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#!/usr/bin/env python2
from __future__ import print_function
import os, subprocess, re
from distutils.core import setup, Command
from distutils.command.sdist import sdist as _sdist
from distutils.command.build import build as _build
# The following code is taken from
# https://github.com/warner/python-ecdsa/blob/f03ab... | mineo/edaboweb | setup.py | Python | mit | 3,540 | [
"Brian"
] | 399e9595e778764915a901e82ee3a3cfa9f862730a3a6ac7e24738f04c263af8 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_compiled_1000.py | Python | gpl-3.0 | 3,912 | [
"Brian"
] | f683073ea17d03e76c1038d1723e5619657d9a05d32efbbd8a635465ad341345 |
import urllib, sys,CoolProp, json
sys.path.append('C:\RDKit_2014_09_2')
from rdkit import Chem
from collections import Counter
for fluid in CoolProp.__fluids__:
CAS = CoolProp.CoolProp.get_fluid_param_string(fluid, "CAS")
print fluid, CAS,
if '.ppf' in CAS or '.PPF' in CAS or 'o' in CAS or 'p' in CAS:
... | JonWel/CoolProp | dev/scripts/get_molecular_formulas.py | Python | mit | 1,054 | [
"RDKit"
] | 060b2a8043e66f499215870cf534da854b8adaaa2daea444c0d7b8111f24d656 |
#randomGal.py
from astropy import units as u
from astropy import coordinates
from astroquery.ned import Ned
from astroquery.irsa_dust import IrsaDust
from astropy.coordinates import Angle,ICRS,SkyCoord
from astropy.coordinates.name_resolve import NameResolveError
import math
import os.path
import sys
import itertools... | TateWalker/Galactic-Data | randomGal.py | Python | apache-2.0 | 4,808 | [
"Galaxy"
] | b88a095b450f154e51e199acea5d52b50abc99a51a5fec6f3a777da90cf5228d |
# Copyright 2016 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... | AsimmHirani/ISpyPi | tensorflow/contrib/tensorflow-master/tensorflow/contrib/linalg/python/ops/linear_operator_test_util.py | Python | apache-2.0 | 24,186 | [
"Gaussian"
] | 396852c6c20db90fb371e49fc700c43a0e82bc2baca0c5510e0e7bf5d3bf246a |
#!/usr/bin/env python3
# Copyright (C) 2016, 2017(H)
# Max Planck Institute for Polymer Research
#
# 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, ei... | espressopp/espressopp | examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/hadress.py | Python | gpl-3.0 | 10,383 | [
"CRYSTAL",
"ESPResSo"
] | 90e023efd20db91c0f740d0509c201d8b64465673dd227548372366502f03228 |
from src.utils import customLogger
from src.api.workers import mongoDriver
from dateutil.relativedelta import relativedelta
import datetime
from datetime import datetime
import calendar
workerLogger = customLogger.getWorkerLogger()
def getResponse(hostname = None, scale = None, time_from = None, time_to = None):
if ... | deccanhosts/log_analytics | api/src/api/workers/dbWorker.py | Python | apache-2.0 | 8,257 | [
"VisIt"
] | 431b22cffa164d397b5f6617a05ad48c1d4c328df0ae34aaec8e00e62c413b8f |
from i3pystatus.core.util import internet, require
from i3pystatus.scores import ScoresBackend
import copy
import json
import pytz
import re
import time
from datetime import datetime
from urllib.request import urlopen
LIVE_URL = 'https://www.nhl.com/gamecenter/%s'
SCOREBOARD_URL = 'https://www.nhl.com/scores'
API_URL... | schroeji/i3pystatus | i3pystatus/scores/nhl.py | Python | mit | 14,693 | [
"COLUMBUS"
] | 99f4cde11c964a9e7b21cf6ce99126105110a19b25a0f0080a4d47f82951e4fc |
from toontown.toonbase.ToonPythonUtil import randFloat, normalDistrib, Enum
from toontown.distributed.PythonUtil import clampScalar
from toontown.toonbase import TTLocalizer, ToontownGlobals
import random, copy
TraitDivisor = 10000
def getTraitNames():
if not hasattr(PetTraits, 'TraitNames'):
traitNames = ... | silly-wacky-3-town-toon/SOURCE-COD | toontown/pets/PetTraits.py | Python | apache-2.0 | 9,416 | [
"Gaussian"
] | 6cb473cc2eea316164969a0bf4cffe65676592ac2901577e578b62fbf1f413d3 |
"""
Diversity calculations (:mod:`skbio.diversity`)
===============================================
.. currentmodule:: skbio.diversity
This package provides functionality for calculating community diversity,
including various alpha- and beta-diversity measures.
Subpackages
-----------
.. autosummary::
:toctree: ... | SamStudio8/scikit-bio | skbio/diversity/__init__.py | Python | bsd-3-clause | 842 | [
"scikit-bio"
] | 3bbda75e927b9786999dded52918c368f387534c8833bc52922491a62d2c3e93 |
# $Id$
#
# Copyright (C) 2003-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | ptosco/rdkit | rdkit/Dbase/UnitTestStorageUtils.py | Python | bsd-3-clause | 1,301 | [
"RDKit"
] | c21926a223450ecfc5ad0237ce5327dadc1f7f84037f0c0d23971dbea8802443 |
#
# Attempting to replicate lane detection results described in this tutorial:
# http://www.kdnuggets.com/2017/07/road-lane-line-detection-using-computer-vision-models.html
# https://github.com/vijay120/KDNuggets/blob/master/2016-12-04-detecting-car-lane-lines-using-computer-vision.md
#
# This first version just proce... | guydavis/lane-detect | older/lane_detect.v1.py | Python | mit | 6,929 | [
"Gaussian"
] | 72f6bf25fee6f78910a67696d1edd8603ada6e377aa5b4f2d731557d0675d92e |
'''
Update the transformation files of active transformations,
given an InputDataQuery fetched from the Transformation Service.
Possibility to speedup the query time by only fetching files that were added since the last iteration.
Use the CS option RefreshOnly (False by default) and set the DateKey (empty by default) ... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Agent/InputDataAgent.py | Python | gpl-3.0 | 7,177 | [
"DIRAC"
] | 339b94674b64c39bb2eb6b5c8629ef07c385646cb6054377c7a7abdd6a704d91 |
#!/usr/bin/env python
import multiprocessing as mp
import rospy
from visualization_msgs.msg import MarkerArray, Marker
from geometry_msgs.msg import Point, Quaternion
import numpy as np
from sklearn.cluster import KMeans, DBSCAN
from sklearn import svm
from move_base_loiter import Loiter
from move_base_waypoint import ... | reinaldomaslim/Singaboat_RobotX2016 | robotx_nav/nodes/task2_toplevel.py | Python | gpl-3.0 | 4,821 | [
"VisIt"
] | cbe2b2116830816e9c9c0e72c156c14e8798985e3cbedf37ac80a1b764eec700 |
import sys
import numpy as np
from gpaw import debug
from gpaw.mpi import world
from gpaw.utilities.tools import L_to_lm, lm_to_L
from gpaw.sphere import lmiter
from gpaw.sphere.csh import C, Y, dYdtheta, dYdphi, \
intYY, intYY_ex, intYY_ey, intYY_ez, \
intYdYdtheta_ex, intYdYdtheta_ey, intYdYdtheta_ez, \
... | robwarm/gpaw-symm | gpaw/test/ut_csh.py | Python | gpl-3.0 | 17,947 | [
"ASE",
"GPAW"
] | f48bb977a791d4f38b289c69d70b359a1e3d6bdca25198a5b67b241c93eca23f |
# qmpy/analysis/vasp/calculation.py
import os
import copy
import json
import gzip
import numpy as np
import numpy.linalg
import logging
import re
import subprocess
from collections import defaultdict
from os.path import exists, isfile, isdir
from lxml import etree
from django.db import models
from django.db import t... | wolverton-research-group/qmpy | qmpy/analysis/vasp/calculation.py | Python | mit | 66,831 | [
"CRYSTAL",
"VASP"
] | a572ea8f7eea54de5a460a9caf49bde01d231a354556953d85ba37f6fcbca217 |
from __future__ import print_function, division, absolute_import
import os
import io
import bz2
import gzip
from mdtraj.utils.six import PY2, StringIO
def open_maybe_zipped(filename, mode, force_overwrite=True):
"""Open a file in text (not binary) mode, transparently handling
.gz or .bz2 compresssion, with u... | rmcgibbo/mdtraj | mdtraj/utils/zipped.py | Python | lgpl-2.1 | 1,899 | [
"MDTraj"
] | 95bb70d1d9cc3d135c0121e827dd8bc5f3a52f0b34795223a16a236d40548a60 |
"""
test_transformations
--------------------
"""
import numpy as np
from ..artificial_data.create_artificial_timeseries import create_random_ts,\
create_random_raster, create_brownian_noise_regular_ts
from ..utils.util_operations import format_as_regular_ts
from ..Transformation.filtering import general_filteri... | tgquintela/TimeSeriesTools | TimeSeriesTools/tests/test_transformations.py | Python | mit | 11,832 | [
"Gaussian"
] | 83cc3ac73dc7f663908cddd243033b81a3c4e4901517c20244e533f3ce619680 |
import numpy
from test import V2NUnitTest
from numpy2vtk.data.raw import points
from numpy2vtk.data import mesh
from numpy2vtk.exceptions import Numpy2VtkFormatException
class TestMeshData(V2NUnitTest):
def test_mesh_with_2d_input_data(self):
numpy_points = numpy.array([
[0.0, 0.0],
... | selaux/numpy2vtk | test/data/mesh_test.py | Python | lgpl-3.0 | 5,537 | [
"VTK"
] | 7b1f65b4367836b621c1d69c37f7be3b245b6983dd864bcab5250be4cdadf661 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/delegates/comboboxdelegate.py | Python | gpl-2.0 | 2,127 | [
"VisIt"
] | 70469f4afe377efe98000019290d1a409aa2e80884345f6a5cb1984217ef6ac1 |
#!/usr/bin/env python
#
# Copyright 2008 Jose Fonseca
#
# This program 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 3 of the License, or
# (at your option) any later version.
#
# This ... | nagyistoce/netzob | src/netzob/ExternalLibs/xdot.py | Python | gpl-3.0 | 89,743 | [
"FLEUR"
] | 842695e1bbba741e036d5bc7e78968906ee148d8b4e2ad6f6adb1a33b9543a5d |
#!/usr/bin/env python
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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
... | Multiscale-Genomics/mg-process-fastq | process_damidseq.py | Python | apache-2.0 | 15,359 | [
"BWA"
] | fc87d388120ededdf0116f32ee9c08f52c064de22e6d177a4b07acba065de6d1 |
#!/usr/bin/env python
"""Work in progress: gets all tensors for David King's Summer 2011 project
Right now this only gets all in the volume tensors;
plan on it getting individual fibers eventually. This is just to
get David started"""
import vtk
import sys
def get_num_fibers(filename):
#reader = vtk.vtkDataSetRe... | reckbo/ppl | pipeline-lib/measuretracts/getTensorData.py | Python | bsd-3-clause | 2,583 | [
"VTK"
] | 004472950f81cf3fca001fb3272d1d1c517b4539bef28bd6aac55ac94e0ec534 |
#!/usr/bin/env python
import sys
import numpy as np
from gpaw import debug
from gpaw.mpi import world
from gpaw.utilities.tools import tri2full
from gpaw.hs_operators import MatrixOperator
from gpaw.utilities import compiled_with_sl
from gpaw.utilities.scalapack import scalapack_set
from gpaw.blacs import Redistribut... | qsnake/gpaw | gpaw/test/parallel/ut_hsblacs.py | Python | gpl-3.0 | 16,695 | [
"ASE",
"GPAW"
] | 6533513767d85ac40210911082785b4f84b65a10dac9188c4b9ecb946a5e3afe |
# -*- coding: utf-8 -*-
# This file is part of MOOSE simulator: http://moose.ncbs.res.in.
# MOOSE 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 lat... | dilawar/moose-core | python/moose/moose_constants.py | Python | gpl-3.0 | 1,966 | [
"MOOSE"
] | 311699a2edcec824734b009962a4f64c9a505c483f38d047ae7288b7c9710322 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | kbrebanov/ansible | lib/ansible/modules/network/avi/avi_pkiprofile.py | Python | gpl-3.0 | 5,324 | [
"VisIt"
] | 6db25b58c44ce236df03c70fadec51ac59af6835859fe4786e975137cf85919c |
#!/usr/bin/env python
import sys
import pyzbar
SCRIPTS = ['read_zbar']
# Optional dependency
PILLOW = 'Pillow>=3.2.0'
URL = 'https://github.com/NaturalHistoryMuseum/pyzbar/'
def readme():
# TODO IOError on Python 2.x. FileNotFoundError on Python 3.x.
try:
with open('README.rst') as f:
... | NaturalHistoryMuseum/pyzbar | setup.py | Python | mit | 2,230 | [
"VisIt"
] | 0abc435501ff073c2e48d784190d5c14954daac20c9a986feae1ea93dcb916db |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Magnetic space groups.
"""
import os
import sqlite3
import textwrap
from array import array
from fractions import Fraction
import numpy as np
from monty.design_patterns import cached_class
from pymatgen.... | davidwaroquiers/pymatgen | pymatgen/symmetry/maggroups.py | Python | mit | 23,612 | [
"CRYSTAL",
"pymatgen"
] | c9cba6705fb28e9a9585e07c3806c7a3d4601e86ec7c68ccf8d639f477597d88 |
from __future__ import print_function, division
from sympy.core import S, sympify, Dummy
from sympy.core.function import Function, ArgumentIndexError
from sympy.core.logic import fuzzy_and
from sympy.core.numbers import Integer
from sympy.ntheory import sieve
from math import sqrt as _sqrt
from sympy.core.compatibili... | pandeyadarsh/sympy | sympy/functions/combinatorial/factorials.py | Python | bsd-3-clause | 24,934 | [
"VisIt"
] | c60a00db89a554e44c1c11ad811a70cab6d3fa1acca2972c261ebf4b7659e4f2 |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['CRL', 'CRL_Watchpoint', 'Watchpoint', 'Fiber', 'Fiber_Watchpoint2', 'Watchp... | mkeilman/sirepo | tests/template/srw_generate_data/boron-fiber-crl-with-3-lenses.py | Python | apache-2.0 | 23,950 | [
"Gaussian"
] | 8a6c3f4780536076cd0250cb4524f30d4d5e09cd716b385b23b379f59da91e64 |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import warnings
import threading
import sys
import timeit
from . import sigtools, dlti
from ._upfirdn import upfirdn, _output_len
from scipy._lib.six import callable
from scipy._lib._version import NumpyVersion
... | pbrod/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 116,559 | [
"Gaussian"
] | 5fe9e4fab6846125993142614c21ad771389d10ce3421f8c55cb7c70fb6b23cb |
# -*- coding: utf-8 -*-
#
# Pulsar documentation build configuration file, created by
# sphinx-quickstart on Sun Dec 16 23:16:23 2012.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All ... | jmchilton/pulsar | docs/conf.py | Python | apache-2.0 | 7,875 | [
"Galaxy"
] | 671d7b3a4ca53e91f1d2ee77a1de9c09b040e08518bee8d478fb406e543a7599 |
# -*- coding: utf-8 -*-
# regex patterns for substitutions
XU__PATTERN = ur'ッ(.)' # 小さい u'ッ' は直後の文字を２回に変換
LTU_PATTERN = ur'ッ$' # 最後の小さい u'ッ' は消去(?)
ER__PATTERN = ur'(.)ー' # u'ー'は直前の文字を２回に変換
N___PATTERN = ur'n(b|p)([aiueo])' # n の後ろ... | ian-wilson/python-kana-conversion | kana_conversion/conversion_models.py | Python | mit | 8,389 | [
"BWA"
] | 492cee99fe6598ca2e1c4ff6219d409c9a553bf51b1a06b42aed57cfee7b4024 |
#!/usr/bin/env python
#pylint: disable=missing-docstring, anomalous-backslash-in-string
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Mu... | Chuban/moose | python/MooseDocs/tests/latex/test_elements.py | Python | lgpl-2.1 | 8,341 | [
"MOOSE"
] | 59183bad9c3c71c556bc3be2b33f82276408364abdc6e7520afcd3e731fbd75c |
from aces.materials import Material
from aces.modify import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt,atan
import numpy as np
class structure(Material):
def set_parameters(self):
pass
def setup(self):
pass
def lmp_structure(self):
col=self.unitcell(self.laty,self.latx)
col.set... | vanceeasleaf/aces | aces/materials/C3N-rotate.py | Python | gpl-2.0 | 5,514 | [
"ASE"
] | bec39bd64ede84f36b47269fe125147bde8c8bace547259996ea99e763f45e95 |
# Copyright 2002 by Andrew Dalke. All rights reserved.
# Revisions 2007-2014 copyright by Peter Cock. All rights reserved.
# Revisions 2009 copyright by Cymon J. Cox. All rights reserved.
# Revisions 2013-2014 copyright by Tiago Antao. All rights reserved.
# This code is part of the Biopython distribution and gover... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/BioSQL/BioSeqDatabase.py | Python | apache-2.0 | 30,416 | [
"BioPerl",
"Biopython"
] | d95aef869de6ad5dcaf79bc459a216faa9c080c0ee5eb803ee4bfb5abf255e0a |
# -*- coding: utf-8 -*-
""" Functions related to handling FVCOM outputs. """
from __future__ import print_function, division
import copy
import inspect
import sys
from datetime import datetime, timedelta
from pathlib import Path
import matplotlib.path as mpath
import numpy as np
import pandas as pd
from netCDF4 imp... | pwcazenave/PyFVCOM | PyFVCOM/read.py | Python | mit | 138,166 | [
"NetCDF",
"ParaView"
] | fff4cde06987a85bfad0c32a739e8821d272bebfacb5aca58f1dbaed1df5849c |
# Copyright 2013 by Kamil Koziara. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Module containing resolvers for ambigious entities ids.
"""
import c... | arkatebi/SwissProt-stats | Ontology/IdResolver.py | Python | gpl-3.0 | 1,860 | [
"Biopython"
] | 35e9e40177fbbd72d3430378ed106cba282d2962de3b98e4fab37c853baf9876 |
# coding: utf-8
#
# Copyright 2014 The Oppia 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 requi... | kevinlee12/oppia | core/domain/email_manager.py | Python | apache-2.0 | 80,809 | [
"VisIt"
] | 2d396576fca0d69e2df3ccc35aa70a3d607c59c55d2e0ed2467d5b8d59090c2f |
from neuron import Neuron
from PIL import Image
import os
import sys
import glob
import pickle
# neuron attributes
threshold = 1
width = 35
l_rate = 0.005
err_margin = 0.1 # does nothing so far
a_func = "step"
f_stretch = 1
def main():
print "=============="
print "TRAINING PHASE"
print "===... | TeKrop/PyDigR | reseau_neurones/digit_recog.py | Python | gpl-2.0 | 5,074 | [
"NEURON"
] | 95f0376e6fdb46329735a50bccf4cf32aabc7dcde9c32c0a6725ebe5578b10d2 |
# Copyright 2017 Google Inc. 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 applicable law or a... | cloudendpoints/endpoints-python | test/testdata/sample_app/data.py | Python | apache-2.0 | 10,260 | [
"COLUMBUS",
"TINKER"
] | 2d555222149f4ae5e8a583d3ccfeac1b0694c90d2a1551fde25959e51095ed0b |
from scrapy.spiders import CrawlSpider, Rule
from scrapy.linkextractors import LinkExtractor
out_file = 'urls_out'
class NetCDF_Spider(CrawlSpider):
name = 'netcdf'
allowed_domains = ['uchicago.edu']
start_urls = [
'http://users.rcc.uchicago.edu/~davidkelly999/'
]
rules = ( Rule(LinkExtrac... | RDCEP/EDE | ede/crawler/crawler/spiders/netcdf_spider.py | Python | mit | 600 | [
"NetCDF"
] | be782f7e7db4ccb2c4596e4f11cb9b190649d54697ea545fbea652fb8f767604 |
"""
Tally atoms in each given region.
Regions are given by X, Y, or Z coordinates dividing the space up. The number
of atoms will be counted and written to the output.
"""
import argparse
def main():
"""Drive the main functionality."""
# Parse the command line arguments.
parser = argparse.ArgumentPars... | tschijnmo/lammps_scripts | tally_regions.py | Python | mit | 3,786 | [
"LAMMPS"
] | 6e826c4dabb7798025025cd9dbe794f4f08553fe1161af37d2836749fc9b2118 |
# -*- coding: utf-8 -*-
"""
Created on Thu Oct 23 15:54:36 2014
This file is part of pyNLO.
pyNLO 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 optio... | ycasg/PyNLO | src/validation/dfg_unit_test.py | Python | gpl-3.0 | 9,014 | [
"CRYSTAL"
] | 03f90f0191417f042f9035c00621ccb952ff6bb3ed1efcbfe6f26345b430ed44 |
# experimental data for tv analysis
# hyperparameter for variance of weights trajectory:
# 0.0015
import sys
sys.path.append("/Users/roger/Dropbox/pyglm-master")
sys.path.append("/Users/roger/Dropbox/TVpgGLM-v1/TVpgGLM/libs")
import numpy as np
np.random.seed(5)
import pickle
import seaborn as sns
sns.set_style("w... | sheqi/TVpgGLM | runtime/exp_tv_demo1.py | Python | mit | 6,625 | [
"NEURON"
] | 799ffd7fe8494f532ccfe4eaada131f202d6be4ec953bf22f3f898233c593733 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | andreaso/ansible | lib/ansible/modules/network/avi/avi_serviceenginegroup.py | Python | gpl-3.0 | 24,318 | [
"VisIt"
] | e9ab05bb3505f78d6ec1e96f03b92c869e18f84adfe72ce9f0b9b0dfd73955f5 |
'''
Created on Sep 10, 2012
@author: mkiyer
'''
import argparse
import logging
import sys
import shelve
import operator
import pysam
from chimerascan.lib import config
from chimerascan.lib.chimera import parse_discordant_cluster_pair_file, \
ORIENTATION_5P, ORIENTATION_3P
from chimerascan.lib.sam import get_clip... | tectronics/chimerascan | chimerascan/pipeline/process_spanning_alignments.py | Python | gpl-3.0 | 11,479 | [
"pysam"
] | aa2704a06e2b678e5834ff7c181ac1b718f416dc1ac7dc5e13b887e566be96bd |
#!/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... | sunqm/pyscf | pyscf/fci/test/test_addons.py | Python | apache-2.0 | 21,528 | [
"PySCF"
] | 02f93845db233a7aceedf11850edf5862ea6d697a21884c11820c37c152ddcf5 |
#
# GMSK modulation and demodulation.
#
#
# Copyright 2005,2006,2007 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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 v... | levelrf/level_basestation | gr-digital/python/gmsk.py | Python | gpl-3.0 | 10,998 | [
"Gaussian"
] | 07de7a765cb66dae1e96a9d1c9f9e6d8d082fb2c63d03323ee2f37f69d44b895 |
"""
Sample script that runs netcdf4 functions logged by recipy.
"""
# Copyright (c) 2016, 2018 University of Edinburgh and Netherlands eScience
# Center
from __future__ import (nested_scopes, generators, division,
absolute_import, with_statement,
print_function, unicode... | recipy/recipy | integration_test/packages/run_netcdf4.py | Python | apache-2.0 | 1,726 | [
"NetCDF"
] | 48c39d58933278d5bcfdddbeb1b84775e6d0b444670308df01487739365bda37 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Code to support writing parsers.
Classes:
AbstractParser Base class for parsers.... | asherkhb/coge | bin/last_wrapper/Bio/ParserSupport.py | Python | bsd-2-clause | 15,536 | [
"Biopython"
] | 376f23a0b9999e450f7ee080aabd4071c5ea3d295c09f211fb8e3d4763404b24 |
#!/usr/bin/env python
import sys
import math
from functools import partial
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
from Tkinter import Pack
VTK_DATA_ROOT = vtkGetDataRoot()
import Tkinter
#from vtk.tk.vtkTkRenderWindowInteractor import vtkTkRenderWindowInteractor
from vtk.tk.v... | msmolens/VTK | Rendering/Tk/Testing/Python/TestTextActor3D.py | Python | bsd-3-clause | 8,355 | [
"VTK"
] | 6682f48fbb1a91dc165d0a7cae33855df18b52bb6f85ffc148538ee09aba68ca |
#!/usr/bin/env python
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Script to plot density of states (DOS) generated by an FEFF run
either by site, element, or orbital
"""
__author__ = "Alan Dozier"
__credits__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyr... | vorwerkc/pymatgen | pymatgen/cli/feff_plot_dos.py | Python | mit | 2,268 | [
"FEFF",
"pymatgen"
] | ae1849330f4939304a0a15d9c7bdcd9c1d7ec3172eb5dd3e7e020ccaaa03f2f5 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | yipenggao/moose | python/chigger/tests/exodus/labels/points.py | Python | lgpl-2.1 | 1,353 | [
"MOOSE"
] | 98a36231dbe39565e923f1b2a88dc9cdc336874fa9e83e559a9ed51011c36b28 |
"""
some random tools, slow code.
"""
import collections
import imp
import os
import time
import types
import numpy as np
import scipy.signal as signal
import sparco.mpi as mpi
# TODO docstrings for all methods
###################################
########### OBJECTIVE
###################################
# TODO giv... | smackesey/sparco | sparco/util.py | Python | gpl-2.0 | 4,235 | [
"Gaussian"
] | e9c396d15c4e5fd6e409c9263da95bfc9193bf277428452c336ee8bc9027ffc1 |
# Sebastian Raschka 2015
# mlxtend Machine Learning Library Extensions
import numpy as np
class Adaline(object):
""" ADAptive LInear NEuron classifier.
Parameters
------------
eta : float
Learning rate (between 0.0 and 1.0)
epochs : int
Passes over the training dataset.
learning... | YoungKwonJo/mlxtend | mlxtend/classifier/adaline.py | Python | bsd-3-clause | 4,507 | [
"NEURON"
] | 85d9e28be1657459bce1394fbdb566475a33baffba0b6a870ce16dc23ee92bea |
# 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 PyRseqc(PythonPackage):
"""RSeQC package provides a number of useful modules that can
... | LLNL/spack | var/spack/repos/builtin/packages/py-rseqc/package.py | Python | lgpl-2.1 | 1,238 | [
"pysam"
] | 6559d824bbc8fe4458d9abd4a09a5d248dc8a8648aecf04c8031bf03dbfb95dd |
#! /usr/bin/env python
########################################################################
# File : dirac-admin-bdii-info
# Author : Aresh Vedaee
########################################################################
"""
Check info on BDII for a given CE or site
"""
from __future__ import print_function
__... | fstagni/DIRAC | ConfigurationSystem/scripts/dirac-admin-bdii-info.py | Python | gpl-3.0 | 4,617 | [
"DIRAC"
] | 9243dbfe2b4c2a4bcf2e45f8ef05adc02d8584f6a6e1878a923932e146e681a0 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2018, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | subutai/htmresearch | projects/union_path_integration/entorhinal/gaussian_simulation.py | Python | agpl-3.0 | 9,160 | [
"Gaussian"
] | f18c08fcfc32f464f283178ca1c7a5232f88a255858c9fb02faa3731c9cdcc72 |
import os
import simulation.weathergen as weathergen
import simulation.dairy_herd as dairy
import simulation.financials as financials
import simulation.forage as forage
import simulation.maize as maize
import simulation.farm_admin as admin
import simulation.models as models
from csvReader.csvReader import CsvReadErro... | BenLatham/FLOSS-Agricultural-Simulation | simulation/simulation.py | Python | mit | 2,359 | [
"ADF"
] | 1ddd640216c72ae32f3a6e401db789e2688b9c867c39136cc1c81ff457cad901 |
# -*- coding: utf-8 -*-
"""
wiritten by Till A. Hoffmann <http://tillahoffmann.github.io>.
"""
import numpy as np
from scipy.spatial.distance import cdist
class Gaussian_kde(object):
"""Representation of a kernel-density estimate using Gaussian kernels.
Kernel density estimation is a way to estimate the pro... | kklmn/xrt | xrt/kde.py | Python | mit | 11,419 | [
"Gaussian"
] | 43ccf0a5581b8c0b77a890b90a48163a6aef0a9283d32d9a8ed9de75fce496f0 |
import pytest
from pytest import raises
from viper import compiler
from viper.exceptions import StructureException, \
TypeMismatchException
# These functions register test cases
# for pytest functions at the end
fail_list = []
def must_fail(code, exception):
fail_list.append((code, exception))
pass_list ... | NedYork/viper | tests/parser/syntax/test_invalids.py | Python | mit | 2,967 | [
"MOOSE"
] | 83d2e1163a77362c64b75415c84bee07435d4b803830a7ad864fe45ea12c6d70 |
# -*- coding: utf-8 -*-
#LICENCE
#
# This File is part of the Webbouqueteditor plugin
# and licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported
# License if not stated otherwise in a files head. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc-sa/3.0... | pli3/e2-openwbif | plugin/controllers/BouquetEditor.py | Python | gpl-2.0 | 25,951 | [
"VisIt"
] | 266da03ea059f3bfebcd327ef7caade156b4c0555bb78ebe1176bf2bdf48f623 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Analytical nuclear gradients of CASCI excited state.
'''
from pyscf import gto
from pyscf import scf
from pyscf import mcscf
from pyscf import lib
import inspect
mol = gto.M(
atom = [
["O" , (0. , 0. , 0.)],
[1 , (0. ... | sunqm/pyscf | examples/grad/12-excited_state_casscf_grad.py | Python | apache-2.0 | 3,547 | [
"PySCF"
] | 392ad7c8009a0f67356eca8010234c9c96559dab24f7f000e0f1212f013838b8 |
#
# interface.py: support for generating XML with interface description
#
# Copyright (C) 2017
# Red Hat, Inc. All rights reserved.
#
# 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 ver... | vathpela/anaconda | pyanaconda/dbus/interface.py | Python | gpl-2.0 | 16,681 | [
"VisIt"
] | f413d74e5aee6fc6b8fab2c0cc92ec62bc93a45f25fa1944e7c9d76165cd57b7 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.courseware import CoursewarePage
from ...pages.... | beni55/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 3,301 | [
"VisIt"
] | 4f8a67e63e73b243c8e052ee7fc4643351c24c1f8959680ec5de7acd9789c739 |
"""Provide estimates of sample purity and subclonal copy number using THetA.
Identifying cellularity and subclonal populations within somatic calling using
tumor normal pairs.
https://github.com/raphael-group/THetA
"""
import os
import sys
import subprocess
import pybedtools
import pysam
import toolz as tz
from bcb... | elkingtonmcb/bcbio-nextgen | bcbio/heterogeneity/theta.py | Python | mit | 10,093 | [
"pysam"
] | a6c46376d693e74830054b633e34a41d1d198aa1ecd20d47c6b6b7414c3b705b |
from urllib2 import urlopen, HTTPError
from urllib import quote
import lxml.html
import requests
import json
import csv
import pprint
import time
import os
import pandas as pd
import traceback
from collections import defaultdict
DATA_DIR = 'data'
DATA_REPORTS = ["DataRequest","DataExemption","DataAppeal","DataProcess... | sunlightlabs/foia-data | data/foia.gov/scrape_foia_data_officialx_double_output_clayton.py | Python | gpl-3.0 | 6,903 | [
"ADF"
] | ee3513243ab82a9ebe112df3e6dfc5639927829feb8a37d442863ccf50755712 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
import check
import time
import random
@choice
def action(assertCheck, id, channel_input=... | runefriborg/pycsp | test/commtest.py | Python | mit | 5,924 | [
"Brian"
] | 715f0e902fd21d497b9c3e6b7866232a9e08c30865d4d73c71ea86708b3e48d3 |
"""
.. inheritance-diagram:: pyopus.problems.mgh
:parts: 1
**More-Garbow-Hillstrom test functions with first derivatives
(PyOPUS subsystem name: MGH)**
Translated from MATLAB implementation (with bugs omitted).
All test functions in this module are maps from :math:`R` to :math:`R^n`.
Every function... | blorgon9000/pyopus | pyopus/problems/mgh.py | Python | gpl-3.0 | 52,180 | [
"Gaussian"
] | 4d726d3185ea0ea1bec40114648ae11f6f312ff5e8760cfe9b929c0548943936 |
#
# Copyright (C) 2000 Stephen Davies
# Copyright (C) 2000 Stefan Seefeld
# All rights reserved.
# Licensed to the public under the terms of the GNU LGPL (>= 2),
# see the file COPYING for details.
#
from Synopsis.Processor import Parameter
from Synopsis import FileTree
from Synopsis.Formatters.HTML.View import View
f... | stefanseefeld/synopsis | Synopsis/Formatters/HTML/Views/FileListing.py | Python | lgpl-2.1 | 2,722 | [
"VisIt"
] | b2c7e439aa01471e55fd74c9f4b1cf856595f866cec23e3ed2dddb3971cf1bbb |
"""
Performance test created using multi-mechnize to analyze time
for update processing with ElasticSearch.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import random
import string
import time
from DIRAC.WorkloadManagementSystem.DB.ElasticJobParamete... | yujikato/DIRAC | tests/Performance/ESJobMonitoring/test_scripts/update.py | Python | gpl-3.0 | 1,043 | [
"DIRAC"
] | fde6c0ea4753bccc8a83d5a6385eddc02e315e04ef16307ab496286673ec18b5 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/task.py | Python | lgpl-2.1 | 29,861 | [
"MDTraj"
] | a635fa42548d8f41a73fd0e9c6c70bc3e9a9bed1b91d2fff90d9e85a7015a8c2 |
# Read .Mat Files
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz as ... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/AI_Surface_Recognition/src/state_accuracy_variation.py | Python | mit | 1,192 | [
"Mayavi"
] | 855fe46ec8c754b9b0d15c4d658c60258d80df44b90583279dcd55b9e832295d |
from __future__ import unicode_literals
from __future__ import print_function
import logging
import requests
import utilities
from bson.objectid import ObjectId
import json
def query_cliff(sentence, host, port):
"""
Takes a sentence from a news article, passes it to the ... | openeventdata/phoenix_pipeline | geolocation.py | Python | mit | 16,025 | [
"BWA"
] | 2afccc8bf0e32894d5a720c635afa2f500f7cc24dd3f9904a3e3d8d418b7d24a |
import numpy as np
from scipy import stats
import matplotlib.pyplot as plt
# Ignore the unused warning: Axes3D import
# enables projection='3d' to be used without error
from mpl_toolkits.mplot3d import Axes3D
#ignore the warning from * (import all functionality utils)
from brownian_manifold.utils import *
class Mani... | hankbesser/brownian-manifold | brownian_manifold/manifold.py | Python | mit | 22,725 | [
"Gaussian"
] | 78073278e70591d203ed71e4519cef629a6f9b4e53f97af04fc95c0a3f22624c |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 8 20:25:18 2017
@author: sitibanc
"""
import numpy as np
from scipy import signal
from PIL import Image
def gen2DGaussian(stdv, mean, h, w):
x, y = np.meshgrid(np.linspace(-1, 1, w), np.linspace(-1, 1, h))
d = np.sqrt(x ** 2 + y ** 2)
... | SitiBanc/1061_NCTU_IOMDS | 1108/HW7/HW7.py | Python | apache-2.0 | 3,177 | [
"Gaussian"
] | 4a9d60d79209644295e63b28268075b971caa45c226db4bad25ecea798eb5cc0 |
import numpy as np
from ase.lattice.spacegroup import crystal
# A diamond unit cell
diamond = crystal('C', [(0,0,0)], spacegroup=227,
cellpar=[3.57, 3.57, 3.57, 90, 90, 90])
assert len(diamond) == 8
correct_pos = np.array([[ 0. , 0. , 0. ],
[ 0. , 0.5 , 0.5 ],
... | grhawk/ASE | tools/ase/test/crystal.py | Python | gpl-2.0 | 2,573 | [
"ASE",
"CRYSTAL"
] | 16cd46155f253a71ea96359701d66763c1a9d328e2e209e82b6452e56c9f2244 |
"""
Examples:
To smear an already smeared spectrum with a light yield of 200 to a
a light yield of 190 then the following lines are required::
>>> smearer = smear.SmearEnergySmearLY()
>>> ly = smearer.calc_smear_ly(190., cur_ly=200.)
>>> smearer.set_resolution(ly)
>>> smeared_spec = smearer.weighte... | mjmottram/echidna | echidna/core/smear.py | Python | mit | 29,217 | [
"Gaussian"
] | 54d9b10ad44019974998dfb240c9de094b1cfffee917e70876a171e75b83293f |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/presentations/lib/mediaitem.py | Python | gpl-2.0 | 15,551 | [
"Brian"
] | c0825f9f4b8c2bbd41752b4d94bfca3ab3f3cca97b7597c4c62a76db5e683fcf |
#!/usr/bin/python
#
# Copyright 2012 Google Inc. 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 b... | nearlyfreeapps/python-googleadwords | examples/adspygoogle/adwords/v201109_1/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,934 | [
"VisIt"
] | 67cb83fbd1e0f9f8653327cf8f23e5fb2b12f6813bae32cad9de118ffa4716c6 |
"""
Test for MlabSource and its subclasses.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
import unittest
import numpy as N
from mayavi.tools import sources
################################################################################
# `Tes... | dmsurti/mayavi | mayavi/tests/test_mlab_source.py | Python | bsd-3-clause | 28,306 | [
"Mayavi"
] | 4ca811f02e9f4ddea893dd8b4ac74d6ad36bb26d4d8c04a6dbd58a780ac525ef |
"""The base source object from which all MayaVi sources derive.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import List, Str
from apptools.persistence.state_pickler import set_state
from traitsu... | dmsurti/mayavi | mayavi/core/source.py | Python | bsd-3-clause | 9,253 | [
"Mayavi",
"VTK"
] | 33d5b38c661b0960b22ded360a2443a40f6d018d45b19c3e459461001a44e99a |
#!/usr/bin/python
# (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# most of it copied from AWX's scan_packages module
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': ... | t794104/ansible | lib/ansible/modules/packaging/os/package_facts.py | Python | gpl-3.0 | 11,246 | [
"Brian"
] | 81d239b529c44a72c4bd25b4bd55d34a3feefdf32362002c9760d6edf60785fb |
import sys
import os
from PySide.QtGui import (QWidget, QDialog, QListWidget, QListWidgetItem,
QVBoxLayout, QStackedWidget, QListView,
QHBoxLayout, QDialogButtonBox, QCheckBox,
QMessageBox, QLabel, QLineEdit, QSpinBox,
... | zenotech/MyClusterUI | myclusterui/myclusterui.py | Python | bsd-3-clause | 12,952 | [
"ParaView"
] | 86fbb56a88743dee9383e2c57334b8249ee8e9595702fbd0b90681868ae214f9 |
# 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... | horance-liu/tensorflow | tensorflow/contrib/bayesflow/python/ops/hmc_impl.py | Python | apache-2.0 | 28,497 | [
"Gaussian"
] | eaa67374f7cc6d68cd936c4e880e2fb11d6aa8af37ffc45388dab461a6c769bc |
from lammps_data.crystal import Packing
def test_cubic_unit_cell_should_return_cubic_vectors():
# Parameters for ECOLEP_clean from CoRE database and expected results from Avogadro
expected_vectors = [[18.64000, 0.00000, 0.00000],
[0.00000, 18.64000, 0.00000],
[0... | kbsezginel/lammps-data-file | tests/test_unit_cell_vectors.py | Python | mit | 4,119 | [
"Avogadro",
"CRYSTAL"
] | 00c3444884f7303426ba13b6b3fcb1b21f2c27d83b25644387c40f6dcb3ff816 |
'''
@file : plurals.py
@author (A) : Anirudh Gopu
@project : Social List
this file is not used anywhere
This work is licensed under the
Creative Commons Attribution-NonCommercial-ShareAlike 4.0
International License. To view a copy of this license,
visit http://creativecommons.org/licenses/by-nc-sa/4.0/.
'''
#To chec... | SummerProject16/project | CMUTweetTagger/testFile3.py | Python | cc0-1.0 | 1,107 | [
"VisIt"
] | 45564b232a2521356fad17c159301952283da708c3b5836700f1bcb7dde62d2a |
""" The SiteSEMapping module performs the necessary CS gymnastics to
resolve site and SE combinations. These manipulations are necessary
in several components.
Assumes CS structure of: /Resources/Sites/<GRIDNAME>/<SITENAME>
"""
from __future__ import absolute_import
from __future__ import division
fro... | yujikato/DIRAC | src/DIRAC/Core/Utilities/SiteSEMapping.py | Python | gpl-3.0 | 5,714 | [
"DIRAC"
] | 0a1475d10e9c4fe598a86526b6018545f1f2eaa263044769ed495d6d12e637ea |
""" Test class for plugins
"""
# pylint: disable=protected-access, missing-docstring, invalid-name,
# line-too-long
# imports
import pytest
from mock import MagicMock
from DIRAC.DataManagementSystem.Client.test.mock_DM import dm_mock
from DIRAC.Resources.Catalog.test.mock_FC import fc_mock
from DIRAC import gLogger... | fstagni/DIRAC | TransformationSystem/Agent/test/Test_Plugins.py | Python | gpl-3.0 | 6,130 | [
"DIRAC"
] | 3fd131fe2900b24971de0d867b72be91d3300d39a193e157f898da1aff7592ff |
# -*- coding: utf-8 -*-
#
# Copyright 2014 David Emms
#
# This program (OrthoFinder) is distributed under the terms of the GNU General Public License v3
#
# 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 Sof... | davidemms/OrthoFinder | scripts_of/util.py | Python | gpl-3.0 | 18,566 | [
"BLAST"
] | 20359ed421296275db66f3f109864a18ba0d203af27e1b88241d844d0b528c04 |
import json
from datetime import timedelta
from glob import glob
from os.path import join, exists
import numpy as np
import pandas as pd
from grib2io import Grib2Message
from netCDF4 import Dataset, num2date
from scipy.interpolate import interp1d
from scipy.ndimage import gaussian_filter
from scipy.signal import fftco... | djgagne/hagelslag | hagelslag/processing/EnsembleProducts.py | Python | mit | 26,206 | [
"Gaussian",
"NetCDF"
] | f7b637d66d3180dc31af7a326bfa3834e0873d5c6736f8e2a3e9b8725427ce95 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: TJ Lane
# Contributors: Robert McGibbon and Jason Swails
#
# M... | dwhswenson/mdtraj | tests/test_crd.py | Python | lgpl-2.1 | 1,409 | [
"MDTraj"
] | fa9928939c36cd1f7590aadf3db55c39eb94566ee3af6b3bbafe9e595ce7496d |
'''
Created on Jun 10, 2013
Updated Sept 22, 2014
@author: Graham Rockwell
@summary:
Method for working through sequencing of recombination strains.
Focused on comparing recombination oligos used with sequencing results
Searching multiple file and running analysis in parallel.
!Currently broken an... | bionomicron/Redirector | core/genetic/RecSeqAnalysis.py | Python | mit | 14,668 | [
"BLAST"
] | 944217676578a058b2ba8b8f6c3732c3d57e30ef11866cb379d0cede2d1a0386 |
""" GOCDBClient module is a client for the GOC DB, looking for Downtimes.
"""
__RCSID__ = "$Id$"
import urllib2
import time
import socket
from datetime import datetime, timedelta
from xml.dom import minidom
from DIRAC import S_OK, S_ERROR, gLogger
def _parseSingleElement( element, attributes = None ):
"""
Given... | miloszz/DIRAC | Core/LCG/GOCDBClient.py | Python | gpl-3.0 | 11,488 | [
"DIRAC"
] | ce18caeaa09b9562a82bf5ee4a6c1d1ada5aa607946f33099fde46857ef3b858 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement local access classes for the CPU."""
from hoomd.data.local_access import (ParticleLocalAccessBase,
BondLocalAc... | joaander/hoomd-blue | hoomd/data/local_access_cpu.py | Python | bsd-3-clause | 3,666 | [
"HOOMD-blue"
] | 067aa5c8f3201ca11aaf7239302d303f2bb41505cf7ce12c8dbb6d9c2d0a6a00 |
"""
network
~~~~~~~
Some basic "network" / graph theory tools.
We roll our own graph class as we don't need much, and we are particularly
interested in "embedded planar" graphs, that is, the exact way our graph is
presented in the plane is vital.
"""
import numpy as _np
import scipy.spatial as _spatial
from . import... | QuantCrimAtLeeds/PredictCode | open_cp/network.py | Python | artistic-2.0 | 50,830 | [
"VisIt"
] | ba77aa7239a2134d9d9f2465c36c6bc893a30a6644e55507b9e9724856ada33a |
# -*- coding: utf-8 -*-
"""
eve.io.mongo.parser
~~~~~~~~~~~~~~~~~~~
This module implements a Python-to-Mongo syntax parser. Allows the MongoDB
data-layer to seamlessy respond to a Python-like query.
:copyright: (c) 2017 by Nicola Iarocci.
:license: BSD, see LICENSE for more details.
"""
impo... | bcrochet/eve | eve/io/mongo/parser.py | Python | bsd-3-clause | 4,462 | [
"VisIt"
] | db499f44582e954d5fd83f10001d31f4f8f124744f04da364b4de0ff18901f34 |
# coding=utf-8
# Copyright 2022 GradMax 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 ag... | google-research/growneuron | growneuron/growers.py | Python | apache-2.0 | 21,505 | [
"Firefly",
"NEURON"
] | d6e4fd374216894e9fb0b180dbcc7a4762cd9ba2f14891bc4ae8a4da231c2c75 |
"""
==========================================
Outlier detection with several methods.
==========================================
When the amount of contamination is known, this example illustrates two
different ways of performing :ref:`outlier_detection`:
- based on a robust estimator of covariance, which is assumin... | beepee14/scikit-learn | examples/covariance/plot_outlier_detection.py | Python | bsd-3-clause | 3,891 | [
"Gaussian"
] | eec712403f6ec854de21503f362884880cbdfd6a8894e6bc2abe25303fe6aeae |
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