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#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
##!/mnt/lustre_fs/users/mjmcc/apps/python2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
import sys
import numpy as np
import MDAnalysis
from MDAnalysis.analysis.align import *
from... | rbdavid/RMSF_calc | rmsf_calc.py | Python | gpl-3.0 | 11,988 | [
"MDAnalysis"
] | 15ceafb9f6f7e8d0295b2999d4f9bc3a24ee22f9cf3bf750b11ace02157e30a6 |
from __future__ import absolute_import, print_function
import os
import numpy as np
from ase.db.core import Database, ops, parallel, lock, now
from ase.db.row import AtomsRow
from ase.io.jsonio import encode, read_json
from ase.parallel import world
class JSONDatabase(Database):
def __enter__(self):
ret... | suttond/MODOI | ase/db/jsondb.py | Python | lgpl-3.0 | 5,904 | [
"ASE"
] | feca6c8a408f8ca2e52957d7c22be0c63f64048b8b048cca6f6666134c938d4b |
__author__ = 'xiaoxiaol'
import sys
import os
import platform
if (platform.system() == "Linux"):
WORK_PATH = "/local1/xiaoxiaol/work"
else:
WORK_PATH = "/Users/xiaoxiaoliu/work"
p = WORK_PATH + '/src/morphology_analysis'
sys.path.append(p)
import bigneuron.recon_prescreening as rp
import bigneuron.plot_di... | XiaoxiaoLiu/morphology_analysis | bigneuron/tmp_conesnsus_comparison_ave.py | Python | gpl-3.0 | 3,852 | [
"NEURON"
] | fc8c5038656beefc719acf5a380d37c5ea7bfcf9ac64a859b26af45fc10830cc |
# TLE
class Solution(object):
def findLadders(self, beginWord, endWord, wordlist):
"""
:type beginWord: str
:type endWord: str
:type wordlist: Set[str]
:rtype: List[List[int]]
"""
bw = beginWord
ew = endWord
visit = set()
un... | sogapalag/problems | leetcode/126.Word-Ladder-II.py | Python | mit | 1,451 | [
"VisIt"
] | e7886698a22ba5cd23a2bbd0b358d225117f5df77aaab58b7d5109d57b24254d |
from copy import deepcopy
class GraphicFeature:
"""Genetic Feature to be plotted.
Parameters
----------
start, end
Coordinates of the feature in the final sequence.
strand
Directionality of the feature. can be +1/-1/0 for direct sense,
anti-sense, or no directionality.
lab... | TAMU-CPT/galaxy-tools | tools/genome_viz/dna_features_viewer/GraphicFeature.py | Python | gpl-3.0 | 4,933 | [
"Biopython"
] | dde3ce04fe3f48890f118465ad2c8c3cc8473345d2a693d84dd002cc6ecb6073 |
# -*- 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... | ericvandenbergfb/spark | python/pyspark/ml/tests.py | Python | apache-2.0 | 100,846 | [
"Gaussian"
] | 3c633da4fd95c212fb4884d5149ae8a911a15cc2e28a85627f8738433664ffc9 |
import time
import collections
from datetime import timedelta
import GangaCore.Utility.logging
from GangaCore.GPIDev.Base.Objects import GangaObject
from GangaCore.GPIDev.Base.Proxy import export
from GangaCore.GPIDev.Schema import Schema, Version
from GangaCore.Core.exceptions import CredentialsError, GangaKeyErro... | ganga-devs/ganga | ganga/GangaCore/GPIDev/Credentials/CredentialStore.py | Python | gpl-3.0 | 12,863 | [
"DIRAC"
] | d878dc2ab02aeab6515b90313408733451b72ad5e503a9560b72455e3e727eab |
#!/usr/bin/python
import argparse
import re
import pysam
import pickle
import os
import string
from pysam import VariantFile
import itertools
#import gzip
def main():
args = process_input()
index_dbsnp = args.index_dbsnp
vcf_file = args.vcf_file
out_file = args.out_file
marker_ids = args.marker_ids
dbsnp_index... | christopher-gillies/VCFScripts | extract_haplotypes.py | Python | apache-2.0 | 7,549 | [
"pysam"
] | 224f7b16454b676ac4620868517f3ce6c6bcd28b838873ee08fad3abb789a0d2 |
#!/usr/bin/env python
"""
IHNIL main parsing module.
Provides the interface for evaluating a given target file.
"""
import argparse
import os
import ast
import codegen
__version__ = "1.0.0"
def command_line_call():
"""Provide access to command line argument inputs."""
parser = argparse.ArgumentParser(des... | forstmeier/pythonistics | ihnil/ihnil.py | Python | mit | 15,424 | [
"VisIt"
] | 2f61ca465ad5449c587da2aa6e97fbbdac456f23152249842e4bff21c46c9d1b |
"""Properties once used for transcription and translation (DEPRECATED).
This module is deprecated, and is expected to be removed in the next release.
If you use this module, please contact the Biopython developers via the
mailing lists.
"""
#NOTE - Adding a deprecation warning would affect Bio.Alphabet.IUPAC
# Set up... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Encodings/IUPACEncoding.py | Python | gpl-2.0 | 5,460 | [
"Biopython"
] | a28859d112a67626a51b666b290ad18d1cedfd9c0c9420d7cc461043d2a71440 |
import numpy as np
from matplotlib import pyplot
import rft1d
#(0) Set parameters:
np.random.seed(0)
nResponses = 10000
nNodes = 101
FWHM = 13.1877
### generate a field mask:
nodes_full = np.array([True]*nNodes) #nothing masked out
nodes = nodes_full.copy()
nodes[20:45] = False #thi... | 0todd0000/rft1d | rft1d/examples/val_broken_0_gauss.py | Python | gpl-3.0 | 1,486 | [
"Gaussian"
] | 176c7131e2a14fdc2dcffca960a7bc7dcfcc96c6a02f8e7fd8288c6ab353cb73 |
#
# Copyright (C) 2011-2017 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import os
import sys
import tempfile
import unittest
f... | rvianello/rdkit | rdkit/Chem/Draw/UnitTestDraw.py | Python | bsd-3-clause | 6,738 | [
"RDKit"
] | 99a88ca79e18f4826119d50d8870745607b370fd3c8cdf73c025538321e29808 |
"""A VTK file reader object.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import basename
# Enthought library imports.
from traits.api import Instance
from tvtk.api import tvtk
# Local imports.
fro... | liulion/mayavi | mayavi/sources/vtk_file_reader.py | Python | bsd-3-clause | 3,665 | [
"Mayavi",
"VTK"
] | 327bd65058fbbd7132679abef104818381fed95e9c886b9012bdf954e4753808 |
#!/usr/bin/env python
"""
Deploy all scripts and extensions
Options:
* --symlink: this will create symlinks instead of wrappers
* <python path>: you can specify the folder where your python installation should be fetched from
to replace the shebang
"""
__RCSID__ = "$Id$"
import getopt
import os
imp... | andresailer/DIRAC | Core/scripts/dirac-deploy-scripts.py | Python | gpl-3.0 | 7,643 | [
"DIRAC"
] | df9d9ab740d05f252d887ad7017f120df7f974808024939a0645a9a3f457a8d5 |
import numpy as np
import scipy.stats as ss
import scipy.special as sp
from .family import Family
from .flat import Flat
from .normal import Normal
from .gas_recursions import gas_recursion_laplace_orderone, gas_recursion_laplace_ordertwo
from .gas_recursions import gasx_recursion_laplace_orderone, gasx_recursion_lap... | RJT1990/pyflux | pyflux/families/laplace.py | Python | bsd-3-clause | 13,158 | [
"Gaussian"
] | 3a57ce1f2068f72d92c36d5acdf656d563941b053346635abb822a5bd6d6e317 |
#!/usr/bin/env python
# $Id: buildhtml.py 7037 2011-05-19 08:56:27Z milde $
# Author: David Goodger <goodger@python.org>
# Copyright: This module has been placed in the public domain.
"""
Generates .html from all the .txt files in a directory.
Ordinary .txt files are understood to be standalone reStructuredText.
Fil... | stevejefferies/robotframework-selenium2library | doc/buildhtml.py | Python | apache-2.0 | 9,935 | [
"VisIt"
] | 8dfef5abe8f18bd9af5524a4574b674066a3e6e8af44feffd262d030099b3a92 |
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems Inc.
# 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.o... | stevenliuit/neon | neon/backends/gpu.py | Python | apache-2.0 | 34,358 | [
"Gaussian"
] | ceb34308000f5e88b1e489f6f76e32387f08337a7312dbfdeb5546235727f037 |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# 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.
import unittest
from Bio.Phylo.PAML import chi2
class ModTest(unittest.TestCase):
d... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Chi2.py | Python | gpl-2.0 | 1,211 | [
"Biopython"
] | 62fab78c2b9aedc8564a20c2cd3e2918bad5fbc17245ad959e7cd9d0c3854010 |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## 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 Softwar... | ostrokach/biskit | scripts/Biskit/1pdb2model.py | Python | gpl-3.0 | 2,638 | [
"Amber"
] | 719b95fa26887171a03869a34b04227eb2cc6f37d53efd6227837209674e2230 |
# shamelessly copied from pliExpertInfo (Vali, Mirakels, Littlesat)
from enigma import iServiceInformation, iPlayableService
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tools.Transponder import ConvertToHumanReadable
from Tools.Ge... | popazerty/EG-2 | lib/python/Components/Converter/PliExtraInfo.py | Python | gpl-2.0 | 24,837 | [
"Galaxy"
] | 7181ce086ebe9ad9d647f38a98b01970dda2615ad433d9ecfc09a60566526d44 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
#
# 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 version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/ekiga/script.py | Python | gpl-3.0 | 3,335 | [
"ORCA"
] | 3e525eee08bd6e07da0199465f58b3de14c7c7db97e828d51afd99da8c65b9ed |
# -*- coding: utf-8 -*-
"""
Generators for random graphs.
"""
# Copyright (C) 2004-2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
__author__ = "\n".join(['Aric Hagberg (hagberg@lanl.gov)',
... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/networkx/generators/random_graphs.py | Python | agpl-3.0 | 27,558 | [
"VisIt"
] | 5f7851277f5f443368b2a8a2d6c37b516cdd97d3a68250bd5e4f2faeec18fd2e |
import numpy as np
from ss_generator import numeric
from ss_generator import geometry
from . import basic
D_MEAN = 3.80
def get_internal_coordinates_for_ideal_strand(R, delta, alpha, eta):
'''Get 4 internal coordinates for an ideal beta strand.
The inputs are the screw redius R, the angle alpha which is
... | xingjiepan/ss_generator | ss_generator/ca_tracing/beta_sheet.py | Python | bsd-3-clause | 26,718 | [
"Gaussian"
] | 734e9ba42e8a22efaf0df4c6d1cc82e41896bd85bd1fcc8846913b66da9a39c5 |
"""
Acceptance tests for Studio's Setting pages
"""
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from ...pages.studio.settings_advanced import AdvancedSettingsPage
from ...pages.studio.settings_group_configurations import GroupConfigurationsPage
@attr('shard_1')
class ContentG... | olexiim/edx-platform | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 11,964 | [
"VisIt"
] | 509f29c2d11938e3f480775a2d30c075639785e48d63f72836244063bd9f5e90 |
# -*- 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/topology/test_topology_str_types.py | Python | gpl-2.0 | 2,389 | [
"MDAnalysis"
] | ef32230969fc984caca7e7eb10a7e1fa526aac82bdd82d1b9ccbe1733f441095 |
# Copyright 2009 by David Winter. 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.
import os
import sys
import unittest
from Bio import MissingExternalDependencyError
from Bio i... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_EmbossPhylipNew.py | Python | gpl-2.0 | 12,717 | [
"Biopython"
] | 564a3b0f34e5bc02c6c15e255dbff974bf006faca460dac1d16267d4ed458282 |
# Copyright 2016-2020 The GPflow Contributors. 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 appli... | GPflow/GPflow | gpflow/models/svgp.py | Python | apache-2.0 | 10,361 | [
"Gaussian"
] | 0a0221e4be7bd0bb749fc349a33cce384e5e4c989f2613e53e1afbd25660b5ad |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
from pycsp.common.trace import *
from random import random
from functools import reduce
T... | runefriborg/pycsp | examples/MCPiTrace.py | Python | mit | 1,263 | [
"Brian"
] | 3848c2afb01dbe3038a026e46a04441bbfd5157ac601160009ad9661269e1398 |
##############################################################################
# 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... | matthiasdiener/spack | var/spack/repos/builtin/packages/chombo/package.py | Python | lgpl-2.1 | 5,936 | [
"Brian"
] | a972760d087a10b1ac8244327d4938ab033f13ff844829baf2daaafd6347c900 |
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distribu... | jarrodmcc/OpenFermion | src/openfermion/__init__.py | Python | apache-2.0 | 882 | [
"VisIt"
] | cc9577190257198a315517b23bb9585870d36e4be4fe43caf6cc7917c3c67dd6 |
#!/usr/local/epd/bin/python
#------------------------------------------------------------------------------------------------------
# Dirac propagator based on:
# Fillion-Gourdeau, Francois, Lorin, Emmanuel, Bandrauk, Andre D.
# Numerical Solution of the Time-Dependent Dirac Equation in Coordinate Space without Ferm... | cabrer7/PyWignerCUDA | GPU_Dirac3D.py | Python | mit | 47,438 | [
"DIRAC",
"Gaussian",
"Psi4"
] | 6db2c9ed357038f95e88e488cd87fb200b9a56ebd3912fc97e587eadbec31718 |
# Lint as: python2, python3
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... | ppwwyyxx/tensorflow | tensorflow/tools/compatibility/ast_edits.py | Python | apache-2.0 | 40,126 | [
"VisIt"
] | 00104501e24b79d92ffff9d473cc807aa636e2b736f619bedd455dcba7172874 |
# coding: utf-8
###################################################################
# Copyright (c) 2016-2022 European Synchrotron Radiation Facility #
# #
# Author: Marius Retegan #
# ... | mretegan/crispy | crispy/quanty/hamiltonian.py | Python | mit | 23,228 | [
"CRYSTAL"
] | ffa7580a5909da387dbbe9cc64944c0b0739656cdc2da506394a9895d690905a |
#!/usr/bin/env python
import getpass
import config
import sys
import loggers
import json
import argparse
import utils
import os
import readline
import shutil
from request import Request
from parsers import base as base_parser
readline.parse_and_bind('tab: complete')
readline.parse_and_bind('set editing-mode vi')
def ... | digicert/digicert_express | digicert_express/digicert_express.py | Python | mit | 19,639 | [
"VisIt"
] | d5d052597ad93551f90cd9c9a55f27b927e82d0e5f3e28832dc32d28c837f161 |
import numpy as np
import tensorflow as tf
### constructing and composing layers
def make_layer(dot, activation):
def layer(W, b):
def apply(h):
return activation(dot(h, W) + b)
return apply
return layer
# TODO - a stochastic layer is really a composition of a deterministic layer... | andymiller/vae-flow | vae/nnet.py | Python | mit | 3,389 | [
"Gaussian"
] | 2a5257aa879f0e77430aa2a2e002302259ac253fb4bca2071588dbb038c8b6ea |
# -*- coding: utf-8 -*-
#########################################################################
#
# Copyright (C) 2018 OSGeo
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 ... | kartoza/geonode | geonode/tests/bdd/e2e/conftest.py | Python | gpl-3.0 | 1,906 | [
"VisIt"
] | 28df2601f016ff80ad4d62d277942291730346e86d8b051611b8493f2649b4e3 |
"""Unit test for util.py"""
from ..util import lat2W, nonplanar_neighbors, fuzzy_contiguity
from .. import util
from ..weights import W, WSP
from ..distance import DistanceBand, KNN
from ..contiguity import Queen, Rook
from ...io.fileio import FileIO as psopen
from ... import examples
import numpy as np
import unittest... | lixun910/pysal | pysal/lib/weights/tests/test_util.py | Python | bsd-3-clause | 10,115 | [
"COLUMBUS"
] | 8305c74a74e8de88f1e553e3c132d0f9aa72f254e59d697bfcdad14ff8fbeaab |
# -*- coding: utf-8 -*-
#
# scikit-nano documentation build configuration file, created by
# sphinx-quickstart on Wed Oct 30 00:26:16 2013.
#
# This file is execfile()d with the current directory set to its containing dir
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
#... | androomerrill/scikit-nano | doc/source/conf.py | Python | bsd-2-clause | 15,819 | [
"pymatgen"
] | 4284d56c6cda5fca2c05d5353fd32426a462a62e596780f40d9f39a2c5b94bfc |
#!/usr/bin/env python
import sys
import unittest
from PyQt5 import QtWidgets
import vtk
from peacock.ExodusViewer.plugins.ClipPlugin import main
from peacock.utils import Testing
class TestClipPlugin(Testing.PeacockImageTestCase):
"""
Testing for FileControl widget.
"""
qapp = QtWidgets.QApplication(... | liuwenf/moose | python/peacock/tests/exodus_tab/test_ClipPlugin.py | Python | lgpl-2.1 | 4,943 | [
"VTK"
] | b571d61f8c3ca8ec6179e7c8e762ac80b8f6bfec57be4fa9f5866b1f59245d28 |
#!/usr/local/bin/python2.6
###AltAnalyze
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Softwar... | kdaily/altanalyze | AltAnalyze.py | Python | apache-2.0 | 493,577 | [
"Cytoscape"
] | e8fcab3f3e7343e654a666719aa747561bf674687ab4489632f1af94e616b626 |
#
# This code is taken from the code by Luca Tornatore
# (C) Luca Tornatore http://qe-forge.org/gf/user/tornatore/
# This is not used by the qe-util library and is kept here
# for reference and verification.
#
"""
This module defines an ASE interface to QUANTUM-ESPRESSO
http://www.quantum-espresso.org
"""
# the s... | jochym/qe-util | qeutil/quantumespresso.py | Python | gpl-3.0 | 50,150 | [
"ASE",
"CRYSTAL",
"DIRAC",
"ESPResSo",
"Gaussian"
] | 6d13e37ddf3a6d83ab836e696e2161fb32154cf3c961cbbdbca03880a1948e7a |
#! /usr/bin/env python
# D.J. Bennett
# 26/05/2014
"""
setup.py for pglt
"""
import os
import pglt
from setuptools import setup, find_packages
# PACAKAGE INFO
PACKAGES = find_packages()
PACKAGE_DIRS = [p.replace(".", os.path.sep) for p in PACKAGES]
# SETUP
setup(
name="pglt",
version=pglt.__version__,
aut... | DomBennett/pG-lt | setup.py | Python | gpl-2.0 | 1,466 | [
"Biopython"
] | 1690a448f142cfd334cb1dc235d7fd1cd27bb7ba2bd2cd1f47a42c1ace5ecd79 |
# Filename: cider.py
#
# Description: Describes the class to compute the CIDEr (Consensus-Based Image Description Evaluation) Metric
# by Vedantam, Zitnick, and Parikh (http://arxiv.org/abs/1411.5726)
#
# Creation Date: Sun Feb 8 14:16:54 2015
#
# Authors: Ramakrishna Vedantam <vrama91@vt.edu> and Tsung... | MeteorKepler/RICGA | ricga/eval_tools/pycocoevalcap/cider/cider.py | Python | apache-2.0 | 1,667 | [
"Gaussian"
] | 8749e316a756833561b7fda9004d747de9ade17a64d590d359c16a2f99aea069 |
__RCSID__ = "$Id$"
# FIXME: if it requires a dirac.cfg it is not a unit test and should be moved to TestDIRAC
import unittest, types, time, os, shutil
from DIRAC.Resources.Storage.StorageFactory import StorageFactory
from DIRAC.Core.Utilities.File import getSize
class StoragePlugInTestCase( uni... | marcelovilaca/DIRAC | Resources/Storage/test/TestRFIOPlugIn.py | Python | gpl-3.0 | 28,890 | [
"DIRAC"
] | aa769444e38b9094b31b1fca6fbf1ff9b4c85ea4c85f47d58414ec228b1521e7 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/commoncode/test_functional.py | Python | apache-2.0 | 2,065 | [
"VisIt"
] | fafe24eccdf4ea3ded368c6d276982d9ea6d29f2e2f62a90f0e82a7834cee080 |
#!/usr/bin/env python
import fileinput
import sys
import os
import re
import math
import json
import numpy as np
import subprocess
from optparse import OptionParser
# These kernels have guaranteed correct Jacobians
whitelisted_kernels = ['Diffusion', 'TimeDerivative']
# regular expressions to parse the PETSc debug... | danielru/moose | python/jacobiandebug/analyzejacobian.py | Python | lgpl-2.1 | 12,102 | [
"MOOSE"
] | eb8d622cc7f44ed655ee2389019cd26a68a197a7abf55ce5926e2400e4144f53 |
#* 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
from sympy ... | nuclear-wizard/moose | python/mms/evaluate.py | Python | lgpl-2.1 | 6,455 | [
"MOOSE"
] | 6a73e5ba3d15c5109ab0b66aba3695509874d127c94f709f0d30efc3aad0bc00 |
# Copyright 2008-2015 Nokia Networks
# Copyright 2016- Robot Framework Foundation
#
# 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
... | alexandrul-ci/robotframework | src/robot/reporting/xunitwriter.py | Python | apache-2.0 | 3,441 | [
"VisIt"
] | cc063915e77aa51130e65a1ebd5dcf37f762684bb3b8ba7d1c6115b5aba60c72 |
#!/usr/bin/env python
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Implementation for `pmg plot` CLI.
"""
from collections import OrderedDict
from pymatgen.core.structure import Structure
from pymatgen.analysis.diffraction.xrd import XRDCalculator
from pymatgen.ele... | vorwerkc/pymatgen | pymatgen/cli/pmg_plot.py | Python | mit | 2,807 | [
"VASP",
"pymatgen"
] | 12edae358f68f9118aa6ae11922eb3653754c2243cd5d76aeac5e44f410675a5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
<<<<<<< HEAD
Development script to get the multiplicity of the separation planes for some model coordination environments
=======
Development script to get... | Bismarrck/pymatgen | dev_scripts/chemenv/plane_multiplicity.py | Python | mit | 1,995 | [
"pymatgen"
] | e19d33218856ee172a93925517cd027e241a9e6ea63e23e2bec1195b90dfc1bd |
import scipy.constants as spc
# Speed of light in m/s
C = spc.c
# ħ = h / 2π in J/s
HBAR = spc.hbar
# Conversion factor for momentum in SI to atomic units
P_AU = spc.value("atomic unit of momentum")
# Bohr radius in m
BOHR2M = spc.value("Bohr radius")
# Bohr -> Å conversion factor
BOHR2ANG = BOHR2M * 1e10
# Å -> Bohr... | eljost/pysisyphus | pysisyphus/constants.py | Python | gpl-3.0 | 1,456 | [
"Avogadro"
] | 3925471c49ac95755c656b1ed8d1eeb9369075dd6c61168357acb60ff9938403 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
#... | cchurch/ansible-modules-core | files/find.py | Python | gpl-3.0 | 12,335 | [
"Brian"
] | 9cd2a19640ae3e02ec2cf13bdf4ca1ee9f5d1f3bd64ea23976ce6482cb4f1a1b |
# Copyright 2019 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... | googlegenomics/gcp-variant-transforms | gcp_variant_transforms/libs/vcf_header_definitions_merger_test.py | Python | apache-2.0 | 9,257 | [
"pysam"
] | c3e73ba00f393c93221dd82d574fc92fdfed34aa2a49ad5e9e683d3e7cc70e82 |
#!/usr/bin/env python
import re
import sys
import time
import math
import urllib2
import urlparse
import optparse
import hashlib
from cgi import escape
from traceback import format_exc
from Queue import Queue, Empty as QueueEmpty
from BeautifulSoup import *
class Link (object):
def __init__(self, src, dst, lin... | vishnumani2009/SiteSpider | crawler.py | Python | mit | 12,772 | [
"VisIt"
] | 6e3d7636b0bf319349b2a8609f1920ba544b94d9d64fa04fb53b2c62c3f2e3f4 |
import re
from galaxy import util
from ..instrumenters import InstrumentPlugin
from ...metrics import formatting
MEMINFO_LINE = re.compile(r"(\w+)\s*\:\s*(\d+) kB")
# Important (non-verbose) meminfo property titles.
MEMINFO_TITLES = {
"memtotal": "Total System Memory",
"swaptotal": "Total System Swap"
}
c... | ssorgatem/pulsar | galaxy/jobs/metrics/instrumenters/meminfo.py | Python | apache-2.0 | 2,056 | [
"Galaxy"
] | 27bf0854ccfaa871f80b33a2013e2242ff9aabbb4a481d1b8778e31958f134b2 |
"""
Acceptance tests for Studio.
"""
import uuid
from selenium.webdriver.common.keys import Keys
from base_studio_test import StudioCourseTest
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acc... | Stanford-Online/edx-platform | common/test/acceptance/tests/studio/test_studio_general.py | Python | agpl-3.0 | 13,130 | [
"VisIt"
] | da21de9c4743784f99ca26ce57f7ed3e094e80340b1f20813da11e9ab1406838 |
# -*- coding: utf-8 -*-
"""test_muparser.py:
odified from https://elifesciences.org/articles/25827
Fig4.py
"""
import sys
import re
import numpy as np
import moose
import rdesigneur as rd
print( "[INFO ] Using moose from %s" % moose.__file__ )
def parseExpr( expr, params, hasCa ):
if hasCa:
expr = expr.r... | upibhalla/moose-core | tests/python/test_function_chemsys.py | Python | gpl-3.0 | 13,073 | [
"MOOSE",
"NEURON"
] | 300b85653df5af8bad16215428f7dc3bfdbdab2c7986c6de7f8ac7ecaa070414 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import numpy as np
from pymatgen.optimization.linear_assignment import LinearAssignment # type: ignore
class LinearAssignmentTest(unittest.TestCase):
def test(self):
w0 = np.array(
... | vorwerkc/pymatgen | pymatgen/optimization/tests/test_linear_assignment.py | Python | mit | 9,619 | [
"pymatgen"
] | 9c6eeed75f7636fbe83e18fc7f671f8eedee6fe73c6f6b6f5768339696805ccd |
# Draw samples from the distribution:
mu, beta = 0, 0.1 # location and scale
s = np.random.gumbel(mu, beta, 1000)
# Display the histogram of the samples, along with
# the probability density function:
import matplotlib.pyplot as plt
count, bins, ignored = plt.hist(s, 30, normed=True)
plt.plot(bins, (1/beta)*np.exp(-... | leesavide/pythonista-docs | Documentation/numpy/reference/generated/numpy-random-gumbel-1.py | Python | apache-2.0 | 1,082 | [
"Gaussian"
] | ba3f074891254acced0d9c193a476ba97e1ad6fe4671dbec1befd711fefaafda |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import clawpack.geoclaw.util as util
try:
CLAW = os.environ['CLAW']
except:
raise Exception("*** Must first set CLAW envior... | mandli/sumatra-tsunami | setrun.py | Python | mit | 14,161 | [
"NetCDF"
] | 815fa79fcaf23750a671ed9043cbbc7ff0ef8b1ce19ac9bec2a09bd3c349c018 |
#!/usr/bin/env
import os, string, codecs
from sklearn import svm, tree
from sklearn.naive_bayes import MultinomialNB, GaussianNB
from sklearn.feature_extraction.text import CountVectorizer, TfidfTransformer
from sklearn.metrics import accuracy_score
from nltk.corpus import stopwords
from nltk.stem.snowball import Snow... | aorti017/Genre-Identification | main.py | Python | bsd-3-clause | 3,012 | [
"Gaussian"
] | 385a5f964c7507fa1b2972a97e6027335e9faa35027823dac14a4aae051b4ae0 |
# Copyright 2020 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | petewarden/tensorflow | tensorflow/python/keras/engine/keras_tensor.py | Python | apache-2.0 | 25,155 | [
"VisIt"
] | 16a83b69aa460e116b207526b6a1ade2bffcd1720c79fb6b16e771b36428c6f2 |
"""Demonstrate the usage of IDTxl's core estimators."""
import numpy as np
from idtxl.estimators_jidt import (JidtDiscreteAIS, JidtDiscreteCMI,
JidtDiscreteMI, JidtDiscreteTE,
JidtKraskovAIS, JidtKraskovCMI,
JidtKra... | pwollstadt/IDTxl | demos/demo_core_estimators.py | Python | gpl-3.0 | 4,402 | [
"Gaussian"
] | 3b5f35bf1ca5d81ff42468d601b89bce3f21b070181cf6af984775bb1051e5df |
r"""``sphobjinv`` *data class for full inventories*.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
7 Dec 2017
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
https://github.com/b... | bskinn/sphobjinv | src/sphobjinv/inventory.py | Python | mit | 22,643 | [
"Brian"
] | b9880cc42c41852a3a3298072cf64d052851168eb2033aa48b0ace0e31d7dd0e |
"""Utility functions for plotting M/EEG data
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# ... | jniediek/mne-python | mne/viz/utils.py | Python | bsd-3-clause | 58,956 | [
"Mayavi"
] | dd19cc12fd28ee20de97d6c3b5e90ec3f4c65cd6c977aaea06d4d3a77ea7be4f |
#!/usr/bin/env python
calendarId = 'me36k96u55g9gts6fmu4tgq4ts@group.calendar.google.com'
#bfly-client_id='633559698772.apps.googleusercontent.com'
#bfly-client_secret='9iqW9BTnwTt8rWg4fQtJL3CG'
#bfly-user_agent='bragato-cal-2013/v1'
#bfly-developerKey='AIzaSyCjPID1d7hKLiRCjMTWYj6DjagF8viG8wM'
client_id='222573514309... | relic7/prodimages | python/drafts/gcal_scrap/gcal_again.py | Python | mit | 2,933 | [
"VisIt"
] | 82e35a73aaf6c97be346dcd1dbae6e8082febb48762a8fc10c64904ec9ce62d3 |
# Made by Mr. - Version 0.3 by DrLecter
import sys
from net.sf.l2j.gameserver.model.quest import State
from net.sf.l2j.gameserver.model.quest import QuestState
from net.sf.l2j.gameserver.model.quest.jython import QuestJython as JQuest
FLAME_SHARD = 1020
ICE_SHARD = 1021
ADENA = 57
DROPLIST={
109:[30,FLAME_SHARD],
110... | Barrog/C4-Datapack | data/jscript/quests/306_CrystalOfFireice/__init__.py | Python | gpl-2.0 | 2,338 | [
"CRYSTAL"
] | 7cbbafc634b47131446d6f0949f68cc9909cfbed65f056504edb373b83387fb8 |
# -*- coding:utf-8 -*-
#
# Copyright 2012 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 vers... | lucasmachadorj/pypln.web | pypln/web/core/tests/views/test_document.py | Python | gpl-3.0 | 11,044 | [
"NAMD"
] | b28944fadfac98aa56408c981b7e19822ef1aa57f27b5da9b203c80632239adb |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | mgeplf/NeuroM | neurom/io/utils.py | Python | bsd-3-clause | 7,482 | [
"NEURON"
] | 9194d70be51952f1d49ad7fb9aa0f22a2a4fbb185d5e8fcc48948c1695c7f3a5 |
# (c) Dan La Russa & Randy Taylor
# routines for fitting histograms
import numpy as np
import scipy.special as sps
MAX_NEWTON_ITERATIONS = 1000
def gauss_fit(data, binwidth=None):
"""
Fits a Gaussian pdf to a set of independent values (data) using
maximum likelihood estimators. If fitting to a histogram... | sharifelguindi/qatrackplus | qatrack/qa/control_chart/maximumlikelihoodfit.py | Python | mit | 2,817 | [
"Gaussian"
] | 44eda9600d96059c49cd3145376f2aeb98f817ef00983ef51b2eca2bd310fe9b |
import unittest
from collections import UserDict
import pytest
from sickchill.oldbeard.numdict import NumDict
class NumDictTest(unittest.TestCase):
"""
Test the NumDict class
"""
def test_constructors(self):
"""
Test NumDict constructors
"""
# dicts for testing
... | h3llrais3r/SickRage | tests/test_numdict.py | Python | gpl-3.0 | 17,963 | [
"Octopus"
] | 55436bf0f4fb7d706fbc642b5067d95d8836cd8a2298c866e9d634ac6175faf4 |
"""This module implements a linear response calculator class."""
__all__ = ["ResponseCalculator"]
import numpy as np
from gpaw.transformers import Transformer
from gpaw.dfpt.mixer import BaseMixer
from gpaw.dfpt.sternheimeroperator import SternheimerOperator
from gpaw.dfpt.scipylinearsolver import ScipyLinearSolver
... | robwarm/gpaw-symm | gpaw/dfpt/responsecalculator.py | Python | gpl-3.0 | 14,928 | [
"GPAW"
] | 21046aa94115a67abe941707cf83add62bd41b6edd2cd6ba92a7fd2e107ae85c |
"""
This module implements error handlers for Nwchem runs. Currently tested only
for B3LYP DFT jobs.
"""
from pymatgen.io.nwchem import NwInput, NwOutput
from custodian.ansible.interpreter import Modder
from custodian.custodian import ErrorHandler
from custodian.utils import backup
class NwchemErrorHandler(ErrorHan... | materialsproject/custodian | custodian/nwchem/handlers.py | Python | mit | 3,146 | [
"NWChem",
"pymatgen"
] | c90a47a099cadc16771947723995f1369c0ac39691f0f7ee35e23b222dc28123 |
import os
import sys
import pkgutil
def LoadFolder(inputFolderPath):
infilePathList=[]
try:
for root, dirs, files in os.walk(inputFolderPath):
for file in files:
infilePathList.append(inputFolderPath+file)
except:
print('Error Code: 0015')
return infilePathLi... | liutairan/eMolFrag | Old versions/eMolFrag_2017_01_13_01/loader.py | Python | gpl-3.0 | 3,639 | [
"RDKit"
] | 2574bee9a5108263f68f26510355815ce682bd2372dd940e946a1ad5af5ac9bf |
'''
Calculates the average number of water contacts for each residue across the trajectory.
For each residue the waters are selected in a specified cutoff distance and then the counts are averaged
for that residue.
Output:
a .csv file with indexed by resid including residue names and the average water contacts
e.g.
re... | dkoes/md-scripts | waters.py | Python | bsd-3-clause | 2,414 | [
"MDAnalysis"
] | 055f9905daa6318bbc8c0e9b31fad60e454a4a1d63c7095933a199eb8671e9a5 |
from tests.test_helper import *
from datetime import date
from braintree.dispute import Dispute
from braintree.credit_card import CreditCard
from braintree.paypal_account import PayPalAccount
from braintree.venmo_account import VenmoAccount
class TestWebhooks(unittest.TestCase):
def test_granted_payment_method_rev... | braintree/braintree_python | tests/unit/test_webhooks.py | Python | mit | 42,036 | [
"Amber"
] | c9684b21c72efe9330ff648a62fd63ca6d8f5b535787b3633f3701f28b3f3f24 |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | fabio-otsuka/invesalius3 | invesalius/data/styles.py | Python | gpl-2.0 | 86,613 | [
"Gaussian",
"VTK"
] | 381de80d151f082b83d1be2c7056cbd2016df2dde1b93c727f82a23410b3846d |
#!/usr/bin/env python
'''CREATED:2014-05-22 16:43:44 by Brian McFee <brm2132@columbia.edu>
Pitch-shift a recording to be in A440 tuning.
Usage: ./adjust_tuning.py [-h] input_file output_file
'''
from __future__ import print_function
import argparse
import sys
import librosa
def adjust_tuning(input_file, output_fil... | ebattenberg/librosa | examples/adjust_tuning.py | Python | isc | 1,701 | [
"Brian"
] | 18f97a8667bf8a4f74b7f9534fc68a12cd4a06470db436a30b766365aebddad4 |
# ----------------------------------------------------------------------
# Copyright (c) 2016, The Regents of the University of California All
# rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | drichmond/tinker | python/GlobalMemoryInterface.py | Python | bsd-3-clause | 9,852 | [
"TINKER"
] | 9b1f09024b61badcfdbcb94861dbe573c18a338122bdd7da08b5ee4bfddef5a4 |
#!/usr/bin/env python
import numpy as np
import ply.yacc as yacc
import data.calculated_parser.functions as functions
import data.calculated_parser.lexer
class Parser:
"""The parsing portion of the domain specific language"""
def __init__(self, **kwargs):
self.lexer = data.calculated_parser.lexer.L... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | data/calculated_parser/parser.py | Python | gpl-3.0 | 5,165 | [
"NetCDF"
] | 3a03d30fa5c4233a1d2cd4889d40b5739b5712a72f5d8717fb93860e60edf559 |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" unit testing code for the C++ ExplicitBitVects... | strets123/rdkit | rdkit/DataStructs/UnitTestcBitVect2.py | Python | bsd-3-clause | 10,189 | [
"RDKit"
] | 6b63ad0c38313babf36fa8c44a136c0cd73e6bb7c83d4aeba4c3a26cde6593af |
#!/usr/bin/env python
import vtk
def main():
colors = vtk.vtkNamedColors()
# Create the polydata geometry
sphereSource = vtk.vtkSphereSource()
sphereSource.Update()
# Set up the actor to display the untransformed polydata
originalMapper = vtk.vtkPolyDataMapper()
originalMapper.Se... | lorensen/VTKExamples | src/Python/Filtering/TransformPolyData.py | Python | apache-2.0 | 1,732 | [
"VTK"
] | de8b48501d81d36663d0971b367ba8bf7bd06fcf3a57d27a393a8d34352adc91 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
#
# PCR-GLOBWB (PCRaster Global Water Balance) Global Hydrological Model
#
# Copyright (C) 2016, Edwin H. Sutanudjaja, Rens van Beek, Niko Wanders, Yoshihide Wada,
# Joyce H. C. Bosmans, Niels Drost, Ruud J. van der Ent, Inge E. M. de... | UU-Hydro/PCR-GLOBWB_model | model/ncConverter.py | Python | gpl-3.0 | 8,768 | [
"NetCDF"
] | 77af496985d37c78fc0900fdd93c9054c645e3c0afadb978376ebe8d30d369a0 |
# coding: utf-8
"""
This module is used to estimate the cost of various compounds. Costs are taken
from the a CostDB instance, for example a CSV file via CostDBCSV.
For compounds with no cost listed, a Phase Diagram style convex hull
optimization is performed to determine a set of compositions that can be mixed
to giv... | Dioptas/pymatgen | pymatgen/analysis/cost/cost.py | Python | mit | 6,014 | [
"pymatgen"
] | aca462c084ae4e1149a35a563d91ceea4ce8d0aebecc5741808301ab4f729015 |
##!/usr/bin/env python
#! -*- coding: utf-8 -*-
### Copyright Paul Brian 2013
# This program is licensed, without under the terms of the
# GNU General Public License version 2 (or later). Please see
# LICENSE.txt for details
###
"""
"""
import doctest
import json
from optparse import OptionParser
import saffli... | lifeisstillgood/saffrondigital | main.py | Python | gpl-2.0 | 1,430 | [
"Brian"
] | b35bebf6107c4c4206404dfbe8db41f4c3cdc1b5ff444e628010877a7b4ac826 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.core.exceptions import ValidationError
from django.test import SimpleTestCase
from localflavor.nl import forms, models, validators
from .forms import NLPlaceForm
from .models import NLPlace
class NLLocalFlavorValidatorTests(SimpleTestCase)... | thor/django-localflavor | tests/test_nl/tests.py | Python | bsd-3-clause | 7,254 | [
"BWA"
] | 6010a43efc6bc676291254f72fd45ef14009dccb043d3f40522a0800d1ede1a9 |
# Copyright 2002 by Yves Bastide and Brad Chapman.
# Copyright 2007 by Sebastian Bassi
# 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.
"""Functions to calculate assorted sequen... | zjuchenyuan/BioWeb | Lib/Bio/SeqUtils/CheckSum.py | Python | mit | 4,004 | [
"BioPerl",
"Biopython"
] | f03a40d11af245e5d7a99e0d9343c8c8fb04d9c15297f8a143773ebdaea715da |
#
# 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 us... | markflyhigh/incubator-beam | sdks/python/apache_beam/examples/snippets/snippets.py | Python | apache-2.0 | 49,662 | [
"VisIt"
] | 796a60b860c6c1571506b6cc9c86364ae5558ed7643e8d8db1137caadbbd8f0c |
#!/usr/bin/env python
#
# Copyright 2016 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 requir... | Aloomaio/googleads-python-lib | examples/adwords/v201806/error_handling/handle_policy_violation_error.py | Python | apache-2.0 | 6,157 | [
"VisIt"
] | c878c89fc94d8ac61049aa62b2e46548890e793543a16efc868238701e303393 |
# app imports
from oweb.models import Supply1, Supply2, Supply3, Supply4, Supply12, Station14, Station15, Civil212, Research113, Research122
from oweb.libs.production import get_metal_production, get_crystal_production, get_deuterium_production, get_plasma_bonus, get_capacity, get_sat_production, get_energy_production
... | Mischback/django-oweb | oweb/libs/queue.py | Python | mit | 13,231 | [
"CRYSTAL"
] | c7cf4bfa7bfb937516815ef1eead40916eda8a60145dcc5c415606c7983b27ef |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Prepare input files for Celera Assembler, dispatch based on file suffix::
*.fasta: convert-fasta-to-v2.pl
*.sff: sffToCA
*.fastq: fastqToCA
"""
import logging
import os.path as op
import sys
from pickle import dump, load
import networkx as nx
from collections import ... | tanghaibao/jcvi | jcvi/assembly/ca.py | Python | bsd-2-clause | 34,986 | [
"BLAST"
] | ae5c2b125fd36f06842ae6039cef12e22c0d7983488b620535d8424a2790d449 |
import numpy as np
from collections import defaultdict
from scipy.stats import norm
from bokeh.plotting import show, figure
from bokeh.models import ColumnDataSource, HoverTool, TapTool
from bokeh.layouts import gridplot
from bokeh.palettes import Viridis6
mass_spec = defaultdict(list)
RT_x = np.linspace(118, 123, n... | draperjames/bokeh | examples/plotting/file/multi_line.py | Python | bsd-3-clause | 1,691 | [
"Gaussian"
] | 64f3e42f62a233e0a6ce8aa14000b610d47b62c24f351b0969d3b04b62cd0d05 |
# -*- 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 th... | kain88-de/mdanalysis | package/MDAnalysis/lib/formats/__init__.py | Python | gpl-2.0 | 1,106 | [
"MDAnalysis"
] | 0260529dd541f2a5a3376e40bfd3578e2b1135d5767e9ce4deda1fecba561386 |
import astropy.cosmology as co
aa=co.Planck15
import astropy.io.fits as fits
import astropy.units as u
from astropy.coordinates import angles
#import AngularSeparation
from astropy import coordinates as coord
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as p
import numpy as n
import os
import sys
... | JohanComparat/pySU | spm/bin_spiders/spiders_last_burst_vs_radius.py | Python | cc0-1.0 | 5,578 | [
"Galaxy"
] | 803790443ddfddaa362b266a14ef863bafebb4be1b8cf860c5f5c5770f8e5d42 |
#-----------------------------------------------------------------
# pycparser: func_defs.py
#
# Using pycparser for printing out all the functions defined in a
# C file.
#
# This is a simple example of traversing the AST generated by
# pycparser. Call it from the root directory of pycparser.
#
# Eli Bendersky [http://... | CtheSky/pycparser | examples/func_defs.py | Python | bsd-3-clause | 1,342 | [
"VisIt"
] | d21968ec39cb0410c4bb49ec779b1fbedcd88c15b4bfb6645c09c942b3544358 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#======================================================================
#
# file_time_sync.py -
#
# Created by skywind on 2020/12/08
# Last Modified: 2020/12/08 01:08:36
#
#======================================================================
from __future__ im... | skywind3000/collection | script/filesync2.py | Python | mit | 16,309 | [
"VisIt"
] | 8c35c398710eb850d3eb8d6a3d3833244e2382752122ebdedcddddb0f165bf30 |
import numpy as np
import bayesianoracle as bo
import bayesianoracle.plot as boplotter
# Import function information
from function_data import *
execfile("function_data.py")
def plot(bmao, X, k_fig, x_next, y_next):
""" Auxillary plotting function
Parameters
----------
bma : EnrichedBayesianModel... | altaetran/bayesianoracle | tests/quadraticBayesianAveraging/paper_examples/FullyBayesianBMAO1D.py | Python | apache-2.0 | 10,021 | [
"Gaussian"
] | 4a259bdea339a531803631f25270e57999f498f19dde1380bd405f8a9629ab95 |
import pytest
import io
from CommonServerPython import *
from CommonServerPython import DemistoException, Common
TAG_IDS_LISTS = [([1, 2, 3], [2, 3, 4, 5], [1, 2, 3], [4, 5]),
([1, 2, 3], [4, 5], [1, 2, 3], [4, 5])]
ATTRIBUTE_TAG_LIMIT = [{'ID': '1', 'Name': 'Tag1'}, {'ID': '2', 'Name': 'misp-galaxy:... | demisto/content | Packs/MISP/Integrations/MISPV3/MISPV3_test.py | Python | mit | 22,332 | [
"Galaxy"
] | ee255f0fe9a31443921bc9d7fba7a99768e3e728aa304859761c8627ace6807f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
The human data file is taken from:
https://github.com/Slicer/Slicer/blob/master/Base/Logic/Resources/OrientationMarkers/Human.vtp
Thanks to the Slicer people for providing this.
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName = get_pro... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/AnatomicalOrientation.py | Python | apache-2.0 | 12,414 | [
"VTK"
] | 0e0911eac7057590f619dad29f03f6c7dc7854359dd192636992a6438d7c8a71 |
#!/usr/bin/python
# Use python and scipy to check if the CLM spun-up
import gridtrans as gt
from scipy.io import netcdf
import numpy as np
def num_of_time(num_stps, num_dif_h, num_y, num_m, num_d, num_h ,if_ic, if_silence=True):
# dif_hr: out put interval
# num_y,m,d,h: start Y,M,D,H for calculation
if if_ic:
... | metalpen1984/SciTool_Py | chk_clm_energ.py | Python | lgpl-3.0 | 4,596 | [
"NetCDF"
] | c15241bf45e78c11a0d0acfc12afb969f61611838d115a758584130343624699 |
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