text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
#!/usr/bin/env python
import sys, os
sys.path.append("../")
from demo_runner import Demo
class CDKDemo(Demo):
def run_demo(self):
self.print_comment(
"""first we install Vagrant from the regular Fedora repositories. Vagrant is available in
the main Fedora repos since Fedora 21.... | whitel/summit-cdk-demo-2015 | demo_cdk_install/demo_cdk_install.py | Python | gpl-2.0 | 3,232 | [
"CDK"
] | 93cf314ec8d3a30a7705c15918f713d42cc917e02a5beb770c4abd7ba9f47776 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Views tests for the OSF.'''
from __future__ import absolute_import
import unittest
import json
import datetime as dt
import mock
import httplib as http
import math
import time
from nose.tools import * # noqa PEP8 asserts
from tests.test_features import requires_search... | samanehsan/osf.io | tests/test_views.py | Python | apache-2.0 | 184,038 | [
"Brian"
] | 5ceb68fa1e455cbd2bedc9f934c9aaf5eb546e25acbe0ef0f64d045479e57f79 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/build/component.py | Python | agpl-3.0 | 11,804 | [
"Galaxy"
] | 67e6079009622fb53613f00eb11da82c0bf77e3f8ff039a2d6e684326d2a9af7 |
#!/usr/bin/env python3
########################################################################
# Solves problem 26 from projectEuler.net.
# Finds the number below 1000 which has the longest cycle when 1/d.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribute it and... | sanSS/programming-contests | project-euler/problem026.py | Python | gpl-3.0 | 1,669 | [
"VisIt"
] | f7b42f81f6c41eafaff14afed7e7c5de519549d3f89b8a2d50dbed60a9aa83eb |
import sys
import antlr
class Visitor(antlr.ASTVisitor):
def __init__(self,*args):
super(Visitor,self).__init__(*args)
self.level = 0
if not args:
self.cout = sys.stdout
return
if isinstance(args[0],file):
self.cout = args[0]
return
assert 0
... | bamboo/boo | lib/antlr-2.7.5/examples/python/java/java.py | Python | bsd-3-clause | 1,835 | [
"VisIt"
] | 5e665e222884b5a149b624543fa16bd362dee5db49be33955619b30aa0b4d1c5 |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
import lxml.etree
import requests
from werkzeug.tes... | bird-house/PyWPS | pywps/tests.py | Python | mit | 6,132 | [
"NetCDF"
] | 3e1a43a1078dff11f13e2dbbaaf298c396929ad1702af1bdfd68cfa5295a8a18 |
# coding=utf-8
from __future__ import absolute_import
from flask_restful import Resource
from firefly.models.topic import Comment
from firefly.views.utils import short_timesince
from firefly.views.api.consts import OK
from firefly.views.api.utils import generate_status_fields
class ReplyApi(Resource):
def get(s... | mozillazg/firefly | firefly/views/api/comment.py | Python | mit | 1,060 | [
"Firefly"
] | 7d189264a0fe6e5e0fb2505a2c74684f9051e7948be19365cc7b82fe57075208 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Query-Parser.
# Copyright (C) 2014 CERN.
#
# Invenio-Query-Parser 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 ... | egabancho/invenio-query-parser | invenio_query_parser/contrib/spires/walkers/tree_printer.py | Python | gpl-2.0 | 1,411 | [
"VisIt"
] | 65bb150e142ba7d3095587af76124b96806a5ea8be63ab19f0a800fc86f653f6 |
from toee import *
from utilities import *
from Co8 import *
## How this works:
##
## A variable is set in moduels\ToEE\delayed_blast_fireball.txt, that determines how many rounds the fireball is delayed.
## If it's 0, the spell works just like ordinary Fireball, except the damage is limited to 20d6 rather than 10d6.
... | GrognardsFromHell/TemplePlus | tpdatasrc/kotbfixes/scr/Spell105 - Delayed Blast Fireball.py | Python | mit | 4,699 | [
"BLAST"
] | bd1849194bb886d2401b4d06ba8132ff626076117c1db7d785d05c3bdd68024c |
from __future__ import division
import numpy as np
import subprocess
# The bash script for Torque
script = """#!/bin/bash
#PBS -q parallel
#PBS -l nodes=1:ppn=6
#PBS -l mem=5gb
#PBS -l cput=400:00:00
#PBS -N calc_C60
ulimit -s unlimited
export NPROCS=`wc -l < $PBS_NODEFILE`
export OMP_NUM_THREADS=${NPROCS}
export... | gkc1000/pyscf | doc_legacy/source/nao/examples/submit_jobs.py | Python | apache-2.0 | 2,393 | [
"ASE",
"PySCF",
"SIESTA"
] | 2e6f858b31bde5d6f76a410159d137c1852b0731f05b81770450235be95d9fff |
# Author : Fabian Jakobs
"""
Functions for solving linear systems.
The library provides simple linear algebra operations which operate
directly on the gsl_vector and gsl_matrix objects. These are intended
for use with "small" systems where simple algorithms are acceptable.
Anyone interested in large systems will want... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/pygsl/linalg.py | Python | apache-2.0 | 24,076 | [
"Gaussian"
] | 8fa24764b79de678994c6dc7960a8438b83dd7c5c58350ebe5de886e519c4bda |
class MLPView(object):
def __init__(self, mlpdata):
self.__mlp = mlpdata
def layers(self):
'''
return a generator object that is capable of iterating over
the layers of the perceptron
'''
for l in xrange(self.__mlp.layer_count()):
yield LayerV... | aolsux/DeepThought | deepthought/views.py | Python | gpl-3.0 | 1,594 | [
"NEURON"
] | 5155a8fa069acefcf1f1f50fdb353c032b5d4dfed91ab68d5909c1e0f3470810 |
import logging
log = logging.getLogger(__name__)
from markdown.util import etree
from MooseSyntaxBase import MooseSyntaxBase
import MooseDocs
class MooseActionList(MooseSyntaxBase):
"""
Creates dynamic lists for Moose syntax.
Examples:
!systems
!systems framework phase_field
"""
RE = r'^... | backmari/moose | python/MooseDocs/extensions/MooseActionList.py | Python | lgpl-2.1 | 3,773 | [
"MOOSE"
] | b0b02dba9687348b97ebc2eb54e3f62569710a639650601f3cff96c71a448a6a |
import os
import pickle
import time
import types
from decimal import Decimal
from io import StringIO
import pytest
from django.core.cache import CacheKeyWarning, cache, caches
from django.core.management import CommandError, call_command
from django.db import IntegrityError, OperationalError, connection
from django.db... | arnau126/django-mysql | tests/testapp/test_cache.py | Python | bsd-3-clause | 48,949 | [
"Brian"
] | 0098e1f64c59c0def4cea014cc8b0a8b2fceb20c5f4c3a536d31b91f9dae4ead |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | qjflores/state_of_health | config/urls.py | Python | mit | 1,439 | [
"VisIt"
] | b5b397648c48846a202a8fe317adf16da22221312dd17fe1f5234a74cd908619 |
from distutils.core import setup
setup(name='greeker',
version='0.3.2-git',
description="scrambles nouns in an XML document to produce a specimen for layout testing",
author="Brian Tingle",
author_email="brian.tingle.cdlib.org@gmail.com",
url="http://tingletech.github.com/greeker.py/",
... | tingletech/greeker.py | setup.py | Python | bsd-3-clause | 486 | [
"Brian"
] | dbdbb65f39bbd64d68af18e996359728db70f4ed9939784d9cde8cb576d78dbc |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | PatrickOReilly/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 34,762 | [
"Gaussian"
] | 250d7166f1b1d29f2b403a716ea61a7eafdfa2b2e44c4b25a7bc841bcc2bd993 |
import matplotlib.pyplot as plt
from yambopy import *
y = YamboOut('bse',save_folder='bse/SAVE')
energy = y.files['o-yambo.eps_q1_diago_bse']['E/ev[1]']
im_eps = y.files['o-yambo.eps_q1_diago_bse']['EPS-Im[2]']
plt.plot(energy,im_eps)
plt.show()
| alexmoratalla/yambopy | tutorial/bn/plot-bse.py | Python | bsd-3-clause | 249 | [
"Yambo"
] | 4b0efee3cabe3a9ec874c32bbaefde28a29e5c934bc62d292f40fb5d4d6e03f4 |
"""GNG regressor"""
from . import gng2
from .kde import density
from .__gaussian_custom import norm_pdf_multivariate
from numpy import array,diag,matrix
import time
from pygraph.classes.graph import graph
from pygraph.algorithms.accessibility import connected_components
import itertools
from .gks import GKS
from copy i... | sbxzy/pygks | pygks/reg_gng.py | Python | bsd-3-clause | 6,639 | [
"NEURON"
] | 7b9b5ae80b37e5990682aa439f7135721f9391eb56a1b51a73eeb2329bd4ee7c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Clean fasta DNA sequence alignment for sequencing errors
__authors__ = "Eric Normandeau"
__program_name__ = "alignment_clean"
__version_info__ = ('0', '0', '1')
__version__ = '.'.join(__version_info__)
__copyright__ = "Copyright (c) 2011 Eric Normandeau"
__license__ = "GPLv... | enormandeau/ngs_genotyping | scripts/alignment_clean.py | Python | gpl-3.0 | 9,499 | [
"Biopython"
] | 89ab5593dbff7357af7ae0675fc570dd7f325fa7edab5122fdedd89bb59cd564 |
import os
import tempfile
from Bio.Blast import NCBIXML
from django.test import TestCase
from blastplus import utils
from blastplus.features import record
from blastplus.settings import SAMPLE_DIR
class UtilsTestCase(TestCase):
def setUp(self):
self.fastfile = tempfile.NamedTemporaryFile(mode="w+", dele... | michal-stuglik/django-blastplus | blastplus/tests/tests.py | Python | mit | 2,182 | [
"BLAST"
] | cff7aaf038a8547f18b2952ddd3089d86a4fb551cb012bb1fca4d1cc8b55197d |
#!/usr/bin/env python
# coding: utf-8
"""Test suite for autopep8.
Unit tests go in "UnitTests". System tests go in "SystemTests".
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import os
import re
import sys
... | MeteorAdminz/autopep8 | test/test_autopep8.py | Python | mit | 209,330 | [
"Psi4"
] | 5e607f8a74122b6fa8e69d5d2cffbffa31ba137dea59525d5c3e8f4d23809af0 |
# coding=utf-8
# (The line above is necessary so that I can use 世界 in the
# *comment* below without Python getting all bent out of shape.)
# Copyright 2007-2009 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may o... | MinFu/lantern | src/code.google.com/p/winsvc/codereview.py | Python | apache-2.0 | 111,664 | [
"VisIt"
] | d3706328b856f82a546aadab55ca6b35cd79e49f2dabf2be8d2c77dd36f15a3c |
##############################################################################
# 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... | TheTimmy/spack | var/spack/repos/builtin/packages/espresso/package.py | Python | lgpl-2.1 | 5,850 | [
"ESPResSo"
] | c658817abf5bbf50d8e84b800eedf8bd0885d68e9de1e9d60c9d43d444abf05a |
# ----------------------------------------------------------------------------
# Copyright 2015-2016 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apa... | Jokeren/neon | tests/test_lstm.py | Python | apache-2.0 | 15,387 | [
"Gaussian"
] | 07c123fe72686f15ac2643157c33ebf25d29d84ae14828ffc9d5b9e4025dc702 |
#Created by Vineet Tiruvadi, 2010 - 2015
#This is a script that has, embedded, the modules that need to be extracted out into a library
#!/usr/bin/env python
import networkx as nx
import matplotlib.pyplot as plt
import numpy as nm
import time
import sys
import random
import math
import pdb
#import astroglia_net
disp... | virati/pyNetGL | astrocyte_network.py | Python | mit | 8,216 | [
"NEURON"
] | 3aa6cec8d0fd906879a8d7d96484ddf8663ccb6e1ab19e50f253594a0f4595c4 |
from __future__ import print_function
import functools
from copy import copy
import numpy as np
from scipy.stats import norm as ndist
import regreg.api as rr
from ..algorithms.sqrt_lasso import solve_sqrt_lasso, choose_lambda
from .query import gaussian_query
from .randomization import randomization
from ..base im... | selective-inference/selective-inference | selectinf/randomized/lasso.py | Python | bsd-3-clause | 33,753 | [
"Gaussian"
] | 59e89168bd0bfc637b1fd473873bcf3b21471ab0e1cef164e2b4ea0b8b3f8422 |
# -*- coding: utf-8 -*-
#
# hl_api_stdp.py
"""
Functions for spike-timing dependent plasticity.
"""
import nest
def HelloSTDP():
"""Enable all spiking-time dependent plasticity features."""
nest.Install("stdpmodule")
# save old functions
nest_connect = nest.Connect
def _connect(pre, post, conn... | zifeo/nest-stdpmodule | pynest/hl_api_stdp.py | Python | gpl-2.0 | 2,304 | [
"NEURON"
] | 4386f203b5c43fb88c659270be2ac67e0a60f1bf01f13469755a40dbb280fc06 |
#!/usr/bin/env python
from vtk import *
source = vtkRandomGraphSource()
view = vtkGraphLayoutView()
view.AddRepresentationFromInputConnection(source.GetOutputPort())
view.GetRenderWindow().SetSize(600, 600)
view.ResetCamera()
view.Render()
view.GetInteractor().Start()
| HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Infovis/Python/hello_world.py | Python | gpl-3.0 | 275 | [
"VTK"
] | a3186542f74827642674cfec87315b102c88c382e31c24faf9d6dcc3124cb910 |
# -*- coding: utf-8 -*-
import numpy as np
from numpy.random import RandomState
from fakespikes.util import to_spikes
from fakespikes.rates import constant
class Spikes(object):
"""Simulates statistical models of neural spiking
Params
------
n : int
Number of neurons
t : float
Sim... | voytekresearch/fakespikes | fakespikes/neurons.py | Python | mit | 4,820 | [
"NEURON"
] | ea79ee5307d3f716149caaebb00758072dde1fe7799580a8f96c373417a4387e |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 2000
n = 4000
display = True
... | sg0/Elemental | examples/interface/BP.py | Python | bsd-3-clause | 1,926 | [
"Gaussian"
] | 6d441b23923ba1526380403c1913056d7e8585ed38e364880bbf57612daa3906 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
import os
from lettuce import world, step
from nose.tools import assert_true, assert_in # pylint: disable=no-name-in-module
from django.conf import settings
from student.roles import CourseStaffRole, CourseInstructorRole, GlobalStaff
from stu... | zadgroup/edx-platform | cms/djangoapps/contentstore/features/common.py | Python | agpl-3.0 | 12,752 | [
"VisIt"
] | 46ab4764729ba2122131ccffea27519f5d08cc7ebb8de2f7aee554add241ffd5 |
"""
Acceptance tests for course creation.
"""
import uuid
from nose.plugins.attrib import attr
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.index import DashboardPage
from common.test.acceptance.pages.studio.overview import CourseOutlinePage
from comm... | BehavioralInsightsTeam/edx-platform | common/test/acceptance/tests/studio/test_studio_course_create.py | Python | agpl-3.0 | 6,057 | [
"VisIt"
] | 758328e1bfc1138583abd697248ac4db89609acc524e3c8d82169f9261ce2f74 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
import os
from DIRAC import gLogger
from DIRAC.Core.Security import Locations
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Security.X509Chain import... | yujikato/DIRAC | src/DIRAC/Core/DISET/private/Transports/SSLTransport.py | Python | gpl-3.0 | 3,966 | [
"DIRAC"
] | 85dd1adcd792cca0d9403cd4eea01d10adcddb7c5edb9683c208a8e7db61d8d3 |
from django.apps import AppConfig
class VisitConfig(AppConfig):
name = 'visit'
| anhelus/emw-museum-output | visit/apps.py | Python | gpl-3.0 | 85 | [
"VisIt"
] | be59e57be748eee28b3df091b6493f30a0c25376d4594dcb1007a2f0c5720f7d |
"""
@name: Modules/Schedules/_test/test_auto_update.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2019 by D. Brian Kimmel
@note: Created on Dec 31, 2013
@license: MIT License
@summary: Handle the automatic updating of PyHouse
Passed all 5 tests - DBK - 2015-11-21... | DBrianKimmel/PyHouse | Project/src/Modules/House/Schedule/_test/test_auto_update.py | Python | mit | 4,942 | [
"Brian"
] | f2272e99262bddd2be069becd26b29bde043369d909f2099203e9147236f234a |
from ase.test import NotAvailable
from ase.lattice import bulk
from ase.calculators.calculator import get_calculator
required = {'abinit': dict(ecut=200, toldfe=0.0001, chksymbreak=0),
'aims': dict(sc_accuracy_rho=5.e-3),
'elk': dict(tasks=0, rgkmax=5.0),
'gpaw': dict(mode='pw'),
... | suttond/MODOI | ase/test/calculator/al.py | Python | lgpl-3.0 | 1,282 | [
"ABINIT",
"ASE",
"CP2K",
"Elk",
"GPAW"
] | fe8bb967747f71a6f7eafb7a271c11aa791905aa8e388426c6534fa5f21fc9cc |
import numpy as np
from PIL import Image
from line_functions import line_corners, get_angle, sort_quad, getsquares, keep_ratio, round_results, warp_perspective, remove_duplicate_lines, remove_duplicate_corners
from os import listdir
from os.path import isfile, join
import sys
import time
#sys.path.append('/usr/loca... | nishij66/Strutagio | semSegInfer.py | Python | mit | 18,824 | [
"Gaussian"
] | 180f75044ca7c5af40c114b3a40c39ec89b1babfcb929e2f8f93b9a226a7e8c0 |
# 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)
import llnl.util.cpu
class Gromacs(CMakePackage):
"""GROMACS (GROningen MAchine for Chemical Simulations) is a molecu... | rspavel/spack | var/spack/repos/builtin/packages/gromacs/package.py | Python | lgpl-2.1 | 10,315 | [
"Gromacs"
] | a873b3f8d1c5bced6d1d3e8012a0f501a621008254c84e27a0348f578973620c |
# BSD 3-Clause License
#
# Copyright (c) 2016-18, University of Liverpool
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notic... | fsimkovic/conkit | conkit/io/casp.py | Python | bsd-3-clause | 8,972 | [
"PyMOL"
] | 61b782c69530e08a478a65f17dcf5301a68c316eb5bf212cdc8e3ae8a936fa4e |
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
from builtins import range
import os.path
import os
import mock
import random
from io import BytesIO as StringIO
from zipfile import ZipFile... | remind101/stacker | stacker/tests/hooks/test_aws_lambda.py | Python | bsd-2-clause | 14,190 | [
"VisIt"
] | 67d62ab3141240ca741db641aec6910a4611b7e468f5c5731e04994679cd63dd |
"""
Tests i18n in courseware
"""
from __future__ import absolute_import
import json
import re
import six
from django.conf import settings
from django.contrib.auth.models import User
from django.test.client import Client
from django.urls import reverse, reverse_lazy
from django.utils import translation
from openedx.... | ESOedX/edx-platform | lms/djangoapps/courseware/tests/test_i18n.py | Python | agpl-3.0 | 9,383 | [
"VisIt"
] | c202777cada3e709964cf94c1b985b266a29b6565f02b93f870fcc6877e514d2 |
# $Id$
#
"""unit testing code for 3D stuff
"""
from rdkit import RDConfig
import unittest,os
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import TorsionFingerprints
class TestCase(unittest.TestCase):
def testConformerRMS(self):
m1 = Chem.MolFromSmiles('CNc(n2)nc(C)cc2Nc(cc34)ccc3[nH]nc... | soerendip42/rdkit | rdkit/Chem/UnitTestMol3D.py | Python | bsd-3-clause | 6,659 | [
"RDKit"
] | 585a9bf3e159245ad0f42438b5907d6f371adb7a37810e83ba4562af7e78bebf |
class AdalineGD(object):
"""ADAptive LInear NEuron classifier.
Parameters
----------
eta : float
Learning rate between 0 and 1
n_iter : int
Passes over the training dataset
Attributes
----------
w_ : 1d-array
Weights after fitting
errors_ : list
Numb... | southpaw94/MachineLearning | Adaline/AdalineGD.py | Python | gpl-2.0 | 1,619 | [
"NEURON"
] | 8ced2635cab0b501d5eeb1d2bc1ae08a71a989b290a4fa24ba725d10fdfbefda |
#! /usr/bin/env python
#
# pymetar
# (c) 2002 Tobias Klausmann
# (c) 2002 Jerome Alet <alet@librelogiciel.com>
# You're welcome to redistribute this software under the
# terms of the GNU General Public Licence version 2.0
# or, at your option, any higher version.
#
# You can read the complete GNU GPL in the file COPYIN... | theswitch/pymetar3 | setup.py | Python | gpl-2.0 | 1,041 | [
"VisIt"
] | 5b35b9fc1cf1e1b7d236f3d5e127a7c3306da669ac98900a3e64d9e62ca2725f |
from collections import OrderedDict
from keras import backend as K
from keras.layers.core import Layer
from keras import initializations, activations
from keras.layers.convolutional import MaxPooling1D
from seya.regularizers import GaussianKL, LambdaRegularizer
class VariationalDense(Layer):
"""VariationalDense... | EderSantana/seya | seya/layers/temp.py | Python | bsd-3-clause | 6,796 | [
"Gaussian"
] | b77ee6c37ded51525434ad548d68d967726089a60ddb287abcceb382f54d774a |
from __future__ import division
from __future__ import print_function
from past.utils import old_div
import sys
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gam import H2OGeneralizedAdditiveEstimator
from h2o.grid.grid_search import H2OGridSearch
# In this test, we chec... | michalkurka/h2o-3 | h2o-py/tests/testdir_algos/gam/pyunit_PUBDEV_7367_gridsearch_error.py | Python | apache-2.0 | 3,610 | [
"Gaussian"
] | 3e8d8ac63a5ffafd7f8620f5e3fc7fa7ce08bed8e8efafe536b5228ebf4f32b2 |
import datetime
import time
import zlib
import hashlib
import redis
import re
import mongoengine as mongo
import random
import requests
import HTMLParser
from collections import defaultdict
from BeautifulSoup import BeautifulSoup
from mongoengine.queryset import Q
from django.conf import settings
from django.contrib.au... | petecummings/NewsBlur | apps/social/models.py | Python | mit | 144,598 | [
"BLAST"
] | 4f36603251670d917391d689eba5e92200e0259a53ccc57e9fbd924a6be19522 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.vaibhav.brocadeswitches | setup.py | Python | gpl-2.0 | 3,285 | [
"VisIt"
] | 8a3428588ecbd72c69ab1696eb21fe07492678b66bbeefbeced813f07e2c6498 |
# 2-electron VMC code for 2dim quantum dot with importance sampling
# Using gaussian rng for new positions and Metropolis- Hastings
# No energy minimization
from math import exp, sqrt
from random import random, seed, normalvariate
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes... | CompPhysics/ComputationalPhysics2 | doc/Programs/ConjugateGradient/python/qdotimportance.py | Python | cc0-1.0 | 6,026 | [
"Gaussian"
] | b5d91b4c3463bbd043607b253f19b2a66bb9c4ee6850e711ef27aaef6959c755 |
"""NetCDF file reader.
This is adapted from Roberto De Almeida's Pupynere PUre PYthon NEtcdf REader.
classes changed to underscore_separated instead of CamelCase
TODO:
Add write capability.
"""
#__author__ = "Roberto De Almeida <rob@pydap.org>"
__all__ = ['netcdf_file', 'netcdf_variable']
import struct
import... | huard/scipy-work | scipy/io/netcdf.py | Python | bsd-3-clause | 8,702 | [
"NetCDF"
] | 870f7160ccc568e271a6cf6ad85436a63bcacbc652caf57d27400b0cf730cd4a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Tools for the submission of Tasks."""
from __future__ import unicode_literals, division, print_function
import os
import time
import ruamel.yaml as yaml
import pickle
from collections import deque
from date... | matk86/pymatgen | pymatgen/io/abinit/launcher.py | Python | mit | 47,862 | [
"ABINIT",
"pymatgen"
] | 3e4c704b4297ccc154b7a5eaeee6b9739dc65c04d3f931b2adb6ec1dd54b029c |
#!/usr/bin/env python
import os
try:
__IPYTHON__
import sys
del sys.argv[1:]
except:
pass
import srwl_bl
import srwlib
import srwlpy
import srwl_uti_smp
def set_optics(v=None):
el = []
pp = []
names = ['M1', 'M1_Grating', 'Grating', 'GA', 'GA_M3A', 'M3A', 'M3', 'M3_SSA', 'SSA', 'SSA_KBAp... | radiasoft/sirepo | tests/template/srw_import_data/nsls-ii-esm-beamline.py | Python | apache-2.0 | 33,733 | [
"Gaussian"
] | 171f00c916f4a4d2ff97c0136bd31459a8b87063cb57f3450cfb084d57558d1a |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jH0ward/psi4 | psi4/driver/qcdb/dbproc.py | Python | lgpl-3.0 | 3,933 | [
"Psi4"
] | 20c4f9fad6cb5d982ca18a1906860d1198fb9ff27ecd5454b4540612875ca16b |
# Copyright (C) 2010, Joao Rodrigues (anaryin@gmail.com)
# 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.
__doc__ = """
Interface for servers provided at http://swift.cmbi.kun.nl/.
Available Function... | nmih/ssbio | ssbio/biopython/Bio/Struct/WWW/WHATIF.py | Python | mit | 4,083 | [
"Biopython"
] | ab11f6e5cd5db75c90d94500175e309f2871011d6c7dbc9ae7988a9c3fa96095 |
# This file is part of Indico.
# Copyright (C) 2002 - 2022 CERN
#
# Indico is free software; you can redistribute it and/or
# modify it under the terms of the MIT License; see the
# LICENSE file for more details.
import re
import pytest
from indico.modules.events.abstracts.models.abstracts import Abstract, AbstractS... | indico/indico | indico/modules/events/abstracts/notifications_test.py | Python | mit | 8,838 | [
"VisIt"
] | fafbb35cac1f25b9a86f4c4300574dd157992a3bea2166f592c846cd7be45dc7 |
from distutils.core import setup
setup(
name='debacl',
version='0.2.0',
author='Brian P. Kent',
author_email='bpkent@gmail.com',
packages=['debacl', 'debacl.test'],
scripts=['bin/gauss_demo.py'],
url='https://github.com/CoAxLab/DeBaCl',
license='LICENSE.txt',
description='Density-Ba... | nicolasfauchereau/DeBaCl | setup.py | Python | bsd-3-clause | 527 | [
"Brian"
] | 215c0602ecd4ccb58269cef7baee7fcd58e2388a35d3f0c43dd96b4086302bdc |
#!/usr/bin/env python
import os, sys, time, db_conf, getopt, getpass
class options:
def __init__(self, argv):
try:
opts, args = getopt.getopt(argv, "hpu:s:d:r:a:", ["help", "password", "user=","server=","database=","refresh=","alignment_type="])
except getopt.GetoptError:
print 'error running ge... | byuphamerator/phamerator-dev | phamerator/phamServer_progress.py | Python | gpl-2.0 | 3,158 | [
"BLAST"
] | 8c9ff54fa3df967184373ff4a9705fab33327eb8c27b663571c1109fce4061d6 |
# Author: Harish Mohan <harishprofile001@gmail.com>
# Name: GMaps Scrapper
# Version: 3.0
# Description: Scraps data(name, category, address, geocode) from google maps
from splinter import Browser
from easygui import *
from sys import exit
from time import sleep
from re import sub
from os import path, makedirs
# Rec... | harish0507/GMapsScrapper | GMaps_Scrapper_V3.py | Python | mit | 5,317 | [
"VisIt"
] | 73fec5d35570b968dc887fbbf6506bc196db50f327d5730619fc772878619b21 |
#!/usr/bin/env python
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# 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 c... | hitdong/pyvision | src/pyvision/gui/EyePicker.py | Python | bsd-3-clause | 11,763 | [
"VisIt"
] | d15222bbf4adf0fa1e29379220d15fc95b27342fd43b6986235a89acff1f4032 |
"""
The GA4GH data model. Defines all the methods required to translate
data in existing formats into GA4GH protocol types.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import base64
import collections
import glob
import os
import ga4gh.exceptions a... | srblum/hackathon-server | ga4gh/datamodel/__init__.py | Python | apache-2.0 | 15,403 | [
"pysam"
] | caff559a6187721b5ab1197b513e1d69e551eb9b3b2ada085ede4bf1aa9be9bb |
"""
Callable objects that generate numbers according to different distributions.
$Id$
"""
__version__='$Revision: 8943 $'
import random
import operator
from math import e,pi
import param
class NumberGenerator(param.Parameterized):
"""
Abstract base class for any object that when called produces a number.
... | ioam/svn-history | numbergen/__init__.py | Python | bsd-3-clause | 11,067 | [
"Gaussian"
] | 0b2512556fa0df6490c8cc448979bdf46d35252f82549ecb537e79e4ecda881f |
# Copyright 2014 Diamond Light Source Ltd.
#
# 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... | FedeMPouzols/Savu | savu/plugins/filters/fitters/base_fluo_fitter.py | Python | gpl-3.0 | 9,704 | [
"Gaussian"
] | 0639148b72340a135e7758faf01c85b18552f830223141528375640954b6ad29 |
## Aditya Gilra, NCBS, Bangalore, 2012
"""
Inside the .../Demos/GranuleCell/ directory supplied with MOOSE, run
python testNeuroML_Gran98.py
(other channels and morph xml files are already present in this same directory).
The soma name below is hard coded for gran98, else any other file can be used by modifying this s... | dilawar/moose-full | moose-examples/neuroml/GranuleCell/Granule98.py | Python | gpl-2.0 | 1,922 | [
"MOOSE"
] | 8daa5fb9e43b7547f1caf495f6659757f8483b823efd3446aab92dad22b0d567 |
##########################################################################
## # The Coq Proof Assistant / The Coq Development Team ##
## v # Copyright INRIA, CNRS and contributors ##
## <O___,, # (see version control and CREDITS file for authors & dates) ##
## \VV/ #########... | coq/coq | doc/tools/coqrst/notations/regexp.py | Python | lgpl-2.1 | 2,514 | [
"VisIt"
] | c628478e77e672da2274f35b02d779e0bc46259322d038d8a24f637f0f8e8c13 |
# -*- coding: utf-8 -*-
"""
Shortest paths and path lengths using A* ("A star") algorithm.
"""
__author__ =\
"""Salim Fadhley <salimfadhley@gmail.com>
Matteo Dell'Amico <matteodellamico@gmail.com>"""
# Copyright (C) 2004-2008 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter... | rainest/dance-partner-matching | networkx/algorithms/shortest_paths/astar.py | Python | bsd-2-clause | 4,495 | [
"VisIt"
] | 0bf558f159217f5c04851c053396b8e23bcd5635092a4981f6843ecc115ad7e0 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/lib/chkfile.py | Python | apache-2.0 | 1,703 | [
"PySCF"
] | 28e9d4471c0bf69bbcb7914fd33a010663b4ce2517b7f4af9829cfc52ae75ca4 |
""" DIRAC.Resources.Storage package """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
| yujikato/DIRAC | src/DIRAC/Resources/Storage/__init__.py | Python | gpl-3.0 | 149 | [
"DIRAC"
] | 210b24ad02cb8135a5cc232f957d460416f88ca290517efa04468b32ee65259b |
#!/usr/bin/python
#
# Simple script to iterate over the -m 8 results from a
# BLAST and spits out the number of hits at each base of the
# query database.
#
# Peter Skewes-Cox
# February 3, 2009
# *** modified by Charles Chiu, Feburary 8, 2013 to only include bases from the actual BLAST match to the genome ***
# SURP... | chiulab/surpi | mapPerfectBLASTtoGenome.py | Python | bsd-2-clause | 1,290 | [
"BLAST"
] | 6905644fdeb2a6342a6470c6ec663723e133aca886aa4b4455445f85a0d0a198 |
# Copyright (c) 2015-2017 Cisco Systems, Inc.
#
# 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... | kharkevich/molecule | test/unit/conftest.py | Python | mit | 6,733 | [
"Galaxy"
] | 3f244dc1640c58643b587cd0fa632239a5eb7017b6b54ae31e21f6da69c80698 |
import glob
import logging
import os
import sys
import traceback
from urllib import quote_plus
import signal
import time
from PyQt5 import uic
from PyQt5.QtCore import Qt, pyqtSignal, QStringListModel, QSettings, QPoint, QCoreApplication, pyqtSlot, QUrl, QObject
from PyQt5.QtGui import QIcon, QDesktopServices
from PyQ... | vandenheuvel/tribler | TriblerGUI/tribler_window.py | Python | lgpl-3.0 | 30,106 | [
"VisIt"
] | 9dfdf16cbcfb608e57c79a8cac4cfa5cb1642012b0d06b1c64772dc4231ed1c6 |
# -*- coding: utf-8 -*-
"""This module provides the views for the portal."""
import os
import gzip
import json
import boto3
import nbformat
import requests
import urllib
from redis import Redis
from io import BytesIO
from copy import deepcopy
from pathlib import Path
from shutil import make_archive, rmtree
from nbcon... | materialsproject/MPContribs | mpcontribs-portal/mpcontribs/portal/views.py | Python | mit | 18,117 | [
"VisIt"
] | 3ac926de7a6797eaa8c7d703c5d20d2df4fe56c5161e212c4583852260608b49 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
'''Finds yaml tests, converts them to Go tests.'''
from __future__ import print_function
import sys
import os
import os.path
import re
import time
import ast
from re import sub, match, split, DOTALL
import argparse
import codecs
import logging
import process_polyglot
impo... | codepope/transporter | vendor/gopkg.in/gorethink/gorethink.v3/internal/gen_tests/gen_tests.py | Python | bsd-3-clause | 36,833 | [
"VisIt"
] | 3c3f7558aa09b0e93e2ea77455d2cae779940c413db9de8216a8f6b6c4b745c3 |
#!/usr/bin/env python -i
from __future__ import print_function
infile = 'in.simple'
me = 0
from lammps import lammps
lmp = lammps()
# run infile one line at a time
lines = open(infile,'r').readlines()
for line in lines: lmp.command(line)
lmp.command("run 10")
x = lmp.gather_atoms("x",1,3)
epsilon = 0.1
x[0] += ep... | arielzn/lammps | test/lib_python/in.simple-001.py | Python | gpl-2.0 | 555 | [
"LAMMPS"
] | 7d58bff40c6aa70cc707cdc070e203cbef80fbcd135bca40ca8ecf171efe662e |
# Copyright 2004 by Frank Kauff and Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Parser for ACE files output by PHRAP.
Written by Frank Kauff (fkauff@duke.e... | bryback/quickseq | genescript/Bio/Sequencing/Ace.py | Python | mit | 18,866 | [
"Biopython"
] | ac868d1c799e8c935ed40bd70b5210dbc46a97c2445753d70ed7020c32b8874d |
###############################################################################
# Application to run DSCensor #
# Connor Cameron (ctc@ncgr.org) #
# Andrew Farmer (adf@ncgr.org) #
... | ncgr/DSCensor | dscensor/server/dscensor.py | Python | mit | 2,031 | [
"ADF"
] | 4cae9b77a6a8a7a41b186a27225d544185b5c590a9065c651c3bdaf1c8329328 |
# This file is part of BHMM (Bayesian Hidden Markov Models).
#
# Copyright (c) 2016 Frank Noe (Freie Universitaet Berlin)
# and John D. Chodera (Memorial Sloan-Kettering Cancer Center, New York)
#
# BHMM is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public Licen... | jchodera/bhmm | bhmm/hmm/gaussian_hmm.py | Python | lgpl-3.0 | 4,517 | [
"Gaussian"
] | 60fe9a469054447d75b25537351337965b202b42c44eec83d1249885e009f643 |
# MIT License
#
# Copyright (c) 2016 Anders Steen Christensen, Felix Faber
#
# 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 ... | qmlcode/qml | qml/arad.py | Python | mit | 13,619 | [
"Gaussian"
] | bb4a35ccae16777b1b0416a62c2166cafb57cb045a5f90ac6b5263ba797956a5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
Module for reading Lobster output files. For more information
on LOBSTER see www.cohp.de.
"""
import collections
import fnmatch
import os
import re
import warnings
from collections import defa... | davidwaroquiers/pymatgen | pymatgen/io/lobster/outputs.py | Python | mit | 60,061 | [
"VASP",
"pymatgen"
] | 8d19361aea57fc6d632d1fe673673866938a54cd560162c83481e38c3cb3c5ab |
"""
Acceptance tests for Studio related to course reruns.
"""
import random
from bok_choy.promise import EmptyPromise
from nose.tools import assert_in
from ...pages.studio.index import DashboardPage
from ...pages.studio.course_rerun import CourseRerunPage
from ...pages.studio.overview import CourseOutlinePage
from ..... | solashirai/edx-platform | common/test/acceptance/tests/studio/test_studio_rerun.py | Python | agpl-3.0 | 4,244 | [
"VisIt"
] | 9fba07f3a1e006d8585a13f0b50ca5e8687d5206f3ab6d5e4151a40df33e9163 |
# -*- coding: utf-8 -*-
#
# evaluate_tsodyks2_synapse.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 t... | mdjurfeldt/nest-simulator | pynest/examples/evaluate_tsodyks2_synapse.py | Python | gpl-2.0 | 4,181 | [
"NEURON"
] | 294649801f78b4a7ca8d650df0ceedd49c4467e21d2b4cf60826d4159d59ddf3 |
"""
With molecular inversion probes, we map reads to the genome that include the
ligation and extension arms, along with a molecular tag (AKA UMI).
This script takes:
1) ref.fasta
2) mips design file (likely from MIPgen)
3) de-multiplxed, paired-end fastqs
and moves the UMI into the read-name, aligns the r... | brentp/bwa-mips | bwamips.py | Python | mit | 20,414 | [
"BWA"
] | 993d7b6da21153e014bdbfadffc48ed410d5f4b860e577908219bdf6d8c45ae2 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | BlueBrain/NeuroM | neurom/apps/morph_stats.py | Python | bsd-3-clause | 12,150 | [
"NEURON"
] | 7bba9d1a784c2b23a0af93856927aac323c987430ab6a3db382da820d2183bf4 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/line/single_point.py | Python | lgpl-2.1 | 679 | [
"MOOSE"
] | fa5e5c3a004b2b403114ffb86db412e9a200fb008610879a327a640715e99611 |
from __future__ import unicode_literals
from __future__ import absolute_import
from functools import reduce
import logging
from docker.errors import APIError
from .config import get_service_name_from_net, ConfigurationError
from .const import DEFAULT_TIMEOUT, LABEL_PROJECT, LABEL_SERVICE, LABEL_ONE_OFF
from .containe... | lukemarsden/compose | compose/project.py | Python | apache-2.0 | 12,276 | [
"VisIt"
] | fff608676896f78144ad5580324c091b54cf4fa52676bfd7d1d90b108d4ceb70 |
"""The suite of window functions."""
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
'blackmanharris', 'flattop', 'bartlett', 'hanning', 'barthann',
'hamming', 'kaiser', 'gaussian', 'gene... | teoliphant/scipy | scipy/signal/windows.py | Python | bsd-3-clause | 44,370 | [
"Gaussian"
] | 0f8821ca2da691387a8b64b7750cfc972123be36c5a346d7cf431901d2bc6417 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from rest_framework.routers import DefaultRouter, Route
... | TraMZzz/baby-w | server/project/urls.py | Python | bsd-3-clause | 1,861 | [
"VisIt"
] | dee3b27150d82b14ce26f8df983e9729744e19ba3eb09ec4464465d9f8573306 |
import unittest
import numpy as np
from nineml.visitors.base import BaseVisitorWithContext
from nineml.abstraction.dynamics import Dynamics
from nineml.user.multi import MultiDynamics
from nineml.utils.comprehensive_example import instances_of_all_types
from nineml.exceptions import NineMLUsageError
class IDsVisitor(... | INCF/lib9ML | test/unittests/temporary_ids_test.py | Python | bsd-3-clause | 2,484 | [
"VisIt"
] | 900dfde778027986210c945ab382c0a205c078b755043b33da458afc210c3c3a |
# proxy module
from __future__ import absolute_import
from mayavi.core.component import *
| enthought/etsproxy | enthought/mayavi/core/component.py | Python | bsd-3-clause | 90 | [
"Mayavi"
] | b1fc83f6405420123c387ed380f3cf3cfe0f511b1bc71d313b9af29ba8b6da62 |
import fmn.lib.models
from fmn.consumer.backends.base import BaseBackend, shorten
import fedmsg.meta
import arrow
import time
import twisted.internet.protocol
import twisted.words.protocols.irc
from twisted.internet import reactor
from bleach import clean
import logging
logging.basicConfig(level=logging.DEBUG)
log ... | fedora-infra/fmn.consumer | fmn/consumer/backends/irc.py | Python | gpl-2.0 | 18,871 | [
"VisIt"
] | 018b69c67619a81e8c7ab6986681da63d1957b794d829f2ca5460de68149abac |
from __future__ import division
import pytest
import numpy as np
from scipy import sparse
from scipy.stats import kstest
import io
from sklearn.utils._testing import assert_allclose
from sklearn.utils._testing import assert_allclose_dense_sparse
from sklearn.utils._testing import assert_array_equal
from sklearn.uti... | shyamalschandra/scikit-learn | sklearn/impute/tests/test_impute.py | Python | bsd-3-clause | 49,648 | [
"Gaussian"
] | aa8b4db1c987b11b19b45e687a945b72bf64965a80a00611f4af411073485118 |
import matplotlib
if __name__ == '__main__':
matplotlib.use('Agg')
#matplotlib.rc('font', family='computer modern roman')
matplotlib.rc('font', family='serif')
fontsize = 14
matplotlib.rc('font', size=fontsize)
matplotlib.rc('text', usetex=True)
import numpy as np
import pylab as plt
import os... | dstndstn/unwise-coadds | fourier.py | Python | gpl-2.0 | 31,248 | [
"Gaussian"
] | c3ad16fc8f5fa93c921653ac2ddb2fbeb86c8af2f716f55273ea4035797301ab |
import os, sys
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
from collections import OrderedDict
import time
import numpy as np
import SimpleITK as sitk
import math
import itertools
from CIP.logic.SlicerUtil import SlicerUtil
from CIP.logic import Util
#
# CIP_... | acil-bwh/SlicerCIP | Scripted/CIP_TracheaStentPlanning/CIP_TracheaStentPlanning.py | Python | bsd-3-clause | 54,907 | [
"VTK"
] | 958c005676986111648f2035869eb65866ba792b978a1517d087aec7bea9efaf |
""" This module contains various functions that are special cases
of incomplete gamma functions. It should probably be renamed. """
from __future__ import print_function, division
from sympy.core import Add, S, C, sympify, cacheit, pi, I
from sympy.core.function import Function, ArgumentIndexError
from sympy.func... | ojengwa/sympy | sympy/functions/special/error_functions.py | Python | bsd-3-clause | 64,781 | [
"Gaussian"
] | d8595044bbaa12a6ad12bcc1e4812005271cee7dbffecb31a1a2bfcdd5d7c5fe |
"""
This module contains the AmberWriter class and associated methods,
which outputs a prmtop/inpcrd file with CHARMM names and parameters
for use with simulation with the AMBER molecular dynamics package.
It does this by using the chamber functionality of ParmEd API.
Author: Robin Betz
Copyright (C) 2019 Robin... | Eigenstate/dabble | dabble/param/amber.py | Python | gpl-2.0 | 32,598 | [
"Amber",
"CHARMM",
"VMD"
] | a4c65f521eb235774eeab335c2e33025f49f54e28ea27438168acd5a9cd05801 |
#!/usr/bin/env python3
import subprocess
import time
import argparse
if __name__ == '__main__':
bwa_is_recorded = False
smb_is_recorded = False
htvc_is_recorded = False
parser = argparse.ArgumentParser(description='A SOFA wrapper which supports event-driven recording.')
parser.add_argument('--trac... | cyliustack/sofa | tools/sofa-edr.py | Python | apache-2.0 | 1,975 | [
"BWA"
] | 98ea8962a5891f7a7a9503b9c7164aae882934f898bb026d092442c6d2216f8b |
from __future__ import print_function
from __future__ import absolute_import
import os
import numpy as nm
from sfepy.base.base import get_default, Struct, output
from sfepy.base.ioutils import get_print_info
from sfepy.base.timing import Timer
from sfepy.discrete.fem import extend_cell_data, Mesh
from sfepy.homogeniz... | vlukes/sfepy | sfepy/homogenization/recovery.py | Python | bsd-3-clause | 25,124 | [
"VTK"
] | 59767596ef5723750ccd800a25bceb5ea0321534d417c7fd6dcd4bebbab18fde |
"""
Author: Willem Wybo
Date: 18/08/2015
Place: BBP, Geneva
"""
import numpy as np
import math
import scipy.optimize
import sympy as sp
from sys import argv, stdout
import os
import time
import copy
import unittest
import btstructs
import ionchannels as ionc
import functionFitter as funF
import neuronModels as neur... | WillemWybo/SGF_formalism | source/morphologyReader.py | Python | mit | 193,511 | [
"NEURON"
] | a23aa6753e05d9587d0f96e95de8e4f300511720a33c415caac4e3fac9fe9d8b |
"""
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... | Andrew-McNab-UK/DIRAC | Interfaces/API/Job.py | Python | gpl-3.0 | 48,974 | [
"DIRAC"
] | 9fdfc7c2361f6770c78250482853ed3313d834c48e0cad581ac72faea2b81b9b |
#!/usr/bin/env python
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Script to plot density of states (DOS) generated by an FEFF run
either by site, element, or orbital
"""
__author__ = "Alan Dozier"
__credits__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyri... | materialsproject/pymatgen | pymatgen/cli/feff_plot_dos.py | Python | mit | 2,220 | [
"FEFF",
"pymatgen"
] | 33f1b5a0b36a0104a4203c523c2725b348409e19d4a68e7c62f382d385b3f696 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.