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#!/usr/bin/env python
############################################################################
# Copyright (c) 2015-2016 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
###########################################... | INNUENDOWEB/INNUca | src/SPAdes-3.10.1-Linux/share/spades/spades_pipeline/support.py | Python | gpl-3.0 | 37,437 | [
"BWA"
] | b8ad5c581dd113ba5dff491e8d5251dd5d4eada9d2f1f3fef088d29b4097ca34 |
# proxy module
from __future__ import absolute_import
from mayavi.modules.glyph import *
| enthought/etsproxy | enthought/mayavi/modules/glyph.py | Python | bsd-3-clause | 89 | [
"Mayavi"
] | f8ee516a7c17e4a2605475412efd5c6beaf18f5c0d61f9ae7df7326977b22427 |
from sqlalchemy.sql import table, column, ClauseElement, operators
from sqlalchemy.sql.expression import _clone, _from_objects
from sqlalchemy import func, select, Integer, Table, \
Column, MetaData, extract, String, bindparam, tuple_, and_, union, text,\
case, ForeignKey, literal_column
from sqlalchemy.testing... | Abi1ity/uniclust2.0 | SQLAlchemy-0.9.9/test/sql/test_generative.py | Python | bsd-3-clause | 58,459 | [
"ADF",
"VisIt"
] | a69173cfdf2f7f8d30b50bbfbbf67f4107b72817ede0dafa6b98536869c9718c |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | jralls/gramps | gramps/plugins/webreport/surnamelist.py | Python | gpl-2.0 | 10,613 | [
"Brian"
] | a9b7fb452f9b42b841a149b3b364f5e97c65a2299132e2d9ddaa68d2bb8b1c5e |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawLoops(myscreen, loops, loopcolor):
nloop = 0
for lop in loops:
n = 0
N = len(lop)
first_point=ocl.Point(-1,-1,5)
previous=ocl.Point(-1,-1,5)
for p in lop:
if n==0: # don't dra... | AlanZatarain/opencamlib | scripts/waterline/waterline_7_cavity.py | Python | gpl-3.0 | 3,887 | [
"VTK"
] | 0810e9272c75c1dad0a60267b8116b83262db810215108d04ead1b8d09953ce4 |
""" Module that holds DISET Authorization class for services
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
from DIRAC.ConfigurationSystem.Client.Config import gConfig
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.F... | yujikato/DIRAC | src/DIRAC/Core/DISET/AuthManager.py | Python | gpl-3.0 | 12,276 | [
"DIRAC"
] | afe9064007b490991d8a3453ae7e3746247db27b4dce177c0076e115f1d41f58 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.... | ashray/VTK-EVM | IO/Core/Testing/Python/TestGlobFileNames.py | Python | bsd-3-clause | 3,167 | [
"VTK"
] | 6ce6ceee969683d5710e9fbd2599a15ef9d0f85251e8078191b4d57ebb38e12c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2017- Serge Noiraud
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | gramps-project/gramps | gramps/gen/filters/rules/place/__init__.py | Python | gpl-2.0 | 2,348 | [
"Brian"
] | dbd8fbf06f5e5513c0dbc2d242126aa3dc3ac7cea0d40f15d40aa96d87dd6e1c |
# Copyright (c) 2012-2014 Stephanie T. Douglas
# under the MIT License (see LICENSE.txt for full details)
import numpy as np
import cPickle
import emcee
import matplotlib.pyplot as plt
def quantile(x,quantiles):
""" Calculates quantiles - taken from DFM's triangle.py """
xsorted = sorted(x)
qvalues = [xs... | stephtdouglas/fit-rossby | fit_rossby.py | Python | mit | 7,182 | [
"Gaussian"
] | 299b963d6039af1fbe9fc96e44395b82dcd916f99a24f54e08b19aba272d7317 |
"""**Utilities for storage module**
"""
import os
import re
import copy
import numpy
import math
from osgeo import ogr
from safe.common.numerics import ensure_numeric
from safe.common.utilities import verify
# Default attribute to assign to vector layers
DEFAULT_ATTRIBUTE = 'Affected'
# Spatial layer file extension... | ingenieroariel/inasafe | safe/storage/utilities.py | Python | gpl-3.0 | 28,632 | [
"NetCDF"
] | 66969c8375af8a60d6b37535023292428c778ae1b190977a2f730aa63a329fe9 |
from pybrain.structure import FeedForwardNetwork
from pybrain.structure import LinearLayer, SigmoidLayer
from pybrain.structure import BiasUnit,TanhLayer
from pybrain.structure import FullConnection
from pybrain.datasets import SupervisedDataSet
from pybrain.supervised.trainers ... | fxsjy/pybrain | examples/supervised/test_network_read_write/jpq2layersWriter.py | Python | bsd-3-clause | 3,945 | [
"NEURON"
] | a4784f247035f5074ea9cf769258045093caf317aa9fbb4625f36699d9670a83 |
# Copyright (C) 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 versio... | psci2195/espresso-ffans | testsuite/scripts/tutorials/test_01-lennard_jones.py | Python | gpl-3.0 | 1,119 | [
"ESPResSo"
] | 556c1826c4bf483eb7f397d4e138f9fd06f50d9dd0b6b84965d35b8c666d4d7b |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2014 Paul Franklin
# Copyright (C) 2010-2015 Craig J. Anderson
#
# This program is free software; you can redistrib... | jralls/gramps | gramps/plugins/drawreport/ancestortree.py | Python | gpl-2.0 | 42,285 | [
"Brian"
] | 7e2c0053b31cca3ab901ba7415757a109451ca74c3887fa3e39c505307b370b0 |
# 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.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | junmin-zhu/chromium-rivertrail | PRESUBMIT.py | Python | bsd-3-clause | 22,478 | [
"VisIt"
] | 3e4def88c932d64e279a957b216b71af5f2005eff62654b687c7dd9b9a590f63 |
#!/usr/bin/env python
# Copyright 2014-2019 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/lo/boys.py | Python | apache-2.0 | 14,458 | [
"PySCF"
] | a9afe3efabc3e89220b44598e5c9d9fa4a27df9a2dbedc11495ef8c69bd7ec20 |
"""Support for control of Elk-M1 connected thermostats."""
from __future__ import annotations
from elkm1_lib.const import ThermostatFan, ThermostatMode, ThermostatSetting
from homeassistant.components.climate import ClimateEntity
from homeassistant.components.climate.const import (
ATTR_TARGET_TEMP_HIGH,
ATTR... | rohitranjan1991/home-assistant | homeassistant/components/elkm1/climate.py | Python | mit | 6,616 | [
"Elk"
] | c14c317141eb0a2b5bd146f7fe5bbecaa67e96b97334ce800d68112205eabe88 |
#!/usr/bin/env python
# general imports
from numpy import *
from random import *
# imp general
import IMP
# our project
from IMP.isd import *
# unit testing framework
import IMP.test
class MockFunc:
def __init__(self, setval, evaluate, evalargs=1, update=None):
self.__set = setval
self.__eva... | shanot/imp | modules/isd/test/medium_test_GaussianProcessInterpolationRestraintNumericallyNoSigma.py | Python | gpl-3.0 | 15,384 | [
"Gaussian"
] | bb405f9a49c50a647f2fba96143709a46ad3b5ec41f0835717a298bbe79aba5f |
#!/usr/bin/env python
"""
function:
parse the block of thermo data in a lammps logfile and perform auto- and
cross correlation of the specified column data. The total sum of the
correlation is also computed which can be converted to an integral by
multiplying by the timestep.
output:
stand... | qipa/lammps | doc/doc2/Scripts/correlate.py | Python | gpl-2.0 | 2,537 | [
"LAMMPS"
] | 24e9a46deae3ad00db5a6dfbffdd38b9a71f313e52c8264c1ef234de14400ec7 |
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
urlpatterns = [
url(r'^$', TemplateView.as_view(template_name='page... | markliederbach/blog-backend | config/urls.py | Python | mit | 1,552 | [
"VisIt"
] | 7351c2742df27069f88e85e8ae511c5f1977b62a3ffda4b50cd1359c29d68ba1 |
from .fgir import *
from .optimize import FlowgraphOptimization
from .error import Warn
import asyncio
class PCodeOp(object):
'''A class interface for creating coroutines.
This helps us keep track of valid computational elements. Every coroutine in
a PCode object should be an method of PCodeOp.'''
@staticmet... | cs207-project/TimeSeries | pype/pcode.py | Python | mit | 5,337 | [
"VisIt"
] | 9ae87e3a8fca58898b5268c7ca6f23cacc1d0405d22e90293e19db3eabe22bb9 |
# Copyright (C) 2017 Alex Nitz
#
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in t... | hagabbar/pycbc_copy | pycbc/noise/reproduceable.py | Python | gpl-3.0 | 6,953 | [
"Gaussian"
] | b4f4f24b548b6f27b57b112009df959191856425ee2121b4afc2614a2e7183bc |
import vtk
import math
vtk_major_version = vtk.VTK_MAJOR_VERSION
"""
vtk.vtkPoints(): A set of points cam be collected in a vtkPoints
object by first setting the number of points with the
vtk_points.SetNumberOfPoints(npts) method and then enumerating
through the points and using the vtk_points.SetPoint(i, point) metho... | saullocastro/pyNastran | pyNastran/gui/vtk_examples/tube_filter_helix.py | Python | lgpl-3.0 | 5,741 | [
"VTK"
] | 44c86c01ad35c6b3ccd66c32845f18eb9f65318d68cab35b6400e9e32d621f0c |
from selenium import webdriver
from torProfile import TorProfile
from pyvirtualdisplay import Display
import selenium
from random import randint
import subprocess
import os
import signal
import sys
import time
training_data = "Dumps/training/"
experiment_data = "Dumps/experiment/"
iface = "eth1"
sleep_time = 2.0
load... | chhans/tor-automation | capture.py | Python | mit | 3,679 | [
"VisIt"
] | 4be440b8e9d901f16ce595be7812812627d006ea29b13f7f10b6454c0844be9f |
# Copyright (c) 2017, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
ha2ev = 27.211396132
class YamboGreenDB():
"""
Read the green's functions calculated using yambo
These green's functions describe the spectral function of the quasiparticles.... | alexmoratalla/yambo-py | yambopy/dbs/greendb.py | Python | bsd-3-clause | 4,251 | [
"Yambo"
] | 9c68e436736ca51d07e2b325faf25ca17c978153c24561a087152290b542f1e9 |
APP_NAME = "mvp_chw_visits"
CHW_VISIT_ACTIVE_CASES_INDICATORS = dict(
app=APP_NAME,
indicators=dict(
all_cases=dict(
household_cases_90days=dict(
description="No. of active households in the past 90 days",
title="# Households in past 90 days",
... | puttarajubr/commcare-hq | custom/_legacy/mvp/static_definitions/couch/chw_visits.py | Python | bsd-3-clause | 6,673 | [
"VisIt"
] | 05c83a578bf489faa101803f08f4299eb1ede52f187a96759360f1b92219e324 |
"""
This is the Data Integrity Client which allows the simple reporting of
problematic file and replicas to the IntegrityDB and their status
correctly updated in the FileCatalog.
"""
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.DataManagementSystem.Client.DataManag... | andresailer/DIRAC | DataManagementSystem/Client/DataIntegrityClient.py | Python | gpl-3.0 | 10,020 | [
"DIRAC"
] | 5bf11fbe4e44bfd7eaeb6dca867a69c139dd4c10625b2bf088f30b7c49f7e2e4 |
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 7 14:56:14 2017
@author: yesf
"""
##############################################################################
#为方便与logistic模型结果的比对，评分卡为“颠倒型”，也就是分数越高，违约可能越大
#散度最大化的基本想法是将评分卡设置为特征的线性组合后，最大化好人群和坏人群的散度
#好人群和坏人群的散度定义为：
# 目标函数：max [f(s,G)-f(s,B)]ln[f(s,G)/f(s,B)]ds (Diverg... | allinpaybusiness/ACS | allinpay projects/creditscoredivmax/classdivmax.py | Python | apache-2.0 | 6,745 | [
"Gaussian"
] | 06bc26beadfb86935d4fe91a031c66e7a5ca262c46537213046bee1680118de0 |
#!/usr/bin/env python
from __future__ import print_function
from optparse import OptionParser
import sys
import numpy as np
import pandas as pd
import pysam
from dna_io import dna_one_hot
################################################################################
# bvcf.py
#
# Methods and classes to support .vc... | davek44/Basset | src/bvcf.py | Python | mit | 9,551 | [
"pysam"
] | 1382ddd8214fbbbfb644e7f80098c36b521bfc91c3e86c66262f7690167fe59f |
#!/usr/bin/env python
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspath(path.dirname(__file__))
# Get the long description from the README file
with open(path.join(here, 'README.md'), en... | foolcage/fooltrader | setup.py | Python | mit | 7,553 | [
"VisIt"
] | 4eb877916e5aabb0c3c18dac26b893ac8afdf3b9c2d09dab78818abd8bf35699 |
# -*- coding: utf-8 -*-
# QuickFF is a code to quickly derive accurate force fields from ab initio input.
# Copyright (C) 2012 - 2019 Louis Vanduyfhuys <Louis.Vanduyfhuys@UGent.be>
# Steven Vandenbrande <Steven.Vandenbrande@UGent.be>,
# Jelle Wieme <Jelle.Wieme@UGent.be>,
# Toon Verstraelen <Toon.Verstraelen@UGent.be>,... | molmod/QuickFF | quickff/tests/test_examples.py | Python | gpl-3.0 | 10,660 | [
"Gaussian"
] | 7dc4e21c4aa6c65d6505e8108ec6bc641339c1cf7da084ef26a0b9f18218e781 |
BASAL_NAME_FOLDER = "RUN_EVOEVO"
BASAL_NAME_PARENT_FOLDER = "./RESULTS"
FILE_NAME_SEPARATOR = "_"
SEP_IN_FILE = "\t"
END_OF_LINE_FILE = "\n"
COMMENTS_IN_FILE = '# '
GAUSSIAN = 0
UNIFORM = 1
TRANSITION_MATRIX = 2
GENE_SIZE = 4
FITNESS_COPY_FUNCTION_WITH_DOTS... | speignier/suppositoire | definitions.py | Python | gpl-2.0 | 3,228 | [
"Gaussian"
] | 11b4746855294abae24a2f4d7d9fddd5874bb3ba40287c0e26746799d6d20140 |
import collections
import os
from xml.etree import ElementTree
from galaxy.util.submodules import submodules
from galaxy import util
from ..metrics import formatting
import logging
log = logging.getLogger( __name__ )
DEFAULT_FORMATTER = formatting.JobMetricFormatter()
class JobMetrics( object ):
def __init... | jmchilton/lwr | galaxy/jobs/metrics/__init__.py | Python | apache-2.0 | 5,101 | [
"Galaxy"
] | f813e73d970db18e0f8d70e80e12b91a2d55a180c2b9eb62591885c41944bcae |
#! /usr/bin/python
# -*- coding: utf-8 -*-
# import funkcí z jiného adresáře
import os.path
import sys
path_to_script = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.join(path_to_script, "../extern/sed3/"))
# from ..extern.sed3 import sed3
# import featurevector
from loguru import logger
# logge... | mjirik/lisa | lisa/virtual_resection.py | Python | bsd-3-clause | 29,738 | [
"VTK"
] | 8f692d9d64cbc504b5dd9e5bff16a23a202a8dd9725708921adcd88e6746109f |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Change directory to p... | mick-d/nipype_source | nipype/interfaces/fsl/model.py | Python | bsd-3-clause | 82,941 | [
"Gaussian"
] | 34ae8bc97a1ec40524bd24ce088108f890e03ce2a939b763d948edf781664377 |
import pytest
from .utils import *
import psi4
from qcengine.testing import using
@pytest.mark.parametrize('engine', [
pytest.param('optking'),
pytest.param('geometric', marks=using('geometric')),
]) # yapf: disable
@pytest.mark.parametrize('inp', [
pytest.param({'name': 'hf', 'options': {'scf_type': '... | ashutoshvt/psi4 | tests/pytests/test_geometric.py | Python | lgpl-3.0 | 3,139 | [
"Psi4"
] | 8ac63fcbfcb7adbf7e7dbba9c2d4f1f77f6ef412988fc24ba759a9323bdbbccf |
# Copied from https://github.com/PX4/ecl/commit/264c8c4e8681704e4719d0a03b848df8617c0863
# and modified for ArduPilot
from sympy import *
from code_gen import *
import numpy as np
# q: quaternion describing rotation from frame 1 to frame 2
# returns a rotation matrix derived form q which describes the same
# rotation
... | lthall/Leonard_ardupilot | libraries/AP_NavEKF3/derivation/main.py | Python | gpl-3.0 | 29,240 | [
"DIRAC"
] | c55fc857465fd4806ab2df2e693339cd48146d482e5138511a7046e1ae75d174 |
"""
======================================
Plotting sensor layouts of MEG systems
======================================
In this example, sensor layouts of different MEG systems
are shown.
"""
# Author: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD (3-clause)
import os.path as op
from mayavi import mlab
im... | jniediek/mne-python | examples/visualization/plot_meg_sensors.py | Python | bsd-3-clause | 1,463 | [
"Mayavi"
] | 0072f6f174412a50eebe9bfa512a3f99d1349ed525f9bf64ea3c96c746109c53 |
# IM - Infrastructure Manager
# Copyright (C) 2011 - GRyCAP - Universitat Politecnica de Valencia
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your... | indigo-dc/im | IM/CtxtAgentBase.py | Python | gpl-3.0 | 21,525 | [
"Galaxy"
] | c61eee070026176f966d0a8f86456eae41e1aa09c7ba58107548ad5308195fcf |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
"""
This module provides classes to run and analyze boltztrap on pymatgen band
structure objects. Boltztrap is a software interpolating band structures and
computing materials properties from this band structure using Boltzmann
semi-cla... | Dioptas/pymatgen | pymatgen/electronic_structure/boltztrap.py | Python | mit | 44,658 | [
"BoltzTrap",
"pymatgen"
] | 8cf70500387577120e2186821c8d45c72e45630820d0d3fcba7996ddde0095ae |
# Copyright 2014 The Oppia Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable ... | brianrodri/oppia | core/domain/email_manager_test.py | Python | apache-2.0 | 274,978 | [
"VisIt"
] | 87a04676910c1b7beb921e3c0303d03537746a4e57ddc2d9e090aa672a7ab21d |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from .fake_webapp import EXAMPLE_APP
class IsTextPresentTest(object):
def test_is_text_present(self):
"should verify if tex... | bmcculley/splinter | tests/is_text_present.py | Python | bsd-3-clause | 1,967 | [
"VisIt"
] | 1dca7f9e838e950926469e70a42629feb73846afbe2d4a2235b7fd381ca27cd1 |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-05-19 17:56:30
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-07-06 14:43:00
# from __future__ import print_function, division, absolute_import
# from marvin.tests.ap... | albireox/marvin | python/marvin/tests/api/test_spaxel.py | Python | bsd-3-clause | 6,974 | [
"Brian",
"Galaxy"
] | 4d3bd7ddac67e7f246afffd940edea3ac9d3d9373827a9e65e0984fd4ae7d11d |
# f90wrap: F90 to Python interface generator with derived type support
#
# Copyright James Kermode 2011-2018
#
# This file is part of f90wrap
# For the latest version see github.com/jameskermode/f90wrap
#
# f90wrap is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser Gene... | jameskermode/f90wrap | f90wrap/f90wrapgen.py | Python | lgpl-3.0 | 35,177 | [
"VisIt"
] | bf16460a958f238e9588ade2f997a17111b3c4144c69633fea11421cd181d493 |
#!/usr/bin/env python
# Copyright (c) 2012 ARM Limited
# All rights reserved
#
# The license below extends only to copyright in the software and shall
# not be construed as granting a license to any other intellectual
# property including but not limited to intellectual property relating
# to a hardware implementation... | tiagormk/gem5-hmp | util/cpt_upgrader.py | Python | bsd-3-clause | 12,383 | [
"VisIt"
] | 12ba8a12b1027acbbd5f2c58d29f380bb92626852fb153739af966149eb9d990 |
#!/usr/bin/env python
"""
This file tests vtk.util.vtkImageExportToArray and
vtk.util.vtkImageImportFromArray. It tests the code by first
exporting a PNG image to a Numeric Array and then converts the array
to an image and compares that image to the original image. It does
this for all PNG images in a particular dir... | ashray/VTK-EVM | Common/DataModel/Testing/Python/TestNumericArrayImageData.py | Python | bsd-3-clause | 2,101 | [
"VTK"
] | bf5c12b1b3358a5c0c641c293da10619b64191d5f536a4b5629d41ecaf9a7fbb |
import ast
import os
from jaspyx.ast_util import ast_load, ast_store, ast_call
from jaspyx.visitor import BaseVisitor
class Import(BaseVisitor):
import_path = ['.']
def load_module(self, pieces):
module_name = '.'.join(pieces)
if module_name in self.registry:
return
if le... | iksteen/jaspyx | jaspyx/visitor/import_.py | Python | mit | 4,183 | [
"VisIt"
] | 69764f6a67434c065fdbc60678944556943fadf769b134689b23bb9dc400f480 |
#!/usr/bin/env python
#----------------------------------------------------------------------------
# Name: test7.py
# Purpose: A minimal wxPython test program
#
# Author: Robin Dunn
#
# Created: A long time ago, in a galaxy far, far away...
# Copyright: (c) 1998 by Total Control Software
# L... | cestaberous/lbgprg | py/gui/0_information/wxPythonTest.py | Python | gpl-2.0 | 2,859 | [
"Galaxy"
] | a365e87a571929754c75e84d1a2e670ddc73fdb43b3bf7588db7d40bf2c8f74f |
# -*- coding:utf-8 -*-
from brian import Equations
from brian.units import *
from brian.stdunits import *
from model import PARAMETERS as ps
# If the model parameters have been initialized
if ps != None:
N_subpop = ps['Common']['N_subpop']
PSSYN = ps['Synapse']
V_E = PSSYN['V_E']
V_act_E = PSS... | neuro-lyon/multiglom-model | src/model/synapse.py | Python | mit | 3,066 | [
"Brian"
] | c303f64dad6308c9531eb7e44f3084838a3c4f90a47b32166d7326b0aa29861e |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
"""Implement MD Integrator."""
import itertools
from hoomd.md import _md
from hoomd.data.parameterdicts import ParameterDict
from hoomd.data.typeconverter impo... | joaander/hoomd-blue | hoomd/md/integrate.py | Python | bsd-3-clause | 8,904 | [
"HOOMD-blue"
] | 4de1a222d150fcafd74ac5d84a31112444736cc3d6098d95e90a7fdec2c4cff9 |
""" Collection of user jobs for testing purposes
"""
# pylint: disable=invalid-name
from __future__ import print_function
import os
from DIRAC import rootPath
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.tests.Utilities.utils import find_all
# parameters
# Commo... | petricm/DIRAC | tests/Utilities/testJobDefinitions.py | Python | gpl-3.0 | 2,690 | [
"DIRAC"
] | 906afb7b99460bd9d68077d27f25ea3c8dfea77acc3647268becdbfac208babb |
# Copyright 2009 by Cymon J. Cox. 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.
"""Command line wrapper for the multiple alignment program DIALIGN2-2.
"""
from __future__ impo... | zjuchenyuan/BioWeb | Lib/Bio/Align/Applications/_Dialign.py | Python | mit | 9,585 | [
"Biopython"
] | 7b156a3ba5634b5c08bfdf3899a6667783bf6c316b9d02d1d0b094cf5984d1a2 |
########################################################################
# $HeadURL $
# File: OperationHandlerBaseTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/25 08:09:08
########################################################################
""" :mod: OperationHandlerBaseTests
==============... | yujikato/DIRAC | src/DIRAC/RequestManagementSystem/Service/test/OperationHandlerBaseTests.py | Python | gpl-3.0 | 2,636 | [
"DIRAC"
] | b74e9f7d844a1459dae8f3202492f4a0e57678201026e5cbeb95b9bdc246b0d6 |
#!/usr/bin/python
import os
import shutil
# from testutil import run_gasoline, test_result
import pynbody as pyn
import numpy as np
import matplotlib.pyplot as plt
import pynbody.plot.sph as p_sph
#Parameters for the test
testdir='sedov'
files = ["data/sedov.std", "data/sedov.param"]
exe = "./ChaNGa"
testname = "Sedov... | ibackus/compare-changa-builds | tests/sedov/sedovblast_ch.py | Python | mit | 3,236 | [
"BLAST"
] | 91d72749f93d6eb004be54d1a899173c75674defb4e279aa41df95fec52f3a33 |
from gpaw.xc.gllb.contribution import Contribution
#from gpaw.xc_functional import XCRadialGrid, XCFunctional, XC3DGrid
#from gpaw.xc_correction import A_Liy, weights
from gpaw.sphere.lebedev import weight_n
from gpaw.utilities import pack
from gpaw.xc.gllb import safe_sqr
from math import sqrt, pi
from gpaw.mpi import... | ajylee/gpaw-rtxs | gpaw/xc/gllb/c_response.py | Python | gpl-3.0 | 20,645 | [
"GPAW"
] | 714155190386b5d05ecd4649d954c7e3fb977a46ccdf05a832bc74beea867999 |
#!/usr/bin/env python3
import os,sys,string,subprocess,signal,shutil,argparse
from subprocess import PIPE, run
#psutil
mcdir = sys.path[0]
#1 READ/PARSE COMMAND LINE ARGUMENTS
#1.1 PROCESS COMMAND LINE ARGUMENTS
parser = argparse.ArgumentParser(description="MetaCompass metagenome assembler version 2.0.0 by Victoria C... | marbl/MetaCompass | go_metacompass2.py | Python | artistic-2.0 | 16,636 | [
"BLAST"
] | 67e46cf523b8939960ceb6a3cfe7d4bbb673d0dd6b6daf0dffff28ceae41d8e9 |
# -*- coding: utf-8 -*-
import contextlib
import pyjade
def process_param(key, value, terse=False):
if terse:
if (key == value) or (value is True):
return key
if isinstance(value, basestring):
value = value.decode('utf8')
return '''%s="%s"''' % (key, value)
TYPE_CODE = {
... | xlk521/cloudguantou | pyjade/ext/html.py | Python | bsd-3-clause | 5,096 | [
"VisIt"
] | 8e93d6941d6805481e50dd00126f0e183728e974ffc69ad528b18a4eac58d105 |
"""
Regression tests for Studio's Setting page.
"""
from bok_choy.web_app_test import WebAppTest
from edxapp_acceptance.pages.studio.users import UsersPageMixin
from edxapp_acceptance.pages.studio.settings_advanced import (
AdvancedSettingsPage
)
from edxapp_acceptance.pages.studio.settings_group_configurations imp... | raeeschachar/edx-e2e-mirror | regression/tests/studio/test_schedule_and_details_settings.py | Python | agpl-3.0 | 5,952 | [
"VisIt"
] | 4733a8a4e03e4ea19894c216b98d4af4244c315e62f621ff70169f7a26197edf |
#!/usr/bin/env python
#
# texttable - module for creating simple ASCII tables
# Copyright (C) 2003-2011 Gerome Fournier <jef(at)foutaise.org>
#
# 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 Foundat... | ClusterHQ/dvol | dvol_python/texttable.py | Python | apache-2.0 | 21,967 | [
"Brian"
] | 91c39a332a7bfebf7db0bb4fc41686fe9a270d774cc14a8950b1e52a2ce7311f |
from __future__ import print_function
# module cubicSpline
''' k = curvatures(xData,yData).
Returns the curvatures of cubic spline at its knots.
y = evalSpline(xData,yData,k,x).
Evaluates cubic spline at x. The curvatures k can be
computed with the function 'curvatures'.
From:
http://www... | mzechmeister/serval | src/cubicSpline.py | Python | mit | 10,659 | [
"Gaussian"
] | c72890e6cb0dd9a2f6944d61209e351ff2962350ea8acdd36e5d1ad2efc13c81 |
# -*- coding: utf-8 -*-
# ***********************************************************************
# Copyright (C) 2016 - 2017 Oscar Gerardo Lazo Arjona *
# <oscar.lazoarjona@physics.ox.ac.uk> *
# ***********************************************************************
... | oscarlazoarjona/quantum_memories | examples/hyperfine_orca/simple_example_rb.py | Python | gpl-3.0 | 2,109 | [
"ORCA"
] | 4a18849a5097406e352cd63ef5da19ed7835855b1f0eb1b8ff3e51fbd458b1af |
# -*- coding: utf-8 -*-
from abc import ABC, abstractmethod
import argparse
from collections import defaultdict
import inspect
import logging
import progressbar
from typing import Any, DefaultDict, Dict, List, Set, Type
from catmaid.apps import get_system_user
from catmaid.control.annotationadmin import copy_annotati... | tomka/CATMAID | django/applications/catmaid/management/commands/catmaid_import_data.py | Python | gpl-3.0 | 41,280 | [
"NEURON"
] | ab02b49861ad86337a80358d9fbea19c24e687e687edfa26a9b59360a0751281 |
# This is to be used in the CloudServer deployment,
# it currently has all the urls for lems_ui, cenet, results_viewer, rtw_ui
from django.conf.urls import patterns, include, url
import lems_ui.views
import cenet.views
import results_viewer.views
import rtw_ui.views
import worm_conf.views
# Uncomment the next two lin... | Si-elegans/Web-based_GUI_Tools | lems_ui/urls.py | Python | apache-2.0 | 4,731 | [
"NEURON"
] | 0c577d7fce145fe76018bdc82965f3301ec0275cac70346c9fc634d3b05a5289 |
'''
Brian-specific extension to the Sphinx documentation generation system.
'''
| brian-team/brian2genn | brian2genn/sphinxext/__init__.py | Python | gpl-2.0 | 80 | [
"Brian"
] | 821822cc97555e34c39e32fd42e38a1715182e28c1b09f1fc71d5f46969adef8 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | wtanaka/beam | sdks/python/apache_beam/runners/direct/direct_runner.py | Python | apache-2.0 | 8,397 | [
"VisIt"
] | 2ef580275b46892efa2d2cb53abc15786de976374d90bba06e6e8623c7d20746 |
import json
import logging
from difflib import ndiff
import waffle
from django import forms
from django.conf import settings
from django.core.exceptions import ObjectDoesNotExist
from django.forms.widgets import CheckboxSelectMultiple
from django.template.loader import render_to_string
from django.utils import transla... | ollie314/kuma | kuma/wiki/forms.py | Python | mpl-2.0 | 37,414 | [
"VisIt"
] | b585ff14857a6525488aee4542a4fc1fa57520414af3ba652ad9823bf100b6fc |
import numpy as np
import tensorflow as tf
from yadlt.models.boltzmann import dbn
from yadlt.utils import datasets, utilities
# #################### #
# Flags definition #
# #################### #
flags = tf.app.flags
FLAGS = flags.FLAGS
# Global configuration
flags.DEFINE_string('dataset', 'mnist', 'Which datas... | blackecho/Deep-Learning-TensorFlow | cmd_line/boltzmann/run_dbn.py | Python | mit | 6,820 | [
"Gaussian"
] | eb1fa072b0d00c8d62c153a2674b40ad1510d2fe2258bf4587e19c8ca2e229c0 |
# $Id$
#
# Copyright (C) 2003-2006 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 Lipinski par... | soerendip42/rdkit | rdkit/Chem/UnitTestLipinski.py | Python | bsd-3-clause | 3,208 | [
"RDKit"
] | 6b4ee94e728e20f16b5d788746d1eb88ae33a650a46bbb5da7e56e46a7d2d72e |
# -*- 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-talent | tests/unit/gapic/talent_v4/test_tenant_service.py | Python | apache-2.0 | 92,876 | [
"Octopus"
] | ccd004438582b5bde9ef833efe423c66f75eef3d149b3113d319aff1e36e92e9 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/friesian/feature/conftest.py | Python | apache-2.0 | 1,289 | [
"ORCA"
] | 5b9d0625b5d33424c02950ca0c66a14aeb9e5da514040baae527b7641ae1edeb |
# SPDX-License-Identifier: BSD-3-Clause
#
# Config file for GUS config generator.
#
# Names of GUS instrument files to use for playing MIDI.
# These are the names of the .pat files in the \ultrasnd\midi directory
# that are loaded into the card.
GUS_INSTR_PATCHES = {
0: "acpiano", # #001 - Acoustic Grand Piano
... | CWolfRU/freedoom | lumps/dmxgus/config.py | Python | bsd-3-clause | 14,982 | [
"CRYSTAL"
] | 9520e8f3983d03bf5309a7a7fbf487705b3dd401890603d4014c7e9536aaacde |
"""
=========================================
Image denoising using dictionary learning
=========================================
An example comparing the effect of reconstructing noisy fragments
of a raccoon face image using firstly online :ref:`DictionaryLearning` and
various transform methods.
The dictionary is fi... | chenyyx/scikit-learn-doc-zh | examples/zh/decomposition/plot_image_denoising.py | Python | gpl-3.0 | 5,878 | [
"Gaussian"
] | cac9a763471a7761a296128b36e54623e5679bdbbbc2faf7e28e8d09785ba2c2 |
import os
from math import pi, cos, sin
from ase import Atom, Atoms
from ase.parallel import rank, barrier
from gpaw import GPAW
from gpaw.test import equal, gen
import numpy as np
# Generate setup for oxygen with half a core-hole:
gen('O', name='hch1s', corehole=(1, 0, 0.5))
if 1:
a = 5.0
d = 0.9575
t = ... | robwarm/gpaw-symm | gpaw/test/h2o_xas_recursion.py | Python | gpl-3.0 | 1,259 | [
"ASE",
"GPAW"
] | 11d9285d902ff95401265c18a94b1a4f42db90e989ffff2280b76b14d3bb5719 |
# Copyright (c) 2020 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | luotao1/Paddle | python/paddle/fluid/dygraph/dygraph_to_static/break_continue_transformer.py | Python | apache-2.0 | 14,751 | [
"VisIt"
] | 6c2afcb726ab0e5b42134014b747b9e16f08685c303ff81ffc56a0e2ac657317 |
#* 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, ... | nuclear-wizard/moose | python/TestHarness/testers/AnalyzeJacobian.py | Python | lgpl-2.1 | 3,154 | [
"MOOSE"
] | 56d1a840db06af91b8fe512d1713fa9f184f860e1c8b98e130aca90c79cc634c |
# -*- coding: utf-8 -*-
"""
Called by ~/local/vim/rc/custom_misc_functions.vim
References:
# The vim python module documentation
http://vimdoc.sourceforge.net/htmldoc/if_pyth.html
ToLookAt:
https://github.com/ivanov/ipython-vimception
FIXME:
the indexing is messed up because some places row2 means th... | Erotemic/local | vim/rc/pyvim_funcs.py | Python | gpl-3.0 | 56,333 | [
"Galaxy"
] | f13ca7bf7a524d4dd9a52ada91ff9582895606c12813ea4bf91b666c8f92fe37 |
# coding=utf-8
# Copyright 2018 The DisentanglementLib 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
#
# Un... | google-research/disentanglement_lib | disentanglement_lib/visualize/visualize_util.py | Python | apache-2.0 | 6,783 | [
"Gaussian"
] | fe2f12187a56ca96c3e0de6736eee1aee0e16dfd6522449025d5688ba8d6a745 |
"""Visitor/traversal interface and library functions.
SQLAlchemy schema and expression constructs rely on a Python-centric
version of the classic "visitor" pattern as the primary way in which
they apply functionality. The most common use of this pattern
is statement compilation, where individual expression classes m... | obeattie/sqlalchemy | lib/sqlalchemy/sql/visitors.py | Python | mit | 7,999 | [
"VisIt"
] | 61fdf5b4a724a2dd4097e6028a2a1b0096cf20bc0d12d751277bd095cc3628e2 |
#!/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/grad/test/test_dhf.py | Python | apache-2.0 | 2,886 | [
"PySCF"
] | 53dc1bf02e730616678d91663a8c25472fcf38b0091908992b82ba131df5c268 |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import math
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['ApM1', 'M1', 'M1_Watchpoint', 'Watchpoint', 'ApKB', 'VFM', 'VFM_HFM', 'HFM'... | mkeilman/sirepo | tests/template/srw_generate_data/gaussian-x-ray-beam-through-a-beamline-containing-imperfect-mirrors.py | Python | apache-2.0 | 26,637 | [
"Gaussian"
] | ee54682e8dd80275b5eb755b59d0132c041abf6d793954650cbbc9e07dd08637 |
r"""
Definition
----------
This model describes a Gaussian shaped peak on a flat background
.. math::
I(q) = (\text{scale}) \exp\left[ -\tfrac12 (q-q_0)^2 / \sigma^2 \right]
+ \text{background}
with the peak having height of *scale* centered at $q_0$ and having a standard
deviation of $\sigma$. The FWH... | SasView/sasmodels | sasmodels/models/gaussian_peak.py | Python | bsd-3-clause | 1,720 | [
"Gaussian"
] | 46afaa704097e6fbf64f2540e2a0102187dd00a3f345d0813c5eec1ff296d635 |
import os
import logging
from sklearn.cluster import KMeans, SpectralClustering, DBSCAN, MeanShift,\
Birch, AffinityPropagation, AgglomerativeClustering
# Type checkers taken from here. http://stackoverflow.com/questions/25039626/find-numeric-columns-in-pandas-python
def is_type(df, baseTyp... | greytip/data-science-utils | datascienceutils/utils.py | Python | gpl-3.0 | 8,765 | [
"Gaussian"
] | 3a9d7869e282f0de46c5d208012e73c92a644d533c73ad2fd0a139c99c19fc6f |
########################################################################
# $HeadURL$
########################################################################
""" DIRAC FileCatalog utilities
"""
__RCSID__ = "$Id$"
try:
import hashlib
md5 = hashlib
except:
import md5
import random, os, time
from types import S... | avedaee/DIRAC | DataManagementSystem/DB/FileCatalogComponents/Utilities.py | Python | gpl-3.0 | 2,862 | [
"DIRAC"
] | b52839b29e8231d9de5b95020c9378cd841d164d478df04a1453971f626c2c5e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module is used for analysis of materials with potential application as
intercalation batteries.
"""
__author__ = "Anubhav Jain, Shyue Ping Ong"
__co... | xhqu1981/pymatgen | pymatgen/apps/battery/insertion_battery.py | Python | mit | 20,634 | [
"pymatgen"
] | cf920e56d008b8cd87a48665b572fc8395cb159c993aa32e354d9d933bcbd3d6 |
#!/usr/bin/env python
# encoding: utf-8
r"""
Simple fit
==========
This tutorial shows how to do the simplest inversion case, a curve fit, by
setting up a custom forward operator. The function to be fitted is`
.. math::
f(x) = A * e^{-x/X}
with the two unknown coefficients A (a signal amplitude) and X (a deca... | gimli-org/gimli | doc/tutorials/3_inversion/plot_0-expfit.py | Python | apache-2.0 | 6,241 | [
"Gaussian"
] | a3c250f3e13d80804d8f09c41d66fc34ca909855c8f61bca730225d830e0255d |
import sys, json, os
from solver.commonSolver import CommonSolver
from logic.smbool import SMBool
from logic.smboolmanager import SMBoolManagerPlando as SMBoolManager
from logic.helpers import Pickup
from rom.rompatcher import RomPatcher
from rom.rom_patches import RomPatches
from graph.graph import AccessGraphSolver ... | theonlydude/RandomMetroidSolver | solver/interactiveSolver.py | Python | mit | 55,648 | [
"VisIt"
] | 3c1e519dc418a075751085cdfb67987192a1410647a5623222a47dfc9f7a2c82 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | MrTheodor/espressopp | testsuite/interaction_potentials/unittest/PTestFENE.py | Python | gpl-3.0 | 1,424 | [
"ESPResSo"
] | 0ec43c982d9c2c15394a8e519ade99f2840785aadd3a793c7349d1229da72baa |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | 0x46616c6b/ansible | lib/ansible/modules/network/avi/avi_healthmonitor.py | Python | gpl-3.0 | 6,100 | [
"VisIt"
] | 2aafe9cc0824eb189828b706b043d8026c4c192ac56acd4ecebec7586368218f |
#__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 ... | andim/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 96,383 | [
"Gaussian"
] | 8bcb8ac765e7ce76ddad3478928ad74164f5e7c5c67f637c076e95ba1df0bfda |
#!/usr/bin/env python
"""
Cross-check energies of molecules from AlkEthOH set using SMIRNOFF xml file
versus energies from AMBER .prmtop and .crd files (parm@frosst params).
"""
import os
# datapath = './AlkEthOH_tripos/AlkEthOH_chain_filt1'
# datapath = './AlkEthOH_tripos/AlkEthOH_rings_filt1'
datapath = './AlkEthO... | open-forcefield-group/openforcefield | examples/deprecated/SMIRNOFF_comparison/compare_molecule_energies.py | Python | mit | 1,818 | [
"Amber"
] | 24c47efcedef7b81736bd518ab93234f1cdf3869fe0d872983d664314d69a056 |
# coding: utf-8
__all__ = [
'__version__',
'name',
'description',
'long_description',
'license',
'__author__',
'author',
'author_email',
'url',
]
__version__ = '4.6.0'
name = "ElectronPhononCoupling"
description = "Python module to analyze electron-phonon related quantities.... | abinit/abinit | scripts/post_processing/ElectronPhononCoupling/ElectronPhononCoupling/config/release.py | Python | gpl-3.0 | 989 | [
"ABINIT"
] | d1c84e3c012c6bdbc09c3db42d945c79e6ce79c386ae38a0e5460c6cdddc7968 |
# -*- coding: utf-8 -*-
'''Views of site pages'''
from django.shortcuts import render_to_response
from amber.mongo_db import MAIN_COLLECTION, SERVERS_COLLECTION, split_words
from django.conf import settings
from datetime import datetime
def sizeof_fmt(num):
'''Formatting file or folder size'''
for size in ['b... | yl3dy/amber | amber/views.py | Python | bsd-3-clause | 4,799 | [
"Amber"
] | 24ea947653a9092ac1bdd05377886e86c46412821642e7b19e6820946402a773 |
class mutation_stability(object):
'''
check mutation and format it so that it's compatible with foldx structure 1HA0 and 2YP7
'''
def __init__(self, mut, structure):
self.mut = mut # list of mutations
self.mut_set = set(mut) # set of mutations
self.mut_chain_info_set = set(... | blab/stability | augur/mutator/mutate_everything_2YP7/foldx_essentials/mutation_stability.py | Python | agpl-3.0 | 2,540 | [
"FoldX"
] | fbde5863cc982e3ce0a0f61795cee1971c9d4abbaefcf4942ca858b9e72399e7 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2009 Jan Decaluwe
#
# The myhdl 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 t... | cordoval/myhdl-python | myhdl/_always_comb.py | Python | lgpl-2.1 | 6,955 | [
"VisIt"
] | 83c585e3dbab48d0b160125b294dc3ebfa755920c328470901d6fcacccac711f |
# -*- mode: python; -*-
##
## sashimi_plot
##
## Utility for visualizing RNA-Seq densities along gene models and
## for plotting MISO output
##
import os
import sys
import glob
import warnings
with warnings.catch_warnings():
warnings.filterwarnings("ignore",category=UserWarning) ### hides import warnings
import... | wuxue/altanalyze | misopy/sashimi_plot/sashimi_plot.py | Python | apache-2.0 | 11,215 | [
"pysam"
] | 5fe36acc350788cf14484b9167a7fb074e6c9d1fd84fadb7079f872b0aa8bf5e |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | leeping/mdtraj | tests/test_hbonds.py | Python | lgpl-2.1 | 5,463 | [
"MDTraj",
"PyMOL"
] | acb832184755f24ae520ea8b38afd81fc4c3671948b4189de2d92467c55ec69b |
# Copyright 2019 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... | petewarden/tensorflow | tensorflow/python/keras/layers/kernelized.py | Python | apache-2.0 | 11,190 | [
"Gaussian"
] | 8bd29219d121f90567ad2cbbaed36468b2fa29525cd72f1c174fd7eae1c3340a |
import copy
import random
import logging
import numpy as np
import scipy.sparse as spp
from itertools import repeat, combinations
from collections import defaultdict
from indigo.operators import (
CompositeOperator, Product,
Eye, BlockDiag, Kron,
VStack, SpMatrix,
Adjoint, UnscaledFFT,
)
log = logging... | mbdriscoll/indigo | indigo/transforms.py | Python | bsd-3-clause | 8,789 | [
"VisIt"
] | f64909e9dd3c8291983e39f44ff351dc862e6619b6ff1308a1f25c614380a52c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Package for analysis of magnetic structures.
"""
from pymatgen.analysis.magnetism.analyzer import * # noqa
| gmatteo/pymatgen | pymatgen/analysis/magnetism/__init__.py | Python | mit | 223 | [
"pymatgen"
] | 5cc16a0bc4d38ed3a672395fa4b4766ef20479983d72b0621fae223099579f6d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import multiselectfield.db.fields
class Migration(migrations.Migration):
dependencies = [
('branch', '0044_auto_20141204_1126'),
]
operations = [
migrations.AlterField(
m... | MaximeBiset/care4care | branch/migrations/0045_auto_20141204_1708.py | Python | agpl-3.0 | 1,281 | [
"VisIt"
] | 558b45b0af964dbd85e9e2b9d879483a78947bc979c39b9bd213447db383d733 |
# -*- coding: utf-8 -*-
'''auto ordering call chain test mixins'''
from inspect import ismodule
from twoq.support import port
class ARandomQMixin(object):
def test_choice(self):
self.assertEqual(len(list(self.qclass(1, 2, 3, 4, 5, 6).choice())), 1)
def test_sample(self):
self.assertEqual(l... | lcrees/twoq | twoq/tests/auto/ordering.py | Python | bsd-3-clause | 2,838 | [
"MOE"
] | 2dcf060e7bf5ea9c7477d81d62b1bb133524d969eb923875b50c3b5553014a26 |
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