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from openmm_systems.test_systems import LennardJonesPair
import simtk.openmm.app as omma
import simtk.openmm as omm
import simtk.unit as unit
from wepy.runners.openmm import gen_sim_state
import time
import trio
def create_sim():
test_sys = LennardJonesPair()
integrator = omm.LangevinIntegrator(300.0*unit... | ADicksonLab/wepy | jigs/trio_mapper/source/trio_openmm.py | Python | mit | 1,420 | [
"OpenMM"
] | bcc69289f6d99074b192b6c803db730994e5cfbd4405050a7986779ecc3ca8fc |
"""Support for the Amazon Polly text to speech service."""
import logging
import boto3
import voluptuous as vol
from homeassistant.components.tts import PLATFORM_SCHEMA, Provider
import homeassistant.helpers.config_validation as cv
_LOGGER = logging.getLogger(__name__)
CONF_REGION = "region_name"
CONF_ACCESS_KEY_ID... | joopert/home-assistant | homeassistant/components/amazon_polly/tts.py | Python | apache-2.0 | 6,945 | [
"Brian"
] | 1aa765855a9fded5b3e1d70c149a5ce5dffb0147eefaeb06633143f6597f0919 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2017--2018 Amazon.com, Inc. or its affiliates. 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. A copy of the License
# is located at
#
# http://aws.... | mlperf/training_results_v0.7 | Google/benchmarks/gnmt/implementations/gnmt-research-TF-tpu-v4-512/utils/sacrebleu.py | Python | apache-2.0 | 96,093 | [
"COLUMBUS"
] | 4c0c49f8feee4a8c93bd5b6e81c0b311b6cfb4ee280d3ca02834efb873367da1 |
"""
Job Base Class
This class provides generic job definition functionality suitable for any VO.
Helper functions are documented with example usage for the DIRAC API. An example
script (for a simple executable) would be::
from DIRAC.Interfaces.API.Dirac import Dirac
from DIRAC.Interfaces.API.J... | fstagni/DIRAC | Interfaces/API/Job.py | Python | gpl-3.0 | 49,591 | [
"DIRAC"
] | a386659c9c9e3ad7aef8e9ae39d9de0d1783f7bb13af42d199c6802b1e9afef9 |
data = (
'mya', # 0x00
'myag', # 0x01
'myagg', # 0x02
'myags', # 0x03
'myan', # 0x04
'myanj', # 0x05
'myanh', # 0x06
'myad', # 0x07
'myal', # 0x08
'myalg', # 0x09
'myalm', # 0x0a
'myalb', # 0x0b
'myals', # 0x0c
'myalt', # 0x0d
'myalp', # 0x0e
'myalh', # 0x0f
'myam', # ... | samuelmaudo/yepes | yepes/utils/unidecode/x0ba.py | Python | bsd-3-clause | 4,765 | [
"MOE"
] | e20b9b89fa01789514af05c4238962b49ca07a4b9f1327265832eb27e42fb35e |
"""
Wrapper for gaussian filter that supports padding of the
boundary with voxel values inside the brain boundary. The
purpose of padding is so that gaussian filter results
are not distorted too badly nearly the brain boundary because
of the extremely low fMRI measurements outside the brain
boundary.
"""
import sys, o... | nhejazi/project-gamma | code/utils/gaussian_filter.py | Python | bsd-3-clause | 1,482 | [
"Gaussian"
] | 0b1d547adf5818e204a8f258e5833f825da26b2c3ca4f3348a7d5e11428a0ce4 |
#poly_gauss_coil model
#conversion of Poly_GaussCoil.py
#converted by Steve King, Mar 2016
r"""
This empirical model describes the scattering from *polydisperse* polymer
chains in theta solvents or polymer melts, assuming a Schulz-Zimm type
molecular weight distribution.
To describe the scattering from *monodisperse* ... | SasView/sasmodels | sasmodels/models/poly_gauss_coil.py | Python | bsd-3-clause | 4,158 | [
"Avogadro"
] | c2d03dbb251ecc876fce968e138b3f6d581c32b7140a38d02013db614d3535cd |
# Copyright 2016 Brian Innes
#
# 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 in writing, ... | brianinnes/vPiP | python/vPiP/generators/__init__.py | Python | apache-2.0 | 612 | [
"Brian"
] | 49c484484269ade89d476e59c562cf909342b2767919d81f17e2653120d40fc4 |
"""Participation model tests."""
from django.db.utils import IntegrityError
from tests.utils import ModelTestCase
from users.factory import UserFactory
from visits.factory import VisitFactory
from visits.models import Participation
class ParticipationTest(ModelTestCase):
"""Test the Participation model."""
... | oser-cs/oser-website | tests/test_visits/test_participation.py | Python | gpl-3.0 | 1,554 | [
"VisIt"
] | 0b45d7392b19fbcb7d30ab8580499d8a0541c581069e60d2e5b4895d3491798b |
# Compute a particle concentration
# and save as netCDF
import datetime
import numpy as np
from netCDF4 import Dataset
from postladim import ParticleFile
# import gridmap
# ----------------
# User settings
# ----------------
particle_file = "/hexagon/vol1/bjorn_rhea/out.nc"
grid_file = "/data/model_data006/anneds/... | bjornaa/ladim | models/zladim/aggregate2nc.py | Python | mit | 2,622 | [
"NetCDF"
] | e40158e2d8018b9b7ac88c2e8d5341e92c83ba32a728fb27b64e0d950063795b |
from django.contrib import admin
from .models import APIKey, Short, Visit
class APIKeyAdmin(admin.ModelAdmin):
list_display = ('user', 'key', )
model = APIKey
class VisitAdmin(admin.TabularInline):
extra = 0
model = Visit
readonly_fields = ('remote_addr', 'user_agent', 'referrer', 'created_at',... | sneeu/little | little/admin.py | Python | mit | 733 | [
"VisIt"
] | 901fc3c1f2d016b7d10ed34008df191931e3a0dbbe14501f5ccca5dfbd6b2fef |
"""
This Module is the graphic user interface wrapper for accessing the all small molecules database
Current Problems:
Compatibility issues and quick fix:
Issues with upgraded version of matplotlib:
for ubuntu:
sudo apt-get install tk-dev libpng-dev libffi-dev dvipng texlive-... | azariven/BioSig_SEAS | SEAS_Aux/Visualizer/Spec_Gui.py | Python | gpl-3.0 | 24,054 | [
"RDKit"
] | 8bdaac6f0bd6e1a35073cc78c522201769b62e3fc499e385d89cb1caf3e33b6d |
# -*- coding: utf-8 -*-
"""Release data for the IPython project."""
#-----------------------------------------------------------------------------
# Copyright (c) 2008, IPython Development Team.
# Copyright (c) 2001, Fernando Perez <fernando.perez@colorado.edu>
# Copyright (c) 2001, Janko Hauser <jhauser@zscout.de>... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/IPython/core/release.py | Python | mit | 4,272 | [
"Brian"
] | f211e085d581e7690cf91c4b1aa54f2e867fd0d199dd27f4242cec29d92ab111 |
#!/usr/bin/env python
#
# SPDX-FileCopyrightText: 2014-2022 Fredrik Ahlberg, Angus Gratton, Espressif Systems (Shanghai) CO LTD, other contributors as noted.
#
# SPDX-License-Identifier: GPL-2.0-or-later
from __future__ import division, print_function
import argparse
import base64
import binascii
import copy
import h... | espressif/esptool | esptool.py | Python | gpl-2.0 | 267,470 | [
"CRYSTAL",
"VisIt"
] | 59816efb6fbf9ed7d8565bc9fa6ce9d79e832045b0c0f1b16d9f164b15953609 |
#__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 ... | apbard/scipy | scipy/optimize/optimize.py | Python | bsd-3-clause | 105,325 | [
"Gaussian"
] | 449ebb2732985aeba73009354b48af4f364d9845274a5db359f92635718b07ac |
##################################################################
## 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... | dilawar/moose-full | moose-examples/snippets/testWigglySpines.py | Python | gpl-2.0 | 8,167 | [
"MOOSE",
"NEURON"
] | 956d0b26e713208efad287aff69458f062b435d527654754615aa9fc2a54e91d |
# SimpleCV Image Object
#load required libraries
from SimpleCV.base import *
from SimpleCV.Color import *
from numpy import int32
from numpy import uint8
import pygame as pg
class ColorSpace:
"""
This class is used to encapsulates the color space of a given image.
This class acts like C/C++ sty... | intelie/pycollector | src/third/SimpleCV/ImageClass.py | Python | bsd-3-clause | 96,392 | [
"Gaussian"
] | eb042f52edf4196a6d5f33c783ecc12bfa7d78f93391539c09668388b784686c |
# -*- coding: utf-8 -*-
#
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as pu... | thica/ORCA-Remote | src/scripts/system/system_debuglogger/script.py | Python | gpl-3.0 | 4,025 | [
"ORCA"
] | 4f1f1025ec8869d0c1a0c3f0437d683e530329c10d7c8ac0358cd437bc8277d8 |
from abc import ABCMeta, abstractmethod
class NeuralViewerConsole(metaclass=ABCMeta):
@staticmethod
@abstractmethod
def show_connection(connection):
pass
@staticmethod
@abstractmethod
def show_neuron(neuron):
pass
@staticmethod
@abstractmethod
def show_neural_netw... | mcasl/AMORE | pyAmore/cython/viewers.py | Python | gpl-3.0 | 3,229 | [
"NEURON"
] | c7983b09e3dd8f203b324a8138bb08355cb9340ad7117a1b78bd5e513f81a595 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
from .math import fit_gaussian
import warnings
from scipy.ndimage import center_of_mass, shift
from scipy.optimize import minim... | DanHickstein/pyBASEX | abel/tools/center.py | Python | gpl-2.0 | 23,101 | [
"Gaussian"
] | 93c263212a3535e5fed6c24e3167a47aff209aa1acabee125d3d9118ae6f3f08 |
import pytest
from pysisyphus.calculators.AnaPot import AnaPot
from pysisyphus.helpers import geom_loader
from pysisyphus.optimizers.LBFGS import LBFGS
from pysisyphus.testing import using
from pysisyphus.calculators.PySCF import PySCF
@pytest.mark.skip
@using("pyscf")
@pytest.mark.parametrize("line_search", [True, ... | eljost/pysisyphus | tests/test_lbfgs/test_lbfgs.py | Python | gpl-3.0 | 1,871 | [
"PySCF"
] | d2b53e75428bef8ee378bf7751d69a88cee62d7aec4006fc6fe4a7a27657df23 |
"""Core visualization operations."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
import sys
import os
from contextlib im... | bloyl/mne-python | mne/viz/backends/renderer.py | Python | bsd-3-clause | 12,076 | [
"Mayavi"
] | e587f3fec53c28abe34f8bd953b40141031cf1c6f6d0882d97648a63cba5a7c5 |
# MP1 Application 1
# Brian T. Bailey
# Define get and put functions
def get(list):
t = list.pop(0)
print "Removed a task from the queue: %s with priority %s" % (t.keys()[0], t[t.keys()[0]])
return t
def put(list, task):
list.append(task)
list.sort(key=lambda pv: pv.values()[0], reverse=True)
print "Added... | briantbailey/ITM-513 | mp1/mp1_app1.py | Python | mit | 1,442 | [
"Brian"
] | f680b9a4915303e9195d18a135623cac5400b0483877cbae800e3b55c0eb313b |
#!/usr/bin/python2
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
... | yasharmaster/scancode-toolkit | etc/scripts/json2csv.py | Python | apache-2.0 | 9,466 | [
"VisIt"
] | b126380be39733bc3e890871ec84736e0e341bbb8cc3a29340c89e06438c68b9 |
import StringIO
from volatility.renderers.basic import Renderer
try:
import ujson as json
except ImportError:
import json
__author__ = 'mike'
# additional author Tran Vien Ha
class HTMLRenderer(Renderer):
def __init__(self):
pass
def render(self, outfd, data):
"""Renders the treegri... | tranvienha/volatility-osint | misc/html.py | Python | gpl-3.0 | 5,971 | [
"VisIt"
] | d6eba921f0bb1fa9c094dff65d436b86e4a32fae44ec805e6dd7ce81aec9049b |
# -*- coding: utf-8 -*-
## Description: class MorphML for loading MorphML from file or xml element into MOOSE
## Version 1.0 by Aditya Gilra, NCBS, Bangalore, India, 2011 for serial MOOSE
## Version 1.5 by Niraj Dudani, NCBS, Bangalore, India, 2012, ported to parallel MOOSE
## Version 1.6 by Aditya Gilra, NCBS, Bangalo... | dilawar/moose-core | python/moose/neuroml/MorphML.py | Python | gpl-3.0 | 40,827 | [
"MOOSE",
"NEURON"
] | 0a628dba77697715700ba214ccb2ebbe42ed9c0741b356a3fecdb89501b8800c |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under t... | kain88-de/mdanalysis | package/MDAnalysis/exceptions.py | Python | gpl-2.0 | 2,321 | [
"MDAnalysis"
] | 6d45149badebd6d03f124dc84d93abfb3eedf6a6a893494de46aa9e414e13302 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/tree/tests/test_tree.py | Python | bsd-3-clause | 51,540 | [
"scikit-bio"
] | 0e38e47914d4a8e0902d2d019ab6008ba26535cabf397cf3bb5b9fcc050acbe9 |
import difflib
from test.test_support import run_unittest, findfile
import unittest
import doctest
import sys
class TestWithAscii(unittest.TestCase):
def test_one_insert(self):
sm = difflib.SequenceMatcher(None, 'b' * 100, 'a' + 'b' * 100)
self.assertAlmostEqual(sm.ratio(), 0.995, places=3)
... | HiSPARC/station-software | user/python/Lib/test/test_difflib.py | Python | gpl-3.0 | 11,497 | [
"MOOSE"
] | 11224893850d5318135dae6f0b7d62121f72d1bd03224b6a881daf25ba34c3fb |
########################################################################
# $HeadURL$
########################################################################
"""
Utilities to execute a function with a given proxy.
executeWithUserProxy decorator example usage::
@executeWithUserProxy
def testFcn( x, i, kw = 'qwerty... | marcelovilaca/DIRAC | Core/Utilities/Proxy.py | Python | gpl-3.0 | 3,866 | [
"DIRAC"
] | d31f51915ae87464768017b8c25f7e972d03500e5d59c7e11a4cff23bde6369f |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/bowtie/package.py | Python | lgpl-2.1 | 2,175 | [
"Bowtie"
] | 84cc96f76a81275251ef8cee28dfd3c972f41510d290c67c385ee31e5bb78cf3 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2011 Adam Stein <adam@csh.rit.edu>
#
# This program is free software; you... | beernarrd/gramps | gramps/plugins/docgen/rtfdoc.py | Python | gpl-2.0 | 21,776 | [
"Brian"
] | a4ed9e0a1cdc112f3dfbb7d579142eb17aa14c6e2a1d79a24772f5cffb5a5e04 |
import numpy as np
from mesonh_atm.mesonh_atmosphere import MesoNHAtmosphere
import matplotlib.pyplot as plt
from scipy.interpolate import RegularGridInterpolator
import scipy.optimize as sciopt
import modules.cloud as ModCloud
import pickle
font = {'size' : 26}
plt.rc('font', **font)
#Data without advection
path ... | DiegoSelle/master_thesis | radial_variograms.py | Python | mit | 18,921 | [
"Gaussian"
] | 9454b8143df5e844e64667767fd2944581496c7ccc41e5e818dfa73ae0200849 |
#! /usr/bin/env python
"""
Script to pre-average data using a sliding Gaussian kernel in time
"""
import argparse
from argparse import RawTextHelpFormatter
import numpy as np
import glob
import sys
import os
import itertools
import pickle
from scipy.ndimage.filters import gaussian_filter1d as gfilter
import casacore.ta... | darafferty/factor | factor/scripts/pre_average_time.py | Python | gpl-2.0 | 17,676 | [
"Gaussian"
] | d97cea1b7da904008334f36a975b8743503f109463dd2e7476e8bbecdbb02fc7 |
#
# linter.py
# Linter for SublimeLinter version 4.
#
# Written by Brian Schott (Hackerpilot)
# Copyright © 2014-2019 Economic Modeling Specialists, Intl.
#
# License: MIT
#
"""This module exports the D-Scanner plugin class."""
from SublimeLinter.lint import Linter, STREAM_STDOUT
class Dscanner(Linter):
"""Pro... | economicmodeling/SublimeLinter-dscanner | linter.py | Python | mit | 649 | [
"Brian"
] | f582b63e868de58784578fa49bd48244e4abccf12af73a44f649a7f3bd2e229a |
#!/usr/bin/env python
"""Module for the reciprocal blast step."""
from shared import create_directory, concatenate
from versions import MAKEBLASTDB, BLASTN, BLASTP
from subprocess import check_call, STDOUT
import logging as log
import os
import tempfile
import shutil
__author__ = "Tim te Beek"
__copyright__ = "Copyri... | ODoSE/odose.nl | reciprocal_blast_local.py | Python | mit | 2,955 | [
"BLAST"
] | 7a126b72f19aafab9cff6a71a94277a55a0f150ae3e37589944aed3f1cb904bc |
"""Copyright 2012 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.8'
__date__ = 'May 17 2010'
import threading
from ctypes ... | danielsuo/mobot | src/move/PhidgetsPython/Phidgets/Devices/Spatial.py | Python | mit | 25,537 | [
"VisIt"
] | a7b25f375048f5596f208b0b2627061c855f8a25a8b6568a559ccbe351b34e1c |
import HTMLParser
import json
import random
import re
import urllib2
import urlparse
import requests,os,time
import xbmc,xbmcaddon
USERDATA_PATH = xbmc.translatePath('special://home/userdata/addon_data')
ADDON_DATA = os.path.join(USERDATA_PATH,'script.module.universalscrapers')
full_file = ADDON_DATA + '/Log.txt'
def ... | repotvsupertuga/tvsupertuga.repository | script.module.universalscrapers/lib/universalscrapers/common.py | Python | gpl-2.0 | 16,257 | [
"MOE"
] | 10f974eadd9ea597d91fe3de16032e9e90c69eff4f1cc7f0f68401c75c7c7c52 |
import mdtraj as md
import numpy as np
import tensorflow as tf
import tftraj.rmsd
def test_against_mdtraj_diff_xy(sess, traj):
inds = [5, 19, 234]
target = np.array(traj.xyz[inds])
frames = tf.constant(traj.xyz)
target = tf.constant(target)
prmsd = tftraj.rmsd.pairwise_msd(frames, target)
re... | mdtraj/tftraj | tests/test_rmsd_tf.py | Python | mit | 554 | [
"MDTraj"
] | 62254dc53c51e153c6333139a003610d16300b76183878f3b1439920aa38c440 |
"""
=======================================================
Reading an inverse operator and view source space in 3D
=======================================================
"""
# Author: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License: BSD (3-clause)
print(__doc__)
from mne.datasets import sam... | effigies/mne-python | examples/inverse/plot_read_inverse.py | Python | bsd-3-clause | 1,462 | [
"Mayavi"
] | 4850b95114eafcf9e912911cb1746c8f609f978b095068a76871d0b347e50928 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import os.path as op
import sys
import re
import logging
from astropy.table import Table, Column
from maize.apps.base import AttrDict, str2bool, eprint, sh, mkdir, which
from maize.formats.base import must_open
from maize.formats.pbs import PbsJob, create_job_ch... | orionzhou/robin | old/pipelines/rnaseq.py | Python | gpl-2.0 | 24,757 | [
"ASE",
"BWA",
"Bowtie",
"HTSeq",
"pysam"
] | 24c7a230e7e92f9999cc30c7df2d4e2608e338eecb674579fa77912beacf08bc |
"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import functools
import re
import warnings
i... | ryfeus/lambda-packs | pytorch/source/numpy/lib/polynomial.py | Python | mit | 40,292 | [
"Gaussian"
] | 1a6f9722f6a5252d81d4a311bf205d7738961ed77c6429967f166527490e8b27 |
#!/usr/bin/env python
from opsimsummary import summarize_opsim as oss
import matplotlib.pyplot as plt
import os
import numpy as np
import copy
from astropy.table import Table
from astropy.units import Unit
import sncosmo
from lsst.sims.photUtils import BandpassDict
from lsst.sims.catUtils.supernovae import SNObject
... | rbiswas4/Cadence | quality/metrics.py | Python | mit | 9,758 | [
"VisIt"
] | 573f5a620c58f748bf1a1ffb270c1578c2bc9405553f63c322db240a264717c1 |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import json
import analytics
from io import BytesIO
import pytz
import logging
import smtplib
import StringIO
import csv
from boto... | vismartltd/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 83,588 | [
"VisIt"
] | 4316d3ae4a5afee22a50b741e52bb32c1a34fa3e4cf36a68228a3019ac3a47a6 |
# 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... | BackupTheBerlios/espressopp | src/integrator/MDIntegrator.py | Python | gpl-3.0 | 2,056 | [
"ESPResSo"
] | 3f2abc0bf80a8eaa6f1a7001a674ee8727d0788121aaa1a1cc5dec3f93dec491 |
# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
from logging import getLogger
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from pulsar.util im... | natefoo/pulsar | pulsar/managers/util/cli/job/slurm.py | Python | apache-2.0 | 2,937 | [
"Galaxy"
] | 08a3c197fab5fdf488b1063ac0acc23dc14e24244e458a458327fb4155dba486 |
# Copyright (c) 2015, Riverbank Computing Limited
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of c... | LumPenPacK/NetworkExtractionFromImages | win_build/nefi2_win_amd64_msvc_2015/tools/pyqtdeploy/pyqtdeploy/project/project.py | Python | bsd-2-clause | 25,486 | [
"VisIt"
] | 47426f7435a25aebdf85a93108d9d697c2ec303c7b3764b78ff081a09c117360 |
#!/usr/bin/env python
# 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 the hope that ... | dmnfarrell/smallrnaseq | smallrnaseq/aligners.py | Python | gpl-3.0 | 4,322 | [
"Bowtie"
] | f548dcae91efd096b8e6b79e4094285c22f1ea87e2f5b114cbccc09bbbd3dd47 |
from __main__ import vtk, qt, ctk, slicer
import LASegmentationResources
import PythonQt
#
# LASegmentationWorkflow
#
class LASegmentationWorkflow:
def __init__(self, parent):
parent.title = "LA Segmentation Workflow"
parent.categories = ["Cardiac MRI Toolkit"]
parent.dependencies = []
... | carma-center/carma_slicer_extension | LASegmentationWorkflow/LASegmentationWorkflow.py | Python | bsd-2-clause | 4,949 | [
"VTK"
] | 3de4735946ccfa53dc80454549472ac0db9c0223c3af96628548345692226111 |
# Copyright 2018 Dave Eddy <dave@daveeddy.com>
# 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 the rights to use, copy, modify, merge, publish, ... | EternityForest/KaithemAutomation | kaithem/src/thirdparty/hardline/gui/colornames.py | Python | gpl-3.0 | 76,222 | [
"Amber",
"ESPResSo",
"Firefly",
"Jaguar"
] | 96d2be10a9a2a816d0fe1cabbccd7809d9443c3656d8cabca58b3fbb741d3137 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-get-normalized-queue-length.py
# Author : Ricardo Graciani
########################################################################
"""
Report Normalized CPU length of queue
This script was used by the... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_wms_get_normalized_queue_length.py | Python | gpl-3.0 | 1,365 | [
"DIRAC"
] | b7548e86a5050659abe3b5b42933a6868e8e98d6c58995eab8daaa98a3f51d8b |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-genomeinfodb/package.py | Python | lgpl-2.1 | 2,180 | [
"Bioconductor"
] | dee4827020a325d0bbe8fd3643b4f223e55e42e02bd2b1bb4603eba0c7381765 |
__author__ = 'Brian Wickman'
from twitter.common.rpc.finagle.protocol import (
TFinagleProtocol,
TFinagleProtocolWithClientId)
__all__ = [
'TFinagleProtocol',
'TFinagleProtocolWithClientId'
]
| foursquare/commons-old | src/python/twitter/common/rpc/finagle/__init__.py | Python | apache-2.0 | 202 | [
"Brian"
] | 273e4e2163427471e2c45de327a249e262ca60348f49559ad1dde725015f8f38 |
#!/usr/bin/python
# Copyright (C) 2019 Red Hat, Inc.
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['preview... | wgwoods/lorax | share/lifted/providers/aws/library/ec2_snapshot_import.py | Python | gpl-2.0 | 7,425 | [
"Brian"
] | 2be2130abc819fb32740c957e7edacf37fc9a87b6b4421443422aa5442f268e9 |
#!/usr/bin/python
import sys
import misc_utils as utils
from Bio import AlignIO
############################# CLASSES ##################################
class consensAlign():
'Consensus alignment object'
#Default constructor
def __init__(self, alignment, threshold=0.1, mask=0.1):
self.alnVars = []
self.conSeq... | tkchafin/fst_filter.py | alignment_tools_v2.py | Python | gpl-3.0 | 4,675 | [
"Biopython"
] | e88b7ac6ba1967bf2d99553982b6e2fc3912a551454a2fe5ac3eb0adb208b63b |
# This tests calculates the force on the atoms of a small molecule.
#
# If the test fails, set the fd boolean below to enable a (costly) finite
# difference check.
import numpy as np
from ase.data.molecules import molecule
from gpaw import GPAW
from gpaw.atom.basis import BasisMaker
obasis = BasisMaker('O').generate(... | qsnake/gpaw | gpaw/test/lcao_force.py | Python | gpl-3.0 | 1,753 | [
"ASE",
"GPAW"
] | dc23be2b375f438f04d62f5d4a5f52722387e17ee52dffed3b56984097fa5b65 |
from __future__ import division, print_function, absolute_import
__all__ = ['Sphere', 'HemiSphere', 'faces_from_sphere_vertices', 'unique_edges']
import numpy as np
import warnings
from ..utils.six.moves import xrange
from dipy.core.geometry import cart2sphere, sphere2cart, vector_norm
from dipy.core.onetime import... | mdesco/dipy | dipy/core/sphere.py | Python | bsd-3-clause | 19,979 | [
"Gaussian"
] | fbf145c71a4dcad890d5a207d96908a29c085457ae65fe67a11abd9c93fdcf9c |
# Copyright (c) 2014-2016 Genome Research Ltd.
#
# This file is part of IVA.
#
# IVA 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.
# ... | sanger-pathogens/iva | iva/assembly.py | Python | gpl-3.0 | 29,056 | [
"pysam"
] | e30d8c87d681b08dd6d99c33dba0bfeb8717e23fa37ea712562b7057509957c7 |
"""
Course Outline page in Studio.
"""
import datetime
from bok_choy.javascript import js_defined, wait_for_js
from bok_choy.page_object import PageObject
from bok_choy.promise import EmptyPromise
from selenium.webdriver import ActionChains
from selenium.webdriver.common.keys import Keys
from selenium.webdriver.suppor... | fintech-circle/edx-platform | common/test/acceptance/pages/studio/overview.py | Python | agpl-3.0 | 38,571 | [
"VisIt"
] | 9ad29ac156b7638a5de5c97b35dbddf9a03f1be3e7398eda74a51bb1c440ab94 |
"""SIESTA calculator interface."""
# Copyright (C) 2015 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions o... | atztogo/phonopy | phonopy/interface/siesta.py | Python | bsd-3-clause | 9,218 | [
"CRYSTAL",
"SIESTA",
"VASP",
"phonopy"
] | 60303757fc98e749ae68b39ea66c851e07cb061c152fdda6f99e248d0eb2607c |
import os
import tempfile
import numpy as np
import tables
from mdtraj.testing import eq
from msmbuilder3.base import BaseModeller, EstimatorMixin
fn = None
def setup():
global fn
fn = tempfile.mkstemp()[1]
def teardown():
os.unlink(fn)
class MyEstimator(BaseModeller, EstimatorMixin):
def __init__(... | rmcgibbo/msmbuilder3 | tests/test_to_from_pytables.py | Python | gpl-3.0 | 1,495 | [
"MDTraj"
] | bff4d622ce9d381e9c38afb8026e37796348c8bd8539fd3140b4ff2b1dee5292 |
#!/usr/bin/env python
#
# This example demonstrates how to use multiple renderers within a
# render window. It is a variation of the Cone.py example. Please
# refer to that example for additional documentation.
#
import vtk
import time
#
# Next we create an instance of vtkConeSource and set some of its
# properties.... | b3c/VTK-5.8 | Examples/Tutorial/Step3/Python/Cone3.py | Python | bsd-3-clause | 2,693 | [
"VTK"
] | 25d394531c30df76fab6c7f353d4b0177de94574ed6517faadf635e56d156315 |
"""A base class notebook manager.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed as part of th... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/html/services/notebooks/nbmanager.py | Python | apache-2.0 | 8,907 | [
"Brian"
] | 4446e0b50c4021fef1822e96c8d5b79d2b9a406139a08dc6e8d7e3fb8f0ca68b |
""" Test the API for Gyms """
from app.tests.api.personalised.gym_gym_visit_collection.gym_visit_common \
import GymVisitAPICommonCase
class TestGymVisitCollectionModelData(GymVisitAPICommonCase):
""" Test the API methods for the Gym """
def test_gym_visit_list(self):
"""
Test that a lis... | Gimpneek/exclusive-raid-gym-tracker | app/tests/api/personalised/gym_gym_visit_collection/test_model_data.py | Python | gpl-3.0 | 1,102 | [
"VisIt"
] | 0d5ed60f0117c043584d6250664ca4a958449456357fa69d372db75990e28c26 |
# Copyright 2006 by Tiago Antao <tiagoantao@gmail.com>. 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.
from Bio._py3k import _universal_read_mode
import os
import unittest
fro... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_PopGen_SimCoal_nodepend.py | Python | gpl-2.0 | 2,072 | [
"Biopython"
] | 54fd5f0957de0c41c68147236c093d29b4697b373ab7ab4f1b569374021445f4 |
""" JobMonitoringHandler is the implementation of the JobMonitoring service
in the DISET framework
The following methods are available in the Service interface
"""
from __future__ import print_function
__RCSID__ = "$Id$"
from datetime import timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.DISET.Re... | chaen/DIRAC | WorkloadManagementSystem/Service/JobMonitoringHandler.py | Python | gpl-3.0 | 20,321 | [
"DIRAC"
] | 3f306aac8ec93c4b4a58d7c6e6bc5015f7d5fb64ea91e2820e120c44c65ebe2e |
#!/usr/bin/env python3
import sys
from pathlib import Path
import jinja2
import pypandoc
import pytoml as toml
from common import list_ops, list_mods, validate_toml
if (sys.version_info.major, sys.version_info.minor) < (3, 6):
raise Exception("need Python 3.6 or later")
THIS_FILE = Path(__file__).resolve()
ROO... | burnsauce/teletype | utils/docs.py | Python | gpl-2.0 | 5,376 | [
"ORCA"
] | 6d6da9834dd69317396b25f13768056de6b62622b7aef7d775b06f3a2d5cd4e4 |
from ase.structure import molecule
from ase.neb import NEB
from ase.calculators.emt import EMT
from ase.optimize.fire import FIRE as QuasiNewton
from ase.visualize import view
#Optimise molecule
initial = molecule('C2H6')
initial.set_calculator(EMT())
relax = QuasiNewton(initial)
relax.run(fmax=0.05)
view(initial)
#C... | misdoro/python-ase | doc/tutorials/neb/idpp2.py | Python | gpl-2.0 | 777 | [
"ASE"
] | 552e576a07bd7beb2d90a5857538850773e5ec5b172cb0a44c9b521c632a2f02 |
# python3
# pylint: disable=g-bad-file-header
# Copyright 2021 DeepMind Technologies Limited. 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... | deepmind/neural_testbed | neural_testbed/generative/gp_regression_envlikelihood.py | Python | apache-2.0 | 4,574 | [
"Gaussian"
] | 93b2272b9717dbc3ea2e0b520463869c86f3df53fab2105e0da1293cf92c2b56 |
"""
Tests for discussion pages
"""
import datetime
from uuid import uuid4
from nose.plugins.attrib import attr
from pytz import UTC
from flaky import flaky
from common.test.acceptance.tests.discussion.helpers import BaseDiscussionTestCase
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.... | deepsrijit1105/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 61,938 | [
"VisIt"
] | 4abb13fd3baa0c3cf23f1ad7145bf028e2714e4cb5b4a512a59ef95a45c73e93 |
#!/usr/bin/env python2
"""
Copyright (C) 2015-2016 Jakub Krajniak <jkrajniak@gmail.com>
This file is distributed under free software licence:
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 ... | MrTheodor/bakery | src/start_backmapping.py | Python | gpl-3.0 | 23,286 | [
"Gaussian",
"Gromacs"
] | 4d52e678b725e22eb01cf8cf7ee570b8124e1e3d4aae90c46deb64d565347c3f |
'''
Functions for creating archives of all basis sets
'''
import os
import copy
import zipfile
import tarfile
import io
import datetime
from . import api, writers, refconverters, misc
from .writers.write import _writer_map
_readme_str = '''Basis set exchange: Basis set bundle
=========================================... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/bundle.py | Python | bsd-3-clause | 6,812 | [
"NWChem",
"TURBOMOLE"
] | 8870d6d8e5f46568991380aa1051dbc75bd66d24011255b977f2094c0b0943d4 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your optio... | zenodo/invenio | invenio/ext/script/__init__.py | Python | gpl-2.0 | 8,079 | [
"VisIt"
] | 78e1ab47e2fcd78df0bb3e86a3bf07348cc23e2aa62faae73e2e5149efcf3f4f |
#!/usr/bin/env python3
import pyro
from ..gp import GP
from ._pyro_mixin import _PyroMixin
class PyroGP(GP, _PyroMixin):
"""
A :obj:`~gpytorch.models.ApproximateGP` designed to work with Pyro.
This module makes it possible to include GP models with more complex probablistic models,
or to use likeli... | jrg365/gpytorch | gpytorch/models/pyro/pyro_gp.py | Python | mit | 4,679 | [
"Gaussian"
] | f3a64759410de942aa48752e84b1f28545445b8f7ac1a887e2b5f83ce11fa04a |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'preferences.ui'
#
# Created by: PyQt5 UI code generator 5.10.1
#
# WARNING! All changes made in this file will be lost!
from PyQt5 import QtCore, QtGui, QtWidgets
class Ui_Dialog(object):
def setupUi(self, Dialog):
Dialog.setOb... | alexisflesch/texamator | partielatormods/guis/guiprefs.py | Python | gpl-3.0 | 37,869 | [
"VisIt"
] | b2ab673ea7c020a2e6827a92a74be2bc029a8ce8aed4fbab1e74b78e0a0d7799 |
#!/usr/bin/env python
import sys, os
import cnavgpost.mergehistories.event_cycles_module as histseg
import pysam
import cPickle as pickle
import re
def merge_segments_into_regions(event):
if len(event.segs) ==0:
event.make_segs_from_str()
mylocs=[]
for seg in event.segs:
if seg.adj:
mylocs.append((seg.c... | dzerbino/cn-avg | paper_figures/cnavgpost/genehistory/annotate_events.py | Python | bsd-3-clause | 2,821 | [
"pysam"
] | 6338bd782a262b37c7a1f496a21cd14a427b7211803f264feffefa81706b4730 |
# -*- 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
urlpatterns = [
url(r'^$', TemplateView.as_view(tem... | willingc/succulent-pups | config/urls.py | Python | bsd-3-clause | 1,303 | [
"VisIt"
] | b9ea9aea0ca6655e1bbe74bfc04857663924733d4cc6a1f023fa545b9b7ed6e5 |
#
# Copyright (c) 2017 Intel Corporation
#
# 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... | NervanaSystems/coach | rl_coach/exploration_policies/additive_noise.py | Python | apache-2.0 | 5,318 | [
"Gaussian"
] | 93347e03de32304997064027694386714a06957456e7925dba30b97db515a888 |
import numpy as np
def gaussian(x, p):
'''
gaussian(arr,p): p[0] = norm, p[1] = mean, p[2]=sigma
'''
return p[0] * np.exp( -1 * (x - p[1])**2 / (2 * p[2]**2))
def double_gaussian(x, p):
'''
gaussian(arr,p): p[0] = norm1, p[1] = mean1, p[2]=sigma1
p[3] = norm2, p[4] = mean2... | philrosenfield/TPAGB-calib | functions.py | Python | bsd-3-clause | 777 | [
"Gaussian"
] | 89ddd5742b6ec8f58a6d6144bdf061959647c5f7476ff3c363c735b4d76ad05e |
import types
import os
import re
import logging
import urllib
import hmac
import hashlib
from urlparse import urlparse
from email import header
from datetime import timedelta, datetime
from hashlib import sha256
import iso8601
import pymongo
from pylons import c, g, request
from ming import schema as S
from ming impo... | leotrubach/sourceforge-allura | Allura/allura/model/auth.py | Python | apache-2.0 | 21,852 | [
"VisIt"
] | 2896d7051a6c9daf2ca17f92db32ac36a2b2530f48b02068975b5c07e7053448 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | fingeronthebutton/RIDE | src/robotide/lib/robot/result/merger.py | Python | apache-2.0 | 3,024 | [
"VisIt"
] | 9f44819afc34db34b9452c27a7e71442d8d1ef3bcd9ddf705c0c18139be5799c |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Xeralux/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 41,167 | [
"VisIt"
] | 3a9445dc80dbf54fbb8a00161e43314c96350fdd5b6b0cd3a8572217cd2dd95e |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageMathematics(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | nagyistoce/devide | modules/vtk_basic/vtkImageMathematics.py | Python | bsd-3-clause | 510 | [
"VTK"
] | eead7f56d49c9ed29f167818fd7b462ece29cecbf24fdfa90b83a1b7c8af8679 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2014, 2015, 2016, 2018 Adam.Dybbroe
# Author(s):
# Adam.Dybbroe <adam.dybbroe@smhi.se>
# Panu Lahtinen <panu.lahtinen@fmi.fi>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | pytroll/mpop | mpop/satin/nc_pps_l2.py | Python | gpl-3.0 | 41,291 | [
"Bowtie",
"NetCDF"
] | 5ee5ca5160f5b8f16978779cac131015caa96300cbeae96c57c3a71b25d58cd1 |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empir... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/covariance/robust_covariance.py | Python | mit | 30,680 | [
"Gaussian"
] | 44d85e530a1307a431a2926ae4116ccf7f74aab6734be28ddd438c8cbd4ee67a |
# proxy module
from __future__ import absolute_import
from mayavi.filters.decimatepro import *
| enthought/etsproxy | enthought/mayavi/filters/decimatepro.py | Python | bsd-3-clause | 95 | [
"Mayavi"
] | 4d2a02b48b641956f6eb45b03ac5a5985d066382d508e6f9e49ec4ce417b2214 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
from monty.json import MontyDecoder
from pymatgen.apps.battery.conversion_battery import (
ConversionElectrode,
ConversionVoltagePair,
)
from pymatgen.core.composition import Co... | materialsproject/pymatgen | pymatgen/apps/battery/tests/test_conversion_battery.py | Python | mit | 3,687 | [
"pymatgen"
] | 4107e78895084b9ed8f1a1612aa1883ccccd92575aca67c7c069b041257a0cfc |
'''
Created on Oct 25, 2010
@author: joel
'''
import pypyr.utils as pu
import pypyr.mesh as pm
import pypyr.physics.stokes as pps
import pypyr.extra.poisson as pep
import numpy as np
import enthought.mayavi.mlab as emm
import matplotlib.pyplot as mpl
class MeshPlotter(pm.MeshBase):
def __init__(self):
pm... | joelphillips/pypyramid | src/scripts/stokesplot.py | Python | bsd-3-clause | 3,545 | [
"Mayavi"
] | 50339e52a173168b9204029d39ddca569f481bbe3eeb22f628657de73ff1fb61 |
#!/usr/bin/env python
"""
DataSet
"""
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
$Revisi... | chunshen1987/iSS | utilities/for_paraview/lib/DataSet.py | Python | mit | 3,486 | [
"VTK"
] | 842336ae465498edf091ccdb47952994a16b3da25c46ff984804b47089aa4fa6 |
"""Module to configure and run CP2K jobs.
Index
-----
.. currentmodule:: nanoqm.schedule.scheduleCP2K
.. autosummary::
prepare_job_cp2k
API
---
.. autofunction:: prepare_job_cp2k
"""
import fnmatch
import logging
import os
from os.path import join
from pathlib import Path
from typing import Any, Dict
from nood... | SCM-NV/qmworks-namd | nanoqm/schedule/scheduleCP2K.py | Python | mit | 3,247 | [
"CP2K"
] | b17c5cd7e7a750aaffa886979cf7ef457bb1f2cc70cde228b8b3aa6b4039b821 |
import cv2
import numpy as np
scale = 1
delta = 0
ddepth = cv2.CV_16S
blur_scale = 3
img = cv2.imread('muscle_matrix.png')
img = cv2.GaussianBlur(img,(blur_scale,blur_scale),0)
img = cv2.imwrite('muscle_matrix.png')
gray = cv2.cvtColor(img,cv2.COLOR_BGR2GRAY)
# Gradient-X
grad_x = cv2.Sobel(gray,ddepth,1,0,ksize... | SlideAtlas/SlideAtlas-Server | slideatlas/plugins/ipython/notebooks/image_orientations.py | Python | apache-2.0 | 966 | [
"VisIt"
] | 694a1c8ec905a4ef36e9fde3f280baffb7640a7d3eaeda5d9aee014fc1bc305d |
"""User-friendly public interface to polynomial functions. """
from __future__ import print_function, division
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy, Tuple
)
from sympy.core.mul import _keep_coeff
from sympy.core.symbol import Symbol
from sympy.core.basic import preorder_traversal
... | MridulS/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 171,947 | [
"Gaussian"
] | ba8bef30bcb43d3cfdfb3f468d01f6e6bf98fa0416881889d7452ed86647f342 |
# -*- coding: utf-8 -*-
"""
Mdi sub window for displaying VTK render window.
@author: Chris Scott
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import unicode_literals
from __future__ import division
import logging
import platform
import ctypes
from PySide2 import ... | chrisdjscott/Atoman | atoman/gui/rendererSubWindow.py | Python | mit | 38,687 | [
"VTK"
] | af7fd7c792b26e18088f5a297c668f71c42c493dc06debfc31efc22e420eea5c |
#
# Copyright (C) 2000 Stefan Seefeld
# All rights reserved.
# Licensed to the public under the terms of the GNU LGPL (>= 2),
# see the file COPYING for details.
#
from Synopsis import IR, ASG
from Synopsis.QualifiedName import QualifiedCxxName as QName
from Synopsis.SourceFile import *
import idlast, idltype, idlvisi... | stefanseefeld/synopsis | Synopsis/Parsers/IDL/omni.py | Python | lgpl-2.1 | 18,192 | [
"VisIt"
] | 7cae196893f8f5ab0cb28a1bc799c670365115b1e1c852200609755e3933d951 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2015 by Tobias Houska
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Tobias Houska
Holds functions to analyse results out of the database.
Note: This part of SPOTPY is in alpha status and not ready for production use.
'''
import numpy as ... | gitporst/spotpy | spotpy/analyser.py | Python | mit | 38,680 | [
"Gaussian"
] | 149934c96891195bad8d52758052a34e9681cb40bb0f284de9197307bc3f96b7 |
# Encoding utf-8
import sys
import os
import pymatgen as pmg
import pymatgen.io.nwchem as nw
from cage.core import Cage
"""
Script to set up the directories and input files to calculate the minimum
energy paths for all non-equivalent facet combinations in a Cage molecule.
"""
# Cation parameters
CATION = 'Na'
STA... | mbercx/cage | cage/scripts/pathsetup.py | Python | mit | 3,134 | [
"NWChem",
"pymatgen"
] | e34a55093ff34379f3b7e10a3cefcc201bc3650479c630e117968fa466e5b30a |
#!/usr/bin/env python
#----------------------------------------------------------------------
# Copyright (c) 2013-2015 Raytheon BBN Technologies
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and/or hardware specification (the "Work") to
# deal in the Work without ... | plantigrade/geni-tools | src/gcf/omnilib/stitch/objects.py | Python | mit | 298,389 | [
"ORCA"
] | caf2a0d14d09b8079c5cad13874943d8d90d82b9b199f5f7d2380cbef50249f2 |
#
# Copyright (C) 2001 greg Landrum
#
from rdkit.ML.Data import Quantize
from rdkit.Dbase import DbConnection
from rdkit import RDConfig
def runIt(namesAndTypes,dbConnect,nBounds,resCol,typesToDo=['float']):
results = map(lambda x:x[0],dbConnect.GetColumns(namesAndTypes[resCol][0]))
nPossibleRes = max(results)... | rdkit/rdkit-orig | rdkit/ML/Data/FindQuantBounds.py | Python | bsd-3-clause | 1,670 | [
"RDKit"
] | 32307df7b653959129f07c4454415d3763685aa82506261d6d9d3dae3df7acb4 |
import unittest
import numpy as np
import pysal
#from pysal.spreg.twosls import TSLS, BaseTSLS
from scipy import sparse as SP
from pysal.contrib.handler import Model
from functools import partial
TSLS = partial(Model, mtype='TSLS')
class TestTSLS(unittest.TestCase):
def setUp(self):
db = pysal.open(pysal... | TaylorOshan/pysal | pysal/contrib/handler/tests/test_twosls_sparse.py | Python | bsd-3-clause | 8,763 | [
"COLUMBUS"
] | b09150983ab7c1407dc0fc1b388b1dbb25941e190dab464765b8139d82c516b7 |
import editdist
import pandas as pd
def observed_wellbc_extraction(line, AD1='GGAAGCCTTGGCTTTTG'):
'''
This function returns the sequence (observed wellbc) before the first adaptor sequence
ToDo, fix alignments to well bc
Parameters
----------
line: Panda... | SuLab/RASLseqAligner | src/RASLseqWellbc.py | Python | mit | 6,807 | [
"BLAST"
] | 05fdda0c7a1be904de8830facf4801a6a46acc84defe282cdf850106ccde7ceb |
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