle
import sys
class litelistTest(unittest.TestCase):
def test_len(self):
a = litelist([])
self.assertEqual(len(a), 0)
a = litelist([1])
self.assertEqual(len(a), 1)
def test_items(self):
a = ... |
#!/usr/bin/python
# -*- coding:utf-8 -*-
import os
import os.path
import logging
import logging.handlers
import sqlite3
import tweepy
import requests
from six.moves.urllib.request import urlretrieve
from six.moves.urllib.parse import urlencode
DB_FILENAME = 'aladin.db'
LOG_FILENAME = 'aladin.log'
ALADIN_ITEM_ENDPOI... |
#!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
import json
import os
from os.path import join as pjoin
from os.path import isfile, isdir
from parlai.core.params impor... |
import statistics
import numpy as np
import os
import json
def load_config():
config_file = os.path.abspath(os.path.join(os.curdir, 'config2.json'))
with open(config_file, 'r', ) as config_file:
config_string = config_file.read()
return json.loads(config_string)
def solve(graph, labels):
"... |
# -*- coding: utf-8 -*-
# Copyright (C) 2014-2016 <NAME> <<EMAIL>>
# Copyright (C) 2014-2016 <NAME> <<EMAIL>>
# Copyright (C) 2014-2016 <NAME> <<EMAIL>>
# Copyright (C) 2014-2016 <NAME> <<EMAIL>>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public... |
# tests/test_trees.py
#
# forestry: Python Tree data structures and tools
#
# Copyright (C) 2019 by <NAME>
#
# This module is part of `forestry` and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Unit tests for module trees.py"""
# Third-party library imports
import pytest
... |
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