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"""
@name: /home/briank/PyHouse/src/Modules/Families/Insteon/_test/test_Insteon_security.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Nov 2, 2016
@summary: Test
"""
__updated__ = '2016-11-02'
# Im... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Insteon/_test/test_insteon_security.py | Python | mit | 615 | [
"Brian"
] | be76cf33496a35023f392cedb808a779ffb3fb74d90fb689e23d679c37b5e004 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose-examples | snippets/changeFuncExpression.py | Python | gpl-2.0 | 4,475 | [
"MOOSE"
] | 22eb948798dd86463a5f648195b612b9a1d0544801cedee1ae0c7cb6b91acac1 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/aetemplate/aeasglossytemplate.py | Python | mit | 2,621 | [
"VisIt"
] | 2edc12075d5558a933f7aaf86a03fb38d462c3c754790165f435b08f215f2743 |
# -*- coding: utf-8 -*-
import urlparse
from lib import unshortenit
SERVICES_SHORT = ["adf.ly", "sh.st", "bit.ly", "ul.to"]
def expand_url(url):
e = unshortenit.UnshortenIt()
while Es_Corto(url):
long_url, estado = e.unshorten(url)
url = long_url
return long_url
def Es_Corto(url):
... | pitunti/alfaPitunti | plugin.video.alfa/servers/decrypters/expurl.py | Python | gpl-3.0 | 418 | [
"ADF"
] | dcb66254c0e77e85d5c8ad154b7aacce1ae31a5102f560b44966019e2f6bfe85 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/texinfo/package.py | Python | lgpl-2.1 | 2,028 | [
"Brian"
] | 525940dafe270ee67bc80b27d979cc35542173bb7ec8f2375f0e89cadbb8e108 |
#!/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/Rendering/Volume/Testing/Python/TestFixedPointRayCasterNearestCropped.py | Python | bsd-3-clause | 2,049 | [
"VTK"
] | f79b23a37e8ffb8c62e8ef3f5d92949a2167fe861bc99a2dda966a06377226bf |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | caio2k/RIDE | src/robotide/lib/robot/model/itemlist.py | Python | apache-2.0 | 2,805 | [
"VisIt"
] | 92a742d83dde4b906df22535d025474dfb0831465a73f3e482c3b93f074ea55a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import astropy.time as time
import datetime, os,math,sys
import pickle
import subprocess
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.dates as mdates
os.chdir(os.path.dirname(__file__))
def discrete_t(t):
dt = t - datetime.... | nushio3/UFCORIN | script/reproduce-past-probability.py | Python | mit | 4,743 | [
"Gaussian"
] | e75f2910339b9c86ac34a973387a19007624baac3dd86e42656ac5999bcaa818 |
"""
This module defines an ASE interface to gromacs
http://www.gromacs.org
It is VERY SLOW compared to standard Gromacs
(due to slow formatted io required here).
Mainly intended to be the MM part in the ase QM/MM
Markus.Kaukonen@iki.fi
See accompanying license files for details.
"""
import os, sys
import glob
fr... | grhawk/ASE | tools/ase/calculators/gromacs.py | Python | gpl-2.0 | 18,264 | [
"ASE",
"GROMOS",
"Gromacs"
] | e901e3ceea64e39adfefc2374aedde77a67da9f6e15f81da46e05a549e70019a |
# coding: utf-8
from __future__ import unicode_literals
import types
import unittest
from collections import OrderedDict
import rows.fields as fields
from rows.utils import create_table, ipartition, slug
class UtilsTestCase(unittest.TestCase):
def test_slug(self):
self.assertEqual(slug('Álvaro Justen... | tilacog/rows | tests/tests_utils.py | Python | gpl-3.0 | 2,168 | [
"MOE"
] | 9aefb0112ee3045bd54c549c0c5d670c9d96ece4e95bfedfcda7b0b9ea0ca941 |
# Copyright 2016 Mark Raasveldt
#
# 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 writin... | Mytherin/Tibialyzer | Database Scan/parseXML.py | Python | apache-2.0 | 32,356 | [
"CRYSTAL"
] | 74db4cd7f98f23f71bd5a5120ceac01b2918f56c4707cb5e5bee95f8bf38b061 |
#
# 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... | retrography/scancode-toolkit | tests/scancode/test_cli.py | Python | apache-2.0 | 6,515 | [
"VisIt"
] | bba04248d7c440ce7cfd361b4d84160c65f0e116589ad72719b2f6fa20826eba |
# 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 t... | BackupTheBerlios/espressopp | src/bc/OrthorhombicBC.py | Python | gpl-3.0 | 2,332 | [
"ESPResSo"
] | 6fa2060399b86c3260682cf9cb43dda0663cbf9103d6aba0feebf7a0f375c1a7 |
"""Test OpenBabel executables from Python
Note: Python bindings not used
On Windows or Linux, you can run these tests at the commandline
in the build folder with:
"C:\Program Files\CMake 2.6\bin\ctest.exe" -C CTestTestfile.cmake
-R pytest -VV
You could also "chdir" into bui... | torcolvin/openbabel | test/testsym.py | Python | gpl-2.0 | 15,129 | [
"RDKit"
] | 9d2f4694ca4fc5f66edd869610d1a4d7f8d9a6f75252941867265729c6c2c8a4 |
"""Test file for conversation system"""
import unittest
import pygame
import os
import time
from helper import *
import serge.events
import serge.blocks.conversation
pygame.init()
class TestConversation(unittest.TestCase):
"""Tests for the Conversation"""
def setUp(self):
"""Set up the tests"""
... | smmosquera/serge | test/testconversation.py | Python | lgpl-3.0 | 8,535 | [
"VisIt"
] | fa9873d724bc0e24dbc8d722aea72aefe4af4f71b7c535f0e3824e38ac473ac9 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
__doc__ = """Code by Benjamin S. Murphy
bscott.murphy@gmail.com
Dependencies:
numpy
scipy
matplotlib
Classes:
OrdinaryKriging3D: Support for 3D Ordinary... | basaks/PyKrige | pykrige/ok3d.py | Python | bsd-3-clause | 35,966 | [
"Gaussian"
] | 642a8a4bf107fcbd582f8edc97df5ae74e6b5832d9d4b70cd8047dcf15ed2bef |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Tue Feb 25 06:01:55 2020
@author: deborahkhider
Contains all relevant functions for correlation analysis
"""
__all__ = [
'corr_sig',
'fdr',
]
import numpy as np
from scipy.stats import pearsonr
from scipy.stats.mstats import gmean
from scipy.stat... | LinkedEarth/Pyleoclim_util | pyleoclim/utils/correlation.py | Python | gpl-3.0 | 24,459 | [
"Gaussian"
] | dbcd4976535257e701678903d00a54546df24105da579a0a401b5d7a5c633432 |
from PyQt5.QtCore import pyqtSlot, Qt
from PyQt5.QtWidgets import QWidget, QVBoxLayout, QHBoxLayout, QPushButton, QTreeWidget, QTreeWidgetItem
from PyQt5.QtGui import QIcon
from .xnova.xn_world import XNovaWorld_instance
from .xnova import xn_logger
from .widget_utils import number_format
logger = xn_logger.get(__na... | minlexx/xnovacmd | ui/imperium_widget.py | Python | gpl-2.0 | 22,457 | [
"CRYSTAL",
"Galaxy"
] | 76ca2a9f3d6c18de8dc6dda1324a5ca8bd661bc6c64efcc87a9f8bab227b1e65 |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
# Create a cube.
cubeSource = vtk.vtkCubeSource()
shrink = vtk.vtkShrinkFilter()
shrink.SetInputConnection(cubeSource.GetOutputPort())
shrink.SetShrinkFactor(.9)
# Create a mapper and actor.
mapper = vtk.vt... | lorensen/VTKExamples | src/Python/GeometricObjects/ShrinkCube.py | Python | apache-2.0 | 1,357 | [
"VTK"
] | 51ce1f08a4ed13a6e67a5314a3349de028a3aa21739595cc8683a365654f041e |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008,2012 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 ... | beernarrd/gramps | gramps/plugins/textreport/simplebooktitle.py | Python | gpl-2.0 | 7,651 | [
"Brian"
] | 7600dc242477e932f3e06807a38a502a3b98138905cf5edbf8ba8273a9d17e4d |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/pmv_dev/colorCommands.py is part of ePMV.
ePMV 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
... | corredD/ePMV | pmv_dev/colorCommands.py | Python | gpl-3.0 | 99,114 | [
"RasMol"
] | 05dd885d228a6bc12fc2e32bb5a3ad586361f8d1d2711017dd0547528cb934c7 |
import pytest
import os
from threeML.plugins.FermiGBMTTELike import FermiGBMTTELike
from threeML.plugins.OGIPLike import OGIPLike
from threeML.data_list import DataList
from threeML.classicMLE.joint_likelihood import JointLikelihood
from threeML.bayesian.bayesian_analysis import BayesianAnalysis
from threeML.io.plott... | volodymyrss/3ML | threeML/test/test_gbm.py | Python | bsd-3-clause | 11,985 | [
"Gaussian"
] | 01ec966195c91506af040760417f39095973f7c36566798d250026a7f2c06ce4 |
########################################################################
# File: File.py
# Date: 2012/08/03 15:02:53
########################################################################
"""
:mod: File
.. module: File
:synopsis: RMS operation file
operation file
"""
# Disable invalid names warning
# pylint: disa... | fstagni/DIRAC | RequestManagementSystem/Client/File.py | Python | gpl-3.0 | 5,418 | [
"DIRAC"
] | b23ae38d22cd332ccad5ce5f7f208fde7924dfac5dca0d5a40848e219177fc6f |
#!/usr/bin/env python
#
# 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
# "L... | gouravshenoy/airavata | airavata-api/airavata-client-sdks/airavata-python-sdk/src/main/resources/samples/AiravataClient.py | Python | apache-2.0 | 10,414 | [
"Amber"
] | 1ab8dcb52e98a3555622a19644ca8c38078c5a63e9b8e41d8cd6b768356b4d91 |
# Copyright 2004 by Thomas Hamelryck.
# 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.
"""KD tree data structure for searching N-dimensional vectors.
The KD tree data structure ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/KDTree/KDTree.py | Python | apache-2.0 | 8,462 | [
"Biopython"
] | 027c26600301120909fe66e42817d059215a3f3931d29b265285d7a1d8dccdc2 |
#!/usr/bin/env python
# Returns N50 (or N of your choice) and other stats of a fasta/q (can be gzipped)
# file of sequences. N50 is calculated as the sequence length above which 50%
# of the total sequence length lies when the sequences are sorted in order of
# descending length.
import getopt, sys
import copy
import... | sandyjmacdonald/fast_stats | fast_stats.py | Python | mit | 4,322 | [
"Biopython"
] | 236af7cd45bc25b8615d5735f8c43b85ed689f12b8fcfeda4092d283b7b536eb |
from __future__ import print_function
from operator import attrgetter as attr
from functools import partial
import sh
from toolz import compose
from Bio import SeqIO
import sys
import os
import mock
try:
import unittest2 as unittest
except:
import unittest
THISD = os.path.dirname(os.path.abspath(__file__))
he... | VDBWRAIR/biotest | biotest/biotest.py | Python | gpl-2.0 | 2,823 | [
"Biopython"
] | 04e990c0c1159950c994b40e2fa14c0a149d8fdf4c847f5a19009d6b6b8312bc |
"""
Clone an undirected graph. Each node in the graph contains a label and a list
of its neighbors.
"""
# Definition for a undirected graph node
# class UndirectedGraphNode(object):
# def __init__(self, x):
# self.label = x
# self.neighbors = []
class Solution(object):
def cloneGraph(self, nod... | shichao-an/leetcode-python | clone_graph/solution2.py | Python | bsd-2-clause | 1,272 | [
"VisIt"
] | 73dd28a0e07b70494255de3eb03f9a95080e9bb2703b9055e461e92c61317669 |
'''
Created on Jul 18, 2011
@author: sean
'''
from graphlab.meta.asttools import Visitor, visit_children
import _ast
from graphlab.meta.asttools.visitors.symbol_visitor import get_symbols
try:
from networkx import DiGraph
except ImportError:
DiGraph = None
def collect_(self, node):
names = set()
for ... | ypkang/Dato-Core | src/unity/python/graphlab/meta/asttools/visitors/graph_visitor.py | Python | agpl-3.0 | 10,400 | [
"VisIt"
] | 2df1fb790c41950ff217054e942daaf7534c958c103beddf01986633120bc408 |
"""
Project
FPGA-Imaging-Library
Design
MeanFilter
Function
Local filter - Mean filter, it always used for smoothing images.
Module
Software simulation.
Version
1.0
Modified
2015-05-16
Copyright (C) 2015 Tianyu Dai (dtysky) <dtysky@outlook.com>
This library is free software; you can redistribute it and/or
modif... | jaechoon2/FPGA-Imaging-Library | LocalFilter/MeanFilter/SoftwareSim/sim.py | Python | lgpl-2.1 | 4,416 | [
"MOE"
] | d6b7cbcd67a7e8c93d21bffc551097384762f4ce0346acdfde50f434a1e7830b |
import sys
if sys.version_info < (3,):
range = xrange
import numpy as np
import pandas as pd
import scipy.stats as ss
from scipy import optimize
from .. import inference as ifr
from .. import families as fam
from .. import output as op
from .. import tsm as tsm
from .. import data_check as dc
from .. import covar... | RJT1990/pyflux | pyflux/ssm/nllt.py | Python | bsd-3-clause | 30,987 | [
"Gaussian"
] | a602d356ff12adc9533d3b490300b9706b99eeab974e7613ac6ccea0676c40c5 |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | theochem/horton | horton/meanfield/test/test_libxc.py | Python | gpl-3.0 | 15,355 | [
"DIRAC"
] | 5c4868b0e33311489f4cb2f7418a06db6d8a8bf84f3151d7a1fef4124e1adfbd |
from django.test import TestCase, tag
from edc_appointment.models import Appointment
from edc_base.utils import get_utcnow
from edc_facility.import_holidays import import_holidays
from edc_reference.site import site_reference_configs
from edc_visit_schedule.site_visit_schedules import site_visit_schedules
from edc_visi... | botswana-harvard/edc-entry | edc_metadata/tests/test_metadata_getter.py | Python | gpl-2.0 | 4,392 | [
"VisIt"
] | ce9980525bd79c3361b4311518797a8bf666dca74c2cae2af091ea6750d501e1 |
"""
=========
structure
=========
"""
import numpy as np
from pandas import DataFrame
from javelin.unitcell import UnitCell
from javelin.utils import (get_atomic_number_symbol, is_structure, get_unitcell, get_positions,
get_atomic_numbers)
class Structure:
"""The structure class is ma... | rosswhitfield/javelin | javelin/structure.py | Python | mit | 26,259 | [
"ASE"
] | 0ed3ddddb90bd2380c02ff0d8ccb2a6c1b96fce2f9af118a0222e2620b9044dd |
"""
Copyright (c) 2017 Sam Witte
Created on Jan 19, 2017
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any late... | SamWitte/Codds_DarkMatter | src/Data/LZ.py | Python | gpl-2.0 | 3,262 | [
"Gaussian"
] | d13730d86d2959e589fee689734c37f2753218911c42b05dd1d42fc8c4b30cca |
#!/usr/bin/env python3
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | espressopp/espressopp | examples/lj_cos/lj_cos.py | Python | gpl-3.0 | 7,442 | [
"ESPResSo"
] | feabee06ba7948411449511cf405ff0946e36ff516438df0a3e20d88129cae8c |
# Copyright 2008-2013 by Peter Cock. 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.
"""AlignIO support module (not for general use).
Unless you are writing a new parser or writ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/AlignIO/Interfaces.py | Python | gpl-2.0 | 6,030 | [
"Biopython"
] | 5f37b1e07c65c8797381dde5096ea6c5446682f168b3ef3f4041fc86d70e8578 |
import datetime
import time
import web
from nose.tools import *
database = web.database(dbn='postgres', db='authenticationpy_test', user='postgres')
web.config.authdb = database
web.config.authmail = {'sender': 'admin@mysite.com',
'activation_subject': 'MySite.com Activation E-Mail',}
from aut... | foxbunny/acl.py | authenticationpy/test_auth.py | Python | gpl-3.0 | 29,052 | [
"VisIt"
] | a4a708f0c2df18bab2cc4d34c026a09d2b2bbc995baf0e9ebdf771bc53f593fa |
import inspect
import os
import textwrap
import types
import warnings
from .reference import Reference
from .shim import ModuleShim
class XTracebackFrame(object):
FILTER = ("__builtins__", "__all__", "__doc__", "__file__", "__name__",
"__package__", "__path__", "__loader__", "__cached__")
FUN... | Hypernode/xtraceback | xtraceback/xtracebackframe.py | Python | mit | 8,621 | [
"xTB"
] | 940c3d0ed37bb1ffde29aa07598ade50e483b019ef5651aff9155287a9e5a43a |
#!/usr/bin/env python3
# This file is part of the Minecraft Overviewer.
#
# Minecraft Overviewer 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 o... | tswsl1989/Minecraft-Overviewer | overviewer.py | Python | gpl-3.0 | 29,519 | [
"VisIt"
] | 21e60e4a22a8604553774eda034a71dfb74a3691b0af3a1a8a371361275c517f |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2015 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | atodorov/anaconda | pyanaconda/pwpolicy.py | Python | gpl-2.0 | 6,910 | [
"Brian"
] | e2b1e8daa0953d0c6694d65d780bd8c7304481bc6a5fb18f9825a39609f25f87 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements the Quasi-harmonic Debye approximation that can
be used to compute thermal properties.
See the following papers for more info:
http://doi.org/10.1016/j.comphy.2003.12.001 (2004... | fraricci/pymatgen | pymatgen/analysis/quasiharmonic.py | Python | mit | 13,291 | [
"pymatgen"
] | 0cbf22cb7447a47cd2866a7bcb1931318356ef272e7ba1da47cb8ada96a7c626 |
# Copyright (c) 2003-2010 LOGILAB S.A. (Paris, FRANCE).
# Copyright (c) 2009-2010 Arista Networks, Inc.
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# ... | jheld/pylint | checkers/base.py | Python | gpl-2.0 | 33,139 | [
"VisIt"
] | 195176a58fe0fdd8173aedd0dd0122a2b5e84bc9f49365de09263bdbf7f84b7f |
# Copyright 2020 DeepMind Technologies Limited.
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed... | deepmind/ferminet | ferminet/pretrain.py | Python | apache-2.0 | 10,362 | [
"PySCF"
] | f1e968d1c4dc1328d511c4f0f5e66fe09df65485488eb5be1b9d7b754720c1f7 |
# -*- coding: utf-8 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later ve... | FedoraScientific/salome-hexablock | doc/test_doc/quadRevolution/revolution_quad.py | Python | lgpl-2.1 | 1,794 | [
"VTK"
] | 59b52962fd782313d91e2c493c49507ecadfa33f134742430f275881576de757 |
#!/usr/bin/env python
# test_cursor.py - unit test for cursor attributes
#
# Copyright (C) 2010-2011 Daniele Varrazzo <daniele.varrazzo@gmail.com>
#
# psycopg2 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 Foun... | nwokeo/supysonic | venv/lib/python2.7/site-packages/psycopg2/tests/test_cursor.py | Python | agpl-3.0 | 20,887 | [
"GULP"
] | c3726e58039745be2e5311282d1bf83a5d54434d8e71e507d589127525280fa3 |
# ft/tests/item_form/ui/test_element.py: FT for item form page UI elements
#
# Copyright 2014 Sudaraka Wijesinghe <sudaraka.org/contact>
#
# This program 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 Foundat... | sudaraka/sopin-web | ft/item_form/ui/test_elements.py | Python | agpl-3.0 | 10,074 | [
"VisIt"
] | aee08afb5a1754486bfff36a4d5cc1321bbc77113e0420fbd162f6e00cd3e063 |
#!/usr/bin/python
"""
Copyright 2015 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/postFeedback.py | Python | gpl-3.0 | 5,119 | [
"Galaxy"
] | 8f38840b936870ce62d961ee59d0784588179b1085d12059646a66a952567ed7 |
#!/usr/bin/env python
# encoding: utf-8
# vim: tabstop=4:softtabstop=4:shiftwidth=4:expandtab
from __future__ import division, print_function
import numpy as np
import math
import scipy.linalg as sl, scipy.special as ss
from piccard import *
class likelihoodWrapper(object):
"""
Wrapper class of the likelih... | vhaasteren/piccard | piccard/transformations.py | Python | gpl-3.0 | 28,839 | [
"Gaussian"
] | 40ce345f7c1dbca3b54fb63f230b467d4e9a1a44ce82186303d4cb4a993ce182 |
# -*- coding: utf-8 -*-
r"""
.. _disc-filtering:
===================================
Background information on filtering
===================================
Here we give some background information on filtering in general,
and how it is done in MNE-Python in particular.
Recommended reading for practical applications ... | mne-tools/mne-tools.github.io | 0.18/_downloads/50ca168736a7f5e0ade7d4d0af520755/plot_background_filtering.py | Python | bsd-3-clause | 50,019 | [
"Gaussian"
] | db7a4ac81d9b97cc1dde11871325e9e58f870aa3d60ccff3eef7102ab44eb0e9 |
from Firefly import logging
from Firefly.components.zwave.zwave_device import ZwaveDevice
from Firefly.const import (EVENT_ACTION_OFF)
TITLE = 'Aeotec ZW117 Range Extender'
DEVICE_TYPE = 'UNKNONW'
AUTHOR = 'Zachary Priddy'
COMMANDS = []
REQUESTS = []
INITIAL_VALUES = {
'_state': EVENT_ACTION_OFF
}
def Setup(firefl... | Firefly-Automation/Firefly | Firefly/components/zwave/aeotec/zw117_range_extender_6.py | Python | apache-2.0 | 812 | [
"Firefly"
] | 63d54811b9ec23e6da7647ba9b311322c221d5a182350deff84970ed2efa2d27 |
# -*- coding: utf-8 -*-
import os
import sys
try:
import urlparse
except ImportError:
import urllib.parse as urlparse
from django.utils.translation import ugettext_lazy as _
from celery.schedules import crontab
from constance import config
from datetime import timedelta
from path import path
DJANGO_PROJECT_R... | KlubJagiellonski/Politikon | politikon/settings/base.py | Python | gpl-2.0 | 13,736 | [
"VisIt"
] | 49815205fcb43fceef545dffa30b0edd897c782d6cebec05b5043f79fb27c3de |
from pymongo import MongoClient
from collections import Counter
import datetime
import numpy as np
import operator
import pprint
from matplotlib import pyplot as plt
from matplotlib.pyplot import cm
from scipy.ndimage.filters import maximum_filter
from scipy import stats
from scipy.ndimage.morphology import generate_bi... | willettk/rgz-analysis | python/checksum.py | Python | mit | 13,446 | [
"Galaxy"
] | 870d9eb0895a2e3adf1ff55211b692f5bacaabaf3675c87aef4a1612ea2644d5 |
import six
from contextlib import contextmanager
from collections import Counter, defaultdict
from pysam import (
AlignmentFile, CMATCH, CINS, CDEL, CREF_SKIP, CSOFT_CLIP, CHARD_CLIP, CPAD,
CEQUAL, CDIFF)
from dark.reads import Read, DNARead
class UnequalReferenceLengthError(Exception):
"The references... | terrycojones/dark-matter | dark/sam.py | Python | mit | 32,184 | [
"pysam"
] | 12b603469a21eb29c67194f482c3dc2945f5b669caeb6284b80d5db5e25a2002 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'NeuronEphysDataMap.exp_fact_concept_map'
db.delete_colu... | lessc0de/neuroelectro_org | neuroelectro/south_migrations/0082_auto__del_field_neuronephysdatamap_exp_fact_concept_map.py | Python | gpl-2.0 | 35,909 | [
"NEURON"
] | 142c57db6b9462dde740582a92688fb330bdfd60117994f2790bfd6ca35476b9 |
"""
Copyright (C) <2010> Autin L.
This file ePMV_git/PyMol/pymolAdaptor.py is part of ePMV.
ePMV 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
... | corredD/ePMV | PyMol/pymolAdaptor.py | Python | gpl-3.0 | 18,256 | [
"PyMOL"
] | 0bd854672ce2ae2b449a75ad14045399ac578b496abc1e67a982a5b3bef9f908 |
#
#@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 your option) any later ver... | spring01/libPSI | lib/python/qcdb/psiutil.py | Python | gpl-2.0 | 3,972 | [
"Psi4"
] | c8ed8f50c9f772b29e8d455b8d70621a86c0e86decf78d7ed735c9d83179ecb8 |
import datetime, platform, pytz, os, json
from lbcmain.mailntf import MailBuilder, MailType
from lbcmain.lbcmonitor import Monitor
from lbcmain.config import Config
from lbcmain.dataexplorer import DataExplorer
Config.readconfig()
Config.setpath(os.path.dirname(os.path.abspath(__file__)))
mail = MailBuilder(type = M... | panyz522/lbc-autotrader | test.py | Python | mit | 1,639 | [
"ADF"
] | c88540eea1f1c48c83b778c676eed7fb4704c52dc414f0e150c72427633b2230 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/lib/logger.py | Python | apache-2.0 | 6,296 | [
"PySCF"
] | f7b705b184d4dd3771b1f86c3581d543ca4f66f1dfb6eea86a52fce4a8e92545 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | alxgu/ansible | lib/ansible/modules/network/avi/avi_snmptrapprofile.py | Python | gpl-3.0 | 3,551 | [
"VisIt"
] | 9e2addc67cad35b3198d8e974cc9d2745c965d8243b6b9984ad032f16864eb6d |
# Copyright (C) 2015-2020 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU Affero General Public License version 3, or any later version
# See top-level LICENSE file for more information
from typing import Any, Dict, List, Optional, Tuple
from dja... | SoftwareHeritage/swh-web-ui | swh/web/api/utils.py | Python | agpl-3.0 | 11,379 | [
"VisIt"
] | 64a761ce10bb6d95f5320dc9452f42f70259295e4cef1be094444a79eabaa4da |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Mask low complexity regions in the genome.
"""
import os.path as op
import sys
from jcvi.formats.fasta import Fasta
from jcvi.utils.cbook import depends, percentage
from jcvi.apps.base import OptionParser, ActionDispatcher, sh
@depends
def wm_mk_counts(infile=None,... | sgordon007/jcvi_062915 | apps/mask.py | Python | bsd-2-clause | 2,948 | [
"BLAST"
] | 37d809abb315334ebc932f5a5d7bf04f023fc171db71ba5abd3b7dcbae24297a |
# coding: utf-8
# In[1]:
import matplotlib
matplotlib.use('Agg')
import numpy as np
from scipy.cluster.vq import kmeans2
import pylab as plt
plt.style.use('ggplot')
import astropy.units as au
import os
import gpflow as gp
from heterogp.latent import Latent
from gpflow import settings
from gpflow.decors import ... | Joshuaalbert/IonoTomo | src/ionotomo/notebooks/itoh_gp/itoh_gp.py | Python | apache-2.0 | 35,362 | [
"Gaussian"
] | 27a821ae78be840d6549c45a2a05ddb9c5564d799db074c020991f8fa5084d92 |
import logging
import os
import shutil
import json
import numpy as np
import time
import warnings
from copy import deepcopy
from datetime import datetime
from shutil import copyfile
from typing import List, Tuple, Union
import flare
import flare.predict as predict
from flare import struc, gp, env, md
from flare.dft_i... | mir-group/flare | flare/otf.py | Python | mit | 23,786 | [
"ASE",
"CP2K",
"ESPResSo",
"Gaussian",
"VASP"
] | 1ef4d40551ff3150b124e529eb1c11c2fe1c6d1929f91f9453581a1d939858ac |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from forocacao.app.views import HomeView
urlpatterns = [... | javierwilson/resilienciacafe | config/urls.py | Python | bsd-3-clause | 1,621 | [
"VisIt"
] | 6c0ab3f640df88795fcc67a069197c0639f39112ee9d7e5f05598f72401512b3 |
__RCSID__ = "$Id: UsersAndGroups.py 34413 2011-02-19 06:10:18Z rgracian $"
"""
Update Users and Groups from VOMS on CS
"""
import os
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.ConfigurationSystem.Client.CSAPI import CSAPI
from DIRAC.FrameworkSystem.Client.NotificationC... | Sbalbp/DIRAC | ConfigurationSystem/Agent/UsersAndGroups.py | Python | gpl-3.0 | 16,302 | [
"DIRAC"
] | b3ae5254eb4192bb0507548d9a692a524a52c9ab4a71676815e6a35d8d5eb826 |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
from rdkit import RDConfig
import sys,os,types
from rdkit import Chem
from rdkit.VLib.Transform import TransformNode
class SmartsRemover(TransformNode):
""" transforms molecules by removing atoms matching smarts patterns
Assumption... | soerendip42/rdkit | rdkit/VLib/NodeLib/SmartsRemover.py | Python | bsd-3-clause | 3,785 | [
"RDKit"
] | fb98bc0bdb7472f459cec18dd9a7d9b9201aedc112e9aa40f44ac995b4ba077d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import warnings
import numpy as np
from pymatgen import Lattice, Structure, Specie, Element
from pymatgen.transformations... | gpetretto/pymatgen | pymatgen/transformations/tests/test_advanced_transformations.py | Python | mit | 25,899 | [
"VASP",
"pymatgen"
] | ba22190235430eff63d847415ac8c3a27d38388fe9c0cd95b226e1b1a4f542d4 |
from __future__ import division, print_function
from interpolation import *
from interpolation import __find_hosts
def rungekutta(self):
"""
** Rungekutta4 solver. Moves particles one timestep.**
Inputs:
- pyticleClass
"""
grid = self.grid
particles = self.particles
mstage = 4
... | moflaher/pyticle_tracker | pyticle_tracker/solvers.py | Python | agpl-3.0 | 4,470 | [
"Gaussian"
] | 96876d6686e718470c9b098c05b8c5d06cb40e542f388b2f3bc5c54a3d8b6160 |
"""
Generate a magnitude distribution from the template based on the fits from the SN(oo)Py module
"""
import numpy as np
import matplotlib.pyplot as plt
import sys
import os
from glob import glob
#imports from within the package
from lsst import discover
from jwst import filters, z_sne
#simlc is the euclid filter... | sdhawan21/euclidIR | euclidIR/gen_mc.py | Python | mit | 5,398 | [
"Gaussian"
] | 78394bc2cd9b2157980e2656b89d3957c0415167112024f0bca305fea7282faf |
# (c) 2016, Adrian Likins <alikins@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 Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | caphrim007/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 21,211 | [
"Galaxy"
] | b85b7c3af8cb5c7aaaff62f660dc40d888abbc1fe704e1e207bf9f7b83b23730 |
#!/usr/bin/env python
from itertools import takewhile
import logging
import os
from random import randint
import re
import sys
from urllib.parse import urlencode
from urllib.request import urlopen
from bs4 import BeautifulSoup
import yaml
import typos
# http://www.foia.gov/foiareport.js
# Excludes "ALL" (All agenc... | sunlightlabs/foia-data | new/new-more/foia-master/contacts/scraper.py | Python | gpl-3.0 | 16,836 | [
"ADF"
] | 7526107817c88ee810ac647b87ce4829b60a278a1f69185ecb567c28d0fe6023 |
"""
============================================================
Empirical evaluation of the impact of k-means initialization
============================================================
Evaluate the ability of k-means initializations strategies to make
the algorithm convergence robust as measured by the relative stan... | manhhomienbienthuy/scikit-learn | examples/cluster/plot_kmeans_stability_low_dim_dense.py | Python | bsd-3-clause | 4,338 | [
"Gaussian"
] | 185e034e0ce7ea215793fbf76e456450e3fe74bfe8ad9653ca9db5911068bad5 |
#! /home/caleb/.anaconda3/bin/python
import sys
import os
import rdkit
from rdkit import Chem
from rdkit.Chem import Descriptors, inchi
from rdkit.Chem.rdMolDescriptors import CalcMolFormula
from pubchempy import get_compounds, Compound
import json
import db_preprocessor
from collections import Counter
from chemicals ... | CalebBell/chemical-metadata | generate_db.py | Python | mit | 7,180 | [
"RDKit"
] | 54ddea92abc4c9ffd53bf08774e4a9573466dd57d2303f457c44eed452009982 |
#! /usr/bin/env python
"""
Module with cosmetics procedures. Contains the function for bad pixel fixing.
Also functions for cropping cubes.
"""
__author__ = 'Carlos Alberto Gomez Gonzalez, V. Christiaens'
__all__ = ['cube_crop_frames',
'cube_drop_frames',
'frame_crop',
'cube_correct... | carlgogo/vip_exoplanets | vip_hci/preproc/cosmetics.py | Python | bsd-3-clause | 12,607 | [
"Gaussian"
] | 3c38ca41a6b8ead45f642ccbd862e1544790fd5d1bf5c69a5f2226cdbdd32376 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | KonradBreitsprecher/espresso | testsuite/lj.py | Python | gpl-3.0 | 2,736 | [
"ESPResSo"
] | e4d220fe2979e4fe7daa8d94fcf3b6e41aed25610c39a887b2e16fc224261395 |
#
# The Python Imaging Library.
# $Id$
#
# the Image class wrapper
#
# partial release history:
# 1995-09-09 fl Created
# 1996-03-11 fl PIL release 0.0 (proof of concept)
# 1996-04-30 fl PIL release 0.1b1
# 1999-07-28 fl PIL release 1.0 final
# 2000-06-07 fl PIL release 1.1
# 2000-10-20 fl PIL release 1.1.1... | nwokeo/supysonic | venv/lib/python2.7/site-packages/PIL/Image.py | Python | agpl-3.0 | 89,185 | [
"Gaussian"
] | 9da3483fb88c67ca741d1a91864fa91c50bccce11e00c331d7f2e14a0d47f5b9 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'Visit'
db.create_table('visits_visit', (
('id', self.gf('django.db.models.fiel... | marklocklear/Online-Student-Profile | osp/visits/migrations/0001_initial.py | Python | lgpl-3.0 | 6,099 | [
"VisIt"
] | 192aeb93023016e7f423438d657e6850dd72676eacd3b25e85fb1dbe7bf95f81 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
#import numpy as np
#import pandas as pd
#from unittest import TestCase
#from exatomic.base import resource
#from exatomic.adf.nmr.output import Output
#
#class TestOutput(TestCase):... | exa-analytics/atomic | exatomic/adf/nmr/tests/test_output.py | Python | apache-2.0 | 1,185 | [
"ADF"
] | fcbb4adadf77cfd750269fba8dfa76208484d8579b782461f5c79f9d365d60b0 |
# -*- coding: utf-8 -*-
#
# brunel_alpha_evolution_strategies.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 versio... | wschenck/nest-simulator | pynest/examples/brunel_alpha_evolution_strategies.py | Python | gpl-2.0 | 20,704 | [
"Gaussian",
"NEURON"
] | ad01486d23aa2768d7c5bb70365158a7ad55df6b4a25b562f0ef4b3f4591680d |
"""Sensitive variant calling using VarDict.
Defaults to using the faster, equally sensitive Java port:
https://github.com/AstraZeneca-NGS/VarDictJava
if 'vardict' or 'vardict-java' is specified in the configuration. To use the
VarDict perl version:
https://github.com/AstraZeneca-NGS/VarDict
specify 'vardict-perl'.... | brainstorm/bcbio-nextgen | bcbio/variation/vardict.py | Python | mit | 15,794 | [
"BWA"
] | 32ba730c09b3ae62fc2153a2415c9da2cdea3f1300d56b2313a27238b0cec602 |
#
# 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 = 500
n = 250
display = True
wo... | sg0/Elemental | examples/interface/NNLSDense.py | Python | bsd-3-clause | 1,550 | [
"Gaussian"
] | b1863a289bb880135e226444435f512979a8151e85d4fba4425f1c432c44cf73 |
import os
import sys
import random
import time
import math
import torchvision
from torch import optim
import io
from PIL import Image
import visdom
vis = visdom.Visdom()
import matplotlib.ticker as ticker
import socket
hostname = socket.gethostname()
from .pssm3go_model import *
from .baselines import *
from ... | yotamfr/prot2vec | src/python/pssm3go_train.py | Python | mit | 27,211 | [
"BLAST"
] | b244747c7cd87c2ae3dbb2bead8929af3fcf0b6b5d5b18d92fc508387b5cc7b1 |
#!/usr/bin/env python
# encoding: UTF-8
"""
This file is part of Commix Project (http://commixproject.com).
Copyright (c) 2014-2017 Anastasios Stasinopoulos (@ancst).
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 Soft... | hackersql/sq1map | comm1x/src/utils/menu.py | Python | gpl-3.0 | 25,803 | [
"Galaxy"
] | d2f6257e3603e9c35c6c0b77a283c366a7f236779c9e6edc7b7e4d53b74a1d69 |
# Tutorial 17: Neuron Models
# Nengo supports multiple different types of neurons. The default is the
# "Leaky Integrate-and-Fire" or LIF neuron. Other supported ones are shown
# here. The LIFRate neuron acts like the LIF neuron, but does not have spikes.
# The Sigmoid is a standard model used in machine learning. ... | tcstewar/nengo_assignments | groningen_2018/sig_test.py | Python | gpl-3.0 | 1,691 | [
"NEURON"
] | b3be5fd70731305ee18b46670ed8625107ec163418c9e399de7f5a2fd1a3c795 |
# Copyright (C) 2012-2018
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 GNU General... | espressopp/espressopp | src/interaction/Harmonic.py | Python | gpl-3.0 | 21,129 | [
"ESPResSo"
] | 9dddb95fadd96d0caba9612e4ee06f38637aaf30db988be3567dde6beb4fc4b2 |
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | googlecodelabs/migrate-python2-appengine | mod15-blobstore/main.py | Python | apache-2.0 | 2,607 | [
"VisIt"
] | 740817a3b7fd625ba3d2c174d8470692f273c3153b5966e33585a8ee77263978 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Mads Jensen <mje.mads@gmail.com>
#
# License: BSD (3-clause)
import copy
import os.path as op
from math import ceil
import warn... | jniediek/mne-python | mne/source_estimate.py | Python | bsd-3-clause | 109,664 | [
"Mayavi"
] | 2412866cb333ef400be36f3ff36b97e01abad954d6f997b2cfcf62ccdbe8e6fc |
# $HeadURL: $
''' AccountingCacheCommand
The AccountingCacheCommand class is a command module that collects command
classes to store accounting results in the accounting cache.
'''
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIR... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Command/AccountingCacheCommand.py | Python | gpl-3.0 | 33,632 | [
"DIRAC"
] | c9371e7c7dd716c57dde15524221c27b63b4a5a7e1b55b39c258087e0ddcdcf5 |
# 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]
... | blaze/partd | versioneer.py | Python | bsd-3-clause | 68,607 | [
"Brian"
] | 9cbac05ca131ceff00f5dbcb1806b68ce98a979854004a43f5c47013d972c3d0 |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list ... | jameswatt2008/jameswatt2008.github.io | python/Python核心编程/网络编程/截图和代码/概述、SOCKET/多进程copy文件/test/mimetypes.py | Python | gpl-2.0 | 20,847 | [
"NetCDF"
] | 086a5b748a658c4148cc071bb31a006cb033adda559c04c5ec975e315d2a2694 |
#
# Copyright 2019 the original author or 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 agre... | opencord/voltha | voltha/adapters/openolt/openolt_data_model.py | Python | apache-2.0 | 23,725 | [
"VisIt"
] | e88d1ae74b57036eb854f71f0bb46a6a63c969d29359786727dec39344586475 |
import csv
import math
import numpy as np
import random
from .base import classifier
from numpy import asarray as arr
# Bayes classifiers
# Current implementation only includes a Gaussian class-conditional model,
# "gaussClassify"
# TODO: data weights
##############################################################... | sameersingh/ml-discussions | week9/mltools/bayes.py | Python | apache-2.0 | 6,600 | [
"Gaussian"
] | c80802253ec6c1aef2833d1501997b4903a0d048c80f846c352d8b1d48518996 |
#!/usr/bin/env python
import sys
import pysam
import random
__doc__ = """Count the number of cells in a 10X BAM file."""
class CellCounter(object):
infile = ""
outfile = "/dev/stdout"
mincount = 100 # Mimimum reported count
maxreads = 0 # Number of reads to be examined... | albertoriva/bioscripts | count_cells.py | Python | gpl-3.0 | 3,917 | [
"pysam"
] | 5b6c7ebbab874000288329196f27f20bc7c558f9759c09acae608eaa1fa71718 |
from __future__ import print_function
import time, re, json, sys
from collections import Counter
from svtyper.statistics import mean, stdev, median, upper_mad
# ==================================================
# VCF parsing tools
# ==================================================
def confidence_interval(var, tag... | hall-lab/svtyper | svtyper/parsers.py | Python | mit | 46,403 | [
"pysam"
] | 90371f5ff6e4fadebdb4d2cff7230a4f7acae79be857aafc1560b3b7f4c0cb4d |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2021, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""A library for parsing and interpreting results from computational chemistry packages.
The goals of cclib are centered ... | cclib/cclib | cclib/__init__.py | Python | bsd-3-clause | 1,712 | [
"ADF",
"Firefly",
"GAMESS",
"Gaussian",
"Jaguar",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Q-Chem",
"cclib"
] | 60fa163bafeca3e4c5032b448801d9f5a8db86e0a867e00a9cf765d21f4bbf7a |
import matplotlib
matplotlib.use('Agg')
import os
import tensorflow as tf
import fid
import numpy as np
import math
import utils
import fidutils
from glob import glob
import argparse
#
# parse params
#
parser = argparse.ArgumentParser()
parser.add_argument('--path_IncNet', type=str, help='Path to inception net.')
pars... | bioinf-jku/TTUR | FIDvsINC/main.py | Python | apache-2.0 | 9,675 | [
"Gaussian"
] | 1000892a459011da77858485a1520d630111d9738cf8c4c51f473400c78fe865 |
"""
@name: PyHouse/src/Modules/Housing/Entertainment/panasonic/_test/test_panasonic.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2018-2018 by D. Brian Kimmel
@note: Created on Aug 17, 2018
@license: MIT License
@summary:
"""
__updated__ = '2019-12-24'
# Import system... | DBrianKimmel/PyHouse | Project/src/Modules/House/Entertainment/Panasonic/_test/test_panasonic.py | Python | mit | 16,467 | [
"Brian"
] | f102c6cd7bcd825e2428328bd6b3af66ab3fabfec0ad567e360b99eb3882b111 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import glob
from io import StringIO
import numpy as np
import pandas as pd
from monty.json import MSONable
from monty.io import zopen
from pymatgen.io.lammps.data import LammpsBox
"""
This module i... | dongsenfo/pymatgen | pymatgen/io/lammps/outputs.py | Python | mit | 5,960 | [
"LAMMPS",
"pymatgen"
] | df8092d21179a4c428602715d52aa99d258f9c5c3b6590b990d7a8240265d06f |
from collections import OrderedDict
import itertools
import numpy as np
from scipy.spatial.distance import cdist
from chargetools.constants import AXES_NAMES
from chargetools.exceptions import InputError
from chargetools.utils.utils import chained_or
class Cube(object):
"""
A object that stores information ... | jincheng95/charges-tools | chargetools/grids.py | Python | mit | 15,085 | [
"Gaussian"
] | 9ffa14cad82b6b99cb5e462d606796800138894ce9748233fb3cc7640f68c62c |
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