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#
# Copyright (C) 2003-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" contains factory class for... | greglandrum/rdkit | rdkit/Chem/Pharm2D/SigFactory.py | Python | bsd-3-clause | 11,319 | [
"RDKit"
] | efa3f7b49528886e04ded0a8d75a0b051686c7119c2fdd1714e1e9e9aeed97b7 |
from __future__ import absolute_import
from . import ir as I
from .walk import IRWalker, propigate_location
class EvaluateCompileTime(IRWalker):
descend_into_functions = True
def __init__(self, eval_ir):
super(EvaluateCompileTime, self).__init__()
self.eval_ir = eval_ir
def visit_compi... | matthagy/Jamenson | jamenson/compiler/preeval.py | Python | apache-2.0 | 564 | [
"VisIt"
] | afe4cd54e22b48fbf11190a4a0a8fb86503b1e03e5c5703cc5a619e51edeb2fa |
from __future__ import unicode_literals
import unittest
from django.utils import html
class TestUtilsHtml(unittest.TestCase):
def check_output(self, function, value, output=None):
"""
Check that function(value) equals output. If output is None,
check that function(value) equals value.
... | chrisfranzen/django | tests/regressiontests/utils/html.py | Python | bsd-3-clause | 6,410 | [
"ADF"
] | 23d29c5cff55e5e82587448f2408942b0fea7ef1d5229cbc27cc25403689e05c |
#!/usr/bin/env python
#
import webapp2
import re
from google.appengine.ext import db
from google.appengine.ext import blobstore
from google.appengine.ext.webapp import blobstore_handlers
import xml.etree.ElementTree as ET
import logging
headers = '''<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang=... | westurner/schemaorg | headers.py | Python | apache-2.0 | 4,372 | [
"ESPResSo"
] | f3664359ba353503660e703004f3cd14a41f913f61926a1e5b787ca6b6cab694 |
#!/usr/local/bin/python
# -*- python -*-
#
# HPCToolkit MPI Profiler
# this script is adapted from mpiP MPI Profiler ( http://mpip.sourceforge.net/ )
#
# Please see COPYRIGHT AND LICENSE information at the end of this file.
#
#
# make-wrappers.py -- parse the mpi prototype file and generate a
# series o... | zcth428/hpctoolkit111 | src/tool/hpcrun/sample-sources/make-wrappers.py | Python | bsd-3-clause | 48,342 | [
"VisIt"
] | 50d7d78256d0912010a21b3592852a6d752714276f596f2c8bcb5f6f7c6e3f1e |
# Print Class
# - Will Print GroupFinder Events via PDF.
#
# Notes:
# - PDF strings, lines, and rectangles are a nightmare to move.
# - Editing PDF = Time Consuming.
from zope.interface import Interface
from Products.CMFCore.utils import getToolByName
from Products.Five import BrowserView
from Products.... | uwosh/uwosh.librarygroupfinder | uwosh/librarygroupfinder/browser/print.py | Python | gpl-2.0 | 13,673 | [
"VisIt"
] | 9c9babb23d9b7c865acdd88774869d92f27dc63faab4e630d041920611783072 |
# 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 u... | pwcberry/climate | ocw/data_source/local.py | Python | apache-2.0 | 13,413 | [
"NetCDF"
] | 0d35d6efc97af67d8dbaed6f45cacb0f42fe74fa766ae652f05d88a7664b8472 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
"""
test_parallel.py
================
Trying to task farming parameter exploration
99% inspired by parameter_search_example.py from Michael Schmuker
To run this script, you first have to invoke an IPython controller and
computation engines. If IPython is installed corre... | NeuralEnsemble/NeuroTools | examples/retina/test_parallel.py | Python | gpl-2.0 | 4,502 | [
"NEURON"
] | 706d8896f407213c429b27b2c4cbe97db67173b3daaea2ddea238e7a5ec8b9c2 |
import pybullet as p
import time
#you can visualize the timings using Google Chrome, visit about://tracing
#and load the json file
p.connect(p.GUI)
t = time.time() + 3.1
logId = p.startStateLogging(p.STATE_LOGGING_PROFILE_TIMINGS, "chrome_about_tracing.json")
while (time.time() < t):
p.stepSimulation()
p.submitP... | MadManRises/Madgine | shared/bullet3-2.89/examples/pybullet/examples/profileTiming.py | Python | mit | 598 | [
"VisIt"
] | b74b676726b7032e3e6ee754c7f7f6ad3f833d1fff0786718d981be62858ba00 |
#!/usr/bin/env python
# Purpose: Demonstrates different plots from the matplotlib examples collection
# Author: Ken McIvor <mcivor@iit.edu>, deriving from the matplotlib examples
# collection
#
# Copyright 2002-2004 John D. Hunter, 2005 Illinois Institute of Technology
#
# Distributed under the license agreement for ma... | digitie/magneto | native/wxmplplot/plotting.py | Python | unlicense | 9,658 | [
"Gaussian"
] | 118b26347cf32c7cf37924ca8cc9c3af7b29f7423133f0a5a8593b215382d46f |
"""
The more times we visit a hypothesis, the more we decrease its prior
TODO
----
* Try version where penalty decreases with time!
* This currently only extends LOTHypotheses, since we have to handle casting inside of h0 to WrapperClass.
... HOWEVER, we could make WrapperClass just dispatch the right methods if the... | ebigelow/LOTlib | LOTlib/Inference/Samplers/TabooMCMC.py | Python | gpl-3.0 | 1,569 | [
"VisIt"
] | 36a51b8cc4c6b6e858466b19439d23ae6573355a4934e979617fa9b617876cb2 |
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import numpy as np
import math
def mass_frac_cut(datas, mn):
ageend=datas['AGEEND']
print('I THINK I DID IT WOOHOO')
TM=get_tot_mass(datas, 'MASS','SPECOBJID')
#data1=datas[(ageend==np.max(ageend))&(datas['MASS']/datas['M_STELLAR']>=mn)]
data1... | anewmark/galaxy_dark_matter | def_ages.py | Python | mit | 5,004 | [
"Galaxy"
] | 9ecebe3a6bd5aacf8486c6604b460e555eb9144f121daded31801dbb1828ba7e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
import csv
import collections
import itertools
from io import open
import math
from six.moves import zip
import logging
from monty.json import MSONa... | czhengsci/pymatgen | pymatgen/analysis/phase_diagram.py | Python | mit | 84,711 | [
"pymatgen"
] | b0da6f5b1d2501a4e56a3f1371c81847aaffd334a464805e688459bf43db3356 |
# being a bit too dynamic
# pylint: disable=E1101
from __future__ import division
import warnings
import re
from collections import namedtuple
from distutils.version import LooseVersion
import numpy as np
from pandas.util._decorators import cache_readonly
import pandas.core.common as com
from pandas.core.base import... | louispotok/pandas | pandas/plotting/_core.py | Python | bsd-3-clause | 126,383 | [
"Gaussian"
] | 860c06b590c82d3f78466b18f361c799182264ec2ed9f05c48eb8c3553dd10ed |
"""
revlog.py - storage back-end for mercurial
This provides efficient delta storage with O(1) retrieve and append
and O(changes) merge between branches
Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
This software may be used and distributed according to the terms
of the GNU General Public License, incorporated ... | carlgao/lenga | images/lenny64-peon/usr/share/python-support/mercurial-common/mercurial/revlog.py | Python | mit | 46,218 | [
"VisIt"
] | 21bd256dbbf87c9cfccbe529835f8e0532551f64aa19540cf1d2cc62dace20d0 |
import argparse
import logging
import multiprocessing
import time
from functools import partial, update_wrapper
from defaults import EXTRACTION_MAX_READ_PAIRS, EXTRACTION_MAX_NM, EXTRACTION_MAX_INTERVAL_TRUNCATION, EXTRACTION_TRUNCATION_PAD
import pysam
compl_table = [chr(i) for i in xrange(256)]
compl_table[ord('A')... | msahraeian/metasv | metasv/extract_pairs.py | Python | bsd-2-clause | 8,155 | [
"pysam"
] | f944f4198024613b040a80f137e2055fd190ebd0c5e5c2c69a01c717f40114ba |
import numpy as np
import time
import matplotlib.pyplot as plt
import os, pdb, sys
import scipy.optimize
import scipy.interpolate
import scipy.ndimage
import glob
import atpy
# TODO - wrap these routines up as attributes of spectroscopy
# opjects somehow.
def calc_spectra_variations( spectra, ref_spectrum, max_wavsh... | tomevans/spectroscopy | spectroscopy/wfc3_routines_BACKUP.py | Python | gpl-2.0 | 6,854 | [
"Gaussian"
] | cc6fa403e2797216932bebb0cd30ab8da4d3357d05d2b3813f2fd255e36802cd |
from __future__ import print_function
import string
import sys
from collections import deque
import numpy as np
from sklearn.base import BaseEstimator
from sklearn.utils import check_random_state
from sklearn.utils.extmath import logsumexp
from . import _hmmc
from .utils import normalize
decoder_algorithms = froze... | matthiasplappert/hmmlearn | hmmlearn/base.py | Python | bsd-3-clause | 21,078 | [
"Gaussian"
] | 809af31c57a4fcbccae2fbf59eda6df1e048a7b4ebfae43df2dcb2b52356d688 |
import time
import hashlib
from flask import redirect, flash, url_for, request
from flask.ext.admin import BaseView, expose
from flask.ext.login import current_user
from application import app
def generate_whmcs_url(goto=None):
""" Creates a link that allows an user to visit their billing account
http://... | pawl/MakerManager2 | application/views/billing_redirect.py | Python | mit | 1,276 | [
"VisIt"
] | 00ee55f93c87f13097d5a88b8dd3f0fdd97f5bbc610989b5a98299b081a235ed |
# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Nodes.py
#
# Provides functionality of a linked list.
# Each node has one ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Nexus/Nodes.py | Python | gpl-2.0 | 5,759 | [
"Biopython"
] | b453174e4f47d573ca4be825b4e6cb63a3dd452d02c61439562fd11ddb445dfd |
# -*- coding: utf-8 -*-
import typing as T
import moose._moose as _moose
_tick = 8
_base = "/_utils"
_path = _base + "/y{0}"
_counter = 0
_plots : T.List[_Plot] = []
_moose.Neutral(_base)
_defaultFields = {
_moose.Compartment: "Vm",
_moose.ZombieCompartment: "Vm",
_moose.HHChannel: "Gk",
_moose.Zomb... | dilawar/moose-core | python/moose/recording.py | Python | gpl-3.0 | 5,054 | [
"MOOSE"
] | bf29287c44cfceefb81897b8192ce41efd2da39d37f6351cb72b0e0fd0842679 |
import galaxy.model
from base.twilltestcase import TwillTestCase
from base.test_db_util import (
get_user,
get_private_role,
get_latest_history_for_user,
get_default_history_permissions_by_history,
get_latest_dataset,
refresh,
get_default_user_permissions_by_user,
get_dataset_permissions... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/functional/test_data_security.py | Python | gpl-3.0 | 12,947 | [
"Galaxy"
] | 36c80cddde1bcf78c14b8650233e38a7cb961778b587b0c75c2a18f18f493e41 |
"""
Imports all the functions in the various files.
Doing this explicitly for clarity
"""
from .array_help import (
find_nearest,
find_nearest_index,
copy_range,
copy_range_array,
copy_range_yarray,
sort_by_list,
find_nearest_tolerance,
sort_array_column,
split_columns,
)
from .bac... | rohanisaac/spectra | spectra/__init__.py | Python | gpl-3.0 | 2,083 | [
"Gaussian"
] | 8c69df1f3f0627a764185c6e93c0d3be260520871af55ae7bba4db211043920c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (C) 2012-2014 Bitergia
#
# 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 v... | jgbarah/Automator | launch.py | Python | gpl-3.0 | 76,615 | [
"Octopus"
] | 6e1c28c8bd1452863ac97cab01dde4fb7439106ae9184e6c26f997fcd6539d42 |
from WebAppDIRAC.Lib.WebHandler import WebHandler, asyncGen
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC import gConfig, gLogger
from DIRAC.Core.Utilities import Time
import json
class PilotSummaryHandler(WebHandler):
AUTH_PROPS = "authenticated"
@asyncGen
def web_getPilotSummaryData(self):
... | zmathe/WebAppDIRAC | WebApp/handler/PilotSummaryHandler.py | Python | gpl-3.0 | 6,823 | [
"DIRAC"
] | abf9c5566d14a82c9340a3b4e2a928a21c5f88149095c0cea8993dcbb55d46ba |
# 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_sigmaPreprocessing16.py | Python | cc0-1.0 | 7,833 | [
"Gaussian"
] | 61387c1f970416612ba2ba83952a655bde55bd4188579e98323c62d2e40c0f02 |
# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to LWR ones.
from galaxy.util import enum
job_states = enum(R... | jmchilton/lwr | lwr/managers/util/cli/job/slurm.py | Python | apache-2.0 | 2,840 | [
"Galaxy"
] | 9b7a9d587de78e9f9f2d3787030938d95d2e120dfcdadea5aeca8efd57dcc2cb |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | etherkit/OpenBeacon2 | client/linux-x86/venv/lib/python3.8/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 89,903 | [
"VisIt"
] | d2563c020c5efbb22032dc60c45b8e63536b0e507339496908ab2f6b25e54d86 |
"""
Enterprise Login tests
"""
from datetime import datetime
from bok_choy.web_app_test import WebAppTest
from regression.pages import LOGIN_EMAIL, LOGIN_PASSWORD
from regression.pages.enterprise.course_about_page import CourseAboutPageExtended
from regression.pages.enterprise.ent_course_enrollment_page import Enter... | edx/edx-e2e-tests | regression/tests/enterprise/ent_test_base.py | Python | agpl-3.0 | 10,648 | [
"VisIt"
] | a78657d9a5c5d994cd86fe2c0d7289450529f63571cafb6d5b5a77b4fae3be25 |
#!/usr/bin/env python
########################################################################
# $HeadURL: svn+ssh://svn.cern.ch/reps/dirac/DIRAC/trunk/DIRAC/WorkloadManagementSystem/private/DIRACPilotDirector.py $
# File : test_wrapperScript.py
# Author : Ricardo Graciani
############################################... | Sbalbp/DIRAC | Resources/Computing/test/test_writeScript.py | Python | gpl-3.0 | 1,628 | [
"DIRAC"
] | aec2131cb1f1d9db8dd97ae14bae9cac92f8bebfc71268178c919fbd42762daf |
import pandas as pd
import matplotlib as mpl
mpl.use('Agg') # drop tkinter dependecy
import matplotlib.pyplot as plt
import matplotlib.ticker as ticker
import matplotlib.dates as dates
from time import time, mktime
from datetime import datetime
from sqlalchemy import create_engine, select as sqlselect, between
from s... | qtto/big-brother | plot.py | Python | mit | 3,440 | [
"ADF"
] | 49115467faf2f33192157496963810fced32de4cd9b394ff0dce25afcb9313d8 |
# Copyright (C) 2014
# Pierre de Buyl
# 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 ... | capoe/espressopp.soap | src/interaction/LennardJones93Wall.py | Python | gpl-3.0 | 4,584 | [
"ESPResSo"
] | 9b19ece6202ce1096ac7169f871ea5d0c9577fcce60052994d92da2e4a6b70a8 |
from __future__ import absolute_import
from __future__ import print_function
from __future__ import division
import unittest
import os
import numpy as np
from pymatgen.analysis.elasticity.elastic import *
from pymatgen.analysis.elasticity.strain import Strain, IndependentStrain, Deformation
from pymatgen.analysis.el... | xhqu1981/pymatgen | pymatgen/analysis/elasticity/tests/test_elastic.py | Python | mit | 17,054 | [
"pymatgen"
] | a9a8bda8b5a11592442403044904ad1652f26c1e44e176195b1078256f4d1b8e |
# Copyright 2014, Brian Coca <bcoca@ansible.com>
# Copyright 2017, Ken Celenza <ken@networktocode.com>
# Copyright 2017, Jason Edelman <jason@networktocode.com>
# Copyright 2017, Ansible Project
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of ... | azaghal/ansible | lib/ansible/plugins/filter/mathstuff.py | Python | gpl-3.0 | 8,097 | [
"Brian"
] | 1cd0ef68bd0a649f7ac10b3ce48a91eec67e7e506090efc4b8f882fdeac53c08 |
"""
fitpack --- curve and surface fitting with splines
fitpack is based on a collection of Fortran routines DIERCKX
by P. Dierckx (see http://www.netlib.org/dierckx/) transformed
to double routines by Pearu Peterson.
"""
# Created by Pearu Peterson, June,August 2003
from __future__ import division, print_function, abs... | sargas/scipy | scipy/interpolate/fitpack2.py | Python | bsd-3-clause | 48,821 | [
"Gaussian"
] | a03e67d6ec5d226f10e3677854ce647c8800158127c49ebd00ba594f5cfd9c6a |
import numpy as np
import scipy.misc
import argparse
from PIL import Image, ImageFont, ImageDraw
def main():
parser = argparse.ArgumentParser(
description = 'This program will generate a bmp of Gaussian Noise')
parser.add_argument('width', help='The width of the image',
type=int)
parser.add_argument('height', ... | mitre-cyber-academy/2013-forensics-500 | src/genNoiseImg.py | Python | apache-2.0 | 3,106 | [
"Gaussian"
] | 31c615ea9ba082c7e0d14e41e340e5e73224cee15e28c50b3633e2c27f0e2330 |
# -*- coding: utf-8 -*-
from __future__ import annotations
from statsmodels.compat.pandas import (
Appender,
Substitution,
call_cached_func,
to_numpy,
)
from collections.abc import Iterable
import datetime
import datetime as dt
from types import SimpleNamespace
from typing import Any, Literal, Sequenc... | statsmodels/statsmodels | statsmodels/tsa/ar_model.py | Python | bsd-3-clause | 79,633 | [
"Gaussian"
] | 7297f0e0e3e4e9810dbbe4deeffdea7cb4b8679cfe2078444f42b84880ed808a |
from MafiaBot.MafiaRole import MafiaRole
from MafiaBot.MafiaAction import MafiaAction
class Sleepwalker(MafiaRole):
def GetRolePM(self):
ret = 'You are a Sleepwalker. You have to visit another player at night. This action does nothing.'
if self.limiteduses > -1:
ret += ' You may only ... | LLCoolDave/MafiaBot | MafiaBot/Roles/Sleepwalker.py | Python | mit | 2,173 | [
"VisIt"
] | a90e01a75ce46659d619e8bd0f5f3d3b9e1ccc3cad42a1a15c25ad6466c588b8 |
# FIXME: to bring back to life
from DIRAC.Resources.Catalog.FileCatalogClient import FileCatalogClient
import cmd
import sys
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.AbstractFileSystem import DFCFileSystem
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.DirectoryCompletion import DirectoryComp... | Andrew-McNab-UK/DIRAC | tests/Integration/DataManagementSystem/FIXME_dfc_dir_completion.py | Python | gpl-3.0 | 1,214 | [
"DIRAC"
] | 9048c9ff52211a33cb112fc0ba659138749217dfdfec4be4d01e28dd76b8fb4e |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
# Copyright (c) 2016 Mikkel Schubert <MikkelSch@gmail.com>
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without ... | MikkelSchubert/paleomix | paleomix/pipelines/zonkey/build_db.py | Python | mit | 11,228 | [
"pysam"
] | a41e309c876512562bd79e89d993fa62fe8c2ecef6aaa5ec327453cfe9c4ecf3 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | tests/crystal/test_third_order.py | Python | gpl-3.0 | 1,819 | [
"CRYSTAL",
"VASP"
] | c54533869f56b7a75ca39cb0508a9ab03752d426593c1654b54ed7c6d00cfa38 |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
#
# This library 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 2.1 of the License, or (at your option) any later version.
#
# This library i... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/Thunderbird/script_utilities.py | Python | gpl-3.0 | 4,032 | [
"ORCA"
] | a1b41a4c8f4143fa64b283034673387dddf032092943a6418cb368def709f59b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import numpy as np
import unittest2 as unittest
from pymatgen.analysis.eos import EOS
def have_scipy():
try:
import scipy
... | Bismarrck/pymatgen | pymatgen/io/abinit/tests/test_eos.py | Python | mit | 927 | [
"pymatgen"
] | d0c57f7811e6252b4ecc73b8be123071a9912594b3e79d25b69d898638afc623 |
"""Contains time series code
"""
import os
import gzip
import numpy as np
import pandas as pd
from scipy.stats import zscore
from scipy.stats import spearmanr
from scipy.stats import pearsonr
from scipy.stats import multivariate_normal
from scipy.stats import chi2
from ggr.util.parallelize import setup_multiprocessi... | vervacity/ggr-project | ggr/analyses/timeseries.py | Python | mit | 34,599 | [
"Gaussian"
] | ab53f2400382e9d7190ac925e83cd4302f8c31d0888e3ffd336c26ea2f68b1a6 |
# This file is part of Merlin/Arthur.
# Merlin/Arthur is the Copyright (C)2009,2010 of Elliot Rosemarine.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; you can redistribute it an... | d7415/merlin | Arthur/views/__init__.py | Python | gpl-2.0 | 1,785 | [
"Galaxy"
] | c0ce8c033357a61ae8ac2474c048d1749ea212c49145b43128be4de6e58e8dbe |
#!/usr/bin/env python3
import itertools
from collections import defaultdict
import logging
from operator import mul
import networkx as nx
import numpy as np
import pandas as pd
from pgmpy.base import DirectedGraph
from pgmpy.factors.discrete import TabularCPD, JointProbabilityDistribution, DiscreteFactor
from pgmpy.... | khalibartan/pgmpy | pgmpy/models/BayesianModel.py | Python | mit | 39,747 | [
"VisIt"
] | cc6ceed385843667962f6ae53e052c3678ac86fc4d617bfbf58060865d46f7c9 |
"""
.. _tut_forward:
Head model and forward computation
==================================
The aim of this tutorial is to be a getting started for forward
computation.
For more extensive details and presentation of the general
concepts for forward modeling. See :ref:`ch_forward`.
"""
import mne
from mne.datasets i... | jaeilepp/mne-python | tutorials/plot_forward.py | Python | bsd-3-clause | 8,258 | [
"Mayavi"
] | 53d8779e55b547b54e60c8b14c62bbd145c4b55c3ac971bbb4a4f819a95f6c3f |
# -*- coding: utf-8 -*-
#import sys # for devel only
#
#import numpy
#import json
#
from aiida.parsers.parser import Parser
from aiida.parsers.exceptions import OutputParsingError
from aiida.common.datastructures import calc_states
#
from aiida.orm.calculation.job.vasp.vasp import VaspCalculation
from aiida.orm.calcul... | abelcarreras/aiida_extensions | plugins/parsers/vasp/__init__.py | Python | mit | 8,544 | [
"VASP"
] | a13518304ea6c2a6ec9f480825e848325647b2bd3e8d4fdfdd3339b1d475b3c4 |
# generics/DogsAndRobots.py
# (c)2017 MindView LLC: see Copyright.txt
# We make no guarantees that this code is fit for any purpose.
# Visit http://OnJava8.com for more book information.
class Dog:
def speak(self):
print("Arf!")
def sit(self):
print("Sitting")
def reproduce(self):
p... | mayonghui2112/helloWorld | sourceCode/testMaven/onjava8/src/main/java/generics/DogsAndRobots.py | Python | apache-2.0 | 618 | [
"VisIt"
] | b00824e8b2205a3a7ea19d94fab4b04c7383d6daa2d6b49ce515feb9c4bdc8a1 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os.path
import itertools
import numpy as np
from numpy.testing import assert_equal, assert_allclose
from scipy.ndimage.interpolation import shift
import abel
from abel.tools.center import find_origin,... | DanHickstein/pyBASEX | abel/tests/test_tools_center.py | Python | gpl-2.0 | 12,986 | [
"Gaussian"
] | c9b517094e4831efd5aee789b73766f70331f5cb69986b7e06647ac1e89ed001 |
#!/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 | modules/porous_flow/examples/thm_example/paper_solns.py | Python | lgpl-2.1 | 25,361 | [
"MOOSE"
] | 1887ba692c015c0cc5ab3fc42bdfb72cdea63073cbfba5303a3c2afdf1b07026 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | tbereau/espresso | samples/python/lj_liquid.py | Python | gpl-3.0 | 6,659 | [
"ESPResSo"
] | 5fa6678785c091eba73483590f8a7e23df5206bac8512abebeffe03d2db76ae0 |
#Script to run at set intervals to check on the status of condor jobs, submit them, and collate results if necessary
from web_frontend.condor_copasi_db import models
from web_frontend.copasi.model import CopasiModel
from web_frontend import settings, condor_log, condor_status, email_notify
import subprocess, os, re, da... | Nucleoos/condor-copasi | condor-copasi-daemon/background_run.py | Python | artistic-2.0 | 32,291 | [
"COPASI"
] | 7012c866e607bd53fc080ae598e545b1289689154fbb8db0a7ab721bb9793722 |
#get the default AMI's and titles for the 8 EC2 datacenters through endless screen scraping
#please destroy me when EC2 provides this data through JSON ;)
import time, datetime, sys, re
try:
from splinter import Browser
except:
sys.exit('install splinter, ./bin/pip install splinter')
EC2_USER = ""
EC2_PASS = "... | Lao-liu/mist.io | scripts/get_ec2_amis.py | Python | agpl-3.0 | 2,135 | [
"VisIt"
] | a6ceff426abc3bae997ce964bf7c68fb632d8b75dcc7fdc4ec7dd1de14ab749a |
# -*- coding: utf-8 -*-
import random
import chatbot
from commands import general_chat, send_whisper
__all__ = [ 'PLUGIN', 'init' ]
PLUGIN = {
'name': 'lazytree',
'requires': ('chatbot',),
'blocks': (),
}
# -----------------------------------------------------------------------------
greetings = {
... | mekolat/manachat | plugins/lazytree.py | Python | gpl-2.0 | 9,027 | [
"Galaxy"
] | cd16cd34d6de0edd5e556fdd5db436032070d9b5cda2114a36ddc26f37296c4d |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ThreadPoolExecutor."""
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
import atexit
from concurrent.futures import _base
import itertools
import queue
import threading
import weakref
im... | prefetchnta/questlab | bin/x64bin/python/36/Lib/concurrent/futures/thread.py | Python | lgpl-2.1 | 5,664 | [
"Brian"
] | fdd0148415b07091194349d1fe22fc4b56ba48d8e336524b7bc46c68126e5800 |
# sql/elements.py
# Copyright (C) 2005-2014 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core sql expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | ncdesouza/bookworm | env/lib/python2.7/site-packages/sqlalchemy/sql/elements.py | Python | gpl-3.0 | 121,469 | [
"VisIt"
] | d64dd26b0e978fd25c515d718e7f5bd2b4424182e5dbfb967c7d5b56152e42d8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
:synopsis: Prompts the user to add network paths and username passwords for
e.g. smb paths
"""
from __future__ import absolute_import, division, unicode_literals
from logging import getLogger
import re
import socket
import urllib
import xbmc
from .. import ... | croneter/PlexKodiConnect | resources/lib/windows/direct_path_sources.py | Python | gpl-2.0 | 7,136 | [
"VisIt"
] | 1c60ab32c1cac3bd6134f5be3172420eaaa5c3feebe5f7a4305759414287ff20 |
#!/usr/bin/env python
#
# Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
# $Id: std.py,v 1.1 2002/01/29 20:07:05 zooko Exp $
# This is a silly hack to get around Python'... | zooko/egtp | common/std.py | Python | agpl-3.0 | 862 | [
"VisIt"
] | 79b78b5b3b0e30e5d1598031390b1ba2304a8d22e60821fc664a47649ec4a2ca |
""" Testing the FCConditionPaserClass
"""
import unittest
from DIRAC.Resources.Catalog.FCConditionParser import FCConditionParser
__RCSID__ = "$Id $"
class TestLogicEvaluation( unittest.TestCase ):
""" Tests all the logic evaluation
"""
def setUp( self ):
self.fcp = FCConditionParser()
self.lfns = ['/... | andresailer/DIRAC | Resources/Catalog/test/Test_FCConditionParser.py | Python | gpl-3.0 | 9,153 | [
"DIRAC"
] | 2313d3183d37fbad954ae23318452057e5a9ede23210558ec8299621505d98fe |
"""
font data tables for truetype and afm computer modern fonts
"""
# this dict maps symbol names to fontnames, glyphindex. To get the
# glyph index from the character code, you have to use get_charmap
"""
from matplotlib.ft2font import FT2Font
font = FT2Font('/usr/local/share/matplotlib/cmr10.ttf')
items = font.get_... | SpaceKatt/CSPLN | apps/scaffolding/mac/web2py/web2py.app/Contents/Resources/lib/python2.7/matplotlib/_mathtext_data.py | Python | gpl-3.0 | 89,917 | [
"Bowtie"
] | 5eab7e8f6e7c8192a720764420f7c480d0996fc98435d1504d1d107d3dad5e3d |
#!/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... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_cloud.py | Python | gpl-3.0 | 11,134 | [
"VisIt"
] | 28d1299bec0a82b980ca2e44507ae61a160c2f1d48c278e835e47bebd6c6e0ca |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Unit tests for the :class:`iris.experimental.ugrid.cf.CFUGridAuxiliaryCoordinateVariable` class.
todo: fold these tests in... | SciTools/iris | lib/iris/tests/unit/experimental/ugrid/cf/test_CFUGridAuxiliaryCoordinateVariable.py | Python | lgpl-3.0 | 8,596 | [
"NetCDF"
] | fad4cb7244972af3a189587a92fb475e96ba40066c7fcd1867e36badceaa6562 |
import re
from .. import factories as f
from .. utils import create_user_verify_login
def get_captcha_value(html_body):
captcha_text = re.split(r'What is', html_body)[1]
main_text = re.split(r'\?', captcha_text)
a = main_text[0].strip().split(' ')
if a[1] == '+':
return int(a[0]) + int(a[2])
... | pythonindia/wye | tests/functional/test_contact_page.py | Python | mit | 2,764 | [
"VisIt"
] | e41f58e819a1530de646f681ab6850d171fcea12091bd7d31940ee6f9899f4c0 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Popularity Contest (popcontest) parser."""
from __future__ import unicode_literals
import unittest
from plaso.lib import definitions
from plaso.parsers import popcontest
from tests.parsers import test_lib
class PopularityContestUnitTest(test_lib.Pars... | rgayon/plaso | tests/parsers/popcontest.py | Python | apache-2.0 | 6,523 | [
"ORCA"
] | aaabfb981b88cd72f8dc1dcf1167c25269d1346ed4b0082951457b548bd06018 |
import argparse
import requests
from twisted.internet import reactor
try:
import ConfigParser as configparser
except ImportError:
import configparser
from pipes.connector import MatchPlayer
parser = argparse.ArgumentParser(description="connect to a casino")
parser.add_argument('--key', help="secret key for y... | gnmerritt/poker-plumbing | play.py | Python | mit | 2,768 | [
"CASINO"
] | 3746872351f7046d63f6efc89b9f8eed44a10e60a64f9f82bd78b1c507fa022f |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | zimmermant/dlvo_lammps | python/lammps.py | Python | gpl-2.0 | 9,129 | [
"LAMMPS"
] | 28ad9659ac2aec2b97ff8c267c8790dd04f71367a2b96b958d037d8219fb7224 |
"""Ranks cog.
Keep track of active members on the server.
"""
import logging
import os
import random
import MySQLdb # The use of MySQL is debatable, but will use it to incorporate CMPT 354 stuff.
import discord
from discord.ext import commands
from __main__ import send_cmd_help # pylint: disable=no-name-in-m... | Injabie3/lui-cogs | ranks/ranks.py | Python | gpl-3.0 | 17,074 | [
"MOE"
] | 97a8127fed4c25ad0fcc0a65524eb0292c446f35ac0940c74863be9f3d920beb |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains objects that are used to describe the environments in a structure. The most detailed object
(StructureEnvironments) contains a very thorough analysis of the environments of a given atom but is difficul... | materialsproject/pymatgen | pymatgen/analysis/chemenv/coordination_environments/structure_environments.py | Python | mit | 104,682 | [
"pymatgen"
] | 9fe8aeb5c8996e32d9174bc1b72493819934853439d963bc176d1850d8471015 |
from skimage import feature, io, filters, transform
img_file = "../data/similar_objects/4.JPG"
# load the image and convert it to a floating point data type
image = io.imread(img_file)
image = transform.rescale(image, 0.4)
from matplotlib import pyplot as plt
from skimage import data
from skimage.feature import blo... | m3rik/nn | CNTK/GeneralizedHoughTransform/blobs.py | Python | apache-2.0 | 1,228 | [
"Gaussian"
] | a16c9e6708596e3ad79f45a1e205f3d094595959ba6b99a45fbdd6e3ddb6dc0e |
import sys
import os
import pysam
import difflib
IS_PYTHON3 = sys.version_info[0] >= 3
if IS_PYTHON3:
from itertools import zip_longest
from urllib.request import urlopen
else:
from itertools import izip as zip_longest
from urllib2 import urlopen
def checkBinaryEqual(filename1, filename2):
'''r... | nlhepler/pysam | tests/TestUtils.py | Python | mit | 3,260 | [
"pysam"
] | ab7e83d06c716e728048ce5deb45dcadc206210bc0de5d5c48fa7862aed6b7e8 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Variable_Stiffness_Variable_Velocity/HMM/with 2s/hmm_crossvalidation_force_motion_10_states_scaled_wrt_all_data.py | Python | mit | 39,761 | [
"Mayavi"
] | 96eb7ac2533b76fbe16c02d84d82909d641dd21ce55596c02c428cae00d3469f |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose | moose-examples/tutorials/ChemicalBistables/simpleBis.py | Python | gpl-3.0 | 8,484 | [
"MOOSE"
] | 02f31f9dc3390e712da0b59bc58c28e0fbb9751af458e7f946d0f61a57459ae6 |
import os
import itertools
import mdtraj
import pandas as pd
cos = np.cos
sin = np.sin
ave = lambda x: x.mean(0).mean(0)
phi0 = np.deg2rad(0.0)
amino_acids = ["A" , "C" , "D" , "E" , "F" , "G" , "H" , "I" , "K" , "L" , "M" , "N" , "Q" , "R" , "S" , "T" , "V" , "W" , "Y"]
labels = ["%s%s" % (a0,a1) for (a0, a1) in ite... | hainm/open-forcefield-group | nmr/code/analyze_dcd.py | Python | gpl-2.0 | 2,427 | [
"MDTraj"
] | ef7c5b5ca861094e5d7dcc1a5104ccd11b03ca069bf2d5095935be0c55bbc082 |
# vim: fileencoding=utf-8 et ts=4 sts=4 sw=4 tw=0
"""
Base RPC service class
Authors:
* Brian Granger
* Alexander Glyzov
* Axel Voitier
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2012-2014. Brian Granger, Min Ragan-Kelley, Alexander Glyzov,
# Axel Voitier
#
... | srault95/netcall | netcall/base_service.py | Python | bsd-3-clause | 12,879 | [
"Brian"
] | 138321514797a22287c22d2d523b6a865f8a3f585abd37825a7f05607f9dbdab |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# 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... | steckdenis/rlglue-py3 | rlglue/agent/Agent.py | Python | apache-2.0 | 1,491 | [
"Brian"
] | 5af13b0986d6b6bda1c94a3ab156d8d6f80a365627bdd3ea77107b4fbf7456d4 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
#
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Math... | sknepneklab/SAMoS | FormerAnalysis/nematic_defects_analysis.py | Python | gpl-3.0 | 28,489 | [
"VTK"
] | eb94031a15c050326650d200fbead44d78248f0786c7316af60531da6fc22bdd |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkShrinkFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | chrisidefix/devide | modules/vtk_basic/vtkShrinkFilter.py | Python | bsd-3-clause | 492 | [
"VTK"
] | 3445702ed54f25467cdb5f9d93a9263b919da20f82a547aa9bc044a71e4b79f4 |
#!/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,... | kkreis/espressopp | testsuite/ewald/ewald_eppDeserno_comparison.py | Python | gpl-3.0 | 7,543 | [
"ESPResSo"
] | eff709ab89d89e824fa35e37199292032c53c53347687334fd3a1d161870817c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Simple peak fitting utility with PyMCA/SILX
===========================================
Current fitting backends: PyMca_ or SILX_
.. _PyMca: https://github.com/vasole/pymca
.. _SILX: https://github.com/silx-kit/silx
"""
from sloth.gui.jupyx import run_from_ipython
i... | maurov/xraysloth | sloth/fit/peakfit_silx.py | Python | bsd-3-clause | 11,844 | [
"Gaussian"
] | b54346be38f9d1edbeedf12a853b8e94976a70e4a7a367236f794f420059afc0 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2014 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 Foundati... | LunarLanding/Pythics | pythics/control_helpers.py | Python | gpl-3.0 | 12,528 | [
"Brian"
] | 74bbbda57743098551bf143cdfe94b5700122d1c8eea544b72ff33a7e9d1a3a5 |
"""
Acceptance tests for Content Libraries in Studio
"""
from ddt import ddt, data
from nose.plugins.attrib import attr
from flaky import flaky
from .base_studio_test import StudioLibraryTest
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.utils ... | antoviaque/edx-platform | common/test/acceptance/tests/studio/test_studio_library.py | Python | agpl-3.0 | 28,054 | [
"VisIt"
] | 1cf182ed44307367356324fb84719ddacc0314335c8ecbd0a7a8ced8343b1bfa |
########################################################################
# File: ReplicateAndRegister.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 18:49:12
########################################################################
""" :mod: ReplicateAndRegister
==========================
.. mo... | arrabito/DIRAC | DataManagementSystem/Agent/RequestOperations/ReplicateAndRegister.py | Python | gpl-3.0 | 28,823 | [
"DIRAC"
] | ca0c2c23401940cedcd1ec00065d2d75e6ffa3c68c7e91ed41781527eefe58e9 |
import cgen as c
from sympy import Not
from devito.arch import AMDGPUX, NVIDIAX
from devito.ir import (Block, Call, Conditional, List, Prodder, ParallelIteration,
ParallelBlock, PointerCast, While, FindNodes, Transformer)
from devito.mpi.routines import IrecvCall, IsendCall
from devito.passes.ie... | opesci/devito | devito/passes/iet/languages/openmp.py | Python | mit | 6,258 | [
"VisIt"
] | f32970fa5960986598bb6a810aa72a5f449068d8444a8c96b5b54303e994bed8 |
"""
Voronoi analysis of atom positions
author Gerd and Rama
part of pycrosocpy
"""
import numpy as np
import sys
# from skimage.feature import peak_local_max
from skimage.feature import blob_log
from sklearn.cluster import KMeans
from scipy.spatial import cKDTree
import scipy.optimize as optimization
import pyTEM... | pycroscopy/pycroscopy | pycroscopy/image/image_atoms.py | Python | mit | 7,225 | [
"Gaussian"
] | 642f98fa5934fbc95717459a2a2c8c648090de4c508aa7e2b6e29d90926ee471 |
#!/usr/bin/python
# -- Content-Encoding: UTF-8 --
"""
iPOPO component factories repository
:author: Thomas Calmant
:license: Apache Software License 2.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the L... | isandlaTech/cohorte-demos | led/dump/led-demo-yun/cohorte/dist/cohorte-1.0.0-20141216.234517-57-python-distribution/repo/cohorte/repositories/python/ipopo.py | Python | apache-2.0 | 11,559 | [
"VisIt"
] | 13f7e24601443ee78a6d4b51e5fd553f3925f7ccb002935162fff49a4e08a112 |
#!/usr/bin/env python
import sys, os, time, ConfigParser, shutil
from datetime import datetime, timedelta
from time import strftime
from optparse import OptionParser
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy impor... | dbcls/dbcls-galaxy | scripts/cleanup_datasets/cleanup_datasets.py | Python | mit | 16,195 | [
"Galaxy"
] | 24872fb8acac2cc27bbef893a81ddce1aba13559598c57d046a1e0488e655c95 |
# -*- coding: utf-8 -*-
#
# connections.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or... | zifeo/nest-simulator | topology/doc/user_manual_scripts/connections.py | Python | gpl-2.0 | 18,038 | [
"Gaussian"
] | 63afe2e5ad46ed52477faf07ddf5140ee94d7f05ff31c6f5d82a6a1d06584473 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
# CreateTime: 2016-09-21 16:51:48
import numpy as np
from Bio import SeqIO, Seq, SeqUtils
#from Bio.SeqUtils.CodonUsage import CodonAdaptationIndex
from Bio.SeqUtils import GC
from Bio.SeqUtils.CodonUsage import SynonymousCodons
import math
from math impo... | Rinoahu/POEM | deprecate/lib/deep_operon.py | Python | gpl-3.0 | 21,697 | [
"Biopython"
] | 75e884a1b853240736e658c78f04e528f48d407f13826ca8a8a84e2178b5d3e5 |
from paraview.simple import *
import os
import numpy as np
model = GetActiveSource()
renderView1 = GetActiveViewOrCreate('RenderView')
renderView1.CameraParallelProjection = 1
Hide(model, renderView1)
# waves
extractBlock1 = ExtractBlock(Input=model)
extractBlock1.BlockIndices = [1, 2]
extractBlock1Display = Show(ext... | ratanakso/WEC-Sim | source/paraview_macros/WEC-Sim.py | Python | apache-2.0 | 2,530 | [
"ParaView"
] | 2c97c546001aa4726f9a440b43f929a39d0d786fb2809bcfa63ecc67ba0f2977 |
# encoding: utf-8
"""
Class for reading data from NeuroExplorer (.nex)
Documentation for dev :
http://www.neuroexplorer.com/code.html
Depend on: scipy
Supported : Read
Author: sgarcia,luc estebanez
"""
from .baseio import BaseIO
from ..core import *
from .tools import create_many_to_one_relationship
import nu... | tkf/neo | neo/io/neuroexplorerio.py | Python | bsd-3-clause | 13,880 | [
"NEURON"
] | c0bbead020ed904e0b629abfd3a52fcc1f56ae44bd15eca942c3396ac8435fd5 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | adityacs/ansible | lib/ansible/modules/network/avi/avi_networkprofile.py | Python | gpl-3.0 | 3,671 | [
"VisIt"
] | fe97524a706bdce03a4766200b4c827294dbda802b45098582951ec81c41b821 |
import glob
import pandas as pd
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
import matplotlib
import os
os.chdir('/Users/evanbiederstedt/Downloads/RRBS_data_files')
mcell = glob.glob("RRBS_NormalBCD19pCD27mcell*")
newdf1 = pd.DataFrame()
for filename in mcell:
df = pd.read_table(file... | evanbiederstedt/RRBSfun | scripts/mcell_regions.py | Python | mit | 25,304 | [
"MCell"
] | 97f029bb036b688859fc5264b387c116a064b0044f71f7155bdaf1c3fd575ca4 |
'''
Identify people and umbrellas moving down the street - using top down static video.
Bare bones version of the program created by - https://github.com/jlark/rainAlert
track and detect umbrellas (to detect rainy days). The original version included
a significantly more advanced training model along with hooks to mak... | AnthonyHonstain/SimpleRainAlert | basic_tracker.py | Python | mit | 6,890 | [
"Gaussian"
] | de9db2e6fece4c62e3e20615b359150c14f97fca1d44d0264291d57ca72cbec5 |
from pathlib import Path
from clldutils.sfm import SFM, Entry
def test_Dictionary(tmp_path):
p = Path(__file__).parent.joinpath('fixtures', 'test.sfm')
d = SFM.from_file(p, keep_empty=True)
assert d[1].get('empty') is not None
d = SFM.from_file(p)
assert len(d) == 2
assert d[1].get('empty') ... | clld/clldutils | tests/test_sfm.py | Python | apache-2.0 | 1,223 | [
"VisIt"
] | 52b20fce38a9c656f407af006115f688e7848911a7870f9d834740922acc0660 |
#!/usr/bin/env python
"""
Simple script for testing various SfePy functionality, examples not
covered by tests, and running the tests.
The script just runs the commands specified in its main() using the
`subprocess` module, captures the output and compares one or more key
words to the expected ones.
The output of fai... | sfepy/sfepy | test_install.py | Python | bsd-3-clause | 10,002 | [
"VTK"
] | 80483ae5cf8315684836f7eb4911bc3679d7170def27c4ae742e8ebfbbf1f208 |
__author__ = 'robert'
import sys
if (sys.version_info < (2, 7, 0)):
import unittest2 as unittest
else:
import unittest
try:
import brian
import pypet.brian
from pypet.brian import *
except ImportError as exc:
#print('Import Error: %s' % str(exc))
brian = None
from pypet.tests.testutils.i... | nigroup/pypet | pypet/tests/unittests/briantests/module_test.py | Python | bsd-3-clause | 1,053 | [
"Brian"
] | 64a528b14bdb9dd790a96d85fdee6b7e428343bd3516e34be37b486c0c2fdfc9 |
from jasp import *
from ase.io import read, write
from ase.io.vasp import read_vasp, write_vasp
'''
code for running NEB calculations in jasp
here is typical code to set up the band:
with jasp('../surfaces/Pt-slab-O-fcc') as calc:
initial_atoms = calc.get_atoms()
with jasp('../surfaces/Pt-slab-O-hcp') as calc:
... | prtkm/jasp | jasp/jasp_neb.py | Python | gpl-2.0 | 14,770 | [
"ASE",
"VASP"
] | 020344cc26d536fdb046ad3f505f3a86f06c603b5fb2645d87d4c0a94fc4891b |
import os
from setuptools import setup
# Utility function to read the README file.
# Used for the long_description. It's nice, because now 1) we have a top level
# README file and 2) it's easier to type in the README file than to put a raw
# string in below ...
def read(fname):
return open(os.path.join(os.path.... | JoeOsborn/hyped | setup.py | Python | mit | 1,206 | [
"Brian"
] | f178439207c59f68b31ac367f861dabf53d5260309b68f95b2dd74d20d6679a4 |
#!/usr/bin/env python
'''
Online example from :
http://www.vtk.org/Wiki/VTK/Examples/Python/Graphs/EdgeWeights
Going to heavly comment out the steps to understand how to edit
this into what we need to make other graphs
'''
import vtk # Manditory on all python VTK
import random
g = vtk.vtkMutableUndirectedG... | espinm2/interactive-vtk | pysrc/PlanarGraph.py | Python | mit | 1,648 | [
"VTK"
] | f6c870e0b6d56a4236a8f936e82c4817554e2c978505f6380cf6547c530dc2f5 |
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