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###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/Community-Zenpacks | ZenPacks.AndreaConsadori.Netasq/setup.py | Python | gpl-2.0 | 3,296 | [
"VisIt"
] | 8b95588f307602ea5f531eee1e85e60013acdc25fa295594c55f094b10a49726 |
# Copyright 2021 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | GoogleCloudPlatform/anthos-ai | serving/resnet_client_grpc.py | Python | apache-2.0 | 33,634 | [
"Bowtie",
"ESPResSo",
"Jaguar",
"ORCA"
] | ed497391b8699296936b0dd663a06c14e441c8844fe7a1f526d030622b08222f |
#!/usr/bin/env python
import matplotlib
matplotlib.use('Agg')
# import h5py as h5
import numpy as np
import pylab as plt
from random import sample, seed
from os.path import getsize as getFileSize
# ================================================================================
# Basic variables
# ==================... | darrencroton/sage | output/history.py | Python | mit | 27,194 | [
"Galaxy"
] | b3438479a5e82be12284ad448efe0d6406eba85680d59166d6b906bede269aed |
#!/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 (th... | apache/libcloud | contrib/scrape-gce-prices.py | Python | apache-2.0 | 17,016 | [
"VisIt"
] | 51dbd1440c0fc4365902e284d0906ef44ff65def56973325442650ea2d2fdf2e |
#!/usr/bin/env python
from vtk import *
reader = vtkXMLTreeReader()
reader.SetFileName("vtkclasses.xml")
view = vtkGraphLayoutView()
view.AddRepresentationFromInputConnection(reader.GetOutputPort())
view.SetVertexLabelArrayName("id")
view.SetVertexLabelVisibility(True)
view.SetVertexColorArrayName("vertex id")
view.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Examples/Infovis/Python/cone_layout.py | Python | gpl-3.0 | 723 | [
"VTK"
] | 5a374fd6312796d006872845046b7c3c5fd9c5b80bd7617c0e2b529b407cdec3 |
"""
Copyright (C) 2014, Jaguar Land Rover
This program is licensed under the terms and conditions of the
Mozilla Public License, version 2.0. The full text of the
Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
Maintainer: Rudolf Streif (rstreif@jaguarlandrover.com)
"""
from logging import Handler
f... | dvthiriez/rvi_backend | web/dblog/handlers.py | Python | mpl-2.0 | 2,680 | [
"Jaguar"
] | d0c2df58c4d60270e8b17a4f553ec79bc9aa2f7bfaa57f4f1068ae083d818b68 |
import copy
import logging
import os
import sys
from datetime import datetime
import coloredlogs
import pandas as pd
import pytz
from inicheck.config import MasterConfig, UserConfig
from inicheck.output import print_config_report, generate_config
from inicheck.tools import get_user_config, check_config, cast_all_varia... | USDA-ARS-NWRC/AWSF | awsm/framework/framework.py | Python | gpl-3.0 | 31,367 | [
"NetCDF"
] | e55794743a4d1903e760e6bd3d2f82a59e249b5d4c068a5b3ecebea332b3c5f1 |
# -*- coding: utf-8 -*-
"""
flaskbb.utils.helpers
~~~~~~~~~~~~~~~~~~~~
A few helpers that are used by flaskbb
:copyright: (c) 2014 by the FlaskBB Team.
:license: BSD, see LICENSE for more details.
"""
import re
import time
import itertools
import operator
from datetime import datetime, timedelta
... | mattcaldwell/flaskbb | flaskbb/utils/helpers.py | Python | bsd-3-clause | 10,745 | [
"VisIt"
] | 1c2f1c14b4ed7e728d1c7be781142c6935d74e7d1f9d3ffd09d42f3766ad8f49 |
# jhbuild - a build script for GNOME 1.x and 2.x
# Copyright (C) 2001-2006 James Henstridge
#
# tinderbox.py: build logic for a non-interactive reporting build
#
# 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 So... | oliver/jhbuild | jhbuild/frontends/tinderbox.py | Python | gpl-2.0 | 12,724 | [
"VisIt"
] | 6217773d73c63ed0c12d941304c16bc4276c33d0408d1ce62fc1fe10213b6e3f |
def ORR_line(pH):
"""
"""
#start_fold - ORR_line
intercept = 1.23
slope = -0.0591
V = slope*pH + intercept
return V
#end_fold
def stable_mat_one_elem(pH,V,mat):
"""
Returns pymatgen pourbaix entry object corresponding to most stable species
Args:
pH: pH of system
V: Potential with ref... | raulf2012/pourbaix_pymatgen | pd_screen_tools.py | Python | mit | 5,815 | [
"pymatgen"
] | 4fd7fad81dd0d377c3bc193447a64a0c3bf9c332720eb830dfa6a1523b681f60 |
"""
==========================================
Outlier detection with several methods.
==========================================
This example illustrates two ways of performing :ref:`outlier_detection`
when the amount of contamination is known:
- based on a robust estimator of covariance, which is assuming that the
... | cdegroc/scikit-learn | examples/covariance/plot_outlier_detection.py | Python | bsd-3-clause | 3,882 | [
"Gaussian"
] | 8bab20ea6143afb6113ef401d38a04cf89826ed7132b7815d4cf44c7216ed15d |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of t... | pmghalvorsen/gramps_branch | gramps/gui/displaystate.py | Python | gpl-2.0 | 20,893 | [
"Brian"
] | 5668a78fec15c95ebb0866c4eb9bf7dedbdd9a990de7b79f6aa837966eccbca5 |
#!/usr/bin/env python
# http://blog.magiksys.net/parsing-email-using-python-content
# https://github.com/mailgun/flanker
# https://pregmatch.org/read/python-procmail
# http://stackoverflow.com/questions/557906/want-procmail-to-run-a-custom-python-script-everytime-a-new-mail-shows-up
# http://stackoverflow.com/question... | aeppert/py-cifsdk | cifsdk/procmail.py | Python | lgpl-3.0 | 5,003 | [
"Amber"
] | 22e47c9e8d1dee547a20229785e8ad103b46b23edfb3039decff1a9647414778 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | alejob/mdanalysis | package/MDAnalysis/coordinates/XYZ.py | Python | gpl-2.0 | 15,300 | [
"MDAnalysis",
"VMD"
] | 03d47e62a6e6e2c09758dee5efdcc9f5ff802e51bffdbba11251c2019369f255 |
"""Test the Amber Electric Sensors."""
from typing import AsyncGenerator, List
from unittest.mock import Mock, patch
from amberelectric.model.current_interval import CurrentInterval
from amberelectric.model.range import Range
import pytest
from homeassistant.components.amberelectric.const import (
CONF_API_TOKEN,... | aronsky/home-assistant | tests/components/amberelectric/test_sensor.py | Python | apache-2.0 | 10,621 | [
"Amber"
] | 3f72e57d74e2530e98230d2a6bd82c59c85f1e88e9a0365f4a310571564d7b1a |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
#
# Copyright (c) 2015 Steffen Deusch
# Licensed under the MIT license
# Beilage zu MonitorNjus, 07.05.2015 (Version 0.7.1)
import random # Random Modul importieren
rancolor = ['red','indigo','blue','light-blue','cyan','teal','green','light-green','l... | SteffenDE/monitornjus-classic | modules/colors.py | Python | mit | 2,933 | [
"Amber"
] | 54440da890f2c4921109d97347c5082f2cf63f1e0234d831e26963f582eacf63 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core import Specie, Element, Lattice, Structure
from pymatgen.io.cif import CifParser
from pymatgen.analysis.magnetism import *
from monty.os.path import which
import os
import unittest
test_di... | gVallverdu/pymatgen | pymatgen/analysis/magnetism/tests/test_analyzer.py | Python | mit | 13,974 | [
"pymatgen"
] | 284b59871e16f8a9f866cc742a153833d6366a58488f8e6fbb4fda5acabc7c7f |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_numba_utils.py | Python | apache-2.0 | 3,689 | [
"PySCF"
] | d93f1a9ebfb2a15f0138313e7a5ba9f4b5368b0ff490eaaa818467c21218662e |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from textwrap import dedent
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from... | pepeportela/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 37,713 | [
"VisIt"
] | 59eb2407243c8287e2bc9c390672efe969bc142f55ba31e2a0a1f904c4eec5f1 |
#
# 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/dllib/src/bigdl/dllib/keras/layers/torch.py | Python | apache-2.0 | 34,210 | [
"Gaussian"
] | 77c58a2fd4b887ec1a322c8f8031c67a85cb36be1cd4e359d5741b3209c5f842 |
#!/usr/bin/env python3
"""The influence of windowing of bandlimited log. sweep signals when using a
Kaiser Window by fixing beta (=7) and fade_in (=0).
fstart = 100 Hz
fstop = 5000 Hz
Deconvolution: Windowed
"""
import sys
sys.path.append('..')
import measurement_chain
import plotting
import calculatio... | franzpl/sweep | log_sweep_kaiser_window_bandlimited_script6/log_sweep_kaiser_window_bandlimited_script6.py | Python | mit | 2,166 | [
"DIRAC"
] | b1409beedc54bf0c3b41b823f2e3b5ed0425007ab3fd45951348f72f8106b022 |
#!/usr/bin/env python
'''
GAEUnit: Google App Engine Unit Test Framework
Usage:
1. Put gaeunit.py into your application directory. Modify 'app.yaml' by
adding the following mapping below the 'handlers:' section:
- url: /test.*
script: gaeunit.py
2. Write your own test cases by extending unittest.TestCas... | DrZoot/pglib | gaeunit.py | Python | gpl-3.0 | 18,839 | [
"VisIt"
] | e82c04f3a9c554265c0c184588dad45e27192e1a188d658e3af1406e80119b1a |
# -*- coding: utf-8 -*-
"""Various Statistical Tests
Author: josef-pktd
License: BSD-3
Notes
-----
Almost fully verified against R or Gretl, not all options are the same.
In many cases of Lagrange multiplier tests both the LM test and the F test is
returned. In some but not all cases, R has the option to choose the ... | rgommers/statsmodels | statsmodels/sandbox/stats/diagnostic.py | Python | bsd-3-clause | 52,890 | [
"ADF"
] | 8d30fc297d3ae10f455b138239dff049024a92d68fbb1f2c4ef2775dbc0db3fd |
'''This script runs the iterative procedure that follows the workflow: steric assessment - alchembed - steric assessment, etc.'''
import glob
import argparse
import time
import sys
import subprocess
import cPickle as pickle
import numpy as np
import generate_mdp
import collections
import MDAnalysis
import matplotlib
m... | tylerjereddy/steric-conflict-resolution | docker_build/run_steric_resolution.py | Python | mit | 30,823 | [
"Gromacs",
"MDAnalysis"
] | 47ccc4bcc59cd61f87f9ca9fdc3564e981c32c7527157de2db500c1ac78507a4 |
import matplotlib
matplotlib.use('PS')
matplotlib.rc('text', usetex = True)
matplotlib.rcParams['font.size'] = 17
matplotlib.rc('xtick', labelsize = 13)
matplotlib.rc('ytick', labelsize = 13)
matplotlib.rc('axes', linewidth = 1.2)
matplotlib.rcParams['legend.fontsize'] = 12
matplotlib.rcParams['legend.handlelength'] ... | sniemi/SamPy | herschel/plotFluxDistribution.py | Python | bsd-2-clause | 5,322 | [
"Galaxy"
] | 4e12b75149e81f28226a7e666b1a60269860dd9fd6dd52db881f8c0f25cfd72f |
"""Module containing specific irradiance modeling functions and tools.
More work probably needs to be done to improve the computation speed here, and
in theory a big part of ``perez_diffuse_luminance`` should be handled by pvlib
"""
import numpy as np
import pandas as pd
from pvlib import atmosphere, irradiance
from pv... | SunPower/pvfactors | pvfactors/irradiance/utils.py | Python | bsd-3-clause | 13,218 | [
"Gaussian"
] | 739a8f800fc68a30c9f7c9799a93d1b686f8cbebde5e18ff974ca74eb5927e9e |
import pytest
import numpy as np
import os
from tests.test_gp import get_random_structure
from flare.struc import Structure
from json import loads, dumps
from flare.utils.element_coder import Z_to_element, NumpyEncoder
from .test_gp import dumpcompare
def test_random_structure_setup():
struct, forces = get_rando... | mir-group/flare | tests/test_struc.py | Python | mit | 10,616 | [
"ASE",
"pymatgen"
] | 86270c077292b58127d31aacb1f3f14158389974a1974d0e1a117fb0d8462a97 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from diraccfg import CFG
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import List
def loadJDLAsCFG(jdl):
"""
Load a JDL as CFG
"""
def cleanValue(value):
... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/JDL.py | Python | gpl-3.0 | 5,764 | [
"DIRAC"
] | 073aa2dab9a907e07ef243292cc8f62a29aefa9d3d42bf9b35b4f48f9be021b4 |
import threading, time, types
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.ReturnValues import isReturnStructure
from DIRAC.Core.Utilities.ThreadScheduler import gThreadScheduler
class ExecutorState:
def __init__( self, log = False ):
if log:
self.__log = log
else:
self.__... | calancha/DIRAC | Core/Utilities/ExecutorDispatcher.py | Python | gpl-3.0 | 28,735 | [
"DIRAC"
] | 66be65a0def93dafa4e9e10e453e6214ca9d0540b6e9c42493564008e4d5ab03 |
# -*- coding: utf-8 -*-
# aboutdialog.py
#
# Copyright (C) 2007 Marcos Mobley ('markybob') <markybob@gmail.com>
#
# Deluge is free software.
#
# You may 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, ... | EiNSTeiN-/deluge-gtk3 | deluge/ui/gtkui/aboutdialog.py | Python | gpl-3.0 | 19,136 | [
"Gaussian"
] | f2f07abbe9ce76bdf897c42374eb27743ce6be2854c00d467f5eae0debe063de |
from mayavi import mlab
from traits.api import Range, on_trait_change
from traits.api import HasTraits, Instance, List, Enum, Str, Bool
from traitsui.api import View, Item, Group, HGroup, Spring, CheckListEditor, Label
from mayavi.core.ui.api import SceneEditor, MlabSceneModel, MayaviScene
import numpy as np
from threa... | recursix/spearmint-salad | spearmint_salad/analyze/plot_nd.py | Python | bsd-3-clause | 16,401 | [
"Gaussian",
"Mayavi"
] | 9428fd1c0866f94c733abf316140a0b4d0a0c5beb71cd13d3b2600666028f900 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/search/commissionsearch.py | Python | gpl-2.0 | 7,384 | [
"VisIt"
] | 027f922cb25e03bfd24d687f903cb5bc7c3bf3ce5555aed770bc1f4f179d484a |
from math import sqrt
from ase import Atoms, Atom
from ase.constraints import FixAtoms
from ase.optimize import FIRE, QuasiNewton, BFGS
from ase.neb import SingleCalculatorNEB
from ase.calculators.emt import EMT
Optimizer = BFGS
# Distance between Cu atoms on a (111) surface:
a = 3.6
d = a / sqrt(2)
fcc111 = Atoms(sy... | suttond/MODOI | ase/test/COCu111_2.py | Python | lgpl-3.0 | 1,853 | [
"ASE"
] | b14bea5d25c15c627e3851107721b3db9446c6cd9a5a6913e13142824e882a3e |
from ANN_simulation import *
import datetime, os, argparse
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
from sys import stdout
import ast
from config import *
############################ PARAMETERS BEGIN ###############################################################
parser = ar... | weiHelloWorld/accelerated_sampling_with_autoencoder | MD_simulation_on_alanine_dipeptide/current_work/src/biased_simulation_general.py | Python | mit | 23,527 | [
"OpenMM"
] | d7abfd66b156165685500a61119d934441feeb61f98e671f0dff36b3b4a7becf |
#
# @BEGIN LICENSE
#
# ccambit by Psi4 Developer, a plugin to:
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribu... | lothian/ccambit | __init__.py | Python | gpl-3.0 | 1,296 | [
"Psi4"
] | 09a14aabc04dfa275965a0c380bff64fe7951e73a1b40180755d678003cda6ac |
# 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.
#
"""Classes to help deal with stopping training a neural network.
One of the key issues with training a neural network is knowning when to
stop the t... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/NeuralNetwork/StopTraining.py | Python | gpl-2.0 | 3,072 | [
"Biopython"
] | 527243be6804c724a8af0a2be16f35adf67b651cd08ad49501f6100b4114e05b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
__author__ = 'Ignacio Arroyo-Fernandez'
from mklObj import *
from ast import literal_eval
from sys import stdout
import argparse
#from sys import stderr
#import pdb
# [feats_train, feats_test, labelsTr, labelsTs] = generate_binToy()
# [feats_train, feats_test, labelsTr, l... | iarroyof/distributionalSemanticStabilityThesis | mklCall.py | Python | gpl-2.0 | 7,526 | [
"Gaussian"
] | 20df8eb045701b40a39f4c90c5ccea51d2fa0a982b2f8baf7765f9f2fe04c37a |
import os
import datetime
import traceback
import gzip
import sys
import subprocess
import yaml
from yaml.scanner import ScannerError
import warnings
import socket
from collections import deque
from copy import deepcopy
import numpy as np
import Bio
import ensembler
import ensembler.version
from ensembler.core import m... | jchodera/ensembler | ensembler/refinement.py | Python | gpl-2.0 | 48,857 | [
"MDTraj",
"OpenMM"
] | 85df0c09920e5deecceb45f3178bf45708fb6f549e761f25a5ae2afb004a8e33 |
#
# 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)... | dschwoerer/espresso | samples/python/p3m.py | Python | gpl-3.0 | 6,355 | [
"ESPResSo"
] | 35cafee0849cc3582547dd81f6f70822b0f825748152d23dc1d18727575d1a3e |
from dirac.lib.base import *
from dirac.lib.credentials import getUserDN, getUsername, getAvailableGroups
from dirac.lib.credentials import getProperties, checkUserCredentials, getSelectedGroup
from DIRAC import gConfig, gLogger
from DIRAC.FrameworkSystem.Client.SystemAdministratorClient import SystemAdministratorClien... | DIRACGrid/DIRACWeb | dirac/controllers/systems/SystemAdministration.py | Python | gpl-3.0 | 16,925 | [
"DIRAC"
] | ba79786f47e1e904410ac0bcff31a4070feddb6524e483fe70b41bec56018b55 |
import numpy as np
import interpolation
def smooth(data,smooth,smoothtype='gaussian',downsample=True,downsample_factor=None,
convmode='same'):
"""
Smooth and downsample the data array
Parameters
----------
smooth : float
Number of pixels to smooth by
smoothtype : [ 'gaussian... | keflavich/pyspeckit-obsolete | pyspeckit/spectrum/smooth.py | Python | mit | 2,911 | [
"Gaussian"
] | ae3805019ea2752cd8a62f1e66f62f2db9c8d35d4923afa66a651005c5e78df4 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
import warnings
from monty.os.path import which
from monty.serialization import loadfn
from pymatgen.electronic_structure.bandstructure import BandStructure
from pymatgen.electronic_str... | vorwerkc/pymatgen | pymatgen/electronic_structure/tests/test_boltztrap.py | Python | mit | 15,673 | [
"ASE",
"BoltzTrap",
"pymatgen"
] | ed097faf54c32617e5a4168adb0a4fc44a7b944c68e2f7d42e6cceee39a25b80 |
#!/usr/bin/env python3
# Copyright (C) 2012-2017(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/simpleGromacs/simpleGromacs.py | Python | gpl-3.0 | 8,199 | [
"ESPResSo",
"Gromacs"
] | c2f70fab8eaba59f0a4b22663031b5d7a87b99fda0ddc74f12b2b61a2e06297f |
# $Id$
"""
This is a comment
"""
__RCSID__ = "$Revision: 1.30 $"
import os, time, types, traceback, sys
#try: # this part to inport as part of the DIRAC framework
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Workflow.Module import *
from DIRAC import S_OK, S_ERROR
#except: # this part is to import c... | marcelovilaca/DIRAC | Core/Workflow/Step.py | Python | gpl-3.0 | 17,147 | [
"DIRAC"
] | 55fa04dbeb2d1e6549a2e2698fad8e5fe8ab8898976cc9bbe69cabea8b3b149a |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@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, either... | k0ste/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 62,220 | [
"VisIt"
] | dba39683f9f24c961521eee8c9b5c1c40a24e24fefa5a9b7800c2c2cabe6edaa |
#!/usr/bin/env python
# Copyright 2014-2019 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/pbc/dft/gen_grid.py | Python | apache-2.0 | 9,710 | [
"PySCF"
] | bcc88110902167831719975662b034370454e7c1c36799da7f3fccb661551bdb |
# Copyright (c) 2012 - 2014 the GPy Austhors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ..core import SparseGP
from ..inference.latent_function_inference import VarDTC
from .. import kern
from .. import util
class SparseGPCoregionalizedRegression(SparseGP):
... | befelix/GPy | GPy/models/sparse_gp_coregionalized_regression.py | Python | bsd-3-clause | 3,024 | [
"Gaussian"
] | e8f3b5469eeb594bc23b49cd94ad53ac66e3e966f03fd9b2268e0dd774ad02f2 |
import os
from tibanna import top
top_contents = """
Timestamp: 2020-12-18-18:55:37
top - 18:55:37 up 4 days, 3:18, 2 users, load average: 2.00, 2.00, 2.30
Tasks: 344 total, 1 running, 343 sleeping, 0 stopped, 0 zombie
%Cpu(s): 6.6 us, 0.1 sy, 0.0 ni, 93.2 id, 0.0 wa, 0.0 hi, 0.0 si, 0.0 st
KiB Mem :... | 4dn-dcic/tibanna | tests/tibanna/unicorn/test_top.py | Python | mit | 7,672 | [
"BWA"
] | 76dbc8252589f8b9f23b6758150b170afc4fd6512925357c956ee926e7ec088a |
import dataset_adapter as dsa
import numpy
from vtk.util import numpy_support
import vtk
def _cell_derivatives (narray, dataset, attribute_type, filter):
if not dataset :
raise RuntimeError, 'Need a dataset to compute _cell_derivatives.'
# Reshape n dimensional vector to n by 1 matrix
if len(narray... | msmolens/VTK | Wrapping/Python/vtk/numpy_interface/internal_algorithms.py | Python | bsd-3-clause | 19,342 | [
"VTK"
] | 0491f0080861afda70b0172f5afb714b5beb331202a413ae45a7917e7c3e9dbd |
# !/usr/local/bin/python3.4.2
# ----Copyright (c) 2017 Carnegie Hall | The MIT License (MIT)----
# ----For the full license terms, please visit https://github.com/CarnegieHall/linked-data/blob/master/LICENSE----
## Argument[0] is script to run
## Argument[1] is path to json query results from data.carnegiehall.org
im... | CarnegieHall/linked-data | scripts/create_ch_toWikiDict.py | Python | mit | 958 | [
"VisIt"
] | 1dd4a49f4ed69942f939201fd9106bcf42bd084cbe2f56310d5a143602420e27 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/core/exception.py | Python | gpl-2.0 | 3,629 | [
"VisIt"
] | 71eb6cc1e91f52bc607d258bdf1db1e77dc828f17838f5757c3d1fd4d4776901 |
import pysam
import collections
import multiprocessing
from general_python import toolbox
from ngs_python.variant import annovar
import pandas as pd
from scipy.stats import fisher_exact
import re
def extract_fasta(fasta, chrom, start, end):
''' Function to extract sequence from FASTA file using the pysam
modul... | adam-rabinowitz/ngs_python | bam/pysamfunc.py | Python | gpl-2.0 | 35,840 | [
"pysam"
] | 64be45fc6f4ccd993589ef12cfaa4519e8c6dfde8c67a329ff7f65fd6867f953 |
"""
test_galaxy.py
Copyright 2016 Brian Romanchuk
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... | brianr747/Simple4Xpygame | tests/test_galaxy.py | Python | apache-2.0 | 3,554 | [
"Brian",
"Galaxy"
] | 9efbc7fbcf13356fc95fdbff908569168943eeb2e625888501cbe7d6b75cf162 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | sg00dwin/origin | vendor/k8s.io/kubernetes/hack/verify-flags-underscore.py | Python | apache-2.0 | 4,683 | [
"VisIt"
] | 6fd63b3f3ac7755927f69f4c262de9161a4ebb5bde8450bfa48736ea3c3a1d17 |
#!/usr/bin/env python
# =============================================================================================
# MODULE DOCSTRING
# =============================================================================================
"""
Tests for cheminformatics toolkit wrappers
"""
# ==============================... | open-forcefield-group/openforcefield | openff/toolkit/tests/test_toolkits.py | Python | mit | 163,747 | [
"RDKit"
] | dd4c0c44dadce65afab8b8d3849ec7892e84e4415b54ce3f7ed118c7dfea8e92 |
# -*- coding: utf-8 -*-
import inspect
import os.path as op
from ....interfaces import io as nio # Data i/o
from ....interfaces import utility as util # utility
from ....pipeline import engine as pe # pypeline engine
from ....interfaces import camino as camino
from ....interfaces import fsl as fsl
from .... | mick-d/nipype | nipype/workflows/dmri/camino/connectivity_mapping.py | Python | bsd-3-clause | 25,841 | [
"DIRAC",
"ParaView",
"VTK"
] | b635958a40682ab86a0a99ac406248cc8ef40e3753bb7ad604c51b07ab5b009f |
# 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... | Laurawly/tvm-1 | python/tvm/relay/testing/__init__.py | Python | apache-2.0 | 7,200 | [
"VisIt"
] | f7e8528984f59e59fcb5914869309f9e50a60360016cad165975f921f6181958 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Neuron(CMakePackage):
"""NEURON is a simulation environment for single and networks of neu... | LLNL/spack | var/spack/repos/builtin/packages/neuron/package.py | Python | lgpl-2.1 | 5,773 | [
"NEURON"
] | c825ef3f401a3ca0a4e880b4d95e60e653d6649a3364a5754a27731d87fd2006 |
"""
Tests for analysis of spatial autocorrelation within vectors
"""
__author__ = 'Taylor Oshan tayoshan@gmail.com'
import unittest
import numpy as np
from libpysal.weights.distance import DistanceBand
from ..vec_SA import VecMoran
class TestVecMoran(unittest.TestCase):
"""Tests VecMoran class"""
def setU... | TaylorOshan/spint | spint/tests/test_vec_SA.py | Python | bsd-3-clause | 2,204 | [
"VMD"
] | 18e40df2f33b5242154f9b7fa5a8d26d2bb8221492c0bb7151ae50bbce2059a0 |
"""
This transform implements time management functions (delay_mu/now_mu/at_mu)
using an accumulator 'now' and simple replacement rules:
delay_mu(t) -> now += t
now_mu() -> now
at_mu(t) -> now = t
The function delay(), that uses seconds, must be lowered to delay_mu() before
invoking this transfor... | kgilmo/penning_artiq | artiq/transforms/lower_time.py | Python | gpl-3.0 | 2,028 | [
"VisIt"
] | b252e8711ed592605e21ed37de8cc1017dbc490cbdc8cd172caa61fb68794cfb |
#!/usr/bin/python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it ... | andysim/psi4 | doc/sphinxman/extract_changeset.py | Python | gpl-2.0 | 1,797 | [
"Psi4"
] | 7b3e60acaaef3f128259e31e552439fe865e60978ff0cbb4a289dc01946b8eb3 |
from pyibex.thickset import *
from pyibex_thickset.image import *
from pyibex import Interval, IntervalVector
from vibes import vibes
import numpy as np
import time
class Timer(object):
""" A quick tic-toc timer
Credit: http://stackoverflow.com/questions/5849800/tic-toc-functions-analog-in-python
"""
... | benEnsta/pyIbex | pyibex/thickset/examples/thickSet_transform2.py | Python | lgpl-3.0 | 2,634 | [
"VisIt"
] | 6c49c979aa9004d4728276589c333d4e5f9c3c91bb9ec4bb9cdacfa5027987a1 |
""" Test for StorageManagement clients
"""
# pylint: disable=protected-access,missing-docstring,invalid-name
import unittest
from mock import MagicMock, patch
from DIRAC import S_OK, S_ERROR
from DIRAC.StorageManagementSystem.Client.StorageManagerClient import getFilesToStage
from DIRAC.DataManagementSystem.Client.te... | DIRACGrid/DIRAC | src/DIRAC/StorageManagementSystem/Client/test/Test_Client_StorageManagementSystem.py | Python | gpl-3.0 | 8,176 | [
"DIRAC"
] | bff94e6450b5fb158c0f654ba7614d71d6b464a012d79e73ecd7aa1ead8abd8f |
import sys
import antlr
class Visitor(antlr.ASTVisitor):
def __init__(self,*args):
super(Visitor,self).__init__(*args)
self.level = 0
if not args:
self.cout = sys.stdout
return
if isinstance(args[0],file):
self.cout = args[0]
return
assert 0
... | BillHally/boo | lib/antlr-2.7.5/examples/python/includeFile/incfile.py | Python | bsd-3-clause | 2,507 | [
"VisIt"
] | 00f8d5d2e9561e1e78fdb16457a23a0a48c6f7c6c4d7fac487a2f7a68b3b9ce8 |
from math import sqrt,log
import numpy as np
from matplotlib import pyplot
import rft1d
eps = np.finfo(float).eps
def here_cca_single_node(y, x):
N = y.shape[0]
X,Y = np.matrix(x.T).T, np.matrix(y)
Z = np.matrix(np.ones(N)).T
Rz = np.eye(N) - Z*np.linalg.inv(Z.T*Z)*Z.... | 0todd0000/rft1d | rft1d/examples/val_upx_4_X2_set.py | Python | gpl-3.0 | 2,822 | [
"Gaussian"
] | a51e8b9a432711643cc9a3e5d716ba4c5235f74dda5c57c22dc6aa4004b78567 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jan 07 11:08:41 2016
@author: Radu
"""
import numpy
import simrun
import time
from ballandstick_clarke_new import ClarkeRelay
#from neuron import h,gui
from neuron import h
h.load_file('stdgui.hoc')
#h.load_file("stdrun.hoc")
from math import sin, cos, pi
from matplotlib im... | penguinscontrol/Spinal-Cord-Modeling | ClarkesNetwork/test1_plot.py | Python | gpl-2.0 | 5,699 | [
"NEURON"
] | 821c3c6f65639adaa8c9b10d63c5140f069343c0783dcf6b96d3f228a12c2058 |
#!/usr/bin/python
# File created on Nov 27 Jan 2012
from __future__ import division
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
from os import makedirs, sys, remove, rename
... | wholebiome/MetaPathways_Python_Koonkie.3.0 | libs/python_scripts/MetaPathways_annotate_fast.py | Python | mit | 38,426 | [
"BLAST"
] | d009138bc13fb6354214f9250df6461f71e0061df769125f701fd6dfe9d43809 |
"""
Copyright 2007, 2008, 2009 Free Software Foundation, Inc.
This file is part of GNU Radio
SPDX-License-Identifier: GPL-2.0-or-later
"""
from gi.repository import Gtk, Gdk, GObject, Pango
from . import Actions, Utils, Constants
from .Dialogs import SimpleTextDisplay
class PropsDialog(Gtk.Dialog):
"""
A ... | mbr0wn/gnuradio | grc/gui/PropsDialog.py | Python | gpl-3.0 | 11,674 | [
"VisIt"
] | f6d5e87f08c2f14ecb6e98606f0584f9f7d0d46b20adb86a85a41c5560252e11 |
import requests
API_ROOT = 'http://api.nytimes.com/svc/search/v2/articlesearch.'
API_SIGNUP_PAGE = 'http://developer.nytimes.com/docs/reference/keys'
class NoAPIKeyException(Exception):
def __init__(self, value):
self.value = value
def __str__(self):
return repr(self.value)
class articleAPI(... | MattDMo/NYTimesArticleAPI | NYTimesArticleAPI/search_api.py | Python | mit | 2,843 | [
"VisIt"
] | 1230f45b149232d2a225ed262d9dd1f238cf4d1ce82c846dee1393fd3909ecbe |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/core/test_groups.py | Python | gpl-2.0 | 59,291 | [
"MDAnalysis"
] | acded786445ff143e8345d4b4f95dc4eae168363ebed966be5c7582a2af3358c |
#
# 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) 2016-2019 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaini... | est77/appleseed-maya | scripts/appleseedMaya/xgenseed.py | Python | mit | 4,751 | [
"VisIt"
] | bde3e61cc7c7758fcc60aabbd9c25431cb159d55ff6020d880b62a63a1f18c8f |
# procedure for existing halos, after the first snapshot was initiated :
import sys
# only input parameter is the numbering of the snapshot. These have to be processed in sequence, cannot be done in parallel ... First 1, 2, 3, ...
ii = int(sys.argv[1])
#ii = 10
import time
t0 = time.time()
import h5py
import os
... | JohanComparat/pyEmerge | bin_rzg_v0/emerge_iterate.py | Python | unlicense | 17,361 | [
"Galaxy"
] | d647c02a0fb4bdb4d604457db76ff3d2088fcf08a486784cb2ab956fd5c83195 |
# Copyright (C) 2011 Jeremy S. Sanders
# Email: Jeremy Sanders <jeremy@jeremysanders.net>
#
# 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
# ... | arichar6/veusz | veusz/utils/colormap.py | Python | gpl-2.0 | 18,221 | [
"VisIt"
] | 86efe56f04262dee1c7616c0fd201583d50b4f0a9324e7a5d53bcf081a7260d1 |
#! /usr/bin/python
#Done by: Guru
"""
Get Flanking regions.
usage: %prog input out_file size direction region
-l, --cols=N,N,N,N: Columns for chrom, start, end, strand in file
-o, --off=N: Offset
"""
import sys, re, os
from galaxy import eggs
import pkg_resources; pkg_resources.require( "bx-python" )
from bx.c... | volpino/Yeps-EURAC | tools/new_operations/get_flanks.py | Python | mit | 9,711 | [
"Galaxy"
] | 058fbec5a4f71ba3ade0f437d125e51f15938fe9a043feab1d0dfbc6298d8742 |
from django.test import TestCase
from splinter import Browser
from .models import UserActivation, User
class AuthenticationLoginBrowserTestCase(TestCase):
def setUp(self):
self.browser = Browser('django')
self.test_user_id = 'test-user@pergenie.org'
self.test_user_password = 'test-user-pa... | knmkr/perGENIE | pergenie/apps/authentication/test_browser.py | Python | agpl-3.0 | 8,254 | [
"VisIt"
] | ef937c7a0628b797a4a74f0dca6279678b28e4bdc7f32fa0fba6004f224b4b65 |
import numpy as np
def genRandomFunction(dim=1):
'''
Generates a random multi-dimensional fourier sine series on the periodic domain [0,1)
parameterized by random coefficients that fall off exponentially with the degree of
the sinusoid
'''
depth = 5
m = np.meshgrid(*(range(1,depth+1),)*dim)
m = np.stac... | pvarin/Dynamics-LGP | src/genData.py | Python | mit | 1,845 | [
"Gaussian"
] | cb8bbfb699751fc81ceb1a05ad80a11a0bfff986a21153e4f416ac36406c0fd1 |
#!/usr/bin/env python
"""
synfig_output.py
An Inkscape extension for exporting Synfig files (.sif)
Copyright (C) 2011 Nikita Kitaev
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 o... | piksels-and-lines-orchestra/inkscape | share/extensions/synfig_output.py | Python | gpl-2.0 | 48,326 | [
"Gaussian"
] | d7bb542c11c0db58005d09a834bc93239b7244948152cbb6cc9e729d3b22fcd1 |
# -*- coding: utf-8 -*-
#
# 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... | janewangfb/spark | python/pyspark/ml/tests.py | Python | apache-2.0 | 93,226 | [
"Gaussian"
] | c8b736bf94a1f819e156a9c45a1d1f6364cbbc67c2af3964686cbfdde258f94f |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import sys
i... | nuclear-wizard/moose | python/MooseDocs/extensions/bibtex.py | Python | lgpl-2.1 | 11,343 | [
"MOOSE"
] | 28cf9a02df87568470786b9386fd03de1e3747fa822140104e34d2ef6287376a |
##
# Copyright 2016-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | akesandgren/easybuild-easyblocks | easybuild/easyblocks/a/adf.py | Python | gpl-2.0 | 3,997 | [
"ADF"
] | aec9a4eb152d4791b041bb1a028dd4219757da38f05fe60ec2f19cfdf2e32f16 |
# *****************************************************************************
# Copyright (c) 2020, Intel Corporation All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# Redistributions of sou... | IntelLabs/hpat | sdc/hiframes/aggregate.py | Python | bsd-2-clause | 73,006 | [
"VisIt"
] | f9e0fff0f5655e3776ec79b71994a5522b59f5c64352724b4cfdde8281577c75 |
# -*- coding: utf-8 -*-
"""
pySEBAL_3.3.8
@author: Tim Hessels, Jonna van Opstal, Patricia Trambauer, Wim Bastiaanssen, Mohamed Faouzi Smiej, Yasir Mohamed, and Ahmed Er-Raji
UNESCO-IHE
September 2017
"""
import sys
import os
import re
import shutil
import numpy as np
import datetime
from osgeo impo... | wateraccounting/SEBAL | EESEBAL/EESEBAL_LS_input.py | Python | apache-2.0 | 98,673 | [
"ADF"
] | 0e3343967aaf392bfe8ae88a513dcc0972b249308b0e8e27b0f032dfe4bcf221 |
from ase.test import cli
from ase.db import connect
cmd = """
ase-build H | ase-run emt -d y.json &&
ase-build H2O | ase-run emt -d y.json &&
ase-build O2 | ase-run emt -d y.json &&
ase-build H2 | ase-run emt -f 0.02 -d y.json &&
ase-build O2 | ase-run emt -f 0.02 -d y.json &&
ase-build -x fcc Cu | ase-run emt -E 5 -d... | askhl/ase | ase/test/db.py | Python | gpl-2.0 | 1,223 | [
"ASE"
] | c13fbcfee1525690090dca35c19ed957881b5003a8c0592597af2f420846a878 |
# 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):
db.rename_column('core_patient','user_id', 'owner_id')
db.rename_column('core_historicalpatient', 'user_id', 'owner... | praekelt/txtalert | txtalert/core/migrations/0007_rename_patient_user_to_owner.py | Python | gpl-3.0 | 13,069 | [
"VisIt"
] | 3cd8d28d4b7c2ef5ffa0cbf75177e675474f2687916df5e71cebcabf2f545695 |
from setuptools import setup
setup(
name='blender-chemicals',
version='0.3.0',
description="Imports chemicals into blender with open babel.",
url='http://github.com/patrickfuller/blender-chemicals/',
author="Patrick Fuller",
author_email='patrickfuller@gmail.com',
entry_points={
'co... | patrickfuller/blender-chemicals | setup.py | Python | mit | 733 | [
"Open Babel"
] | bfd3e61ef5027588910a64330d2d3cec48b96cd1942a5a39d9452afbcb695e2c |
"""
Test dashboard search
"""
import os
import json
from bok_choy.web_app_test import WebAppTest
from ..helpers import generate_course_key
from ...pages.common.logout import LogoutPage
from ...pages.studio.utils import add_html_component, click_css, type_in_codemirror
from ...pages.studio.auto_auth import AutoAuthPage... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/lms/test_lms_dashboard_search.py | Python | agpl-3.0 | 7,031 | [
"VisIt"
] | 378ebe9cf5c9dc37b71218af22a5d7f8ec70c308a998b16eafbf606a088476bb |
#!/usr/bin/env python
# Standard packages
import sys
import argparse
# Third-party packages
from toil.job import Job
# Package methods
from ddb import configuration
from ddb_ngsflow import gatk
from ddb_ngsflow import annotation
from ddb_ngsflow import pipeline
from ddb_ngsflow.align import bwa
from ddb_ngsflow.vari... | dgaston/ddb-ngsflow-scripts | workflow-var_call_exome.py | Python | mit | 3,785 | [
"BWA"
] | 993ae508939ed72f635daf37f6a1de10cff8333bda883cd51cfd5c824c888213 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Jun 14 05:54:11 2020
@author: mathieumoog
"""
import cpmd
import filexyz
import numpy as np
import matplotlib.pyplot as plt
# MSMbuilder ( lacks CK validation )
from msmbuilder.msm import MarkovStateModel
from msmbuilder.msm import BayesianMarkovState... | CondensedOtters/PHYSIX_Utils | Projects/Moog_2016-2019/CO2/CO2_NN/forces.py | Python | gpl-3.0 | 2,995 | [
"CPMD"
] | 7737205ebe3bd724a139287c5edbac6e7252f9573d70f62fc56b2e4ffeef314a |
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Dbase import DbModule
from rdkit.Dbase.DbConnection import DbConnect
import pickle
if RDConfig.usePgSQL:
dbName = "::RDTests"
else:
dbName = "data.sqlt"
molTblName = 'simple_mols1'
fpTblName = 'simple_mols1_fp'
conn = DbConnect(dbName, molTblName)... | bp-kelley/rdkit | rdkit/SimDivFilters/test_data/genfps.py | Python | bsd-3-clause | 650 | [
"RDKit"
] | 77e08eb150ee0406f6eaa491b02e89a674ef7f55d65a36f03351f5b568001806 |
from plotly.basedatatypes import BaseTraceHierarchyType as _BaseTraceHierarchyType
import copy as _copy
class Marker(_BaseTraceHierarchyType):
# class properties
# --------------------
_parent_path_str = "scattercarpet"
_path_str = "scattercarpet.marker"
_valid_props = {
"autocolorscale",... | plotly/python-api | packages/python/plotly/plotly/graph_objs/scattercarpet/_marker.py | Python | mit | 57,935 | [
"Bowtie"
] | 39ed641b19dc42ac5dda0bf30eb01b18783987964cadde815964135aa265b544 |
import json
from django.test import TestCase
from django.utils import timezone
from datetime import timedelta
from myvoice.core.tests import factories
from .. import forms
class TestFeedbackForm(TestCase):
"""
Requirements from TextIt Generic feedback flow
Clinic ID comes as numeric category with label... | myvoice-nigeria/myvoice | myvoice/clinics/tests/test_forms.py | Python | bsd-2-clause | 15,424 | [
"VisIt"
] | fdbc8b13c1ca83adc1ea8dc189460480a78f76cbbdaba2c69382e1c4672f68c5 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Input Cholesky decomposed integrals for SCF module by overwriting the _cderi attribute.
See also:
examples/df/40-precompute_df_ints.py
'''
import tempfile
import h5py
from pyscf import gto, df, scf
mol = gto.M(atom='H 0 0 0; F 0 0 1', basis='... | sunqm/pyscf | examples/scf/41-hf_with_given_densityfit_ints.py | Python | apache-2.0 | 1,697 | [
"PySCF"
] | 45c16ebe5d2dfc9f9c8bc9a15cfc8593d10583f9228518974d874301015b143a |
#-------------------------------------------------------------------------------
# Cloud-COPASI
# Copyright (c) 2013 Edward Kent.
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the GNU Public License v3.0
# which accompanies this distribution, and is available... | edkent/cloud-copasi | cloud_copasi/web_interface/aws/ec2_config.py | Python | gpl-3.0 | 2,212 | [
"COPASI"
] | 6a19ab1f2668084233ecf723330e732b56d0e66691830c437e7d06ba77acea39 |
from ovito.io import import_file
from ovito.modifiers import LoadTrajectoryModifier
# Load static topology data from a LAMMPS data file.
node = import_file('input.data', atom_style = 'bond')
# Load atom trajectories from separate LAMMPS dump file.
traj_mod = LoadTrajectoryModifier()
traj_mod.source.load('trajectory.d... | srinath-chakravarthy/ovito | doc/python/example_snippets/load_trajectory_modifier.py | Python | gpl-3.0 | 428 | [
"LAMMPS",
"OVITO"
] | d4b9866a9e073d8fe744522d91ecf245a5c32fb22e392e179e63f30cc9b93e9c |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2015 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/dialogs/returnedsaledialog.py | Python | gpl-2.0 | 6,044 | [
"VisIt"
] | 9787a017efea2a46b1d46b3a7db2ac422d713a708dfe631bb986c3e869907509 |
# -*- coding: utf-8 -*-
# Copyright (c) 2008, 2010, 2013 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014 Google, Inc.
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2014-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelmc.ro>
... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/test/unittest_pyreverse_writer.py | Python | apache-2.0 | 4,453 | [
"VisIt"
] | f2fa57904b8073c71d959156fcae302189f7dbba7bf0308f14a64fb930254f9b |
#!/usr/bin/env python
import sys
import os
import logging
import tempfile
import shutil
import glob
import HTSeq
from HTSeq import GenomicInterval
import collections
from bx.intervals.cluster import ClusterTree
import subprocess
import bz2
import re
from shutil import rmtree
from subprocess import PIPE
from collect... | schelhorn/virana | virana/vhom.py | Python | apache-2.0 | 70,901 | [
"Biopython",
"HTSeq",
"pysam"
] | 74ac57da01089f25b156cb631cd451190477b23347f1f828921879686c58c0fa |
from Bio.SubsMat import MatrixInfo
from Bio import SeqIO
def fasta_to_list(path_to_alignment):
"""Parse through a fasta formatted file and store its contents in a
list. Uses SeqIO from Biopython.
:param path_to_alignment: a string representation of the path to the
fasta formatted file
:return: a ... | Adriel-M/Clustal-MUSCLE-Iterator | Sum_of_Pairs.py | Python | gpl-3.0 | 5,510 | [
"Biopython"
] | 48160f15a889ee0d4238e71310d3e3ad64b20c0889422a74e8f77df64c1f23e7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
**sIBL_GUI_For_Maya.py
**Platform:**
Windows, Linux, Mac Os X.
**Description:**
Maya sIBL_GUI Helper Script for Maya 2011 and higher.
**Others:**
"""
#***********************************************************************************************... | KelSolaar/sIBL_GUI_For_Maya | src/scripts/sIBL_GUI_For_Maya.py | Python | gpl-3.0 | 14,004 | [
"VisIt"
] | 5308dabfa645313635c9916a29b003ba5b2013d46df4a9cae8b8bd43b1be6dd5 |
import ast
def _get_attr_node(names):
"""Builds an Attribute node, or a Name node if names has just one entry."""
node = ast.Name(id=names[0], ctx=ast.Load())
for name in names[1:]:
node = ast.Attribute(value=node, attr=name, ctx=ast.Load())
return node
def _get_long_name(node):
# If th... | HyperloopTeam/FullOpenMDAO | lib/python2.7/site-packages/openmdao.main-0.13.0-py2.7.egg/openmdao/main/printexpr.py | Python | gpl-2.0 | 11,186 | [
"VisIt"
] | 727996311cdae31fabf4e0a27d6e0fa36426b14f808971a544c7ac2a4b4bafc1 |
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