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#!/usr/bin/env python
# coding: utf-8
"""Floating bodies to be used in radiation-diffraction problems."""
# Copyright (C) 2017-2019 Matthieu Ancellin
# See LICENSE file at <https://github.com/mancellin/capytaine>
import logging
import copy
from itertools import chain, accumulate, product, zip_longest
import datetime
... | mancellin/capytaine | capytaine/bodies/bodies.py | Python | gpl-3.0 | 20,164 | [
"VTK"
] | f2e660a9b11391e331404fcc7a2c632788b86b482a00af654689192b355a1c70 |
#!/usr/bin/python2
from os import system
from hashlib import sha256
from base import *
from bedrock import *
from globs import *
from types_builtin import *
from vat import *
import types
types_by_name['set'] = lambda: t_DT(Set)
# Shouldn't this be an env or something?
BUILTINS = {}
RUNTIME = {}
Builtin = DT('Builti... | pshc/archipelago | atom.py | Python | mit | 17,314 | [
"VisIt"
] | 60d0565ba111c657d569c6a9849b0f493c6c6a5fce896bbf6e09b1772c336bb0 |
from __future__ import print_function
class RBM:
def __init__(self, rng, configFile, cloneFrom=None)
"""
initializing the RBM from the specified configFile
:type rng: numpy.random.RandomState
:param rng: a random number generator used to initialize weights
:type... | mohsenmalmir/DeepLearningStack | DeepLearningStack/RBM/RBM.py | Python | mit | 1,034 | [
"NEURON"
] | 14403d2d65f6eed6c09577152aa1edd8115704c1325589fa873524f04845fcaa |
import numpy as np
from pandas import DataFrame, Series
def generate_qmatrix(concepts, problems):
""" Generates a Q-matrix of size "concepts x problems" with values
sampled from a continuous uniform distribution between 0 and 1."""
return np.random.rand(concepts, problems)
def generate_skills(concepts, ... | jniznan/edami | edami/synthetic.py | Python | mit | 2,007 | [
"Gaussian"
] | 149cc9c24c9e26d63e2b5c09acdb5f89f322d57feb734ac56d0d103fee9559c3 |
from gaussian import noise_from_psd, noise_from_string, frequency_noise_from_psd # noqa
| hagabbar/pycbc_copy | pycbc/noise/__init__.py | Python | gpl-3.0 | 88 | [
"Gaussian"
] | 0c728b8b501b93e90387656c531bf82518967ace3351b418964d690fe9cfb8f6 |
from StoryModels import StoryModels
from AllDBFields import ZoneDBFields
from ZoneDefinitions import ZoneDefinition
from ZoneDefinitions import AllZones
from bson.objectid import ObjectId
from OrphanedModelException import OrphanedModelException
import DatabaseLayer
import random
class Zone(StoryM... | joelliusp/SpaceHabit | SpaceHabitRPG/Models/Zone.py | Python | mit | 14,252 | [
"VisIt"
] | 566c80a333d824aa3212c889a7b7a3c6240b35e8ab21b8a226e08c3353dfc3a7 |
#!/usr/bin/env python
################################################################################
#
# A bunch of regression type tests for the builder and parser.
#
################################################################################
ident = '$Id: SOAPtest.py,v 1.19 2004/04/01 13:25:46 warnes Exp $'
... | nagyistoce/devide.johannes | extra/soappy-cvp/tests/SOAPtest.py | Python | bsd-3-clause | 140,087 | [
"MOOSE"
] | 19c98cc2b664f04b66eb68fce29992b47e9d2f36de739905322389dfad275ba6 |
########################################################################
# File : IdProviderFactory.py
# Author : A.T.
########################################################################
""" The Identity Provider Factory instantiates IdProvider objects
according to their configuration
"""
from __future__ ... | ic-hep/DIRAC | src/DIRAC/Resources/IdProvider/IdProviderFactory.py | Python | gpl-3.0 | 4,216 | [
"DIRAC"
] | 12b5759bcf783660c5810a9caea12ad50f0c9954bbb476b3ce32cad32bfee0af |
#import matplotlib as plt
#from numpy import *
## Force matplotlib to not use any Xwindows backend.
#matplotlib.use('Agg')
#import matplotlib.pyplot as plt
#def plot_cov_contour(S, m):
## plots equidensity contor of a gaussian
## S: covariance matrix
# phi=arange(0,2*pi+.01,.01)
# points=zeros((size(phi), 2)
# ... | zsomko/visualcortex | python/plotting/covariance_ellipse.py | Python | gpl-2.0 | 3,091 | [
"Gaussian"
] | f0dc3e971f856fd9583e6cc84b035d22a78f1a8d0e255edd0cfe706cde1e2f4b |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_featurestore_online_serving_service.py | Python | apache-2.0 | 69,458 | [
"Octopus"
] | 331f9cd511d5e2606c93a537fa72a9c796172dcd84fe4d919dd8f964d9ec97a6 |
#!/usr/bin/python2.4
# Copyright (c) 2006-2008 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""This is a simple HTTP server used for testing Chrome.
It supports several test URLs, as specified by the handlers in TestPa... | kuiche/chromium | net/tools/testserver/testserver.py | Python | bsd-3-clause | 36,527 | [
"VisIt"
] | 3f1bad71ca579f7b92859b0bb3720a4ec1c3bc4b8d48d463ff60435fa609fbab |
# Copyright 2001 by Tarjei Mikkelsen. 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.
# get set abstraction for graph representation
#TODO - Subclass graph?
class MultiGraph(ob... | bryback/quickseq | genescript/Bio/Pathway/Rep/MultiGraph.py | Python | mit | 6,729 | [
"Biopython"
] | 3669300064e9bc034f87569a62cf1882d9345ab4c3ec9ff6d4ea62cc5bc2cb17 |
from __future__ import print_function
from bokeh.browserlib import view
from bokeh.models import ColumnDataSource, DataRange1d, Plot, LinearAxis, Grid, GlyphRenderer, Circle, HoverTool, BoxSelectTool
from bokeh.models.widgets import (
Select, HBox, VBox, DataTable, TableColumn, StringFormatter,
NumberFormatter... | lukebarnard1/bokeh | examples/glyphs/data_tables_server.py | Python | bsd-3-clause | 6,815 | [
"VisIt"
] | bac92349a5189f78f4d468875aaedf3f665a60cad48d8e2f9cb8285ad266254a |
#! /usr/bin/env python
#------------------------------------------------------------------------------
# THIS FILE HAS BEEN MODIFIED FROM THE ORIGINAL (freeze.py).
# THE MODIFICATIONS ENABLE FREEZING OF MODULES/PACKAGES WITHOUT IMPORTING THEM.
# THAT MAKES IT POSSIBLE TO FREEZE PARAVIEW MODULES WITHOUT IMPORTING THE
# ... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/ThirdParty/FreezePython/freeze/freeze_paraview.py | Python | gpl-3.0 | 19,322 | [
"ParaView"
] | 4bf1ec4eb0c296136efb67f8eb988f24641f2b08e88a0925049226739b726843 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | symbolic_functionals/syfes/xc/lda_test.py | Python | apache-2.0 | 5,545 | [
"PySCF"
] | d4a663b5b289c8e1b5f9cf6005c6f12c7d9561a0bb11d6f1ff44da5e12cd75ac |
""" gpr_fit_2d.py
An example that uses functionality from the GPR module
to regress a 2-Dimensional Function
"""
# ------------------------------------------------------------
# Imports
# ------------------------------------------------------------
import time, os, sys, copy
import numpy as np
... | aerialhedgehog/VyPy | tests/_experimental/activesubspace_tests_01.py | Python | bsd-3-clause | 8,500 | [
"Gaussian"
] | be74c0067c0a4fc406baf5cd08731a440d0ec8cc013f371440ddb88729a2b1d4 |
#!/usr/bin/python
import numpy as np
import numpy.linalg as lg
import sys
import subprocess as sp
import os
import errno
import shutil
import re
import numpy.linalg as lg
from __tools__ import MyParser
from __tools__ import make_sure_path_exists
from __tools__ import XmlParser
from __tools__ import cd
from __tools__ i... | 12AngryMen/votca-scripts | xtp/xtp_Polarisation.py | Python | apache-2.0 | 9,256 | [
"Gaussian"
] | 19dcae3dbefc3e7db843df220369839d99596df882c08aaf050b2c38fdc372eb |
# -*- coding: utf-8 -*-s
"""
module to transform raw vtk to rotated vtk along mom bud axis
THIS IS FOR OLD DATASET (2015 , thesis YPD, YPE, YPL and YPR WT cells)
"""
import os
import os.path as op
import cPickle as pickle
import numpy as np
from mayavi import mlab
import pandas as pd
from tvtk.api import tvtk
from momb... | moosekaka/sweepython | cell_pick_viz/vtk_rotate_mombud_old.py | Python | mit | 5,336 | [
"Mayavi",
"VTK"
] | 476d46cef446cf20532f32966258ec1129caf2fce28d70bd534e422e1557d82a |
from __future__ import division
import numpy as np
import scipy.io
import pylab as plt
def sparse_nmf(X, r, maxiter, spar, W = None, H = None):
"""Input data and the rank
Learns a sparse NMF model given data X and the rank r.
Parameters
----------
X : {array}, shape = [n_features, n_samples]
... | ismav/sparseNMF | sparse_nmf.py | Python | bsd-3-clause | 4,259 | [
"Gaussian"
] | 958b5cf7de743aedf0899ae229715dd6d9e4770bee13633ad0d9e23c4274e89b |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
The instrument module:
defines the inputset and the job
"""
import os
import shutil
import subprocess
import logging
from pymatg... | henniggroup/MPInterfaces | mpinterfaces/instrument.py | Python | mit | 12,676 | [
"VASP",
"pymatgen"
] | 3cea30cd239a3782758e8c50c543d91daff16b32e07dcddc791f9bed5c618f37 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | Eraldo/sandbox | config/urls.py | Python | bsd-3-clause | 1,285 | [
"VisIt"
] | 669b8fd4c41aacc9a1118d17b0731c3551b1c508fa1cbdd7ad9b6e0d87b0740e |
"""
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revision: 879 $"
import StringIO
try:
import bz2 # New in Python 2.3.
except ImportError:
bz2 = None
import fileinput
import gzip
import inspect
i... | faribas/RMG-Java | source/cclib/parser/logfileparser.py | Python | mit | 11,017 | [
"ADF",
"Avogadro",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"ORCA",
"cclib"
] | 93a998b2b155a64be79f71c696b2859b4e3c0cef5aa3d498c338934114f421d6 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# _generate_pyx.py to generate the docstrings for the ufuncs in
# scipy.special at the C level... | e-q/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 242,499 | [
"Gaussian"
] | 56870c9d7f63910f534be2f1f6b6e47fbd1f14582851b7d4332fcc43ab8f14e2 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | ovidner/cookiecutter-django | {{cookiecutter.repo_name}}/config/urls.py | Python | bsd-3-clause | 1,472 | [
"VisIt"
] | 0c5b7f4b567d56eae8bb4a60aaff404790f98299cdfd0d1ecdc1f99f708d1a35 |
#
# @file TestRDFAnnotationC.py
# @brief RDFAnnotation parser unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id: TestRDFAnnotationC.py 11441 2010-07-09 02:22:23Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/python/test/annot... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/annotation/TestRDFAnnotationC.py | Python | gpl-3.0 | 10,360 | [
"VisIt"
] | 51a73c3440b798a74cb526be3d914b30d5c879abac0bb4864e3c051898048cfc |
#__docformat__ = "restructuredtext en"
# ******NOTICE***************
# optimize.py module by Travis E. Oliphant
#
# You may copy and use this module as you see fit with no
# guarantee implied provided you keep this notice in all copies.
# *****END NOTICE************
# A collection of optimization algorithms. Version 0... | grlee77/scipy | scipy/optimize/_optimize.py | Python | bsd-3-clause | 134,753 | [
"Gaussian"
] | 57b31d5190bfa974a4c6babc62f85be2a31286ffe4c80d5c48fe971ca001402d |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2009 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
"""
Mantid system testing framework. This mod... | mganeva/mantid | Testing/SystemTests/lib/systemtests/systemtesting.py | Python | gpl-3.0 | 50,994 | [
"ParaView"
] | 5756056410af62e3cdb69d829fa7f82beba35aaaa3ad57a749b63fd16207d88d |
# -*- coding: utf-8 -*-
# md_format_converter.Mol2TrajOutput.py
#
# Copyright (C) 2012-2016 Karl T Debiec
# All rights reserved.
#
# This software may be modified and distributed under the terms of the
# BSD license. See the LICENSE file for details.
"""
Manages addition of mol2 output information to segments... | KarlTDebiec/md_format_converter | Mol2TrajOutput.py | Python | bsd-3-clause | 3,820 | [
"VMD"
] | 84e206d637d1a2ab91cfbeffd559cb4339885156dbd2a800eed24f223cab439c |
#* 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
from TestHa... | harterj/moose | python/TestHarness/tests/test_RequiredObjects.py | Python | lgpl-2.1 | 872 | [
"MOOSE"
] | 61b2761002fbc6bff022dd85e7efddc48271013b8fbeff4c64e06acd5ad0f67d |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/converters/ParmEdParser.py | Python | gpl-2.0 | 10,806 | [
"MDAnalysis",
"OpenMM"
] | 1824f7a72591f59479457b049ee1c0d72a94c679a74bdc1994ab175a03406316 |
# pyenchant
#
# Copyright (C) 2004-2011, Ryan Kelly
#
# This library 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 version.
#
# This ... | halfak/pyenchant | enchant/__init__.py | Python | lgpl-2.1 | 35,236 | [
"VisIt"
] | 5309d5ca2cc87c5dcd4538f8d42a578fe2ea3d92d70af2faf9ba119cc93fee46 |
# -*- coding: utf-8 -*-
# This file is part of beets.
# Copyright 2016, Adrian Sampson.
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation t... | jcoady9/beets | beetsplug/discogs.py | Python | mit | 14,464 | [
"VisIt"
] | 975636ce12c53541c91736b2e4513f71a07ec4c443bcc7eb5cf37a8ad2d3614d |
########################################################################
# $HeadURL$
########################################################################
""" Legend encapsulates a graphical plot legend drawing tool
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phed... | andresailer/DIRAC | Core/Utilities/Graphs/Legend.py | Python | gpl-3.0 | 7,924 | [
"DIRAC"
] | bef0dcfc8d8d91add9b94c84a6bb1ef253f2e92d93df3817aa01c1b494bb48b6 |
# encoding:utf-8
import re
import os
def is_md_file(filename):
pattern = re.compile(r'.[Mm]{1}[Dd]{1}')
return len(re.findall(pattern, filename)) > 0
def deal_with(filename):
with open(filename) as f:
content = f.read()
# print content
p_img = re.compile(r'(\[code=img\].+\[/code\])+?', r... | EManual/EManual.github.io | android-tmp/cleanup.py | Python | apache-2.0 | 1,333 | [
"VisIt"
] | 11331a11514fe588059324a9418c76a1f74f1a2151ea78cbd771545b7afaad4b |
import os, time
import numpy as np
from ase import Atoms
from ase.parallel import paropen
from ase.units import Hartree, Bohr
from ase.io.trajectory import PickleTrajectory
from ase.calculators.singlepoint import SinglePointCalculator
from gpaw import GPAW
from gpaw.mpi import world
from gpaw.tddft import TDDFT
from ... | robwarm/gpaw-symm | gpaw/test/big/ehrenfest/h2_osc.py | Python | gpl-3.0 | 2,549 | [
"ASE",
"GPAW"
] | 36d917a505f7556fd33fd04b9fbcb284239a603409c6c38073b98bdb38ece5fa |
from __future__ import print_function
from pybrain.structure import FeedForwardNetwork
from pybrain.tools.validation import ModuleValidator,Validator
from pybrain.utilities import percentError
from pybrain.tools.customxml import NetworkReader
from pybrain.datasets import SupervisedDataSet
i... | affordablewindurbines/jarvisproject | pybrain/examples/supervised/test_network_read_write/jpq2layersReader.py | Python | gpl-3.0 | 2,034 | [
"NEURON"
] | 342f8f1a2e491c942cdd1c8c5093fb5fa2c394b30437c0b3dff166bbdec4424d |
import tensorflow as tf
def cat_id_column(train_x, test_x, unlabeled, col_name):
train_set = set(train_x[col_name])
test_set = set(test_x[col_name])
unlabeled_set = set(unlabeled[col_name])
id_max = max(train_set.union(test_set).union(unlabeled_set))
return tf.feature_column.indicator_column(
... | matthiasn/iWasWhere | src/tensorflow/feature_columns.py | Python | agpl-3.0 | 3,305 | [
"VisIt"
] | fd06b855940ad3193f4c90ca32e8dadcda55faba7b004c8f4d851bdd6454471e |
"""Github two-factor authentication requirement was disabled for a user."""
from streamalert.shared.rule import rule
@rule(logs=['ghe:general'])
def github_disable_two_factor_requirement_user(rec):
"""
author: @mimeframe
description: Two-factor authentication requirement was disabled for a user.
... | airbnb/streamalert | rules/community/github/github_disable_two_factor_requirement_user.py | Python | apache-2.0 | 555 | [
"VisIt"
] | 3279c0629714a4ec3a22e8c25a819e3251cfaaf4974366d18753658b5b0c29ac |
# -*- coding: utf-8 -*-
from ....interfaces import utility as util # utility
from ....pipeline import engine as pe # pypeline engine
from ....interfaces import camino as camino
from ....interfaces import fsl as fsl
from ....interfaces import camino2trackvis as cam2trk
from ....algorithms import misc as mis... | mick-d/nipype | nipype/workflows/dmri/camino/diffusion.py | Python | bsd-3-clause | 10,861 | [
"ParaView",
"VTK"
] | 80a44cef35b6a11b356ea0ade3acd94988c8e82b6b4ef5f1cea4e1f456df8df6 |
#################################################################
# Code written by Edward Choi (mp2893@gatech.edu)
# For bug report, please contact author using the email address
#################################################################
import sys, random
import numpy as np
import cPickle as pickle
from colle... | mp2893/doctorai | doctorAI.py | Python | bsd-3-clause | 24,190 | [
"VisIt"
] | 05769fdf34b8f14f16ee003fad1e9a25f78a7df687aae0c6073af4d034cdf66f |
from lib.typecheck import *
import lib.visit as v
import lib.const as C
from .. import util
from ..meta import class_lookup
from ..meta.program import Program
from ..meta.clazz import Clazz
from ..meta.method import Method
from ..meta.field import Field
from ..meta.statement import Statement
from ..meta.expression imp... | plum-umd/java-sketch | java_sk/decode/collection.py | Python | mit | 1,855 | [
"VisIt"
] | a9f5d5acad63ab9ec46f9369d8b545254e0e979091eabbe9f83e02498329a41d |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/test_qcprot.py | Python | gpl-2.0 | 6,133 | [
"MDAnalysis"
] | fad52c4755916f0db3c7aa3834f48aee9d2732e4461f2eac9f9083da3a017a10 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from common import *
from terrain.steps import reload_the_page
from selenium.common.exceptions import InvalidElementStateException
from contentstore.utils import reverse_course_url
from nose.tools import assert_i... | B-MOOC/edx-platform | cms/djangoapps/contentstore/features/grading.py | Python | agpl-3.0 | 7,217 | [
"VisIt"
] | 1991d8e6f2d44bda59daec11d3b662d71c09bba2f809ffeab2ac62c9f84a36ed |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | hmenke/espresso | testsuite/python/electrostaticInteractions.py | Python | gpl-3.0 | 5,238 | [
"ESPResSo"
] | a1ace35d78809061f820fbac7b23093784589d0b6c4c0ad437b504f666a1c8be |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/getcurrlocation.py | Python | gpl-2.0 | 5,020 | [
"VisIt"
] | 63c70a5eb3b6bf08cdfca0a2f8b9884b2ee19bf1cbc67f48daa1e66215f779e9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# Convolve MTSS rotamers with MD trajectory.
# Copyright (c) 2011-2017 Philip Fowler and AUTHORS
# Published under the GNU Public Licence, version 2 (or higher)
#
# Includ... | MDAnalysis/RotamerConvolveMD | rotcon/convolve_pre.py | Python | gpl-2.0 | 7,731 | [
"MDAnalysis"
] | 09a937e4ba193038e4ca190949277f9d7e3eae79d41d56fdab1ee5a4d21fb1a6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Initialization of LFPy, a Python module for simulating
extracellular potentials.
Group of Computational Neuroscience,
Department of Mathematical Sciences and Technology,
Norwegian University of Life Sciences.
Copyright (C) 2012 Computational Neuroscience Group, NMBU.
... | espenhgn/LFPy | LFPy/__init__.py | Python | gpl-3.0 | 3,646 | [
"NEURON"
] | 535349461bb4a969ae96de167aaf7b6c37ecbf1b24d6ecd3baf72439e551a97b |
# ============================================================================
#
# 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/editors/onetomanychoiceseditor.py | Python | gpl-2.0 | 1,903 | [
"VisIt"
] | 1808de1c3a7da4dbfb80a861ef8dad5cf61d39e6a2eb3c1626897384fd2d6b53 |
#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import sys, os, shutil, gzip
import pysam
import unittest
import itertools
import subprocess
class TestVCFIterator( unittest.TestCase ):
filename = "example.... | pkaleta/pysam | tests/vcf_test.py | Python | mit | 4,827 | [
"pysam"
] | 6b3005ce19f7ad3f86d9ae94cd6643eaee260660a476a00d65242fb192bde0e9 |
# -*- coding: utf-8 -*-
#
# MOOSE documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 1 19:05:47 2014.
# updated on Thr Jan 21 00:30:10 2016
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in ... | BhallaLab/moose | docs/source/conf.py | Python | gpl-3.0 | 10,678 | [
"MOOSE"
] | dfc8b8457143b23fa9152dd3093d9b7ebe039fb65e33adedad09ef5de2f77731 |
"""Monitoring Daemon."""
import logging
import time
from datetime import datetime
import requests
from daemonize import Daemonize
from lzproduction.utils import logging_utils
from lzproduction.sql.statuses import LOCALSTATUS, SERVICESTATUS
from lzproduction.sql.utils import db_session
from lzproduction.sql.tables imp... | alexanderrichards/LZProduction | lzproduction/monitoring/MonitoringDaemon.py | Python | mit | 4,656 | [
"DIRAC"
] | 74277cefc0de52471d10957ae2dcf9a430a2f3b455ba2f69fb19952053cb5412 |
# -*- coding: utf-8 -*-
#
# pyrubberband documentation build configuration file, created by
# sphinx-quickstart on Mon Oct 19 10:40:20 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 file.
... | bmcfee/pyrubberband | docs/conf.py | Python | isc | 8,734 | [
"Brian"
] | 8afa1906cfbf5232d9cdf63e9a8ef7b64ba3fed9e07a3aeccda5a0a67b6d7a16 |
#!/usr/bin/env python
import argparse
import logging
import time
from bioblend.galaxy import GalaxyInstance
from bioblend.galaxy.client import ConnectionError
import datetime as dt
import yaml
# Omit (most of the) logging by external libraries
logging.getLogger('bioblend').setLevel(logging.ERROR)
logging.getLogger(... | gvlproject/gvl.ansible.filesystem | files/scripts/install_genome_indices.py | Python | mit | 6,317 | [
"Galaxy"
] | 640e59c23ce287edb84a139ccf9ca96034a28e62adcdb4931cbf8705d80e84a4 |
#-------------------------------------------------------------------------------
# Name: sample_nansatBasemap
# Purpose:
#
# Author: asumak
#
# Created: 28.01.2013
# Copyright: (c) asumak 2013
# Licence: <your licence>
#---------------------------------------------------------------------... | yuxiaobu/nansat | sample_nansatBasemap.py | Python | gpl-3.0 | 5,942 | [
"Gaussian"
] | e387803bb7883c5743d9a37d94e70294c6626b61dd1e24993ddf9c0eb49ffe77 |
from datetime import datetime
import hashlib
from werkzeug.security import generate_password_hash, check_password_hash
from itsdangerous import TimedJSONWebSignatureSerializer as Serializer
from markdown import markdown
import bleach
import json
from flask import Flask, current_app, request, url_for, jsonify, session
f... | Spandex-at-Exeter/demography_database | app/models.py | Python | mit | 151,567 | [
"Amber"
] | a738c739ecd9863af4a84df4b41491ca2c2a50e836e7d4626f8f5a8ebe82660f |
#-*- coding=utf-8 -*-
#-----------------------
# Named: Price Models
# Created: 2016-08-11
# @Author: Qianfeng
#-----------------------
from random import random,randint
import math
import numpy as np
from pylab import *
def wineprice(rating, age):
peak_age = rating-50
# 根据等级来计算计算价格
price = rating/2
if a... | qianfengzh/ML-source-code | algorithms/CollectiveIntelligence/CH08-Price Models/numpredict.py | Python | gpl-2.0 | 5,428 | [
"Gaussian"
] | 5b4baa47e959e5148d0dce81a654d6715d61f5c7321b0f5239070c51df95664f |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | hehongliang/tensorflow | tensorflow/python/autograph/converters/call_trees.py | Python | apache-2.0 | 11,904 | [
"VisIt"
] | 0b77c478b6d41bbf31efbdd6704790a677a2a3e2a2cd17345b242c6ce07db6e7 |
# TODO: Determine which tests are valid for GLSAR, and under what conditions
# TODO: Fix issue with constant and GLS
# TODO: GLS: add options Iterative GLS, for iterative fgls if sigma is None
# TODO: GLS: default if sigma is none should be two-step GLS
# TODO: Check nesting when performing model based tests, lr, wald,... | DonBeo/statsmodels | statsmodels/regression/linear_model.py | Python | bsd-3-clause | 92,206 | [
"Gaussian"
] | 1070d5350c612b44f38811879cafcc27f46b9c848f6f832947a3f8ac19afc5bb |
import random
import string
from django.contrib.auth import get_user_model
from django.db import models
from django.utils import timezone
import base32_crockford
API_KEY_LENGTH = 32
def generate_key(length):
return ''.join(
random.choice(string.digits + string.ascii_lowercase)
for __ in xrange... | sneeu/little | little/models.py | Python | mit | 1,848 | [
"VisIt"
] | 20e1925da52ecd91b3af8a48cfddd8b0df8395cfd6e457288363f97cf291a81a |
from traits.api import HasTraits, Instance, ListStr, Str, Dict, Property
from traitsui.api import View, Group, Item
from mayavi.core.trait_defs import DEnum
from simphony.cuds.abc_modeling_engine import ABCModelingEngine
class EngineManager(HasTraits):
"""A basic container of Simphony Engine that comes with a G... | simphony/simphony-mayavi | simphony_mayavi/plugins/engine_manager.py | Python | bsd-2-clause | 3,024 | [
"Mayavi"
] | 16ca04cc0026b58369770a8aec737b9c7fc9c0c67343f47bd19fd767d30b24ce |
# 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... | xiaoyuanW/gem5 | src/python/m5/stats/__init__.py | Python | bsd-3-clause | 4,535 | [
"VisIt"
] | a949f954de9d1d72ea3093df23f1ea23d5dc3aa485bdc3f20c63a176f49e9e75 |
# -*- coding: utf-8 -*-
##############################################################################
#
# Copyright (C) 2014 Eficent (<http://www.eficent.com/>)
# <contact@eficent.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero ... | Eficent/odoo-operating-unit | purchase_request_procurement_operating_unit/__openerp__.py | Python | agpl-3.0 | 2,045 | [
"VisIt"
] | f0af185fbb5fc06105e5e7975a0b7b003a185235500fe155113b6f4b9b3d9925 |
#!/usr/bin/env python
"""Spectral indicator definition and measurements."""
import sys
import numpy as N
from scipy.interpolate import LSQUnivariateSpline, UnivariateSpline
from snspin.spectrum import smoothing
from snspin.spectrum import covariance
class Craniometer(object):
"""Initialization function."""
... | nicolaschotard/snspin | snspin/spin.py | Python | mit | 82,655 | [
"Gaussian"
] | 290d550b67daa049f3b4833aee9f71d612e393db19e120707be28715290739fb |
from sklearn.feature_extraction import DictVectorizer
from collections import defaultdict
import evaluateFile
import loading
import evaluation
import sys, os
import classification
import shutil
from utils import Stream
from sklearn.grid_search import GridSearchCV
import itertools
from sklearn.preprocessing.data import ... | TurkuNLP/CAFA3 | learning/ensemble.py | Python | lgpl-3.0 | 17,859 | [
"BLAST"
] | 37920eaefc59650a4fadeafa24e660f8f3c95dbcfb94042129447b7466332a18 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | martinbede/second-sight | tensorflow/python/ops/control_flow_grad.py | Python | apache-2.0 | 7,938 | [
"VisIt"
] | 5b95e543129e1ff346b14495e8831ac419351eaa2be904033173fc60a941b274 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import datetime
import itertools
import os
from django.contrib.auth.models import User
from django.contrib.auth.signals import user_logged_in, user_logged_out
from django... | BMJHayward/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 67,625 | [
"VisIt"
] | 1cf2a781093673174492590f3c80c4930b433c8c35f575dc36158a25f8b9a8e0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.structure import Structure
from pymatgen.core.units import Ha_to_eV, bohr_to_ang
from pymatgen.io.abinit.abiobjects import *
import ... | dongsenfo/pymatgen | pymatgen/io/abinit/tests/test_abiobjects.py | Python | mit | 5,537 | [
"ABINIT",
"pymatgen"
] | f614c5d8bd69b5926d492ee361d8c2d5a34029259407aec13b58fc5d1f435d5b |
#!/usr/bin/python
# Use 1 or 2 arguments:
# 1 (read): generic input file
# 2 (write): Molcas input file (default: append ".mol" to generic input)
import sys
#=============================
# CHANGE THIS DATA AS NEEDED
Q_root = 1
seward_header = """\
*** Usa el directorio de bases (6-31G* con funciones esfericas)... | Jellby/ASEP-MD | Tests/scripts/gen2molcas6.py | Python | gpl-3.0 | 5,951 | [
"MOLCAS"
] | 0b56bdd73820bff4d706ed9b841f4b72d5926de5bab9ea51e2854398ba5043ec |
"""Utilities for handling PDBQT files."""
from typing import Dict, List, Optional, Set, Tuple
from deepchem.utils.typing import RDKitMol
def pdbqt_to_pdb(filename: Optional[str] = None,
pdbqt_data: Optional[List[str]] = None) -> str:
"""Extracts the PDB part of a pdbqt file as a string.
Either ... | miaecle/deepchem | deepchem/utils/pdbqt_utils.py | Python | mit | 10,872 | [
"RDKit"
] | 3c3b2d81d0df00fb78a81a12a81323e9cf92c1606b5b32735616206dcc56055e |
import unittest
import os
import json
import scipy
from io import open
from pymatgen.phonon.dos import CompletePhononDos
from pymatgen.phonon.plotter import PhononDosPlotter, PhononBSPlotter, ThermoPlotter
from pymatgen.phonon.bandstructure import PhononBandStructureSymmLine
test_dir = os.path.join(os.path.dirname(... | dongsenfo/pymatgen | pymatgen/phonon/tests/test_plotter.py | Python | mit | 3,658 | [
"pymatgen"
] | 97bfd777da2fa187851872ca4561e5b8312a5a3b9082c0abe0c7e14c8ea8eb3c |
#!/usr/bin/python2
# -*- Mode: Python; py-indent-offset: 8 -*-
# (C) Copyright Zack Rusin 2005
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, ... | CPFDSoftware-Tony/gmv | utils/Mesa/Mesa-7.8.2/src/mesa/glapi/gen/gl_enums.py | Python | gpl-3.0 | 6,491 | [
"Brian"
] | c5b17fd853c9c1447eb66855da263dcb53a35ed03d2fa90d16c217174520fc02 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
from InteractorSuperclass import InteractorSuperclass
class Interactor3rdPerson(InteractorSuperclass):
'''
Inherit the VTK class vtkInteractorStyleUser and extend it to be a 3rd-person camera that tracks a specified SceneObject.
This class will on... | GearsAD/semisorted_arnerve | sandbox/bot_vis_platform_oculus/scene/Interactor3rdPerson.py | Python | mit | 3,581 | [
"VTK"
] | d58787e9be0450f289c748291bff714fd5d81755f54a4c72063d25646df76226 |
# -*- coding: utf-8 -*-
"""
Created on Sun Nov 15 15:24:39 2015
Functions for single-cell TCRseq analysis for paired-end fastq data
@author:David Redmond (email david.redmond@outlook.com)
"""
import sys, os, commands, csv, commands, operator, tempfile, subprocess, numpy
from itertools import groupby, count
from collec... | ElementoLab/scTCRseq | sctcrfuncs.py | Python | agpl-3.0 | 13,655 | [
"BLAST",
"BWA"
] | e202b79a396398bc66afab0253cb8bf1092bbc20d14717a95e901e42d57e16e1 |
# Philip Bailey
# 2 October 2019
# loops over all files listed in the CHaMP Workbench and reports whether they exist on the local system
import os
import sys, traceback
import argparse
import sqlite3
import json
from lib.sitkaAPI import APIGet
from lib import env
from lib.loghelper import Logger
from datetime import da... | SouthForkResearch/CHaMP_Metrics | scripts/download_champ_data.py | Python | gpl-3.0 | 4,178 | [
"VisIt"
] | 5fc100b8efc72b7d23bced560fd80f92659ebb68233f228c6a856560d788460c |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
import pyglet
import cocos
from cocos.director import director
from cocos.actions import *
from cocos.layer import *
from cocos.particle_systems import *
cl... | adamwiggins/cocos2d | test/test_particle_fire.py | Python | bsd-3-clause | 784 | [
"Galaxy"
] | 240e3e3a051907c9dc1fcd4458ebdd04a9afa725e7c6cf46c39e307db5dbebcf |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by XXX.
Craig Markwardt converted the FORTRAN code to IDL. The information for the
IDL version is:
... | segasai/astrolibpy | mpfit/mpfit.py | Python | gpl-3.0 | 78,287 | [
"Gaussian"
] | ad24d39d37524feff44fd8e1907cc2cc8e1c199dfa3b80fe2672b99194550171 |
##################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2015 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2.1
## S... | BhallaLab/moose-examples | snippets/rxdSpineSize.py | Python | gpl-2.0 | 10,748 | [
"MOOSE",
"NEURON"
] | d39be95b57f77875c026e5e917737155041ac30463ab0972ba93b4b7f03a2b73 |
import tempfile
from copy import deepcopy
import numpy as np
from numpy import cos, sin, pi
import gmin_ as GMIN
from pele.potentials import GMINPotential
from pele.potentials import LJ
from pele.angleaxis import RBTopology, RBSystem, RigidFragment
from pele.utils.xyz import write_xyz
class OTPPotential(LJ):
d... | js850/pele | playground/otp/otp.py | Python | gpl-3.0 | 4,872 | [
"PyMOL"
] | 12c307114f029f9a82c7b8f8f63b7c1ee3b1c0bd29a2d43aafde4f83c009e9f3 |
# import modules
import mcpi.minecraft as minecraft
from time import sleep
# connect python to minecraft
mc = minecraft.Minecraft.create()
# create CONSTANTS for block and light colours
AIR = 0
STONE = 1
WOOL = 35
BLACK = 15
RED = 14
AMBER = 4
GREEN = 5
# clear area in middle of map and move player there
mc.setBlock... | NeilCFord/CPD4T_Minecraft_Workshop | trafficlights.py | Python | cc0-1.0 | 1,305 | [
"Amber"
] | 8b19b1693ff02872aa3ae9e832118c37217f6d0c19923073f89bf99897d8ef13 |
from flow_workflow.perl_action import actions
from flow_workflow.perl_action import adapter_base
from flow_workflow.perl_action import future_nets
from lxml import etree
import mock
import unittest
PARALLEL_BY_XML = '''
<operation name="test_op_name" parallelBy="foo">
<operationtype commandClass="NullCommand"
... | genome/flow-workflow | unit_tests/perl_action/test_adapter_base.py | Python | agpl-3.0 | 2,054 | [
"exciting"
] | 052925a4d5ab2e3d1cfd6269e3def53d52c0f3892ab754af11d72df4018310d4 |
from Sire.IO import *
from Sire.Mol import *
from Sire.Base import *
import Sire.Config
import subprocess
import shlex
import sys
import os
from nose.tools import assert_equal
sire_python = getBinDir() + "/sire_python"
gromacs_path = StringProperty("../io/gromacs")
def _test_broken_pdb():
try:
verbos... | michellab/SireUnitTests | unittests/SireIO/test_locale.py | Python | gpl-3.0 | 4,886 | [
"Gromacs"
] | d17d211cfdb69ac2413436d9aacdc0f4116f35c494c1ebeb6074081af12b48e4 |
import numpy as np
from scipy.ndimage.interpolation import shift as scipy_shift
from skued import register_time_shift, register_time_shifts
import pytest
np.random.seed(23)
def test_time_shift_trivial():
"""Test that the time-shift between two identical traces is zero."""
trace1 = np.sin(2 * np.pi * np.lins... | LaurentRDC/scikit-ued | skued/time_series/tests/test_time_zero.py | Python | gpl-3.0 | 3,135 | [
"Gaussian"
] | bef5b6132a0c11f577029fd459218f36af31b5cfd0f59b92dae4dbe31e3cd5d8 |
# -*- coding: utf-8 -*-
"""
A VTK RenderWindowInteractor widget for wxPython.
Find wxPython info at http://wxPython.org
Created by Prabhu Ramachandran, April 2002
Based on wxVTKRenderWindow.py
Fixes and updates by Charl P. Botha 2003-2008
Updated to new wx namespace and some cleaning up by Andrea Gavana,
December 2... | KristoferHellman/gimli | python/pygimli/gui/vtk/wxVTKRenderWindowInteractor.py | Python | gpl-3.0 | 24,578 | [
"VTK"
] | f25866a7d4d3bb08b10733598f6e1a1b08cb2260f71564f52f921b2a8c662c94 |
#Author : Lewis Mervin lhm30@cam.ac.uk
#Supervisor : Dr. A. Bender
#All rights reserved 2014
#Protein Target Prediction Tool trained on SARs from PubChem (Mined 08/04/14) and ChEMBL18
#Molecular Descriptors : 2048bit Morgan Binary Fingerprints (Rdkit) - ECFP4
#Dependencies : rdkit, sklearn, numpy
#libraries
from rdkit... | lhm30/PIDGIN | predict_binary.py | Python | mit | 3,324 | [
"RDKit"
] | 3a7f593b57f1ad7dbec6bddaa2d9f0a947fda63b599cd0e4df606002ab3adfff |
#!/usr/bin/env python
# Copyright 2014-2018 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/lo/test/test_nao.py | Python | apache-2.0 | 2,294 | [
"PySCF"
] | 86792f46fc0534a1b10c2f86ab8cdb7bd9b0d044463e1fd3b8d16be0f9b41d2f |
"""This module contains functional tests for the Home Page."""
import datetime
from django.contrib.auth import get_user_model
from mezzanine.core.models import CONTENT_STATUS_PUBLISHED
from mezzanine.blog.models import BlogPost
from communities.models import Community
from fec.utils import SeleniumTestCase
from homepa... | FederationOfEgalitarianCommunities/FECWebsite | fec/functional_tests/home_page_tests.py | Python | gpl-3.0 | 5,254 | [
"VisIt"
] | 0f5d3184bf394f95a971f671c39a5bdfc220185ae10862fbb70cd32874cc1090 |
import tensorflow as tf
import numpy as np
import time
def get_batch(X, Xn, size):
a = np.random.choice(len(X), size, replace=False)
return X[a], Xn[a]
class Denoiser:
def __init__(self, input_dim, hidden_dim, epoch=10000, batch_size=50, learning_rate=0.001):
self.epoch = epoch
self.batch... | BinRoot/TensorFlow-Book | ch07_autoencoder/denoiser.py | Python | mit | 3,422 | [
"Gaussian"
] | 5c0ccb6f3d2914b32c8c091503de60621f11561a71ac5d3a66a077ef9293bd23 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | samples/dpd.py | Python | gpl-3.0 | 2,365 | [
"ESPResSo"
] | a1ab0a9ab633ca356f60ac3fedc81341941645f7b6765f556d014778a8c9dec5 |
from __future__ import (absolute_import, division, print_function)
import unittest
from mantid.simpleapi import logger
import AbinsModules
class AbinsLoadCRYSTALTest(unittest.TestCase, AbinsModules.GeneralLoadAbInitioTester):
def tearDown(self):
AbinsModules.AbinsTestHelpers.remove_output_files(list_of_n... | ScreamingUdder/mantid | scripts/test/AbinsLoadCRYSTALTest.py | Python | gpl-3.0 | 2,066 | [
"CRYSTAL"
] | abe5d41be0391fef6731211c01d4254b978ad8834c68b09aaadca12f797f47d2 |
import truetypetracer as ttt # https://github.com/aewallin/truetype-tracer
import openvoronoi as ovd # https://github.com/aewallin/openvoronoi
#import ovdvtk
import time
#import vtk
import random
import string
import sys
def translate(segs,x,y):
out = []
for seg in segs:
seg2 = []
... | aewallin/openvoronoi | src/test/pytest_ttt_random_chars/ttt_random_chars.py | Python | lgpl-2.1 | 5,444 | [
"VTK"
] | 09ac2c918dee198b4c50c8eb63cd7395d279a7e337639130a44ef262d993def8 |
import flask
from views import *
from lookups import *
import rest as annotation
import requests
from config import config
if config.IMPORT_PYSAM_PRIMER3:
import pysam
import primer3
import myvariant
import re
from utils import *
import itertools
import csv
#hpo lookup
import phizz
import random
import orm
impo... | Withington/phenopolis | views/variant.py | Python | mit | 9,280 | [
"pysam"
] | a163dc2c0f8d7fa1ca602f20520f68c27149cd6d6b1f2924a602c2c49f4d45b0 |
# Copyright 2004 by James Casbon. 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.
"""
Code to deal with COMPASS output, a program for profile/profile comparison.
Compass is des... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Compass/__init__.py | Python | gpl-2.0 | 14,941 | [
"Biopython"
] | f42ca4d62116bf12852f8655a50aa72fbe8520b0e2630d960e79e4a1aa018712 |
# Copyright 2017 Battelle Energy Alliance, LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | idaholab/raven | framework/DataObjects/DataSet.py | Python | apache-2.0 | 107,450 | [
"NetCDF"
] | f69a1c67c3285ef68d55b76a6dd180e57c976726ac2309fa4daa786dcccf1d14 |
from collections import OrderedDict
class GenInput:
def __init__(self):
self.rtRange = self.setRtRange()
self.cycles=[] # number of iterations in each for loop
self.rtvar=[] # variable rt parameter [ {"TCLOUD":[0,10,20]}, {"SZA":[0,30,60]}, {"ALBCON":[0,0.5,1.0]}]
self.rtcons={} ... | paulricchiazzi/SBDART | RunRT/GenInput.py | Python | gpl-3.0 | 14,678 | [
"Gaussian"
] | 7e552c6a9c618b013911874ee7d948bbfb7ec5d381ca52becd48b5e4683b9e13 |
""" This module loads all the classes from the VTK Charts library into
its namespace. This is an optional module."""
from vtkChartsPython import *
| b3c/VTK-5.8 | Wrapping/Python/vtk/charts.py | Python | bsd-3-clause | 149 | [
"VTK"
] | e88e3142f387f5b11a889e4b5a2933dd7d07a768ed2ddd54aef863f0e7cfd689 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Generates .h and .rc files for strings extracted from a .grd file.
This script generates an rc file and header (NAME.{rc,h}) to... | ric2b/Vivaldi-browser | chromium/base/win/embedded_i18n/create_string_rc.py | Python | bsd-3-clause | 27,808 | [
"xTB"
] | 887cad6273faca31a4cd1108912115b377478535ca8e63661a433eb0b58b4eb8 |
# ============================================================================
#
# Copyright (C) 2007-2012 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... | jeroendierckx/Camelot | camelot/model/fixture.py | Python | gpl-2.0 | 11,034 | [
"VisIt"
] | c77fd9a664b26d952960fc76f6610453af065ff5b1f534d9e2bb4593b2e64f40 |
from django.shortcuts import render_to_response, get_object_or_404
from django.db import models
from django.http import Http404, HttpResponseRedirect
from django.core.urlresolvers import resolve, reverse
from pprint import pprint
from django.template.context import Context, RequestContext
from forms import TellAFriendF... | gregplaysguitar/glamkit | glamkit/incubated/tellafriend/views.py | Python | bsd-3-clause | 5,531 | [
"VisIt"
] | e055725d9608325943c95fd3d463a4e04073daef00fc86febdd193b02231b388 |
# Copyright 1999 by Jeffrey Chang. All rights reserved.
# Copyright 2000 by Jeffrey Chang. All rights reserved.
# Revisions Copyright 2007 by Peter Cock. All rights reserved.
# Revisions Copyright 2009 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# l... | bryback/quickseq | genescript/Bio/ExPASy/Prosite.py | Python | mit | 10,917 | [
"Biopython"
] | bdddc23ac6aedf0e55b7579507d9e90c8570a965967b52157f8d0be956d80049 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/questions/models.py | Python | gpl-3.0 | 2,701 | [
"Brian"
] | f3f97162fb8f2720e191dfca4f67f407c67e5c21c5ca92582ebd955777ca3a8e |
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