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#! /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-orchestration-airflow | scripts/fixup_service_v1beta1_keywords.py | Python | apache-2.0 | 6,383 | [
"VisIt"
] | 2d56530f837148886c384f054031b2cab35627b8fbafe4e16e30bf9a18d04f14 |
"""
===============
GMM covariances
===============
Demonstration of several covariances types for Gaussian mixture models.
See :ref:`gmm` for more information on the estimator.
Although GMM are often used for clustering, we can compare the obtained
clusters with the actual classes from the dataset. We initialize th... | RPGOne/Skynet | scikit-learn-0.18.1/examples/mixture/plot_gmm_covariances.py | Python | bsd-3-clause | 4,724 | [
"Gaussian"
] | f22ae19ed87dada29d036d11445b71bac12d02ced2a4be4f1c6f6a772c329dd5 |
import numpy as np
import matplotlib.pyplot as plt
import time
import h5py
from ..doublyPeriodic import doublyPeriodicModel
from numpy import pi
class model(doublyPeriodicModel):
def __init__(self, name = None,
# Grid parameters
nx = 128, ny = None, Lx = 2.0*pi, Ly = None,
# ... | glwagner/py2Periodic | py2Periodic/physics/linearizedBoussinesq_xy.py | Python | mit | 11,854 | [
"Gaussian"
] | 8772d51fe2412c875c3715235eeffd7036ec02eb2b1b619064d3a057a6f27a79 |
# Copyright 2013 by Leighton Pritchard. 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 classes and functions to parse a KGML pathway map.
The KGML path... | zjuchenyuan/BioWeb | Lib/Bio/KEGG/KGML/KGML_parser.py | Python | mit | 6,552 | [
"Biopython"
] | b1edbfb7c18d255db402ac5f6b1da3dfe6f5c17bf265a2ba4c482eb57db3efa1 |
#
# Copyright (c) 2018, 2021, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# The Universal Permissive License (UPL), Version 1.0
#
# Subject to the condition set forth below, permission is hereby granted to any
# person obtaining a copy of this sof... | smarr/Truffle | truffle/mx.truffle/mx_truffle.py | Python | gpl-2.0 | 40,988 | [
"VisIt"
] | 4ffed93b2d16cfc512a8939480714750c482877f1123557daa5c38c336afa9f1 |
import random
# coding: utf-8
import math
def randomrange(*args):
"""
.. function:: randomrange(start, end, step) -> int
Returns a random number in the defined range
Examples:
>>> sql("select randomrange(0, 68, 1)") # doctest: +ELLIPSIS
randomrange(0, 68, 1)
---------------------
..... | openaire/iis | iis-3rdparty-madis/src/main/resources/eu/dnetlib/iis/3rdparty/scripts/madis/functions/row/mathops.py | Python | apache-2.0 | 2,177 | [
"Gaussian"
] | 0ba7b1b8c911ec89825cb3f60975e57af3f65d0741dc52f84c0214557141b8c8 |
import ResolvedStellarPops as rsp
import numpy as np
import os
import pyfits
from sfhs.vary_sfh import VarySFHs
import time
from IPython import parallel
import matplotlib.pylab as plt
def plot_lf_files():
import plotting as pl
from astropy.io import fits
def translate_model_name(model, small=False):
... | philrosenfield/TPAGB-calib | tpagb_calibration/snap_data.py | Python | bsd-3-clause | 10,491 | [
"Galaxy"
] | ac4039861afc20947cd20549478418a60ba4c5b3a8d67c7ff357e4b8c9eee93e |
# -*- coding: utf-8 -*-
#-------------------------------------------------------------------------------
# Name: omnifocuslib.py
# Purpose: helper functions for simulation of omnifocus image synthesis
# using Zemax and PyZDDE. In particular, the results presented in
# the pa... | indranilsinharoy/cosi2016_omnifocus | omnifocuslib.py | Python | mit | 91,496 | [
"Gaussian"
] | b806a67d4889e7f0ba23e1192bf6ebddcb53292b09af847931be2074ddd2dc21 |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
import os
import sys
import fnmatch
import ast
import doctest
import collections
import os.path as pathlib
from .log import logger
from .helpers import parse_git_config, trim_suffix
import nbformat
Module = collections.namedtu... | Damnever/pigar | pigar/parser.py | Python | bsd-3-clause | 11,861 | [
"VisIt"
] | 07535ddaba639cbbdee50979fa72aa4a6b887b209028f58ff540c2f482ea0d0c |
# -*- coding: utf-8 -*-
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008-2009 Brian G. Matherly
# Copyright (C) 2009 Rob G. Healey <robhealey1@gmail.com>
# Copyright (C) 2014 Vlada Perić <vlada.peric@gmail.com>
#
# This program is free softwar... | sam-m888/gprime | gprime/plugins/lib/libholiday.py | Python | gpl-2.0 | 17,741 | [
"Brian"
] | 75e6088e268fe6e5aa832e13399ec0b9b38be401736377d0e0b5c2a7874b3019 |
# -*- coding: utf-8 -*-
# Copyright 2010 Dirk Holtwick, holtwick.it
#
# 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 ... | atn9/xhtml2pdf | xhtml2pdf/parser.py | Python | apache-2.0 | 24,428 | [
"VisIt"
] | c281a9e43a18b991f65a80a69973508fedfa614e3a2197e0aa65c1f0d4cc12de |
import numpy as np
import six
import sys
import matplotlib as mpl
from ...config import kafe2_rc
from ...core.confidence import ConfidenceLevel
from .._base import FitBase
from .._base.format import ScalarFormatter as ScalarBaseFormatter
from matplotlib import pyplot as plt, rcParams
from matplotlib import gridspec as... | dsavoiu/kafe2 | kafe2/fit/tools/contours_profiler.py | Python | gpl-3.0 | 37,347 | [
"Gaussian"
] | 45e9e7a7c9271ba0ad99026295d5f8380a5f80faa0aa7ce1d014d7f91502c923 |
from __future__ import absolute_import, division
import numpy as np
import os
import shutil
import tempfile
import matplotlib
matplotlib.use('Agg', warn=False)
from matplotlib.pyplot import Artist, savefig, clf, cm, get_cmap
from matplotlib.testing.noseclasses import ImageComparisonFailure
from matplotlib.testing.com... | IamJeffG/geopandas | geopandas/tests/test_plotting.py | Python | bsd-3-clause | 10,101 | [
"COLUMBUS"
] | 49ba17262b174c91f837a551deaaa94428a1f4b177954df057e33850a5bb9caa |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | yasharmaster/scancode-toolkit | etc/scripts/dejacode.py | Python | apache-2.0 | 2,405 | [
"VisIt"
] | 01c8c1faaf31e631c0e5c552ac3b5afd992047b6eb7b828389c5418b4e789476 |
from math import cos, sin, pi
from ase import Atoms
from ase.optimize import QuasiNewton
from ase.vibrations import Vibrations
from gpaw import GPAW
# Water molecule:
d = 0.9575
t = pi / 180 * 104.51
H2O = Atoms('H2O',
positions=[(0, 0, 0),
(d, 0, 0),
(d * c... | robwarm/gpaw-symm | doc/exercises/vibrations/vibH2O.py | Python | gpl-3.0 | 743 | [
"ASE",
"GPAW"
] | 9f096a4e6276709f63b51fad52d59b0c8c174169b8e519cc39286addc62abbc0 |
import gzip
import os
import shutil
from asyncio import gather
from pathlib import Path
import pytest
from aiohttp.test_utils import make_mocked_coro, make_mocked_request
from sqlalchemy.ext.asyncio import AsyncEngine, AsyncSession
import virtool.uploads.db
from virtool.db.transforms import apply_transforms
from virt... | igboyes/virtool | tests/samples/test_db.py | Python | mit | 14,378 | [
"Bowtie"
] | b016e01f0db554886cd9ab48be59d6ef6f38b00e6c9ee3604900d04f7ee27bd7 |
"""
Import utilities
Exported classes:
ImportManager Manage the import process
Importer Base class for replacing standard import functions
BuiltinImporter Emulate the import mechanism for builtin and frozen modules
DynLoadSuffixImporter
"""
# note: avoid importing non-builtin modules
import... | xbmc/atv2 | xbmc/lib/libPython/Python/Lib/imputil.py | Python | gpl-2.0 | 25,675 | [
"BLAST"
] | cfd62be9f3b429a2e4e48d58e04ebb4c7af72cf0af226a3fead036faa40c7b1b |
#!/usr/bin/env python
#=========================================================================
#
# 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
... | prasadvagdargi/med_image_analysis | Examples/FilterProgressReporting/FilterProgressReporting.py | Python | apache-2.0 | 2,125 | [
"Gaussian"
] | 82822e0f8b6fe5deae7a9a0a714661dd6ab896ec84c943f7dd72a03138d7773c |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/servicelistreload.py | Python | gpl-2.0 | 5,286 | [
"VisIt"
] | c60cae4bb6fb640431909d64815a3c5d8bba7c305a0b28e399eef8ecb53d7818 |
# coding=UTF-8
"""Copyleft 2010-2015 Forrest Sheng Bao http://fsbao.net
Copyleft 2010 Xin Liu
Copyleft 2014-2015 Borzou Alipour Fard
PyEEG, a Python module to extract EEG feature.
Project homepage: http://pyeeg.org
**Data structure**
PyEEG only uses standard Python and numpy data structures,
so you need to i... | bnaul/pyeeg | pyeeg/__init__.py | Python | gpl-3.0 | 32,322 | [
"VisIt"
] | 3ba9517fbbade2413303477a2946b6078ef50119f3728d7dce55c8487ecb3216 |
from setuptools import setup, find_packages
from mfr import __version__
def parse_requirements(requirements):
with open(requirements) as f:
return [l.strip('\n') for l in f if l.strip('\n') and not l.startswith('#')]
requirements = parse_requirements('requirements.txt')
setup(
name='mfr',
vers... | TomBaxter/modular-file-renderer | setup.py | Python | apache-2.0 | 51,290 | [
"VTK"
] | 9327a3760dc09980210444bfe3b842e74f6a950a652ef1cfd8f7704b8be6a995 |
LANGUAGE_NAMES = {
u"Afar": "aa",
u"Ghotuo": "aaa",
u"Arum-Tesu": "aab",
u"Ari": "aac",
u"Amal": "aad",
u"Arbëreshë Albanian": "aae",
u"Aranadan": "aaf",
u"Ambrak": "aag",
u"Abu' Arapesh": "aah",
u"Arifama-Miniafia": "aai",
u"Ankave": "aak",
u"Afade": "aal",
u"Aramani... | radomd92/botjagwar | conf/entryprocessor/languagecodes.py | Python | mit | 186,322 | [
"ADF",
"ASE",
"BWA",
"Elk",
"MOE",
"MOOSE",
"VMD",
"xTB"
] | 42e2fff6911ea44f9d3c64e5b00c59d8769304edb89bd8a92f7e2bba987d520c |
"""Builds the Adience network.
Summary of available functions:
# Compute input images and labels for training. If you would like to run
# evaluations, use input() instead.
inputs, labels = distorted_inputs()
# Compute inference on the model inputs to make a prediction.
predictions = inference(inputs)
# Comput... | NumesSanguis/MLTensor | adience/adience.py | Python | apache-2.0 | 18,728 | [
"Gaussian"
] | c375d6af05139cab85885c203eb4505adce7d2526746a20a3db7e646e1aeda6c |
"""The pylab module of ipvyolume."""
from __future__ import absolute_import
from __future__ import division
import pythreejs
__all__ = [
'current',
'clear',
'controls_light',
'figure',
'gcf',
'xlim',
'ylim',
'zlim',
'xyzlim',
'squarelim',
'set_box_aspect',
'set_box_aspe... | maartenbreddels/ipyvolume | ipyvolume/pylab.py | Python | mit | 68,979 | [
"Gaussian"
] | 2884ec6f8b25ca822c6c980a4b25570534fc29ec8eaf24cc68eb5ed5b33aaa19 |
__source__ = 'https://leetcode.com/problems/spiral-matrix-iii/'
# Time: O()
# Space: O()
#
# Description: Leetcode # 885. Spiral Matrix III
#
# On a 2 dimensional grid with R rows and C columns, we start at (r0, c0) facing east.
#
# Here, the north-west corner of the grid is at the first row and column,
# and the sout... | JulyKikuAkita/PythonPrac | cs15211/SpiralMatrixIII.py | Python | apache-2.0 | 5,684 | [
"VisIt"
] | 31047d4a28e16380398755d10da1684cae558f0bc2f97216a9d6ac21c9bbe2c8 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2019 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | dictoon/blenderseed | properties/lamps.py | Python | mit | 7,951 | [
"VisIt"
] | 6179c66fa4e5e4d82b360b75e51a023e3a135921fdfdfdc02411125a9293084a |
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2014 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation; either version 2.1 of the
# License, or... | forrestv/myhdl | myhdl/conversion/_toVHDL.py | Python | lgpl-2.1 | 74,865 | [
"VisIt"
] | b56aca5392ce3a3dd01cc71c3e0e95c76df3e22864536fbc3bfb3450f9b14c3a |
########################################################################
# $Id$
########################################################################
""" The LSF TimeLeft utility interrogates the LSF batch system for the
current CPU and Wallclock consumed, as well as their limits.
"""
__RCSID__ = "$Id$"
from ... | sposs/DIRAC | Core/Utilities/TimeLeft/LSFTimeLeft.py | Python | gpl-3.0 | 9,232 | [
"DIRAC"
] | 43b417db348eb08ef486e3fef4f55f3dbcfc25140dd718eb43c311c6e03c2554 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/learn/ray/pytorch/test_estimator_pyspark_backend.py | Python | apache-2.0 | 18,616 | [
"ORCA"
] | 546489f28f0cb69a30c5dfd8b33d603bfe1afe6b07aaa9a8e7d4eed37b933e29 |
#!/usr/bin/python
"""
Copyright 2017 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/verifyUser.py | Python | gpl-3.0 | 2,719 | [
"Galaxy"
] | b9d1396ac21e30e0a1bdc127deb3c464f6ce8492cade1a58a7b5f8755b61b293 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
import time
m = 4000
n = 2000
display = True
... | sg0/Elemental | examples/interface/NNLS.py | Python | bsd-3-clause | 2,114 | [
"Gaussian"
] | 57237e354ddce3f4cdf3c9a9ff335a2f2131ab8db0a39d18e743184338979981 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
##===-----------------------------------------------------------------------------*- Python -*-===##
##
## S E R I A L B O X
##
## This file is distributed under terms of BSD license.
## See LICENSE.txt for more information.
##
##===---------... | thfabian/serialbox2 | test/serialbox-python/serialbox/test_serializer.py | Python | bsd-2-clause | 18,226 | [
"NetCDF"
] | 2cdb6d79a4de2b88c6599e7741f68ce6eef429e428a159bdb9e648b90cb141aa |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('backend', '0001_initial'),
]
operations = [
migrations.AlterField(
model_name='automatedmessage',
na... | I-TECH-UW/mwachx | backend/migrations/0002_auto_20160122_1618.py | Python | apache-2.0 | 1,172 | [
"VisIt"
] | 1286776670c299d2824565d0b11758a7be07d36ea71c9da8766489c8601941f7 |
import logging
from typing import List
import numpy as np
from deepchem.utils.typing import RDKitMol
from deepchem.utils.molecule_feature_utils import one_hot_encode
from deepchem.feat.base_classes import Featurizer
from typing import Any, Iterable, Optional
logger = logging.getLogger(__name__)
ZINC_CHARSET = [
... | deepchem/deepchem | deepchem/feat/molecule_featurizers/one_hot_featurizer.py | Python | mit | 5,709 | [
"RDKit"
] | 319c6fd4c09e966c6cdb00f8652e5b3d0aa65c20e43238c4db95c64776c3aaff |
"""
Test Logger Wrapper
"""
__RCSID__ = "$Id$"
import logging
from six import StringIO
from DIRAC.FrameworkSystem.private.standardLogging.LoggingRoot import LoggingRoot
from DIRAC.FrameworkSystem.private.standardLogging.Logging import Logging
gLogger = LoggingRoot()
def cleaningLog(log):
"""
Remove date and ... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/private/standardLogging/test/TestLogUtilities.py | Python | gpl-3.0 | 2,232 | [
"DIRAC"
] | 92cff259e606e22b7a29b8588608b222c7474c0a0886f2c10b340cc0e06847c7 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | arunkgupta/gramps | gramps/plugins/textreport/simplebooktitle.py | Python | gpl-2.0 | 7,495 | [
"Brian"
] | 88d777d749a0ca3714880578de518b025ea947137fbb54b834b913f9725f1299 |
import glob
import logging
import os
import subprocess
from plugins import BaseAligner
from yapsy.IPlugin import IPlugin
from assembly import get_qual_encoding
class Bowtie2Aligner(BaseAligner, IPlugin):
def run(self):
"""
Map READS to CONTIGS and return alignment.
Set MERGED_PAIR to True ... | levinas/assembly | lib/assembly/plugins/bowtie2.py | Python | mit | 2,404 | [
"Bowtie"
] | f0ff34ea9a9c71530414e76c1f544256140f60a24a8cf1c681908c5fa8f96b59 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/licensedcode/saneyaml.py | Python | apache-2.0 | 7,133 | [
"VisIt"
] | 1b8c0e053fca1b1b4e246016c11633569625af6259e9ab45ddcd73a8b44dd86b |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Quadric definition
quadric = vtk.vtkQuadric()
quadric.SetCoefficients([.5,1,.2,0,.1,0,0,.2,0,0])
sample = vtk.vtkSampleFunction()
sample.SetSampleDimensions(30,30,30)
sam... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/DataModel/Testing/Python/scalarConn.py | Python | bsd-3-clause | 1,921 | [
"VTK"
] | 1b2310d6713527d578af5de38e812c951d915e1b1c133fdea9ed2cf3ed42b730 |
"""
.. Copyright (C) 2009 Inspired Intelligence Initiative
.. This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) ... | tectronics/ecspy | ecspy/variators/mutators.py | Python | gpl-3.0 | 5,602 | [
"Gaussian"
] | f4cbb6fa4aa68ff190ddeff1207545a7999bab3b480eece60fb5df62c4276e2c |
"""Utilities used in the Kadenze Academy Course on Deep Learning w/ Tensorflow.
Creative Applications of Deep Learning w/ Tensorflow.
Kadenze, Inc.
Parag K. Mital
Copyright Parag K. Mital, June 2016.
"""
import matplotlib.pyplot as plt
import tensorflow as tf
import urllib
import numpy as np
import zipfile
import os
... | goddoe/super_resolution | src/libs/utils.py | Python | mit | 20,943 | [
"Gaussian"
] | 97f343b8dc9b66cc4b5406bc76e17c6dadb74b7c149074a25898d7b3c2c0c963 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | bgoli/pysces | pysces/core2/PyscesCore2.py | Python | bsd-3-clause | 53,588 | [
"PySCeS"
] | d2f624d5f1c8af46c8e16abcf5fc8b9039ac1c11337df47e0065f7099b41a3d8 |
import unittest
import numpy as np
import scipy.signal
import sys
sys.path.append("..")
import features
def zeros(sig_len=1024):
signal = np.zeros(sig_len)
return (signal, np.fft.rfft(signal))
def ones(sig_len=1024):
signal = np.ones(sig_len)
return (signal, np.fft.rfft(signal))
def sine(periods=1... | bastibe/MusicTagger | tests/test_features.py | Python | bsd-3-clause | 8,916 | [
"DIRAC"
] | 3f9616ac5b00ed17df6b088023002fb0f1b82618ab2e09634498264d227420f6 |
import numpy as np
import multiprocessing
import time
from deeptools import countReadsPerBin
from deeptools.utilities import getTLen
from deeptoolsintervals import GTF
class SumCoveragePerBin(countReadsPerBin.CountReadsPerBin):
r"""This is an extension of CountReadsPerBin for use with plotFingerprint.
There,... | fidelram/deepTools | deeptools/sumCoveragePerBin.py | Python | gpl-3.0 | 9,902 | [
"pysam"
] | d5d5a826acb8d10518244ccc63f4d8dcc044190262288e9e5930c801c311ac78 |
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.PyMol import MolViewer
from rdkit.Chem.Subshape import SubshapeBuilder,SubshapeObjects,SubshapeAligner
from rdkit.six.moves import cPickle
import copy
m1 = Chem.MolFromMolFile('test_data/square1.mol')
m2 = Chem... | adalke/rdkit | rdkit/Chem/Subshape/testCombined.py | Python | bsd-3-clause | 1,702 | [
"PyMOL",
"RDKit"
] | 1d3fb166fc7292e041f019140a760eca55bab95883ec01fbb085598ede043a2e |
from collections import deque
graph = {
"1": ["2", "5"],
"2": ["1", "3", "5"],
"3": ["2", "4"],
"4": ["3", "5", "6"],
"5": ["1", "2", "4"],
"6": ["4"],
}
graph2 = [
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0]
]
def traverse_bfs(graph, root, tar... | pieteradejong/joie-de-code | graphs.py | Python | mit | 1,287 | [
"VisIt"
] | b081507613a944ec800685a787436f05f9dacee61ff397d94bfe35d1c15f3a44 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Mar 18, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date__ = "Mar 18, 2012"
import unittest
import ... | yanikou19/pymatgen | pymatgen/apps/borg/tests/test_hive.py | Python | mit | 4,670 | [
"pymatgen"
] | 8d7ad6d29473ad508c0b28e3efe1da8944672d219a02b671a9c6af8e0b3f44ea |
# Lint as: python2, python3
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... | xzturn/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2.py | Python | apache-2.0 | 102,324 | [
"Gaussian",
"VisIt"
] | 12a4902bb8db25dcbb3a9edb4df849e7fba4a3ae75243002a404b48a7e3c65dd |
# -*- coding: utf-8 -*-
#
# brunel_exp_multisynapse_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 o... | weidel-p/nest-simulator | pynest/examples/brunel_exp_multisynapse_nest.py | Python | gpl-2.0 | 13,514 | [
"NEURON"
] | 6d8960c4e6651ef65178cf13c9e2134c02284ac16c1a8f7d5f8e9b8432648f6e |
#!/usr/bin/env python3
#
# Script to convert VASP output or XDATCAR to ASE-extxyz trajectory
# by Patrick Melix
# 2018/03/13
#
# You can import the module and then call .main() or use it as a script
from ase import io
import os
def main(outFile, inFiles):
#if output exists mv to .bak
if os.path.isfile(outFile)... | patrickmelix/Python4ChemistryTools | vasp2traj.py | Python | mit | 1,274 | [
"ASE",
"VASP"
] | c8014aeb3308868f7eb692df49196f2532ba57645d443afc6201082169808030 |
from sqlalchemy import create_engine, select, text
from sqlalchemy.orm import sessionmaker
import psycopg2
import sys
import os
from os.path import join, dirname
from datetime import date, timedelta, datetime
from urllib import parse
from pandas import DataFrame, ExcelWriter
import pandas as pd
sql_dir = os.path.... | UWPCE-PythonCert/IntroPython2016 | students/heb2016/Python2016_project/uw_project/uw_project.py | Python | unlicense | 2,127 | [
"CDK"
] | f24bf2153cc1ba23abdbf531f1c368cd2cd39383936940a7d86fe85b29542f7c |
from __future__ import annotations
import json
import logging
import math
import os
from xia2.Driver.DriverFactory import DriverFactory
from xia2.Handlers.Phil import PhilIndex
logger = logging.getLogger("xia2.Wrappers.Dials.Integrate")
try:
from typing import Optional
except ImportError:
pass
class DIALS... | xia2/xia2 | src/xia2/Wrappers/Dials/Integrate.py | Python | bsd-3-clause | 9,898 | [
"Gaussian"
] | fc449981c39b813f989d7f364528aacb1778fd5f8458a53a3160a6fcaa5be8ac |
from collections import OrderedDict
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
"{{first_name_male}} {{last_name}}",
"{{first_name_male}} {{last_name}}",
"{{first_name_male}} {{last_name}}",
"{{first_name_male}} {{last_name}}",
"{{... | joke2k/faker | faker/providers/person/en_GB/__init__.py | Python | mit | 22,799 | [
"Amber",
"Brian"
] | adfcd88bad7c5220c0292188e03bc5c81f7d7e1c6c483f15370457bd30ce9a05 |
from __future__ import absolute_import
import datetime
import pytest
import six
import unittest
from datetime import timedelta
from django.utils import timezone
from freezegun import freeze_time
from sentry.api.event_search import (
convert_endpoint_params,
event_search_grammar,
get_snuba_query_args,
... | mvaled/sentry | tests/sentry/api/test_event_search.py | Python | bsd-3-clause | 54,960 | [
"VisIt"
] | 45483302cbc20b3eb65c85e74345133ca5e86c3b373a73a6c4b93f09c969d404 |
from bpython.curtsiesfrontend.manual_readline import \
left_arrow, right_arrow, beginning_of_line, forward_word, back_word, \
end_of_line, delete, last_word_pos, backspace, delete_from_cursor_back, \
delete_from_cursor_forward, delete_rest_of_word, delete_word_to_cursor, \
transpose_character_before_cur... | wevial/bpython | bpython/test/test_manual_readline.py | Python | mit | 9,842 | [
"ADF"
] | 7fe831cf9ccde93aef39ff8578ad6c840d44eec70fc3d7cf53cb5f97ca131fa0 |
import os
import tempfile
from netCDF4 import Dataset
from pynwm import nwm_data, constants
def test_get_schema():
'''Should identify schema from id dimension in netCDF file.'''
tempdir = tempfile.gettempdir()
v1_0_dim = 'station'
v1_1_dim = 'feature_id'
v1_0_file = os.path.join(tempdir, 'v1_0... | twhiteaker/pynwm | src/pynwm/test/test_pynwm/test_nwm_data_get_schema.py | Python | mit | 822 | [
"NetCDF"
] | 9335eece1f64fe2d93cbccc8170baf63e4152f49733670154a781d90ac0d5231 |
# 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... | apache/incubator-singa | python/singa/initializer.py | Python | apache-2.0 | 11,753 | [
"Gaussian"
] | cf8eb95c796736e9004c4926fac2826ae1923f0433c0e0d01c6cfdf6cdd298bd |
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import fnmatch
import json
import operator
import os
import shutil
import tarfile
import tempfile
... | hyperized/ansible | lib/ansible/galaxy/collection.py | Python | gpl-3.0 | 38,648 | [
"Galaxy"
] | 24eefb97aea82168818be9b6e7a36c1677d2feb8309deea6654db879fdf2b969 |
import os
import unittest
import multiprocessing
import time
from urllib.parse import urlparse
from werkzeug.security import generate_password_hash
from splinter import Browser
# Configure app to user the testing database
os.environ["CONFIG_PATH"] = "fight_simulator.config.TestingConfig"
from fight_simulator import ... | tydonk/fight_simulator | tests/test_views_acceptance.py | Python | mit | 3,358 | [
"VisIt"
] | 9b60d9f9a12116104757fbb67965c0747808e1454115f5d0abcdaf80cb624559 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','license','co... | protez/Titanium-Image-Gallery | Module/ios/imagegallery/build.py | Python | apache-2.0 | 5,861 | [
"VisIt"
] | a0411457e03491669ef3a82fabb2fdef89ecc376410f38636309dcd418744009 |
# -*- coding: utf-8 -*-
"""Functions to make 3D plots with M/EEG data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <maina... | Teekuningas/mne-python | mne/viz/_3d.py | Python | bsd-3-clause | 129,054 | [
"Mayavi"
] | df73220b1430f7fd5e2b78ac01080647ae1c69be28410cae08449a773ae9fc85 |
# -*- coding: utf-8 -*-
"""Factories for the OSF models, including an abstract ModularOdmFactory.
Example usage: ::
>>> from tests.factories import UserFactory
>>> user1 = UserFactory()
>>> user1.username
fred0@example.com
>>> user2 = UserFactory()
fred1@example.com
Factory boy docs: http://f... | rdhyee/osf.io | tests/factories.py | Python | apache-2.0 | 30,059 | [
"Brian"
] | 080c6165ca45a7257d467f08164cb4b30589ee64b578c2c36074920b59a93701 |
"""Compatibility fixes for older versions of libraries
If you add content to this file, please give the version of the package
at which the fix is no longer needed.
# originally copied from scikit-learn
"""
# Authors: Emmanuelle Gouillart <emmanuelle.gouillart@normalesup.org>
# Gael Varoquaux <gael.varoquau... | Teekuningas/mne-python | mne/fixes.py | Python | bsd-3-clause | 40,124 | [
"Gaussian",
"Mayavi"
] | 63f44d20eb5510a69ed23000eb734619f593a77d340ad0eb0b1ffc2c7b98e9ce |
"""
docstring needed
:copyright: Copyright 2010-2017 by the NineML Python team, see AUTHORS.
:license: BSD-3, see LICENSE for details.
"""
from ...base import Parameter
from nineml.abstraction.expressions import Alias, Constant
from nineml.visitors import BaseVisitor
from nineml.units import Dimension, Unit
class T... | INCF/lib9ML | nineml/abstraction/componentclass/visitors/validators/types.py | Python | bsd-3-clause | 1,176 | [
"VisIt"
] | 28f9e31e5f74667c4e26963c18bccb469e00b8f6e515f3a7851affff59cd1dc0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import z2pack
# Creating the System. Note that the SCF charge file does not need to be
# copied, but instead can be referenced in the .files file.
# The k-points input is appended to the .... | Z2PackDev/Z2Pack | examples/fp/vasp/Bi/run.py | Python | gpl-3.0 | 1,535 | [
"VASP",
"Wannier90"
] | 3ea130c6c04e58c2b29bd4a3ff27b61d999e461debf60b2ae498b30d399a4dc9 |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ve... | francisco-dlp/hyperspy | hyperspy/tests/model/test_model_as_dictionary.py | Python | gpl-3.0 | 8,908 | [
"Gaussian"
] | 3587628a6032baa094e6f9049f2eded5254145faefb40c4ddeb75cda3de9e391 |
import math
import process_base as base
import myalgorithm as alg
def cal_dif_pair(line_from,line_to,n_dig=4):
res=[]
length_f=len(line_from)
length_t=len(line_to)
if length_f==0 or length_t==0:
return res
j=0
start_p=0
while start_p<length_f and line_from[start_p]<line_to[0]:
start_p+=1
for i in range(sta... | yanxiangtianji/Neuron | dataAnalysis/activation.py | Python | gpl-2.0 | 2,635 | [
"NEURON"
] | 331bbcb5a171287f55baddb5277f8a11e9ed883d6d411c77fb31f687fea13c3f |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
'''
Description: ARP poisons a LAN victim and prints all the interesting unencrypted info like usernames, passwords and messages. Asynchronous multithreaded arp spoofing packet parser.
Prerequisites: Linux
nmap (optional)
nbtscan (optional)
... | AlvinChiou/LANs.py | LANs.py | Python | gpl-3.0 | 67,680 | [
"VisIt"
] | ba5e0c310b74471b5bbdb39e04f0cf82cc7773d056a3b64f675d05bb4e5d3039 |
#!/usr/bin/env python
# Copyright (c) 2014, Jelmer Tiete <jelmer@tiete.be>.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# 1. Redistributions of source code must retain the above copyright
#... | daniel-k/RIOT | dist/tools/cc2538-bsl/cc2538-bsl.py | Python | lgpl-2.1 | 26,597 | [
"CRYSTAL"
] | 8eb55d31078dc3370ec6553a045e97333d8b9d2754afc42c5ee1e30b894253bb |
'''
Module docstring goes here.
'''
from __future__ import print_function
import numpy as np
import desc.slcosmo
c = 3.00e5
class SLCosmo(object):
'''
Master class for handling cosmological parameter inference given
strong lens time delay and Fermat potential data.
In the TDC2 scheme (and perhaps ot... | DarkEnergyScienceCollaboration/SLCosmo | python/desc/slcosmo/SLCosmo.py | Python | bsd-3-clause | 12,777 | [
"Gaussian"
] | e8b41c2f408ee019b6a2f9edb5c13b6e72a860773b361ae463a9ac1d4961b438 |
from builtins import object
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# 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 Softw... | mdiener/grace | grace/py27/slimit/visitors/nodevisitor.py | Python | gpl-3.0 | 2,858 | [
"VisIt"
] | 4aa22fb023c6154875880b4ca2de2fdd8a0c171b16d7ca558aa2238f324343a6 |
"""
This script is used to design the design matrix for our linear regression.
We explore the influence of linear and quadratic drifts on the model
performance.
Script for the filtered data.
Run with:
python noise-pca_filtered_script.py
from this directory
"""
from __future__ import print_function, division
im... | timothy1191xa/project-epsilon-1 | code/utils/scripts/noise-pca_filtered_script.py | Python | bsd-3-clause | 14,837 | [
"Gaussian"
] | fd3a12161bfc702c4637d9d831c9a970ac53e2c74153f69bef801534920f7e99 |
#!/usr/bin/env python
"""
http://msmbuilder.org/latest/examples/hmm-and-msm.html
"""
import pdb
import os
import matplotlib
from matplotlib.pyplot import *
import matplotlib.pyplot as plt
plt.style.use("ggplot")
from msmbuilder.featurizer import SuperposeFeaturizer
from msmbuilder.example_datasets import AlanineDipept... | jeiros/Scripts | MSManalysis/hmm-vs-msm.py | Python | mit | 2,759 | [
"MDTraj"
] | bb3d0c783117bd6389c385a7608aeb875c00d38bac1d1fa597dec84d49d5c57b |
# $Id$
#
# Copyright (C) 2002-2006 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.
#
"""unit testing code f... | rdkit/rdkit-orig | rdkit/Chem/Pharm2D/UnitTestGobbi.py | Python | bsd-3-clause | 5,463 | [
"RDKit"
] | dea8a7087d8e639a854d787d112756df6d07f3f03a4f9d7d48af1cb4ae60711e |
# test20140716.py
# constructing the objects for the report
"""
COMPREF: march 20140311.0000
-1. COMPREF Intensity plot:Scale = 2
0. COMPREF Intensity plot:Scale = 4
1. COMPREF Max Intensity:Scale plot (Scale 1=0.05deg)
20140311.0000
2. COMPREF Max Intensity:Intensity plot (corresp. to scale)
3. COMPREF: Ma... | yaukwankiu/armor | tests/test20140716.py | Python | cc0-1.0 | 8,978 | [
"Gaussian"
] | aced62ee6cb06c7f4dcf608e4411dd783c35e460806fb71c5ca04abe0c39ea1a |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
Script.setUsageMessage( """
Show storage quotas for specified users or f... | Sbalbp/DIRAC | DataManagementSystem/scripts/dirac-admin-user-quota.py | Python | gpl-3.0 | 1,250 | [
"DIRAC"
] | a5fd1dd8ecea421a7fd42bd8f02ab7a921d779ea5374c33d4dc8d84d7c20399f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import logging, math, time
from psycopg2 import sql
from . import constants, geometry, statistics
from .config import Config
from .constants import ReturnCode
from .db_control import DBControl
from .helper import WebserverException
from .translator import Translator
class ... | scheibler/WalkersGuide-Server | webserver/poi.py | Python | gpl-3.0 | 72,325 | [
"CASINO"
] | 1c7c787b51892dbe05fd93fee370171a718ad3bab95256684864f04daebbcd9f |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@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 Foundation... | shakamunyi/ansible | v2/ansible/galaxy/role.py | Python | gpl-3.0 | 11,286 | [
"Brian",
"Galaxy"
] | c7eb38151c2fad54ddd3417a3602ceafa68c7e4f3bf834a80b821f2a4358b018 |
# -*- coding: utf-8 -*-
"""
Copyright 2015 by Johannes Leugering (jleugeri@uos.de)
This file is part of the adaptive LN Neurons package.
The adaptive LN Neurons package is free software:
you can redistribute it and/or modify it under the terms of the
GNU Lesser General Public License as published by the... | jleugeri/nengo-adaptiveLN-models | nengo_adaptiveLN_models/__init__.py | Python | gpl-3.0 | 3,205 | [
"NEURON"
] | 94321743e7825a381a73b7b12f102fab2efb7716c541c928be858cfca93e9322 |
#!/usr/bin/env python
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
import sys
import getopt
from omg.gaussian.gaussian import GaussianLog as GL
from omg import geom
def usage():
print('usage:')
print(' gsurf.py 1.log 2.log 3.log ... N.log')
print('opti... | eduardoftoliveira/oniomMacGyver | scripts/gau_plot2dscan.py | Python | gpl-3.0 | 7,569 | [
"Gaussian"
] | fec15914a3590583b6f176b66cb454594b9a1f2beef72d9383337c3b1101a1ed |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.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 ... | wkeeling/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 32,322 | [
"Galaxy"
] | f66c9e4d45140ba5d544ff89fe2bbcc4c09908f0cd6a9e852ce3b79a0ee8aed7 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/gui/widgets/calculator.py | Python | gpl-2.0 | 12,074 | [
"VisIt"
] | bcb48485e3a5029de6234a4a93ac05e54c391bc815ccfc5737cf43f4540136ed |
#!/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/Interaction/Style/Testing/Python/TestStyleTerrain.py | Python | bsd-3-clause | 1,940 | [
"VTK"
] | a93ed079a3b95377286898ef14549cc3788620dc41722c143f2a4a65c321d9d1 |
from Neuron import Neuron
from Neuron import Node
from NeuronCollection import collection
from MCMC import MCMC
from visualize import get_all_path, plot_2D
import data_transforms
| RoozbehFarhoodi/McNeuron | McNeuron/__init__.py | Python | mit | 179 | [
"NEURON"
] | 00db98bdd885550bce6087bb1d8f5248b998f998d286d763884dffb10a9b0bfa |
# -*- coding: utf-8 -*-
# Author: Óscar Nájera
# License: 3-clause BSD
"""
Backreferences Generator
========================
Parses example file code in order to keep track of used functions
"""
from __future__ import print_function
import ast
import os
# Try Python 2 first, otherwise load from Python 3
try:
im... | chenyyx/scikit-learn-doc-zh | doc/zh/sphinxext/sphinx_gallery/backreferences.py | Python | gpl-3.0 | 6,291 | [
"VisIt"
] | 62d6235dc709c3f53731f6eaf3331424a03e636c082f9a060436cffbf589f304 |
from __future__ import (absolute_import, division,
print_function, unicode_literals)
from .plotting import *
from .outputs import *
from .slit import Slit
from .mask import Mask
from .galaxy import Galaxy
| adwasser/masktools | masktools/superskims/__init__.py | Python | mit | 232 | [
"Galaxy"
] | 568ba615e6ef8c047d584461fd3b00942e541eb4fc287dfb0afbb1585f5a1ff7 |
#!/usr/bin/python
from __future__ import division
from psutil import virtual_memory
import subprocess
import time
import multiprocessing
import random
import os
import socket
import syslog
import datetime as dt
FNULL = open(os.devnull, 'w')
traffic_sink = "192.168.66.230"
CPU_Offset_Dict= {'normal-server': 70, 'priori... | DTUbigdata/Thesis_Source_Code | thesis_package/Workload_Generator/workload_source.py | Python | apache-2.0 | 3,725 | [
"Gaussian"
] | a8facf9d1a4b99893539f19863881c8c36a0a65c1814a2752c99336e2ce981e1 |
# Author: Matthew Harrigan <matthew.harrigan@outlook.com>
# Contributors:
# Copyright (c) 2015, Stanford University and the Authors
# All rights reserved.
from ..base import BaseEstimator
from sklearn.base import TransformerMixin
import numpy as np
class FeatureUnion(BaseEstimator, TransformerMixin):
def __init_... | rmcgibbo/msmbuilder | msmbuilder/featurizer/feature_union.py | Python | lgpl-2.1 | 2,744 | [
"MDTraj"
] | 7dfdbf7bbf8fa5f600c7f912c96984c760f60a7b0e62eb511db05f66b218a917 |
import numpy as np, matplotlib as mpl
try:
import vtk, vtk.util.numpy_support as npsup
#import SimPEG.visualize.vtk.vtkTools as vtkSP # Always get an error for this import
except Exception, e:
print 'VTK import error. Please ensure you have VTK installed to use this visualization package.'
import SimPEG as simpeg
c... | simpeg/simpegviz | simpegViz/vtkView.py | Python | mit | 12,231 | [
"VTK"
] | fc72ed21d0409e781f715ee9e19ebdfbf025194a6fef2379f5fcf9091bd537a6 |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# 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 applicabl... | petrutlucian94/nova | nova/tests/unit/policy_fixture.py | Python | apache-2.0 | 4,109 | [
"TINKER"
] | 25ea6800de8c30981842e4f9165c7760e11bbb861de52775b32cce0d8c1b2adf |
########################################################################
# File : ARCComputingElement.py
# Author : A.T.
# Update to use ARC API : Raja Nandakumar
########################################################################
""" ARC Computing Element
Using the ARC API now
"""
__RCSID__ = "58c42fc (2... | vmendez/DIRAC | Resources/Computing/ARCComputingElement.py | Python | gpl-3.0 | 17,612 | [
"DIRAC"
] | 493adc417624e034744f355d1d3985d389220e513dce7893ea8d07da60f0ce04 |
'''Transform code s.t. the resulting code object can be marshalled
'''
from __future__ import absolute_import
from __future__ import with_statement
import cPickle as pickle
from ..runtime.symbol import gensym
from ..runtime.marshalp import marshalp
from . import ir as I
from . import bind
from .walk import IRWalker,... | matthagy/Jamenson | jamenson/compiler/Attic/marshal_trans.py | Python | apache-2.0 | 2,932 | [
"VisIt"
] | 0e2a3fe32dd096df1495d32e2a7f318905cff9b4d8d0e7f819273fa5ed49132d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements representations of slabs and surfaces, as well as
algorithms for generating them. If you use this module, please consider
citing the following work::
R. Tran, Z. Xu, B. Radhakris... | gVallverdu/pymatgen | pymatgen/core/surface.py | Python | mit | 87,911 | [
"pymatgen"
] | 5be7473be70b91aa253513dad118bfa5f7c1a69f723b8d18ad3e339bfe3777ce |
# -*- coding: utf-8 -*-
from resources.lib.modules import control, cleantitle, client, playcount
import requests
import os,sys,re,json,urllib.request,urllib.parse,urllib.error
import urllib.parse as urlparse
import xbmc, xbmcaddon, xbmcgui, xbmcvfs
import time
import datetime
from difflib import SequenceMatcher... | tvaddonsco/tva-release-repo | matrix/plugin.video.premiumizerx/resources/lib/api/premiumize.py | Python | gpl-3.0 | 74,550 | [
"VisIt"
] | 4800c789ffe4625d811beab2fc528357437eb5297dcd0686b405df30d87fca30 |
"""
This module provides GOCDB2CSAgent code.
The agent is used to synchronize information between GOCDB and DIRAC configuration System (CS)
Right now it only adds perfosonar endpoints
The following options can be set for the GOCDB2CSAgent.
.. literalinclude:: ../ConfigTemplate.cfg
:start-after: ##BEGIN GOCDB2CSAge... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Agent/GOCDB2CSAgent.py | Python | gpl-3.0 | 11,547 | [
"DIRAC"
] | 248db093a6d2a9900821297154a289b82e86f2c0df92aabd1a449673f7f667c8 |
"""
Logging
"""
__RCSID__ = "$Id$"
import logging
import os
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.Resources.LogBackends.AbstractBackend import AbstractBackend
class Logging(object):
"""
Logging is a wrapper of... | arrabito/DIRAC | FrameworkSystem/private/standardLogging/Logging.py | Python | gpl-3.0 | 17,321 | [
"DIRAC"
] | a134f6dc946ed2eb2fff7dc86c865c67c5f11afbb7c280e466cba49e5c0ef573 |
#!/usr/bin/python
# PumpkinPi, an LED Jack-O'-Lantern for Raspberry Pi
# https://github.com/begillespie/Pumpkin_Pi
# To access the GPIO on the Raspberry Pi, you must run this program as root.
# by Brian Gillespie, 2012
# @begillespie
# GPL license, see README for more details.
import RPi.GPIO as GPIO, sys,... | begillespie/Pumpkin_Pi | pumpkinPi.py | Python | gpl-3.0 | 9,309 | [
"Amber",
"Brian"
] | f5c1fe34ee7fea54462abd999ca6d1b1239e6c4ebd19828c2ad60633ef17179a |
# -*- test-case-name: pyflakes -*-
# (c) 2005-2010 Divmod, Inc.
# See LICENSE file for details
import __builtin__
import os.path
import _ast
from pyflakes import messages
# utility function to iterate over an AST node's children, adapted
# from Python 2.6's standard ast module
try:
import ast
iter_child_nod... | isohybrid/dotfile | vim/bundle/git:--github.com-klen-python-mode/pylibs/pyflakes/checker.py | Python | bsd-2-clause | 22,266 | [
"VisIt"
] | f288f5b0f7813f9b1b6bbcfe819b5af339e7a8a23cc4598e311fca52eb5771e9 |
# Orca
#
# Copyright 2016 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your o... | GNOME/orca | src/orca/scripts/web/sound_generator.py | Python | lgpl-2.1 | 4,135 | [
"ORCA"
] | e138257d1304c060c40634bc1655cd9420707892974b01fb7841674950e86bbe |
#!/usr/bin/env python
## Example usage: python get_tool_yml_from_gi.py -g https://mississippi.snv.jussieu.fr/ -a <api_key> -o tool_list.yml
from operator import itemgetter
from argparse import ArgumentParser
import bioblend.galaxy
import yaml
class GiToToolYaml:
def __init__(self, url,
api_key,... | ARTbio/tools-artbio | scripts/helper_scripts/get_tool_yml_from_gi.py | Python | mit | 11,810 | [
"Galaxy"
] | 7a5c2afd200b30bdb6b60e3114a19d880fceb871f9d360fee95cc40010d92338 |
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