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# -*- coding: utf-8 -*-
# Author: Braden Czapla (2019)
# Last modified: 2019-04-29
# Original data: Kaiser et al. 1962, https://doi.org/10.1103/PhysRev.127.1950
from __future__ import absolute_import, division, print_function
import numpy as np
import matplotlib.pyplot as plt
#########################################... | polyanskiy/refractiveindex.info-scripts | scripts/Kaiser 1962 - SrF2.py | Python | gpl-3.0 | 3,299 | [
"CRYSTAL"
] | 0135bc3a94f293f37aa89617e1211121ff00ef0d2f4124a72e63ffe76821d1e0 |
"""
This class deal with the relation between every three balls in n-dimensional world
"""
__author__ = 'Yinan Zhang'
__revision__ = '$Revision$'
import sys, os, math, time
sys.path.append('../basics/math')
from numpy.linalg import matrix_rank
from hyper_geometry import *
from l1_geometry import *
from Triangle ... | Yinan-Zhang/RichCSpace | alphashape/hyper_alpha_shape.py | Python | mit | 13,140 | [
"Gaussian"
] | 8103885ff542256cc96f792c16c2fc858d6b30b57df66f9849fb56a150bcbf63 |
import itertools
import logging
import re
import time
import urllib
from collections import defaultdict
from datetime import datetime, timedelta
from decimal import Decimal
from typing import Any, Callable, Dict, List, \
Optional, Set, Tuple, Type, Union
import pytz
from django.conf import settings
from django.ur... | tommyip/zulip | analytics/views.py | Python | apache-2.0 | 51,930 | [
"VisIt"
] | fbade33b1d93e2c8c34ab489dda41ed2e847555039f287195b1a77e8a7f71600 |
#!/usr/bin/env python
############################################################################
# Copyright (c) 2015-2019 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
###########################################... | B-UMMI/INNUca | src/SPAdes-3.14.0-Linux/share/spades/spades_pipeline/stages/correction_stage.py | Python | gpl-3.0 | 5,676 | [
"BWA"
] | d10a5208aff33e66b4581bebb9bc618afd7f81fd1c3f34144394eacb83d70f19 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
import unittest
import os
from pymatgen.alchemy.transmuters import CifTransmuter, PoscarTransmuter
from pymatgen.alchemy.filters import ContainsSpecieFilter
from pymatgen.transformations.standa... | dongsenfo/pymatgen | pymatgen/alchemy/tests/test_transmuters.py | Python | mit | 4,616 | [
"pymatgen"
] | 32824dba742a855973a7a9110eae22af6e70c21ca5ea1720a704dbab6ccdd799 |
"""This file provides enhanced support for editing Python files
Nothing is done if the projects do not support python, otherwise, the
following are provided:
- Create highlight rules for python files
- Defines a convenient filter "Python File" to use when defining your
own actions
- New menu to reload the cu... | qunying/gps | share/support/languages/python_support.py | Python | gpl-3.0 | 15,959 | [
"VisIt"
] | 542fdfab384e3bfe282e556eec02b656948801a85090062baeb39e6d1344d989 |
# Copyright (c) 2013,Vienna University of Technology, Department of Geodesy and Geoinformation
# 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 a... | christophreimer/pytesmo | tests/test_grid/test_netcdf.py | Python | bsd-3-clause | 6,962 | [
"NetCDF"
] | 71f2b1192fd9f0420c08f5fc6aaa3a0333bac4917710ecac4c0e85bfbbfa6e18 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | Bhaal22/blog.drylm.org | conf.py | Python | mit | 30,140 | [
"VisIt"
] | 46e46035d40d0187a34380b9bc70589aa156f4bea39723173a4fa089843c1fc3 |
from pathlib import Path
import platform
import warnings
import numpy as np
import pandas as pd
from pkg_resources import parse_version
import pytest
import pvlib
pvlib_base_version = \
parse_version(parse_version(pvlib.__version__).base_version)
# decorator takes one argument: the base version for which it sh... | anomam/pvlib-python | pvlib/tests/conftest.py | Python | bsd-3-clause | 10,997 | [
"pysam"
] | 8597a94ca01a780d757ec4ea93fc93d01cdffa40d1ad554e7063eb90a0dbad7b |
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
from statapp.views import dcv_validation
urlpatterns = [
url(r'^$',... | AndrewBorst/statapp | config/urls.py | Python | mit | 1,917 | [
"VisIt"
] | f6459c944abed4fbb2458fa7f820d4a2a6a07254bd6ce58dfc1597c504af64e1 |
#!/usr/bin/env python3
import re
import requests
from urllib.parse import urlsplit
def get_content(url):
spit_base_url = "https://spit.mixtape.moe/view/download/"
paste_info = {
'site': 'mixtape',
'url': url,
}
fragments = urlsplit(url)
subdomain = fragments.netloc.split(".")[0]... | luceatnobis/harvester | harvester/mixtape/__init__.py | Python | unlicense | 891 | [
"MOE"
] | 065ac74d67a65364da2dd42e22542fc7ddba3d1c76ba009543982e15ba38cee9 |
"""HTTP related handlers.
Note that some other HTTP handlers live in more specific modules: _auth.py,
_gzip.py, etc.
Copyright 2002-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt included w... | Masood-M/yalih | mechanize/_http.py | Python | apache-2.0 | 10,064 | [
"VisIt"
] | 0ba5bc641774071dc9fe2a306f4508b80bdf39d0e777dbaf730c9e22d479925b |
#!/usr/bin/env python
import rospy
from geometry_msgs.msg import Twist
from turtlesim.msg import Pose
from math import pow,atan2,sqrt
import numpy as np
class turtle():
def __init__(self):
#Creating our node,publisher and subscriber
rospy.init_node('turtlebot_controller', anonymous=True)
s... | kribe48/wasp-mbse | WASP-turtlebot-DSL/ros_node_old.py | Python | mit | 3,221 | [
"VisIt"
] | d70c2cea8c8ea66d3b3cb0c4ce03ec61d5259fffc018a97c452bba371154f5a0 |
"""Classes for ODHQLs Abstract Syntax Tree."""
from collections import Sequence
from enum import Enum
from hub.odhql.exceptions import TokenException
class ASTBase(object):
"""Base class for all AST classes."""
def accept(self, visitor):
""" Basic support for the visitor pattern. """
visit... | hsr-ba-fs15-dat/opendatahub | src/main/python/hub/odhql/ast.py | Python | mit | 23,543 | [
"VisIt"
] | c15eefea9cfd96427bcecf21ef4157a223b649dd5fba84074d0204cbf0b0ad6b |
from ScriptingLanguage.Parser.AstNode import Ast
from ScriptingLanguage.Visitors.FunctionVisitor import visit_func_call
__author__ = 'chronium'
class FunctionCallNode(Ast):
def __init__(self, value):
super(FunctionCallNode, self).__init__(value, 'Function Call')
def visit(self):
return visit_... | chronium/ChronoScript | ScriptingLanguage/Parser/AstNodes/FunctionNodes.py | Python | gpl-2.0 | 584 | [
"VisIt"
] | 77c2f9e9f0ea8b5932c8fb4c5bc94d3fb85dab27065c2ae52bcdc63f73a6e943 |
# Copyright 2003, 2007 by Sebastian Bassi. sbassi@genesdigitales.com
# All rights reserved. This code is part of the Biopython
# distribution and governed by its license.
# Please see the LICENSE file that should have been included as part
# of this package.
"""Local Composition Complexity."""
import math
__docforma... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SeqUtils/lcc.py | Python | gpl-2.0 | 6,135 | [
"Biopython"
] | 9d480e03316dc3a3b95305406dada74c84105aae43ca99b2b9b298ff1461c641 |
#!/usr/bin/python
from math import ceil
class OverlapException:
pass
class OutOfRackException:
pass
class RackFullException:
pass
unitsize = 43.5
class Rack(object):
def __init__(self, name, attr, units):
self._name = name
self.units = units
self.affinity = "bottom"
self._elements = {}
self.__att... | jaqx0r/fengshui | rack.py | Python | gpl-2.0 | 10,254 | [
"VisIt"
] | 96356b4272332240186f0ec9233ed2db53a981bf7b2b10b374848737fd39af87 |
""" :mod: RegisterReplica
==================
.. module: RegisterReplica
:synopsis: register replica handler
RegisterReplica operation handler
"""
__RCSID__ = "$Id $"
from DIRAC import S_OK, S_ERROR
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.DataManagementSystem.Age... | rajanandakumar/DIRAC | DataManagementSystem/Agent/RequestOperations/RegisterReplica.py | Python | gpl-3.0 | 5,015 | [
"DIRAC"
] | 1c329d02e7b7cd2133085733fbda72016d32d68aa5c2e6a81057445498a487fb |
'''
Created on Nov 7, 2010
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3... | tectronics/chimerascan | chimerascan/deprecated/merge_spanning_alignments_v1.py | Python | gpl-3.0 | 10,842 | [
"pysam"
] | 5eaa723625ff8c438387f3917930aa6cd8bee20c388664549ab15faf17157891 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Scaled_Features/results/2_categories/test10_cross_validate_categories_mov_fixed_1200ms_scaled_method_iii.py | Python | mit | 4,633 | [
"Mayavi"
] | e9867bd11dceea32906d6464fff22190ea59057b182c55882c949e70aa686e15 |
# -*- coding: utf-8 -*-
init_intro = """
_____ _ __
|_ _| __ __ _ _ __ ___(_)/ _| _____ __
| || '__/ _` | '_ \/ __| | |_ / _ \ \/ /
| || | | (_| | | | \__ \ | _| __/> <
|_||_| \__,_|_| |_|___/_|_| \___/_/\_\\
Welcome to the Transifex Client! Please follow the instructions to
initia... | transifex/transifex-client | txclib/messages.py | Python | gpl-2.0 | 4,233 | [
"VisIt"
] | 3f697aa10593b91343688547bb302e0c2715c1d60cb545139ef4c5d7a8eb4a2a |
"""
Simulates Izhikevich's neuron model using the Runge-Kutta method.
Parameters for regular spiking, fast spiking and bursting
neurons extracted from:
http://www.izhikevich.org/publications/spikes.htm
"""
import numpy as np
IZ_PARAMETERS = {
'regular': {
'a': 0.02,
'b': 0.2,
'c': -65,
... | lawrencejones/neuro | iz/IzNeuron.py | Python | gpl-3.0 | 2,752 | [
"NEURON"
] | 108fc41bbde394f4d541882eb96332b9a96425abdf309b83b8f25219ae3a58b4 |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
import warnings
from sklearn.datasets import load_digits
from sklearn.cross_validation import cross_val_score
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.testing import assert_array_equal
from sklearn.utils.testi... | depet/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 12,739 | [
"Gaussian"
] | b9649f58577ae9046a0912087982964e9a62a8de7ee9778929ab5d21ca552309 |
#!/usr/bin/env python
'''
Fly Copter in SITL
AP_FLAKE8_CLEAN
'''
from __future__ import print_function
import copy
import math
import os
import shutil
import time
import numpy
from pymavlink import mavutil
from pymavlink import mavextra
from pymavlink import rotmat
from pysim import util
from pysim import vehiclei... | samuelctabor/ardupilot | Tools/autotest/arducopter.py | Python | gpl-3.0 | 326,096 | [
"Gaussian"
] | 225bccad737b23be470b0fa3d73d6fc548c4d8ec26bcf623d8831c2988e64cf2 |
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not... | bolkedebruin/airflow | airflow/utils/log/logging_mixin.py | Python | apache-2.0 | 6,012 | [
"Elk"
] | f37e7ee981d024ccc564a1e1438955fb4f1b8c5f0db4be55bc11abdf02270c7e |
import numpy as np
import devito as dv
from devito.tools import as_tuple, as_list
from devito.builtins.utils import nbl_to_padsize, pad_outhalo
__all__ = ['assign', 'smooth', 'gaussian_smooth', 'initialize_function']
def assign(f, rhs=0, options=None, name='assign', **kwargs):
"""
Assign a list of RHSs to a... | opesci/devito | devito/builtins/initializers.py | Python | mit | 11,728 | [
"Gaussian"
] | 6d641bf87638855f3404e182c7a8fce118cf42cf3c91bd9c7216b79fac6cddf6 |
"""HandleImport transformation takes care of importing user-defined modules."""
from pythran.passmanager import Transformation
from pythran.tables import cxx_keywords, MODULES, pythran_ward
from pythran.syntax import PythranSyntaxError
import ast
import importlib
import inspect
import logging
logger = logging.getLogg... | pbrunet/pythran | pythran/transformations/handle_import.py | Python | bsd-3-clause | 16,323 | [
"VisIt"
] | 7e7700e5bbd5124affaa67fcb2cdfffae298d7be99a80b53d6c35c143a9db43e |
# -*- coding: iso-8859-1 -*-
"""
MoinMoin - convert content in 1.6.0alpha (rev 1844: 58ebb64243cc) wiki markup to 1.6.0 style
by using a modified 1.6.0alpha parser as translator.
PLEASE NOTE: most moin users will never need to execute this code,
because it is just for users of 1... | RealTimeWeb/wikisite | MoinMoin/script/migration/_conv160a_wiki.py | Python | apache-2.0 | 19,189 | [
"Brian"
] | bc1f8dda94485f05e694cbc44496aa59c65da11319e0defc029df69f7c5bf16a |
import os
import json
import requests
import multiprocessing
cwd = os.path.dirname(os.path.realpath(__file__))
num_requests = 3
key = ''
headers = {'Cache-Control': 'no-cache'}
post_url = ''
def get_code(url):
# Try loaing the site in 1 second
try:
requests.get(url, timeout=1, headers=headers, verify... | cloughrm/HTTP-Uptime-Monitor | status.py | Python | gpl-2.0 | 1,764 | [
"Amber"
] | aed0f0a724ef1bf00aed5d16b5cfb8396496630017ac9c60040740567819c791 |
import hashlib
import itsdangerous
import rollbar
from boto3.session import Session
from django.conf import settings
from django.http import HttpResponseBadRequest
from django.utils.translation import ugettext
from .signatures import signer
from .helpers import render
CONFIRMATION_PARAM = '__ctx'
def _send_mail(t... | Pinecast/pinecast | pinecast/email.py | Python | apache-2.0 | 4,330 | [
"VisIt"
] | 11df6239b31c0ac26346f7ab9309ca541c7c7f2316ff15901cf3c8012be0a457 |
# Copyright 2017-2020 The GPflow Contributors. 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 appli... | GPflow/GPflow | gpflow/expectations/sums.py | Python | apache-2.0 | 4,488 | [
"Gaussian"
] | 04509f87f210a29ea2f294589d7418cdad204351f957de0a668e632e326c1735 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/peacock/PeacockMainWindow.py | Python | lgpl-2.1 | 7,195 | [
"MOOSE"
] | b20d97d5c0710afaf8e55e694827abcf3dae3cd6217a5825783d906374195371 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/mooseutils/civet_results.py | Python | lgpl-2.1 | 6,960 | [
"MOOSE"
] | c316a66b675d7ad695918d2aa7edf99059bd6dbc31c31afaf2d280978e578036 |
# -*- coding: utf-8 -*-
"""Unit tests for functions calling bowtie externally."""
from pathlib2 import Path
import pytest
from imfusion.external import star
# pylint: disable=no-self-use,redefined-outer-name
class TestStarIndex(object):
"""Unit tests for the star_index function."""
def test_call(self, mo... | NKI-CCB/imfusion | tests/imfusion/external/test_ext_star.py | Python | mit | 4,343 | [
"Bowtie"
] | 5b60400c02c0084710395aebe4dca8ae124c64ae509b9906cd87a89e1b4ea812 |
import numpy
import scipy.stats.kde as kde
import scipy.ndimage as ndimage
def viterbi(p_observations_given_state, p_transition, p_initial):
"""Given an HMM and set of observations, identify the most likely state
sequence to have generated the observations using the Viterbi algorithm.
This implements a ge... | zpincus/zplib | zplib/scalar_stats/hmm.py | Python | mit | 9,561 | [
"Gaussian"
] | 2985be5a584f38d8006f61333325a3e39d956a5abfd202457797cfc3478d0cdb |
'''upgrade to numpy 1.8.1
instal pyper # bridge to R
install numexpr # http://code.google.com/p/numexpr/downloads/detail?name=numexpr-2.1.win32-py2.7.exe
install pytables aka tables 3.1.1 # http://www.lfd.uci.edu/~gohlke/pythonlibs/
easy_install pandas
# IN R do this to install rhdf5:
> source("http://bioconductor.org... | ConvergenceDA/visdom-web | test/pandasTools.py | Python | mit | 1,802 | [
"Bioconductor"
] | ae695988e8f2285efafca6f4b700f764fb7efcaf01b840aa8570ca4cb8a81baf |
# Copyright (c) 2016, the GPyOpt Authors
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from .base import AcquisitionBase
from ..util.general import get_quantiles
class AcquisitionLCB(AcquisitionBase):
"""
GP-Lower Confidence Bound acquisition function with constant exploration weight.
See:
... | SheffieldML/GPyOpt | GPyOpt/acquisitions/LCB.py | Python | bsd-3-clause | 1,851 | [
"Gaussian"
] | b7bb1613cb19d546a3203134792454cfc0508c6bf9b2567e67f56ca8718f10e7 |
""" SummarizeLogsAgent module
This agents scans all the log tables ( SiteLog, ResourceLog and NodeLog ) on the
ResourceStatusDB and summarizes them. The results are stored on the History
tables (SiteHistory, ResourceHistory and NodeHistory) and the Log tables
cleared.
In order to summarize the logs, all ent... | arrabito/DIRAC | ResourceStatusSystem/Agent/SummarizeLogsAgent.py | Python | gpl-3.0 | 7,460 | [
"DIRAC"
] | 793cf82d4e4c6b18490dd6317e46d62005b0e27b3f9fff7be17d12348d12e627 |
from sqlobject import *
from sqlobject.converters import sqlrepr
from sqlobject.sqlbuilder import RLIKE, AND, OR, INNERJOINOn
from turbogears import identity, config
from datetime import datetime
import time
from string import strip
import IPy
from mirrormanager.lib import uniqueify, append_value_to_cache
from mirrorma... | docent-net/mirrormanager | server/mirrormanager/model.py | Python | gpl-2.0 | 37,615 | [
"VisIt"
] | bdd01dc5264f0dc92c7c34fa6145fc9522f3b9aa28ec7a3beea5dabc31897bfd |
# Look at sdf_example.py in the examples/ directory for more detail
from sdfpy import load_sdf
from thingking import loadtxt
import vtk
import numpy as np
# Load N-body particles from a = 1.0 dataset. Particles have positions with
# units of proper kpc, and velocities with units of km/s.
particles = load_sdf("../dat... | ryanpbrewster/SciVis-2015 | examples/displayParticleGlyphs.py | Python | mit | 1,043 | [
"VTK"
] | 05a10212c8eff9dc464c0aacfac3f6c828be784a784882e109d32971bfa5b9fa |
#!/usr/bin/env python
########################################################################
# File : dirac-configure
# Author : Ricardo Graciani
########################################################################
"""
Main script to write dirac.cfg for a new DIRAC installation and initial download of CAs a... | fstagni/DIRAC | Core/scripts/dirac-configure.py | Python | gpl-3.0 | 20,249 | [
"DIRAC"
] | fd4fc3304df1191169742cf2408eae0b4a2f33ef12a9368705be47b3fdf382bb |
"""Importers for bookmarks"""
import json
import os
import random
import string
import time
import transaction
from datetime import datetime
from dateutil import parser as dateparser
from BeautifulSoup import BeautifulSoup
from lxml import etree
from lxml.etree import XMLSyntaxError
from bookie.lib.urlhash import gene... | charany1/Bookie | bookie/lib/importer.py | Python | agpl-3.0 | 20,851 | [
"VisIt"
] | f091eca57452bb4c99110cd7607bd9adda95fba90796c4ff3320bde6a19725c5 |
# -*- coding: utf-8 -*-
"""
Created on Sun Dec 03 21:54:41 2017
@author: TUNTUNGAN
"""
from datetime import timedelta,datetime
import numpy as np
import re
import os.path
from scipy import signal
import pandas as pd
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
def step_removal_process(data,thres... | ragabhumi/MRDP | step_remove.py | Python | gpl-3.0 | 12,400 | [
"Gaussian"
] | 7a08fd1ce5dda859a69ae64680456a55c2779b902c698041acb349abe76b794f |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/mooseutils/csvdiff.py | Python | lgpl-2.1 | 18,912 | [
"MOOSE"
] | 3b3bd5a8f351abd84e6312f693ea20dae762bee7aeeeee1c1517c494acbb57b9 |
from django.db import models
from django.core.mail import send_mail
from django.core.urlresolvers import reverse
import os
import urllib
import uuid
# Create your models here.
class Subscriber(models.Model):
email = models.EmailField(max_length=254)
active = models.BooleanField(default=False)
confirm_key... | nolanzandi/webapp-public | webapp/apps/register/models.py | Python | mit | 1,396 | [
"VisIt"
] | 6444d84f911ee444d82403bb90a4ab303f474cab16d8d4f93c868aa8a007f630 |
import logging
import math
from galaxy.model.item_attrs import RuntimeException, UsesAnnotations, UsesItemRatings
from galaxy.util import sanitize_text
from galaxy.util.json import loads, dumps
from galaxy.util.odict import odict
from galaxy.web.framework import decorators
from galaxy.web.framework import url_for
from... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/framework/helpers/grids.py | Python | gpl-3.0 | 41,060 | [
"Galaxy"
] | f02d57e45f80f086f6811a3df3efd762a3a57b163265447e6d9c5a0805a76253 |
"""
Author: Remy D <remyd@civx.us>
Ralph Bean <rbean@redhat.com>
Mike Nolan <me@michael-nolan.com>
License: AGPLv3+
"""
import ConfigParser
import feedparser
import json
import urllib2
import re
from flask import Flask
from flask.ext.mako import MakoTemplates, render_template
from flask import redirect... | FOSSRIT/everline | run.py | Python | agpl-3.0 | 8,576 | [
"VisIt"
] | 3e5bc52b88b53b32b1ed3626169b6ab962143b19f10eb2189adb9ed13d1f81e1 |
## Alarm Server
## Supporting Envisalink 2DS/3
##
## This code is under the terms of the GPL v3 license.
import ctypes
c_uint16 = ctypes.c_uint16
class IconLED_Bitfield( ctypes.LittleEndianStructure ):
_fields_ = [
("alarm", c_uint16, 1 ),
("alarm_in_memory", c_uint16, 1 ),
... | jnimmo/pyenvisalink | pyenvisalink/honeywell_envisalinkdefs.py | Python | mit | 15,602 | [
"FEFF"
] | e94d04ab767b5f1684ed56f53a5242a5423c30e7414e27bdc9a9cd294b985c1e |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
class NhkVodIE(InfoExtractor):
_VALID_URL = r'https?://www3\.nhk\.or\.jp/nhkworld/(?P<lang>[a-z]{2})/ondemand/(?P<type>video|audio)/(?P<id>\d{7}|[a-z]+-\d{8}-\d+)'
# Content available only for a limited period of time. Visit... | hakatashi/youtube-dl | youtube_dl/extractor/nhk.py | Python | unlicense | 3,776 | [
"VisIt"
] | f03ae6723245e9a0960799d7138d1a041eccb954193214b6f70b9c8a253f2f5f |
import ast
__author__ = 'Mathias Claus Jensen'
__maintainer__ = 'Mathias Claus Jensen'
__all__ = ['TransformVisitor']
ATOMIC_SOURCES = ['SQLSource', 'CSVSource', 'TypedCSVSource']
WRAPPERS = ['ConnectionWrapper']
class TransformVisitor(ast.NodeVisitor):
"""
Class responsible for making changes to an AST so ... | Betaboxguugi/P6 | code/framework/reinterpreter/transform_visitor.py | Python | gpl-3.0 | 3,321 | [
"VisIt"
] | c1115b0bc77f8f72b0b2e28a9500303075b68cd1547a5f07987d7b86bbb5eefc |
import pandas as pd
from sklearn.ensemble import RandomForestRegressor
from sklearn.ensemble import BaggingRegressor
from sklearn.ensemble import ExtraTreesRegressor
from sklearn.ensemble import AdaBoostRegressor
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.ensemble import RandomTreesEmbedding
fr... | rupakc/Kaggle-Compendium | Winton Stock Market Challenge/stock-baseline.py | Python | mit | 2,904 | [
"Gaussian"
] | 5b01cb2ed2f42657ba1bebc72c24b9e05574b0ec578fdeae197900eebb9616b1 |
"""
This module provides the generic functionality of tracing code by
modifying its AST. Eventually this will become a separate package.
This is similar to the standard library module bdb, while birdseye
itself would correspond to pdb.
Most of the work is in TreeTracerBase.
"""
import ast
import inspect
import sys
fro... | alexmojaki/birdseye | birdseye/tracer.py | Python | mit | 26,076 | [
"VisIt"
] | db555262a013f922a8d60c5618f424dc20999149b142a499d065705af0c749b3 |
"""
:mod: DataManager
.. module: DataManager
:synopsis: DataManager links the functionalities of StorageElement and FileCatalog.
This module consists of DataManager and related classes.
"""
# # imports
from datetime import datetime, timedelta
import fnmatch
import os
import time
import errno
# # from DIRAC
import... | andresailer/DIRAC | DataManagementSystem/Client/DataManager.py | Python | gpl-3.0 | 75,470 | [
"DIRAC"
] | 8c4767a42a6a12d1814081c1b957251de7fe4ce38e6206e1886bb90303cc0888 |
# Copyright (C) 2018
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, o... | espressopp/espressopp | src/interaction/TabulatedSubEnsDihedral.py | Python | gpl-3.0 | 6,904 | [
"ESPResSo"
] | 37b53882936376b49f227f58828ebc05d8cec78e4b9777cea1e53b45d8aa3965 |
#!/usr/bin/env python
import sys
import unittest
import vtk
from PyQt5 import QtWidgets
from peacock.ExodusViewer.plugins.MediaControlPlugin import main
from peacock.utils import Testing
class TestMediaControlPlugin(Testing.PeacockImageTestCase):
"""
Testing for MeshControl widget.
"""
qapp = QtWidget... | Chuban/moose | python/peacock/tests/exodus_tab/test_MediaControlPlugin.py | Python | lgpl-2.1 | 12,428 | [
"VTK"
] | 788f6df5426b607c68b005649189a953a1a115ac4ad6923ac08bf3460bb47782 |
import os
from visitor.Visitor import Visitor
from data.Category import Category
from data.Test import Test
class FileExplorer(Visitor):
@staticmethod
def visit(obj):
if isinstance(obj, Category):
FileExplorer.visit_category(obj)
@staticmethod
def visit_category(obj: Category):
... | Sildra/PyTester | PyTester/visitor/FileExplorer.py | Python | apache-2.0 | 668 | [
"VisIt"
] | 2c8cd944bc7cb744fc68ccc9314826bafb0af1326a290316bd72cddb655e0e1c |
"""Mayavi/traits GUI for averaging two sets of KIT marker points."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD-3-Clause
import os
import sys
import numpy as np
from mayavi.tools.mlab_scene_model import MlabSceneModel
from pyface.api import confirm, error, FileDialog, OK, YES
from tr... | pravsripad/mne-python | mne/gui/_marker_gui.py | Python | bsd-3-clause | 15,406 | [
"Mayavi"
] | 8d6a3a04cbeb5eec7d88e04ec5a8eeb98b2a5f939793e206dc7fb6f993ab78cf |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0035_bse_nonin_nao.py | Python | apache-2.0 | 1,705 | [
"PySCF"
] | fe9f333ab73facd5353705c490bdbc058094055c4b2879f15cbd4b10885ee615 |
'''WeenieBot's Setup!'''
import json
import subprocess
import time
import sys
with open("settings.json", 'w+') as outfile:
outfile.write(json.dumps({}))
with open("settings.json", "r") as infile:
settings = json.loads(infile.read())
print('Welcome to WeenieBot\'s setup!\nIf you need any help just refer to the in... | Beefywhale/WeenieBot | setup.py | Python | mit | 1,308 | [
"VisIt"
] | 4bccb143edf55d47dcfaaa3043100b8d0afe0ae2852761f64ca80a3cff0f9485 |
# -*- coding: utf-8 -*-
"""Various text used throughout the website, e.g. status messages, errors, etc.
"""
# Status Messages
#################
# NOTE: in status messages, newlines are not preserved, so triple-quotes strings
# are ok
# Status message shown at settings page on first login
# (upon clicking primary e... | kushG/osf.io | website/language.py | Python | apache-2.0 | 5,549 | [
"VisIt"
] | 24720641d45b1a06683f42bc09aa1dd9b8d2f59ff178b79f305116de9fc2479c |
import os
import sys
import time
import platform
from math import log
import numpy as np
import ase
from ase.units import Bohr, Hartree
from ase.data import chemical_symbols
from ase.version import version as ase_version
import gpaw
import _gpaw
from gpaw.version import version
from gpaw.utilities import devnull
from... | robwarm/gpaw-symm | gpaw/output.py | Python | gpl-3.0 | 20,573 | [
"ASE",
"CRYSTAL",
"GPAW"
] | 4ff740f0a79bf92dab2570e32c06f2476739311d3d79db41d6dbfdc795f0d204 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/learn/ray/mxnet/test_mxnet_symbol.py | Python | apache-2.0 | 2,514 | [
"ORCA"
] | 504c81493161dbc2b7085985e7c5b1030b5204a6af110cd4582d5e2081ed890d |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Read a maf file and print the regions covered to a set of bed files (one for
each sequence source referenced in the maf). Only blocks with a positive
percent identity are written out.
TODO: Can this be generalized to be made more useful?
usage: %prog bed_outfile_prefix... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_covered_regions.py | Python | bsd-3-clause | 1,700 | [
"Galaxy"
] | 53dcf83ffb37ba8d344852c2533b70b8cfc17db96a71e6517fea9f2314b98a91 |
#!/usr/bin/python
import argparse, sys, re, random, os, gzip
from multiprocessing import Pool, Lock, cpu_count, Queue
from subprocess import Popen, PIPE
import SimulationBasics
from VCFBasics import VCF
from SequenceBasics import read_fasta_into_hash
from TranscriptomeBasics import Transcriptome
from GenePredBasics imp... | jason-weirather/py-seq-tools | seqtools/cli/legacy/simulate_biallelic_transcriptome.py | Python | apache-2.0 | 22,656 | [
"ASE"
] | 8027b3633d268ec7df97231d4c93c834a7811eece114643f7775cbb142ac1cdc |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | scripts/clobber.py | Python | lgpl-2.1 | 4,034 | [
"MOOSE"
] | 543f8b5903de2718424e576911200b7af9ee39fb0f6cfb870cb2f74abce28df1 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/python/ops/image_grad_test.py | Python | apache-2.0 | 18,282 | [
"Gaussian"
] | 8ba4a34a26c459eb546cb074903432e1b265acc0323ab8b7fd0f26731ea37029 |
"""
Converting the 'parse-tree' output of pyparsing to a SPARQL Algebra expression
http://www.w3.org/TR/sparql11-query/#sparqlQuery
"""
import functools
import operator
import collections
from rdflib import Literal, Variable, URIRef, BNode
from rdflib.plugins.sparql.sparql import Prologue, Query
from rdflib.plugi... | dbs/rdflib | rdflib/plugins/sparql/algebra.py | Python | bsd-3-clause | 20,961 | [
"VisIt"
] | f284ddcfc72e33526448abf2f6914deebb4af72d4414a39f1e287640a8d84233 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/learn/ray/tf/test_tf_ray_estimator.py | Python | apache-2.0 | 25,326 | [
"ORCA"
] | dc1ce54805722915f8fc696bf6c482b7661ba673b2cfc9ca7fd2bb18a43dd7a6 |
# modified mexican hat wavelet test.py
# spectral analysis for RADAR and WRF patterns
# NO plotting - just saving the results: LOG-response spectra for each sigma and max-LOG response numerical spectra
# pre-convolved with a gaussian filter of sigma=10
import os, shutil
import time, datetime
import pickle
imp... | yaukwankiu/armor | tests/modifiedMexicanHatTest15_march2014_sigmaPreprocessing20.py | Python | cc0-1.0 | 7,833 | [
"Gaussian"
] | 84afd4822ebf7fc765d3bb4d5d270e54f0e369559b54524fd74be2740060ccf8 |
# This file is generated by /afs/bx.psu.edu/home/nate/galaxy/py27/scripts/scramble/build/py2.7-linux-x86_64-ucs4/numpy/scramble.py
# It contains system_info results at the time of building this package.
__all__ = ["get_info","show"]
blas_info={}
lapack_info={}
atlas_threads_info={}
blas_src_info={}
blas_opt_info={}
la... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg/numpy/distutils/__config__.py | Python | gpl-3.0 | 977 | [
"Galaxy"
] | 0d4cc6a7d25cbda7bdad50424900f040e4c63a3eac8537cc70409720fa06f822 |
#
# MuPIF: Multi-Physics Integration Framework
# Copyright (C) 2010-2015 Borek Patzak
#
# Czech Technical University, Faculty of Civil Engineering,
# Department of Structural Mechanics, 166 29 Prague, Czech Republic
#
# This library is free software; you can redistribute it and/or
# modify i... | mupif/mupif | mupif/field.py | Python | lgpl-3.0 | 27,647 | [
"Mayavi",
"ParaView",
"VTK"
] | 9ec16d92d4f2e74969fbf39adad6f5d6b370413dbf31b9466d0cfe795bc3f8fd |
#!/usr/bin/python
# encoding: utf-8
'''
Licensed under a 3-clause BSD license.
'''
from __future__ import print_function, division
import os
# Flask imports
from flask import Flask, Blueprint, send_from_directory, request
import flask_jsglue as jsg
# Marvin imports
from brain.utils.general.general import getDbMachine
... | albireox/marvin | python/marvin/web/__init__.py | Python | bsd-3-clause | 5,684 | [
"Galaxy"
] | 1aa4aab9250527e3c57c266fead2989f82911e59ec2492612578092303edd376 |
from veidt.elsie.preprocessing import Preprocessing
from pymatgen.core.spectrum import Spectrum
import numpy as np
import unittest
from copy import deepcopy
class PreprocessingTest(unittest.TestCase):
def setUp(self):
self.x_range = np.linspace(-np.pi, np.pi, 201)
self.spectrum = Spectrum(self.x_r... | materialsvirtuallab/veidt | veidt/elsie/tests/test_preprocessing.py | Python | bsd-3-clause | 3,214 | [
"pymatgen"
] | cb407ce1e45de2899686e86a21f7b5c04bee609e8d837775073e018f60ce6e59 |
from enum import Enum
"""
Adds an Enum for MIME_TYPE and LINKED_DATA_RESOURCE_DEFINING_NETCDF for use
in Schema.org and DCAT outputs
"""
class BaldDistributionEnum(Enum):
MIME_TYPE = "application/x-netcdf"
LINKED_DATA_RESOURCE_DEFINING_NETCDF = "http://vocab.nerc.ac.uk/collection/M01/current/NC/" | binary-array-ld/bald | lib/bald/distribution.py | Python | bsd-3-clause | 307 | [
"NetCDF"
] | 86500c01d3fe773e5f5286210481684492b5aa4d998d5b8dd8de3d3313433e90 |
"""
This is the file for diverse helper functions.
Copyright 2015 Markus Oberweger, ICG,
Graz University of Technology <oberweger@icg.tugraz.at>
This file is part of DeepPrior.
DeepPrior is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the F... | moberweger/deep-prior | src/util/helpers.py | Python | gpl-3.0 | 6,072 | [
"Gaussian"
] | ede9244901deef938b9674d2b746c5f9e7783e50cca81d81fb65b33dea1d1ec2 |
"""
This file contains a few demo functions for easily showing some nice examples
in hermes and also showing that things work.
"""
def demo_layer(lib="mayavi"):
"""
Shows off the example 22-layer.
It adaptively refines things and shows the final solution and a convergence
graph.
"""
from herme... | certik/hermes2d | python/hermes2d/demos.py | Python | gpl-2.0 | 3,220 | [
"Mayavi"
] | eec5e800e65aadc56017dd481f2d30cecebb6347ee0b02791b8d5f4a844d9b5e |
"""
Implement -f aka looponfailing for py.test.
NOTE that we try to avoid loading and depending on application modules
within the controlling process (the one that starts repeatedly test
processes) otherwise changes to source code can crash
the controlling process which should best never happen.
""... | vicky2135/lucious | oscar/lib/python2.7/site-packages/xdist/looponfail.py | Python | bsd-3-clause | 8,713 | [
"VisIt"
] | f1042583e47531d8e27216b8779e5e387128b3f4ba8a9a2e09b1146ec501ca6b |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, 2009 Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License ... | jcurry/ZenPacks.ZenSystems.olsonPower | ZenPacks/ZenSystems/olsonPower/modeler/plugins/OlsonNewDeviceMap.py | Python | gpl-2.0 | 4,058 | [
"VisIt"
] | 3ba121612c802b3d284459f4376da82074ef2ba7a6820a058d82ef66707b99a3 |
# -*- coding: utf-8 -*-
#
# brunel_alpha_nest.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 Licen... | espenhgn/nest-simulator | pynest/examples/brunel_alpha_nest.py | Python | gpl-2.0 | 13,724 | [
"NEURON"
] | 64a758f2204fff8018567601882ddccec4b4c9502a41bdfa3d9dbcd3ac18c355 |
from sqlalchemy import *
from sqlalchemy.sql import table, column, ClauseElement
from sqlalchemy.sql.expression import _clone, _from_objects
from sqlalchemy.test import *
from sqlalchemy.sql.visitors import *
from sqlalchemy import util
from sqlalchemy.sql import util as sql_util
from sqlalchemy.test.testing import eq... | obeattie/sqlalchemy | test/sql/test_generative.py | Python | mit | 38,671 | [
"ADF"
] | 30e167addb32a282504934da473782a6284aa1a9622347c2f147538cdda1e321 |
# Copyright 2016 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 ag... | Sorsly/subtle | google-cloud-sdk/lib/googlecloudsdk/command_lib/app/deploy_util.py | Python | mit | 22,926 | [
"VisIt"
] | 1edb4f13cc60e4ea952bc7b8fe9717c7c5104b2550248c3bd7d2d8ce9d7c79f4 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | manuzhang/incubator-beam | sdks/python/apache_beam/pipeline.py | Python | apache-2.0 | 22,256 | [
"VisIt"
] | 67945089b4e3616c65a4aaf603f7ba90d5599b9a6d3f118683c55f56bb84a527 |
"""
Stuff to make multi-D dispersion spectra, for instance for Mayavi ...
For now this works only for 4 curves, to give 3 dimensions.
"""
import sys
import numpy as np
#import matplotlib.pyplot as plt
import pycs.gen.util as util
import pycs.gen.lc as lc
import pycs.gen.polyml as ml
def dispcube(lcs, rawdisper... | COSMOGRAIL/PyCS | pycs/disp/old/multispec.py | Python | gpl-3.0 | 4,026 | [
"Mayavi"
] | ad81d34069031d62672eeeab52619e89b0611a3b7213f9e05bde70d8b10009a2 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | caio2k/RIDE | src/robotide/lib/robot/result/visitor.py | Python | apache-2.0 | 3,924 | [
"VisIt"
] | aaaad08680ece9d4cc735276afbcfeeda21eb8d6003365b8f01cce847a23366a |
# ***** 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... | samn/spectral-workbench | webserver/public/lib/bespin-0.9a2/lib/dryice/tool.py | Python | gpl-3.0 | 22,134 | [
"VisIt"
] | 7ba1abe577598185d40923aaab7eba0cf629c3982d23cc078e41d70bdd0bf53e |
# coding=utf-8
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public ... | Clyde-fare/cclib | src/cclib/method/lpa.py | Python | lgpl-2.1 | 4,979 | [
"cclib"
] | dfbeed2e625b9fde59e77703ad215ba21e28f8db0872aa712481c9ac6e6fdce3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides the Stress class used to create, manipulate, and
calculate relevant properties of the stress tensor.
"""
import math
import numpy as np
from pymatgen.core.tensors import SquareTenso... | gmatteo/pymatgen | pymatgen/analysis/elasticity/stress.py | Python | mit | 3,442 | [
"pymatgen"
] | d2a5f2b137b445863a4104960fe8e053f668bc6a50efecd3b9bf64d42a6a0d9f |
# -*- coding: utf-8 -*-
#
# test_rate_neuron_communication.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... | mschmidt87/nest-simulator | pynest/nest/tests/test_rate_neuron_communication.py | Python | gpl-2.0 | 9,225 | [
"NEURON"
] | b69ddd1fc547a5edef5948722f900484d890d38898943158367815e93995d710 |
#!/usr/bin/env python
"""
Input
- reference sequence (fasta with samtools fai index)
- annotations (gff3, has to contain exon entries)
- filtered variants (vcf, primers are designed for variants with PASS)
Output
- PCR and genotyping primers selected using primer3 (gff3)
Algorithm
- there is only a few selected v... | libor-m/scrimer | scripts/design_primers.py | Python | agpl-3.0 | 18,284 | [
"pysam"
] | 640ead9c97407c80762e555b5e5ced5842df5510de54df373b846ed510bd3568 |
import unittest
from test.support import (verbose, refcount_test, run_unittest,
strip_python_stderr, cpython_only, start_threads)
from test.script_helper import assert_python_ok, make_script, temp_dir
import sys
import time
import gc
import weakref
try:
import threading
except ImportEr... | technologiescollege/Blockly-rduino-communication | scripts_XP/Lib/test/test_gc.py | Python | gpl-3.0 | 33,389 | [
"VisIt"
] | 75d695d230c6b4c4acb53fcda3ca00ee1ca6cc5a4de74aae6d901ded741dbe29 |
import numpy as np
import matplotlib.pyplot as plt
from NumpyArrayHandler import *
class ModalNoise():
def __init__(self, image_obj, camera='nf'):
self.plot_buffer = 1.1
self.setImageObject(image_obj)
self.setCamera(camera)
def setImageObject(self, image_obj):
self.ima... | rpetersburg/FiberProperties | legacy_code/ModalNoise.py | Python | mit | 20,835 | [
"Gaussian"
] | 68de0178d36130f389d3be1032325418b5e250e37a9b7c22a9267d660d22f3b1 |
__author__ = 'stonerri'
'''
This code acts as the application's primary controller, and provides links to the following:
'''
import tornado.escape
import tornado.ioloop
import tornado.options
import tornado.web
import tornado.websocket
import tornado.gen
import tornado.auth
import tornado.autoreload
from tornad... | richstoner/incf_engine | frontend/app/app.py | Python | mit | 13,249 | [
"Firefly",
"VisIt"
] | cfda63f30e453b923b59be797354135faa2a6fa3244652b530a14c3e9980abd7 |
################################################################################
# #
# Copyright (C) 2010,2011,2012,2013,2014,2015,2016 The ESPResSo project #
# ... | KonradBreitsprecher/espresso | doc/tutorials/09-swimmer_reactions/EXERCISES/reaction.py | Python | gpl-3.0 | 9,461 | [
"ESPResSo"
] | d0d210b7eaa085430403a03a41f7c974d1fd1cea41f44780306641ce3b86efe4 |
import caching.base as caching
import jingo
import jinja2
from tower import ugettext_lazy as _
import amo
from addons.models import Addon
from api.views import addon_filter
from bandwagon.models import Collection, MonthlyPick as MP
from versions.compare import version_int
# The global registry for promo modules. Ma... | Joergen/zamboni | apps/discovery/modules.py | Python | bsd-3-clause | 10,559 | [
"VisIt"
] | e0bf1b89bf78d11af2298fa1d5e49f3b0d911bc0615f814cad122919cfd616f0 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/TestHarness/testers/bench.py | Python | lgpl-2.1 | 14,805 | [
"MOOSE"
] | ee9a67e7a556b4e0335fed1621c91aecb7bbe6de0e54846423048e4861a3ddf9 |
"""
API operations on remote files.
"""
import os
import time
import hashlib
from galaxy import web
from galaxy import exceptions
from galaxy.web import _future_expose_api as expose_api
from galaxy.util import jstree
from galaxy.web.base.controller import BaseAPIController, url_for
from operator import itemgetter
impo... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/ftp_files.py | Python | gpl-3.0 | 6,231 | [
"Galaxy"
] | 6fa0187171730a466bd9422f488f692dee5841bb3ced6555fe05462b312fb103 |
#! /usr/bin/python
import os;
import sys;
import math;
import random;
class StructEvent:
def __init__(self, size=0, type='', position=0):
self.size = size;
self.type = type;
self.position = position;
self.position_final = position;
self.open_cov = 0;
self.close_cov = 0;
self.max_cov = 0;
self.max_eve... | isovic/test-scripts | src/evaluate_events.py | Python | mit | 12,260 | [
"BWA"
] | efe049f412afaa07c6d14c5e2a6fa5209353f22244f79df6b9f0a858dc3d4fa8 |
"""
Module for managing the installation of DIRAC components:
MySQL, DB's, NoSQL DBs, Services, Agents, Executors
It only makes use of defaults in LocalInstallation Section in dirac.cfg
The Following Options are used::
/DIRAC/Setup: Setup to be used for any operation
/LocalInstallation/InstanceName: ... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/Client/ComponentInstaller.py | Python | gpl-3.0 | 102,343 | [
"DIRAC"
] | c3bafd71de4c22aa6dc0c9403fbd84f26d24b1d50f2adb09081d34a3e597ca67 |
""" X509Request is a class for managing X509 requests with their Pkeys
"""
__RCSID__ = "$Id$"
import GSI
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.X509Chain import X509Chain
class X509Request( object ):
def __init__( self, reqObj = None, pkeyObj = None ):
... | andresailer/DIRAC | Core/Security/X509Request.py | Python | gpl-3.0 | 4,466 | [
"DIRAC"
] | 029dc52b83176a50e1338e2fb779d806c20e4e8f2f325a86a0402bb0ba8a11f8 |
from ..codes import CodeOutput
import numpy as np
class OctopusOutput(CodeOutput):
@property
def is_finished(self):
return False
def __init__(self, dirname):
self.dirname = dirname
CodeOutput.__init__(self)
def read(self):
coords = coordinates(self.dirname)
e... | MaterialsDiscovery/PyChemia | pychemia/code/octopus/output.py | Python | mit | 2,529 | [
"Octopus"
] | f3c0925db517026d0f32eca0a6c7bf5b181dabb40584bb877fdc51f89c642c4a |
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