text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | jkettleb/iris | lib/iris/tests/test_pickling.py | Python | lgpl-3.0 | 4,614 | [
"NetCDF"
] | 25cb173fe7ec51d26326c4eb234c717380c72ed01e9bf39544d515bb88be3ef6 |
#!/usr/bin/env python2
# Copyright 2011, 2012 Alexandre Gravier (al.gravier@gmail)
# This file is part of PyCogMo.
# PyCogMo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, o... | agravier/pycogmo | tests/pynn_to_visu_tests.py | Python | gpl-3.0 | 7,283 | [
"Brian"
] | 45ef31f01be303faac027206c2612f9daf052330eb07418aadbced78db931262 |
""" Test the SSLTransport mechanism """
import os
import select
import socket
import threading
from pytest import fixture
from DIRAC.Core.Security.test.x509TestUtilities import CERTDIR, USERCERT, getCertOption
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.Core.Utilit... | chaen/DIRAC | Core/DISET/private/Transports/test/Test_SSLTransport.py | Python | gpl-3.0 | 7,191 | [
"DIRAC"
] | 8006350bb946637e2937dcad33b94fe5203aaa6ea60515810747a84c27bf1074 |
# -*- coding: utf-8 -*-
import logging
import os
import bpy
from mathutils import Matrix
from mmd_tools import bpyutils
from mmd_tools.core import vmd
from mmd_tools.core import vpd
class VPDExporter:
def __init__(self):
self.__osm_name = None
self.__scale = 1
self.__bone_util_cls = vmd... | powroupi/blender_mmd_tools | mmd_tools/core/vpd/exporter.py | Python | gpl-3.0 | 4,716 | [
"VMD"
] | 34fc317b1c3dbd29c8b4abaa016f6de6a7c531edea80ffb04ab70d5f9a262b0f |
##############################################################################
# MSIBI: A package for optimizing coarse-grained force fields using multistate
# iterative Boltzmann inversion.
# Copyright (c) 2017 Vanderbilt University and the Authors
#
# Authors: Christoph Klein, Timothy C. Moore
#
# Permission is her... | mosdef-hub/msibi | msibi/utils/find_exclusions.py | Python | mit | 3,343 | [
"MDTraj"
] | 056b53bb0a64c85df1644c877f21171555e34bf2d8826a45acd0ac9b6015523b |
"""
Generate coulomb matrices for molecules.
See Montavon et al., _New Journal of Physics_ __15__ (2013) 095003.
"""
import numpy as np
import deepchem as dc
from deepchem.feat.base_classes import MolecularFeaturizer
from deepchem.utils import pad_array
from deepchem.feat.atomic_coordinates import AtomicCoordinates
... | miaecle/deepchem | deepchem/feat/coulomb_matrices.py | Python | mit | 10,564 | [
"RDKit"
] | 02852b95779af99618e1bead9836ade225a5ae59b3578fcdcb5b1d3b504538d9 |
# -*- coding: utf-8 -*-
# Copyright (c) 2006, 2009-2010, 2012-2015 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2012, 2014 Google, Inc.
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015 Ionel Cristian Maries <cont... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/checkers/design_analysis.py | Python | apache-2.0 | 13,994 | [
"VisIt"
] | 147261389dc57affb5d456e6de53655d32000b3d5b9c265ccee70184c19b9691 |
# coding: utf-8
# Copyright (c) Materials Virtual Lab
# Distributed under the terms of the BSD License.
import warnings
from veidt.abstract import Model
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process import kernels
from sklearn.externals import joblib
class GaussianProces... | czhengsci/veidt | veidt/model/gaussian_process.py | Python | bsd-3-clause | 3,601 | [
"Gaussian"
] | f5f0fb47d9e63d99428177988b5b65b4105f5437b716b2799ec6a25ad214c7a8 |
try: paraview.simple
except: from paraview.simple import *
from paraview import coprocessing
#--------------------------------------------------------------
# Code generated from cpstate.py to create the CoProcessor.
# ----------------------- CoProcessor definition -----------------------
def CreateCoProcessor()... | tfogal/freeprocessing | pvsim/pvimage.py | Python | lgpl-3.0 | 7,091 | [
"ParaView"
] | fbdc279532d6a18f9893fd2f71935d610ba2ee76450050d2bf225f43aeb34fa4 |
# slicer imports
from __main__ import vtk, qt, ctk, slicer
# vmtk includes
import SlicerVmtkCommonLib
#
# Level Set Segmentation using VMTK based Tools
#
class LevelSetSegmentation:
def __init__( self, parent ):
parent.title = "Level Set Segmentation"
parent.categories = ["Vascular Modeling Toolkit", ]
... | jcfr/SlicerExtension-VMTK | PythonModules/LevelSetSegmentation.py | Python | apache-2.0 | 31,688 | [
"VTK"
] | 23fbbe4d9f0d875db55a8dd0e5022b081d01d086e81b7c5d0c508002674ec903 |
"""
This migration script adds the request_event table and
removes the state field in the request table
"""
# Need our custom types, but don't import anything else from model
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.exc import *
from migrate import *
from migrate.changeset import *
import ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0027_request_events.py | Python | gpl-3.0 | 3,542 | [
"Galaxy"
] | fc22011f0884fd57c5aa6002983eb1851623c7ddf9bfdb52ba2e16569f9ae246 |
# Copyright 2013-2019 The Meson development team
# 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 agree... | QuLogic/meson | mesonbuild/dependencies/misc.py | Python | apache-2.0 | 22,949 | [
"NetCDF"
] | aebc96e3a7e40fd3cb9a7c604128893ca5db20fa852416c4d0e3486e294cf849 |
import astropy.io.fits as pyfits
import astropy.wcs as pywcs
import os
import numpy as np
import montage_wrapper as montage
import shutil
import sys
import glob
import time
from matplotlib.path import Path
from scipy.ndimage import zoom
from pdb import set_trace
_TOP_DIR = '/data/tycho/0/leroy.42/allsky/'
_INDEX_DIR ... | arlewis/galaxy_cutouts | versions/extract_stamp_v2.py | Python | mit | 23,234 | [
"Galaxy"
] | 88546be8312873a514343f2bfc848a9a5ebdc129d10ec988d377c272e723fff3 |
########################################################################
# File: Operation.py
# Date: 2012/07/24 12:12:05
########################################################################
"""
:mod: Operation
.. module: Operation
:synopsis: Operation implementation
Operation implementation
"""
# Disable inva... | fstagni/DIRAC | RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 10,442 | [
"DIRAC"
] | 3d7f83c6e66ad9c7ef4ba25562cb4f635ef10460e361a5e54192a6a7101b7489 |
import lb_loader
import numpy as np
import pandas as pd
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
collision_rate = 1.0 / u.picoseconds
n_steps = 1500
temperature = 300. * u.kelvin
system, positions = lb_loader.load_lb()
hmc_integrators.guess_force_group... | kyleabeauchamp/HMCNotes | code/old/test_ghmc.py | Python | gpl-2.0 | 1,915 | [
"OpenMM"
] | 8bd607eb8279999a3b9f886c5d343a0437148d3295c820eb23bacfd6e435ad92 |
'''
Created on Jul 31, 2012
@author: arenduchintala
'''
import math
import pickle
import numpy
from scipy import stats
def dbgprint(*args):
return
class GaussianNaiveBayes(object):
'''
classdocs
gaussian naive bayes classifier
a single training instance tuple:
(label, [(feature,value), (fe... | alexf101/indoor-tracking | FingerprintsREST/views/MatchLocation/GaussianNB.py | Python | gpl-2.0 | 4,630 | [
"Gaussian"
] | be46ab4d000478ee61dbd09fb02ba7071973508fd8c301c73bd65f05863073d3 |
import numpy as np
import cvxopt as co
def load_mnist_dataset():
import torchvision.datasets as datasets
mnist_train = datasets.MNIST(root='../data/mnist', train=True, download=True, transform=None)
mnist_test = datasets.MNIST(root='../data/mnist', train=False, download=True, transform=None)
test_labe... | nicococo/tilitools | tilitools/utils_data.py | Python | mit | 5,881 | [
"Gaussian"
] | 2756fc10b985b244ecb6c0364438df37acbacd9ebb2911705234501461f1e30a |
# -------------------------------------------------------------------------
# Name: Land Cover Type module
# Purpose:
#
# Author: PB
#
# Created: 15/07/2016
# Copyright: (c) PB 2016
# -------------------------------------------------------------------------
from cwatm.management_modules.data_handling... | CWatM/CWatM | cwatm/hydrological_modules/landcoverType.py | Python | gpl-3.0 | 46,001 | [
"NetCDF"
] | 77e656c06a4d4aaa0fcad9b9c01e1d17dab561307e75b80476d29bb2b7fa79f8 |
from django.conf.urls import patterns, include, url
from django.views.generic import DetailView, ListView
from tastypie.serializers import Serializer
from tastypie.api import Api
import neuroelectro.api
import inspect
from django.contrib import admin
# Uncomment the next two lines to enable the admin:
#from d... | lessc0de/neuroelectro_org | neuroelectro/urls.py | Python | gpl-2.0 | 4,885 | [
"NEURON"
] | d63ca2740787891108e5ab01111980c3a0d5c88c70b8848356023b2ed007e26f |
import pysam
from svviz.tabix import ensureIndexed
class AnnotationSet(object):
def __init__(self, tabixPath, preset="bed"):
self.preset = preset
self.tabixPath = ensureIndexed(tabixPath, self.preset)
self._tabix = None
self.usingChromFormat = False
self._checkChromFormat(... | svviz/svviz | src/svviz/annotations.py | Python | mit | 2,368 | [
"pysam"
] | ec8ebfcf64a9764d77697f8841c153f0f49e1c92b827280e23430df877ae3054 |
""" ProxyProvider implementation for the proxy generation using local a PUSP
proxy server
"""
import urllib
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security.X509Chain import X509Chain # pylint: disable=import-error
from DIRAC.ConfigurationSystem.Client.Helpers import Registry
from DIRAC.Resources.ProxyPr... | chaen/DIRAC | Resources/ProxyProvider/PUSPProxyProvider.py | Python | gpl-3.0 | 3,140 | [
"DIRAC"
] | 82cfd4370fdfe752b7bbe455f910c297cd7349e3e66dff7207a10ae79d547c0e |
#!/usr/bin/env python
"""
lttree_postprocess.py
This is a stand-alone python script which checks the files created by
lttree.py to insure that the standard instance-variables ($variables)
have all been defined. This script performs a task which is very similar
to the task performed by lttree_check... | ibethune/lammps | tools/moltemplate/moltemplate/lttree_postprocess.py | Python | gpl-2.0 | 15,992 | [
"LAMMPS"
] | 70e41b1123b3351505ee5bb41bdd1132ea778d1e5c5642b8038462ad786d2718 |
from __future__ import print_function
import numpy as np
from chemlab.core import System, Atom, Molecule
from chemlab.io import datafile, add_default_handler
from chemlab.io.handlers import GromacsIO
from chemlab.io.handlers import EdrIO
from nose.tools import assert_raises, eq_
from nose.plugins.skip import SkipTest... | chemlab/chemlab | tests/test_io.py | Python | gpl-3.0 | 4,636 | [
"GAMESS",
"Gromacs",
"cclib"
] | 1e54c92dc37140cc8099a0c8ac08678611dec4701e5db5f5e80ae03c198786cc |
# -*- coding: utf-8 -*-
# benchmark.py ---
#
# Filename: benchmark.py
# Description: Script for performance benchmarking
# Author:
# Maintainer:
# Created: Thu Jan 23 16:06:25 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Chan... | dharmasam9/moose-core | tests/python/mpi/benchmark.py | Python | gpl-3.0 | 4,984 | [
"MOOSE"
] | 71bf6439fe1f4e6c43a3ab40a42a322ac074d7aec185063148613b8499dd36a0 |
import numpy as np
import pandas as pd
returns = prices.pct_change()
returns.dropna()
returns.std()
deviations = (returns - returns.mean())**2
squared_deviations = deviations ** 2
variance = squared_deviations.mean()
volatility = np.sqrt(variance)
me_m = pd.read_csv('./Data/Portfolios_Formed_on_ME_monthly_EW.csv',... | nealchenzhang/Py4Invst | EDHEC/CourseOne.py | Python | mit | 2,869 | [
"Gaussian"
] | 1411790a3a4194d463abc2ea6258e806096a31fe37097123e61dba30e647ee16 |
"""
Ax_Metrics - EROut plugin 'geckoboard_bullet'
Writes Geckoboard JSON output for various charts for use with
http://www.geckoboard.com.
Contents:
- EROut_geckoboard_bullet - bullet chart
See:
- https://developer.geckoboard.com/#bullet-graph
----------------------------------------------------------------... | axonchisel/ax_metrics | py/axonchisel/metrics/io/erout/plugins/ero_geckoboard/bullet.py | Python | mit | 10,675 | [
"Amber"
] | 3613b136dafbef377dc5823ff358a9a5b5ee9ba37f84029b6c8ef657f9f3aea1 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a BSE calculation using yambo
#
from __future__ import print_function
import sys
from yambopy import *
from qepy import *
from schedulerpy import *
import argparse
import shutil
yambo = "yambo"
p2y = "p2y"
prefix = 'bn'
scheduler = Scheduler.factory
def create_save(... | henriquemiranda/yambopy | tutorial/bn/bse_conv_bn.py | Python | bsd-3-clause | 6,243 | [
"Yambo"
] | 49fc980315fb1f756498d13fd4f88238050f163662e095321dbc01c75d39e1c9 |
'''Copyright(C): Leaf Johnson 2011
This file is part of makeclub.
makeclub 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 versi... | cardmaster/makeclub | controlers/member.py | Python | agpl-3.0 | 5,244 | [
"VisIt"
] | f8ef2d049d48e9f2caec79a64f357cb82ca9fce37cd5c8620b2c670c616774bc |
from matplotlib.axes import Axes
from matplotlib import colors as mpl_colors
from matplotlib import path
from scipy import optimize
import numpy as np
import sys
from matplotlib import __version__
from . import colors
from . import _tools
mpl_2 = __version__[0] == "2"
class Axes_bpl(Axes):
name="bpl"
d... | gillenbrown/betterplotlib | betterplotlib/axes_bpl.py | Python | mit | 69,193 | [
"Gaussian"
] | 004eb6d6f83f6e1273393333f6b202eebab6d34cf9e2d6e1e458abcd95fd4a37 |
#coding:utf8
'''
Created on 2013-8-2
@author: lan (www.9miao.com)
'''
from firefly.utils.singleton import Singleton
class GlobalObject:
__metaclass__ = Singleton
def __init__(self):
self.netfactory = None#net前端
self.root = None#分布式root节点
self.remote = {}#remote节点
self... | yangdw/PyRepo | src/annotation/Firefly/firefly/server/globalobject.py | Python | mit | 2,453 | [
"Firefly"
] | befa344d8948ef1e2ea24fce1c413a1620aef2aac2330ccc85c951479ddc731e |
import os
import time
import math
import director.vtkAll as vtk
import PythonQt
from PythonQt import QtCore
from PythonQt import QtGui
from director import getDRCBaseDir as getDRCBase
from director import botspy
from director import openscope
import functools
_mainWindow = None
_defaultRenderView = None
def getMainW... | mitdrc/director | src/python/director/applogic.py | Python | bsd-3-clause | 8,862 | [
"VTK"
] | a950b98da52b725c746957192c40724d4563c740be70b49ac0610b3423ac274b |
from umibukela.importer.mavc import cycle1_2
"""
_________ _____ _________ _________ _____
/ _____/ / _ \ / _____// _____/ / _ \
\_____ \ / /_\ \ \_____ \ \_____ \ / /_\ \
/ \/ | \/ \/ \/ | \
/_______ /\____|__ /_______ /_______ /\____|__ /
... | Code4SA/umibukela | umibukela/importer/mavc/cycle1_2_sassa.py | Python | mit | 9,658 | [
"VisIt"
] | 21854bd5336c4fb8cbd03add09cb7158cb54bb3a5c2813a919ea4fa6a3735716 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | stacked_capsule_autoencoders/capsules/plot.py | Python | apache-2.0 | 10,874 | [
"Gaussian"
] | 32bab5ca1afcba0ec0be18fac34249417e69210944a65591ec9d87e2bc8da3fe |
# config.py ---
#
# Filename: config.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Sat Feb 13 16:07:56 2010 (+0530)
# Version:
# Last-Updated: Mon Nov 15 09:53:00 2010 (+0530)
# By: Subhasis Ray
# Update #: 145
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
... | BhallaLab/moose-thalamocortical | gui/config.py | Python | lgpl-2.1 | 3,143 | [
"MOOSE"
] | 02725f10c66bc1b05c29836b0aade806aa86056dfa4c4471d03202cff6a4e5f9 |
# 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/engine_lb.py | Python | gpl-3.0 | 6,177 | [
"ESPResSo"
] | a6e3c8fd802f9c721529a01657f228e802bdba3f968c954b7b3b78e003e88b4a |
#!/usr/bin/python
from multiprocessing import Pool
import time
import os
import sys
import argparse
import math
from homolog4 import *
from collections import defaultdict
import itertools
from collections import Counter
from Levenshtein import distance
import cPickle as pickle
# Copyright(C) 2014 David Ream
# Releas... | reamdc1/gene_block_evolution | make_event_distance_matrix.py | Python | gpl-3.0 | 23,885 | [
"BLAST"
] | 3bb98ec4dedbfcfccbaea2fd00989a9b414f117a46cda0c47e9416399b0eab3f |
from __future__ import print_function
# -*- coding: utf-8 -*-
"""This module defines I/O routines with CASTEP files.
The key idea is that all function accept or return atoms objects.
CASTEP specific parameters will be returned through the <atoms>.calc
attribute.
"""
from numpy import sqrt, radians, sin, cos, matrix, ... | suttond/MODOI | ase/io/castep.py | Python | lgpl-3.0 | 23,925 | [
"ASE",
"CASTEP"
] | 32122a632914007ecf90a702c6e6ffb31d007d46e1e67d1357b7efa7969ea8d5 |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import webnotes
import webnotes.utils
from webnotes.utils import add_days, cint, cstr, flt, getdate, nowdate, _round
from webnotes.utils import cst... | Tejal011089/med2-app | selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 23,576 | [
"VisIt"
] | e940111e17eb96515eb2750d870dad09df04a2216feecfe82aa882b7fa50317a |
"""
Provides rolling statistical moments and related descriptive
statistics implemented in Cython
"""
from __future__ import division
from functools import wraps
from collections import defaultdict
from numpy import NaN
import numpy as np
from pandas.core.api import DataFrame, Series, Panel, notnull
import pandas.al... | bdh1011/wau | venv/lib/python2.7/site-packages/pandas/stats/moments.py | Python | mit | 39,028 | [
"Gaussian"
] | 21a76d8d4038162fd5019ed4028287ddcec2bb0035f24e4373a9b57dfa2cac45 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | doc/sphinxman/source/psi4doc/ext/relbar_toc.py | Python | lgpl-3.0 | 2,511 | [
"Psi4"
] | 3a0045740158c51f12ba99adb082270d9bc3c48c7192ac43998d4cded44adefa |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_lb_profile.py | Python | gpl-3.0 | 1,170 | [
"ESPResSo"
] | ab54e0ec07f27b7f7cc8ea3b12ec1c303881cddc529e0986c6a703072234ff82 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# LAMMPS documentation build configuration file, created by
# sphinx-quickstart on Sat Sep 6 14:20:08 2014.
#
# 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
# aut... | ramisetti/lammps | doc/utils/sphinx-config/conf.py | Python | gpl-2.0 | 10,029 | [
"LAMMPS"
] | a2eddb24ea4974b2f3118c724fc2cf81daffc98002dfc78ce690f38d5216b90b |
import types
import os
import sys
import imp
from DIRAC.Core.Utilities import List
from DIRAC import gConfig, S_ERROR, S_OK, gLogger
from DIRAC.ConfigurationSystem.Client.Helpers.CSGlobals import Extensions
from DIRAC.ConfigurationSystem.Client import PathFinder
class ModuleLoader( object ):
def __init__( self, im... | avedaee/DIRAC | Core/Base/private/ModuleLoader.py | Python | gpl-3.0 | 9,914 | [
"DIRAC"
] | a242f08f9b6aeac5279e96934be57efdd58f14d451a7ed1d60260f196a131231 |
from __future__ import unicode_literals
import unittest
import os
import json
from pymatgen.core.periodic_table import Element
from pymatgen.phonon.dos import PhononDos, CompletePhononDos
from pymatgen.util.testing import PymatgenTest
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
... | xhqu1981/pymatgen | pymatgen/phonon/tests/test_dos.py | Python | mit | 2,515 | [
"pymatgen"
] | 4a53705227cfe1c9a5fb840fc9bca8a38e79b6b87d4b693e0b7218e1ed0e2dbd |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | amir-qayyum-khan/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 109,839 | [
"VisIt"
] | ff0e395b02cab72f9b1609b38cfc1abd6eeecd0f2f44e16e290c4597fbe7a5ca |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed ... | JWDebelius/scikit-bio | skbio/tree/tests/test_majority_rule.py | Python | bsd-3-clause | 6,695 | [
"scikit-bio"
] | 402821596829665c197a49f7354951cfc74013d059a80cb8121c716673aab037 |
#!/usr/bin/python
from __future__ import division
import numpy as np
import argparse, itertools
import matplotlib.pyplot as plt
from sklearn import svm
from template_speech_rec import configParserWrapper
from scipy.spatial.distance import pdist, squareform, cdist
def main(args):
"""
"""
config_d = configP... | markstoehr/phoneclassification | local/CSVMTrain.py | Python | gpl-3.0 | 6,956 | [
"Gaussian"
] | 69e0c4f58c0d56f0c6383de66c0460a1c1462174f82073f3e63557308d9bbbd4 |
# Copyright 2012 by Eric Talevich. All rights reserved.
# This code is part of the Biopython distribution and governed by its license.
# Please see the LICENSE file that should have been included as part of this
# package.
"""Command-line wrapper for the tree inference program RAxML.
Derived from the help page for RA... | bryback/quickseq | genescript/Bio/Phylo/Applications/_Raxml.py | Python | mit | 19,768 | [
"Biopython"
] | 24ac08cc61fcd3c658ae99ca93f76cb19a65015e45145bd2cdb98e0270591edf |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO support for Exonerate output formats.
This module adds support for handli... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SearchIO/ExonerateIO/__init__.py | Python | gpl-2.0 | 13,014 | [
"Biopython"
] | 78fe17b09c6fb9e4c82c3b6bf8848ba74c812d2815525df12cceff1600696b2a |
#!/usr/bin/env python
from __future__ import division
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout", "Greg Caporaso", "Meg Pirrung"]
__license__ = "GPL"
__version__ = "1.5.0-dev"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"... | cuttlefishh/emp | legacy/code/emp/most_wanted_otus.py | Python | bsd-3-clause | 17,837 | [
"BLAST"
] | efffb3917d06faee469a185802703b69ec6f280a52db82da55ead1649336ccf2 |
'''
Show how to do box generation on the fly
I try to use the least dependency but there still remains some
pls, if this cannot work by default, run :
pip install biopython pyparsing numpy scipy matplotlib prody
in your clean python environment.
'''
from vector import vector_generator,Box
def generate_box_onfly(r... | Reimilia/pdb_sth | vector_generation/example.py | Python | mit | 1,890 | [
"Biopython"
] | 1f7c5210fba444dba2b7d4c444cfaaf9274b6fc7dc0e4640c7c5c339bcf0e368 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | sxjscience/tvm | python/tvm/script/meta_unparser.py | Python | apache-2.0 | 1,702 | [
"VisIt"
] | 08408e0b70db8508b8211d13db7a8cf0724ae9640449005f6484b8300ef06a6f |
# Authors: Denis Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import numpy as np
from os import path as op
import glob
import tempfile
from shutil import rmtree
import atexit
def create_chunks(sequence, size):
"""Generate chunks from a sequence
Note. copied from MNE-Python
Parameters... | drammock/pyeparse | pyeparse/utils.py | Python | bsd-3-clause | 3,374 | [
"Gaussian"
] | 13f11f447cd46d66028a561cdc423ca6106b367feacba7a6e8016ecf140c9fe9 |
#
# Copyright (C) 2004 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import rdBase
try:
from rdkit.SimDivFilters import rdSimDivPickers
from rdkit.SimDivFilters.rdSimDivPickers import *
except ImportError:
import traceback
rdSimDivPickers=None
| adalke/rdkit | rdkit/SimDivFilters/__init__.py | Python | bsd-3-clause | 269 | [
"RDKit"
] | 5194bd3a72268363594f53fc20cc26b807c981cc4ee036a530cedc696f8386e6 |
"""
Tests for Normalizing Flows.
"""
import os
import sys
import pytest
import deepchem
import numpy as np
import unittest
from deepchem.data import NumpyDataset
try:
import tensorflow as tf
import tensorflow_probability as tfp
from deepchem.models.normalizing_flows import NormalizingFlow, NormalizingFlowModel... | deepchem/deepchem | deepchem/models/tests/test_normalizing_flows.py | Python | mit | 1,505 | [
"Gaussian"
] | dc09816dd0c92baac195faa9a336fb649aa03f08a14a761f4cedb860ad7e43f9 |
import ast
import pydot
class GraphNodeVisitor(ast.NodeVisitor):
def __init__(self):
self.graph = pydot.Dot(graph_type='graph', **self._dot_graph_kwargs())
def visit(self, node):
if len(node.parents) <= 1:
self.graph.add_node(self._dot_node(node))
if len(node.parents) == ... | librallu/RICM4Projet | parser/astmonkey/astmonkey-0.1.1/build/lib/astmonkey/visitors.py | Python | gpl-3.0 | 19,017 | [
"VisIt"
] | 9c35a0b1541c03c79281dfe50c90c94631a9b2e9816179f57047eb47755b8388 |
from i3pystatus.core.util import internet, require
from i3pystatus.weather import WeatherBackend
from datetime import datetime
from urllib.request import urlopen
GEOLOOKUP_URL = 'http://api.wunderground.com/api/%s/geolookup%s/q/%s.json'
STATION_QUERY_URL = 'http://api.wunderground.com/api/%s/%s/q/%s.json'
class Wun... | richese/i3pystatus | i3pystatus/weather/wunderground.py | Python | mit | 11,545 | [
"VisIt"
] | e3bfa284aa4e0276c627c07dd5305218787eeb588ed8cd5d0e7d7827775394b9 |
import numpy as np
from NeuronNetworkLayer import NeuronNetworkLayer
def add_dirac_pulse(V, firings, dirac_pulse=30):
"""
Given a record of when neurons fired, will add Dirac pulses of the given magnitude to the
membrane potentials in V.
"""
if firings.size > 0:
V[firings[:, 0], firings[:... | lawrencejones/neuro | Exercise_4/neuro/NeuronNetwork.py | Python | gpl-3.0 | 3,528 | [
"DIRAC",
"NEURON"
] | 26a82caa2cd6d293721561e3649663f38249fd4918837eac91f6dcd310777f77 |
"""Tests for composite filter """
from __future__ import (print_function, absolute_import, division, unicode_literals)
import os
import pytest
import numpy as np
import nebulio
import pysynphot
from nebulio.tests.utils import this_func_name
from matplotlib import pyplot as plt
def plot_filterset(fs):
title = thi... | deprecated/nebulio | nebulio/tests/test_composite.py | Python | mit | 3,402 | [
"Gaussian"
] | c61d29e6dfe9e4aa3d348d154768da83d5ca18e5f24a35f56fe40b60cccd201b |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'Prescription'
db.create_table(u'patient_prescription', (
(u'id', self.gf('django... | aazhbd/medical_info01 | patient/migrations/0009_auto__add_prescription__chg_field_routinecheckup_date__chg_field_labor.py | Python | bsd-3-clause | 30,927 | [
"VisIt"
] | b67ce273139217b4901b4190d5aa240d68a7ad2d6acfead8618e66940661b098 |
"""Prototype pattern
"""
import copy
from collections import OrderedDict
class Book:
def __init__(self, name, authors, price, **kwargs):
"""Examples of kwargs: publisher, length, tags, publication date"""
self.name = name
self.authors = authors
self.price = price
self.__dic... | jackaljack/design-patterns | prototype.py | Python | mit | 1,912 | [
"Brian"
] | be4613f83a2acc0ba38bd6a86ab374482d1053627ac4584fab15eaac74f59283 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Quantum ESPRESSO
#####################
"""
from .cp.dynamics import parse_symbols_from_input, parse_evp, parse_xyz
| exa-analytics/atomic | exatomic/qe/__init__.py | Python | apache-2.0 | 257 | [
"Quantum ESPRESSO"
] | 63405e2f2f0c941f62163de8d88cf8d846c60fb6b4862939d614edc063ae5c19 |
"""
Tabular datatype
"""
import pkg_resources
pkg_resources.require( "bx-python" )
import logging
import data
from galaxy import util
from cgi import escape
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
from sniff import *
log = logging.getLogger(__name__)
class Tabular... | volpino/Yeps-EURAC | lib/galaxy/datatypes/tabular.py | Python | mit | 15,751 | [
"Galaxy"
] | cdf3c23cc82c98eaec01fa64fffe7a0fc770a59261a80a7afb41393579c32167 |
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary for... | Nikea/VisTrails | vistrails/gui/mashups/mashup_app.py | Python | bsd-3-clause | 27,120 | [
"VTK"
] | 985103b33e7f1ea4754bf1512597d4dfc107108f6af12e049a4f6ea1617adb2d |
#
# This file is a part of the normalize python library
#
# normalize is free software: you can redistribute it and/or modify
# it under the terms of the MIT License.
#
# normalize is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FI... | hearsaycorp/normalize | tests/test_record.py | Python | mit | 7,177 | [
"VisIt"
] | 1e19a75b986364b8cd097356f879783acc43b470aa42f646b0ec13b96f5b9c01 |
""" Test_RSS_Command_GOCDBStatusCommand
"""
__RCSID__ = '$Id$'
from datetime import datetime, timedelta
import mock
from DIRAC import gLogger, S_OK
from DIRAC.ResourceStatusSystem.Command.DowntimeCommand import DowntimeCommand
"""
Setup
"""
gLogger.setLevel('DEBUG')
# Mock external libraries / modules not interes... | andresailer/DIRAC | ResourceStatusSystem/Command/test/Test_RSS_Command_GOCDBStatusCommand.py | Python | gpl-3.0 | 11,902 | [
"DIRAC"
] | 71c000fc1e923c285f18de88ee123faeddf805785c8ed6596c7886cc5908f968 |
# Copyright (C) 2010-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library ... | FedoraScientific/salome-paravis | test/VisuPrs/SWIG_scripts/A8.py | Python | lgpl-2.1 | 2,064 | [
"ParaView",
"VTK"
] | e69a7fd4b85cc163df3cb606e0e1a9af6145314dd4030578f250c2095dd758b5 |
"""
The :mod:`sklearn.lda` module implements Linear Discriminant Analysis (LDA).
"""
from __future__ import print_function
# Authors: Matthieu Perrot
# Mathieu Blondel
import warnings
import numpy as np
from scipy import linalg
from .base import BaseEstimator, ClassifierMixin, TransformerMixin
from .utils.e... | soulmachine/scikit-learn | sklearn/lda.py | Python | bsd-3-clause | 9,517 | [
"Gaussian"
] | 180a85fd1243c1579826db0b5403aca94890d228b75f69b377166ed1ee8be12d |
"""
This is the XROOTD StorageClass
"""
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Resources.Storage.Utilities import checkArgumentFormat
from DIRAC.Resources.Storage.StorageBase import StorageBase
from DIRAC.Core.Utilities.Pfn ... | vmendez/DIRAC | Resources/Storage/XROOTStorage.py | Python | gpl-3.0 | 56,979 | [
"DIRAC"
] | 5f51d3715b17f591271c9f17821f0b4bebba56b20145127b98a01b3c64b8c804 |
# Makes print and division act like Python 3
from __future__ import print_function, division
# Import the usual libraries
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
from copy import deepcopy
#from .nrc_utils import S, stellar_spectrum, jupiter_spec, con... | JarronL/pynrc | pynrc/nb_funcs.py | Python | mit | 54,609 | [
"Gaussian"
] | 153620e141963795442e69723c9a8a39376767994fb128fd2e6845a8ef4ee034 |
# coding: utf-8
"""
Demonstrate how to use MPI with kombine. Run this module with
mpiexec -n <nprocesses> python mpi-demo.py
where <nprocesses> is the number of processes to spawn.
"""
from __future__ import division, print_function
__author__ = "adrn <adrn@astro.columbia.edu>"
# Third-party
imp... | bfarr/kombine | examples/mpi-demo.py | Python | mit | 1,082 | [
"Gaussian"
] | 49b929909d80869aecd3b19954deac0c073a19d60f14c9bd255d232caf572933 |
# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Robert Layton <robertlayton@gmail.com>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Philippe Gervais <philippe.gervais@inria.fr>
# Lars Buitinck
... | meduz/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 46,724 | [
"Gaussian"
] | cc013557800356ff9967657fbcbd0e8100bac0e82fcada3502a83921ce4ed229 |
## Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
import rdkit.Numerics.rdAlignment as rdAlg
from rdkit import Geometry
from rdkit import RDConfig
import os,sys
import unittest
import numpy.oldnumeric as Numeric
import math
import copy
def lstFeq(l1, l2, tol=1.e-4):
if (len(list(l1)) != len(list(l2))... | rdkit/rdkit-orig | Code/Numerics/Alignment/Wrap/testAlignment.py | Python | bsd-3-clause | 7,036 | [
"RDKit"
] | 62ab60d0f94e33c5c9db1cb05cafb857954b97fe86b8fc20f2c98e84a5f6fff9 |
#!/usr/bin/env python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Version: 0.7+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
For developers who work from ... | isislovecruft/leekspin | versioneer.py | Python | mit | 25,770 | [
"Brian"
] | 6c8c351b97dafad5f4787047dd08f1adf58bd5fe6350b199e7028bd6eaf508e6 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module defines the base aperture classes.
"""
import abc
import copy
import numpy as np
from astropy.coordinates import SkyCoord
import astropy.units as u
from .bounding_box import BoundingBox
from ._photometry_utils import (_handle_units, _pre... | astropy/photutils | photutils/aperture/core.py | Python | bsd-3-clause | 26,226 | [
"Gaussian"
] | 9dd5372066fefeca3a1b89c900e01fde7a5d1bf3357890341bbb8ef02e4b3f15 |
import openvoronoi as ovd
import ovdvtk # comes with openvoronoi
import time
import vtk
import datetime
import math
import random
import os
import sys
import pickle
import gzip
import ovdgenerators as gens # comes with openvoronoi
import randompolygon as rpg # random polygon generator see https://github.com/aewallin... | aewallin/openvoronoi | python_examples/chain_3_rpg_loop.py | Python | lgpl-2.1 | 3,649 | [
"VTK"
] | 6eaea0b719ca422b9dadaebe47d237725c7166ebb61f16fb2730610142552ebf |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements more advanced transformations.
"""
import logging
import math
import warnings
from fractions import Fraction
from itertools import groupby, product
from math import gcd
from string import ascii_lower... | vorwerkc/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 88,361 | [
"ASE",
"CRYSTAL",
"pymatgen"
] | 3ee9d06ce4af6a3be9b7c08f87d4c9afced68d9cd311f39ce209be1e6e83a83b |
from __future__ import absolute_import
from __future__ import division
import deprecation
import numpy as np
import scipy.ndimage as scind
from scipy.ndimage import (
binary_erosion,
convolve,
gaussian_filter,
generate_binary_structure,
label,
map_coordinates,
)
from . import _filter
from .rank... | CellProfiler/centrosome | centrosome/filter.py | Python | bsd-3-clause | 71,074 | [
"Gaussian"
] | bbf7fa52014efd858e7b03f49ad7edf3d7f4833e8ca73f89631651b32e98200d |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. 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; either ... | sam-m888/gprime | gprime/filters/rules/person/_regexpname.py | Python | gpl-2.0 | 2,185 | [
"Brian"
] | b22b9ec021d4b24a308e1af95d7c1fea06f1601977912fc959b192c46fb74eea |
from behave import *
import uuid as uuid
from django.contrib.auth.models import User
from page_actions import *
from page_objects import *
username = 'user999999999'
uid = uuid.uuid4()
email_address = 'ureport@webpro.com'
password = 'password'
@given(u'I am a logged into wep-pro')
def step_impl(context):
login_... | rapidpro/ureport-web-participation | features/steps/shout_step.py | Python | agpl-3.0 | 655 | [
"VisIt"
] | 1188b18faaee38afd69451650e764ae455fbd107190c1ecacd6bbf54cb62b381 |
import os
import shutil
import logging
import re
from functools import partial, wraps
import netCDF4
import numpy as np
from django.db import models, transaction
from django.core.exceptions import ValidationError
from django.core.files.uploadedfile import UploadedFile
from django.template import Template, Context
fro... | ResearchSoftwareInstitute/MyHPOM | hs_file_types/models/netcdf.py | Python | bsd-3-clause | 44,192 | [
"NetCDF"
] | d96ae856dbce75e1507fd53a37c95afff1f056f4579fc1f298b7dd2fd99e5a53 |
import MDAnalysis
import numpy as np
try:
from MDAnalysis.analysis import psa
except:
pass
class PSA_sqnormBench(object):
"""Benchmarks for MDAnalysis.analysis.psa.
sqnorm
"""
params = ([2,3,4],
[100,1000,10000],
[None, 0, 1, -1])
#... | MDAnalysis/mdanalysis | benchmarks/benchmarks/analysis/psa.py | Python | gpl-2.0 | 4,688 | [
"MDAnalysis"
] | 9b3839f1378b3ed9c70bcdd857d6c5e7d98db4a4c4c0a32a16d9ec1c8f3d9ee8 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0007_auto_20150429_0341'),
]
operations = [
migrations.AddField(
model_name='visit',
name='... | koebbe/homeworks | visit/migrations/0008_visit_is_completed.py | Python | mit | 406 | [
"VisIt"
] | 9524f8a9fe6194cfd5d2c4c4fa53a22bad9959d9c339d8d459736bebfc752294 |
# Copyright (C) 2015-2017,2019
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free... | bakery-cg2at/bakery | src/gromacs_topology.py | Python | gpl-3.0 | 51,694 | [
"ESPResSo",
"Gromacs"
] | 97c7532369c8d2fd3347f6b8701d0bd0c697f63bf8599ee5bc65a9dc345c0677 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/test/bigdl/chronos/model/test_arima.py | Python | apache-2.0 | 4,423 | [
"ORCA"
] | 2513e1270762876b668de1d1f8f52e544dadd1ebd8cb83a1f9d1e60ad39225d2 |
########################################################################
# $HeadURL$
# File : AgentModule.py
# Author : Adria Casajus
########################################################################
"""
Base class for all agent modules
"""
__RCSID__ = "$Id$"
import os
import threading
import types
import... | Sbalbp/DIRAC | Core/Base/AgentModule.py | Python | gpl-3.0 | 17,594 | [
"DIRAC"
] | 443b378dc07d95046facc08ad411b8a99b0dda926d90d89c0e6e1f56c9d5cbbd |
#!/usr/bin/python
import os
import sys
import time
import glob
import trace
import tempfile
tmpdir = tempfile.mkdtemp(prefix='ase-')
os.chdir(tmpdir)
def build():
if os.system('svn checkout ' +
'https://svn.fysik.dtu.dk/projects/ase/trunk ase') != 0:
raise RuntimeError('Checkout of ASE fa... | slabanja/ase | tools/sphinx.py | Python | gpl-2.0 | 2,767 | [
"ASE"
] | 9dfe0de966c3b4367f6cd5894b493c97953d126d04610a3ae6eb8e2a37b55ad4 |
# -*- coding: utf-8 -*-
#
# test_synaptic_elements.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 ... | magnastrazh/NEUCOGAR | nest/serotonin/research/C/nest-2.10.0/pynest/nest/tests/test_sp/test_synaptic_elements.py | Python | gpl-2.0 | 3,448 | [
"Gaussian",
"NEURON"
] | 80bace34e2d71d3556c87cc61a10ed56695c9f91916c866b5939a5ee28f5fec5 |
"""
Finding a signal in a background
--------------------------------
Figure 5.26
Fitting a model of a signal in an unknown background. The histogram in the
top-right panel visualizes a sample drawn from a Gaussian signal plus a
uniform background model given by eq. 5.83 and shown by the line. The remaining
panels sho... | kcavagnolo/astroML | book_figures/chapter5/fig_signal_background.py | Python | bsd-2-clause | 3,660 | [
"Gaussian"
] | d53b8b4be667606a4c568fd9c375996416a929c3452ad57d51ee83951e305edf |
from __future__ import print_function
import time
from bokeh.browserlib import view
from bokeh.models import ColumnDataSource, DataRange1d, Plot, LinearAxis, Grid, GlyphRenderer, Circle, HoverTool, BoxSelectTool
from bokeh.models.widgets import Select, HBox, VBox, DataTable, TableColumn, StringFormatter, NumberFormat... | zrhans/python | exemplos/Examples.lnk/bokeh/glyphs/data_tables_server.py | Python | gpl-2.0 | 6,919 | [
"VisIt"
] | 6811f80ee3cda8987473cc25bf0cfb6d81ed1ce853f4b5c7628da4c0af530610 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
import numpy as np
import bob.ip.gabor
import skimage.measure
from braincode.util import configParser
from braincode.math import make_2d_gaussian
#from braincode.math import img_resize
def get... | sealhuang/brainCodingToolbox | braincode/prf/tfrecon_util.py | Python | bsd-3-clause | 5,942 | [
"Gaussian"
] | 2b4f76528e54b26715af2948283b8da703c0c08aca0f9dab9e38d29929b53155 |
#!/usr/bin/env python
# general imports
from numpy import *
from random import *
# imp general
import IMP
# our project
from IMP.isd import *
# unit testing framework
import IMP.test
class MockFunc:
def __init__(self, setval, evaluate, evalargs=1, update=None):
self.__set = setval
self.__eva... | shanot/imp | modules/isd/test/medium_test_GaussianProcessInterpolationRestraintNumericallyNoMean.py | Python | gpl-3.0 | 10,128 | [
"Gaussian"
] | 4b426ffa94ff2b011b60055cc0642737230b82141c5daeabf84d7a163a84f4e1 |
# LICENSE: Simplified BSD https://github.com/mmp2/megaman/blob/master/LICENSE
from __future__ import division ## removes integer division
import os
import numpy as np
from numpy.testing import assert_allclose, assert_equal, assert_raises
from scipy.spatial.distance import cdist, pdist, squareform
from scipy.sparse ... | jakevdp/megaman | megaman/geometry/tests/test_affinity.py | Python | bsd-2-clause | 3,661 | [
"Gaussian"
] | 6c833e71417dd05061fd6454bed4165925aa61eb14a50becf4a0c94dfa67c16b |
"""
Copyright (C) 2009-2015 Jussi Leinonen, Finnish Meteorological Institute,
California Institute of Technology
Permission is hereby granted, free of charge, to any person obtaining a copy of
this software and associated documentation files (the "Software"), to deal in
the Software without restriction, including wit... | jleinonen/pytmatrix | pytmatrix/orientation.py | Python | mit | 4,905 | [
"Gaussian"
] | 8e8255533245de0ec6948dbc719c78be22f6f51b6a12763d9ffeee0592e482b2 |
# -*- coding: utf-8 -*-
__docformat__='restructuredtext'
from popserver.tests.nodb_model import *
from popserver.tests import *
from fixture import DataTestCase
from popserver.tests import popfixtures
from popserver.agents.lastfm_agent import LastFmAgent
from popserver.agents.lastfm_client import LastFMClient
import p... | santisiri/popego | popego/popserver/popserver/tests/agents/test_lastfm.py | Python | bsd-3-clause | 6,723 | [
"Brian"
] | 1658015ab7d6f363748a34c74137e4ee1e7c1f564e9f6a6d02ac77794fcc0d06 |
import datetime
import hashlib
import itertools
import logging
import os
import time
from collections import defaultdict
from dataclasses import asdict, dataclass, field
from operator import itemgetter
from typing import (
IO,
AbstractSet,
Any,
Callable,
Collection,
Dict,
Iterable,
List,... | rht/zulip | zerver/lib/actions.py | Python | apache-2.0 | 296,769 | [
"Octopus"
] | 832e93507d1e8bd3102d83231e5e41a918e3cf0b08df13d2b19f95b7a5bbb730 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2006 Donald N. Allingham
# Copyright (C) 2007 Brian G. 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; ... | prculley/gramps | gramps/gen/filters/rules/note/__init__.py | Python | gpl-2.0 | 1,568 | [
"Brian"
] | ccbd12ccec0833c5b7ddb1dd69342e544b529b7e182e769dca0b9191c333fd97 |
"""
Module for running simulations
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
from __future__ import absolute_import
from builtins import round
from builtins import range
from builtins import str
from future import standard_library
standard_libr... | Neurosim-lab/netpyne | netpyne/sim/run.py | Python | mit | 10,719 | [
"NEURON"
] | d4c1ce1648241d3df2253482605143c0e43019fab3f021182b2dfcd28612a58d |
"""Base class for mixture models."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
import warnings
from abc import ABCMeta, abstractmethod
from time import time
import numpy as np
from .. import cluster
from ..base import BaseEstima... | chrsrds/scikit-learn | sklearn/mixture/base.py | Python | bsd-3-clause | 18,167 | [
"Gaussian"
] | 8b154c1662b6fb0f80345a71bdaea1a142ee680cb452e9b3888550424b49257e |
#!/usr/bin/env python
#* 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/lgpl... | harterj/moose | python/moosesqa/test/test_documents.py | Python | lgpl-2.1 | 2,645 | [
"MOOSE"
] | 866cb4c5fb8f55a9f2395fcb9877473fc0001ffc38e7c1e842ffdf1d1b4f8308 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.