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from __future__ import print_function
import numpy as np
import pdb
from . import BuiltinProposals
from . import Utils
"""
This module contains definitions for algorithms to be used by MCMC objects
to sample from the posterior distribution of models. Currently, it only contains
the definition for a basic Metropolis sa... | tomevans/pyhm | pyhm/BuiltinStepMethods.py | Python | gpl-2.0 | 1,875 | [
"Gaussian"
] | e8efb8b1d3934a0c7b27f57e7eeb9240581343711b3445952a02821a262db01d |
# -*- 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_pos.py | Python | gpl-2.0 | 28,475 | [
"VisIt"
] | ca0241838599c62e4d85327e4d579ad91667d8ea2838ba0c3df7a6d7b55d001d |
#!/usr/bin/env 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
"""
impo... | OpenWinCon/OpenWinNet | web-gui/myvenv/lib/python3.4/site-packages/setuptools/command/easy_install.py | Python | apache-2.0 | 75,200 | [
"VisIt"
] | b66e9cfc942459b7d9c3877c9646a2fe4addc5207295f1c8009c440137f31627 |
# The MIT License
#
# Copyright 2014, 2015 Piotr Dabkowski
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the 'Software'),
# to deal in the Software without restriction, including without limitation the rights
# to use, copy, modif... | maxive/erp | doc/_extensions/pyjsparser/parser.py | Python | agpl-3.0 | 107,859 | [
"VisIt"
] | 8f0a320b1616bce0f9e409251996943df5f3008bed14b199bee609603baec80c |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011-2012 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 Fou... | renatonlima/PySPED | tests/test_pyflakes.py | Python | lgpl-2.1 | 3,822 | [
"VisIt"
] | ed75af8a500efcaf28079465691a851881abf575fd1df5cdbe8f2cd0a1953ec3 |
import numpy as np
from blaze.expr import visitor, paterm
from blaze.engine import executors
from blaze.engine import llvm_execution
class ExecutorDispatcher(visitor.BasicGraphVisitor):
"""
Evaluate an expression.
TODO: execute each executor on a single chunk before moving to the next
executor... | davidcoallier/blaze | blaze/engine/dispatch.py | Python | bsd-2-clause | 1,291 | [
"VisIt"
] | 8d5631d0f79e6f3fbaaf5ff8f4d49bbe528a438f5cd7162a54e77f587d557d60 |
#! /usr/bin/env python
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
import sys
# check biopython module
try:
from Bio.PDB import PDBParser
from Bio.PDB.DSSP import DSSP
from Bio import SeqIO... | zhujianwei31415/dcnnfold | scripts/training_test/convert_pdb_to_image.py | Python | gpl-3.0 | 1,683 | [
"Biopython"
] | 7509dca4acdae436b23a40a2bfe20ab0635cb8b3d269163110f16dc74e21830d |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Two Body Properties Computations
#####################################
"""
import numpy as np
import numba as nb
import pandas as pd
from IPython.display import display
from ipyw... | exa-analytics/exatomic | exatomic/algorithms/angles.py | Python | apache-2.0 | 2,542 | [
"ADF"
] | c8431262e25fd236b4c86a8e7730b4424e5ee310bc262846b9a18bfc56967a28 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# 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... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_poolgroupdeploymentpolicy.py | Python | gpl-3.0 | 6,364 | [
"VisIt"
] | e174c0fa4b3b3de255957e6470d52591e5c74fe0c27caa1fe4a9c97021d79b61 |
# Copyright 2021, Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing... | google-research/public-data-in-dpfl | mirror_descent_convex_v2.py | Python | apache-2.0 | 19,702 | [
"Gaussian"
] | 89d57028a2bd29bd31e2250ec622ccac7b560decef2cb10a9b42d102d2ac885f |
# -*- coding: utf-8 -*-
"""This module tests various ways how to set up the provisioning using the provisioning dialog."""
import re
from datetime import datetime
from datetime import timedelta
import fauxfactory
import pytest
from widgetastic.utils import partial_match
from widgetastic_patternfly import CheckableBoot... | RedHatQE/cfme_tests | cfme/tests/infrastructure/test_provisioning_dialog.py | Python | gpl-2.0 | 17,390 | [
"VisIt"
] | 09c13bfbea73d0bf545ee646430b18b3cdd7f924b4f063cdd004003b15266f7a |
#! /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-network-security | scripts/fixup_network_security_v1beta1_keywords.py | Python | apache-2.0 | 6,975 | [
"VisIt"
] | b2915a085a729db424e952e4747bfe6aa2220c544bacc20270886008ad3f8d68 |
from pyboof import gateway
from pyboof.common import *
from pyboof.image import dtype_to_Class_SingleBand
from pyboof.image import ImageType
from py4j.java_gateway import is_instance_of
class Border:
SKIP=0
EXTENDED=1
NORMALIZED=2
REFLECT=3
WRAP=4
ZERO=5
class GradientType:
SOBEL="sobel... | lessthanoptimal/PyBoof | pyboof/ip.py | Python | apache-2.0 | 24,552 | [
"Gaussian"
] | 47d1dd7269dc4f0b4ab864aa5a74171d10903446e1f2910d6b103785e24a25eb |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | marmyshev/transitions | openlp/plugins/bibles/__init__.py | Python | gpl-2.0 | 2,203 | [
"Brian"
] | 3bce1427daa10195e85385f3b2c19c172bc07392b613c7671bd90a5f3d9a61c7 |
################################################################################
# SCFGP: Sparsely Correlated Fourier Features Based Gaussian Process
# Github: https://github.com/MaxInGaussian/SCFGP
# Author: Max W. Y. Lam (maxingaussian@gmail.com)
####################################################################... | MaxInGaussian/SCFGP | experiments/boston_housing/boston_housing.py | Python | bsd-3-clause | 4,809 | [
"Gaussian"
] | 6d45bd4f16b41cff207481683d044d2affe7c8297666d3e95e0ae41846e9c4be |
"""
Functions to create initializers for parameter variables.
Examples
--------
>>> from lasagne.layers import DenseLayer
>>> from lasagne.init import Constant, Glorot
>>> l1 = DenseLayer((100,20), num_units=50, W=GlorotUniform(), b=Constant(0.0))
"""
import numpy as np
from .utils import floatX
class Initializer(... | Richi91/nntools | lasagne/init.py | Python | mit | 11,237 | [
"Gaussian"
] | aa40a507fcd278c0bdc7caf8dc44f767035bef66f85a441c43302f05b407f30c |
""" codecs -- Python Codec Registry, API and helpers.
Written by Marc-Andre Lemburg (mal@lemburg.com).
(c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
"""#"
import builtins, sys
### Registry and builtin stateless codec functions
try:
from _codecs import *
except ImportError as why:
raise SystemErro... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.1/Lib/codecs.py | Python | mit | 34,798 | [
"FEFF"
] | f1810757196096949ead048e818148e00cbd6ce2234c894316c4152f60d6c306 |
# { -1, -1}: On entry to PDLASRT parameter number 9 had an illegal value
# works with 'sl_default': (2, 2, 32)
from ase.lattice.surface import fcc100, add_adsorbate
from gpaw import GPAW, ConvergenceError
from gpaw.mpi import world
from gpaw.utilities import compiled_with_sl
assert world.size == 4
slab = fc... | robwarm/gpaw-symm | gpaw/test/parallel/scalapack_pdlasrt_hang.py | Python | gpl-3.0 | 703 | [
"ASE",
"GPAW"
] | 7535f7d0aed76136ea52df2a05be7a5fb8c231265d9c23e8243fbedb7358fff7 |
#!/usr/bin/env python
"""
Demo pipeline for processing voltage imaging data. The processing pipeline
includes motion correction, memory mapping, segmentation, denoising and source
extraction. The demo shows how to construct the params, MotionCorrect and VOLPY
objects and call the relevant functions. See inside for det... | simonsfoundation/CaImAn | use_cases/volpy_paper/Fig4&5/demo_voltage_simulation.py | Python | gpl-2.0 | 11,496 | [
"Gaussian"
] | 08d10b0e463f4d51e7039093d83bf97d8634dfeb8b8a85155cb62548b971b875 |
"""
all reusable image processing should be here
"""
from rescaler import cx,cy
import ImageGrab
import time
from makinreusable.winfunction import *
class ImageManager(object):
screen_size = (970,632)
def __init__(self):
#default image
self.screen_save = ImageGrab.grab()
self.screen_loading = self.screen_save... | imakin/PersonalAssistant | GameBot/src_py/image.py | Python | mit | 57,437 | [
"CRYSTAL"
] | cb770c19c31b7b12a62ffc717d58751d9f7ddf8b5b28c68cd35e092276b77aa1 |
#!/usr/bin/python
# -*- encoding: utf-8; py-indent-offset: 4 -*-
# +------------------------------------------------------------------+
# | ____ _ _ __ __ _ __ |
# | / ___| |__ ___ ___| | __ | \/ | |/ / |
# | | | | '_ \ / _ \/ __| |/ /... | huiyiqun/check_mk | web/plugins/dashboard/dashlets.py | Python | gpl-2.0 | 39,357 | [
"VisIt"
] | e87ec6fa10e244d307301abdc66d0552c11dad9e5960199c052e9bbd208fd69a |
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# Modifications Copyright 2010 Jeffrey Finkelstein. 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.
""" Handle the SC... | bryback/quickseq | genescript/Bio/SCOP/Cla.py | Python | mit | 3,938 | [
"Biopython"
] | 5c3335b01973bfc8262e3f2806c775515a4106278cd26980e070f3d9ad16c4a0 |
from numpy import *
#from scipy.stats import truncnorm, erfc
from scipy.stats import truncnorm
from scipy.special import erfc
from scipy.special import erf
class RandomGenerator():
"""B
Abstract class to ensure the definition of the function generate.
"""
def __call__(self, size):
return self... | philouc/pyhrf | python/pyhrf/stats/random.py | Python | gpl-3.0 | 6,240 | [
"Gaussian"
] | 68eb197cba96bdfa12ad57cd8c7d8608b8476510fa76b89b5a5ceeffc7ac8c4d |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-09-13 16:05:56
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: 2018-08-06 11:45:33
from __future__ import absolute_import, division, print_function
im... | sdss/marvin | python/marvin/utils/datamodel/dap/MPL6.py | Python | bsd-3-clause | 22,569 | [
"Brian",
"Galaxy",
"Gaussian"
] | d574432e282ea0ce766a78527df50ccaf2ab6129265ec1dbf2338898cd586db7 |
"""Configuration file for eruption scenario
Tephra modelling validation worksheet
Scenario Name: Mount Tambora 1815 (VEI 6 eruption)
Run Date: 2010_05_06
Run number:1 ... | GeoscienceAustralia/PF3D | testing/tambora.py | Python | gpl-3.0 | 3,480 | [
"Gaussian"
] | 13f59286bf406d301e30802c41ed70d418b2c8f797f5c9ab27d371739d76d5bd |
# -*- 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)
#
... | alejob/mdanalysis | testsuite/MDAnalysisTests/core/test_topologyattrs.py | Python | gpl-2.0 | 14,967 | [
"MDAnalysis"
] | 20c911732bc54b2744e679cd2532b77ddb9605478a9cbb57b2862f1a8c58d5c9 |
#!/usr/bin/python
# File created on Nov 27 Jan 2012
from __future__ import division
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
import os
from sys import path
import ... | kishori82/MetaPathways_Python.3.0 | libs/python_scripts/MetaPathways_extract_pathways.py | Python | mit | 12,753 | [
"BLAST"
] | 8c0dae423d0ee6c3622fd72dcfa8f08fe406261011bd5d64f55aded20a090e3a |
import pytest
from ethereum import tester
from ethereum import utils
from ethereum._solidity import get_solidity
serpent_contract = """
extern solidity: [sub2:[]:i]
def main(a):
return(a.sub2() * 2)
def sub1():
return(5)
"""
solidity_contract = """
contract serpent { function sub1() returns (int256 y) {} ... | harlantwood/pyethereum | ethereum/tests/test_solidity.py | Python | mit | 23,090 | [
"MOOSE"
] | d68f67b371ecf01ffea9a8568197e45cba37a119a1757a6f8781401b0018118b |
# Copyright 2016 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... | npuichigo/ttsflow | third_party/tensorflow/tensorflow/tools/compatibility/ast_edits.py | Python | apache-2.0 | 18,961 | [
"VisIt"
] | 58b7228ae055639a994999305c42851804036ca50c18b1479a2e1ac3fccab892 |
#!/usr/bin/env python
# encoding: utf-8
"""
CijUtil.py
Bits to help with elastic constants manipulation.
polyCij(Cij): Given an elastic constants matrix for a single crystal,
calculate the Voight and Reuss bounds on the bulk and
shear moduli for a random polycrystal.
Copyright (c) 2010 A... | andreww/theia_tools | CijUtil.py | Python | mit | 13,840 | [
"CRYSTAL"
] | ca8546f708e71d0f694971b6111a9dae7b13fc21c56f7d5ee217a6a7f7c2f71a |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer, and RenderWindowInteractor
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.SetMultiSamples(0)
renWin.AddRenderer(ren1)
iren = vtk... | collects/VTK | Filters/General/Testing/Python/testDataSetTriangleFilter.py | Python | bsd-3-clause | 2,009 | [
"VTK"
] | 8792d6e2db8aa220119867816632883dcf07020c0185efccf4c202b09b68a2a7 |
"""
Course import test
"""
from bok_choy.web_app_test import WebAppTest
from regression.pages.studio.course_outline_page import CourseOutlinePageExtended
from regression.pages.studio.import_course_page import ImportCoursePageExtended
from regression.tests.helpers.api_clients import LmsLoginApi
from regression.tests.h... | edx/edx-e2e-tests | regression/tests/studio/test_course_import.py | Python | agpl-3.0 | 1,724 | [
"VisIt"
] | e64b18b5abc89e3c8a66b9d2945502ef604cfbbac4d2aa0b53878dc2e6858635 |
#* 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
# To create... | harterj/moose | modules/navier_stokes/test/tests/ins/mms/pspg/plot_convergence.py | Python | lgpl-2.1 | 1,863 | [
"MOOSE"
] | 346b9a5a38509eb2b2132d10e78a05c1491f030385032d5ab28952814697851b |
# -*- coding: utf8 -*-
"""Users frontend tests.
:license: AGPL v3, see LICENSE for more details
:copyright: 2014-2021 Joe Doherty
"""
import io
from flask import url_for
import json
from pjuu import mongo as m, storage
from pjuu.auth.backend import create_account, delete_account, activate
from pjuu.lib import key... | pjuu/pjuu | tests/test_users_frontend.py | Python | agpl-3.0 | 44,915 | [
"VisIt"
] | 8ca8bf5cc8fb2ef5055f883b68e937ed2b33e57650ba5afd30ed42fa071f6df3 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
required_module_keys = ['name','version','moduleid','description','copyright','license','copyright','platform','minsdk']
module_def... | rubenfonseca/titanium-keychain | build.py | Python | mit | 5,744 | [
"VisIt"
] | dd7cbb41d39047abce39f394598a87341ab07735ff596937a0d22d774ef5956f |
#!/usr/bin/env python
#
# @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 program is free software; you can redistribute it and/or modify
#... | mhlechner/psi4 | psi4/share/psi4/fsapt/fsaptdiff.py | Python | gpl-2.0 | 4,162 | [
"Psi4"
] | dc01372cd9483f37f6072334e12df3eb22aac7fdaf7716e5f89087d662a45b6f |
from moogli.core import NetworkViewer
from moogli.extensions.swc import SwcNetwork
from PyQt4.QtGui import QApplication
from matplotlib.cm import gnuplot
import sys
app = QApplication(sys.argv)
network = SwcNetwork("VHC-neuron.CNG.swc")
network.write("VHC-neuron.3ds")
viewer = NetworkViewer(network)
viewer.set_backgro... | dilawar/moogli | examples/colorbar.py | Python | gpl-2.0 | 2,488 | [
"NEURON"
] | f9cbd9669c133bb383e32b9f04bf2b60243b9bfde2a316f7109e4fe1fa3ddaad |
from .model import Model
from .powerlaw import PowerLaw
from .wilmsabs import WilmsAbs
from .gaussian import Gaussian
from .rgscat import RGScat
| eblur/xpysis | pyxsis/models/__init__.py | Python | lgpl-3.0 | 145 | [
"Gaussian"
] | 97ed80ba06370f969c8cd8a6f07bdf2c07484aa181538014c9e8e811a6ef18d6 |
"""
Maximum likelihood covariance estimator.
"""
# Author: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Gael Varoquaux <gael.varoquaux@normalesup.org>
# Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
# avoid division truncation
import warnings
import numpy as np
from scipy... | chrsrds/scikit-learn | sklearn/covariance/empirical_covariance_.py | Python | bsd-3-clause | 9,848 | [
"Gaussian"
] | 5b43676469c96d0f3adbdb6b6ae3b71e4ddce62702bf80d69b2657b75a5a415c |
import pathlib
import pytest
import kgrid.cli
data_dir = pathlib.Path('test/data')
sio2 = data_dir / 'POSCAR'
def test_calc_grid_output(capsys):
kgrid.cli.calc_grid(15., filename=str(sio2), pretty_print=True)
captured = capsys.readouterr()
assert captured.out == ' 8 8 12\n'
def test_calc_grid_fo... | WMD-group/kgrid | test/test_kgrid_cli.py | Python | gpl-3.0 | 2,106 | [
"CASTEP",
"VASP"
] | 73c57e119708be1f34d31e3ca792765d4e74f47f59eb6c49aa54c0d37c63ecc6 |
"""Timeseries plotting functions."""
from __future__ import division
import numpy as np
import pandas as pd
from scipy import stats, interpolate
import matplotlib as mpl
import matplotlib.pyplot as plt
from .external.six import string_types
from . import utils
from . import algorithms as algo
from .palettes import c... | yarikoptic/seaborn | seaborn/timeseries.py | Python | bsd-3-clause | 13,054 | [
"NEURON"
] | 0571a839cf0e28e676b4f7d77669087e24eea1bb28d6be614d38ccdee4e528c3 |
import density_container as dc
import itertools as it
class PymolDensity(object):
"""docstring for PymolDensity"""
surface_colors = ['blue', 'brightorange', 'cyan', 'forest', 'orange',
'lightmagenta', 'deepteal', 'oxygen', 'purple', 'yellow']
def __init__(self, pymol_vis):
s... | luminescence/PolyLibScan | Analysis/PymolDensity.py | Python | mit | 3,557 | [
"PyMOL"
] | 995020975120137f49c85e6f41e397e50a4472961858fb17e707db2a1a96aa92 |
"""Generalized linear mixed model"""
import warnings
import re
import numpy as np
import pandas as pd
from sklearn.base import BaseEstimator
from sklearn.utils.random import check_random_state
from category_encoders.ordinal import OrdinalEncoder
import category_encoders.utils as util
import statsmodels.formula.api as s... | scikit-learn-contrib/categorical-encoding | category_encoders/glmm.py | Python | bsd-3-clause | 13,548 | [
"Gaussian"
] | d0b47829ae9d51743969045d707ef80c4961d404a8d20863e313774d91f13146 |
# Test ase.utils.eos without ASE (eoswoase)
# This test will run if numpy is in the default sys.path
# because PYTHONPATH is overwritten under os.system call!
import os
import sys
import ase
dir = os.path.abspath(os.path.dirname(ase.__file__))
utilsdir = os.path.join(dir, 'utils')
sjeos = os.path.join(utilsdir, 'sj... | grhawk/ASE | tools/ase/test/eoswoase.py | Python | gpl-2.0 | 437 | [
"ASE"
] | 9fae1e3acb5a2db655d092a02776bda843b2cf6e66eae97426e769e9da8f7159 |
import sys; import os.path; sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
import numpy
from bigfile import BigFile
from mpi4py import MPI
from pypm.transfer import TransferFunction
from pypm.tools import FromRoot
import numba
from genic import GridIC
from qpm import QPM
import logging
LOG = l... | rainwoodman/pypm | nbody/gravpm.py | Python | gpl-3.0 | 6,261 | [
"Gaussian"
] | 4fe807810726c5bb31e5f954e936f6bd7e4a73d51529c4779b69e5e943bf5174 |
# Copyright (c) 2018, Henrique Miranda
# All rights reserved.
#
# This file is part of the phononwebsite project
#
""" Read phonon dispersion from quantum espresso or abinit """
from .qephonon import *
from .anaddbphonon import *
| henriquemiranda/phononwebsite | phononweb/__init__.py | Python | bsd-3-clause | 230 | [
"ABINIT",
"Quantum ESPRESSO"
] | 5f8e26ef74365e16656c932efa1a5be87d3e2679ebe2f3066e150538137d8903 |
import base64
import sys
import json
import pytest
import numpy as np
from plotly import io as pio
import plotly.graph_objs as go
from plotly.offline.offline import _get_jconfig
if sys.version_info >= (3, 3):
import unittest.mock as mock
else:
import mock
plotly_mimetype = "application/vnd.plotly.v1+json"
... | plotly/python-api | packages/python/plotly/plotly/tests/test_orca/test_image_renderers.py | Python | mit | 4,325 | [
"ORCA"
] | b32efcf46b659e6a1942b7eb2444bff9d8d95ac86ae29364d420e4762d1623d0 |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019-2021, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
"""Installed collections management package."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import errno
import f... | felixfontein/ansible | lib/ansible/galaxy/collection/__init__.py | Python | gpl-3.0 | 65,231 | [
"Galaxy"
] | bd560f78c433ed5b10dede254dffe31e938526aca6ff5dfd18fe99b9c84ed5ed |
#!/usr/bin/python2.4
#
# CDDL HEADER START
#
# The contents of this file are subject to the terms of the
# Common Development and Distribution License (the "License").
# You may not use this file except in compliance with the License.
#
# You can obtain a copy of the license at usr/src/OPENSOLARIS.LICENSE
# or http://w... | marcellodesales/svnedge-console | ext/windows/pkg-toolkit/pkg/vendor-packages/pkg/server/feed.py | Python | agpl-3.0 | 16,865 | [
"VisIt"
] | 352dc07d4b4af76c1c08b20d32253a7a2bf65f505d68d62bdac1e282876382e7 |
import os
## os.chdir('c:/mypysces/kraken')
os.chdir('/home/bgoli/mypysces/kraken')
from Kraken import *
import itertools
import scipy.io
#investigate using vstack with type/range checking
def concatenateArrays(array_list):
output = None
for arr in range(len(array_list)):
if type(array_list... | asttra/pysces | pysces/kraken/controllers/kraken_scanner2.py | Python | bsd-3-clause | 14,078 | [
"Mayavi",
"VTK"
] | 3f5091187c0bc42def83bcd72737fb4a0f7df82578c4bf1959459e6373ba4dde |
# Copyright (c) 2013, the GPy Authors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from ..core import GP
from .. import likelihoods
from .. import kern
from ..inference.latent_function_inference.expectation_propagation import EP
class GPClassification(GP):
"""
Gaussian Process... | mikecroucher/GPy | GPy/models/gp_classification.py | Python | bsd-3-clause | 1,009 | [
"Gaussian"
] | eddd04a3e552c9bfda8ebe94dfa4ce1c9f5d76e85ad7bb27e31ae604cc5fbfc9 |
# Copyright (C) 2012,2013,2014,2015,2016,2017,2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it... | espressopp/espressopp | src/storage/Storage.py | Python | gpl-3.0 | 25,097 | [
"ESPResSo"
] | ab9db91cd80c90b8aeff2497e3ad13babcef6d957e527b67985dde0c05a0c181 |
import ocl
import pyocl
import camvtk
import time
import vtk
import datetime
import math
if __name__ == "__main__":
print(ocl.version())
myscreen = camvtk.VTKScreen()
a=ocl.Point(1,0,0)
myscreen.addActor(camvtk.Point(center=(1,0,0), color=(1,0,1)));
b=ocl.Point(0,1,0)
myscreen.addAct... | aewallin/opencamlib | examples/python/drop-cutter/drop_cutter_tst_4.py | Python | lgpl-2.1 | 2,382 | [
"VTK"
] | 58b2c43b344f936473a8e2a3545e42657ce7eedb4fae97471720fd3d92617818 |
# Copyright (c) 2011, Alex Krizhevsky (akrizhevsky@gmail.com)
# 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 notice,
# this ... | tund/kaggle-galaxy-zoo | cuda_convnet/shownet.py | Python | bsd-3-clause | 22,427 | [
"NEURON"
] | 6e2980c0ad9dc2ecb697ec2be80777f2393a79c131224ac60a980bfeb6e35eb1 |
import dataclasses
from typing import Union
from argparse import Namespace
import rapidjson as json
import os
import toml
import yaml
from pkg_resources import resource_stream
from .configurator import create_cluster_config, load_and_validate_config
from . import print_config
from .daijin_configuration import DaijinCon... | lucventurini/mikado | Mikado/configuration/daijin_configurator.py | Python | lgpl-3.0 | 11,565 | [
"pysam"
] | 3f6b1c1b04a787dbd42fb5a70d838c47ae9b9fceb7add69ca26758640c2fcba5 |
from html.parser import HTMLParser
from urllib.request import urlopen
from urllib import parse
from bs4 import BeautifulSoup
# We are going to create a class called LinkParser that inherits some
# methods from HTMLParser which is why it is passed into the definition
class LinkParser(HTMLParser):
# This is a f... | chunlaw/GeoNews | models/applespider.py | Python | mit | 5,145 | [
"VisIt"
] | 7fb9bea337a3cd0b8ae7859b5070367067992f0dbe05b3105c14bf523051298d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Name:
Power_wb, a command-line tool for Weibo.
Version:
beta, nothing reserved
Author:
Lane(zhanglintc)
Description:
Based on "lxyu/weibo", work on Python 2.x.x, support Linux/Mac/Windows.
Support automatic installation by using "python setup.py".
More d... | zhanglintc/wb | src/wb.py | Python | gpl-2.0 | 26,942 | [
"VisIt"
] | f9b5cb3c7e388a9869744399f16a7603a43f737c6dcf3a9bb7bd9a070a6086ff |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <mainak@neuro.hut.fi>
# Mark Wronkiewicz <wronk.mark@gmail.com>
#
# Lice... | Teekuningas/mne-python | mne/viz/tests/test_3d.py | Python | bsd-3-clause | 36,261 | [
"Mayavi"
] | 94411f770d83a1ce3c0a999377a66549cb681d8c2bd6204c2d3df5284cc3cb70 |
"""Example code to convert Structured Commons objects to Python objects."""
from __future__ import print_function
import sys
from sc import fp
class pyrepr_visitor(object):
"""Convert an abstract object tree to a Python concrete object.
- object files are transformed to bytearray
- object dictionaries are ... | structured-commons/tools | sc/py.py | Python | unlicense | 3,072 | [
"VisIt"
] | 236800ca8a5a07a90dcba51d165894a39bd0bc9b580985aa0c9b2dde246ac4c6 |
import cPickle, gzip, numpy as np
# semi-functional
#py 3
# u = pickle._Unpickler(f)
# train_set, valid_set, test_set = u.load()
f = gzip.open('mnist.pkl.gz', 'rb')
#f2 = open('matplot-text.txt', 'w+')
train_set, valid_set, test_set = cPickle.load(f)
f.close()
print 'train_set length: ', len(train_set[0])
# perce... | xR86/ml-stuff | labs-neural-networks/hw-lab4/mnist-perceptron-classes.py | Python | mit | 4,243 | [
"NEURON"
] | 70aa13c8cd7fc33a2114db44971dd1f7b62b35d2fee542b032eae1a72e6f19bd |
"""Definitions of workflows for translation into common workflow language.
This organizes the metadata and other information about workflows,
providing the necessary information to translate into CWL. The goal is to
eventually replace pipeline/main.py workflows with generalized
versions of this code.
Ideally we could... | biocyberman/bcbio-nextgen | bcbio/cwl/defs.py | Python | mit | 27,173 | [
"BWA"
] | d1710e81f58099ed0e45c6b2fbd45a6ef2cdf9a87d7278f7ea9c90c834d54e21 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.
# Revisions copyright 2014 by Melissa Gymrek <mgymrek@mit.edu>.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""This ... | zjuchenyuan/BioWeb | Lib/Bio/PopGen/SimCoal/Controller.py | Python | mit | 11,979 | [
"Biopython"
] | 71d3ef6400038152a5d4cfa7faf490fea8dde249cda7450ec8916f1c09407056 |
"""
Generate molecular scaffolds.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
from . import Featurizer
from ..utils import ScaffoldGenerator
class Scaffold(Featurizer):
"""
Molecular scaffolds.
Parameters
----------
Parame... | rbharath/pande-gas | vs_utils/features/scaffolds.py | Python | bsd-3-clause | 878 | [
"RDKit"
] | 949d3d6e7f904127e0d23124db2ece1daee8eef11467a50a140a67cbafb93a6c |
""" FileCatalogFactory class to create file catalog client objects according to the
configuration description
"""
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.Helpers.Resources import getCatalogPath
from DIRAC.Resources.Catalog.FileCatalogProxyClient import FileCatalogPr... | andresailer/DIRAC | Resources/Catalog/FileCatalogFactory.py | Python | gpl-3.0 | 2,630 | [
"DIRAC"
] | ef4728a019f37ef614df46386f781c895d4e14a375df78abf7c1172da74afb6f |
"""
Browser set up for acceptance tests.
"""
# pylint: disable=no-member
# pylint: disable=unused-argument
from lettuce import before, after, world
from splinter.browser import Browser
from logging import getLogger
from django.core.management import call_command
from django.conf import settings
from selenium.common.e... | ahmadiga/min_edx | common/djangoapps/terrain/browser.py | Python | agpl-3.0 | 10,130 | [
"VisIt"
] | fab72565324e4fe5820cf61a76b63a77f5adbb5f00b64a69627b5dc3f495d611 |
import pandas as pd
from sklearn.datasets import make_regression, \
make_blobs, \
make_classification, \
make_multilabel_classification, \
make_gaussian_quantiles, \
make_hastie_10_2, \
make_circles, \
make_moons, \
make_biclusters, \
make_s_curve, \
make_checkerboard, \
make... | timkpaine/lantern | lantern/data/data_sklearn.py | Python | apache-2.0 | 10,655 | [
"Gaussian"
] | b9516594120a4600d327857e6b9e7ddc827aeb5ab3be7defceb47d40dd0e0568 |
import cobble.env
import cobble.target
import os.path
from itertools import chain
from cobble.plugin import *
DEPS_INCLUDE_SYSTEM = cobble.env.overrideable_bool_key(
name = 'c_deps_include_system',
default = True,
readout = lambda x: '-MD' if x else '-MMD',
help = ('Whether to recompile in response to ... | cbiffle/cobble-build | src/cobble/target/c.py | Python | bsd-2-clause | 9,205 | [
"VisIt"
] | 4cbb90e64d2a9dea27cf14bf034b6c6f122e1a925545f36962140e3655835be7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Compare orientation matrices
Uses the mat3 and vec3 classes from Python Computer Graphics Kit v1.2.0
module by Matthias Baas (see http://cgkit.sourceforge.net).
License: http://www.opensource.org/licenses/bsd-license.php
"""
__author__ = "Pierre Legra... | RAPD/RAPD | src/plugins/subcontractors/xdsme/new/xdsme-0.4.9/XOconv/XOcompare.py | Python | agpl-3.0 | 9,108 | [
"CRYSTAL"
] | c76392e38b5d422abc6147eb80f2eef93efa656c0b6d10bdd25812181066c698 |
### pypixel - Python educational graphics library
### Copyright 2009-2011 Brian Mock <mock.brian@gmail.com>
###
### This library is free software; you can redistribute it and/or
### modify it under the terms of the GNU Library General Public
### License as published by the Free Software Foundation; either
### version 2... | wavebeem/pypixel | pypixel.py | Python | lgpl-2.1 | 11,062 | [
"Brian"
] | bab24cfe5152114abf9a4a6efa94159f7dddf4f322a66535a1808f695c727804 |
# crc32 and crc64
# crc64 is adapted from BioPerl
import warnings
warnings.warn("Bio.crc is deprecated; use crc32 and crc64 in Bio.SeqUtils.CheckSum instead", DeprecationWarning)
from binascii import crc32
_table_h = []
def crc64(s):
crcl = 0
crch = 0
for c in s:
shr = (crch & 0xFF) << 24
... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/crc.py | Python | apache-2.0 | 772 | [
"BioPerl"
] | 764293803b45d232877673c44625ff26fe1a861a95b9f5124197081003aa7928 |
import scipy.io as sio
import numpy as np
import pandas as pd
from tqdm import tqdm
import argparse
def main():
parser = argparse.ArgumentParser(description='RNN for modeling neuron populations')
parser.add_argument('infile', metavar='infile', type=str,
help='Input data file path')
... | elijahc/ml_v1 | load_data.py | Python | mit | 4,089 | [
"NEURON"
] | ab8c22fe4a085b2ae1258f7eed501615c6c42ca1a6b3d4a247e5a5d51948f934 |
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import labrad
from labrad.units import Unit
V, mV, us, ns, GHz, MHz = [Unit(s) for s in ('V', 'mV', 'us', 'ns', 'GHz', 'MHz')]
import pyle
from pyle.pipeline import returnValue, FutureList
from pyle.dataking import util
from py... | McDermott-Group/LabRAD | LabRAD/TestScripts/fpgaTest/pyle/pyle/dataking/hadamard.py | Python | gpl-2.0 | 13,824 | [
"Gaussian"
] | ac42c3b10040081a2d47beda096196db0b3c82b0eac5651c70f9e152896ebdf2 |
""" Contains a class used for evaluating policies for accessing jobs/WMS/pilots accounting
"""
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Security import Properties
from DIRAC.AccountingSystem.private.Policies.FilterExecutor import FilterExecutor
class JobPolicy(object):
def __init__(self):
self.__ex... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/private/Policies/JobPolicy.py | Python | gpl-3.0 | 3,508 | [
"DIRAC"
] | 1c05e742adca731b60a0c1cf45fa19871d1c09594badc13402d39b189614f988 |
#!/usr/bin/env python3
# -*- encoding: utf-8 -*-
import pyautogui, time
# Set these to the correct coordinates for your computer
nameField = (648, 319)
submitButton = (651, 817)
submitButtonColor = (75, 141, 249)
submitAnotherLink = (760, 224)
formData = [
{'name': 'Alice', 'fer': 'eavesdroppers', 'source': 'wan... | xu6148152/Binea_Python_Project | automate the boring stuff with python/auto_gui/formFiller.py | Python | mit | 2,625 | [
"CRYSTAL"
] | a3b38f1353b9c7ea232d5499341da2e307a6ae67de610cd081b8d76a475071c0 |
import sys
for i in range(0, len(sys.argv)):
if sys.argv[i] == "-vtkdir" and i < len(sys.argv)-1:
input_file = sys.argv[i+1]
if not input_file:
print "Usage: %s [-vtkdir <path to the vtk source tree>] [-k ...] ..." % sys.argv[0]
print "Got Args: %s" % `sys.argv`
sys.exit(1)
inpu... | dlrdave/activizdotnet | Testing/TclToCsScript/GenerateVtkCommandList.py | Python | bsd-3-clause | 1,597 | [
"VTK"
] | e9cbb2ad971ca88bb67b34689e69c9d50f129eb51c4c56cd89052a295467c4c4 |
# Copyright 2015 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import print_function
from __future__ import absolute_import
from moose.horn import horn_object
class Moose(object):
def __init__(self):
... | catapult-project/catapult | telemetry/telemetry/internal/testing/dependency_test_dir/other_animals/moose/moose/moose_object.py | Python | bsd-3-clause | 450 | [
"MOOSE"
] | b230dfb370cff6aa74e4ce108bd1c129519a2563c154ff5eae47ae899109e6da |
# Natural Language Toolkit: Decision tree
#
# Copyright (C) 2001 University of Melbourne
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# URL: <http://nltk.sf.net>
# For license information, see LICENSE.TXT
#
# $Id: decisiontree.py,v 1.3 2003/10/27 04:41:29 trevorcohn1 Exp $
"""
Decision tree classifier using the flip-flo... | ronaldahmed/robot-navigation | neural-navigation-with-lstm/MARCO/nltk_contrib/unimelb/tacohn/classifier/decisiontree.py | Python | mit | 23,792 | [
"VisIt"
] | 5985fc750185590eec09df87aef6816b609c1a609dc76437143381ae6093e89e |
""" This is a test of the chain
FileCatalogClient -> FileCatalogHandler -> FileCatalogDB
It supposes that the DB is present, and that the service is running
"""
# pylint: disable=invalid-name,wrong-import-position
from __future__ import print_function
from __future__ import absolute_import
from __future__ imp... | ic-hep/DIRAC | tests/Integration/DataManagementSystem/Test_Client_DFC.py | Python | gpl-3.0 | 40,086 | [
"DIRAC"
] | d92e1b5322c76234bea046fe9c606604b140e2e8f9c256bb86d403239d758d68 |
"""Test cases for BADBAM intersection and difference. It is suffiicent to generate a test case for one chromosome
as the badbams code operates on reads on a chromosome by chromosome basis"""
import tempfile
import os
import pysam
import numpy as np
from mitty.benchmarking.badbams import intersect_and_diff_of_bams
fro... | latticelabs/Mitty | mitty/tests/benchmarking/badbam_test.py | Python | gpl-2.0 | 6,621 | [
"pysam"
] | fe3ffed2fda20a433a8a35acd5c272f7e824fa58a9aef6f65ac98cc3a0a7514b |
from django.conf.urls import patterns, url
from django.contrib.auth.decorators import login_required
from django.views.generic import TemplateView
from catmaid.views import CatmaidView, ExportWidgetView
# A regular expression matching floating point and integer numbers
num = r'[-+]?[0-9]*\.?[0-9]+'
integer = r'[-+]?[... | htem/CATMAID | django/applications/catmaid/urls.py | Python | agpl-3.0 | 21,264 | [
"NEURON"
] | 201598cc25ef74702681ab2720b560b6ab65122f7a29366e32c5993bb09b6a6f |
import MDAnalysis
import numpy as np
try:
from MDAnalysisTests.datafiles import GRO
except:
pass
try:
from MDAnalysis.analysis import distances
except:
pass
class DistancesBench(object):
"""Benchmarks for MDAnalysis.analysis.distances
functions.
"""
# TODO: eventually we should inclu... | MDAnalysis/mdanalysis | benchmarks/benchmarks/analysis/distances.py | Python | gpl-2.0 | 4,884 | [
"MDAnalysis"
] | ac1d5b13f168473fb8252fb15e899676be3f99e741925fb856422d8d44942ff5 |
# texttable - module for creating simple ASCII tables
# Copyright (C) 2003-2015 Gerome Fournier <jef(at)foutaise.org>
#
# 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.... | mdeff/ntds_2017 | projects/reports/stackoverflow_survey/texttable.py | Python | mit | 22,111 | [
"Brian"
] | e3e842efe880571dcc3d663bc5d08397f242301ae177264120409ae76b693d05 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a GW calculation using Yambo
#
from __future__ import print_function
import sys
from yambopy import *
from qepy import *
import argparse
yambo = 'yambo'
p2y = 'p2y'
prefix = 'si'
def create_save():
#check if the nscf cycle is present
if os.path.isdir('nscf/%s... | palful/yambopy | tutorial/si/gw_conv_si.py | Python | bsd-3-clause | 2,652 | [
"Yambo"
] | e824feddeb23d18edd2d4e3dec1ab3a814cc0e8ae2f66946e1b914132f42aba6 |
"""
@file outputs.py
@author Yun-Pang Wang
@author Daniel Krajzewicz
@author Michael Behrisch
@date 2007-12-25
@version $Id: outputs.py 13811 2013-05-01 20:31:43Z behrisch $
This script is for generating the outputs from the choosed traffic assignment.
SUMO, Simulation of Urban MObility; see http://sumo.sour... | rudhir-upretee/Sumo17_With_Netsim | tools/assign/outputs.py | Python | gpl-3.0 | 6,838 | [
"MOE"
] | 4727f9e776199febe3f645b161236925b4792804aab30968b2a14388827bf4d5 |
#!/usr/bin/env python3
"""
Copyright 2021 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/myResources.py | Python | gpl-3.0 | 1,841 | [
"Galaxy"
] | c8124a10435f8b0918dac35a296af46295f09131bb30d5df31876650a6575f71 |
"""
The B{0install man} command-line interface.
"""
# Copyright (C) 2012, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import sys, os
from zeroinstall import support, logger
syntax = "NAME"
def add_options(parser):
pass
def handle(config, ... | timdiels/0install | zeroinstall/cmd/man.py | Python | lgpl-2.1 | 1,222 | [
"VisIt"
] | f1ccefb8ce397eddd2d1fdd269d3e1f76983a9f0debd7762a8f2eb96acb8e0ef |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Run parser unit tests for cclib."""
import sys
import unittest
sys.path.append('parser')
from testdata import *
from ... | Schamnad/cclib | test/test_parser.py | Python | bsd-3-clause | 420 | [
"cclib"
] | 25f932d71997a4ca0800f5cd5d47bc057e2b8c3c09e7a56e6adc2e55760f3e04 |
# Copyright 2016 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... | aselle/tensorflow | tensorflow/contrib/autograph/converters/asserts.py | Python | apache-2.0 | 1,736 | [
"VisIt"
] | e90f1511cdffd8edc808cc5c9d53b82ab62a093dcb1d28ae09650b917542013f |
"""
Feature calculations.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
import numpy as np
import types
from rdkit import Chem
from rdkit.Chem import rdGeometry, rdMolTransforms
from ..utils.ob_utils import Ionizer
def get_featurizers():
"... | rbharath/pande-gas | vs_utils/features/__init__.py | Python | bsd-3-clause | 10,567 | [
"RDKit"
] | dbc562b878b1fb3bb51d5f9cb10178f300c7895d813fa0e5960cf52ca88fb62f |
### ANR CARD SCRIPTS ###
# 5 Equal Signs (=) signifiies a break between the description (what you're currently reading) and the code
# 5 Dashes (-) signifies a break between the card name, the GUID and the card scripts. The card name is ignored by the code, only the GUID and Scripts are used.
# 5 Plus Signs (+) sig... | Khudzlin/Doomtown-Reloaded-OCTGN | o8g/Scripts/CardScripts.py | Python | agpl-3.0 | 20,292 | [
"BLAST",
"CASINO"
] | 2ff6992821f97ebcd8bfae12fd05a25eaa50a18d53f00cb62d9e39727ccb2125 |
# Orca
#
# Copyright 2005-2008 Google 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 library i... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/outloud.py | Python | gpl-3.0 | 10,940 | [
"ORCA"
] | 68da8327056dd3a4e4021c499fd5f8d4079afd18bdbb2feb81d83fa32dd381b6 |
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input dimension
of D, a hidden dimension of H, and perform... | UltronAI/Deep-Learning | CS231n/reference/CS231n-master/assignment2/cs231n/classifiers/fc_net.py | Python | mit | 15,248 | [
"BLAST",
"Gaussian"
] | 702e84ff5c9dc60526a750205bf9be4c08236efa1adb0d8e176c92a7305f3023 |
# Copyright (c) 2015, Julian Straub <jstraub@csail.mit.edu>
# Licensed under the MIT license. See the license file LICENSE.
import numpy as np
from scipy.linalg import eig, logm
import subprocess as subp
import matplotlib.pyplot as plt
import mayavi.mlab as mlab
from matplotlib.patches import Ellipse
import pdb, re, ... | jstraub/dpMM | python/dpSphereMM.py | Python | mit | 19,932 | [
"Mayavi"
] | 1b364f2727a5ec574cab509fd1f471e80cca02e3337c7c5245c9f5ce9bf55803 |
"""
Python Interchangeable Virtual Instrument Library
Copyright (c) 2012-2014 Alex Forencich
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the... | sephalon/python-ivi | ivi/agilent/agilent3000A.py | Python | mit | 6,792 | [
"Gaussian"
] | c6eb81ea1367d8704b1a067dc2768bde92b3922ba3988cb93b88ea52426ee91c |
# -*- 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 required by applicable law or... | googleapis/python-life-sciences | tests/unit/gapic/lifesciences_v2beta/test_workflows_service_v2_beta.py | Python | apache-2.0 | 54,713 | [
"Octopus"
] | fa29a70f3eeaf33be1be436361e9683d0c8fc8894f8c80a3b45efcaedd5ea13c |
# coding: utf-8
from mod_python import apache # @UnresolvedImport
import time
import os
import json
import netCDF4 # @UnresolvedImport
import urllib
import datetime
# ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
def readData(req, fileType="1", dimCols="time,p,lat,lon", varCols="temp,rh", gridStep=5, zAdjustment=1000):
di... | makinux/GridVIz | readData.py | Python | gpl-2.0 | 2,916 | [
"NetCDF"
] | 836ac592fd20163586819d101e5a963cfc0fe07921de344d09b9eb7d37f76d6a |
#!/usr/bin/env python
import sys,os,errno,argparse,subprocess
from Bio import SeqIO
helptext = """
usage: python distribute_targets.py baitfile\n
Given a file containing all of the "baits" for a target enrichment, create separate
FASTA files with all copies of that bait. Multiple copies of the same bait can be
sp... | mossmatters/HybPiper | distribute_targets.py | Python | gpl-3.0 | 7,649 | [
"BLAST",
"BWA"
] | 56945a0c5535747aaea618a2e0e5c96190b523102270a9dd4ff54b3db7557a5c |
from DIRAC.ConfigurationSystem.private.ConfigurationData import ConfigurationData
gConfigurationData = ConfigurationData()
| DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/Client/ConfigurationData.py | Python | gpl-3.0 | 124 | [
"DIRAC"
] | dc18546549ded8a88c29236ab3578faa273329d4fbb00876d740a659b6c8621c |
'''
This script shows how to implement a new grid based quantity.
Here, we implement the reduced density gradient as proposed by
Johnson et al., J. Am. Chem. Soc. 132, 6498 (2010).
'''
from orbkit import read, grid, display, core, output
'''
Identify the non-covalent interaction regions
using the reduced density g... | orbkit/orbkit | examples/orbkit_applications/H2O-dimer_reduced_density_gradient/reduced_density_gradient.py | Python | lgpl-3.0 | 2,141 | [
"VMD"
] | 07a6c9a566715ddc21fef9e4b7e0642b2e9d0dd257619d57e7c36d91f62f8219 |
import numpy as np
from astropy.modeling import fitting, models
__all__ = ['fit_gaussian1d', 'fit_multi_gaussian1d']
def fit_gaussian1d(x, y, init_amp=1.0, init_mean=0.0, init_std=0.45,
xcrop=None):
"""Fit a Gaussian 1D kernel to the data.
Parameters
----------
x: array-like
... | piyanatk/sim | opstats/utils/fitting.py | Python | mit | 2,364 | [
"Gaussian"
] | 287a24d74df3797050d07669677691d775274c9eddef2cdd428c7a5f3128f7de |
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