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# Copyright (C) 2016 Peloton
#########################
# Library for spectra
# author: julien@sussex
# Date of creation: 10/2015
# See 1611.01446
#########################
import glob, copy, sys, os
import numpy as np
import lib_covariances
from loop_lensing import loop_lensing
from util import binner, split_block_n0
... | JulienPeloton/lenscov | src/lib_spectra.py | Python | gpl-3.0 | 32,367 | [
"Gaussian"
] | 76805fe94239f1df3f71cafc1769484600f2137f26c222ba9380152264dd3ccc |
# 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 software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/Version.py | Python | gpl-3.0 | 2,306 | [
"ESPResSo"
] | e8d3b9d6f7effecd00020481964e7eeb158e0338bd3263a81f8ebd34109cf000 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | Freeseer/freeseer | src/freeseer/framework/config/persist/configparser.py | Python | gpl-3.0 | 2,083 | [
"VisIt"
] | 8a798b59228d096cedeba0848c8290778a86ef159f19380b34a01001596534d1 |
"""Simple test for the contour related modules.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from io import BytesIO
import copy
import numpy
# Local imports.
from common import TestCa... | dmsurti/mayavi | integrationtests/mayavi/test_contour.py | Python | bsd-3-clause | 7,774 | [
"Mayavi",
"VTK"
] | 1ef738a459aa526c0df1ab178136d2f8795ba386dcf677be0d5d3899d8ab5b9b |
#
# Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyrigh... | rvianello/rdkit | rdkit/Chem/MolKey/MolKey.py | Python | bsd-3-clause | 15,512 | [
"RDKit"
] | 39bca14b132de32657d4752b171fe6fbb61a21540d60cb2d518b103315be1961 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import llnl.util.tty as tty
class Qmcpack(CMakePackage, CudaPackage):
"""QMCPACK, is a modern hi... | rspavel/spack | var/spack/repos/builtin/packages/qmcpack/package.py | Python | lgpl-2.1 | 16,625 | [
"QMCPACK"
] | 43e4b733a9bdac8b7b29ade893177da6440e40d9beb2cdc738c8e79a6f9f709c |
#!/usr/bin/env python
"""
Copyright 2001 Pearu Peterson all rights reserved,
Pearu Peterson <pearu@ioc.ee>
Permission to use, modify, and distribute this software is given under the
terms of the LGPL. See http://www.fsf.org
NO WARRANTY IS EXPRESSED OR IMPLIED. USE AT YOUR OWN RISK.
$Revision: 1.1 $
$Date:... | chunshen1987/iSS | utilities/for_paraview/lib152/ColorScalars.py | Python | mit | 1,405 | [
"VTK"
] | e9319a8ae67f2cff1986056c874a7ef1e343dfc5930eda8dc3de4f3bd8d1d6b6 |
''' Basic implementation of locator for use on computers
that don't have OpenCL.'''
import numpy
from numpy import float32, abs, maximum, minimum
from math import pi, radians
class Locator(object):
def __init__( self, north, east, length, size, sigma ):
north = numpy.linspace(north-length/2., north+lengt... | cuauv/software | locator/locator_numpy.py | Python | bsd-3-clause | 4,056 | [
"Gaussian"
] | 69a5b2b3e3aec1bf5f4b844e17f3d9173c8f8ddc08ee3472e17b43bc430e8dea |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# trilegal - Waqas Bhatti (wbhatti@astro.princeton.edu) - Dec 2017
# License: MIT. See the LICENSE file for more details.
'''
This downloads and interacts with galaxy models generated by the TRILEGAL
web-form by Prof. Leo Girardi. This module requires the `requests` and `... | lgbouma/astrobase | astrobase/services/trilegal.py | Python | mit | 30,095 | [
"Galaxy"
] | 0be297d4d2dc94a282c567eb5cb2a6452ad0c0304ebb98a0a14d0b349c8f2408 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
from brian import *
from pylab import figure, plot, hist, show
def brun():
eqs="""
dZ/dt = xi*second**-.5 : 1
"""
nn = NeuronGroup(1, model=eqs)
print nn._eqs
mon = {}
for par in ['Z']:
mon[par] = StateMonitor(nn, par, record=... | neuro-lyon/multiglom-model | src/tests/test_mini.py | Python | mit | 695 | [
"Brian"
] | 757f0287e666d86f48d23cea78887221d01638dae04be47e73de79a3968cd92d |
# 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... | mkuron/espresso | testsuite/python/observable_profileLB.py | Python | gpl-3.0 | 4,696 | [
"ESPResSo"
] | b873b0881393201e9912e893dca534a67e3bed15103fb316c733b3285a777bbe |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
import pandas as pd
import numpy as np
import csv as csv
from sklearn.ensemble import RandomForestClassifier
def handlerData(filepath):
# Carrega o CSV e seta algumas colunas como object (factor).
df = pd.read_csv(filepath,
sep = ';',
... | UFCGProjects/analise-dados-2-p5 | problem6.py | Python | mit | 4,713 | [
"ADF"
] | 7462b3328503259916c4500b9c73950767ed7423496e5883a5bbab278f664c4c |
# Copyright (c) OpenMMLab. All rights reserved.
import mmcv
import torch.nn as nn
from ..builder import LOSSES
from .utils import weighted_loss
@mmcv.jit(derivate=True, coderize=True)
@weighted_loss
def gaussian_focal_loss(pred, gaussian_target, alpha=2.0, gamma=4.0):
"""`Focal Loss <https://arxiv.org/abs/1708.0... | open-mmlab/mmdetection | mmdet/models/losses/gaussian_focal_loss.py | Python | apache-2.0 | 3,312 | [
"Gaussian"
] | 95c16c6fbd706bc9d13bd2dd712f96d76ed62c03f257f57f3b37954e731b2918 |
from __future__ import print_function
from utils import file_transaction, file_exists
from collections import defaultdict, Counter
import os
import gzip
import HTSeq
def count_umi(sam_file, gtf_file, barcode_to_well, multimappers=False):
"""
stripped down implementation of the HTSeq algorithm for counting
... | roryk/singlecell | singlecell/count.py | Python | mit | 4,159 | [
"HTSeq"
] | 27ea801b6a8448937b8b951a94f32d15d5941fbe93c3d27c53cdf4d69daa6008 |
# $Id$
#
# Copyright (C)2003-2010 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Hybrid EState-VSA de... | ptosco/rdkit | rdkit/Chem/EState/EState_VSA.py | Python | bsd-3-clause | 3,565 | [
"MOE",
"RDKit"
] | 203ff525d678c85eb9a22856ca993ed7a0c6f30de9334cdd8ec1f1a32d85b56a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2013 Spotify AB
#
# 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... | wavelets/annoy | setup.py | Python | apache-2.0 | 1,429 | [
"VisIt"
] | 15125a66ece87a8dbfc00df03ae93d237ae51b495bd5cef26504524dc6523610 |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
colors.SetColor("ActorColor", [235, 235, 235, 255])
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
... | lorensen/VTKExamples | src/Python/ImageProcessing/IsoSubsample.py | Python | apache-2.0 | 3,854 | [
"VTK"
] | e39c570998042771e4df3871c72e5987a92346a634a392666bc41328f6998826 |
#!/usr/bin/env python
''' VIC exact restart testing '''
import numpy as np
import datetime
import os
import glob
import xarray as xr
import warnings
from test_utils import read_vic_ascii
from tonic.testing import VICTestError
def prepare_restart_run_periods(restart_dict, state_basedir):
''' For restart tests, re... | dgergel/VIC | tests/test_restart.py | Python | gpl-2.0 | 16,164 | [
"NetCDF"
] | 57c8809b257f75a5ab05fd8067b158a36a2e6c0cf311654bccb447d6e6c10de0 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/qcdb/parker.py | Python | lgpl-3.0 | 6,554 | [
"Psi4"
] | b9e18841bf582eab08312dccc1377356ed998c3b42a71705b07ef7fdea173f5a |
"""
KeepNote
Functions for iterating and inserting into textbuffers
"""
#
# KeepNote
# Copyright (c) 2008-2009 Matt Rasmussen
# Author: Matt Rasmussen <rasmus@alum.mit.edu>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as pu... | brotchie/keepnote | keepnote/gui/richtext/textbuffer_tools.py | Python | gpl-2.0 | 18,607 | [
"VisIt"
] | 4b730886ac31e045a0913ec92f58054b99fd87c3880062c6a64e354c98bd065c |
# module pyparsing.py
#
# Copyright (c) 2003-2018 Paul T. McGuire
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, cop... | sserrot/champion_relationships | venv/Lib/site-packages/setuptools/_vendor/pyparsing.py | Python | mit | 226,313 | [
"VisIt"
] | 4b451826d448625408ae38f14af9f80c89024014107592d2c636e3c656f46bc8 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
#sphere 1
sphereSource = vtk.vtkSphereSource()
sphereSource.SetCenter(0.0, 0.0, 0.0)
sphereSource.SetRadius(4.0)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(sphereSource.GetOutputPort())
... | lorensen/VTKExamples | src/Python/Geovis/CompassWidget.py | Python | apache-2.0 | 1,362 | [
"VTK"
] | da119aa437f368b8c416e292dad9b1d823550477c7be2eb201d7775a38474b80 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import glob
import os
from spack import *
class Magics(CMakePackage):
"""Magics is the latest generation of the ECM... | LLNL/spack | var/spack/repos/builtin/packages/magics/package.py | Python | lgpl-2.1 | 8,853 | [
"NetCDF"
] | d5c9cfb53478e5229d27152a4e87333a64214b931b1d690d280e282b65973162 |
import matplotlib.pyplot as plt
import random
files = ['results_alpha1', 'results_alpha2', 'results_alpha3', 'sim']
data = []
for f in files:
with open(f, 'r') as r:
print(f)
content = r.read().split('\n')[:-1]
data.append([float(c)/10000 for c in content])
print(data)
names = ['alpha-step1', '... | OPU-Surveillance-System/monitoring | master/scripts/planner/solvers/alpha_boxplot.py | Python | mit | 673 | [
"Firefly"
] | 94f4ecf22a876e904e7b54049a0c50f7593ca0825979ed9d61691c6f2e26fa4e |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 30 08:57:31 2016
@author: nicholas
"""
import sys
import logging
import shutil
import os
import unittest
from riboSeed.classes import Exes
sys.dont_write_bytecode = True
logger = logging
@unittest.skipIf(shutil.which("bwa") is None or
shutil.which("... | nickp60/riboSeed | tests/test_Exes.py | Python | mit | 2,727 | [
"BWA",
"Bowtie"
] | 4c09973b666c62a7195b1562c01d3c66279b1d2702db22d05d6895e5c0ba8fd0 |
import pytest
import psi4
pytestmark = pytest.mark.quick
@pytest.mark.smoke
def test_psi4_basic():
"""tu1-h2o-energy"""
#! Sample HF/cc-pVDZ H2O computation
h2o = psi4.geometry("""
O
H 1 0.96
H 1 0.96 2 104.5
""")
psi4.set_options({'basis': "cc-pVDZ"})
psi4.energy('scf')
... | CDSherrill/psi4 | tests/pytests/test_psi4.py | Python | lgpl-3.0 | 8,715 | [
"Psi4"
] | 7a2af0051f1cff4b55c6cbfca1f8975a1b7d7f63fe9b3373cf764a97ba320056 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 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; ... | beernarrd/gramps | gramps/gen/filters/rules/person/_searchname.py | Python | gpl-2.0 | 2,208 | [
"Brian"
] | 0b6443d16dbf23525e064e4fc8219e3c19421e945554fd0e95d42987a3b6ea27 |
#!/usr/bin/env python2.7
"""
vg_mapeval.py: Compare alignment positions from gam or bam to a truth set
that was created with vg sim --gam
"""
from __future__ import print_function
import argparse, sys, os, os.path, errno, random, subprocess, shutil, itertools, glob, tarfile
import doctest, re, json, collections, time,... | glennhickey/toil-vg | src/toil_vg/vg_mapeval.py | Python | apache-2.0 | 144,358 | [
"BWA",
"pysam"
] | c7a16e507cbbda5af7f7d85c51957abb92cf7039fc7886a7aeeb6fab47b6ed4f |
#!/usr/bin/env python
"""
Just a demo script to test out the DIMACS reader/writer function
"""
from __future__ import print_function
import time
from vtk import *
# generate a random graph
source = vtkRandomGraphSource()
source.SetNumberOfVertices(100)
source.SetAllowSelfLoops(False)
source.SetEdgeProbabil... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/dimacs.py | Python | bsd-3-clause | 1,557 | [
"VTK"
] | 6dbf3dc6f1aacae44a0a33b14eb35ab9818aa87cfaa014c003596dd9f8f8cb49 |
import os, sys
from nltk.corpus import wordnet as wn
import numpy as np
from bisect import bisect_left
import h5py
from basic.constant import ROOT_PATH
from basic.util import readImageSet, bisect_index
_min_freq = {'train10k': 50, 'train100k': 250, 'train1m': 750, 'mirflickr08': 50, 'flickr81test': 50, 'flickr81': 50... | li-xirong/jingwei | tools/wordnet_frequency_tags.py | Python | mit | 7,590 | [
"Elk",
"Jaguar"
] | c53f43e54f43d84a7b4c0d250cf6e1f937296ca90179117c5c10a35aa6e162ab |
#
# EOVSA_MOUNTCAL
# Routine to convert pointing measurements analyzed with calibration.py
# routines calpntanal() and calpnt_multi(), to the appropriate pointing
# parameters used in the antennas.
#
# History
# 2018-01-20 DG
# Finally wrote a purely EOVSA version of mountcal that can handle all
# of the... | dgary50/eovsa | eovsa_mountcal.py | Python | gpl-2.0 | 22,419 | [
"Elk"
] | d52c9638876a1674bf99a916148188f9b77399d670e2e6f02390de71b3020c51 |
# 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/.
import operator
from ..node import NodeVisitor
from ..parser import parse
class Compiler(NodeVisitor):
"""Compile... | GreenRecycleBin/servo | tests/wpt/harness/wptrunner/wptmanifest/backends/static.py | Python | mpl-2.0 | 6,583 | [
"VisIt"
] | be7e26ee04387b473a4d01fe62722ec4e3bc473d9e94c42c7e8a07176ca292a8 |
# coding: utf-8
"""
This module provides objects to inspect the status of the Abinit tasks at run-time.
by extracting information from the main output file (text format).
"""
from __future__ import unicode_literals, division, print_function
import collections
import numpy as np
import yaml
import six
from six.moves i... | rousseab/pymatgen | pymatgen/io/abinitio/abiinspect.py | Python | mit | 18,454 | [
"ABINIT",
"CRYSTAL",
"pymatgen"
] | ce34426a24efa2c733bd45fce44133d7669ca9b6bdcac46658d97c81ddba86b9 |
#!/usr/bin/env python
# In this example we show the use of the
# vtkBandedPolyDataContourFilter. This filter creates separate,
# constant colored bands for a range of scalar values. Each band is
# bounded by two scalar values, and the cell data laying within the
# value has the same cell scalar value.
import vtk
fro... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/VisualizationAlgorithms/Python/BandContourTerrain.py | Python | gpl-3.0 | 4,296 | [
"VTK"
] | e0d082e6844b64bd917c3b82d4b561e09a2469d001ab53edc5d9951513330ae3 |
#!/usr/bin/env python
# -*- coding: iso-8859-15 -*-
# generated by wxGlade 0.6.3 on Wed Sep 10 21:49:20 2008
import wx
# begin wxGlade: extracode
# import the RWI (why does this line appear twice?)
from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowInteractor
# import the RWI (why does this line appear... | nagyistoce/devide | modules/viewers/resources/python/DICOMBrowserPanels.py | Python | bsd-3-clause | 5,474 | [
"VTK"
] | bd932e20efc7c210460f7945c5dafd6610cec0a8f6aec6c2a946afe84bdf92a1 |
import numpy as np
np.seterr(divide='ignore') #ignore errors in log division
np.seterr(all='ignore') #ignore errors in log division
import sys
import time
##########################################################################################
def MCMC_N(LogPosterior,gp,post_args,ch_len,ep,N=1,chain_filenames=['MC... | nealegibson/Infer | src/MCMC_SimN.py | Python | gpl-3.0 | 11,175 | [
"Gaussian"
] | 6805b76c4c42741ce5fdbc6f25561b0887f091ed5ef22012324a64ff2b2565c3 |
# -*- coding: utf-8 -*-
"""
=====================
Cython related magics
=====================
Magic command interface for interactive work with Cython
.. note::
The ``Cython`` package needs to be installed separately. It
can be obtained using ``easy_install`` or ``pip``.
Usage
=====
To enable the magics below,... | andreasvc/cython | Cython/Build/IpythonMagic.py | Python | apache-2.0 | 12,044 | [
"Brian"
] | 176e5fe4c4886ec83e129d866cfaad194a9bcd8e5a20b5a4db1e62804a0a8cc1 |
"""
Basic molecular features.
"""
import numpy as np
from deepchem.feat.base_classes import MolecularFeaturizer
class RDKitDescriptors(MolecularFeaturizer):
"""RDKit descriptors.
This class comptues a list of chemical descriptors using RDKit.
See http://rdkit.org/docs/GettingStartedInPython.html
#list-of-a... | miaecle/deepchem | deepchem/feat/rdkit_descriptors.py | Python | mit | 3,257 | [
"RDKit"
] | 0bd3de1361fd1f8aa88e13cff6d0877aa095aae54c50d040613bcab86033dbdd |
from direct.directnotify import DirectNotifyGlobal
from direct.distributed.ClockDelta import *
from direct.gui import DirectGuiGlobals
from direct.gui.DirectGui import *
from direct.interval.IntervalGlobal import *
from direct.showbase import PythonUtil
from direct.showbase.PythonUtil import *
from direct.task import T... | Spiderlover/Toontown | toontown/toon/LocalToon.py | Python | mit | 86,710 | [
"VisIt"
] | 277120ba04f4f69d4fbb94b3071259835ae8391b3a2530ef673e03444163c9dc |
#!/usr/bin/env python
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 you... | loriab/qcdb | bin/ixyz2database.py | Python | lgpl-3.0 | 18,622 | [
"Psi4"
] | 7b480c0591dc3e7fca610c411979c925b074986a84b2e2b02de8bab01a6335ab |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import copy
from bashlint import bast, flags, tokenizer, errors
def _recursiveparse(parserobj, base, sindex, tokenizerargs=None):
# TODO: fix this hack that prevents mutual import
from bashlint import... | TellinaTool/awesome_nmt | bashlint/subst.py | Python | gpl-3.0 | 13,318 | [
"VisIt"
] | 702273446178c38dcef1165fdc132b2e93099d57919e4b54437a758b21e74c29 |
#!/usr/local/sci/bin/python2.7
#*****************************
#
# convert to complete dataset files (pentad and monthlies)
#
#
#************************************************************************
'''
Author: Robert Dunn
Created: March 2016
Last update: 12 April 2016
Location: /project/hadobs2/hadisdh/marine/PROGS/... | Kate-Willett/HadISDH_Marine_Build | EUSTACE_SST_MAT/make_complete_data_files.py | Python | cc0-1.0 | 28,878 | [
"NetCDF"
] | 2d2023eca96a1c69cd84a2fe765ade2fdd0767481b2480da07a02ef0b5c1ad01 |
# -*- coding: iso-8859-1 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Conector para linkbucks
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import re, sys
import urlparse, urllib, urllib2
from... | jose36/plugin.video.live.ProyectoLuzDigital- | servers/linkbucks.py | Python | gpl-2.0 | 2,053 | [
"ADF"
] | 38a4c29c7f3f53a6e08d1a0cc63885478e4ecf30988bc4928c15bbe0ff3f493d |
# sane.py
#
# Python wrapper on top of the _sane module, which is in turn a very
# thin wrapper on top of the SANE library. For a complete understanding
# of SANE, consult the documentation at the SANE home page:
# http://www.mostang.com/sane/ .
__version__ = '2.0'
__author__ = ['Andrew Kuchling', 'Ralph Heinkel']
... | zhaochl/python-utils | verify_code/Imaging-1.1.7/Sane/sane.py | Python | apache-2.0 | 10,210 | [
"ADF"
] | 7a4c65e6cf5f9b44b5ea0e99a686823ee4419abc6e9cc16e0df29d36c8df7d56 |
"""Utilities to evaluate pairwise distances or affinity of sets of samples"""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# License: BSD Style.
import numpy as np
from scipy.spatial import distance
from scipy.sparse import csr_matrix, issparse
from ..u... | joshbohde/scikit-learn | sklearn/metrics/pairwise.py | Python | bsd-3-clause | 9,343 | [
"Gaussian"
] | 84b11108c6472bc7092e5ae81e8f3ba34f7a6bbcaa7cc3f03ac421bce5ae705f |
"""
This is the Data Integrity Client which allows the simple reporting of
problematic file and replicas to the IntegrityDB and their status
correctly updated in the FileCatalog.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.DataMana... | vmendez/DIRAC | DataManagementSystem/Client/DataIntegrityClient.py | Python | gpl-3.0 | 20,649 | [
"DIRAC"
] | c6d62e816e89f4f7f8d4bb080de25959d2bfe326af732abd7a7f9a45aa460395 |
#!/usr/bin/env python
'''
Scan Cr2 molecule singlet state dissociation curve.
Simliar tthe example mcscf/30-hf_scan, we need to control the CASSCF initial
guess using functions project_init_guess and sort_mo. In this example,
sort_mo function is replaced by the symmetry-adapted version
``sort_mo_by_irrep``.
'''
imp... | gkc1000/pyscf | examples/mcscf/31-cr2_scan/cr2-scan.py | Python | apache-2.0 | 2,329 | [
"PySCF"
] | 8eeff01d07577907f916246f44174192d3e0402e264ee835ff9f1e632c22123d |
#
#
# prepares HTML files
# Only supports the new MCS PSF.
#
#
#
execfile("../config.py")
import shutil
from kirbybase import KirbyBase, KBError
import variousfct
import star
import lookback_fct
import combibynight_fct
import numpy as np
from glob import glob
import ds9reg
import f2n
###### config ########
start... | COSMOGRAIL/COSMOULINE | pipe/8_pyMCS_lookback_scripts/1_buildpages.py | Python | gpl-3.0 | 14,944 | [
"VisIt"
] | 910d7bc879eecf349aa2fa52d3f8a36c2d56f03430de74ea48f27581b00ce836 |
#!/usr/bin/env python
# coding=utf-8
"""508. Integers in base i-1
https://projecteuler.net/problem=508
Consider the Gaussian integer i-1. A **base i-1 representation** of a Gaussian
integer a+bi is a finite sequence of digits dn-1dn-2...d1d0 such that:
* a+bi = dn-1(i-1)n-1 \+ dn-2(i-1)n-2 \+ ... + d1(i-1) + d0
... | openqt/algorithms | projecteuler/pe508-integers-in-base-i-1.py | Python | gpl-3.0 | 1,027 | [
"Gaussian"
] | 978760dfb7a65828b1edfef470052a292be2e48a335d0ae5612a1135bf1d0ee6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 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; ... | dermoth/gramps | gramps/plugins/quickview/filterbyname.py | Python | gpl-2.0 | 18,773 | [
"Brian"
] | a8351f7ffed71b4f4d060d0d3fea080ec36e09809f997b29c999cbe043057f1f |
import os
import time
import tempfile
__doc__ = """ Create/modify a file locally while a file with the same name gets downloaded from the server.
"""
from smashbox.utilities import *
from smashbox.utilities.hash_files import *
tinker_wait = int(config.get('fileTinkerDownload_tinker_wait',2))
filesize = config.get('... | mrow4a/smashbox | lib/test_fileTinkerDownload.py | Python | agpl-3.0 | 1,517 | [
"TINKER"
] | 259705293acbe989ac411396039a9f6d3935b77defe0aab18bfe368daf075605 |
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from DIRAC.FrameworkSystem.Client import ProxyUpload
from DIRAC.Core.Security.X509Chain import X509Chain
from DIRAC.Core.DISET.RPCClient import RPCClient
from WebAppDIRAC.Lib.SessionData import SessionData
from DIRAC import gConfig, S_OK, S_ERROR, ... | chaen/WebAppDIRAC | WebApp/handler/ProxyUploadHandler.py | Python | gpl-3.0 | 8,467 | [
"DIRAC"
] | bebafa021c90925c0f7541f5a51f56ff7b74d31333fc1dd0e4196a89688a6cba |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
#
# This is a based largely on the Homebrew science formula:
# https://github.com/Homebrew/homebrew-science/blob/master/bl... | iulian787/spack | var/spack/repos/builtin/packages/blast-plus/package.py | Python | lgpl-2.1 | 7,271 | [
"BLAST"
] | 9438a6bc53049f59b8953a6b2fb399d144381d4e0347524357d3ebd4daca294a |
#!/usr/bin/env python
from __future__ import print_function
try:
from ..Priithon.all import N, U, Y, F, Mrc
except ValueError:
from Priithon.all import N, U, Y, F, Mrc
from scipy import optimize
from . import imgFit
import os
#try:
# from packages import Eext
#except:
# pass
# basic contrast operations
... | macronucleus/chromagnon | Chromagnon/PriCommon/imgFilters.py | Python | mit | 36,930 | [
"Gaussian"
] | eb0e26276bead362ee20ccda2e6bc31c5abef6984b5875655b440520ec71291a |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','desc... | tapitapps/CEStripe | build.py | Python | mit | 8,783 | [
"VisIt"
] | 29268d0d8623bc0de497046d1fdb201f3179ff49a2678ca5d41e9274f88b19c9 |
# -*- coding: utf-8 -*-
#
# secret_key.py
#
# Copyright (C) 2011-2013 Linaro Limited
# Author: Zygmunt Krynicki <zygmunt.krynicki@linaro.org>
# Copyright 2013 Neil Williams <codehelp@debian.org>
#
# This file is part of LAVA Server.
#
# LAVA Server is free software: you can redistribute it and/or modify
# it under ... | Linaro/lava-server | lava_server/settings/secret_key.py | Python | agpl-3.0 | 2,218 | [
"VisIt"
] | fed2278081523d7000ecdae86903da50894a5fa8562fdbe5368d8caf38c71842 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
from django.conf import settings
class Migration(migrations.Migration):
dependencies = [
('snisi_core', '0001_initial'),
migrations.swappable_dependency(settings.AUTH_USER_MODEL),
]
... | yeleman/snisi | snisi_trachoma/migrations/0001_initial.py | Python | mit | 8,755 | [
"VisIt"
] | 11de50bf7de07e3eb1f9a4aed3134b3fb8d75b1d3041a6d78b96f9c1e15d4ce6 |
#!/usr/bin/env python
'''
@author: Deniz Altinbuken, Emin Gun Sirer
@note: concoord script
@date: January 20, 2012
@copyright: See LICENSE
'''
import argparse
import signal
from time import sleep,time
import os, sys, time, shutil
import ast, _ast
import concoord
from concoord.enums import *
from concoord.safetychecker ... | tempbottle/concoord | concoord/main.py | Python | bsd-3-clause | 5,986 | [
"VisIt"
] | de0e58cf51531b86741a360018200b08b181a22b474ee7363de81bc6e855d180 |
#Apache OCW lib immports
from ocw.dataset import Dataset, Bounds
import ocw.data_source.local as local
import ocw.data_source.rcmed as rcmed
import ocw.dataset_processor as dsp
import ocw.evaluation as evaluation
import ocw.metrics as metrics
import ocw.plotter as plotter
import ocw.utils as utils
import dat... | MJJoyce/climate | examples/subregions_portrait_diagram.py | Python | apache-2.0 | 5,313 | [
"NetCDF"
] | a41563958621bb9d7a08af9338d083df6bfc3a038ec8fb77bf38e47a9a1db658 |
#!/usr/bin/python
__author__="cooke"
__date__ ="$02-Feb-2012 15:26:23$"
"""
Initialize a basic broadcast slave channel for listening to
an ANT+ Bicycle cadence and speed senser, using raw messages
and event handlers.
"""
import logging
import optparse
from time import sleep
import os.path
from ant.core import event
f... | agcooke/ExperimentControl | bin/experiment-control.py | Python | bsd-3-clause | 6,240 | [
"VisIt"
] | eec4e11156b57a1d27009a9dac22a0fbee47be2373213bbb6d7b5194cd5f7b0e |
# Copyright 2015 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... | jhseu/tensorflow | tensorflow/python/ops/image_ops_test.py | Python | apache-2.0 | 203,373 | [
"Gaussian"
] | e01ca0b76fd94026331ddaf919e82309fd033836f84057b736ae6f07f3875dd8 |
r"""
==================================
Constants (:mod:`scipy.constants`)
==================================
.. currentmodule:: scipy.constants
Physical and mathematical constants and units.
Mathematical constants
======================
================ ===========================================================... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/constants/__init__.py | Python | mit | 12,203 | [
"Avogadro"
] | c6df32c17e45c676050ad2694ffcbd1109b40edd8fb2ccb92b31fbfae9f395f6 |
"""
Django settings for pyconuk project.
Generated by 'django-admin startproject' using Django 1.9.6.
For more information on this file, see
https://docs.djangoproject.com/en/1.9/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.9/ref/settings/
"""
import os
#... | PyconUK/2017.pyconuk.org | pyconuk/settings.py | Python | mit | 3,532 | [
"Amber"
] | 8516f5c6a5e951ad7d15ce07edc89b596496956f7fbc8ee5fa7e150bfc6a5999 |
#a whole bunch of i/o functions
#jared@well.ox.ac.uk
import csv, sys,copy,gzip,numpy as np,os,math,time,cStringIO,io,itertools
import numpy as np
import subprocess,string
import string,random#,pysam
csv.field_size_limit(1000000000)
def read_genetic_map(fname):
return np.genfromtxt(ropen(fname),dtype=np.dtype([('p... | jaredo/gwas | iolib.py | Python | mit | 46,973 | [
"pysam"
] | 5e3b8422524b29dab6e044048d6b3c0de31bb726aefcb3fbd756176cf94bc924 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/mp/ump2.py | Python | apache-2.0 | 28,136 | [
"PySCF"
] | 8db987ef8d797c6357da3408433a30a960df11bb43cfcaffc4b72dc2ee582c50 |
########################################################################
# Author: Stuart Paterson
# eMail : Stuart.Paterson@cern.ch
########################################################################
""" The Watchdog class is used by the Job Wrapper to resolve and monitor
the system CPU and memory consumed... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/JobWrapper/WatchdogLinux.py | Python | gpl-3.0 | 3,840 | [
"DIRAC"
] | fc367b806147ad5fe89f8b49b5be47b5cd35dc1917869b6e8ca2a94ffe503647 |
#! /usr/bin/env python
"""Generate C code from an ASDL description."""
import os, sys
import asdl
TABSIZE = 4
MAX_COL = 80
def get_c_type(name):
"""Return a string for the C name of the type.
This function special cases the default types provided by asdl.
"""
if name in asdl.builtin_types:
... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.5.9/Python-3.5.9/Parser/asdl_c.py | Python | apache-2.0 | 44,419 | [
"VisIt"
] | 17ff7bae0742a23370324ec76dd4ce7e11d65db2fdd8dcf7602b84da2df3acc4 |
########################################################################
# File: FTSDB.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 15:13:51
########################################################################
""" :mod: FTSDB
===========
.. module: FTSDB
:synopsis: FTS DB
.. modul... | Sbalbp/DIRAC | DataManagementSystem/DB/FTSDB.py | Python | gpl-3.0 | 22,029 | [
"DIRAC"
] | c1920df1fe7cebe461f7f9fea8c1ef74416be96d1d228323c6efef112e43389f |
import ast
class CombineImports(ast.NodeTransformer):
"""
Combine multiple import statements where possible
This doesn't change the order of imports
"""
def __call__(self, node):
return self.visit(node)
def visit_ClassDef(self, node):
node.body = self.suite(node.body)
... | listyque/TACTIC-Handler | thlib/side/python_minifier/transforms/combine_imports.py | Python | epl-1.0 | 3,278 | [
"VisIt"
] | 296489fb38a733c438a5130312f088796da1ae368ca1ff1185da35923e914623 |
import unittest
import re
from pynhost import grammarbase
from pynhost import ruleparser
class TestRegexConvert(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.num_text = ''
def test_compile0(self):
input_str = 'hello'
r = ruleparser.Rule('')
self.assertEqual(r.c... | evfredericksen/pynacea | pynhost/test_pynhost/test_regex_compile.py | Python | mit | 6,801 | [
"Galaxy"
] | 058e245ed0ce7c19f663328e8be33eb1523652feacd7e77fa94b1219f8df9b82 |
from pyscf.pbc.gto import Cell
from pyscf.pbc.scf import KRKS
from pyscf.pbc.tdscf import KTDDFT
from pyscf.pbc.tdscf import kproxy_supercell
from pyscf.tdscf.common_slow import eig, format_frozen_k, format_frozen_mol
from test_common import retrieve_m, ov_order, assert_vectors_close
import unittest
from numpy import... | gkc1000/pyscf | pyscf/pbc/tdscf/test/test_kproxy_supercell_ks.py | Python | apache-2.0 | 9,930 | [
"PySCF"
] | a91aba0130bd1b96f55bcf09a96c7b9df2306f553d9ef80441e8e4bfcbc3482c |
import copy
import scipy.misc
import scipy.integrate
import lb_loader
import pandas as pd
import simtk.openmm.app as app
import numpy as np
import simtk.openmm as mm
from simtk import unit as u
from openmmtools import hmc_integrators, testsystems
sysname = "ljbox"
system, positions, groups, temperature, timestep = lb... | kyleabeauchamp/HMCNotes | code/correctness/old/test_integrals.py | Python | gpl-2.0 | 1,289 | [
"OpenMM"
] | abefc3e343eda1b08ce96560167392fe8ee291c127d6d6257b47749af88bd1cf |
#!/usr/bin/env python
# Copyright (c) 2002 Bryce "Zooko" Wilcox-O'Hearn
# portions Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
__cvsid = '$Id: EGTPtest.py,v 1.14 200... | zooko/egtp | EGTPtest.py | Python | agpl-3.0 | 5,759 | [
"VisIt"
] | df417278f00de76bd9374c0ed1b62e312543a612f5300e16d15f91c7ebca2f53 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/lib/dockwidget.py | Python | gpl-2.0 | 3,058 | [
"Brian"
] | cb59f7159fe57d229ae09291ba6a2b9d8ccde5fc5942245fcc69335303729602 |
'''
Created on 20 Jul. 2018
@author: Alex Ip
Utility to read metadata from netCDF files under a specified directory into dataset metadata cache
'''
import sys
import os
from glob import glob
from geophys_utils.dataset_metadata_cache import get_dataset_metadata_cache, Dataset, Distribution
import logging
import netCDF... | alex-ip/geophys_utils | geophys_utils/dataset_metadata_cache/netcdf2dataset_metadata_cache.py | Python | apache-2.0 | 10,417 | [
"NetCDF"
] | 22579f6809dc5c3348e613b08a2a87838dfd6ab8727424c1cebc180b65b12a95 |
""" This provides some useful code used by other modules. This is not to be
used by the end user which is why it is hidden. """
import string, sys
class LinkError(Exception):
pass
def refine_import_err(mod_name, extension_name, exc):
""" Checks to see if the ImportError was because the library
itself was... | b3c/VTK-5.8 | Wrapping/Python/vtk/__helper.py | Python | bsd-3-clause | 981 | [
"VTK"
] | cd45b4616f1dd3995e488e9d018379f56b79d14920ef21daa51d9a19c7a935df |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import os
from spack import *
class Molcas(CMakePackage):
"""Molcas is an ab initio quantum chemistry software pack... | LLNL/spack | var/spack/repos/builtin/packages/molcas/package.py | Python | lgpl-2.1 | 888 | [
"MOLCAS"
] | 993907d01ec99dcca68a250075b21bed432c23c681fe274d8795e6b69f516cea |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Gaussian White Noise Restoration via CSC
========================================
This example demonstrates t... | bwohlberg/sporco | examples/scripts/csc/gwnden_clr.py | Python | bsd-3-clause | 5,086 | [
"Gaussian"
] | 6bacda11aa041f2d42ff4b651c38213f5190e08a800e696bb3e9179ff03f8475 |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
account = "ACXXXXXXXXXXXXXXXXXXXXX... | teoreteetik/api-snippets | notifications/rest/services/delete-service/delete-service.6.x.py | Python | mit | 497 | [
"VisIt"
] | 7c3b2ce865a25c4ad6016ee5eb1fec156603b77e1a41958498e2fc21503ec46f |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors:
#
# MDTraj is free software:... | leeping/mdtraj | tests/test_thermodynamic_properties.py | Python | lgpl-2.1 | 6,431 | [
"Gromacs",
"MDTraj"
] | 6761dad66e8a868d2b9c00d6bd92e494b7c1b21aab64c7d3981c58eb45a5f82d |
# -*- coding: utf-8-*-
import datetime
import re
import facebook
from client.app_utils import get_timezone
WORDS = ["BIRTHDAY"]
def handle(text, mic, profile):
"""
Responds to user-input, typically speech text, by listing the user's
Facebook friends with birthdays today.
Arguments:
... | benhoff/jasper-client | client/modules/Birthday.py | Python | mit | 2,016 | [
"VisIt"
] | 227941cda9a1163b464a95a8fb5656d12cf7076fe4a9a16b815e51f17dd880e5 |
## Python script to make a table that includes the sequence id for OTU centroids, the OTU number (as used in usearch) and the taxonomy that was assigned in motur
import sys
#file1="../results/Divided_by_primers/All_libs_combined_OTUs_picked/18s_OTUs.fasta"
#file2="../results/Divided_by_primers/All_libs_combined_OTUs_... | jooolia/phylo_temporal_jericho | sequence_processing/Mapping_taxonomy_to_OTUs.py | Python | mit | 1,959 | [
"Biopython"
] | fa27bed24fe9a1dde4e971d8aa359aa469ac04c3f14c7a0f5be012507d1a06a9 |
# Copyright (C) 2010-2019 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... | KaiSzuttor/espresso | testsuite/python/constraint_shape_based.py | Python | gpl-3.0 | 36,175 | [
"ESPResSo"
] | 5502286f971f10fe189e1c80c46174b456cb021b1ec96f7a85cb32bb6490c01c |
import abc, sys, io
import numpy as np
import pandas as pd
from cvxopt import solvers, matrix
from numpy import linalg
from scipy.stats import multivariate_normal
from ..utils import create_logger, is_level_debug
from classifip.representations.voting import Scores
try:
import matlab.engine
except Exception as e:
... | sdestercke/classifip | classifip/models/qda.py | Python | gpl-2.0 | 26,091 | [
"Gaussian"
] | e39db588c17fdc69f0e4a6983626ea53214d0c052127390256a5f81674718aff |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or ... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Core/Testing/Python/SliceOrder.py | Python | bsd-3-clause | 3,120 | [
"VTK"
] | 7a1ee7011ab74d696e913e03b1c10acd4495f55a611d367a0283af330ed8caa6 |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2021, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2-plugins/normalize | q2_feature_table/_summarize/_visualizer.py | Python | bsd-3-clause | 11,912 | [
"BLAST"
] | 13d2a9b3e9f2cfbe7850bbbe98cafa32780a4b5dea907d94545004b8fbbb0350 |
#!/usr/bin/python
doc_name = 'CfA.SNIbc.BIGINFO.list'
#doc_name = 'test'
USR='fedhere'
PWD='*******'
import sys,os
sys.path.append('mypython')
import pylab as pl
import gdata.docs
import gdata.docs.service
import gdata.spreadsheet.service
import re
import optparse
from numpy import array, ma, mean, std, m... | fedhere/SESNCfAlib | getCfASNtable/getfromtable.py | Python | mit | 12,898 | [
"Galaxy"
] | 9cd83bbbbb1208bf3d499be88fa990dfc34ff63750ea561464e02d53c33228a4 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/songusage/forms/songusagedetaildialog.py | Python | gpl-2.0 | 5,817 | [
"Brian"
] | 63aa5cbfa44fd82db48094b1b3900eb00d44a474e1cb60fb5632e6a2c66d6618 |
from __future__ import print_function
from __future__ import division
import os
import sys
import numpy as np
from scipy import optimize
from numpy.linalg import solve, LinAlgError
from numpy.linalg import cholesky as chol
from six import with_metaclass
from abc import ABCMeta, abstractmethod
try: # Run as a packag... | amarquand/nispat | pcntoolkit/model/gp.py | Python | gpl-3.0 | 15,337 | [
"Gaussian"
] | 975d8a3a1883910b5d48cbda6e0a127926d5695ae25c1459b8c597a65a73e922 |
"""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:... | kenshay/ImageScript | Script_Runner/PYTHON/Lib/inspect.py | Python | gpl-3.0 | 117,120 | [
"VisIt"
] | a345b8ee726b32c7966a6d5c148e969fe012c5fb6484a36a8c2e787223f2b78b |
import itertools as it
import difflib
import glob
import os
from pkg_resources import resource_filename
from lxml import etree as ET
import parmed as pmd
import pytest
from foyer import Forcefield, forcefields
from foyer.forcefield import generate_topology
from foyer.forcefield import _check_independent_residues, _s... | iModels/foyer | foyer/tests/test_forcefield.py | Python | mit | 22,431 | [
"OpenMM"
] | 713df22b127216838969dfc71834bbf9f6144f55ad92396da909fe172f10b6e4 |
''' EmailAction
This action writes all the necessary data to a cache file ( cache.db ) that
will be used later by the EmailAgent in order to send the emails for each site.
'''
__RCSID__ = '$Id$'
from DIRAC import S_ERROR
from DIRAC.ResourceStatusSystem.Client.ResourceStatusClient import ResourceStatusClient
fro... | chaen/DIRAC | ResourceStatusSystem/PolicySystem/Actions/EmailAction.py | Python | gpl-3.0 | 2,949 | [
"DIRAC"
] | 2e3b828ea758f33e42d2fd40730f20731c788e58a1d7ba427f61c01076fdf218 |
#!/usr/bin/python
#
# Filename: dumpsterFireFactory.py
#
# Version: 1.0.1
#
# Author: Joe Gervais (TryCatchHCF)
#
# Summary:
#
# Create and execute time-delayed, distributed security incidents for Red- and Blue
# Team exercises. Allows repeatable, trackable
#
# User interface for creating, reviewing, editing, and... | TryCatchHCF/DumpsterFire | dumpsterFireFactory.py | Python | mit | 49,392 | [
"VisIt"
] | 3ea24c6e5768a387cef4eca88dcb5bd881b81046c0590526c37a5809a2a79a76 |
# -*- coding: utf-8 -*-
from __future__ import print_function
import collections
import multiprocessing
import os
import time
try:
from cStringIO import StringIO
except ImportError:
from io import StringIO
from . import exceptions
from . import g2g
from . import g2g_utils
import pysam
from bx.intervals.int... | churchill-lab/g2gtools | g2gtools/vci.py | Python | mit | 14,480 | [
"pysam"
] | 2d8ad6297914678fa6917e96e3c2108f24776f44e775273acc618dd9a01a6a51 |
import itertools
import math
import random
import mixins
import dice
class Character(mixins.AppearanceMixin):
def __init__(self, *args, **kwargs):
super(Character, self).__init__(*args, **kwargs)
self.role = random.choice(self.ROLES)
self.occupation = random.choice(self.OCCUPATIONS)
... | funkaoshi/randomcharacter | demoncity.py | Python | mit | 42,366 | [
"CASINO",
"VMD"
] | 69aaa483917d8d0ca176fe5619eb780145fb5421bb3560eab55f4c58440c7e68 |
# 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]
(... | great-expectations/great_expectations | versioneer.py | Python | apache-2.0 | 68,458 | [
"Brian"
] | 8a0a207482be13c587f5c4f75380719ec21d2332a093b3abdc4fd4a3881713b3 |
from __future__ import division, print_function, absolute_import
import numpy as np
from scipy.ndimage import map_coordinates
from dipy.viz.colormap import line_colors
# Conditional import machinery for vtk
from dipy.utils.optpkg import optional_package
# import vtk
# Allow import, but disable doctests if we don't ... | JohnGriffiths/dipy | dipy/viz/utils.py | Python | bsd-3-clause | 7,389 | [
"VTK"
] | 6a2f03aa4eb76769666dbe2293b0050cc292644bef5dc45adfe16a2ac1e48efe |
'''
* Created by Zhenia Syryanyy (Yevgen Syryanyy)
* e-mail: yuginboy@gmail.com
* License: this code is under GPL license
* Last modified: 2017-02-27
'''
import os
from feff.libs.dir_and_file_operations import runningScriptDir, get_folder_name
from feff.libs.load_chi_data_file import load_and_apply_xftf, load_chi_data
... | yuginboy/from_GULP_to_FEFF | feff/libs/class_Spectrum.py | Python | gpl-3.0 | 16,880 | [
"FEFF"
] | e6930995e1749909f491880fc169696c798ad796e10b07bd75ad91582afec42c |
# encoding:utf-8
"""
:synopsis: views diplaying and processing main content post forms
This module contains views that allow adding, editing, and deleting main textual content.
"""
import datetime
import logging
import os
import os.path
import random
import sys
import tempfile
import time
import urlparse
from django.s... | tvenkat/askbot-devel | askbot/views/writers.py | Python | gpl-3.0 | 26,756 | [
"VisIt"
] | e99da0998d397f73bd186ec873839b5804cfea59e637ef1e5d5597ae2be1a205 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/wait/StartWait.py | Python | gpl-3.0 | 1,952 | [
"ORCA"
] | 9b5741b7b0a959913614242efd50ab6e1905219ac2397e8de1e03c49896dbbdb |
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