text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
import datetime
import itertools
import logging
import os
import time
from collections import defaultdict
from operator import itemgetter
from typing import (
AbstractSet,
Any,
Callable,
Dict,
Iterable,
List,
Mapping,
MutableMapping,
Optional,
Sequence,
Set,
Tuple,
Un... | showell/zulip | zerver/lib/actions.py | Python | apache-2.0 | 263,469 | [
"Octopus"
] | 7ceb874e8bdb731e1ce360b517274f59ceed4c57016d1103abb71496b5323021 |
__RCSID__ = "$Id$"
import os
import time
import GSI
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.DISET.private.Transports.BaseTransport import BaseTransport
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.DISET.pr... | fstagni/DIRAC | Core/DISET/private/Transports/GSISSLTransport.py | Python | gpl-3.0 | 6,441 | [
"DIRAC"
] | b24734147926530a8b0c736b0a30f773d4829d74045152f539825c9a31bc62cd |
try:
import smbus
except ImportError:
raise ImportError("python-smbus not found. Install with 'sudo apt-get install python-smbus'")
import re
__all__ = ['ADCHelper']
class ADCHelper:
def get_smbus(self):
''' Detect the i2c port number and assign to i2c_bus '''
i2c_bus = 0
for line in open('/proc/cpuinfo').r... | dhhagan/ADCPi | ADCPi/adc_helper.py | Python | mit | 844 | [
"VisIt"
] | d78b8355b3462afbcd9e2cd5d6a48f2ce18696e21e1424a7818a6f10174747af |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-dialogflow-cx | tests/unit/gapic/dialogflowcx_v3/test_experiments.py | Python | apache-2.0 | 115,643 | [
"Octopus"
] | 719c1357db3ac8b3e4e25ae4eb5c16a709b05d7750a97915861390fc86f22dff |
# -*- coding: utf-8 -*-
#
# test_rate_copy_model.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 2 of the Li... | terhorstd/nest-simulator | pynest/nest/tests/test_rate_copy_model.py | Python | gpl-2.0 | 3,319 | [
"NEURON"
] | 65e2dc9a7937677f328b0781896851e345136f84b874d7ec34244ef3e02f5aea |
########################################################################
# $HeadURL $
# File: ReplicateAndRegister.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 18:49:12
########################################################################
""" :mod: ReplicateAndRegister
=========================... | marcelovilaca/DIRAC | DataManagementSystem/Agent/RequestOperations/ReplicateAndRegister.py | Python | gpl-3.0 | 19,165 | [
"DIRAC"
] | b9b8a16380c5f460d4bae7f7f1142f906ed67ba05c1535bb1177b12c15305ec7 |
import logging
import json
import copy
logger = logging.getLogger(__name__)
logger.setLevel(logging.DEBUG)
matchingList = { #key: entry field. value: don't care value.
'srcMac': '00:00:00:00:00:00', \
'dstMac': '00:00:00:00:00:00', \
'dlType': '0x0', \
'srcIP': '0.0.0.0', \
'dstIP': '0.0.0.0', \
'srcPort': '0', \
'ds... | dlinknctu/OpenADM | core/src/floodlight_modules/simulate.py | Python | gpl-2.0 | 9,183 | [
"VisIt"
] | adc13b01a6715e05991b65512f88463bbe7e747a63d2731993db903fe1217574 |
from __future__ import division
import numpy as np
from scipy.ndimage import uniform_filter, gaussian_filter
from ..util.dtype import dtype_range
from ..util.arraycrop import crop
from .._shared.utils import warn
__all__ = ['compare_ssim']
def compare_ssim(X, Y, win_size=None, gradient=False,
data... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/skimage/measure/_structural_similarity.py | Python | gpl-3.0 | 7,497 | [
"Gaussian"
] | 1b3374f0f715b20667e5d2949b7b0f3932edfd59be300e2cb3d9a7597a429f56 |
# CTL analysis for GN2
# Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
import sys
from numpy import *
import rpy2.robjects as ro # R Objects
import rpy2.rinterface as ri
import simplejson as json
from base.webqtlConfig import GENERATED_IMAGE_DIR
from utility import webqtlUtil ... | DannyArends/genenetwork2 | wqflask/wqflask/ctl/ctl_analysis.py | Python | agpl-3.0 | 9,969 | [
"Cytoscape"
] | 33db0de994d6b2add473384dd7f7a5f631c7405ddef472437c2752c663ef38d0 |
import os.path as op
from collections import defaultdict, Counter
import pysam
from pybedtools import BedTool
from bcbio.utils import splitext_plus
def _complementary(nt):
if nt.lower() == "a":
return "T"
if nt.lower() == "t":
return "A"
if nt.lower() == "c":
return "G"
if nt... | lpantano/ASMfinder | asm/show.py | Python | mit | 8,248 | [
"pysam"
] | 8022961ed623c336d9c402f3946b0d36bba0e82fc82e3ab76799563208414e22 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2014 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | LunarLanding/Pythics | pythics/slave.py | Python | gpl-3.0 | 4,160 | [
"Brian"
] | 7eae0686a1b74155c3924600cffb8b19121ca3866ff12f2830123c969c7ab588 |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# 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... | barnabytprowe/great3-public | metrics/calculate_plot_const_shear_metrics.py | Python | bsd-3-clause | 8,063 | [
"Galaxy"
] | ff41441480979d582d6b94d39cb96971c4decf3a02a6b8995977d85e8bfc624f |
""" This is a test of the chain
ResourceManagementClient -> ResourceManagementHandler -> ResourceManagementDB
It supposes that the DB is present, and that the service is running
The DB is supposed to be empty when the test starts
"""
# pylint: disable=invalid-name,wrong-import-position
import sys
import d... | DIRACGrid/DIRAC | tests/Integration/ResourceStatusSystem/Test_ResourceManagement.py | Python | gpl-3.0 | 13,262 | [
"DIRAC"
] | 65739bc7ab630d7bdbb247b9b2525335e30bc557bf19ab6221270782bfbf4a65 |
###########################################################################
#
# 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
#
# https://www.apache.org/l... | google/starthinker | dags/google_ads_segmentology_dag.py | Python | apache-2.0 | 11,850 | [
"VisIt"
] | de8129f9559ecd890a52219ed1d70f39f1ff6482ce8423c446d096cabf8a8e31 |
#!/usr/bin/env python
"""
hycom.py
Functions for dealing with the HYCOM model for importation into ROMS
Written by Brian Powell on 07/24/15
Copyright (c)2017 University of Hawaii under the MIT-License.
"""
import numpy as np
from datetime import datetime
import netCDF4
from seapy.lib import default_epoch, c... | ocefpaf/seapy | seapy/model/hycom.py | Python | mit | 4,912 | [
"Brian"
] | 31bb812496b28bc9a3091ee7452bd2a80859bdb2eaa162f5c50e7ca0c632ebcb |
#! /usr/bin/python
#Adapted and expanded from https://github.com/pontikos/uclex_browser/blob/master/load_vcfs/uclex_to_vcf.py
from __future__ import print_function
import argparse
import os
import os.path
import sys
import re
#import tabix
import pysam
from pysam import VCF
import csv
import numpy
import cPickle as ... | danchubb/CanVar | vcf_to_site_canvar.py | Python | mit | 20,137 | [
"pysam"
] | 42c84cedea719755b6062080d49c9de8cad140424fd5552b87bb4c5659786f55 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'VisitRegistrationError.error_count'
db.delete_column(u'... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0016_auto__del_field_visitregistrationerror_error_count.py | Python | bsd-2-clause | 13,187 | [
"VisIt"
] | 348e0e807b5fda766e0a352dd982051c22728ed45e4e25fd5c26dafbc21964e9 |
#!/usr/bin/env python
__author__ = "waroquiers"
import json
import os
import shutil
import unittest
import numpy as np
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
AngleNbSetWeight,
CNBiasNbSetWeight,
DeltaCSMNbSetWeight,
DistanceAngleAreaNbSetWeight,
Mul... | gmatteo/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py | Python | mit | 11,171 | [
"pymatgen"
] | 228dacde4ebfe0b93b61ba53fcbbc1c5b0146a8b4fd05e3a10779784b88c1b5b |
#!/usr/bin/env python3
"""
http://adventofcode.com/day/20
Part 1
------
To keep the Elves busy, Santa has them deliver some presents
by hand, door-to-door. He sends them down a street with infinite
houses numbered sequentially: 1, 2, 3, 4, 5, and so on.
Each Elf is assigned a number, too, and delivers presents to hou... | rnelson/adventofcode | advent2015/day20.py | Python | mit | 3,037 | [
"VisIt"
] | 5440bb2509744f70ebe533bde4d754511cb49e49744c25eca11fec5e5a5b7a95 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
class Migration(DataMigration):
def forwards(self, orm):
"Write your forwards methods here."
# Note: Don't use "from appname.models imp... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0048_serial_to_tempserial.py | Python | bsd-2-clause | 13,745 | [
"VisIt"
] | 67e2623297b89bbed17beaad1223660f9a43de3faecf9344e895e258b8d4b143 |
# -*- coding: utf-8 -*-
"""Ansible Terraform Inventory."""
# batteries included
from __future__ import absolute_import
from glob import glob
from os.path import basename, splitext
from setuptools import find_packages, setup
doc_requirements = []
install_requirements = [
'boto3>=1.4.4,<2',
'sh>=1.12.13,<2']
... | CiscoCloud/terraform.py | setup.py | Python | apache-2.0 | 2,086 | [
"Brian"
] | 32260585a3f235e894f11903329e13f77e2001e07b794787af77a5b4f3e8e4a8 |
#-*- coding:utf-8 -*-
"""
This file is part of OpenSesame.
OpenSesame 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) any later version.
OpenSesame is distri... | SCgeeker/OpenSesame | extensions/update_checker/update_checker.py | Python | gpl-3.0 | 3,335 | [
"VisIt"
] | 068859c769b2e97273788bc8e9b78de1ccca70dd58fb6225993bd636299d7b0c |
import asyncio
import discord
import random
import pprint
import yaml
import time
import re
import io
from collections import OrderedDict
from discord.abc import PrivateChannel
from psycopg2.extras import Json
from youtube_dl import YoutubeDL
from tinytag import TinyTag
from jshbot import data, utilities, configurati... | jkchen2/JshBot-plugins | tags/tags.py | Python | mit | 53,209 | [
"MOE"
] | 53c44d0321ecb56e237a4010647af00205fa4460f04c9827084a5fe5c1e33f52 |
# Copyright (C) 2012 Guilhem Ribeill
#
# This program 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 2 of the License, or
# (at your option) any later version.
#
# This program is distributed i... | McDermott-Group/LabRAD | LabRAD/Measurements/General/pulse_shapes.py | Python | gpl-2.0 | 2,149 | [
"Gaussian"
] | 02878c719ef31a95d3065848ba1f7ce801b8834c7d0087cab1584f2f7d718a0e |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/selectaudiotrack.py | Python | gpl-2.0 | 5,023 | [
"VisIt"
] | f85fff3be30c5c7d42409243e8ca9d4e9f2a4405f3393dd6317e9319274a9fff |
import numpy
from scipy.stats import kde
def kd_distribution(data, x_min=None, x_max=None, num_points=200, CDF=False,
estimator_class=kde.gaussian_kde, **kws):
"""Use Kernel Density Estimation to estimate a density or CDF from data.
Parameters:
data: 1-dimensional list or array of data points
... | zplab/zplib | zplib/scalar_stats/kde.py | Python | mit | 5,517 | [
"Gaussian"
] | d1c9d75202906ac37de0ea51dcde14cde04a4a3b28a15c20c3e2d41237c3fc60 |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | chrisfranzen/django | django/conf/global_settings.py | Python | bsd-3-clause | 21,365 | [
"VisIt"
] | f7b2a676d6fd16174bed1852ea60148a218cbaeecd1515e57384f5e11ebf974e |
"""Safe Resolwe process parser."""
import ast
import collections
import json
import asteval
from . import runtime
from .descriptor import ProcessDescriptor, SchedulingClass
from .fields import get_available_fields
class StaticMetadata:
"""Process metadata item."""
def get_value(self, node):
"""Conv... | jberci/resolwe | resolwe/process/parser.py | Python | apache-2.0 | 7,257 | [
"VisIt"
] | 80ebf07a3d7404c40261b0c47582313e81add52b34458ae2bb6b8ee137d36ab1 |
# Author: Travis Oliphant
# 1999 -- 2002
import operator
import math
import timeit
from scipy.spatial import cKDTree
from . import sigtools, dlti
from ._upfirdn import upfirdn, _output_len, _upfirdn_modes
from scipy import linalg, fft as sp_fft
from scipy.fft._helper import _init_nd_shape_and_axes
from scipy._lib._uti... | pizzathief/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 146,890 | [
"Gaussian"
] | a7400b70d65ceda61e18808902b7f945f851f3109970395d3758d4d6a36e3634 |
from __future__ import division
from warnings import warn
import numpy as np
binary_erosion = None # expensive, from scipy.ndimage
binary_dilation = None # expensive, from scipy.ndimage
from menpo.base import MenpoDeprecationWarning, copy_landmarks_and_path
from menpo.transform import Translation
from menpo.visuali... | grigorisg9gr/menpo | menpo/image/masked.py | Python | bsd-3-clause | 60,008 | [
"Gaussian"
] | d139b19cbe7dda88ffffe26e8c35e50741c311f1cc3044ab130285d33c6ef060 |
##
# Copyright 2009-2017 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ULHPC/easybuild-easyblocks | easybuild/easyblocks/b/bioconductor.py | Python | gpl-2.0 | 2,250 | [
"Bioconductor"
] | 1f5631c106124b5b52b98b8b491b166e96cb9d230678de03564db8e6a31e5e96 |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-pubsublite | tests/unit/gapic/pubsublite_v1/test_publisher_service.py | Python | apache-2.0 | 49,493 | [
"Octopus"
] | 70c785790b4f15fffc8355fd61ba4e6944b0eb3465a45270421f0af74766d3b5 |
#!/usr/bin/python
# TODO - python path - assuming condo here
## HEALTH WARNING - BETA CODE IN DEVELOPMENT ##
'''
This standalone application will build a mesh from a nifti classification file.
To keep the procedure as similar as possible to the way mrMesh used to do this,
we will keep this as a standalon applicatio... | andregouws/mrMeshPy | matlabRoutines/pyMeshBuild_test.py | Python | mit | 10,547 | [
"VTK"
] | 01a950ee5d6f1bc62eec0206cca4b8724641a108b3cd6c0ca1f8243968bd0649 |
# Copyright 2022 The jax3d 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 wr... | google-research/jax3d | jax3d/projects/nesf/nerfstatic/models/nerf_utils.py | Python | apache-2.0 | 13,141 | [
"Gaussian"
] | 0439f54eb583b797225b74a1c928ea98003a528ca0c881dac47565af8ea37baf |
#!/usr/bin/env python
##get_RSCU_for_fasta.py
##written 9/8/15 by Groves Dixon
ProgramName = 'get_RSCU_for_fasta.py'
LastUpdated = '9/8/15'
By = 'Groves Dixon'
VersionNumber = '1.0'
print "\nRunning Program {}...".format(ProgramName)
VersionString = '{} version {} Last Updated {} by {}'.format(ProgramName, VersionNumb... | grovesdixon/metaTranscriptomes | scripts/get_RSCU_for_fasta.py | Python | mit | 9,506 | [
"BLAST"
] | 9ea2b95bb0c5d87aacb333a3c277354422c4285e8c6fee6fbb0bd3b78eb6ef1d |
########################################################################################################################
#
# Toolbox for batch downloading and preprocessing of Sentinel satellite data from Sentinels Scientific Data Hub
# Contributors: Thomas Stark & Tatjana Buergmann (TU Munich)
# Adaption of ... | sendobox/sendobox | scripts/snappy_01_mosaic.py | Python | gpl-3.0 | 12,941 | [
"NetCDF"
] | 200a0de24a4f511c4ba9bd6366781b46c6d981d1addbfac0d59461c3506b290a |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | markovmodel/PyEMMA | pyemma/coordinates/tests/test_stride.py | Python | lgpl-3.0 | 4,387 | [
"MDTraj"
] | e210d84c8085617d678779eab431f04dd3320a24e11db732e4f67ca93e77cb0a |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | fabio-otsuka/invesalius3 | invesalius/data/slice_data.py | Python | gpl-2.0 | 5,990 | [
"VTK"
] | 9f1a5cceab8ef5a759bbcec5269d6b6efca2e12fddccef3fe7fd4caa49110a23 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2012-2013 Esteban Tovagliari, Jupiter Jazz Limited
# Copyright (c) 2014-2018 Esteban Tovagliari, The appleseedhq Organization
#
# ... | est77/appleseed | sandbox/examples/python/helloworld/helloworld.py | Python | mit | 12,218 | [
"VisIt"
] | 26480c93c91244ddef00f11f06af2a459b0ae99a483d24b2cdae0ada8fafd46b |
# -*- coding: utf-8 -*-
'''
This module (mostly) uses the XenAPI to manage Xen virtual machines.
Big fat warning: the XenAPI used in this file is the one bundled with
Xen Source, NOT XenServer nor Xen Cloud Platform. As a matter of fact it
*will* fail under those platforms. From what I've read, little work is needed
t... | smallyear/linuxLearn | salt/salt/modules/xapi.py | Python | apache-2.0 | 25,212 | [
"VMD"
] | 6ea7b8acfb9b7f031878630842987c4570b56ceeaf6b0858b182874ab2fd9959 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004 Martin Hawlisch
# Copyright (C) 2005-2006, 2008 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | beernarrd/gramps | gramps/plugins/export/exportvcalendar.py | Python | gpl-2.0 | 9,568 | [
"Brian"
] | edb2e0433b276f56de25bbf15324a5d239d5e476902397de31cc808044ef8514 |
import logging
from keras.preprocessing.image import ImageDataGenerator
from keras.models import Sequential
from keras.layers.core import Dense, MaxoutDense, Dropout, Activation, Flatten, Merge
from keras.layers.convolutional import Convolution2D, MaxPooling2D
from keras.optimizers import SGD, Adadelta, Adagrad
from k... | ml-slac/deep-jets | convtrain.py | Python | mit | 5,894 | [
"Gaussian"
] | 1c00b98e64656186a13a9b41551f2eafbc0ada13b59da92fefe37dd6155c5ef9 |
#!/usr/bin/env python
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# 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 c... | svohara/pyvision | src/pyvision/gui/EyePicker.py | Python | bsd-3-clause | 11,624 | [
"VisIt"
] | c8df7e28cb9d666f4f506fd79d515da824d1998fc7e5703d8fa9c6e4a8bf5ee0 |
from direct.directnotify import DirectNotifyGlobal
from direct.fsm import StateData
import CogHQLoader
from toontown.toonbase import ToontownGlobals
from direct.gui import DirectGui
from toontown.toonbase import TTLocalizer
from toontown.toon import Toon
from direct.fsm import State
import BrutalFactoryInterior
import ... | Spiderlover/Toontown | toontown/coghq/SellbotCogHQLoader.py | Python | mit | 10,427 | [
"VisIt"
] | 5c01de15c5390fcbc719ff168efd54a860c63a9c91a3ade8fbb3f2319e382775 |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/lib/aifh/__init__.py | Python | apache-2.0 | 976 | [
"VisIt"
] | e932e64e9dad670d7811668d5b1096363e76fffd915887a5bbbcd408c755f185 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This script shows how to use vtkImageEuclideanDistance
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/fullhead15.png")
cast = vtk.v... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestEuclideanDistance.py | Python | gpl-3.0 | 902 | [
"VTK"
] | 70768b6124e3ecdb7cf5a9224c12670d11ea870481ce41bc17c5e53d05345319 |
#
# This file is protected by Copyright. Please refer to the COPYRIGHT file
# distributed with this source distribution.
#
# This file is part of GNUHAWK.
#
# GNUHAWK is free software: you can redistribute it and/or modify is under the
# terms of the GNU General Public License as published by the Free Software
# F... | RedhawkSDR/integration-gnuhawk | qa/tests/qa_bpsk.py | Python | gpl-3.0 | 4,987 | [
"Gaussian"
] | 3ea4b6e2c348fc2981a48bd83df5d5649df528b4ccfc2676cdf8c8a795709930 |
# coding=utf-8
''''''
import os
import ast
import sys
import time
import signal
import argparse
import asyncio
from datetime import datetime, timedelta
from collections import defaultdict
from functools import reduce, partial
from slacker import Slacker
from tornado.ioloop import IOLoop
from apscheduler.job import Job... | dongweiming/slack-alert | slack_alert.py | Python | mit | 9,349 | [
"VisIt"
] | 78ba6e358ebad53f087b08944bae5026397d0b7fb0f06c0f4cd4a47890f4deee |
# This file helps to compute a version number in source trees obtained from
# git-archive tarball (such as those provided by githubs download-from-tag
# feature). Distribution tarballs (built by setup.py sdist) and build
# directories (produced by setup.py build) will contain a much shorter file
# that just contains t... | bioconda/bioconda-utils | bioconda_utils/_version.py | Python | mit | 18,467 | [
"Bioconda"
] | 309f84aa7422637f978869578b2ea8afb38c222c32dbb4ceb43b1827af5ff9e7 |
# -*- coding: utf-8 -*-
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
# Copyright 2011 The Orca Team.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the ... | GNOME/orca | src/orca/brlmon.py | Python | lgpl-2.1 | 6,601 | [
"ORCA"
] | d9fe8e79c7ba5234b7b74fbeed6d79fc527bd2936300d453b0cdfe6ec6f1838e |
# Copyright (c) Amber Brown, 2015
# See LICENSE for details.
import os
from subprocess import call
from textwrap import dedent
from twisted.trial.unittest import TestCase
from click.testing import CliRunner
from ..build import _main
from .._shell import cli
def setup_simple_project():
with open("pyproject.toml... | hawkowl/towncrier | src/towncrier/test/test_build.py | Python | mit | 25,891 | [
"Amber"
] | d3dd5b0e627bcb0afa11e27671d0af044a21a2346f12080f0abb5572d9828aa9 |
# -*- coding: utf-8 -*-
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
from __future__ import absolute_import, print_function, unicode_literals
import unittest
from... | Yukarumya/Yukarum-Redfoxes | taskcluster/taskgraph/test/test_graph.py | Python | mpl-2.0 | 5,948 | [
"VisIt"
] | c780c098234c38531f3c1e5b59f72a0df310a36248b6958ad48f021598d8c990 |
"""
kmerfreq_ha_2_wrapper.py
A wrapper script for KmerFreq_HA_v2.0
Peter Li - GigaScience, BGI-HK
"""
import optparse, os, shutil, subprocess, sys, tempfile
def stop_err(msg):
sys.stderr.write(msg)
sys.exit()
def cleanup_before_exit(tmp_dir):
if tmp_dir and os.path.exists(tmp_dir):
shutil.rmtree(... | gigascience/galaxy-bgisoap | tools/kmerfreq_ha_2/kmerfreq_ha_2_wrapper.py | Python | gpl-3.0 | 6,446 | [
"Galaxy"
] | 138368d2068553f6687881634bcb8dde1d96ca34e82ff0e1e86ba0222145fc97 |
"""
This file contains the multi-fidelity deep Gaussian process model from:
Deep Gaussian Processes for Multi-fidelity Modeling (Kurt Cutajar, Mark Pullin, Andreas Damianou, Neil Lawrence, Javier González)
The class intended for public consumption is MultiFidelityDeepGP, which is an emukit model class.
This file requ... | EmuKit/emukit | emukit/examples/multi_fidelity_dgp/multi_fidelity_deep_gp.py | Python | apache-2.0 | 18,171 | [
"Gaussian"
] | 6f5b71274e6437762b9ce9ca404bf3ab71d39b049ad4d626da3707e990f22fc0 |
# -*- coding: UTF-8 -*-
import datetime
import os
import os.path
import subprocess
from collections import defaultdict
from django.conf import settings as dsettings
from django.core import exceptions
from django.core.cache import cache
from django.db import connection
from django.db import models
from django.db import... | pythonitalia/conference | conference/models.py | Python | bsd-2-clause | 47,624 | [
"ESPResSo"
] | 2bbef81339dc0cdcd01517c5f05a8b1f43109b5852f05747e9d96e45fb4eb63c |
import locale
import datetime
from unittest import skip
from bok_choy.promise import EmptyPromise
from analyticsclient.client import Client
from acceptance_tests import API_SERVER_URL, API_AUTH_TOKEN, DASHBOARD_FEEDBACK_EMAIL, SUPPORT_URL, LMS_USERNAME, \
LMS_PASSWORD, DASHBOARD_SERVER_URL, ENABLE_AUTO_AUTH, DOC_... | open-craft/edx-analytics-dashboard | acceptance_tests/mixins.py | Python | agpl-3.0 | 14,599 | [
"VisIt"
] | 231224df95fd6ca0b2f7ca3f9c1071fd60b86c68feb0a3b7cabb3fdf05a49c2e |
import os
import orca
from activitysim import activitysim as asim
from .util.misc import add_dependent_columns
"""
Auto ownership is a standard model which predicts how many cars a household
with given characteristics owns
"""
@orca.injectable()
def auto_ownership_spec(configs_dir):
f = os.path.join(configs_dir... | bhargavasana/activitysim | activitysim/defaults/models/auto_ownership.py | Python | agpl-3.0 | 801 | [
"ORCA"
] | 17bfa4d6bf25c0023be6e105cb3ff954bdc8ac7e739b852b5ecf09250355a6bd |
#!/usr/bin/env python
# Encoding: UTF-8
"""Part of qdex: a Pokédex using PySide and veekun's pokedex library.
Column groups: Columns, grouped together. Yeah.
"""
# XXX: Better name for ColumnGroup: should take the leaf objects into account
from PySide import QtGui, QtCore
Qt = QtCore.Qt
from pkg_resources import re... | encukou/qdex | qdex/columngroup.py | Python | mit | 6,474 | [
"VisIt"
] | 3161d10a1944433cb07545fa49ae25a79d3ef9fcd66d67cd1bb9825dde6bc6c7 |
from vtk import *
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
reader = vtkXGMLReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/Infovis/fsm.gml")
reader.Update()
strategy = vtkSpanTreeLayoutStrategy()
strategy.DepthFirstSpanningTreeOn()
view = vtkGraphLayoutView()
view.AddRepresentat... | collects/VTK | Examples/Infovis/Python/graph3d.py | Python | bsd-3-clause | 2,289 | [
"VTK"
] | 19f5a769ec9d5443be2d652f648a98d4acaa3aec928345b08f28911c4f43664a |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
#
"""
Scripts to manipulate Quantum Espresso input files
Also able to read output files in xml format (datafile.xml or datafile-schema.xml)
"""
from qepy.lattice import *
from qepy.pw import *
fr... | alexandremorlet/yambopy | qepy/__init__.py | Python | bsd-3-clause | 529 | [
"Quantum ESPRESSO"
] | f23b9bf3606398cf791deb7d6e4679279ca814c70d83b388b7cf2b96c5a664ea |
TRUCKS = [
"ACMAT",
"AEC",
"AIL",
"AWD",
"Albion",
"Argyle",
"Askam",
"Astra",
"Atkinson",
"Austin",
"Automiesse",
"BMC",
"Barkas",
"Baron",
"Barreiros",
"Bean",
"Beardmore",
"Bedford",
"BelAZ",
"Berliet",
"Berna",
"Bernard",
"B... | wikkiewikkie/elizabeth | elizabeth/intd/trans.py | Python | mit | 5,047 | [
"Jaguar"
] | 0f60b50ea332f80d52fa32547835829694bea543ab374b80f20429ecbc0e3b4b |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | dmlc/mxnet | example/reinforcement-learning/a3c/a3c.py | Python | apache-2.0 | 9,718 | [
"Gaussian"
] | 8be79d97e3d1389e1c9b86d65813c86dce3111a859accad8e6e7d15eca778b14 |
###########################################################################
#
# 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
#
# https://www.apache.org/l... | google/starthinker | dags/iam_dag.py | Python | apache-2.0 | 4,159 | [
"VisIt"
] | 52d42401594ea90fb783ae410295c168a4d1c5f7875328df258a0ee227bcaa89 |
'''
Created on Oct 11, 2014
@author: federico
'''
import os
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
import milkyway
URL = "https://github.com/FedericoRessi/milkyway"
class Tox(TestCommand): # pylint: disable=too-many-public-methods
'''
Command... | FedericoRessi/milkyway | setup.py | Python | gpl-3.0 | 1,746 | [
"Galaxy"
] | e8ccb3407b7de253c9f04f68b1e36dca57e7f886dd91e4f6b002543d992b8600 |
""" Soft implementation of a Direct Acyclic Graph (DAG)
Nota Bene: It is NOT fully checked if valid (i.e. some cycle can be introduced)!
"""
import copy
from DIRAC import gLogger
__RCSID__ = "$Id $"
class DAG( object ):
""" a Direct Acyclic Graph (DAG)
Represented as a dictionary whose keys are nodes, ... | andresailer/DIRAC | Core/Utilities/DAG.py | Python | gpl-3.0 | 3,321 | [
"DIRAC"
] | 14ad19122a806963cd1c92e965f2e0e69e068123ef245870b69b99c07655a467 |
# Common imports
import os
# Where to save the figures and data files
PROJECT_ROOT_DIR = "Results"
FIGURE_ID = "Results/FigureFiles"
DATA_ID = "Results/VMCQdotImportance"
if not os.path.exists(PROJECT_ROOT_DIR):
os.mkdir(PROJECT_ROOT_DIR)
if not os.path.exists(FIGURE_ID):
os.makedirs(FIGURE_ID)
if not os.pa... | CompPhysics/ComputationalPhysics2 | doc/src/MCsummary/src/qdotimportance.py | Python | cc0-1.0 | 6,476 | [
"Gaussian"
] | 6ea24c179026d787306ec30199708979216753b695601ab910f9e8526a217e70 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | lib/spack/spack/spec.py | Python | lgpl-2.1 | 142,903 | [
"VisIt"
] | d64474e3362bb85859758bbedbe0be6d8248cf5d9046be9eeb0b8c0ba3cd139b |
"""Tests for pytd.py."""
import itertools
import textwrap
import unittest
from pytype.pytd import pytd
from pytype.pytd.parse import parser
from pytype.pytd.parse import visitors
class TestPytd(unittest.TestCase):
"""Test the simple functionality in pytd.py."""
def setUp(self):
self.int = pytd.ClassType("in... | pombredanne/pytype | pytype/pytd/pytd_test.py | Python | apache-2.0 | 3,507 | [
"VisIt"
] | 7638c0974cc127d9f73f76c0e9cbdbf201bfc2232fcd7f33278884de655d5548 |
import logging
import logging.config
import threading
import abc
from ambercommon.common import runtime
import os
import drivermsg_pb2
__author__ = 'paoolo'
LOGGER_NAME = 'AmberClient'
pwd = os.path.dirname(os.path.abspath(__file__))
logging.config.fileConfig('%s/amber.ini' % pwd)
class AmberProxy(object):
... | project-capo/amber-python-clients | src/amberclient/common/amber_proxy.py | Python | mit | 3,783 | [
"Amber"
] | be34daea228b535d2e37f7b9d0ff856718e87fc43e80bf3c37343aeb36924e0c |
# -*- coding: utf-8 -*-
# Copyright (C) 2017-2018 CIRCL Computer Incident Response Center Luxembourg (smile gie)
# Copyright (C) 2017-2018 Christian Studer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published... | FloatingGhost/MISP | app/files/scripts/stix2misp.py | Python | agpl-3.0 | 62,288 | [
"Galaxy"
] | 170966bd0959d44a670ab60f117028881ef8f4099406f0b9ec6e4ff820d35895 |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Application context management for the cr tool.
Contains all the support code to enable the shared context used by the cr tool.
This includes the configu... | endlessm/chromium-browser | tools/cr/cr/base/context.py | Python | bsd-3-clause | 6,709 | [
"VisIt"
] | 5c789e4e728f28d10750b3385e1ef85baf1b3ee4331f0ca75dc690fd3aa31ecb |
#!/usr/bin/python
#
# Copyright 2010 Brian Dolbec <brian.dolbec@gmail.com>
# Copyright(c) 2010, Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
#
"""Provides a rebuild file of USE flags or keywords used and by
what packages according to the Installed package database"""
from __f... | dol-sen/gentoolkit | pym/gentoolkit/enalyze/rebuild.py | Python | gpl-2.0 | 11,973 | [
"Brian"
] | a662b2e7721bb61748eea23a59d7a8e20a33adb58616bfbbac7fed8d530fd7f9 |
from electrum.i18n import _
fullname = _('Two Factor Authentication')
description = ''.join([
_("This plugin adds two-factor authentication to your wallet."), '<br/>',
_("For more information, visit"),
" <a href=\"https://api.trustedcoin.com/#/electrum-help\">https://api.trustedcoin.com/#/electrum-help</a>... | romanz/electrum | plugins/trustedcoin/__init__.py | Python | mit | 420 | [
"VisIt"
] | 37c0fa0612cc09c52d274f9ffa6d19d511627e32717b093780c4ce54a1124693 |
SmsTrip = 16274,14708
trip_date = object.trip_id.trip_start or False
rs = True
prefix = {
1:'971',
17:'975',
6:'86',
4:'20',
7:'91',
8:'91',
16:'254',
11:'996',
5:'373',
13:'212',
9:'95',
14:'977',
15:'63',
12:'40',
3:'94',
10:'216'
... | nishad-jobsglobal/odoo-marriot | openerp/addons/mkjosms/smsscripts/new9b1.py | Python | agpl-3.0 | 13,061 | [
"VisIt"
] | a800bbefadc02ea9a6e464ec0b71ff1eb495a9c7dc4391e21481e3657f5962ef |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <http://cjkpython.i18n.org... | kasparg/lawcats | libs/feedparser.py | Python | gpl-3.0 | 166,787 | [
"NetCDF",
"VisIt"
] | af05d4afeff0cf4225f52762f24a468ff2b878016c554b1dff3e98a7b6a14e0b |
'''
Created on Oct 23, 2013
@author: drnorris
'''
#import Galaxy
from Galaxy import *
class Space():
def __init__(self, size):
self.size = size
self.galaxys = []
self.massMaps = []
def createGalaxies(self, count):
for c in range(count):
xpos = self.size / 2
... | a8ksh4/solar | Rev-1/Space.py | Python | gpl-3.0 | 748 | [
"Galaxy"
] | 3f4369305c951c88642b9d8677f68ba61829a3f786c9ce5f22105bd1d62f8132 |
from elements.models import Rank, GameBaseValues, Region, TravelMethod, Transport, Armor, Gun, Car
from elements.models import SinglePlayerJob, FailedSinglePlayerJob, RegionPrices, Housing
from characters.models import Character
from django.contrib.auth.models import User
from users.models import ExtendUser
def add_r... | Sult/Mercenaries | data.py | Python | gpl-2.0 | 28,969 | [
"CASINO"
] | 327ef39405ec374381b896ee18e53a1f0c7c42a1d5bc9b883c2d26c4bd342933 |
import numpy as np
from paraview.util.vtkAlgorithm import (
VTKPythonAlgorithmBase,
smdomain,
smhint,
smproperty,
smproxy,
)
from vtkmodules.numpy_interface import dataset_adapter as dsa
from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid
import meshio
paraview_plugin_version = meshio.__... | nschloe/meshio | tools/paraview-meshio-plugin.py | Python | mit | 6,728 | [
"ParaView"
] | 050fb432582e154901ce47147c2d1f8dc8dec4cab81349061ea56f18927d5a43 |
# utf8
"""
This module contains the core functionality of the CIM to Matpower import tool.
.. note::This module is based partially on the started but never finished open source project Cim2BusBranch https://www.versioneye.com/Python/Cim2BusBranch/0.1
.. seealso:: :py:mod:`Topology_NodeBreaker` and :py:mod:`CIM2Matpo... | SanPen/GridCal | src/research/CIM/cim_to_matpower/CIM2Matpower.py | Python | lgpl-3.0 | 63,866 | [
"VisIt"
] | 840d4b7a01122df35cffdf28a62f8b538571212f8449604890f304b302a53786 |
#!/eecs/research/asr/mingbin/python-workspace/hopeless/bin/python
"""
Author : Mingbin Xu (mingbin.xu@gmail.com)
Filename : kbp-ed-trainer.py
Last Update : Jul 26, 2016
Description : N/A
Website : https://wiki.eecs.yorku.ca/lab/MLL/
Copyright (c) 2016 iNCML (author: Mingbin Xu)
License: MIT License (see .... | nanalelfe/fofe-ner | kbp-ed-trainer.py | Python | mit | 19,781 | [
"Gaussian"
] | e2531e43abdd08773de23284e828e293d68f5a00fee85d4b20d560411e71a4f5 |
"""TIP3P potential, constraints and dynamics."""
from math import pi, sin, cos
import numpy as np
import ase.units as units
from ase.parallel import world
from ase.md.md import MolecularDynamics
qH = 0.417
sigma0 = 3.15061
epsilon0 = 0.1521 * units.kcal / units.mol
rOH = 0.9572
thetaHOH = 104.52 / 180 * pi
class T... | suttond/MODOI | ase/calculators/tip3p.py | Python | lgpl-3.0 | 5,957 | [
"ASE"
] | 9989e79366ddb2bba23c97df1ddc9b47990f452372f5b58e3ed1489094746609 |
"""
Acceptance tests for the teams feature.
"""
import json
import random
import time
from dateutil.parser import parse
import ddt
from flaky import flaky
from nose.plugins.attrib import attr
from uuid import uuid4
from ..helpers import EventsTestMixin, UniqueCourseTest
from ...fixtures import LMS_BASE_URL
from ...fi... | Semi-global/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 64,204 | [
"VisIt"
] | 3b1ac992558fc2d9694e9b84999a560be11b33e79652fbe96aeb25136eb4b036 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/model/tagstatistics.py | Python | mit | 5,134 | [
"VisIt"
] | 935d57f70f06aa2f4e08cf3f9a99997aa20be95a9ed96c45cba8634b63f10978 |
"""
Calculate the kurtosis of a bam file. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424905/ for the definition
"""
import os
import sys
import argparse
import pysam
from roblib import mean, stdev
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Read a bamfile calculate average co... | linsalrob/EdwardsLab | bam/kurtosis.py | Python | mit | 2,120 | [
"pysam"
] | 46afebd85b291c2f57b7cebb518a3ca89ee53de22ff801991c407584462310f7 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import sys
i... | nuclear-wizard/moose | python/MooseDocs/tree/app_syntax.py | Python | lgpl-2.1 | 4,070 | [
"MOOSE"
] | 9a0565083d9a87229d6cca9d55a376803361d6850019f7644b7de015ecb50bc0 |
#
# Copyright (C) 2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo 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) any later vers... | mkuron/espresso | testsuite/python/actor.py | Python | gpl-3.0 | 3,041 | [
"ESPResSo"
] | 7ecbfe67cc3296883b2b5d51d2b68b037f7c1bf01866708f76b0e069bc8ec3a6 |
from __future__ import print_function, division, unicode_literals
import os
import numpy as np
from scipy import interpolate
import math
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.core.structure import Structure
import warnin... | ashtonmv/twod_materials | twod_materials/friction/analysis.py | Python | gpl-3.0 | 14,880 | [
"VASP",
"pymatgen"
] | c9f8c787eb69c46395f3f1453efc20b308bff17f4b7b1065e792a2058ef67893 |
"""Next-gen alignments with TopHat a spliced read mapper for RNA-seq experiments.
http://tophat.cbcb.umd.edu
"""
import os
import shutil
import sys
import glob
import subprocess
import numpy
import pysam
from bcbio.pipeline import config_utils
from bcbio.ngsalign import bowtie, bowtie2
from bcbio.utils import safe_m... | biocyberman/bcbio-nextgen | bcbio/ngsalign/tophat.py | Python | mit | 14,156 | [
"Bowtie",
"pysam"
] | 10bd08f2b24a93ae61bd2aac73d9faa848b136e8351a29071dd722d8e6f00e60 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2018 David Arroyo Menéndez
# Author: David Arroyo Menéndez <davidam@gnu.org>
# Maintainer: David Arroyo Menéndez <davidam@gnu.org>
# This file is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | davidam/python-examples | chempy/balancingreactions.py | Python | gpl-3.0 | 1,408 | [
"ChemPy"
] | 01cbea1bf3f4205503ca0d9d76bc3f9fa652204198eacd9d0167551bf1a806f5 |
from django.conf.urls import patterns, include, url
from django.contrib import admin
from django.contrib.staticfiles.urls import staticfiles_urlpatterns
from django.contrib.auth.views import login, logout
from django.conf import settings
from django.views.generic import RedirectView
from .views import index
admin.aut... | dwagon/Scheduler | scheduler/scheduler/urls.py | Python | gpl-2.0 | 1,303 | [
"VisIt"
] | c091dd5728076d0547e100985d876e577f57c2091d3f0d400e9be22c696b53a9 |
# 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
# d... | Thingee/cinder | cinder/flow_utils.py | Python | apache-2.0 | 1,392 | [
"VisIt"
] | 0d2bde33d1fdbc38107daef50d14ec9739e55a437a4e9ecfe472565537461b4b |
from __future__ import annotations
import logging
from math import floor, sqrt
import numpy as np
from numpy.linalg import inv, norm
from cctbx.array_family import flex
from dxtbx import flumpy
from scitbx import matrix
from dials.algorithms.profile_model.ellipsoid import chisq_quantile
from dials.algorithms.statis... | dials/dials | algorithms/profile_model/ellipsoid/indexer.py | Python | bsd-3-clause | 7,181 | [
"CRYSTAL"
] | 7a76328b7f0bffb30d17f17a7c89663d0f0db2fe583252b57e68bc7e86eda0ec |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | demis001/scikit-bio | skbio/stats/evolve/_hommola.py | Python | bsd-3-clause | 11,168 | [
"scikit-bio"
] | 23951b96f328b5aee71928a620d6843e3845f305945d4e4db00df5fa5b418148 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/integrator/DPDThermostat.py | Python | gpl-3.0 | 1,962 | [
"ESPResSo"
] | 955ad596c2b23108dee69ff9a9d38173df86f5fd6e7e5f66b2f433e0b8d41109 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from lettuce.django import django_url
import time
@step('I register for the course "([^"]*)"$')
def i_register_for_the_course(_step, course):
url = django_url('courses/%s/about' % world.scenario_dict['COURS... | ahmadiga/min_edx | lms/djangoapps/courseware/features/registration.py | Python | agpl-3.0 | 2,357 | [
"VisIt"
] | f0bbdc48562b792abb89722350568db963e47823d223def9cc8597a5117c242a |
"""
docstring needed
:copyright: Copyright 2010-2017 by the NineML Python team, see AUTHORS.
:license: BSD-3, see LICENSE for details.
"""
from itertools import chain
from nineml.exceptions import NineMLUsageError
from ..base import BaseDynamicsVisitor
class EventPortsDynamicsValidator(BaseDynamicsVisitor):
"""... | INCF/lib9ML | nineml/abstraction/dynamics/visitors/validators/ports.py | Python | bsd-3-clause | 4,686 | [
"VisIt"
] | a9437051cdbdc9508f36197f83b8590d5b616a1000603271d53f0d1d177da963 |
import numpy as np
import pylab as plt
from scipy.stats import norm#is it poisson
import glob,os
#import BeamDeconvolution
import numpy as np
from scipy.optimize import minimize
def ecliptic2quadratic(xc,yc,bmaj,bmin,pa,k=np.log(2)):
'''a*x**2 + b*x*y + c*y**2 + d*x + e*y + f = k
pa in deg'''
#unrotated solution
... | Joshuaalbert/RadioAstronomyThings | src/rathings/notebooks/combine_images.py | Python | apache-2.0 | 8,865 | [
"Gaussian"
] | 4220c6232a309a517d6067481e82bdd10fc2ed37017864769c2a97a63e074b42 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/cc/rintermediates.py | Python | apache-2.0 | 12,286 | [
"PySCF"
] | e17fa0a479f1bc02dcc875619dec79c6234cf953d91059b95ae9558155e4c0a2 |
# Copyright (c) 2010 OpenStack Foundation
#
# 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 ... | larsbutler/swift | test/unit/common/middleware/test_staticweb.py | Python | apache-2.0 | 39,780 | [
"VisIt"
] | 6c434f531153ca1037033e05ff62e5aaaa584527588f19ed4e21a0783b76ff00 |
from flask import Flask, request, g, render_template, redirect, url_for, session, jsonify, json
from apscheduler.scheduler import Scheduler
from flask_oauth import OAuth
import requests
import arduino
import time
import pytz
import datetime
from dateutil.parser import parse
from settings import *
import logging
import ... | beiju/thekindleonthewall | src/python/web.py | Python | mit | 13,234 | [
"VisIt"
] | dbb41046bf5485cb5a6c0c1911facf32ad044096a6b0944a8a5bcafe0b2c32c7 |
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