text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#
# co_co_all_variables_defined.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at y... | kperun/nestml | pynestml/cocos/co_co_all_variables_defined.py | Python | gpl-2.0 | 6,476 | [
"NEURON"
] | ed3ce97420c8d70b2c825d79c50f91bb7be34f2260990f59a5628f54139cc04b |
"""Align protein to arbitrary axis with atom selection at origin.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
from __future__ import division
import ast
from pymol import cmd, stored
from pymol.cgo import *
import numpy as np
AXES = {"x": [1., 0., 0.], "y": [0., 1., 0.], "z": [0., 0., 1.]}
def get_com(selec... | sdaxen/pymol_scripts | align_to_axis.py | Python | lgpl-3.0 | 4,994 | [
"PyMOL"
] | 7172ac17ee7ff815e7bdb85a1481a3bc8a77ecb6ba2aee90ed65f9ed45ca5fd3 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 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 requi... | googleapis/python-websecurityscanner | scripts/fixup_websecurityscanner_v1beta_keywords.py | Python | apache-2.0 | 6,616 | [
"VisIt"
] | 1d7df7e65048a3781514be92c9af61f571b0a05a29420fd791207166744700bd |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
#####################################
# ╔╗ ┬ ┬ ┬┌─┐ ╔╦╗┌─┐┌┬┐ #
# ╠╩╗│ │ │├┤ ║║│ │ │ #
# ╚═╝┴─┘└─┘└─┘ ═╩╝└─┘ ┴ #
# ╔═╗┌─┐┌─┐┌┬┐┬ ┬┌─┐┬─┐┌─┐ #
# ╚═╗│ │├┤ │ │││├─┤├┬┘├┤ #
# ╚═╝└─┘└ ┴ └┴┘┴ ┴┴└─└─┘ #
###... | Starkiller4011/tsat | tsat/core/lcutils.py | Python | mit | 7,214 | [
"Gaussian"
] | 08c2c24422e6ec67a11aacadb215f7cabef52f14e5173de9364ed67a84cd96a4 |
from __future__ import print_function, division
INPUT_LAYERS = ['Data', 'ImageData', 'Input']
# Layers that only support elwise
ELWISE_LAYERS = ['Deconvolution']
# Layers that support parameters
PARAMETER_LAYERS = ['Convolution', 'InnerProduct']+ELWISE_LAYERS
# All supported layers
SUPPORTED_LAYERS = ['ReLU', 'Sigmoid... | kl456123/machine_learning | utilsToLearn/caffe/magic_init.py | Python | mit | 18,435 | [
"Gaussian"
] | 6f9345297d18980a978e4800e1a4d0cb21e14adc1e4b14c7326adf96f57d64e9 |
from brian import *
eqs = '''
dv/dt = (ge+gi-(v+49*mV))/(20*ms) : volt
dge/dt = -ge/(5*ms) : volt
dgi/dt = -gi/(10*ms) : volt
'''
P = NeuronGroup(4000, eqs, threshold=-50*mV, reset=-60*mV)
P.v = -60*mV
Pe = P.subgroup(3200)
Pi = P.subgroup(800)
Ce = Connection(Pe, P, 'ge', weight=1.62*mV, sparseness=0.02)
Ci = Connecti... | achilleas-k/brian-scripts | brian_demo.py | Python | apache-2.0 | 444 | [
"Brian"
] | 29405cee5db82b6e740d5826ef529d69bb2eae658cac9ec63a2d03a8273f8295 |
"""
"""
from cloudbio.galaxy.utils import _chown_galaxy
from fabric.contrib.files import *
from shared import _write_to_file
def install_protvis(env):
""" Installs Andrew Brock's proteomics visualize tool.
https://bitbucket.org/Andrew_Brock/proteomics-visualise/
"""
_setup_protvis_env(env)
prot... | averagehat/cloudbiolinux | cloudbio/custom/galaxyp.py | Python | mit | 2,285 | [
"Galaxy"
] | 729a3df2a3ba7a12cc6f1e01ac5ae4d8689f32b3681ab9450e128f7788c97a20 |
"""
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
>>> os.chdir(datadir)
"""
from nipype.interfaces.base import (CommandLineInputSpec, C... | wanderine/nipype | nipype/interfaces/camino/dti.py | Python | bsd-3-clause | 51,551 | [
"DIRAC",
"Gaussian"
] | 76d0593c5f4477a78bb1c2f9a070ec67d3b78330d9a868ff7b10cb3d3e01dcb1 |
from __future__ import division
from __future__ import print_function
from past.utils import old_div
import sys
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gam import H2OGeneralizedAdditiveEstimator
# In this test, we check and make sure that the scale parameter is app... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/gam/pyunit_PUBDEV_7932_gam_scale_parameter.py | Python | apache-2.0 | 2,866 | [
"Gaussian"
] | 90ca7845e7e0045388c920d013aa4e2dd38317eb5593421619f6eedf55d104ee |
import numpy as np
"""
wrapper around unstructured netcdf output with various
helper functions. mostly just a place to collect relevant
bits of code.
"""
import netCDF4
import trigrid
from matplotlib.dates import date2num
import datetime
import pytz
def cf_to_datenums(nc_t_var):
""" parse the 'units since epoch'... | rustychris/stomel | src/ugrid.py | Python | gpl-2.0 | 9,422 | [
"NetCDF"
] | e2873d24ea494ed2ba6726312138ca8551c022431b5fe8190412c9b0f5686c34 |
#!/usr/bin/env python3
#Program fitting the exchange interaction
#Model curve: Bethe-Slater function
import numpy as np, pylab, tkinter
import matplotlib.pyplot as plt
from scipy.optimize import curve_fit
from decimal import *
import sys, string, os
argv = sys.argv
if len(argv) != 3:
print("Syntax: ./plot_precessi... | pastewka/lammps | examples/SPIN/test_problems/validation_langevin_precession/plot_precession.py | Python | gpl-2.0 | 948 | [
"LAMMPS"
] | 54169bbac78075964dc2a19c2ab0bc0984a233eef0b264307899c47e469944b2 |
"""
GPoFM: Gaussian Process Training with
Optimized Feature Maps for Shift-Invariant Kernels
Github: https://github.com/MaxInGaussian/GPoFM
Author: Max W. Y. Lam [maxingaussian@gmail.com]
"""
import numpy as np
import matplotlib.pyplot as plt
from matplotlib import offsetbox
from scipy.interpolate import gridda... | MaxInGaussian/GPoFM | GPoFM/utils/Visualizer.py | Python | bsd-3-clause | 6,333 | [
"Gaussian"
] | 8c9a0b91ba5d6e56319a190bb673979ba0f040bbd6996d4c59d3bf226c145e3c |
#!/usr/bin/env python3
# Copyright (c) 2018 The Bitcoin Core developers
# Distributed under the MIT software license, see the accompanying
# file COPYING or http://www.opensource.org/licenses/mit-license.php.
"""Verify commits against a trusted keys list."""
import argparse
import hashlib
import os
import subprocess
im... | vergecurrency/VERGE | contrib/verify-commits/verify-commits.py | Python | mit | 7,872 | [
"Octopus"
] | 2a313858e499dd198081a289a3395bd647034242fae76460b7df19417ad33da3 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from .posterior import Posterior
from ...util.linalg import mdot, jitchol, backsub_both_sides, tdot, dtrtrs, dtrtri, dpotri, dpotrs, symmetrify
from ...util import diag
from GPy.core.parameterization.variat... | avehtari/GPy | GPy/inference/latent_function_inference/var_dtc.py | Python | bsd-3-clause | 10,718 | [
"Gaussian"
] | 0a53158badace5ba36789194fcf80ed22a498374fd953a733b81615823f8f9a7 |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014-2017 CERN.
#
# INSPIRE 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 ... | Glignos/inspire-next | inspirehep/modules/authors/views.py | Python | gpl-3.0 | 13,369 | [
"VisIt"
] | 1bce94a233094e2331a7a294447e8397825bd97ce6d4895917d0fa4ea1070123 |
from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
__author__ = 'stripathy'
def get_major_brain_region(structure_path_str, onto):
""" Returns a dictionary of region attributes given structure path from allensdk API
:param structure_path_str: a region's structure path from the allensdk ... | neuroelectro/neuroelectro_org | aba_functions/get_brain_region.py | Python | gpl-2.0 | 2,090 | [
"NEURON"
] | d68eee97c2774aa654ecda1a39449eee1c0cd332f83e64efe08d6b97b9c34b0e |
import numpy as np
from ase.md import MolecularDynamics
class VelocityVerlet(MolecularDynamics):
def __init__(self, atoms, dt, trajectory=None):
MolecularDynamics.__init__(self, atoms, dt, trajectory)
def step(self, f):
atoms = self.atoms
p = self.atoms.get_momenta()
... | freephys/python_ase | ase/md/verlet.py | Python | gpl-3.0 | 956 | [
"ASE"
] | ae740a949aa7eaa7892ccad34ec07629dd02f174e6294734cd180ae3566ce413 |
"""
This example shows how to create a vtkPolyData object with multiple
scalar attributes (strength and time), and how to efficiently extract
quakes within a specified time interval.
Author: Johan Nysjo
"""
import ReadPointsCSV
import vtk
# Load the earthquake data
points, strength, time_, = ReadPointsCSV.readPoin... | RDeckers/ScientificVisualization-1TD389 | Assignments/Project/threshold_quakes_by_time.py | Python | gpl-3.0 | 1,518 | [
"VTK"
] | 9969e80f87563284fcbebb92543e1d8d4156d3ee3b90a7ad7fda75661c5b13ca |
""" SystemLoggingDB class is a front-end to the Message Logging Database.
The following methods are provided
insertMessage()
getMessagesByDate()
getMessagesByFixedText()
getMessages()
"""
import re
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Base.D... | Andrew-McNab-UK/DIRAC | FrameworkSystem/DB/SystemLoggingDB.py | Python | gpl-3.0 | 22,375 | [
"DIRAC"
] | fa9d1138609219be77b25bca71d3fa895496a143ee46a56707f5fa877eb4d177 |
#!/usr/bin/env python
'''
This example covers different ways to input basis
1. A universal basis set for all elements.
2. Different basis for different elements.
3. Different basis for same elements (different atoms).
4. Default basis for all elements, except the given basis of specific element.
5. gto.basis.parse and... | sunqm/pyscf | examples/gto/04-input_basis.py | Python | apache-2.0 | 8,842 | [
"Gaussian",
"NWChem",
"PySCF"
] | 87db3b7aa03605399afed7509f53f7ffb516fc8ef2649e1933c69f53474d3238 |
"""Very basic example of a simulation without a resampler or boundary
conditions"""
from copy import copy
import simtk.openmm as omm
import simtk.unit as unit
from openmm_systems.test_systems import LennardJonesPair
from wepy.resampling.resamplers.resampler import NoResampler
from wepy.runners.openmm import OpenMMR... | ADicksonLab/wepy | info/examples/Lennard_Jones_Pair/source/trivial_run.py | Python | mit | 1,541 | [
"OpenMM"
] | bddac6d4771772a0b6514391251f5561fe8f4e3ad7208a708e7b635341c8abaf |
# coding=utf-8
"""Molecule manipulation using rdkit."""
from __future__ import print_function
from collections import Iterable
from collections import defaultdict
import numpy as np
from rdkit import Chem
from rdkit.Chem import Descriptors, AllChem
from rdkit.Chem.PropertyMol import PropertyMol
from whatami import wha... | sdvillal/manysources | manysources/common/rdkit_utils.py | Python | bsd-3-clause | 10,249 | [
"RDKit"
] | ca45f841ce427f41b62646ec501d473aef3c5ed916aa4e631e7dbc3a7d45d9ec |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import copy
import json
import os
import py... | jctanner/ansible | test/units/galaxy/test_collection_install.py | Python | gpl-3.0 | 45,630 | [
"Galaxy"
] | 9cf55d9848eddb0fed3f9906d697cdd1516d77fbc25e8207abfdfd07734aba71 |
# Copyright 2014-2020 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
#
# Unless required by appl... | sunqm/pyscf | pyscf/agf2/test/test_c_agf2.py | Python | apache-2.0 | 4,413 | [
"PySCF"
] | 34946c77e88cc5e94a373ec3254c1c868822d1329141122d1566cb6e2be9574e |
# 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/func_tests/test_timeouts.py | Python | lgpl-3.0 | 2,266 | [
"VisIt"
] | b9a8cb8ebe8b2606d46468e03b4364d8c6f5b32612a15d4d21ed9e1b467e2845 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Written for python 3, not tested under 2.
"""
Deep mutational scan primer design for Carlos Acevedo-Rocha based on this paper: http://nar.oxfordjournals.org/content/43/2/e12.long
"""
__author__ = "Matteo Ferla. [Github](https://github.com/matteoferla)"
__email__ = "matte... | matteoferla/mutational_scanning | deep_mut_scanning.py | Python | gpl-3.0 | 8,241 | [
"Biopython"
] | 0c4dc36a8fff5120c375f12bba43bf961d5c8028fedb6be14006f34bc8ff1ed5 |
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# Version: MPL 1.1/GPL 2.0/LGPL 2.1
#
# The contents of this file are subject to the Mozilla Public License
# Version 1.1 (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.mozil... | dostavro/dotfiles | sublime2/Packages/SublimeCodeIntel/libs/textinfo.py | Python | mit | 82,250 | [
"VisIt"
] | 7b47fa8be333c27728ec268e436ca7c127c73fa0ece4ff1316aa75804c7d9b0c |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import json
import re
from .common import InfoExtractor
from ..compat import compat_urllib_parse_unquote
from ..utils import (
int_or_none,
parse_duration,
remove_end,
try_get,
)
class MailRuIE(InfoExtractor):
IE_NAME = 'mailru'
IE_DESC ... | valmynd/MediaFetcher | src/plugins/youtube_dl/youtube_dl/extractor/mailru.py | Python | gpl-3.0 | 8,911 | [
"Galaxy"
] | c4fe5b628b80eed3f1cee4ce28335dd5d8312c28738893f62213f53356259aae |
"""Simple Echo State Network
"""
# Copyright (C) 2015 Sylvain Chevallier <sylvain.chevallier@uvsq.fr>
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or... | sylvchev/simple_esn | simple_esn/simple_esn.py | Python | gpl-3.0 | 7,835 | [
"NEURON"
] | 4f7c42227d718636764d8f4826098ec6e1670282aa0e8b9e7b185a1abd06b4ef |
#!/usr/bin/env python
########################################################################
# File : dirac-dms-replicate-lfn
# Author : Stuart Paterson
########################################################################
"""
Replicate an existing LFN to another Storage Element
Example:
$ dirac-dms-replica... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_dms_replicate_lfn.py | Python | gpl-3.0 | 2,005 | [
"DIRAC"
] | d8f355499d076eef83b522e8014484e12918436c7f38d43363fc880004062c79 |
#!/usr/bin/python
# 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) any later version.
#
# Ansible is distributed... | garyjyao1/ansible | lib/ansible/modules/core/cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,928 | [
"Dalton"
] | 987d617ec99f31642dc878aac2207c12e07379970d6e04c270397f8dd01eade1 |
#
# 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.
#
# Written (C) 2012 Heiko Strathmann, based on interactive_svm_demo by ... | MikeLing/shogun | examples/undocumented/python/graphical/interactive_gp_demo.py | Python | gpl-3.0 | 14,167 | [
"Gaussian"
] | e3e91882f8fddda84bc1d6656f464ef719a345f6a96419ba6f65d4eaebd5c0fe |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/force_codes/resolution/hmm_crossvalidation_force_1.py | Python | mit | 16,210 | [
"Gaussian",
"Mayavi"
] | 050a4f05cc283ec0bb8408b5ab912d9cdf40f888e8bf371bc7d6021c9b2cc978 |
HTTP_METHODS = [
'GET',
'POST',
'PUT',
'DELETE',
'OPTIONS'
]
HTTP_STATUS_CODES = [
"100 Continue",
"101 Switching Protocols",
"200 OK",
"201 Created",
"202 Accepted",
"203 Non Authoritative Information",
"204 No Content",
"205 Reset Content",
"206 Partial Content... | wikkiewikkie/elizabeth | elizabeth/intd/net.py | Python | mit | 34,724 | [
"Bowtie",
"Galaxy",
"Octopus"
] | eaea84ce1b915155bf488b19cb20e52465252f753f6a860feadbec2664dc9716 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2008 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/lib/test/test_validators.py | Python | gpl-2.0 | 5,919 | [
"VisIt"
] | 09c394f37df1ec722597c6e3719d0b712bd2dc8f54f8e175220a319d005761c4 |
# Reverend -- Practical Bayesian Inference with Kernel Embeddings
# Copyright (C) 2013 Lachlan McCalman
# lachlan@mccalman.info
# Reverend 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 t... | lmccalman/reverend | demo/visualise_filtering.py | Python | gpl-3.0 | 1,882 | [
"Mayavi"
] | b9735f05b208db298286e8c182477c7ab1e3ba572f2d081d1879cec531a741b7 |
'''
Gaussian Process utils. Design inspired by GPflow.
'''
import numpy as np
import tensorflow as tf
import zhusuan as zs
class RBFKernel:
def __init__(self, n_covariates, name='rbf_kernel', dtype=tf.float32):
k_raw_scale = tf.get_variable('k_log_scale_{}'.format(name),
... | thu-ml/zhusuan | examples/gaussian_process/utils.py | Python | mit | 3,319 | [
"Gaussian"
] | dc999554d3fadd49e1947ba5ff4839c0f0338f436eff315a149e03d057a3bbca |
from datetime import datetime
import pytz
import logging
import smtplib
from model_utils.managers import InheritanceManager
from collections import namedtuple
from boto.exception import BotoServerError # this is a super-class of SESError and catches connection errors
from django.db import models
from django.conf imp... | heran7/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 21,313 | [
"VisIt"
] | f596b4cf9bd4ec5869e2ef30b455f70d3d297c7ebbe51fd41f55070f3b820b6a |
"""
An example in which 3 functions of x and y are displayed with a surf plot,
while the z scaling is kept constant, to allow comparison between them.
The important aspect of this example is that the 3 functions should not
be displayed on top of each other, but side by side. For this we use the
extent keyword argumen... | wright-group/WrightData | 2015-12 Czech/TOC_Figure.py | Python | cc0-1.0 | 12,706 | [
"Mayavi"
] | eb0b252cddc4831632cf09fd83bc0a42f5a7652fe8fb6e34b127bdb1b7dbe675 |
#!/usr/bin/env python3
# Software License Agreement (BSD License)
#
# Copyright (c) 2020, UFACTORY, Inc.
# All rights reserved.
#
# Author: Vinman <vinman.wen@ufactory.cc> <vinman.cub@gmail.com>
import time
from ..core.utils.log import logger
from .code import APIState
from .utils import xarm_is_connected, check_modbu... | xArm-Developer/xArm-Python-SDK | xarm/x3/robotiq.py | Python | bsd-3-clause | 10,366 | [
"OpenMM"
] | d345756516404567879cc42409f541cc15c62b1d0df7a2b4096ef6fba8886ce0 |
#!/usr/bin/env python
##output_ortholog_seqs.py
##written 10/15/14 by Groves Dixon
ProgramName = 'output_ortholog_seqs.py'
LastUpdated = '12/14/14'
#revised to output seqs headed by only first 10 characters of species label to match with RAxML style
By = 'Groves Dixon'
VersionNumber = '1.0'
print "\nRunning Program {}.... | grovesdixon/metaTranscriptomes | scripts/output_ortholog_seqs.py | Python | mit | 11,148 | [
"BLAST"
] | 4d24e104c082b62282fb7810b172922d38166428d0792169a70dbd9245fbc47e |
#
# Copyright (C) 2008, Brian Tanner
#
#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 requ... | GarethNelson/rl-glue-ext | projects/codecs/Python/src/tests/test_1_experiment.py | Python | apache-2.0 | 3,698 | [
"Brian"
] | cd013405a59e83896b830749fd74d38c43c4fb02f811c80978959b2287a14957 |
import ast
import asyncio
from abc import ABC, abstractmethod
from collections import defaultdict
from concurrent.futures import Executor, ThreadPoolExecutor, ProcessPoolExecutor
from contextlib import contextmanager
from datetime import datetime
from enum import Enum
from functools import lru_cache, partial, wraps
imp... | TeamSPoon/logicmoo_workspace | packs_web/butterfly/lib/python3.7/site-packages/black/__init__.py | Python | mit | 230,988 | [
"VisIt"
] | 8d5e2537af1c185a00a4ad3a2e6bfea07a027acbdb2fa110e130b1a66b093ce8 |
# Copyright (c) 2012, GlaxoSmithKline Research & Development Ltd.
# 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 copyright
# ... | InformaticsMatters/squonk | components/rdkit-camel/src/main/python/mmp_code/index.py | Python | apache-2.0 | 19,816 | [
"RDKit"
] | bb35a783850eaf26131a71b7f0c8756149fdf85a772855689c84a6a81cc4f47c |
# -*- coding: utf-8 -*-
"""
Acceptance tests for studio related to the outline page.
"""
from __future__ import absolute_import
import itertools
import json
from datetime import datetime, timedelta
from unittest import skip
from pytz import UTC
import six
from six.moves import range
from common.test.acceptance.fixtu... | ESOedX/edx-platform | common/test/acceptance/tests/studio/test_studio_outline.py | Python | agpl-3.0 | 87,465 | [
"VisIt"
] | b837b27c2369340f1fcdb617f1fe7eeda8e0b364e1f5f05266d3cae2edf9ef02 |
import platform, re, os
from TestHarness import util
from FactorySystem.MooseObject import MooseObject
from tempfile import TemporaryFile
import subprocess
from signal import SIGTERM
class Tester(MooseObject):
"""
Base class from which all tester objects are instanced.
"""
@staticmethod
def validPa... | Chuban/moose | python/TestHarness/testers/Tester.py | Python | lgpl-2.1 | 27,923 | [
"MOOSE",
"VTK"
] | 3b5169d61e58cc96d652e67337620bb5f101889ce22afd73bdd9ddc51bf5067f |
# -*- coding: utf-8 -*-
from selenium_tests.RemoteAppDriverTest import RemoteAppDriverTest
from selenium.webdriver.common.by import By
class AdminDriverTest(RemoteAppDriverTest):
def setUp(self):
RemoteAppDriverTest.setUp(self)
self.login("admin")
def wait_until_visibility_of_row(self, row):
... | simphony/simphony-remote | selenium_tests/AdminDriverTest.py | Python | bsd-3-clause | 2,649 | [
"Mayavi"
] | b3ba4643ea71016b0772086ca63895b390ed4ea25c303e81cdee8b981e3c1d71 |
#!/usr/bin/env python
"""
================================================
ABElectronics RTC Pi Real-time clock
Requires smbus2 or python smbus to be installed
================================================
"""
try:
from smbus2 import SMBus
except ImportError:
try:
from smbus import SMBus
except ... | abelectronicsuk/ABElectronics_Python_Libraries | RTCPi/RTCPi.py | Python | gpl-2.0 | 10,476 | [
"TINKER"
] | 776934b0ee6b6bcebcce2cae48a7c8346c4444c9892bf049379e70333b2ecd00 |
#!/usr/bin/python
"""rss2email: get RSS feeds emailed to you
http://rss2email.infogami.com
Usage:
new [emailaddress] (create new feedfile)
email newemailaddress (update default email)
run [--no-send] [num]
add feedurl [emailaddress]
list
reset
delete n
pause n
unpause n
opmlexport
opmlimport file... | onecore/rss2email-gui | rss2email.py | Python | mit | 31,127 | [
"Brian"
] | 773b5efc8694502961359f6bf01e0b4e72f6bac87d459295ccf5849f28a57e91 |
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
from __future__ import division, print_function, absolute_import
from scipy._lib.six import string_types, exec_
import sys
import keyword
import re
import inspect
import types
import warnings
from scipy.misc impor... | nvoron23/scipy | scipy/stats/_distn_infrastructure.py | Python | bsd-3-clause | 108,689 | [
"Gaussian"
] | e6287f7b583c057754dcf6ae4d9f56007705aa999c1552f367a25dfa77137b46 |
# encoding: utf-8
"""
Prefiltering components.
Prefilters transform user input before it is exec'd by Python. These
transforms are used to implement additional syntax such as !ls and %magic.
Authors:
* Brian Granger
* Fernando Perez
* Dan Milstein
* Ville Vainio
"""
#-----------------------------------------------... | Vvucinic/Wander | venv_2_7/lib/python2.7/site-packages/IPython/core/prefilter.py | Python | artistic-2.0 | 26,042 | [
"Brian"
] | 04c8661642de0b83f53125b159fc27ee8ec1d8ed848349787aec5ccd7f7dd370 |
#!/usr/bin/env python
# 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 hope that ... | dmnfarrell/smallrnaseq | smallrnaseq/analysis.py | Python | gpl-3.0 | 12,574 | [
"HTSeq"
] | 6a19b4523cb07c96c32cfe3036a55cb2b5999a3ebb191266120a3fa88f3a9926 |
#!/usr/bin/env python
# Copyright 2020 Informatics Matters Ltd.
#
# 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... | InformaticsMatters/pipelines | src/python/pipelines/xchem/featurestein_generate.py | Python | apache-2.0 | 6,018 | [
"RDKit"
] | 5ed1aa5188d191163f6e2a581ab7d42dd5528e0d77e22920a3892bfd9bff1f87 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from datetime import timedelta
from collections import defaultdict
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth import logout, authe... | martynovp/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 92,733 | [
"VisIt"
] | 513bcfa2fb2ec2399900b514482ac1deeaa246e431307f6759a9ab0d513efaa5 |
from __future__ import print_function
#from scipy.io import netcdf
import numpy as np
import sys
import os
import struct
import scipy.ndimage.filters as filters
import matplotlib.pyplot as plt
from scipy.interpolate import griddata
from mpl_toolkits.mplot3d import axes3d
#=====================================
# ... | geodynamics/specfem3d | utils/dynamic_rupture/Visualization/Present_specfem3D_results.py | Python | gpl-3.0 | 10,397 | [
"NetCDF"
] | da4ebd48fd71c0309662ea0ef40919b64aae5cce6cbc509abee0dada4909224b |
#!/usr/bin/env python3
#
# Copyright (c) 2012 Brian Yi ZHANG <brianlions at gmail dot com>
#
# This file is part of pynebula.
#
# pynebula 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 th... | brianlions/python-nebula | nebula/asyncevent/_socket_dispatcher.py | Python | gpl-3.0 | 15,806 | [
"Brian"
] | 098ed8ea37a54a6b5b50aa68ab5415e0426477916d88c3dd2a6e2a044b865006 |
import random
import numpy
from utils.constants import Constants
grouped_hotel_context_words = {
'airport': {'airport', 'shuttle', 'plane', 'flight', 'transportation',
'bus'},
'holiday': {'holiday', 'vacation', 'staycation', 'getaway', '@', '@@'},
'conference': {'conference', 'convention... | melqkiades/yelp | source/python/utils/utilities.py | Python | lgpl-2.1 | 6,294 | [
"CASINO"
] | fc129441b4bd9c7caaefa5ce3990f9f81d095a6288598d55515d37df82e0bc81 |
import numpy as np
import batoid
from .utils import bilinear_fit, fieldToDirCos
def _reciprocalLatticeVectors(a1, a2, N):
norm = 2*np.pi/(a1[0]*a2[1] - a1[1]*a2[0])/N
b1 = norm*np.array([a2[1], a2[0]])
b2 = norm*np.array([a1[1], a1[0]])
return b1, b2
def dkdu(
optic, theta_x, theta_y, wavelengt... | jmeyers314/batoid | batoid/analysis.py | Python | bsd-2-clause | 31,486 | [
"Gaussian"
] | c679f80455741069eab1e95b252d0f54e1df8cb412efd8f73ef5f9de7a68d3c6 |
import numpy as np
import pylab as pl
from scipy.optimize import leastsq
from lmfit import minimize, Parameters, Parameter,\
report_fit, Model
from lmfit.models import StepModel,PolynomialModel, ExponentialModel, PowerLawModel, DonaichModel, GaussianModel, LorentzianModel, ConstantModel, RectangleMo... | DiamondLightSource/auto_tomo_calibration-experimental | old_code_scripts/measure_resolution/fit_data.py | Python | apache-2.0 | 6,119 | [
"Gaussian"
] | f28d2e4822dc103575e5c8c6cef14978cc0f38afccc15fd89c458b73c76f9992 |
#!/usr/bin/env python
""" update local cfg
"""
from DIRAC.Core.Base import Script
Script.setUsageMessage('\n'.join([__doc__.split('\n')[1],
'Usage:',
' %s [option|cfgFile] ... DB ...' % Script.scriptName]))
Script.parseCommandLine()
args = Script.... | arrabito/DIRAC | tests/Jenkins/dirac-cfg-JobDBESFlag.py | Python | gpl-3.0 | 592 | [
"DIRAC"
] | f4e189d116b89f530ad57a6434c756157eea5063dc8892a1ceef329c34e0186a |
# -*- Mode: Python; coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Sof... | tiagocardosos/stoq | stoq/gui/accounts.py | Python | gpl-2.0 | 11,345 | [
"VisIt"
] | 5443706dc423201064dbdd1e1c3b19a82bb3100c9a3ef1321ce10e83720a2a13 |
"""
Diversity calculations (:mod:`skbio.diversity`)
===============================================
.. currentmodule:: skbio.diversity
This package provides functionality for analyzing biological diversity. It
implements metrics of alpha and beta diversity, and provides two "driver
functions" that are intended to be ... | gregcaporaso/scikit-bio | skbio/diversity/__init__.py | Python | bsd-3-clause | 17,124 | [
"scikit-bio"
] | 9fc4aae62fb98c168f68980d4c063b277af4a9d64afa3f1c80899e756ddb55e6 |
# -*- coding: utf-8 -*-
import numpy as np
import pickle
import json
import copy
from .inputparser import InputParser
from .knn import KNN
from ..converter import Converter
from ..pitchdistribution import PitchDistribution
class KNNClassifier(InputParser):
def __init__(self, step_size=7.5, kernel_width=15.0, fea... | altugkarakurt/morty | morty/classifiers/knnclassifier.py | Python | agpl-3.0 | 17,794 | [
"Gaussian"
] | 8c179a00139fc3a84aa49edfb53a4f1599375d35f45e7400ab993948796903a8 |
''' Mercurial revision DAG visualization library
Implements a gtk.TreeModel which visualizes a Mercurial repository
revision history.
Portions of this code stolen mercilessly from bzr-gtk visualization
dialog. Other portions stolen from graphlog extension.
'''
import gtk
import gobject
import pango
import treem... | tdjordan/tortoisegit | gitgtk/vis/treeview.py | Python | gpl-2.0 | 16,818 | [
"MCell"
] | 5d58f8a00a24afccbbbc5dc2f1ce990aaf648f3ce76272f5a0b441b1dab8af83 |
#!/usr/bin/env python
"""
Block mesh generator.
"""
from __future__ import absolute_import
import sys
sys.path.append('.')
from argparse import ArgumentParser
import numpy as nm
from sfepy.base.base import output
from sfepy.mesh.mesh_generators import gen_block_mesh
from sfepy.discrete.fem.meshio import MeshIO
helps... | lokik/sfepy | script/blockgen.py | Python | bsd-3-clause | 2,683 | [
"VTK"
] | 952d72c5140ac5439b267d263c6178f2a126df30a11f474d91a64ee782cd17ab |
# -*- coding: utf-8 -*-
"""
Created on Mon May 15 09:57:29 2017
@author: S.Y. Agustsson
"""
import os
import re
import numpy as np
import pandas as pd
import scipy.io as spio
import scipy.signal as spsignal
from matplotlib import cm, pyplot as plt
from scipy.optimize import curve_fit
from lib import utils
def mai... | steinnymir/RegAscope2017 | lib/transient.py | Python | mit | 46,836 | [
"Gaussian"
] | 246324fb0509a1efd147a780e7791e16ca337df964814d37acd68bc3dc2b9a27 |
""" Utilities for the MessageQueue package
"""
__RCSID__ = "$Id$"
import Queue
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.ConfigurationSystem.Client.CSAPI import CSAPI
def getMQParamsFromCS(mqURI):
""" Function gets parameters of a MQ destination (queue/topic) from the CS.
Args:
mqURI(str):Pseudo ... | andresailer/DIRAC | Resources/MessageQueue/Utilities.py | Python | gpl-3.0 | 3,168 | [
"DIRAC"
] | f4a1905d34967321d215e5bee633dc64520dcb32f23abb61ae06507fb691e3a2 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathem... | sknepneklab/SAMoS | analysis/batch_nematic/batch_analyze_nematic_longa.py | Python | gpl-3.0 | 2,492 | [
"VTK"
] | 80195be63d8f56b5835937c6f9c2a05415bf73d0d4570d91cb047e7f13ed46ff |
import numpy as np
np.random.seed(42)
import chainer
from chainer import functions as F
from chainer import links as L
from chainer import initializer
from chainer.initializers import Normal
from time import time
import pandas as pd
eps = 1e-8
def phi(obs):
"""
Feature extraction function
"""
xp = c... | naripok/cryptotrader | cryptotrader/models/cn_models.py | Python | mit | 10,789 | [
"Gaussian"
] | ab7c13fa2ae4c711c7d4d3ee974ef655b516c01e5ec777d318b4a2b86044d403 |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... | 99cloud/keystone_register | horizon/base.py | Python | apache-2.0 | 29,033 | [
"VisIt"
] | aa688d1cdc56e029478f54ed8b3cc6e0cd865d6668706ffa1440c0491c7bc035 |
##############################################################################
# Copyright (c) 2013-2018, 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... | krafczyk/spack | var/spack/repos/builtin/packages/mfem/package.py | Python | lgpl-2.1 | 21,344 | [
"NetCDF"
] | 0b7b831301808e8bc17313a98ca489b0a5cb093674ffc9f3a8c7f01e199a5931 |
'''Helper module in popmodel containing constants and functions for OH
calculations.
'''
## Literature cited:
# Bradshaw et al, Appl Opt, 23, 2134 (1984)
# Daily et al., Applied Optics 16 (3), 568-571 (1977)
# Fuchs et al., Atmos Meas Tech, 1611-1626(2012)
# Schlosser et al., J Atmos Chem, 56, 187-205 (2007)
# Tsuji ... | awbirdsall/popmodel | src/popmodel/ohcalcs.py | Python | mit | 19,426 | [
"Gaussian"
] | 045cda414b39cc21ee759d3fd30aa533833f4b2b56f57645e1c1fcc6cceb4ed1 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list ... | bruderstein/PythonScript | PythonLib/min/mimetypes.py | Python | gpl-2.0 | 22,624 | [
"NetCDF"
] | 9a0adce97a4d2f793a021733fb13c21678870b8d3adcf39fbbb9a586e3ff3286 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Copyright (c) 2012-2013, Dennis Sun <dlsun@stanford.edu>
# Copyright (c) 2012, Kinjal Basu <kinjal@stanford.edu>... | jonathan-taylor/ohms | ohms/homeworks/Example_Homework.py | Python | mpl-2.0 | 4,748 | [
"CASINO"
] | e1193ebc0b325435698ff2b23aac47b4705780eefba7c3c5b40624b2850837bc |
"""
Very quick and dirty script to insert FMI PM data from CSV file into InfluxDB.
"""
import sys
import os
import math
import csv
import datetime
import influxdb
from dateutil.parser import parse
import pytz
if len(sys.argv) < 2:
print("Usage:\n\tpython {} pm_min PM10_PM25_min.csv".format(sys.argv[0]))
exit(... | aapris/IoT-Web-Experiments | TempStuff/fmi_pm_csv2inluxdb.py | Python | mit | 2,209 | [
"FEFF"
] | 7ec4e68160ffc7e6061a4ea5a5befdf07f56d4ffa47fdbd55c5cc3f19ab841fe |
import series_io, series_transform, series_stats_calc
from common import *
logger = logging.getLogger(__name__)
def main(config):
logger.info('main start')
dump_test_series(config)
calculate_statistics(config, 'sample_bics_1_tech')
calculate_statistics(config, 'sample_xchng_us')
calculate_statistics(config, ... | candide-guevara/programming_challenges | compression_fun_and_profit/stats_calc/main.py | Python | gpl-2.0 | 3,649 | [
"Gaussian"
] | cd4598c515f892ff2d59f0910615a7066d32cfb5009a0c16f55cdc2e8fe6e9ed |
'''
Created on Aug 28, 2013
@author: anuvrat
'''
from bs4 import BeautifulSoup
import urllib.request
import urllib.parse
import codecs
import json
import pickle
from datetime import datetime
import urllib2
def loadState():
try:
state_file = open( "state_dump", "rb" )
apps_discovered = pickle.load... | anuvrat/scrape-google-play | src/crawlPlay.py | Python | mit | 8,983 | [
"VisIt"
] | 1ff4a2f06a802320e24cf351b977dbc5231bd5c8676d67ce3c7d074cf12b7280 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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
# ... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/lenovo/cnos_command.py | Python | bsd-3-clause | 5,666 | [
"VisIt"
] | 1d8fa78b19b34de182639139ceb307d18e1511d0011bef6d5815486258e2cc24 |
# textrender.py
# module to render text, tries to understand a basic LateX-like syntax
# Copyright (C) 2003 Jeremy S. Sanders
# Email: Jeremy Sanders <jeremy@jeremysanders.net>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as... | veusz/veusz | veusz/utils/textrender.py | Python | gpl-2.0 | 50,320 | [
"Bowtie"
] | 28908c96ca786cfcde51302d2d5fe5b371381fbae33feb318228119c578a85a5 |
"""Gaussian processes classification."""
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve
import scipy.optimize
from scipy.special import erf, expit
from ..base import BaseEst... | kevin-intel/scikit-learn | sklearn/gaussian_process/_gpc.py | Python | bsd-3-clause | 34,992 | [
"Gaussian"
] | d6a87950f55739da1f708225af05e29bdcd1f89f12cf21e070f63458c7b5367d |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | hainm/scikit-xray | skxray/core/fitting/xrf_model.py | Python | bsd-3-clause | 46,079 | [
"Gaussian"
] | 2b96f5609f605129b2bd473ad110662c6099be0786b81c14803963ec495b2fe1 |
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | tensorflow/neural-structured-learning | research/carls/dynamic_normalization.py | Python | apache-2.0 | 11,677 | [
"Gaussian"
] | 111616c124467baad5a45060710220a05df03aaee3b6ea5380059245428370ed |
from vtk.util import vtkMethodParser
class Tester:
def __init__(self, debug=0):
self.setDebug(debug)
self.parser = vtkMethodParser.VtkDirMethodParser()
self.obj = None
def setDebug(self, val):
"""Sets debug value of the vtkMethodParser. 1 is verbose and
0 is not. 0 i... | Wuteyan/VTK | Wrapping/Python/vtk/test/BlackBox.py | Python | bsd-3-clause | 2,793 | [
"VTK"
] | 32daebde8c6e111fe2b879ec86d53062c9e07e2cb306b453a4ecbdcbf947c056 |
from setuptools import find_packages, setup
setup(
name='pythomics',
version='0.3.46',
description='A multi-omic python package',
url='https://github.com/pandeylab/pythomics',
author='Chris Mitchell',
author_email='chris.mit7@gmail.com',
install_requires=[
'lxml',
'six',
... | pandeylab/pythomics | setup.py | Python | gpl-3.0 | 981 | [
"pysam"
] | 84a683eb1b233fdf93cad93e34bebb418d70b748a324f44b995082c8fb069cf8 |
#
# ImageViewTk.py -- a backend for Ginga using a Tk canvas widget
#
# This is open-source software licensed under a BSD license.
# Please see the file LICENSE.txt for details.
#
import PIL.Image as PILimage
have_pil_imagetk = False
try:
# sometimes this is not installed even though PIL is
from PIL.ImageTk imp... | pllim/ginga | ginga/tkw/ImageViewTk.py | Python | bsd-3-clause | 15,381 | [
"FLEUR"
] | a42c2c95cff03e5f932e2c4a5c93e3ee41567696d8652ca285181831b1f008b4 |
"""Test the dirac-transformation-replication script and helper"""
import unittest
from mock import MagicMock as Mock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.TransformationSystem.Utilities.ReplicationTransformation import createDataTransformation
from DIRAC.TransformationSystem.Utilities.ReplicationCLIPara... | chaen/DIRAC | TransformationSystem/test/Test_replicationTransformation.py | Python | gpl-3.0 | 10,335 | [
"DIRAC"
] | d2ade20129885e9e37f06d236c98c587612931c4d711223de32b43ee1236e7f3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
DIRAC and GridPP: perform a query on the CERN@school clusters.
"""
#...for the operating system stuff.
import os
#...for parsing the arguments.
import argparse
#...for the logging.
import logging as lg
# Import the JSON library.
import json
# The DIRAC import st... | gridpp/dirac-getting-started | perform_cluster_query.py | Python | mit | 2,617 | [
"DIRAC"
] | 9732bdf9da513b2d0f956ff4ff3481e389326e4170f2b337f3e0aee9b963fdc1 |
# coding: utf-8
from __future__ import print_function, division, unicode_literals, absolute_import
executable = "multibinit"
from abimkdocs.variables import ValueWithUnit, MultipleValue, Range
#from abipy.abio.abivar_database.variables import ValueWithUnit, MultipleValue, Range, ValueWithConditions
ValueWithCondition... | abinit/abinit | abimkdocs/variables_multibinit.py | Python | gpl-3.0 | 51,651 | [
"ABINIT",
"NetCDF",
"VASP"
] | eb22098e5302e6d9e12a7670acb72a8b00bf11b1a958be79bfe8245824f3c629 |
from BlockDevice import BlockDevice
import ctypes
import gzip
import io
class ADFBlockDevice(BlockDevice):
def __init__(self, adf_file, read_only=False, fobj=None):
self.adf_file = adf_file
self.read_only = read_only
self.fobj = fobj
self.dirty = False
lo = adf_file.lower()
self.gzipped = lo.... | alpine9000/amiga_examples | tools/external/amitools/amitools/fs/blkdev/ADFBlockDevice.py | Python | bsd-2-clause | 3,365 | [
"ADF"
] | 0fd3d4c384b4046a5890442f7b5adfba95acf576e4f5aa09e8d0448998f1da79 |
"""
Exploration strategies
"""
from gym.spaces import Box
import numpy as np
import numpy.random as nr
class OUStrategy(object):
"""
This strategy implements the Ornstein-Uhlenbeck process, which adds
time-correlated noise to the actions taken by the deterministic policy.
The OU process satisfies the ... | justinjfu/chaos_theory | chaos_theory/models/exploration.py | Python | gpl-3.0 | 2,011 | [
"Gaussian"
] | a0754cd3c634aba7ec685a99a0e4744512cb3d78f1c1529d80171a456e5b226f |
import director
import director.objectmodel as om
from director import visualization as vis
from director.visualization import PolyDataItem
from director import filterUtils
from director import ioUtils
from director import meshmanager
from director import transformUtils
from director.uuidutil import newUUID
from direct... | mitdrc/director | src/python/director/affordanceitems.py | Python | bsd-3-clause | 12,122 | [
"VTK"
] | 848fc2bd9adb678749912bf80ed3171dad3922fef7e3cf0695eb3e7ddb57b144 |
# ------------------------------------------------------------------------------
# Name: analytics_engine.py
# Purpose: Analytical Engine
#
# Author: Peter Wang
#
# Created: 14 July 2015
# Copyright: 2015 Commonwealth Scientific and Industrial Research Organisation
# (CSIRO)
# License: T... | ceos-seo/Data_Cube_v2 | agdc-v2/datacube/analytics/analytics_engine.py | Python | apache-2.0 | 16,960 | [
"NetCDF"
] | c1aab7f75abc95e3f0a221b2339ab49c47bcf595b4b5f15bf41b7d08b027ee44 |
#
# Copyright (C) 2004-2008 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 numpy
from rdkit impor... | rvianello/rdkit | rdkit/Chem/Pharm3D/Pharmacophore.py | Python | bsd-3-clause | 5,917 | [
"RDKit"
] | c1ef71fd2c7028262f87d041d6fa6e8ef582473ad13ce12cc55ad6e8767b9bf2 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# 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 PyBioMed source tree.
"""
The c... | gadsbyfly/PyBioMed | PyBioMed/PyInteraction/PyInteraction.py | Python | bsd-3-clause | 3,660 | [
"MOE",
"RDKit"
] | bcbee45fc4dea940c51899f7153c422b6bf878f192ca62fa654e964315318ad5 |
#!python
# coding=utf-8
from pyaxiom.netcdf import CFDataset
from pyaxiom import logger
class ContiguousRaggedTimeseries(CFDataset):
@classmethod
def is_mine(cls, dsg):
try:
rvars = dsg.get_variables_by_attributes(cf_role='timeseries_id')
assert len(rvars) == 1
as... | axiom-data-science/pyaxiom | pyaxiom/netcdf/sensors/dsg/timeseries/cr.py | Python | mit | 1,599 | [
"NetCDF"
] | cf4ff5c8a905e571ad5ec0c085bfe4ef035f660a6c14f71b4b7d9f17e01f2a93 |
#!/usr/bin/env python
# ORCA1 -> eORCA1 has 40 gridpoint offset
# L. Brodeau, april 2010
import sys
import numpy as nmp
from netCDF4 import Dataset
from string import replace
if len(sys.argv) != 2:
print 'Usage: '+sys.argv[0]+' <mesh_mask_eORCA1_file.nc>'
sys.exit(0)
cf_mm = sys.argv[1]
cf_out = replace(cf_... | plesager/barakuda | python/exec/eorca1_create_basin_mask_from_meshmask.py | Python | gpl-2.0 | 4,972 | [
"NetCDF"
] | c4e621b60b4cc40e0c18d1c3f25daaae308aee59d0824b90ce7ab2e230945cc1 |
"""Incremental version of the MiniMark GC.
Environment variables can be used to fine-tune the following parameters:
PYPY_GC_NURSERY The nursery size. Defaults to 1/2 of your cache or
'4M'. Small values
(like 1 or 1KB) are useful for debugging.
PYPY_GC_NUR... | jptomo/rpython-lang-scheme | rpython/memory/gc/incminimark.py | Python | mit | 129,040 | [
"VisIt"
] | c4c472947e0ecc04584b268f42f66700bfa71366c302f05a38a3db13c61afad8 |
# -*- coding: utf8 -*-
from testrun import cfiles
import os
PDB_CONTENT = """CRYST1 15.000 15.000 15.000 90.00 90.00 90.00
ATOM 1 O X 1 0.417 8.303 11.737 0.00 0.00
ATOM 2 H X 1 1.320 8.480 12.003 0.00 0.00
ATOM 3 H X 1 0.332 8.726 10.88... | chemfiles/chrp | tests/convert.py | Python | mpl-2.0 | 2,489 | [
"Chemfiles"
] | a5badd52babeba38173dd6de7c6db407e4898b27983218ec07be12314a948fa7 |
# Copyright (c) 2012-2015 The GPy authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from scipy import stats,special
import scipy as sp
from . import link_functions
from ..util.misc import chain_1, chain_2, chain_3, blockify_dhess_dtheta, blockify_third, blockify_h... | SheffieldML/GPy | GPy/likelihoods/likelihood.py | Python | bsd-3-clause | 36,595 | [
"Gaussian"
] | 0b90ac97bf68071601c4ed73dbf6119df2b691eda79c90e821d4dc92f42c25c7 |
"""
sentry.web.frontend.accounts
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:copyright: (c) 2012 by the Sentry Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
from __future__ import absolute_import
import logging
import six
from django.conf import settings
from django.contrib import messages
... | JamesMura/sentry | src/sentry/web/frontend/accounts.py | Python | bsd-3-clause | 19,916 | [
"VisIt"
] | 4d0091b2a1292c7346b46678f33bdcc24c56f9067c3392084cb2e44819339f63 |
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