text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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"""
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... | 10clouds/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 31,218 | [
"VisIt"
] | 2f9adfb14409ce2dd9e2fe7d01784af7596b758c9f2fc7758c4e610b4af6a8c1 |
#* 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/lgpl-2.1.html
import os
f... | harterj/moose | python/MooseDocs/extensions/alert.py | Python | lgpl-2.1 | 7,034 | [
"MOOSE"
] | 3d646523df50591d53d8fba417e6146aa55e5468daf9867b13707c25859b2142 |
# -*- coding: utf-8 -*-
#
# __init__.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# ... | niltonlk/nest-simulator | pynest/nest/__init__.py | Python | gpl-2.0 | 15,517 | [
"NEURON",
"VisIt"
] | eef9a0775d575ad743b132754aeac385e2565a40a3d4dab1aa924675fd89cb61 |
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import os.path
import unitte... | greglandrum/rdkit | rdkit/Chem/Pharm2D/UnitTestMatcher.py | Python | bsd-3-clause | 3,370 | [
"RDKit"
] | 8ba5fdb763dd6d267f8a9e606b26def76668b23a5e9a4cefbc5ba1bc677f1664 |
#!/usr/bin/env python3
# ver 0.1 - copy from massf_1d.py (v1.1) and modify codes on 1/22/2018
import argparse
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='partial rdf(s) at interfaces using various domain info. from domain.py')
## args
parser.add_arg... | jht0664/Utility_python_gromacs | python/rdf_itf.py | Python | mit | 9,604 | [
"MDAnalysis"
] | 2e0b0ecef7e0cb0ed3aea01713e90e460b5e79a4264baea5f7a0077a5d1786c0 |
"""
This module use used to extend genes predicted with Genemark and then annotate them using
the function extendGenes.
"""
"""
Copyright 2010 Jarl Haggerty
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 Lic... | jarl-haggerty/profelis | src/main/jython/profelis/extend.py | Python | apache-2.0 | 7,042 | [
"BLAST"
] | 77c1b556ea87590d3b0f29ebdb3f3d87be27c124c85252dc042cf95d54ed2f91 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2013 Zuza Software Foundation
# Copyright 2014 Evernote Corporation
#
# This file is part of Pootle.
#
# Pootle 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
# F... | evernote/pootle | pootle/core/initdb.py | Python | gpl-2.0 | 10,571 | [
"VisIt"
] | c9820e175db51b4ce311ae270e6b7b64192c5ff68f50a010b7ad5cf8996ece40 |
#
# @file TestSpecies.py
# @brief Species unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestSpecies.py | Python | gpl-3.0 | 8,165 | [
"VisIt"
] | cc24de1818c89526c7a78ec2d53ff2a15848b5826ea05b30f15310cc81488f69 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/EnggFitPeaks.py | Python | gpl-3.0 | 28,172 | [
"Gaussian"
] | 8e70103c5d66ff9440be01fc8d9f1520002002db6c3d7db2e1a763369e506d3d |
"""
Acceptance tests for Studio's Setting pages
"""
from unittest import skip
from .base_studio_test import StudioCourseTest
from ...pages.studio.settings_certificates import CertificatesPage
class CertificatesTest(StudioCourseTest):
"""
Tests for settings/certificates Page.
"""
def setUp(self): # py... | jbassen/edx-platform | common/test/acceptance/tests/studio/test_studio_settings_certificates.py | Python | agpl-3.0 | 8,448 | [
"VisIt"
] | 86281647a961b27ba8ef9ef7a36bc28991ad9d2592f7aed43a6538128acf7844 |
"""
Tests for kpoint functions.
"""
# pylint: disable=redefined-outer-name
import pytest
import numpy as np
import z2pack
@pytest.fixture
def kpt(line):
"""
Return a list of k-points for a given 'line' fixture.
"""
kpt = [
np.array(line(tval))
for tval in [0., 0.125, 0.25, 0.375, 0.5... | Z2PackDev/Z2Pack | tests/fp/test_fp_kpoint.py | Python | gpl-3.0 | 3,820 | [
"ABINIT",
"VASP",
"Wannier90"
] | 4a73b32d781ad23817fc3cff2c9752c1d0974fd01ba7e22bd8fc74a1321e59fd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the VaspInputSet abstract base class and a concrete
implementation for the parameters developed and tested by the core team
of pymatgen, including the Materials Virtual Lab, Materials Pr... | dongsenfo/pymatgen | pymatgen/io/vasp/sets.py | Python | mit | 86,776 | [
"BoltzTrap",
"VASP",
"pymatgen"
] | 8e997456685ff1ff4d05b094162afafd7af0ccf0413f81bcc96af0ebcea7a15c |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/plan_medicare.py | Python | apache-2.0 | 20,037 | [
"VisIt"
] | c69dd6c12ef74c661a338f8df6d89d6b6b7386e9c44d2b0d8a8c4b53ad294cb6 |
""" Encapsulate here the logic for limiting the matching of jobs
Utilities and classes here are used by the Matcher
"""
from DIRAC import S_OK, S_ERROR
from DIRAC import gLogger
from DIRAC.Core.Utilities.DictCache import DictCache
from DIRAC.Core.Utilities.DErrno import cmpError, ESECTION
from DIRAC.Configuration... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Client/Limiter.py | Python | gpl-3.0 | 10,119 | [
"DIRAC"
] | 0658d71c300e5683d13d2248b3984b8c277d7982ec6dbeb5526478b8732665c6 |
# -*- coding: utf-8 -*-
#
# tsodyks_facilitating.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | tobikausk/nest-simulator | pynest/examples/tsodyks_facilitating.py | Python | gpl-2.0 | 4,981 | [
"NEURON"
] | 61cbccffb41ac931069ee54e0f28f80bb29ec37668de7752682842692d6453d6 |
#!/usr/bin/env python
import json
import os
import sys
import shutil
from setuptools import setup, find_packages
import pyct.build
setup_args = {}
install_requires = [
"param >=1.9.3,<2.0",
"numpy >=1.0",
"pyviz_comms >=0.7.4",
"panel >=0.9.5",
"colorcet",
"pandas >=0.20.0",
]
extras_requir... | ioam/holoviews | setup.py | Python | bsd-3-clause | 5,692 | [
"VisIt"
] | d6e8a0c9284a57464c1458e4edae577d1953757e7ffe3977371c14898a82512d |
""" Main class for doing consistency checks, between files in:
- File Catalog
- TransformationSystem
Should be extended to include the Storage (in DIRAC)
"""
import os
import time
import sys
import re
import errno
import DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.DataManagementSystem.Clien... | fstagni/DIRAC | DataManagementSystem/Client/ConsistencyInspector.py | Python | gpl-3.0 | 28,413 | [
"DIRAC"
] | 2726d2512aa3eb3fb63c3b15589e9d81576aa137049f7bccec362166db61b4c7 |
"""Tools easing the work with OpenBabel
Copyright (C) 2010 Troels Kofoed Jacobsen
Code released under GPLv2 (or later). See COPYING for details.
"""
import numpy as np
import pybel
import openbabel as ob
from ase import Atom, Atoms, units
from obcalc.obwrap import forces_ni
def get_forces(mol):
N = mol.NumAtoms... | tkjacobsen/obcalc | obcalc/tools.py | Python | gpl-2.0 | 3,308 | [
"ASE",
"Pybel"
] | fc7b1673a808693fd2a7170ef1e31ba8abb3541b00637c92444e64ee036a305c |
# -*- coding: utf-8 -*-
u"""
Functions to mask spatial coordinates.
“Geographic masking is the process of altering the coordinates of point
location data to limit the risk of reidentification upon release of the
data. In effect, the purpose of geographic masking is to make it much
more difficult to a... | sjorek/geoanonymizer.py | geoanonymizer/spatial/mask.py | Python | mit | 20,449 | [
"Gaussian"
] | 0b470573270f4f7504b7ae4a776053ab9f689a574518f9d671af995d3d033cb0 |
# $Id$
#
# Copyright (c) 2007-2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the ... | soerendip42/rdkit | Projects/DbCLI/SearchDb.py | Python | bsd-3-clause | 24,186 | [
"RDKit"
] | 20de1dce08eeb8c408fa877a4ca4d3cffd21160485a879c7a8604a1fdb04637a |
# -*- coding: utf-8 -*-
"""
Created on Tue Sep 26 00:09:21 2017
@author: Mayukh Sarkar
"""
import math
import matplotlib.pyplot as plt
N= 6.022e23 # Avogadro's number
k= 1.3806488e-23 # in SI base units
atm= 101325 # atmospheric pressure in Pa
L= .001 # 1 L = .001 m^3
plt.xlabel("Volume (m^3)")
p... | blackburn66/Carnot-cycle | engines.py | Python | gpl-3.0 | 3,391 | [
"Avogadro"
] | a5d2564cc07a9df4f4035917c74ef1d7ae9d91a71b05ded7e9c313b5c323d1e4 |
import numpy as np
import orthopy
import pytest
import quadpy
@pytest.mark.parametrize(
"scheme",
[quadpy.enr2.cools_haegemans_1(n) for n in range(1, 6)]
+ [quadpy.enr2.cools_haegemans_2(n) for n in range(1, 6)]
+ [quadpy.enr2.cools_haegemans_3(n) for n in range(2, 6)]
+ [quadpy.enr2.lu_darmofal_... | nschloe/quadpy | tests/test_enr2.py | Python | mit | 3,693 | [
"VTK"
] | c69a3b5f38d9adcb132b8d6a08fb7b4e07df232d7eee44d9afe69c2604050075 |
# ==========================================================================
#
# Copyright NumFOCUS
#
# 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/... | BRAINSia/ITK | Wrapping/Generators/Python/itk/support/extras.py | Python | apache-2.0 | 67,567 | [
"VTK"
] | 90d814650947e82faaebcdbc982019d32ae39c9bad97db275c13af463f588a1d |
import unittest
from phevaluator.tables import NO_FLUSH_6
from .utils import BaseTestNoFlushTable
class TestNoFlush6Table(BaseTestNoFlushTable):
TOCOMPARE = NO_FLUSH_6
TABLE = [0] * len(TOCOMPARE)
VISIT = [0] * len(TOCOMPARE)
NUM_CARDS = 6
@classmethod
def setUpClass(cls):
super().s... | HenryRLee/PokerHandEvaluator | python/tests/table_tests/test_hashtable6.py | Python | apache-2.0 | 474 | [
"VisIt"
] | 0dfff4779f31c7c3e9bb867bd1280e6133ee104962febdb167e80dc599ce14a5 |
# $Id$
#
# Copyright (C) 2007 by Greg Landrum
# All rights reserved
#
from rdkit import Chem
from rdkit import Geometry
class SkeletonPoint(object):
location = None
shapeMoments = None
shapeDirs = None
molFeatures = None
featmapFeatures = None
fracVol = 0.0
def __init__(self, *args, **kwargs):
se... | jandom/rdkit | rdkit/Chem/Subshape/SubshapeObjects.py | Python | bsd-3-clause | 2,462 | [
"RDKit"
] | bd4ea03ae164bc3e2d9859aaa920d799de9833e82029c0168d2a61313c143fc3 |
# -*- coding: utf-8 -*-
# This code is part of Qiskit.
#
# (C) Copyright IBM 2017, 2019.
#
# This code is licensed under the Apache License, Version 2.0. You may
# obtain a copy of this license in the LICENSE.txt file in the root directory
# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
#
# Any... | QISKit/qiskit-sdk-py | qiskit/pulse/pulse_lib/continuous.py | Python | apache-2.0 | 11,951 | [
"Gaussian"
] | 20b40a131ff71625a8083944d485b3e478345214302db4b997cd597a71e6c6aa |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems 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
#
# ... | dongjoon-hyun/neon | examples/multi_optimizer.py | Python | apache-2.0 | 2,657 | [
"Gaussian"
] | d8db16b96f9a1bdc79a7a5a3ffc9d6c5b428e2032017ca6f65729a97b5d3ac07 |
# Copyright 2013 anthony cantor
# This file is part of pyc.
#
# pyc 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.
#
# pyc is distr... | cantora/pyc | pyc_astvisitor.py | Python | gpl-3.0 | 3,969 | [
"VisIt"
] | 07788500b67ff8bc247dc38dd334770313494d890ac36f78436a0d5bb422e058 |
import pysam
import sys
import Pyrex
import os
import math
BamFile = sys.argv[1]
samFile = pysam.Samfile(BamFile,"rb")
AllMapped = samFile.mapped
headerOriginal = samFile.header
Range1C = 0
Range2C = 0
Range3C = 0
Range4C = 0
Range5C = 0
count = 0
outfileRange1 = pysam.Samfile(str(BamFile)+"Range1.bam","wb",header=hea... | hjanime/mrcchip | CountIszie.py | Python | gpl-2.0 | 1,781 | [
"pysam"
] | dfbcdb5b3fedcd4306c3d0ff0f53800d02645c208a1cd5898443ac7a44ed7a82 |
# -*- coding:Utf-8 -*-
import numpy as np
from traits.api import HasTraits, Instance, Array, on_trait_change
from traitsui.api import View, Item, HGroup, Group
from tvtk.api import tvtk
from tvtk.pyface.scene import Scene
from mayavi import mlab
from mayavi.core.api import PipelineBase, Source
from mayavi.core.ui.ap... | buguen/pylayers | pylayers/util/mayautil.py | Python | lgpl-3.0 | 8,758 | [
"Mayavi",
"VTK"
] | 39fe85407383df715e5a045fff299f880a7f063f05631eb87e378565a79b962b |
#!/usr/bin/env python
#import argparse
#from glob import glob
#-s test_samples.txt
#-b /mnt/lfs2/hend6746/devils/reference/sarHar1.fa
#-k /mnt/lfs2/hend6746/taz/filtered_plink_files/export_data_150907/seventy.1-2.nodoubletons.noparalogs.noX.plink.oneperlocus.vcf
from os.path import join as jp
from os.path import absp... | shendri4/devil_wgs | BQSR_perInd_Devils.py | Python | apache-2.0 | 3,647 | [
"BWA"
] | 4cf1c6c82ed65d70af61387fb85433141170158816c1f333a80f6705b89e121f |
"""
Linear Discriminant Analysis and Quadratic Discriminant Analysis
"""
# Authors: Clemens Brunner
# Martin Billinger
# Matthieu Perrot
# Mathieu Blondel
# License: BSD 3-Clause
from __future__ import print_function
import warnings
import numpy as np
from .utils import deprecated
from sci... | BiaDarkia/scikit-learn | sklearn/discriminant_analysis.py | Python | bsd-3-clause | 27,666 | [
"Gaussian"
] | a51095bc8a33f3e0fb24ede77e8c1cb13cbe2776a5037dddd637a535adafaf7c |
from ase.lattice.cubic import FaceCenteredCubic
from gpaw import GPAW, PW
element = 'Pt'
atoms = FaceCenteredCubic(symbol=element,
size=(2, 2, 2),
directions=[[1, 1, 0],
[-1, 1, 0],
[0, 0, 1]]... | robwarm/gpaw-symm | gpaw/test/big/scf/trouble/pt13.py | Python | gpl-3.0 | 512 | [
"ASE",
"GPAW"
] | 0044fd0ef36e5a8db0e9514bc47412f426530e85fe8f3d7f2a3e2ce320cd92e9 |
# 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/converters/ifexp.py | Python | apache-2.0 | 1,621 | [
"VisIt"
] | a7bf36ee9d385689d79c735f8d4e94e03e46c8777eb809824008cf75700be0c1 |
# -*- coding: utf-8 -*-
"""Compiles nodes from the parser into Python code."""
from collections import namedtuple
from functools import update_wrapper
from itertools import chain
from keyword import iskeyword as is_python_keyword
from markupsafe import escape
from markupsafe import Markup
from . import nodes
from ._c... | chromium/chromium | third_party/jinja2/compiler.py | Python | bsd-3-clause | 66,300 | [
"VisIt"
] | 200147eb3e7710f4e233e23bf65a9f69d8e2bc24b61a68631df5992bdcb003d5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import re
import itertools
import warnings
import logging
import math
import six
import numpy as np
from numpy.linalg import det
from collections im... | tallakahath/pymatgen | pymatgen/io/vasp/inputs.py | Python | mit | 72,033 | [
"VASP",
"pymatgen"
] | e50d5f7952dc74ea116f170d4e8d1ed309c5faba2deb340725ae459591e6c026 |
__author__ = 'stephen'
# ===============================================================================
# GLOBAL IMPORTS:
import os,sys
import numpy as np
import argparse
# ===============================================================================
# LOCAL IMPORTS:
#HK_DataMiner_Path = os.path.relpath(os.pardir)
... | stephenliu1989/HK_DataMiner | hkdataminer/scripts/test_kcenters.py | Python | apache-2.0 | 4,271 | [
"MDTraj"
] | 873889e83ab1de4e3a90a8096052da71caa1b14194eb721c51c2d3dcdf720812 |
#!/usr/bin/env python
# Run as
# ./switzerland/client/webgui/WebGUI.py --fake
# Where --fake optionally specifies the bogus demo
# that can run without a network
import web
import time
import math
import sys
import os
import random
import logging
import getopt
import socket as s
import base64
import switzerland.commo... | isislovecruft/switzerland | switzerland/client/webgui/WebGUI.py | Python | gpl-3.0 | 46,962 | [
"Brian"
] | ab8951580ea14348a127008ec71b9ad037add7e22f9d00cc7813979cc64b15c8 |
#!/usr/bin/python
# This code is just for educational only ;)
# coder by jimmyromanticdevil
# code for tutorial Python [ Membuat Bot Auto Clicker ]
import urllib2
import urllib
import sys
import time
import random
import re
import os
import time
proxylisttext = "proxylist.txt"
useragent = ['Mozilla/4.0 (co... | elangoverdosis2/autoclickpython | bot.py | Python | mpl-2.0 | 2,826 | [
"ADF"
] | 763d8963b4f0411948b69341400eda618ab1675a597336efd536a467311f5a25 |
#!/usr/bin/env yamtbx.python
"""
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
"""
Add staturation flags (SATURATED_PART, SATURATED_ALL) to mtz file.
Read MAXC column from INTEGRATE.HKL and compare it with user-specified overload= ... | keitaroyam/yamtbx | yamtbx/dataproc/xds/command_line/add_saturation_info_to_mtz.py | Python | bsd-3-clause | 5,858 | [
"CRYSTAL"
] | c18d151c8fe6da173fad95bca673dac034d106de873fff9cf2346143ce0e9596 |
"""
===============
GMM covariances
===============
Demonstration of several covariances types for Gaussian mixture models.
See :ref:`gmm` for more information on the estimator.
Although GMM are often used for clustering, we can compare the obtained
clusters with the actual classes from the dataset. We initialize th... | imaculate/scikit-learn | examples/mixture/plot_gmm_covariances.py | Python | bsd-3-clause | 4,723 | [
"Gaussian"
] | 0b99ea916c69e2aecc185e35cb71130308d689225feda2e86da8d032de968ec2 |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You shou... | Clyde-fare/cclib_bak | src/cclib/parser/gaussianparser.py | Python | lgpl-2.1 | 54,260 | [
"Gaussian",
"cclib"
] | 9760cc2cfda72b5924921627515473a91f8ae907a482e6deae2c66e78e1f21b0 |
from django.db import models
from vendor.models import Store
class Driver(models.Model):
id = models.AutoField(primary_key=True)
username = models.CharField(max_length=40, unique=True)
password = models.CharField(max_length=30)
first_name = models.CharField(max_length=30, blank=True)
last_name = ... | rayhu-osu/vcube | valet/models.py | Python | mit | 1,459 | [
"VisIt"
] | c44150b6f58d20cf89939922ac5faa61bb325b2f5ff68d63096be282744ee495 |
from ase.transport.calculators import TransportCalculator
import numpy as np
#Aux. function to write data to a text file.
def write(fname,xs,ys):
fd = open(fname,'w')
for x,y in zip(xs,ys):
print >> fd, x, y
fd.close()
H_lead = np.zeros([4,4])
# On-site energies are zero
for i in range(4):
H_... | grhawk/ASE | tools/ase/transport/test_transport_calulator.py | Python | gpl-2.0 | 2,162 | [
"ASE"
] | 386a186e87aaea9df28dd444a09ff7f034069bce7bfa00c7ce4d7ceab21ac065 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/vasp/test_runrelax.py | Python | gpl-3.0 | 2,647 | [
"CRYSTAL",
"VASP"
] | d768355b158513ece8cf67a3c023212f0912c192bc00ef5199e97288a6f7694d |
"""This module contains the "Viz" objects
These objects represent the backend of all the visualizations that
Superset can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import copy
import hashlib
import l... | asdf2014/superset | superset/viz.py | Python | apache-2.0 | 52,742 | [
"VisIt"
] | c8ebf1dc716d37c98fbade0552305ac6fafdce5afe177d0ed4efe720fd16879a |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-api-gateway | scripts/fixup_apigateway_v1_keywords.py | Python | apache-2.0 | 6,756 | [
"VisIt"
] | cfa11b3ba86dff58a77bbd8fda6d9b27d58e78b53f09b1626524e00489b5df52 |
from functools import reduce
from operator import add
from os.path import dirname, join
import arviz as az
import numpy as np
import pandas as pd
import pytest
from formulae import design_matrices
from bambi.models import Model
from bambi.terms import Term, GroupSpecificTerm
from bambi.priors import Prior
@pytest.... | bambinos/bambi | bambi/tests/test_model_construction.py | Python | mit | 13,347 | [
"Gaussian"
] | 1ba72f9c00938041b5c86850afe34d2e449ab76caeead3073719d95b7f0f917b |
"""IO methods for radar data from MYRORSS or MRMS.
MYRORSS = Multi-year Reanalysis of Remotely Sensed Storms
MRMS = Multi-radar Multi-sensor
"""
import os
import glob
import warnings
import numpy
import pandas
from netCDF4 import Dataset
from gewittergefahr.gg_io import netcdf_io
from gewittergefahr.gg_utils import ... | thunderhoser/GewitterGefahr | gewittergefahr/gg_io/myrorss_and_mrms_io.py | Python | mit | 38,214 | [
"NetCDF"
] | 4d21b0fb9729d972650a61729c8ea3dafc6bfd2f1233cf9a30da3f9a1da8a752 |
import re
import pymol
import cmd
import setting
import parsing
import threading
from cmd import DEFAULT_ERROR, DEFAULT_SUCCESS, _raising, \
is_list, is_string, is_error
QuietException = parsing.QuietException
_prefix = "_tmp_editor"
tmp_wild = _prefix + "*"
tmp_editor = _prefix + "0"
tmp_connect = _prefix + "... | gratefulfrog/lib | python/pymol/editor.py | Python | gpl-2.0 | 16,247 | [
"ChemPy",
"PyMOL"
] | c5b444eedf1c810e6ce040d9205809cb891c9460dd1d5b6ba49795573846c28f |
# http://curtis.schlak.com/2012/01/04/python-visitor-pattern-helper.html
# http://curtis.schlak.com/2013/06/20/follow-up-to-python-visitor-pattern.html
# visit.py
# Updated 2013-06-20 to fix bug on line 41
import inspect
__all__ = ['on', 'when']
def on(param_name):
def f(fn):
dispatcher = Dispatcher(param_nam... | plum-umd/java-sketch | lib/visit.py | Python | mit | 1,481 | [
"VisIt"
] | 5a6c1d8598f27e29904b35e1c639cccca7431a8f9b19eef3ec218e4fb1884172 |
################################################################################
# The Neural Network (NN) based Speech Synthesis System
# https://svn.ecdf.ed.ac.uk/repo/inf/dnn_tts/
#
# Centre for Speech Technology Research
# ... | ashmanmode/TTSDNNRepo | src/layers/layers.py | Python | apache-2.0 | 23,616 | [
"Gaussian"
] | 945689fc7b6ed502cf405fd714f6468feb3fff42bc3bd3ff6e3ce7e04d04b8b8 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
#
# This program is free software; you can redistribute i... | pmghalvorsen/gramps_branch | gramps/gen/plug/docgen/paperstyle.py | Python | gpl-2.0 | 6,428 | [
"Brian"
] | 3ebbd4d3302414b62f1318265283748b372bbaa6898de7586b16a3a2b99790ca |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
"""
A row of Artificial Neural Network (ANN)
to recognize smiley faces as follow :
- 1: Happy :)
- 2: Sad :(
- 3: Mischievous >)
- 4: Mad >(
Generate pydoc by running :
`$ pydoc -w faces`
"""
__author__ = 'Benjamin Sientzoff'
__date__ = '11 December 2015'
__versio... | blasterbug/SmileANN | faces.py | Python | gpl-2.0 | 9,564 | [
"NEURON"
] | c109a08f0d15a74bd673f5af19dfe7fa7b1973ee7fb512ec4f0df214c3253cd7 |
../../../../../../../share/pyshared/orca/scripts/apps/planner/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/planner/script.py | Python | gpl-3.0 | 71 | [
"ORCA"
] | af76dd540d95a333d2bf069070fe5a0c60fbbc9d4a189ea5602d0886229c341d |
#! /bin/usr/env python
# D.J. Bennett
# 26/05/2014
"""
Tests for download tools.
"""
import unittest
import pickle
import logging
import os
import pglt.tools.download_tools as dtools
# DIRS
working_dir = os.path.dirname(__file__)
# DUMMIES
# expected terms and term search results
t1_term = '(txid1[PORGN]) OR txid2[... | DomBennett/pG-lt | tests/test_tools_download.py | Python | gpl-2.0 | 8,457 | [
"BLAST"
] | 50a06fa172c6739cc4a99661cd358ba1c80b8ecef46e7291d28cdb6180856f0d |
from Firefly import logging
from Firefly.components.zwave.device_types.water_sensor import ZwaveWaterSensor
from Firefly.const import SENSOR_DRY, WATER
ALARM = 'alarm'
BATTERY = 'battery'
TITLE = 'DSB45 Aeotec Water Sensor'
COMMANDS = []
REQUESTS = [ALARM, BATTERY, WATER]
INITIAL_VALUES = {
'_alarm': False,
'... | Firefly-Automation/Firefly | Firefly/components/zwave/aeotec/dsb45_water_sensor.py | Python | apache-2.0 | 1,889 | [
"Firefly"
] | b56bb50d1f9c6d298c57e59030c3804c700c061581a6ae9fe5b6f07b77214e21 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from six.moves import map
from six.moves import zip
import math
import itertools
import logging
import time
from monty.json import MSONable
import numpy as ... | matk86/pymatgen | pymatgen/transformations/site_transformations.py | Python | mit | 20,996 | [
"pymatgen"
] | f08b06b9a4fecbe690181cfda7c102ca0820bbf85e5016010968b27a4b3d381c |
"""
Test courseware search
"""
import os
import json
from ...pages.common.logout import LogoutPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms.courseware_search import CoursewareSearchPage
from ...pages.lms.course_nav import CourseNavPage
from ...fixtures.course import XBlockFixtureDesc
fr... | B-MOOC/edx-platform | common/test/acceptance/tests/lms/test_lms_split_test_courseware_search.py | Python | agpl-3.0 | 6,940 | [
"VisIt"
] | e6633c73690146dd9882a12e939eb1ac0b227bc18e54c4a8ad0d4c008868da75 |
"""
-- Policy Network for decision making [more general]
"""
from nmt_uni import *
from layers import _p
import os
import time, datetime
import cPickle as pkl
# hyper params
TINY = 1e-7
PI = numpy.pi
E = numpy.e
A = 0.2
B = 1
class Controller(object):
def __init__(self, trng,
option... | nyu-dl/dl4mt-simul-trans | policy.py | Python | bsd-3-clause | 23,644 | [
"Gaussian"
] | 41c543f78fd49e54729dea809183d7436040842db2b3871af9dbfa26461ab896 |
# -*- coding: utf-8 -*-
#
#Created on Fri Apr 14 13:37:08 2017
#
#author: Elina Thibeau-Sutre
#
from .base import BaseMixture
from .base import _log_normal_matrix
from .kmeans import dist_matrix
from megamix.batch.initializations import initialization_plus_plus
from megamix.batch.initializations import initialization_... | 14thibea/megamix | megamix/online/VBGMM.py | Python | apache-2.0 | 20,937 | [
"Gaussian"
] | e876076f8c38f6d72ee02b29db79632790f2f59db680aa25e660dba33f1052f5 |
from sklearn.preprocessing import *
import pandas as pd
from sys import argv
file_path = argv[1]
verbose = argv[2] == "true"
scaler = argv[3]
#####################################################################################
# Scaler Options
# (https://scikit-learn.org/stable/auto_examples/preprocessing/plot_all_s... | srp33/ShinyLearner | scripts/Scale.py | Python | mit | 4,259 | [
"Gaussian"
] | f34d1f4420e1e6084d6dcb9535390aaffd977e67a7b15fda9740305910356a2e |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
red= (1,0,0)
green= (0,1,0)
blue= (0,0,1)
cyan= (0,1,1)
yellow= (1,1,0)
pink = ( float(255)/255,float(192)/255,float(203)/255)
grey = ( float(127)/255,float(127)/255,float(127)/255)
orange = ( float(255)/255,float(165)/255,float(0)/255... | davidwusea/opencamlib | src/attic/oct_test1.py | Python | gpl-3.0 | 6,424 | [
"VTK"
] | ffa498a892eef6551298b1c7e2d3920069836df12bd25a796dfa5ede1211c170 |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
import warnings
import numpy as np
import pandas as pd
from scipy import ndimage
from scipy.spatial import cKDTree
from pandas import DataFrame
from .preprocessing import bandpass, scale_to_gamut, s... | daniorerio/trackpy | trackpy/feature.py | Python | bsd-3-clause | 32,400 | [
"Gaussian"
] | 208797f777e34b22d86761c2d25954ae3a40e24261b329e199308ea26f1873f6 |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/task_plugins/plugins/raw_mode/plugin.py | Python | gpl-3.0 | 8,902 | [
"COPASI"
] | 742813c08a3e39e7c2d2675d462432cad1fd8b035723d7e509259d99317b2059 |
import random
from sympy.core.basic import Basic
from sympy.core.compatibility import is_sequence, as_int
from sympy.core.function import count_ops
from sympy.core.decorators import call_highest_priority
from sympy.core.singleton import S
from sympy.core.symbol import Symbol
from sympy.core.sympify import sympify
from... | lidavidm/mathics-heroku | venv/lib/python2.7/site-packages/sympy/matrices/dense.py | Python | gpl-3.0 | 43,924 | [
"DIRAC"
] | 3e661954ac1ffb76bd7f7c2157eb86d4509af9756eba5ee12426c54e00c88240 |
#
# Copyright (C) 2003-2006 Greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code for fin... | greglandrum/rdkit | rdkit/Chem/Fingerprints/UnitTestFingerprints.py | Python | bsd-3-clause | 2,918 | [
"RDKit"
] | 525d31dc830d137a7514c1eea04cff9dc003256f9eff5ad37106290b88438e84 |
#
# Copyright 2005,2006,2007 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio 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, or (at your option)
# any later ... | tyc85/nwsdr-3.6.3-dsc | dsc-gmsk-rs/cat_packet_utils.py | Python | gpl-3.0 | 29,805 | [
"cclib"
] | 389d68ae80335eb116e2f5688fdf363ff7ca72ac3a1995bee7b63b5a4fbb39d2 |
"""Module for calculating electron-phonon couplings.
Electron-phonon interaction::
__
\ l + +
H = ) g c c ( a + a ),
el-ph /_ ij i j l l
l,ij
where the electron phon... | robwarm/gpaw-symm | gpaw/elph/electronphonon.py | Python | gpl-3.0 | 35,302 | [
"ASE",
"GPAW"
] | 822459ade4df98155bf3db6e1386e82d6bd8a4b940e851b20b1619bbd4079722 |
###
# Copyright 2015-2020, Institute for Systems Biology
#
# 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 la... | isb-cgc/ISB-CGC-Webapp | scripts/get_mendeley_papers.py | Python | apache-2.0 | 4,930 | [
"VisIt"
] | 5aac311a292cc406f77ba57fd64309a2ab7f99da1f71209f3944587561701a12 |
"""Create Common Workflow Language (CWL) runnable files and tools from a world object.
"""
from __future__ import print_function
import collections
import copy
import dateutil
import functools
import json
import math
import operator
import os
import tarfile
import requests
import six
import toolz as tz
import yaml
fr... | a113n/bcbio-nextgen | bcbio/cwl/create.py | Python | mit | 40,458 | [
"BWA",
"Bioconda"
] | b0ca9494824c67f22d3d0038148e67097431e60f87dd3c9b199203e33c9329d2 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import copy
import os
import unittest
import warnings
from shutil import which
from monty.serialization import loadfn
from pymatgen.analysis.graphs import (
MoleculeGraph,
MolGraphSplitError,
PeriodicSite,
S... | materialsproject/pymatgen | pymatgen/analysis/tests/test_graphs.py | Python | mit | 38,777 | [
"pymatgen"
] | ad63ba51d46b16c6a3d4ae10c5e91f493c6c3945ebbdf0ab970895d2ec6fd858 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | greglandrum/rdkit | rdkit/Chem/EState/UnitTestFingerprints.py | Python | bsd-3-clause | 2,008 | [
"RDKit"
] | 80444ffa7ad625e5907149992caa6aa4208eeedcd2709d78f19b661e72f462b6 |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
""" Various bits and pieces for calculating Molecular descriptors
"""
from rdkit import RDConfig
from rdkit.ML.Descriptors import Descriptors
from rdkit.Chem import Descriptors as DescriptorsMod
from rdkit.RDLogger import logger
logger = l... | jandom/rdkit | rdkit/ML/Descriptors/MoleculeDescriptors.py | Python | bsd-3-clause | 3,308 | [
"RDKit"
] | 381e5735df359799187442f988b9c010b951679c04c2391de0f39935218c9d84 |
# 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 PyVcfKit(PythonPackage):
"""VCF-kit is a command-line based collection of utilities for pe... | rspavel/spack | var/spack/repos/builtin/packages/py-vcf-kit/package.py | Python | lgpl-2.1 | 1,832 | [
"BLAST",
"BWA",
"Biopython"
] | bc54ca154e4d4434206aac9521f208df08e5938013f9624f4741fc3b6ecbdcc9 |
#
from env import ABSPATH
import os
import json
from neuronjs import Neuron
dependency_tree = {}
dependency_file = os.path.normpath(
os.path.join(ABSPATH, './test/fixtures/dependency.json')
)
try:
dependency_json = open(dependency_file).read()
dependency_tree = json.loads(dependency_json)
except Exception as... | neuron-js/pyneuron | test/all.py | Python | mit | 1,346 | [
"NEURON"
] | e31efcaa382a55f406ce033d327e3447cc6d5cbd028a7c325db281ce698e8c1d |
import IMP
import IMP.core
import IMP.algebra
import IMP.atom
import IMP.pmi
import sys
import os.path
import IMP.display
import numpy as np
import math
import matplotlib.pyplot as plt
import time
colors = [(1,.4,.4),(.4,.4,1),(.4,1,.4),(1,.4,1),(.4,1,1),(1,.7,.4),(1,.4,.7)]
class MassSpecSystem:
def __init__(self,m... | jEschweiler/Urease | urease_software/IMMSonly_restraints/sampler.py | Python | gpl-3.0 | 17,964 | [
"PyMOL"
] | 429315b9028c9fc7245c190c10cfdbe658eb069f3da7d73d614a8a7451042aed |
#!/usr/bin/env python
# -*- 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 ... | molmod/tamkin | tamkin/examples/001_ethane/thermo.py | Python | gpl-3.0 | 2,326 | [
"Gaussian"
] | 268879b38f7fe6043a7a0ed96eaee66de2bba42466fb94c9e7f17b68e65362bb |
"""A notebook manager that uses the local file system for storage.
Authors:
* Brian Granger
* Zach Sailer
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full li... | wusung/ipython-notebook-store | bookstore/filenotebookmanager.py | Python | apache-2.0 | 20,614 | [
"Brian"
] | 2ead2999bf99454326079a07011d5867482830f99f3ca78874f4ab3302fe4c76 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-kill
# Author : Stuart Paterson
########################################################################
"""
Issue a kill signal to a running DIRAC job
Usage:
dirac-wms-job-kill [options] ... Job... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_job_kill.py | Python | gpl-3.0 | 1,677 | [
"DIRAC"
] | b83d1243bef27406ecfda1ce28d844e44f1be6b0f900561860f89a42660f5177 |
##
# 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... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/b/bowtie.py | Python | mit | 2,657 | [
"Bowtie"
] | 408c50d58fe91110ac635339c4cee8304d146ed69ad471f6cf160b4b809202d2 |
#
# Copyright (C) 2013,2014,2015,2016 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option)... | richter-t/espresso | samples/python/slice_input.py | Python | gpl-3.0 | 2,860 | [
"ESPResSo"
] | d36244c20f5f06d6df54c0598e1befda9855aa0af1acfdc09d1a79ddb92e7be5 |
"""
call the python built-in compile to convert a python program to an ast structure, then convert that structure
to a simplified structure using the classes in parsetree.py
"""
from parsetree import *
import _ast
import os
from os.path import split, splitext, join
import codecs
import sys
from jslib import pystorm_m... | treeform/pystorm | pyfrontend.py | Python | mit | 20,299 | [
"VisIt"
] | a036863a969794eb9b2342e8047f4f1ece189685b5c5924120d8179e5a7467b6 |
"""
Module for recoding matrices.
date: 25/08/2016
"""
import sys
import os
import types
import subprocess
import re
import copy
import warnings
from Bio.Data import CodonTable
from p4 import Alignment
from p4 import func
from p4 import var
from p4 import P4Error
from p4 import read
from p4.code_utils import \
... | blaiseli/p4-phylogenetics | p4/alignment_recoding.py | Python | gpl-2.0 | 46,750 | [
"Biopython"
] | f3ac5350efe09dc5ff52ef296cc1f2030e677455f4258c13585d5b4b5f269451 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/delegates/labeldelegate.py | Python | gpl-2.0 | 2,178 | [
"VisIt"
] | 7dbdaab260c29eb871ba533fe1bdd6f69a0269dfeb8999514f3b9c3bcfc94c84 |
#!/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... | sunqm/pyscf | pyscf/cc/dfccsd.py | Python | apache-2.0 | 9,438 | [
"PySCF"
] | 9406b503ded1dafc5014a939498ad9ba6b2af97bd78295776e667342c7b012ba |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
"""Simple protein analysis.
Example,
X = ProteinAnalysis("MAEGEITTFTALTEKFNLPPGNYKKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKSTETGQYLAMDTSGLLYGSQTPSEECLFLERLEENHYNTYTSKKHAEKNWFVGLKKNGSCKRGPRTHYGQKAILFLPLPV")
print X.... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SeqUtils/ProtParam.py | Python | gpl-2.0 | 10,842 | [
"Biopython"
] | 8f1fe2f1284c3fa7cc9c002502e25ca93d98c69407b78bfcbf2c7eb6d38f8502 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.StereoCapableWindowOn()
iren = vtk.vtkRenderWindowInte... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/EnSight/Testing/Python/EnSight6ElementsBin.py | Python | gpl-3.0 | 1,233 | [
"VTK"
] | 28febc0b530517bf15ef56136c3c2b89da1e6b7aaa724c2b2d99b73debe97c0c |
import logging
import urllib
from functools import partial
from collections import defaultdict
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User
f... | pku9104038/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 28,526 | [
"VisIt"
] | c7513d40a19274cdacab9e45cc6516940db96aa0de48b597c5025c5bad67973a |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/crystal/__init__.py | Python | gpl-3.0 | 6,379 | [
"CRYSTAL",
"VASP"
] | 2991bc82008d2e8a4a92b5c90d53978e1031d50295674990ce5c82f3f1fc991c |
##############################################################################
##############################################################################
# Default settings and helpers for
# Particle filtering
#
# Copyright (c) 2016 Johan Dahlin [ johan.dahlin (at) liu.se ]
# Distributed under the MIT license.
#
##... | compops/pmmh-correlated2015 | state/smc_helpers.py | Python | gpl-3.0 | 5,924 | [
"Gaussian"
] | af9fde41d9b9be13b4684c593f9f6f3379131877a5a264635858b0791752144d |
# -*- coding: utf-8 -*-
"""
Created on Mon May 03 14:53:54 2010
@author: a1185872
"""
import numpy as np
import scipy.signal as sps
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
def padzeros(f,npad=None,padpattern=None):
"""
padzeros(f) will return a function that is padded wi... | geophysics/mtpy | mtpy/legacy/tftools.py | Python | gpl-3.0 | 60,744 | [
"Gaussian"
] | 73f1940b7be0d6403fac3db5a69d77429fbf74a4fe2ea9eab79aea54b72df204 |
##############################################################################
# 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 | lib/spack/spack/url.py | Python | lgpl-2.1 | 29,937 | [
"HOOMD-blue",
"VTK"
] | dcbda43554aeb451e4ccbf1a9658df7a65e32b0aae2e30414d880c4bf662e017 |
from __future__ import print_function
import fileinput
import os
import shutil
import subprocess
import click
def _get_version():
with open('flexget/_version.py') as f:
g = globals()
l = {}
exec(f.read(), g, l) # pylint: disable=W0122
if not l['__version__']:
raise click.Cli... | oxc/Flexget | dev_tools.py | Python | mit | 2,861 | [
"GULP"
] | 3551b7e774da48efc30818b8f01726e83c863fc9b202cdc5374d141f47145680 |
#!/usr/bin/env python2
import sys
import os
from parmed.tools import changeLJSingleType
from parmed.tools import parmout
from parmed.tools import change
from parmed.amber import AmberParm
from parmed.structure import Structure
def parmed_topology(top_file, param_type, param_list,TIP3P_param_list, index):
"""
U... | Janeyin600/WaterBot | waterbot_parmed.py | Python | gpl-3.0 | 3,304 | [
"Amber"
] | 6ea39e7739e11ece6695c775ef48b59229bd8bc86b61820bdbcdfbaf4abd06fe |
# 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... | annarev/tensorflow | tensorflow/python/keras/activations.py | Python | apache-2.0 | 18,023 | [
"Gaussian"
] | 945aad1829be37d434de863b0b87444ed6ca3d706efd3b00b4df3ae438c7eefb |
import json
from django.core.context_processors import csrf
from django.http import HttpResponse, HttpResponseRedirect
from django.shortcuts import render, render_to_response
from django.template import Template, Context
from django.template.loader import get_template
from pathgenerator.models import Place, Path, Use... | Earthstar/double-d | pathgenerator/views.py | Python | mit | 5,967 | [
"CASINO"
] | 3b824a521a76c61ca9d75d2b3b270161e6912bd76bc2a44bc2bf0b5ed2a9b671 |
from GenericRequest import GenericRequest
from kol.manager import PatternManager
class CharpaneRequest(GenericRequest):
"Requests the user's character pane."
def __init__(self, session):
super(CharpaneRequest, self).__init__(session)
self.url = session.serverURL + 'charpane.php'
def parse... | ijzer/cwbot-ndy | kol/request/CharpaneRequest.py | Python | bsd-3-clause | 7,273 | [
"MOOSE"
] | 3d43d473bc6c1e8528acafa9768756cf8ec4941270b32beb3d46101fb88115b0 |
from tkinter import *
from tkinter.filedialog import *
from tkinter.messagebox import *
##from tkinter.filedialog import askopenfilenames
##from tkinter.filedialog import asksaveasfilename
import GEToperant
GETprofile = None
MPC_filenames = None
#Define functions for the menus
def openprofile():
globa... | SKhoo/GEToperant | GEToperantGUI.py | Python | mit | 24,091 | [
"VisIt"
] | 3e623385072b064673c964480aca55630ab75501b79073de3b978f67eede70c6 |
'''
Define the public 'draw' function to be used to draw
morphology using plotly
'''
from __future__ import absolute_import # prevents name clash with local plotly module
from itertools import chain
import numpy as np
try:
import plotly.graph_objs as go
from plotly.offline import plot, iplot, init_notebook_m... | lidakanari/NeuroM | neurom/view/plotly.py | Python | bsd-3-clause | 4,380 | [
"NEURON"
] | 70f81d95ddce2128d896a3d76b78c98ceb61d6f743ed26b204d43a70f590227e |
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