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#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# createresource - Create resource from user request file
# Copyright (C) 2003-2011 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gen... | heromod/migrid | mig/server/createresource.py | Python | gpl-2.0 | 1,967 | [
"Brian"
] | d1cfc7c3a271a957247dc0df7f000c27b896a0328982633ed33684b8fb695a80 |
# ----------------------------------------------------------------------
# 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... | rbberger/lammps | python/lammps/formats.py | Python | gpl-2.0 | 6,821 | [
"LAMMPS"
] | c4d1381d234f972efdc29b0c4d685a98a9ae5fcc884dfd3dfdda67f0d361c2c6 |
"""
source.py
Source object for GALFACTS transiet search
04 June 2014 - Trey Wenger - creation
11 June 2014 - Joseph Kania - Modification
"""
import sys
import numpy as np
import make_plots
from scipy.optimize import curve_fit
class Source(object):
"""Source object for GALFACTS transient search"""
def __init__... | tvwenger/galfacts | source.py | Python | mit | 4,159 | [
"Gaussian"
] | 172e4df8e6aa938b8e898d610beb93c356827bd11d354bfe5142a0b0c82b5f9f |
#!/usr/bin/python
"""This script applies parsed BLAST results from a CSV file (produced by
parseblast.pl) to a series of GenBank files.
Oct 26, 2009 by Simon Eng
Changed the method of outputting statistics.
"""
try:
import optparse, csv, re, sys
from os import path
import logging.handlers
from... | kishori82/MetaPathways_Python.3.0 | libs/python_scripts/MetaPathways_create_amino_sequences.py | Python | mit | 16,158 | [
"BLAST"
] | fea21d49bd185ae5d95a5a97ff73130f3e7f3be96d966fa34ea20ac8b7244abb |
import numpy as np
import itertools
import scipy
from scipy.ndimage.filters import gaussian_filter
def smoothing(data, sigma, time):
'''
Return a smoothed array that has the same shape as our input.
Parameters
----------
data: A numpy array. It is the image data for one subject, one run.
sigma: Scalar or ... | timothy1191xa/project-epsilon-1 | code/utils/functions/smoothing.py | Python | bsd-3-clause | 820 | [
"Gaussian"
] | 77c86c54191ea9372eea00bc7e9379f717fa46fe7bf042501c674ecfa99e4fd2 |
#!/usr/bin/env python
#
# Copyright (C) 2016, the ximpol team.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# Thi... | lucabaldini/ximpol | ximpol/examples/gk_per.py | Python | gpl-3.0 | 8,004 | [
"Gaussian"
] | 84285ac9aea7648420b04c1d9aca9d0137e9f17ea7844648e92fb1cc2380b549 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-reportingtools/package.py | Python | lgpl-2.1 | 3,428 | [
"Bioconductor",
"VisIt"
] | a596a57b4ab8f6045274c40bb8ba6fac7b831b0a2eec7ad7d95a1a7b049b3698 |
"""
See the image regression notes in doc/extras/developer_notes.rst
"""
import time
import platform
import warnings
import inspect
import pathlib
import os
from weakref import proxy
from pathlib import Path
from PIL import Image
import imageio
import numpy as np
import pytest
import vtk
import pyvista
from pyvista._... | akaszynski/vtkInterface | tests/plotting/test_plotting.py | Python | mit | 61,956 | [
"VTK"
] | 7f16bb28219e345a97c617bfb838911bb11ecb24f02ae3209c80611092db6009 |
#!/usr/bin/env python
'''
TODO:
write all the atoms of the solvent molecule to the index file.
'''
import math
import sys
import numpy
import copy
import string
import MDAnalysis
import MDPackage
from MDPackage import Index
from MDPackage import Simple_atom
from MDPackage import usage
import time as Time
from MDAn... | zhuhong/Closest-solvent | Closest_solvent.py | Python | gpl-2.0 | 14,275 | [
"MDAnalysis"
] | 9f2bc9e1ae36fb3159806586aa4fa42e5de2c8738f00e56128729cebc18276ba |
from barak.utilities import between
from barak.io import parse_config, readtxt
from scipy.integrate import simps
import numpy as np
from barak.constants import Ryd_Ang, pi, hplanck
import os
def get_data_path():
""" Return the path to the data directory for this package.
"""
return os.path.abspath(__file_... | nhmc/cloudy | utils.py | Python | bsd-3-clause | 11,356 | [
"Galaxy"
] | dd5f434cb270e9dc3403ef4043745359305e631f7472ca8a9ba2ff5d1bf21701 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# In this example, an image is centered at (0,0,0) before a
# rotation is applied to ensure that the rotation occurs about
# the center of the image.
reader = vtk.vtkPNGReade... | timkrentz/SunTracker | IMU/VTK-6.2.0/Imaging/Core/Testing/Python/TestChangeInformation.py | Python | mit | 1,265 | [
"VTK"
] | 6dd1f7c138b5519cb08e08ee4c48be27eee0b1463465c456c63a9a0038b8b9b2 |
# the following items had incorrect stats and should be corrected now
# necklace of strife
# wind dancer tunic
# dispersing belt
# storm rider's boots
# wind dancer gloves
# Uhn'agh Fash
# Poison Protocol Pauldrons
# Wind Dancer's Spaulders
# lots of necks/heads
import math
class Item(object):
reforgable_stats = ... | dazer/ShadowCraft-Engine | test_ui/ui_data.py | Python | lgpl-3.0 | 23,019 | [
"Amber",
"CRYSTAL"
] | c3601cddd9488a1f67b69132a90d685b250b77b2f58d56628189d11f217d28b9 |
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause License.
""" Apply external fields to HPMC simulations.
"""
from hoomd import _hoomd
from hoomd.hpmc import _hpmc
from hoomd.hpmc import integrate
from hoomd.operation imp... | joaander/hoomd-blue | hoomd/hpmc/field.py | Python | bsd-3-clause | 45,911 | [
"CRYSTAL",
"HOOMD-blue"
] | 21947f9c38cb14f4bd044b8c47c265f8c3571bb48832c1e800a7a7749f512f70 |
from PyQt4 import QtCore, QtGui
#import acq4.Manager
import acq4.pyqtgraph as pg
import numpy as np
import acq4.util.functions as fn
import MapConvolverTemplate
import scipy
from acq4.analysis.tools import functions as afn
class MapConvolver(QtGui.QWidget):
sigOutputChanged = QtCore.Signal(object, object)
... | hiuwo/acq4 | acq4/analysis/modules/MapImager/MapConvolver.py | Python | mit | 10,053 | [
"Gaussian"
] | a28a18408e345e30dd0ba26c0272e59729d38bf95f36b3f7f6a1bf3078f482a2 |
# coding: utf-8
# Copyright 2013 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | wavemind/gcb17ml | tests/functional/test_classes.py | Python | apache-2.0 | 211,119 | [
"VisIt"
] | 570e2052dab28ca8a093c2777c62e2a112d819be1e68bbdb2cc9bad3a6fd9ef0 |
#!/usr/bin/env python
from argparse import ArgumentParser
from argparse import RawDescriptionHelpFormatter
import logging
import textwrap
import os.path
import os
from datetime import datetime, timedelta
from pprint import pprint
import json
import requests
from . import VERSION
from csirtg_indicator import Indicator
... | csirtgadgets/apwgsdk-py | apwgsdk/client.py | Python | mpl-2.0 | 8,943 | [
"Amber"
] | b3c7a0ab86daba3e80eae6c17477419eafcc236fc1833b087313903c69f5f5b4 |
# Demonstrate a non-parametric (parzen) density estimator in 1D
# Author: Gerardo Durán Martín
import superimport
import numpy as np
import matplotlib.pyplot as plt
from scipy.linalg import norm
plt.rcParams["axes.spines.right"] = False
plt.rcParams["axes.spines.top"] = False
def K(u, axis=0): return np.all(np.abs... | probml/pyprobml | scripts/parzen_window_demo2.py | Python | mit | 2,303 | [
"Gaussian"
] | 19afc95c5c3dc87b731697b6c5b06b4e55348de2db4c3061f633b14dc49102a4 |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_compiled_250.py | Python | gpl-3.0 | 3,909 | [
"Brian"
] | 8f3b56d225365924e6d90bfe48c56fb1bd78f16082fe66b2a0a2869db1be062f |
#!/usr/bin/env python
from __future__ import division
import sys
import csv
import random
# import required modules
import numpy as np
from scipy import signal
import pylab as plt
import math
# ------------------------------------------------------------
# Some elementary functions
# ---------------------------------... | Ralf3/samt2 | stats/stat_bw2.py | Python | gpl-3.0 | 30,435 | [
"Gaussian"
] | 0711a0c26e7224aee77da2d35cd389a3d3716cbaf09b39ccb7253ba7e862fbae |
# Copyright 2017 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... | DavidNorman/tensorflow | tensorflow/python/ops/linalg/linalg_impl.py | Python | apache-2.0 | 44,585 | [
"Gaussian"
] | ffda622c71a16dda9f507d8a8f42dd71b24b26c3ca9be77cd6965d4c11fed6db |
# -*- coding: utf8 -*-
import re
ACCESS_DENIED = 'ACCESS_DENIED'
ALREADY_REFUNDED = 'ALREADY_REFUNDED'
BANGO_ALREADY_PREMIUM_ENABLED = 'BANGO_ALREADY_PREMIUM_ENABLED'
BANK_DETAILS_EXIST = 'BANK_DETAILS_EXIST'
CANCEL = 'CANCEL'
CANT_REFUND = 'CANT_REFUND'
INTERNAL_ERROR = 'INTERNAL_ERROR'
# There is one of these for ev... | muffinresearch/solitude | lib/bango/constants.py | Python | bsd-3-clause | 4,047 | [
"BWA"
] | 131c7085d9b46f32b6907d5d10cb1be72ceb77754e8fcabe784777ee4d500f4b |
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2014-2016 Pierre Bélissent
#
# This program is heavily based on "narrativeweb.py" included in Gramps
# Copyrights for "narrativeweb.py":
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <j... | sam-m888/addons-source | DynamicWeb/dynamicweb.py | Python | gpl-2.0 | 202,986 | [
"Brian"
] | baaae2de4ee743d5f1c8f943e91d3f5ea9585285655164768ecb60f2a88fb69c |
from ase import Atoms
from gpaw import GPAW
from gpaw.test import equal
from ase.units import Bohr, Hartree
a = 7.5 * Bohr
n = 16
atoms = Atoms('He', [(0.0, 0.0, 0.0)], cell=(a, a, a), pbc=True)
calc = GPAW(gpts=(n, n, n), nbands=1, xc='PBE')
atoms.set_calculator(calc)
e1 = atoms.get_potential_energy()
niter1 = calc.g... | robwarm/gpaw-symm | gpaw/test/revPBE.py | Python | gpl-3.0 | 734 | [
"ASE",
"GPAW"
] | 0b811c8acc9867f56c3bec47435cb56a555433b4d903b1a5b59f4fbfd01bee51 |
import unittest
from src.underscore import _
class TestArrays(unittest.TestCase):
def test_first(self):
res = _([1, 2, 3, 4, 5]).first()
self.assertEqual(1, res, "first one item did not work")
res = _([1, 2, 3, 4, 5]).first(3)
self.assertEqual([1, 2, 3], res, "first multi item did... | serkanyersen/underscore.py | tests/test_arrays.py | Python | mit | 8,244 | [
"MOE"
] | 62f07289e37f037731708b7774f79ec8bc6e0aefd7c1cab3788e8f6376641c5f |
import requests
import tornado.web
from common.web import requestsManager
class handler(requestsManager.asyncRequestHandler):
MODULE_NAME = "seasonal"
@tornado.web.asynchronous
@tornado.gen.engine
def asyncGet(self):
self.write(requests.get("http://s.ripple.moe/bg.json", timeout=5).text)
| osuripple/lets | handlers/seasonalHandler.py | Python | agpl-3.0 | 299 | [
"MOE"
] | 9e4c3ccc68fdb7bb26ceb8f66e3490e9aee3041408d03cc584a02e9e263b5ba2 |
#!/usr/bin/env python
# This example shows how to use the InteractorStyleImage and add your
# own event handling. The InteractorStyleImage is a special
# interactor designed to be used with vtkImageActor in a rendering
# window context. It forces the camera to stay perpendicular to the
# x-y plane.
import vtk
from v... | naucoin/VTKSlicerWidgets | Examples/ImageProcessing/Python/ImageInteractor.py | Python | bsd-3-clause | 4,257 | [
"VTK"
] | d36034b8bdf0b296a4447885820b2257209eb1a29f4f67ac46fcb375f436a5f7 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""Unit tests for the `iris.fileformats.netcdf._load_cube` function."""
# Import iris.tests first so that some things can be i... | SciTools/iris | lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py | Python | lgpl-3.0 | 6,687 | [
"NetCDF"
] | 7677b902222a43f870ee83c2702cd99b2eb254ca9b4cac00b0ac32cc6ef664e8 |
import os
import numpy as np
import json
import ParameterContainer
from copy import deepcopy as dc
import pprint
##
# By convention, the parameters are named as, when applicable: "parameter"_"source"_"target" or along this line.
class global_parameters(ParameterContainer.ParameterContainer):
#class global_p... | pierreberthet/bg_dopa_nest | simulation_parameters.py | Python | gpl-2.0 | 40,826 | [
"NEURON"
] | accc9827c2845174e36dee39bdea4051175f44169d2513e983a9e65562c5e5a3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
TODO: Modify module doc.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "... | xhqu1981/pymatgen | pymatgen/analysis/tests/test_energy_models.py | Python | mit | 3,178 | [
"pymatgen"
] | 5799e041c496acf452316058a31f09519205377fb19cc3346eced5aa1b0cadc7 |
"""Example of NaCl calculation."""
from typing import List
import numpy as np
from phonopy import Phonopy
from phonopy.file_IO import parse_BORN, parse_FORCE_SETS
from phonopy.interface.vasp import read_vasp
# from phonopy.structure.atoms import PhonopyAtoms
def _append_band(bands, q_start, q_end):
band = []
... | atztogo/phonopy | example/NaCl/NaCl.py | Python | bsd-3-clause | 4,060 | [
"CRYSTAL",
"VASP",
"phonopy"
] | c36554248e475e8d981ffa6082afc74ec46128869765ff034889aa628bf6bc38 |
from django.db import models
class Color(models.TextChoices):
DARK_RED = "aa1409", "Dark red"
RED = "f44336", "Red"
PINK = "e91e63", "Pink"
ROSE = "ffe4e1", "Rose"
FUSCHIA = "ff66ff", "Fuschia"
PURPLE = "9c27b0", "Purple"
DARK_PURPLE = "673ab7", "Dark purple"
INDIGO = "3f51b5", "Indigo... | respawner/peering-manager | utils/enums.py | Python | apache-2.0 | 1,093 | [
"Amber"
] | eae08430e1c8c79ed8486a79735b1c3722532b6a23ad97cfc752c60f81042638 |
# Copyright (c) 2013-2015 University Corporation for Atmospheric Research/Unidata.
# Distributed under the terms of the MIT License.
# SPDX-License-Identifier: MIT
"""Test NCSS access code."""
from contextlib import contextmanager
from datetime import datetime
import numpy as np
from siphon.ncss import NCSS, NCSSQue... | dopplershift/siphon | siphon/tests/test_ncss.py | Python | mit | 6,833 | [
"NetCDF"
] | d953b556e8644ad69a43c15191b337fb220b1b6a4aa17cf4aa48f2113ea03239 |
import vtk
def main():
colors = vtk.vtkNamedColors()
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# cr... | lorensen/VTKExamples | src/Python/PolyData/Outline.py | Python | apache-2.0 | 1,142 | [
"VTK"
] | 1e4eab70c5e8c1d071d56e0728e976eb0b32a21b9ea6a29472be11a7fa39ea32 |
"""Takes an unrolled StencilModel and converts it to a C++ AST.
The third stage in processing. Input must be processed with
StencilUnrollNeighborIter first to remove neighbor loops and
InputElementZeroOffset nodes. Done once per call.
"""
import ast
import asp.codegen.cpp_ast as cpp_ast
import asp.codegen.ast_tools a... | richardxia/asp-multilevel-debug | specializers/stencil/stencil_convert.py | Python | bsd-3-clause | 9,865 | [
"VisIt"
] | 2cddfa287b29590aeb0f121a9d78c3062c31e72d0bb708caa3e6f4123ea66e3e |
#Copyright (C) 2013 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the h... | pannarale/pycbc | pycbc/strain/strain.py | Python | gpl-3.0 | 77,041 | [
"Gaussian"
] | f62f09c3320031bd4a37359e6d44aabbce250f5c9ae7f251273e50cefc6aafb1 |
"""
This module contains methods for the validation of production definitions
"""
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.TransformationSystem.Client.TransformationClient import TransformationClient
from DIRAC.Resources.Catalog.FileCatalog import FileCatalog
class ProdValidator(object):
def __init__... | DIRACGrid/DIRAC | src/DIRAC/ProductionSystem/Utilities/ProdValidator.py | Python | gpl-3.0 | 5,598 | [
"DIRAC"
] | 5209e2f49b9e3e466e326f7a8530488e647db59ce15c8316bcfc04a60ebbc0ae |
# -*- coding: utf-8 -*-
from pyramid.renderers import get_renderer
from pyramid.response import Response
from pyramid.view import view_config
class ViewTemplate(object):
def __init__(self, context, request):
self.context = context
self.request = request
renderer = get_renderer("templates/... | AnneGilles/agx_pyramid_example2 | src/pyramidonal/views.py | Python | bsd-3-clause | 2,494 | [
"Brian"
] | b666f7299ac6f86e25a99da38d8aba7206a7e18a0c9aa000e937905cd2d4a66f |
#!/usr/bin/env python
# encoding: utf-8
"""
bed_from_genbank.py
grab the gene records from a genbank file (edit for other record types).
- requires: biopython
"""
from __future__ import division
import os
from sys import argv
import baselib as b
class Rabbit:
def __init__(self,age,m):
self.age = age
... | KoenHoogendoorn1994/rosalind | 11.py | Python | gpl-3.0 | 1,384 | [
"Biopython"
] | 33fa7b5066eed4a728d0361ae719fdac25222570a92e4791caac21bf3b2400f4 |
import pdb
import numpy as np
import math
import time
import chainer
import chainer.functions as F
import chainer.links as L
from chainer import cuda
from util import gaussian_kl_divergence_standard
from util import gaussian_logp
class VAE(chainer.Chain):
def __init__(self, dim_in, dim_hidden, dim_latent, num_... | ashwindcruz/dgm | vae_pose/model.py | Python | mit | 3,753 | [
"Gaussian"
] | a7210dcd33712f49b68685c3eb307d3fa4dbb215eb7aac725228e2a24aef90c3 |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Multidimensional models: making 2/3 dimensional plots of p.d.f.s and datasets
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++ version)
import ROOT
# Create 2D model and dataset
# --------------------------------... | karies/root | tutorials/roofit/rf309_ndimplot.py | Python | lgpl-2.1 | 3,814 | [
"Gaussian"
] | b0c790487d480a542f486a46c01e0640c7cc690b20c8673b566d7c922345fd6d |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
import itk
import module_kits.itk_kit as itk_kit
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
class symmetricDemonsRegistration(ScriptedConfigModuleMixin, ModuleBase):
def __init_... | nagyistoce/devide | modules/insight/symmetricDemonsRegistration.py | Python | bsd-3-clause | 4,001 | [
"Gaussian"
] | 2ee92bbf67a8cdf97b5e802a44be5661da32cd325fe9d3105e82f76c3a822a3c |
"""
JSMN Renderer
"""
from . import jsmn_template
from ... import renderer_result
from ....visitors import data_visitor as dv
def get_name_from_qname(qname):
return qname.split('.')[-1]
class JsmnPrimitiveRenderer(dv.DataVisitor):
def __init__(self, load_stream, dump_stream, calcsize_stream,
... | svperbeast/plain_data_companion | src/templates/json/jsmn/jsmn_renderer.py | Python | mit | 29,648 | [
"VisIt"
] | 852cedb011cde2d268d8f8bd52683d146cc2ce7b3a84f4dc279374ba0064f432 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# searchusers - Search in MiG user database
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Li... | heromod/migrid | mig/server/searchusers.py | Python | gpl-2.0 | 3,367 | [
"Brian"
] | 738bd60843bddc608f669d05073bb6643d60dc035be9c20e76e8a9ba437683a1 |
#!/usr/bin/env python3
# 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 is distributed in the... | FluidityStokes/fluidity | python/fluidity/diagnostics/structured_fields.py | Python | lgpl-2.1 | 10,762 | [
"VTK"
] | 31459a13523cd8cfdc10abf0088c18a817d1053d02ef2f258464c12fa9faeb0c |
""" Plotting Service generates graphs according to the client specifications
and data
"""
import os
import hashlib
from DIRAC import S_OK, S_ERROR, rootPath, gConfig, gLogger
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.ConfigurationSystem.Client import PathFinder
from DIRAC.Core.D... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/Service/PlottingHandler.py | Python | gpl-3.0 | 2,516 | [
"DIRAC"
] | ae9dfb73a8b1a764bfd2276b9ae0f974f2165ceaf1be8116fdbba0d4cb7cf196 |
# 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... | pkreissl/espresso | testsuite/python/polymer_linear.py | Python | gpl-3.0 | 8,285 | [
"ESPResSo"
] | 3c13dab7d71c06a5927f0f0cec86df94771743445af1d5f44df14655dae7e2c4 |
# -*- coding: utf-8 -*-
__author__ = "Konstantin Klementiev"
__date__ = "14 October 2014"
import os, sys; sys.path.append(os.path.join('..', '..', '..')) # analysis:ignore
import numpy as np
#import matplotlib as mpl
import matplotlib.pyplot as plt
import xrt.backends.raycing.materials as rm
cases = []
band = 'narro... | kklmn/xrt | examples/withRaycing/06_AnalyzerBent1D/flux-dE.py | Python | mit | 6,397 | [
"CRYSTAL"
] | 860d6cc75868a969fe7f94e444d40e674f7e3dea36c5560f653197ac0015086d |
from __future__ import annotations
import logging
import sys
from io import StringIO
from iotbx.phil import parse
from libtbx import Auto
from dials.util import log, show_mail_handle_errors
logger = logging.getLogger("dials.command_line.export")
help_message = """
This program is used to export the results of dia... | dials/dials | command_line/export.py | Python | bsd-3-clause | 17,380 | [
"CRYSTAL"
] | eabbb474c3e7ed27907d91e71265639779008b801fa20af713b52344ab0b5ed0 |
#####################################
## mQC (MappingQC): ribosome profiling mapping quality control tool
## Author: S. Verbruggen
## Supervised by: G. Menschaert
##
## Copyright (C) 2017 S. Verbruggen & G. Menschaert
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of ... | Biobix/mQC | mqc_tools/mQC.py | Python | gpl-3.0 | 57,236 | [
"Galaxy",
"Mayavi",
"VisIt"
] | 556334f942431b6fe360e71e095cac4c8ab4dc12940fc67a03a072e42307d38e |
from __future__ import absolute_import
import os
import os.path
import sys
from django.conf import settings
from django.core.management.commands.runserver import Command as RunserverCommand
from optparse import make_option
from subprocess import Popen
class Command(RunserverCommand):
"""
ALmost identical to... | jokey2k/sentry | src/sentry/management/commands/runserver.py | Python | bsd-3-clause | 1,848 | [
"GULP"
] | d11ab5451ae0dd4b07f17860844efe11b4f004c53a7e9de16ab9152cb763b3d8 |
#!/usr/bin/env python
# ******************************************************************************
# Copyright 2014-2018 Intel Corporation
#
# 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
... | NervanaSystems/neon | examples/mnist_hdf5.py | Python | apache-2.0 | 3,625 | [
"Gaussian"
] | f866f6e642ec8a38abf59d6242bd8eac9a9c5d42470866ea00806e1763a85c01 |
import core.modules
import core.modules.module_registry
from core.modules.vistrails_module import Module, ModuleError
from scipy import sparse
from Array import *
from Matrix import *
from wrapper import VTKInstanceWrapper
class ArrayConvertModule(object):
my_namespace = 'numpy|array|convert'
class ArrayDumpToFil... | VisTrails/VisTrails | contrib/NumSciPy/ArrayConvert.py | Python | bsd-3-clause | 6,147 | [
"VTK"
] | a919ca897e87312555f49cdcc9ad97b5d9eec363e04d9ff79140b87c357552a8 |
# Gaussian Naive Bayes Example
from matplotlib import pyplot as plt
from sklearn.datasets import load_iris
from sklearn.metrics import plot_confusion_matrix
from sklearn.model_selection import train_test_split
from sklearn.naive_bayes import GaussianNB
def main():
"""
Gaussian Naive Bayes Example using sklea... | TheAlgorithms/Python | machine_learning/gaussian_naive_bayes.py | Python | mit | 1,068 | [
"Gaussian"
] | 4ffa3e5feb025cc07172a0ea49dfefb16b13c64dcf4d1a95f5bdf5532fd22cc1 |
from ..sql_models.statistics import Flowline
from ..sql_models.statistics import FlowlineStats
from ..sql_models.statistics import ManholeStats
from ..sql_models.statistics import Node
from ..sql_models.statistics import PipeStats
from ..sql_models.statistics import PumplineStats
from ..sql_models.statistics import Sta... | nens/threedi-qgis-plugin | tool_statistics/tools/statistics.py | Python | gpl-3.0 | 59,565 | [
"NetCDF"
] | e7b89a12d4509c140334a9948271076a70b3e0f5ab12ebe53091054820a633d4 |
# Generated from VarDef.g4 by ANTLR 4.6
from antlr4 import *
from Study import Study
from Var import Var
from collections import defaultdict
import collections
from antlr4.error import Err
import numpy as np
# This class defines a complete generic visitor for a parse tree produced by VarDefParser.
clas... | kuckaogh/csclpp | csclpp/src/csclpp/dts/VarDefVisitor.py | Python | gpl-3.0 | 5,166 | [
"VisIt"
] | 4050c1e7c58167257ecdd976f3e182f6fbcacee1b248cddeaedf267c0e7a68c9 |
# Copyright 2005 by Jonathan Taylor.
# 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.
"""This module deals with CAPS markers.
A CAPS marker is a location a DifferentialCutsite a... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/CAPS/__init__.py | Python | gpl-2.0 | 3,833 | [
"Biopython"
] | 7788765c7d0eac58374a6f3e3b9851c6098be5697e93aeaf4277e898592d7884 |
# Copyright (C) 2008-2011 Canonical Ltd
#
# 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.
#
# This program is distribute... | Distrotech/bzr | bzrlib/groupcompress.py | Python | gpl-2.0 | 96,546 | [
"VisIt"
] | e8626927158f4464884b9868773f7d972cf7a8e19843d27014448afb4602e305 |
# coding=utf-8
# Copyright 2020 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/proteinfer | proteinfer_test.py | Python | apache-2.0 | 8,657 | [
"Biopython"
] | 9cbc84249e87bbb6187cca2b7acbef1eff73c9266d03f3f02c2f6f2b322552b2 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests for utilities."""
import unittest
from cclib.parser.utils import WidthSplitter
class WidthSplitterTest(u... | gaursagar/cclib | test/test_utils.py | Python | bsd-3-clause | 1,646 | [
"cclib"
] | 09728f0029c4bc26f63ce121b02dba4757d48a26151bf93b67a89c682dfd5b6b |
import os
import datetime as dt
import pandas as pd
import sys
from matplotlib import pyplot as plt
from netCDF4 import Dataset
os.environ['SHYFTDATA'] = '/home/johnbur/workspace/shyft_workspace/shyft-data/'
sys.path.insert(0, '/home/johnbur/workspace/shyft_workspace/shyft')
from shyft import api
import shyft
from ... | statkraft/shyft-doc | notebooks/nea-example/simulation-api.py | Python | lgpl-3.0 | 18,932 | [
"NetCDF"
] | 5e48bc00db27726693f88e50cb9683a8f6cecb239571c9cccd4cc736d39dc439 |
from src.Log import Log
class Sort(object):
def __init__(self, header):
self.header = header
def sort_column(self, variable):
print variable
if 'csvcolumn' in variable and variable['csvcolumn'] != "" and variable['csvcolumn'] in self.header:
return 'csvcolumn'
elif... | plocan/netCDF-Generator | src/Sort.py | Python | gpl-3.0 | 946 | [
"NetCDF"
] | 2a4896aa4362f3b4c46452c8da0e17aa2fc85a8777a86ccaa3a2ce5d0d800507 |
import inspect
from contextlib import contextmanager
from functools import partial
from types import MethodType
from typing import Any, Callable, Dict, List, Tuple
from typing import Union, Optional, Sequence
import numpy as np
import tensorflow as tf
from tensorflow import keras
from tensorflow.python.keras.layers im... | imito/odin | odin/bay/vi/autoencoder/hierarchical_vae.py | Python | mit | 41,844 | [
"Gaussian"
] | 18a412ee21dee1ff9c703da03d669ff61205419ff7639af91ee992394e1fb6a8 |
# -*- coding: utf-8 -*-
"""Tests for PyBEL filter functions."""
| pybel/pybel | tests/test_struct/test_filters/__init__.py | Python | mit | 65 | [
"Pybel"
] | bbdcec81d4fcd56d0ff4ff5a0c576db02707efaa20a059ed5d60124dfa2cc925 |
import subprocess
from itertools import dropwhile
import re
def CallBWA(str_f_fwdfq, str_f_revfq, str_refgem, str_of_psam,
bln_long=True, int_thrds=1):
str_f_revfq = str_f_revfq.strip()
str_bwa_l = r'bwa mem -t %d ${BWADB}/%s.fa %s %s > %s'% (int_thrds, str_refgem, str_f_fwdfq, str_f_revfq, str_o... | bm2-lab/cage | src/core/prep/fqmapper.py | Python | mit | 2,939 | [
"BWA"
] | fd63f092704b487e518624414c378a17900ceb227eee52af2917d3854c178f69 |
#
#
# File to test current configuration of CA1Pyramidal cell project.
#
# To execute this type of file, type '..\..\..\nC.bat -python XXX.py' (Windows)
# or '../../../nC.sh -python XXX.py' (Linux/Mac). Note: you may have to update the
# NC_HOME and NC_MAX_MEMORY variables in nC.bat/nC.sh
#
# Author:... | pgleeson/TestArea | models/LarkumEtAl2009/pythonScripts/RunTestsDescret3.py | Python | gpl-2.0 | 3,074 | [
"NEURON"
] | 699930ef189ce72d2e3d2647f87d841747d5fb3f8a68d513fae84d8f67b93cfe |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or l... | Clyde-fare/cclib | src/cclib/method/density.py | Python | lgpl-2.1 | 3,249 | [
"cclib"
] | 7cdaa8634d1f17afe5df09cca406c834c8b6749a4dfdc6ccc07a61903c28ece9 |
## SNGP model, adapted from https://www.tensorflow.org/tutorials/understanding/sngp
import numpy as np
import tensorflow as tf
import tf_import
class DeepResNet(tf.keras.Model):
"""Defines a multi-layer residual network."""
def __init__(self, num_classes, num_layers=3, num_hidden=128,
dropout_rat... | gagnonlg/explore-ml | sngp/sngp.py | Python | gpl-3.0 | 3,321 | [
"Gaussian"
] | 6b7745f466a3bc4b6b50265f7edd49c57e929549c892764d83731d5dba170b6a |
import pyspeckit
import numpy as np
from pyspeckit.spectrum.models import voigtfitter
# technically, the voigt fitter works as a singlefitter (i.e., you can fit the
# background level and the peak simultaneously)
# in practice, however, you need to fit the background independently except for
# gaussians. I don't kno... | keflavich/pyspeckit-obsolete | examples/voigt.py | Python | mit | 1,760 | [
"Gaussian"
] | d9113f04e184c0e6448a9f70c0fe418031d5645499bb4e90b976a77d96167832 |
#!/usr/bin/env python
#
# This script borrows a great deal of code from the azure_rm.py dynamic inventory script
# that is packaged with Ansible. This can be found in the Ansible GitHub project at:
# https://github.com/ansible/ansible/blob/devel/contrib/inventory/azure_rm.py
#
# The Azure Dynamic Inventory script was ... | sgerhart/ansible | contrib/vault/azure_vault.py | Python | mit | 23,794 | [
"Galaxy"
] | 7cbdb6c4e4e68dcd422c4af19a3d582c1ec93fc8821f5ac4f2709ca5cb0ec1cb |
#!/usr/bin/env python
#
# $File: statHaploFreq.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistrib... | BoPeng/simuPOP | docs/statHaploFreq.py | Python | gpl-2.0 | 1,400 | [
"VisIt"
] | 5f2476ed21af40e1cb3c059568b2872810571e523c8d0c57926bdaf177e6edc4 |
"""
SDSS Spectroscopic Galaxy Sample
--------------------------------
Figure 1.3.
The r vs. u-r color-magnitude diagram for the first 10,000 entries in the
catalog of spectroscopically observed galaxies from the Sloan Digital Sky
Survey (SDSS). Note two "clouds" of points with different morphologies
separated by u-r ~... | kcavagnolo/astroML | book_figures/chapter1/fig_SDSS_specgals.py | Python | bsd-2-clause | 2,041 | [
"Galaxy"
] | 5e27e63a2efcb75914ac1610f1c0e0fe128d9f283a7d40b039b7c2d6ca673b89 |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe,
# Brian Holt,
# Andreas Mueller,
# Arnaud Joly
# License: BSD 3 clause
import pickle
from collections import defaultdict
from itertools import combinations
from itertools import product
import numpy ... | zorroblue/scikit-learn | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 43,490 | [
"Brian"
] | 5d10a4d69a9116cb26b3aa1843ae425aebc0d46de3c0c535cf9d6cac7214fdea |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | jralls/gramps | gramps/plugins/webreport/introduction.py | Python | gpl-2.0 | 3,788 | [
"Brian"
] | 87efa8b7063eaf87190ee9808c34ff8e60ee9c13b1f7edbb3bdccccf26067f11 |
from pymatgen.io.vasp import Vasprun
def parse_xml():
v = Vasprun("../test_files/vasprun.xml")
if __name__ == "__main__":
import timeit
print(timeit.timeit("parse_xml()", setup="from __main__ import parse_xml",
number=1))
| matk86/pymatgen | dev_scripts/profile_xml.py | Python | mit | 245 | [
"VASP",
"pymatgen"
] | 62bc73a5f26ab70679d62bec399e3ea8b2e670cc868a982b266663a52de68e9c |
#
#
# File to test current configuration of CA1Pyramidal cell project.
#
# To execute this type of file, type '..\..\..\nC.bat -python XXX.py' (Windows)
# or '../../../nC.sh -python XXX.py' (Linux/Mac). Note: you may have to update the
# NC_HOME and NC_MAX_MEMORY variables in nC.bat/nC.sh
#
# Author:... | pgleeson/TestArea | models/LarkumEtAl2009/pythonScripts/RunTests.py | Python | gpl-2.0 | 2,884 | [
"NEURON"
] | fcbefa236d4e3471b713463e1eea4080a56b0ee13e18e59274d67a4479bc4d05 |
#!/usr/bin/env python
# coding=utf-8
"""584. Birthday Problem Revisited
https://projecteuler.net/problem=584
A long long time ago in a galaxy far far away, the Wimwians, inhabitants of
planet WimWi, discovered an unmanned drone that had landed on their planet. On
examining the drone, they uncovered a device that soug... | openqt/algorithms | projecteuler/pe584-birthday-problem-revisited.py | Python | gpl-3.0 | 2,413 | [
"Galaxy"
] | 7be104c0c4031cad4bcb688e5241a22be497428a9cb3f4a83787a3a299f41715 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
from sbol import Document, SO_CDS, SO_RBS
from synbiochem.utils import dna_utils
from synbiochem.utils.seq_u... | neilswainston/PathwayGenie | pathway_genie/sbol_utils.py | Python | mit | 3,538 | [
"VisIt"
] | 04b86d30230cc0081098175b1caa2d25f16e3f0a02abe096f6482bdf6c9c8249 |
#!/usr/bin/env ipython -wthread
from enthought.mayavi.mlab import *
from neuron3d import *
#===============================================================================
# Create a mayavi figure
#===============================================================================
fig = figure(bgcolor=(0.1, 0.1, 0.1))
##... | tfoutz99/Neuron3D | Examples/4_DBS_Electrode.py | Python | gpl-3.0 | 573 | [
"Mayavi"
] | 7ddb587f1b86f802b15f069b0315411723da8db27050110d699d88775bc102e9 |
# Copyright (c) 2016 Robert Bosch LLC, USA.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
# This source code is based on Neon
# https://github.com/NervanaSystems/neon/
# Copyright 2015 Nervana Systems Inc., lice... | DL-Benchmarks/DL-Benchmarks | neon/LeNet/lenet.py | Python | mit | 4,601 | [
"Gaussian"
] | cb33e42e5411c492c996ceca84779aa8fa1ec27668e118e633d2b400f0397893 |
#!/usr/bin/env python
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or later
Recommended:... | pbarton666/buzz_bot | bot_project/buzzbot/feedparser.py | Python | mit | 126,889 | [
"NetCDF",
"VisIt"
] | 3ac336c2c7e2516a73a5633b967f2cc22d4d631f9234e23f5347dd04e4b8d3aa |
#* 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-2.1.html
import os, ... | harterj/moose | python/TestHarness/XMLDiffer.py | Python | lgpl-2.1 | 12,194 | [
"MOOSE",
"VTK"
] | 4ee41c204bddbf94821628e2af77f42b9c623aaa7816affa6018b3075e5beec5 |
#!/usr/bin/env python
"""
Simple operating code for Turbomole
Reads input, sets up job via define, generates the submit script
depending on number of cores requested, and submits.
Future watch jobs & do sequential calculations (ie opt then freq).
Input files are formatted as gaussian, with additional/alternative keywor... | pbulsink/turbocontrol | bin/turbogo.py | Python | mit | 18,430 | [
"Gaussian",
"TURBOMOLE"
] | 7c2e263a90d71ac064af4ca4af341ee3d3163f64bbcbdf25bc61b4301ee4bdd5 |
import sys
from DIRAC import S_OK, S_ERROR, gLogger
from RESTDIRAC.RESTSystem.Client.OAToken import OAToken
from DIRAC.Core.Base import Script
class Params:
def __init__( self ):
self.cid = ""
self.name = ""
self.redirect = ""
self.url = ""
self.icon = ""
self.disableLocal = False
def setC... | DIRACGrid/RESTDIRAC | RESTSystem/scripts/dirac-rest-register-client.py | Python | gpl-3.0 | 2,466 | [
"DIRAC"
] | b411fc72ce885db8749e11350895ea1659680328df7a75d0ab8769c2236d4999 |
import sys
import utils
import caffe
import argparse
import numpy as np
import _init_paths
def get_position_probabilities(position_maps, boxes):
box_i = 0
probs = np.zeros((boxes.shape[0],len(position_maps)),dtype=np.float32)
for box_i in range(boxes.shape[0]):
for cls in range(len(position_maps)... | gogartom/TextMaps | tools/test.py | Python | mit | 5,412 | [
"Gaussian"
] | d18b47d371c428765eefa303628b6b17e2eca9c5821c5bf4f32a3cf3db683d54 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/models.py | Python | gpl-2.0 | 24,768 | [
"ChemPy",
"PyMOL"
] | 497ea4beada89483fdca16cfffa6f326b78832b9050db931458cbf51fd529558 |
#! /usr/bin/env python
"""
outputs FASTA sequence corresponding to subject start and subject end in m8 file
if subject has match over E value cutoff
some subjects will be written multiple times, depending on how many hits they have
Copyright:
blast_e5_wite_subjs_nt.py Output FASTA seqs from BLAST alignment
... | Brazelton-Lab/lab_scripts | blast_e5_write_subjs_nt.py | Python | gpl-2.0 | 4,038 | [
"BLAST"
] | 4a125cd079c98b6411b06c783d1447daafce671b68ba559225bfd46b9fdf82a7 |
import itertools
import random
import pandas as pd
import os
class RASLseqProbes(object):
'''
This class creates a pandas DataFrame for RASLseq Probes and
offers functions to create a fasta file and blast database
using the cartesian product of the Donor and Acceptor probes.
Parameters
... | erscott/RASLseqTools | RASLseqTools/RASLseqProbes.py | Python | mit | 9,400 | [
"BLAST"
] | 3c8c37c15dff79c94015548da99077f00b1e00fed9d71b6a0213bf14dbeae84f |
# Software License Agreement (BSD License)
#
# Copyright (c) 2008, Willow Garage, Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above... | MangoMangoDevelopment/neptune | lib/ros_comm-1.12.0/tools/topic_tools/test/args.py | Python | bsd-3-clause | 2,904 | [
"Brian"
] | 65eb88fe715b9c5fb916ec0fce6650cb07de3608ca83f828494198849f6a00fe |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | imosquera/spinnaker | testing/citest/tests/google_smoke_test.py | Python | apache-2.0 | 15,357 | [
"ORCA"
] | f0bfaad06b0b23b9b5f8a094e8c571df42ffe2cfb45ec73d9a22ee89ea241899 |
# -*- coding: utf-8 -*-
# Author: Subha
# Maintainer: Dilawar Singh
# Created: Tue May 21 16:34:45 2013 (+0530)
# This test is fragile.
from __future__ import print_function, division, absolute_import
import numpy as np
import unittest
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import moo... | dilawar/moose-core | tests/support/test_hhfit.py | Python | gpl-3.0 | 6,029 | [
"MOOSE"
] | 126a041541e757d3f9e6fe0561d2877f1383c5ce92a39183e2e66669601c6f3d |
from Module import AbstractModule
class Module(AbstractModule):
def __init__(self):
AbstractModule.__init__(self)
def run(
self, network, antecedents, out_attributes, user_options, num_cores,
out_path):
import os
import shutil
#from genomicode import config
... | jefftc/changlab | Betsy/Betsy/modules/index_reference_rsem.py | Python | mit | 4,423 | [
"Bowtie"
] | 3cb3ae52d43a04535a28963be56d7f83b88e6bb40fd8aecdfd3a4550d2112c89 |
import numpy as np
import ase
from ase.parallel import paropen
cfg_default_fields = np.array( [ 'positions', 'momenta', 'numbers', 'magmoms' ] )
def write_cfg(f, a):
"""Write atomic configuration to a CFG-file (native AtomEye format).
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
if isin... | grhawk/ASE | tools/ase/io/cfg.py | Python | gpl-2.0 | 6,819 | [
"ASE"
] | 0b1d115debf2f55fff493a9b4798ff567cc163a848d2d27583f314abf570e1da |
#
# Copyright 2014-2015, 2017, 2021 Lars Pastewka (U. Freiburg)
# 2018, 2020 Jan Griesser (U. Freiburg)
# 2014, 2020 James Kermode (Warwick U.)
# 2018 Jacek Golebiowski (Imperial College London)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/... | libAtoms/matscipy | matscipy/numerical.py | Python | lgpl-2.1 | 4,249 | [
"ASE",
"Matscipy"
] | 6e2f56c5d500c26241c5195e9f5cea3a8e1c5aa0fd366e537a173871e3f945fc |
######################################################################
# Copyright (C) 2015 Jaakko Luttinen
#
# This file is licensed under the MIT License.
######################################################################
"""
Module for Bernoulli using the logistic function for Gaussian
"""
import numpy as np
... | bayespy/bayespy | bayespy/inference/vmp/nodes/logistic.py | Python | mit | 6,069 | [
"Gaussian"
] | d1b19161eed4a0367eb8c7d859f39c93761f3d86b60d1ad6eb0f8ee380eeec5a |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/GridVTKData/griddeddata_from_vtk.py | Python | lgpl-2.1 | 7,398 | [
"MOOSE",
"VTK"
] | fe79c8e7738e4ceaf11266d52cf570540808d806d9e7ab8afcdd29173afe4d53 |
from pylayers.antprop.rays import *
from pylayers.gis.layout import *
from pylayers.antprop.signature import *
import pylayers.signal.bsignal as bs
import pylayers.signal.waveform as wvf
import matplotlib.pyplot as plt
from pylayers.antprop.antenna import *
from pylayers.antprop.channel import *
import copy
import t... | pylayers/pylayers | pylayers/simul/tests/test_saveh5.py | Python | mit | 1,840 | [
"Mayavi"
] | 2f852dacee6494778797d7e1c7f1b1624883fdc6d79b13de70a1afa048109acd |
# -*- coding: utf-8 -*-
#This is generated code - do not edit
encoding = 'utf-8'
dict = {
' of ': ' de ',
'&About...': '&Quant a...',
'&Close Document': '&Tanca el document',
'&Comment Region': '&Comenta Regi\xc3\xb3',
'&Delete Window': '&Esborra Finestra',
'&Describe Action': '&Descriu Acci\xc3\xb3',
'&Execute Action'... | robmcmullen/peppy | peppy/i18n/ca.py | Python | gpl-2.0 | 6,125 | [
"Gaussian"
] | 1997cf3c31dab5b46d74315821abe96c0f172b7092cc1fe203063ab80666a54a |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | Bashar/django | django/conf/global_settings.py | Python | bsd-3-clause | 22,740 | [
"VisIt"
] | 1d8d3b1b62812e7052b9b59db7ddeef6207ee9e807abc081f6f472c65d38119d |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2015, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | mur47x111/GraalVM | mx.graal/mx_graal_makefile.py | Python | gpl-2.0 | 13,099 | [
"VisIt"
] | 2dadef1273c4e65b2ad1302cdf93200d40b8e92639f95aa010814360cc5a6f49 |
__author__ = 'Ahmed Hani Ibrahim'
from LearningAlgorithm import *
class Backpropagation(LearningAlgorithm):
def learn(self, learningRate, input, output, network):
"""
:param learningRate: double
:param input: list
:param output: list
:param network: [[Neuron]]
:retu... | AhmedHani/Python-Neural-Networks-API | OptimizationAlgorithms/Backpropagation.py | Python | mit | 2,236 | [
"NEURON"
] | 8532bd19616ddedb11485da010d5e0481a8f34e3569dd7a1d5e3a0d814bfc473 |
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