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# Finding coefficients in ranking algorithm by comparing results to actual ranking
# Improvements to make
# 1) use enumerate to remove arguments from functions.
# 2) *Consider exercises that were completed more often to be easier and others more difficult (a lot of error here).*
# 3) Implement householder QR decomp... | easyCZ/SLIP-A-2015 | respiratory/Processed Datasets/Processed Datasets/uptoweek9.py | Python | mit | 13,161 | [
"Gaussian"
] | b62db48e54077b58daec42476ea29b56d18690287e6c7082a2889e4f28891d03 |
import warnings
import matplotlib.pyplot as plt
import numpy as np
from sklearn.preprocessing import normalize
class RandomWalk2D:
''' Class for SARSA random walk '''
def __init__(self, grid_size=3, end_states=[(0,0)], rewards=[1], \
exploration=.1, move_cost=0, alpha=.3, gamma=.9):
self.n =... | rahulsrma26/code-gems | RL/randomWalk/sarsa.py | Python | mit | 5,442 | [
"VisIt"
] | 1d29b08a797af1239080e3264ca282227e86600344b24302bcca8ee95c80860e |
""" The Request Task Agent takes request tasks created in the transformation database
and submits to the request management system
"""
from DIRAC import S_OK
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.TransformationSystem.Agent.TaskManagerAgentBase import TaskManager... | Sbalbp/DIRAC | TransformationSystem/Agent/RequestTaskAgent.py | Python | gpl-3.0 | 1,537 | [
"DIRAC"
] | d3436ae93b341a546b041b36edc96e5dae7015dd688f1a8c92881ee7e2e04af5 |
# -*- coding: utf-8 -*-
import re
import urllib2
import httplib, urllib
import random
import json
import sys
from bs4 import BeautifulSoup
import sys
reload(sys)
sys.setdefaultencoding("utf-8")
# Some User Agents
hds = [{'User-Agent': 'Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.1.6) Geck... | autumnz613/HangzhoulLianjia | server_ershoufang.py | Python | mit | 8,609 | [
"VisIt"
] | 8d2391d3e46d6b55a1734940b1c497b3a0f8677e362ee4f08c016e71a913ace6 |
"""
Tests for discussion pages
"""
import datetime
from unittest import skip
from uuid import uuid4
from flaky import flaky
from nose.plugins.attrib import attr
from pytz import UTC
from .helpers import BaseDiscussionTestCase
from ..helpers import UniqueCourseTest
from ...pages.lms.auto_auth import AutoAuthPage
from... | franosincic/edx-platform | common/test/acceptance/tests/discussion/test_discussion.py | Python | agpl-3.0 | 52,729 | [
"VisIt"
] | fad9a8b8598391491dab17ce076a08d3ae96bb76896676ac3fa3216565ca9121 |
#!/usr/bin/env python
from Asap import *
from Asap.Setup.Lattice.Cubic import FaceCenteredCubic
from Asap.Setup.Dislocation import Dislocation
from Asap.Filters.TimeAveragedPositions import TimeAveragedPositions
from Asap.Filters.RestrictedCNA import RestrictedCNA
from Asap.Dynamics.Langevin import Langevin
from Asap.... | auag92/n2dm | Asap-3.8.4/Examples/CNA.py | Python | mit | 2,024 | [
"ASE"
] | 9068b32a5b2c116b5b3e39a3c8f11894834183d3d57014c0ebb7b2c3f58b1fc9 |
#!/usr/bin/python
# Reads ACGTrie and dumps it into value file format. In value file format
# each record is stored into 32 bits. Value of the record represent frequency
# of the chain in DNA. We use bijective numbers notation with base 4 to map from index
# into chain. This system has only four digits A < C < G < T; T... | anvaka/actg | utils/dumpValueFile.py | Python | mit | 5,133 | [
"VisIt"
] | b1656e41fbb2a200c5822cafe9ba3da89fef14ea1cdef3990918fa4c2726dc99 |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def link_incompatible_error():
print("Reading in original prostate data.")
prostate = h2o.import_file(path=h2o.locate("smalldata/prostate/prostate.csv.zip"))
print("Throw error when trying to create model with incompatible logit link... | brightchen/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_link_incompatible_errorGLM.py | Python | apache-2.0 | 987 | [
"Gaussian"
] | 7e421f8c4b0a5f5402543f3fb708fcdbb2a7983a33d5cade9a43e43e7a1a6d9b |
#!/usr/bin/env python
# encoding: utf-8
# Thomas Nagy, 2010-2016 (ita)
"""
Classes and functions required for waf commands
"""
import os, re, imp, sys
from waflib import Utils, Errors, Logs
import waflib.Node
# the following 3 constants are updated on each new release (do not touch)
HEXVERSION=0x1081300
"""Constant ... | mattaw/SoCFoundationFlow | admin/waf/waf-1.8.19/waflib/Context.py | Python | apache-2.0 | 19,546 | [
"VisIt"
] | e481c37d329591134350db55ffeeabe75b159bf53851d9afc33f40ada26d2ade |
import sys
sys.path.append('..')
import numpy as np
from sklearn.svm import SVC
import sklearn.preprocessing as preprocessing
from sklearn.metrics import recall_score, accuracy_score, confusion_matrix, classification_report
import os
import sys
import utils.dataset_manupulation as dm
import utils.utils as utl
import w... | vespero89/Snoring_Challenge | Supervectors/gridsearch_ivec.py | Python | gpl-3.0 | 6,323 | [
"Gaussian"
] | b847ee35b7624913ac008e1d9f4a6e914adb5b234f5424fb564759894bda495d |
#!/usr/bin/env python
"""Post weather update to WeatherUnderground
::
%s
.. Warning::
This module has been superseded by the :doc:`pywws.toservice`
module. It will be deleted from pywws in the next release.
Introduction
------------
`Weather Underground <http://www.wunderground.com/>`_ is a USA based
web s... | edk0/pywws | pywws/ToUnderground.py | Python | gpl-2.0 | 4,393 | [
"VisIt"
] | b0e294222dc4d9cefabc003e2024c9b0c1613071ba6816510faa92c34fc5ced1 |
List_of_plants = []
class ambrosia():
name = 'ambrosia'
plantname = 'Ambrosia Vulgaris'
Description = "These seeds grow into common ambrosia, a plant grown by and from medicine."
icon_state = 'seed-ambrosiavulgaris'
lifespan = 60
endurance = 25
production = 6
plant_yield = 6
potency = 5
weed_growth_rate = 1
... | Necromunger/unitystation | Tools/python DM botany to json/plans.py | Python | agpl-3.0 | 51,496 | [
"Galaxy"
] | 06eebc02489865d591f0cebedce901d42e56cf2e640e08d571179c3627b846a9 |
#!/usr/bin/env python
from setuptools import setup
from glob import glob
import sys
setup(name='Glutton',
version='0.1',
description='Transcriptome scaffolding and postprocessing for comparative analysis using evolutionary alignment',
author='Alan Medlar',
author_email='alan.j.medlar@helsinki.f... | ajm/glutton | setup_with_extras.py | Python | gpl-3.0 | 1,214 | [
"Biopython",
"pysam"
] | b9cc66f276f26264317396a5d2c04483d3bff4842d5eb8d94146069de33c9f83 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Hall
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Genera... | arunkgupta/gramps | gramps/plugins/textreport/tagreport.py | Python | gpl-2.0 | 21,726 | [
"Brian"
] | ed60b0af1110db51f53f45a4d8aa168918f1e41b249b11c5e0fcba824dfb784e |
# coding: utf-8
import copy
import datetime as dt
import furl
import mock
import httpretty
import github3.repos
import github3.git
from flask import url_for
import kozmic.builds.tasks
from kozmic.models import (User, DeployKey, Project, Membership, Hook,
HookCall, Build, Job, TrackedFile)
f... | abak-press/kozmic-ci | tests/func_tests.py | Python | bsd-3-clause | 29,170 | [
"VisIt"
] | 6560919459db73bb6eaaf1d9b875a24295a9e1149d1211a719d05de710be2f6b |
"""Axis binary sensor platform tests."""
from homeassistant.components import axis
import homeassistant.components.binary_sensor as binary_sensor
from homeassistant.setup import async_setup_component
from .test_device import NAME, setup_axis_integration
EVENTS = [
{
"operation": "Initialized",
"t... | postlund/home-assistant | tests/components/axis/test_binary_sensor.py | Python | apache-2.0 | 1,798 | [
"VMD"
] | 65d03640697b9446adbf08d0e506f345449957e33cb008f4908c39e36d9087fa |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | maheshakya/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 54,070 | [
"Gaussian"
] | 93c43ba90f3a77381ce4dc179019f9cdb9e559ecf7f10721baf62124f69fd7d5 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/LennardJones.py | Python | gpl-3.0 | 10,773 | [
"ESPResSo"
] | 3a38daf65a0b51b154978889521a4f108ec33b176d0ca5751c3c4ff1da2fd122 |
#!/usr/bin/env python
#coding: utf8
import os
from splinter import Browser
from sys import exit
import time
username = raw_input("Nombre de usuario: ")
pswd = raw_input("Contraseña: ")
alias = raw_input("Alias: ")
with Browser('chrome') as browser:
browser.visit("https://www.corporativo.telcel.com/pcorporativo/logi... | ianchesu/Adendum-Download | adendum.py | Python | mit | 1,566 | [
"VisIt"
] | 5bebd479abed0cc57b1794a1b1de7b70d0639f609977cfde10a5cafb10c9b408 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from mock import patch
from fakeldap import MockLDAP
from zilencer.models import Deployment
from zerver.views import do_change_password, create_homepag... | vikas-parashar/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 47,788 | [
"VisIt"
] | 5556c0e98c7fe848e898c4b5dfa9d945baf5403d54a46edc2814cd070ed55926 |
"""
Naive Bayes with MapReduce
Algorithm calculates multinomial distribution for discrete features and Gaussian distribution for numerical features.
The output of algorithm is consistent with implementation of Naive Bayes classifier in Orange and scikit-learn.
Reference:
MapReduce version of algorithm is proposed by ... | romanorac/discomll | discomll/classification/naivebayes.py | Python | apache-2.0 | 11,861 | [
"Gaussian"
] | b85faefe1aeed2a905ffff1a129c412e835d25bfc5cdfb45474a8dec6f30afc3 |
"""
Django settings for neuron project.
Generated by 'django-admin startproject' using Django 1.10.5.
For more information on this file, see
https://docs.djangoproject.com/en/1.10/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.10/ref/settings/
"""
import os
... | chugunovyar/factoryForBuild | neuron/settings.py | Python | gpl-3.0 | 4,902 | [
"NEURON"
] | 47aeca4f330eed13259599728ad45ea185b32922ca0d36b479384aef0ab81594 |
"""Support for control of ElkM1 tasks ("macros")."""
from homeassistant.components.elkm1 import (
DOMAIN as ELK_DOMAIN, ElkEntity, create_elk_entities)
from homeassistant.components.scene import Scene
DEPENDENCIES = [ELK_DOMAIN]
async def async_setup_platform(
hass, config, async_add_entities, discovery_... | HydrelioxGitHub/home-assistant | homeassistant/components/elkm1/scene.py | Python | apache-2.0 | 743 | [
"Elk"
] | e6a6baff50aef811755a502677dbd0e13ea6dba3de4e49184392f994b3536e70 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2004-2005 Eero Tamminen
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2008 Peter Landgren
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2016 Paul Franklin
#
# This program is free ... | sam-m888/gprime | gprime/plugins/drawreport/statisticschart.py | Python | gpl-2.0 | 47,300 | [
"Brian"
] | bfb3c0340e1988225354605b19280e68e44b36c47c6af70828927826c9bfeeea |
#!/usr/bin/env python
# Copyright (C) 2011 Tianyang Li
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This... | tianyang-li/meta-transcriptome | sam_filter.py | Python | gpl-3.0 | 1,610 | [
"HTSeq"
] | 2ba71f0ad45db95ba89ad7d040aeeff51cc538049df34e3cc01422d89d63eb64 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from ...pages.lms.account_settings import AccountSettingsPage
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.da... | simbs/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 17,483 | [
"VisIt"
] | c1602704debed07dc05ca17ccaf73ddbda81601bed75ad8999d6ac2a30fa7d4b |
from brian import Clock, Hz, second, PoissonGroup, network_operation, pA, Network
import numpy as np
from perceptchoice.model.monitor import WTAMonitor
from perceptchoice.model.network import default_params, pyr_params, inh_params, simulation_params, WTANetworkGroup
class VirtualSubject:
def __init__(self, subj_... | jbonaiuto/perceptual-choice-hysteresis | src/python/perceptchoice/model/virtual_subject.py | Python | gpl-3.0 | 3,437 | [
"Brian"
] | 7e2e300c6652e260dcf9fec657f9c0794d6cd2ef572dc46b09f83415c287c60d |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2005-2012 Julio Sanchez
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU Genera... | Forage/Gramps | gramps/plugins/rel/rel_es.py | Python | gpl-2.0 | 36,185 | [
"Brian"
] | 44d7d9f50c59aee44759b963088db4352bd52cc378c038a6a79bdb25e00767dd |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | alexlo03/ansible | lib/ansible/modules/network/avi/avi_gslbapplicationpersistenceprofile.py | Python | gpl-3.0 | 3,672 | [
"VisIt"
] | ac9827db1853832042ebbd96967276ba5b825611d6d8266c17b093740de266b0 |
import os
import tarfile
import cStringIO
from DIRAC import S_OK, gLogger
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.Core.DISET.TransferClient import TransferClient
from DIRAC.Core.Security import Locations, CS
class BundleDeliveryClient:
def __init__( self, rpcClient = False, transferClient = Fal... | Sbalbp/DIRAC | FrameworkSystem/Client/BundleDeliveryClient.py | Python | gpl-3.0 | 3,497 | [
"DIRAC"
] | 8f5e9ec4545ad0655e5ba3c7afdb89fdfbb0dac0da9d6f38d302bbfa6b4755e0 |
"""This module defines input and output functions for NMD format.
.. _nmd-format:
NMD Format
-------------------------------------------------------------------------------
Description
^^^^^^^^^^^
NMD files (extension :file:`.nmd`) are plain text files that contain at
least normal mode and system coordinate data.
... | Shen-Lab/cNMA | Manual/Modified/nmdfile.py | Python | mit | 15,465 | [
"VMD"
] | 05b33c75ee31452acfeabced2292a5f30c487ac6b7a302da0afa40795422579f |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/examples/example_eca.py | Python | apache-2.0 | 3,365 | [
"VisIt"
] | f86f56278d7fd83208fcca3b18e517145be8fd8ecb25fb2ccf400d1296aaa63e |
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 04 13:48:11 2015
This file is part of pyNLO.
pyNLO is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your optio... | ycasg/PyNLO | src/pynlo/light/DerivedPulses.py | Python | gpl-3.0 | 12,433 | [
"Gaussian"
] | 86fe6bdbe9af9c47482ea43c354cdcf7d3326350b65a4bfcaa5f5d2483ede8a0 |
"""
Manage pools of connections so that we can limit the number of requests per site and reuse
connections.
@since: 1.6
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import urlparse
from collections import defaultdict
import threading, gobject
from zeroinst... | dabrahams/zeroinstall | zeroinstall/injector/scheduler.py | Python | lgpl-2.1 | 3,901 | [
"VisIt"
] | aca73010f097311fdae8bcfee171654287550f19ece497645462aa1eb81a4839 |
'''
Author: Fernando Luiz Neme Chibli
Name: pyTreeBee
Version: 0.6
License: GNU LGPL v2.1
'''
'''
Asgard Defense is the first game made with pyTreeBee.
Asgard Defense by Asgardian AGES is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
To view a copy of this licens... | FernandoLuizNemeChibli/pyTreeBee | pyTreeBee.py | Python | lgpl-2.1 | 25,228 | [
"VisIt"
] | ef551a39629fe6fac1044b8def805deddfcdbf33b582786560fb2eec056a648d |
# Copyright (c) 2012 - 2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from scipy.special import gammaln, digamma
from ...util.linalg import pdinv
from paramz.domains import _REAL, _POSITIVE, _NEGATIVE
import warnings
import weakref
class Prior(obj... | SheffieldML/GPy | GPy/core/parameterization/priors.py | Python | bsd-3-clause | 48,125 | [
"Gaussian"
] | cbefd017ebdd5b67b9464cd2f63c280c96d0f7f6fe71a86ae1bf507ee3a5f5f6 |
from hamcrest import *
from test.features import BrowserTest
from test.features.support import table_from
class Javascript(BrowserTest):
def test_all_services_table(self):
self.browser.visit("http://0.0.0.0:8000/SpecRunner")
tests_passing = self.browser.find_by_css('.symbolSummary .passed')
... | alphagov/transactions-explorer | test/features/test_javascript.py | Python | mit | 549 | [
"VisIt"
] | bba3d97adced9d33a83aa9ce5aa1e59f478743c4d4e0e71a794ed5697cf86110 |
"""
Copyright 2013 Appurify, Inc
All rights reserved
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS, WITHOUT
WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the
License for the specific la... | appurify/appurify-python | appurify/constants.py | Python | apache-2.0 | 6,341 | [
"ESPResSo"
] | 800c1413b68a013594b2ae5a0e46b7652dcb60ef5dfeb96966bfec4da3df296a |
import os, random, string
from fabric.api import run, env, cd, settings, put, local, shell_env
# load ~/.ssh/id_rsa
env.key_filename = os.getenv('HOME', '/root') + '/.ssh/id_rsa'
# determine hosts
branch = os.getenv('DRONE_BRANCH', '')
if branch == "master":
env.hosts = ["marge.lavaboom.io:36104"]
api_uri... | MartinCote1978/web | fabfile.py | Python | gpl-3.0 | 2,240 | [
"GULP"
] | 0a83e3fb54744c839fa808c5478d0ed2b22200760b28dd156784e86953130535 |
from lxml import html
import requests
import click
import os
import sys
import logging
import re
from pprint import pprint
from collections import OrderedDict as odict
import json
import database
import utils
from models import *
from sqlalchemy import func
logging.basicConfig(
level=logging.DEBUG,
format="%(... | fre-sch/collector-drone | collectordrone/inara.py | Python | gpl-3.0 | 5,636 | [
"BLAST",
"Galaxy"
] | b44be1c2b6b7cc0d86ede1a6f4a7029996b20eb11ed1d94378ee53adb82c5554 |
import psi4
from psi4 import *
from psi4.core import *
def run_myplugin1(name, **kwargs):
r"""Function encoding sequence of PSI module and plugin calls so that
myplugin1 can be called via :py:func:`~driver.energy`.
>>> energy('myplugin1')
"""
lowername = name.lower()
kwargs = p4util.kwargs_l... | andysim/psi4 | tests/psithon2/psiaux1/myplugin1/pymodule.py | Python | gpl-2.0 | 790 | [
"Psi4"
] | 7bb781de8d960df52d111a82b6c0ead294203993314b51d24cdd5ff7f71ebfb3 |
#!/usr/bin/env python
#
# Python Y86 Assembler
# Copyright (c) 2012 Linus Yang <laokongzi@gmail.com>
#
# ** Compatible with Shedskin **
# Shedskin is an RPython to C++ compiler
# Visit https://code.google.com/p/shedskin/wiki/docs for more info
#
# This program is free software: you can redistribute it... | linusyang/python-y86 | yas.py | Python | gpl-3.0 | 15,193 | [
"VisIt"
] | 567e61e82864f02ec596563829baca40cce51a986abc0a79ba70a4776cc3f8d5 |
# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
from compmod.distributions import Rayleigh, Triangular, Rectangular
from compmod.rheology import SaintVenant, Bilinear
E = 1.
sigmay = .01
n = .1
sigma_sat = .02
epsilon = np.linspace(0., 0.2, 1000)
sigmay_mean = sigmay
ray = Rayleigh(sigmay_m... | lcharleux/compmod | doc/example_code/rheology/demo.py | Python | gpl-2.0 | 1,561 | [
"DIRAC"
] | 15576acd69a4eb2188f6cfcb173f630aab8f03fe6422ae96459489a585352992 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=1>
# Aging Analysis of Cytokine and SNP data
# <markdowncell>
# This analysis will look at how aging effects HIV-1 disease progression. This will include looking at things like clinical parameters, LTR SNPs, Cytokine Profiling, and NeuroCog Imp... | JudoWill/ResearchNotebooks | AgingAnalysis.py | Python | mit | 16,158 | [
"VisIt"
] | e2ac0fe70f298dc079223e81883a50f4b329e5d9df692e63a5516b5b5fd21ea1 |
def read_aims(filename):
"""Import FHI-aims geometry type files.
Reads unitcell, atom positions and constraints from
a geometry.in file.
"""
from ase import Atoms
from ase.constraints import FixAtoms, FixCartesian
import numpy as np
atoms = Atoms()
fd = open(filename, 'r')
li... | grhawk/ASE | tools/ase/io/aims.py | Python | gpl-2.0 | 10,468 | [
"ASE",
"FHI-aims"
] | 6ad083b950e9f8b3447c85084b2367b6e7d66eec1ba4c4223c63128a8033a8d5 |
"""Convolutional/Variational autoencoder, including demonstration of
training such a network on MNIST, CelebNet and the film, "Sita Sings The Blues"
using an image pipeline.
Copyright Parag K. Mital, January 2016
"""
import tensorflow as tf
import numpy as np
import os
from libs.dataset_utils import create_input_pipel... | pkmital/CADL | session-3/libs/vae.py | Python | apache-2.0 | 19,312 | [
"Gaussian"
] | 8534212f46bcf9b268738a3ec68aa15aac8cdf2a10b3c115b81d4bd401e3c730 |
# Simulacion de sistema MM1 usando la libreria SimPy
from SimPy.Simulation import *
from random import expovariate, seed
from numpy.random import normal
import matplotlib.pyplot as plt
queue_size = []
service_size = []
## Componentes del modelo ------------------------
class Source(Process):
""" Este codigo genera... | milardovich/simulacion | mm1.py | Python | mit | 2,636 | [
"VisIt"
] | 29a16ddba0b3bdb5296235ef2968b89e32f708fdfc3255e25993f69459197612 |
from multiprocessing import freeze_support
from rdkit import Chem
from mordred import Calculator
from mordred.RingCount import RingCount
# for parallel calculation on windows only
if __name__ == "__main__":
freeze_support()
# Start Code 5
calc = Calculator()
calc.register(RingCount())
print(calc... | mordred-descriptor/mordred | examples/article/Code5.py | Python | bsd-3-clause | 444 | [
"RDKit"
] | 2c0ac66b65103cd62032dfeb31861aabe1df10c48718a88247353fa7fe3c7f12 |
"""
Subraph centrality and communicability betweenness.
"""
import networkx as nx
from networkx.utils import not_implemented_for
__all__ = [
"subgraph_centrality_exp",
"subgraph_centrality",
"communicability_betweenness_centrality",
"estrada_index",
]
@not_implemented_for("directed")
@not_implemented... | SpaceGroupUCL/qgisSpaceSyntaxToolkit | esstoolkit/external/networkx/algorithms/centrality/subgraph_alg.py | Python | gpl-3.0 | 10,125 | [
"Desmond"
] | af1c0d1fac2d9457c59fa0d9626a7178b80fb5f7ce3ea86a6fd52ccd0691c018 |
# Copyright 2012, 2013 by the Micromagnum authors.
#
# This file is part of MicroMagnum.
#
# MicroMagnum is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) a... | MicroMagnum/MicroMagnum | src/magnum/micromagnetics/io/vtk/__init__.py | Python | gpl-3.0 | 742 | [
"VTK"
] | 6c0c62e2733cc7eacd708df3a7e34290d622bf2ffb8f0ad2dc0451876af8d413 |
import numpy as np
from alis import almsgs
from alis import alfunc_base
from scipy.signal import convolve
msgs=almsgs.msgs()
class APOD(alfunc_base.Base) :
"""
Convolves the spectrum with a Gaussian with full-width at half-maxium AFWHM (in Angstroms):
p[0] = AFWHM
"""
def __init__(self, prgname="",... | rcooke-ast/ALIS | alis/alfunc_apod.py | Python | gpl-3.0 | 14,420 | [
"Gaussian"
] | 54cf4bd3ecbc92cc3a74029f8e229cb05a4d53ea30411e72b384064935df923e |
##############################################################################
#
# Copyright (C) 2018 Compassion CH (http://www.compassion.ch)
# @author: Emanuel Cino <ecino@compassion.ch>
#
# The licence is in the file __manifest__.py
#
#########################################################################... | eicher31/compassion-switzerland | website_event_compassion/forms/group_visit_payment.py | Python | agpl-3.0 | 3,408 | [
"VisIt"
] | c12e9fb4d7b60513010b48f1557ea228b2e446ad58d83261b33b49bab6586ff2 |
"""
Kernel Density Estimation
-------------------------
"""
# Author: Jake Vanderplas <jakevdp@cs.washington.edu>
import numpy as np
from scipy.special import gammainc
from ..base import BaseEstimator
from ..utils import check_array, check_random_state, check_consistent_length
from ..utils.extmath import row_norms
fr... | vortex-ape/scikit-learn | sklearn/neighbors/kde.py | Python | bsd-3-clause | 9,452 | [
"Gaussian"
] | 2ab5fecccebed2fac0240780cf1e667805a91554295fa54351ebe076d1db3355 |
#!/usr/bin/python3
# Copyright 2020 Uraniborg 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 ... | android/security-certification-resources | ioXt/uraniborg/scripts/python/package_whitelists.py | Python | apache-2.0 | 9,989 | [
"Galaxy"
] | 9561fbc0187312dbedd91b1114a2668d16cd0eaacf1415f9429986203fbe888e |
# $HeadURL$
__RCSID__ = "$Id$"
import types
import os
from DIRAC import gLogger, gConfig, rootPath, S_OK, S_ERROR
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.Core.Utilities import DEncode, Time
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.ConfigurationSystem.Cl... | Sbalbp/DIRAC | FrameworkSystem/Service/MonitoringHandler.py | Python | gpl-3.0 | 7,836 | [
"DIRAC"
] | b52e163e75140fa1271a716bde42fcbcb0006d600ee930f733f422ec74371040 |
# (C) British Crown Copyright 2010 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | duncanwp/iris | lib/iris/tests/test_pickling.py | Python | lgpl-3.0 | 5,105 | [
"NetCDF"
] | 74c34731adcf96404ccf5938c4b052bb29c56bb5f12572e8839da440e441b4ee |
#!/usr/bin/env python
"""
Copyright 2014 Jirafe, 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.apache.org/licenses/LICENSE-2.0
Unless required by applicab... | concerned3rdparty/jirafe-python | jirafe/models/Visit.py | Python | mit | 1,119 | [
"VisIt"
] | fc272538d2b7c0f5fe3b9f3482b3f4d0350cc583119124ae0dc3bed6c0eb6467 |
#
# 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... | jasonkuster/incubator-beam | sdks/python/apache_beam/runners/runner.py | Python | apache-2.0 | 13,090 | [
"VisIt"
] | 44b56a7aec5d526647a0f847600563bb40c50c21dff0dbf6eeedf7d86af6a4df |
#!/ysr/bin/env python
from __future__ import division
import numpy as np
import theano
import theano.tensor as T
from theano import tensor
#-----------------------------------------------------------------------------
def my_batched_dot(A, B):
"""Batched version of dot-product.
... | langholz/draw | draw/attention.py | Python | mit | 9,303 | [
"Gaussian"
] | 650e8ded1758e070a184e4a980cc8db37f3e30a59b1ca224f86e6ffd58a03208 |
"""
API operations on Group objects.
"""
import logging
from galaxy.web.base.controller import BaseAPIController, url_for
from galaxy import web
log = logging.getLogger( __name__ )
class GroupAPIController( BaseAPIController ):
@web.expose_api
@web.require_admin
def index( self, trans, **kwd ):
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/api/groups.py | Python | gpl-3.0 | 5,237 | [
"Galaxy"
] | 2f6b3441978a3b853643b79ea6539dcefeb0df7e126a9e4d46d6479aef051e63 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements an interface to the Henkelmann et al.'s excellent
Fortran code for calculating a Bader charge analysis.
This module depends on a co... | xhqu1981/pymatgen | pymatgen/command_line/bader_caller.py | Python | mit | 6,078 | [
"VASP",
"pymatgen"
] | 26ed81fabf0ae795d92bdb5166f0552efe6c4fe65c8409a2911cd63ae93f3cb7 |
import ghmm
# example code for a continuous HMM with gaussian emissions
F = ghmm.Float() # emission domain of this model
A = [[0.0,1.0,0],[0.5,0.0,0.5],[0.3,0.3,0.4]] # transition matrix
B = [[0.0,1.0],[-1.0,0.5], [1.0,0.2]] # parameters of emission distributions in pairs of (mu, sigma)
pi = [1.0,0.0,0.0] # i... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Misc/continuousHMM.py | Python | mit | 1,157 | [
"Gaussian"
] | 6a417323564893bfa4f312250ad4d6c96b830302e84ff79ed6ebfa20adf07348 |
#!/usr/bin/env python
# Copyright (c) 2015 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""The 'grit xtb' tool.
"""
import getopt
import os
from xml.sax import saxutils
from grit import grd_reader
from grit import la... | CrankWheel/grit-i18n | grit/tool/xtb.py | Python | bsd-2-clause | 9,411 | [
"xTB"
] | 5b449bd9b1b41acbe64b928a58f19ee4fd3ba04f6ae6e6b6a0725f5a3b09fcad |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | samples/dpd.py | Python | gpl-3.0 | 2,464 | [
"ESPResSo"
] | 7b9691c9bf0c7e5f05b51e9c1f944fadf4e9fd590aeab077d5fa7bd492f352bd |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | src/python/espressomd/virtual_sites.py | Python | gpl-3.0 | 2,232 | [
"ESPResSo"
] | 1b445d346e2e5665551d94d246c767e4b100f377b4c99b4fb2f92b08ac4d02e9 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/test_checkpoint.py | Python | gpl-3.0 | 18,699 | [
"ESPResSo"
] | 34990f1faf2d49ea644baacf8e52b952e0d129d6f4dbd4f24f72ebf46abe7c70 |
"""Wrapper around different ASE calculators to perform simple QM/MM calculations"""
def __init__(self, atoms):
| PHOTOX/fuase | ase/ase/calculators/qmmm.py | Python | gpl-2.0 | 112 | [
"ASE"
] | 582c5f74e5a6481066ed0989d9cc1e5341ab04987a1eae2c81fbd94f43080f3b |
""" The POOL XML File module provides a means to extract the GUID of a file or list
of files by searching for an appropriate POOL XML Catalog in the specified directory.
"""
import os
import glob
import tarfile
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Resource... | chaen/DIRAC | Resources/Catalog/PoolXMLFile.py | Python | gpl-3.0 | 4,803 | [
"DIRAC"
] | a4c05b47612366747c01531f839c523026d9e47451be52e34a1519427626899c |
# ----------------------------------------------------------------------------
# cocos2d
# Copyright (c) 2008-2012 Daniel Moisset, Ricardo Quesada, Rayentray Tappa,
# Lucio Torre
# Copyright (c) 2009-2015 Richard Jones, Claudio Canepa
# All rights reserved.
#
# Redistribution and use in source and binary forms, with o... | dangillet/cocos | cocos/skeleton.py | Python | bsd-3-clause | 14,881 | [
"VisIt"
] | c2533f2f9617f8ce69d661f9e0e35d57206d2084b00c429dacc797a6aecc6aa0 |
from django.apps import apps as django_apps
from django.db import models
from edc_visit_schedule.site_visit_schedules import site_visit_schedules
from ...constants import REQUIRED, NOT_REQUIRED
class MetadataError(Exception):
pass
class UpdatesMetadataModelMixin(models.Model):
updater_cls = None
metad... | botswana-harvard/edc-meta-data | edc_metadata/model_mixins/updates/updates_metadata_model_mixin.py | Python | gpl-2.0 | 2,915 | [
"VisIt"
] | 464ffc24ad16b7cf9ccd992e238626ac37e6b78bd08e84607fefcd124f7652f1 |
"""
.. module: FSRStools.uvvis
:platform: Windows
.. moduleauthor:: Daniel Dietze <daniel.dietze@berkeley.edu>
Load and process UV/VIS spectra and related formats. Supports PerkinElmers old Lambda format.
Provides also some short cuts to useful functions from the :py:mod:`FSRStools.raman` module.
..
Th... | ddietze/FSRStools | uvvis/__init__.py | Python | gpl-3.0 | 15,078 | [
"Gaussian"
] | a0e201b8d1a3bed417aebc0739809511754332929d10690d511d148c6a190be9 |
import models
import util
class ReportLine():
''' Generic report line'''
def __init__(self, **kwds):
self.__dict__.update(kwds)
class PatientReport():
def __init__(self, org, visit_date_from, visit_date_to, default_country, residence):
self.org = org
self.visit_date_from = visit_date_from
self.... | avastjohn/maventy_new | healthdb/reports.py | Python | bsd-3-clause | 8,101 | [
"VisIt"
] | d441e749c9f6a5e95c9b23b98c70f5cc1cc32336488b0b9e1c5b2f5d62be531f |
import numpy as np
import inspect
import sys
small = .000000000001
class NeighborhoodFactory(object):
@staticmethod
def build(neighborhood_func):
for name, obj in inspect.getmembers(sys.modules[__name__]):
if inspect.isclass(obj):
if hasattr(obj, 'name') and ... | sevamoo/SOMPY | sompy/neighborhood.py | Python | apache-2.0 | 1,239 | [
"Gaussian"
] | 832447f1ed86346970cbb5334d7e0f225b1c62b513f178064671ded322017801 |
"""
Histogram-related functions
"""
from __future__ import division, absolute_import, print_function
import operator
import warnings
import numpy as np
from numpy.compat.py3k import basestring
__all__ = ['histogram', 'histogramdd', 'histogram_bin_edges']
# range is a keyword argument to many functions, so save the ... | Eric89GXL/numpy | numpy/lib/histograms.py | Python | bsd-3-clause | 35,040 | [
"Gaussian"
] | 06e575642b0e7c8f54e741a2eb178a927f643bd09d10e811e9c307e0d2754c3b |
# coding: utf-8
"""
The initial version of this module was based on a similar implementation
present in FireWorks (https://pypi.python.org/pypi/FireWorks).
Work done by D. Waroquiers, A. Jain, and M. Kocher.
The main difference wrt the Fireworks implementation is that the QueueAdapter
objects provide a programmatic in... | rousseab/pymatgen | pymatgen/io/abinitio/qadapters.py | Python | mit | 59,656 | [
"ABINIT",
"pymatgen"
] | 3be5107dd560c54ea6c6c624838b78ba9fca95599f372df00bc111276dc36afc |
"""
RDKit Utilities.
This file contains utilities that compute useful properties of
molecules. Some of these are simple cleanup utilities, and
others are more sophisticated functions that detect chemical
properties of molecules.
"""
import os
import logging
import itertools
import numpy as np
from io import StringIO
... | lilleswing/deepchem | deepchem/utils/rdkit_utils.py | Python | mit | 18,305 | [
"OpenMM",
"RDKit"
] | 7f79355d2e4525a61c41bdedbe40aed20dc6a93558103b7eafa8f28412bc9380 |
from abc import abstractmethod, ABCMeta
import logging
import os
import urlparse
logger = logging.getLogger(__name__)
class ProductInstance(object):
"""
Configuration object for a product's instance.
"""
def __init__(self, instance_id, base_url):
"""
Constructor.
@type insta... | butfriendly/friendly-pageobjects | friendly/pageobjects/product.py | Python | bsd-3-clause | 3,450 | [
"VisIt"
] | e1b6b69a47dbd1004bf72551c7770fa258bd9f9f7e04d15f8f390105fd554f0a |
from .core import OneHaloTerm, TwoHaloTerm
from .core import GalaxyPowerTerm, DampedGalaxyPowerTerm
class ZeroShotNoise(object):
"""
Class to manage the handling of `N` when computing component spectra
"""
def __init__(self, model):
self.model = model
self._N = self.model.N
... | nickhand/pyRSD | pyRSD/rsd/power/gal/__init__.py | Python | gpl-3.0 | 996 | [
"Galaxy"
] | 18f6873962f0cebd09c0c5520ec0af93213f3df7ffdb4af179540477ae3990a8 |
# -*- coding: utf-8 -*-
'''python3.3/html/entities.py, plus HTMLParser.decode(), for Python 2 compat'''
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import re
def unescape(s):
'''Decode HTML entities.'''
if '&' not in s:
return s
re... | ollyc/kajiki | kajiki/entities.py | Python | mit | 58,439 | [
"Bowtie"
] | ba8ac0221a50e13053c5fb759f5fdc3f3ca1a490b8be353bdc9cc29cd6215c6f |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | mkrupcale/ansible | lib/ansible/modules/cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 53,270 | [
"Dalton"
] | 7f825946e8d28b1aaa2eeb707d04b8a748c8e7c1a9f330a09a152da248ca6288 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os, sys
def open_in_browser(link):
browser = os.environ.get('BROWSER', 'firefox')
child = os.fork()
if child == 0:
# We are the child
try:
os.spawnlp(os.P_NOWAIT, browser, browser, link)
os._exit(... | pombredanne/zero-install | zeroinstall/0launch-gui/browser.py | Python | lgpl-2.1 | 419 | [
"VisIt"
] | ac0a460501b2c4709bdacb3f3844d65733e993467a46a18e5f94c78f5e965fa8 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# 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,... | govarguz/espressopp | testsuite/LangevinThermostat/test_LangevinThermostat.py | Python | gpl-3.0 | 6,355 | [
"ESPResSo"
] | 2f45fa3ed1311ca4826a855ebe443f83300560917d652d2483d4da64ef5b4ed4 |
# Dual4BitVerticalBargraph3x.py
#
# A DEMO DUAL 4 bit slow analogue bargraph generator in colour for STANDARD Python 3.x.x
# and Linux... This is a DUAL vertical version of the SINGLE one also given away by myself.
# It is written so that anyone can understand how it works.
#
# (Original copyright, (C)2011, B.Walker, G... | ActiveState/code | recipes/Python/577685_DUAL_4_Bit_Vertical_Coloured_Analogue_Bar_Graph_/recipe-577685.py | Python | mit | 7,602 | [
"Amber"
] | 6036e84656480d28ec39678a0cb10c14d8479354a89b5d82310a0e9f5992ff43 |
from __future__ import print_function
import sys
import random
import os
import numpy as np
from builtins import range
import time
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
from h2o.grid.grid_search import H2OGridSearch
cl... | mathemage/h2o-3 | h2o-py/dynamic_tests/testdir_algos/glm/pyunit_glm_gridsearch_over_all_params_large.py | Python | apache-2.0 | 33,225 | [
"Gaussian"
] | 189b9386cc2c7dec30982da7e38a238f358e067b3ae58388bd5bde5e14db8b94 |
from __future__ import print_function
from __future__ import unicode_literals
from builtins import str, bytes, dict, int
import os
import sys
sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", ".."))
from pattern.graph.commonsense import Commonsense
# A semantic network is a graph in which each node r... | clips/pattern | examples/06-graph/06-commonsense.py | Python | bsd-3-clause | 2,601 | [
"Octopus"
] | d5dca4dc1ef32280aa3a298e5a311b696222d6faa57c31c996b5425feaae78b3 |
from DIRAC.WorkloadManagementSystem.Client.SandboxStoreClient import SandboxStoreClient
from DIRAC.FrameworkSystem.Client.SystemAdministratorClient import SystemAdministratorClient
from DIRAC.FrameworkSystem.Client.NotificationClient import NotificationClient
from DIRAC.FrameworkSystem.Client.SystemAdministratorIntegr... | chaen/WebAppDIRAC | WebApp/handler/SystemAdministrationHandler.py | Python | gpl-3.0 | 26,553 | [
"DIRAC"
] | 5fcd7beae06c68162212b440960959897ff7419d552845000e13b0151771b0bd |
"""Support for Konnected devices."""
import copy
import hmac
from http import HTTPStatus
import json
import logging
from aiohttp.hdrs import AUTHORIZATION
from aiohttp.web import Request, Response
import voluptuous as vol
from homeassistant import config_entries
from homeassistant.components.binary_sensor import DEVI... | rohitranjan1991/home-assistant | homeassistant/components/konnected/__init__.py | Python | mit | 14,301 | [
"VisIt"
] | 204aef4d4fa00d45f5226b7a735533ae6f31943ae0b3b7e857e84b2822e14453 |
from __future__ import print_function
import sys
import random
import os
from builtins import range
import time
import json
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.random_forest import H2ORandomForestEstimator
from h2o.grid.grid_search import H2OGridSearch
class... | michalkurka/h2o-3 | h2o-py/dynamic_tests/testdir_algos/rf/pyunit_rf_gridsearch_sorting_metrics.py | Python | apache-2.0 | 14,484 | [
"Gaussian"
] | 5bc6d00ccef89b768c2360d2b9168d5b4ab256de5efea8f63f08b1b5b55badff |
#!/usr/bin/python
import os, sys # low level handling, such as command line stuff
import string # string methods available
import re # regular expressions
import getopt # comand line argument handling
from low import * # custom functions, written by myself
from Bio.Seq import Seq
from Bio.Alpha... | lotharwissler/bioinformatics | python/fasta/fasta-extract-fragment.py | Python | mit | 5,139 | [
"BLAST"
] | e4eb8eb5883dfa7c378917ecaa1a80442848a34fbf7a5a197dc5fdaa01e654ed |
""" Class that contains client access to the StorageManagerDB handler.
"""
import six
import random
import errno
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.ConfigurationSystem.Client.Helpers.Registry import getVOForGroup
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC.Core.Utilities.DErrno ... | DIRACGrid/DIRAC | src/DIRAC/StorageManagementSystem/Client/StorageManagerClient.py | Python | gpl-3.0 | 9,832 | [
"DIRAC"
] | 1fb4e6738cf50306ef2703fac0a756503e24e9a8c7cbf453df6f4fba3045714a |
try:
import cPickle as pickle
except ImportError:
import pickle
from stagecraft.tools import get_credentials_or_die
import requests
import django
django.setup()
from collections import defaultdict
from django.db import connection
from pprint import pprint
from stagecraft.apps.organisation.models import Node,... | alphagov/stagecraft | stagecraft/tools/import_organisations.py | Python | mit | 12,682 | [
"VisIt"
] | a02edb39995595ae93e5a25f9f29dfe26a18488b48e7375940e90fcc55b0f6ab |
from shinymud.lib.world import World
from shinymud.data.config import *
from shinymud.commands.emotes import *
from shinymud.commands.attacks import *
from shinymud.commands import *
from shinymud.lib.battle import Battle
import re
# ************************ GENERIC COMMANDS ************************
command_list =... | shinymud/ShinyMUD | src/shinymud/commands/commands.py | Python | mit | 101,475 | [
"Brian"
] | d40875cefd1e41a2ed41d748384a8d2b51adaa06942f5b8a26962c90fa61c183 |
import sys,logging,json,signal,hashlib,time
import xml.dom.minidom, xml.sax.saxutils
from BaseHTTPServer import BaseHTTPRequestHandler, HTTPServer
import SocketServer
import urllib
import splunk.entity as entity
import ssl
def signal_handler(signal, frame):
try:
httpd.server_close()
except NameError:... | damiendallimore/SplunkModularInputsPythonFramework | implementations/meraki/bin/meraki.py | Python | apache-2.0 | 13,395 | [
"VisIt"
] | 1b69329e04095f7153d24d37abf8c418c88fac9a3133c2ad2e49207788dacfe7 |
import code
from code import softspace
import os
import sys
import wx
import new
def sanitise_text(text):
"""When we process text before saving or executing, we sanitise it
by changing all CR/LF pairs into LF, and then nuking all remaining CRs.
This consistency also ensures that the files we save have the ... | nagyistoce/devide | module_kits/wx_kit/python_shell_mixin.py | Python | bsd-3-clause | 9,948 | [
"VTK"
] | 2c240761562db8b6d1119fd5dd143193d41c2b3fe4122d324d1fa8e461614eb0 |
# Copyright (C) 2012 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the... | hagabbar/pycbc_copy | pycbc/waveform/waveform.py | Python | gpl-3.0 | 38,346 | [
"Gaussian"
] | c90478cccc14fbb928e15f0ba137e8c04f9792d79b6b7dcc31149007b519653e |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RXmapbridge(RPackage):
"""Export plotting files to the xmapBridge for visualisation in X:M... | LLNL/spack | var/spack/repos/builtin/packages/r-xmapbridge/package.py | Python | lgpl-2.1 | 1,076 | [
"Bioconductor"
] | 05fffb971f7dc26472b6135df8cc9359febe99e4f933f03d2400a1d20ffecd48 |
#Needs to:
# Manage the notebook/worksheet object.
# Communicate to the javascript in the WebView object.
# Open and save .sws files.
# Delete the internal notebook object on disk when done.
import os
try:
# simplejson is faster, so try to import it first
import simplejson as json
except ImportError:
... | rljacobson/Guru | guru/WorksheetController.py | Python | mit | 43,950 | [
"Jmol"
] | 7b9599b80f89e17fbd1a2dae5ccd7f3b9828078f8892f30b38fe311417a8bef7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""transforms.py -- This module contains parameter transformations that may be
useful to transform from parameters that are easier to _sample_ in to the
parameters required for building SED models.
They can be used as ``"depends_on"`` entries in parameter specifications.
... | bd-j/bsfh | prospect/models/transforms.py | Python | gpl-2.0 | 12,300 | [
"Galaxy"
] | 5d9a20f78c2c22599078b41eadf1ed579bb4a282c585ba31a2acfd43a04b3e55 |
#! /usr/bin/env python
import os
import sys
import logging
import logging.config
import sketch
import util
from encoder import Encoder
from jskparser.jskparser import parse
import rewrite, decode
pwd = os.path.dirname(__file__)
root_dir = os.path.join(pwd, "..")
res_dir = os.path.join(root_dir, "result")
log_lvls = ... | plum-umd/java-sketch | java_sk/main.py | Python | mit | 7,160 | [
"VisIt"
] | 4e2a6a31c5dbb9d176b476d4ac5328dd9bb69f44be15fa89ac99b47fd0a6853a |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | pkreissl/espresso | testsuite/scripts/benchmarks/test_lb.py | Python | gpl-3.0 | 1,176 | [
"ESPResSo"
] | 5390add4296c569696f8a4817df960898b1c0560be0189d42cad450f7fc4cb54 |
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