text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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__all__ = ['gaussian']
| harpolea/pyro2 | diffusion/problems/__init__.py | Python | bsd-3-clause | 23 | [
"Gaussian"
] | 4e4f49eba249053b2fdd34efdb16c88cbaaa7a27ce7d30132ff669354fb94374 |
from nose.plugins.attrib import attr
import simtk.unit as u
from simtk.openmm import app
import simtk.openmm as mm
import numpy as np
from mdtraj.testing import eq
from unittest import skipIf
from openmoltools import utils, packmol
import os
import openmoltools.openeye
import pandas as pd
import mdtraj as md
from mdtra... | jchodera/openmoltools | openmoltools/tests/test_openeye.py | Python | gpl-2.0 | 11,798 | [
"Amber",
"MDTraj",
"OpenMM"
] | 8c00f314e361a58160c4c531761d3492d43969974e3c5eaa7d4357d08a449e35 |
"""
Processes and execution
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
# Imports
import types
import uuid
import threading
from pycsp.parallel.dispatch import Soc... | runefriborg/pycsp | pycsp/parallel/process.py | Python | mit | 17,098 | [
"Brian"
] | 0725184d5fe90f3346ce294c306dd3a29728219741d63b3516720133eb761f74 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2018, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | neuroidss/nupic.research | htmresearch/regions/Guassian2DLocationRegion.py | Python | agpl-3.0 | 17,678 | [
"Gaussian"
] | 587b116632047bf3830db08eba37d711658bb078be3471402777d4e019a7e2a5 |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2014 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | LunarLanding/Pythics | pythics/master.py | Python | gpl-3.0 | 22,230 | [
"Brian"
] | 5a5e6abef410d437a52b435ccaff00ed067d11641ed4ace9bb538203a8bcb711 |
# -*- coding: utf-8 -*-
"""
flaskbb.utils.helpers
~~~~~~~~~~~~~~~~~~~~
A few helpers that are used by flaskbb
:copyright: (c) 2014 by the FlaskBB Team.
:license: BSD, see LICENSE for more details.
"""
import re
import time
import itertools
import operator
import struct
from io import BytesIO
from ... | KevinHock/rtdpyt | profiling/test_projects/flaskbb_lite_3/flaskbb/utils/helpers.py | Python | gpl-2.0 | 16,443 | [
"VisIt"
] | 2b56ad83d9440b9261af041d2785ee3beeb66df1397d3e9027685214dfcf58c2 |
#!/usr/bin/env python3
from scipy.version import version as SciPyVersion
if tuple(int(x) for x in SciPyVersion.split('.')) < (0, 9, 0):
from Scientific.IO.NetCDF import NetCDFFile as netcdf_file
else:
from scipy.io.netcdf import netcdf_file
from numpy import arange, zeros
import height
f = netcdf_file('heig... | FluidityStokes/fluidity | tests/netcdf_read_free_surface/createnetcdf.py | Python | lgpl-2.1 | 854 | [
"NetCDF"
] | bd82762b46454c5ef5b3ad714f305f5116dfb202c5ac45ced2e9310ed5b73438 |
from __future__ import division
__all__ = ['write_lammpsdata']
import re
import numpy as np
from .hoomdxml import RB_to_OPLS
from collections import OrderedDict
def write_lammpsdata(structure, filename, forcefield, box):
"""Output a LAMMPS data file.
Note: Output supports 'real' units and 'full' atom s... | sallai/mbuild | mbuild/formats/lammpsdata.py | Python | mit | 8,048 | [
"LAMMPS"
] | 73a5e522f278bcab6b97b822af96ce2913a686de844fa46f01eacd0dfc25f8d1 |
import inspect
from inspect import getsource
import os.path as op
from pkgutil import walk_packages
import re
import sys
from unittest import SkipTest
import pytest
import mne
from mne.utils import (run_tests_if_main, _doc_special_members,
requires_numpydoc)
from mne.fixes import _get_args
pub... | adykstra/mne-python | mne/tests/test_docstring_parameters.py | Python | bsd-3-clause | 10,211 | [
"Mayavi"
] | d94c3a21d6d3fe92e908d698bf7e186f9ff1fbfe8676c80f207c7958ed524148 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/remote_signals.py | Python | gpl-2.0 | 7,148 | [
"VisIt"
] | 615de4a1ed59d91f248cb6c405ad397bfd115aa04ad466213be067c09c015507 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/worker.py | Python | lgpl-2.1 | 26,353 | [
"MDTraj"
] | ecfb820f932cb24056325f1a9342cdf0ad4e17fe92efde9ae884329f6eff29fd |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2012 Jan Decaluwe
#
# The myhdl 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 t... | hgomersall/myhdl | myhdl/conversion/_toVerilog.py | Python | lgpl-2.1 | 51,950 | [
"VisIt"
] | c41bc5969abc1bf5182101e2ffad234f69b1906543828f153cbe76d94af4b530 |
"""This program is currently set up to approximate the uniformly convex solution of the Monge--Ampere optimal mass transport equation, coinciding with the prescribed Gaussian curvature equation
det( D^2 u(x, y) ) = f(x,y)*(|grad(u)|^2+1)^2,
on the unit disk, with the boundary condition |grad(u)|^2-1=0, as well ... | ekawecki/Monge--Ampere | MA-no-gradient-recovery.py | Python | gpl-3.0 | 14,680 | [
"Gaussian",
"ParaView"
] | b89db2186f0140a9aeee0ccabbb543c0b9349bb4f7a3bb7a0be5740d925c06fe |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Module fo... | nuclear-wizard/moose | python/MooseDocs/base/executioners.py | Python | lgpl-2.1 | 22,966 | [
"MOOSE"
] | f5a705c1ffd4312dc23dd65523a3e2b64a63f4ac3455ca49875b1a1484bc08c0 |
# Copyright 2018 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, ... | google/jax | examples/mnist_vae.py | Python | apache-2.0 | 5,048 | [
"Gaussian"
] | b583f2096bc3664087a3d723801d937f2ad879536f8ebebb22e75726bae6a5ce |
from __future__ import division
import numpy as np
from menpo.shape import TriMesh
from menpo.image import MaskedImage
from menpo.transform import Scale, Translation
from menpo.transform.piecewiseaffine import PiecewiseAffine
from menpo.transform.thinplatesplines import ThinPlateSplines
from menpo.model import PCAMode... | jabooth/menpo-archive | menpo/fitmultilevel/aam/builder.py | Python | bsd-3-clause | 27,729 | [
"Gaussian"
] | 60d2d7fcff28b47658f349b7a5f28d1c861ca4cc2b023b4e985126af66b6a681 |
#!/bin/env python
"""
Module simtk.unit.quantity
Physical quantities with units, intended to produce similar functionality
to Boost.Units package in C++ (but with a runtime cost).
Uses similar API as Scientific.Physics.PhysicalQuantities
but different internals to satisfy our local requirements.
In particular, there i... | leeping/mdtraj | mdtraj/utils/unit/quantity.py | Python | lgpl-2.1 | 27,291 | [
"OpenMM"
] | c99ed107dcf8dd65f387336e7fe04764798e3292ef2f7667c4a2254c55d86628 |
# 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... | xzturn/tensorflow | tensorflow/python/autograph/pyct/transformer_test.py | Python | apache-2.0 | 9,724 | [
"VisIt"
] | 40fa904500d8ae68619cd7e313b7e02bae87e311c115630554461559595371b8 |
import os.path as op
import pytest
import ssbio.io
import shutil
import pandas as pd
from ssbio.pipeline.atlas2 import ATLAS2
@pytest.fixture(scope='class')
def reference_gempro(test_files_gempro):
gp = ssbio.io.load_json(op.join(test_files_gempro, 'test_id_dir_json', 'model', 'mini_gp.json'))
gp.root_dir = t... | nmih/ssbio | ssbio/test/test_pipeline_atlas.py | Python | mit | 6,237 | [
"Biopython"
] | 3b2d33af55d1c1ab02d01bceb4bc06e9933814e42a691b2960cc634efda32ad9 |
#
# 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... | bravo-zhang/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 66,013 | [
"Gaussian"
] | 1003f566fbd68953be78e5c9b215fddc5f4410ebe04eb0215d50ccb86200bb46 |
#!/usr/bin/env python
########################################################################
# File : dirac_proxy_get_uploaded_info.py
# Author : Adrian Casajus
########################################################################
"""
Print information about uploaded proxies.
Example:
$ dirac-proxy-get-uplo... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_proxy_get_uploaded_info.py | Python | gpl-3.0 | 3,704 | [
"DIRAC"
] | f6b729f639d888825e1a2939200fc508f1dadbf703fb8fb9274f79ea94570ec5 |
#
# QAPI types generator
#
# Copyright IBM, Corp. 2011
# Copyright (c) 2013-2016 Red Hat Inc.
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2.
# See the COPYING file in the top-level directory.
from qapi ... | SPICE/qemu | scripts/qapi-types.py | Python | gpl-2.0 | 8,843 | [
"VisIt"
] | 16581766484876086a22e29f48dceba4dc45efee72efe4d5f55d9b4ce93d08fa |
# Copyright 2008 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parser for XML results returned by NCBI's Entrez Utilities.
This parser is used by the r... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Entrez/Parser.py | Python | gpl-2.0 | 21,857 | [
"Biopython"
] | 4fcf2b29bcaa526678963919ead4da84fea83d0b8b6901c1ddf01d7e907324bb |
# Licensed to the StackStorm, Inc ('StackStorm') 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 use th... | armab/st2 | st2common/st2common/hooks.py | Python | apache-2.0 | 14,043 | [
"GULP"
] | 0ca44f1c48e92a418f9e16f04ac871c59a4fa7e2f06087085fc4f2dfee18d03c |
"""Utility modules for the VTK-Python wrappers."""
__all__ = ['colors', 'misc', 'vtkConstants', 'vtkImageExportToArray',
'vtkImageImportFromArray', 'vtkMethodParser']
| sgh/vtk | Wrapping/Python/vtk/util/__init__.py | Python | bsd-3-clause | 179 | [
"VTK"
] | 249d5dde8b3f54e073e2dba8d71b47b91455912339be89e2896d49fc1ac41066 |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2014 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | pbokoc/pykickstart | tests/commands/sshkey.py | Python | gpl-2.0 | 2,613 | [
"Brian"
] | f2585bbf50c2963509d550505cd8d0e85339644c388f54c2b2806834ea744bcf |
from __future__ import absolute_import
import unittest2 as unittest
import math
import json
import os
import numpy as np
from pymatgen.analysis.elasticity.tensors import TensorBase, SquareTensor
from pymatgen.core.operations import SymmOp
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.te... | aykol/pymatgen | pymatgen/analysis/elasticity/tests/test_tensors.py | Python | mit | 17,143 | [
"pymatgen"
] | ce35714fae6a77f3326a64f017c68f7b0caa00ea088dc9630a1a660b6444aa97 |
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/... | harterj/moose | python/chigger/filters/RotationalExtrusionFilter.py | Python | lgpl-2.1 | 1,471 | [
"MOOSE",
"VTK"
] | 17075a000ca964cab9816f789af18995bac90bbd50943c3b5e1cd14c0b50dda2 |
from collections import OrderedDict
import datetime
import json
__author__ = 'rjs'
class Visitor:
def visit(self, node, *args, **kwargs):
method = None
for cls in node.__class__.__mro__:
method_name = 'visit_' + cls.__name__
method = getattr(self, method_name, None)
... | rob-smallshire/trailer | trailer/writers/json/renderer.py | Python | mit | 7,594 | [
"VisIt"
] | 482869673a3207c385cc657c597ba3318bac098b15f5ba240f217630bcb0785c |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py | Python | gpl-2.0 | 2,285 | [
"Amber",
"MDAnalysis"
] | 6a24077090086fdf4eb2e662fd3ea880e7b2ad7a0639d35e10fa4ee587f9d537 |
"""
Pass two csv file, first moose and second neuron.
The first column in each file is time vector which is our reference column
for further processing.
This script assumes that columns of both files have been sorted in a way
that each column in one file has its equivalent in second file at the s... | BhallaLab/benchmarks | moose_nrn_equivalence_testing/comparision_with_simple_HH_model_additional_mechanism/compare_moose_nrn_single_vector.py | Python | gpl-2.0 | 4,145 | [
"MOOSE",
"NEURON"
] | af8cd057392aa4209c53c9e54a0b288ade1be19f6370573c8ace0f5342c64ab4 |
# 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, software
# distributed under th... | hammerlab/isovar | isovar/read_collector.py | Python | apache-2.0 | 22,490 | [
"pysam"
] | 315d50015dde808e78b50e6530a5a973bbf1357b411c20125d51490a95ac0d02 |
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import ast
import sys
import glob
import json
import errno
import socket
import shutil
import string
from builtins import range
import six
from six import reraise as raise_
import numpy as np
import mdtraj as md
from scipy impo... | AdaptivePELE/AdaptivePELE | AdaptivePELE/utilities/utilities.py | Python | mit | 34,434 | [
"MDTraj",
"VMD"
] | da0820fb9cac70f4829549d1efbd8520fb462c4da022e10438c2277ef6cfdd34 |
from pytradelib.utils import batch
from pytradelib.downloader import Downloader
from urllib import urlencode
try:
import simplejson as json
except ImportError:
import json
def get_yql_url(yql):
base_url = 'http://query.yahooapis.com/v1/public/yql?'
url = base_url + urlencode({'q': yql,
... | briancappello/PyTradeLib | pytradelib/yahoo/yql.py | Python | gpl-3.0 | 2,036 | [
"ASE"
] | 7269b0dc74bafdf331bf9a5342ce6c6a1e55cb271f14bc18aaa75a21a6f5c9e0 |
###############################################################################
# #
# Copyright (C) 2004-2005, 2008-2009 Edward d'Auvergne #
# #
... | Igor-Rast/printipi | util/rotation_matrix.py | Python | mit | 11,304 | [
"Gaussian"
] | 5fcf3a02ce3cc1f5330230a1ceaee24d4dec7e2127a3cb2a4207851cf6567038 |
# Author: Travis Oliphant
# 2003
#
# Feb. 2010: Updated by Warren Weckesser:
# Rewrote much of chirp()
# Added sweep_poly()
from numpy import asarray, zeros, place, nan, mod, pi, extract, log, sqrt, \
exp, cos, sin, polyval, polyint
def sawtooth(t, width=1):
"""
Return a periodic sawtooth waveform.
... | scipy/scipy-svn | scipy/signal/waveforms.py | Python | bsd-3-clause | 11,609 | [
"Gaussian"
] | 7a721f1c44b9847e822dbb1324b7a66208ef377fde0671f38e7bdded4f936ea9 |
# -*- coding: utf-8 -*-
"""Various text used throughout the website, e.g. status messages, errors, etc.
"""
# Status Messages
#################
# NOTE: in status messages, newlines are not preserved, so triple-quotes strings
# are ok
# Status message shown at settings page on first login
# (upon clicking primary e... | jolene-esposito/osf.io | website/language.py | Python | apache-2.0 | 7,757 | [
"VisIt"
] | 7541bdca1426e956ff97e65e9f56e3b97945f41f560f97fbdf44008808de999e |
""" Python test discovery, setup and run of test functions. """
import fnmatch
import py
import inspect
import sys
import pytest
from _pytest.mark import MarkDecorator, MarkerError
from py._code.code import TerminalRepr
import _pytest
import pluggy
cutdir2 = py.path.local(_pytest.__file__).dirpath()
cutdir1 = py.path... | bubenkoff/pytest | _pytest/python.py | Python | mit | 80,512 | [
"VisIt"
] | b3b52bad5556acc4c1ca3e4bcc9aeaa5f3df55c8e4d78db678ace52e1d80dc64 |
# Copyright 2010 The Closure Library 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 a... | LeoLombardi/tos-laimas-compass | tos-laimas-compass-win32-x64/resources/app/node_modules/closure-util/.deps/library/b06c979ecae7d78dd1ac4f7b09adec643baac308/closure/bin/build/jscompiler.py | Python | mit | 4,107 | [
"VisIt"
] | ed5d057f8aa17c2f9a05ea65f9e8650f706d6ab42d3f601f993eb81b82ff0cb0 |
# Copyright (c) 2014, James Hensman, Alan Saul
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core.model import Model
from ..core.parameterization import ObsAr
from .. import likelihoods
class GPKroneckerGaussianRegression(Model):
"""
Kronecker GP regression
Take tw... | ptonner/GPy | GPy/models/gp_kronecker_gaussian_regression.py | Python | bsd-3-clause | 4,383 | [
"Gaussian"
] | f0707d4463baffc4c4bb9ad8bf54c286e1b2c8a791bcd5733174fe78cd6bcfc6 |
""" The CS! (Configuration Service)
Modified to work with Tornado
Encode data in base64 because of JSON limitations
In client side you must use a specific client
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from base64 import b6... | yujikato/DIRAC | src/DIRAC/ConfigurationSystem/Service/TornadoConfigurationHandler.py | Python | gpl-3.0 | 4,137 | [
"DIRAC"
] | 6205a8376d729f480e371264ca5eb2579799ead2527956195a9501d1d45e3892 |
# Copyright 2018 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... | kobejean/tensorflow | tensorflow/contrib/eager/python/examples/l2hmc/main.py | Python | apache-2.0 | 7,799 | [
"Gaussian"
] | 86d815c83f82606f6a237f611ab173063b83607876dc3624c257bd4311bea197 |
# Copyright 2003 Iddo Friedberg. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import sys
# Add path to Bio
sys.path.append('../..')
"""A parser for the NCBI blastpgp version... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Blast/ParseBlastTable.py | Python | gpl-2.0 | 3,773 | [
"Biopython"
] | 0faa2759a4a61e5dde73ed34acaa96bcfa18945e486afdf58c6bfa986223ab50 |
#!/usr/bin/env python
""" Which - locate a command
* adapted from Brian Curtin's http://bugs.python.org/file15381/shutil_which.patch
* see http://bugs.python.org/issue444582
* uses ``PATHEXT`` on Windows
* searches current directory before ``PATH`` on Windows,
but not before an explicitly passed ... | jeremiahyan/odoo | odoo/tools/which.py | Python | gpl-3.0 | 6,723 | [
"Brian"
] | f3bac99222bdffb144a4bd998e0fa4407553555deaefe9cf434b81e61caef17e |
import os, time, sys
import numpy as np
import cv, cv2
import scipy
import scipy.ndimage as nd
from copy import deepcopy
from pyKinectTools.utils.DepthReader import DepthReader
from pyKinectTools.algs.PersonTracker import Tracker
from pyKinectTools.utils.DepthUtils import *
from pyKinectTools.algs.BackgroundSubtract... | colincsl/pyKinectTools | pyKinectTools/scripts/mainICU.py | Python | bsd-2-clause | 22,204 | [
"Gaussian"
] | 79290e90bee1dbe7cd3c3e05a87cc3687840b6adc1e81abe7bd6db91d069b453 |
# convcmd - convert extension commands definition
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from common import NoRepo, MissingTool, SKIPREV, mapfile
from cvs import conv... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/mercurial-2.2.3-py2.7-linux-x86_64-ucs4.egg/hgext/convert/convcmd.py | Python | gpl-3.0 | 16,673 | [
"VisIt"
] | 141646e3a7341e9a7e452679a5af3aeb77e224e4f2a05f55cb109719370a4ca8 |
# GromacsWrapper: test_example.py
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
# Ian Kenney's pytest-gmx plugin
# https://github.com/ianmkenney/pytest-gmx/
import distutils.spawn
import os
import pytes... | Becksteinlab/GromacsWrapper | tests/conftest.py | Python | gpl-3.0 | 3,042 | [
"Gromacs"
] | f140b39e1b28bd30cc7227399d78c99737fe27d2a6af109f4c82f019f03ca3b4 |
import tensorflow as tf
import numpy as np
import part_detector
import settings
import utils
import os
from abc import abstractmethod
from functools import lru_cache
from scipy.stats import norm
from inception_resnet_v2 import inception_resnet_v2_arg_scope, inception_resnet_v2
import tensorflow.contrib.layers as lay... | marian-margeta/gait-recognition | human_pose_nn.py | Python | bsd-3-clause | 18,957 | [
"Gaussian"
] | 23e428ac18b0299b8e99e7f2af9ae789f1de2bb6f74611c73306208e50a0e15c |
#!/usr/bin/env python
# Copyright 2014-2019 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/cc/eom_rccsd.py | Python | apache-2.0 | 83,813 | [
"PySCF"
] | 9a15be8563221d668e61742c6d1dc0f00736ffaeaf60db4570abea986f4d7be6 |
"""Tools for reading writing and manipulating GMTK parameter files
@author: Arthur Kantor
@contact: akantorREMOVE_THIS@uiuc.edu
@copyright: 2008
@license: GPL version 3
@date: 11/18/2008
@version: 0.2
History:
This module is derived from a piece of the SVC library
which is Copyright (C) 2006... | satwik77/tree-hmm | gmtkParam/__init__.py | Python | bsd-3-clause | 58,284 | [
"Gaussian"
] | a1eaef6dc58bfadc0b8d7155eec9409dd71b168f8c7dcb1de1f8a105779fb30c |
from __future__ import absolute_import
from typing import Any, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet
from dja... | sonali0901/zulip | zerver/models.py | Python | apache-2.0 | 60,338 | [
"VisIt"
] | 982389114c76b519c126a35ec1c467bc6159de721c7ce9c5104cbb78060c6ec2 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | kosso/TiTranslucentView | build.py | Python | mit | 6,806 | [
"VisIt"
] | 9ce2a9765a4476ebd7a159075f4457a8d1d3787f0913103cdc040c79c21a5020 |
import re
import mdtraj
from mdtraj.testing.docstrings import docstring_verifiers, import_all_modules
from mdtraj.testing.docstrings import import_all_modules
import pytest
SKIP_MODULES = [
'mdtraj\.utils\.external',
'mdtraj\.utils\.six',
'mdtraj\.utils\.unit\.unit_math',
'mdtraj\.utils\.unit\.baseunit... | leeping/mdtraj | tests/test_docstrings.py | Python | lgpl-2.1 | 1,018 | [
"MDTraj"
] | fcc59ee00a134d931cf879d7ff87c74083b246221178656d51ff73f223a1f3bd |
# -*- encoding: utf-8 -*-
# Copyright 2013 Red Hat, Inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless re... | stackforge/watcher | watcher/api/controllers/v1/action_plan.py | Python | apache-2.0 | 23,796 | [
"VisIt"
] | 740616ecf761400ec877f18421d8c59ff161e587ac110d1a2181d6fcfe972448 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoq/gui/test/test_production.py | Python | gpl-2.0 | 3,913 | [
"VisIt"
] | 7e6c04c9da80460e7a216d6f51893383220376a3941d63aec1363bea62c65668 |
"""Functionality to query and extract information from aligned BAM files.
"""
import collections
import contextlib
import os
import itertools
import signal
import subprocess
import numpy
import pysam
import toolz as tz
from bcbio import utils
from bcbio.bam import ref
from bcbio.distributed import objectstore
from bc... | Cyberbio-Lab/bcbio-nextgen | bcbio/bam/__init__.py | Python | mit | 19,381 | [
"pysam"
] | 9123a30811315dc658eb41caf2711f5131291a12b0f727d6f4d9bb7a50a2ce15 |
"""
Cross section plots
===================
This example demonstrates contour plots of a cross-sectioned multi-dimensional
cube which features a hybrid height vertical coordinate system.
"""
import matplotlib.pyplot as plt
import iris
import iris.plot as iplt
import iris.quickplot as qplt
def main():
# Enable... | SusanJL/iris | docs/iris/example_code/General/cross_section.py | Python | gpl-3.0 | 1,297 | [
"NetCDF"
] | 8419b8447ccba4226e9780f859335590bb95fa169c9135e8a366efb131ec19d4 |
""" DIRAC.ProductionSystem package """
| DIRACGrid/DIRAC | src/DIRAC/ProductionSystem/__init__.py | Python | gpl-3.0 | 39 | [
"DIRAC"
] | ce605b1bd3f56078ea1caa46d2fcbb00e1b8a3e1c3c9e9166af0c0c3822cdbbd |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
from scipy._lib.six import string_types
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
... | efiring/scipy | scipy/signal/windows.py | Python | bsd-3-clause | 51,595 | [
"Gaussian"
] | 79bed0a9ab083d19e41bcafd84febdd47c6246a8ebb89dd608121c10fdbc9907 |
import numpy as np
from matplotlib import pyplot
import rft1d
eps = np.finfo(float).eps #smallest float
#(0) Set parameters:
np.random.seed(0)
nResponses = 12
nNodes = 101
nIterations = 2000
FWHM = 8.5
interp = True
wrap = True
heights = [2.0, 2.2, 2.4]
c = 2
... | 0todd0000/rft1d | rft1d/examples/val_upx_1_t_set.py | Python | gpl-3.0 | 1,687 | [
"Gaussian"
] | 2490249d66ad0e4a7632f78e55aae1cd28f438dd48e34764b29de23d9613bb66 |
#!python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
import sys
import... | bobeirasa/virtualenvs | pyzabbixhue/lib/python2.7/site-packages/setuptools/command/easy_install.py | Python | mit | 73,097 | [
"VisIt"
] | aecad447011e6de97b5845bb61279e85137ddfac4605bf72b3ebc829460ca0f7 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import collections
import os
import gyp
import gyp.common
import gyp.msvs_emulation
import json
import sys
generator_supports_multiple_toolsets = True
generator_... | guorendong/iridium-browser-ubuntu | tools/gyp/pylib/gyp/generator/dump_dependency_json.py | Python | bsd-3-clause | 3,394 | [
"VisIt"
] | a47049a43317bfef5d766b4252bb20574bce6e30990059ff85d2e7ac5425eb71 |
from time import time
import sys
import numpy as np
from gpaw import parsize, parsize_bands
from gpaw.band_descriptor import BandDescriptor
from gpaw.grid_descriptor import GridDescriptor
from gpaw.kohnsham_layouts import BandLayouts
from gpaw.mpi import world, distribute_cpus
from gpaw.utilities import gcd
from gpaw.u... | qsnake/gpaw | gpaw/test/parallel/overlap.py | Python | gpl-3.0 | 3,461 | [
"GPAW"
] | 04c1941852b85316414ebee12c443687946caf607fe1356b9300e057aa1a7644 |
# 2-electron VMC code for 2dim quantum dot with importance sampling
# Using gaussian rng for new positions and Metropolis- Hastings
# Added energy minimization
from math import exp, sqrt
from random import random, seed, normalvariate
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import A... | CompPhysics/ComputationalPhysics2 | doc/src/MCsummary/src/qdotBroyden.py | Python | cc0-1.0 | 8,051 | [
"Gaussian"
] | 6b4f0a7c797658a26b77ee0ed39f2c3abf5d6dd20f28defb2634c115709e9ddc |
# -*- coding: utf8 -*-
# Copyright (C) 2015 - Philipp Temminghoff <phil65@kodi.tv>
# This program is Free Software see LICENSE file for details
from __future__ import absolute_import
from __future__ import unicode_literals
import urllib
import xbmcgui
from kodi65 import utils
from kodi65 import addon
from kodi65 i... | phil65/script.maps.browser | resources/lib/googleplaces.py | Python | gpl-2.0 | 7,062 | [
"CASINO"
] | a0e3575b87d50e9820fd65e18ce3d30339dae2e6a1daebe5cf3d908bae2817b9 |
# ./sdf_dom.py
# -*- coding: utf-8 -*-
# PyXB bindings for NM:e92452c8d3e28a9e27abfc9994d2007779e7f4c9
# Generated 2017-10-02 18:13:38.461234 by PyXB version 1.2.5 using Python 3.5.2.final.0
# Namespace AbsentNamespace0
from __future__ import unicode_literals
import pyxb
import pyxb.binding
import pyxb.binding.saxer
i... | HBPNeurorobotics/BlenderRobotDesigner | robot_designer_plugin/resources/xsd_sdf/sdf_dom.py | Python | gpl-2.0 | 1,021,753 | [
"Gaussian"
] | 495a953f32d9901577c38490a24c53b0a643e63ab49d7fea4236424344dae53e |
import sys
from functools import partial
from .._requires import click
from .._requires import jinja2
from ..run import run
from ..types import Command, LocalPath, Mode
from ..images import docker_image
from ..status import Status
from ..console import config_tty
from ..network import ensure_network
from ..resolve i... | vmagamedov/pi | pi/ui/custom.py | Python | bsd-3-clause | 5,966 | [
"VisIt"
] | afd40c2da2e6969b641ed915b7dfa45ec02783c7cb58715b382b1a2cc76e180b |
#!/usr/bin/env python
'''
Created on 2011 uzt 7
@author: peio
'''
from optparse import OptionParser
import sys
from franklin.seq.alignment_result import (filter_alignments,
get_alignment_parser)
def parse_options():
'It parses the command line arguments'
parser = Op... | JoseBlanca/franklin | scripts/get_similar_seqs.py | Python | agpl-3.0 | 4,752 | [
"BLAST"
] | 831fe879f239f84f973a47184ecc93199ae46ec613d17e97f8134bad820c73d5 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import warnings
from pymatgen.analysis.structure_prediction.volume_predictor import (
DLSVolumePredictor,
RLSVolumePredictor,
)
from pymatgen.core import Structure
from pymatgen.util.testing ... | vorwerkc/pymatgen | pymatgen/analysis/structure_prediction/tests/test_volume_predictor.py | Python | mit | 5,277 | [
"pymatgen"
] | 62974683648737c3299ee6ba5cf3a16e88b964b62b5ca5f1994529787ceabecf |
#!/usr/bin/env python
import os
import sys
import time
from optparse import OptionParser, OptionValueError
import math
import vtk
# parse command line
p = OptionParser(usage="""usage: %prog [options] <gridfile> <vtrfile_base>
Converts the griddata file (suitable for PiecewiseMultilinear functions) into vtr format.
... | liuwenf/moose | python/GridVTKData/griddeddata_to_vtk.py | Python | lgpl-2.1 | 4,365 | [
"VTK"
] | f7fee2f189c5194c592a5a9ea235eddaf185ad46fe3438406ae6864c370e0516 |
from django import forms
from edc_constants.constants import POS, YES
from microbiome.apps.mb.constants import LIVE
from ..models import MaternalEligibility, PostnatalEnrollment, AntenatalEnrollment
from .base_enrollment_form import BaseEnrollmentForm
from microbiome.apps.mb_maternal.models.maternal_visit import Ma... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/forms/postnatal_enrollment_form.py | Python | gpl-2.0 | 5,152 | [
"VisIt"
] | 78bcdafe0ec62cb3df533835ca8ff44844981a1b6514fc75b90d15c56289b10b |
"""
UI-level acceptance tests for OpenAssessment.
"""
import os
import unittest
import time
from functools import wraps
from nose.plugins.attrib import attr
from bok_choy.web_app_test import WebAppTest
from bok_choy.promise import BrokenPromise
from auto_auth import AutoAuthPage
from pages import (
SubmissionPage, ... | EDUlib/edx-ora2 | test/acceptance/tests.py | Python | agpl-3.0 | 6,500 | [
"VisIt"
] | b084134e3e27fe7e9ba3922e2ccd5acf982e03ef45a1ba203891e46e3262e4dc |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/peacock_app/BasePeacockMainWindow/test_BasePeacockMainWindow.py | Python | lgpl-2.1 | 3,596 | [
"MOOSE"
] | 7923608ae6f8ae63523fc92e2223c1bcdc7a4c75e70689a32854a42279c33b7d |
import sys,getopt,time
#Define Default Values
Ntries = 100
Naddrs = 4
ExpectedCoinsToSend = 1.
minCoinsMultiplier = .00000001
coinBinResolution = 1
#Take command line arguments
opts, args = getopt.getopt(sys.argv[1:], 'o:v', ['addr=','tries=','coins=','multiplier=','resolution='])
for opt,arg in opts:
if opt in (... | stafur/TRUSTplus-AT-PoC | TRUSTplus-PoC.py | Python | apache-2.0 | 5,974 | [
"Mayavi"
] | 5ca101ffdd8fd52b85cf79ac365b8884111dbbb9b19781e00ccf7fb55801dfc9 |
# coding: utf8
""" Implementation of the meta-class :class:`BetaEnsemble` see :math:`\\beta-`:ref:`Ensembles<beta_ensembles>` with children:
- :class:`HermiteEnsemble`
- :class:`LaguerreEnsemble`
- :class:`JacobiEnsemble`
- :class:`CircularEnsemble`
- :class:`GinibreEnsemble`
Such objects have 4 main methods:
- :py:... | guilgautier/DPPy | dppy/beta_ensembles.py | Python | mit | 53,803 | [
"Gaussian"
] | 11a82d5d27786d5e97a84b1b62c4704e2a390814e6c3b693bb31864e894a0260 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/network_search_response.py | Python | apache-2.0 | 12,817 | [
"VisIt"
] | 4e1f1642f61afe392b657b66f1ed8c0ed1c4674783d5fb027cf1aa813162a603 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | sam-m888/gramps | gramps/plugins/tool/rebuild.py | Python | gpl-2.0 | 3,621 | [
"Brian"
] | 4a64a763eebe47ce590a081c0bb15b87ddc3fc0cfffc46554d0ae74e7d6e3636 |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Addons modules by CLEARCORP S.A.
# Copyright (C) 2009-TODAY CLEARCORP S.A. (<http://clearcorp.co.cr>).
#
# This program is free software: you can redistribute... | sysadminmatmoz/odoo-clearcorp | project_issue_helpdesk/project_issue_helpdesk.py | Python | agpl-3.0 | 28,634 | [
"VisIt"
] | 756fe8fd37092d1568cd36fa5172b63bb0bd2701dd614ddadf7db08a9f92f267 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/stats.py | Python | gpl-3.0 | 3,864 | [
"Galaxy"
] | 8e1d9f17201c61f6edcbd58a28744dba542c8b95ab1bf18756bf80b45083c1e5 |
# -*- coding: utf-8 -*-
"""Define function to make hyperparameter search space.
"""
# Author: Taku Yoshioka
# License: MIT
import numpy as np
"""Define search space of hyperparameters
"""
class InferParams(object):
"""Parameters for causal inference with the bayesian mixed LiNGAM.
The fields... | taku-y/bmlingam | bmlingam/hparam.py | Python | mit | 16,567 | [
"Gaussian"
] | b8021007d491ed00ab2d6ba8167427e505749aaddd227b1ed35421f9507e2a34 |
import logging
import numpy as np
import sys
import time
import platform
import nengo
from pacman103.core import control
from . import assembler
from . import builder
from . import node
from . import spinn_io
from . import probe
from .config import Config
import utils
logger = logging.getLogger(__name__)
class Sim... | ctn-archive/nengo_spinnaker_2014 | nengo_spinnaker/simulator.py | Python | mit | 12,890 | [
"NEURON"
] | 064655fb956329d4e2d85fcc98e878c8ceeb2fce50e94afdf3a26c1484b5acd5 |
import unittest, time, sys
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_glm, h2o_util, h2o_hosts, h2o_import as h2i
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_for_errors()
@classmethod
def setUpClass(cls):
global localhost
localhost = h2o.dec... | janezhango/BigDataMachineLearning | py/testdir_single_jvm/test_GLM2_umass.py | Python | apache-2.0 | 2,634 | [
"Gaussian"
] | cf799ede590ed37ad8d0523cdca312251a66c30566d0cef961c731cddb4803c1 |
# flake8: noqa
crawlers = [ # precluded from normal url tracking
"'Mozilla/5.0 (compatible; DuckDuckBot-Https/1.1; https://duckduckgo.com/duckduckbot)'",
": Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)",
"Aboundex/0.3 (http://www.aboundex.com/crawler/)",
"ArchiveTeam ArchiveBot/20... | ddierschow/bamca | bin/crawls.py | Python | mit | 18,699 | [
"VisIt"
] | a806eeeb0ac6f7bc9c379d1a950587d5c623332a1a446bd5e5ab10a1a5d20296 |
from modshogun import *
from numpy import *
from sklearn.metrics import r2_score
from scipy.stats import randint
from scipy.stats import randint as sp_randint
from scipy.stats import expon
from mkl_regressor import *
from time import localtime, strftime
if __name__ == "__main__":
import Gnuplot, Gnuplot.funcutil... | iarroyof/distributionalSemanticStabilityThesis | mkl.py | Python | gpl-2.0 | 6,182 | [
"Gaussian"
] | c8f7d139f4f2cd1bda37d118b85e9527c710895abd00f6d41cd5fe09f87a7471 |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/keynames.py | Python | gpl-3.0 | 9,840 | [
"ORCA"
] | 89c2e1a8ebf66aa12048b7241a1424431140c6c184a1a57869390e8c40de983a |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RBiomformat(RPackage):
"""An interface package for the BIOM file format.
This is a... | iulian787/spack | var/spack/repos/builtin/packages/r-biomformat/package.py | Python | lgpl-2.1 | 1,714 | [
"Bioconductor"
] | a4dd6c7c38d7450f7f816541601febc80f43d2f606105e10c14f9b37b21346ca |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2016 OSGeo
#
# 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 ... | kartoza/geonode | geonode/base/enumerations.py | Python | gpl-3.0 | 13,754 | [
"BWA"
] | ef59f8381d9c79937db156fb2bf518dc1f18157326334cbeae15056771aa622b |
# description: code for working with motifs
import os
import gzip
import numpy as np
import pandas as pd
from scipy.stats import pearsonr
from scipy.cluster.hierarchy import linkage, leaves_list, fcluster
from scipy.spatial.distance import squareform
from multiprocessing import Pool
def read_pwm_file(pwm_file, v... | vervacity/ggr-project | ggr/analyses/motifs.py | Python | mit | 30,872 | [
"Gaussian"
] | 5a910244ccbb98713774aebb15b6aec2cb1c5ba0483ee9329611455df3d8189e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Matt Flood
import os
import random
import sys
import time
from urllib.parse import urlparse
from selenium import webdriver
from webdriver_manager.chrome import ChromeDriverManager
from bs4 import BeautifulSoup
from random import shuffle
from os.path import join, di... | MattFlood7/LinkedInBot | LinkedInBot.py | Python | mit | 15,728 | [
"VisIt"
] | ac329cbd8e511e703d7a47f34c0ae87feda4a17ca49508844b2de09cee6d0606 |
# coding: utf-8
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getp... | uannight/reposan | plugin.video.tvalacarta/lib/youtube_dl/extractor/common.py | Python | gpl-2.0 | 118,491 | [
"VisIt"
] | 7682d2e28e840772df710e1ad3d0af3caa50733cad0a52b21e00e00ee4c5c8a7 |
"""
Unit tests for the utility module.
Thomas Ogden <t@ogden.eu>
"""
import os
import unittest
import numpy as np
from maxwellbloch import utility, t_funcs
class TestHalfMaxRoots(unittest.TestCase):
def test_gaussian(self):
""" Tests a Gaussian pulse for the correct half max and width. """
t_l... | tommyogden/maxwellbloch | maxwellbloch/tests/test_utility.py | Python | mit | 1,056 | [
"Gaussian"
] | 8e692164024359cf4ca3bf4aa99ae87843b17b2f5179d58382971059a2a2b0eb |
# Copyright 2018 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... | jendap/tensorflow | tensorflow/contrib/tpu/python/tpu/tensor_tracer.py | Python | apache-2.0 | 58,783 | [
"VisIt"
] | 2634184b25d2696c7c21bf2006b4166291695290339d5d1234f4d56fd809967d |
import sys, pickle
sys.path.append('./mobtypingmodules')
from mobmods import runsubprocess
#sys.argv[1] dataprefix; sys.argv[2]/[3] 0 0 (no id/coverage thresholds); sys.argv[4] evalue; sys.argv[5] maxiter
#extract sequence ids, alignment lengths and gapopen from blast table
fileObj=open('./output_intermediate/%s_BLAS... | AlexOrlek/MOBtyping | blastfilter.py | Python | mit | 17,174 | [
"BLAST"
] | 4f981762d18e26ea533bba0a7b1c1db27435bc1dc0b9a8283f5856c5b1dbf947 |
# fr_CA.po
val = {" days." : " jours.",
"(all)" : "(tous)",
"(any)" : "(n'importe lequel)",
"(anyone)" : "(n'importe qui)",
"(available)" : "(disponible)",
"(blank)" : "(vide)",
"(both)" : "(tous)",
"(everyone)" : "(tout le monde)",
"(master user, not editable)" : "(Utilisateur principal, non modifiable)",
"(no change... | bobintetley/asm3 | src/asm3/locales/locale_fr_CA.py | Python | gpl-3.0 | 218,348 | [
"Amber",
"VisIt"
] | 273499289c73e3dff93efb1d6ea2817be7006d498d43a0659e5ad99a6160364e |
##########################################################################
## # The Coq Proof Assistant / The Coq Development Team ##
## v # INRIA, CNRS and contributors - Copyright 1999-2018 ##
## <O___,, # (see CREDITS file for the list of authors) ##
## \VV/ #########... | letouzey/coq-wip | doc/tools/coqrst/notations/html.py | Python | lgpl-2.1 | 2,864 | [
"VisIt"
] | 9202bda9437710f3b51f4acb32bab89170ea6c6dfba08d4d6e7fa8278e5e81ba |
from pele.amber import amberSystem
# create new amber system
system = amberSystem.AMBERSystem('coords.prmtop', 'coords.inpcrd')
database = system.create_database("optimdb.sqlite")
#start the gui
from pele.gui import run as gr
gr.run_gui(system, db=database)
| khs26/pele | playground/amber/aladipep/start_gui.py | Python | gpl-3.0 | 272 | [
"Amber"
] | 6852a9fbb455f1f52b243abf34897af13bd85875befcf96a71be3ca560b82bdb |
''' DIRAC Transformation DB
Transformation database is used to collect and serve the necessary information
in order to automate the task of job preparation for high level transformations.
This class is typically used as a base class for more specific data processing
databases
'''
import re, time, thre... | coberger/DIRAC | TransformationSystem/DB/TransformationDB.py | Python | gpl-3.0 | 80,992 | [
"DIRAC"
] | c229d139be09cfd7b88f45a2a74dabcb38a225f923dbb227b76fd7cbac61c2fb |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/qcdb/vecutil.py | Python | lgpl-3.0 | 11,230 | [
"Psi4"
] | 8200619e105279accb024d907ec68b7d68068592de66fd26590d534cd2fb95fa |
from setuptools import setup
setup(name='shoelace',
version='0.2',
description='A python package for RNA sequence data and expression level analysis and utilities for querying the NCBI Gene Expression Omnibus (GEO) database',
url='http://github.com/ChellyD65/shoelace',
author='Marcello DiStasio... | ChellyD65/shoelace | python/setup.py | Python | gpl-2.0 | 685 | [
"Biopython"
] | 37d3818425d18b5bf0500f9732163a3e712d8c6f3a4605816eb5ef2cce565f8d |
'''
Report either the best hits, best equal hits or all hits from a blast search.
FOR THIS VERSION WE ARE USING THE BLAST WITH TAXID ADDED AT THE END OF THE LINE (e.g. from GI to TAX)
Note that we use the HIGHEST bit score here for this calculation.
We generate a table of [phage NC_ id, host tax id]. We need to r... | linsalrob/PhageHosts | code/blast_hits.py | Python | mit | 2,273 | [
"BLAST"
] | f722522c58ee993ecfed618085035bec198c1a7f258e8ca14154360d91e4fec1 |
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