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# coding=utf-8
from __future__ import unicode_literals
import capybara
class TestText:
def test_returns_the_text_of_the_page(self, session):
session.visit("/with_simple_html")
assert session.text == "Bar"
def test_ignores_invisible_text_by_default(self, session):
session.visit("/with... | elliterate/capybara.py | capybara/tests/session/test_text.py | Python | mit | 2,053 | [
"VisIt"
] | ff99920e326bd39a1677e8b2b77e3dfd8897b4842c53680534a8fc43d8eee328 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines standard transformations which transforms a structure into
another structure. Standard transformations operate in a structure-wide manner,
rather than site-specific manner.
All transformations should inherit the AbstractTransfor... | yanikou19/pymatgen | pymatgen/transformations/standard_transformations.py | Python | mit | 26,470 | [
"pymatgen"
] | 4c412b5eaf56b7dd12efe95f7e73b0d17b98b0ec6d4b29033ace6ebe22852bfc |
from PyQt5 import QtCore as QC
from PyQt5 import QtGui as QG
from PyQt5 import QtWidgets as QW
import numpy
from lsjuicer.data.pipes.tools import PipeChain
from lsjuicer.ui.plot.pixmapmaker import PixmapMaker
from lsjuicer.static.constants import ImageSelectionTypeNames as ISTN
from lsjuicer.ui.widgets.plot_with_axe... | ardoi/datajuicer | lsjuicer/ui/tabs/sparkdetecttab.py | Python | gpl-3.0 | 44,401 | [
"Gaussian"
] | 7d307b5c19454d75efa4df928d8f1b4524eb59f8ebdc5a71bd5bc613b5978b83 |
""" This module contains functions for calculating single-ifo ranking
statistic values
"""
import numpy
def newsnr_sgveto_psdvar_scaled(snr, bchisq, sgchisq,
psd_var_val, scaling=0.33):
""" Combined SNR derived from NewSNR, Sine-Gaussian Chisq and scaled PSD
variation statistic... | stevereyes01/pycbc | pycbc/events/ranking.py | Python | gpl-3.0 | 7,214 | [
"Gaussian"
] | 11b0cbd2251a0452178ebe5bf08b95f0aed1178309cfb18afb28f35d303d040c |
import os.path
import sys
import yaml
import subprocess
from ruffus.proxy_logger import *
import logging
import os
from shell_command import shellCommand
from cluster_job import (PBS_Script, runJobAndWait)
import re
defaultOptionsFile = 'ngs_pipeline.opt'
defaultWalltime = None # use the default walltime of the schedu... | bjpop/ngs-pipeline | src/ruffus/utils.py | Python | bsd-3-clause | 5,271 | [
"BWA"
] | 00627a839d5598c18aa7f53f7c239a4a8e192501361864ef73a7ecace71dfd40 |
""" JobManagerHandler is the implementation of the JobManager service
in the DISET framework
The following methods are available in the Service interface
submitJob()
rescheduleJob()
deleteJob()
killJob()
"""
__RCSID__ = "$Id$"
from types import StringTypes, IntType
from DIRAC.Core.DISET.Req... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Service/JobManagerHandler.py | Python | gpl-3.0 | 15,300 | [
"DIRAC"
] | 4c8c0851083d46c895dd0cb712df8431f9be95425091e8031a91f3e4024e2b7f |
__all__ = [
'TensorMeshReader',
'TensorMeshAppender',
'TopoMeshAppender',
]
__displayname__ = 'Tensor Mesh'
import os
import sys
import numpy as np
import pandas as pd
import vtk
from .. import _helpers, interface
from ..base import AlgorithmBase
from .two_file_base import ModelAppenderBase, ubcMeshRead... | banesullivan/ParaViewGeophysics | PVGeo/ubc/tensor.py | Python | bsd-3-clause | 21,910 | [
"VTK"
] | b41be86688be0295b58d431577d2058f08b5be4849b048623bd2f28dab053552 |
from collections import OrderedDict
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{... | danhuss/faker | faker/providers/person/en_GB/__init__.py | Python | mit | 18,303 | [
"Amber",
"Brian"
] | 7193372565ca23942f8993e57d2f911e4c61af2b544bc7ec9e4025e8fc31cbd7 |
"""
Load and save a set of chosen implementations.
@since: 0.27
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, zerostore
from zeroinstall.injector import model
from zeroinstall.injector.namespaces import XMLNS_IFACE
class Selection... | pombredanne/0install | tests/selections.py | Python | lgpl-2.1 | 4,920 | [
"VisIt"
] | 1916ac6781b6f9064d0b02eaa102590ff7e139dfa956af4896884ffccf87afa6 |
""" This is a test of the chain
FTSClient -> FTSManagerHandler -> FTSDB
It supposes that the DB is present, and that the service is running
"""
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
import unittest
#import mock
import uuid
from DIRAC import gLogger
from DIRAC.DataManagementS... | Andrew-McNab-UK/DIRAC | tests/Integration/DataManagementSystem/Test_Client_FTS.py | Python | gpl-3.0 | 8,332 | [
"DIRAC"
] | 734bcde357aba29833cda356e7958efe987e6d7332304b3becc5162db4a67ce1 |
from importlib import reload
import pandas as pd
import numpy as np
from textblob import TextBlob
from sklearn.decomposition import LatentDirichletAllocation
from sklearn.feature_extraction.text import TfidfVectorizer, CountVectorizer
from scipy.spatial.distance import pdist
from sklearn.preprocessing import MultiLabe... | Christoph/tag-connect | keyvis_add/lda_creator.py | Python | mit | 5,222 | [
"Gaussian"
] | 0e351e8e131c26753d896c01eaf149aef40718bb26cd7683139e6cef59b08a28 |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A convenience script engine to read Gaussian output in a directory tree.
"""
from __future__ import division, print_function
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright... | aykol/pymatgen | pymatgen/cli/gaussian_analyzer.py | Python | mit | 3,346 | [
"Gaussian",
"pymatgen"
] | a8e8bd70c790fc26afe6d67e1f7a8d12b9b4b7fcb866a8ae749e56dcf90210ff |
"""
Egg save utilities.
Note that :mod:`pickle` can't save references to functions that aren't defined
at the top level of a module, and there doesn't appear to be a viable
workaround. Normally :mod:`pickle` won't handle instance methods either,
but there is code in place to work around that.
When saving to an egg, ... | DailyActie/Surrogate-Model | 01-codes/OpenMDAO-Framework-dev/openmdao.util/src/openmdao/util/eggsaver.py | Python | mit | 28,767 | [
"VisIt"
] | a5d935c6736663358d1134e78bbe3d419bb35dcd5e41afd60b947208c43c480d |
import numpy as np
import mayavi.mlab as mlab
def test_triangular_mesh():
"""An example of a cone, ie a non-regular mesh defined by its
triangles.
"""
n = 15
t = np.linspace(-np.pi, np.pi, n)
z = np.exp(1j * t)
x = z.real.copy()
y = z.imag.copy()
z = np.zeros_like(x)
triangles = [(0, i, i + ... | kayarre/dicomwrangle | plotMesh.py | Python | bsd-2-clause | 552 | [
"Mayavi"
] | 97b2752affcefb599f36618d07f90e49e866cbf68a2ed9fb2c1d5e07ae234479 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2009 Peter G. Landgren
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as pu... | Forage/Gramps | gramps/gen/constfunc.py | Python | gpl-2.0 | 4,455 | [
"Brian"
] | 4a4f7243b24478035822a6f51a88c830ede7b782445d968e361f76289d58d3d2 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | magic/tests/Sky/test.py | Python | agpl-3.0 | 28,260 | [
"Galaxy",
"Gaussian"
] | 9b9e202851f388692b787dfa3e84b69183d92b219a623d46d49d1d88928c8a00 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-datacatalog | tests/unit/gapic/datacatalog_v1/test_policy_tag_manager_serialization.py | Python | apache-2.0 | 68,099 | [
"Octopus"
] | f75ee6a60c451ea01ce43533a9baec000f48a4c8f6a2e7cd7a42ad8182bbcbfd |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | dagwieers/ansible | lib/ansible/modules/cloud/kubevirt/kubevirt_vm.py | Python | gpl-3.0 | 10,418 | [
"Galaxy"
] | 96c506461a793a21f6cbec8dd415a47b4438c7cecc4d33e1b7d95f538e51e946 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2011, 2012, 2015, 2018, 2019 CERN.
#
# Invenio 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 (a... | inspirehep/invenio | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 148,233 | [
"VisIt"
] | 6fb7b855af1afa02efd5a2ea54973a5f069d5cf9acc199b0c5c6ee3a67f2b204 |
import numpy as np
from scipy.stats import bernoulli
from scipy.linalg import eigh
import random
import matplotlib.pyplot as plt
import itertools, math
def generateWignerMatrix(matrix_size):
matrix = np.zeros((matrix_size, matrix_size)) #Form a symmetric matrix
newSize = (matrix_size*(matrix_size+1))/2
ber... | krishnasripada/HighDimDataSet | Assignment1/problem25.py | Python | gpl-2.0 | 3,750 | [
"Gaussian"
] | b19ede987daee04bdad0f47459024c2092e5b23414286a6518829778e393f95d |
##
# Copyright 2013 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://vscentrum.be/nl/en),
# the Hercules foundation (http://w... | hajgato/easybuild-easyblocks | easybuild/easyblocks/b/bowtie.py | Python | gpl-2.0 | 2,599 | [
"Bowtie"
] | ab51d6654fbbbe8f96e00f72c2a692380287640303ba151cb2aea9e023012d52 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | marscher/mdtraj | MDTraj/geometry/tests/test_geometry.py | Python | lgpl-2.1 | 7,406 | [
"MDTraj",
"PyMOL"
] | 32a2a538e32c507823bf2c58117b7519524028e03008d375f84ace0b4282a19a |
#!/usr/bin/env python
#=========================================================================
#
# Copyright Insight Software Consortium
#
# 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
... | prasadvagdargi/med_image_analysis | Examples/Python/SimpleGaussianProcedural.py | Python | apache-2.0 | 1,300 | [
"Gaussian"
] | ea90e910b4447d7bd5f804ba085a0f70c27fa560d92f1cb4a2eef22994a91a8c |
"""This module/class contains functionality for computing (and plotting) radial
velocities and creating reference spectra for extracted fluxes. This should
ideally remain independent of the extraction method, such that it does not
matter which spectrograph took the data, nor what "Spectrograph" object was
used for e... | mikeireland/pymfe | pymfe/rv.py | Python | mit | 37,463 | [
"Gaussian"
] | d50b5d746a2b25c893a405b0c15d7258a84d8fab6f30174ecfc20a9971c34a8f |
# -*- coding: utf-8 -*-
# YAFF is yet another force-field code.
# Copyright (C) 2011 Toon Verstraelen <Toon.Verstraelen@UGent.be>,
# Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>, Center for Molecular Modeling
# (CMM), Ghent University, Ghent, Belgium; all rights reserved unless otherwise
# stated.
#
# This file is pa... | molmod/yaff | yaff/conversion/test/test_raspa.py | Python | gpl-3.0 | 1,493 | [
"RASPA"
] | 0a7bb6efcac22ac77e56556263ad1277989382249edb6aecf5b2fcab874c5cb5 |
'''
* Author: Lukasz Jachym
* Date: 9/15/13
* Time: 5:20 PM
*
* This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
* To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
'''
import requests
BASE_URL = 'http://openexchang... | b1r3k/recruitment-challanges | data-hacking/src/task1/exchange/openexchange.py | Python | mit | 690 | [
"VisIt"
] | dcdc36976944e2426db36e52141c0b29d09188f233ba8ebdcf14b7201fb8bb06 |
#
# @file TestRequiredElements.py
# @brief Test hasRequiredElements unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converti... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestRequiredElements.py | Python | bsd-3-clause | 7,241 | [
"VisIt"
] | d34cfc07874bea20130475d0d0d021f2ac4b8538b73af51e1e62374c5a9995c1 |
# -*- coding: utf-8 -*-
import datetime
import random
import re
import string
from lxml.html import parse
from urllib import urlencode
from urllib2 import urlopen
from urlparse import urljoin
from urlparse import urlparse
from openerp import models, fields, api, _
URL_REGEX = r'(\bhref=[\'"]([^\'"]+)[\'"])'
def VAL... | zbqf109/goodo | openerp/addons/link_tracker/models/link_tracker.py | Python | gpl-3.0 | 9,915 | [
"VisIt"
] | e0838d626ebd3e0996d026252e825c50068326dad6b59d8d5991b46f94d02b52 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py | Python | gpl-2.0 | 79,175 | [
"Amber",
"Gromacs",
"MDAnalysis"
] | a2dd00bdc0159532576f21d90ad2d3deddb92725597e8a04b4f0f6df6c1da2c4 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-a4core/package.py | Python | lgpl-2.1 | 1,743 | [
"Bioconductor"
] | 614069efbb8f67b42763f42b5cf4ee369b5b30d862fa4bade10fa68202676ca1 |
from __future__ import absolute_import, division, print_function
from typing import List, Union, Callable
import numpy as np
import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow.python import keras
from tensorflow_probability.python.internal import \
distribution_util as dist_util
from tensor... | imito/odin | odin/bay/layers/mixture_layers.py | Python | mit | 26,277 | [
"Gaussian"
] | 8a7b44fa10a1b145f2f6dc0a85114645e760df929db31c0fe33c3a7104f5de1a |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | heke123/chromium-crosswalk | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 25,419 | [
"Galaxy"
] | a4589f462bdb09301a7463e2cbe9c959d04b91075de55afbbd66547667e6eac7 |
"""This module provides an interface class for phonon calculations."""
__all__ = ["PhononCalculator"]
import time
import os
import pickle
from math import pi, sqrt, exp, sin
import numpy as np
import numpy.random as rand
import numpy.linalg as la
import ase.units as units
from ase.io.trajectory import PickleTraject... | qsnake/gpaw | gpaw/dfpt/phononcalculator.py | Python | gpl-3.0 | 18,564 | [
"ASE",
"GPAW"
] | 3a8371d2d3ab3947ffc9643d632681e6376c9352e5b7ed74e5d8fa3a11d9edb3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
DICOM2FEM - organ segmentation and FE model generator
Example:
$ dicom2fem -d sample_data
"""
# TODO:
# recalculate voxelsize when rescaled
# import unittest
from optparse import OptionParser
from scipy.io import loadmat, savemat
from scipy import ndimage
import nump... | mjirik/dicom2fem | dicom2fem/dicom2fem.py | Python | bsd-3-clause | 29,842 | [
"VTK"
] | 0c2f9376cd49338a25ff26f9b89f230101dd9b0b1b37c1fce5bcca8518a34ad6 |
import re
import pytest
import urllib
import datetime
from redwind.models import User
from testutil import FakeResponse, assert_urls_match
def test_empty_db(client):
"""Make sure there are no articles when the database is empty"""
rv = client.get('/')
assert '<article' not in rv.get_data(as_text=True)
d... | Lancey6/redwind | tests/views_test.py | Python | bsd-2-clause | 8,136 | [
"Firefly"
] | a2cc1ed75271631768b0d4955544e919ebdf5c71470ada67edf1b27e67dbc0e8 |
# Copyright (c) 2012-2014 The GPy authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
# Multioutput likelihood structure is similar to the
# corresponding structure in GPstuff. If building complex
# multioutput models on top of this class and need a reference,
# check GPstuff project.... | SheffieldML/GPy | GPy/likelihoods/multioutput_likelihood.py | Python | bsd-3-clause | 10,610 | [
"Gaussian"
] | 7aa06d08051799cfaf290e20fb828b5eba6e4b00822865f478e322cab9343117 |
# Copyright (C) 2012,2013
# 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 t... | fedepad/espressopp | src/storage/Storage.py | Python | gpl-3.0 | 18,150 | [
"ESPResSo"
] | fc3b1b07e43505c4d68f917490d779151f31f14a5dba2f2cae3ee318ccd7f283 |
"""GPAW I/O
Change log for version:
1)
2) GridPoints array added when gpts is used.
3) Different k-points now have different number of plane-waves. Added
PlaneWaveIndices array.
"""
import os
import warnings
try:
from ase.units import AUT # requires rev1839 or later
except ImportError:
from ase.... | robwarm/gpaw-symm | gpaw/io/__init__.py | Python | gpl-3.0 | 30,444 | [
"ASE",
"GPAW",
"NetCDF"
] | 00b930e1d8092a0ecabf2fe964e82b7b80791a805c74d29448eeab32dc1430c8 |
"""
CBMPy: CBTools module
=====================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Publi... | SystemsBioinformatics/cbmpy | cbmpy/CBTools.py | Python | gpl-3.0 | 62,009 | [
"PySCeS"
] | b8db52387564c1756c46c5c805ec9b08f7a14f5378f961036f67275984645ada |
# Copyright (c) 2015, 2016 Timothy Savannah under terms of LGPLv3. You should have received a copy of this with this distribution as "LICENSE"
'''
GlobalEnv - Methods/Classes related to the "global" env,
i.e. the environment used for on-demand imports
'''
# vim: ts=4 sw=4 expandtab
import imp
import sys
imp... | kata198/VirtualEnvOnDemand | VirtualEnvOnDemand/GlobalEnv.py | Python | lgpl-3.0 | 10,443 | [
"Biopython"
] | 991af09762d2df135a712f1f4b585c457c740e726bff394844d3acd6184c1468 |
# coding: utf-8
#
# Copyright 2015 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | flavioamieiro/pypln.backend | tests/test_celery_task.py | Python | gpl-3.0 | 1,543 | [
"NAMD"
] | 9fb37b75dc9509d50346042923c3ea91faad28eee1385979d414d962362194bd |
import math
import string
import sys
import struct
import matplotlib
import matplotlib.pyplot as pyplot
import matplotlib.colors as pycolors
import matplotlib.cm as cm
from matplotlib.ticker import FormatStrFormatter
import numpy as np
import numpy.ma as ma
import numpy.random as nprand
import asciitable
import scipy.n... | gsnyder206/synthetic-image-morph | morphology_analysis/illcan_multiplots.py | Python | gpl-2.0 | 163,083 | [
"Galaxy"
] | 6c02af90f8ce454983f01160d2190d1c4b73510fe06c132d8d58f3f9e44201bd |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Bayesian Blocks for Time Series Analysis
========================================
Dynamic programming algorithm for solving a piecewise-constant model for
various datasets. This is based on the algorithm presented in Scargle
et al 2012 [1]_. This cod... | kelle/astropy | astropy/stats/bayesian_blocks.py | Python | bsd-3-clause | 18,837 | [
"Gaussian"
] | 23a76b575f7af4e094d4ad3c085243b7a7cbf7c5e1b22828e386c1fbdfb9b796 |
#!/usr/bin/env python3
import numpy as np
## these lines are anachronistic and should be fixed at some point
from LoLIM import utilities
utilities.default_raw_data_loc = "/exp_app2/appexp1/lightning_data"
utilities.default_processed_data_loc = "/home/brian/processed_files"
#refractivity = 0.000293*2
#utilities.v_air... | Bhare8972/LOFAR-LIM | LIM_scripts/stationTimings/examples/run_stochasticFitter_translator.py | Python | mit | 4,987 | [
"Brian"
] | d70ee97eccb3148f71c179af176b083b6f740ad543b54d4de10ad1c28430fbb0 |
#! /usr/bin/env python3
from __future__ import print_function
"""Writes lines from the B6/M8 file under the given E-value to output
Usage:
b6_evalue_filter.py --b6 <b6 file> --e_value <max e_value>
--output <output file>
Copyright:
filter_b6_evalue.py filter lines of B6/M8 file by ... | Brazelton-Lab/bio_utils | bio_utils/blast_tools/filter_b6_evalue.py | Python | gpl-3.0 | 3,410 | [
"BLAST"
] | 2f9b8bd2c5bda7336be4b24e9b795b7b176d3d0cc37714d890a404f6f75a0c22 |
#
# The XBUILD tester.
#
# (c) 2012 The XTK Developers <dev@goXTK.com>
#
import json
import os
import platform
import re
import shutil
import sys
import subprocess
import tempfile
import time
import config
from _cdash import CDash
from _colors import Colors
from _jsfilefinder import JSFileFinder
from _licenser import... | rherrick/XNATImageViewer | src/main/scripts/viewer/X/utils/_core/_tester.py | Python | bsd-3-clause | 16,358 | [
"VisIt"
] | b0092dab13ec010ae6230f9f90ff7e94fc3a337be34aae1cee428e7b6e5659c3 |
#!/usr/bin/env python
"""Script to run all the tests each in its own subprocess to ensure
maximal correctness and minimal pain. This does make running the tests
quite slow but the tests will be run correctly -- which is the important
thing.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copy... | liulion/mayavi | mayavi/tests/runtests.py | Python | bsd-3-clause | 6,609 | [
"Mayavi"
] | b67fa115d5cb8a65596a09503876a536adf02e6788e173d2b72a5d9293e3823e |
# -*- coding: utf-8 -*-
# Copyright (C) 2012, Almar Klein, Ant1, Marius van Voorden
#
# This code is subject to the (new) BSD license:
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of s... | callowayproject/Transmogrify | transmogrify/images2gif.py | Python | apache-2.0 | 36,344 | [
"NEURON"
] | e1b69249f4803248e22a36ff806062e45b0425e829e8167997fadd6940753d04 |
# Copyright 2020 The FedLearner 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... | bytedance/fedlearner | fedlearner/data_join/example_id_visitor.py | Python | apache-2.0 | 12,785 | [
"VisIt"
] | 8e929e03ef30f235d5b8e1bc64e6b80a713327b814d124737566835e3dbf03eb |
# Written by Lauri Lehtovaara, 2007
"""This module implements classes for time-dependent variables and
operators."""
import numpy as np
from gpaw.external_potential import ExternalPotential
from gpaw.utilities import pack2, unpack
from gpaw.mpi import run
from gpaw.fd_operators import Laplace, Gradient
from gpaw.ove... | robwarm/gpaw-symm | gpaw/tddft/tdopers.py | Python | gpl-3.0 | 27,530 | [
"GPAW"
] | 8f86c588eab1139aa96857757b93c7fc2877e188edbcd7928cd3c56f25daf3cd |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
# TODO: Add support for a C++11 enabled installation that filters out the
# TODO: "C++11-Disabled" fl... | iulian787/spack | var/spack/repos/builtin/packages/exodusii/package.py | Python | lgpl-2.1 | 2,317 | [
"NetCDF"
] | 70ad38ec0d70c566201923062ca459200e62702ca9d6897169b9f04cb58fb931 |
"""Tests for query.py."""
import datetime
import os
import unittest
from .google_imports import datastore_errors
from .google_imports import namespace_manager
from .google_imports import users
from .google_test_imports import datastore_stub_util
from . import model
from . import query
from . import tasklets
from . i... | bslatkin/8-bits | appengine-ndb/ndb/query_test.py | Python | apache-2.0 | 61,766 | [
"MOE"
] | 6c959b525747fad9e905a34258a2763bb5f59f1860410c521adde04ea2d85815 |
#! /usr/bin/env python
# Copyright (c) 2012, Julian Straub <jstraub@csail.mit.edu>
# Licensed under the MIT license. See LICENSE.txt or
# http://www.opensource.org/licenses/mit-license.php
import numpy as np
import matplotlib.pyplot as plt
import time
import pickle
from robo import *
from robo_SAM import *
from rob... | jstraub/easyRobo | simulate.py | Python | mit | 3,257 | [
"Gaussian"
] | 0d1a207f4652c21c8458c8686fbc6296c51f91a1264e48ee4878dfa2f0f8ba5b |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | elkingtonmcb/nupic | src/swarming/permutationhelpers.py | Python | agpl-3.0 | 26,044 | [
"Gaussian"
] | 1da45e4202d04644cbb0fc6d058d422d109ca317688db1cc363ebe0f214b761c |
# -*- coding: utf-8 -*-
from collections.abc import Iterable
import numpy as np
from scipy._lib._util import _asarray_validated
from scipy.linalg import block_diag, LinAlgError
from .lapack import _compute_lwork, get_lapack_funcs
__all__ = ['cossin']
def cossin(X, p=None, q=None, separate=False,
swap_sig... | WarrenWeckesser/scipy | scipy/linalg/_decomp_cossin.py | Python | bsd-3-clause | 9,111 | [
"Brian"
] | 54a3249faa2f103b14a69cfe3d5f7a5c3f932c3928ae5b50b7c3e7611fcb100f |
# Copyright (c) 2012 OpenStack Foundation.
#
# 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 agreed to... | sebrandon1/neutron | neutron/tests/unit/test_policy.py | Python | apache-2.0 | 28,623 | [
"BLAST"
] | 9eb9aaf4641304a67aa0e25b7e959d9143199d02fe74274b5fbbc73056eb3b80 |
# 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... | Xeralux/tensorflow | tensorflow/contrib/py2tf/pyct/qual_names.py | Python | apache-2.0 | 6,448 | [
"VisIt"
] | a0198fcfa9023152dddd92a6fb7cac4df255fcee520f0a08e3e7893e000fe433 |
# $HeadURL$
__RCSID__ = "$Id$"
import types
import copy
import os
import re
try:
import zipfile
gZipEnabled = True
except ImportError:
gZipEnabled = False
try:
from DIRAC.Core.Utilities import List, ThreadSafe
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
gCFGSynchro = ThreadSa... | vmendez/DIRAC | Core/Utilities/CFG.py | Python | gpl-3.0 | 32,241 | [
"DIRAC"
] | 65f422c78b17eb4001980fc7335f52de33c578a58c03f1991fbca3b256c8539c |
#! /usr/bin/env python
"""
Script to pre-average data using a sliding Gaussian kernel in frequency
"""
import argparse
from argparse import RawTextHelpFormatter
import numpy as np
import sys
import os
from scipy.ndimage.filters import gaussian_filter1d as gfilter
from scipy.special import erf
import casacore.tables as ... | darafferty/factor | factor/scripts/pre_average_freq.py | Python | gpl-2.0 | 6,132 | [
"Gaussian"
] | dc855dcd46e8fb0581022f7ef9553d68d177a2aa49bddeed5efb92a218058dc0 |
#!/usr/bin/python
from cgi import escape
import cherrypy
class Page:
def __init__(self,title):
self.title = title
def header(self):
yield '''<html>
<head><title>%s</title><head>
<body><h2>%s</h2>''' % (self.title, self.title)
yield '<a href="/">home</a>'
def footer(self):
yield '<div class="footer">... | MaxTyutyunnikov/lino | obsolete/src/sandbox/cherrypy/2/hello2.py | Python | gpl-3.0 | 1,108 | [
"exciting"
] | 4ab59d1a184131e7d2a676aac4219745d0c7983706f79f60f92f25f23e5c4bd2 |
# 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/_agf2.py | Python | apache-2.0 | 18,199 | [
"PySCF"
] | 9a2e07c9fdb27102977f9f18482d9904963c2b6297c0b15a555be8b8448d5687 |
from numpy import *
from pylab import *
import scipy.optimize.lbfgsb as lbfgsb
import numpy.linalg
from scipy.fftpack.realtransforms import dct, idct
import numpy as np
import numpy.ma as ma
def smoothn(
y,
nS0=10,
axis=None,
smoothOrder=2.0,
sd=None,
verbose=False,
s0=None,
z0=None,
... | alexlib/openpiv-python | openpiv/smoothn.py | Python | gpl-3.0 | 26,473 | [
"Gaussian",
"VisIt"
] | f1432e643d23978039f026654187794dba201ac599de4226d544baf544bc15c0 |
import _gpaw
from gpaw.xc.kernel import XCKernel
from gpaw.xc.libxc_functionals import libxc_functionals
from gpaw import debug
short_names = {
'LDA': 'LDA_X+LDA_C_PW',
'PW91': 'GGA_X_PW91+GGA_C_PW91',
'PBE': 'GGA_X_PBE+GGA_C_PBE',
'revPBE': 'GGA_X_PBE_R+GGA_C_PBE',
'RPBE': 'GGA_X_RP... | qsnake/gpaw | gpaw/xc/libxc.py | Python | gpl-3.0 | 3,223 | [
"GPAW"
] | 745f1df0f1b95db8a0e6c5ea18b4bbcd227adec3779ed7b151986ea3c3a054b7 |
import ANNarchy.core.Global as Global
import ANNarchy.parser.report.LatexParser as LatexParser
from ANNarchy.core.Neuron import Neuron
from ANNarchy.extensions.bold.BoldModel import BoldModel
from ANNarchy.core.Synapse import Synapse
import numpy as np
import os
##################################
### Templates
#####... | vitay/ANNarchy | ANNarchy/parser/report/LatexReport.py | Python | gpl-2.0 | 22,678 | [
"NEURON"
] | 70e1f661f43533a83c87545792da7d082be37f19bb4282a75d5d97e3a43f6e37 |
#### import the simple module from the paraview
import os
from paraview.simple import *
from ParaviewLoad import ShowData
Cmap_name = 'u'
Cmap_title = 'The stuff'
Cmap = [-100, 100]
Thr_Neg = [-100, -50]
Thr_Pos = [25, 40]
Bkg_Op = 0.1
VTKnames=['../../resources/vtk/nn1.vtk','../../resources/vtk/nn2.vtk','../../res... | EIT-team/Reconstruction | src/python/load_test_animate.py | Python | gpl-3.0 | 778 | [
"ParaView",
"VTK"
] | d3491024457782ca873d3fca2c0b5e04e42249fcbe65cdd5cd421d70717fdbec |
"""
revlog.py - storage back-end for mercurial
This provides efficient delta storage with O(1) retrieve and append
and O(changes) merge between branches
Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
This software may be used and distributed according to the terms
of the GNU General Public License, incorporated ... | pombredanne/SmartNotes | mercurial_gae/revlog.py | Python | gpl-3.0 | 47,247 | [
"VisIt"
] | e3af0543d5adca533924627cf8eb1c0e4f2b30df463803cc9d000693b8e51731 |
# deepaxoaxonic.py ---
#
# Filename: deepaxoaxonic.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Fri Oct 16 11:11:39 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 17:18:59 2011 (+0530)
# By: Subhasis Ray
# Update #: 58
# URL:
# Keywords:
# Compatibility:
#
#
# Commentar... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/deepaxoaxonic.py | Python | lgpl-2.1 | 5,126 | [
"MOOSE",
"NEURON"
] | ca9b6d000f24544e3efb8d74315f1ab2cb461c8059612a78783865eed91e4d84 |
from src.constant.Constant import Constant
class Number(Constant):
value = -1
def getValue(self):
return self.value
def accept(self,visitor):
return visitor.visit(self)
| charleshamel73/diceroller | src/constant/Number.py | Python | mit | 201 | [
"VisIt"
] | 34cb06fc6b329be0219f32803075f64bb10c6c1370dd7e88b69d7bae6401cff2 |
import time, os, gc, sys, copy
import cPickle as pickle
import numpy as np
from numpy import pi
import pylab as plt
import VyPy
from VyPy.regression import gpr
from VyPy.tools import atleast_2d
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import cm
import matplotlib.pyplot as plt
from ... | aerialhedgehog/VyPy | tests/_experimental/regression_tests_01.py | Python | bsd-3-clause | 16,950 | [
"Gaussian"
] | fac4db99b659efd3e2b7578b5c19a3bd556580e48ee7cfc867ed3fd3526607ce |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Views tests for the OSF."""
from __future__ import absolute_import
import datetime as dt
from rest_framework import status as http_status
import json
import time
import unittest
from future.moves.urllib.parse import quote
from flask import request
import mock
import p... | brianjgeiger/osf.io | tests/test_views.py | Python | apache-2.0 | 216,976 | [
"Brian",
"VisIt"
] | faf3b70f5c264c5442234b9c46dfeb4136da9212917c01383b4a099c89c7a48e |
# Copyright (c) 2015 Universidade Federal Fluminense (UFF)
# Copyright (c) 2015 Polytechnic Institute of New York University.
# This file is part of noWorkflow.
# Please, consult the license terms in the LICENSE file.
from __future__ import (absolute_import, print_function,
division, unicode_li... | paopao74cn/noworkflow | capture/noworkflow/now/graphs/trial_graph.py | Python | mit | 12,765 | [
"VisIt"
] | d2cec6a06250705864db26ee8b39976b05d3ab5dc966b716f1d4db47b4432141 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose | moose-examples/snippets/scaleVolumes.py | Python | gpl-3.0 | 6,376 | [
"MOOSE"
] | 717a81cdc8937ef4d349c677319a8642bb1df6364abeeb272fef695f967e24e3 |
from setuptools import setup, find_packages
import sys, os
version = '0.0'
setup(name='maml',
version=version,
description="Mako Abstract Markup Language",
long_description="""\
HAML-alike for Mako""",
classifiers=[], # Get strings from http://pypi.python.org/pypi?%3Aaction=list_classifiers
... | brianhawthorne/maml | setup.py | Python | gpl-3.0 | 747 | [
"Brian"
] | 77155329a28f191cb51a1531844f4890175aacfac54f0dd666a290dba95e4717 |
#!/usr/bin/python2.4
# Copyright (c) 2006-2008 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Fast and efficient parser for XTB files.
'''
import sys
import xml.sax
import xml.sax.handler
class XtbContentHandler(xm... | meego-tablet-ux/meego-app-browser | tools/grit/grit/xtb_reader.py | Python | bsd-3-clause | 4,505 | [
"xTB"
] | d109ccc70d787e23648c256679ff53b13f77c382ebf8f63656a27640d1822564 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2008-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | Clyde-fare/cclib | src/cclib/parser/psiparser.py | Python | lgpl-2.1 | 39,708 | [
"NWChem",
"Psi4",
"cclib"
] | 1c8637bd96bb4d6ee9e0027296f2c995fc1741d5b59563f2887b6fbf1a2c4dd1 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/xmlf90/package.py | Python | lgpl-2.1 | 2,136 | [
"SIESTA"
] | c8a41bb2c9dfdc7fe82f69edc2bd24747a14a3cc1a19583325cc51721d4eec4c |
""" RemoveComprehension turns list comprehension into function calls. """
from pythran import metadata
from pythran.analyses import ImportedIds
from pythran.passmanager import Transformation
import ast
class RemoveComprehension(Transformation):
"""
Turns all list comprehension from a node into new function ... | artas360/pythran | pythran/transformations/remove_comprehension.py | Python | bsd-3-clause | 5,506 | [
"VisIt"
] | a840bf6a4a05ced68b0d53a637000fe80b150bbbc1d73a2602b04bfca11ae729 |
#!/usr/bin/env python
"""
Read the table of chimeric fragments and find regions that are over-represented
in their interactions. This script should remove non-specific chimeras using
Fisher excat's test by counting the number of fragments that support a pair of
genomic reginos and comparing to the expected number of i... | asafpr/pro_clash | bin/pro_clash_significant_regions.py | Python | mit | 9,238 | [
"Amber"
] | ef56b5748149749ac473e47a80b0e2fb6dba1a706691da5086565421310bde7a |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/input_tab/TimeStepEstimate/test_TimeStepEstimate.py | Python | lgpl-2.1 | 1,677 | [
"MOOSE"
] | 1184a14b91377f77fe6a5a20271fa800c0f73c663f0debf43331010e1cb85742 |
import pytest
from functools import partial
import numpy as np
import psi4
from psi4.driver import qcdb
pytestmark = pytest.mark.quick
_arrs = {
'a1234_14': np.arange(4),
'blip14': np.arange(4) + [0., 0.02, 0.005, 0.02],
'a1234_22': np.arange(4).reshape((2, 2)),
'blip22': (np.arange(4) + [0., 0.02,... | CDSherrill/psi4 | tests/pytests/test_testing.py | Python | lgpl-3.0 | 11,541 | [
"Psi4"
] | 9d091dcb7a4d67f0fa9920871d73c87009c240b246ada33ff99ce6b5d13739d7 |
#### PATTERN | WEB #################################################################################
# Copyright (c) 2010 University of Antwerp, Belgium
# Author: Tom De Smedt <tom@organisms.be>
# License: BSD (see LICENSE.txt for details).
# http://www.clips.ua.ac.be/pages/pattern
####################################... | piskvorky/pattern | pattern/web/__init__.py | Python | bsd-3-clause | 95,460 | [
"VisIt"
] | 4bdf3b0ef49eee2bcbf9924b73c3d19e45e3f6806612e9c9e627db9f7420a3f2 |
def straight_line_log_likelihood(x, y, sigmay, m, b):
'''
Returns the log-likelihood of drawing data values *y* at
known values *x* given Gaussian measurement noise with standard
deviation with known *sigmay*, where the "true" y values are
*y_t = m * x + b*
x: list of x coordinates
y: list ... | dbouquin/AstroHackWeek2015 | inference/straightline_log_likelihood.py | Python | gpl-2.0 | 588 | [
"Gaussian"
] | 9739b56e3a939b08f830382c0ca3bbabedb734e68df6c3df87ece775e3993ab7 |
import wx
import wx.grid
import wx.lib.scrolledpanel
import os
import os.path
import time
import platform
import multiprocessing
import Bio.PDB
import webbrowser
from threading import Thread
from tools import *
class ConstraintPanel(wx.lib.scrolledpanel.ScrolledPanel):
'''A panel allowing for the selection of cons... | schenc3/InteractiveROSETTA | InteractiveROSETTA/scripts/constraints.py | Python | gpl-2.0 | 32,493 | [
"PyMOL"
] | bbc6e51597aa6dba2368eedd4759f605b1f1ebd21f7e4236764d4289cb6f05cc |
import sys
import traceback
from ase.asec.asec import run
def main(calculator=None):
try:
run(calculator=calculator)
except (KeyboardInterrupt, SystemExit):
raise
except Exception:
traceback.print_exc()
sys.stderr.write("""
An exception occurred! Please report the issue t... | alexei-matveev/ase-local | ase/asec/__init__.py | Python | gpl-2.0 | 493 | [
"ASE"
] | be565b102ed2ba64616a21e00095dc1eac47bdeed461c646e0a8ebbcf5d1287e |
from __future__ import division
from builtins import range
from past.utils import old_div
import scipy.ndimage.filters as ndimf
import numpy as np
import scipy.interpolate as scint
"""
Author: Jack Griffiths 0ct 2019
Function to automatically choose the level of gaussian smoothing to apply to a signal as to supress ... | nanophotonics/nplab | nplab/analysis/Auto_Gaussian_Smooth.py | Python | gpl-3.0 | 2,529 | [
"Gaussian"
] | af31ae9a57aa987911e2ed60eb380db6529537385f32a539af881467e8856dc8 |
"""
Acceptance tests for Content Libraries in Studio
"""
from ddt import ddt, data
from nose.plugins.attrib import attr
from flaky import flaky
from .base_studio_test import StudioLibraryTest
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.utils ... | shashank971/edx-platform | common/test/acceptance/tests/studio/test_studio_library.py | Python | agpl-3.0 | 27,320 | [
"VisIt"
] | 979a23a71d5b18ef34b898a5b09207a27f06f72301e521c1425e56d15bdbfbc0 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Nebula, Inc.
#
# 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
#
# ... | andrewsmedina/horizon | horizon/horizon/base.py | Python | apache-2.0 | 24,197 | [
"VisIt"
] | 4597fbf6534b19508ed25dfa65684be853aa266ec67dbaf4d793015d2492e6ab |
from ase import Atoms, Atom
from ase.data.molecules import molecule
from ase.parallel import barrier
from ase.units import Hartree, mol, kcal
from gpaw import GPAW, setup_paths
from gpaw.mixer import Mixer, MixerSum
from gpaw.occupations import FermiDirac
from gpaw.atom.generator import Generator
from gpaw.atom.configu... | qsnake/gpaw | gpaw/test/AA_exx_enthalpy.py | Python | gpl-3.0 | 7,519 | [
"ASE",
"GPAW"
] | 18611647fb79ba68aae02e4b9f3073e4596fc8d612185b8829d1521eb1c52d14 |
"""The decision module handles the three planning levels
Currently, only pre-specified planning is implemented.
The choices made in the three planning levels influence the set of interventions
and assets available within a model run.
The interventions available in a model run are stored in a dict keyed by name.
"""... | nismod/smif | src/smif/decision/decision.py | Python | mit | 22,745 | [
"CRYSTAL"
] | 4be5171236d6dab1f4f4e000a930ad3cdca0eb5fb4907c63ac64725f93ddc6a3 |
#!/usr/bin/python
# vim: tabstop=9 expandtab shiftwidth=3 softtabstop=3
# Downsample MTs
# Chang Xu. 07DEC2015
import os
import sys
import datetime
import subprocess
import shutil
import time
import math
import pysam
from collections import defaultdict
import argparse
import random
bamHeader = "/qgen/home/xuc/Variant... | xuchang116/smCounter | ds.mt.py | Python | mit | 2,923 | [
"pysam"
] | f064d995723c17827db2cc3acd3cc3804354eb526edfb93fd58cbaa082463bf8 |
#
# Copyright (C) 2001 greg Landrum
#
""" unit testing code for variable quantization
"""
import unittest
from rdkit import RDConfig
from rdkit.ML.Data import Quantize
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
pass
def testOneSplit1(self):
"""... | rdkit/rdkit-orig | rdkit/ML/Data/UnitTestQuantize.py | Python | bsd-3-clause | 12,296 | [
"RDKit"
] | 6f465de6e4dac9084313d63d8ba33d9bbc094b85a30de992e0a35f11f0da8aa7 |
# Copyright iris-grib contributors
#
# This file is part of iris-grib and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Integration tests to confirm data is loaded correctly.
"""
# import iris_grib.tests first so that some things c... | SciTools/iris-grib | iris_grib/tests/integration/load_convert/test_data_section.py | Python | lgpl-3.0 | 2,335 | [
"Gaussian"
] | d70cf2f1eced80093fa3799e2fc9c465bd4bc9834af478401d9cd537b5fdf87d |
"""
Tests for binding pocket detection.
"""
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import sys
import logging
import unittest
import os
import numpy as np
import deepchem as dc
fr... | ktaneishi/deepchem | deepchem/dock/tests/test_binding_pocket.py | Python | mit | 7,585 | [
"MDTraj"
] | df5f80060eb3e7a579c4c9bb592c865dbaa79603b850905b99cdf64ffb1b2eb4 |
#!/usr/bin/env python
"""This is an example of yapyNFFT.
yapyNFFT is a simple python wrapper of NFFT (http://www.nfft.org).
I think the license has to be GPL to distribute because NFFT employs
GPL. But if it is not the case, I want to change the license to BSD-3.
nfft_plan is stored in yapyNFFT modlue as a static v... | atztogo/yapyNFFT | example/simple_example.py | Python | gpl-2.0 | 4,162 | [
"Gaussian"
] | 7fcc3f0c68489d45392b56848853813b3b9baa1ae8d9af9c3adcc4c09b983256 |
""" Module for core algorithms related to tracing slits/orders
These should primarily be called by the TraceSlits class
"""
from __future__ import (print_function, absolute_import, division, unicode_literals)
import inspect
import copy
from collections import Counter
import numpy as np
from scipy import ndimage
from... | PYPIT/PYPIT | pypeit/core/trace_slits.py | Python | gpl-3.0 | 123,065 | [
"Gaussian"
] | 845cc89b034d7e99a310cf673c4e2132e4713e6ae293918fe8d9ffa15b9dd5bd |
"""Plot the xy-velocity along the y-axis for all cfd datasets and the piv
image."""
import os
import vtk
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.axes_grid1.inset_locator import zoomed_inset_axes, mark_inset
from matplotlib.ticker import MaxNLocator
from utils import iolib
from ut... | ajgeers/visc11 | code/lineplot_yaxis.py | Python | bsd-2-clause | 3,912 | [
"VTK"
] | 190ac7614f2928b5b2c2f039aa931df41d50b85ba7fdea4614878aef3a34f79f |
#! /usr/bin/env python
###=============================================================
### Multifit 2
### Nicola Ferralis <feranick@hotmail.com>
### The entire code is covered by GNU Public License (GPL) v.3
###=============================================================
### Uncomment this if for headless servers.
... | feranick/MultiFit | Archive/multifit_2/multifit.py | Python | gpl-3.0 | 25,274 | [
"Gaussian"
] | 38309acb3177bbad3cee26aee6a34109ccfc2be29f9fae000e3ddaa6512aa862 |
import random
import synapse.common as s_common
import synapse.neuron as s_neuron
import synapse.lib.cell as s_cell
import synapse.lib.crypto.vault as s_vault
import synapse.tools.neuron as s_tools_neuron
from synapse.tests.common import *
logger = logging.getLogger(__name__)
class TstCell(s_cell.Cell):
def ... | vivisect/synapse | synapse/tests/test_neuron.py | Python | apache-2.0 | 15,951 | [
"NEURON"
] | d0c68c98a6e4ec4ecf8701185eb9ab72291f8bdd0528d1d42a9d47d5b4c0fb92 |
# coding: utf-8
from flask import url_for
from flask.ext.admin import Admin
from flask.ext.admin.base import MenuLink as BaseMenuLink
from flask import Blueprint, abort
from david.ext.babel import lazy_gettext
from config import SITE_ROOT
from .model import *
translations = {}
def _(string):
if string in trans... | ktmud/david | david/ext/admin/__init__.py | Python | mit | 859 | [
"VisIt"
] | 8d7ebdbdd43f2b258c1ead0dceaff099303bd115be65c8f4d77fcf0ba1bad7b4 |
from setuptools import setup, find_packages
import codecs
import os
here = os.path.abspath(os.path.dirname(__file__))
version_file = open(os.path.join(here, 'pyrepo', 'VERSION'))
version = version_file.read().strip()
# Get the long description from the relevant file
with codecs.open('DESCRIPTION.rst', encoding='utf-... | dghubble/pyrepo | setup.py | Python | mit | 2,048 | [
"Dalton"
] | d80905ab278c64f19d0cd7ba742e14ca58d9afa95a8e02c8bcb40fe501a7587a |
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