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""" Metrics for Symmetric Diffeomorphic Registration """
from __future__ import print_function
import abc
import numpy as np
import scipy as sp
from scipy import gradient, ndimage
from dipy.utils.six import with_metaclass
from dipy.align import vector_fields as vfu
from dipy.align import sumsqdiff as ssd
from dipy.al... | StongeEtienne/dipy | dipy/align/metrics.py | Python | bsd-3-clause | 46,544 | [
"Gaussian"
] | 9646f1961ec0798fc22e447831947aa433031dfd99c34cddf04ce5fed0dfbb47 |
"""
End-to-end test for cohorted courseware. This uses both Studio and LMS.
"""
import json
from nose.plugins.attrib import attr
from studio.base_studio_test import ContainerBase
from common.test.acceptance.pages.studio.settings_group_configurations import GroupConfigurationsPage
from common.test.acceptance.pages.st... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/test_cohorted_courseware.py | Python | agpl-3.0 | 9,840 | [
"VisIt"
] | edc359fd67cea089b3c42b24fa9961909fbccd00c59e18712575a5d7a3282e00 |
#!/usr/bin/env python
"""
Loprop model implementation (J. Chem. Phys. 121, 4494 (2004))
"""
import os
import sys
import math
import numpy
from daltools import one, mol, dens, prop, lr, qr, sirifc
from daltools.util import full, blocked, subblocked, timing
#full.matrix.fmt = "%14.6f"
xtang = 0.5291772108
angtx = 1.0/xt... | fishstamp82/loprop-1 | loprop/loprop.py | Python | gpl-3.0 | 54,871 | [
"Dalton"
] | b81452e1660f4f3d701acb2b7900ab12b53f7e450239179da624782e1d42ab51 |
from ase import *
from hotbit import *
from pylab import *
atoms = Atoms('Au2',[(0,0,0),(2.2,0,0)])
atoms.center(vacuum=10)
traj = PickleTrajectory('dimer_curve.traj','w',atoms)
R = [2.2,2.4,2.54,2.8,3.0,3.2,3.4]
E = [-1.06,-2.08,-2.22,-1.99,-1.66,-1.31,-1.00]
class Calc:
def __init__(self):
pass
... | pekkosk/hotbit | examples/CH_parametrization/Au2.py | Python | gpl-2.0 | 914 | [
"ASE"
] | 1ce68245a42811b24cdd0f9b77e6aa407959e18fbcba663624ebcda052a1ee3d |
#!/usr/bin/env python
#
# LSST Data Management System
# Copyright 2008-2015 AURA/LSST.
#
# This product includes software developed by the
# LSST Project (http://www.lsst.org/).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published ... | yalsayyad/obs_decam | tests/getId.py | Python | gpl-3.0 | 2,055 | [
"VisIt"
] | 1fe926f1334116b08776f64e598126dcd2c72b06b7c57ed993466aead87e563d |
"""
Visualizations (:mod:`skbio.draw`)
==================================
.. currentmodule:: skbio.draw
This module provides functionality for visualization of data.
Distribution visualizations
---------------------------
Functions
^^^^^^^^^
.. autosummary::
:toctree: generated/
boxplots
grouped_distribu... | Achuth17/scikit-bio | skbio/draw/__init__.py | Python | bsd-3-clause | 864 | [
"scikit-bio"
] | fd2699ec440142bfe82db9a335a29a57e4c2dbc7ae0d7c54cf8cdbe965e6ed51 |
from copy import deepcopy
from warnings import warn
from itertools import chain
from ast import NodeTransformer
from six import iteritems
from .. import Reaction, Metabolite, Gene
from .delete import get_compiled_gene_reaction_rules
from ..core.Gene import ast2str
_renames = (
(".", "_DOT_"),
("(", "_LPAREN... | aebrahim/cobrapy | cobra/manipulation/modify.py | Python | lgpl-2.1 | 14,568 | [
"VisIt"
] | 6eae24cda223de1b1625afd6b0553ed21791380a65c2102b2fe3cdffab058f57 |
# Copyright 1999 by Jeffrey Chang. 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 module provides code to work with Medline.
Classes:
Record A dictionary ho... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Medline/__init__.py | Python | gpl-2.0 | 4,985 | [
"Biopython"
] | d4a6f4869a4a350c11aa6e724b23a67b6a6f0de177fb43f50f0544c9f9644226 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import platform
from matplotlib.font_manager import FontProperties
from matplotlib.ticker import FormatStrFormatter
"""
This module provides classes for plot... | tallakahath/pymatgen | pymatgen/analysis/pourbaix/plotter.py | Python | mit | 34,827 | [
"pymatgen"
] | 920511d1c2daa210a37465617ea621dc334ad5140e78252052ee7f6956ae7c1c |
""" Code that looks for mayavi contributions on sys.path or other
standard places, making it easy for users to add contributions to load
on startup.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2008, Prabhu Ramachandran
# License: BSD Style.
import sys
from os.path import isdir, exists, ... | liulion/mayavi | mayavi/preferences/contrib_finder.py | Python | bsd-3-clause | 3,216 | [
"Mayavi"
] | b77e6d3f5cdfc9213352420f5877cfd19f89b54fbc21554bba1e40676b9f8c8e |
#!/usr/bin/env python
import os, sys
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require( "SQLAlchemy >= 0.4" )
import time, ConfigParser, shutil
from datetime impor... | volpino/Yeps-EURAC | scripts/cleanup_datasets/cleanup_datasets.py | Python | mit | 25,034 | [
"Galaxy"
] | 1da98f211f9430267e867d99ee0439bd1c3973604c111e2c048b544c03aacc3a |
#
# Copyright (C) 2010-2020 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... | espressomd/espresso | testsuite/python/lb_vtk.py | Python | gpl-3.0 | 8,220 | [
"ESPResSo",
"VTK"
] | 6697c02435dc081fceed6d51f1e593eab9ef1a48c8fe0b5a48b288898d5d79c9 |
from django.core.management.base import BaseCommand
from django.conf import settings
from django.utils.timezone import now
from ...models import Replay
from twython import Twython
import os
import random
import praw
class Command(BaseCommand):
help = "Send out the most exciting replay of the day to Twitter."
... | rocket-league-replays/rocket-league-replays | rocket_league/apps/replays/management/commands/social_post.py | Python | gpl-3.0 | 2,215 | [
"exciting"
] | dc98fd383d09b7d597b1e06f5cfc5b6a7a1ce8d2ec1d988b774f0c95b6c434ca |
# -*- 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/topology/test_hoomdxml.py | Python | gpl-2.0 | 1,991 | [
"MDAnalysis"
] | 82f07a9562661eb7384c5cfa786c72e70490a56e7530e34e17bc97b377c54bf2 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | patpatpatpatpat/digestus | config/urls.py | Python | bsd-3-clause | 1,479 | [
"VisIt"
] | c294710045cc54c674ec648bc99ea5a171301a15f8b43eef061dc41b97e18241 |
#!/usr/bin/env python3
#
# Copyright (C) 2017, 2018 Jaguar Land Rover
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
# Authors: Shane Fagan - shane.fagan@collabora.co... | GENIVI/vehicle_signal_manager | tests.py | Python | mpl-2.0 | 25,241 | [
"Jaguar"
] | 90181fa61987f03de9f329028f438b8e2e2a63af8d06fec441e8385efe7a353a |
#! /usr/bin/env python
#
# Copyright (C) 2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD
import os
import zipfile
import logging
LOGGER = logging.getLogger(__name__)
import pandas as pd
import numpy as np
import skchem
from .base import Converter
from ... import standardizers
PATCHES = {
'820-75-7': ... | richlewis42/scikit-chem | skchem/data/converters/muller_ames.py | Python | bsd-3-clause | 3,856 | [
"RDKit"
] | c8e9cc3049a1d9da63bc4090148c71ee8cf54f83e6b40e3bc5901f3966612c7e |
from ase import *
from ase.lattice import bulk
from ase.dft.kpoints import monkhorst_pack
from gpaw import *
from gpaw.mpi import serial_comm
from gpaw.test import equal
from gpaw.xc.rpa import RPACorrelation
from gpaw.xc.fxc import FXCCorrelation
import numpy as np
a0 = 5.43
cell = bulk('Si', 'fcc', a=a0).get_cell()
... | robwarm/gpaw-symm | gpaw/test/ralda_energy_Si.py | Python | gpl-3.0 | 1,208 | [
"ASE",
"GPAW"
] | 45499a6c9eab81e01b6da8a58b5ab1433fc2995ab318138f189db825251773b9 |
"""
DISPERSAO_AVANCADO.PY
Material de apoio para a série de posts "Gráficos de dispersão complexos
no Python", no Programando Ciência.
* Autor: Alexandre 'Jaguar' Fioravante de Siqueira
* Contato: http://www.programandociencia.com/sobre/
* Material de apoio:
http://www.github.com/alexandrejaguar/programandocienci... | alexandrejaguar/programandociencia | 2016/0508-scatteradv/dispersao_avancado.py | Python | gpl-2.0 | 5,453 | [
"Jaguar"
] | 7a35324eee765114d8ed6b879a06bbd2f3db3cb44294f9be54cc41ac89f3ab14 |
# encoding: utf-8
"""colors.py - select how to color the atoms in the GUI."""
import gtk
from gettext import gettext as _
from ase.gui.widgets import pack, cancel_apply_ok, oops, help
import ase
from ase.data.colors import jmol_colors
import numpy as np
import colorsys
named_colors = ('Green', 'Yellow', 'Blue', 'Red... | askhl/ase | ase/gui/colors.py | Python | gpl-2.0 | 30,815 | [
"ASE",
"Jmol"
] | 522c46b17a642df1f9502c49b3e5ea7615ae668b93f177aa9904a8885429f97f |
import argparse
import pysam
from collections import Counter
from pomoxis.summary_from_stats import qscore
from pomoxis.stats_from_bam import stats_from_aligned_read
def get_errors(aln, ref_seq=None):
seq = aln.query_sequence
errors = {}
insertions = ''
pairs = aln.get_aligned_pairs(with_seq=True)
... | nanoporetech/pomoxis | pomoxis/common_errors_from_bam.py | Python | mpl-2.0 | 6,482 | [
"pysam"
] | 31f8af26d3c61dd8b65f8c2b902b04a189574573ec2bb7feba8557334703ad4e |
#!/usr/bin/env python
"""
Runs Ben's simulation.
usage: %prog [options]
-i, --input=i: Input genome (FASTA format)
-g, --genome=g: If built-in, the genome being used
-l, --read_len=l: Read length
-c, --avg_coverage=c: Average coverage
-e, --error_rate=e: Error rate (0-1)
-n, --num_sims=n: Number of ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/tools/ngs_simulation/ngs_simulation.py | Python | gpl-3.0 | 12,156 | [
"Galaxy"
] | 903641305a9457a6feafd080358c9393ba6f7b026ce2a304f303cbf017d26caf |
########################################################################
# $HeadURL$
# File : Watchdog.py
# Author: Stuart Paterson
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system resource consumption. ... | fibbo/DIRAC | WorkloadManagementSystem/JobWrapper/Watchdog.py | Python | gpl-3.0 | 34,697 | [
"DIRAC"
] | 0b71f86ec5450db69d2a6f08d6debde4395a320fca0c23f1c50a1c03812e619b |
# 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... | ijingo/incubator-singa | test/python/test_operation.py | Python | apache-2.0 | 11,386 | [
"Gaussian"
] | 0f4cf03e119ce7cae635d1155b1fde8451f3c46b167af0683c367465e804da54 |
# -*- coding: utf-8 -*-
import os
import glob
import inspect
import fnmatch
import datetime
from warnings import warn
import numpy as np
import matplotlib.pyplot as plt
from netCDF4 import Dataset as ncfile
import copy
import tempfile
from altimetry.tools.nctools import load_ncVar, load_ncVar_v2, nc a... | rdussurget/py-altimetry | altimetry/data/hydro.py | Python | lgpl-3.0 | 91,403 | [
"NetCDF"
] | c8bd7ba9152f732c180cef4cbe3b1208ff773c21094e80b2e5dfe6cea99594c7 |
#==========================================================================
#
# Copyright Insight Software Consortium
#
# 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... | stnava/ITK | Wrapping/Generators/Python/Tests/SpatialObjectTest.py | Python | apache-2.0 | 2,675 | [
"Gaussian"
] | 655e25ea2e680c46d74f766149625374510489491406a53423be047c6cc658ff |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# PCR-GLOBWB (PCRaster Global Water Balance) Global Hydrological Model
#
# Copyright (C) 2016, Ludovicus P. H. (Rens) van Beek, Edwin H. Sutanudjaja, Yoshihide Wada,
# Joyce H. C. Bosmans, Niels Drost, Inge E. M. de Graaf, Kor de Jong, Patricia Lopez Lopez,
# Stefanie Pes... | openstreams/wflow | wflow/pcrglobwb/landSurface.py | Python | gpl-3.0 | 106,368 | [
"NetCDF"
] | 199992e3f5106a1591794ae25d5e2f0cd671416821a522c3081957c70e000bb8 |
# -*- coding: utf-8 -*-
"""Release data for the IPython project."""
#-----------------------------------------------------------------------------
# Copyright (c) 2008, IPython Development Team.
# Copyright (c) 2001, Fernando Perez <fernando.perez@colorado.edu>
# Copyright (c) 2001, Janko Hauser <jhauser@zscout.de>... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/core/release.py | Python | lgpl-3.0 | 5,422 | [
"Brian"
] | 08da7187f78650c99c89703d38a46ab4de43d45fb1d4c91b9d241eff56e71d72 |
# Copyright 2021 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/distributions/mvn_diag_plus_low_rank_covariance.py | Python | apache-2.0 | 8,348 | [
"Gaussian"
] | 392a907488ad0a45a80dd870c06581cfa7a2f81f7e1d4443567c5f6e84896f9e |
# encoding: utf-8
from __future__ import unicode_literals
import mimetypes
import os
import re
from tempfile import NamedTemporaryFile
import requests
from twitter import TwitterError
TLDS = [
"ac", "ad", "ae", "af", "ag", "ai", "al", "am", "an", "ao", "aq", "ar",
"as", "at", "au", "aw", "ax", "az", "ba", "... | IKholopov/HackUPC2017 | hackupc/env/lib/python3.5/site-packages/twitter/twitter_utils.py | Python | apache-2.0 | 14,700 | [
"CASINO",
"MOE"
] | f7d04e676185e3a707ea2129cbc2b3f178b6692404e7510e7415ccf8e2f51611 |
""" Test the FilenamePlugin class"""
import unittest
from DIRAC.Resources.Catalog.ConditionPlugins.FilenamePlugin import FilenamePlugin
class TestfilenamePlugin(unittest.TestCase):
"""Test the FilenamePlugin class"""
def setUp(self):
self.lfns = ["/lhcb/lfn1", "/lhcb/anotherlfn", "/otherVo/name"]
... | DIRACGrid/DIRAC | src/DIRAC/Resources/Catalog/ConditionPlugins/test/Test_FilenamePlugin.py | Python | gpl-3.0 | 1,428 | [
"DIRAC"
] | 1a629c6f11289641a1d5783d2faadd2c4876ac9e9ec711127ae0fcc7e09abb9b |
#-*-coding:utf-8-*-
"""
Copyright (c) 2012 wong2 <wonderfuly@gmail.com>
Copyright (c) 2012 hupili <hpl1989@gmail.com>
Original Author:
Wong2 <wonderfuly@gmail.com>
Changes Statement:
Changes made by Pili Hu <hpl1989@gmail.com> on
Jan 10 2013:
Support captcha.
Permission is hereby granted, free of... | BigRocky/xiaohuangji | renren.py | Python | mit | 11,873 | [
"VisIt"
] | 1573638c38a8ff64727830960bdebcf658f4a7f7e92120160c6992fd023385c1 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
import pyro
import pyro.distributions as dist
from pyro.contrib.gp.likelihoods.likelihood import Likelihood
class Poisson(Likelihood):
"""
Implementation of Poisson likelihood, which is used for count data.
... | uber/pyro | pyro/contrib/gp/likelihoods/poisson.py | Python | apache-2.0 | 1,884 | [
"Gaussian"
] | 5c130a00cc22c50d705e8dd63334290b7f9febec39edec190dbf3bbce85371df |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawLoops(myscreen, loops, loopcolor):
nloop = 0
for lop in loops:
n = 0
N = len(lop)
first_point=ocl.Point(-1,-1,5)
previous=ocl.Point(-1,-1,5)
for p in lop:
if n==0: # don't dra... | aewallin/opencamlib | examples/python/cutter_shapes.py | Python | lgpl-2.1 | 5,396 | [
"VTK"
] | a5c9181a59f0c5d3ffdd29e242d3ca6c55b6ba9b0d7f248abb7ad667315c0a88 |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from .stationary import Stationary
from .psi_comp import PSICOMP_RBF, PSICOMP_RBF_GPU
from ...core import Param
from paramz.transformations import Logexp
class RBF(Stationary):
"""
... | avehtari/GPy | GPy/kern/src/rbf.py | Python | bsd-3-clause | 4,138 | [
"Gaussian"
] | da4ab5bfc343709f73640806767602d5510520456bcafcd71146d2d37e2100ff |
import analysis.event
import analysis.beamline
import analysis.pixel_detector
import analysis.hitfinding
import utils.cxiwriter
import simulation.ptycho
import ipc.mpi
import numpy as np
import os,sys
import time
import h5py
# Physical constants (from http://physics.nist.gov/)
h = 6.626070040e-34 # [J s]
c = np... | SPIhub/hummingbird | examples/ptychography/write2cxi.py | Python | bsd-2-clause | 5,705 | [
"Gaussian"
] | 2289342823136496158ce99b5b4139695dc1753f9ceedbf66d878ebbf42e1cde |
"""
Command Line Parameters for creating the Replication transformations Script
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DIRAC.ConfigurationSystem... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Utilities/ReplicationCLIParameters.py | Python | gpl-3.0 | 6,238 | [
"DIRAC"
] | 7e945bd48a336ad9b5f70b059e60d010eb305af41431c71c8c1644840d8e9599 |
# coding: utf-8
from __future__ import unicode_literals, division
import unittest
import os
import shutil
import glob
from monty.tempfile import ScratchDir
from monty.os import cd
import multiprocessing
from custodian.vasp.jobs import VaspJob, VaspNEBJob, GenerateVaspInputJob
from pymatgen.io.vasp import Incar, Kpoint... | specter119/custodian | custodian/vasp/tests/test_jobs.py | Python | mit | 6,616 | [
"VASP",
"pymatgen"
] | 8f6fdc54392cb5df44032514cd27d8ed752477da500a5f0f71f76bdb63fc356d |
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distribu... | jarrodmcc/OpenFermion | src/openfermion/utils/_sparse_tools.py | Python | apache-2.0 | 51,858 | [
"Gaussian"
] | 1112e74d65c0ececd263c8f7a9c7bd785e13077443c9d212fad4eae2c3409b19 |
#! /usr/bin/env python
#-*- coding: utf-8 -*-
"""
Integrated Python GUI for spectral analysis.
Designed functionalities:
> Plot spectra (x,y) file
> Fit spectral lines to common lineshape functions (Gaussian/Lorentzian/Voigt)
> Baseline removal
> Peak selection
> Catalog simulation (JPL/CDMS)
... | luyaozou/PySpec | PySpec.py | Python | gpl-3.0 | 24,448 | [
"Gaussian"
] | fd48a1105a029febed8044af352c93f67eda863f69c4780dfc2bfd43bda35858 |
#!/usr/bin/env python
"""
C.7 Mathematical Formulas (p187)
"""
from Arrays import Array
from plasTeX import Command, Environment, sourceChildren, Macro
from plasTeX import DimenCommand, GlueCommand
from plasTeX.Logging import getLogger
from plasTeX.DOM import Node
#
# C.7.1
#
class MathEnvironment(Environment):
... | hao-han/LaTex2Docx | plasTeX/Base/LaTeX/Math.py | Python | mit | 17,215 | [
"Bowtie"
] | 9f04d52d4be623e81152a689b0fefd662bf268b746e95f5af17716e5530116d8 |
#!/usr/bin/env python
import math, numpy as np
#from enthought.mayavi import mlab
import matplotlib.pyplot as pp
import matplotlib.cm as cm
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz as hv
import... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/Cody_Data/time_varying_data_two_objects.py | Python | mit | 10,020 | [
"Mayavi"
] | 911a36a4dd5bc4689433918988607efbdc71a2a27803805d8c4611df7d96fa00 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songs/forms/topicsdialog.py | Python | gpl-2.0 | 3,674 | [
"Brian"
] | 213d1703ec55bbcb7745cf279e3a08dd8cbb8fc4fd21926bd83e0e78620cb6ac |
# This script processes MIMIC-III dataset and builds longitudinal diagnosis records for patients with at least two visits.
# The output data are cPickled, and suitable for training Doctor AI or RETAIN
# Written by Edward Choi (mp2893@gatech.edu)
# Usage: Put this script to the foler where MIMIC-III CSV files are locate... | mp2893/doctorai | process_mimic.py | Python | bsd-3-clause | 3,673 | [
"VisIt"
] | c32064e72e81471d282765725d36bfeab725e2f00542a0129773e242d069c3b0 |
"""
Photovoltaic
"""
import os
import time
from itertools import repeat
from math import *
from multiprocessing import Pool
import numpy as np
import pandas as pd
from geopandas import GeoDataFrame as gdf
from scipy import interpolate
import cea.config
import cea.inputlocator
import cea.utilities.parallel
from cea.a... | architecture-building-systems/CEAforArcGIS | cea/technologies/solar/photovoltaic.py | Python | mit | 39,532 | [
"EPW"
] | e4c9b386a0e10f3d4c25e8a9a44522e97a7a90e2ae98c0bf38251d9ed86cd8bf |
from rdkit.Chem import PandasTools
from rdkit import Chem
from rdkit.Chem import AllChem
import cirpy
import pandas as pd
import bs4
def parse_page(soup):
for x in soup.find_all("td"):
t = x.get("class")
if t is not None and "term2TD" in t:
if "CAS No." in x.next:
a0 = x... | choderalab/open-forcefield-group | densities/CHERIC/parse.py | Python | gpl-2.0 | 2,515 | [
"RDKit"
] | 0b38ed730a97fe84d81b4bdc9e31b674e619e37798eacdd1476aa778dda5ded8 |
import argparse
import ast
import symtable
import sys
from template import T
def lambda_function(arguments_to_values, prettyprinted=False):
# arguments_to_values :: {argument_i: value_i}
# :: string
if prettyprinted:
raise NotImplementedError
else:
return T('(lambda {}: {})({})').forma... | lizhuoli1126/MarkdownScript | Oneliner/main.py | Python | mit | 28,019 | [
"VisIt"
] | 248d284a008cd7062c4595e98fd317550ba1d0f72c6dbe7346adbe62618183ce |
#!/usr/bin/env python3
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, eit... | espressopp/espressopp | examples/water_gromacs/water.py | Python | gpl-3.0 | 7,049 | [
"ESPResSo",
"Gromacs"
] | ff33c549d299f76b507d7d7fb641a2aa9e5c482c51cd73d8ca21ecf4bdb69d30 |
"""Acceptances tests using py.test fixtures.
All fixtures from ../conftest.py and :mod: `pytest_splinter.plugin` are
available.
The test case structure should follow the If-When-Then pattern.
"""
#########
# Tests #
#########
def test_user_want_to_explore_news(browser):
# import ipdb; ipdb.set_trace() # pytho... | FabiApfelkern/policycompass | tests-acceptance-frontend/test_example_story.py | Python | agpl-3.0 | 1,073 | [
"VisIt"
] | 3f9578de9092261c19fd4dd4b26e69ab127996357e9f691a3f07a96f9ab22613 |
# -*- coding: utf-8 -*-
"""
This module contains a custom streamlining class derived from the MayaVi2
streamlining class, modified to accept an array of seed points for visulaisation
using mayavi.
.. warning::
The documentation for this class cannot be built on Read The Docs, it is possible to build it locally.
Y... | SWAT-Sheffield/pysac | pysac/plot/mayavi_seed_streamlines.py | Python | bsd-2-clause | 7,479 | [
"Mayavi"
] | b1ccba6db26dc5c3cc73421175c456e381e0ef9688bbdc2afa4cfaaa40f23f98 |
""" What's this...?
"""
__RCSID__ = "$Id"
import datetime
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.WorkloadManagementSystem.Client.JobState.JobManifest import JobManifest
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC.WorkloadManagementSystem.Service.JobPolicy import RIGHT_GET_INFO, RIGHT_RESC... | arrabito/DIRAC | WorkloadManagementSystem/Client/JobState/JobState.py | Python | gpl-3.0 | 17,242 | [
"DIRAC"
] | 357568aef153788e1b2230bf564987210b320e36a20b64164e17ba415cee9da7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of t... | gramps-project/gramps | gramps/gui/displaystate.py | Python | gpl-2.0 | 25,554 | [
"Brian"
] | bac529da89523d59b2fea97213b98683b2fafa5299f1b86314bdc948ff96964e |
# Copyright 2003 by Bartek Wilczynski. 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.
"""
Consumers for AlignACE and CompareACE parsers.
"""
class AlignAceScanner:
"""Scann... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/AlignAce/Scanner.py | Python | apache-2.0 | 3,011 | [
"Biopython"
] | 2b9073bfa482ba44affc1ec1afb32b95802f9673f92781557a41dbf4ac3c88cc |
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![Latest Version]
(... | pyoceans/python-oceans | versioneer.py | Python | bsd-3-clause | 68,638 | [
"Brian"
] | 80ab01f473859652602ca280f2d245eed1670a11260aa97efc39bd09e1d67f3e |
import os
import sys
import time
import logging
import datetime
import numpy as np
from data import *
from time import clock
from parameters import *
from collections import defaultdict
SAVE_PATH = "" # path to save results
spike_generators = {} # dict name_part : spikegenerator
spike_detectors = {} # dict name_... | vitaliykomarov/NEUCOGAR | nest/visual/V4/scripts/func.py | Python | gpl-2.0 | 9,243 | [
"NEURON"
] | 7a5a3e645aae2348c9cd3cccec88644d864a48a4462d066739ba8e5f07d2df02 |
import pytest
from biothings.web.options import Option, OptionError, ReqArgs
def test_01():
reqargs = (
ReqArgs.Path(
args=("gene", "1017"),
kwargs={
"host": "mygene.info",
"version": "v3"}),
{
"size": "10",
"dotfield"... | biothings/biothings.api | tests/web/options/test_options.py | Python | apache-2.0 | 3,211 | [
"CDK"
] | 7f2fdf11922146d0a2e21bd52043c081fc25bf376abd524b1105ac5437b523dd |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import random
import re
import shutil
import subprocess
import sys
import tempfile
from argparse import ArgumentParser
from os import listdir
import numpy as np
from adderror import adderror
"""ENSAMBLE, -d directory -n number of models """
"""-k number of sele... | spirit01/SAXS | testing_ensamble_krabik.py | Python | mit | 9,282 | [
"PyMOL"
] | c46ef9a07ae905c549e111f5557cc7b8b9cab9414d554baa2801668232c328e7 |
# -*- coding: utf-8 -*-
# Copyright 2014 Diamond Light Source Ltd.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by a... | FedeMPouzols/Savu | savu/plugins/reconstructions/base_astra_recon.py | Python | gpl-3.0 | 9,521 | [
"Gaussian"
] | 7a2150082729dda7b8750b1c0d9a8037f38ec05aeb7c72d37910d497feb85508 |
"""
############################################################
Pyndorama - Model
############################################################
:Author: *Carlo E. T. Oliveira*
:Contact: carlo@nce.ufrj.br
:Date: 2013/09/13
:Status: This is a "work in progress"
:Revision: 0.1.5
:Home: `Labase <http://labase.selfip.org/>... | labase/pyndorama | src/model.py | Python | gpl-2.0 | 12,473 | [
"VisIt"
] | 25a3062efc41ba6fbca2db3f8bfe2ebdad9ac0e63b671ea24db5fe9889c91a97 |
"""gro.py: Used for loading Gromacs GRO files.
"""
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Robert McGi... | hainm/mdtraj | mdtraj/formats/gro.py | Python | lgpl-2.1 | 19,920 | [
"Gromacs",
"MDTraj",
"OpenMM"
] | 5e3120dc1ce57c731d92d1446acceaf9e6853affeb74fd52accbd43751467079 |
from ..utils import *
##
# Minions
# Goblin Auto-Barber
class GVG_023:
play = Buff(FRIENDLY_WEAPON, "GVG_023a")
# One-eyed Cheat
class GVG_025:
events = Summon(CONTROLLER, PIRATE - SELF).on(Stealth(SELF))
# Iron Sensei
class GVG_027:
events = OWN_TURN_END.on(Buff(RANDOM(FRIENDLY_MINIONS + MECH - SELF), "GVG_0... | liujimj/fireplace | fireplace/cards/gvg/rogue.py | Python | agpl-3.0 | 979 | [
"TINKER"
] | 77421a182dcc360cb16961aed1c6000fd223ae9b1b53d9c3d3c9cc7746080790 |
import searchengine as se
import ast
eval_tests = [
"a and b",
"a or b",
"a and (b or c)",
]
class MyVisitor(ast.NodeVisitor):
def visit_Name(self, node):
print 'Found string "%s"' % node
def visit_BoolOp(self, node):
if isinstance(node, ast.BinOp) and \
isinstance(nod... | vinjn/MLStudy | miner/main.py | Python | mit | 1,770 | [
"VisIt"
] | 38c64c8dbf1c38f55a3a1b48059c92ca8f73550205dc287faf08b24d57512e72 |
"""Structured Commons fingerprinting utilities."""
from __future__ import print_function
import base64
import codecs
import hashlib
import re
import sys
if hasattr(int, 'from_bytes'):
# python 3
long = int
def bytes_to_long(barray):
return int.from_bytes(barray, 'big')
def long_to_bytes(val):
... | structured-commons/tools | sc/fp.py | Python | unlicense | 14,159 | [
"VisIt"
] | 12158c3e369a0c69c5c80a97870f45b2f6a4d8de5f8d71118c82b56a9cebf017 |
import re
from math import log
from time import sleep
import subprocess
from io import StringIO
from pathlib import Path
from operator import itemgetter
from Bio import SearchIO, SeqIO
from Bio.Blast import NCBIXML, NCBIWWW
from RecBlast import print, merge_ranges
from RecBlast.WarningsExceptions import *
class Searc... | docmanny/RecBlast | RecBlast/Search.py | Python | mit | 43,643 | [
"BLAST",
"Biopython"
] | b7dd4c8c752259a64c2ab688c06ab3ceded41c2abb5c70871b68b233df848641 |
class Record:
def __init__(self, elem):
"""
this class simply represents a list record linked to his next/prev elems
:param elem: elem stored in the record
"""
self._elem = elem
self._next = None
self._prev = None
def getElem(self):
"""
:... | IA-MP/KnightTour | libs/graph/DLinkedList.py | Python | mit | 6,415 | [
"VisIt"
] | 965e4239162895604707a66c400b859eae2110456495129814a2c50f798bb367 |
import pysam
class AnnotateMateInformation(object):
"""Reads along a file that has a complete set of alignments and a file that should be annotated for mates of interest."""
def __init__(self, target, source, output_path=None, mate_sequence_tag='MS'):
"""
Add mate sequence into MS tag.
... | bardin-lab/readtagger | readtagger/mateoperations.py | Python | mit | 2,303 | [
"pysam"
] | ac1fcb1b6c81f6d585fe2f1b0568ebdbb46ca70dec3585ac606d69828bf1527a |
#!/usr/bin/env python3
#
# Code related to ESET's Linux/Moose research
# For feedback or questions contact us at: github@eset.com
# https://github.com/eset/malware-research/
# Olivier Bilodeau <bilodeau@eset.com>
#
# This code is provided to the community under the two-clause BSD license as
# follows:
#
# Copyright (C)... | eset/malware-research | moose/parse_cnc1_wordlist.py | Python | bsd-2-clause | 2,280 | [
"MOOSE"
] | bed7b00fda1a71bb3c2db7bcd88e9b9ffac6639b9a554ef979d47b90edc8f3c8 |
#!/usr/bin/env python
################################################################################
#
# castep_constrain.py
#
# Usage: castep_constraints.py some.cell threshold --axis=(a, b or c)
#
# Generates constraints on all atoms below "threshold" (units fractional by default) along
# the specified axis (c axis... | HSINWEI/physics | python/castep_constrain.py | Python | gpl-3.0 | 3,080 | [
"CASTEP"
] | fb092e9593935639fcffa73cf724c3b60887e212828e20bab7255d504dfad766 |
""" Here, we need some documentation...
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import threading
import time
import select
import socket
from concurrent.futures import ThreadPoolExecutor
try:
import selectors
except Impo... | ic-hep/DIRAC | src/DIRAC/Core/DISET/private/MessageBroker.py | Python | gpl-3.0 | 16,514 | [
"DIRAC"
] | 3c0fa205e5288ff8abb9eb60f371b0960d6b5ccfd3fad1f0dac91db7af615547 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2015--, The Horizomer Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------... | qiyunzhu/horizomer | setup.py | Python | bsd-3-clause | 1,948 | [
"scikit-bio"
] | 8d1d4d9a2fd2c747cef12c6f91e7b4ad8664f10501ac0218779eccc1aabfe580 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This code is copied from https://github.com/vsvinayak/mnist-helper.
It requires Scipy to perform convolve2d.
Default parameters are modified.
"""
import numpy as np
import math
from scipy.signal import convolve2d
from deepy.utils import global_rand
def create_2d_ga... | ZhangAustin/deepy | deepy/utils/elastic_distortion.py | Python | mit | 3,676 | [
"Gaussian"
] | a3b967a376e57eaec25a64c9a113bd22d4ffe699cd2567d9e1f0ef5b7cceb854 |
#
# This file is a part of the normalize python library
#
# normalize is free software: you can redistribute it and/or modify
# it under the terms of the MIT License.
#
# normalize is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FI... | samv/normalize | normalize/visitor.py | Python | mit | 28,858 | [
"VisIt"
] | 62bf8a1c942ff67e7f33d2bede6b8083f40cf1e95c1dd213db2326d9cb7d0454 |
# encoding: utf-8
"""
Prefiltering components.
Prefilters transform user input before it is exec'd by Python. These
transforms are used to implement additional syntax such as !ls and %magic.
Authors:
* Brian Granger
* Fernando Perez
* Dan Milstein
* Ville Vainio
"""
#-----------------------------------------------... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/IPython/core/prefilter.py | Python | mit | 25,935 | [
"Brian"
] | 06e72889b5250970be89666691332af84f3255de62bc65640a20cc072206cc6a |
__problem_title__ = "Jumping frog"
__problem_url___ = "https://projecteuler.net/problem=490"
__problem_description__ = "There are stones in a pond, numbered 1 to . Consecutive stones are " \
"spaced one unit apart. A frog sits on stone 1. He wishes to visit " \
"each... | jrichte43/ProjectEuler | Problem-0490/solutions.py | Python | gpl-3.0 | 2,062 | [
"VisIt"
] | 48dcb7ef5835710942a44bff63ecb373edb9c780fc1055247cdbadcf7aca3f5e |
"""Get useful information from live Python objects.
This module encapsulates the interface provided by the internal special
attributes (co_*, im_*, tb_*, etc.) in a friendlier fashion.
It also provides some help for examining source code and class layout.
Here are some of the useful functions provided by this module:... | munyirik/python | cpython/Lib/inspect.py | Python | bsd-3-clause | 112,277 | [
"VisIt"
] | bbb960e6500b59a223af85d98fe88d8ed41af893904e0db3baa112ca6cc96b68 |
import subprocess,os,sys
sys.path.append('/home/shangzhong/Codes/Pipeline')
from Modules.f05_IDConvert import extract_from_gene2ref,prIDMap2geneIDMap
from Modules.p04_ParseBlast import blastName2ID
def rosetta_pair(group):
"""
This functions detects rosetta pairs, given a list of lines which have same 2nd colu... | shl198/Pipeline | CHOGeneId2HumanId/rosetta_stone.py | Python | mit | 4,396 | [
"BLAST"
] | 43fd8e01c698517d0fd30a2f30c1dde85b3ddc16c58b0b0dc0b67df88d7f39d8 |
import numpy as np
import pytest
from conftest import skipif
from devito import (Grid, Dimension, Function, TimeFunction, Eq, Inc, solve,
Operator, switchconfig, norm, cos)
from devito.exceptions import InvalidOperator
from devito.ir.iet import Block, FindNodes, retrieve_iteration_tree
from devito.... | opesci/devito | tests/test_gpu_openmp.py | Python | mit | 13,943 | [
"VisIt"
] | 8b3b7798f9f71b705368f04fdfbc78d769b051580203d1761cdcb84c70e1daab |
# 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.
try:
from numpy import corrcoef
del corrcoef
except ImportError:
from Bio import MissingExternalDependencyError
raise MissingExternalDe... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SubsMat.py | Python | gpl-2.0 | 3,379 | [
"Biopython"
] | 4503b8ccd76c0ef4abdb9e87b9fa8b6db0de8c32bde50ab92b9c5830e8557030 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the PyNCulture project, which aims at providing tools to
# easily generate complex neuronal cultures.
# Copyright (C) 2017 SENeC Initiative
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Genera... | SENeC-Initiative/PyNCulture | backup_shape.py | Python | gpl-3.0 | 18,852 | [
"NEURON"
] | bb7608cfd492c56c6b3f4f4681ba4b06b39e94480788d42f2e781a7bbbca4632 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module contains some utils for the main script of the chemenv package.
"""
__author__ = "David Waroquiers"
__copyright__ = "Copyright 2012, The Mater... | tallakahath/pymatgen | pymatgen/analysis/chemenv/utils/scripts_utils.py | Python | mit | 15,858 | [
"VTK",
"pymatgen"
] | 42a51541dd4b7a6865ef69ad483b3dfe3af77fc5bf22fcca58d86f1fea610ef5 |
# Version: 0.16+dev
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.3, 3.4, 3.5, and pypy
* [![Latest Version]
(https... | kdmurray91/radhax | radsim/versioneer.py | Python | gpl-3.0 | 64,445 | [
"Brian"
] | a5321d1811c2bc3008e3ac838f4f57acbdaeab87332b99275425eb5be59feae3 |
#!/usr/bin/env python
from __future__ import print_function, division
import os
import scipy as sp
import scipy.linalg as LA
import scipy.spatial.distance as sp_dist
from ase import units
from sklearn.kernel_ridge import KernelRidge
# import pdb
from matplotlib import pyplot as plt
import PES_plotting as pl
from time ... | marcocaccin/LearningMetaDynamics | MD_unconstrained/mock_sampling.py | Python | gpl-2.0 | 5,083 | [
"ASE",
"Gaussian"
] | 437f86d839e793175183892c4a1ecdc142a6cad558bbb3f589b1adc648aa570a |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
#####################################... | gviejo/ThalamusPhysio | python/figure_talk/main_talk_7_corr2.py | Python | gpl-3.0 | 14,903 | [
"Gaussian"
] | 714241afbc44b94cfb2c79c79f176a622188a7a08bd9ab3ac5b018defd50f85f |
"""
A set of classes for specifying input parameters for the Ember solver.
Create a :class:`.Config` object to be passed to :func:`~ember.utils.run` or
:func:`~ember.utils.multirun`.
Sane defaults are given for most input parameters. Create a customized
configuration by passing :class:`.Options` objects to the constru... | speth/ember | python/ember/input.py | Python | mit | 65,505 | [
"Gaussian"
] | 59d30b7212cc8d8d21056362fbbb8e79fd1bd1306294805ab4ad8251d759fc14 |
# Copyright 2018 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/sts/components/autoregressive.py | Python | apache-2.0 | 17,359 | [
"Gaussian"
] | b24a09ceba82f0bb95d9ce16b41ddf543e1af80034f605dff9a9f05b9e09d2a4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import sys
from setuptools import setup, Extension
from pybind11.setup_helpers import Pybind11Extension, build_ext
# Publish the library to PyPI.
if "publish" in sys.argv[-1]:
os.system("python setup.py sdist upload")
sys.exit()
# Default compile argum... | dfm/celerite | setup.py | Python | mit | 1,642 | [
"Gaussian"
] | 02d1813d6b5726705ea3737b464f5da9c3f63218c30700a834df3b20480cb61d |
#!/usr/bin/env python
"""
Provides PeakFitter class for fitting of gaussian peaks in 1D spectra.
"""
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.gridspec import GridSpec
from matplotlib.font_manager import FontProperties
from lmfit import models
import panda... | bearing/radwatch-analysis | peak_fitting.py | Python | mit | 21,235 | [
"Brian",
"Gaussian"
] | a52027d8313db5f8e355e603e48e201bb9dec287dfd921927d9e7849c687edfe |
import os,glob,h5py,astropy,numpy,scipy
from astropy.time import Time
from datetime import datetime,timedelta
from glue.segments import segment,segmentlist
from gwpy.segments import DataQualityDict,DataQualityFlag
from gwpy.timeseries import TimeSeries,TimeSeriesList
from pycbc import types
def... | GNOME-physics/gdas | gdas/retrieve.py | Python | mit | 6,442 | [
"Gaussian"
] | 4e69804bb3bd8736d136839f2e4df8549eaeb7e84dad7da5688fe267034f01d3 |
# interpol2d.py ---
#
# Filename: interpol2d.py
# Description:
# Author:
# Maintainer:
# Created: Thu Jun 28 15:19:46 2012 (+0530)
# Version:
# Last-Updated: Thu Jun 28 17:11:42 2012 (+0530)
# By: subha
# Update #: 49
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change... | dilawar/moose-full | moose-examples/snippets/interpol2d.py | Python | gpl-2.0 | 1,991 | [
"MOOSE"
] | b1cf09e985a4d0a0a39d129fe35eb7ea8b9536a996c6f864fcd7ab78dd5e5348 |
import scipy as sp
import pdb
import scipy.linalg as la
import fastlmm.util.util as utilx
import sys
def genphen(y_G0,G1,covDat,options,nInd,K1=None,fracCausal=None,randseed=None):
'''
Generate synthetic phenotype with a LMM and linear kernels, using SNPs in G1 for signal,
snps in GO for backgroun... | zhonghualiu/FaST-LMM | fastlmm/util/genphen.py | Python | apache-2.0 | 3,540 | [
"Gaussian"
] | d4220f703e486f2da7abad681869d90684aa5d6a743bfbb466b444a586844af2 |
"""Collection of DIRAC useful file related modules.
.. warning::
By default on Error they return None.
"""
__RCSID__ = "$Id$"
import os
import hashlib
import random
import glob
import sys
import re
import errno
# Translation table of a given unit to Bytes
# I know, it should be kB...
SIZE_UNIT_CONVERSION = {
... | andresailer/DIRAC | Core/Utilities/File.py | Python | gpl-3.0 | 7,879 | [
"DIRAC"
] | 08ee42ed53ed3195641027cee4bb9fa6777527eaa124b0a746c30e90fec154d0 |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | wizmer/NeuroM | setup.py | Python | bsd-3-clause | 3,142 | [
"NEURON"
] | 5a620c3691b18209d026b85d7336e401dce6f3eb952e26062d2225c40b1c0888 |
"""This tests the linked_list module."""
import pytest
INSTANTIATION_TABLE = [
([3, 7, 5, 6, 4], 4),
((7, 6, 5, 4), 4),
([4], 4)
]
POP_TABLE = [
([7, 9], 9),
([33, 0, 10], 10),
((3, 2, 1, 34), 34),
]
SIZE_TABLE = [
([795]),
([2, 33]),
([3, 4, 5]),
((5, 3, 2, 23))
]
SEARCH_TA... | Copenbacon/data-structures | src/test_linked_list.py | Python | mit | 4,621 | [
"ADF"
] | d7f1ca43e0b4f696a68db6e5bbcacaefa25881274b5cfd2d11bd48a5f650dd4f |
#! /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-grafeas | scripts/fixup_grafeas_v1_keywords.py | Python | apache-2.0 | 6,683 | [
"VisIt"
] | bac23ad20a766f67c320f8f78d4ed016d591ce50205d917a199f409fc2dfeb14 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/tree/tests/test_nj.py | Python | bsd-3-clause | 8,287 | [
"scikit-bio"
] | 292ee3d4b89bf55cbe96769fa3cc80478a88da1dcbbea3790893360fd72717ad |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software ... | garyjyao1/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 24,555 | [
"Galaxy"
] | 43fc83cd592f9dcdd067486a91326fdc47e691a4c4c08f7729ae48b6805c9bf6 |
import ast
import token
import tokenize
from os.path import islink
from StringIO import StringIO
from dxr.build import unignored
from dxr.filters import FILE, LINE
from dxr.indexers import (Extent, FileToIndex as FileToIndexBase,
iterable_per_line, Position, split_into_lines,
... | gartung/dxr | dxr/plugins/python/indexers.py | Python | mit | 10,644 | [
"VisIt"
] | e618005f94d92464dccf214f91a0541346e53c84b13c692bf129c8bace5df24b |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | AnishShah/tensorflow | tensorflow/contrib/distributions/python/ops/bijectors/masked_autoregressive.py | Python | apache-2.0 | 23,611 | [
"Gaussian"
] | 083502f36ca5e694193105a39d194cdc9883f8f36e2208c29e1d2bc4821c793f |
# -*- coding: utf-8 -*-
import sys
import time
import httplib2
AUTO_RECONNECT_TIMES = 5
crawl_tips_json = {}
SERVER = 'http://api.cn.faceplusplus.com/'
category_Arts_Entertainment = ['Aquarium', 'Arcade', 'Art Gallery', 'Bowling Alley', 'Casino', 'Circus', 'Comedy Club',
'Concert Hall... | chenyang03/Foursquare_Crawler | foursq_utils.py | Python | mit | 18,877 | [
"CASINO"
] | 403d880426f16c6afb0a06cb67c5880b1db034e69778e9f8e414ae22b8eb9083 |
"""
Windowed operators that can be expressed as convolutions
"""
import numpy as np
from .window import OpWindow
class OpFilter(OpWindow):
"""
base class for filter operations
subclasses provide the get_filter() method
"""
@classmethod
def apply_window_function(cls, input_array, window_size... | burgerdev/hostload | tsdl/features/filter.py | Python | mit | 2,189 | [
"Gaussian"
] | a2fe30722c8b1f9b71ba5c5f6919807e6553404b9e0f38220e4dec634ce7669e |
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