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# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | chemelnucfin/tensorflow | tensorflow/python/keras/optimizer_v2/learning_rate_schedule.py | Python | apache-2.0 | 38,679 | [
"Gaussian"
] | 363e9d78f9a82bb494b08ef0a636fbd97d2cf0df32094aeb667fd263f326d4d9 |
# -*- coding: utf-8 -*-
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
if __name__ == '__main__':
print """\
You are using the wrong setup.py script! This setup.py defines a
Setup class used to hold the atomic data needed for a specific atom.
For building the GPAW c... | ajylee/gpaw-rtxs | gpaw/setup.py | Python | gpl-3.0 | 39,336 | [
"ASE",
"GPAW"
] | c44c848ac90d9d62d2cdc820e4e1a3fc87b5b89cb0b9b9db20fc1c737ce15072 |
#! /usr/bin/python
"""
Split into windows.
usage: %prog input size out_file
-l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
"""
import sys, re, os
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.cookbook import doc_optparse
from galaxy.tools.util.galax... | volpino/Yeps-EURAC | tools/regVariation/windowSplitter.py | Python | mit | 2,834 | [
"Galaxy"
] | 46357c98e6f042cd621c25421d8fb5fb08649b46947dbf48a83223dc43cfaf95 |
import sys
sys.path.append('../../..')
sys.path.append('.')
from mupif import VtkReader2
from mupif import Model
from mupif import FieldID
import pyvtk
import logging
log = logging.getLogger()
import mupif.physics.physicalquantities as PQ
timeUnits = PQ.PhysicalUnit('s', 1., [0,0,1,0,0,0,0,0,0])
##
vtkreader2.pyv... | mupif/mupif | obsolete/examples/Example07-micress-local/Micress.py | Python | lgpl-3.0 | 1,447 | [
"VTK"
] | 22089c97f9ebfd6d13e99d5af2e31e2cffaa50e4614ed5fd609ac447214e5be1 |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Wed Nov 19 00:18:55 2014
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 2 of the License, or
(at your option) any later version.
... | SamWitte/Codds_DarkMatter | src/Data/CDMSlite2013CoGeNTQ.py | Python | gpl-2.0 | 11,135 | [
"Gaussian"
] | d1facc7c2d405d47383f6182896dfae6c5d8d364156a3e6f120638c892284717 |
# Copyright (c) 2012-2015 The GPy authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
import scipy
from ..util.univariate_Gaussian import std_norm_cdf, std_norm_pdf
import scipy as sp
from ..util.misc import safe_exp, safe_square, safe_cube, safe_quad, safe_three_ti... | mikecroucher/GPy | GPy/likelihoods/link_functions.py | Python | bsd-3-clause | 4,019 | [
"Gaussian"
] | 23f41069264c15b13dfb0556ddb6d339f9c8bec01c18c462c9bfebe85b12ce51 |
from django.conf.urls import include, url
# from django.conf import settings
from django.contrib import admin
from wagtail.wagtailadmin import urls as wagtailadmin_urls
from wagtail.wagtaildocs import urls as wagtaildocs_urls
from wagtail.wagtailcore import urls as wagtail_urls
from wapps import urls as wapps_urls
f... | apihackers/wapps | tests/app/urls.py | Python | mit | 1,001 | [
"VisIt"
] | 2eda3ff657bbbf02a9540c59d0a16d311332d42a5ed5af49ccbf8c11ddc23189 |
import os, sys
sys.path.append(os.getcwd())
import random
import time
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import tensorflow as tf
import sklearn.datasets
import tflib as lib
import tflib.ops.linear
import tflib.plot
MODE = 'wgan-gp' # wgan or wgan-gp
DATASET = ... | aalitaiga/improved_wgan_training | gan_toy.py | Python | mit | 7,675 | [
"Gaussian"
] | 780ef574882abff5f29aadd2001ef205aaafd44efa7a7cff5ebfb36c8060a2b7 |
# 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 Grass(AutotoolsPackage):
"""GRASS GIS (Geographic Resources Analysis Support System), is a... | LLNL/spack | var/spack/repos/builtin/packages/grass/package.py | Python | lgpl-2.1 | 10,619 | [
"NetCDF"
] | b0ce8f70226af8fc98bedd6f0b915a77ea155a2b096b7bebe85cd2d2c01f8be5 |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Scaled_Features/best_kNN_PCA/2_categories/test11_cross_validate_categories_mov_fixed_1200ms_scaled_method_iii.py | Python | mit | 5,012 | [
"Mayavi"
] | dafc16279e4960909d137d444a7bcf165949961f3b9c80283a3d16d40e538429 |
#!/usr/bin/env python
from __future__ import nested_scopes
import visitor
"""Compiler from ASN.1 specification to the Python format acceptable
to my asn1.py module. Loosely based on esnacc grammar. We ignore
MACROs, CONSUMER INVOKES, SUPPLIER INVOKES, and a lot of stuff, for simplicity.
We also ignore the {...} sy... | seblefevre/testerman | plugins/codecs/ber/compiler.py | Python | gpl-2.0 | 29,456 | [
"ASE"
] | bfd9c6f515bd4c21a89617fe85f19a69d3b92a785c2d8896c90caef9a5c4f5a6 |
#-----------------------------------------------------------------------------
# Copyright (c) 2013, PyInstaller Development Team.
#
# Distributed under the terms of the GNU General Public License with exception
# for distributing bootloader.
#
# The full license is in the file COPYING.txt, distributed with this softwa... | TeamSWAP/swap | external/pyinstaller/PyInstaller/hooks/hookutils.py | Python | apache-2.0 | 17,250 | [
"VisIt"
] | 9aa7aaf4dbf54f1a058131d8e9657b97c4d19f95d6760fe4600cb7867a3a746a |
#
# QAPI event generator
#
# Copyright (c) 2014 Wenchao Xia
# Copyright (c) 2015-2016 Red Hat Inc.
#
# Authors:
# Wenchao Xia <wenchaoqemu@gmail.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from qa... | gongleiarei/qemu | scripts/qapi-event.py | Python | gpl-2.0 | 5,702 | [
"VisIt"
] | 28a8edd81c74c2353c05d83f1641724fa8e059fe6bd47125a9bf710a96663015 |
import os
import numpy as np
from scipy.io import loadmat
from mindboggle.utils.io_vtk import read_vtk
from mindboggle.utils.compute import point_distance
G = loadmat('/Users/arno/Dropbox/MB/data/allen/H0351.2002.mat')
values = G['expr']
gene_mni = G['mni']
path = os.environ['MINDBOGGLE_DATA']
genes = []
gene_values =... | binarybottle/mindboggle_sidelined | load_gene_data.py | Python | apache-2.0 | 1,078 | [
"VTK"
] | 2ee5212d6bc70ef9f6305afc8e0e738240b7b0e8c33981fe459200ab55489a1a |
# Copyright 2013 by Rackspace Hosting, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | cdepman/falcon_api | site-packages/falcon/http_error.py | Python | mit | 8,482 | [
"VisIt"
] | ffe8363d604bb1c7658e66cb6c9f0a1701a90eec3d3c5c0c9b5b33b50b0ac378 |
"""
Original code by @philopon
https://gist.github.com/philopon/a75a33919d9ae41dbed5bc6a39f5ede2
"""
import sys
import os
import requests
import subprocess
import shutil
from logging import getLogger, StreamHandler, INFO
logger = getLogger(__name__)
logger.addHandler(StreamHandler())
logger.setLevel(INFO)
default_ch... | deepchem/deepchem | scripts/colab_install.py | Python | mit | 3,457 | [
"MDTraj",
"OpenMM",
"RDKit"
] | 020295dee27522d2a868a52b7b97a5f5ea348e250dd05aa0d8459991859749dd |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import functools
import glob
import itertools
import jinja2
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib2
import zlib
from xml.etree import ElementTree
from cStringIO import Stri... | trabacus-softapps/openerp-8.0-cc | openerp/addons/web/controllers/main.py | Python | agpl-3.0 | 74,305 | [
"VisIt"
] | f891b4a97c81aac9ccd0d7c41a1c921fff636ef69f8dbffab1fbcd67004a6081 |
# Copyright (c) 2017, Zhenwen Dai
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core.sparse_gp_mpi import SparseGP_MPI
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference.vardtc_md import VarDTC_MD
from GPy.core.parameterization.variational... | SheffieldML/GPy | GPy/models/sparse_gp_regression_md.py | Python | bsd-3-clause | 4,136 | [
"Gaussian"
] | 480c15f1584a37a3387987019c9998ecc29a284280539d1080f5b41bad42bbd6 |
import math
from matplotlib import pyplot as plt
from matplotlib.colors import LogNorm
from matplotlib.ticker import LogLocator
from scipy.optimize import curve_fit
import numpy as np
iFilename = 'cry_entrance.dat'
# Reading file ----------------------------------------------------------------------------------------... | SixTrack/SixTrack | test/collimation_cry_si_vr_ver_b2/EntCheck.py | Python | lgpl-2.1 | 3,261 | [
"CRYSTAL"
] | e9d254b4faa336af8ef26831032325a614876d8205dd6f064aa771813427bd18 |
#! /usr/bin/python
"""
Copyright (c) 2015, The Cinder Project, All rights reserved.
This code is intended for use with the Cinder C++ library: http://libcinder.org
Redistribution and use in source and binary forms, with or without modification, are permitted provided that
the following conditions are met:
*... | 2666hz/Cinder | docs/generateDocs.py | Python | bsd-2-clause | 127,835 | [
"VisIt"
] | e38e8d2fc92569e2780493242bdaa442e91c5b72eb7cfd018ab147be79d09b5c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
import unittest2 as unittest
import os
from numbers import Number
from pymatgen.core.composition import Composition
from pymatgen.core.periodic_table import Element
fr... | aykol/pymatgen | pymatgen/phasediagram/tests/test_pdanalyzer.py | Python | mit | 5,113 | [
"pymatgen"
] | 61f1b37a49f1e721a0d74ea6e6a513dbfaf1504c246078d65d9fc60e321c23fe |
# -*- coding: utf-8 -*-
from datetime import datetime
from operator import itemgetter
from urlparse import urlparse
from urllib import unquote_plus
from pyga import utils
from pyga import exceptions
__author__ = "Arun KR (kra3) <the1.arun@gmail.com>"
__license__ = "Simplified BSD"
class Campaign(object):
'''
... | steeve/xbmctorrent | resources/site-packages/pyga/entities.py | Python | gpl-3.0 | 19,442 | [
"VisIt"
] | d8583aa567224e7f1335578a93c62c2898c60fdd3ab68e3c81c6676f340c3fb4 |
import math
from ..libmp.backend import xrange
class QuadratureRule(object):
"""
Quadrature rules are implemented using this class, in order to
simplify the code and provide a common infrastructure
for tasks such as error estimation and node caching.
You can implement a custom quadrature rule by ... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sympy/mpmath/calculus/quadrature.py | Python | agpl-3.0 | 38,274 | [
"Gaussian"
] | a29a71567feb375ef20d04ec3fabb076bba1d1223e1712ebc9f7ba9c7bf67df5 |
# ----------------------------------------------------------------------
# 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... | yidongxiainl/lammps | python/lammps.py | Python | gpl-2.0 | 35,412 | [
"LAMMPS"
] | 2efadae96b621ae14fa44a9875c214d7835db8e481f5a84689eada5d086bfd68 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_crashreportdialog.py | Python | gpl-2.0 | 1,180 | [
"VisIt"
] | 2a6d145ba5e48d4cf9a990e416d221dff1aea971c9f54a1584b98a14c5162ec3 |
"""Evaluation metrics."""
import numpy as np
from sklearn.metrics import matthews_corrcoef # noqa
from sklearn.metrics import recall_score # noqa
from sklearn.metrics import cohen_kappa_score
from sklearn.metrics import r2_score # noqa
from sklearn.metrics import mean_squared_error
from sklearn.metrics import mean_... | lilleswing/deepchem | deepchem/metrics/score_function.py | Python | mit | 5,680 | [
"RDKit"
] | b0053931b5ba5a03b0d23a8a31680db77252ec44277a761ad6c62da2df1bba98 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import numpy as np
import pymatgen.io.ase as aio
from pymatgen.core.composition import Composition
from pymatgen.core.structure import Molecule
from pymatgen.io.vasp.inputs import Poscar
from pymatg... | vorwerkc/pymatgen | pymatgen/io/tests/test_ase.py | Python | mit | 6,225 | [
"ASE",
"VASP",
"pymatgen"
] | 6375b21b11b0e73a472c604b349376e1ef96721a0ea4355bee53b44d22127d15 |
import json
try:
from urllib.request import urlopen
except ImportError:
from urllib2 import urlopen
from mdtraj import version
if not version.release:
print("This is not a release.")
exit(0)
URL = 'http://www.mdtraj.org'
data = urlopen(URL + '/versions.json').read().decode()
versions = json.loads(dat... | leeping/mdtraj | devtools/travis-ci/update_versions_json.py | Python | lgpl-2.1 | 732 | [
"MDTraj"
] | f839d7199794d2aeebea7aeb6e8575b6a4fee8a86138f994f9cba97ec0ee87b2 |
"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import functools
import re
import warnings
i... | jorisvandenbossche/numpy | numpy/lib/polynomial.py | Python | bsd-3-clause | 40,755 | [
"Gaussian"
] | bab5a3759f1d02f9050ca47ebe448898922c9214d77bd5e5542972d1a097eef3 |
from math import sqrt
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack, help
graph_help_text = _("""\
Help for plot ...
Symbols:
<c>e</c>:\t\t\t\ttotal energy
<c>epot</c>:\t\t\tpotential energy
<c>ekin</c>:\t\t\tkinetic energy
<c>fmax</c>:\t\t\tmaximum force
<c>fave</c>:\t\t\taverage forc... | grhawk/ASE | tools/ase/gui/graphs.py | Python | gpl-2.0 | 4,750 | [
"ASE"
] | 64d2d47f53d858cfc08353f2cb04a446d5fc4b9f33afca21f4a680e91a07893f |
"""Gromacs parser tests.
"""
from alchemlyb.parsing.gmx import extract_dHdl, extract_u_nk
from alchemtest.gmx import load_benzene
from alchemtest.gmx import load_expanded_ensemble_case_1, load_expanded_ensemble_case_2, load_expanded_ensemble_case_3
from alchemtest.gmx import load_water_particle_with_total_energy
from... | alchemistry/alchemlyb | src/alchemlyb/tests/parsing/test_gmx.py | Python | bsd-3-clause | 6,231 | [
"Gromacs"
] | fd6eb5a77ead720ee0d6a75770de2d1eba2eb4b7db236f7a5a47c266fb83feac |
#!/usr/bin/env python
"""
castep.py
Various bits of python to read/write castep files
Copyright (c) 2010 Andrew Walker (a.walker@ucl.ac.uk)
All rights reserved.
"""
import re
import scipy as S
version = 0.1
# regular expression to match the whole of the final cell from a .castep file
dotcastep_latt_RE = re.compile... | andreww/elastic-constants | castep.py | Python | bsd-3-clause | 6,008 | [
"CASTEP",
"CRYSTAL"
] | 4df9193002ee33afcba6820c82a42a330afce06ea45f4e9df72932c059d2b9fb |
""" DIRAC FileCatalog component representing a directory tree with simple nodes
"""
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.DirectoryManager.DirectoryTreeBase import DirectoryTreeBase
class DirectoryNodeTree(DirectoryTreeBase):
"""Class managing Director... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/DirectoryManager/DirectoryNodeTree.py | Python | gpl-3.0 | 5,866 | [
"DIRAC"
] | 17ccab40d3db527df4871e83b6454394ed5950d6ccd5a93e7341f6ee91dbba6f |
# Copyright 2015 Allen Institute for Brain Science
# This file is part of Allen SDK.
#
# Allen SDK 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, version 3 of the License.
#
# Allen SDK is distributed in the ... | wvangeit/AllenSDK | allensdk/model/glif/simulate_neuron.py | Python | gpl-3.0 | 5,862 | [
"NEURON"
] | bef7522357adf09f9880d910dccbc1dd1cf2b8f0c15efd4a17cebe0c237be788 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/plugins/kgapplications/views/project.py | Python | gpl-3.0 | 6,844 | [
"Brian"
] | 8389a715c36d98ef34d6515aa66699400e3b2db62aace2a4936b6068f19e3fb5 |
# -*- coding: utf-8 -*-
__all__ = [
"StretchMove",
"WalkMove",
"DEMove",
"KDEMove",
"MHMove",
"GaussianMove",
"HamiltonianMove",
"NoUTurnsMove",
]
from .walk import WalkMove
from .stretch import StretchMove
from .de import DEMove
from .kde import KDEMove
from .mh import MHMove
from .g... | jellis18/emcee3 | emcee3/moves/__init__.py | Python | mit | 413 | [
"Gaussian"
] | c85ac07d2405f91abc817545975647d2dae82126dcaaadee689e0b4a9d755e5d |
from __future__ import print_function
import copy
import warnings
import graphviz
import matplotlib.pyplot as plt
import numpy as np
def plot_stats(statistics, ylog=False, view=False, filename='avg_fitness.svg'):
""" Plots the population's average and best fitness. """
if plt is None:
warnings.warn... | drallensmith/neat-python | examples/memory-variable/visualize.py | Python | bsd-3-clause | 5,965 | [
"NEURON"
] | fa317a34b9d4f844cadfd280f8d2ef31cd706a7518a6ce37067827ac8774da1a |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import unittest
import numpy as np
import GPy
class MiscTests(unittest.TestCase):
def setUp(self):
self.N = 20
self.N_new = 50
self.D = 1
self.X = np.random.uniform(-3.... | avehtari/GPy | GPy/testing/model_tests.py | Python | bsd-3-clause | 32,449 | [
"Gaussian"
] | 4ade88958a901bc853d5b63225a12cd120f2b7cd3fb5570b0cb4558638da19a8 |
#!/usr/bin/python
################################################################
# .___ __ _______ .___ #
# __| _/____ _______| | __ ____ \ _ \ __| _/____ #
# / __ |\__ \\_ __ \ |/ // ___\/ /_\ \ / __ |/ __ \ #
# / /_/ | / __ \| | \/ <\ \___\... | knightmare2600/d4rkc0de | others/shellgen.py | Python | gpl-2.0 | 2,341 | [
"VisIt"
] | 324e1c398760a9f8382b08a0e9e6ec7a02dde6d53ac1787b22d217e9eb6bda8b |
'''
A suite of common exponential family distributions.
'''
import numpy as np
import scipy.sparse as sps
from scipy.special import psi, polygamma, gammaln, gammasgn
from copy import deepcopy
from utils import pretty_str, safe_exp, safe_sq
import csv
def get_node(name):
if name == 'bernoulli' or name == 'b':
... | redreamality/vsmrfs | vsmrfs/exponential_families.py | Python | mit | 11,657 | [
"Gaussian"
] | 2263f82647e4cff5e23455ea86014ad954b319a91f171600c40d5d79c5e407bf |
"""
Common code for mayavi tests.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
import os.path
from traits.api import HasTraits, Any, Event, Callable
def fixpath(filename):
"""Given a relative file path it sets the path relative to this
... | dmsurti/mayavi | mayavi/tests/common.py | Python | bsd-3-clause | 692 | [
"Mayavi"
] | f14b8879f19dfaaa747c4a35b14d4665f563bc1739b069839d1891096b9fe540 |
########################################
# Read ECMWF netcdf files for heat fluxes
#
# Created by: Peter Willetts
# Created on: 12/06/2014
#
# ECMWF heat and radiation flux - Read from netcdf
# filter by date, latitude and longitude
# calculate mean and t... | peterwilletts24/Python-Scripts | era_interim/netcdf_fileread_heat_fluxes_6hourly_rad.py | Python | mit | 4,215 | [
"NetCDF"
] | 4767434a966fa2ebae7ccd48af2f39a9883e767c7d7227257aa027a35926c073 |
# Copyright (c) 2007, Enthought, Inc.
# License: BSD Style.
# all_traits_features.py --- Shows primary features of the Traits
# package
#--[Imports]--------------------------------------------------------------------
from traits.api import Delegate, HasTraits, Instance, Int, Str
#--[Cod... | burnpanck/traits | examples/tutorials/doc_examples/examples/all_traits_features.py | Python | bsd-3-clause | 1,454 | [
"MOE"
] | 2d4611e8b0718049781f9b9f345f6ad18b8e8cfba05391a56ad76eb9479a66e1 |
#!/usr/bin/python
import sys,os
nonbonded = '/home/fuqy/Software/gromacs-5.1.4/share/top/amber99sb.ff/ffnonbonded.itp'
rtp = '/home/fuqy/Software/gromacs-5.1.4/share/top/amber99sb.ff/aminoacids.rtp'
watermodel = '/home/fuqy/Software/gromacs-5.1.4/share/top/amber99sb.ff/tip3p.itp'
class gmxtop:
# private variables
... | hnlab/fpdb | fpdb/gmx_top.py | Python | mit | 7,752 | [
"Amber",
"Gromacs"
] | ed6e930196960272c4609cd2ffe0fe67646d7ee7ee7a8e19adabf6b818322fce |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/data/component.py | Python | agpl-3.0 | 2,859 | [
"Galaxy"
] | 11ab1b59dadae9314a29eefd2df416d2b6c6c6860d32ed73de674ce369d78cae |
import glob
import os
import textwrap
from setuptools.package_index import PackageIndex
from setuptools.sandbox import run_setup
import pytest
from . import run_cmd, testpackage
from ..utils import silence
TEST_SETUP_PY = """\
#!/usr/bin/env python
from __future__ import print_function
import os
import sys
impor... | eteq/astropy-helpers | astropy_helpers/tests/test_ah_bootstrap.py | Python | bsd-3-clause | 11,986 | [
"VisIt"
] | c90e5db5bc8afc8c9da36d40b4a7025bfba1912c672c39c1364a6edf0183b142 |
#!/usr/local/sci/bin/python
#***************************************
# 1 April 2014 KMW - v1
# Plots global time series from netCDF - cannot work with uncertainties right now
#
#************************************************************************
# START
#***************************... | Kate-Willett/Climate_Explorer | PYTHON/PlotNiceTimeSeries_APR2016.py | Python | cc0-1.0 | 16,514 | [
"NetCDF"
] | da621d9e006d79ff8e80e446359a12df208b256a8b495cdb04ac3b57e089447f |
#
# ImageViewTk.py -- classes for the display of FITS files in Tk surfaces
#
# Eric Jeschke (eric@naoj.org)
#
# Copyright (c) Eric R. Jeschke. All rights reserved.
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
import numpy
import PIL.Image as PILimage
im... | eteq/ginga | ginga/tkw/ImageViewTk.py | Python | bsd-3-clause | 14,732 | [
"FLEUR"
] | dd489685af67b5b22ee0cc18f29ff1d821c143b34fcbe9898eb6d6482da7ea73 |
# Purpose: make masks based on 12CO ancillary data for data reduction
# and analysis.
# Date Programmer Description of Changes
# ----------------------------------------------------------------------
# 4/14/2020 A.A. Kepley Original Code
# 4/8/2021 A.A. Kepley Upd... | low-sky/degas | scripts/process_12CO.py | Python | gpl-3.0 | 12,171 | [
"Galaxy"
] | 095446f71ab24477a069ec42acabc7fa77fcd36844e40809d55b0f4eb381cd48 |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
from SceneObject import SceneObject
class Text(SceneObject):
'''
A text object.
'''
# The camera texture
cameraVtkTexture = None
def __init__(self, renderer, parent, text, scale, position):
'''
Initialize the Came... | GearsAD/semisorted_arnerve | arnerve/scene/Text.py | Python | mit | 799 | [
"VTK"
] | 7d9ef08004844d50f7fc4a946e272deaa091c9e4fcf6ee43efb6443d5b57fb8c |
from enum import IntEnum
from hashkernel.bakery import (
CakePath, HasCake, Cake, CakeRack, CakeRole)
from hashkernel import Str2Bytes
class NodeState(IntEnum):
"""
>>> list(NodeState) #doctest: +NORMALIZE_WHITESPACE
[<NodeState.unknown: 0>, <NodeState.scanning: 1>,
<NodeState.scanned: 2>, <NodeS... | walnutgeek/hashstore | hashstore/bakery/cake_tree.py | Python | apache-2.0 | 9,430 | [
"NEURON"
] | 98a27a5437acada37b9d362557e6ac63117166a4a5f865d8c23e9884e21bcd4d |
from paraview.simple import *
import glob
import re
opacityBaffles=0.6
opacityImpeller=1.0
opacityTank=0.2
liste = glob.glob('./post/VTK/mixer_*.vtk')
listeImpl = glob.glob('./post/VTK/impeller_*.stl')
listeTank = glob.glob('/home/bruno/doctorat/mesh/PBT_Manon/tank.stl')
listeBafflesB = glob.glob('/home/bruno/doctora... | mendax-grip/cfdemUtilities | paraview/mixerParticlesBaffles.py | Python | lgpl-3.0 | 5,661 | [
"ParaView",
"VTK"
] | 8cd70c44700c584601ff337ee00d86349819d933ee9a69429bb695580e8853cf |
# -*- coding: utf-8 -*-
"""
Tests the "preview" selector in the LMS that allows changing between Staff, Learner, and Content Groups.
"""
from textwrap import dedent
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPag... | philanthropy-u/edx-platform | common/test/acceptance/tests/lms/test_lms_user_preview.py | Python | agpl-3.0 | 17,913 | [
"VisIt"
] | f4246c3e31579ba529b2bc07cb06af2cfb9791205cb147a7f0d1d1351ebc17d2 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/Community-Zenpacks | ZenPacks.AndreaConsadori.ASSP/setup.py | Python | gpl-2.0 | 3,327 | [
"VisIt"
] | 514c0b7f6d699457587545c4b0f2f7cc8badc7b3be2f6414066d2e19884e967e |
# -*- coding: utf-8 -*-
#
# Asterisk IVR documentation build configuration file, created by
# sphinx-quickstart on Mon Nov 14 16:14:39 2016.
#
# 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.
#
... | invitecomm/asterisk-ivr | docs/conf.py | Python | gpl-3.0 | 6,709 | [
"Brian"
] | 83894ba7dd98eeb8b05cf433ab1753b422a90865b1ee3eabbae5260e8ce793b9 |
#!/usr/bin/env python
import os
import numpy as np
from astropy.io import fits
import scipy.optimize
import scipy.signal
from scipy.misc import imsave
import scipy.ndimage
def gaussian(coordinates, height, *centroid_and_width):
"""
The n-dimensional symmetric Gaussian distribution
Expects coordinates x t... | Saethlin/astrotools | vectorize_starfield.py | Python | mit | 3,096 | [
"Gaussian"
] | 7e782631efb8b5ffb096f4b60b38d9703734d3891c4683c70317dc0619211899 |
# -- coding: utf-8 --
# ===========================================================================
# eXe
# Copyright 2012, Pedro Peña Pérez, Open Phoenix IT
#
# 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 Softwar... | tquilian/exeNext | exe/jsui/mainpage.py | Python | gpl-2.0 | 57,162 | [
"VisIt"
] | 5d8a17fb4f42e47afeda4cdd1eb57a603fc4c27e8264e3c9fdac67e3ee9e2b94 |
# -*- coding: utf-8 -*-
# Ported and tweaked from Java to Python, from Better Arabic Reshaper [https://github.com/agawish/Better-Arabic-Reshaper/]
# This work is licensed under the GNU Public License (GPL).
# To view a copy of this license, visit http://www.gnu.org/copyleft/gpl.html
# Written by Abd Allah Diab (mpcabd)... | faisal-oead/conky-arabic-support | conkyar/arabic_reshaper.py | Python | gpl-2.0 | 13,842 | [
"VisIt"
] | 5946efabd65c3e1e11945f0af410f9dd63f33c4f567ab4deb0986b4962c066c6 |
from moves import DamagingMove
from moves import Move
from moves import BoostingMove
from moves import HealingMove
from handlers import *
moves = {
"Noop": Move("Noop"),
"Absorb": DamagingMove("Absorb",
power=20,
category="Special",
... | vasumv/pokemon_ai | showdownai/move_list.py | Python | mit | 135,020 | [
"BLAST"
] | e47ea03d31986b263aab701de68443c59e15b6c9d536a3438f71e1e493026417 |
# -*- coding: utf-8 -*-
#
# neuronview.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
... | magnastrazh/NEUCOGAR | nest/serotonin/research/C/nest-2.10.0/examples/neuronview/neuronview.py | Python | gpl-2.0 | 10,544 | [
"NEURON"
] | 317cbfbd2fa614d5a331e1eff079e10bc75f9f1a2c4c202b17207b9ca6cdc2ab |
from __future__ import print_function
from builtins import range
"""
SECTION 1 : Load and setup data for training
"""
import csv
import random
import math
random.seed(113)
# Load dataset
with open('../Datasets/iris/iris.csv') as csvfile:
csvreader = csv.reader(csvfile)
next(csvreader, None) # skip header
... | rianrajagede/simplesamplecode | Python/iris_plain_mlp.py | Python | mit | 4,759 | [
"NEURON"
] | 63e229d48bf44e3113f2b8574e03f9f12833ae25c896669a443ea0bf9185820a |
import os
import sys
import vtk
import numpy as np
from vtk.util.colors import red, green, black, white, grey, blue, orange, peacock
from vtk.util import numpy_support
# see if some of the stuff needs to be moved to the Microstructure module
from pymicro.crystal.lattice import Lattice, HklPlane
def to_vtk_type(type)... | heprom/pymicro | pymicro/view/vtk_utils.py | Python | mit | 103,117 | [
"CRYSTAL",
"ParaView",
"VTK"
] | 14ee52c91113f9166485ee646fa647c7d8cd5445ac4199933b718ce92a6202f5 |
# Copyright 2012 by Kai Blin.
# 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.
"""Bio.SearchIO parser for HMMER 2 text output."""
import re
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio... | zjuchenyuan/BioWeb | Lib/Bio/SearchIO/HmmerIO/hmmer2_text.py | Python | mit | 12,055 | [
"Biopython"
] | 99da5763519dd548e67e3cc83a4ced8f5efef90cb49a190947cf7c566b6fa989 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import copy as cp
import os
from math import floor, ceil, log
import itertools as itt
import warnings
import ... | andyh616/mne-python | mne/cov.py | Python | bsd-3-clause | 70,741 | [
"Gaussian"
] | 12f1db2da3b39d57290a3581ab5b46ad6487c386fb179ec6b5f19233c1060573 |
# Copyright 2015 gRPC authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | ctiller/grpc | src/python/grpcio/grpc_core_dependencies.py | Python | apache-2.0 | 88,940 | [
"ORCA"
] | 1539327e7f6064081c95826e0ba9119d511e8d89f0497d82885e164322a648d3 |
from __future__ import print_function
import vtk
def main():
# setup sphere
sphereSource = vtk.vtkSphereSource()
sphereSource.Update()
polydata = vtk.vtkPolyData()
polydata.ShallowCopy(sphereSource.GetOutput())
normals = polydata.GetPointData().GetNormals()
normal0 = normals.GetTuple3(0... | lorensen/VTKExamples | src/Python/Arrays/GetValues.py | Python | apache-2.0 | 452 | [
"VTK"
] | e94f9b66ec09d284e1a05ffb600b31b7157029f32fb82950653726ef4010b35e |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.abspa... | DentonJC/virtual_screening | setup.py | Python | gpl-3.0 | 8,119 | [
"VisIt"
] | 0d30a3130dfb4a4ca121c7e290d1c6cb730237ba08f1b95fbb929ff153ff8144 |
#!/usr/bin/env python
"""
Filename: version_safe_cdscan.py
Description: Create a xml catalogue of NetCDF files using cdscan
Input: List on XML files
Output: XML catalogue file suitable for use with CDAT/UV-CDAT (cdms python library)
Author: David Kent David.Kent@csiro.au
Revisions: Tim Bedin T... | paolap/cwsl-ctools | aggregation/version_safe_cdscan.py | Python | apache-2.0 | 6,261 | [
"NetCDF"
] | ee2f86def5502082882b5de2cfa42c0697dfc2e77ec952271695307b27a0fd22 |
"""
Test courseware search
"""
import json
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.acceptance.pages.common.utils import c... | ahmedaljazzar/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware_search.py | Python | agpl-3.0 | 7,715 | [
"VisIt"
] | 2c6ec259cc52a547740fc36deac9a24a1445d157fdffad624501c38f12f1a4e1 |
###############################################################################
# ilastik: interactive learning and segmentation toolkit
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# mod... | nielsbuwen/ilastik | tests/test_applets/featureSelection/testOpFeatureSelection.py | Python | gpl-3.0 | 6,640 | [
"Gaussian"
] | 96ed3df462eb27e82571864b76fe38e9eaeaf2d07d49cb11e2a0fae7d17acce6 |
from collections import Counter, namedtuple
import copy
import itertools as it
import re
import subprocess
import tempfile
import sys
import h5py
import numpy as np
from scipy.spatial.distance import pdist
from scipy.spatial.transform import Rotation
import rmsd
try:
from thermoanalysis.QCData import QCData
f... | eljost/pysisyphus | pysisyphus/Geometry.py | Python | gpl-3.0 | 45,861 | [
"ASE",
"Jmol"
] | 9b62562645acf0a652defaf9b62c174b40b132a8a8a36a16b1f569956fd1fb5c |
import web
from web import form
render = web.template.render('templates/')
urls = ('/', 'index')
app = web.application(urls, globals())
myform = form.Form(
form.Textbox("boe"),
form.Textbox("bax",
form.notnull,
form.regexp('\d+', 'Must be a digit'),
form.Validator('Must be more than 5... | ivanortegaalba/DAI_2014-2015 | practica-webpy/form-exercise5.py | Python | gpl-2.0 | 1,112 | [
"MOE"
] | a3730d96b0bd95eaac84cebc8a215fb4799693763d18a905d1c2899b994cd46e |
#! /usr/bin/env python2.5
# -*- coding: latin-1 -*-
# Copyright (C) 2006-2008 Universitat Pompeu Fabra
# Copyright (C) 2009 Universidad Simon Bolivar
#
# Permission is hereby granted to distribute this software for
# non-commercial research purposes, provided that this copyright
# notice is included with any such... | PlanTool/plantool | code/Uncertainty/T0/translator/translator/translator.py | Python | gpl-2.0 | 68,757 | [
"VisIt"
] | 44c82bfafc77ede013a0c443dd65050fa05995ca5655579f0a3a7eb72fcc9bcf |
"""Helper methods to import yelp data"""
import json
from pprint import pprint
import numpy as np
import re
import cPickle as pickle
import os.path
VEGAS_RESTAURANTS_PATH = "pickles/get_restaurants_vegas.p"
PHOENIX_RESTAURANTS_PATH = "pickles/get_restaurants_phoenix.p"
EDINBURGH_RESTAURANTS_PATH = "pickles/get_restau... | harinisuresh/yelp-district-clustering | DataImporter.py | Python | mit | 7,566 | [
"CASINO"
] | dd3b136f0e9b89d8d7cdc5cf60293b8735fe17ee41ae8ae090cb86fb3607ad25 |
# This is the code that visits the warehouse.
import sys
import Pyro4
import Pyro4.util
from person import Person
sys.excepthook = Pyro4.util.excepthook
warehouse = Pyro4.Proxy("PYRONAME:example.warehouse")
janet = Person("Janet")
henry = Person("Henry")
janet.visit(warehouse)
henry.visit(warehouse)
| irmen/Pyro4 | examples/warehouse/phase3/visit.py | Python | mit | 305 | [
"VisIt"
] | bfd836dfc2a5c495d07b2c4f168d5a7609bfec99f11a73e4a6b588ae5ac73f01 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | samples/visualization_charged.py | Python | gpl-3.0 | 4,820 | [
"Avogadro",
"ESPResSo"
] | e2b73afb93dfba7d50c9424e54f0fe76093c5a5fae6f7c5ce76c935f01b6bea4 |
# -*- coding: utf8
"""Random Projection transformers
Random Projections are a simple and computationally efficient way to
reduce the dimensionality of the data by trading a controlled amount
of accuracy (as additional variance) for faster processing times and
smaller model sizes.
The dimensions and distribution of Ra... | RomainBrault/scikit-learn | sklearn/random_projection.py | Python | bsd-3-clause | 22,969 | [
"Gaussian"
] | 7ce7dda6b9f7e3f3194cac6d6d966fb23a6e148123250ecd06a64561b2408854 |
"""Define a helper function for running tests
The skeleton for making a new setup is as follows:
from ase.optimize.test import run_test
def get_atoms():
return Atoms('H')
def get_calculator():
return EMT()
run_test(get_atoms, get_calculator, 'Hydrogen')
"""
import time
import matplotlib
matplotlib.rcPara... | conwayje/ase-python | ase/optimize/test/__init__.py | Python | gpl-2.0 | 4,860 | [
"ASE"
] | a6903138ae8b50d7025767e471f95e54f6b849472507937ae6744e1ea7c2e8f9 |
from __future__ import print_function, absolute_import
from .script_interface import ScriptInterfaceHelper, script_interface_register
import numpy as np
@script_interface_register
class MeanVarianceCalculator(ScriptInterfaceHelper):
"""
Accumulates results from observables.
Parameters
----------
... | KonradBreitsprecher/espresso | src/python/espressomd/accumulators.py | Python | gpl-3.0 | 9,736 | [
"exciting"
] | b5e8484d3c3ef30006a61ad7bb6c1dd22b4643ce21f07a6b499fc9299da87036 |
#******************
# MODULE DOCSTRING
#******************
"""
LOMAP: fingerprint calculations
=====
Alchemical free energy calculations hold increasing promise as an aid to drug
discovery efforts. However, applications of these techniques in discovery
projects have been relatively few, partly because of the diffi... | nividic/Lomap | lomap/fp.py | Python | lgpl-2.1 | 3,370 | [
"RDKit"
] | a51135b2923edf7306a5fa3654e777775fb1fe8d62cbc0b6215c46636c5b5f05 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/array_properties.py | Python | gpl-3.0 | 8,586 | [
"ESPResSo"
] | 0eb5f562603dbdd3ce4036b9b2998e095401602d195504f9b4ce64333629024e |
__author__ = 'Mario'
__author__ = 'Mario'
import numpy as np
from scipy.stats import multivariate_normal as norm
import pandas as pd
import matplotlib.pyplot as plt
dataTraining = pd.read_table('./Data/iris_training.txt',delim_whitespace=True, header=None)
dataTest = pd.read_table('./Data/iris_test.txt',delim_whites... | marioharper182/Patterns | PatternRecognition/ProgrammingProject1/MaxLiklihood.py | Python | apache-2.0 | 2,560 | [
"Gaussian"
] | 768c204e9c2f00ae95bb5bac8816156348c5e3a7e4af07d32bac8471425b1f38 |
# This file is generated by mk-codemirror-language-list.py.
# Probably don't edit it by hand.
# List of (mode_name, human_label, js_url)
CODEMIRROR_MODES = [
('apl', 'APL', '/static/codemirror/mode/apl/apl.js'),
('asn.1', 'ASN.1', '/static/codemirror/mode/asn.1/asn.1.js'),
('clike', 'C, C++, C#', '/static/... | sfu-fas/coursys | courselib/codemirror_language_list.py | Python | gpl-3.0 | 8,008 | [
"CRYSTAL"
] | 275ab487ebfc73c8f6c63bd622834b5b32997add7226ea7150d8d968739e6fab |
"""Support for Ecobee sensors."""
from pyecobee.const import ECOBEE_STATE_CALIBRATING, ECOBEE_STATE_UNKNOWN
from homeassistant.components.sensor import SensorEntity
from homeassistant.const import (
DEVICE_CLASS_HUMIDITY,
DEVICE_CLASS_TEMPERATURE,
PERCENTAGE,
TEMP_FAHRENHEIT,
)
from .const import _LOG... | w1ll1am23/home-assistant | homeassistant/components/ecobee/sensor.py | Python | apache-2.0 | 4,823 | [
"VisIt"
] | 284c6c041981ab5548577fa849674c3b2a8e1a506100fd2e89b6754abed0e9e9 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Development script of the ChemEnv utility to get the explicit permutations for coordination environments identified
with the separation plane algorithms (typically with coordination numbers >= 6)
"""
import itertools
impo... | materialsproject/pymatgen | dev_scripts/chemenv/explicit_permutations_plane_algorithm.py | Python | mit | 5,857 | [
"pymatgen"
] | eaf54af0f2cf94387c12835917fbd9722fbf12f3dc6f25c9294906a4347a6040 |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# 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 2 of the License, o... | Shouqun/node-gn | tools/depot_tools/third_party/pylint/checkers/classes.py | Python | mit | 42,518 | [
"VisIt"
] | 5e925fe6b6efb45173c63f8025935b19004f7498771d12c0bbd11df58790ce65 |
'''
One summer Felicia was visiting her granny's summer house. There were several old and withered vines growing in the garden, that no longer produced grapes.
Felicia found it sad, and decided to decorate the vines with wooden grapes she carved out herself. She also watered them with cola, since cola makes everything ... | chuckinator0/Projects | scripts/vines.py | Python | gpl-3.0 | 3,983 | [
"VisIt"
] | 83ddb29bb580c39b85110ba27b2d39e4ba0c00ff394d076125465f611335113b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
=============================================================
Compare the effect of different scalers on data with outliers
=============================================================
Feature 0 (median income in a block) and feature 5 (number of households) of
the :... | glemaitre/scikit-learn | examples/preprocessing/plot_all_scaling.py | Python | bsd-3-clause | 13,721 | [
"Gaussian"
] | ade3c8dfc63f2ffaa974036ef80a82d8d900574fc44b590a6d616615096c6e70 |
"""Only External Repos url specific constants module"""
CUSTOM_FILE_REPO = 'https://fixtures.pulpproject.org/file/'
CUSTOM_KICKSTART_REPO = 'http://ftp.cvut.cz/centos/8/BaseOS/x86_64/kickstart/'
CUSTOM_RPM_REPO = 'https://fixtures.pulpproject.org/rpm-signed/'
CUSTOM_RPM_SHA_512 = 'https://fixtures.pulpproject.org/rpm... | SatelliteQE/robottelo | robottelo/constants/repos.py | Python | gpl-3.0 | 1,448 | [
"Galaxy"
] | 756aedeb5cbe79fb858e2737f0911f4b2597eee2328a4b53939c1d1de843a6ea |
#!/usr/bin/env python
import sys
import argparse
import multiprocessing
import logging
import vcf
import random
import math
import pysam
def annotate_vcfs(bam, chromosomes, vcfs):
func_logger = logging.getLogger("%s-%s" % (annotate_vcfs.__name__, multiprocessing.current_process()))
random.seed(0)
# Load ... | msahraeian/metasv | scripts/annotate_vcf_bam.py | Python | bsd-2-clause | 7,661 | [
"pysam"
] | 33ec9b34a23d8f60e149ae1090109bc95628ae7049d55cea7f3e038cba4c6cb4 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-parameters
# Author : Stuart Paterson
########################################################################
"""
Retrieve parameters associated to the given DIRAC job
"""
from __future__ import... | fstagni/DIRAC | Interfaces/scripts/dirac-wms-job-parameters.py | Python | gpl-3.0 | 1,263 | [
"DIRAC"
] | df33b76db2e7bd11e1b49d48e8c54c02df7fe23057a2c1db2fc9dbbd9b7f0e38 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Common test support for pymatgen test scripts.
This single module should provide all the common functionality for pymatgen
tests in a single location, so that test scripts can just import it and work
right... | mbkumar/pymatgen | pymatgen/util/testing.py | Python | mit | 7,992 | [
"pymatgen"
] | 6ac0cd7723fc49021e4ec5490b3a7663be33d1487e47a1ebe1aae0c59682593e |
"""
Instructor Dashboard Views
"""
import datetime
import logging
import uuid
from urlparse import urljoin
import pytz
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.urls import reverse
from django.http import Http404, HttpResponseServerError
from django.utils.h... | philanthropy-u/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 36,922 | [
"VisIt"
] | ba5740853f52f8f4891c5f82cd739a5c5a6b5e5c67e1add671732895bb564cc8 |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.absp... | pivotal-energy-solutions/geopy | setup.py | Python | mit | 8,055 | [
"VisIt"
] | 2da093a5ea6ca78c45f6a8622980d3fe58259cb2138b33058436ee8bb6fe2e3e |
# This neural class creates the fundamentals of a
# neural network. All of the classes are to achieve
# standard, plain bread and butter goals of a
# standard backpropogation supervised learning
# network.
#
# It can work out of the box for basic stuff, but to extend it
# beyond just the plain standard, you can extend ... | limdingwen/neural | neural.py | Python | mit | 4,992 | [
"NEURON"
] | 726e7d2035fa374d8cbdce9741da0a48e0e1b7a7d4432c0a28cc2f214fef7df2 |
""" X509CRL is a class for managing X509CRL
This class is used to manage the revoked certificates....
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import stat
import os
import tempfile
import re
import datetime
import M2Crypto
fr... | ic-hep/DIRAC | src/DIRAC/Core/Security/m2crypto/X509CRL.py | Python | gpl-3.0 | 3,804 | [
"DIRAC"
] | fd1e7367a9f1aa072d2a6a29f30f063e426b18633a2cd9d6be1ae5f715f3ee6f |
import pybullet as p
from time import sleep
import pybullet_data
physicsClient = p.connect(p.GUI)
p.setAdditionalSearchPath(pybullet_data.getDataPath())
p.setGravity(0, 0, -10)
planeId = p.loadURDF("plane.urdf", [0,0,-2])
boxId = p.loadURDF("cube.urdf", [0,3,2],useMaximalCoordinates = True)
bunnyId = p.loadSoftBody(... | nrz/ylikuutio | external/bullet3/examples/pybullet/examples/load_soft_body.py | Python | agpl-3.0 | 902 | [
"VTK"
] | 1d0eb975823a3ef5f4f0f50f73aea6b05db19e794abf64aa18de116c85cd224d |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/core/test_group_traj_access.py | Python | gpl-2.0 | 16,540 | [
"Gromacs",
"MDAnalysis"
] | 566ee88ddcda62447d290c32a8a5a708a9f40cb954d945765c7d5b84391176ba |
"""Grid out dailyc for a daily climatology on PRISM grid.
Note: PRISM's climatology is monthly/annual, so no daily :/
"""
import datetime
import os
import numpy as np
from pyiem import prism
from pyiem.util import ncopen, logger
LOG = logger()
BASEDIR = "/mesonet/data/prism"
def init_year(ts):
"""
Create a... | akrherz/iem | scripts/prism/init_prism_dailyc.py | Python | mit | 3,234 | [
"NetCDF"
] | 80a738e6a21665759bbfa6994da6002e8caeeed1da3dc23cb3bb993c5c3e795e |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
class Pilot(BaseAccountingType):
def __init__(self):
super(Pilot, self).__init__()
... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/Client/Types/Pilot.py | Python | gpl-3.0 | 775 | [
"DIRAC"
] | 1d32f4152552d3d7ca68fe6e7b90fca09f9125614a8f4b74c22c445fda9dd42f |
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