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# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
import time
import os
from urllib import parse
import pytest
from selenium import webdriver
from selenium.common.exceptions import WebDr... | cobrateam/splinter | tests/base.py | Python | bsd-3-clause | 12,388 | [
"VisIt"
] | ccec3323d98285172d851ba8c36d8fd9b7da9cd120b273a8462c3764a0127b84 |
ROOOT_Domain_List = { ".aaa" : "[.]aaa",
".aarp" : "[.]aarp",
".abb" : "[.]abb",
".abbott" : "[.]abbott",
".abbvie" : "[.]abbvie",
".able" : "[.]able",
".abogado" : "[.]abogado",
".abudhabi" : "[.]abudhabi",
".ac" : "[.]ac",
".academy" : "[.]academy",
".accenture" : "[.]accenture",
".accountant" : "[.]accoun... | johestephan/CTI-Toolbox | redactit_zone.py | Python | apache-2.0 | 31,191 | [
"CASINO",
"Jaguar",
"MOE"
] | 1afc9861eafb0b5ec812bda731dccfc989eb8276a4b3d5701c2b05b132797f85 |
#!/usr/bin/env python
# Copyright (c) 2015-2018
# Jakub Krajniak (jkrajniak at gmail.com)
#
# 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 versio... | espressopp/espressopp | testsuite/FileIOTests/h5md/dump_topology_test.py | Python | gpl-3.0 | 7,316 | [
"ESPResSo"
] | ede57dd8f2b1554474857ad01acfab4b6b8894a3d3a0dc087ca97290b8b5e987 |
# -*- coding: utf-8 -*-
# Author : Jean-Michel Begon
# Date : Apr 02 2014
"""
A custom filter container
"""
import numpy as np
from math import sqrt
from randconv.image import Finite3SameFilter
__all__ = ["custom_filters", "custom_finite_3_same_filter"]
def shape2D(squareIterable, normalisation=None):
"""
... | jm-begon/randconv | randconv/image/filter_holder.py | Python | bsd-3-clause | 5,931 | [
"Gaussian"
] | a603fed1673402ab343f7723388beb4b820e70ada4ed1df696c38e8e6856c3ee |
#!/usr/local/sci/bin/python
#*****************************
#
# general utilities & classes for Python QC.
#
#
#************************************************************************
# SVN Info
#$Rev:: 117 $: Revision of last commit
#$Author:: rdunn ... | rjhd2/HadISD_v2 | qc_utils.py | Python | bsd-3-clause | 30,588 | [
"Gaussian",
"NetCDF"
] | edf29d8358cb8e912fc9bfd661d51a7d4cff4350b9c86e923f72d9c9d0a52ebf |
#!/usr/bin/env python
"""Tests for Howdoi."""
import gzip
import json
import os
import re
import unittest
from pathlib import Path
from unittest.mock import patch
import requests
from cachelib import NullCache
from pyquery import PyQuery as pq
# pylint: disable=no-name-in-module
from howdoi import howdoi
# pylint... | gleitz/howdoi | test_howdoi.py | Python | mit | 16,354 | [
"MOE"
] | 5b72ef2814ce7a5e85d8888a2da60aed36a872afb390f791203e06121df46326 |
#-*- coding:utf-8 -*-
from builtins import map
from builtins import range
import logging
import warnings
from collections import namedtuple
from builtins import int as int_types
from future.utils import viewitems, viewvalues
from miasm.expression.expression import ExprId, ExprInt, get_expr_locs
from miasm.expression... | serpilliere/miasm | miasm/core/asmblock.py | Python | gpl-2.0 | 51,507 | [
"VisIt"
] | c308282045337422d0fadff4cbfd1ee5ce20c6ebee405fab800d8b6410ffc07c |
## Automatically adapted for numpy.oldnumeric May 17, 2011 by -c
# Natural Language Toolkit: Clusterers
#
# Copyright (C) 2004 University of Melbourne
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# URL: <http://nltk.sf.net>
# For license information, see LICENSE.TXT
#
# $Id: __init__.py,v 1.1.1.1 2004/09/29 21:58:25 ada... | ronaldahmed/SLAM-for-ugv | neural-navigation-with-lstm/MARCO/nltk/clusterer/__init__.py | Python | mit | 39,218 | [
"Gaussian"
] | 1a28ff27db6451e49ddc27b7088b41cb637cc2d165a4744c1b62ff94a17f197f |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | s-hertel/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 9,119 | [
"Brian"
] | bf3d45c810f2c08be6706e258a41def94e4312bc0aa247879f532fe8174302e8 |
# -*- coding: utf-8 -*-
"""
Created on Wed May 18 11:55:27 2016
@author: Ashley Zhou
"""
import sys
sys.path.append('/home/nzhou/git')
import os
from os import walk
from CAFAAssess.precRec import GOPred,PrecREC,read_benchmark
from Ontology.IO import OboIO
import gzip
import zipfile
import tarfile
pred_folder = "/h... | arkatebi/SwissProt-stats | CAFAAssess/confidence.py | Python | gpl-3.0 | 6,698 | [
"BLAST"
] | 45d6bcc164150b64c6fafb93b1c79ba93080655b4554d42307371b32f367c0a6 |
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from builtins import * # NOQA
from future import standard_library
standard_library.install_aliases() # NOQA
from logging import getLogger
import chainer
from chainer i... | toslunar/chainerrl | chainerrl/policies/gaussian_policy.py | Python | mit | 12,463 | [
"Gaussian"
] | 10846243cc35369aef9d9b0ec260bc64f2c448fd16f4deda768d5315c39bab7f |
__author__ = 'dan'
import networkx as nx
from datetime import datetime
import numpy as np
import pandas as pd
import itertools
import scipy.stats as stats
import os
nets = [('small','fluorescence_iNet1_Size100_CC01inh.txt.diff.csv')]
out_dir = '/Users/dan/dev/datasci/kaggle/connectomix/out/'
#nets = {'valid':'fluores... | ecodan/kaggle-connectomix | cnct_pearson.py | Python | apache-2.0 | 1,717 | [
"NEURON"
] | 458bf07439d9e47960a366a24bcee566574dff75b22cd52ec9f73f798e8d0fcf |
##
# Copyright 2009-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/n/nwchem.py | Python | gpl-2.0 | 25,378 | [
"Amber",
"NWChem"
] | be6067fbf5dacd1fc571d1db699f8dac02619bc6bf774a9fbaccd327e8cf8e43 |
"""
Extended math utilities.
"""
# Authors: G. Varoquaux, A. Gramfort, A. Passos, O. Grisel
# License: BSD 3 clause
import warnings
import numpy as np
from scipy import linalg
from scipy.sparse import issparse
from distutils.version import LooseVersion
from . import check_random_state
from .fixes import qr_economic
f... | Eric89GXL/scikit-learn | sklearn/utils/extmath.py | Python | bsd-3-clause | 18,706 | [
"Gaussian"
] | 866f9f08ea9a2171f7209a6259dabfc4c6649ccdde8d343a63a23b641c280270 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# inputMaker_v3.py
#
# Copyright 2015 Carlos Eduardo Sequeiros Borja <casebor@gmail.com>
#
# 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... | casebor/labioscripts | python/inputMakerX2.py | Python | gpl-3.0 | 17,475 | [
"Amber"
] | 7fb6470e3330739b695e7d130c5068aa91b4b2e27a963920a374271e3e945eaa |
import os
from ase.io import read
from ase.neb import NEB
from ase.calculators.turbomole import Turbomole
from ase.optimize import BFGS
initial = read('initial.coord')
final = read('final.coord')
os.system('rm -f coord; cp initial.coord coord')
#restart
configs = read('neb.traj@-5:')
band = NEB(configs, climb=True)... | grhawk/ASE | tools/doc/ase/calculators/turbomole_ex3_restart_diffuse_usingNEB.py | Python | gpl-2.0 | 478 | [
"ASE",
"TURBOMOLE"
] | bdbc85c15af810ab5fa2eb058e6c654615529b8ec5450a72290ad3750b117fdb |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
from scipy._lib.six import string_types
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/scipy/signal/windows.py | Python | gpl-2.0 | 53,971 | [
"Gaussian"
] | 5168610b7ad5f07891192a7e574ae8e7a438afa076df331c835181fb816680cc |
#!/usr/bin/env python3
########################################################################
# Solves problem 11 from projectEuler.net.
# Finds 4 adyacent numbers whose product is the greatest.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or modify... | salessandri/programming-contests | project-euler/problem011.py | Python | gpl-3.0 | 4,059 | [
"VisIt"
] | 82df9a7a13aec91a77f443d33f3675388e493b0df0c56358efd62256a1a1aaad |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf.nao import mf
class KnowValues(unittest.TestCase):
def test_fireball(self):
""" Test computation of matrix elements of overlap after fireball """
sv = mf(fireball="fireball.out", gen_pb=False)
s_ref = sv.hsx.s4_csr.... | gkc1000/pyscf | pyscf/nao/test/test_0100_fireball.py | Python | apache-2.0 | 441 | [
"PySCF"
] | d7521809f48f83891507a515d835b0c89c0931948a141987142b57796484d738 |
# -*- encoding: utf-8 -*-
"""Test class for Remote Execution Management UI
:Requirement: Remoteexecution
:CaseAutomation: Automated
:CaseLevel: Acceptance
:CaseComponent: CLI
:TestType: Functional
:CaseImportance: High
:Upstream: No
"""
from datetime import datetime, timedelta
from fauxfactory import gen_string... | sghai/robottelo | tests/foreman/cli/test_remoteexecution.py | Python | gpl-3.0 | 41,735 | [
"Galaxy"
] | 19ae0c27b9c7a4d310198596d246ecc7d73d44bac803d0df6dcc972c3a4baa1e |
""" SandboxHandler is the implementation of the Sandbox service
in the DISET framework
"""
__RCSID__ = "$Id$"
import os
import time
import threading
import tempfile
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from... | chaen/DIRAC | WorkloadManagementSystem/Service/SandboxStoreHandler.py | Python | gpl-3.0 | 18,672 | [
"DIRAC"
] | d2966cb754d0157958e3e1d39f819e25d0f42e87e009868b3bd40a78932f46ff |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | double12gzh/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 61,878 | [
"exciting"
] | ecf206ee3a9646e57b2f88d74b0ea51d7f495e10f8072ce75a72ee6c0c9b15b3 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/alerts/forms/alertdialog.py | Python | gpl-2.0 | 5,961 | [
"Brian"
] | d45a93e21ddec31c23d76ab63e7fa99031c052cc8fa6b46e609dddeb8d790677 |
#!/usr/bin/env python
# Script which removes the strange entities from the nt-database which causes the retrieve taxonomy to fail
# It is about ID;ID. That part needs to be removed
# Example of running:
# - python RemoveDoubleEntityNCBI.py /home/hagel003/Downloads/CITES/Output/BlastTest/OTU_26.filtered.blast.out /hom... | RIKILT/CITESspeciesDetect | RemoveDoubleEntityNCBI.py | Python | bsd-3-clause | 1,236 | [
"BLAST"
] | f7f3006f67129d75124ef9bc3564a79663839865f1b01f47e8421c8056deed01 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Extensions to Iris' CF variable representation to represent CF UGrid variables.
Eventual destination: :mod:`iris.fileform... | SciTools/iris | lib/iris/experimental/ugrid/cf.py | Python | lgpl-3.0 | 12,667 | [
"NetCDF"
] | a899e63c01173e8dd33d22482062df2fe99256ab6bc968638fe8af1956211730 |
"""
Execute each notebook as a test, reporting an error if any cell throws an exception.
Adapted from https://gist.github.com/minrk/2620876.
"""
from __future__ import print_function
import os
import sys
import nbformat
import pytest
from jupyter_client import KernelManager
from six.moves.queue import Empty
FLAKEY_LI... | leeping/mdtraj | examples/test_examples.py | Python | lgpl-2.1 | 2,098 | [
"OpenMM"
] | 6a7ca0f9c8d8733bde51cf90b0a5b1c40d44cd7cb98ea330ea35504cf69cc88f |
_mod_txt = """
NEURON {
POINT_PROCESS ExpSynMorphforge
RANGE tau, e, i
NONSPECIFIC_CURRENT i
RANGE peak_conductance
}
UNITS {
(nA) = (nanoamp)
(mV) = (millivolt)
(uS) = (microsiemens)
}
PARAMETER {
tau = 0.1 (ms) <1e-9,1e9>
e = 0 (mV)
peak_conductance = -100000 ()
}
ASSIGNED {
v (mV)
i (nA)
... | mikehulluk/morphforge | src/morphforgecontrib/simulation/synapse_templates/exponential_form/expsyn/postsynaptic_mechanisms_expsyn_modfile.py | Python | bsd-2-clause | 599 | [
"NEURON"
] | 23faccb74d65b19bf85a076a0894a2c417395466c6a4a6afb761931e3d75a762 |
import os
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
precision = "single"
sysname = "ho"
system, positions, groups, temperature, timestep = lb_loader.load(sysname)
i... | kyleabeauchamp/HMCNotes | code/correctness/old/test_hmc_correctness_ljbox_converger_fullgrid.py | Python | gpl-2.0 | 1,984 | [
"OpenMM"
] | 91a9bccdc3acfa32a86cc85f5c968ae545ccd3610aa48a50fd25f909c60a32ff |
"""
Base class for plugins - frameworks or systems that may:
* add code at startup
* allow hooks to be called
and base class for plugins that:
* serve static content
* serve templated html
* have some configuration at startup
"""
import os.path
import sys
import imp
import pkg_resources
pkg_resources.require( 'M... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/base/pluginframework.py | Python | gpl-3.0 | 25,225 | [
"Galaxy"
] | f26ec12ad4ca9b2360619f09c9581e80eb9e4a0d10963279d9236e4f8d0387e7 |
"""Functionality to query and extract information from aligned BAM files.
"""
import collections
import os
import itertools
import signal
import subprocess
import numpy
import pybedtools
import pysam
import toolz as tz
from bcbio import broad, utils
from bcbio.bam import ref
from bcbio.distributed import objectstore
... | biocyberman/bcbio-nextgen | bcbio/bam/__init__.py | Python | mit | 21,282 | [
"BWA",
"pysam"
] | b87067c272922e4c840af58acc481c02a58748ace75fd2b44b4effebf4ca44ba |
# -*- coding: utf-8 -*-
#
# Cherokee-admin
#
# Authors:
# Alvaro Lopez Ortega <alvaro@alobbs.com>
# Taher Shihadeh <taher@unixwars.com>
#
# Copyright (C) 2001-2014 Alvaro Lopez Ortega
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of version 2 of the GNU General ... | lmcro/webserver | admin/PageIndex.py | Python | gpl-2.0 | 10,179 | [
"VisIt"
] | e0953f44a6628f44a0d0436920edf4e807c169a401c0fee13395ba41353a4a01 |
# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Bug reports welcome: fkauff@biologie.uni-kl.de or on Biopython's bugzilla.
... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Nexus/Nexus.py | Python | gpl-2.0 | 74,994 | [
"Biopython"
] | bc57fc7691f958acccfd09b446e403c266d6e042f219306c1719ec29c93fd97e |
"""
Contains the user interface in the Universe class
"""
import glob
import logging
import os
import socket
import string
import random
import urllib
from galaxy import web
from galaxy import util
from galaxy import model
from galaxy.model.orm import and_
from galaxy.security.validate_user_input import validate_email... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/user.py | Python | gpl-3.0 | 99,743 | [
"Galaxy",
"VisIt"
] | f7daf9ca5084dbbf48b2776c4379a8846466703ae4048d6ce6e37ae83f6a2936 |
"""
Parses an XML feed into a Python representation. You should probably use L{iface_cache.iface_cache} rather than the functions here.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import os
from logging import debug, info, warn
f... | timdiels/zeroinstall | zeroinstall/injector/reader.py | Python | lgpl-2.1 | 8,848 | [
"VisIt"
] | 0ef0ef58796f59e0b2f63f46299f44f3cf0c4c7b5de0afadece6a9a1a922917c |
from .source.syntax_tree import *
from .source.expression import Block
class Unit(Node):
def __init__(self, parent, filename):
self.parent = parent
self.filename = filename
class Module(Node):
def __init__(self, parent, identifier):
self.parent = parent
self.identifier = identifier
self.source_dirs = [... | jdavidls/uScript | uscript/model/module.py | Python | cc0-1.0 | 1,670 | [
"VisIt"
] | 2cb05e3e333f1a32b94adbb188ba061561d2de04f8b5d3027b3bc648c5892f1f |
import numpy as np
from scipy.ndimage import gaussian_filter
from menpo.base import name_of_callable
from menpo.model import PCAModel
from menpo.feature import no_op, ndfeature
from menpo.transform import Scale
from menpo.visualize import print_dynamic
from menpofit import checks
from menpofit.builder import (build_r... | grigorisg9gr/menpofit | menpofit/unified_aam_clm/base.py | Python | bsd-3-clause | 32,035 | [
"Gaussian"
] | 04dffb8e68dd3cd1e039020e26e0d70794a9877aa83a57ed1474b629694024a4 |
# coding=utf-8
import logging
from random import randint
try:
from ujson import dumps
except ImportError:
from json import dumps
import inspect
from .web_utils import Status, get_engine_version
from ..engine.types_ import Room, Description, Item, Blueprint
from ..engine.exceptions import NoSuchBlueprint, IdMis... | DefaltSimon/Amber | amber/web_modules/handler.py | Python | mit | 13,618 | [
"Amber"
] | eff7e23b48be3f63953143340ea41c8d1b038c016e12a4f1ab7e6de8e6760bda |
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# --------------------------------------------------------------------... | kuvinodms/vsts-cd-manager-demo | vsts_cd_manager/continuous_delivery_manager.py | Python | mit | 15,538 | [
"GULP"
] | f974c8eef281def63f42f0d438cc94c8345e9d55689b4f3c6ec807e50a991ea2 |
'''
Contains the classes BeliefNetwork, GaussianBeliefNetwork and the inherited (less general) PyramidGaussianBeliefNetwork
BeliefNetwork is a rudimentary class that makes no assumptions about the random variables it includes
A GaussianBeliefNetwork is a Bayesian Network where all the conditional distributions are G... | szwieback/nlscaling | core/GaussianBeliefNetwork.py | Python | gpl-3.0 | 29,410 | [
"Gaussian"
] | 9612a69eceefec9650736b7a95dd5277fbdad81d72a8648eba7eef006ca0fff2 |
#!/usr/bin/python
"""Test of line navigation output of Firefox on the Orca wiki."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
#sequence.append(WaitForDocLoad())
sequence.append(PauseAction(5000))
# Work around some new quirk in Gecko that causes this test to fail if
# run via the test... | chrys87/orca-beep | test/keystrokes/firefox/line_nav_wiki_up.py | Python | lgpl-2.1 | 42,749 | [
"ORCA"
] | 6b34e7ca67a12c4e046285273aceddfa020376519abd6a7cf12b2f0d33009644 |
#!/usr/bin/env python
# -*- mode: python; coding: utf-8; -*-
# ---------------------------------------------------------------------------##
#
# Copyright (C) 1998-2003 Markus Franz Xaver Johannes Oberhumer
# Copyright (C) 2003 Mt. Hood Playing Card Co.
# Copyright (C) 2005-2009 Skomoroh
#
# This program is free softwa... | jimsize/PySolFC | pysollib/options.py | Python | gpl-3.0 | 24,332 | [
"CRYSTAL"
] | 1e88796a74854196ea44ed9f1a21c631ca68377dfa2767acb365fe2489861112 |
#!/usr/bin/python3
import argparse
import os
import re
from multiprocessing import cpu_count
from subprocess import run
from timeit import default_timer as timer
from Bio import SearchIO, SeqIO
from Bio.Blast.Applications import NcbiblastnCommandline as nb
def safe(old):
return re.sub(r'\W', '_', old)
def get_... | wpwupingwp/filter | filter.py | Python | gpl-3.0 | 9,766 | [
"BLAST"
] | 21fa71bdebe00ddc5719f712fce0f275786a01da6e5266c7c6773def56e4b0ce |
'''This example shows how to use importance sampling and how to
adapt the proposal density using the pmc algorithm in an MPI
parallel environment.
In order to have a multiprocessing enviroment invoke this script with
"mpirun -n 10 python pmc_mpi.py".
'''
from mpi4py.MPI import COMM_WORLD as comm
import numpy as np
... | fredRos/pypmc | examples/pmc_mpi.py | Python | gpl-2.0 | 8,806 | [
"Gaussian"
] | d12b966e095073f815cfb76cfff54d18be2744299c939490968a056b31bac33b |
#!/usr/bin/env python
import time
import numpy as np
from .utils import kmeans, orthonormalize_rows, random_rotation
from joblib import Memory
_memory = Memory('.', verbose=0)
# ================================================================ PQ
@_memory.cache
def learn_pq(X, ncentroids, nsubvects, subvect_len, m... | dblalock/bolt | experiments/python/product_quantize.py | Python | mpl-2.0 | 14,544 | [
"Gaussian"
] | 492a233c73e4dabc3da6a4691f6f6ef11b12186dc61bf0f41fefe538d785081f |
#!/usr/bin/env python
#
# This code was copied from the data generation program of Tencent Alchemy
# project (https://github.com/tencent-alchemy).
#
#
# #
# # Copyright 2019 Tencent America LLC. All Rights Reserved.
# #
# # Licensed under the Apache License, Version 2.0 (the "License");
# # you may not use this file e... | gkc1000/pyscf | pyscf/df/hessian/uks.py | Python | apache-2.0 | 5,381 | [
"PySCF"
] | 371c081a6d34466baa13bec7f5fe78cdae322cc64a3a4c1de2b422203fd878ba |
from pysam.utils import PysamDispatcher
# samtools command line options to export in python
SAMTOOLS_DISPATCH = {
# samtools 'documented' commands
"view": ("view", None),
"sort": ("sort", None),
"mpileup": ("mpileup", None),
"depth": ("depth", None),
"faidx": ("faidx", None),
"fqidx": ("fqi... | pysam-developers/pysam | pysam/samtools.py | Python | mit | 1,671 | [
"pysam"
] | 6f692f4b268cbe2156fb771e24328e4d628f834d95e0ef2026dedd04200ac948 |
import warnings
warnings.filterwarnings('ignore') #because of plotly in pymzml
import os, sys, pandas, pyteomics, glob, numpy, subprocess, shutil, re, optparse
from itertools import izip_longest
from subprocess import Popen, STDOUT
from array import array
import numpy
import sqlite3, zlib
from pymzml import run
######... | wohllab/milkyway_proteomics | galaxy_milkyway_files/tools/wohl-proteomics/msplit-dia/msplit_dia.py | Python | mit | 16,427 | [
"Galaxy"
] | d1fdb5bc3fa9a750f4bb34c1d37df21c3ab2c3876476447c0cbd7216777e71ef |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A pedestrian version of The Cannon.
"""
from __future__ import (division, print_function, absolute_import,
unicode_literals)
__all__ = ["CannonModel"]
import logging
from numpy.linalg import inv
import numpy as np
import scipy.optimize as op
... | peraktong/Cannon-Experiment | AnniesLasso_2/cannon.py | Python | mit | 38,188 | [
"Gaussian"
] | 7a80785aa27ea5126ea259ad7bdbe242b156351832c18cba144a22710367e49a |
"""
23/05/2015
Plots to compare results from different Gaussian processes. Using data in
band 'r'.
"""
import classes as cl
import util
import matplotlib.pyplot as plt
import utilities as ut
dictR = dict([('g', 3.237), ('r', 2.176), ('i', 1.595), ('z', 1.217)])
band = 'i'# 'r'
snid = 2896 # 3644 # 3776
xlim = [-36, ... | mdepasca/miniature-adventure | thesis_plot.py | Python | unlicense | 4,299 | [
"Gaussian"
] | c8467233227d9434f4fe69f58ae4a8631f6725f2ff02a514c226fa55103a1bde |
# $Id$
__revision__ = '$Rev$'
import sys
import math
import numpy
from itcc.molecule import read
from itcc.tinker import parameter, analyze, tinker, molparam
from itcc.torsionfit import tools
from itcc.core import tools as extra_tools
def torene(tor, param):
"""torene(tor, param) -> Float
tor: Float
para... | lidaobing/itcc | itcc/torsionfit/parmfit.py | Python | gpl-3.0 | 3,540 | [
"TINKER"
] | a54c09690ba2d8a4ee2656b4ac923c1aa6dd550689ac51cf634cd61d07fc26be |
#! /usr/bin/env python
########################################################################
# File : dirac-admin-kill-pilot
# Author : A.T.
########################################################################
"""
Kill the specified pilot
"""
import DIRAC
from DIRAC.Core.Base.Script import Script
@Script()... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_admin_kill_pilot.py | Python | gpl-3.0 | 931 | [
"DIRAC"
] | 9aaf82d460bf540006f4ecbb709025a5fc7524a419a7ab0dbf4679d6e7978cb5 |
#!/usr/bin/env python3.7
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law ... | GoogleCloudPlatform/gke-istio-telemetry-demo | test/verify_boilerplate.py | Python | apache-2.0 | 11,481 | [
"VisIt"
] | 355fd30fd4a323204a211437bc5d80eb15ff5be63285231fc29779c0426c7cc4 |
# This file is part of SGS-Flask.
# SGS-Flask 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.
# SGS-Flask is distributed in the hope ... | TheLetterN/sgs-flask | app/auth/views.py | Python | gpl-3.0 | 26,867 | [
"VisIt"
] | 8de8afc1b5f766d5c86891f473368b9f69e569c016ed61200111577aa412ea24 |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | zaina/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 58,737 | [
"exciting"
] | 90b7e2364e2144c8eea9689b3e6680212ea30b641e6a7994053e245e80580689 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Provides a class for interacting with KPath classes to
generate high-symmetry k-paths using different conventions.
"""
import itertools
from warnings import warn
import networkx as nx
import numpy as np
... | richardtran415/pymatgen | pymatgen/symmetry/bandstructure.py | Python | mit | 14,625 | [
"pymatgen"
] | fcb19b0344dadc4d000adeb549f2702aa27c9cf7be852adf55965164601f4da6 |
from func import *
# ATTTENTION! Maybe there are some mistakes in neuron parameters!
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True,
'local_num_threads': 8,
'resolution': 0... | research-team/NEUCOGAR | NEST/cube/dopa+sero/scripts/neuromodulaton.py | Python | gpl-2.0 | 16,120 | [
"NEURON"
] | 73f4d8607b65eac8e6ca0f0a1f4b106e840d7f549a4df3447c29e2efc4456775 |
import sys
import gdb
# Update module path.
dir_ = '/home/wbj/project/mt7621/firewrt_build_all_app/FireWRT-OpenWrt-Firefly-FireWRT-SDK/staging_dir/host/share/glib-2.0/gdb'
if not dir_ in sys.path:
sys.path.insert(0, dir_)
from glib import register
register (gdb.current_objfile ())
| michalliu/OpenWrt-Firefly-Libraries | staging_dir/host/share/gdb/auto-load/libglib-2.0.so.0.4304.0-gdb.py | Python | gpl-2.0 | 288 | [
"Firefly"
] | 7172fa537cf6f5defcc4e4c78f4ac40ed98a56721be4026336e29f7219f3f22a |
#!/usr/bin/python
#
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required b... | donspaulding/adspygoogle | examples/adspygoogle/adwords/v201306/misc/use_oauth2.py | Python | apache-2.0 | 5,056 | [
"VisIt"
] | 36408a75d21125a535e0a2a12629776ab65d90cb8a69bff5ac64e258605a82d6 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
########################################################################
# Solves problem 56 from projectEuler.net.
# Finds the maximum digital sum amon a ** b for a,b < 100
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redis... | salessandri/programming-contests | project-euler/problem056.py | Python | gpl-3.0 | 1,300 | [
"VisIt"
] | e844e5d01e516e663f781bb866109d90a61d34922bd2d69265781adde7d69c52 |
#!/usr/bin/env python
# encoding: utf-8
#| Copyright Inria May 2015
#| This project has received funding from the European Research Council (ERC) under
#| the European Union's Horizon 2020 research and innovation programme (grant
#| agreement No 637972) - see http://www.resibots.eu
#|
#| Contributor(s):
#| - Jean-Bap... | jbmouret/limbo | waf_tools/plot_bo_benchmarks.py | Python | gpl-3.0 | 9,879 | [
"Gaussian"
] | e21e530cb1b2a6eb19ed283757b9ca488b3a1e9c6f1a9acb1703e2f9c457f879 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of smartoptim.
# https://github.com/thumby/smartoptim
# Licensed under the MIT license:
# http://www.opensource.org/licenses/MIT-license
# Copyright (c) 2015, Thumby <dev@thumby.io>
from setuptools import setup, find_packages
from smartoptim import __... | thumby/smartoptim | setup.py | Python | mit | 1,615 | [
"Octopus"
] | 632d00370ad2ea83fe4d0e544aa57f7c39b40137c9359a5add2ce77ae095b6fa |
#!/usr/bin/python
"""This module wraps up communication with the light controller.
Lights -- a connection to the light controller
Error -- the exception we can raise
Author: J.Cupitt
Created as part of the AHRC RTI project in 2011
GNU LESSER GENERAL PUBLIC LICENSE
"""
import glob
import os
import serial
import time... | rti-capture/rtiacquire | rtiacquire/lights.py | Python | lgpl-2.1 | 4,017 | [
"Firefly"
] | 0e6e8bf67f5cd680eacfa690c0ac61ea7e991175229bcd6592c3bd09b9d9dc23 |
#!/usr/env python
import math
import sys
import numpy
import scipy
import _gfrd
from _gfrd import (
CuboidalRegion,
SphericalSurface,
CylindricalSurface,
DiskSurface,
PlanarSurface,
Surface
) # to perform instance checks
from utils import *
import os
import logging
import logging.hand... | Seynen/egfrd | gfrdbase.py | Python | gpl-2.0 | 36,931 | [
"Gaussian"
] | 7430b3ad1174b539bac9df3e5164cd1a807e6bfcc2c57f2a8ae32cb93632b822 |
import requests
import os
import json
import datetime
import time
from loghelper import Logger
from sslverify import verification
from exception import *
from tempfile import NamedTemporaryFile
from tokenator import Tokenator
import zipfile
import logging
logging.getLogger("requests").setLevel(logging.ERROR)
from metri... | SouthForkResearch/CHaMP_Metrics | lib/sitkaAPI.py | Python | gpl-3.0 | 8,540 | [
"VisIt"
] | 52eb8a43db09a568871748c3dacc2cc02594ea521e83936fa61f77e76b653151 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/sequence/_nucleotide_mixin.py | Python | bsd-3-clause | 10,796 | [
"scikit-bio"
] | 4aae85e4db7d35f7b995f63059c5ea6282d1df0279c6e8ea7c517d260436e661 |
import os
import pathlib
from .. import ansys, cgns, gmsh, h5m, mdpa, ply, stl, vtk, vtu, xdmf
from .._common import error
from .._helpers import _filetypes_from_path, read, reader_map
def add_args(parser):
parser.add_argument("infile", type=str, help="mesh file to compress")
parser.add_argument(
"--... | nschloe/meshio | src/meshio/_cli/_compress.py | Python | mit | 2,391 | [
"VTK"
] | 68220e016c34c60afad13f306301c9202fbe47154fafe92d5cfaa8d9eaca1bad |
"""
Instructor Dashboard Views
"""
import datetime
import logging
import uuid
import pytz
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.core.urlresolvers import reverse
from django.http import Http404, HttpResponseServerError
from django.utils.html import escap... | procangroup/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 36,131 | [
"VisIt"
] | ec85d2913602469ab4256416152cc84ad5f107ad23d250894e8dce77909176f2 |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, unicode_literals, print_function)
__all__ = ['Regressor', 'Classifier', 'Layer', 'Convolution']
import os
import sys
import time
import logging
import itertools
import collections
log = logging.getLogger('sknn')
import numpy
import theano
class ans... | jgdwyer/ML-convection | sknn_jgd/nn.py | Python | apache-2.0 | 26,071 | [
"Gaussian"
] | 455b551e5dbbc0e741d9d5c5231a861ecd2ed128a06b64103908a391c6e4dc71 |
#!/usr/bin/env python
import pyemma
import numpy as np
import mdtraj
import time
import os
# Source directory
source_directory = '/cbio/jclab/projects/fah/fah-data/munged3/no-solvent/11406' # CK2
#source_directory = '11406' # CK2
################################################################################
# Load... | jchodera/MSMs | jchodera/CK2/pyemma/cluster.py | Python | gpl-2.0 | 3,359 | [
"MDTraj"
] | a8b10485f6a85aa994043788609d5cb04d367d315af9063d8c0ac4ef52ecd93f |
# -*- coding: utf-8 -*-
"""test email tracking"""
from datetime import datetime
from django.conf import settings
from django.contrib.sites.models import Site
from django.core import management
from django.core import mail
from django.urls import reverse
from model_mommy import mommy
from coop_cms.models import Newsl... | ljean/coop_cms | coop_cms/apps/newsletters/tests/test_tracking.py | Python | bsd-3-clause | 6,681 | [
"VisIt"
] | e11ef9fa87812193fcab5796c9e7f947e62f24f352fea082cad4d0bfd0e3c5f5 |
# -*- coding: utf-8 -*-
import os
import unittest
from dateutil.parser import parse as dtparse
import numpy as np
from pyaxiom.netcdf.sensors.dsg import IncompleteMultidimensionalProfile
import logging
from pyaxiom import logger
logger.level = logging.DEBUG
logger.handlers = [logging.StreamHandler()]
class TestInco... | axiom-data-science/pyaxiom | pyaxiom/tests/dsg/profile/test_profile_im.py | Python | mit | 1,768 | [
"NetCDF"
] | e3dafaa51abc20d233ce2eb9d88abe8e596656f7d1b38849fd5baf71676b2e67 |
import pylab as pl
# first plot the gaussian results
P = pl.load('ec2117ans_2_cc.dat')
X = pl.load('Ha.dat')
t = int(X[:,0][0])
E = 2453964.3307097
# calculate t in terms of orbital phase
# period in days
period = 0.1545255
phase = (X[:,0]-E)/period - int(((X[:,0]-E)/period)[0])
print phase
# velocities
pl.figu... | ezietsman/msc-thesis | spectroscopy/extracted/plot_velocities.py | Python | mit | 2,420 | [
"Gaussian"
] | 9d912e1673156ae92fcd4ede2259d07c8be4ce393580eb977682c7168ee007ff |
../../../../../../../share/pyshared/orca/scripts/toolkits/Gecko/keymaps.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/Gecko/keymaps.py | Python | gpl-3.0 | 74 | [
"ORCA"
] | 21f9d146fb856e6956c5f90acf72518d84f35255f5b6043df3d80addc6db074a |
# coding: utf-8
from pycalphad import Database, binplot, equilibrium, variables as v
dbf = Database('NI_AL_DUPIN_2001.TDB')
comps = ['AL', 'NI', 'VA']
phases = ['BCC_B2']
eq = equilibrium(dbf, comps, phases, {v.P: 101325, v.T: 1804, v.N: 1, v.X('AL'): 0.4798})
print(f'GM {eq.GM.values.squeeze():0.3f}')
print(f'MU {eq.... | richardotis/pycalphad-sandbox | al-ni_sundman_convergence.py | Python | mit | 827 | [
"pycalphad"
] | 814a11c6a04ea9eaa69c83a2eb0a6e9ccc809138b34c03dcc1698b938186cd53 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jbedorf/tensorflow | tensorflow/python/autograph/core/unsupported_features_checker.py | Python | apache-2.0 | 1,864 | [
"VisIt"
] | fb05ee387163c89ca60930beee7bd35f0b37b45b91c65ed52dea7387d2c1ecce |
import ast
import json
import os, os.path
import sys
from modulefinder import ModuleFinder
from importvisitor import ImportVisitor
def invertBadmodules(finder):
missing = {}
for mod, where in finder.badmodules.iteritems():
for name in where.iterkeys():
if name not in missing:
missing[name] = []
missing[... | jmorse/cyanide | lint-imports/getimportsinfo.py | Python | mit | 2,289 | [
"VisIt"
] | b405b68fa086848ba09f551c89384fbf0c8824e1235828b44d79871debcabd5d |
#!/usr/bin/python2
"""This script will call LAMMPS to calculate and visualize (with matplotlib) the Gay-Berne potential
for the side-by-side (ll), end-to-end(z),tee(T) and cross(X) configurations for a uniaxial ellipsoid.
Note:
If the default intermolecular distances for a configuration are too far from it's minimum,
... | EtiCui/Msc-UdeS | theory/gayberne.py | Python | mit | 7,437 | [
"LAMMPS"
] | beb697bdc664252d0ab041c59d2e677f105bf99b22ec6b50ac0562f3b26761e6 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-02-12 18:00:11
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-07-05 20:37:53
from __future__ import print_function, division, absolute_import
from marvin.api.api impo... | albireox/marvin | python/marvin/tests/api/test_interaction.py | Python | bsd-3-clause | 337 | [
"Brian"
] | a9b9c1a423cf17e86fd5d73a32c2e65f3659b087c25fcbf160ff1b34a10df5db |
import re
from pycp2k import CP2K
from ase.build import fcc111
from ase import Atoms
from ase.constraints import FixAtoms
import numpy as np
#===============================================================================
# Creating Cu (111) surface with 4 layers 2x2 supercell in orthogonal cell
# through Atomic Simul... | SINGROUP/pycp2k | examples/example_slab_kpts_vdw.py | Python | lgpl-3.0 | 7,457 | [
"ASE",
"CP2K"
] | d5f019c3728476c23fdacc5d107049b08af4d535c2e23875509606f2c263871a |
#!/usr/bin/env python
""" Data Extraction"""
_author_ ="Hector H Corzo"
_copyright_ = "Copyright 2017, Auburn, AL"
import os
import re
import openpyxl
import sys
#My current path
path=os.path.dirname(os.path.realpath(__file__))
os.chdir(path)
#
U_proc=8
U_char=1
U_mult=1
U_meth='CCSD(T)'
U_basis='Aug-cc-pvDz'
U_gjf... | hhcorzo/Extraction_Script | Extraction.py | Python | gpl-3.0 | 10,924 | [
"Gaussian"
] | e3b5bb3bf3beefb431782ade626d0f3a02d2a8e2ec1d6a31c84e3573df3ced79 |
#!/usr/bin/env python
"""mut2read.py
Author -- Gundula Povysil
Contact -- povysil@bioinf.jku.at
Takes a tabular file with mutations and a BAM file as input and prints
all tags of reads that carry the mutation to a user specified output file.
Creates fastq file of reads of tags with mutation.
======= ========== ==... | loraine-gueguen/tools-iuc | tools/variant_analyzer/mut2read.py | Python | mit | 5,803 | [
"pysam"
] | 43f4c3b70cb48c5a9f1f0f80d2d3914713e82bc5e1f06f5ac6767024b3e9dac9 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageCityBlockDistance(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkImageCityBlockDistance.py | Python | bsd-3-clause | 507 | [
"VTK"
] | b7a1f8f294836fa2685107f44a57a4a825a9da482cd97c6412ab9d373c500536 |
#
# Copyright (c) 2014, Novartis Institutes for BioMedical Research Inc.
# 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 copyri... | adalke/rdkit | rdkit/Chem/SimpleEnum/Enumerator.py | Python | bsd-3-clause | 9,028 | [
"RDKit"
] | 4ab3787ef1bdba162043a44c0833e8bdc1e6b63a4760e625b561dff662f6035f |
# Copyright (C) 2012,2013,2015
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of ... | fedepad/espressopp | src/VerletListAdress.py | Python | gpl-3.0 | 7,649 | [
"ESPResSo"
] | 329310308b97157755450158a3c9095fa84d811c190160c1a2831228e1dc8272 |
"""
dihedrals.py -- Calculate the dihedral angles between peptide bond planes.
Author: Clay McClure <clay@daemons.net>
Usage:
python dihedrals.py [--chain=CHAIN] <pdb_file>
Requirements:
- numpy (for linear algebra)
- BioPython (for PDB access)
Tested with:
TIM barrel (1B9B)
porin (2F1C)
ox... | claymation/dihedrals | dihedrals.py | Python | bsd-2-clause | 5,534 | [
"Biopython",
"CRYSTAL"
] | e38910cef23d0ff9edbbccefd5b72c3f713ed4f61802d862c6e04660e6d13106 |
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/mpi_helper.py | Python | apache-2.0 | 4,376 | [
"PySCF"
] | 95dd74e7c0a8930b0c58050fb1be0fe8908d289cef3aa5477c23741f2c9f38fd |
"""t-Student Mixture Models Module (smm).
- This module allows you to model data by a mixture of t-Student \
distributions, estimating the parameters with \
Expectation-Maximisation. \
It is an implementation of the paper: 'Robust mixture modelling using \
the t distribution', D. Peel and G. J. McLachlan. Published at... | luiscarlosgph/t-Student-Mixture-Models | src/smm.py | Python | bsd-3-clause | 55,095 | [
"Gaussian"
] | 0376da29ef347fac348ae6e8955f197b431533c5d405827c96e85d9df5b2e049 |
# BurnMan - a lower mantle toolkit
# Copyright (C) 2012, 2013, Heister, T., Unterborn, C., Rose, I. and Cottaar, S.
# Released under GPL v2 or later.
import numpy as np
import mie_grueneisen_debye as mgd
import birch_murnaghan as bm
import warnings
import slb
import equation_of_state as eos
import composite
class mat... | tjhei/burnman_old2 | burnman/minerals_base.py | Python | gpl-2.0 | 12,348 | [
"Avogadro"
] | bdb9ded6cfd71cfd41b1380db8c7cacc837eb970c1a6c4c9464cd0092a9b1ba7 |
# Copyright (c) 2015 TachyonNZ
# Copyright (c) 2015 Florian Limberger <flo@snakeoilproductions.net>
#
# 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 ... | flimberger/textcom | textcom/soldier.py | Python | mit | 17,865 | [
"CASINO",
"MOOSE"
] | 53484f753bccee89ae298c530e7e0ae39f2af43328141d0281ccad2c85c63315 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
import socket
import sys
from os import environ as env
import llnl.util.tty as tty
from spack import *
def ... | LLNL/spack | var/spack/repos/builtin/packages/vtk-h/package.py | Python | lgpl-2.1 | 13,130 | [
"VTK"
] | 6a71406f88bbb4aef204190006d6744b4dc99616d0ffc742450e1ca360fb0905 |
from collections import deque
import numpy as np
import pickle
from baselines.her.util import convert_episode_to_batch_major, store_args
class RolloutWorker:
@store_args
def __init__(self, venv, policy, dims, logger, T, rollout_batch_size=1,
exploit=False, use_target_net=False, compute_Q=F... | openai/baselines | baselines/her/rollout.py | Python | mit | 6,782 | [
"Gaussian"
] | 566cc4dba745a44a294a6dad663ca7ee486217ac882d083974013e7df0e67da6 |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | mo-g/iris | lib/iris/fileformats/grib/_load_convert.py | Python | gpl-3.0 | 77,972 | [
"Gaussian"
] | fcff41f872758df05996985855e9bb8302563f96aa965fd4ba18b16c011477da |
from ase.structure import molecule
from gpaw import GPAW
from gpaw import dscf
from gpaw.test import equal
# Ground state calculation
#------------------------------------------------------------------
calc_mol = GPAW(nbands=8, h=0.2, xc='PBE', spinpol=True,
convergence={'energy': 100,
... | ajylee/gpaw-rtxs | gpaw/test/big/miscellaneous/dscf_CO.py | Python | gpl-3.0 | 2,345 | [
"ASE",
"GPAW"
] | d420bd599984782199c4ad58576e881d3d3cb2f4d2bba7973a554777d50ca50b |
"""
Views for the verification flow
"""
import decimal
import json
import logging
import urllib
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.staticfiles.storage import staticfiles_storage
from django.db import transaction
from django.http import Http40... | EDUlib/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 53,361 | [
"VisIt"
] | 12f618a30547c9a17d48fa0ae8d0c7310cb77f35341cf3499fd1d32a643fa276 |
import types
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.PromptUser import promptUser
from DIRAC.Core.Base.API import API
from DIRAC.TransformationSystem.Client.TransformationClient import TransformationClient
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.... | avedaee/DIRAC | TransformationSystem/Client/Transformation.py | Python | gpl-3.0 | 19,943 | [
"DIRAC"
] | de3d76e60ba9fc273accb1720007f1045a7c41b34cef5b86f3abeaa0791ebd50 |
#Copyright ReportLab Europe Ltd. 2000-2004
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/docs/userguide/ch1_intro.py
from reportlab.tools.docco.rl_doc_utils import *
import reportlab
title("ReportLab PDF Library")
title("User Guide")
centr... | alexissmirnov/donomo | donomo_archive/lib/reportlab/docs/userguide/ch1_intro.py | Python | bsd-3-clause | 31,880 | [
"VisIt"
] | 9d506f4f319bff5fc6611fd5798eeffe592c2cedd0b4a8778e552ba89641938a |
########################################
# Read TRMM netcdf files.py
#
# Created by: Peter Willetts
# Created on: 12/11/2013
#
########################################
#
#
###################################################
from mpl_toolkits.basemap import Basemap
import matplotlib.pyplot as plt
import numpy as np
from... | peterwilletts24/Python-Scripts | era_interim/netcdf_fileread.py | Python | mit | 6,024 | [
"NetCDF"
] | 3d7fb981aade4ca71485e9e841995a035da21c15f2c959c531bd104cff1eb6fa |
import os
import sys
cwd = os.getcwd()
sys.path.append( cwd )
new_path = [ os.path.join( cwd, "lib" ),
os.path.join( cwd, 'test' ),
os.path.join( cwd, 'lib', 'tool_shed', 'scripts', 'api' ) ]
new_path.extend( sys.path )
sys.path = new_path
from galaxy import eggs
eggs.require( 'mercurial' )
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/install_and_test_tool_shed_repositories/base/util.py | Python | gpl-3.0 | 69,912 | [
"Galaxy"
] | 612543ec6867587eed124f36148eeff7119f2871b46c322ffe0cdc08cf865f21 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
## Dependencies: python-mechanize, python-keyring, curses
## Author: Gijs Timmers: https://github.com/GijsTimmers
## Contributors: Gijs Timmers: https://github.com/GijsTimmers
## Jo Van Bulck: https://github.com/jovanbulck
##
## Licence: ... | GijsTimmers/kotnetcli | kotnetcli.py | Python | gpl-3.0 | 12,072 | [
"VisIt"
] | 68f61b14532f6e89124e973be4bec2ccf6bf393611c194dfff2970628db9cdb7 |
import numpy as np
import nest
import nest.voltage_trace as plot
# Reset simulation
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True}) # set to True to permit overwriting
# Set up simulation time limits
T = 10000.0
dt = 10.0
# Set basic params
delay = 1. # the delay in ms
g = 3.83
K = 10000
f_ex ... | vitaliykomarov/NEUCOGAR | nest/serotonin/test5HT.py | Python | gpl-2.0 | 2,950 | [
"NEURON"
] | 9c2ca0657af653c95d97e768ac5a3e09846429abaf756de9b5ace29dcd4f314b |
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