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#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy o... | jwallen/ChemPy | chempy/graph.py | Python | mit | 37,438 | [
"ChemPy"
] | e50c16bcbfeef23ea110806071a5087ba26c20fed45589f5ac37ce104051713c |
import numpy as np
import scipy.linalg as la
from dora.regressors.gp import linalg
from dora.regressors.gp import types
from time import time
def alpha(Y, L):
result = la.solve_triangular(
L.T, la.solve_triangular(L,Y, lower=True, check_finite=False),
check_finite=False)
return resu... | NICTA/dora | dora/regressors/gp/predict.py | Python | apache-2.0 | 2,721 | [
"Gaussian"
] | 419e7e860a071c5d32a590d76279bfb5152de4b2f39a38c04cde8779a2c0e25f |
"""
System class for biomolecules using AMBER ff.
Set up using prmtop and inpcrd files used in Amber GMIN and Optim.
Potential parameters (e.g. non-bonded cut-offs are set in
TODO:
Parameters
----------
prmtopFname : str
prmtop file name
inpcrdFname : str
inpcrd file name
... | js850/PyGMIN | pygmin/amber/amberSystem.py | Python | gpl-3.0 | 26,533 | [
"Amber",
"OpenMM",
"PyMOL"
] | 17c52d9372132c0eae83ac74a52234ece7cc3d111c91087144e369e5f4111fdd |
# Kristen Laguana
# CS294 Project
# Galaxy Sky Spaxel Logger
import argparse
def create_new_file():
print("Creating new file...\n")
pass
def begin_working_file():
print("Retrieving file...\n")
pass
def classify():
# goes through 15x15 grid
for column in range(1, 16):
for row in range... | klaguana/project | logger.py | Python | mit | 2,729 | [
"Galaxy"
] | 2a1db58e87686955cd81e9de811c1d13ad7d6fbec49b6cb6038a603a1cdc7255 |
########################################################################
# $HeadURL$
# File: RequestValidator.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/09/18 07:55:16
########################################################################
""" :mod: RequestValidator
======================
.. mod... | avedaee/DIRAC | RequestManagementSystem/private/RequestValidator.py | Python | gpl-3.0 | 8,649 | [
"DIRAC"
] | e31f72b553d3f7ac0f3d52273f96aceaa589c5dd12a659c25f353c616ff246ea |
# -*- coding: utf-8 -*-
# Messier Catalog
# number.
# FIXME: Need to convert this into a dictionary such that we can more efficiently obtain
# the astronomical data (including common name) when looking up the catalog
# number.
# Key to Type representation:
# SNR = supernova remnant
# GCl = glo... | walterbender/starchart | dso1.py | Python | gpl-2.0 | 8,531 | [
"Galaxy"
] | 88ed2ea27dddbc33e0fb70a240e2952808173d98c4a97d493fd8da191164c2b3 |
"""
Process an input dataset into a format suitable for machine learning.
"""
import os
import gzip
import pandas as pd
import numpy as np
import csv
import numbers
import tempfile
import time
import sys
import logging
import warnings
from typing import List, Optional, Dict, Tuple, Any, Sequence, Union
from deepchem.u... | miaecle/deepchem | deepchem/data/data_loader.py | Python | mit | 36,370 | [
"RDKit"
] | ddb0f80016c6bc3cf54355e6bcfec6079c99b681c28f861e1e86508885c65d4b |
# -*- coding: utf-8 -*-
""" *==LICENSE==*
CyanWorlds.com Engine - MMOG client, server and tools
Copyright (C) 2011 Cyan Worlds, Inc.
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... | TOC-Shard/moul-scripts | Python/plasma/Plasma.py | Python | gpl-3.0 | 263,729 | [
"VisIt"
] | 8b916d7c3f374ab365e1515349a2818013debfc9d2ea191eae7f6b5d12ef437e |
#!/usr/bin/env python
import sys
import subprocess as sb
import numpy as np
import argparse
from utilities import filesFromList, writeLog
from plotTools import userLabels, extractFromCSV, addToPlot
import matplotlib.pyplot as plt
'''
Description:
Author: Mikko Auvinen
mikko.auvinen@helsinki.fi
Unive... | saskartt/P4UL | pyAnalyze/approachAnalysis.py | Python | mit | 8,459 | [
"ParaView"
] | 2bbc8ba22826622aabea1619a0f8053f35e7060327fa62ff1cf9571e0df7a5a7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import itertools
import logging
from operator import mul
import functools
from monty.json import MSONable
from pymatgen.core.periodic_table import get_el_sp
from pymatgen.analysis.structure_prediction.substitu... | dongsenfo/pymatgen | pymatgen/analysis/structure_prediction/substitutor.py | Python | mit | 10,806 | [
"pymatgen"
] | 39db3adf3cc374290f1c468f3694315d24a13583d7a78454af43662ca9c7c826 |
# Copyright (c) 2012-2014, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .model import Model
from .parameterization.variational import VariationalPosterior
from .mapping import Mapping
from .. import likelihoods
from .. import kern
from ..inference.l... | befelix/GPy | GPy/core/gp.py | Python | bsd-3-clause | 32,440 | [
"Gaussian"
] | 512f4fd88ce8c3e544f1329c78e61c5c6644f668760bd08d0d220693398f9bb2 |
import math
from scipy.integrate import quad
from scipy.integrate import odeint
from scipy.interpolate import spline
import numpy as np
import matplotlib.pyplot as plt
# System Definitions
# Chemical Properties
MW = 100.0 # g / mol
MW /= 1000 # Convert to kg / mol.
T = 298.15 # K
R = 8.314 # J / mol K
Z_air = 1 / R ... | StephenAWood/SWEnvironmentalFate | SWEnvironmentalFateLevel4.py | Python | mit | 2,301 | [
"Gaussian"
] | beefa03f725a7d4e1d6a568f6d53b0dbf8824b113bc775fef6169a248ffd6388 |
#!/usr/bin/env python
from optparse import OptionParser
import copy
import math
import os
import random
import string
import subprocess
import sys
import h5py
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from scipy.cluster import hierarchy
from scipy.stats import spearmanr
import seaborn as s... | davek44/Basset | src/dev/basset_kmers.py | Python | mit | 11,132 | [
"scikit-bio"
] | 62e24a2eaa3f30f1a46c752a7b884769e846ce73328a501713398effb3a96df7 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | sunqm/pyscf | pyscf/lib/gto/test/test_ecp.py | Python | apache-2.0 | 28,317 | [
"PySCF"
] | 8205c2d0ece406abfd92879c1dde6e1d63f9daf8a9f6d0e208a8bc6156d8177b |
# -*- coding: utf-8 -*-
#
# brunel_alpha_evolution_strategies.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 versio... | apeyser/nest-simulator | pynest/examples/brunel_alpha_evolution_strategies.py | Python | gpl-2.0 | 20,542 | [
"Gaussian",
"NEURON"
] | 0cd8edf91811c9a102025e2fae85115c9b64d46865e17794bace13a9c1b865de |
#=== CONTROLS ========================================================================================
# Native GUI controls.
# Authors: Tom De Smedt, Frederik De Bleser
# License: BSD (see LICENSE.txt for details).
# Copyright (c) 2008 City In A Bottle (cityinabottle.org)
# http://cityinabottle.org/nodebox
import os
... | est/nodebox-gl | gui/controls.py | Python | bsd-3-clause | 47,034 | [
"VisIt"
] | ba45741034e992b2fa5a183ffa1528e70341a0a288773cd1b8401ff1f4ae017d |
from os import path
import sys
import traceback
import cStringIO
import webbrowser
import base64
import urllib
import gzip
from pprint import pformat
from PodSix.Resource import *
from PodSix.Game import Game
from engine.NetMonitor import NetErrorException, NetDisconnectionException, NetBadVersionException
from engin... | chr15m/Infinite8BitPlatformer | engine/ExceptionHandler.py | Python | gpl-3.0 | 2,783 | [
"VisIt"
] | 373a906510d9d89612b2a85f84a541fba6e06eb2c8b133ed139a0b037f1859ac |
# -*- coding: utf-8 -*-
"""
Models used to implement SAML SSO support in third_party_auth
(inlcuding Shibboleth support)
"""
import json
import logging
import re
from config_models.models import ConfigurationModel, cache
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.e... | appsembler/edx-platform | common/djangoapps/third_party_auth/models.py | Python | agpl-3.0 | 37,862 | [
"VisIt"
] | a6d5307072333f2c8b280cf09fe4c662eff5352a638e22f6355c2f19ac3c5a98 |
# SVI for a mixture of 3 Gaussians in 2d
# https://github.com/brendanhasz/svi-gaussian-mixture-model/blob/master/BayesianGaussianMixtureModel.ipynb
import superimport
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
import tensorflow as tf
import tensorflow_probability as tfp
tfd = tfp.distri... | probml/pyprobml | scripts/svi_gmm_demo_2d_tfp.py | Python | mit | 1,943 | [
"Gaussian"
] | 7975572afd49fd8e50fbe54e537396f352117ee509ac454894cf0e0c4ca17968 |
#!/usr/bin/env python
"""
@package coverage_model.persistence_helpers
@file coverage_model/persistence_helpers.py
@author Christopher Mueller
@brief Helper functions and classes for the PersistenceLayer
"""
from pyon.core.interceptor.encode import encode_ion, decode_ion
from ooi.logging import log
from coverage_model... | ooici/coverage-model | coverage_model/persistence_helpers.py | Python | bsd-2-clause | 11,604 | [
"VisIt"
] | c3f993cb402434f85b811b32a2eeefdcd383b564b847e4d21b142bf8358a7535 |
#
# 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 us... | maropu/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 62,447 | [
"Gaussian"
] | 59ac943638e9741ed9c12ff73ad5fc0377e5382779617af627ff4a870caf9d0e |
# ----------------------------------------------------------------------------
# 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 with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/test.py | Python | bsd-3-clause | 437 | [
"scikit-bio"
] | b4fe5423379981e33bafecf97e8f4fd3176852850a368de5a67e8dee24f59af2 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | tests/unit_tests/test_random_port.py | Python | lgpl-3.0 | 1,677 | [
"VisIt"
] | 8d302cc3bf1ce52e3d051b87ce273cdc5e248bf8267c4da77e04501950508535 |
## \file
## \ingroup tutorial_roofit
## \notebook
## Addition and convolution: decay function pdfs with optional B physics effects (mixing
## and CP violation) that can be analytically convolved with e.g. Gaussian resolution functions
##
## ```
## pdf1 = decay(t,tau) (x) delta(t)
## pdf2 = decay(t,tau) (x) gauss(t,m,s)... | root-mirror/root | tutorials/roofit/rf209_anaconv.py | Python | lgpl-2.1 | 2,658 | [
"Gaussian"
] | 736eb5bc72f7ae56bce9990bae77f0609a616113cb77e756e6dd37a52f3e956d |
# 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... | tensorflow/tensorflow | tensorflow/python/ops/linalg/linalg_impl.py | Python | apache-2.0 | 65,567 | [
"Gaussian"
] | 54cdf7370d29a6f69d549e88ab9768773a89f49eb72dc27432ff3197fae81798 |
# $Id$
#-----------------------------------------------------------------------
# Copyright (C) 2006,2009,2019
# Associated Universities, Inc. Washington DC, USA.
#
# 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 Fr... | kernsuite-debian/obit | python/ConvUtil.py | Python | gpl-2.0 | 5,627 | [
"Gaussian"
] | 6cd659f51091c922cfa464642f4dcdd85df50dc868e55848ad29cf1b8d694a13 |
"""
Migration script to add the ctx_rev column to the tool_shed_repository table.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything else from model
from galax... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0097_add_ctx_rev_column.py | Python | gpl-3.0 | 1,498 | [
"Galaxy"
] | f0d23cdd478b5b0421696a32051785d4dafe4571f7fee4e2daf3b642acfba10a |
"""
Voxelize Points
~~~~~~~~~~~~~~~
This example will demonstrate how to connect a set of points defined on a
regular grid to create a `vtkUnstructuredGrid` which can be used to perform
volumetric operations.
This example demos :class:`PVGeo.filters.VoxelizePoints`
"""
# sphinx_gallery_thumbnail_number = 2
import py... | banesullivan/ParaViewGeophysics | examples/filters-general/voxelize-points.py | Python | bsd-3-clause | 4,302 | [
"VTK"
] | 41adc54f92daaabeb7704e19a5c19cef14159c38ba0778e0b10ef4aa63841195 |
#!/usr/bin/env python
'''
Looks at a hydrogen metallic lattice and looks at using the level shift in
k-point ccsd. While for most systems the level shift will not affect results,
this is one instance where the system will converge on a different ccsd solution
depending on the initial guess and whether one is using a ... | gkc1000/pyscf | examples/pbc/36-ccsd_level_shift.py | Python | apache-2.0 | 2,593 | [
"PySCF"
] | eea00ae44ba820f0fb80b02e64f4b9ffbb4e8e55a8fd88ac9347f4de4765617a |
import argparse
import datetime
import time
import tensorflow as tf
from tensorflow.keras import layers
from tensorflow.keras.datasets import fashion_mnist
parser = argparse.ArgumentParser()
parser.add_argument("--batch_size", type=int, default=200)
parser.add_argument('--gpu_option', action='store_true')
parser.add_a... | bytedance/fedlearner | example/privacy/embedding_protection/FMNIST_Embedding_Protection_Framework_Demo.py | Python | apache-2.0 | 31,162 | [
"Gaussian"
] | 2d84187b6bf457a3c784bb57650afd670fecc13ec794ba24a9edee59b09b617b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from setuptools import find_packages, setup
with open("README.rst") as readme_file:
readme = readme_file.read()
changelog_header = """
*********
Changelog
*********
"""
with open("CHANGELOG.rst") as changelog_file:
changelog = changelog_file.read()
setup(
a... | xia2/i19 | setup.py | Python | bsd-3-clause | 1,986 | [
"CRYSTAL"
] | 8df18dc80f9654c428ee99b6ea795a27d4dc874a017d70d69243a493c85f21be |
# -*- coding: utf-8 -*-
"""Fake data generator.
To use:
1. Install fake-factory.
pip install fake-factory
2. Create your OSF user account
3. Run the script, passing in your username (email).
::
python -m scripts.create_fakes --user fred@cos.io
This will create 3 fake public projects, each with 3 fake con... | AndrewSallans/osf.io | scripts/create_fakes.py | Python | apache-2.0 | 16,186 | [
"Galaxy"
] | 5b67b40144c9c6354f41d41df951c7306392832e9b1e8da9bcda34435a79f9da |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
import random
def cv_carsGLM():
# read in the dataset and construct training set (and validation set)
cars = h2o.import_file(path=h2o.locate("smalldata/junit/cars_20mpg.csv"))
# choose the type model-building exercise (multinomial classificati... | printedheart/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_cv_carsGLM.py | Python | apache-2.0 | 6,744 | [
"Gaussian"
] | 1ff1964669ff9f74d0d1e1d7992ef6ab8d0eb736b351abc1c5d99e1567147065 |
#encoding: utf-8
import unittest
from ase import Atoms
from ase.io import read
from ase.calculators.neighborlist import NeighborList
from numpy import dot
from math import atan2,pi
class testAse(unittest.TestCase):
def setUp(self):
pass
def tearDown(self):
pass
def testRead(self):
atoms=read('range',format='l... | vanceeasleaf/aces | aces/unittest/testAse.py | Python | gpl-2.0 | 1,134 | [
"ASE",
"LAMMPS"
] | dab4c1e1085fe371d57505f3778d3f3d9456906f9bd5b213bcaf7db520bf1c18 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | jbedorf/tensorflow | tensorflow/python/ops/gradients_util.py | Python | apache-2.0 | 41,830 | [
"VisIt"
] | 4a2d3e715ce958df88a8ccc46dab93f254dfe82b4d304fca6be1c2c3fdf5a385 |
# -*- coding: utf-8 -*-
"""This script generates Slicer Interfaces based on the CLI modules XML. CLI
modules are selected from the hardcoded list below and generated code is placed
in the cli_modules.py file (and imported in __init__.py). For this to work
correctly you must have your CLI executabes in $PATH"""
from __f... | carolFrohlich/nipype | nipype/interfaces/slicer/generate_classes.py | Python | bsd-3-clause | 21,792 | [
"VTK"
] | 1eba58ded56959a0e26430f6788962de5b27c290d9308a27d1b64fe47b6af13d |
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import os.path
import unitte... | rvianello/rdkit | rdkit/Chem/Pharm2D/UnitTestMatcher.py | Python | bsd-3-clause | 3,090 | [
"RDKit"
] | 9441f380978a12d2a1fc9fa369f219150a690ad5b4c708c40288470dc8cc15e8 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/core/test_accumulate.py | Python | gpl-2.0 | 6,638 | [
"MDAnalysis"
] | b66f112ef77e9f929d2633df09f49abaff28da9f18a876dd475ee1dc322e064f |
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
precision = "mixed"
sysname = "switchedaccuratewater"
system, positions, groups, temperature, timestep, langevin_timestep, ... | kyleabeauchamp/HMCNotes | code/correctness/old/test_langevin.py | Python | gpl-2.0 | 1,095 | [
"OpenMM"
] | 840a2ec3a1809d011f0784c8488ddffddea8db512ad697f49cc760793fc9d7d9 |
#!/usr/bin/env python2
#
# Copyright 2001 - 2016 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space 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 ... | ospaceteam/outerspace | tools/osclient_tui.py | Python | gpl-2.0 | 14,651 | [
"Galaxy"
] | 6ef6c7b37a420d9826b8053f84afe60b488a21237c348666ddb2640e80905915 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/driver/p4util/python_helpers.py | Python | lgpl-3.0 | 44,094 | [
"Psi4"
] | 35558e371dd30329c11ec535fec108e0324db73f93dfe2efc62c82ff4abc3a88 |
from numpy import exp, array, random, dot
class NeuronLayer():
def __init__(self, number_of_neurons, number_of_inputs_per_neuron):
self.synaptic_weights = 2 * random.random((number_of_inputs_per_neuron, number_of_neurons)) - 1
class NeuralNetwork():
def __init__(self, neural_layers):
self.ne... | abhishekkr/tutorials_as_code | talks-articles/machine-learning/toolbox/numpy/multi-layer-neural-network.py | Python | mit | 4,859 | [
"NEURON"
] | d40f10e5eb3cedaba5a50e00e51122c1360885b21e7600250669b440efa1dee2 |
"""
Copyright (c) 2017 Sam Witte
Created on Jan 19, 2017
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 late... | SamWitte/Codds_DarkMatter | src/Data/DarkSideG2.py | Python | gpl-2.0 | 1,829 | [
"DIRAC"
] | 89e4d32e7eaede4b5ea2d90979049ced64fc7b268234079f9aa73118ca6f08b4 |
"""
==================================
Bayesian optimization with `skopt`
==================================
Gilles Louppe, Manoj Kumar July 2016.
Reformatted by Holger Nahrstaedt 2020
.. currentmodule:: skopt
Problem statement
-----------------
We are interested in solving
.. math::
x^* = arg \min_x f(x)
und... | scikit-optimize/scikit-optimize | examples/bayesian-optimization.py | Python | bsd-3-clause | 7,424 | [
"Gaussian"
] | 5abce7cd8f6ab6816727bb97548196278ebb165f70cec23857ca6bbcf8948e1f |
import copy
import itertools
import inspect
import numpy as np
from scipy.sparse import lil_matrix, csc_matrix
from conny import utility
class Function:
def compute(self, inputs):
raise NotImplemented
def derive(self, activation, input_):
raise NotImplemented
def gradient(self, num_in... | danijar/conny | conny/core.py | Python | gpl-3.0 | 5,408 | [
"NEURON"
] | ecb02b029ec163f56481442a9755516d0d89b39a07f6f30196611f16d5cac2d3 |
# -*- coding: utf-8 -*-
"""
Create an initial ATP Profile for an ECs Mesh and write it out as .vtp.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the GenerateATPMap script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__... | BlueFern/DBiharMesher | meshes/c8064Smooth/Generate8064ATPMapV2.py | Python | gpl-2.0 | 1,134 | [
"VTK"
] | 1625633f781078b786be1f5d656b441e46a56427a96fca9c00247ec1038d1dd3 |
# this one was generated with:
# for i in *.py; do n=`echo $i | cut -f 1 -d .`; \
# echo -e "class $n:\n kits = ['vtk_kit']\n cats = ['Filters']\n" \
# >> blaat.txt; done
class appendPolyData:
kits = ['vtk_kit']
cats = ['Filters']
help = """DeVIDE encapsulation of the vtkAppendPolyDataFilter that
... | nagyistoce/devide | modules/filters/module_index.py | Python | bsd-3-clause | 18,517 | [
"Gaussian",
"ParaView",
"VTK"
] | 77bcf9ed39a4f8c595cbcb5c65baf8d0cac1c5fe5aa4209c3cf72b30fac23700 |
# -*- coding: utf-8 -*-
import os, sys
COMMON_DIR = os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
PROJECT_DIR = os.path.dirname(COMMON_DIR)
ZIP_PACKAGES_DIRS = (os.path.join(PROJECT_DIR, 'zip-packages'),
os.path.join(COMMON_DIR, 'zip-packages'))
# Overrides for os.environ
env_ext = {... | lstoll/XMPPtweets | src/common/appenginepatch/aecmd.py | Python | mit | 4,777 | [
"VisIt"
] | 24e925ea0afdaff0866b2507306f848ea641e72e9f20f2211f116571e2558ca7 |
from django.contrib.auth.models import User
from lettuce import step, world
from questionnaire.features.pages.questionnaires import QuestionnairePage
from questionnaire.features.pages.users import LoginPage
from questionnaire.models import Questionnaire, Section, SubSection, Question, QuestionGroup, QuestionGroupOrder,... | testvidya11/ejrf | questionnaire/features/responses_steps.py | Python | bsd-3-clause | 6,990 | [
"VisIt"
] | a81025ce5027524d2844991e294b5104d582b8940efd28c7209be366b85edcaa |
#!/usr/bin/env python
"""
lib.py
State Estimation and Analysis for PYthon
Library of utilities for general seapy module, imported into the namespace
when importing the seapy module
Written by Brian Powell on 10/18/13
Copyright (c)2017 University of Hawaii under the BSD-License.
"""
import numpy as np
f... | dalepartridge/seapy | lib.py | Python | mit | 22,993 | [
"Brian",
"NetCDF"
] | eb96c6637ba13fe68789273ee34c0d5088ef8578e5264445d50601a87445b256 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
cc_plugin_ncei/ncei_trajectory_profile.py
'''
from compliance_checker.base import BaseCheck
from cc_plugin_ncei.ncei_base import TestCtx, NCEI1_1Check, NCEI2_0Check
from cc_plugin_ncei import util
from isodate import parse_duration
class NCEITrajectoryProfileOrthogon... | ioos/cc-plugin-ncei | cc_plugin_ncei/ncei_trajectory_profile.py | Python | apache-2.0 | 15,889 | [
"NetCDF"
] | 250181bc74add83a9cd0fbe6080342ff878db2cd1b88791998f3b67583d5f861 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
"""This file contains code for use with "Think Stats" and
"Think Bayes", both by Allen B. Downey, available from greenteapress.com
Copyright 2014 Allen B. Downey
License: GNU GPLv3 http://www.gnu.org/licenses/gpl.html
"""
from __future__ import print_function, division
"""... | qrsforever/workspace | python/learn/thinkbayes/thinkstats2.py | Python | mit | 70,069 | [
"Gaussian"
] | 042f9405db46ca42d3d18d26e4424f4edbe55d0487c1579a8c1bdeadabebea4e |
##
# title: BreadInterface.Prototype.py
# by: Brian Kim
# description: the main BreadInterface app that help end-developers design their
# button layouts
#
import pygtk
pygtk.require('2.0')
import gtk
from App import App
from Controller import Controller
from Lifecycle import Lifecycle
from BreadInter... | briansan/BreadInterface | py/BreadInterface/Prototype.py | Python | bsd-2-clause | 10,927 | [
"Brian"
] | 39edff96cc6a66b2a0f9edede47d37fe5399ce1c2b385ef0cd8a2af820f76d0a |
"""
Acceptance tests for Studio.
"""
from unittest import skip
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from ..pages.studio.asset_index import AssetIndexPage
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.studio.checklists import ChecklistsPage
from ..pages.stu... | TangXT/edx-platform | common/test/acceptance/tests/test_studio_general.py | Python | agpl-3.0 | 7,371 | [
"VisIt"
] | 61de5f1f2d6f6502e3a462c133af446209e8b510ad2855a84e5f7dd317ee5be6 |
#!/usr/bin/env python
import sys
from distutils.core import setup
# this affects the names of all the directories we do stuff with
sys.path.insert(0, './')
from layman.version import VERSION
setup(name = 'layman',
version = VERSION,
description = 'Python script for retrieving gentoo ov... | jmesmon/layman | setup.py | Python | gpl-2.0 | 735 | [
"Brian"
] | 41eb1c3b64ce50d2728ffae8dd16ce30fd7891bb14b3f01721eacdd30bba453e |
#This program will output permanent red blob counts
#Hematoxylin (Basic blue)= binds to nuclei
#CD3 (T cells) are DAB
import numpy as np
from numpy import linalg
from math import sqrt
import matplotlib.pyplot as plt
from skimage import data
from skimage.color import separate_stains, rgb2grey
from skimage.exposure i... | griffincalme/MicroDeconvolution | ScriptsUsedInPaper/BlobCounterRedPaper.py | Python | apache-2.0 | 1,813 | [
"Gaussian"
] | 457f65f66cac9aa35713d7e0bb03393d1a2949d95fb194bd5c214f7c714ae5f4 |
#!/usr/bin/env python
"""Oink is a Python to Javascript compiler.
It differs from Pyjamas in that it tries to be as thin a layer as possible
between Python and Javascript.
"""
import ast
import optparse
import os
import sys
from textwrap import dedent
from contextlib import contextmanager
class Error(Exception):
... | alecthomas/oink | oink.py | Python | mit | 15,506 | [
"VisIt"
] | 956f3e5b7f944a5e34b78ee6c34e83751c00417af0f271d945f466047352a372 |
import moose
def deleteSolver(modelRoot):
compts = moose.wildcardFind(modelRoot+'/##[ISA=ChemCompt]')
for compt in compts:
if moose.exists(compt.path+'/stoich'):
st = moose.element(compt.path+'/stoich')
st_ksolve = st.ksolve
moose.delete(st)
if moose.exists((st_ksolve).path):
moose.delete(st_ksolve... | BhallaLab/moose | moose-gui/plugins/setsolver.py | Python | gpl-3.0 | 3,007 | [
"MOOSE"
] | e1d9ef1fa061fd7671582d12764a5ed81c55db41e796526d6730eb59473cfe56 |
# 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... | MJJoyce/climate | examples/simple_model_tstd.py | Python | apache-2.0 | 3,639 | [
"NetCDF"
] | 99643b3f289172b177934c2b26a6a60f6d4d32f1f18fba6a2c7e0f6316ccd8b7 |
# $HeadURL $
""" PublisherHandler
This service has been built to provide the RSS web views with all the information
they need. NO OTHER COMPONENT THAN Web controllers should make use of it.
"""
from datetime import datetime
from types import NoneType
# DIRAC
from DIRAC ... | vmendez/DIRAC | ResourceStatusSystem/Service/PublisherHandler.py | Python | gpl-3.0 | 9,452 | [
"DIRAC"
] | 08b9656084c40ab22b9297d12960074dd030db8912934eba05f016d0ebbf8c79 |
# -*- coding: utf-8 -*-
"""
====================
ZenTools
====================
* Tools for reading and writing files for Zen and processing software
* Tools for copying data from SD cards
* Tools for copying schedules to SD cards
Created on Tue Jun 11 10:53:23 2013
@author: jpeacock-pr
"""
#===... | geophysics/mtpy | mtpy/usgs/zen.py | Python | gpl-3.0 | 252,541 | [
"Gaussian"
] | fac3f6685cd4ecc37d281f2939decf4f231abb71b0a5b54b41c566d80111ff54 |
""" The TimeLeft utility allows to calculate the amount of CPU time
left for a given batch system slot. This is essential for the 'Filling
Mode' where several VO jobs may be executed in the same allocated slot.
The prerequisites for the utility to run are:
- Plugin for extracting information from lo... | Andrew-McNab-UK/DIRAC | Core/Utilities/TimeLeft/TimeLeft.py | Python | gpl-3.0 | 9,585 | [
"DIRAC"
] | a3829a0705f3e5cb8f0cf122b0124fc11e75c5f10e009859fdf16df87448cc19 |
# Test the Brenner potential with some hydrocarbons. -*- encoding: utf-8 -*-
from ase.structure import molecule
from ase.optimize import BFGS
from asap3 import BrennerPotential
from asap3.testtools import ReportTest
import ase.data.g2
import numpy as np
C60_data = {
'C60': {
'description': "Buckminsterf... | auag92/n2dm | Asap-3.8.4/Test/Hydrocarbons.py | Python | mit | 4,854 | [
"ASE",
"GPAW"
] | a26fbc8675ed82faca4d9b93c45a2f44b1cc5ed2b780d82b8579a8f6134512fe |
import numpy as np
import math
import sys
import random
# Star position in parsecs
class Star:
velocity = np.array([0., 0., 0.])
force = np.array([0., 0., 0.])
def __init__(self, mass, x, y, z, origin):
self.mass = mass
self.pos = np.array([x, y, z])
self.origin = origin
class Ga... | samhollenbach/Galaxy2 | SimComponents.py | Python | mit | 5,780 | [
"Galaxy"
] | b9508e572c01f1c6a17c97bd67149c876859cf79361265ab6e4d4ea451453e01 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/symm/addons.py | Python | apache-2.0 | 12,136 | [
"PySCF"
] | 24e342d315ead8bc7d69d659de6842a95ffe2bd79a43d781df9dae21226d39d7 |
"""
BLAST+6 format (:mod:`skbio.io.format.blast6`)
==============================================
.. currentmodule:: skbio.io.format.blast6
The BLAST+6 format (``blast+6``) stores the results of a BLAST [1]_ database
search. The results are stored in a simple tabular format with no column
headers. Values are separate... | gregcaporaso/scikit-bio | skbio/io/format/blast6.py | Python | bsd-3-clause | 12,815 | [
"BLAST",
"scikit-bio"
] | f04104ef8330d3980518d4c732dc81fb9c37dc910ff746107053f302d0ef9fe4 |
#!/usr/bin/env python
"""
dirac-rss-query-db
Script that dumps the DB information for the elements into the standard output.
If returns information concerning the StatusType and Status attributes.
Usage:
dirac-rss-query-db [option] <query> <element> <tableType>
Queries:
[select|add|... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/scripts/dirac-rss-query-db.py | Python | gpl-3.0 | 17,572 | [
"DIRAC"
] | 8bcd41794fc81cab38d563786f3a176cd2e06d2cbc80439e4fc5aa17c23987f5 |
from twisted.enterprise import adbapi
from twisted.internet import reactor
from twisted.internet.defer import Deferred
from twisted.words.protocols import irc
from txircd.modbase import Command
from txircd.server import RegisterUser, RemoveUser, ModuleMessage, SetIdent, SetHost, SetName
from txircd.utils import chunk_m... | DesertBus/txircd | txircd/modules/db_services.py | Python | bsd-3-clause | 98,469 | [
"VisIt"
] | df634c0561950e35d3b59873f5f28ac2bf02305b1096de3a68c48bcca88c10ac |
"""
Utility functions for manipulating neuprint-python output.
"""
import sys
import inspect
import functools
import warnings
from textwrap import dedent
from collections.abc import Iterable, Iterator, Collection
import numpy as np
import pandas as pd
class NotNull:
"""Filter for existing properties.
Transl... | connectome-neuprint/neuprint-python | neuprint/utils.py | Python | bsd-3-clause | 13,938 | [
"NEURON"
] | 8ad043eabccfb1a3b06b97e00743e9cebc1a4e0c72c01e3c14d9be17879363c7 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld."""
import json
import ... | DarrelHsu/cvsClient | git_cl.py | Python | bsd-3-clause | 64,418 | [
"VisIt"
] | 6a74b8fb420e9fffd9f38128b389eee2b8f5f9eb9b2dcd5d945bc1339c17c7bf |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Script to convert database structured txt-files into netCDF format.
For usage from command line see
python convert_db2nc.py -h
Requirements:
- numpy
- netCDF4
- argparse
Converter class: DB2NC
Check out current version at
https://github.com/Chilipp/Co... | Chilipp/Convert-Database-to-NetCDF | convert_db2nc.py | Python | gpl-2.0 | 38,805 | [
"NetCDF"
] | 73caad4c30fa636538d866fec1dbf3751796dea5e352def28f9e0ca9d0b73358 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | Slezhuk/ansible | lib/ansible/playbook/conditional.py | Python | gpl-3.0 | 10,551 | [
"VisIt"
] | b6f5c5cd921ad35eaa4f6f4a7f33e8865345a6fe4dead82003cf5719cac97752 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2017-10-31
# @Filename: base_quantity.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified t... | albireox/marvin | python/marvin/tools/quantities/base_quantity.py | Python | bsd-3-clause | 6,492 | [
"Brian"
] | 193a0dd6c84c3f3779358727686821a72f0424511957658773150197e29287f7 |
# encoding: 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 'IonChannelSyn'
db.create_table('neuroelectro_ionchannelsyn', (
('i... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0008_auto__add_ionchannelsyn__add_ionchannel__add_superprotein.py | Python | gpl-2.0 | 12,704 | [
"NEURON"
] | 7adc9a616fc230b712b1cd9873a13997d4171f01adab0ba839825cfa0658536e |
# -*- coding: utf-8 -*-
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, softwar... | clusterdock/framework | clusterdock/utils.py | Python | apache-2.0 | 9,738 | [
"Gaussian"
] | ed89850b673f85805ae2adcd8dd5ac2157dc5f5ba4cc51963a88061e1685c460 |
''' -- imports from installed packages -- '''
import json
import datetime
''' -- imports from django -- '''
from django.shortcuts import render_to_response, render
from gnowsys_ndf.ndf.models import NodeJSONEncoder
from django.template import RequestContext
from django.template import Context
from django.template.defa... | AvadootNachankar/gstudio | gnowsys-ndf/gnowsys_ndf/ndf/views/forum.py | Python | agpl-3.0 | 43,873 | [
"VisIt"
] | c495c904788d5c7c98b6ad46b25ccd8602e0ed0a53d51e87946ceeaa9f2598a1 |
# This is the instrument-specific file for the PS3000a series of instruments.
#
# pico-python is Copyright (c) 2013-2014 By:
# Colin O'Flynn <coflynn@newae.com>
# Mark Harfouche <mark.harfouche@gmail.com>
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are p... | ElOceanografo/pico-python | picoscope/ps3000a.py | Python | bsd-2-clause | 16,341 | [
"Gaussian"
] | a8d0539c9cb0f639a06ac84c79279694cfcef4da82bdd31cb2784380c70a7a49 |
import numpy
from matplotlib.pyplot import figure, show, rc
from kmpfit import kmpfit
def my_model(p, x):
#-----------------------------------------------------------------------
# This describes the model and its parameters for which we want to find
# the best fit. 'p' is a sequence of parameters (array/list... | aoeftiger/kmpfit | kmpfit/example2.py | Python | bsd-3-clause | 2,326 | [
"Gaussian"
] | a1555cdbecaf3bb45ad347fb49c30759838d1a2c57f405bbea35ce29dfcdd9f5 |
"""
Define common steps for instructor dashboard acceptance tests.
"""
# pylint: disable=C0111
# pylint: disable=W0621
from __future__ import absolute_import
from lettuce import world, step
from mock import patch
from nose.tools import assert_in # pylint: disable=E0611
from courseware.tests.factories import StaffF... | dsajkl/reqiop | lms/djangoapps/instructor/features/common.py | Python | agpl-3.0 | 4,537 | [
"VisIt"
] | 0533977eb322960acb3b86ae26d080b30ca9309e536a332809cc0dc3951b7fae |
import os
import sys
import numpy as np
import pupynere as netcdf
import csv
import math
import json
SAVE_TO_COUCH = False
SAVE_JSON = True
IN_FOLDER = "../netcdf/v4/"
if SAVE_TO_COUCH:
import couchdb
couch = couchdb.Server()
couch.delete('euporias')
db = couch.create('euporias')
# db = couch['euporias']
outp... | MoritzStefaner/project-ukko-os | data/python/couchify.py | Python | apache-2.0 | 4,625 | [
"NetCDF"
] | f9b9a05a11fd1b915221401c01136b9efcacce3af87e2ca0380c9236155d1e1f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#This module calculates statistics and saves it to a file
import numpy as np
from scipy import stats as scstats
from tkinter import font as tkfont
import tkinter as tk
import stat_functions as stat
import functions as fu
import model_parser
STANDARD_LENGTH=8
class ou... | espensirnes/paneltime | build/lib.win-amd64-3.7/paneltime/output.py | Python | gpl-3.0 | 20,054 | [
"ADF"
] | 3668a77850dd8e1b13c83304a1f5bc67d4f2b2299c338eb7e137617cbddb65ae |
# encoding: utf-8
industry_list = {
'150' : u'基金/证券/期货/投资',
'210' : u'家具/家电',
'200' : u'服装服饰/纺织/皮革',
'090' : u'房地产服务(物业管理/地产经纪)',
'310' : u'石油/石化/化工',
'190' : u'食品/饮料/烟酒/日化',
'010' : u'计算机软件',
'130' : u'银行',
'110' : u'中介服务',
'030' : u'IT服务/系统集成',
'050' : u'电子技术/半导体/集成电路',
... | followcat/predator | sources/liepin_industry.py | Python | lgpl-3.0 | 97,374 | [
"BLAST"
] | 0fec7f1aa5d7bc1b743e613cf2fcbda944cccdc84f4160ffaabbcd815bbe4a15 |
#
# Copyright (C) 2013-2019 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... | pkreissl/espresso | testsuite/python/tabulated.py | Python | gpl-3.0 | 3,393 | [
"ESPResSo"
] | a1ebe7a22379229e2543ee1ef31ede34f6bfdbc4ba6868834e49df2a546744b5 |
#!/usr/bin/env ipython -wthread
from enthought.mayavi.mlab import *
from neuron import h as nrn
from neuron import gui
from neuron3d import *
##==============================================================================
# Cell
##==============================================================================
nrn.load... | tfoutz99/Neuron3D | Examples/6_Subthalamic_Neuron.py | Python | gpl-3.0 | 395 | [
"Mayavi",
"NEURON"
] | 5b822ef280d79eb3cff75e59d8448d1c4fc23ff825ab8797a2e122154f91a5b6 |
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | googlecodelabs/migrate-python2-appengine | mod7-gaetasks/main.py | Python | apache-2.0 | 2,374 | [
"VisIt"
] | dc270f807c54e12107d584d86c937e78b9f2e28f23c1a213bd77a3f22c80f104 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-CAs
# Author : Ricardo Graciani
########################################################################
"""
Refresh the local copy of the CA certificates and revocation lists.
Connects to the Bu... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_admin_get_CAs.py | Python | gpl-3.0 | 1,569 | [
"DIRAC"
] | ac7f60baf49190ea2cb272085288d40dc4b0bad5e9341fe59731eb6c1a6a8314 |
""" This is a test of the FileCatalogDB
It supposes that the DB is present.
"""
# pylint: disable=invalid-name,wrong-import-position
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import unittest
import itertools
import os
import sys
from collections ... | yujikato/DIRAC | tests/Integration/DataManagementSystem/Test_FileCatalogDB.py | Python | gpl-3.0 | 64,072 | [
"DIRAC"
] | 549a0e098ffc60903965c65e0e6a9dfa72ef9e557b77f180929d70ff9e628ac1 |
import sys
import os.path
#sys.path.insert(0, '/home/andy/theano/tool_examples/theano-lstm-0.0.15')
from theano_lstm import Embedding, LSTM, RNN, StackedCells, Layer, create_optimization_updates, masked_loss
from utilities import *
import dill
import argparse
#import cPickle
import pickle
import numpy
from collections... | darongliu/Lstm_Turing_LM | lstm-neural-turing-machines-lm/analysis/v1-one-weight-same-entropy/lm_v4.py | Python | mit | 26,033 | [
"NEURON"
] | 9e558ccfa59c44e4680df6fefb5c81713b240cb653eb92a220f7075e2b770726 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/core/ScrollableLabelLarge.py | Python | gpl-3.0 | 15,619 | [
"ORCA"
] | d9233284c81ba4f6376ffd77dc94ce117e6947982dc0e021d6107e251d9082e2 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# PMDA
# Copyright (c) 2018 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher ve... | MDAnalysis/pmda | pmda/leaflet.py | Python | gpl-2.0 | 11,864 | [
"MDAnalysis"
] | 0119322030513f679bdea7ca184094808fb60aa51b8bef2f3eab60f9ef910935 |
"""
How to reference supporting evidence for some object in the database.
See: "Metadata in PyOpenWorm" for discussion on semantics of what giving
evidence for an object means.
"""
from __future__ import absolute_import
from __future__ import print_function
import PyOpenWorm as P
from PyOpenWorm.evidence import Evide... | gsarma/PyOpenWorm | examples/add_reference.py | Python | mit | 1,637 | [
"NEURON"
] | fd3f88ad92e8b5b842b37ad483277b054aa45c9cbfd24d2b46c3a2a36920e15b |
# 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... | dmlc/tvm | tests/python/contrib/test_ethosn/infrastructure.py | Python | apache-2.0 | 12,799 | [
"VisIt"
] | 7a04a6c53711873f1a58ec119daa4532f50bc9ff19c2d058aea9d837833a0267 |
#!/usr/bin/env python3
import os
import argparse
import sys
from time import sleep
import subprocess
import glob
mypath = os.environ["PATH"]
os.environ["PATH"] = "/home/wl45/python/bin:/home/wl45/opt:" + mypath
my_env = os.environ.copy()
parser = argparse.ArgumentParser(
description="This is a python3 script ... | luwei0917/awsemmd_script | final_move.py | Python | mit | 2,154 | [
"PyMOL"
] | 644e950860f1d78e564a1abc6a657a500d598a774002775d992d59d7fb6e286f |
import sublime
import sublime_plugin
import os.path
is_sublime_text_3 = int(sublime.version()) >= 3000
if is_sublime_text_3:
from .progress_notifier import ProgressNotifier
from .cross_platform_codecs import CrossPlaformCodecs
else:
from progress_notifier import ProgressNotifier
from cross_platform_co... | nickgzzjr/sublime-gulp | base_command.py | Python | mit | 5,668 | [
"GULP"
] | 8bfb19d35910d23bb2953733044c2c222b59add19dd42eccc38d4319f0e1cab0 |
#!/usr/bin/env python
# -*- coding: us-ascii -*-
#----------------------------------------------------------------------------
# Copyright (C) 2009 BigDFT group (TD)
# This file is distributed under the terms of the
# GNU General Public License, see ~abinit/COPYING
# or http://www.gnu.org/copyleft/gpl.txt .
# For the i... | SamKChang/abinit-7.10.5_multipole | tests/Scripts/memcheck.py | Python | gpl-3.0 | 2,739 | [
"ABINIT"
] | f8002ca1553c610d846ee3737ed5bec1d76143bbf25b8ff07d2dff059389ca4a |
"""
SP3 format:
https://kb.igs.org/hc/en-us/articles/201096516-IGS-Formats
"""
import xarray
import numpy as np
import logging
from pathlib import Path
from datetime import datetime, timedelta
import typing as T
from .rio import first_nonblank_line
# for NetCDF compression. too high slows down with little space ... | scienceopen/pyrinex | src/georinex/sp3.py | Python | mit | 4,540 | [
"NetCDF"
] | 85cd2d965ba798da63b27a9648938ce66b65af3d4bc5d4c612de453a575eb9b2 |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required... | mguzdial3/MineCode | python-codec/src/rlglue/agent/ClientAgent.py | Python | apache-2.0 | 4,648 | [
"Brian"
] | 4321d544b658f820d2a8953b06d967de4d39cd99a5ac79fea444909e4f924966 |
# CREATED:2013-08-13 12:02:42 by Brian McFee <brm2132@columbia.edu>
'''
Evaluation criteria for structural segmentation fall into two categories:
boundary annotation and structural annotation. Boundary annotation is the task
of predicting the times at which structural changes occur, such as when a verse
transitions to... | faroit/mir_eval | mir_eval/segment.py | Python | mit | 43,678 | [
"Brian"
] | c991e30d9c802501d301d7aca0f48bae8d2d60b5fb4607dd35f7ef79eaccd647 |
from util import *
from InputParameters import InputParameters
class Tester(object):
# Static Method
def getValidParams():
params = InputParameters()
# Common Options
params.addRequiredParam('type', "The type of test of Tester to create for this test.")
params.addParam('max_time', 300, "The maxi... | amburan/moose | framework/scripts/TestHarness/testers/Tester.py | Python | lgpl-2.1 | 7,826 | [
"VTK"
] | 4d91ee5c4463c8927c28f9c4c88fdd6c3aca25142d7a91083eb7a8e68f113215 |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits, load_iris
from sklearn.cross_validation import cross_val_score, train_test_split
from sklearn.externals.six.moves import zip
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.te... | uglyboxer/linear_neuron | net-p3/lib/python3.5/site-packages/sklearn/tests/test_naive_bayes.py | Python | mit | 16,259 | [
"Gaussian"
] | 0c98ad5abac8962f86873e97e5d8949d24866e0562ec52ce5a3d1f749cf9590c |
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