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#!/usr/bin/python
# Copyright (C) 2012,2013,2014,2015,2016 The ESPResSo project
# Copyright (C) 2011 Olaf Lenz
# Copyright 2008 Marcus D. Hanwell <marcus@cryos.org>
#
# 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 ... | Marcello-Sega/espresso | maintainer/git2changelog.py | Python | gpl-3.0 | 4,736 | [
"ESPResSo"
] | 4773e48bd229e348b7121bb9893920a653ce7dc5caf326c5669159e6055bc096 |
#!/usr/bin/env python
"""
This file provides a more advanced example of vtkTable access and
manipulation methods.
"""
from vtk import *
#------------------------------------------------------------------------------
# Script Entry Point (i.e., main() )
#------------------------------------------------------... | timkrentz/SunTracker | IMU/VTK-6.2.0/Examples/Infovis/Python/tables4.py | Python | mit | 1,331 | [
"VTK"
] | 08fd600c1cd0138972ca71c78609c0b0f1b2f6fd4972deb64b3332772977b135 |
from __future__ import absolute_import
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import Quer... | jainayush975/zulip | zerver/models.py | Python | apache-2.0 | 63,723 | [
"VisIt"
] | 4e856323a4d6e41f60b13bc86ec5d2307ceb5e7fc11871c2ebf50ccd91279829 |
# coding: utf-8
# In[1]:
from __future__ import division
from sys import stdout
import numpy as np
import networkx as nx
from sklearn.metrics import normalized_mutual_info_score
from sklearn.metrics.pairwise import euclidean_distances
from sklearn.metrics import pairwise_distances_argmin_min
import matplotlib.py... | DavidMcDonald1993/ghsom | ghsom_parallel.py | Python | gpl-2.0 | 17,719 | [
"NEURON",
"VisIt"
] | 33f4fff3456c67c3098bbb444e20d7edef0b65dff9883d42b02eecaa584f5688 |
import stl
import traces
from pytest import raises, approx
from lenses import bind
from magnum.solvers.cegis import (solve, MaxRoundsError, encode_refuted_rec,
find_refuted_radius, smt_radius_oracle)
def test_feasible_example2_cegis():
from magnum.examples.feasible_example2 impo... | mvcisback/py-blustl | magnum/solvers/test_cegis.py | Python | bsd-3-clause | 4,263 | [
"Psi4"
] | 61fa5a8abe801e0497663f4b666fca28ed431c227f8c0a8628060ab0ebb35c7b |
tutorial_tests = """
Let's try a simple generator:
>>> def f():
... yield 1
... yield 2
>>> for i in f():
... print i
1
2
>>> g = f()
>>> g.next()
1
>>> g.next()
2
"Falling off the end" stops the generator:
>>> g.next()
Traceback (most recent call la... | wang1352083/pythontool | python-2.7.12-lib/test/test_generators.py | Python | mit | 50,769 | [
"VisIt"
] | 808427b654a2cbdce5932942c6e671e0029fee997851f62cbcb7fae4b577ba4b |
# -*- coding: utf-8 -*-
import sys
import os
import re
import time
"""
Python Nagios extensions
"""
__author__ = "Drew Stinnett"
__copyright__ = "Copyright 2008, Drew Stinnett"
__credits__ = ["Drew Stinnett", "Pall Sigurdsson"]
__license__ = "GPL"
__version__ = "0.4"
__maintainer__ = "Pall Sigurdsson"
__email__ = "p... | evilchili/nagiosnmapper | pynag/Parsers/__init__.py | Python | bsd-2-clause | 37,674 | [
"MOE"
] | 330419632e43cf0e951fd145b85b88b2331e4108da0af92595ff149da28edd58 |
# Copyright (c) 2012, GlaxoSmithKline Research & Development Ltd.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# ... | AlexanderSavelyev/rdkit | Contrib/mmpa/indexing.py | Python | bsd-3-clause | 21,045 | [
"RDKit"
] | 42b341dde820d9abc180e03be6ea14769fc8e548c851425adfe54f499ab34010 |
#!/usr/bin/env python
##!/home/users/sblair/anaconda2/bin/python
##!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Fri Jul 14 08:54:21 2017
@author: sblair
"""
import sys
sys.path.insert(1,'.')
import FluidChannel as fc
import argparse
parser = argparse.ArgumentParser(prog='wmb_geom.py',
... | stu314159/pyNFC | ssTest_geom.py | Python | mit | 1,568 | [
"VTK"
] | 3109a1a84b72170a06b191184449e63f40809a22f1b4b34d4e199993d0cb3574 |
#!/usr/bin/env python
"Merges Bisulphite reads by finding reciprocal pairs for PE watson / crick sequencing reads"
import pysam
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from pyfaidx import Fasta
import argparse
#seq_in = SeqIO.parse(open('/Volumes/data/epiGBS/test_scabi/join_all.fq', 'r'), 'fastq')
... | thomasvangurp/epiGBS | de_novo_reference_creation/mergeBSv3.py | Python | mit | 13,261 | [
"Galaxy",
"pysam"
] | 91c9636684c0759588ef713d0f459892ec8c9de09538451b65c3359ef88511d5 |
# The MIT License (MIT)
# Copyright (c) 2013-2015 Brian Madden and Gabe Knuth
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# ... | town-hall-pinball/project-alpha | scriptlets/attract.py | Python | mit | 1,555 | [
"Brian"
] | 6642808fd6023cd1b42e331c958dc995731059afa3ad0d86391f1921fc19c24f |
'''
SASSIE: Copyright (C) 2011 Joseph E. Curtis, Ph.D.
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 3 of the License, or
(at your option) any later version.
... | madscatt/zazzie | src_2.7/sassie/test_sassie/interface/em_to_sas/test_em_to_sas_filter.py | Python | gpl-3.0 | 8,871 | [
"Gaussian"
] | bd3190fab8998c447e94786d317c25ebd6a60ca18cb7560cb220e4fd3e0e8fec |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 15 18:04:09 2017
@author: AutuanLiu
"""
# pyts的使用
import numpy as np
from scipy.stats import norm
n_samples = 10
n_features = 48
n_classes = 2
delta = 0.5
dt = 1
x = 0.
X = np.zeros((n_samples, n_features))
X[:, 0] = x
for i in range(n_samples):
start = x
... | AutuanLiu/RLang | datapro/python/ppaSax.py | Python | mit | 1,386 | [
"Gaussian"
] | 40734fa1c91c595065b5775c064b77c44de84fbbda69278495548e9d315db3af |
#!/usr/bin/env python
import json
import ntpath
import operator
import os
from functools import reduce
from CTDopts.CTDopts import (
_InFile,
_OutFile,
CTDModel,
ModelTypeError,
Parameter,
ParameterGroup,
Parameters
)
from lxml import etree
from ..common import logger
from ..common.excepti... | WorkflowConversion/CTDConverter | ctdconverter/common/utils.py | Python | gpl-3.0 | 18,108 | [
"Galaxy",
"OpenMS",
"VisIt"
] | 7343f3a4e7968af2077bc45343b102e3ce26addf779bb683da6fa840bbdf58d3 |
# -----------------------------------------------------------------------------
# User configuration
# -----------------------------------------------------------------------------
outputDir = '/Users/seb/Desktop/Geometry-diskout/'
inputFile = '/Users/seb/Downloads/ParaViewData-3.10.1/Data/disk_out_ref.ex2'
# -------... | Kitware/arctic-viewer | scripts/examples/paraview/samples/Geometry-diskout.py | Python | bsd-3-clause | 4,125 | [
"ParaView"
] | 75782691f1543748759d5cd643f73fcfe7691ee60d07db510e095aea488e350f |
#!/usr/bin/env python
"""
PyVTK provides tools for manipulating VTK files in Python.
VtkData - create VTK files from Python / read VTK files to Python
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given und... | chunshen1987/iSS | utilities/for_paraview/lib/__init__.py | Python | mit | 10,057 | [
"VTK"
] | 6c73bd620905b2e1913fcdbafe4f9b395a9908b949874f40fbad1c994d2592e2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2017-03-20
# @Filename: conftest.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: Brian Cherinka
# @Last modified time: 2018-07-21 21:51:06
i... | albireox/marvin | python/marvin/tests/conftest.py | Python | bsd-3-clause | 20,539 | [
"Brian",
"Galaxy"
] | 48bea8e966717c25ae1417d2699090d87b8b1cfcaa6ee4b9847f4ba81fb5bb97 |
import numpy
from time import strftime
from ase.build import bulk
from ase.neighborlist import NeighborList
from ase import units
from expectra.feff import feff_edge_number, run_feff
from mpi4py import MPI
COMM_WORLD = MPI.COMM_WORLD
def getxk(e):
return numpy.sign(e)*numpy.sqrt(numpy.abs(e))
def xk2xkp(xk, vrco... | SamChill/expectra | expectra/exafs.py | Python | mit | 5,769 | [
"ASE",
"FEFF"
] | ac0a8690c26bc3325831ae8912c5fc0d29db718c715bee15729e60bcb13b7f28 |
from setuptools import setup, find_packages
from listen.constants import LIBRARY_URL
from listen import (
__license__ as license,
__author__ as author,
__title__ as title,
__version__ as version
)
setup(
name=title,
version=version,
packages=find_packages("listen"),
url=LIBRARY_URL,
... | GetRektByMe/Listen | setup.py | Python | mit | 908 | [
"MOE"
] | d8be5fd423199473a35574c65ee9394a94be072795690bbe631de67d967a8b94 |
import sys
import ply.yacc as yacc
from Cparser import Cparser
from TreePrinter import TreePrinter
from TypeChecker import TypeChecker
semantic_control = True
print_tree = False
if __name__ == '__main__':
TreePrinter() # Loads printTree definitions
try:
filename = sys.argv[1] if len(sys.argv) > 1 el... | salceson/kompilatory | lab3/main.py | Python | mit | 1,105 | [
"VisIt"
] | 814ba26cd2d0956e57aa22090fc78549425e08ce3219003d2d0391ac27668804 |
#!/usr/bin/env python
#coding=utf-8
from setuptools import setup, find_packages
setup(name='ezfile',
version='0.0.3.4',
description='A one-line file-IO package',
author='moe001',
author_email='i@001.moe',
url='https://github.com/moe001/ezfile',
packages=find_packages(),
licen... | moe001/ezfile | ezfile_main/setup.py | Python | mit | 386 | [
"MOE"
] | dc63aaed1ef338559a949f47bf9d9c751469e4388fa1f754c35fce4e08247d32 |
#
# Copyright (C) 2001-2004 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" The "parser" for compound descriptors.
I almost hesitate to document this, because it's not the prettiest
thing the world has ever seen... but it does work (for at least some
definitions of the word).
Rather than getti... | strets123/rdkit | rdkit/ML/Descriptors/Parser.py | Python | bsd-3-clause | 12,201 | [
"RDKit"
] | cfadd71d0c57650b9f582e3c4187003fe63a4d90e628b56cd16bd4b3c6d2b3ef |
# 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... | chemelnucfin/tensorflow | tensorflow/python/autograph/converters/call_trees.py | Python | apache-2.0 | 6,862 | [
"VisIt"
] | 67224519ee9d39cab31921ea399e9cc1fcd10fc1a1ccc6cce1b5e2ff55f1d15f |
from pygmin.amber import amberSystem as amb
# create a new amber system and load database to be pruned
sys = amb.AMBERSystem('coords.prmtop', 'coords.inpcrd')
dbcurr = sys.create_database(db="aladipep.db")
print 'Collecting minima to delete .. '
listTODel = []
for minimum in dbcurr.minima():
testOutCome1 = ... | js850/PyGMIN | examples/amber/driver_sanitycheck.py | Python | gpl-3.0 | 1,210 | [
"Amber"
] | f7ddbdfa4d60bb1b32b3a85b6672c982ad5bd153fdaa20f791130c269a6a031d |
from __future__ import print_function
import httplib2
import os
from apiclient import discovery
from oauth2client import client
from oauth2client import tools
from oauth2client.file import Storage
from email.mime.text import MIMEText
from email.mime.image import MIMEImage
from email.mime.multipart import MIMEMultipar... | natedileas/ImageRIT | Server/g_api_email.py | Python | gpl-3.0 | 4,571 | [
"VisIt"
] | 1ea6c7ebf009cf6bf13e4b9c8cc2fb3f5070d2eb8b083a7cb00d1a71be116598 |
"""
Provide some basic helper functions.
"""
import cv2
import numpy as np
import matplotlib.image as mpimg
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from scipy.optimize import leastsq
from queue import PriorityQueue
NUM_EVALS = 0
LAST_AVG_ERROR = 0.0
def f2K(f):
""" Convert focal l... | eugeniopacceli/ComputerVision | quiz7/BasicFunctions.py | Python | mit | 23,175 | [
"Gaussian"
] | aee19d4852c4f063a8c5ed7db6c6e9ab08d724fd52209a8143ce0e0db2a6fab0 |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2018 Compassion CH (http://www.compassion.ch)
# @author: Emanuel Cino <ecino@compassion.ch>
#
# The licence is in the file __manifest__.py
#
#################################################... | ecino/compassion-switzerland | website_event_compassion/forms/medical_discharge_form.py | Python | agpl-3.0 | 2,148 | [
"VisIt"
] | b58c3d5cc53cdc09d6bb1531968d72ab3d3c08fedb4c47507c0f0c028d6742a7 |
from typing import Union, Iterable
import numpy
from numpy import ndarray
from numpy.random.mtrand import RandomState
from . import DistributionNonNegative, DistributionBounded, DistributionUnbounded
class Beta(DistributionBounded):
"""
The Beta distribution is bounded and continuous.
The implementatio... | Dubrzr/dsfaker | dsfaker/generators/distributions.py | Python | mit | 26,657 | [
"Gaussian"
] | 101615780e2e490688ed9bf8001d8785fe243bc9049d97f34a4f3bc8b4ae2f15 |
"""
Data-driven tests for references.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os
import glob
import hashlib
# TODO it may be a bit circular to use pysam as our interface for
# accessing reference information, since this is the method we ... | UMMS-Biocore/ga4gh-server | tests/datadriven/test_references.py | Python | apache-2.0 | 4,702 | [
"Biopython",
"pysam"
] | 8b30d03778d8c8fa4d3c1ababc694e2d37518d7eb1ab48ecd05ed3a22a09d2df |
# Copyright 2019 Google LLC. 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... | tensorflow/tfx | setup.py | Python | apache-2.0 | 15,240 | [
"VisIt"
] | 63a821aa3c4603da98e30eeec6e37675446a263c8a0be63b5f6c65b0c7c83645 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Mamba.jl documentation build configuration file, created by
# sphinx-quickstart on Mon Mar 31 10:03:01 2014.
#
# 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
# a... | axsk/Mamba.jl | doc/conf.py | Python | mit | 8,644 | [
"Brian"
] | 07464e3069f9c8370221039a523a0a626598ac12e0d9f313afbec0918efac8ee |
#!/usr/bin/env python
from lims_orca_utils import *
from neuron import h
import numpy as np
import argparse
import matplotlib.pyplot as plt
# Load the morphology
def load_morphology(filename):
swc = h.Import3d_SWC_read()
swc.input(filename)
imprt = h.Import3d_GUI(swc, 0)
h("objref this")
imprt.in... | XiaoxiaoLiu/morphology_analysis | model_fitting/neuron_passive_fit2.py | Python | gpl-3.0 | 3,292 | [
"NEURON"
] | 35f1a18ca5ec30b4a87c1e3ed78870dc52bec7756646fff057a6564e1254d3c8 |
#!/usr/bin/env python
"""
Run this test like so:
$ vtkpython TestGL2PSExporter.py -D $VTK_DATA_ROOT \
-B $VTK_DATA_ROOT/Baseline/Rendering/
$ vtkpython TestGL2PSExporter.py --help
provides more details on other options.
Please note that this test requires that you have PIL (the Python
Imaging Library) module insta... | cjh1/VTK | IO/Export/Testing/Python/TestGL2PSExporter.py | Python | bsd-3-clause | 5,080 | [
"VTK"
] | 75226f6095f80c9025f77f5244deba52820577cd0b6325dbe77c29e1c3e19c59 |
# Copyright 2016 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... | plowman/python-mcparseface | models/syntaxnet/tensorflow/tensorflow/contrib/distributions/__init__.py | Python | apache-2.0 | 2,083 | [
"Gaussian"
] | d5cd605fb84553271171f221eba4d9d8f8c6755bb9dcc46ee284cdf419020cb2 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible 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.
#
# Ansible is distributed... | t0mk/ansible | lib/ansible/modules/cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 53,300 | [
"Dalton"
] | 6ca92a85268403fc586cb53c2eba36a32abb1d10be8fd94a1376af88a9cf0cdb |
import os
from __main__ import slicer
import qt, ctk
from SampleData import *
#
# BenderSampleData
#
# To add new data, edit the ui file to add case to the tree.
# and fill the corresponding information in the BenderSampleDataLogic
# download data dictionnary.
class BenderSampleData:
def __init__(self, parent):
... | ricortiz/Bender | Modules/Scripted/Scripts/BenderSampleData.py | Python | apache-2.0 | 7,801 | [
"VTK"
] | acf4fd50809495a69bc13f4aae10247d811095612ebb31533f0cfa533382bd9d |
# Functions for instrumental resolution corrections and area of illumination
# these are to be included in the Models class and Refl class
# Note that these function assumes a Gaussian spread in both the angular as well
# as in real space
# THis one really needs scipy
from scipy import *
from numpy import *
from scipy... | haozhangphd/genx-py3 | genx/models/lib/instrument.py | Python | gpl-3.0 | 4,675 | [
"Gaussian"
] | a6cce2ed05d61e85a097a5ea1be97f28c691343a5aacc83f3e220781535e1e7a |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## 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 Foundati... | laborautonomo/pyboleto | tests/test_pep8.py | Python | bsd-3-clause | 2,862 | [
"VisIt"
] | 0397b9c76af2d3404bf47496aa15d310c9f70f0b3ad925897067c7750c539bc1 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/chigger/vtk_scripts/elem_block.py | Python | lgpl-2.1 | 1,934 | [
"MOOSE",
"VTK"
] | a82ef042cc23a7c25d83c8e7c55bb67ff9fbd292a7bc113a0391d30298ea2453 |
import numpy as np
# functions and classes go here
def fb_alg(A_mat, O_mat, observ):
# set up
k = observ.size
(n,m) = O_mat.shape
prob_mat = np.zeros( (n,k) )
fw = np.zeros( (n,k+1) )
bw = np.zeros( (n,k+1) )
# forward part
fw[:, 0] = 1.0/n
for obs_ind in xrange(k):
f_row_vec... | karolciba/playground | markov/baumwelch.py | Python | unlicense | 4,027 | [
"CASINO"
] | 11dfceb50c4007cf27bc0e267b3fc4b836467f3db454d21252f1f9262a77a740 |
# (C) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import collections
import datetime
import fun... | s-hertel/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 35,709 | [
"Galaxy"
] | 2f1d5d4fb7f01f35279f64a996db43c8e6a0d5e58a70e4217cc41e17e3a89520 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkIdFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkId... | nagyistoce/devide | modules/vtk_basic/vtkIdFilter.py | Python | bsd-3-clause | 475 | [
"VTK"
] | cfbb14b36a3f1a99a0960004b2f036351c138a88883dda0e362a002d52bca597 |
# -*- coding: utf-8 -*-
'''
Exodus Add-on
Copyright (C) 2016 lambda
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 3 of the License, or
(at your option) any l... | EdLogan18/logan-repository | plugin.video.exodus/resources/lib/sources/torba_mv_tv.py | Python | gpl-2.0 | 6,750 | [
"VisIt"
] | 22901364f41db17ef07ac4e4499d806ffe3cdc9610628053154779f7217c47b9 |
#-*. coding: utf-8 -*-
## Copyright (c) 2008-2011, Noel O'Boyle; 2012, Adrià Cereto-Massagué; 2014, Maciej Wójcikowski;
## All rights reserved.
##
## This file is part of Cinfony.
## The contents are covered by the terms of the BSD license
## which is included in the file LICENSE_BSD.txt.
"""
rdkit - A Cinfony modu... | mwojcikowski/opendrugdiscovery | oddt/toolkits/rdk.py | Python | bsd-3-clause | 31,908 | [
"Pybel",
"RDKit"
] | 0ea256f1c9cd9c7fdd309e62970510183bc0a6f9e39254bfa804ce97bd1aaadc |
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
# Copyright (c) 2006, The Regents of the University of California, through
# Lawrence Berkeley National Laboratory (subject to receipt of any required
# approvals from the U.S. Dept. of Energy). All rights reserved.
# This software is distributed unde... | go-bears/Final-Project | weblogo-3.4_rd/corebio/seq_io/__init__.py | Python | mit | 8,995 | [
"BioPerl"
] | e40ed228f1bba4ad7612e02a1896d994d48e1460953923e5aed03c2c78866977 |
'''Tests for the examples in examples/gaussian_bayesian_networks'''
from bayesian.gaussian_bayesian_network import build_graph
from bayesian.examples.gaussian_bayesian_networks.river import (
f_a, f_b, f_c, f_d)
from bayesian.linear_algebra import zeros, Matrix
from bayesian.gaussian import MeansVector, CovarianceM... | kamijawa/ogc_server | bayesian/test/test_gbn_examples.py | Python | mit | 969 | [
"Gaussian"
] | 27a1b24e4b1bdf4da29dd75826883a6211f976ac68f50c10caad1172fba2e5b4 |
##########################################################################
#
# Copyright (c) 2015, John Haddon. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of so... | chippey/gaffer | python/GafferDispatch/PythonCommand.py | Python | bsd-3-clause | 6,260 | [
"VisIt"
] | 2d4f235ed76e7979155671fcbd8a7dc64629160cf6372cb8e6852f598676a526 |
import tkinter
from tkinter import filedialog
from tkinter import messagebox
from PIL import ImageTk
import PIL.Image
import os
import re
import cv2
import numpy as np
from isd_lib import utils
BACKGROUND_COLOR = '#ededed'
WINDOW_WIDTH = 990
WINDOW_HEIGHT = 720
PREVIEW_SIZE = 256 # height & width of preview in pix... | whitews/image-subregion-detector | image_subregion_detector.py | Python | bsd-3-clause | 29,126 | [
"FLEUR"
] | b03f965007ecac91a0127cde2bfe4ec60ccc3f8f6fa37100f0cadba85a7128e1 |
from gpaw.test import equal
from gpaw.grid_descriptor import GridDescriptor
from gpaw.spline import Spline
import gpaw.mpi as mpi
from gpaw.lfc import LocalizedFunctionsCollection as LFC
s = Spline(0, 1.0, [1.0, 0.5, 0.0])
n = 40
a = 8.0
gd = GridDescriptor((n, n, n), (a, a, a), comm=mpi.serial_comm)
c = LFC(gd, [[s],... | robwarm/gpaw-symm | gpaw/test/lf.py | Python | gpl-3.0 | 665 | [
"GPAW"
] | e1299f7fd9ebf1b59b9581a854ae0b7e224dc52124ebbffbbc6ceb60ffee9f59 |
# Orca
#
# Copyright 2004-2008 Sun Microsystems Inc.
#
# 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 License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/Thunderbird/script.py | Python | gpl-3.0 | 28,065 | [
"ORCA"
] | 71ca3f3f14b5a03d6c5a59d134473aa2edce0bc06b309232fa5fdf3fd1819557 |
# The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
# Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
# WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND... | williamdlees/BioTools | PlotIdentity.py | Python | mit | 6,306 | [
"BLAST"
] | 7e0db6e5327bcc3313827f6354f1303bf816bf38d934ca60b57f24500c753124 |
"""
Module for writing data to NetCDF files
"""
from netCDF4 import Dataset
import logging
types = {'int8': 'i1',
'int16': "i2",
'int32': "i4",
'int64': "i8",
'uint8': 'u1',
'uint16': "u2",
'uint32': "u4",
'uint64': "u8",
'float32': "f4",
... | zak-k/cis | cis/data_io/write_netcdf.py | Python | gpl-3.0 | 5,862 | [
"NetCDF"
] | b7e750948fc5d50581eaf67bb017aad8ecaca5812d0f13150f8541e48df9f70d |
"""
Compute Bra-ket averaged Taylor expansion integrals over trajectories
traveling on adiabataic potentials
"""
import numpy as np
import nomad.core.glbl as glbl
import nomad.compiled.nuclear_gaussian as nuclear
# Let propagator know if we need data at centroids to propagate
require_centroids = False
# Determines t... | mschuurman/FMSpy | nomad/integrals/fms_bat.py | Python | lgpl-3.0 | 4,365 | [
"Gaussian"
] | de242cf9b9730283b2a4951686af64c445d58f9fda12e2dd3b375d695e49bbb1 |
from ase import *
from ase.constraints import StrainFilter
a = 3.6
b = a / 2
cu = Atoms('Cu', cell=[(0,b,b),(b,0,b),(b,b,0)], pbc=1) * (6, 6, 6)
try:
import Asap
except ImportError:
pass
else:
cu.set_calculator(ASAP())
f = UnitCellFilter(cu, [1, 1, 1, 0, 0, 0])
opt = QuasiNewton(f)
t = PickleTra... | freephys/python_ase | ase/test/unitcellfilter.py | Python | gpl-3.0 | 796 | [
"ASE"
] | d5af32acef98aa746cf051b5f0ba0067e1606270b7f7f6107796c98048cb16d4 |
# searchAgents.py
# ---------------
# Licensing Information: You are free to use or extend these projects for
# educational purposes provided that (1) you do not distribute or publish
# solutions, (2) you retain this notice, and (3) you provide clear
# attribution to UC Berkeley, including a link to http://ai.berkeley... | namangoyal6/artificial-intelligence | Search/code/searchAgents.py | Python | mit | 25,423 | [
"VisIt"
] | 7bc30b15096a53213b4f1806258dcf93725db8b970dd8b03229e45dd2790e109 |
#!/usr/bin/env python
import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Now create the RenderWindow, Renderer and Interactor
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWin... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/voxelModel.py | Python | bsd-3-clause | 2,253 | [
"VTK"
] | 653132703325591b9b9e41cd95da2b85bc8f3cdfc1e95e6e60d665cc0d9b11fd |
# -*- coding: utf-8 -*-
# Copyright: (c) 2018, Red Hat | Ansible
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Options for authenticating with the API.
class ModuleDocFragment(object):
DOCUMENTATION = r'''
options:
host:
description:
- Provide a URL f... | andmos/ansible | lib/ansible/plugins/doc_fragments/k8s_auth_options.py | Python | gpl-3.0 | 3,129 | [
"VisIt"
] | f770f2f99fcebe6d2928be292cb455275ec28903ac0d994131299267dfd0eda7 |
from brian import *
import random
# ###########################################
# Configuration
# ###########################################
set_global_preferences(useweave=True)
set_global_preferences(usecodegen=True)
#set_global_preferences(openmp=True)
record = True
plot_all = True
# ############################... | vitay/ANNarchy | benchmarks/brunel/Brian-Brunel-plastic.py | Python | gpl-2.0 | 3,239 | [
"Brian",
"NEURON"
] | 2256c367e4fc537097549ee56dca4f11a8af8959d2c6d2f2190959ea2bee9eb3 |
#! /usr/bin/env python
#
# The purpose of this script is to create a moltemplate lt file for the opls.
# and oplsaa forcefields.
__author__ = 'Jason Lambert and Andrew Jewett'
# (some additional corrections by Miguel Gonzalez, Yue Chun Chiu and others)
__version__ = '0.1'
__date__ = '2016-11-20'
import sys
impor... | lkostler/AME60649_project_final | moltemplate/moltemplate/src/tinkerparm2lt.py | Python | bsd-3-clause | 29,431 | [
"LAMMPS",
"TINKER"
] | 3044bd3ab28f494abaa19ceceab07ef45682c24e413be49af16f74b83c4d309c |
# Portions copyright (c) 2014 ZMAN(ZhangNing)
#
# 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/.
#
# Name: WebZ轻量级自动化框架
# Description: keyword-driven automated testing f... | lsp84ch83/PyText | WebZ轻量级自动化框架/keywords.py | Python | gpl-3.0 | 3,311 | [
"VisIt"
] | 1850ab43ce134a2642f09992cba12d9fe378112c3163476c355f06a1f2dcf8a0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""rna_pdb_toolsx - a swiss army knife to manipulation of RNA pdb structures
Usage::
$ rna_pdb_toolsx.py --delete A:46-56 --inplace *.pdb
$ rna_pdb_toolsx.py --get-seq *
# BujnickiLab_RNApuzzle14_n01bound
> A:1-61
# BujnickiLab_RNApuzzle14_n02bound
... | mmagnus/rna-pdb-tools | rna_tools/rna_pdb_toolsx.py | Python | gpl-3.0 | 40,901 | [
"Biopython",
"PyMOL"
] | 5dca839cb152551141d38f9adad5b4e8873a9d0db2ccf390ec3d715b29580cd5 |
import argparse
import os
from coalib.misc import Constants
from coalib.collecting.Collectors import get_all_bears_names
from coalib.parsing.filters import available_filters
class CustomFormatter(argparse.RawDescriptionHelpFormatter):
"""
A Custom Formatter that will keep the metavars in the usage but remove... | IPMITMO/statan | coala/coalib/parsing/DefaultArgParser.py | Python | mit | 10,541 | [
"VisIt"
] | 7840546ede318cb3c09d9ca5232fb9cfb327c5e1b6dbfefb045086f46934ab35 |
"""
Classes to handle the .bed files
"""
import os
import os.path as op
import sys
import math
import logging
import numpy as np
from collections import defaultdict
from itertools import groupby
from jcvi.formats.base import LineFile, must_open, is_number, get_number
from jcvi.formats.sizes import Sizes
from jcvi.ut... | sgordon007/jcvi_062915 | formats/bed.py | Python | bsd-2-clause | 60,122 | [
"BLAST"
] | 8f70c9b7676b945e40adb889cac930834ed84ee8214c202b2460eda19a26fefc |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 F... | andrebellafronte/stoq | stoqlib/gui/dialogs/progressdialog.py | Python | gpl-2.0 | 3,155 | [
"VisIt"
] | 8d1f80c08d04d8d7802df52bff153c3ed65774f4c3801c3c51f4a80722514a7a |
########################################################################
# $HeadURL$
# File : JobCleaningAgent.py
# Author : A.T.
########################################################################
"""
The Job Cleaning Agent controls removing jobs from the WMS in the end of their life cycle.
"""
from DIRAC ... | avedaee/DIRAC | WorkloadManagementSystem/Agent/JobCleaningAgent.py | Python | gpl-3.0 | 8,926 | [
"DIRAC"
] | 80367924a8fdd52e4aa3703241d634a1cbb0961644a6ef1f3abaa210addfa2bd |
########################################################################
# File : AgentModule.py
# Author : Adria Casajus
########################################################################
"""
Base class for all agent modules
"""
import os
import threading
import time
import signal
import importlib
import i... | DIRACGrid/DIRAC | src/DIRAC/Core/Base/AgentModule.py | Python | gpl-3.0 | 21,572 | [
"DIRAC"
] | 85a580a2ea1c08fbd4616e19f925b2a196a5aa1120cfef09f88d2a7430d2e0c5 |
#!/usr/bin/env python
"""
This script automates the steps needed to debug a MPI executable with the GNU debugger
Note that GNU gdb is not a parallel debugger hence this crude approach may not work properly.
"""
from __future__ import print_function, division
import sys
import os
import argparse
import tempfile
from ... | jmbeuken/abinit | developers/various/paragdb.py | Python | gpl-3.0 | 2,114 | [
"ABINIT"
] | c1ee962a0754e436569cc3e37a59b4bc84a6d8c272488a4077739a531be6b25a |
# -*- coding: utf-8 -*-
from fenics import *
from matplotlib import pyplot
import numpy as np
parameters["plotting_backend"] = "matplotlib"
prm = parameters['krylov_solver']
prm['absolute_tolerance'] = 1e-7
prm['relative_tolerance'] = 1e-4
prm['maximum_iterations'] = 1000
#list_linear_solver_methods()
# Units
cm = ... | akdiem/nvu | fenics_artery.py | Python | bsd-3-clause | 2,083 | [
"VTK"
] | d1387d70ef5650bd1ee30d786d79ffd7806a4ba573550a4c587dc91d862189ca |
"""Joint variant calling with multiple samples: aka squaring off, or backfilling.
Handles the N+1 problem of variant calling by combining and recalling samples
previously calling individually (or in smaller batches). Recalls at all positions found
variable in any of the input samples within each batch. Takes a general... | a113n/bcbio-nextgen | bcbio/variation/joint.py | Python | mit | 11,384 | [
"pysam"
] | d597fbf099020599756d1bce970a85751e420b7ccfdf473bd2eec1a93caea1eb |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
# pylint: disable=E1111
import unittest
import json
import requests
import datetime
import ddt
import random
import io
from urllib import quote
from django.test import TestCase
from nose.tools import raises
from mock import Mock, patch
from django.c... | dsajkl/reqiop | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 148,904 | [
"VisIt"
] | 5bc16524826fae070566ec08a73622e8f7472df08829faf1e76f5631fd992378 |
"""
refcounting
~~~~~~~~~~~
Reference count annotations for C API functions. Has the same
result as the sphinx.ext.refcounting extension but works for all
functions regardless of the signature, and the reference counting
information is written inline with the documentation instead of a
sepa... | glenn-edgar/lua_frame_work | user_libraries/avro-c/avro-c-1.4.1/jansson/doc/ext/refcounting.py | Python | mit | 1,706 | [
"VisIt"
] | cab7013f55f173cddfffa0874ef06dea913dad33c849c41a2f5ba9e656c6007d |
import logging
from future.utils import iteritems
import numpy as np
from scipy.ndimage import map_coordinates
import scipy.ndimage as ndimage
from scipy.interpolate import interp1d, LinearNDInterpolator
logger = logging.getLogger('opendrift') # using common logger
def expand_numpy_array(data):
if isinstance(da... | knutfrode/opendrift | opendrift/readers/interpolation.py | Python | gpl-2.0 | 14,062 | [
"NetCDF"
] | d7a0c27351e9323dedc244cde6520cd37f2343984f5b04a49dfbe048f6bbea5d |
""" Find features in image """
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
import numpy as np
from numpy.testing import assert_allclose
import skimage
try:
from skimage.filters import threshold_otsu
except ImportError:
from skimage.filt... | rbnvrw/circletracking | circletracking/find.py | Python | bsd-3-clause | 5,757 | [
"Gaussian"
] | 21da9763d1a654a06e363e613a769f08f5942cb0da82e0bb8a3a9481c45b71e5 |
"""
primer finder for epride -
easy primer design for multiple sequence alignments
@author: manutamminen
"""
import os
import sys
import subprocess
import itertools
import igraph as ig
import leidenalg as la
from collections import defaultdict
from itertools import zip_longest
import pandas as pd
from . import io... | manutamminen/epride | epride/primer_finder.py | Python | mit | 7,971 | [
"BLAST"
] | 41dc689a2b05c821ca5935f050f62379d8c8f4cbfede5e142a8d28c2f16c66aa |
"""
@author David W.H. Swenson
"""
from .test_helpers import data_filename, assert_close_unit, make_1d_traj, md
import pytest
from nose.plugins.skip import SkipTest
import openpathsampling.engines.openmm as peng
from openpathsampling.netcdfplus import FunctionPseudoAttribute
import openpathsampling as paths
import ... | openpathsampling/openpathsampling | openpathsampling/tests/test_attribute.py | Python | mit | 6,549 | [
"MDTraj",
"OpenMM"
] | 9065ad90543a1f80b40402540405d62cbdce30c89309f0cf03ba62dca37415f5 |
# coding=utf-8
import os
import platform
import sys
from typing import Optional, Dict, Any, List
from dbt.events.functions import fire_event
from dbt.events.types import OpenCommand
from dbt import flags
import dbt.clients.system
import dbt.exceptions
from dbt.adapters.factory import get_adapter, register_adapter
from... | analyst-collective/dbt | core/dbt/task/debug.py | Python | apache-2.0 | 13,733 | [
"VisIt"
] | c9d4faf80e5781b88bfbafb67e820bdfaba31ffb44baedd8065a4b5ae8f5712e |
#!/usr/bin/env python
########################################
# to modify the NetCDF files
########################################
#First import the netcdf4 library
from netCDF4 import Dataset # http://code.google.com/p/netcdf4-python/
import numpy as np
import sys,getopt
#=========================================... | CopyChat/Plotting | Python/modify_netcdf.py | Python | gpl-3.0 | 3,214 | [
"NetCDF"
] | 8a6499ae72c53c7b0a1ea0a4b051aabfdaa9bcfb6f086e00734e148782172b51 |
# -*- coding: utf-8 -*-
#
# test_stdp_triplet_synapse.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 t... | alberto-antonietti/nest-simulator | pynest/nest/tests/test_stdp_triplet_synapse.py | Python | gpl-2.0 | 12,804 | [
"NEURON"
] | 85ae8667daa492be1f2a2f60f82b3759109bea86d9c511aea98cfb047216677b |
"""Nodes that make up parse trees
Parsing spits out a tree of these, which you can then tell to walk itself and
spit out a useful value. Or you can walk it yourself; the structural attributes
are public.
"""
# TODO: If this is slow, think about using cElementTree or something.
from inspect import isfunction
from sys ... | fjalex/parsimonious | parsimonious/nodes.py | Python | mit | 12,898 | [
"VisIt"
] | 187d16ac6d949f7eb6558469c3c3267c5d7c9f988bf8393213df5901b26d182d |
import tensorflow as tf # neural network for function approximation
import gym # environment
import numpy as np # matrix operation and math functions
from gym import wrappers
import gym_morph # customized environment for cart-pole
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import time
star... | GitYiheng/reinforcement_learning_test | test03_monte_carlo/t40_rlvps02.py | Python | mit | 7,664 | [
"NEURON"
] | 85dcd9b708d6b361a51dc57c0350e31b0a0add2714f4a43446dcbdeb27b77bf5 |
# -*- coding: utf-8 -*-
#
# (c) Copyright 2003-2007 Hewlett-Packard Development Company, L.P.
#
# 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 opt... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/hplip/base/status.py | Python | gpl-3.0 | 65,504 | [
"ADF"
] | a288c44a3ac18b15ea3d5d993ec775fdd6610e990f604444d894144cefa69563 |
from math import log
import numpy as np
from nose.tools import assert_equal, assert_almost_equal
from iminuit import describe
from probfit import pdf
from probfit._libstat import xlogyx, wlogyx, csum, integrate1d, _vector_apply
from probfit.functor import construct_arg, fast_tuple_equal
from probfit.funcutil import mer... | mtresch/probfit | test/testfunc.py | Python | mit | 10,590 | [
"Gaussian"
] | f7d5d1a8a8a0a8857ed4a961b1f3902220aed93434b39dee55f94aee725f7b6f |
#!/usr/bin/env python
########################################################################
# File : dirac-proxy-init.py
# Author : Adrian Casajus
########################################################################
from __future__ import print_function
from __future__ import absolute_import
from __future__... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_myproxy_upload.py | Python | gpl-3.0 | 1,783 | [
"DIRAC"
] | ecd07c3943960b6df104ed9f50db35ae7c7ff8eca11db881e962075f83df7934 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under ... | MDAnalysis/mdanalysis | package/MDAnalysis/topology/tpr/setting.py | Python | gpl-2.0 | 8,442 | [
"Gromacs",
"MDAnalysis"
] | e3c8e6b95faecd369958c44b24f8cbb13026426a73251edb1d7e8e8b37cb0de4 |
# The Hazard Library
# Copyright (C) 2012-2014, GEM Foundation
#
# 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 by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
... | mmpagani/oq-hazardlib | openquake/hazardlib/gsim/chiou_youngs_2014.py | Python | agpl-3.0 | 20,221 | [
"Brian"
] | 24580ca092d1f706e4450bfaba97470dbc7466adff5395ef0fd12edc28333d98 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/metadata/_mixin.py | Python | bsd-3-clause | 18,539 | [
"scikit-bio"
] | f91b63f76bca56f13437f56fafe306b3bac702316d2b3f62865450ed660e99a9 |
# -*- coding: utf-8 -*-
"""
This module contains functions for turning a Python script into a .hex file
and flashing it onto a BBC micro:bit.
Copyright (c) 2015-2018 Nicholas H.Tollervey and others.
See the LICENSE file for more information, or visit:
https://opensource.org/licenses/MIT
"""
from __future__ import p... | stestagg/mu | mu/contrib/uflash.py | Python | gpl-3.0 | 653,754 | [
"VisIt"
] | a700120c335dd464f087510372c38ce8bf67d6a4e5344a020c2cf04ec9ec10da |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import pysam
import argparse
from time import clock
from collections import Counter
from sets import Set
parser = \
argparse.ArgumentParser(description='Extract reads with one end mapping to hg19 reference and other end mapping to viral genome'
)
parser.add_... | namphuon/ViFi | scripts/get_trans_new.py | Python | gpl-3.0 | 7,981 | [
"pysam"
] | 4658d3a55b065a004a03d6e9f0dafb2fb0dd95eb0c51106a03dfa27c68872342 |
from math import sqrt
import numpy as np
from scipy import stats
from matplotlib import pyplot
#(0) Set parameters:
np.random.seed(0)
nResponsesA = 5
nResponsesB = 5
nIterations = 5000
### derived parameters:
nA,nB = nResponsesA, nResponsesB
df = nA + nB - 2
#(1) Generate Gaussian data an... | 0todd0000/spm1d | spm1d/rft1d/examples/val_max_2_twosample_t_0d.py | Python | gpl-3.0 | 1,327 | [
"Gaussian"
] | f33de9a8787c5d5de9cf17f786d68c9d3e12804dee946c3e2336430154cc2183 |
# -*- coding: utf-8 -*-
"""
This class controls all the GUI for the player
menu screen.
"""
import sys
import pygame as pg
from . import setup, observer
from . import constants as c
from . import tools
#Python 2/3 compatibility.
if sys.version_info[0] == 2:
range = xrange
class SmallArrow(pg.sprite.Sprite):
... | justinmeister/The-Stolen-Crown-RPG | data/menugui.py | Python | mit | 20,934 | [
"BLAST"
] | 5fd8c137f8d5757c29a3a4414c14db1802a38d5c863adb571e0986df3ebeb6e6 |
"""
Given a binary tree and a sum, determine if the tree has a root-to-leaf path such that adding up all the values along the path equals the given sum.
For example:
Given the below binary tree and sum = 22,
5
/ \
4 8
/ / \
11 13 4
/ \ \... | Ahmed--Mohsen/leetcode | path_sum_2.py | Python | mit | 1,355 | [
"VisIt"
] | d4415b4404aa24fcacda5d57c2c3171ff02337986487494405e941ee23d165f8 |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
from twilio.rest import Client
from datetime import datetime
# Your Account Sid and Auth Token from twilio.com/user/account
acco... | teoreteetik/api-snippets | notifications/rest/bindings/list-binding/list-binding.6.x.py | Python | mit | 653 | [
"VisIt"
] | eb3c2a101fbe86e68082a506b7fb27613afda8ea9cf38b61b6d8eef2950b5cf3 |
"""
The Job Sanity Agent accepts all jobs from the Job
receiver and screens them for the following problems:
- Output data already exists
- Problematic JDL
- Jobs with too much input data e.g. > 100 files
- Jobs with input data incorrectly specified e.g. castor:/
- Input sandbox not correc... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Executor/JobSanity.py | Python | gpl-3.0 | 6,735 | [
"DIRAC"
] | 07ec4b8f3c6e5c497d7ec428b6bc3cca6b9e662ebc8b17fc8f0cdcf0173e742f |
import urlparse
from dryscrape.driver.webkit import Driver as DefaultDriver
class Session(object):
""" A web scraping session based on a driver instance. Implements the proxy
pattern to pass unresolved method calls to the underlying driver.
If no `driver` is specified, the instance will create an instance of
... | nabilbendafi/plugin.video.rainiertamayo | resources/lib/dryscrape/session.py | Python | gpl-3.0 | 1,610 | [
"VisIt"
] | 9aa3b4aabd56752d4ea38fa1a219a49dc1fb119a7a1becdb9cb07d46f9d560ea |
import pytest
import math
from timeit import timeit
from astropy import units as u
from panoptes.pocs.filterwheel.simulator import FilterWheel as SimFilterWheel
from panoptes.pocs.camera.simulator.dslr import Camera as SimCamera
from panoptes.utils import error
@pytest.fixture(scope='function')
def filterwheel():
... | panoptes/POCS | tests/test_filterwheel.py | Python | mit | 8,100 | [
"Gaussian"
] | ae4622fc43290a3cf61d3823c8872e2efbfe736916f2d21dd8e265ad3c9c1255 |
#
# Samples a 2d double-well distribution using Umbrella sampling in the temperature (parallel version)
#
# Usage:
# > mpirun -np N python -u doublewell_mpi.py
# where "N" is the number of cores to run on, e.g. 4
#
import usample.usample
import numpy as np
import emcee
#
# Sample a 2D distribution of the sum of two G... | c-matthews/usample | doublewell_mpi.py | Python | gpl-3.0 | 2,785 | [
"Gaussian"
] | 126a2047a2297a3b87db58b36287ac0bc21783a6b331f8c32af4951061f94a8d |
# This file is part of xrayutilities.
#
# xrayutilies 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... | dkriegner/xrayutilities | setup.py | Python | gpl-2.0 | 7,251 | [
"Mayavi"
] | bba90129aed4de6b075c3093231501e1daf890316ce9db7007138465a451518a |
# Copyright 2015 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... | DailyActie/Surrogate-Model | 01-codes/tensorflow-master/tensorflow/models/image/cifar10/cifar10.py | Python | mit | 14,256 | [
"Gaussian"
] | 1f3ffa035cf7e3a90df8ee0f7b11cf60eef3637dbded05adbf1fc835c25cfa24 |
# revset.py - revision set queries for mercurial
#
# Copyright 2010 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import re
import parser, util, error, discovery, hbisect, phases
import node
import... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg/mercurial/revset.py | Python | gpl-3.0 | 48,655 | [
"VisIt"
] | 69c3ab59ea9ffe266734ec9ab97f221e539996a410f569f6c2c8088f587100bd |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A Beauchamp, Jason Swails... | swails/mdtraj | mdtraj/geometry/distance.py | Python | lgpl-2.1 | 12,042 | [
"MDTraj"
] | fa7e8ed4f91c17777d132bb9de5b8f903a9e5245ce61cddeba4de1e158343066 |
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