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"""
SECTION 1 : Load and setup data for training
"""
import pandas as pd
from sklearn.model_selection import train_test_split
# Load dataset
datatrain = pd.read_csv('../Datasets/iris/iris.csv')
# Change string value to numeric
datatrain.loc[datatrain['species']=='Iris-setosa', 'species']=0
datatrain.loc[datatrain['sp... | rianrajagede/simplesamplecode | Python/iris_scikit_mlp.py | Python | mit | 1,618 | [
"NEURON"
] | 384eee7a1609f51e89a89040155824d0f7596c47c8621d8111b0e750397cd2dd |
"""
Test the about xblock
"""
import datetime
import ddt
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.urls import reverse
from django.test.utils import override_settings
from milestones.tests.utils import MilestonesTestCaseMixin
from mock import patch
from six import ... | ahmedaljazzar/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 27,681 | [
"VisIt"
] | 9c52db1ed9d2794c6980dca54d954b370879ba0c819192e945edf4d5eef64113 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2006 Donald N. Allingham
# Copyright (C) 2007 Brian Matherly
#
# 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; eit... | Forage/Gramps | gramps/gen/filters/rules/person/_isbookmarked.py | Python | gpl-2.0 | 1,876 | [
"Brian"
] | a47b5bd54095ed3972b5474bc007ba46634e22da29e7f6184efc95c4e093cd5b |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
red= (1,0,0)
green= (0,1,0)
blue= (0,0,1)
cyan= (0,1,1)
yellow= (1,1,0)
pink = ( float(255)/255,float(192)/255,float(203)/255)
grey = ( float(127)/255,float(127)/255,float(127)/255)
orange = ( float(255)/255,float(165)/255,float(0)/255... | aewallin/opencamlib | examples/python/offset-ellipse/oellipse3_tst.py | Python | lgpl-2.1 | 13,689 | [
"VTK"
] | 90d7ba808d188ccf5ebade8575be198f1f4ac0b3355586bd8756c738c9a5f745 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | scripts/sqa_check.py | Python | lgpl-2.1 | 1,916 | [
"MOOSE"
] | b6733accd42a5f3f243c7b420a0d4651b98e2449922bb5a5e33b33ee7b98204f |
# -*- coding: UTF-8 -*-
# File: deform.py
# Author: Yuxin Wu <ppwwyyxx@gmail.com>
from .base import ImageAugmentor
from ...utils import logger
import numpy as np
__all__ = ['GaussianDeform', 'GaussianMap']
# TODO really needs speedup
class GaussianMap(object):
""" Generate gaussian weighted deformation map"""
... | yinglanma/AI-project | tensorpack/dataflow/imgaug/deform.py | Python | apache-2.0 | 3,349 | [
"Gaussian"
] | 2dcb411f6f8f33419e41080b4aac943f30ab35603afb5e8dd04b7578f7aa9126 |
# coding: utf-8
# In[3]:
# Example scipt using MesoPy to Download multiple station/variable and save to a netcdf format using xary
# Created by Nic Wayand (https://github.com/NicWayand/MesoWestDownload)
from MesoPy import Meso
get_ipython().magic(u'matplotlib inline')
import matplotlib
import numpy as np
import matp... | mesowx/MesoPy | examples/Examples Source Code/Example_download_MesoWest_data_to_Netcdf.py | Python | mit | 8,941 | [
"NetCDF"
] | abfdbc3f84817058b1462d5f2fff74750bd4d84350a540303cc7747ff39d32f7 |
# -*- coding: utf-8 -*-
"""Curves.
This module provides implementation of various curves, that appear in machine
learning and statistics. These comprise::
* Sigmoidal shaped curves
* Bell shaped curves (e.g. derivatives of sigmoidal shaped functions)
* Multiple Step Functions
.. References:
.. _Gaussian ... | fishroot/nemoa | nemoa/math/curve.py | Python | gpl-3.0 | 13,571 | [
"Gaussian"
] | 7afb0617b860bea21042712181ed18e7a6dfddd64758ec7d020fae0d1e132b77 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Defines parameters for simulation, used by example_parallel_network.py script
Copyright (C) 2018 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publis... | espenhgn/LFPy | examples/bioRxiv281717/figure_7_8/example_parallel_network_parameters.py | Python | gpl-3.0 | 29,338 | [
"NEURON"
] | 99eeab675d423fd605393da0611f21b58ef5878e3fa999e77f189cfa76898fa7 |
"""Mutable formal context creation arguments (object, properties, bools) with set-like operations."""
import fractions
import typing
from . import _common
from . import formats
from . import tools
from . import contexts
__all__ = ['Definition']
StrSequence = typing.Sequence[str]
class Triple:
"""Triple of ``... | xflr6/concepts | concepts/definitions.py | Python | mit | 33,203 | [
"Brian",
"MOOSE"
] | d4d449351a02c3c2cd8479cf5150e913fb8a5dca6d3114b51b410df178d719c0 |
"""
===========
gaussfitter
===========
.. codeauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com> 3/17/08
Latest version available at <http://code.google.com/p/agpy/source/browse/trunk/agpy/gaussfitter.py>
"""
import numpy
from numpy.ma import median
from numpy import pi
#from scipy import optimize,stats,pi
from mpfi... | kirillzhuravlev/atrex | Software/gaussfitter.py | Python | lgpl-3.0 | 23,723 | [
"Gaussian"
] | 0f8d346f598f7890084a92d63cf6bd7e81c4007fa666aca150af9952d0bfd64e |
# miningInfoMultiplier
#
# Used by:
# Charges from group: Mining Crystal (30 of 30)
# Charges named like: Mining Crystal (32 of 32)
type = "passive"
def handler(fit, module, context):
module.multiplyItemAttr("specialtyMiningAmount",
module.getModifiedChargeAttr("specialisationAsteroidY... | Ebag333/Pyfa | eos/effects/mininginfomultiplier.py | Python | gpl-3.0 | 455 | [
"CRYSTAL"
] | 0656faf7abb5c263fb4a9c13872869c0e3f2c0100a0593fad60eefcaf56d7f23 |
#!/usr/bin/python
"""Test of learn mode."""
from macaroon.playback import *
import utils
sequence = MacroSequence()
sequence.append(KeyPressAction(0, None, "KP_Insert"))
sequence.append(TypeAction("h"))
sequence.append(KeyReleaseAction(0, None, "KP_Insert"))
sequence.append(PauseAction(2000))
sequence.append(KeyCo... | pvagner/orca | test/keystrokes/helpcontent/line_nav_main_page.py | Python | lgpl-2.1 | 13,921 | [
"ORCA"
] | 3d2ea157cdfa4566481686a210a2d63e0e3e04f45a2e5b13e58aa946755f6fe5 |
#! /usr/bin/python
import __main__
__main__.pymol_argv = ['pymol','-qc']
#__main__.pymol_argv = ['pymol','']
import sys,time,os
import pymol
pymol.finish_launching()
sys.path.append("/home/scratch/software/Pymol-script-repo-master")
import my_elbow_angle_ab
my_file = sys.argv[1]
chain1 = sys.argv[2]
chain2 = sys.arg... | demharters/git_scripts | calc_elbow_traj_ab.py | Python | apache-2.0 | 865 | [
"PyMOL"
] | 0741970c295a208aad12582add1c275b7c4c34bcfcf1d4494f8b912bd0578a83 |
""" ResourceStatus
Module use to switch between the CS and the RSS.
"""
import datetime
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.DIRACSingleton import DIRACSingleton
from DIRAC.ConfigurationSystem.Client.CSAPI ... | calancha/DIRAC | ResourceStatusSystem/Client/ResourceStatus.py | Python | gpl-3.0 | 9,871 | [
"DIRAC"
] | 3d6a874c0b7f8224b01771b2f955a2d77b123a797b2ec33165e35e92c3d85437 |
"""
Window functions (:mod:`scipy.signal.windows`)
==============================================
The suite of window functions for filtering and spectral estimation.
.. currentmodule:: scipy.signal.windows
.. autosummary::
:toctree: generated/
get_window -- Return a window of a given length and ... | scipy/scipy | scipy/signal/windows/__init__.py | Python | bsd-3-clause | 2,088 | [
"Gaussian"
] | b7ae642c15c5fb9537fb054914c029aed7190e21acb659cbbe5d039b9792af24 |
#!/usr/bin/python2.7
# Copyright 2010 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | google/apis-client-generator | src/googleapis/codegen/api.py | Python | apache-2.0 | 37,820 | [
"VisIt"
] | 39cea4327098ab29c51514c39c78415d8b13cae5f6099a8ad49a2c8cdb486069 |
#!/usr/bin/env python2
# Copyright (C) 2010 by Brian Parma
# Copyright (C) 2006 Adam Olsen
#
# 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 1, or (at your option)
# any later ve... | genodeftest/exaile | plugins/multialarmclock/__init__.py | Python | gpl-2.0 | 15,868 | [
"Brian"
] | f36eb2656c27c75096e1f4b0d213a0fccf020a2cc8280b8a2e4ebdf6e1076cbe |
# Publisher and subscriber design pattern example.
# More information about this design pattern can be found at:
# http://wiki.wxpython.org/ModelViewController
# http://wiki.wxpython.org/PubSub
import wx.lib.pubsub as ps
# The maintainer of Pubsub module is Oliver Schoenborn.
# Since the end of 2006 Pubsub is now main... | dfelinto/invesalius3 | docs/devel/example_pubsub.py | Python | gpl-2.0 | 2,611 | [
"VTK"
] | 0df046a4c21e29a5f7f440b7ff5a2dd26327fe4f9db8c64e5e8b4d7930063441 |
#!/usr/bin/env python
''' Author : Huy Nguyen
Program : providing 2 method to study operon functionality
1) Method 1: predict structure for each genes in each operon
do a docking for the genes structure in an operon
utilize structure alignment to predic... | nguyenngochuy91/class_projects | CS_569_ProteinStructure/project/retrieve_coordinate.py | Python | gpl-3.0 | 10,338 | [
"BLAST"
] | 3bcaa4afc5ea278af2c198f259a5117e95f9e0f7b5720aefc8cac938fce363c8 |
# This is only meant to add docs to objects defined in C-extension modules.
# The purpose is to allow easier editing of the docstrings without
# requiring a re-compile.
# NOTE: Many of the methods of ndarray have corresponding functions.
# If you update these docstrings, please keep also the ones in
# core... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/numpy/add_newdocs.py | Python | agpl-3.0 | 192,537 | [
"Brian"
] | e374be7d266220bec67753ffc6ebc44c302f1704264d3bad7d72c17a61589273 |
#! /usr/bin/python
from slides import Lecture, NumSlide, Slide, Bullet, SubBullet, PRE, URL
class Raw:
def __init__(self, title, html):
self.title = title
self.html = html
def toHTML(self):
return self.html
class HTML(Raw):
def __init__(self, html):
self.html = html
serve... | waseem18/oh-mainline | vendor/packages/twisted/doc/historic/2003/pycon/pb/pb-slides.py | Python | agpl-3.0 | 13,930 | [
"Brian"
] | 4eb8183fc81cbf4dfa94b78aee8ea7bf998447af8d342a6ac23ce7c67af73c27 |
"""Helper functions to handle AMI creation with packer"""
import boto
import os
import shutil
import subprocess
import logging
import urllib2
import csv
LOGGER = logging.getLogger('mmw')
UBUNTU_RELEASE_URL = 'http://cloud-images.ubuntu.com/query/trusty/server/released.current.txt' # NOQA
UBUNTU_RELEASE_FIELD_NAME... | kdeloach/model-my-watershed | deployment/packer/driver.py | Python | apache-2.0 | 4,848 | [
"Galaxy"
] | 9454c392d4d298d5d00814bfb9a558d1ce78a1a43af947451f740237e28c5c51 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/align.py | Python | gpl-2.0 | 54,194 | [
"Biopython",
"MDAnalysis"
] | bf6eaf35de5d285d44e8e5e27cd50747675b0e18a857cb6f8453761a65df4240 |
"""Read all matched data and make some plotting
"""
import os
import re
from glob import glob
import numpy as np
from matchobject_io import (readCaliopImagerMatchObj,
DataObject,
CloudsatImagerTrackObject,
readCloudsatImagerMatchObj,
... | adybbroe/atrain_match | atrain_match/reshaped_files_scr/pps_vrreport_plot_compare_lwp_pps_modislvl2.py | Python | gpl-3.0 | 6,293 | [
"Gaussian"
] | d94833c9877c40089ff626486e651d4ce39e6e8da29b5d38820574c9ee1c0f21 |
import numpy as np
from spectypes import Enum, Spline, Scalar, RefScalar, Map, List
from specs import toplevels
class Wrapper(object):
"""
Weird reverse visitor. Traversals of the tree are normally done externally
(via property accessors, in a lot of cases). This class alters the
returned representati... | stevenrobertson/cuburn | cuburn/genome/use.py | Python | gpl-2.0 | 7,147 | [
"VisIt"
] | e5d4a8011d97b4a486a0e3a23c1a035a30e07cd97510496180fca3f0f1df718c |
import numpy as np
import numpy.linalg as la
from pysal.spreg.utils import RegressionPropsY, spdot
import pysal.spreg.user_output as USER
from .utils import cache_readonly
from .base import LikelihoodModelResults
from . import family
from .iwls import iwls
__all__ = ['GLM']
class GLM(RegressionPropsY):
"""
G... | CartoDB/crankshaft | src/py/crankshaft/crankshaft/regression/glm/glm.py | Python | bsd-3-clause | 11,858 | [
"Gaussian"
] | 9628cdf08daf5f9a09178e9f0203b7f574c7177dce724658a604e7cac72a84e5 |
# ----------------------------------------
# USAGE:
# python input_file (output_file from avg_structure.py) pdb_file
# ----------------------------------------
# PREAMBLE:
import sys
import numpy as np
from numpy.linalg import *
import MDAnalysis
from MDAnalysis.analysis.align import *
from distance_functions import... | rbdavid/DENV-NS3h | Average_structure/weighted_average.py | Python | gpl-3.0 | 4,437 | [
"MDAnalysis"
] | c34e276022b4b9aadb348d4c761d1a49b9220c62c3d9f601ab9fa1ddbd383418 |
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 03 16:03:10 2015
@author: hanbre
"""
#Import required modules
import sys
import numpy as nmp
from mpl_toolkits.basemap import Basemap
import matplotlib
from matplotlib.pylab import *
import matplotlib.colors as colors
from mpl_toolkits.axes_grid1 import make_axes_locatab... | hansbrenna/NetCDF_postprocessor | plotter.py | Python | gpl-3.0 | 4,748 | [
"NetCDF"
] | b65a38bacaba7691c0173d3c7e3a5477880ab5e324d1cc2dfc5d95679692e5a5 |
# -*- coding: utf-8 -*-
#
# pymatgen documentation build configuration file, created by
# sphinx-quickstart on Tue Nov 15 00:13:52 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | specter119/custodian | docs_rst/conf.py | Python | mit | 9,488 | [
"pymatgen"
] | 52b771b3ffef1c2f224db36335a56a666eb309e6802bba4817fcf1f9e4d7fa0c |
# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
# Author: wangtaize@baidu.com
import cgi
import logging
import tempfile
import urllib
import urllib2
import json
from django.http impo... | bluebore/galaxy | platform/src/common/http.py | Python | bsd-3-clause | 10,148 | [
"Galaxy"
] | c6ecc4fc7ee0eb96eba4c6dae157ef9a754c3efbf7ac83898f53fa4d948d2f4f |
import scipy
from scipy import interpolate
from scipy.optimize.minpack import curve_fit
import numpy as np
import matplotlib.pyplot as plt
import sys
import random
from lmfit import Parameters, minimize, fit_report
from mcalculator_mod import calculateMPDF
from getmPDF import j0calc
def cv(x1,y1,x2,y2):... | benfrandsen/mPDFmodules_noDiffpy | fullfitmPDF_rhombo_nyquist_lmfit.py | Python | gpl-3.0 | 10,627 | [
"Gaussian"
] | ea861d8e3b1d1a092aac1fd0e9517c39389c1e64c74ab2ae742d08807b684ee0 |
"""Module level constants specifying available data"""
from datetime import datetime as dt
MIN_SEASON = 2008
"""Oldest season currently supported"""
MAX_SEASON = dt.today().year if dt.today().month < 10 else dt.today().year + 1
"""Year of the most recent season. Seasons are denoted by the year in which they end, i.... | Cophy08/nhlscrapi | nhlscrapi/constants.py | Python | apache-2.0 | 5,881 | [
"COLUMBUS"
] | 775f596112015d547318dd624a66d7d98101468f06912de44b0d9500c759b222 |
# ------------------------------------------------------------
# MC911 - Compiler construction laboratory.
# IC - UNICAMP
#
# RA094139 - Marcelo Mingatos de Toledo
# RA093175 - Victor Fernando Pompeo Barbosa
#
# astnodevisistor.py
# AST Generic Node Visitor
#
# ----------------------------------------------------------... | MC911-MV-1s2016/lya-compiler-python | lyacompiler/astnodevisitor.py | Python | bsd-3-clause | 3,332 | [
"VisIt"
] | 43eee3c34fd18d5bd871ba5a171ae44150c9401c9d5effa2c24884137f13e944 |
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms of the
#** GNU Lesser General Public License ... | BhallaLab/moose-examples | paper-2015/Fig6_NetMultiscale/Fig6BCDE.py | Python | gpl-2.0 | 38,657 | [
"Gaussian",
"MOOSE",
"NEURON"
] | f3e17d4ddce87286a2f9f9a264dd843c3ad30c6c062b5ba993edcd304509b7d0 |
"""Test script for the bsddb C module by Roger E. Masse
Adapted to unittest format and expanded scope by Raymond Hettinger
"""
import os, sys
import unittest
from test import test_support
# Skip test if _bsddb wasn't built.
test_support.import_module('_bsddb')
bsddb = test_support.import_module('bsddb', deprecated... | HiSPARC/station-software | user/python/Lib/test/test_bsddb.py | Python | gpl-3.0 | 11,976 | [
"Brian"
] | 5bd1ef77f0acd1608725982a584a2435f176d5a35b992e307095a8e4112581e8 |
import ckan.lib.helpers as h
import ckan.lib.base as base
import requests
from urlparse import urlparse, parse_qs
from pylons import config
import ckan.plugins.toolkit as tk
import logging
import ckan.model as model
import ckan.logic as logic
import ckan.lib.uploader as uploader
import ckan.lib.navl.dictization_functi... | ccca-dc/ckanext-thredds | ckanext/thredds/controllers/proxy.py | Python | gpl-3.0 | 2,310 | [
"NetCDF"
] | b0abc5567412429ceedd142e375350043cacaac523d5e797696a603fa2839559 |
from scipy.stats import norm
from numpy import array, polyval, inf, asarray
__all__ = ['mackinnonp','mackinnoncrit']
# These are the cut-off values for the left-tail vs. the rest of the
# tau distribution, for getting the p-values
tau_star_nc = [-1.04, -1.53, -2.68, -3.09, -3.07, -3.77]
tau_min_nc = [-19.04,-19.62,-... | detrout/debian-statsmodels | statsmodels/tsa/adfvalues.py | Python | bsd-3-clause | 17,465 | [
"ADF"
] | 4dde9210f0162cfc16849e4f49c42e3e95c614e6b160e208a098464ca8de7132 |
#!/usr/bin/env python
from FIS import *
# Variables
service = LinguisticVariable('service')
service.addMF('poor',MF.Gaussian(1.5,0.0))
service.addMF('good',MF.Gaussian(1.5,5.0))
service.addMF('excelent',MF.Gaussian(1.5,10))
food = LinguisticVariable('food')
food.addMF('rancid',MF.Trapezoidal(0.0, 0.0, 1.0, 3.0))
foo... | mariosky/protoboard | FIS/Tip.py | Python | apache-2.0 | 1,362 | [
"Gaussian"
] | e34ada6426b32562dbc4bea55b6d68bce8cf3410414a104b08083fb9ef813db2 |
"""Prototype routine to read in EEG dataset in EEGlab format, and return in epoched form.
To be integrated into PyMVPA later.
brian.murphy@unitn.it, 17th June 2010.
"""
### DEV NOTES ###
#
#################
# IMPORT LIBRARIES
# python numerical stuff
import scipy.io as Sio
import numpy as N
#import pylab as P
# logg... | vansky/meg_playground | scripts/protoReadExtractEEGlabICAcomps.py | Python | gpl-2.0 | 7,864 | [
"Brian"
] | e68aa635b165fc645d2729c7b70ee27b28c7cc9bfae2915d5cdb6f40d13526ab |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ve... | vidartf/hyperspy | hyperspy/tests/model/test_set_parameter_value.py | Python | gpl-3.0 | 3,909 | [
"Gaussian"
] | 80d6cd23c6ee2cab0a289c1566a4f91e236965b9576abe82ffb2b0e73944d4db |
# vim: set ts=2 expandtab:
# -*- coding: utf-8 -*-
"""
Module: slingbox.py
Desc: Control a local slingbox player in IRC via keypresses
Author: on_three
Email: on.three.email@gmail.com
DATE: Sunday, August 31st 2014
"""
import string
import re
#from pytz import timezone
#from datetime import datetime
... | on-three/weeabot | weeabot/slingbox.py | Python | mit | 16,498 | [
"VisIt"
] | f525e28ca8964a14a5cb6b5fdfea4524e93b4d2c29f55e06504ab768233fe888 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-install-mysql
# Author : Ricardo Graciani
########################################################################
"""
Install MySQL. The clever way to do this is to use the
dirac-admin-sysadmin... | petricm/DIRAC | Core/scripts/dirac-install-mysql.py | Python | gpl-3.0 | 766 | [
"DIRAC"
] | 964a3fc2428f97b85ecad2bc435b4423b0fe0697cc797609a5a04341c05beae2 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to communicate with the device via the adb command.
Assumes adb binary is currently on system path.
"""
# pylint: disable-all
... | sencha/chromium-spacewalk | build/android/pylib/android_commands.py | Python | bsd-3-clause | 72,756 | [
"Galaxy"
] | 67b32f012d20e0b1c12733ad05b023f8a673035e6bfa05d7e10197e48f72dd6e |
# -*- coding: utf-8 -*-
#GSASIImath - major mathematics routines
########### SVN repository information ###################
# $Date: 2018-06-14 01:48:33 +0300 (Thu, 14 Jun 2018) $
# $Author: vondreele $
# $Revision: 3434 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIImath.py $
# $Id: GSASIImath... | AntonGagin/GSAS_USE | patchSystErrors/modifiedOld/GSASIImath.py | Python | gpl-3.0 | 212,391 | [
"CRYSTAL"
] | 5e2a0268765af32ed5c6ef854a99055f5a0e955b89e851cda187d37f44bde422 |
#!/usr/bin/env python
#App="$1" # argument is the application to fixup
#LibrariesPrefix="Contents/Libraries"
#echo ""
#echo "Fixing up $App"
#echo "All required frameworks/libraries will be placed under $App/$LibrariesPrefix"
#echo ""
#echo "----------------------------"
#echo "Locating all executables and dylibs alr... | Sprunth/RGG | superbuild/Projects/apple/fixup_bundle.py | Python | bsd-3-clause | 13,298 | [
"ParaView"
] | 514ff1859a073912cd4598c78205d9e1a4d505972dd21922987a602705828ce9 |
# -*- coding: utf-8 -*-
"""Tests for :mod:`pybel.struct.summary`."""
| pybel/pybel | tests/test_struct/test_summary/__init__.py | Python | mit | 70 | [
"Pybel"
] | cc510049dadd6946b376ca4357a2da1a6da18cf5fb1cdb7cf0a7c9a7941afb1a |
#!/usr/bin/env python
"""
This is a script for quick Mayavi-based visualizations of finite element
computations results.
Examples
--------
The examples assume that run_tests.py has been run successfully and the
resulting data files are present.
- view data in output-tests/test_navier_stokes.vtk
$ python po... | lokik/sfepy | postproc.py | Python | bsd-3-clause | 20,588 | [
"Mayavi",
"VTK"
] | 55539c042f7cc219da919f899eb62484d1b0fae7b2b95345cb4f5dd67bbb6907 |
### author: alessio.marcozzi@gmail.com
### version: 2019_10
### licence: MIT
### requires Python >= 3.6
from Bio import pairwise2, Entrez, SeqIO
from Bio.SubsMat import MatrixInfo as matlist
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast import NCBIXML
import tensorflow as tf
from urllib.r... | 25shmeckles/alefuncs | alefuncs.py | Python | mit | 154,091 | [
"BLAST",
"Dalton"
] | b0e5f0afe0d997a0bc720926ee8d795fcd93b83f35d14108055d6aacc08f3c32 |
# CRU TS3.1 Run -- January 2016
import glob, os, itertools
from downscale import DownscaleCRU
input_path = '/Data/Base_Data/Climate/World/CRU_grids/CRU_TS323'
# static args setup
cru_ts = '/Data/Base_Data/Climate/World/CRU_grids/CRU_TS323/cru_ts3.23.1901.2014.cld.dat.nc'
clim_path = '/workspace/Shared/Tech_Projects/... | ua-snap/downscale | snap_scripts/epscor_sc/older_epscor_sc_scripts_archive/run_cru_snap.py | Python | mit | 1,214 | [
"NetCDF"
] | f4d5891466949b6da0521e84675f7ff11cf6b0eab01848dc3df3ae189250cfde |
"""Test enum support in VTK-Python
Created on Nov 13, 2014 by David Gobbi
"""
import sys
import exceptions
import vtk
from vtk.test import Testing
class TestEnum(Testing.vtkTest):
def testGlobalNamespaceEnum(self):
"""Check that an enum in the global namespace was wrapped.
"""
# defined i... | msmolens/VTK | Common/Core/Testing/Python/TestEnums.py | Python | bsd-3-clause | 1,553 | [
"VTK"
] | 0de01ae41bad0ed0b86fe50e591717958348804de2efe7a8883a6ed154e9125b |
""" Utility for loading plotting types.
Works both for Accounting and Monitoring.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import re
from DIRAC.Core.Utilities.ObjectLoader import loadObjects
from DIRAC.AccountingSystem.Client.Types.BaseAccou... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Plotting/TypeLoader.py | Python | gpl-3.0 | 1,672 | [
"DIRAC"
] | 0c530ca482bf81442532b47dc7b1219a5e37652aa10924416668f7b661f8ab54 |
import operator
import numpy as np
import sys
if sys.argv[0] != "gen_py.py":
from api_autogen import *
import cgt
from . import core, utils
# Every non-underscored function in this file should have a docstring, and it should enforce that the input data is valid
# ==================================================... | hojonathanho/cgt | cgt/api.py | Python | mit | 23,217 | [
"Gaussian"
] | d533dbf3adb3186d491c22def982a19365e191e6cf2caffef30da708f820a0fe |
# 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 PySpglib(PythonPackage):
"""Python bindings for C library for finding and handling
cry... | LLNL/spack | var/spack/repos/builtin/packages/py-spglib/package.py | Python | lgpl-2.1 | 884 | [
"CRYSTAL"
] | 8c6f989e6b29900a4cd42d9846d2a02d47bdd7dd44dd29679c3063101a29f180 |
from dirac.tests import *
class TestConfigurationController(TestController):
def test_index(self):
response = self.app.get(url_for(controller='systems/configuration'))
# Test response...
| DIRACGrid/DIRACWeb | dirac/tests/functional/test_systems_configuration.py | Python | gpl-3.0 | 209 | [
"DIRAC"
] | eb0b671718d03b57f4b2e5f80543bd05893bc82a3061f7c1d2c2a97568cd096e |
#! /usr/bin/env python
from openturns import *
TESTPREAMBLE()
RandomGenerator.SetSeed(0)
try:
# this analitycal example is taken from "Bayesian Modeling Using WinBUGS" - Ioannis Ntzoufras
# 1.5.3: Inference for the mean or normal data with known variance
# Variable of interest: Y=N(mu, sigma)
# Pri... | dbarbier/ot-svn | python/test/t_RandomWalkMetropolisHastings_std.py | Python | gpl-3.0 | 3,003 | [
"DIRAC"
] | 51426fddb8fb7bc978a685c5257e4ea653c5f5882a72bb6462be37b7e8a9fa2a |
# Author: Meduri Venkata Shivaditya
import superimport
import math
import matplotlib.pyplot as plt
import numpy as np
from scipy.special import logsumexp
'''
z = Wx + µ + E
the equation above represents the latent variable model which
relates a d-dimensional data vector z to a corresponding q-dimensional
latent vari... | probml/pyprobml | scripts/mixPpcaDemo.py | Python | mit | 10,716 | [
"Gaussian",
"VisIt"
] | 74ddda2268c8f8b653d8507f9823fdb5bd72bf32a4bdd712bb74092604c888c5 |
import json
from typing import Optional
import pandas as pd
#!!! This giant block of imports should be something simpler, such as:
# from great_exepectations.helpers.expectation_creation import *
from great_expectations.execution_engine import PandasExecutionEngine
from great_expectations.expectations.expectation imp... | great-expectations/great_expectations | contrib/experimental/great_expectations_experimental/expectations/expect_column_pair_values_foreign_keys_in_column_A_to_exist_in_column_B.py | Python | apache-2.0 | 10,723 | [
"VisIt"
] | bc6b364a9c5197f0437825dfe89069cfcac8d002e34118b39595ca1a81dd15e1 |
#!/usr/bin/python
# This function returns an m by n array, X, in which
# each of the m rows has the n Cartesian coordinates
# of a random point uniformly-distributed over the
# interior of an n-dimensional hypersphere with
# radius r and center at the origin. The function
# 'randn' is initially used to generate ... | magicknight/Purgatory | Python/lesion_sphere.py | Python | gpl-2.0 | 1,636 | [
"Mayavi"
] | 66bdbc83b3b3e06c5bf1aa56fae377ee0369f000b8734e9c1663ea64ee0ca0ff |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Brian Coca <briancoca+ansible@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1... | Tatsh-ansible/ansible | lib/ansible/modules/system/debconf.py | Python | gpl-3.0 | 5,418 | [
"Brian"
] | 020eb2b5e6140b8e939b2c8fbebe01f625b12af39dab849c806ed75b1d503672 |
# -*- mode: python; coding: utf-8 -*-
# Copyright 2017 the HERA Collaboration
# Licensed under the 2-clause BSD license.
"""Testing for `hera_mc.qm`."""
import os
import pytest
from astropy.time import Time, TimeDelta
from .. import mc
from .. import utils
from ..tests import checkWarnings
from ..qm import AntMetric... | HERA-Team/hera_mc | hera_mc/tests/test_qm.py | Python | bsd-2-clause | 11,782 | [
"exciting"
] | bed910a820394277ffba19f06d1e1a237465e3f26c4585e3739bff21f9025e74 |
import os
from rdkit import Chem
import glob
import json
import numpy as np
if not os.path.exists('data'):
os.mkdir('data')
print('made directory ./data/')
download_path = os.path.join('data', 'dsgdb9nsd.xyz.tar.bz2')
if not os.path.exists(download_path):
print('downloading data to %s ...' % d... | Microsoft/gated-graph-neural-network-samples | get_data.py | Python | mit | 3,388 | [
"RDKit"
] | 09ce6d8ac0353460c00592a4b5820a7269423994cc103ad5d73b363c56c0d9c5 |
r"""
Sequences (:mod:`skbio.sequence`)
=================================
.. currentmodule:: skbio.sequence
This module provides classes for storing and working with sequences, including
generic/nonbiological sequences which have no alphabet restrictions
(``Sequence``) and sequences based on IUPAC-defined alphabets (`... | kdmurray91/scikit-bio | skbio/sequence/__init__.py | Python | bsd-3-clause | 7,740 | [
"scikit-bio"
] | 95a43bcca27b3095a790b71b6f64845c0c615e1a8b17badd97557225f9c6af1b |
"""Provide the Subreddit class."""
# pylint: disable=too-many-lines
import socket
from copy import deepcopy
from csv import writer
from io import StringIO
from json import dumps, loads
from os.path import basename, dirname, isfile, join
from typing import TYPE_CHECKING, Any, Dict, Generator, Iterator, List, Optional, ... | praw-dev/praw | praw/models/reddit/subreddit.py | Python | bsd-2-clause | 144,740 | [
"VisIt"
] | 4c781efc7ac9c024f64cc63e4176019443f3a42aef5a9f8636eec209e7d8d626 |
"""
sectors.py
==========
Models for standard sectors.
Copyright 2016 Brian Romanchuk
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 requi... | brianr747/SFC_models | sfc_models/sector_definitions.py | Python | apache-2.0 | 23,361 | [
"Brian"
] | 382411f37b53c70cc90c75a12e0923ed8f862752a9b1242ef57283cc3fa50b5e |
import json
import requests
import sys
STOP_MONITORING_ENDPOINT = 'http://bustime.mta.info/api/siri/stop-monitoring.json'
FEET_PER_METER = 3.28084
FEET_PER_MILE = 5280
class StopStatus(object):
def __init__(self, api_key, stop_id, route=None, max_visits=3):
self.api_key = api_key
self.stop_id = stop_id
... | celeryclub/bustime | bustime/stop.py | Python | bsd-2-clause | 2,289 | [
"VisIt"
] | 2b5fc28e73dc57a50b82239e02c11c7dc6e14a67b73b8379a0417d504c68b50b |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 12 11:11:45 2018
@author: epnevmatikakis
"""
import logging
import matplotlib.pyplot as plt
import numpy as np
import scipy.sparse
from typing import List
import time
import caiman
from .utilities import detrend_df_f, decimation_matrix
from .spati... | agiovann/Constrained_NMF | caiman/source_extraction/cnmf/estimates.py | Python | gpl-2.0 | 75,132 | [
"NEURON"
] | 688436ebb36d149a7a701428efefd8fb586aeaf56a34cd9a6c4defac4de01062 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright (c) 2013 Kai Kratzer, Universität Stuttgart, ICP,
# Allmandring 3, 70569 Stuttgart, Germany; all rights
# reserved unless otherwise stated.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public Licen... | freshs/freshs | scripts/ffs_buildTree_success.py | Python | gpl-3.0 | 4,984 | [
"ESPResSo",
"VisIt"
] | ee15a50e733fe4840e5371661e994cb5dfb8ceb08df7b128441cb42753caf764 |
# -*- coding: utf-8 -*-
# IV_curve.py analysis class for IV like transport measurements
# Micha Wildermuth, micha.wildermuth@kit.edu 2019
# 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 ... | qkitgroup/qkit | qkit/analysis/IV_curve.py | Python | gpl-2.0 | 113,949 | [
"Gaussian"
] | addb347976cc503779aee6bd41d958bd2388a198ed746ed6ec94f3aac501759c |
'''
optics elements
'''
# from numpy import sin, cos, pi, sqrt, log, array, random, sign
#from numpy.linalg import norm
import numpy as np
def debug(*args):
print(' '.join( map(str, args) ))
def warn(*args):
print(' '.join( map(str, args) ))
def info(*args):
print(' '.join( map(str, args) ))
class Op... | ocelot-collab/ocelot | ocelot/optics/elements.py | Python | gpl-3.0 | 8,588 | [
"CRYSTAL"
] | 675a6a49e53ba87cadda2e9d247bb773af52bec1a47a7b35bfe9e9344b86df01 |
# Copyright 2012-2014 Brian May
#
# This file is part of python-tldap.
#
# python-tldap 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.... | brianmay/python-tldap-debian | tldap/schemas/rfc.py | Python | gpl-3.0 | 7,232 | [
"Brian"
] | f23cafe6f47ce82e89693677f07cf70ba59cfd2769a672c09f846588264f4409 |
"""
Bok choy acceptance tests for conditionals in the LMS
"""
from __future__ import absolute_import
from capa.tests.response_xml_factory import StringResponseXMLFactory
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAut... | jolyonb/edx-platform | common/test/acceptance/tests/lms/test_conditional.py | Python | agpl-3.0 | 4,891 | [
"VisIt"
] | aec1f9d2d998187ebaadd7e81433d1add58dca25f905f5bc77d171b6cc9d9856 |
#!/usr/bin/env python
# coding=utf-8
''' A module containing code relating to Matrices. '''
from __future__ import division
__author__ = 'Tom Wright <tom.tdw@gmail.com>'
# Copyright 2012 Thomas Wright <tom.tdw@gmail.com>
# This file is part of C1000 Intelligent Calculator.
#
# C1000 Intelligent Calculator is free softw... | twright/C1000-Intelligent-Calculator | cas/matrices.py | Python | gpl-3.0 | 12,590 | [
"Gaussian"
] | 8a14fcedb1eb8752baa7c6f8ade8cd527aa06d8f2a1e27a704c2ee8522510f1c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
from monty.json import MSONable
from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
from pymatgen.analysis.local_env import OpenBabelNN
from pymatgen.io.babel import BabelMol... | dongsenfo/pymatgen | pymatgen/analysis/fragmenter.py | Python | mit | 8,264 | [
"pymatgen"
] | ea7bf96b96a50cfd5a345c18ec0fdf907377ef76c7e6cfde03865d885b5ef479 |
import pysam
import argparse
parser = argparse.ArgumentParser(description='drop pairs that have anomalous insert sizes')
parser.add_argument('--bam_out', type=argparse.FileType('w'), required=True)
parser.add_argument('--bam_in', type=argparse.FileType('rb'), required=True)
parser.add_argument('--mean', type=int, req... | CSB-IG/hmgb1_rna_seq | drop_pairs_with_long_inserts.py | Python | gpl-3.0 | 801 | [
"pysam"
] | 838864d883bffc50221071190a94cdfcc701353871c0afc1e608a2b365576853 |
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING #
# Under development #
# ##WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING###WARNING#... | fstagni/DIRAC | Workflow/Modules/UploadOutputs.py | Python | gpl-3.0 | 3,366 | [
"DIRAC"
] | 446d1d0fc296106d94ad7c01aecf3a7c348a9c92279764a7cc5a74ded70d2fe9 |
'''
This script implements ***part of the "Model C" analyses from:
Pataky TC, Koseki M, Cox PG (2016) Probabilistic biomechanical
finite element simulations: whole-model classical hypothesis testing
based on upcrossing geometry. PeerJ Computer Science. (in press)
See README.txt for a list of steps required to get... | 0todd0000/probFEApy | modelC/modelC.py | Python | mit | 5,349 | [
"VTK"
] | bca41f7f422359949d4a34124fe898d7965c9b63e8a5e717ec307f9b6c7c90aa |
import sys
import time
import atexit
def paropen(name, mode='r', buffering=0):
"""MPI-safe version of open function.
In read mode, the file is opened on all nodes. In write and
append mode, the file is opened on the master only, and /dev/null
is opened on all other nodes.
"""
if rank > 0 and ... | freephys/python_ase | ase/parallel.py | Python | gpl-3.0 | 1,947 | [
"ASE",
"GPAW"
] | 415fe9da4d50cede616ad869ecd92c26f8b7f1e81437e5168d42e29515e761af |
"""
This is a simple demonstration on how to use the SpaceTime VTK output
for levelset-based moving domain problems in 2D. A circle is travelling
around in a squared background domain. A piecewise linear-in-space
approximation of the level set geometry is taken as an initial
approximation. A space-time mesh deformation... | ngsxfem/ngsxfem | demos/spacetime/spacetime_vtk.py | Python | lgpl-3.0 | 3,090 | [
"VTK"
] | 84a1ee7c9800a3fbca36cdcc9c866e47cc4d71dc172d75748bf4cad39d96d481 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Nov 10, 2012
@author: shyue
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__status__ = "Production"
__dat... | ctoher/pymatgen | pymatgen/core/tests/test_composition.py | Python | mit | 16,583 | [
"pymatgen"
] | 6d9a0c2f3ae2698a1546d11674dff19fa3a5eb314acf6c14987cb19fa8a9f9f5 |
"""
This script reproduces Fig. 1 of Izhikevich (2004).
Original implementation references:
Izhikevich E.M. (2004) Which Model to Use for Cortical Spiking Neurons?
IEEE Transactions on Neural Networks, 15:1063-1070 (special issue on temporal coding)
Izhikevich E.M. (2003) Simple Model... | OpenSourceBrain/IzhikevichModel | PyNN/izhikevich2004.py | Python | bsd-3-clause | 16,172 | [
"Brian",
"NEURON"
] | dfc6f746eb5fe652bccffbbf0530c5e4f02d8eafdb3b305214fe2b0bb2990a59 |
#!/usr/env/python
"""
child2vtk.py: Python version of Vincent Godard's child2vtk.f95 utility for
converting CHILD model output to vtk format.
Created GT Oct 2013
"""
import sys # for command-line arguments
import numpy
from readchild import *
_CHILD_REQUIRED_FILES = {
'node' : 'nodes',
'elevation' : 'z',... | childmodel/child | Child/Postproc/childtools/child2vtk.py | Python | mit | 9,805 | [
"VTK"
] | f8e5883c05ce6037e73b3eedd12216023f52fe589fcdde1eaffb035a3162f19c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to interface with the Materials Project REST
API v2 to enable the creation of data structures and pymatgen objects using
Materials Project data.
To make use of the Materials AP... | mbkumar/pymatgen | pymatgen/ext/matproj.py | Python | mit | 63,500 | [
"ABINIT",
"VASP",
"pymatgen"
] | 1c474cdfead4dc64b3fcd9763b00fc8998bce50675a0c426b2138fa17aaaab01 |
import time
import random
import math
def wineprice(rating,age):
peak_age=rating-50
# Calculate price based on rating
price=rating/2
if age>peak_age:
# Past its peak, goes bad in 10 years
price=price*(5-(age-peak_age)/2)
else:
# Increases to 5x original value as it
# approach... | jonhare/COMP6237 | app/src/main/resources/uk/ac/soton/ecs/comp6237/l9/optimization.py | Python | bsd-3-clause | 5,761 | [
"Gaussian"
] | f8aba76b6b6d4bcb7757032a56292ae28a3efbd0beb112828c779fea4ad366a5 |
# -*- coding: utf-8 -*-
# Copyright 2007-2011 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | sem-geologist/hyperspy | hyperspy/tests/model/test_model_selection_criteria.py | Python | gpl-3.0 | 1,804 | [
"Gaussian"
] | 1ca0f10b09c800867e6d56971b1ec50edff0d41a63396bbe58dfd9742bb7e72c |
# Copyright (C) 2012-2015 by the Free Software Foundation, Inc.
#
# This file is part of GNU Mailman.
#
# GNU Mailman is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at you... | yland/mailman3 | src/mailman/runners/tests/test_confirm.py | Python | gpl-2.0 | 10,549 | [
"VisIt"
] | e9d69340251a03c5f45b7aa1ae136ce28f94e8685b95f74f1e2b1927764f5c43 |
# -*- coding: utf-8 -*-
"""Tests for node utilities."""
import unittest
from pybel import BELGraph
from pybel.dsl import Protein
from pybel.testing.utils import n
from pybel_tools.mutation.collapse import collapse_nodes_with_same_names
class TestMerge(unittest.TestCase):
def test_merge_nodes_by_name(self):
... | pybel/pybel-tools | tests/test_node_utils.py | Python | mit | 1,214 | [
"Pybel"
] | f76db595dd7c8052d5ad7f689c277ff005cc21c54108b4d742792397f12c6bb4 |
# -*- coding: utf-8 -*-
""" GIS Module
@requires: U{B{I{gluon}} <http://web2py.com>}
@requires: U{B{I{shapely}} <http://trac.gispython.org/lab/wiki/Shapely>}
@copyright: (c) 2010-2015 Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaini... | Lokke/eden | modules/s3/s3gis.py | Python | mit | 394,601 | [
"Amber"
] | 3a7716688e39c702de109fcea620b217132361a14511a0b9b29cec1faec4a135 |
#!/usr/bin/env python
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | nelsonsar/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 6,195 | [
"Galaxy"
] | 683b09b5a15a06c9ae9307a17aa8be7aaac4c86b19e8b20208e678be3dc02005 |
#!/usr/bin/env python
"""
# Created: Mon, 18 Mar 2013 11:57:13 +1000
Quick example test of Dryad script. Just run 'python Dryad-Example.py -v'.\
Requires reference genes and remote file list. (Default: all_mlst.fna \
and GB-loc in runex dir)
Dependencies include:
* BLAST+
* MUSCLE
* Biopython
Be sure... | happykhan/Dryad-SA | runex/Dryad-Example.py | Python | gpl-3.0 | 6,963 | [
"BLAST",
"Biopython"
] | 9913ddbd71751270af7717a6432458f3d7742c755c7cdd0a50ffd8cd43dd3e7d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Complete pipeline for CaImAn online processing and comparison with consensus
annotation. The script processes one (or more) of the provided datasets and
compares against the consensus annotations. It generates three figures:
i) contour plots of the detected components... | agiovann/Constrained_NMF | caiman/tests/comparison_humans_online.py | Python | gpl-2.0 | 14,161 | [
"NEURON"
] | 40774e4d5f654f15f6abb316c916acc37d9e588e9ea0aa53f88782b2cd5c2864 |
#!/usr/bin/env/python
from __future__ import print_function
import MDAnalysis as mda
import numpy as np
from silicanet import SilicaNetwork
if __name__ == '__main__':
u = mda.Universe('SiO2_protein_0.17.pdb')
ntw = SilicaNetwork(u.select_atoms('resname SIL'))
ntw.set_connections(1.7) # generous bond dista... | jmborr/confinedBSA | simulation/silica/cristobalite/confineBSA/poretop/evaluate_bonding.py | Python | mit | 1,349 | [
"MDAnalysis"
] | 210619559a338c203befcecfc1e66eeb9e55749f8fe5b12a9cdf43277a3db5c5 |
"""Qt implementation of _Renderer and GUI."""
# Authors: Guillaume Favelier <guillaume.favelier@gmail.com>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
from contextlib import contextmanager
from functools import partial
import pyvista
from PyQt5.QtCore import Qt, pyqtSignal, QLocale
... | kambysese/mne-python | mne/viz/backends/_qt.py | Python | bsd-3-clause | 19,863 | [
"VTK"
] | dccad3e6002ff1e62afe046f845f5b746810b3ed98bae1fb88db514f86f6e50f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# /***************************************************************************
# * Copyright (C) 2015 by Thibault Bouttevin *
# * thibault.bouttevin@gmail.com *
# * www.legalethurlant.fr.st ... | TiboLGH/solextronic | firmware/tools/varUpdater.py | Python | gpl-3.0 | 41,610 | [
"ASE",
"VisIt"
] | aa2169b1f02a0af2253417bea571d216d14f1b896ee3500ad76182f33e85c647 |
"""
@name: Modules/Housing/Irrigation/irrigation_data.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2018-2020 by D. Brian Kimmel
@note: Created on Feb 9, 2018
@license: MIT License
@summary:
"""
__updated__ = '2019-12-30'
# Import system type stuff
# Import PyMh fi... | DBrianKimmel/PyHouse | Project/src/Modules/House/Irrigation/irrigation_data.py | Python | mit | 1,659 | [
"Brian"
] | e41a71acd8464300800b5065849387f287994a2e534697878acc72de76f5bd2e |
"""Module for automatic calculation of an equation of state in jasp."""
from jasp import *
from ase.calculators.vasp import Vasp
import json
from ase.utils.eos import EquationOfState
import matplotlib.pyplot as plt
from ase.units import GPa
def get_eos(self, static=False):
'''calculate the equation of state for... | jboes/jasp | jasp/jasp_eos.py | Python | gpl-2.0 | 10,605 | [
"ASE",
"VASP"
] | eb701e89e025af75740bbac81ea18863d33bbbc3eca48dd5d9869dd949b122c3 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# Based on Bio.Nexus, 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 pa... | zjuchenyuan/BioWeb | Lib/Bio/Phylo/NewickIO.py | Python | mit | 12,468 | [
"Biopython"
] | 832dbd41c86edbb219a0fbac8561751f18bedff4218fe6f35947d6c2a3d9672d |
import argparse
from ddapp.consoleapp import ConsoleApp
from ddapp import cameraview
from ddapp import vtkAll as vtk
def parseChannelArgument(defaultChannel='CAMERA_LEFT'):
parser = argparse.ArgumentParser()
parser.add_argument('-c', '--channel', type=str, help='image channel', default=defaultChannel)
ar... | gizatt/director | src/python/tests/testImageView.py | Python | bsd-3-clause | 1,089 | [
"VTK"
] | f808ccbafac7011a5875b26f94e6ee5c7d49f9c7a25b023922cc45b466936588 |
"""
Converts some ActionScript syntax to C# syntax, and some C# to ActionScript.
cd as2cs
"""
import codecs
from collections import Iterable
from os import path
from pprint import pformat, pprint
from pretty_print_code.pretty_print_code import format
from simpleparse.error import ParserSyntaxError
from simplepars... | ethankennerly/as2cs | as2cs.py | Python | mit | 28,285 | [
"VisIt"
] | 7f5840a65c11d04bab53258b12f6bf6ad2fefb10337d2554c113145b53f8378d |
# -*- coding: utf-8 -*-
#
# This file is part of PyGaze - the open-source toolbox for eye tracking
#
# PyGazeAnalyser is a Python module for easily analysing eye-tracking data
# Copyright (C) 2014 Edwin S. Dalmaijer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GN... | esdalmaijer/EyeTribe_test | analysis/pygazeanalyser/gazeplotter.py | Python | gpl-3.0 | 14,263 | [
"Gaussian"
] | 73b9cddd6e0a291363c44d439ecfea1b85296ada7d34fef51ba7968d2ab1d2ce |
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