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# -*- coding: utf-8 -*-
"""Tests for the PyBEL processor."""
import os
from urllib import request
from pybel import BELGraph
from pybel.dsl import *
from pybel.language import Entity
from pybel.io import from_nodelink_file
from pybel.examples import egf_graph
from indra.statements import *
from indra.sources import ... | sorgerlab/belpy | indra/tests/test_pybel_api.py | Python | mit | 30,089 | [
"Pybel"
] | 9adebb0d4ac3378e682f81cccb76478a28a5b4341846c0e1e8229ad2ed6a65ad |
#!/usr/bin/env python
'''
COPYRIGHT 2013 RPS ASA
This file is part of Wicken.
Wicken 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... | ioos/wicken | wicken/dogma.py | Python | apache-2.0 | 8,388 | [
"NetCDF"
] | e064e8a86c39215543944a282c057771f6040ba306e2881f09b18eb227992745 |
"""Timeseries model using FSL's gaussian least squares."""
import re
import os.path as op
import numpy as np
from scipy import stats, signal
import pandas as pd
import nibabel as nib
import matplotlib.pyplot as plt
from moss import glm
from moss.mosaic import Mosaic
import seaborn as sns
from nipype import Node, MapNo... | tuqc/lyman | lyman/workflows/model.py | Python | bsd-3-clause | 20,567 | [
"Gaussian"
] | 2cc2119b8fe9339dae2e56d391ba9016c50aed9600f52368d0ad65ddc2b12017 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Module to test fitting routines
"""
from __future__ import (absolute_import, unicode_literals, division,
print_function)
import os.path
import pytest
import numpy as np
from numpy import linalg
from numpy.testing.utils import... | kelle/astropy | astropy/modeling/tests/test_fitters.py | Python | bsd-3-clause | 25,717 | [
"Gaussian"
] | 8bbefc179f1217e710e173340be1108307c68a1701363df4ed03f03d56c6388a |
import decimal
import gc
import itertools
import multiprocessing
import weakref
import sqlalchemy as sa
from sqlalchemy import ForeignKey
from sqlalchemy import inspect
from sqlalchemy import Integer
from sqlalchemy import MetaData
from sqlalchemy import select
from sqlalchemy import String
from sqlalchemy import test... | kawamon/hue | desktop/core/ext-py/SQLAlchemy-1.3.17/test/aaa_profiling/test_memusage.py | Python | apache-2.0 | 37,168 | [
"VisIt"
] | efb1a45fc3024520c3dac091598b158e48732c9247f77eab3d33812752979011 |
# -*- coding: utf-8 -*-
# Ambry Bundle Library File
# Use this file for code that may be imported into other bundles
class RandomSourcePipe(object):
def __init__(self, bundle, source=None):
if source:
self.year = int(source.time)
self.space = source.space
else:
... | CivicKnowledge/ambry | test/bundle_tests/build.example.com/coverage/lib.py | Python | bsd-2-clause | 1,571 | [
"Gaussian"
] | 792e11e6c40483bff7c97761a2bf1d7edcb4565d90bb0d2b19a778755297b8fb |
# -*- coding: utf-8 -*-
##
## CreateInflowFileFromERAInterimRunoff.py
## spt_lsm_autorapid_process
##
## Created by Alan D. Snow (adapted from CreateInflowFileFromECMWFRunoff.py).
## Copyright © 2015-2016 Alan D Snow. All rights reserved.
## License: BSD-3 Clause
import csv
import netCDF4 as NET
import... | erdc-cm/spt_lsm_autorapid_process | imports/CreateInflowFileFromERAInterimRunoff.py | Python | bsd-3-clause | 10,290 | [
"NetCDF"
] | f6b1a89073d06609840edee0982859ee84a0cf9d45af6d0284f93324019bb74d |
#!/usr/bin/env python
#########################################################################################
#
# Convert binary spinal cord segmentation to trilinear-interpolated segmentation. Instead of simply re-interpolating
# the image, this function oversample the binary mask, then smooth along centerline (to r... | neuropoly/spinalcordtoolbox | spinalcordtoolbox/scripts/isct_convert_binary_to_trilinear.py | Python | mit | 7,321 | [
"Gaussian"
] | 6671dfd4fb85a8bd2e87adf454ba423d759db1bcf36544d9bd8086214e872f49 |
#!/usr/bin/env python
import datetime
import gevent
import os
import re
import urllib2
import urlparse
from gevent import monkey
monkey.patch_all()
from flask import Flask, render_template, send_from_directory, request, make_response
from lxml.html import parse
# initialization
app = Flask(__name__)
#app.config.upd... | alphagov/service-domain-checker | webapp.py | Python | mit | 11,942 | [
"VisIt"
] | 981b23474125c19340652776f12cf1a9560c291070e9ad3e0119c37925f9284d |
"""
Single page performance tests for LMS.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, CourseUpdateDesc, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutP... | Stanford-Online/edx-platform | common/test/acceptance/performance/test_lms_performance.py | Python | agpl-3.0 | 4,431 | [
"VisIt"
] | 0f9c497ddb4a8f64f408393c310228318fed9308329eba7454b19b298b18299c |
from collections import namedtuple
import os
import ase.io
import ase.db
homedir = os.path.expanduser('~')
materials_dir = homedir + '/Documents/Data/materials'
data_dir = homedir + '/Documents/Data/datasets/sulfur_clusters'
pointgroups = {'S8':'D4d', 'S7_branched':'Cs', 'S7_ring':'Cs', 'S6_branched':'Cs',
... | WMD-group/sulfur-model | scripts/gen_sulfur_db.py | Python | gpl-3.0 | 3,122 | [
"ASE"
] | 4e6cb9123486cb30388d0eb734563eaef413397e6a0c6400ab3b52c2c0d9c66f |
"""
Author: Roger Labbe
Copyright: 2014
This code performs various basic statistics functions for the
Kalman and Bayesian Filters in Python book. Much of this code
is non-optimal; production code should call the equivalent scipy.stats
functions. I wrote the code in this form to make explicit how the
computations are d... | maxiee/MyCodes | KalmanAndBesianFiltersInPython/Chapter6_multivariate_kalman_filter/utils/stats.py | Python | gpl-3.0 | 11,807 | [
"Gaussian"
] | 85866ee41b20d420258acc2ed3ef78fdab9bbed8094827c0757161a6de52c2cb |
import math
import os
import sys
import httplib2
import requests
from apiclient.discovery import build
from apiclient.errors import HttpError
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file import Storage
from oauth2client.tools import argparser, run_flow
from bs4 import Beaut... | haxorjim/dormant-youtube-subscriptions | youtube-tools.py | Python | mit | 6,416 | [
"VisIt"
] | 56f417ee5c3ddb38dd493b2f1279b9adbf75fa6ec27881f41d8adac77c684144 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/mpiblast/package.py | Python | lgpl-2.1 | 1,997 | [
"BLAST"
] | ccadbbea827093934d5384cfeee61d08cdb3a7813d9473c1c8936272d616f5d2 |
#
# @file TestSBMLConvert.py
# @brief SBMLConvert unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by conver... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestSBMLConvert.py | Python | gpl-3.0 | 16,780 | [
"VisIt"
] | c6e60c87d1658948c638efb52b85c1b6515ef3dda3d549ee770ef5b0469e0beb |
from twisted.internet import defer, reactor
from nevow import livepage, loaders, tags, rend, static, entities
from nevow.livepage import js, document
testFrameNode = js.testFrameNode
contentDocument = testFrameNode.contentDocument
import os.path
resourceDirectory = os.path.dirname(__file__)
class Driver(object):... | tquilian/exelearningTest | nevow/livetest.py | Python | gpl-2.0 | 8,724 | [
"VisIt"
] | e37703838ea50010c7ac55e8383391531c9111d96bd08c70b7e465194a590db5 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | jandom/rdkit | rdkit/Chem/EState/UnitTestEState.py | Python | bsd-3-clause | 5,001 | [
"RDKit"
] | 23446bb8b4cf2b02702ee04691c6779d172804c8d0a385c966e6b35693c80c96 |
#! /usr/bin/env python
# FIXME: it has to be seen if this is any useful
# FIXME: to bring back to life
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
from DIRAC.Core.Utilities.File ... | Andrew-McNab-UK/DIRAC | tests/Integration/Resources/Catalog/FIXME_Test_CatalogPlugin.py | Python | gpl-3.0 | 18,087 | [
"DIRAC"
] | 15d9b17acdca5cb24b75e4cd4d7e1a46e66bf35dd63d2308405bef46249eab72 |
"""
A setuptools based setup module.
See:
https://packaging.python.org/guides/distributing-packages-using-setuptools/
https://github.com/pypa/sampleproject
"""
"""
THIS FILE IS USED IN THE DOCS BUILDING
DO NOT DELETE!
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
import os
... | SanPen/GridCal | setup.py | Python | lgpl-3.0 | 9,976 | [
"VisIt"
] | dc93abe0677db2e60ffa729d233595597b119f62b9eb40e8d2956b4ed81f3ee8 |
import re, math
from django.contrib.gis.db import models
from gass.bering.utils import *
class Station(models.Model):
'''
Ablatometer station, idealized i.e. designation B01 is re-used each year.
'''
site = models.CharField(max_length=255, unique=True)
operational = models.BooleanField(help_text="I... | arthur-e/gass | bering/models.py | Python | mit | 17,849 | [
"VisIt"
] | c0737b5d2aa6985ff368be36c37dfe67b14f4d2219fb0d3196fe71c7c82a134a |
import logging
import os
from pyjade import Compiler as _Compiler, Parser, register_filter
from pyjade.runtime import attrs
from pyjade.exceptions import CurrentlyNotSupported
from pyjade.utils import process
from django.conf import settings
class Compiler(_Compiler):
autocloseCode = 'if,ifchanged,ifequal,ifnote... | paradoxxxzero/pyjade | pyjade/ext/django/compiler.py | Python | mit | 4,177 | [
"VisIt"
] | 2f940498b336944200b1a93915d84565f19a64da0b460b6716a334c402c73ddc |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The freesurfer module provides basic functions for interfacing with freesurfer tools.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.pa... | satra/NiPypeold | nipype/interfaces/freesurfer/model.py | Python | bsd-3-clause | 33,883 | [
"Gaussian"
] | e1f3e1167ac2a5184be5124702f82dd832370e2b4e63605eb9729a83a8a65e33 |
"""pdbquery RAPD plugin"""
"""
This file is part of RAPD
c
Copyright (C) 2017, Cornell University
All rights reserved.
RAPD is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, version 3.
RAPD is distributed ... | RAPD/RAPD | src/plugins/mr/plugin.py | Python | agpl-3.0 | 36,161 | [
"ADF"
] | fbc0b1a3c85da22f3443eafed279eb61cc17e33d4db34f5ab6fb3e604affcd52 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2017 Prof. William H. Green (whgreen@mit.edu),
# Prof. Richard H. West (r.west@neu.edu) and the RMG Team (rmg_dev@mit.edu)
#
# ... | Molecular-Image-Recognition/Molecular-Image-Recognition | code/rmgpy/qm/gaussianTest.py | Python | mit | 6,890 | [
"Gaussian"
] | f4a0756af3b0df72d8046c2cf8bdd8ada481205f529c52c23ee417892cc765a5 |
# nerd font icon-name to unicode mapping
icons = {
"500px": "\uf26e",
"accessible-icon": "\uf368",
"accusoft": "\uf369",
"acquisitions-incorporated": "\uf6af",
"ad": "\uf641",
"address-book": "\uf2b9",
"address-card": "\uf2bb",
"adjust": "\uf042",
"adn": "\uf170",
"adversal": "\u... | adamatom/dotfiles | .bin/i3_icons.py | Python | apache-2.0 | 34,587 | [
"GULP"
] | 0b6da26d9028a8f0f84118cf76fbe44aea3793afd46430de4328a5f12ed31438 |
"Demonstrates molecular dynamics with constant energy."
from ase import *
from ase.lattice.cubic import FaceCenteredCubic
from ase.md.velocitydistribution import *
from ase.md.verlet import *
# Use Asap for a huge performance increase if it is installed
useAsap = False
if useAsap:
from asap3 import EMT
size ... | freephys/python_ase | doc/tutorials/md/moldyn1.py | Python | gpl-3.0 | 1,250 | [
"ASE",
"CRYSTAL"
] | 6bcfbfc586d1c4dcc34d14fa038ec70e333e48e52ddb3554db2d0c83bb7f13be |
"""
Container page in Studio
"""
from bok_choy.page_object import PageObject
from bok_choy.promise import Promise, EmptyPromise
from . import BASE_URL
from .utils import click_css, confirm_prompt, type_in_codemirror
class ContainerPage(PageObject):
"""
Container page in Studio
"""
NAME_SELECTOR = '.... | valtech-mooc/edx-platform | common/test/acceptance/pages/studio/container.py | Python | agpl-3.0 | 18,991 | [
"VisIt"
] | 14ca9fbcfc24efe3c3b20c61b5bad15f7c3756582ed466e75f11514179ab7a82 |
# htmlwindow-1.py
# Very simple demo of HTMLWindow.
from wax import *
HTML = """\
<h3>HTMLWindow</h3>
<p>Hello friends! This is some simple <b>HTML</b>.</p>
<p>Flourish & Blotts</p>
<p>Also visit <a href="http://www.python.org/">www.python.org</a>!</p>
"""
class MainFrame(Frame):
def Body(self):
... | MSMBA/msmba-workflow | msmba-workflow/srclib/wax/examples/htmlwindow-1.py | Python | gpl-2.0 | 579 | [
"VisIt"
] | d4dce3f5ae542dcdb656c382a3a143d3c158c8a9d6bbee7aedaf3ee07657cecf |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.4 or later
Recommended: CJKCodecs and iconv_codec <http://cjkpytho... | waseem18/oh-mainline | vendor/packages/feedparser/feedparser/feedparser.py | Python | agpl-3.0 | 168,065 | [
"NetCDF",
"VisIt"
] | 0776da7067c22d625aab6e127eaf6cb1ef595acd9875a160f134480632e7e775 |
# lots to do:
# __ native drawLines
# __ add native drawCurve method
# __ native rectangle/round rect method
# __ native drawEllipse
# __ native drawArc
# __ drawImage support (work on Pyart side of things)
from __future__ import print_function
import pyart
from rdkit.sping.pid import *
from rdkit.sping... | adalke/rdkit | rdkit/sping/Pyart/pidPyart.py | Python | bsd-3-clause | 9,324 | [
"RDKit"
] | bdc7a5cc861adacce97c8f774ca38757f18ed483b1bf5bf6ca50418b54fefb83 |
from ast import Attribute, Await, Dict, Expr, NodeTransformer, parse
from inspect import getsource
from textwrap import dedent
from typing import Any
from sanic.log import logger
from .base import BaseScheme
class OptionalDispatchEvent(BaseScheme):
ident = "ODE"
def __init__(self, app) -> None:
sup... | ashleysommer/sanic | sanic/touchup/schemes/ode.py | Python | mit | 2,262 | [
"VisIt"
] | 8505fffae86fdda4ce990afc4abd835113bd10f56873b9c5ff5ada3fd2a0752a |
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License Version
# 1.1 (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.mozilla.org/MPL/
#
# Softwa... | centrumholdings/buildbot | buildbot/db/dbspec.py | Python | gpl-2.0 | 10,328 | [
"Brian"
] | 2b2cc22f06e4c6df5de4342376362738f6d4bcaa880d602dc21df5bcc466f429 |
################################
# Author : septicmk
# Date : 2015/07/23 19:20:57
# FileName : fusion.py
################################
import numpy as np
import math
from MEHI.utils.tool import exeTime
@exeTime
def content_fusion(rdd, sgm1=44, sgm2=81):
'''
Usage:
- a fast impleme... | septicmk/MEHI | MEHI/paralleled/fusion.py | Python | bsd-3-clause | 2,378 | [
"Gaussian"
] | 370d3b91f1ec06582c0e29419dbe0dd61da0cf57e25f98699681d7927b904fc6 |
# Copyright 2014 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | pombreda/syzygy | syzygy/build/gitdeps.py | Python | apache-2.0 | 25,203 | [
"VisIt"
] | 9f711511b98206a570a4faf6bd5bb033a7a88a4ad5e836b50bd5b8ab16ce7b09 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pylid
from collections import Counter
cs = pylid.PyLID(3)
cs.total_ngrams = 84202116
cs.lang = 'cs'
cs.ngrams = Counter({
u'n\xed#': 669406,
u'#po': 531349,
u'#pr': 516175,
u'ch#': 482809,
u'#a#': 479692,
u'pro': 378527,
u'#p\u0159': 374... | dmort27/pylid | pylid/langs/cs.py | Python | mit | 327,925 | [
"ADF",
"ASE",
"BWA",
"EPW",
"Elk",
"MOE"
] | 6572aab9cd95b7219026333b54db8644f8efff46c4561263861030d1c3161f65 |
#-------------------------------------------------------------------------------
# . File : QMCallerGAMESS.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#----------------------------------------------... | mfx9/MolarisTools | MolarisTools/QMMM/QMCallerGAMESS.py | Python | gpl-3.0 | 4,684 | [
"GAMESS"
] | db4c6775ee1daf8d3003c24f5d0692292d80553892547d4c8a7118b5aa7420cf |
#!/usr/bin/env python
"""
author Brian O'Connor
broconno@ucsc.edu
This module first queries a given Redwood instance for metadata document,
downloads them, minimally transforms them, and, finally, loads them into
Elasticsearch ready for querying.
"""
import semver
import logging
import os
import... | briandoconnor/hca-indexing-sandbox | query_and_load.py | Python | apache-2.0 | 5,071 | [
"Brian"
] | 0163bab55f859c726cd52c689a886b89894b3e10b8d8dc3f7a7a9b72397488db |
from ..nodes import CtreeNode
from ..util import flatten
class TemplateNode(CtreeNode):
"""Base class for all template nodes."""
def __init__(self, template_txt, child_dict):
"""
Create a new template node.
:param template_txt: The template as a string.
:param child_dict: A map... | alphaFred/Sejits4Fpgas | sejits4fpgas/src/vhdl_ctree/templates/nodes.py | Python | gpl-3.0 | 3,245 | [
"VisIt"
] | a965f38ced61a3d8969e62cbd91c86a49d0e03b71865477d3b6011441bfb18c9 |
import data
import pycuda.driver as cuda
import numpy as np
from pycuda._driver import MemoryError
import logging
import kernels
from pycuda.compiler import SourceModule
def run( exp, gm, sm, nm, sample_block_size, npairs_block_size, nets_block_size, rms_only=True):
srt = data.SharedSampleRankTemplate( exp.buffer... | JohnCEarls/GPUDirac | gpudirac/device/dirac.py | Python | agpl-3.0 | 3,857 | [
"DIRAC"
] | 50c704061c224cbe91c9c3e798b86419fc9117485593f6d6814e63d50c867379 |
"""Driver for gradient calculations."""
from __future__ import print_function
import six.moves.builtins as builtins
import logging
import time
import traceback
import warnings
import numpy # for numeric_grad
from six import itervalues
from six.moves import StringIO
import theano
from theano import gof
from theano.g... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/Theano-0.7.0-py3.4.egg/theano/gradient.py | Python | gpl-2.0 | 81,192 | [
"VisIt"
] | c2992bf2af7b96682e94f3b82a1e3676b1b194949e27d643135be7d624284703 |
# GridCal
# Copyright (C) 2022 Santiago Peñate Vera
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 3 of the License, or (at your option) any later version.
#
# This pr... | SanPen/GridCal | src/GridCal/Engine/Core/topology.py | Python | lgpl-3.0 | 6,221 | [
"VisIt"
] | 68a3f26f5a023f935af20ec0937566539f51b7c7e3d579273bcbb05efce37935 |
# c: 14.12.2007, r: 03.11.2008
import os
import numpy as nm
from sfepy.base.base import output, default_printer, pause, debug, Struct
from sfepy.fem import MeshIO
from gen_mesh import gen_concentric
is_3D = False
generate_2D = False
fig_suffix = '.pdf'
if is_3D:
filename_mesh = 'database/phono/cube_sphere.mesh'
#... | certik/sfepy | input/phono/band_gaps_rigid.py | Python | bsd-3-clause | 13,456 | [
"VTK"
] | ffba37c7e2784e06f1ed10104be35f57a630576f59acdcabde700720f2e4aee9 |
"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
from autotest.client.shared import error
from virttest import xml_utils
from virttest.libvirt_xml import base, accessors, xcepts
from virttest.libvirt_xml.devices import librarian
class VMXMLDevices(list):... | waynesun09/virt-test | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 49,655 | [
"VisIt"
] | 3368701003a5fedec6f1b5a4a97126d715842841aca9395edd3f41fa67143e9b |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
import osg, osgDB, osgText
from shape import Shape, UnitShape, PathShape
import neuropti... | JaneliaSciComp/Neuroptikon | Source/display/visible.py | Python | bsd-3-clause | 120,493 | [
"NEURON"
] | 729ac57610a3fab61bcbbde96111635385fde22b50fd628bffa5ac0d8a8e80a1 |
import asyncio
import pickle
from datetime import datetime, timedelta
import json
from os import path
from astral import Astral, GoogleGeocoder
from Firefly import logging, scheduler
from Firefly.const import DAY_EVENTS, EVENT_TYPE_BROADCAST, SOURCE_LOCATION, TIME, LOCATION_FILE
from Firefly.helpers.events import Eve... | Firefly-Automation/Firefly | Firefly/helpers/location.py | Python | apache-2.0 | 8,331 | [
"Firefly"
] | bbfe340f052dde613403d01cb44b54a56b290b15a69a3015ae47ebc84d7c248d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program 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 Softw... | andrebellafronte/stoq | stoqlib/gui/search/fiscalsearch.py | Python | gpl-2.0 | 6,159 | [
"VisIt"
] | c65ed0bee31724e5a1e19976077f223d907288618d7f111f81c17c5f38f5df23 |
"""Test of ScaLAPACK diagonalize and inverse cholesky.
The test generates a random symmetric matrix H0 and
positive definite matrix S0 on a 1-by-1 BLACS grid. They
are redistributed to a mprocs-by-nprocs BLACS grid,
diagonalized in parallel, and eigenvalues are compared
against LAPACK. Eigenvectors are not compared.... | robwarm/gpaw-symm | gpaw/test/parallel/scalapack.py | Python | gpl-3.0 | 6,034 | [
"GPAW"
] | e7a5267ff96d1e628440b394a91024a65b4b51d76def2c15839a94f2085a0992 |
# sql/elements.py
# Copyright (C) 2005-2020 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`_expression.ClauseElement`,
:clas... | gltn/stdm | stdm/third_party/sqlalchemy/sql/elements.py | Python | gpl-2.0 | 161,275 | [
"VisIt"
] | 63bad5cc7d36b54d40851d05830041ce328d320e54fa3c897f7f6a6c99d9b30d |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | yipenggao/moose | python/MooseDocs/common/nodes.py | Python | lgpl-2.1 | 20,082 | [
"MOOSE"
] | 12a6e376cdc816d66aa57363b7bd7723193863be53490bd4110be35665a87980 |
# Copyright 2016-2017 Nitor Creations Oy
#
# 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 ... | NitorCreations/nitor-deploy-tools | n_utils/__init__.py | Python | apache-2.0 | 5,020 | [
"CDK"
] | c07e1bef07ab747b160131eda1f8d7b517960d47346c90f323df6b73ba7a08dd |
#* 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 matp... | nuclear-wizard/moose | modules/level_set/examples/vortex/area.py | Python | lgpl-2.1 | 1,388 | [
"MOOSE"
] | f4cd2b2866d1b7e0495cc2ef3ff02ecb30b6833fab3baf81cbf8e31637f6498a |
"""
Results for test_glm.py.
Hard-coded from R or Stata. Note that some of the remaining discrepancy vs.
Stata may be because Stata uses ML by default unless you specifically ask for
IRLS.
"""
import numpy as np
from scikits.statsmodels.compatnp.py3k import asbytes
import glm_test_resids
import os
from scikits.statsm... | wesm/statsmodels | scikits/statsmodels/genmod/tests/results/results_glm.py | Python | bsd-3-clause | 270,087 | [
"Gaussian"
] | 5d9f8563256ef024c9e0dc0f6409915905d62e5d85010db4e302abe5f5ceb526 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/workspace.py | Python | gpl-2.0 | 7,780 | [
"VisIt"
] | 293d41dce708dbf6915941c14344969d26e56b705a4f9d844a0589d4502d14cd |
""" PilotCommand
The PilotCommand class is a command class to know about present pilots
efficiency.
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getSites, getCESiteMapping
from DIRAC.ResourceStatusSystem.Command.Command import Command
from DIRAC.ResourceStatus... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Command/PilotCommand.py | Python | gpl-3.0 | 6,080 | [
"DIRAC"
] | 2daa34881108ab3ce5dba91346ab879972f6cd76ebf93e6117ee555940f79245 |
#!/usr/bin/python
import os
import json
import urllib
import subprocess
import sys
url_base = "http://admin.ci.centos.org:8080"
api_key = os.environ['API_KEY']
count = os.environ['MACHINE_COUNT'] if os.environ.get('MACHINE_COUNT') != None else "1"
ver = "7"
arch = "x86_64"
req_url = "%s/Node/get?key=%s&ver=%s&arch=%s... | navidshaikh/vagrant-service-manager | .ci/jenkins-execute-script.py | Python | gpl-2.0 | 3,164 | [
"CDK"
] | 4bd16cf9fce8bb29cb1757a2a8e46650e757b32953b9374f40e046e31e88bc41 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the main LMS Dashboard (aka, Student Dashboard).
"""
import datetime
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance... | miptliot/edx-platform | common/test/acceptance/tests/lms/test_lms_dashboard.py | Python | agpl-3.0 | 14,461 | [
"VisIt"
] | 2541249637eedcf3ae3f1b17226e1f9b2b44d584094e4cc5c6d35b2ae37ce5a3 |
#!/usr/bin/env python
#coding: utf-8
import json
import sys
import os
import re
import numpy as np
import neuron
from neuron import h
from builtins import range
# This is super annoying: without neuron.gui, need
# to explicit load 'standard' hoc routines like 'run',
# but this is chatty on stdout, which means we get
... | eth-cscs/nestmc-proto | validation/ref/neuron/nrn_validation.py | Python | bsd-3-clause | 8,771 | [
"NEURON"
] | 8ed27dfcee0c6e630cf2a3006f95edce037f7058ac9b79e3d1628534e1924de3 |
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal 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.
#
# Seal is dis... | QwertyManiac/seal-cdh4 | tests/seal/lib/aligner/bwa/testing_utilities.py | Python | gpl-3.0 | 8,921 | [
"BWA",
"Biopython"
] | e2d19e7bf017696c9b9908868dd9fc82556cdffb4bca0cbf60c9fe4d2f9754ee |
"""
K-means Clustering and Vector Quantization Module
Provides routines for k-means clustering, generating code books
from k-means models, and quantizing vectors by comparing them with
centroids in a code book.
The k-means algorithm takes as input the number of clusters to
generate, k, and a set of observation vector... | jasonmccampbell/scipy-refactor | scipy/cluster/vq.py | Python | bsd-3-clause | 25,832 | [
"Gaussian"
] | 47074512896e115a0948316b2a7f69638164eae42a94bf82ef74adf361c84e0f |
# Generated by Django 1.11.2 on 2017-06-22 10:22
import bitfield.models
import django.contrib.auth.models
import django.core.validators
import django.db.models.deletion
import django.utils.timezone
from django.conf import settings
from django.db import migrations, models
from django.db.backends.postgresql.schema import... | eeshangarg/zulip | zerver/migrations/0001_initial.py | Python | apache-2.0 | 35,999 | [
"VisIt"
] | de18a337a304f8b2151e3c880314e943d0a10894505d0e537a6912deafa48821 |
"""//////////////////////////////////////////////////////////////////////////////
// //
// Copyright © 2016 Juan P. Dominguez-Morales //
// ... | jpdominguez/Multilayer-SNN-for-audio-samples-classification-using-SpiNNaker | Main_SNN_Classifier.py | Python | gpl-3.0 | 8,611 | [
"NEURON"
] | e8a04b0cedfd4e89e14714e563bf23455d989629981669a40823e1ef8635c756 |
#!/usr/bin/env python3
# ver 0.1 - copy from rdf_itf.py (v0.1) and modify codes on 2/3/2018
import argparse
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
description='calculation end-to-end distance of molecules you select')
## args
parser.add_argument('-i', '--in... | jht0664/Utility_python_gromacs | python/ree.py | Python | mit | 4,168 | [
"MDAnalysis"
] | 242b2378f88f070d1711958f3a2154ee8758f5992b962544780d91ad06a01ad0 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/modeling/preparation/preparer.py | Python | mit | 21,533 | [
"Galaxy"
] | 78ad23b338517f3acd3423724d92ed88f2176d692e4d8180adacb344d828064e |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import re
class Texinfo(AutotoolsPackage, GNUMirrorPackage):
"""Texinfo is the official documen... | iulian787/spack | var/spack/repos/builtin/packages/texinfo/package.py | Python | lgpl-2.1 | 2,071 | [
"Brian"
] | 9557b258b471f770a0323f41e62dab0113f02dd7c47ba201460e9600f069c939 |
"""
Code for kernel density estimation.
- Source: http://nbviewer.jupyter.org/gist/tillahoffmann/f844bce2ec264c1c8cb5
"""
import numpy as np
from scipy.spatial.distance import cdist
class gaussian_kde(object):
"""Representation of a kernel-density estimate using Gaussian kernels.
Kernel density estimation i... | DamienIrving/ocean-analysis | modules/kde.py | Python | mit | 11,449 | [
"Gaussian"
] | 98968dc4256413e148d7ff194478e20b4da250202434f408fa2945e8fb3c3d18 |
# 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... | leighpauls/k2cro4 | PRESUBMIT.py | Python | bsd-3-clause | 29,745 | [
"VisIt"
] | 6469389707a86d9565dbdb2e80cb5718a42c81936fc6a2d3cb1c068bdd134fab |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# jobobjsubmit - submit helper to submit job objects directly
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU... | heromod/migrid | mig/cgi-bin/jobobjsubmit.py | Python | gpl-2.0 | 1,147 | [
"Brian"
] | 4417621e5e289ecad8a50eb4ce9e19f0c2c2c4dabe6dfab1e273437b99e374c3 |
# -*- coding: utf-8 -*-s
import numpy as np
import create_timeseries as cts
#create grid
manual_grid_option=True
lons,lats,lonbs,latbs,nlon,nlat,nlonb,nlatb=cts.create_grid(manual_grid_option)
p_full,p_half,npfull,nphalf=cts.create_pressures()
#create times
is_climatology=False
num_years=100
time_spacing=num_years
... | jamesp/Isca | src/extra/python/scripts/create_co2_timeseries.py | Python | gpl-3.0 | 1,095 | [
"NetCDF"
] | b81c8cdebe366f521933527281b240edab5e40cf3b758f99c2cd697725a4ad83 |
import optparse
import numpy as np
from ase.atoms import Atoms
from gpaw import FermiDirac
from gpaw.tasks.convergence import ConvergenceTestTask
class EggboxTestTask(ConvergenceTestTask):
taskname = 'eggbox'
def __init__(self, **kwargs):
"""Calculate size of eggbox error.
A single atom is... | ajylee/gpaw-rtxs | gpaw/tasks/eggbox.py | Python | gpl-3.0 | 1,622 | [
"ASE",
"GPAW"
] | a9554f15c521d698fa7e69145c8e37c3d435118e9b5bbff85f2b697a202bf465 |
import numpy as np
from ..geometry.point import Point
class DataGenerator:
@staticmethod
def generate_random_set(n=10, d=2, seed_value=431):
#print('n={}'.format(n))
#print('d={}'.format(d))
np.random.seed(seed_value)
points = np.random.rand(n, d)
return np.array([Point(... | nhonaitran/aries | aries/utils/datagenerator.py | Python | gpl-2.0 | 700 | [
"Gaussian"
] | 6241eb8db41338578543dc9dacc737fc7b7c48a56490ec4d658c3ba3582f56c6 |
"""Handles IMAP operations for tMail, the terminal Gmail client"""
import os
import time
from os import path
from simplecrypt import decrypt, encrypt
import imaplib
from requests_oauthlib import OAuth2Session
CLIENT_ID = '47637480825-5d3ndp33q8m6eojt015p9th1q5cig3bm.apps.googleusercontent.com'
CLIENT_SECRET = 'xjFx... | nortonprojects/terMail | authentication.py | Python | lgpl-2.1 | 5,601 | [
"VisIt"
] | 25f7e34fc1ce86c12e278249d6362387982d4369ed175c8393bd65922ac9f5cb |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | demis001/scikit-bio | skbio/stats/ordination/_redundancy_analysis.py | Python | bsd-3-clause | 9,550 | [
"scikit-bio"
] | 7d988203dce790a4f117ffcba66fe95a810da1f013a1fbac5f4a601100f2a89e |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RGostats(RPackage):
"""Tools for manipulating GO and microarrays
A set of tools fo... | LLNL/spack | var/spack/repos/builtin/packages/r-gostats/package.py | Python | lgpl-2.1 | 1,837 | [
"Bioconductor"
] | 40be587b101737c3cf8a49570e92eeec4600c14a96af9583fb288d7f8a856ff4 |
# Copyright 2020-2021 Peppy Player peppy.player@gmail.com
#
# This file is part of Peppy Player.
#
# Peppy Player 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 you... | project-owner/Peppy | util/imageutil.py | Python | gpl-3.0 | 42,494 | [
"Gaussian"
] | 6add39883de662498ace68146da13005a1cd51d9bef36b7788d33bce1b669810 |
# -*- coding: utf-8 -*-
#
# test_status.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or... | steffengraber/nest-simulator | testsuite/pytests/test_status.py | Python | gpl-2.0 | 7,597 | [
"NEURON"
] | 73408e965e2c6e0ea876be0c52496a3ba59733b81a4104bb0cb026b99c3172e1 |
# $HeadURL: $
''' SpaceTokenOccupancyCommand
The Command gets information of the SpaceTokenOccupancy from the lcg_utils
'''
import lcg_util
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.Subprocess import py... | marcelovilaca/DIRAC | ResourceStatusSystem/Command/SpaceTokenOccupancyCommand.py | Python | gpl-3.0 | 6,123 | [
"DIRAC"
] | ea55c8041c41a3eb929a5d844d96ca8946470753d7e31a79009ba3069386e838 |
__all__ = [
"bedtools",
"bvatools",
"bwa",
"cufflinks",
"differential_expression",
"gatk",
"gq_seq_utils",
"htseq",
"igvtools",
"metrics",
"mummer",
"pacbio_tools",
"picard",
"ray",
"readset",
"rrna_amplicons",
"run_processing_aligner"
"sample",
... | ccmbioinfo/mugqic_pipelines | bfx/__init__.py | Python | lgpl-3.0 | 458 | [
"BWA",
"HTSeq"
] | 0d2d1ef825c96af000330a44cf931e39428a4b24cea4120506ee2539ec81eefd |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://ww... | stuart-knock/tvb-library | tvb/tests/library/datatypes/patterns_test.py | Python | gpl-2.0 | 5,663 | [
"Gaussian"
] | 6d7b3fa8b092ab4ec0dd6818cac2f97a34e3f5a984af790bf75c0c54b17035a2 |
#
# Copyright (C) 2000 greg Landrum
#
""" unit tests for the Neural network trainer implementation
this basically works out **all** of the network code
"""
from __future__ import print_function
import unittest
from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH
from rdkit.ML.Neural.NetNode import NetNode
from r... | rvianello/rdkit | rdkit/ML/Neural/UnitTestOther.py | Python | bsd-3-clause | 2,498 | [
"RDKit"
] | 47392c63726cdc2c661329554c2a741d7daaabfef27b723580df75e7a31530f4 |
import argparse
import pysam
import numpy
def print_sex(bam):
"""
Print sex based on chr x ratio
Args:
bam (str): Path to bam file
"""
idxstats = pysam.idxstats(bam)
chr_ratio = []
# Calculate read / chromosome length ratio per chromosome
for chr in idxstats[0:24]:
chr = chr.st... | CuppenResearch/IAP | scripts/determine_sex.py | Python | mit | 1,337 | [
"pysam"
] | 9a37f1d837eb9a4d3304c9402c8de8e4cbd9f1164a301f1fecaddf61ee3e3554 |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible 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... | emersonsoftware/ansiblefork | lib/ansible/galaxy/role.py | Python | gpl-3.0 | 14,352 | [
"Brian",
"Galaxy"
] | f041eafb4184032030175ed850716ac46d960b8b60683bcf89794413e9a39ead |
# 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... | tensorflow/addons | tensorflow_addons/activations/gelu.py | Python | apache-2.0 | 2,575 | [
"Gaussian"
] | 80b1787c441cd59c8ee3a68f09712176a1e659bb62ca95506fa605c0790700b5 |
# -*- coding: utf-8 -*-
# Copyright 2008-2013 Jaap Karssenberg <jaap.karssenberg@gmail.com>
'''Package with source formats for pages.
Each module in zim.formats should contains exactly one subclass of
DumperClass and exactly one subclass of ParserClass
(optional for export formats). These can be loaded by L{get_pars... | hjq300/zim-wiki | zim/formats/__init__.py | Python | gpl-2.0 | 47,634 | [
"VisIt"
] | 424c74eeae4e7ddf88179f90e99a3cba9f42e26874bfe248d7c90860a8cc975f |
# -*- coding: utf-8 -*-
"""
zine.plugins.eric_the_fish.fortunes
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Erics fortune cookies (ripped and stripped from the ubuntu `fortune`
fortune data file.)
:copyright: (c) 2010 by the Zine Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more ... | mitsuhiko/zine | external-plugins/eric_the_fish/fortunes.py | Python | bsd-3-clause | 20,673 | [
"VisIt",
"exciting"
] | 539e5deebc76041f623e66547016bcc26fb1fa93032035ca91ef7cd3a55fc2ca |
#!/usr/bin/python
#------------------------------------------------------------------------------
# Name: getThresh.py
# Author: Ra Inta, 20150716
# Last Modified: 20150716
# This is a pared down version of lookThresh.py. This is used to give
# an estimate of the (1-alpha confidence) 2F threshold fo... | NotAFakeRa/Front_end_CW_searches | getThresh.py | Python | mit | 3,741 | [
"Gaussian"
] | 02c8d71cb009080f5431970bc47dedc06d62a53a1745497eadbd583cc6a7993e |
#!/usr/local/bin/python
# coding: utf-8
'''
PocketPidge.py - Produce PDF pocket diaries for users.
'''
import datetime
from reportlab.pdfgen.canvas import Canvas
from reportlab.lib.pagesizes import A4
from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle
from reportlab.lib.enums import TA_JUSTIFY, TA_C... | fergusrossferrier/mypidge.com | MyPidge/PocketPidge.py | Python | agpl-3.0 | 30,632 | [
"VisIt"
] | 9cabbf7f9ef33f9d88e05feb8703aac0ec5849ac910cbe7ea53ec575a270c257 |
# -*- coding: utf-8 -*-
import shutil
import tempfile
import os
import optparse
import traceback
import re
import threading
import time
from io import open
from lwr.lwr_client import submit_job
from lwr.lwr_client import finish_job
from lwr.lwr_client import LwrOutputs
from lwr.lwr_client import ClientOutputs
from lwr... | jmchilton/lwr | test/check.py | Python | apache-2.0 | 15,187 | [
"BWA",
"Galaxy"
] | cbda052e219566927e4d7cf87c966ff448fb7823fac2cfe5027f984b21c49c75 |
# -------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for
# license information.
# --------------------------------------------------------------------------
import lo... | Azure/azure-sdk-for-python | sdk/storage/azure-storage-queue/azure/storage/queue/_shared/authentication.py | Python | mit | 5,369 | [
"VisIt"
] | 60f87e28954c535682e41b8e7e232322ebac5ab494d05c18457ca6999f843f9b |
"""
FitPanel class contains fields allowing to display results when
fitting a model and one data
"""
import sys
import wx
import wx.lib.newevent
import numpy as np
import copy
import math
import time
import traceback
from sasmodels.weights import MODELS as POLYDISPERSITY_MODELS
from sas.sasgui.guiframe.event... | lewisodriscoll/sasview | src/sas/sasgui/perspectives/fitting/fitpage.py | Python | bsd-3-clause | 129,061 | [
"Gaussian"
] | 04d3c1cfa55eded8d7edbd7e97451749691bc325c876bcfaaef9eceef4e53539 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0037_visit_key'),
]
operations = [
migrations.AlterField(
model_name='visit',
n... | koebbe/homeworks | visit/migrations/0038_auto_20150722_2116.py | Python | mit | 433 | [
"VisIt"
] | 3aa883eae7f78056b77b8f4014affa3bf963866a26f1695053053cbee23de18f |
# prepare_receptors.py
# Create the .pdbqt files and receptors coordinates file of receptors
# for VinaMPI Docking
# Usage:
# python prepare_receptors.py
#
# Specify the correct paths of prepare_receptor4.py pythonsh VMD
# Make sure the get_AS_grid.tcl file uses the correct residue number
# of the active sites
# Run th... | Xiaofei-Zhang/NAMD_Docking_pipeline | pre_DOCKING/prepare_receptors.py | Python | mit | 1,588 | [
"VMD"
] | f323b1142ed131671bab751f5e483d65892b20a755fb07ecd16edd83fd2fb211 |
#!/usr/bin/env python
import numpy
import subprocess
import vtk
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
class fluid:
def __init__(self, name = 'unnamed'):
'''
A Navier-Stokes two-dimensional fluid flow simulation object. Most
simulation values are assigned ... | anders-dc/ns2dfd | ns2dfd.py | Python | gpl-3.0 | 14,344 | [
"ParaView",
"VTK"
] | 851bfa37276b7442b45f267b0d49db132e4fec835cb68e6b2f8223f2d5633593 |
# Determines perovskite structures: classifies by vacancy and substitutional defects (impurities)
# Author: Evgeny Blokhin
import math
import random
import six
from ase.data import chemical_symbols
from ase.data import covalent_radii
from ase.spacegroup import crystal
from tilde.core.constants import Perovskite_Str... | tilde-lab/tilde | tilde/classifiers/perovskites.py | Python | mit | 6,214 | [
"ASE",
"CRYSTAL"
] | 7445ca7a88d612baea79266224c4f31dc770fde57e22af68c4736b2b3d4d6f7a |
""" This version of the code runs a swarm of simulations of various viscosities and
temperatures per viscosity. Since 5-29, it also includes an adiabatic temperature variance at the LAB.
All quantities are scaled using option B in Cian_RaNotes.pdf until they are written out."""
import math
import os
import errno
from s... | Johnson-A/UNM_Research | mantle_simulation/mantle_3d_no_advection.py | Python | mit | 8,674 | [
"ParaView"
] | 56df94c49ca3b077fcd9994d9b15550448801fb2aee5b86acd8edff252f43a01 |
import os
import pymc
import pymbar
import dipoles
import numpy as np
import pandas as pd
import simtk.openmm.app as app
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
n_molecules = 500
traj = md.load("./dipoles.pdb")
out_dir = os.path.join(os.getenv("HOME"), "dat", "dipoles")
q0 = pymc.Uniform... | kyleabeauchamp/DBayes | dbayes/simulate/simulate_dipoles.py | Python | gpl-2.0 | 1,151 | [
"MDTraj",
"OpenMM"
] | 1d5617a67f8bee2e87b47b2dcfaba47b3eecd1aecea8627842a4eb5664acf85e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to define everything related to band structures.
"""
import collections
import itertools
import math
import re
import warnings
import numpy as np
from monty.json import MSONab... | richardtran415/pymatgen | pymatgen/electronic_structure/bandstructure.py | Python | mit | 45,088 | [
"CRYSTAL",
"pymatgen"
] | f538ca024a3d2ee37b95ad53e51a63198c1d0426b89753afb97e32c4a87c7cbb |
import unittest
import numpy as np
import pysal
import pysal.spreg as EC
from scipy import sparse
PEGP = pysal.examples.get_path
class TestBaseOLS(unittest.TestCase):
def setUp(self):
db = pysal.open(PEGP('columbus.dbf'),'r')
y = np.array(db.by_col("HOVAL"))
self.y = np.reshape(y, (49,1))
... | AlanZatarain/pysal | pysal/spreg/tests/test_ols_sparse.py | Python | bsd-3-clause | 5,118 | [
"COLUMBUS"
] | 54dbad4fc63fd5f4abec2d367401fea6ec3b1c1265a6aa84140c92c48e632a08 |
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Engine(object):
def __init__(self, scene_map):
self.scene_map = scene_map
def play(self):
current_scene = self.scene_... | amolborcar/learnpythonthehardway | ex43.py | Python | mit | 7,999 | [
"BLAST"
] | 57443ef0a15a140551c90fb7df29ebd693da8d0f90054e18a45004006e298779 |
########################################################################
# File : CSCLI.py
# Author : Adria Casajus
########################################################################
import sys
import types
import atexit
import os
import readline
from DIRAC import gLogger
from DIRAC.Core.Utilities.File impor... | andresailer/DIRAC | ConfigurationSystem/Client/CSCLI.py | Python | gpl-3.0 | 16,811 | [
"DIRAC"
] | 2cdfe70a6ad704a035eb968089682c3d151bd12f379a89de82399797cd6e491d |
from os.path import join
from os.path import relpath
from re import compile
from contextlib import contextmanager
from ..staging import COMMAND_VERSION_FILENAME
from ..action_mapper import FileActionMapper
from logging import getLogger
log = getLogger(__name__)
# All output files marked with from_work_dir attribute... | jmchilton/lwr | lwr/lwr_client/staging/down.py | Python | apache-2.0 | 7,030 | [
"Galaxy"
] | c2d2e354a70fe9af8c7d8d91bbff8ae14dc153f040baa2bffe539ef7b98a46cc |
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