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#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | ened/scancode-toolkit | tests/licensedcode/test_detection_datadriven.py | Python | apache-2.0 | 7,147 | [
"VisIt"
] | 99fcfb76cbd9850c1a2d91d3ebb22138c846e8e93a62b0007323467a28fa9bed |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
# The purpose of this test is to detect a change in the _metric_json of MetricsBase objects. Many of the metric
# accessors require _metric_json to have a particular form.
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
from h... | michalkurka/h2o-3 | h2o-py/tests/testdir_misc/pyunit_metric_json_check.py | Python | apache-2.0 | 13,450 | [
"Gaussian"
] | 6166adbe6bfb3149f702d87a09a3dba4c82525446f3ff5a5c6301b6a8c4e1919 |
import os
from astropy.io.fits import open as fits_open
import numpy as np
from astropy.convolution import convolve as ap_convolve
from astropy.convolution import Box1DKernel
from scipy.signal import medfilt # Median Filter from scipy
from scipy.interpolate import interp1d
def open_kepler(filename):
""" Opens a ... | stephtdouglas/k2spin | fix_kepler.py | Python | mit | 4,505 | [
"Gaussian"
] | 4ad02c7a290b5720844827dd9a1d379a8954ba78424c6cd819a6361d6ffefbdf |
try: paraview.simple
except: from paraview.simple import *
import numpy as np
from mpi4py import MPI
import os
import csv
from scipy import interpolate
import gc
import sys
gc.enable()
comm = MPI.COMM_WORLD
label = 'm_50_7'
label = label+'_3Db_particles'
labelo = label+'_particles'
basename = 'mli_checkpoint'
## ... | jungla/ICOM-fluidity-toolbox | Detectors/extract_Tr_3_day.py | Python | gpl-2.0 | 3,166 | [
"ParaView"
] | 469918f4f4c4d51c7f0c284bef0f92d57571f5dde4c8ecd8d909cc15f1ff9956 |
#
# Copyright (C) 2007, Mark Lee
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required... | okkhoy/mo-rlglue-python-codec | rlglue/environment/EnvironmentLoaderScript.py | Python | mit | 1,631 | [
"Brian"
] | e8481c0589f9cc5a425d16f16381790638ea86fbcf98cdc32e03f4e43b746b21 |
# Copyright Anne M. Archibald 2008
# Released under the scipy license
import os
from numpy.testing import (assert_equal, assert_array_equal, assert_,
assert_almost_equal, assert_array_almost_equal,
assert_allclose)
from pytest import raises as assert_raises
import ... | e-q/scipy | scipy/spatial/tests/test_kdtree.py | Python | bsd-3-clause | 48,897 | [
"VisIt"
] | af60e3593b8620c007e28e09c0bc9b151fc03c73c1b53a0efe56b0395a002b9f |
"""
Views for user API
"""
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import Response
from opaque_keys.edx.keys import UsageKey
from opaque_keys import InvalidKeyError
... | ampax/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 11,135 | [
"VisIt"
] | fd70e9762efa81f90c831a4ca956d9207fdd33b117d68f30d0707cf0b9f05fb9 |
#!/usr/bin/env python -u
# Decompose each of the MAGMO spectra into Gaussian components.
#
# This program reads the previously generated spectra summaries and uses GaussPy to fit Gaussian components to
# the spectra. Comparison diagrams are produced for each spectrum.
# Author James Dempsey
# Date 5 Jan 2017
from __... | jd-au/magmo-HI | decompose.py | Python | apache-2.0 | 21,500 | [
"Gaussian"
] | f5a6f205b10532cfc6ce5476dfdf50bbfce6e96bc9fef9618b0a4acdf7f2a6c1 |
# pmx Copyright Notice
# ============================
#
# The pmx source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# pmx is Copyright (C) 2006-2013 by Daniel ... | dseeliger/pmx | pmx/forcefield.py | Python | lgpl-3.0 | 73,752 | [
"Gromacs"
] | d630e4de961c701794c32c1afdb143768e23dc54367092817f5c091ac1a22e9f |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Softw... | andrebellafronte/stoq | stoqlib/domain/service.py | Python | gpl-2.0 | 4,520 | [
"VisIt"
] | 74416c0ee7ec1359b64f4a0a32f43b516aa1536e9c4c3e58f67c9ebf413e5490 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christopher M. Bruns
# Contributors: Peter Eastman, Robert McG... | kyleabeauchamp/mdtraj | mdtraj/formats/pdb/pdbstructure.py | Python | lgpl-2.1 | 37,034 | [
"CRYSTAL",
"Gromacs",
"MDTraj",
"OpenMM",
"VMD"
] | d075a3979e003e2dd5e810699d612d1795ef84f0fb395e10da6d537824c1d71d |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
ImageLuminance()
| jeromevelut/Peavip | Testing/ImageLuminance.py | Python | gpl-3.0 | 127 | [
"ParaView"
] | 7499f41902a74a9e69a22b0db828c88319f1d017dd679f8a0555d6d0a2798ded |
from pywps.Process import WPSProcess
from flyingpigeon.indices import indices, indices_description, calc_indice_single
from flyingpigeon.subset import countries, countries_longname
from flyingpigeon.utils import GROUPING
import logging
class SingleIndicesProcess(WPSProcess):
"""This process calculates a climate ... | sradanov/flyingpigeon | flyingpigeon/processes/wps_indices.py | Python | apache-2.0 | 3,870 | [
"NetCDF"
] | 37ca0a6c83f8b825666395eca41714b7fb31d0047bdb15767cc0ef35e2bf5748 |
#build list of available data
import os, sys
microbe_info= {}
try:
orgs = {}
for line in open( "/depot/data2/galaxy/microbes/microbial_data.loc" ):
if line[0:1] == "#" : continue
fields = line.split('\t')
#read each line, if not enough fields, go to next line
... | jmchilton/galaxy-central | tools/data_source/microbial_import_code.py | Python | mit | 8,633 | [
"Galaxy"
] | b2b28afcdff56ee0794b0dded1d1f11fc60e6a8b12f835eb827d17525339f5b9 |
"""Module for functions in the Vascular Modeling Toolkit (VMTK).
For more details on VMTK, go to www.vmtk.org. For more details specifically on
VMTK scripts, go to www.vmtk.org/vmtkscripts.
To a large extent, function names were chosen to match the names of
corresponding vmtk scripts. Parts of the documentation... | ajgeers/utils | utils/vmtklib.py | Python | bsd-2-clause | 38,412 | [
"Gaussian",
"VTK"
] | f62742dcb2d1a00721764c73068ef640eb2feec712684cb5902469b2b664cf27 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | matthiasdiener/spack | var/spack/repos/builtin/packages/lammps/package.py | Python | lgpl-2.1 | 4,813 | [
"LAMMPS",
"NetCDF"
] | 5ab1909bc56ef23e0186f6f6070ec96aeec310145dcb550740b08adde951dadf |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-affyilm/package.py | Python | lgpl-2.1 | 2,063 | [
"Bioconductor"
] | 1966cff23b21a535ac8029467f1862b45be2e097e6a3badfd12f57ac6df19218 |
import errno
import functools
import itertools
import multiprocessing
import os, os.path
import shlex
import subprocess
import sys
from ndmake import debug
from ndmake import dispatch
from ndmake import files
from ndmake import mtime
from ndmake import mux
from ndmake import space
from ndmake import template
from ndma... | marktsuchida/NDMake | ndmake/depgraph.py | Python | mit | 32,848 | [
"VisIt"
] | 57c2acf3adfe62ce49eeffe3505a7f179f3af6251b1af56312ad76021d00f043 |
from jinja2.visitor import NodeVisitor
from jinja2._compat import iteritems
VAR_LOAD_PARAMETER = 'param'
VAR_LOAD_RESOLVE = 'resolve'
VAR_LOAD_ALIAS = 'alias'
VAR_LOAD_UNDEFINED = 'undefined'
def find_symbols(nodes, parent_symbols=None):
sym = Symbols(parent=parent_symbols)
visitor = FrameSymbolVisitor(sym)... | astaninger/speakout | venv/lib/python3.6/site-packages/jinja2/idtracking.py | Python | mit | 9,197 | [
"VisIt"
] | d866c34b322f180ac40462e4a2f2e4a847e6631996b047fc737419c0ce2e36cc |
# CoordinateMapper -- map between genomic, cds, and protein coordinates
# AUTHOR: Reece Hart <reecehart@gmail.com>
# Modifications: Lenna X. Peterson <arklenna@gmail.com>
# LICENSE: BioPython
# Examples:
# AB026906.1:g.7872G>T
# AB026906.1:c.274G>T
# BA...:p.Asp92Tyr
#
# All refer to congruent variants. A coordinate m... | HaseloffLab/PartsDB | partsdb/tools/CoordinateMapper/CoordinateMapper.py | Python | mit | 12,170 | [
"BioPerl",
"Biopython"
] | 5760f34060c01f1c1b20e4d15b68a5cfc58ab7a166eed1465c2adcb3ddc79451 |
# Copyright 2014-2016 The ODL development group
#
# This file is part of ODL.
#
# ODL is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#... | bgris/ODL_bgris | odl/test/deform/linearized_deform_test.py | Python | gpl-3.0 | 10,465 | [
"Gaussian"
] | 9e4d6df3dfc9ea826f9a69d195cc641544c6a8fd3b255bb908c6a59cad2afd6a |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
#
# Copyright 2010 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2... | nearlyfreeapps/python-googleadwords | tests/adspygoogle/adwords/bulk_mutate_job_service_unittest.py | Python | apache-2.0 | 8,918 | [
"VisIt"
] | 019437651f5b01a2cb49e68780fecacb4ec3adce74147d3d98f6b3fb14e4b3d1 |
# copyright 2003-2013 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of logilab-astng.
#
# logilab-astng is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as publis... | yorvic/.vim | bundle/python-mode/pylibs/pylama/checkers/pylint/logilab/astng/rebuilder.py | Python | gpl-3.0 | 36,633 | [
"VisIt"
] | 672cbddeff303a13dfc7235cae46b1b84eb70122f9aac58006129cd87c10beb9 |
# -*- coding: utf-8 -*-
"""
Created on Sat Aug 26 17:54:12 2017
@author: Eliot
skimage_segmentation.py
"""
import os
from skimage import color, util, filters, io, morphology, segmentation, measure, feature
import cv2
import numpy as np
import matplotlib.pylab as plt
thisfilepath = os.path.dirname(__file__)
loaddirp... | EliotBryant/ShadDetector | shadDetector_testing/Gradient Based Methods/skimage_segmentation.py | Python | gpl-3.0 | 4,924 | [
"Gaussian"
] | c7ccb074d00472bfd1c1edf9c6707665d41941a4e6e37e370f53c66c1edcd7ca |
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/model/arima.py | Python | apache-2.0 | 7,152 | [
"ADF"
] | f898c800219545723bb8093c4087bb821f5bd595326da5d0c7a45e33ac9e994d |
"""Module managing errors."""
import logging
import os
import re
import sys
import numpy as np
import scooby
import pyvista
from pyvista import _vtk
import contextlib
import collections
def set_error_output_file(filename):
"""Set a file to write out the VTK errors."""
filename = os.path.abspath(os.path.ex... | akaszynski/vtkInterface | pyvista/utilities/errors.py | Python | mit | 10,267 | [
"VTK"
] | 5d0cbdd077ccb2139f5af19aa69eac7db17182b6e41c0b81724829d7c8cf56b9 |
# -*- coding: utf-8 -*-
"""
* Copyright (C) 2010-2014 Loïc BLOT, CNRS <http://www.unix-experience.fr/>
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (a... | nerzhul/Z-Eye | service/WebApp/Z_Eye/InterfaceManager/__init__.py | Python | gpl-2.0 | 31,485 | [
"VisIt"
] | e6b542afe6bc3f93933b0fd1054031b72844e7ac55798efa21939a1e031f626b |
"""
It needs as input the final folder of bcbio
python sv-report.py --run report /path/to/final/bcbio
12% chances to work :)
"""
import os
import os.path as op
import yaml
import glob
from argparse import ArgumentParser
from collections import Counter, defaultdict
import pybedtools
from bcbio.distributed.transactio... | lpantano/eggs | svreport/sv-report.py | Python | gpl-2.0 | 3,843 | [
"Galaxy"
] | b6d5102c617d23003d29656756b50984a046dbd91e0db702d6b41770b026ff28 |
# -*- coding: utf-8 -*-
# Part of the psychopy.iohub library.
# Copyright (C) 2012-2016 iSolver Software Solutions
# Distributed under the terms of the GNU General Public License (GPL).
"""iohub wintab util objects / functions for stylus, position traces,
and validation process psychopy graphics.
"""
from __future__ im... | isolver/OpenHandWrite | distribution/getwrite/wintabtest/wintabgraphics.py | Python | gpl-3.0 | 25,925 | [
"Gaussian"
] | 42467077ed34a1ce891a6bf52c5c6a4ebb28791e0744e095b9f93c772c05b845 |
"""
=======================================================
Filter fastq files based on reads unmapped in bam file
=======================================================
:Author: Nick Ilott
:Release: $Id$
:Date: |today|
:Tags: Python
"""
# load modules
from ruffus import *
import CGAT.Experiment as E
import loggin... | CGATOxford/proj029 | Proj029Pipelines/pipeline_fastqfilter.py | Python | bsd-3-clause | 2,937 | [
"pysam"
] | 6857e0aa45a1bc89bdd0dc14b3d6d89f0a0e5873820f6dec0a0e65056a1ab5b0 |
########################################################################
# $HeadURL $
# File: ProcessPoolTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/02/13 07:55:31
########################################################################
""" :mod: ProcessPoolTests
=======================
.... | coberger/DIRAC | Core/Utilities/test/ProcessPoolTests.py | Python | gpl-3.0 | 12,777 | [
"DIRAC"
] | 9997ec42969001875eb9a91c0ffd09d26d1480202af0f1018b3eb8d2eefb0b7b |
from __future__ import division
from builtins import zip
import os.path
import tempfile
import shutil
import neo.io
import numpy as np
from pype9.cmd import simulate
from pype9.utils.units import parse_units
from pype9.utils.arguments import CATALOG_PREFIX
import ninemlcatalog
import quantities as pq
from pype9.simulat... | CNS-OIST/PyPe9 | test/unittests/test_cmds/test_simulate.py | Python | mit | 10,784 | [
"NEURON"
] | 79e12441cd32585f881ceae8872597e56b604da7507492a13ef276114390b2f8 |
# --------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU... | paulojamorim/invesalius3 | invesalius/data/converters.py | Python | gpl-2.0 | 6,144 | [
"VTK"
] | e66ebcc02ceb20ada730882971eecda774ba31826c749314b6bc6c61ed98c849 |
r"""Solve Poisson's equation on a sphere using a mixed formulation
The Poisson equation is in strong form
.. math::
\nabla^2 u &= f \\
u(x, y=\pm 1) &= 0 \\
u(x=2\pi, y) &= u(x=0, y)
We solve using the mixed formulation
.. math::
g - \nabla(u) &= 0 \\
\nabla \cdot g &= f \\
u(x, y=\pm 1) &... | spectralDNS/shenfun | demo/MixedPoissonSphere.py | Python | bsd-2-clause | 2,621 | [
"Mayavi"
] | 51019646c328e1bd43f8e1766c2561ab86fbbb73ac27522142495fc8ceac098e |
"""
Universe configuration builder.
"""
import sys, os
import logging, logging.config
from optparse import OptionParser
import ConfigParser
from galaxy.util import string_as_bool
from galaxy import eggs
import pkg_resources
log = logging.getLogger( __name__ )
def resolve_path( path, root ):
"""If 'path' is rela... | volpino/Yeps-EURAC | lib/galaxy/config.py | Python | mit | 12,546 | [
"Galaxy"
] | 265670c354d21e36846879db4b79564c000c1d988b874627ae255b9eb869bccc |
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import absolute_import
import string
import os
import copy
import sys
import pandas as pds
import numpy as np
from . import _custom
from . import _files
from . import _orbits
from . import _meta
from . import utils
from pysat import data_di... | aburrell/pysat | pysat/_instrument.py | Python | bsd-3-clause | 56,546 | [
"NetCDF"
] | 46bdca0dd68c99237a1cfc2f57bbc5a448a1fb0ea6dc7da283dff9c014dc151c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Public Domain
"""
CairoSVG - A Simple SVG Converter for Cairo
===========================================
CairoSVG is a SVG converter based on Cairo. It can export SVG files to PDF,
PostScript and PNG files.
For further information, please visit the `CairoSVG Website... | tgaillar/CairoSVG | setup.py | Python | lgpl-3.0 | 1,955 | [
"VisIt"
] | 6d2966c6cf8d08a03a830e143f37857dc4987c01444bb1959b6d41c90db9aab3 |
"""
Helper functions which obtain forces and energies
corresponding to atoms in structures. These functions automatically
cast atoms into their respective atomic environments.
"""
import numpy as np
import multiprocessing as mp
from typing import Tuple, List, Union
from flare.env import AtomicEnvironment
from flare.gp... | mir-group/flare | flare/predict.py | Python | mit | 19,367 | [
"ASE",
"Gaussian"
] | bdd83539eec63e4d5c7662be6595c716ad86575aba04847141953d51decc66d7 |
from numpy import zeros, array, eye
from numpy.random import multivariate_normal, uniform, random_integers
from sklearn.covariance import GraphLasso
import sklearn as skl
import matplotlib.pyplot as plt
from neighbor_select import NeighborSelect
from solver import SklearnCDSolver, ActiveSetCDSolver, ProximalGradient... | nicococo/AdaScreen | scripts/test_neighorhood_selection.py | Python | mit | 2,431 | [
"Gaussian"
] | 2fd541d6077372f0053ee6c0426077f51be2b6a96d6c92e9797998d6dd19d5a9 |
def start(forceOptimizer, debug=False):
if debug:
print ""
print "============="
print "Initial Phase"
print "============="
print ""
# the main group is the only group on the highest level, so the queue starts with her
forceOptimizer.groups = sorted(forceOptimize... | daringer/schemmaker | src/force_optimizer/initial_step.py | Python | apache-2.0 | 45,727 | [
"VisIt"
] | 299b57baf25ae632735dfbc56b5249235262a918c222d19ad6bae5d5174d6ea2 |
# -*- coding: utf-8 -*-
#
desc = 'Noise with a horizontal color bar'
phash = '5f5ca33da3816983'
def plot():
from matplotlib import pyplot as pp
import numpy as np
# Make plot with horizontal colorbar
fig = pp.figure()
ax = fig.add_subplot(111)
np.random.seed(123)
data = np.clip(np.random... | dougnd/matplotlib2tikz | test/testfunctions/noise2.py | Python | mit | 628 | [
"Gaussian"
] | ac825d2abb7df46a49f0bf448d835810205bff816878bf2ebdb3cbac8f35657e |
from __future__ import division
import numpy as np
'''
This file contains implementation of various activation functions.
'''
#Random seed for consistency in results.
np.random.seed(32)
def sigmoid(tensor):
'''
Sigmoid transfer.
:param tensor: numpy array
:return: numpy array of same shape, where eac... | prateekbhat91/Neural-Network | neuralnetwork/activation_functions.py | Python | bsd-3-clause | 1,854 | [
"Gaussian"
] | 68f26a81938fa1f93bc17e90f41620c6a4582dbb6f888ea4e385e69ab30e2639 |
# lots to do:
# __ native drawLines
# __ add native drawCurve method
# __ native rectangle/round rect method
# __ native drawEllipse
# __ native drawArc
# __ drawImage support (work on Pyart side of things)
from __future__ import print_function
import pyart
from rdkit.sping.pid import *
from rdkit.sping... | soerendip42/rdkit | rdkit/sping/Pyart/pidPyart.py | Python | bsd-3-clause | 9,314 | [
"RDKit"
] | 6c7f8e39d4caa30f19c65cab1483c7a705e8e259e12cf1dec02df3495ea14444 |
"""
Computes putative binding pockets on protein.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2017, Stanford University"
__license__ = "GPL"
import os
import tempfile
import numpy as np
im... | bowenliu16/deepchem | deepchem/dock/binding_pocket.py | Python | gpl-3.0 | 11,449 | [
"RDKit"
] | 9126bed4ec105a92c7022a22875d1469e6e3c21c889a3c9bf65014b7c4439075 |
import unittest
from catkit import Gratoms
from catkit.gen.utils import to_gratoms
from ase.constraints import FixAtoms
from ase.build import molecule
import networkx as nx
class TestGratoms(unittest.TestCase):
"""Test features of the gratoms module."""
def test_edge_addition(self):
"""Test that edge... | jboes/CatKit | catkit/tests/test_gratoms.py | Python | gpl-3.0 | 1,432 | [
"ASE"
] | 9052d3a519e580da40b50b70ed1682e095495aa43bd328c61f8938da17956982 |
# Attribute basis to MRL - (do not individually apply to MTP)
# http://www.music.mcgill.ca/~jason/mumt621/papers5/fujishima_1999.pdf ?
# https://www.jstor.org/stable/pdf/40285717.pdf
# Zicheng (Brian) Gao
from MusicRoll import *
import TensionModule
import PPMBasis
import numpy as np
import pickle
import pprint
fro... | ichaelm/MusicPrediction | src/midibasis.py | Python | mit | 9,495 | [
"Brian"
] | fcd3b042ea18dcc223255215c05e748c0d9fe09e7e8046c550b9175473c8400a |
#!/usr/bin/python
"""
" @section DESCRIPTION
" Functions for generating various stimuli
"""
import numpy as np
from scipy.special import erf
from scipy.integrate import cumtrapz
def create_step_current_sequence(params):
""" Generates a step current sequence
Args:
sim_time: total simulation time (ms)... | JohanWesto/receptive-field-models | simulation/stimulus_generator.py | Python | mit | 9,656 | [
"Gaussian"
] | 1b8450c3f89ca0a9a3ccfdae7baafe8f99b6f264e9156e3cd0360bddb9160a43 |
# TODO: By PySCF-1.5 release
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.... | gkc1000/pyscf | pyscf/tools/Molpro2Pyscf/example_Pd_atom.py | Python | apache-2.0 | 5,097 | [
"Molpro",
"PySCF"
] | cbd483940cc1fdefd3807c386e784bbddff7effe1a24bbe1e7394e05f2c29119 |
import numpy as np
import scipy.sparse
import os
import sys
import emcee
import copy
from astropy.cosmology import Planck15
from .class_utils import *
from .lensing import *
from .utils import *
from .calc_likelihood import calc_vis_lnlike
arcsec2rad = np.pi/180/3600
def LensModelMCMC(data,lens,source,
... | jspilker/visilens | visilens/LensModelMCMC.py | Python | mit | 19,225 | [
"Gaussian"
] | e8797edfc4712ef142987289f617d763a8e7242ab7790b2faad5e97188be303a |
"""The suite of window functions."""
from __future__ import division, print_function, absolute_import
import numpy as np
from scipy import special, linalg
from scipy.fftpack import fft
__all__ = ['boxcar', 'triang', 'parzen', 'bohman', 'blackman', 'nuttall',
'blackmanharris', 'flattop', 'bartlett', 'hannin... | sargas/scipy | scipy/signal/windows.py | Python | bsd-3-clause | 44,546 | [
"Gaussian"
] | bcff2623493f8c3b020b3b7a1e6c22b9bcabebf8b6686a3fcc19edbf66177e81 |
#!/usr/bin/python3
# Usage example:
# python captions.py --videoid='<video_id>' --name='<name>' --file='<file>' --language='<language>' --action='action'
import httplib2, os, sys, re, datetime
from pprint import pprint
from googleapiclient.discovery import build_from_document
from googleapiclient.errors import HttpE... | danielhollas/AmaraUpload | api/youtube_oauth.py | Python | mit | 20,326 | [
"VisIt"
] | 9affec3fde25bd9eac631bbd38c251b2d1768902ce690e17fd0d816c2463e69e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | qytz/qytz.github.io | conf.py | Python | cc0-1.0 | 47,282 | [
"VisIt"
] | b8f65208e95b43f6f54e32ec0b13f5ef8e3ce1ca6693aa0659a2bd36e60d623f |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/lb_poiseuille.py | Python | gpl-3.0 | 4,895 | [
"ESPResSo"
] | d6fba8b93ca732cebcf79b46c702d025a49c0fc3a8ed0b86346e8da9bb329c97 |
# -*- coding: utf-8 -*-
#
# mpitest_issue_578_sp.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | SepehrMN/nest-simulator | pynest/nest/tests/test_sp/mpitest_issue_578_sp.py | Python | gpl-2.0 | 3,195 | [
"Gaussian"
] | e0963d0fd0cd1ee628029dcffdcc4693023a5a8d6da6a91889c560fdbf4f8b2f |
#!/usr/bin/python
#
# This program is called mconvert2gpx.py. It find the
# files that match *TES and converts them to
# gpx and kmz files
#
# Import modules
#
# 2015 Aug 13 Frank Monaldo Add *CSV files from Columbus v990 receiver
import glob
import os
#
# Find TES and CSV files
inputfiles = glob.glob('*.TES') + gl... | fmonaldo/gpssoftware | mconvert2gpx.py | Python | cc0-1.0 | 445 | [
"COLUMBUS"
] | ad921de49b8b36b1a48fcd8269b8dac95a5abb4dda493b7650d218c87c4e114a |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/examples/friesian/two_tower/train_2tower.py | Python | apache-2.0 | 11,763 | [
"ORCA"
] | 629f66db7b9dd313b11f9940196169cbe3095e37415070764758c4aafea91ba4 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import requests
import logging
import time
import ConfigParser
import os
import base64
import re
logger = logging.getLogger('data')
USER_AGENT = "Andrew Head (for academic research) <andrewhead@eecs.berekeley.edu>"
default_reque... | andrewhead/Package-Qualifiers | fetch/api.py | Python | mit | 3,957 | [
"VisIt"
] | c43a4a5313febe4a2a60a14843f583f9655dbd5cc9bf2d5da25a188bf57c977d |
#! /usr/bin/env python
# ==========================================================================
# This script generates the TS distribution for a particular model based
# on Monte-Carlo simulations.
#
# Copyright (C) 2011-2013 Jurgen Knodlseder
#
# This program is free software: you can redistribute it and/or modif... | cdeil/ctools | scripts/cstsdist.py | Python | gpl-3.0 | 14,295 | [
"Gaussian"
] | f6602f81e0943db22f87694f968e8bea75ce6cdd24af0acf5b9a9fe6a56407c9 |
#!/usr/bin/env python
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published... | mardom/GalSim | examples/input/make_default_input.py | Python | gpl-3.0 | 5,442 | [
"Galaxy",
"Gaussian"
] | 880cef3694f101f203887bb5b42480d57830801474b8bcff9562a8a8fd04ef92 |
'''
=========================================
Inference for Non-Linear Gaussian Systems
=========================================
This module contains "Square Root" implementations to the Unscented Kalman
Filter. Square Root implementations typically propagate the mean and Cholesky
factorization of the covariance mat... | nmayorov/pykalman | pykalman/sqrt/unscented.py | Python | bsd-3-clause | 30,009 | [
"Gaussian"
] | 585e8576635c7822c5157def7ad09b8fa8c599cb880e4bc05a6a48cf5b528b8f |
import copy
import numpy
import sys
import theano
import theano.tensor as T
from theano.sandbox.rng_mrg import MRG_RandomStreams
from grbm import GBRBM
from linear_regression import LinearRegression
from mlp import HiddenLayer
from rbm import RBM
class DBN(object):
"""
Deep Belief Network
A deep belief ... | gdl-civestav-localization/cinvestav_location_fingerprinting | models/classification/deep_models/dbn.py | Python | gpl-3.0 | 9,358 | [
"Gaussian"
] | 8c8a2af5ed60d2fc3fb4eeb75ebf267a4f51ec15bb30d3fab976fcbac2dc7131 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
The initial version of this module was based on a similar implementation
present in FireWorks (https://pypi.python.org/pypi/FireWorks).
Work done by D. Waroquiers, A. Jain, and M. Kocher.
The main differenc... | migueldiascosta/pymatgen | pymatgen/io/abinit/qadapters.py | Python | mit | 71,607 | [
"ABINIT",
"pymatgen"
] | f4ed60c481938f80dd96674c1c1e31961dcca645ab340997aec39cf157707f10 |
import os
import time
import sys
from unittest import skip
from selenium import webdriver
from selenium.webdriver.firefox.firefox_binary import FirefoxBinary
from selenium.webdriver.common.keys import Keys
from selenium.common.exceptions import WebDriverException
from django.test import LiveServerTestCase
from djang... | chiara-paci/costruttoridimondi | costruttoridimondi/functional_tests/base.py | Python | gpl-3.0 | 7,259 | [
"VisIt"
] | 5588b0e71ead56898b480bd3e2d6d9aca1235bdb7ad2fbcfe4aaa8fc1ef0d186 |
__author__ = 'noe'
import numpy as np
from bhmm.hmm.generic_hmm import HMM
from bhmm.hmm.generic_sampled_hmm import SampledHMM
from bhmm.output_models.discrete import DiscreteOutputModel
from bhmm.util import config
from bhmm.util.statistics import confidence_interval_arr
class DiscreteHMM(HMM, DiscreteOutputModel):... | marscher/bhmm | bhmm/hmm/discrete_hmm.py | Python | lgpl-3.0 | 2,678 | [
"Gaussian"
] | 78b584b149572a86e5483d08451b03472863b4c0dd0cd9002bb1c1f1c1745f7c |
"""
Created on April 25 2020
@author: Pedram Tavadze
"""
import os
import numpy as np
from .xml_output import parse_vasprun
from .incar import VaspInput
from ..codes import CodeOutput
from ...core import Structure
from ...visual import DensityOfStates
from ...crystal.kpoints import KPoints
class VaspXML(CodeOutput):
... | MaterialsDiscovery/PyChemia | pychemia/code/vasp/vaspxml.py | Python | mit | 19,297 | [
"CRYSTAL",
"VASP"
] | 8dc7c9e9f763d1f5b1ff74c9e73d5d92c1bc34729f0e6347ab144f3798f41921 |
import numpy as np
import itertools
from sklearn import mixture, metrics
from sklearn.cluster import DBSCAN
from scipy import linalg
from scipy.spatial import distance
import pylab as pl
import matplotlib as mpl
# ToDo: look for better initial clustering, test with real data
#Generating random sample, in two clu... | smorante/continuous-goal-directed-actions | simulated-CGDA/generalization/generalization_old_visual.py | Python | mit | 4,306 | [
"Gaussian"
] | 6478fd21c2b9c777347611cd924988707a1f686e9515f60baebe693d4b05c47d |
#!/usr/bin/python
# -------------------------------------------------------------------
# Import statements
# -------------------------------------------------------------------
import sys
import os
import math
import re
from decimal import *
from operator import *
from astropy.io import fits
from sqlalchemy.orm impo... | albireox/marvin | python/marvin/db/models/DataModelClasses.py | Python | bsd-3-clause | 28,307 | [
"Galaxy"
] | 8299ee7060e02ac9a9983ddd459d789e3a84590303de31006e4e3741d5d65e14 |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
import wx
from library_item import LibraryItem
from network.neuron import Neuron
class Ne... | JaneliaSciComp/Neuroptikon | Source/library/neuron_class.py | Python | bsd-3-clause | 2,528 | [
"NEURON"
] | f27c8d7df543bd4b5a8027757ef86821ed253f990bb2926887007996ec23e9d0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010 Brian G. Matherly
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option... | arunkgupta/gramps | gramps/gui/widgets/progressdialog.py | Python | gpl-2.0 | 19,477 | [
"Brian"
] | 5f2f0c5fa105f4a29ba87c23b7bf89f851671462649d59e59d55ed0196dfbbf8 |
#!/usr/bin/env python2
# Make.py tool for managing packages and their auxiliary libs,
# auto-editing machine Makefiles, and building LAMMPS
# Syntax: Make.py -h (for help)
# Notes: needs python 2.7 (not Python 3)
import sys,os,commands,re,copy
# switch abbrevs
# switch classes = created class for each switch
# lib... | gurkih/lammps | src/Make.py | Python | gpl-2.0 | 70,853 | [
"LAMMPS"
] | b5068e9bbe975040f3ecf8e9165f47ce0fabea52ffaeab67c8809c31e4597c54 |
"""Generate html report from MNE database
"""
# Authors: Alex Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Mainak Jas <mainak@neuro.hut.fi>
# Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import os
import os.path as op
import fnmatch
import re
import codecs
import time
from... | aestrivex/mne-python | mne/report.py | Python | bsd-3-clause | 60,627 | [
"Mayavi"
] | 09959a20e9c63feb5c8e53088f74b161b29e3278ca2edddf8edc214956ba68b3 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | Huyuwei/tvm | python/tvm/relay/_parser.py | Python | apache-2.0 | 27,885 | [
"VisIt"
] | 87791c45cc65d767b7e4a9154ca486f54117b2f8dce6507bde01e4bfc27e9327 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
from shutil import which
import requests
from pymatgen.ext.cod import COD
try:
website_is_up = requests.get("https://www.crystallography.net").status_code == 200
except:
website_is_u... | materialsproject/pymatgen | pymatgen/ext/tests/test_cod.py | Python | mit | 1,234 | [
"pymatgen"
] | 728aa08073ab99265ba592f1d2bb4aac4e89e9d023b5c0f294735403d7277cf4 |
# -*- coding=utf-8 -*-
"""
MDT, a module for protein structure analysis.
Copyright 1989-2021 Andrej Sali.
MDT is free software: you can redistribute it and/or modify
it under the terms of version 2 of the GNU General Public License
as published by the Free Software Foundation.
This program is dist... | salilab/mdt | pyext/mdt/__init__.py | Python | gpl-2.0 | 60,664 | [
"CHARMM",
"Gaussian"
] | adc03f7c88f5722c19e5ec54c84b84aec534b0bf2007652a7feddbc165d0381c |
# -*- coding: utf-8 -*-
#
# testiaf.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (... | tillschumann/nest-simulator | pynest/examples/testiaf.py | Python | gpl-2.0 | 3,991 | [
"NEURON"
] | d41d919616f98e560d2a97c130f23ab14dae8bfece943437ac36487a7dcc9cbe |
# 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... | jjas0nn/solvem | tensorflow/lib/python2.7/site-packages/tensorflow/contrib/learn/python/learn/estimators/__init__.py | Python | mit | 11,510 | [
"Gaussian"
] | 25b4611cefa8af80214c66f58a7b5a636988fd1eae8995c923fdc71c3a17aacd |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010-2017 GEM Foundation
#
# The OQ-CATK (Lite) 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 of the License, or (at ... | GEMScienceTools/CatalogueTool-Lite | OQCatk/Exploration.py | Python | agpl-3.0 | 12,041 | [
"Gaussian"
] | 2ef1b8e16ffa7b1c2014d16d5ab99d688275d5ca8f96a59e57758b8158479e9b |
""" Failover Transfer
The failover transfer client exposes the following methods:
- transferAndRegisterFile()
- transferAndRegisterFileFailover()
Initially these methods were developed inside workflow modules but
have evolved to a generic 'transfer file with failover' client.
The transferAndR... | Andrew-McNab-UK/DIRAC | DataManagementSystem/Client/FailoverTransfer.py | Python | gpl-3.0 | 11,448 | [
"DIRAC"
] | 9d08de36d33c11f2ee9158a319194a634a81d575ff06ee3043aacd7b3724629a |
from datetime import datetime
from django.http import HttpResponse
from hippocampus import HIPPOCAMPUS_COOKIE_NAME
from hippocampus.models import Visit
def log_exit(request):
cookie_id = request.COOKIES.get(HIPPOCAMPUS_COOKIE_NAME)
if cookie_id is not None:
try:
last_visit = Visit.objects.... | marinho/hippocampus | hippocampus/views.py | Python | bsd-3-clause | 619 | [
"VisIt"
] | 46acff07dd07464456a55f0f3c690b8d88638bb8102e911880b3fe9bf1b88d3a |
#! /usr/bin/python
"""
Varmint Pest - Attempts to frighten away varmints such as raccoons
Created 7/04/17 by Greg Griffes
"""
import time, sys, os
import logging
from automat import MethodicalMachine
##import RPi.GPIO as GPIO
##import pigpio # http://abyz.co.uk/rpi/pigpio/python.html
##import spidev
##import Adafru... | griffegg/varmintpest | varmintpest.py | Python | mit | 8,715 | [
"BLAST"
] | 8935db6c4c5d76e35b90eec889c94e14e5587940c3ba88b19b30a9ef73055fdd |
# ----------------------------------------------------------------------------
# Copyright (c) 2015, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# --------------------------------------------------... | josenavas/deblur | deblur/workflow.py | Python | bsd-3-clause | 34,775 | [
"BLAST",
"scikit-bio"
] | 045d654c42552dfc6fedfcb207f1ce1b431ddc4aef4043791a2fdb5c092c31df |
#!/usr/bin/env python
""" MultiQC module to parse output from Samblaster """
from __future__ import print_function
import os
from collections import OrderedDict
import logging
import re
from multiqc.plots import bargraph
from multiqc.modules.base_module import BaseMultiqcModule
# Initialise the logger
log = logging.... | ewels/MultiQC | multiqc/modules/samblaster/samblaster.py | Python | gpl-3.0 | 4,262 | [
"BWA"
] | c80c5029a0628c67bdc8c60692e6eeef65ecda840695bfb81d8cb5ef72df6f75 |
# (C) 2013, Markus Wildi, markus.wildi@bluewin.ch
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
#
# This program is distr... | zguangyu/rts2 | scripts/rts2saf/unittest/rts2_environment.py | Python | gpl-2.0 | 8,243 | [
"VisIt"
] | a5fc5dc66117115930397593e3d49b877b64f71d9e2b42295fc22017e1e4fee1 |
#!/usr/bin/env python
"""
killMS, a package for calibration in radio interferometry.
Copyright (C) 2013-2017 Cyril Tasse, l'Observatoire de Paris,
SKA South Africa, Rhodes University
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published ... | saopicc/killMS | killMS/SmoothSols.py | Python | gpl-2.0 | 28,755 | [
"Gaussian"
] | ef81d54216ced000dc9dad51ac4cf4278067c2b2d2c3c2afad00ca1175af1fc7 |
#lab04_hog.py
from scipy.ndimage import filters
from PIL import Image
from pylab import *
def Gausian_response(img,sigma=1):
""" Compute Gaussian response function
for each pixel in a graylevel image. """
# Gausian response
img_sigma = zeros(img.shape)
filters.gaussian_filter(img, (sigma,s... | wasit7/cs634 | 2016/lab4_matching.py | Python | bsd-2-clause | 1,841 | [
"Gaussian"
] | b42448491a77c7cc6180982ecce328b00921d2b024d27ccfaece123d765083d3 |
r"""
==================================
Constants (:mod:`scipy.constants`)
==================================
.. currentmodule:: scipy.constants
Physical and mathematical constants and units.
Mathematical constants
======================
================ ===========================================================... | lhilt/scipy | scipy/constants/__init__.py | Python | bsd-3-clause | 12,194 | [
"Avogadro"
] | 652aec33804958c190973849e3f361b813ec785b1b55bc0d61169dfd1b55a83a |
from datetime import datetime
from pytz import timezone
WEDDING_DATE = datetime(2015, 04, 10, 14, 0, tzinfo=timezone('US/Central'))
ENGAGEMENT_DATE = 'Sunday, May 11, 2014'
ABOUT_TEXT = {
'about_groom': 'Kyle grew up in Wisconsin until he was 19 years of age. He then moved to San Francisco, California to ' +
... | rockmans/KyleAndEmily | kyleandemily/site_text.py | Python | mit | 3,563 | [
"exciting"
] | 06d249e887ab91520612ec8aa78385d7cc7d2498d8f41bad50cad713d745439f |
from _collections import OrderedDict
import numpy as np
import theano
import theano.tensor as TT
from . import neuron
from .learned_termination import LearnedTermination
class hPESTermination(LearnedTermination):
#theta_tau = 0.02
# The scaling factor is to increase
# the influence of unsupervised lea... | ctn-waterloo/nengo_theano | nengo_theano/hPES_termination.py | Python | mit | 5,171 | [
"NEURON"
] | 6fe77d2949303594677a1627786a934ab0a8e59269fd3aa85fc6c2bdc635162a |
# coding=utf-8
from datetime import datetime
from time import sleep
import plotly.graph_objs as go
import plotly.plotly as py
import ms5637
__author__ = 'Moe'
__copyright__ = 'Copyright 2017 Moe'
__license__ = 'MIT'
__version__ = '0.0.2'
# Bari sensor of MS5637
sensor = ms5637.Chip()
YUPPER = 40
YLOWER = -40
ZER... | wadda/Bari | bari_plotter.py | Python | mit | 5,105 | [
"MOE"
] | 349e6fbe75a8f6ca9d5b9d72d4d213dd35ed9483f23b25100c7f164a26319f79 |
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
# Copyright (C) 2012,2013
# 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 softw... | fedepad/espressopp | src/interaction/Tabulated.py | Python | gpl-3.0 | 11,704 | [
"ESPResSo"
] | afc77e7c109c84e4852d960d2c7e599544529ff933a4e598bd95c9a0703723f1 |
from functools import partial
from gym.spaces import Box, Dict, Tuple
import numpy as np
from scipy.stats import beta, norm
import tree # pip install dm_tree
import unittest
from ray.rllib.models.jax.jax_action_dist import JAXCategorical
from ray.rllib.models.tf.tf_action_dist import (
Beta,
Categorical,
... | ray-project/ray | rllib/models/tests/test_distributions.py | Python | apache-2.0 | 27,352 | [
"Gaussian"
] | c508df630cb576c3b5bb008d38186e3125ceba734a6ff926449ce99b0ddc2194 |
from dateutil.relativedelta import relativedelta
from edc_constants.constants import SCREENED
from edc_registration.models import RegisteredSubject
from edc_identifier.models import SubjectIdentifier
from edc_constants.constants import FAILED_ELIGIBILITY, OFF_STUDY, SCHEDULED
from edc_meta_data.models import Requisitio... | botswana-harvard/tshilo-dikotla | td_infant/tests/test_infant_birth_membership.py | Python | gpl-2.0 | 2,538 | [
"VisIt"
] | 4b81128cf85a672ce557be2e0e1feb4b362e9f13953b6efe1bd8b11590f605df |
#!/usr/bin/python3
#
# Copyright (c) 2012 Mikkel Schubert <MikkelSch@gmail.com>
#
# 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
... | MikkelSchubert/paleomix | paleomix/pipelines/bam/makefile.py | Python | mit | 22,702 | [
"BWA"
] | 374dd41ac34b843f383c0145892fa4b7821f2ef2567fc49a6b0ff613c64ee7f3 |
from django.contrib import admin
from models import (
Item, Buy, UserProfile, Occasion, Visit, MagicLink, MagicLinkClick
)
class ItemAdmin(admin.ModelAdmin):
list_filter = ('multi_item', 'already_given', 'surprise', 'user',)
list_display = ('name', 'multi_item', 'already_given',)
class Meta:
... | honza/wishlist-app | web/admin.py | Python | bsd-2-clause | 1,246 | [
"VisIt"
] | 8df9fa631951d6f2c8c6da1e58e7004a7f33127461b075c73b136f1f81e60735 |
"""
Testing for the forest module (sklearn.ensemble.forest).
"""
# Authors: Gilles Louppe, Brian Holt, Andreas Mueller
# License: BSD 3 clause
from collections import defaultdict
import numpy as np
from numpy.testing import assert_array_equal
from numpy.testing import assert_array_almost_equal
from numpy.testing imp... | loli/sklearn-ensembletrees | sklearn/ensemble/tests/test_forest.py | Python | bsd-3-clause | 19,091 | [
"Brian"
] | dbaafe458c3d88a565d42d52b25b03c9c0e013e1608e08ff468174bf7574734b |
"""
TherMOF command line interface.
"""
import os
import argparse
from thermof import Simulation
from thermof import Parameters
def main():
parser = argparse.ArgumentParser(
description="""
----------------------------------------------------------------------------
████████╗██╗ ██╗███████╗██████... | kbsezginel/tee_mof | thermof/cli/thermof_write.py | Python | mit | 3,588 | [
"LAMMPS"
] | 2714bb0ca38fc07ff96f35c965c59c6753eb10539a7577c02994b727bbe6c0bd |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Jul 22, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date__ = "Jul 22, 2012"
import unittest
impo... | rousseab/pymatgen | pymatgen/command_line/tests/test_enumlib_caller.py | Python | mit | 3,721 | [
"pymatgen"
] | 2bb69e0f98635b790016a6913ae6a1c6553ecc77b1374d05933a43903c4abe1e |
import PolyLibScan.Analysis.pymol_visualisation as pymol
import pathlib2 as pl
import mock
import numpy as np
import unittest as ut
local_path = pl.Path(__file__).absolute().parent
class TestPymolVis(ut.TestCase):
def __init__(self, *args, **kwargs):
super(TestPymolVis, self).__init__(*args, **kwargs)
... | luminescence/PolyLibScan | Analysis/tests/test_pymolvisualise.py | Python | mit | 1,015 | [
"PyMOL"
] | e15126eea11f7d3419545ec48af537d324a3633ae36d73c65149fe45192a19a6 |
'''
SYNBIOCHEM-DB (c) University of Manchester 2015
SYNBIOCHEM-DB is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
from sbcdb.enzyme_utils import EnzymeManager
class ReactionManager(object):
'''Class to implement a manag... | synbiochem/biochem4j | sbcdb/reaction_utils.py | Python | mit | 2,979 | [
"VisIt"
] | 3d1d8d3beb00cfd72e214644c239a4bccf855e8ada9d04fb69874cb0fc9fa659 |
#!/usr/bin/env python
#
# This example demonstrates the creation of multiple actors and the
# manipulation of their properties and transformations. It is a
# derivative of Cone.py, see that example for more information.
#
import vtk
import time
#
# Next we create an instance of vtkConeSource and set some of its
# pr... | arnaudgelas/VTK | Examples/Tutorial/Step4/Python/Cone4.py | Python | bsd-3-clause | 3,059 | [
"VTK"
] | 4851aa0553268aec383f7eab52bcc43bbd44af23599e887c9baad9df55269be5 |
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