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#
# Copyright (C) 2017-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | pkreissl/espresso | testsuite/python/accumulator_time_series.py | Python | gpl-3.0 | 2,210 | [
"ESPResSo"
] | 8b3d06852cb95e3c950ef36a96a2dcf6d441d95873f43b1faed3e1fe2b6bb97b |
#!/usr/bin/env python
# encoding: utf-8
"""An asymmetric SOM. This type of SOM doesn't use a grid, but the nodes are
freely positioned on a plane.
"""
from collections import UserList
from math import exp
import random
from random import choice
from scipy.spatial import Voronoi, voronoi_plot_2d
from .som import SOM, ... | Procrat/som | som/asom.py | Python | mit | 11,606 | [
"Gaussian"
] | 0529f10806f7eb5d51a0abfc9a4b7013a4e9a3668259ce4666c1bb772a90879e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
__author__ = 'Chengwei Luo (cluo@broadinstitute.org)'
__version__ = '0.1.0'
__date__ = 'December 2013'
USAGE = \
"""
This script calculates the significance of orthologs that differentiate categories.
This script takes a multi-newick tree file, in which each leaf is a gene ... | luo-chengwei/utilitomics | taxonomy/ortholog_aln_test.py | Python | gpl-3.0 | 6,383 | [
"Biopython"
] | 7bbbf5e8bcf161b4a721f4fd87d53198946ad10b0b1d1da6deda34d5c078a9ed |
#!/usr/bin/env python
"""
:Author: Martin Kircher
:Contact: mkircher@uw.edu
:Date: *03.06.2014
"""
import sys, os
from optparse import OptionParser
import gzip
import pysam
import random
from collections import defaultdict
from bx.intervals.intersection import Intersecter, Interval
def isSoftClipped(cigar):
#Op ... | shendurelab/cfDNA | expression/extractReadStartsFromBAM_Region_WPS.py | Python | mit | 7,431 | [
"pysam"
] | 4d640a1c7bcf25ce07381664e93569987fad83a512e07988f90af47fd98a2947 |
"""
Cylinders with size distribution
"""
import bornagain as ba
from bornagain import deg, angstrom, nm
def get_sample():
"""
Return a sample with cylinders on a substrate.
The cylinders have a Gaussian size distribution.
"""
m_ambience = ba.HomogeneousMaterial("Air", 0.0, 0.0)
m_particle = ba... | waltervh/BornAgain | Examples/python/simulation/ex01_BasicParticles/CylindersWithSizeDistribution.py | Python | gpl-3.0 | 2,063 | [
"Gaussian"
] | 9900c9e842ba1018c948ae01c97b7102bea4397cffc292170178fca75c678c2f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | beernarrd/gramps | gramps/gen/filters/rules/place/_hasnote.py | Python | gpl-2.0 | 1,754 | [
"Brian"
] | c4251a6dfacb775664c8be67dd6a9be4b99dcca227bb3fbac4d203527d88e98e |
import matplotlib.pyplot as plt
import os
from astropy.table import Table
import numpy as np
# setup information sources
degas = Table.read(os.path.join(os.environ['SCRIPTDIR'],'degas_base.fits'))
stack = Table.read('/lustre/cv/users/akepley/degas/stack_test/stack_IR6p0_mom1.fits')
plotDir = os.path.join(os.environ['... | low-sky/degas | scripts/plot_SFEdense_vs_molmass_combined_nolim.py | Python | gpl-3.0 | 2,340 | [
"Galaxy"
] | 188b874cb98b2bf0122bf1d9d3af3d0e53b27f57773532e57d27122b2721833d |
import sys
import os
this_file = os.path.dirname(os.path.realpath(__file__))
sys.path.append(os.path.join(this_file, "../src/universal/bin"))
import lib
import json
import shutil
import unittest
from config import Configuration
class ConfigTestCase(unittest.TestCase):
def setUp(self):
self.conf_1 = "/tmp/... | hmrc/release | test/test_config.py | Python | apache-2.0 | 3,295 | [
"Brian"
] | 61ae781d5e0f24c43534f2a27c9e520695d243adccd06d7d6971fe2e8a8c8217 |
# Copyright 2013-2020 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 RBiocinstaller(RPackage):
"""Install/Update Bioconductor, CRAN, and github Packages.
... | iulian787/spack | var/spack/repos/builtin/packages/r-biocinstaller/package.py | Python | lgpl-2.1 | 1,067 | [
"Bioconductor"
] | 574d8c5ee0a8f0b1e5a507139ac4509f373ca6fa717d57cfdcc50c888c55497c |
#! /usr/bin/python3 -B
# *************************************************** *
# This file is a part of ccROJ project *
# distributed under GNU General Public License v3.0. *
# Please visit the webpage: github.com/dsp-box/ccROJ *
# for more information. *
# ... | dsp-box/ccROJ | scripts/roj-draw.py | Python | gpl-3.0 | 7,892 | [
"VisIt"
] | 9649033ebffd08213ea616449d063785a5af51c0f1e223eed07072355d7a7723 |
"""
This Service provides functionality to access and modify the
InstalledComponentsDB database
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.FrameworkSystem.DB.InstalledComponentsDB import (
InstalledComponentsDB,
Component,
Host,
InstalledComponent,
HostLogging,
)
from DIRAC.Core.DISET.... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/Service/ComponentMonitoringHandler.py | Python | gpl-3.0 | 13,450 | [
"DIRAC"
] | b91b01f20b19bb7555110b303ab1c3f33dbee84b9dd5f0c4c67bfa332f781f68 |
# -*- coding: utf-8 -*-
# test_neurom2.py, modified from run_cell.py
# Maintainer: P Gleeson, Dilawar Singh
# This test is not robust.
# Code:
from __future__ import absolute_import, print_function, division
# check if neuroml working properly.
# NOTE: This script does not work with python3
# See https://github.com/N... | upibhalla/moose-core | tests/python/test_neuroml2.py | Python | gpl-3.0 | 1,910 | [
"MOOSE"
] | 601d2e9e5c2c536804a95fffbfb1d87b454a61f775f208efc7d2b70b562c3e03 |
from __future__ import absolute_import
from __future__ import unicode_literals
import logging
from functools import reduce
from docker.errors import APIError
from docker.errors import NotFound
from .config import ConfigurationError
from .config import get_service_name_from_net
from .const import DEFAULT_TIMEOUT
from... | viranch/compose | compose/project.py | Python | apache-2.0 | 15,066 | [
"VisIt"
] | 5e3c7d63100a5006c80aa5f304bd08975c64a8e72da6869b9e5e51fe18f10eb8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# xmlrpcinterface - Provides the entire XMLRPC interface over CGI
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the... | heromod/migrid | mig/cgi-bin/xmlrpcinterface.py | Python | gpl-2.0 | 18,453 | [
"Brian"
] | 312e24f3f319a95fdaaa4a2af7c57afb3d390ef1ed609c110c3d43d73b80f529 |
#!/usr/bin/env python
from datamanagerpkg import ProtonCommunication_data_manager
import requests
import json
import pprint
import os
import paramiko
from scp import SCPClient
import subprocess
import time
from shutil import copyfile
##########################
#URL PROTON
##########################
from sequencer.G... | CARPEM/GalaxyDocker | data-manager-hegp/analysisManager/analysismanager/performRunProtonBackup.py | Python | mit | 26,058 | [
"Galaxy"
] | 9c07ce7ac65e9d1927db352348f64387d7ad71f5c7c583ae70480f6da8182aa3 |
from tool_shed.base.twilltestcase import ShedTwillTestCase, common, os
datatypes_repository_name = 'blast_datatypes_0120'
datatypes_repository_description = 'Galaxy applicable datatypes for BLAST'
datatypes_repository_long_description = 'Galaxy datatypes for the BLAST top hit descriptons tool'
tool_repository_name = '... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py | Python | gpl-3.0 | 12,325 | [
"BLAST",
"Galaxy"
] | a9dedeb3dc713d67ab9c5e002310afff87f04ac001d0fd1a920e2e7fe3680e60 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Change directory to p... | carlohamalainen/nipype | nipype/interfaces/fsl/preprocess.py | Python | bsd-3-clause | 71,745 | [
"Gaussian",
"VTK"
] | a8914c94b559d873c4db6ca7559547751f734203e045e128c2e8c4e923d1f874 |
"""
Test functions for multivariate normal distributions.
"""
from __future__ import division, print_function, absolute_import
from numpy.testing import (assert_almost_equal,
run_module_suite, assert_allclose, assert_equal, assert_raises)
import numpy
import numpy as np
import scipy.linalg
import scipy.stat... | juliantaylor/scipy | scipy/stats/tests/test_multivariate.py | Python | bsd-3-clause | 8,597 | [
"Gaussian"
] | 30b56f0f21779830067649c83c523d37bacecef774e12f07c7280ff8a815acce |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
The Atomic Universe
#########################
The :class:`~exatomic.container.Universe` object is a subclass of
:class:`~exatomic.exa.container.Container` that stores data coming... | exa-analytics/exatomic | exatomic/core/universe.py | Python | apache-2.0 | 15,848 | [
"ADF",
"Gaussian",
"MOLCAS",
"NWChem",
"cclib"
] | 66df390d49611e1cda7d7416c4908a707b90268ac79d2921aac9d2bab7b81a02 |
#!/usr/bin/env python
""" Configuration script for MUGS
This script provides a configuration procedure for MUGS.
After starting the script it will draw a dot on the display,
which movements has to be followed by the subject's eyes. Recorded
data is streamed to LSL and can be used to train the
Gaussian process mod... | MPIK-COMMS/mugs | calibration/calibration.py | Python | gpl-3.0 | 19,994 | [
"Gaussian"
] | 4518e3b09246f8586e0959fccd3b725c5226c433ff972a41aec41e7ae07c1f4c |
#
# Coded by Vali, updated by Mirakels for openpli
#
from enigma import iServiceInformation, eServiceCenter, iPlayableService, iPlayableServicePtr
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHuma... | openatv/enigma2 | lib/python/Components/Converter/pliExpertInfo.py | Python | gpl-2.0 | 13,875 | [
"Galaxy"
] | 8b16e4c9c23ce9b9a2ae76808b1fbffc9832992cdd87f5aacde570d536f87e76 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-network-management | scripts/fixup_network_management_v1_keywords.py | Python | apache-2.0 | 6,312 | [
"VisIt"
] | 9193ed0fd59b1fad50037df6a9487d4b89b9c58a15dc667e42b0c6b628d23d42 |
import unittest
import numpy.testing as testing
import numpy as np
import fitsio
import copy
from numpy import random
import time
import tempfile
import shutil
import os
from redmapper import Configuration
from redmapper import GalaxyCatalog
from redmapper import RedSequenceColorPar
from redmapper import ZredColor
fro... | erykoff/redmapper | tests/test_zred.py | Python | apache-2.0 | 8,360 | [
"Galaxy"
] | 6aea20b0690a9365bd5e5ca7801eaebd93dd42838e8d851417c1e420bb9c8fbc |
import numpy as np
import argparse
import cv2
import sys
#CLASS FOR USE AS A MODULE
#Creates a camera object to generate inputs for the
#neural network
#Takes an integer for the camera value, and then number of
#segments width-wise and height-wise in integers as well.
#Optional: crop (Boolean), crops camera to square... | UnionEvoRobo/evofab | src/evalHue.py | Python | gpl-2.0 | 5,266 | [
"Gaussian"
] | 0a9c9c1d2b93dccf381f9dace56a28b142f3d29ef338bbc8b3ba792536a0b61a |
# -*- coding: utf-8 -*-
"""diagnostic_primers
This module provides code to support the pdp package for diagnostic
primer design.
"""
__version__ = "0.2.0.dev"
import json
import os
import re
import sys
import traceback
from Bio import SeqIO
from Bio.Emboss import Primer3
from Bio.Seq import Seq
from Bio.SeqRecord im... | widdowquinn/find_differential_primers | diagnostic_primers/__init__.py | Python | mit | 12,170 | [
"Biopython"
] | 4d24dd60b4613148d79bde9a5bd5a64da353486a64b3b64ab8c75e49c6e3e2d4 |
try:
from django.urls import reverse
except ImportError:
from django.core.urlresolvers import reverse
from tastypie import authorization
from tastypie.authentication import MultiAuthentication
from crits.actors.actor import Actor, ActorIdentifier
from crits.actors.handlers import add_new_actor, add_new_actor_i... | Magicked/crits | crits/actors/api.py | Python | mit | 6,876 | [
"Amber"
] | aab411d56cf1b1274afe79e5e83b10375737590820bf0903f898511352c8e0fc |
from collections import defaultdict
from environment import Action
import matplotlib.pyplot as plt
import numpy as np
import random
class TDLearning:
def __init__(self, env):
self.QList = defaultdict(float) #(s, a)
self.EList = defaultdict(float) #(s, a)
self.NList = defaultdict(int) #(s, a... | ywk991112/easy21-RL | TDLearning.py | Python | mit | 2,187 | [
"VisIt"
] | ddd311bee529198fcc4edef1ef077017de76742d544e0f7f281f363a26757ec9 |
""" Basic unit tests for AuthManager
"""
import unittest
from DIRAC import gConfig
from DIRAC.Core.Utilities.CFG import CFG
from DIRAC.Core.DISET.AuthManager import AuthManager
__RCSID__ = "$Id$"
testSystemsCFG = """
Systems
{
Service
{
Authorization
{
Method = NormalUser
MethodAll = Any
... | petricm/DIRAC | Core/test/Test_AuthManager.py | Python | gpl-3.0 | 8,737 | [
"DIRAC"
] | 6d3f6115adcf4c1c5504d7f7a35b3f26c417118be7b00f027e46a359c886bdba |
"""
This module contains the CharmmMatcher class. It is used to apply
atom names from known topologies to the molecule by using a graph-based
representation of each molecule.
Author: Robin Betz
Copyright (C) 2015 Robin Betz
"""
# This program is free software; you can redistribute it and/or modify it under
# th... | drorlab/dabble | Dabble/param/charmmmatcher.py | Python | gpl-2.0 | 23,665 | [
"CHARMM",
"VMD"
] | 04eb86a26f9d14426262e2d94502ed51c2a0cdeee43f31a5aee9445a5a1b906b |
# -*- coding: utf-8 -*-s
import numpy as np
from calendar_calc import day_number_to_date
from netCDF4 import Dataset, date2num
import pdb
import create_timeseries as cts
resolution_file = Dataset('/scratch/sit204/ozone_cmip5_files/Ozone_CMIP5_ACC_SPARC_1990-1999_T3M_O3.nc', 'r')
lons = resolution_file.variables['lon'... | sit23/Isca | src/extra/python/scripts/create_cmip5_ozone_timeseries.py | Python | gpl-3.0 | 2,218 | [
"NetCDF"
] | fd60a144ca4fffb6b140d5a4de8edcc679c59208d326d8df1d159820ec9fa194 |
import numpy as np
import partio
import collections
from paraview.util.vtkAlgorithm import (
VTKPythonAlgorithmBase,
smdomain,
smhint,
smproperty,
smproxy,
)
from vtkmodules.numpy_interface import dataset_adapter as dsa
from vtkmodules.vtkCommonDataModel import vtkUnstructuredGrid
paraview_plugin_... | InteractiveComputerGraphics/SPlisHSPlasH | Scripts/Paraview/paraview-partio-plugin.py | Python | mit | 5,066 | [
"ParaView"
] | 22c865e7abdb574861f267c42aecbe5ad14abdaf5ab83a594c358fb78c9d730c |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
####################################################################################
### Copyright (C) 2015-2019 by ABLIFE
####################################################################################
#########################################################... | ablifedev/ABLIRC | ABLIRC/bin/Clip-Seq/piranha/filterout_exp_nonoverlap_peaks_with_ctrl.py | Python | mit | 10,689 | [
"HTSeq"
] | 3f0666038b44272d49a77a4fd4648b96573ae21bfbe3cac39c2b91fca98b3695 |
from __future__ import print_function
from __future__ import division
try:
from builtins import str
except:
print("Warning: No str in builtins")
try:
from builtins import range
except:
print("Warning: No range in builtins")
# Requires:
# - boututils
# - NumPy
try:
from boututils.datafile import... | erikgrinaker/BOUT-dev | tools/pylib/boutdata/collect.py | Python | gpl-3.0 | 13,079 | [
"NetCDF"
] | 595db60c0c6824ae050a11b38a03cd59a1662f4cefaae79659463850105d1db7 |
import os
import json
from unittest import mock
import pytest
import scrypt
from conda_smithy.feedstock_tokens import (
generate_and_write_feedstock_token,
read_feedstock_token,
feedstock_token_exists,
register_feedstock_token,
register_feedstock_token_with_proviers,
is_valid_feedstock_token,
... | ocefpaf/conda-smithy | tests/test_feedstock_tokens.py | Python | bsd-3-clause | 16,232 | [
"ADF"
] | 3368fcfa8921eec5b9528f5e424928776bb49c685507cd27a5bc92aff44bba24 |
# -*- coding: utf-8 -*-
# ***********************************************************************
# Copyright (C) 2016 - 2017 Oscar Gerardo Lazo Arjona *
# <oscar.lazoarjona@physics.ox.ac.uk> *
# ***********************************************************************
... | oscarlazoarjona/quantum_memories | quantum_memories/settings_lambda.py | Python | gpl-3.0 | 11,371 | [
"Gaussian"
] | 2df6d6d9e1d84ec1df1935552674bbbde994eddb4de079e607c7b5853d64a435 |
# -*- coding: utf-8 -*-
#
# DiracDocs documentation build configuration file, created by
# sphinx-quickstart on Sun Apr 25 17:34:37 2010.
#
# 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.
#
# A... | yujikato/DIRAC | docs/source/conf.py | Python | gpl-3.0 | 10,291 | [
"DIRAC"
] | ea5fda4dab1b2339a9772e9cba826b8fbf8ee8308b7ec6b1913b30c6601fbd7e |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The freesurfer module provides basic functions for interfacing with
freesurfer tools.
Change directory to provide relative paths for doctests
>>> import os
>>> filepa... | carolFrohlich/nipype | nipype/interfaces/freesurfer/model.py | Python | bsd-3-clause | 65,791 | [
"Gaussian"
] | 73c3fb8283ce0beb78da64b22d2b35ffcd639467843063d58806a5cb2c169d9a |
#
# Mathematical function library.
# Author: James P. Biagioni (jbiagi1@uic.edu)
# Company: University of Illinois at Chicago
# Created: 12/16/10
#
import math
# Normal distribution PDF. Formula obtained from: http://en.wikipedia.org/wiki/Normal_Distribution
def normal_distribution_pdf(x, mu, sigma, numerator=1.0):
... | Vanuan/gpx_to_road_map | edelkamp2003/pylibs/mathfunclib.py | Python | apache-2.0 | 1,560 | [
"Gaussian"
] | af200b306e9fa6bd4c7b507200b047145c4fbc0566cd0905b37a093f936d8f86 |
#!/usr/bin/env python
"""
Generate GEXF configuration of sensory integration LPU.
"""
import networkx as nx
def create_lpu(file_name, lpu_name, N_neu):
"""
Create a LPU for sensory integration.
Creates a GEXF file containing the neuron, synapse and port parameters for
an LPU containing the specified... | cerrno/neurokernel | examples/sensory_int/data/gen_integrate.py | Python | bsd-3-clause | 3,166 | [
"NEURON"
] | 34bb2fe46c1c0715d1573bdd2d329916172217b7d87e33145b3791acc14c46ad |
#!/usr/bin/env python
import pprint
import re
import os, sys
import unittest
sys.path[0:0] = ['.', '..']
from pycparser import c_parser
from pycparser.c_ast import *
from pycparser.c_parser import CParser, Coord, ParseError
_c_parser = c_parser.CParser(
lex_optimize=False,
yacc_debug... | sideeffects/pycparser | tests/test_c_parser.py | Python | bsd-3-clause | 61,008 | [
"MOE",
"VisIt"
] | b7c036a99f30f915a4ba656e229f77de8ea3abccd67c74b16274e902571b9542 |
#!/usr/bin/env python
import time, os
import random
import writeInputs
import threading as mt
import tarfile
import radical.entk as re
import radical.utils as ru
import radical.analytics as ra
#os.environ['RADICAL_VERBOSE'] = 'INFO'
os.environ['RADICAL_ENTK_VERBOSE'] = 'INFO'
os.environ['RADICAL_PILOT_DBURL'] = 'mo... | radical-cybertools/radical.repex | old/examples/async_repex.py | Python | mit | 16,697 | [
"Amber"
] | 597b6a8464d3bf075a6d9947728074b0357ce0798fedb9fe62747dba5086e77e |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | markovmodel/PyEMMA | pyemma/coordinates/tests/test_api_load.py | Python | lgpl-3.0 | 4,052 | [
"MDTraj",
"NetCDF"
] | 513e0fa9f13da6d7e931cdbd62ffe545dc60259d364e2e64f596b7f5fc3593c4 |
from collections import OrderedDict
from pandas import read_csv, Series
from numpy import concatenate, ones, power, searchsorted, sqrt, std, where, loadtxt, linspace, median, max as npmax, True_, False_, bool_, empty, isnan
from uncertainties import ufloat
from DZ_Logs i... | Delosari/dazer | bin/DZ_LineMesurer.py | Python | mit | 61,897 | [
"Gaussian"
] | e0356a04aab1f168a560cb8c312b516bdd0ccc88f655747ee532d87fa4e38dc0 |
'''
Main interface to Basis Set Exchange internal basis sets
This module contains the interface for getting basis set data
and references from the internal data store of basis sets. As much
as possible, this is being kept separate from the typical reading/writing
functionality of the library.
'''
import os
import tex... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/api.py | Python | bsd-3-clause | 22,486 | [
"NWChem",
"Psi4",
"TURBOMOLE"
] | 38b74867b8f56542d49d47386facd47bc53ea2e17a3db7a578c58ac0ccfa04d3 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | wangsheng1001/incubator-singa | examples/mnist/train.py | Python | apache-2.0 | 5,174 | [
"Gaussian"
] | f228984a4045936756788a367aaae32d947850318199f5f995d8149f8ab00e03 |
#from ctx_base import StandardBaseContext
from .libmp.backend import basestring, exec_
from .libmp import (MPZ, MPZ_ZERO, MPZ_ONE, int_types, repr_dps,
round_floor, round_ceiling, dps_to_prec, round_nearest, prec_to_dps,
ComplexResult, to_pickable, from_pickable, normalize,
from_int, from_float, from_str,... | NikNitro/Python-iBeacon-Scan | mpmath/ctx_mp_python.py | Python | gpl-3.0 | 36,704 | [
"Gaussian"
] | 6f26f5017537db7f981991511ec00f35f7b1c54432a7432879d3035e9c677b70 |
import numpy as np
from iminuit import Minuit
import math
import matplotlib.pyplot as plt
from scipy.stats import multivariate_normal
from scipy.special import erf
from scipy.integrate import dblquad
import random
erf = math.erf
def getPoissonVariate(N,tmin,tmax):
rate = N / (float(tmax)-float(tmin))
tt = [tm... | giacomov/XtDac | XtDac/BayesianBlocks/SpaceClusteringLikelihood.py | Python | bsd-3-clause | 10,665 | [
"Gaussian"
] | 05cf3ca237fd5bf650950ba2fc22bfbd035a15b1f00bdbe7d462f6be7014b97c |
# Copyright (c) 2014, the GREAT3 executive committee (http://www.great3challenge.info/?q=contacts)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are permitted
# provided that the following conditions are met:
#
# 1. Redistributions of source code must retain... | barnabytprowe/great3-public | great3sims/builder.py | Python | bsd-3-clause | 89,687 | [
"Galaxy",
"Gaussian"
] | 673322cb81a4b50365a38619ba7e7a1afc00f8ed813eb885531dc6251dc0c071 |
"""
Test atomic coordinates and neighbor lists.
"""
import os
import logging
import numpy as np
import unittest
from rdkit import Chem
from deepchem.utils import conformers
from deepchem.feat.atomic_coordinates import get_coords
from deepchem.feat.atomic_coordinates import AtomicCoordinates
from deepchem.feat.atomic_co... | Agent007/deepchem | deepchem/feat/tests/test_atomic_coordinates.py | Python | mit | 5,599 | [
"RDKit"
] | 622d585649ff2e91f8c994d0d4cd9befa66879a99c9f0c985a8eefdd7e1ea23a |
# -*- coding: utf-8 -*-
#
# lin_rate_ipn_network.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | hakonsbm/nest-simulator | pynest/examples/lin_rate_ipn_network.py | Python | gpl-2.0 | 5,702 | [
"NEURON"
] | fccae821e546e6526b15654950095c3a40711fdd3a720188d5ae867f1b0032e0 |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 02 18:20:40 2015
@author: Konstantin
"""
from scipy import optimize
import numpy as np
import configparser, os, csv
from fabric.api import env, execute, task, get
import cuisine
import vm_control
import pandas
import operator
import pickle
import scip... | icclab/vm-reliability-tester | model_fitter.py | Python | mit | 9,708 | [
"Gaussian"
] | 667c1f42db26c411bafa2ddc2d187a97bc9239fdba83c364a833d241ea4e18ff |
# Copyright 2015 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... | gunan/tensorflow | tensorflow/python/ops/gradients_util.py | Python | apache-2.0 | 38,917 | [
"VisIt"
] | 77be9e8e20617d7543ec8fd43b9a3bd942de4432d920e5ffb9b75aca2af3a604 |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
# Modifications to create of the HMMLearn module: Gael Varoquaux
"""
The :mod:`hmmlearn.hmm` module implements hidden Markov models.
"""
import numpy ... | stringertheory/hmmlearn | hmmlearn/hmm.py | Python | bsd-3-clause | 25,706 | [
"Gaussian"
] | e5c9a3f8ce0e17776f23176305a53db548abfd6024026e4cd86060583a3c94e8 |
import numpy as np
from scipy.special import hyp1f1
from scipy.special import erf as erf_scipy
#import sympy.mpmath as mpm
#import mpmath as mpm
'''
NOTE:
BoysF is used for Coulomb integrals like :
Vpq = Integral{ exp(-p*(r1)^2) * exp(-q*(r2)^2) /|r1-r2| }
Vpq = 2*pi^(5/2) / ( p*q*sqrt(p+q) ) * BoysF( a*r^2 )... | ProkopHapala/SimpleSimulationEngine | python/pyGaussAtom/BoysFunc.py | Python | mit | 10,075 | [
"Gaussian"
] | 38af0ecb0d8dc5065663e05921582cf9eb2d4c0b3a2137bede90a40f46c44b8a |
""" Test class for AccountingDB
"""
# pylint: disable=protected-access
# imports
import unittest
from mock import MagicMock
import DIRAC.AccountingSystem.DB.AccountingDB as moduleTested
class TestCase(unittest.TestCase):
"""Base class for the AccountingDB test cases"""
def setUp(self):
self.module... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/DB/test/Test_AccountingDB.py | Python | gpl-3.0 | 16,639 | [
"DIRAC"
] | 8316a226486f30f12ecb8f66677fdc8ccc24d872ba0b493cf5bde54690e72d49 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-yaqcaffy/package.py | Python | lgpl-2.1 | 1,760 | [
"Bioconductor"
] | a9c573005bc57b652eec225b72e322063869125fc3c5ae5ec2540d90171fd48c |
#!/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... | andreaso/ansible | lib/ansible/modules/cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,520 | [
"Dalton"
] | ac2a482e25a82e76ce183e7fd149e08e9a00b276618e2d22e55cd8867529cb14 |
"""Phonopy input and command option tools."""
# Copyright (C) 2011 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source ... | atztogo/phonopy | phonopy/cui/settings.py | Python | bsd-3-clause | 91,526 | [
"CRYSTAL",
"Jmol",
"phonopy"
] | e6c50fa62915a44ec52a4f320fc758244c36d77385d9cbabcf1a4d6580775202 |
#!/usr/bin/env python
# This example reads a volume dataset, extracts two isosurfaces that
# represent the skin and bone, and then displays them.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the renderer, the render window, and the interactor. The
# renderer... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Medical/Python/Medical2.py | Python | bsd-3-clause | 4,901 | [
"VTK"
] | a1822760068844605608d10d986cb4dad25101ed55b9bcbf029087d290592daf |
#!/usr/bin/python
################################################################################
#
# Module: File.py
#
# Author: Paul Tindle ( mailto:Paul@Tindle.org )
# Joe White( mailto:joe@stoke.com )
#
# Descr: Subs for file IO
#
# Version: (See below) $Id$
#
# Changes: Conversion to Pytho... | white111/CMtestpy | bin/lib/FileOp.py | Python | lgpl-2.1 | 15,194 | [
"VisIt"
] | f1b8f852b3988e57cdc452034b263362c2f778f7ed2a7bb860a650f7a6590bb0 |
"""Fabric deployment file to install genomic data on remote instances.
Designed to automatically download and manage biologically associated
data on cloud instances like Amazon EC2.
Fabric (http://docs.fabfile.org) manages automation of remote servers.
Usage:
fab -i key_file -H servername -f data_fabfile.py inst... | rchekaluk/cloudbiolinux | data_fabfile.py | Python | mit | 3,174 | [
"Galaxy"
] | 91b3bb4bfb40fbb2ffefa403010ebb1eadb9c4af80c36f97d78b335f165d2811 |
# coding: utf-8
# # 3 - 3D Modeling with GemPy
# In[1]:
from matplotlib import use
use("Agg")
import sys
import numpy as np
# These two lines are necessary only if gempy is not installed
sys.path.append("../../gempy/")
sys.path.append("../../../remote-geomod/rgeomod")
sys.path.append("../gempy/")
sys.path.append("... | cgre-aachen/gempy | test/test_addons/TOUPDATE_addons/test_google_earth.py | Python | lgpl-3.0 | 5,572 | [
"VTK"
] | 68f5497891ced3ba9161d27995c988d2f92a345346978e8274b02993f0e6a2d1 |
#!/usr/bin/env python
import numpy as np
from scipy import sparse
import scipy.io as sio
import argparse
import os
import itertools
import smurff.matrix_io as mio
from sklearn import preprocessing
#parser = argparse.ArgumentParser(description='SMURFF tests')
#parser.add_argument('--envdir', metavar='DIR', dest='envd... | ExaScience/smurff | data/synthetic/make.py | Python | mit | 8,259 | [
"Gaussian"
] | 57e95c68f5a00a6ba6da466669a265b4d7dd28e51f1085cdd4f2b2c04326d0fa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from pymatgen.analysis.bond_valence import (
BVAnalyzer,
calculate_bv_sum,
calculate_bv_sum_unordered,
)
from pymatgen.core.composition import Composition
from pymatgen.c... | gmatteo/pymatgen | pymatgen/analysis/tests/test_bond_valence.py | Python | mit | 4,439 | [
"pymatgen"
] | ad18820e4035b09b93c03711e3c31e576fc0a1154be18a847f1f3c3c6eabd9db |
# -*- coding: utf-8 -*-
#
# gap_junctions_two_neurons.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... | sdiazpier/nest-simulator | pynest/examples/gap_junctions_two_neurons.py | Python | gpl-2.0 | 2,829 | [
"NEURON"
] | c4111e5c83e18889cb016f9fdc1bfedc402f41aa4e0ecc5c4f0739e63f866aad |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Intensity-based image registration
"""
from __future__ import absolute_import
from __future__ import print_function
import numpy as np
import scipy.ndimage as nd
from ...core.image.image_spaces import... | alexis-roche/nipy | nipy/algorithms/registration/histogram_registration.py | Python | bsd-3-clause | 21,515 | [
"Gaussian"
] | c8714bde292dd140c3e1f9a184f7fc6b5487c8e3aafe497d1bbd5ad74f18f6cf |
#!/usr/bin/env python
""" Image segmentation algorithms """
from __future__ import division
import cv2
import numpy as np
from matplotlib import pyplot as plt
from skimage import segmentation, color
from skimage.future import graph
from selam.utils import img
from selam import colorconstancy as cc
def felzenszwalb(i... | jinified/selam | examples/segmentation.py | Python | mit | 2,214 | [
"Gaussian"
] | b4ab133edd83d056c11e23e35dd02393d4b89db611bc570e75f3d487b13543ad |
# -*- coding: utf-8 -*-
"""
Created on Wed Sep 23 16:31:33 2015
@author: Rick Berg, University of Washington, School of Oceanography
Script for modeling reaction rates in marine sediments.
Starts with existing sediment column, sediment column building upward is
modeled as a downward flow of porewater.
Bottom bound... | rickdberg/mgmodel | simple_flux.py | Python | mit | 22,071 | [
"Gaussian"
] | af6e439e9512b8ee630855eccec0473d56b3e7035cc53d82cca2f9c855073761 |
#!/usr/bin/env python
# encoding: utf-8
#
# test_maps.py
#
# Created by Brett Andrews on 1 May 2017.
import numpy as np
import matplotlib
import pytest
from marvin import config
from marvin.tools.maps import Maps
import marvin.utils.plot.map as mapplot
from marvin.utils.general import get_plot_params
matplotlib_2 =... | bretthandrews/marvin | python/marvin/tests/utils/plot/test_map.py | Python | bsd-3-clause | 11,539 | [
"Galaxy"
] | 4cd66cbb3915ab5762990a991c93c6f909d7e3975c927e58377285215e924e96 |
# Script to plot sub-surface ocean temperature drift.
# Analysis: using newer python 2.7.3
"""
module purge
module use -a /home/fms/local/modulefiles
module load gcc
module load netcdf/4.2
module load python/2.7.3
"""
import os
import math
import numpy as np
from numpy import ma
from netCDF4 import Dataset, MFDatase... | aidanheerdegen/MOM6-examples | tools/analysis/MOM6_annual_analysis.py | Python | gpl-3.0 | 4,961 | [
"NetCDF"
] | ee43c769cb7581d6a493a4c5edcac7e3f7ba8532fa387a242209037023614e37 |
"""
Support and standalone functions for Robust Linear Models
References
----------
PJ Huber. 'Robust Statistics' John Wiley and Sons, Inc., New York, 1981.
R Venables, B Ripley. 'Modern Applied Statistics in S'
Springer, New York, 2002.
"""
from statsmodels.compat.python import callable, range
import numpy as n... | bert9bert/statsmodels | statsmodels/robust/scale.py | Python | bsd-3-clause | 8,091 | [
"Gaussian"
] | abf77d1ccc4a39d91af709cb247d42ebd149e41c9c9c2ebf4d48e17215aa677a |
# Exercise 43: Basic Object-Oriented Analysis and Design
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self, scene_map):
s... | pwittchen/learn-python-the-hard-way | exercises/exercise43.py | Python | mit | 8,842 | [
"BLAST"
] | eb2b564648bc6510d2ad46fb0bffaa34d8c28a778c48aaacca46d034ed2041e8 |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, or ntpath
- os.name is 'posix', 'nt', 'os2', 'ce' or 'riscos'
- os.curdir is a string representing the current di... | DmitryADP/diff_qc750 | vendor/nvidia/tegra/3rdparty/python-support-files/src/Lib/os.py | Python | gpl-2.0 | 26,235 | [
"VisIt"
] | 329c1530fa7698e3297c1edb5cfed7e87c5f660d65b72f0796cf7cf90dae58eb |
#!/usr/bin/python
import tweetproc
import os
import io
from datetime import *
from tweetproc.sitesdata import *
# Global variable used for processing
siteiter=-1
# Custom process for this script
def process(inputdir,outfilename,tictime1,tictime2):
# Empty dictionary to store the tweet counts for each user... | HPCGISLab/TwitterMethods | workflow-sites-to-mtic.py | Python | bsd-3-clause | 3,166 | [
"Amber"
] | 7d99777416bfa4eac59b02fb1e5feec1c9c4b81ca8a9dbce054b7a570cc02449 |
#!/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... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_pkiprofile.py | Python | gpl-3.0 | 5,974 | [
"VisIt"
] | c6846bbaf681d2c561a01cacdbc78100cd6604cd5a248035e5c67e5e116293d7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import glob
import itertools
import logging
import math
import os
import re
import warnings
import xml.etree.cElementTree as ET
from collection... | tallakahath/pymatgen | pymatgen/io/vasp/outputs.py | Python | mit | 137,250 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | d2ba3e51fd49723368ae9033abfa87949310069cb68455f94b6b74dce6914c5a |
"""
This package implements various Nwchem Jobs and Error Handlers.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "ongsp@ucsd.edu"
__status__ = "Beta"
__date__ = "6/17/13"
| materialsproject/custodian | custodian/nwchem/__init__.py | Python | mit | 283 | [
"NWChem"
] | cd97d6d1aaf933fc3e4fcc71628e00381bf0ba1d8547b7f13823497350864edf |
# -*- coding: utf-8 -*-
import hexchat
import random
__module_name__ = 'Slap'
__module_version__ = '1.0.1'
__module_description__ = 'Slaps people.'
__module_author__ = 'JeDa (based off Frankity\'s code)'
def slap_cb(word, word_eol, userdata):
actions = ["slaps", "whacks", "ˢᵉʳᶦᵒᵘˢ ᵗʳᵒᵘᵇᶫᵉs", "destroys", "Timsons", ... | JeDa/HexChat-addons | addons/slap.py | Python | mit | 1,745 | [
"Galaxy"
] | 5085ce34a1001071aed9cda1d03068de665d33bddd2959f572580c04352cc2e1 |
# Assemble Arybo IR into ASM thanks to LLVM
# Map symbol names to register
# Warning: this tries to do its best to save modified temporary registers.
# There might be errors while doing this. The idea is not to regenerate clean
# binaries, but to help the reverser!
try:
import llvmlite.ir as ll
import llvmlite... | quarkslab/arybo | arybo/lib/exprs_asm.py | Python | bsd-3-clause | 10,636 | [
"VisIt"
] | f80bc998fe0dccdf62b6823098a6eff0ef28a32b018b4015d615af7027dac44b |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-add-resources
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Add resources from the BDII database for a given VO
"""
__RCSID... | Sbalbp/DIRAC | ConfigurationSystem/scripts/dirac-admin-add-resources.py | Python | gpl-3.0 | 16,049 | [
"DIRAC"
] | a9df1c77b97e9bf295262e46cebea340d2e10527746ca4ef1307f237f8f2217d |
# Orca
#
# Copyright 2015 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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 o... | chrys87/orca-beep | src/orca/scripts/apps/soffice/spellcheck.py | Python | lgpl-2.1 | 3,437 | [
"ORCA"
] | 0f4c4056d2d35a5e7dfe3640eff6f7b02e5115405da45280e23f615687e55439 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Changing field 'Article.suggester'
db.alter_column('neuroelectro_article', 'suggester_id', self.gf('djang... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0036_auto__chg_field_article_suggester.py | Python | gpl-2.0 | 25,701 | [
"NEURON"
] | d6945487b5ac58aac98ae8961f69635d95ee875a4dac9629b71ad8a7cd07fee8 |
import characterquests
from characterutil import *
def z_58_80_Hellfire_Peninsula(count,datatree,openfile):
characterquests.charquestheaderfaction(count,"58-80: Hellfire Peninsula","horde",openfile)
characterquests.charquestprint(count,datatree,openfile,28705,"Warchief's Command: Outland!")
characterquests.charques... | DreamsofPeace/WoW-Quests | characterquests2bc.py | Python | mit | 64,642 | [
"BLAST",
"CRYSTAL",
"VisIt"
] | 1603ca7ac0255c62100a2c14a6e226c93c5f3e588417168ccb7a78f5aead4472 |
#!/usr/bin/env python
"""TexCounter.py: Counts the number of garments in a shelf"""
import cv2
import sys
import logging
import numpy as np
import pandas as pd
from matplotlib import pyplot as plt
from sklearn.cluster import MeanShift, estimate_bandwidth
__author__ = "Pradeep Kumar A.V."
logging.basicConfig(filena... | DrigerG/IIITB-ML | project/TexCounter/tex_counter.py | Python | apache-2.0 | 9,127 | [
"Gaussian"
] | 80b8eb11f1a34dff7f6065f77abfe94754fd63cdabb292c3a2176d8858e93dc4 |
"""
@name: PyHouse/src/Modules/Families/Insteon/_test/test_Insteon_HVAC.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2014-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Dec 6, 2014
@Summary:
Passed all 2 tests - DBK - 2015-07-29
"""
__updated__ = '20... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/_test/test_insteon_hvac.py | Python | mit | 1,123 | [
"Brian"
] | e4e283f6c25a57e8a7a9221f561b726aebc94129d05bbf3edd2cc1ddb70b2b7c |
import unittest
import copy
import sys
from nose.tools import assert_true
import numpy as np
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
assert_raises)
from scipy import stats
from sklearn import mixture
from sklearn.datasets.samples_generator import make_spd_ma... | WangWenjun559/Weiss | summary/sumy/sklearn/mixture/tests/test_gmm.py | Python | apache-2.0 | 17,427 | [
"Gaussian"
] | 114a9548bc74b73ae1f3e7f710196e9d0d604c10b9675c99bfeb890b4b7f6aef |
import random
from rlkit.exploration_strategies.base import RawExplorationStrategy
import numpy as np
class GaussianAndEpsilonStrategy(RawExplorationStrategy):
"""
With probability epsilon, take a completely random action.
with probability 1-epsilon, add Gaussian noise to the action taken by a
determi... | vitchyr/rlkit | rlkit/exploration_strategies/gaussian_and_epsilon_strategy.py | Python | mit | 1,241 | [
"Gaussian"
] | ae75c7c066628baa35ed079f13f3a31a4d9324caaed67c045665f6b920f785e2 |
# -*- coding: utf-8 -*-
#
# brunel2000_rand.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License... | magnastrazh/NEUCOGAR | nest/serotonin/research/C/nest-2.10.0/doc/nest_by_example/scripts/brunel2000_rand.py | Python | gpl-2.0 | 5,643 | [
"NEURON"
] | b56fdf7f8dfa856960b6d03321432809e023b4954533f0aa12f355b06445b631 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | yugangzhang/scikit-beam | skbeam/core/fitting/tests/test_background.py | Python | bsd-3-clause | 3,816 | [
"Gaussian"
] | bcf5adffe9d19323bf55b296469bb8bb5882361b8d59b9f29e4bda714e8e8d2c |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/analysis/test_helanal.py | Python | gpl-2.0 | 6,722 | [
"MDAnalysis"
] | 062e4b2d7ca258eb4f0844bceee9f313b1a6b0cad38c63e394c6bd6aeea5c706 |
"""
Copyright (c) 2016 Jet Propulsion Laboratory,
California Institute of Technology. All rights reserved
"""
import json
import logging
import numpy as np
from nexustiles.nexustiles import NexusTileService
# from time import time
from webservice.NexusHandler import nexus_handler, SparkHandler, DEFAULT_PARAMETERS_SP... | dataplumber/nexus | analysis/webservice/algorithms_spark/CorrMapSpark.py | Python | apache-2.0 | 15,444 | [
"NetCDF"
] | 0cc9c20ba4173a85cc928f9c639f2f8b25023a12eb2dd5c7a498bf1d7bf5ee4e |
from contentbase.upgrader import upgrade_step
@upgrade_step('user', '', '2')
def user_1_2(value, system):
pass
@upgrade_step('user', '2', '3')
def user_2_3(value, system):
pass
@upgrade_step('user', '3', '4')
def user_3_4(value, system):
# https://github.com/ClinGen/clincoded/issues/453
if value['ema... | ClinGen/clincoded | src/clincoded/upgrade/user.py | Python | mit | 75,323 | [
"Brian",
"Dalton"
] | fa016308be021c981923a2bc19b202e4ec39119e900cb581ecfc749fa208b977 |
# 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 https://mozilla.org/MPL/2.0/.
"""Phonon related functions and classes
=======================================
In sisl phonon calculations are relying... | zerothi/sisl | sisl/physics/phonon.py | Python | mpl-2.0 | 15,332 | [
"Gaussian"
] | f1c4cce1f154fd09ed8ae3e70d17f902131dabf463155fa69d6246d4c08696b7 |
# -*- coding: utf-8 -*-
############################ Copyrights and license ############################
# #
# Copyright 2012 Christopher Gilbert <christopher.john.gilbert@gmail.com> #
# Copyright 2012 Steve English <steve.english@naveta... | allevin/PyGithub | github/Repository.py | Python | lgpl-3.0 | 133,405 | [
"Brian"
] | b4fd36b7fa5fd1bdcdb4178534300dcd8a42c5e99fad07e644c1105ba898911d |
""" Configuration and utilities for all the X509 unit tests """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import sys
from datetime import datetime
from pytest import fixture
# We use certificates stored in the same folder as this test file
... | ic-hep/DIRAC | src/DIRAC/Core/Security/test/x509TestUtilities.py | Python | gpl-3.0 | 17,296 | [
"DIRAC"
] | 31a5f800563b1754f79a2174d1d253e43a6955b86759fcd0ea2f703f5ff204de |
# This file is part of Androguard.
#
# Copyright (C) 2014 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
... | androguard/androguard | androguard/decompiler/dad/dast.py | Python | apache-2.0 | 23,596 | [
"VisIt"
] | 72ef0709e8a27602808855921a6f3e6fc65d652bee4a083307c29320a263b9e2 |
from sqlalchemy import create_engine
from sqlalchemy.ext.automap import automap_base
from sqlalchemy import orm
from sqlalchemy.sql import functions as sql_func
from airflow import configuration
class Connection:
def __init__(self, db_url=None):
if db_url is None:
db_url = configuration.get(... | LREN-CHUV/mri-meta-extract | data_tracking/connection.py | Python | apache-2.0 | 4,867 | [
"VisIt"
] | 2c6ec478a974c63dd4e3edc7acdb0e0c5295b99f378ff318819ce05cf9b94b7c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# 배열 돌리기 1 - 시계방향
# https://www.acmicpc.net/problem/16926
'''
4 4 1
1 2 3 4
5 6 7 8
9 10 11 12
13 14 15 16
'''
def debug_print(obj):
for d in obj:
print(d)
print("----------------")
def dfs(x, y, dir, r, Range, Orig):
global row
global col
g... | youngjun0528/moheeto | BaekjoonOnlineJudge/acmicpc_16926_시계방향.py | Python | apache-2.0 | 2,501 | [
"VisIt"
] | 464d536d73eb42160d7e07fefbb1b5fbc96dbd7afba2044bd86f1b638b6c0d73 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | retrography/scancode-toolkit | src/typecode/__init__.py | Python | apache-2.0 | 1,490 | [
"VisIt"
] | 9d08eb0d8271a8514f1893eefab77d775b06f78eab164725f5eb3b5ff4dc2869 |
"""Collection of physical units."""
# Copyright (C) 2011 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# 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 ... | atztogo/phonopy | phonopy/units.py | Python | bsd-3-clause | 3,728 | [
"Avogadro",
"CP2K",
"FLEUR",
"TURBOMOLE",
"phonopy"
] | 47f161142d2ea9cc72722bbb44451d5dd3a71a3c5f2f179cb3e246dd3ed38ef1 |
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