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import numpy as np
def MM(i,j,e,A,B,C,a,b):
''' Recursive definition of Hermite Gaussian coefficients.
Returns a float.
a: orbital exponent on Gaussian 'a' (e.g. alpha in the text)
b: orbital exponent on Gaussian 'b' (e.g. beta in the text)
i,j: orbital angular momentum number on Gau... | fhqgfss/MoHa | moha/system/integral/multipole_moment.py | Python | mit | 2,994 | [
"Gaussian"
] | 96872ba3c820fd8399288ccd1b8730ec90deb501b396620145a638eaa3d2792c |
#! /usr/bin/env python
import os,sys
gaff=['br', 'c', 'c1', 'c2', 'c3', 'ca', 'cc', 'cd', 'ce', 'cf', 'cg', 'cl', 'cp', 'cx', 'cy', 'f', 'h1', 'h2', 'h3', 'h4', 'h5', 'ha', 'hc', 'hn', 'ho', 'hs', 'i', 'n', 'n1', 'n2', 'n3', 'na', 'nb', 'nc', 'nd', 'ne', 'nf', 'nh', 'no', 'o', 'oh', 'os', 'p5', 's', 's4', 's6', 'sh', '... | platinhom/DailyTools | scripts/GetTypeAreaPQRTA.py | Python | gpl-2.0 | 2,131 | [
"Amber"
] | 05797e20fb00ce30afd4747112d312bcddace8dc3d8731f9116c150d08583d76 |
#!/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... | harterj/moose | python/MooseDocs/test/common/test_has_tokens.py | Python | lgpl-2.1 | 724 | [
"MOOSE"
] | 8517390942d78ba993f911d643ee145561b7c01816f2fd586b0985ee70d0fe0d |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/alerts/lib/__init__.py | Python | gpl-2.0 | 2,181 | [
"Brian"
] | 48f75020115fbee183ea9efdceadbc7c89a0b8b52cb197aa3c685555b00487f9 |
from pycalphad import Database, Model, variables as v
from pycalphad.tests.datasets import ROSE_TDB
from pycalphad import equilibrium
import numpy as np
my_phases_rose = ['TEST']
comps = ['H', 'HE', 'LI', 'BE', 'B', 'C', 'N', 'O', 'F']
comps = sorted(comps)
conds = dict({v.T: 1000, v.P: 101325})
for comp in comps[1:]:... | richardotis/pycalphad-sandbox | advconds.py | Python | mit | 498 | [
"pycalphad"
] | 73306102dce9a73e7a2efc7bf2d586ff59d776d69652222f3f62afb92a0e0bc0 |
# This file is part of askbot_fedmsg.
# Copyright (C) 2013 Red Hat, Inc.
#
# fedmsg is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later ver... | fedora-infra/askbot-fedmsg | askbot_fedmsg.py | Python | lgpl-2.1 | 5,465 | [
"VisIt"
] | c14e7ad1163e2c09055403db2690246b61423e71ab263a7cd3c59f8228340046 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tntnatbry/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 37,291 | [
"VisIt"
] | 61b7f53f16f660a2ec01acc15db2b9c97092b50026e8b4f3ea8a0026e4903601 |
"""
Examine the distribution of diffraction spot intensities.
This module defines a class IntensityDist, with several methods for exploring
the distribution of measured spot intensities in an X-ray diffraction
experiment. The user may wish to use this information to inform decisions
regarding the error model employed... | dials/dials | util/intensity_explorer.py | Python | bsd-3-clause | 14,961 | [
"CRYSTAL"
] | dbe2661802e2b7fea961a7493639af91641d3a0ba9fbbdf2c8badb2ab5f0aff3 |
# Copyright (c) 2020 PaddlePaddle 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 app... | luotao1/Paddle | python/paddle/fluid/dygraph/dygraph_to_static/call_transformer.py | Python | apache-2.0 | 2,985 | [
"VisIt"
] | bb9ed08d407470379b7fca75efb809bb0dcbb229af85e1363a6a7446ee15e67b |
# vclamptest.py ---
#
# Filename: vclamptest.py
# Description:
# Author:
# Maintainer:
# Created: Wed Feb 6 16:25:52 2013 (+0530)
# Version:
# Last-Updated: Sun Jun 25 14:47:22 2017 (-0400)
# By: subha
# Update #: 149
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Set up a voltag... | BhallaLab/moose-examples | traub_2005/py/vclamptest.py | Python | gpl-2.0 | 4,772 | [
"MOOSE",
"NEURON"
] | 38a29fdd1ef4631789ee009a54d9ded0749d8573903ca80f411f4faf29f56200 |
from random import random
import math
def sigmoid(x):
return 1/(1 + math.exp(-x))
def th(x):
return (math.exp(x) - math.exp(-x)) / (math.exp(x) + math.exp(-x))
class _AbstractNeuron():
def __init__(self):
self.out = 0
self.w = []
self.w0 = 0
self.dw = []
self.dw0... | zshimanchik/unconditioned-reflexes | NeuralNetwork/Neuron.py | Python | mit | 1,726 | [
"NEURON"
] | ce2aa0f23bf362950e70408883c9dfe64bb9285a0040378e3af4216a96a69f4f |
import numpy as np
import numpy.linalg as nl
import numpy.random as nrnd
def log_sum_exp(X):
"""
Computes log sum_i exp(X_i).
Useful if you want to solve log \int f(x)p(x) dx
where you have samples from p(x) and can compute log f(x)
"""
# extract minimum
X0 = np.min(X)
X_without_X0 = np... | karlnapf/kernel_exp_family | kernel_exp_family/tools/numerics.py | Python | bsd-3-clause | 2,797 | [
"Gaussian"
] | 6a0c2bc0e5c958c2526e0d07b7d3051abc747c7cf610fadccb03628f79ceef03 |
import os
import time
from simtk.openmm import app
import simtk.openmm as mm
from simtk import unit as u
from fah_parameters import *
def write_file(filename, contents):
with open(filename, 'w') as outfile:
outfile.write(contents)
rundir = "./RUNS_NVT/RUN0/"
nclones = 500
system_filename = os.path.join(r... | kyleabeauchamp/fah-projects | code/packaging_nvt.py | Python | gpl-2.0 | 1,730 | [
"OpenMM"
] | f731ac7f5d918ba78c4cc7620f9b4b0e06cc94d5f36823bde2ed619c43c7a7c0 |
#!/usr/bin/env python
import commands, sys
# Get path of the toolbox
status, path_sct = commands.getstatusoutput('echo $SCT_DIR')
# Append path that contains scripts, to be able to load modules
sys.path.append(path_sct + '/scripts')
from msct_parser import Parser
import sct_utils as sct
# DEFAULT PARAMETERS
class... | 3324fr/spinalcordtoolbox | dev/tamag/old/sct_function_preprocessing.py | Python | mit | 5,437 | [
"Gaussian"
] | e2c109fe87c9c1c350d7dca0304a547151b34be04db55f11f2312e025fedbcd8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# pyqt4topyqt5.py
# Nov. 12 2013
# Author: Vincent Vande Vyvre <vincent.vandevyvre@swing.be>
# Copyright: 2013 Vincent Vande Vyvre
# Licence: LGPL3
import os
import glob
import re
import shutil
import argparse
import sys
import tokenize
import subprocess
import stat
from... | rferrazz/pyqt4topyqt5 | pyqt4topyqt5/__init__.py | Python | lgpl-3.0 | 97,910 | [
"VisIt"
] | be0b112871bd5bda97ae95a49545305cacc65a6aae38685a06e70543dcb46a50 |
import re
import os, sys
import numpy as np
import pandas as pd
import networkx as nx
from networkx.drawing.nx_agraph import graphviz_layout
def add_graphics_theme_to_nx_graph(
nx_graph,
edge_color=None,
node_size_factor=50,
edge_size_factor=500):
"""adjust nodes and edges
"... | vervacity/ggr-project | scripts/analyze.mpra_summ_w_tfs.py | Python | mit | 6,736 | [
"Cytoscape"
] | b09f9c881d27bab9206755adae4abcf052fbeb5e28b3c336485fcafa7bf109b2 |
"""
Core visualization operations based on Mayavi.
Actual implementation of _Renderer and _Projection classes.
"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric... | olafhauk/mne-python | mne/viz/backends/_pysurfer_mayavi.py | Python | bsd-3-clause | 22,459 | [
"Mayavi",
"VTK"
] | 1d146fd066c4460663e4fe3eef6eac957731d453d7f6bd81ced16ed386af71b0 |
########################################################################
# $HeadURL $
# File: CleanReqDBAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/17 08:31:26
########################################################################
""" :mod: CleanReqDBAgent
=====================
.. modul... | calancha/DIRAC | RequestManagementSystem/Agent/CleanReqDBAgent.py | Python | gpl-3.0 | 5,696 | [
"DIRAC"
] | eece14a918044950a980e15ff56c9d43f39fdf0f504dfbbae141f361ea042504 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest
import os
from pymatgen.io.feff.sets import FeffInputSet
from pymatgen.io.feff import FeffPot
from pymatgen.io.cif import CifParser
test_dir = os.path.... | sonium0/pymatgen | pymatgen/io/tests/test_feffio_set.py | Python | mit | 2,663 | [
"FEFF",
"pymatgen"
] | 0fb4b9a4287ed6a4d28ecb992b715108dcd5a83eecdcab724d06046f6e07b9d0 |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/solvent/test/test_ddcosmo_grad.py | Python | apache-2.0 | 41,443 | [
"PySCF"
] | 594204d0dfe521ee54336beb9417bf26dc6b1e0cb44ed9f7ae6b418f3b99d018 |
''' Significant lifting from https://jmetzen.github.io/2015-11-27/vae.html '''
import time
import numpy as np
import tensorflow as tf
from tensorflow.python.ops import rnn
import random
import matplotlib.pyplot as plt
import re, string
from sklearn.feature_extraction.text import CountVectorizer
from collections impo... | dricciardelli/vae2vec | vae_def_oh.py | Python | mit | 37,009 | [
"Gaussian"
] | 5d46f9d699bb1958792ea1d08796c2c3adec0015af4ceaab9400c3bea868f94a |
"""
Modules used in building workflows
"""
import logging
import re
from galaxy import eggs
eggs.require( "elementtree" )
from elementtree.ElementTree import Element
import galaxy.tools
from galaxy import exceptions
from galaxy import model
from galaxy.dataset_collections import matching
from galaxy.web.framework i... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/workflow/modules.py | Python | gpl-3.0 | 34,906 | [
"Galaxy"
] | 371cb2cc6c04d92c46a6b6bae7d667bf622ba3eea0772141b3d0ceb9390ae3d8 |
# -*- coding: utf-8 -*-
from behave import given, then, when
import selenium.webdriver.support.ui as ui
@given("we have an existing user")
def given_existing_user(context):
context.test_user = {
'fullname': 'Alyssa P Hacker',
'email': 'alyssa@hacker.com',
'username': 'alyssa',
'pas... | hasgeek/lastuser | features/steps/login.py | Python | bsd-2-clause | 1,508 | [
"VisIt"
] | f2a672ac923452e40420c7aa627674cc592d91b001319adac16c47fbd06200c0 |
# GWR Bandwidth selection class
#Thinking about removing the search method and just having optimization begin in
#class __init__
#x_glob and offset parameters dont yet do anything; former is for semiparametric
#GWR and later is for offset variable for Poisson model
__author__ = "Taylor Oshan Tayoshan@gmail.com"
fro... | CartoDB/crankshaft | release/python/0.8.2/crankshaft/crankshaft/regression/gwr/base/sel_bw.py | Python | bsd-3-clause | 11,262 | [
"Gaussian"
] | de777aecd7343677a4479d54a116bb6a1575ef6116fd374d7edf4d77f8ae9bf9 |
# Copyright (C) 2010 CAMd
# Please see the accompanying LICENSE file for further information.
"""This module provides all the classes and functions associated with the
evaluation of exact exchange with k-point sampling."""
from math import pi, sqrt
import sys
import numpy as np
from ase import Atoms
from ase.units i... | robwarm/gpaw-symm | gpaw/xc/hybridq.py | Python | gpl-3.0 | 16,684 | [
"ASE",
"GPAW"
] | fb9f35d1e9824d73ef566fb77a876378e9457ae6480d9d26fb7bd30f1e1ea750 |
#!/usr/bin/env python
from setuptools import setup, find_packages
from codecs import open
from os import path
# Version
MAJOR="0"
MINOR="5"
MICRO="0"
VERSION= MAJOR + "." + MINOR + "." + MICRO
here = path.abspath(path.dirname(__file__))
with open(path.join(here,'README.md')) as f:
long_description = f.read()
# ... | mattcieslak/DSI2 | setupApp.py | Python | gpl-3.0 | 4,592 | [
"VTK"
] | 1410f89fea75968b7f850530a241054415e907bf0a21cb70ee5feb9d63ddd05b |
#!/usr/bin/python3
import sys
def visited(node, path):
return node in path
class CycleFind(object):
def __init__(self, graph, source, **kwargs):
self.graph = graph
self.source = source
self.cycles = []
self.edges, self.weights = self.getEdges(graph)
self.cyclelimit = k... | joequant/cycle-detector | cyclefind.py | Python | bsd-2-clause | 3,465 | [
"VisIt"
] | b4ba01c15ec3fa6c25215d78fd6318dd9c0f1961f13a8d45c6a6789fc5074f9f |
# -*- coding: utf-8 -*-
"""Functions that expose information about templates that might be
interesting for introspection.
"""
from . import nodes
from ._compat import iteritems
from ._compat import string_types
from .compiler import CodeGenerator
class TrackingCodeGenerator(CodeGenerator):
"""We abuse the code ge... | sserrot/champion_relationships | venv/Lib/site-packages/jinja2/meta.py | Python | mit | 4,131 | [
"VisIt"
] | 423c9885f3510f74025e3049a623e5f4a82412419725b024094ab8f94af5d044 |
# Copyright (C) 2016 Collin Capano, Christopher M. Biwer, Alex Nitz
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
#... | cmbiwer/pycbc | pycbc/distributions/__init__.py | Python | gpl-3.0 | 8,268 | [
"Gaussian"
] | fbf12f066c0325b607a45733abc4c056021899f1b3e6b3375aa252fbb68f40dc |
"""RabbitMQAdmin module serves for the management of the internal RabbitMQ
users database. It uses rabbitmqctl command. Only the user with the right
permissions can execute those commands.
"""
import re
from DIRAC import S_OK, S_ERROR
import errno
from DIRAC.Core.Utilities import Subprocess
def executeRabbitmqc... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/RabbitMQAdmin.py | Python | gpl-3.0 | 4,820 | [
"DIRAC"
] | 606ae4ede36d26c98c84287e6017c69379419dcbab91b3159d5784d1ed3a0c20 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
from .elastic import *
from .tensors import *
from .stress import *
from .strain import *
| matk86/pymatgen | pymatgen/analysis/elasticity/__init__.py | Python | mit | 220 | [
"pymatgen"
] | d1d7c21f6463e7211fcebcf9270420634a81a67cc124418a4af6fbff66ed9a0e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
emoji_table = {
':smile:': u'😄',
':smiley:': u'😃',
':grinning:': u'😀',
':blush:': u'😊',
':relaxed:': u'☺️',
':wink:': u'😉',
':heart_eyes:': u'😍',
':kissing_heart:': u'😘',
':kissing_closed_eyes:': u'😚',
':kissing:': u'😗',
... | lord63/pyemojify | pyemojify/emoji.py | Python | mit | 24,661 | [
"Octopus"
] | 7e93dbe5033a136727027c2f3b808035b5bf64d40b1310944a69244ac00b42b8 |
# Import smorgasbord
import os
import sys
sys.path.insert(0, '../')
import gc
import pdb
import time
import math
import random
import re
import copy
import warnings
import multiprocessing as mp
import numpy as np
import scipy.optimize
import scipy.ndimage.measurements
import scipy.stats
import matplotl... | Stargrazer82301/CAAPR | CAAPR/CAAPR_Photom/CAAPR_Photom.py | Python | mit | 58,770 | [
"Galaxy"
] | a645da4eebfc17496a239e0d86efc47997aa14aefa9bf70a7e2c2883e43b6ebc |
#!/usr/bin/env python
import sys
try:
import moose
except ImportError:
print "ERROR: Could not import moose. Please add the directory containing moose.py in your PYTHONPATH"
import sys
sys.exit(1)
has_pylab = True
try:
import pylab
from matplotlib import numpy
except ImportError:
print 'Co... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/pulsegen.py | Python | lgpl-2.1 | 3,288 | [
"MOOSE"
] | 2d90b38eccbba575f7d52eb16c3f4712d4122030d0b229b3bd9c608bc81c930f |
# -*- coding: utf-8 -*-
#
# vmd.training.pers documentation build configuration file, created by
# sphinx-quickstart on Thu Jul 2 09:48:47 2015.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated f... | milieudefensie/vmd.training.pers | source/conf.py | Python | gpl-2.0 | 11,648 | [
"VMD"
] | da245260ef2c5277322ebe1fc1b30cdf436683957ee0e0d9e5b63a747dc355b1 |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | ahmadiga/min_edx | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 29,833 | [
"VisIt"
] | b3417377fde7ee96005d494ba4de6c018f420b82c75e2af82ffad528924ce10f |
import numpy as np
import mymath as Mmath
import scipy.optimize as spo
import mydictionaries as Mdict
r0 = 2**(1/6) # equilibrium distance for nearest neighbor
npoints = 3000
rmin, rmax = 0.1, 2.0 # range for tabulated potential
rvecmaster = np.linspace(rmin,rmax,npoints)
r1bartry = 1.05 # use morse to 5% strain
r1ba... | varun-rajan/python-modules | Obsolete/mdutilities_warnerpotential3d.py | Python | gpl-2.0 | 7,339 | [
"LAMMPS"
] | 3fe64bedc04ea6beed70e6fb5c69d907cb77b3de70546360ab51c6e2932a9ede |
import matplotlib.pyplot as plt
#%matplotlib inline
import nengo
import numpy as np
import scipy.ndimage
import matplotlib.animation as animation
from matplotlib import pylab
from PIL import Image
import nengo.spa as spa
import cPickle
from nengo_extras.data import load_mnist
from nengo_extras.vision import Gabor, Mas... | science-of-imagination/nengo-buffer | Project/mental_rotation_training_clockwise.py | Python | gpl-3.0 | 6,347 | [
"NEURON"
] | 15f7b1ad699203340775b2eb0178842809037b484621b6b5508576347b2b87f2 |
# Copyright (C) 2012,2013,2015,2016
# 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 ... | kkreis/espressopp | src/FixedTripleList.py | Python | gpl-3.0 | 3,429 | [
"ESPResSo"
] | 65e4a18c9dc97b58074d5a4250a6a9d6c8fb66614a925563427bcb2415d1e14a |
#!/usr/bin/env python
"""verification_utils.py:
IT contains a class which runs tests on moose internal data-structures to
check if it is good for simulation.
Last modified: Sun Feb 15, 2015 12:21PM
"""
from __future__ import print_function
__author__ = "Dilawar Singh"
__copyright__ = ... | rahulgayatri23/moose-core | python/moose/verification_utils.py | Python | gpl-3.0 | 10,069 | [
"MOOSE"
] | f1e86205f2a0749564d2f686c88e34f634ec397c32804a3b53b8eaa1d24c5653 |
'''
Created on Apr 28, 2011
@author: mkiyer
'''
from chimerascan import pysam
from math import log10
from string import maketrans
def get_solexa_qual_conversion_table():
"""
return a translation table that can be used by str.translate() for
converting solexa to sanger quality scores
"""
offset = 6... | genome-vendor/chimerascan | chimerascan/lib/fastq_to_bam.py | Python | gpl-3.0 | 3,324 | [
"pysam"
] | 633319b282ed1d90048a3c9ed19b41111df37140848758b6e4e52a7cb5ad2775 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for the CJSON writer."""
import json
import os
import unittest
from math import sqrt
import cclib
__filed... | langner/cclib | test/io/testcjsonwriter.py | Python | bsd-3-clause | 2,855 | [
"ADF",
"GAMESS",
"cclib"
] | f4bee3221f030ec2e09a298dbd74206f166ddd9f15fb5a2f0c7dba7de7672e39 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RStatmod(RPackage):
"""A collection of algorithms and functions to aid statistical
mod... | rspavel/spack | var/spack/repos/builtin/packages/r-statmod/package.py | Python | lgpl-2.1 | 1,194 | [
"Gaussian"
] | 10f0adcbc7d44ba1b2a2a174427b35f8b551d681f48322a7ed7c3e20b212e1e7 |
##############################################################################
# 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... | krafczyk/spack | var/spack/repos/builtin/packages/r-xvector/package.py | Python | lgpl-2.1 | 1,870 | [
"Bioconductor"
] | d2816c160afbf59e30876f50133c1d55e59fa4423af6156c5a9debf9c78b0380 |
from shapes import *
import random
def main():
random.seed()
# Create window
main_window = Container(0, 600, 0, 250, 25)
win = GraphWin("Neuron Mitochondria", main_window.xMax, main_window.yMax, autoflush=False)
# Buffer values for model, label, and arrow containers
model_label_buffer = 30
... | heztet/bio110 | main.py | Python | gpl-3.0 | 5,672 | [
"NEURON"
] | 897c246b2480d2c692637976afb813bbe6e2bec00825d4f2a271f14ab9bc99e0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import base64
import hashlib
import hmac
import json
import time
import urllib2
from datetime import timedelta
from django.conf import settings
from django.contrib.auth.models import User, Group
from django.core import mail
from django.core.cache import ... | Stanford-Legal-Tech-Design/legaltech-rapidpro | temba/channels/tests.py | Python | agpl-3.0 | 78,039 | [
"VisIt"
] | 76893f7ec1e6f8cd433745e715660ec02324d45d683352cce25903c5f9b25558 |
import unittest
from f90wrap import fortran, parser, transform
from . import test_samples_dir
class TestTransform(unittest.TestCase):
def setUp(self):
self.root = parser.read_files([str(test_samples_dir/'circle.f90')])
def test_resolve_interface_prototypes(self):
''' Verify procedures gets m... | jameskermode/f90wrap | test/test_transform.py | Python | lgpl-3.0 | 3,241 | [
"VisIt"
] | d1e717f04f97a091d1bef003c582d8197162f4b75d9377e4d2d6d210fe419bbc |
# 2-electron VMC code for 2dim quantum dot with importance sampling
# Using gaussian rng for new positions and Metropolis- Hastings
# Added energy minimization
from math import exp, sqrt
from random import random, seed, normalvariate
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import A... | CompPhysics/ComputationalPhysics2 | doc/Programs/ConjugateGradient/python/qdoteminim.py | Python | cc0-1.0 | 5,318 | [
"Gaussian"
] | 129a376f503f137e650056167eb88ea994310181022f6a42ace466c8a7eacc41 |
# Copyright 2009-2010 by Peter Cock. 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.
#
# This module is for reading and writing FASTQ and QUAL format files as
# SeqRecord objects... | bryback/quickseq | genescript/Bio/SeqIO/QualityIO.py | Python | mit | 76,159 | [
"BioJava",
"BioPerl",
"Biopython"
] | f75d1a9c0e488b47a2b90330f0c76f285a2c2688907685213db8a624611b172d |
#!/usr/local/bin/python3.4
# ----Copyright (c) 2016 Carnegie Hall | The MIT License (MIT)----
# ----For the full license terms, please visit https://github.com/CarnegieHall/quality-control/blob/master/LICENSE----
# argument 1 is the XML report
import sys
report = sys.argv[1]
import xml.etree.ElementTree as ET
tree =... | CarnegieHall/quality-control | mediaconch/mediaconch-xmlreport-summary.py | Python | mit | 598 | [
"VisIt"
] | 7da44fbba3e32c4ac201b53a2f5253d64f7d63c009c85d08a4e8939348a8088d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Johan Gronqvist (johan.gronqvist@gmail.com)
# copyright (C) 2007 Brian G. Matherly
#
# 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 ... | Nick-Hall/gramps | gramps/gen/filters/rules/person/_missingparent.py | Python | gpl-2.0 | 2,399 | [
"Brian"
] | 4249e015d227dbc47e27a05efe446632c553f299f93ccd53202444e2512608c1 |
# Copyright 2013-2017, Brian May
#
# This file is part of python-alogger.
#
# python-alogger 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 ver... | Karaage-Cluster/python-alogger | alogger/tests/test_slurm.py | Python | gpl-3.0 | 1,193 | [
"Brian"
] | 554d423dffb37f8c31422ebbce68066d2ecf04f35400f7ae35e4f501b19a6125 |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#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... | Excito/audiotools | test/test_core.py | Python | gpl-2.0 | 195,644 | [
"Brian"
] | cf7ad2cf58881aa85974d5aa59796763b047d02b53d04df06170e92f493b36b1 |
##############################################################################
# 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... | wscullin/spack | var/spack/repos/builtin/packages/gaussian/package.py | Python | lgpl-2.1 | 3,390 | [
"Gaussian"
] | 8059ee52ce8547504d79cfbe6882ec355d67431e3fadd5bdd2c7fca7d128233a |
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
... | niktre/espressopp | src/interaction/TabulatedDihedral.py | Python | gpl-3.0 | 6,508 | [
"ESPResSo"
] | e61e069d5380cac9a53f6f017b26a90537fc1a32696e6e37b8b601a1dd14dde4 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
# Documentation is intended to be processed by Epydoc.
"""
Introduction
============
The Munkres module provides an implementation of the Munkres algorithm
(also called the Hungarian algorithm or the Kuhn-Munkres algorithm),
useful for solving the Assignment Problem... | maxkoryukov/headphones | lib/munkres.py | Python | gpl-3.0 | 24,729 | [
"Brian"
] | 06cd5bd01f6f9bf3f49b13c01e19b1d5974b83ad4900a8a3931028ec2eecc9da |
import meshplex
import numpy as np
import pyamg
from numpy import pi
from sympy import sin
import pyfvm
from pyfvm.form_language import Subdomain, dS, dV, integrate, n_dot_grad
def test():
class Gamma0(Subdomain):
def is_inside(self, x):
return x[1] < 0.5
is_boundary_only = True
... | nschloe/pyfvm | examples/poisson_example_test.py | Python | gpl-3.0 | 2,039 | [
"VTK"
] | ae0ebe91537093d1376af5c21bc5e15a632a37c453722d6c52df9acad842f6db |
#!/usr/bin/env python
"""
This is a Nipype pipeline for combining brain surface atlas labels.
It will combine the surface labels in .annot format,
and convert the labels to VTK format.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014620.html
`mris_translate_annotation <subject> <hemi> <in annot> ... | binarybottle/mindboggle_sidelined | relabel_atlas_pipeline.py | Python | apache-2.0 | 11,697 | [
"VTK"
] | 4c304941d487c58af036a54b1a74867ee7a863d88a71b921e2ddd24ce9c4faa3 |
# flake8: noqa
import copy
import math
def distance(p0, p1):
return math.sqrt(math.pow(p0[0] - p1[0], 2) + math.pow(p0[1] - p1[1], 2))
##############################################################################
# Diffing code from:
# http://stackoverflow.com/a/6333972/784831
def dict_diff(merge, lhs, rhs):
... | LikeMyBread/Saylua | saylua/modules/adventure/dungeons/maps/meta/helpers.py | Python | agpl-3.0 | 12,080 | [
"VisIt"
] | 1e256afbfa93e92c9a00e96ecce6f390d4ebd536420ee2869e506d739b710f4b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#2012 Bruno Chareyre <bruno.chareyre@hmg.inpg.fr>
"""Example usage of a TesselationWrapper object for getting microscale quantities."""
# See Catalano2013a for the definition of micro-strain
# (http://dx.doi.org/10.1002/nag.2198 or free-access at arxiv http://arxiv.org/pdf/1304... | ThomasSweijen/yadesolute2 | examples/tesselationwrapper/tesselationWrapper.py | Python | gpl-2.0 | 1,032 | [
"VTK"
] | 45b766b0bcd175d3dcb8b4da2cda0e24f1a0e51d55b0ced7136910ae92e5d12b |
from __future__ import division, print_function
import sys
import os.path
import optparse
import os
import tempfile
import time
import traceback
import numpy as np
from ase.io import read
from ase.parallel import world
from ase.utils import devnull
from ase.constraints import FixAtoms, UnitCellFilter
from ase.op... | askhl/ase | ase/cli/run.py | Python | gpl-2.0 | 11,700 | [
"ASE"
] | a121e3735d9c39926c94d6decf6238b3135c9f211a7be82ffd606469f7019b56 |
# Copyright (c) 2021, TU Wien, Department of Geodesy and Geoinformation
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright notice,... | TUW-GEO/ascat | tests/test_level2.py | Python | mit | 17,088 | [
"NetCDF"
] | 76186c07fd480685592932db68c13ddad5fa810b62521e8fb19be1ee0dcca4ec |
import os
from setuptools import setup
def read(file):
return open(os.path.join(os.path.dirname(__file__), file)).read()
setup(
name="vsut",
version="1.6",
author="Alex Egger",
author_email="alex.egger96@gmail.com",
description="A simple unit testing framework for Python 3.4",
license="MIT... | zillolo/vsut-python | setup.py | Python | mit | 918 | [
"VisIt"
] | ecf308b37971446f18623fbbf4cafd1dd135816ad58aa428b118df4874dbaa0f |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jhseu/tensorflow | tensorflow/python/keras/optimizer_v2/learning_rate_schedule.py | Python | apache-2.0 | 38,681 | [
"Gaussian"
] | 5d62f9ecc9e74aaac4112c85f37657d8cd9f422f2afe44476ba255ce4ca08103 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2018 by Tobias Houska
This file is part of Statistical Parameter Optimization Tool for Python(SPOTPY).
:author: Tobias Houska and Stijn Van Hoey
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ imp... | bees4ever/spotpy | spotpy/algorithms/sceua.py | Python | mit | 17,408 | [
"Gaussian"
] | 9ab614b497dc88f604296b250a3d1a332bf5e9c2dc6e5f727478a055a190ebf5 |
import sys
import unittest
import os
import tempfile
from netCDF4 import Dataset
import numpy as np
from numpy.testing import assert_array_equal
FILE_NAME = tempfile.NamedTemporaryFile(suffix='.nc', delete=False).name
VL_NAME = 'vlen_type'
VL_BASETYPE = np.int16
DIM1_NAME = 'lon'
DIM2_NAME = 'lat'
nlons = 5; nlats = 5... | Unidata/netcdf4-python | test/tst_vlen.py | Python | mit | 7,675 | [
"NetCDF"
] | 9a2063abf4466f21b7ae7d6e31d7fd6900656cef7f8ab00bad2568bacfe87dfc |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2010-2013 Francois Beaune, Jupiter Jazz Limited
# Copyright (c) 2014-2017 Francois Beaune, The appleseedhq Organi... | gospodnetic/appleseed | scripts/updatemany.py | Python | mit | 4,821 | [
"VisIt"
] | 8c277616f4b0c953ba75d95e6767b2537ae8fd53475457c828d67323663b1f18 |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all March 2013 CANON-ECOHAB activities.
Mike McCann
MBARI 13 March 2013
@var __date__: Date of last svn commit
@undocumented: __doc__ parser
@st... | duane-edgington/stoqs | stoqs/loaders/CANON/loadCANON_march2013.py | Python | gpl-3.0 | 25,731 | [
"NetCDF"
] | a50c1d1f284206959cbfee05ff387da7dcd752c9ee9f44f0e605649e96bf8c97 |
from datetime import datetime
from flask import Flask, session
from flask.ext.mosession import MoSessionExtension
app = Flask(__name__)
app.config['MONGODB_HOST'] = '127.0.0.1'
app.config['MONGODB_PORT'] = 27017
app.config['MONGODB_DATABASE'] = 'session_test_db'
mosession = MoSessionExtension(app)
@app.route("/")
d... | bayazee/flask-mosession | example/example.py | Python | bsd-3-clause | 538 | [
"VisIt"
] | dc5b3140ccb0abebc03724041375c2efcc28dad789076058ead6b8cb92080052 |
# inspired by some code by Nathan Denny (1999)
# see http://www.ece.arizona.edu/~denny/python_nest/graph_lib_1.0.1.html
try:
# use reduce against BDFL's will even on python > 2.6
from functools import reduce
except ImportError:
pass
class GraphException(Exception):
"""Base class for exception in the g... | arnaudsj/mdp-toolkit | mdp/graph/graph.py | Python | bsd-3-clause | 13,020 | [
"VisIt"
] | ae0d4f6f68b0425697e95bd22072b01e39d9248da07016e1977d06e8e1dd7a79 |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | toastedcornflakes/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 33,044 | [
"Gaussian"
] | 3a973c65404e3090a0a535fe60645c0d6701008bb683c3b0d209094bf511e9b9 |
# 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 for grib2 file loading.
These tests load various files from iris-test-data, and compare the cu... | SciTools/iris-grib | iris_grib/tests/integration/load_convert/test_sample_file_loads.py | Python | lgpl-3.0 | 7,723 | [
"Gaussian"
] | c8f21e2f9c3eb877410d0c75693837922168a8a0629d5b82eb3686cb39df5793 |
###############################################################################
# Copyright 2017-2021 - Climate Research Division
# Environment and Climate Change Canada
#
# This file is part of the "fstd2nc" package.
#
# "fstd2nc" is free software: you can redistribute it and/or modify
# it under... | neishm/fstd2nc | fstd2nc/__init__.py | Python | lgpl-3.0 | 3,321 | [
"NetCDF"
] | e57886c9b8cf922362bfc806012ce236eddac3479ddbb9010fbd0418d7172445 |
#
# Calc_ElasticModuli_from_VTK.py
#
# Written by Matthew Priddy on March 17, 2015
# Some functions contributed by Noah Paulson
# Input data also contributed by Noah Paulson
#
# Contact information:
# Matthew W. Priddy: mwpriddy (at) gatech (dot) edu
# mwpriddy (at) gmail (dot) com
#
# The purpose of... | mwpriddy/python_scripts_research | Calc_ElasticModuli_from_VTK/Calc_ElasticModuli_from_VTK.py | Python | mit | 13,800 | [
"VTK"
] | f54128d646f9deb370306032e52f50ed6cdbef372745494c2bde11e092f0f808 |
"""
this file does variant calling for RNAseq
"""
#============= import required packages =================
import os
import sys
import subprocess
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from f00_Message import Message
from f01_list_trim_fq import list_files_human,Trimmomatic
from f02_ali... | shl198/Projects | Human_GATK_vari_call/Human_GATK_RNA_vari_call.py | Python | mit | 7,162 | [
"BWA"
] | f84985e31e24e84fb40f7a8a164bc7ab0f03dbce8c47b1f3b62cffe1a72187c9 |
""" This function uses a connected telescope object to take a sequence of images for lightcurve studies.
"""
from astropy.io import fits
from config import config
import datetime
import time
import os
import json
import urllib.request
import re
from astroplan import Observer
import astropy.units as u
from astropy.time ... | yerkesobservatory/seo | routines/lightcurve.py | Python | gpl-3.0 | 21,037 | [
"Galaxy"
] | 5f29cd3f007cee4d598bff6082d788c59caef38c91a6dad0856667efa49bde6c |
# Copyright (c) 2018, Xilinx, Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of con... | Xilinx/PYNQ | pynq/lib/video/clocks.py | Python | bsd-3-clause | 24,085 | [
"CRYSTAL"
] | d25d103ff18229328242fbec3ead9b13e28e57a03266913f2c7efc1e23226721 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
# Create two points, P0 and P1
p0 = [1.0, 0.0, 0.0]
p1 = [0.0, 1.0, 0.0]
lineSource = vtk.vtkLineSource()
lineSource.SetPoint1(p0)
lineSource.SetPoint2(p1)
# Visualize
colors = vtk.vtkNamedColors()
mapper = vt... | lorensen/VTKExamples | src/Python/GeometricObjects/Line.py | Python | apache-2.0 | 1,017 | [
"VTK"
] | 9f0c44f71bb2233434f84e213768c9001b0d0214b3d18acda5ef13226bfa490b |
#!/usr/bin/env python
# coding: utf-8
# Example utilizing the **`LFPykit`** module (https://lfpykit.readthedocs.io,
# https://github.com/LFPy/LFPykit) for predictions of extracellular
# potentials using the line source approximation implementation
# `LineSourcePotential` with a passive neuron model set up in Arbor
# (... | halfflat/nestmc-proto | python/example/single_cell_extracellular_potentials.py | Python | bsd-3-clause | 11,127 | [
"NEURON"
] | ef1c610ec20c3660e6bcf3c0092562af6c7260b77ac6513d0fe7738d9ce95eab |
import lldb
max_depth = 6
#filters = {'_view': 'UIView *', '_layer': 'CALayer *', '_viewFlags': 'struct'}
filters = {'_view': 'UIView *'}
def print_value(var, depth, prefix):
""" print values and recurse """
global max_depth
local_depth = max_depth - depth
pad = ' ' * local_depth
name = var.GetNa... | mauricerkelly/dotfiles | development/lldbpy.symlink/views.py | Python | mit | 2,085 | [
"VisIt"
] | a41d70be4a7031a1655d284dd7113b73573341aff4ec44973703b2b0db2fcc42 |
"""
SystemLoggingHandler is the implementation of the Logging service
in the DISET framework.
The following methods are available in the Service interface::
addMessages()
"""
__RCSID__ = "$Id$"
from types import ListType, StringTypes
from DIRAC import S_OK, S_ERROR, g... | vmendez/DIRAC | FrameworkSystem/Service/SystemLoggingHandler.py | Python | gpl-3.0 | 2,488 | [
"DIRAC"
] | 52d158b7f0081f06142812f68c8d4dce11a2d77223174cf8bd7198f405ae5f7d |
import json
import py
class DummyS3Connection(object):
_temp_path = py.path.local('/tmp')
def __init__(self, **kwargs):
pass
def get_bucket(self, name):
b = DummyS3Bucket(name=name, path=self._temp_path.join(name))
return b
def get_all_buckets(self):
for p in self._temp... | nocarryr/s3-logparser | tests/utils.py | Python | gpl-3.0 | 2,444 | [
"VisIt"
] | cda5007175744a556420a61e31a28509466430b8b204df0d3a6125412be100f2 |
import collect_array as ca
import collect_transformation_info as cti
from processing import collect_device as cd
class FindLoopArrays(object):
def __init__(self):
self.loop_arrays = dict()
self.loop_arrays_parent = dict()
def collect(self, ast):
arr_to_ref = ca.ArrayNameToRef()
... | dikujepsen/OpenTran | v2.0/framework/unused/collect_boilerplate_info_unused.py | Python | mit | 1,612 | [
"VisIt"
] | 938ea0ede095daa9d14a501a6ec1ae419e938c126fbb0cf9ebb5b3648e689a0a |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2015 by Tobias Houska
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Tobias Houska and the SALib team
This class holds the Fourier Amplitude Sensitivity Test (FAST) based on Cukier et al. (1973) and Saltelli et al. (1999):
Cukier, R. I., Fortu... | p-lauer/spotpy | spotpy/algorithms/fast.py | Python | mit | 10,126 | [
"Gaussian"
] | 558403072ca91268ccf319825efd95ea609115832c73c04f871d79c044d5b516 |
import unittest
import scipy
import pysal
import numpy as np
from pysal.spreg import error_sp as SP
class TestBaseGMError(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("HOVAL"))
self.y = np.reshape(y, (49,1))
X... | spreg-git/pysal | pysal/spreg/tests/test_error_sp.py | Python | bsd-3-clause | 14,705 | [
"COLUMBUS"
] | 05cc8383f8633cd7d5bcbf280251d6ecc6200cd40a43d3e73012f69f59fe97fb |
"""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 ... | hitszxp/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 55,028 | [
"Brian"
] | cd82c4d3acd26272158e745af9be834542ce89acc6e516925a3eeaec747e2545 |
# Copyright (c) 2007 The Regents of The University of Michigan
# Copyright (c) 2010 The Hewlett-Packard Development Company
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met: redistributions of sou... | austinharris/gem5-riscv | src/python/m5/stats/__init__.py | Python | bsd-3-clause | 4,584 | [
"VisIt"
] | 8473f6730b39409281bbfab66df2d5e844c75ae8263ed61fb49ea2c85d6bae5e |
# -*- encoding:utf-8 -*-
from django.db import models
from django.utils.translation import ugettext_lazy as _
class DataCenter(models.Model):
"""
A data center is a mapper to backend openstack cluster
the config of project/user/password is for cloud-web api
to create project and user
"""
id ... | eoncloud-dev/eonboard | eoncloud_web/biz/idc/models.py | Python | apache-2.0 | 2,462 | [
"VisIt"
] | e24473e8b608ec5decac561782836ceb49cc26443373787ffc0d3a7017c157d4 |
# -*- coding: utf-8 -*-
"""Make hetionet exports."""
import os
from random import choice
import click
import networkx as nx
import pandas as pd
from tqdm.autonotebook import tqdm
from pybel import (
from_nodelink_gz,
get_hetionet,
to_bel_script,
to_bel_script_gz,
to_graphdati_file,
to_graphd... | pybel/pybel | src/pybel/io/hetionet/cli.py | Python | mit | 3,495 | [
"Pybel"
] | a2f448564fde0d32c41d3c6115972baf5567777b59cd5ac3c2f03288393a0104 |
from base.twilltestcase import TwillTestCase
from functional import database_contexts
import galaxy.model
from base.test_db_util import (
get_user,
get_private_role,
get_all_histories_for_user,
get_latest_history_for_user,
get_default_history_permissions_by_history,
get_latest_dataset,
refre... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/functional/test_admin_features.py | Python | gpl-3.0 | 30,801 | [
"Galaxy",
"VisIt"
] | c2ad50ffbe5230a4b95a5967098a67263cfee42c77866c1b72441f18b41ce31d |
#!/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 Licen... | atsnyder/ITK | Utilities/Maintenance/BuildHeaderTest.py | Python | apache-2.0 | 5,160 | [
"VTK"
] | 7d15c04094790aaed0d1dde6adac0634ca6b88270c08b533b9f4388fdc3a8a7e |
import argparse, os, sys, csv, heapq, string
from automaton import *
from bs4 import BeautifulSoup
done = set()
parser = argparse.ArgumentParser(description='Crawl Google Auto-Complete Query')
parser.add_argument('filename')
parser.add_argument('--query', action='append')
parser.add_argument('--prefix', action='appe... | conceptcreative/free_grants_community | autocomplete/crawl_google_autocomplete.py | Python | mit | 2,542 | [
"VisIt"
] | b8c2cb3f38f6e32657cfef7327f0f719b8418e526ab4cf4fb2421061db334a36 |
from __future__ import with_statement, print_function
__doc__ = \
"""
This module defines an ASE interface to ParaGauss.
"""
import os, sys
from os.path import basename
from os.path import isfile
import numpy as np2
from numpy import array, any
from ase.gxfile import gxread, gxwrite
from ase.units import Bohr, Hartree... | alexei-matveev/ase-local | ase/calculators/paragauss.py | Python | gpl-2.0 | 30,147 | [
"ASE"
] | 8485517205f4b170a76b100021559e181af1e31fbf1e8949a9d466a1c37c7585 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import collections
from pymatgen.core.units import (
ArrayWithUnit,
Energy,
EnergyArray,
FloatWithUnit,
Length,
LengthArray,
Mass,
Memory,
Time,
TimeArray,
Unit,
UnitError,
... | vorwerkc/pymatgen | pymatgen/core/tests/test_units.py | Python | mit | 8,777 | [
"pymatgen"
] | 60658d34947f00f070974808783dca745f3ba3798b46006fa52ce23336fe82bf |
"""
A first test for the ELBO on the diffusion problem.
The target is consisted of an and a Gaussian likelihood.
The approximating mixture has two components.
Author:
Panagiotis Tsilifis
Date:
6/16/2014
"""
import numpy as np
import matplotlib.pyplot as plt
import os
import cPickle as pickle
from scipy.st... | ebilionis/variational-reformulation-of-inverse-problems | unittests/test_optimize_diffusion_upperleft.py | Python | gpl-2.0 | 7,014 | [
"Gaussian"
] | f5c370063e7e7f3576f2010653e414d2e8b00dd4df7c4089ed4f96644d5001b7 |
# coding: utf-8
from StringIO import StringIO
import unicodecsv
from grano.logic import Loader
from grano.logic.schemata import import_schema
# This source URL will be applied to all properties without their own lineage:
DEFAULT_SOURCE_URL = 'http://www.opennews.org/'
DATA = """fellow_name,twitter_handle,start_date... | clkao/grano | grano/test/fixtures.py | Python | mit | 3,340 | [
"Brian"
] | f1044d5d1e80ea4a193aa10ba4004983be0f3f88a92b3f9f9fc04114d3a43eb2 |
#!/usr/bin/python
# check_glider_netcdf.py - Verifies that a glider NetCDF file from a provider
# contains all the required global attributes, dimensions, scalar variables
# and dimensioned variables. Prints out missing items.
#
# Returns:
# 0 - File complies to NGDAC standard
# 1+ - Number of errors
#
# By: Mi... | USF-COT/glider_netcdf_writer | scripts/scripts-bin/check_glider_netcdf.py | Python | mit | 5,287 | [
"NetCDF"
] | 99d2f5778bda64b5f20450a4a89ccfed9d3729ea90b839f210d5ee4bd6ab62b8 |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/test/test_io.py | Python | gpl-3.0 | 28,786 | [
"Avogadro",
"CP2K",
"CPMD",
"Gaussian"
] | f64b9ae5fc4f0c6b51491881d4e5466f2a9df9718a41353f7d9e4b77a2eab474 |
"""
Module for rendering bonds
"""
from __future__ import absolute_import
from __future__ import unicode_literals
import time
import logging
import functools
import vtk
import numpy as np
from . import baseRenderer
from . import povrayWriters
from .. import utils
from .. import _rendering
from ...filtering import b... | chrisdjscott/Atoman | atoman/rendering/renderers/bondRenderer.py | Python | mit | 8,568 | [
"VTK"
] | bcda6c2e05718b1fe07383aef6810e180168c2b8d7bada03cf1713a15ba9bf72 |
# pylint: disable=C0111
# pylint: disable=W0621
import urllib
from lettuce import world
from django.contrib.auth.models import User, Group
from student.models import CourseEnrollment
from xmodule.modulestore.django import modulestore, clear_existing_modulestores
from xmodule.contentstore.django import _CONTENTSTORE
... | LICEF/edx-platform | common/djangoapps/terrain/course_helpers.py | Python | agpl-3.0 | 2,503 | [
"VisIt"
] | 59b4c4afe5bda3d762bbddff07ee5ad785f5c1d6c3c56317ff6efea2aa41183f |
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