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import warnings
from chempy.units import allclose
from ..water_density_tanaka_2001 import water_density
def test_water_density():
warnings.filterwarnings("error")
assert abs(water_density(273.15 + 0) - 999.8395) < 0.004
assert abs(water_density(273.15 + 4) - 999.9720) < 0.003
assert abs(water_density... | bjodah/aqchem | chempy/properties/tests/test_water_density_tanaka_2001.py | Python | bsd-2-clause | 1,349 | [
"ChemPy"
] | a3fb1bdb0695fdf364f98b709fb17c0a03d10b38de618c0f3d223ea9d6fccbb2 |
"""Collection of useful data transforms."""
# Imports
import numpy as np
from McNeuron import Neuron
import scipy
import scipy.linalg # SciPy Linear Algebra Library
from numpy.linalg import inv
def get_leaves(nodes, parents):
"""
Compute the list of leaf nodes.
Parameters
----------
nodes: li... | RoozbehFarhoodi/McNeuron | data_transforms.py | Python | mit | 6,699 | [
"NEURON"
] | 17f363a2fff60b9350218f94554bf030c198f6716c95d9b49b23a9b0704c61a0 |
#
# Copyright (c) 2017 Brian J. Kidney
# Copyright (c) 2017 Jonathan Anderson
# All rights reserved.
#
# This software was developed by BAE Systems, the University of Cambridge
# Computer Laboratory, and Memorial University under DARPA/AFRL contract
# FA8650-15-C-7558 ("CADETS"), as part of the DARPA Transparent Comput... | musec/py-cdg | cdg/simplify.py | Python | apache-2.0 | 1,742 | [
"Brian"
] | 1f6971467bf2a6c9ece0111647bbe195a2a1b0ad34bbe646bcf4cbdc71c80d72 |
import json
from coalib.bearlib.abstractions.Linter import linter
from coalib.bears.requirements.NpmRequirement import NpmRequirement
def bool_or_str(value):
try:
return bool(value)
except:
return str(value)
def bool_or_int(value):
try:
return bool(value)
except:
ret... | mr-karan/coala-bears | bears/js/JSHintBear.py | Python | agpl-3.0 | 17,767 | [
"VisIt"
] | b5c0690dddb5e5039231c282325e971a9c38cc20575cbbc87c09434a930aa8d7 |
# -*- coding: utf-8 -*-
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope tha... | mathstuf/bodhi | bodhi/tests/functional/test_updates.py | Python | gpl-2.0 | 75,491 | [
"VisIt"
] | bea6c8e513568408ab9415529cd477373f8d46098321a65eee5b7913b6489f64 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | samples/visualization_npt.py | Python | gpl-3.0 | 2,684 | [
"ESPResSo"
] | 18768199e9f0a046098db8ec7c107596ba1828095cb100cd83bc7d0d1d7ef5d6 |
""" DIRAC Workload Management System utility module to get available memory and processors from mjf
"""
__RCSID__ = "$Id$"
import os
import re
import multiprocessing
import urllib2
from DIRAC import gLogger, gConfig
from DIRAC.Core.Utilities.List import fromChar
def getJobFeatures():
features = {}
if 'JOBFEATU... | fstagni/DIRAC | WorkloadManagementSystem/Utilities/JobParameters.py | Python | gpl-3.0 | 7,507 | [
"DIRAC"
] | c3cd79fca7216e6e325c9c79af701c1fcfd7361c013527f78798816cf5f6d251 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/domain/attachment.py | Python | gpl-2.0 | 1,691 | [
"VisIt"
] | 46ab0f4906225e22d36fda57045ac30d93a2bfc953b2df7ca54d1a4f7a53057f |
#!/usr/bin/env python2
# * **************************************************************** **
# File: util.py
# Requires: Python 2.7+ (but not Python 3.0+)
# Note: For history, changes and dates for this file, consult git.
# Author: Brian Danilko, Likeable Software (brian@likeablesoftware.com)
# Copyright 2015-2017 Mi... | Bdanilko/EdPy | src/lib/util.py | Python | gpl-2.0 | 4,629 | [
"Brian"
] | 98b95d0f5946038d7fc228890806317bcd7ee4afdd6551de35ef2ea2d0e42cec |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/management/commands/kgcreatesuperuser.py | Python | gpl-3.0 | 7,851 | [
"Brian"
] | bb52ff0b806445904135d6a15456b31f8a475f2f86057b0e980ef3a3ce63acd1 |
from abc import ABC, abstractmethod
from forte.core import flog
from forte.molecule import Molecule
from forte.basis import Basis
from ._forte import StateInfo
from ._forte import Symmetry
from ._forte import make_ints_from_psi4
class Model(ABC):
"""
An abstract base class used to implement a model.
A m... | evangelistalab/forte | forte/model.py | Python | lgpl-3.0 | 6,126 | [
"Psi4"
] | 3eabc90f444234b51e4d60faeb2980a541acf0cc89e8251444be8bc727011864 |
# coding: utf-8
#
# Copyright 2017 The Oppia Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | prasanna08/oppia-ml | core/domain/job_services.py | Python | apache-2.0 | 4,935 | [
"VisIt"
] | 95f72fb814c2add1e541593c45b281f692a69c2f5d1d343999986eb0eb01874d |
# coding=utf-8
# Copyright 2022 RigL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | google-research/rigl | rigl/experimental/jax/shuffled_mask_test.py | Python | apache-2.0 | 3,413 | [
"NEURON"
] | 6d9348073e9496de6917f606b2a2d7c5216dd9af24bdde25c0c3cb8458ce2f3b |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from __future__ import absolute_import
import pytest
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.courseware... | jolyonb/edx-platform | common/test/acceptance/tests/lms/test_lms_acid_xblock.py | Python | agpl-3.0 | 5,768 | [
"VisIt"
] | 25fa795901f08cb3b881cab562c81da8e0438bcfc18b1517f2da8859ced09fe5 |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010 (ita)
"""
Classes and functions required for waf commands
"""
import os, imp, sys
from waflib import Utils, Errors, Logs
import waflib.Node
# the following 3 constants are updated on each new release (do not touch)
HEXVERSION=0x1060b00
"""Constant updated o... | Theragon/kupfer | waflib/Context.py | Python | gpl-3.0 | 16,308 | [
"VisIt"
] | b1ca13887cd82730784a3631e0b2b3d8efec906a1cdae221cbf185836e3e9673 |
"""Testing for Gaussian process regression """
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import numpy as np
from scipy.optimize import approx_fprime
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels \
import RBF, Constan... | Titan-C/scikit-learn | sklearn/gaussian_process/tests/test_gpr.py | Python | bsd-3-clause | 12,435 | [
"Gaussian"
] | 6c9a6fefd33e54244a6e893ee41216e71dcb5cae7b7c1b990951107d65f6f873 |
# Authors: Jonathan Anchell, Ram Balachandran.
# Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN.
import sys
import math
from operator import itemgetter
import numpy as np
import pymatgen as mg
import copy
from collections import namedtuple
from enum import Enum
class densityOf... | ornl-abinitio/codesScripts | ramScripts/phonopyPostProcess.py | Python | lgpl-2.1 | 2,007 | [
"phonopy",
"pymatgen"
] | 47a2c8d4dd365ec4deee485103c677182dd462b70b86cf5711d115a891fd4c00 |
#!/usr/bin/env python
# (C) Copyright 2018 ECMWF.
#
# This software is licensed under the terms of the Apache Licence Version 2.0
# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0.
# In applying this licence, ECMWF does not waive the privileges and immunities
# granted to it by virtue of its status... | Kate-Willett/Climate_Explorer | PYTHON/cdsapi-0.1.4/example-era5.py | Python | cc0-1.0 | 680 | [
"NetCDF"
] | d61e1633fd153c3e2f96465dc61e6bf602c38b8ccc59dc320e9b7b0346c9208c |
########################################################################
# $HeadURL$
# File : dirac-proxy-init.py
# Author : Adrian Casajus
########################################################################
__RCSID__ = "$Id$"
import sys
import getpass
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Ba... | rajanandakumar/DIRAC | FrameworkSystem/Client/ProxyGeneration.py | Python | gpl-3.0 | 9,636 | [
"DIRAC"
] | 0d9757437c6c345b4b7a49b4f513cfa9bab3b43fb63c6388735b9aed31fdd9fb |
from ase import Atoms
from gpaw import GPAW, PW
from gpaw.response.df import DielectricFunction
from gpaw.test import equal, findpeak
# Comparing the plasmon peaks found in bulk sodium for two different
# atomic structures. Testing for idential plasmon peaks. Not using
# physical sodium cell.
a = 4.23 / 2.0
a1 = Atom... | robwarm/gpaw-symm | gpaw/test/response_na_plasmon.py | Python | gpl-3.0 | 2,563 | [
"ASE",
"GPAW"
] | d584b5b3293879b127ddff394b3093de1afd43c8a8833143b67bc44b7be92b4c |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | CraigHarris/gpdb | src/test/tinc/tincrepo/mpp/models/optimizer_sql_performance_tc.py | Python | apache-2.0 | 11,760 | [
"VisIt"
] | 4f9386acb50268fab12fe802cda875d52472916e45566a52548cdefa29ea5743 |
from abc import ABCMeta, abstractmethod
from math import fsum
import numpy as np
from scipy.stats import norm as norm_dist
from collections import namedtuple
from pyx import _hmmc
from hmm.multivariatenormal import MultivariateNormal, MixtureModel
__author__ = 'eranroz'
class HMMModel(object):
"""
base model... | eranroz/dnase | src/hmm/HMMModel.py | Python | mit | 45,994 | [
"Gaussian"
] | 0221aac9d3ff8ed71ffe405f71c88a196a4a3565f16913d240da827cbd5d749b |
from gi.repository import Gtk, Gdk, GObject
import logging
import os
import xapian
from gettext import gettext as _
from softwarecenter.ui.gtk3.session.appmanager import get_appmanager
from cellrenderers import (CellRendererAppView,
CellButtonRenderer,
CellButto... | armikhael/software-center | softwarecenter/ui/gtk3/widgets/apptreeview.py | Python | gpl-3.0 | 24,448 | [
"ORCA"
] | de2aacb8485364508d6639ca9bf3fcb553e9751a12d80c3f487450afc3b80628 |
"""
Example of running optical and contact cluster stuff on gromacs file
"""
from __future__ import absolute_import, division, print_function
import os.path as op
import numpy as np
import numpy.testing as npt
import pdb
import gsd.hoomd
import sys
import clustering as cl
import random
import scipy
import time
#from co... | ramansbach/cluster_analysis | clustering/scripts/analyze_clusters_martini.py | Python | mit | 2,680 | [
"Gromacs"
] | 7d7e73a96429a90d63c9282e08e4a0c4416403e5559c4bf363a28833c0e413ed |
"""Perform validation of final calls against known reference materials.
Automates the process of checking pipeline results against known valid calls
to identify discordant variants. This provides a baseline for ensuring the
validity of pipeline updates and algorithm changes.
"""
import collections
import contextlib
im... | Cyberbio-Lab/bcbio-nextgen | bcbio/variation/validate.py | Python | mit | 23,539 | [
"pysam"
] | fec0d957113c4f35c5aae48b70094c0b059ed570dbb78d323c5c405baa29db05 |
"""
Defines Configuration class for representation of molecular
structure at one particular point in time.
Part of raman package.
Copyright Sean McGrath 2015. Issued under the MIT License.
"""
from .spectrum import Spectrum
from .matrix import DistanceMatrix
class Configuration:
"""
A single molecular Conf... | SeanMcGrath/raman | gparse/configuration.py | Python | mit | 1,862 | [
"Gaussian"
] | 8772674828caa39dc1f230c49f5ca0c36fd966917c00bb7c686a93ac2e10a6b4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import time
import warnings
from . import basex
from . import dasch
from . import direct
from . import h... | stggh/PyAbel | abel/transform.py | Python | mit | 20,437 | [
"Gaussian"
] | da364e3c23abe211664a64eae2e653e1a3b86eafa3c6b250064b47269530a8ca |
from aiida import load_dbenv
try:
load_dbenv()
from aiida.orm import load_node, load_workflow
from aiida.orm import Code, DataFactory
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
ArrayData = DataFactory('array')
KpointsData = DataFactory('array.kpoints... | abelcarreras/aiida_extensions | workflows/tools/commensurate_phonon.py | Python | mit | 13,854 | [
"phonopy"
] | 8bcc973d41f0036587192e3c1dff930369200848b01b7a56a663443056bb3347 |
import numpy as np
import time
def array_basic():
# create 2x3 matrix
print np.array([(1,2,3), (4,5,6)])
# empty array
print np.empty(5) #1x5
print np.empty((5, 4)) # 5x4
# array of 1s
print np.ones((3,3)) # by default is float
print np.ones((3,3), dtype=np.int) # int
... | gietal/Stocker | sandbox/udacity/1-3.py | Python | mit | 3,724 | [
"Gaussian"
] | 68e739f43abcba6e3c5749f149202e52baa4f4922590ab33ef6f39e118581900 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
class ITKtoVTK:
kits = ['itk_kit']
cats = ['Insight']
help = """Use this module to convert from any ITK image type to
the corresponding VTK type.
"""
class VTKtoITK:
kits = ['itk_kit']
cats = ['Ins... | nagyistoce/devide | modules/insight/module_index.py | Python | bsd-3-clause | 12,137 | [
"Gaussian",
"VTK"
] | a14e7b947f136bf66b7fd7ebf86beeecbd98bfb5aee2f1c20fe01da082bf6f42 |
""" This tests only need the TaskQueueDB, and connects directly to it
"""
import unittest
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC import gLogger
from DIRAC.WorkloadManagementSystem.DB.TaskQueueDB import TaskQueueDB
class TQDBTestCase( unittest.TestCase ):
""" Base class f... | Andrew-McNab-UK/DIRAC | tests/Integration/WorkloadManagementSystem/Test_TaskQueueDB.py | Python | gpl-3.0 | 2,614 | [
"DIRAC"
] | 13ebf741985b3891f6824d92043d2f63dc3f9943682e228890b4f12c0110064c |
# Izhikevich.py ---
#
# Filename: Izhikevich.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri May 28 14:42:33 2010 (+0530)
# Version:
# Last-Updated: Tue Sep 11 14:27:18 2012 (+0530)
# By: subha
# Update #: 1212
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# th... | BhallaLab/moose | moose-examples/izhikevich/Izhikevich.py | Python | gpl-3.0 | 23,767 | [
"MOOSE",
"NEURON"
] | ad15d0ed6e996f24a8691f71752f7e61c84f92eba63e830be485b26dde3cc01a |
import xml.dom.minidom
import numpy
import string
def CreateLib():
"""@todo: document me"""
import sys
import time
domimpl = xml.dom.minidom.getDOMImplementation()
doc = domimpl.createDocument(None, "source_library", None)
lib = doc.documentElement
lib.setAttribute("title", "source library"... | davidsanchez/CTAtools | ctoolsAnalysis/xml_generator.py | Python | gpl-3.0 | 21,335 | [
"Gaussian"
] | 056f56079be553949a8a2dbaf6ea4357178dd959a2269029168943e81fab3d3b |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/profiles/urls.py | Python | gpl-3.0 | 1,157 | [
"Brian"
] | bd85120ea8f4114458e835983a71de5b9b8281392c26f639889c29b94e082590 |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import re
from nose.plugins.attrib import attr
from unittest import skipUnless
from urllib import urlencode
import mock
import ddt
from django.conf import settings
from django.core import mail
from django.core.files.uploadedfile import SimpleUploadedFil... | waheedahmed/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 25,209 | [
"VisIt"
] | ad9786ad003f77fc483da6a7132f97f8dce235a134802448ad5f26efa4725867 |
#!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
import MITgcmutils as mit
import scipy.io.netcdf as netcdf
import sys
plt.ion()
iexp = ['6']
dir0 = '../run10_p'
dir1 = dir0 + iexp[0] + '/mnc_test_*/'
#file_s = 'state*.nc'
file_m = 'mean*.nc'
file_g = 'grid*.nc'
#f1 = netcdf.netcdf_file(dir... | bderembl/mitgcm_configs | natl_square/script/compute_mean.py | Python | mit | 2,255 | [
"NetCDF"
] | 9b57fcdbdda27f4baeb676c564ff13c14b8b22726d5848065eaf2d65ff728b2c |
#!/usr/bin/env python
"""
Remove the outputs produced by a transformation
Usage:
dirac-transformation-remove-output transID [transID] [transID]
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import sys
from DIRAC.Core.Base import Script
from DIRAC.... | yujikato/DIRAC | src/DIRAC/TransformationSystem/scripts/dirac_transformation_remove_output.py | Python | gpl-3.0 | 1,144 | [
"DIRAC"
] | ea2dc47f11e812c0d30296311c35b1476b50ffe0aa47a40e02757a25b7238652 |
import sys
from engine.resources.scene import Point3D
from resources.datatables import GalaxyStatus
from services.sui.SUIService import MessageBoxType
from services.sui.SUIWindow import Trigger
from java.util import Vector
import main.NGECore
def setup():
return
def run(core, actor, target, commandString):
core.s... | agry/NGECore2 | scripts/commands/server.py | Python | lgpl-3.0 | 3,083 | [
"Galaxy"
] | e6d7b78427a7fa9751973ef716a423b19c78d81805e62be39dfb80edc789f4c2 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/ilsa/plugins/reslice/reslice.py | Python | lgpl-3.0 | 2,331 | [
"VTK"
] | 36ca6457aca25bfbd9fedfdec5961635f915710eb039567fc1645f5258795fd6 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | zoulianmp/moonstone-pyqt | moonstone/bloodstone/importer/importer.py | Python | lgpl-3.0 | 18,547 | [
"VTK"
] | 6ba70c37b2df58ee03fba682979b8f43f02f0a13522b849ef057ac5efc734400 |
#!/usr/bin/env python
"""Try out the N-queens problem for an arbitrary number of queens.
This program uses Genetic Algorithms to try to solve the N queens
problem, in which you place N different queens on an N by N chess
board such that no two queens will be attacking each other.
We represent queens on the board as a... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_GAQueens.py | Python | gpl-2.0 | 14,662 | [
"Biopython"
] | 78dde304966058ad840d114e8d5556a8f3b15acd4aaf8f2127278c7b2faa05e7 |
from math import ceil
from numpy import apply_along_axis, full, nan
from numpy.random import choice, get_state, seed, set_state
from ._match_target_and_data import _match_target_and_data
from .compute_nd_array_margin_of_error import compute_nd_array_margin_of_error
def _match_randomly_sampled_target_and_data_to_com... | UCSD-CCAL/ccal | ccal/_match_randomly_sampled_target_and_data_to_compute_margin_of_errors.py | Python | mit | 1,318 | [
"MOE"
] | fef0d89fdbacd3dd7f9f245d32303ab41d8b67a56a14f129a0cfc2d7e533a696 |
#! /usr/bin/python2
import subprocess
import sys
import os
import time
from subprocess import PIPE
import socket
default_params = ''
output_file_prefix = 'output'
if len(sys.argv) > 1:
output_file_prefix = sys.argv[1]
#
# SCENARIO
#
# 0: radial dam break
# 1: gaussian
# 2: balanced steady state u
# 3: balanced ste... | schreiberx/sweet | archive/benchmarks_plane/rexi_tests_lrz/2015_12_27_scalability_nr_fd/params.py | Python | mit | 5,305 | [
"Gaussian"
] | 45ac0477c78fa7e91ce236bb2c3f5528aaf00a419950eff879704d0ee284e970 |
from __future__ import annotations
import os
import procrunner
import pytest
from dxtbx.serialize import load
from dials.array_family import flex
def test_slice_sequence_and_compare_with_expected_results(dials_regression, tmpdir):
# use the i04_weak_data for this test
data_dir = os.path.join(dials_regress... | dials/dials | tests/command_line/test_slice_sequence.py | Python | bsd-3-clause | 4,156 | [
"CRYSTAL"
] | e82dfbac62b55b47e6e321b11dfe867c0db996caa474062e8ca2ed60c65599e5 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ag... | flgiordano/netcash | +/google-cloud-sdk/lib/surface/meta/generate_help_docs.py | Python | bsd-3-clause | 5,638 | [
"VisIt"
] | 390c6b4a08d8d3bffeaa220005a01c1a60c2657f41c937b57c88a06352a821f5 |
"""
A dialog box for confirming GPG keys.
"""
# Copyright (C) 2009, Thomas Leonard
# -*- coding: utf-8 -*-
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, translation
import gtk
from zeroinstall.injector.model import SafeException
from zeroinstall.injector import gpg, trust... | pombredanne/zero-install | zeroinstall/gtkui/trust_box.py | Python | lgpl-2.1 | 9,588 | [
"VisIt"
] | cd473c6816403779dcc49931b85ce8e8072b01545e93877a5ccc5d51935b4feb |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/qcdb/modelchems.py | Python | lgpl-3.0 | 30,569 | [
"CHARMM",
"Psi4"
] | d5692a3546b6fbe805fbb26a643f8ea0cee8bf57e8859ba559b67f455505be38 |
#!/usr/bin/python
import urllib2
import sys
import cv
import numpy
# SRGB-linear conversions using NumPy - see http://en.wikipedia.org/wiki/SRGB
def srgb2lin(x):
a = 0.055
return numpy.where(x <= 0.04045,
x * (1.0 / 12.92),
numpy.power((x + a) * (1.0 / (1 + a)), 2... | eirTony/INDI1 | to/lang/OpenCV-2.2.0/samples/python/numpy_array.py | Python | mit | 2,086 | [
"Gaussian"
] | badb1035b949fa8a6d1d87a320698c18140534fdb14f77a3342258c955941600 |
# Author: Samuel Lucidi <mansam@csh.rit.edu>
__version__ = "0.1.113"
import requests
import urllib
import ConfigParser
import liveconnect.conf
import liveconnect.exceptions
config = ConfigParser.SafeConfigParser()
config.read(liveconnect.conf.liveconnect_config_locations)
def connect():
client_id = liveconnect.conf... | mansam/liveconnect | liveconnect/__init__.py | Python | mit | 2,101 | [
"VisIt"
] | 5abe830201ff215c9c84417fd34798c68ea5d88e5009124bfee807c50a6a9aeb |
# Copyright 2010 by Tiago Antao. 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.
"""
Large file parsing of Genepop files
The standard parser loads the whole file into memory. T... | bryback/quickseq | genescript/Bio/PopGen/GenePop/LargeFileParser.py | Python | mit | 3,945 | [
"Biopython"
] | 2fee16f0a4658e2ad21077f0efd08f5a46e04fe5aacc33ba2b608284dc24a3c1 |
"""The basic dict based notebook format.
The Python representation of a notebook is a nested structure of
dictionary subclasses that support attribute access
(IPython.utils.ipstruct.Struct). The functions in this module are merely
helpers to build the structs in the right form.
Authors:
* Brian Granger
"""
#-------... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/nbformat/v3/nbbase.py | Python | apache-2.0 | 7,046 | [
"Brian"
] | 2f6c65316724eb45f495cb7055afd50f6cef6208762b4601e1f96bd0bb4717a4 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | yipenggao/moose | python/chigger/tests/geometric/base/rotation.py | Python | lgpl-2.1 | 1,643 | [
"MOOSE",
"VTK"
] | 132f28b0470600e07be7cce45a2ce05c9c0f5a2a68e5f8c444958efe327a994a |
"""
An example showing how a custom colormap (or look up table) can be used
for a given object.
Although the end user specifies colormaps by giving the name of a set of
predefined colormaps, Mayavi (and VTK) deal with color internally using
'Look Up Tables' (LUT): a table that associate a scalar value to a
color defin... | HPCGISLab/STDataViz | WorkingVersion/LibTry/OtherTry/custom_colormap.py | Python | bsd-3-clause | 1,777 | [
"Mayavi",
"VTK"
] | f0a2419d1c3606a4e6d629838bf1a05d0589c81d930bfb80ff4a2bba7662db19 |
# encoding: 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):
# Adding model 'DataDomainIndex'
db.create_table(u'profiles_datadomainindex', (
(u'id', self.g... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0067_auto__add_datadomainindex__del_field_datadomain_groups.py | Python | mit | 23,543 | [
"MOE"
] | e985de5b9426df9c759d6a71994cdd93fd939a059a55775c118164e804678251 |
#!/usr/bin/env python
# Testing the new parallel scanner class - detection of invalid states
# --jr20101218
import os
backupdir = os.getcwd()
import numpy as np
import pysces
tbox=pysces.PyscesUtils.TimerBox()
import time
m=pysces.model('isola2a')
ser = pysces.Scanner(m)
print "Serial execution..... | asttra/pysces | pysces/examples/testinvalidstate.py | Python | bsd-3-clause | 2,997 | [
"PySCeS"
] | 61ac1b586042f56f40b2b1e7ce39667a153c17f743f78aefb827315563edac05 |
""" The Machine/Job Features TimeLeft utility interrogates the MJF values
for the current CPU and Wallclock consumed, as well as their limits.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import time
from six.moves.ur... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/MJFResourceUsage.py | Python | gpl-3.0 | 4,360 | [
"DIRAC"
] | d779b7eed58c8179e16f9443aa3376ed9d3b0e673e2bb3b80cd55f5ffe57a76b |
# 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... | sarvex/tensorflow | tensorflow/python/tpu/device_assignment.py | Python | apache-2.0 | 21,430 | [
"VisIt"
] | 2fec1395eadfe6feb7b7d41621f846bc55f322455e2ebf794f36905bf4083da1 |
#!/usr/bin/env python
"""
Extract alignment statistics from a SAM/BAM file.
Adapted from the Celloline stats script
available at: https://github.com/Teichlab/celloline/blob/master/lib/stats.py
"""
import os
import sys
import re
import argparse
import pysam
import logging
import cPickle as pickle
from collections impo... | lazappi/binf-scripts | alignStats.py | Python | mit | 18,860 | [
"pysam"
] | 5597529dcdc22f4eddd06f1a030d701c7824f13e1f1df7bb38f5bf827ffe2ef6 |
# !/usr/local/bin/python3.4.2
# ----Copyright (c) 2016 Carnegie Hall | The MIT License (MIT)----
# ----For the full license terms, please visit https://github.com/CarnegieHall/linked-data/blob/master/LICENSE----
## Argument[0] is script to run
## Argument[1] is path to Venues CSV
## Argument[2] is path to entity... | CarnegieHall/linked-data | scripts/OPAS_toRDF_events.py | Python | mit | 11,216 | [
"VisIt"
] | 2bc4ddf7a344f1cb5014c81ef7c6e216d3b4012b5266f265e26db960ae100abd |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-03-28 23:30:14
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-03-28 23:30:14 by Brian Cherinka
Last Modified On: 2016-03-28 23:30:14 by Brian
'''
from __future__ import print_function
from __future__... | bretthandrews/marvin | python/marvin/db/marvindb.py | Python | bsd-3-clause | 6,528 | [
"Brian"
] | 84d7f8da490aa7ec7d7022da848ebc05a6c032cfbe5dc32a5fa0f4e4557b3a2d |
"""
Converting the 'parse-tree' output of pyparsing to a SPARQL Algebra expression
http://www.w3.org/TR/sparql11-query/#sparqlQuery
"""
import functools
import operator
import collections
from rdflib import Literal, Variable, URIRef, BNode
from rdflib.plugins.sparql.sparql import Prologue, Query
from rdflib.plugi... | gloaec/trifle | src/rdflib/plugins/sparql/algebra.py | Python | gpl-3.0 | 20,924 | [
"VisIt"
] | 6a727d3d32312b90aeaf9d2a3deae4583a04d91af0caa1a3101a623780eea9d1 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | lahnerml/espresso | samples/python/lj_liquid_distribution.py | Python | gpl-3.0 | 7,270 | [
"ESPResSo"
] | 02607c30ea46571d27f2e79678702e59fdcf16270c188cee5599ab5384d3eca4 |
__author__ = 'jules'
#see http://nbviewer.ipython.org/github/timstaley/ipython-notebooks/blob/compiled/probabilistic_programming/convolving_distributions_illustration.ipynb
import deepThought.ORM.ORM as ORM
from deepThought.util import list_to_cdf
from deepThought.stats.phase_type import infer_distribution
import nu... | juliusf/Genetic-SRCPSP | tools/stat_inference/mixture_dist.py | Python | mit | 1,592 | [
"Gaussian"
] | f337221a6151d0c97a683c02324a9a4666e571da7d1e88c964d170f9c3a6f682 |
#!/usr/bin/env python
# Copyright (C) 2012, 2014 Moritz Huetten
import sys
import getopt
import math
#from numpy import *
import numpy as np
try:
from netCDF4 import Dataset as NC
except:
print "netCDF4 is not installed!"
sys.exit(1)
# geometry setup MISMIP3D Stnd-experiment
WRIT_FILE = 'MISMIP3D_Stnd... | talbrecht/pism_pik07 | examples/mismip/mismip3d/setup_Stnd.py | Python | gpl-3.0 | 4,700 | [
"NetCDF"
] | 05e54d08fc8528ec1c76d02cc092aa2e88a9ced8c0e1dae174f946a760478eae |
#!/usr/bin/env python
# Description: run job for the backend. result will not be cached
import os
import sys
import subprocess
from libpredweb import myfunc
from libpredweb import webserver_common as webcom
import glob
import hashlib
import shutil
from datetime import datetime
from dateutil import parser as dtparser
fr... | ElofssonLab/web_common_backend | proj/pred/app/run_job.py | Python | mit | 35,277 | [
"BLAST"
] | 4aefe41e6b0ecc99eb0fae03e18c01a5472e37bb3997c4d5385c03186b50ca29 |
# $Id$
#
# Copyright (C) 2007 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import doctest
import unittest
from rdkit import R... | bp-kelley/rdkit | rdkit/Chem/Fingerprints/UnitTestDbFpSupplier.py | Python | bsd-3-clause | 1,059 | [
"RDKit"
] | 3eec9a99a840f06cffb1b0257f0c61d4c941555bcd69abe2e667949949ad55bd |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jendap/tensorflow | tensorflow/python/ops/linalg/linear_operator_test_util.py | Python | apache-2.0 | 30,832 | [
"Gaussian"
] | bdb7b314565a6089759f46247e2a22288a1481e7bb2c41a4eb35fe8cb6024b61 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Image pipeline
reader = vtk.vtkImageReader()
reader.SetDataByteOrderToLittleEndian()
reader.SetDataExtent(0,63,0,63,1,93)
reader.SetFilePrefix("" + str(VTK_DATA_ROOT) + "/Data/heads... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/ContinuousClose2D.py | Python | gpl-3.0 | 772 | [
"VTK"
] | f8c2221d4d48b3c64944ac37c076ca9674165565aed3c2c8cfb8ca17fccc9eb7 |
from splinter.browser import Browser
from time import sleep
import traceback
class Buy_Tickets(object):
# 定义实例属性，初始化
def __init__(self, username, passwd, order, passengers, dtime, starts, ends):
self.username = username
self.passwd = passwd
# 车次，0代表所有车次，依次从上到下，1代表所有车次，依次类推
self... | lsp84ch83/PyText | 公开课/爬虫/用Python抢火车票完整源代码.py | Python | gpl-3.0 | 4,669 | [
"VisIt"
] | 9cdd68d5202f6557cde1124b647172ef50182e3dcc8af6a1a69d3c54755970b0 |
from sympy.core import S, C, sympify
from sympy.core.function import Function, ArgumentIndexError
from sympy.ntheory import sieve
from math import sqrt as _sqrt
from sympy.core.compatibility import reduce, as_int
from sympy.core.cache import cacheit
class CombinatorialFunction(Function):
"""Base class for combi... | lidavidm/mathics-heroku | venv/lib/python2.7/site-packages/sympy/functions/combinatorial/factorials.py | Python | gpl-3.0 | 16,857 | [
"VisIt"
] | fe787db0fe256eb4a3f7a3b6d58f0dd4ff9632ca48b3bde2539015079d13d71f |
#!/usr/bin/env python
import sys, os, gzip
from galaxy.datatypes.checkers import is_gzip
def main():
"""
The format of the file is JSON::
{ "sections" : [
{ "start" : "x", "end" : "y", "sequences" : "z" },
...
]}
This works only for UNCOMPRESSED fastq fil... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/fastq_to_fqtoc.py | Python | gpl-3.0 | 1,317 | [
"Galaxy"
] | 82c9b67c9e7a194ee98ddbecdb783b9324cb453c13c8af56cfd688b7ce08d805 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | clemkoa/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 78,779 | [
"Brian"
] | d3d059f561a955a205103c5ffb6c485e00406697715c85afaf10e6ead9df2204 |
import os
import re
import errno
def colorText(string, color, **kwargs):
"""
A function for coloring text.
Args:
string[str]: The string to color.
color[str]: The color to use (see color_codes variable).
Kwargs:
html[bool]: If true html colored text is returned.
colore... | stimpsonsg/moose | python/mooseutils/mooseutils.py | Python | lgpl-2.1 | 4,939 | [
"MOOSE"
] | d817b1544112fc0dcc0f65d5110eafd0bc0b38e966d0cd25d7a29e4c1063e029 |
""" 2-input XOR example using Izhikevich's spiking neuron model. """
from __future__ import print_function
import multiprocessing
import os
from matplotlib import patches
from matplotlib import pylab as plt
import visualize
import neat
# Network inputs and expected outputs.
xor_inputs = ((0, 0), (0, 1), (1, 0), (1... | CodeReclaimers/neat-python | examples/xor/evolve-spiking.py | Python | bsd-3-clause | 5,782 | [
"NEURON"
] | ab0085c939dad11e978250ec56cff296c872803f9ec435ea91f1b3940703c20d |
#!/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... | MiLk/ansible | lib/ansible/modules/network/avi/avi_gslbservice.py | Python | gpl-3.0 | 7,459 | [
"VisIt"
] | 9d1179829b66472f6a85c677039d5323a651bf58173ab899e409994ca67af376 |
# -*- coding: utf-8 -*-
"""
***************************************************************************
OTBUtils.py
---------------------
Date : 11-12-13
Copyright : (C) 2013 by CS Systemes d'information (CS SI)
Email : otb at c-s dot fr (CS SI)
Contrib... | AsgerPetersen/QGIS | python/plugins/processing/algs/otb/maintenance/OTBSpecific_XMLcreation.py | Python | gpl-2.0 | 29,063 | [
"Gaussian"
] | 85c566b95051d29c0b1ffa16559a23f4178d6149e98a24f666c8fc0f1446b624 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | KonradBreitsprecher/espresso | samples/debye_hueckel.py | Python | gpl-3.0 | 6,305 | [
"ESPResSo"
] | ffe655962b5eab08db8c30c233f0ce5cb3e42e14d53a0a0228fc52644c31f473 |
"""
Viewing MRI data with cut plane and iso surface.
This example downloads an MRI scan, turns it into a 3D numpy array and
visualizes it.
First we extract some internal structures of the brain by defining a
volume of interest around them, and using iso surfaces.
Then we display two cut planes to show the raw MRI da... | liulion/mayavi | examples/mayavi/mlab/mri.py | Python | bsd-3-clause | 3,664 | [
"Mayavi",
"VTK"
] | 68d398e2e06b7b03f7b5f9c1b381c6f8d76dcee0dbe385418eda9510a5d110a4 |
"""
gribTools
======
Import GRIB2 data (must be converted to netCDF) and return a dictionary of variables.
gribImport
gribLevs
"""
import numpy as np
import warnings
warnings.filterwarnings("ignore",category=FutureWarning)
import xarray as xr
from datetime import datetime as dt
def gribImport(gribFile):
... | stechma2/samuraiAnalysis | gribTools.py | Python | gpl-3.0 | 2,550 | [
"NetCDF"
] | d737984745f31a87b55b7de68565d3e83fbca4efbc4b02af33ce4f187064de02 |
#!/usr/bin/env python
import sys, traceback
import pysam
import numpy
from scipy.stats import histogram
import matplotlib.pyplot as plt
if len(sys.argv) != 2:
print 'Usage: [bam file]'
sys.exit(1)
samfile = pysam.AlignmentFile(sys.argv[1], 'rb')
info = []
counts = {'sec': 0, 'unmap': 0, 'rev': 0, 'dup': 0,... | koadman/proxigenomics | simulation/pipeline/bin/info_sam.py | Python | gpl-2.0 | 2,165 | [
"pysam"
] | 19a7a0eeeac9b3342142a89b4588c30db13a3305ef74afc0183fce8491de4250 |
"""
Tests for discussion pages
"""
from uuid import uuid4
from .helpers import UniqueCourseTest
from ..pages.lms.auto_auth import AutoAuthPage
from ..pages.lms.courseware import CoursewarePage
from ..pages.lms.discussion import (
DiscussionTabSingleThreadPage,
InlineDiscussionPage,
InlineDiscussionThreadP... | LICEF/edx-platform | common/test/acceptance/tests/test_discussion.py | Python | agpl-3.0 | 22,502 | [
"VisIt"
] | 6569fdfa341231db78c3526621ebca9aaa9b44ff2f0ae30ffdec5a50a96ae05a |
# $HeadURL$
"""
Collection of DIRAC useful operating system related modules
by default on Error they return None
"""
__RCSID__ = "$Id$"
from types import StringTypes
import os
import DIRAC
from DIRAC.Core.Utilities.Subprocess import shellCall, systemCall
from DIRAC.Core.Utilities impor... | avedaee/DIRAC | Core/Utilities/Os.py | Python | gpl-3.0 | 6,236 | [
"DIRAC"
] | a6d8df382e5a8d38c09d5fda419d89a624d522e4fe02b9ed704758f92e4d7a79 |
"""Helper functions common to all mission tsaks"""
import itertools
from math import radians, sqrt, cos, sin, tan, atan, degrees, atan2
import numpy
import scipy.stats
import shm
from mission.framework.helpers import get_sub_position
# Function returns a list where elements are sorted by their distance from elemen... | cuauv/software | mission/helpers.py | Python | bsd-3-clause | 10,992 | [
"Gaussian"
] | 5eb2834f67947390566a556fc281e59a17ae9fd1b096dd07d40b3d3db00f36e5 |
"""
This module defines a classs for a generic Workflow Parameter. It also defines
a ParameterCollection class as a list of parameters as well as an AttributeCollection
class which is the base class for the main Workflow classes.
"""
from DIRAC.Core.Workflow.Utility import *
__RCSID__ = "$Id$"
# unbound m... | arrabito/DIRAC | Core/Workflow/Parameter.py | Python | gpl-3.0 | 24,393 | [
"DIRAC"
] | 8e7bfa97ef9afbf100fbd5df6fa6224670c7e1e22638d0b9973c4b6a5f0d7f2e |
# 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... | zhreshold/mxnet | python/mxnet/numpy/random.py | Python | apache-2.0 | 40,820 | [
"Gaussian"
] | 7243a74c0b7914123db09c1cf1b1a660becb0bf4ac5dd713e4d210f54461ec4e |
# ==============================================================================
# plot depth slices
# ==============================================================================
import os
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.ticker import MultipleLocator
from mtpy.modeling.modem imp... | MTgeophysics/mtpy | mtpy/imaging/plot_depth_slice.py | Python | gpl-3.0 | 18,092 | [
"VTK"
] | 2045f1d86b7a400f99eed76afc73cce90a99ddf03da438ef7d0fabb6863b9645 |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2015 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2012-2014 Google, Inc.
# Copyright (c) 2013-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Brett Cannon <brett@python.org>
# Copyright (c) 2015 Radu Ciorba <radu@devrandom.ro>
# Copyright ... | rogalski/pylint | pylint/checkers/base.py | Python | gpl-2.0 | 73,250 | [
"VisIt"
] | 055b602229d2c5a0f6f5d37e2ab1976da2af3a46a6e594041675984625989a5d |
# Copyright 2001 by Gavin E. Crooks. 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.
"""Unit test for Astral"""
import unittest
from Bio.SCOP import *
class AstralTests(unitt... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SCOP_Astral.py | Python | gpl-2.0 | 2,234 | [
"Biopython"
] | a7951410eacdc931d8d0cea578607f23b44b718b7d0ad372f22758f97f3affa1 |
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
import mdtraj.reporters
cutoff = 0.95 * u.nanometers
output_frequency = 25000
n_steps = 500000000
temperature = 293.
pressure = 1.0 * u.atmospheres
pdb_filename = "./1am7_equil.pdb"
dcd_filename = "./1am7.dcd"
log_filename = "./1am7.... | choderalab/open-forcefield-group | nmr/code/simulate_T4.py | Python | gpl-2.0 | 1,413 | [
"MDTraj",
"OpenMM"
] | 5c3c46c166ae8823c4b9fcc6f7a9aa60a6ba93d95522f450b07524afc0bb6206 |
#!/usr/bin/python -O
#PBS -N myjob
#PBS -l select=1:ncpus=9:mem=12GB
#PBS -l walltime=70:00:00
import subprocess
import os
import sys
def module_add(modulen... | ThomasCarroll/mrcchip | pairedAlign.py | Python | gpl-2.0 | 2,281 | [
"BWA"
] | f17afbed52a57995e51cf9c061465b90b8d8e1134ae9114b18a263d1dd8b975b |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/plotting/preparation.py | Python | agpl-3.0 | 22,533 | [
"Galaxy"
] | 57fa3d249a1fac2fcb3c342cd26928405d73d6723f210502565a53fced8175a7 |
"""
ARD gplvm with one covaraince structure per dimension (at least implicitly)
"""
import sys
sys.path.append('./../..')
from pygp.gp import GP
import pygp.gp.gplvm as GPLVM
import pdb
from pygp.optimize.optimize_base import opt_hyper
import scipy as SP
import scipy.linalg as linalg
import copy
#Verbose implements al... | PMBio/pygp | pygp/gp/gplvm_ard.py | Python | gpl-2.0 | 13,046 | [
"Gaussian"
] | f4b632fb8c245477e14995fcc8a07429a9c888b45c88e5f4b1af0c7f46794d24 |
"""atom.py: ...
"""
import numpy as np
from numpy import nan
import scipy.linalg as spl
import sympy.physics.units as u
import piratechem as pc
class Atom(pc.atom.Atom):
"""Allow each atom to contain more specific quantum chemical
properties than piratechem can currently handle.
"""
def __init__(se... | berquist/orcaparse | orcaparse/atom.py | Python | mpl-2.0 | 7,226 | [
"ORCA"
] | 3bf3846332074f6bafadefefc9c150e5d0b889d80c89946d50a6613dd8210358 |
import itertools
from math import sqrt
import os
import re
from warnings import warn
# Isotopic abundances from Meija J, Coplen T B, et al, "Isotopic compositions
# of the elements 2013 (IUPAC Technical Report)", Pure. Appl. Chem. 88 (3),
# pp. 293-306 (2013). The "representative isotopic abundance" values from
# col... | shikhar413/openmc | openmc/data/data.py | Python | mit | 19,751 | [
"Avogadro"
] | 6395c5d2efbd65dbd0cf1120833c1f1d3ce83e1798f8908769e720b423d44999 |
import unittest
import scipy
import pysal
import numpy as np
from pysal.spreg import error_sp_regimes as SP
from pysal.spreg.error_sp import GM_Error, GM_Endog_Error, GM_Combo
from pysal.common import RTOL
@unittest.skipIf(int(scipy.__version__.split(".")[1]) < 11,
"Maximum Likelihood requires SciPy version 11 or newe... | ljwolf/pysal | pysal/spreg/tests/test_error_sp_regimes.py | Python | bsd-3-clause | 14,966 | [
"COLUMBUS"
] | 712b7ca3f172d5642ead6547353d6f81cf4ec599c3bf557c88f32148f6ba3576 |
import pyqtgraph as pg
from pyqtgraph.Qt import QtGui, QtCore
import pyqtgraph.parametertree as pt
import numpy as np
import scipy.ndimage as ndi
from ..event_detection import threshold_events, exp_deconvolve
from ..baseline import float_mode
from .filter import SignalFilter
class EventDetector(QtCore.QObject):
... | campagnola/neuroanalysis | neuroanalysis/ui/event_detection.py | Python | mit | 5,335 | [
"Gaussian"
] | 32c58a3aef1e8e0432cebe62e0f11edde7b6fc1a65a7968fdb50cace5b6ef8c0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2015, Adrián Gómez Pueyo and Alberto Castro
# This file is part of maxdft.
# maxdft 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... | albertocbarrigon/maxdft | src/octopus.py | Python | gpl-3.0 | 1,657 | [
"Octopus"
] | be8d58d3b717d3903d19b465cf4403694f992a603c40a5ef25fabaed6373dc1e |
"""Convert to and from Roman numerals
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.2 $"
__date__ = "$Date: 2004/05/05 21:57:20 ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/roman/stage2/roman2.py | Python | mit | 1,300 | [
"VisIt"
] | 9900dd768b3752d1df3a567b987d1b075eba5b9469367c04b623ea25ca0a2434 |
#!/usr/bin/python
import sys,tempfile,os,hashlib,cPickle
sys.path.append(os.path.join(__file__,'..'))
import xmlstore.datatypes,core.scenario,core.simulator
def run(scenariopath):
# Load scenario.
scen = core.scenario.Scenario.fromSchemaName(core.simulator.gotmscenarioversion)
if scenariopath.endswith('.x... | BoldingBruggeman/gotm | gui.py/unittest/simulate.py | Python | gpl-2.0 | 5,624 | [
"NetCDF"
] | 9a84b4819955a94db3c78ba4dadecbfd1b28453c3cb7218d559d1bf06cf5bd05 |
# 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... | gph82/PyEMMA | pyemma/coordinates/tests/test_featurizer.py | Python | lgpl-3.0 | 37,158 | [
"MDTraj"
] | 09c42c3173814f9342566c48f19b5da38ac38c362475aca69473084622f0ed69 |
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