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import os
import io
import csv
import re
########################################################
# #
# Author: Noel Conlisk #
# Email: noecon@gmail.com #
# Script function: Using Stress data and model ... | nconlisk/python | VTK/abq_vtk_inp_v5_with_origins_and_stress.py | Python | gpl-3.0 | 9,161 | [
"VTK"
] | 21e3dc746e266b6f4f0effee1b3b00bed363238b9c3f4d57414d1dde9f664cae |
"""This is a minimal Python client for Mads Haahr's random number generator at www.random.org
# This tiny set of functions only implements a subset of the HTTP interface available. In particular it only uses the 'live'
# random number generator, and doesn't offer the option of using the alternative 'stored' random
# n... | Erotemic/utool | utool/_internal/randomwrap.py | Python | apache-2.0 | 5,537 | [
"VisIt"
] | 27f6c18f339070145e41c2cb7dc3e8d51b7bcbffb931c4c3ef03a6c85b2e9a91 |
##########################################################################
#
# Copyright 2008-2010 VMware, Inc.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software withou... | PeterLValve/apitrace | specs/stdapi.py | Python | mit | 27,491 | [
"VisIt"
] | efaef5a5d790df62fe365e5b0f27df033207415e311388d2b2db1209e831a374 |
# -*- coding: utf-8 -*-
#
# Molecular Blender
# Filename: stylers.py
# Copyright (C) 2014 Shane Parker, Joshua Szekely
#
# This file is part of Molecular Blender.
#
# Molecular Blender is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# ... | smparker/Molecular-Blender | stylers.py | Python | gpl-3.0 | 13,510 | [
"VMD"
] | 785650d2013e9f96785b006b554515aa11dac374eacf033f7a8f0b382dd64d3c |
import os
import time
import pandas as pd
import tushare as ts
import statsmodels.api as sm
import statsmodels.tsa.stattools as sts
TABLE_STOCKS_BASIC = 'stock_basic_list'
DownloadDir = './stockdata/'
def adfuller_check_smols(code1, code2, start_date = '2011-10-10', end_date = '2014-09-30'):
m = str(code1)
n ... | lionelliang/PairTradingSpark | checkpairtradingSingle.py | Python | gpl-2.0 | 5,387 | [
"ADF"
] | 659318a7ead58f58ad9c9cab897435a8eb94b89360a174aeceef3b55df099520 |
"""Tests for the BitField class."""
import unittest
import bitfield
__author__ = 'Brian Landers <brian@packetslave.com>'
class BitFieldTest(unittest.TestCase):
"""Tests for the BitField class."""
def setUp(self):
self.bits = bitfield.BitField(36)
def test_constructor(self):
for i in xr... | Packetslave/bitfield | bitfield_test.py | Python | apache-2.0 | 1,913 | [
"Brian"
] | 6dcf0d60ce957438efd1350f9622548c09a7fb544cbfe2bafef26c10b983381d |
"""
handhRL - table functions
This file contains the table functions needed for main.
"""
import libtcodpy as libtcod
import random
def rolldice(num, sides, highest=0):
# rolls a given number of dice and returns their total
# args: num = number of dice, sides = number of sides on each die,
# highest (o... | jarcane/handhRL | hhtable.py | Python | gpl-3.0 | 13,115 | [
"BLAST",
"CRYSTAL"
] | cbd80280536df220580aa6c04b0e88f8c737ea326e5ea1aee8ec292b8889ea6b |
# coding: utf-8
"""
Acceptance tests for Studio's Setting pages
"""
from __future__ import unicode_literals
import os
from mock import patch
from nose.plugins.attrib import attr
from base_studio_test import StudioCourseTest
from bok_choy.promise import EmptyPromise
from common.test.acceptance.fixtures.course import X... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/studio/test_studio_settings.py | Python | agpl-3.0 | 37,503 | [
"VisIt"
] | 1cf1a125670299e613eece1ce0637ea0579202d1756f49688f48b07909d372ef |
#!/usr/bin/env python
#
# Authors: James D. McClain <jmcclain@princeton.edu>
#
"""Module for running restricted closed-shell k-point ccsd(t)"""
import ctypes
import h5py
import itertools
import numpy as np
import pyscf.pbc.cc.kccsd_rhf
import time
from itertools import product
from pyscf import lib
from pyscf.cc impo... | gkc1000/pyscf | pyscf/pbc/cc/kccsd_t_rhf.py | Python | apache-2.0 | 28,391 | [
"PySCF"
] | 0aa0179bce135e6f769dd0a0a13f05942b4bf1040908438c42245bc5bcefc6f7 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
import itk
import module_kits.itk_kit as itk_kit
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
class gradientMagnitudeGaussian(ScriptedConfigModuleMixin, ModuleBase):
def __init__... | nagyistoce/devide | modules/insight/gradientMagnitudeGaussian.py | Python | bsd-3-clause | 4,029 | [
"Gaussian"
] | fb632b6e98ea2eff054164e3e7e8116432322c3c10947d2e6effe6330e7225a7 |
""" This is a test of the creation of the json dump file
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import os
from diraccfg import CFG
from DIRAC.WorkloadManagementSystem.Utilities.PilotCStoJSONSynchronizer import PilotCStoJSONSynch... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Utilities/test/Test_PilotCStoJSONSynchronizer.py | Python | gpl-3.0 | 4,327 | [
"DIRAC"
] | 7a21c56e393c98fd70bc0057763ce0c5f198bb6771965a5a7bc6a57a5c47ef9a |
# -*- coding: utf-8 -*-
"""
discord.ext.colours.crayon
~~~~~~~~~~~~~~~~~~~~~
An extension class to extend discord.py's colour class with XKCD colour presets.
( From https://xkcd.com/color/rgb/ )
:license: GPL, see LICENSE for more details.
"""
from discord.colour import Colour
class XKCDColour(Colour):
"""Repres... | mgardne8/DiscordPyColours | discord/ext/colours/xkcd.py | Python | gpl-3.0 | 156,381 | [
"Amber",
"VisIt"
] | b086c06a107b0b10891d4cbd77e8ecb1ae99caa17564a4635fc99ea85b970a6e |
"""
Tests for the Matomo template tags and filters.
"""
import pytest
from django.contrib.auth.models import User
from django.http import HttpRequest
from django.template import Context
from django.test.utils import override_settings
from utils import TagTestCase
from analytical.templatetags.matomo import MatomoNode
... | jcassee/django-analytical | tests/unit/test_tag_matomo.py | Python | mit | 5,650 | [
"VisIt"
] | ead0de0fd3f3ad08dbf5161ec3bc5581aa03d42fbf1d393f0e816dbe265af12a |
#!/usr/bin/python
# -- Content-Encoding: UTF-8 --
"""
iPOPO component factories repository
:author: Thomas Calmant
:license: Apache Software License 2.0
..
Copyright 2014 isandlaTech
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the L... | isandlaTech/cohorte-devtools | qualifier/deploy/cohorte-home/repo/cohorte/repositories/python/ipopo.py | Python | apache-2.0 | 12,465 | [
"VisIt"
] | afa4125144338b84082e38e2fa8bf23c63fc2ee90e8d516c643515d137704ea4 |
#!env python
"""
Applies the masks from a netCDF file to another and saves it in a new file.
"""
import sys
import numpy as np
from netCDF4 import Dataset
if len(sys.argv) < 4:
print "Usage: " + sys.argv[0] + " inputfile maskedfile outputfile"
exit(1)
infile = sys.argv[1]
maskedfile = sys.argv[2]
outfile = ... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | scripts/apply_mask.py | Python | gpl-3.0 | 1,675 | [
"NetCDF"
] | a10c46a850f7a32967a4c0114129a8a629d5e565550e3c9608f1b460b2c8f4b4 |
"""
Logging Root
"""
__RCSID__ = "$Id$"
import logging
import time
import sys
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
from DIRAC.FrameworkSystem.private.standardLogging.Logging import Logging
from DIRAC.Resources.LogBackends.StdoutBackend import StdoutBackend
from DIRAC.Core.Uti... | andresailer/DIRAC | FrameworkSystem/private/standardLogging/LoggingRoot.py | Python | gpl-3.0 | 10,258 | [
"DIRAC"
] | b18d062436656421842fb4e3cc04839f6f3bcb6753c0daef4971bf177621008c |
from os import environ as env
import re
# This is a config file for deploying to Heroku.
# Set these values as environment variables in your Heroku environment with:
# $ heroku config:add SOME_VAR=some_value
DEBUG = True
CSRF_ENABLED = True
SECRET_KEY = env['SECRET_KEY']
UPLOAD_FOLDER = '/tmp/'
ALLOWED_EXTENSIONS = ... | publicscience/hive | config_heroku.py | Python | mit | 1,617 | [
"VisIt"
] | 130c7a2b69e6f57b6e86acab3dc18139da18afc8535107b7b872f18b6e8c2ff1 |
########################################################################
# File: RequestValidator.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/09/18 07:55:16
########################################################################
""" :mod: RequestValidator
======================
.. module: Reques... | yujikato/DIRAC | src/DIRAC/RequestManagementSystem/private/RequestValidator.py | Python | gpl-3.0 | 11,219 | [
"DIRAC"
] | 0dd79e553b317d9c153a3b144d3c625473269801d13a8689467cce3ab0d11548 |
import numpy as np
import copy
import numpy.linalg as la
import summary_output as SUMMARY
import robust as ROBUST
import user_output as USER
from utils import spdot, sphstack, RegressionPropsY, RegressionPropsVM
__author__ = "Luc Anselin luc.anselin@asu.edu, David C. Folch david.folch@asu.edu, Jing Yao jingyao... | schmidtc/pysal | pysal/spreg/twosls.py | Python | bsd-3-clause | 19,084 | [
"COLUMBUS"
] | 2e08fafdd4610edd9516cc36a8553d0bafc2d871c5147865f2ef0a725108684f |
import math
ROWS = 8 # rows in maze
COLS = 8 # columns in maze
GRID_DX = 20.0 # x-dimension of the grid world
GRID_DY = 20.0 # y-dimension of the grid world
MAX_STEPS = ROWS * COLS * 40 # max number of steps - no need to visit each cell more then twice! (turns count now!)
STEP_DELAY = 3.0 # number of seconds to wait b... | JiahuiGuo/AIOpenNERO | Maze/constants.py | Python | mit | 1,254 | [
"VisIt"
] | dfdf2ea5e94dbf9b9d68358587a298b67ac5186c4069644035d6c8605c3f4118 |
# !/bin/python
# -*- coding: latin-1 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your opt... | FedoraScientific/salome-hexablock | src/TEST_PY/cas_2013/cas_2013.py | Python | lgpl-2.1 | 5,166 | [
"VTK"
] | 6cf081c6322f30c6ffec0ec2b457552f61a1b9e540315e494fb2f86603db014e |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/py-pybedtools/package.py | Python | lgpl-2.1 | 2,071 | [
"pysam"
] | 4d2c8998bbe25214fd5fdc88514e0615b841fca97884911b92752ad9c5c60dbc |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Exception types for GRIT.
'''
class Base(Exception):
'''A base exception that uses the class's docstring in addition to any
... | JoKaWare/WTL-DUI | tools/grit/grit/exception.py | Python | bsd-3-clause | 3,985 | [
"xTB"
] | 5fd136be4e599ed1a94bbd7fcdb18a57a9ae064dd7d2d8fbb46a6adb6c94f5c1 |
# This file is now deprecated and slated to be deleted.
# Don't add code here anymore. put it in punkin_chunker instead.
import sys
import os
import subprocess
from subprocess import check_output
from os.path import split, join
#import random
#import math
from Bio import SeqIO
#from Bio import SeqRecord... | bmatern/punkin-chunker | src/deprecated/Blast_Minion_Reads.py | Python | gpl-3.0 | 24,133 | [
"BLAST"
] | 1144b4e56a27e11358d33eee672d4a7354d384a85edfdd2c77ec6a96d9cce6fc |
# -*- coding: utf-8 -*-
import numpy as np
from crystals import Crystal
from skued import patterson, powdersim
def test_patterson_output_shape():
"""Test that the output shape is as expected."""
# Simulate a powder pattern first
crystal = Crystal.from_database("vo2-m1")
q = np.linspace(0.2, 10, 102... | LaurentRDC/scikit-ued | skued/tests/test_patterson.py | Python | gpl-3.0 | 509 | [
"CRYSTAL"
] | 6616d243db35ba11936244c738c616a3bc7252f067a3502fe44f3ba193841d2c |
import ast
import _ast
import os
import random
import string
import api
import ast2code
__author__ = 'hiranya'
PREDICATE_SIMILARITY_THRESHOLD = 0.9
PREDICATE_SET_SIMILARITY_THRESHOLD = 0.85
def parse(string):
return ast.parse(string, mode='eval')
class PredicateEvaluator(ast.NodeVisitor):
def evaluate(self, str... | hiranya911/rest-coder | python-lib/predicate_parser.py | Python | apache-2.0 | 20,533 | [
"VisIt"
] | b0fcf70daf17a93fc7ab6161d04a1431e5b22de9e4f95cba5a430b216090c943 |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import gw as gw_c
mol = gto.M( verbose = 1, atom = '''F 0.0 0.0 0.0''', basis = 'aug-cc-pvdz', spin = 1, )
gto_mf = scf.UHF(mol)
e_tot = gto_mf.kernel()
class KnowValues(unittest.TestCase):
def te... | gkc1000/pyscf | pyscf/nao/test/test_0068_gw_f_atom.py | Python | apache-2.0 | 864 | [
"PySCF"
] | c9c8214b50360a177d2646dbc9d801fa0eae1391959509774d51ad200aad9a86 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/qcdb/datastructures.py | Python | lgpl-3.0 | 2,525 | [
"Psi4"
] | 095a81742959a8ae440af2bd48f6789b6e936322bdb74c163b93e1944abaaf12 |
# Copyright (C) 2017 Allen Li
#
# 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,... | darkfeline/mir.anidb | setup.py | Python | apache-2.0 | 1,514 | [
"MOE"
] | d7aace5e1ccb5a34e1c90a602171849fee2da11ecd13407386ce88ee761c3045 |
from csv import reader
import random
import time
def strTimeProp(start, end, format, prop):
stime = time.mktime(time.strptime(start, format))
etime = time.mktime(time.strptime(end, format))
ptime = stime + prop * (etime - stime)
return time.strftime(format, time.localtime(ptime))
def randomDate(sta... | tburgebeckley/phlebotomy | p4/pyscript/buildVisit.py | Python | gpl-3.0 | 1,223 | [
"VisIt"
] | a4e7d7eb5b873862e7bc85cec90d10a99d286994725db66782f74e0ac8c8152c |
#Copyright (c) 2008 Erik Tollerud (etolleru@uci.edu)
from statsmodels.compat.python import zip
import numpy as np
from math import pi
class Pca(object):
"""
A basic class for Principal Component Analysis (PCA).
p is the number of dimensions, while N is the number of data points
"""
_colors=('r','... | hlin117/statsmodels | statsmodels/sandbox/pca.py | Python | bsd-3-clause | 7,098 | [
"Mayavi"
] | 64911fbd37183b3939111a05e2cd6c4cd41161d987e8c7a6faa1baf014b8bdd9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0027_student_key'),
]
operations = [
migrations.AlterField(
model_name='student',
... | koebbe/homeworks | visit/migrations/0028_auto_20150614_1750.py | Python | mit | 437 | [
"VisIt"
] | 49b2675f2496d291f0c22b106404ab6851975a8136cca0c186148f05a9c92bb7 |
"""
Test the Studio help links.
"""
from unittest import skip
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.studio.asset_index import AssetIndexPageStud... | BehavioralInsightsTeam/edx-platform | common/test/acceptance/tests/studio/test_studio_help.py | Python | agpl-3.0 | 42,755 | [
"VisIt"
] | 8e874a8d8b89b09677ae8705e0867f1ff556cc7641eb3dafb0bb940bc7707334 |
from __future__ import absolute_import, division, unicode_literals
import string
import gettext
_ = gettext.gettext
EOF = None
E = {
"null-character":
_("Null character in input stream, replaced with U+FFFD."),
"invalid-codepoint":
_("Invalid codepoint in stream."),
"incorrectly-placed-so... | KrzysztofStachanczyk/Sensors-WWW-website | www/env/lib/python2.7/site-packages/pip/_vendor/html5lib/constants.py | Python | gpl-3.0 | 86,469 | [
"Bowtie"
] | 38cd030ffd8806b5521a4279dd743969091d051f8d8753fa213e63341640dc3d |
# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Scientific Package. This package holds all simulators, and
# analysers necessary to run brain-simulations. You can use it stand alone or
# in conjunction with TheVirtualBrain-Framework Package. See content of the
# documentation-folder for more details. See also http://www... | stuart-knock/tvb-library | contrib/simulator/models/brunel_wang.py | Python | gpl-2.0 | 25,716 | [
"NEURON"
] | 88b32daf41fc6054eae9d83b8b02d01b13f0711dedbc8c6e395f2f1b34b7e832 |
# -*- coding: utf-8 -*-
#
# csa_topology_example.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | tobikausk/nest-simulator | pynest/examples/csa_topology_example.py | Python | gpl-2.0 | 4,026 | [
"Gaussian",
"NEURON"
] | be7545fda30105c39dc624c02ee8a86fb6eb37da8f8cc9080c155f4778eed6d5 |
"""
hmmer3 module
"""
from mungo.mungoCore import *
from mungo.useful import smartopen, extractRootName
import sys, re, warnings
hmmer2frame = {0: 1, 1: 2, 2: 3, 3: -1, 4: -2, 5: -3}
frame2hmmer = dict([(v,k) for k,v in hmmer2frame.iteritems()])
class Domain(AbstractFeature):
"""Domain feature class"""
... | PapenfussLab/Mungo | mungo/hmmer3.py | Python | artistic-2.0 | 4,052 | [
"BLAST"
] | 13c3a619e3b7f2e166ed2cfc63df41885f4d5d511aaa2b05d49ffe2e522ce1b6 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017 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 ... | yashdsaraf/scancode-toolkit | etc/scripts/synclic.py | Python | apache-2.0 | 32,006 | [
"Dalton",
"VisIt"
] | b2df38265ad0045aa78a04d216632e441f2f36b6ba359bd578f9ed88af463dc7 |
import numpy as np
from ase.atoms import Atoms
from ase.units import Hartree
from ase.parallel import paropen
from ase.calculators.singlepoint import SinglePointCalculator
def write_xsf(fileobj, images, data=None):
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstanc... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/io/xsf.py | Python | gpl-2.0 | 5,028 | [
"ASE",
"CRYSTAL"
] | 878b183d639f63a5c0eedbfa8ea0cfa110a46fb5d902eca59c865ee835f9f934 |
"""
This file is part of the KnownSourceMatcher.
KnownSourceMatcher is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
KnownSourceMatcher is d... | scienceguyrob/KnownSourceMatcher | KnownSourceMatcher/src/Match/ProfileOperationsInterface.py | Python | gpl-2.0 | 7,935 | [
"Gaussian"
] | 79df2c390c685a5e768b0fe05f62fca4cea1986e0ff16afad486a168fba37ea8 |
"""
ClangVisitor
"""
import os
class ClangVisitor(object):
def __init__(self):
self.prefixes = []
def run(self, cursor):
self.visit(cursor)
def set_prefixes(self, prefixes):
self.prefixes = prefixes
def is_in_prefixes(self, path):
if len(self.prefixes) == 0:
... | svperbeast/plain_data_companion | src/visitors/clang_visitor.py | Python | mit | 1,033 | [
"VisIt"
] | 7221022bc7782eb34b52c03fe8863c48105ec720e9deb4b32d860cfddb7890f2 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 vers... | marscher/PyEMMA | pyemma/coordinates/tests/test_frames_from_file.py | Python | lgpl-3.0 | 8,147 | [
"MDTraj"
] | 1e67926aa3ca6973f778ae393e5ef1bdac64f6cd90653900f05ee3ad6ab8d262 |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
ImagePermute()
| jeromevelut/Peavip | Testing/ImagePermute.py | Python | gpl-3.0 | 125 | [
"ParaView"
] | 4b1ca4ed39ac8b27d15b26613fcf26610ea04bbda7bdcede8f7e5a0197466300 |
"""
Testing xml sample from noaa catalog: http://www.esrl.noaa.gov/psd/thredds/catalog.xml
"""
import pytest
from threddsclient import read_xml
def test_noaa_catalog():
xml = """
<catalog xmlns="http://www.unidata.ucar.edu/namespaces/thredds/InvCatalog/v1.0" xmlns:xlink="http://www.w3.org/1999/xlink" name="... | bird-house/threddsclient | tests/test_noaa_sample.py | Python | apache-2.0 | 10,499 | [
"NetCDF"
] | 57d1c4f1f7d2ff72c99f573371648f0eb42bd49df94ea8758f5dfbe7061559e7 |
# ======================================================================
#
# Cosmograil: cosmograil.tools.sexcatalog
#
# sexcatalog module.
#
# Author: Laurent Le Guillou <laurentl@ster.kuleuven.ac.be>
#
# $Id: sexcatalog.py,v 1.1 2005/06/29 13:07:41 hack Exp $
#
# ======================================================... | ankanaan/chimera | src/chimera/util/sexcatalog.py | Python | gpl-2.0 | 27,007 | [
"Gaussian"
] | a7ec0051af35ec826032d949d6af28959eb271fadb66f44b0338f1dedc7921ec |
#
# When publishing work that uses these basis sets, please use the following citation:
#
# K.G. Dyall, Theor. Chem. Acc. (1998) 99:366; addendum Theor. Chem. Acc. (2002) 108:365;
# revision Theor. Chem. Acc. (2006) 115:441. Basis sets available from the Dirac web site,
# http://dirac.chem.sdu.dk.
Pt = [[0, -1, [623... | sunqm/pyscf | pyscf/gto/basis/dyall_tz.py | Python | apache-2.0 | 13,052 | [
"DIRAC"
] | 7c48aa6ad67485de29e700df604f5090153cf5eb9417eb1cba7370675f8ac93c |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/colorbar/colorbar.py | Python | lgpl-2.1 | 647 | [
"MOOSE"
] | b9da5239c161265d476787fb20323cf5f9be6985f2b7e06225febebe19c07d9b |
import pytest
from capybara.node.element import Element
@pytest.mark.requires("js")
class TestEvaluateAsyncScript:
def test_evaluates_the_given_script_and_returns_whatever_it_produces(self, session):
session.visit("/with_js")
assert session.evaluate_async_script("arguments[0](4)") == 4
def t... | elliterate/capybara.py | capybara/tests/session/test_evaluate_async_script.py | Python | mit | 1,233 | [
"VisIt"
] | 1db79d842c6345de68676b7e5c6ca17d71f6757f511e6965c1c4adfd85cc2431 |
##############################################################################
# Copyright (c) 2013-2017, 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-analysispageserver/package.py | Python | lgpl-2.1 | 1,943 | [
"Bioconductor"
] | f5108ee24e2ef1bb468361ef8aea9a626fdd276e561527e45a72714aa426d483 |
## Copyright 2011 Luc Saffre
## This file is part of the Lino project.
## Lino is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation; either version 3 of the License, or
## (at your option) any later version.
## L... | MaxTyutyunnikov/lino | lino/utils/mdbtools.py | Python | gpl-3.0 | 6,191 | [
"Brian"
] | 4918887029b7a713aa7ac0c11d727953ba2afeea6f7aaf94b6fe42a24bd47a4f |
# 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_c2r.py | Python | apache-2.0 | 4,037 | [
"PySCF"
] | cf184fc7e849158d25afb98aef0ce528d04dda3ed1b3d86844a963e3adbebc45 |
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
##
## CDS Invenio 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 (... | lbjay/cds-invenio | modules/websession/lib/websession_templates.py | Python | gpl-2.0 | 102,861 | [
"VisIt"
] | b2f817050d48d484fa3794ce5f7c26d623416cfe377dcf9f4c9da1d767419a8e |
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from builtins import zip
from builtins import range
from builtins import object
import itertools as it
import warnings
import numpy as np
from scipy.special import gammaln
try:
from bottleneck import nansu... | jzaremba/sima | sima/motion/hmm.py | Python | gpl-2.0 | 35,830 | [
"Gaussian",
"NEURON"
] | 6ddc234122c30b498a583decba4092da3b38bc9f5ecb679b45afac943959f900 |
import skimage.color
import skimage.measure
import skimage.transform
import skimage.filters
import skimage.morphology
import numpy as np
import io
from PIL import Image
class GameFrameError(BaseException):
pass
class GameFrame:
def __init__(self, frame_data, frame_variants=None, timestamp=None, **kwargs... | SerpentAI/SerpentAI | serpent/game_frame.py | Python | mit | 5,346 | [
"Gaussian"
] | 0aedb8aedac9a05261f7e6b133c572ae7fa37d4528883d2c095b71cf473df7f5 |
import neurokernel.mpi_relaunch
import scipy.io as io
from libSpineML2NK import nk_executable
from libSpineML import smlExperiment
e = nk_executable.Executable('./experiment0.xml')
exp = e.bundle.experiments[0].Experiment[0]
ai = exp.AbstractInput[0]
mutant = io.loadmat('data/MutantBG6Data.mat')
m_input = mutant['rec... | AdamRTomkins/libSpineML2NK | libSpineML2NK/examples/Narx/Narx_Python/run.py | Python | gpl-3.0 | 1,011 | [
"NEURON"
] | 343129243c493cdd974d8f9bdb720acf9e8de9240dcbdf9fe5699b17086603d8 |
#/*
# *
# * TuneIn Radio for XBMC.
# *
# * Copyright (C) 2013 Brian Hornsby
# *
# * This program is free software: you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation, either version 3 of the License, or
# * (at your option) any... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/plugin.audio.tuneinradio.smallplayer/resources/lib/xbmcdownload.py | Python | gpl-2.0 | 4,770 | [
"Brian"
] | a21e5b4504e9e3cd4e520cb5019d0f8e4c4ef697772909312217ff3308c44c36 |
"""
Acceptance tests for the teams feature.
"""
import json
import random
import time
from dateutil.parser import parse
import ddt
from nose.plugins.attrib import attr
from selenium.common.exceptions import TimeoutException
from uuid import uuid4
from common.test.acceptance.tests.helpers import get_modal_alert, Event... | louyihua/edx-platform | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 83,640 | [
"VisIt"
] | 313098dc9a621ae042214c3b9a0c1554651a6b6ba9650f737ffd35d3d0daab78 |
from setuptools import setup
setup(
name='sulley',
packages=['sulley'],
version='0.1.0b0',
description=('With Sulley, you can build SMS bots in just'
' a few lines of code. Powered by Twilio & Plivo,'
' Sulley requires very minimal configuration and '
... | sandeepraju/sulley | setup.py | Python | bsd-3-clause | 1,321 | [
"VisIt"
] | 66354266f5cbfdc798ed9f5b7e4ef2714106ae62390d3ad3e21c3feb62265a38 |
# -*- coding: utf-8 -*-
# Copyright (c) 2013 Kura
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, ... | getpelican-plugins/pelican_youtube | pelican_youtube/youtube.py | Python | mit | 2,902 | [
"Brian"
] | 38e051c3abe29cf20d12136f7524fcc21f3f146611361126311890f40370f10b |
# snippet to be ran in the introspection window of a slice3dVWR to
# export the whole scene as a RIB file. Before you can do this,
# both BACKGROUND_RENDERER and GRADIENT_BACKGROUND in slice3dVWR.py
# should be set to False.
obj._orientation_widget.Off()
rw = obj._threedRenderer.GetRenderWindow()
re = vtk.vtkRIBExp... | nagyistoce/devide | snippets/ribexport.py | Python | bsd-3-clause | 398 | [
"VTK"
] | 8c21f53afe198881ed49790ddd61c8a7615199daae848b562dc51c311bf63f09 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_NVOC_emissions_n96e_360d.py | Python | gpl-3.0 | 19,052 | [
"NetCDF"
] | 0a33f49161092e048732a319154b2153ee9a8a8af54970ec8b50e7382fbad9e9 |
import os
from collections import OrderedDict, deque
from six.moves.cPickle import loads, dumps
import numpy as np
import pandas as pd
import pytest
from numpy.testing import assert_array_equal, assert_array_almost_equal
import oddt
from oddt.spatial import rmsd
from oddt.toolkits.common import canonize_ring_path
t... | oddt/oddt | tests/test_toolkit.py | Python | bsd-3-clause | 21,611 | [
"RDKit"
] | d96b3677b5f1751762e0564556af1b4142a6990728ac1863e65d01c7b0e21f2c |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-oslogin | tests/unit/gapic/oslogin_v1/test_os_login_service.py | Python | apache-2.0 | 99,055 | [
"Octopus"
] | ce10646ae387f1c7868b2a7994b80d4d58d05ba184354824fa0579474697846a |
# Copyright 2017 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... | asimshankar/tensorflow | tensorflow/python/data/experimental/benchmarks/rejection_resample_benchmark.py | Python | apache-2.0 | 2,449 | [
"DIRAC"
] | fd06cdbe75bd9ee434bdbf2065f3323f00c9e3277250b5b614fe33a72d948ff4 |
#!/usr/bin/env python
'''
TracPy class
'''
import tracpy
import numpy as np
from . import tracmass
from matplotlib.mlab import find
class Tracpy(object):
"""TracPy class."""
def __init__(self, currents_filename, grid, nsteps=1, ndays=1, ff=1,
tseas=3600., ah=0., av=0., z0='s', zpar=1, do3d... | kthyng/tracpy | tracpy/tracpy_class.py | Python | mit | 26,569 | [
"NetCDF"
] | 7442dc9f80d10895851e32cfecaf1478985fa02242ddd4ce1deceadf9e7b7d81 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | polish/env/env.py | Python | apache-2.0 | 30,514 | [
"Gaussian"
] | 949edc65b01327cb2a32ab8073ea0763aad2c5d76eda5ad392959fcb6e83ec1e |
"""
The scene consists of
* Four actors: a rectangle, a box, a cone and a sphere.
The box, the cone and the sphere are above the rectangle.
* Two spotlights: one in the direction of the box, another one in the direction of the sphere.
Both lights are above the box, the cone and the sphere.
"""
import vtk
... | lorensen/VTKExamples | src/Python/Visualization/ShadowsLightsDemo.py | Python | apache-2.0 | 5,081 | [
"VTK"
] | 57f2965769f9586ce12fd77abb83b077bb80dd40f90e0bc68d5911951aecced5 |
#!/usr/bin/env python
from optparse import OptionParser
code_choices = ['gpaw', 'dacapo', 'abinit', 'elk']
adsorbate_choices = ['None', 'N', 'O']
geometry_choices = ['fix', 'relax']
mode_choices = ['molecule', 'slab']
xc_choices = ['PW91', 'LDA', 'PBE']
parser = OptionParser(usage='%prog [options] package.\nExample ... | qsnake/gpaw | gpaw/test/big/Ru001/adsRu001.py | Python | gpl-3.0 | 10,021 | [
"ABINIT",
"ASE",
"Elk",
"GPAW"
] | e9f090c9b716439bcaae0db63c228265add92ce578f10cfe1b9c6ff3062d5c56 |
# GromacsWrapper -- cbook.py
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
"""
:mod:`gromacs.cbook` -- Gromacs Cook Book
=========================================
The :mod:`~gromacs.cbook` (cook book) module contains short recipes for tas... | Becksteinlab/GromacsWrapper | gromacs/cbook.py | Python | gpl-3.0 | 90,385 | [
"CHARMM",
"CRYSTAL",
"Gromacs",
"MDAnalysis",
"VMD"
] | d68b4cd7a50b98c556388d255c8bcbbe76b49289dd1d44d83bc418be8fd5ad28 |
# coding: utf-8
"""Release data for the abiflows project."""
from collections import OrderedDict
# Name of the package for release purposes. This is the name which labels
# the tarballs and RPMs made by distutils, so it's best to lowercase it.
name = 'abiflows'
# version information. An empty _version_extra corresp... | davidwaroquiers/abiflows | abiflows/core/release.py | Python | gpl-2.0 | 2,408 | [
"ABINIT",
"pymatgen"
] | ccd0bbc9c28d9cbf0bbc355c0df231cd273e9b881aaa7b260ddf66969a985a60 |
import os
import sys
import vtkAll as vtk
from ddapp import botpy
import math
import time
import types
import functools
import numpy as np
from ddapp import transformUtils
from ddapp import lcmUtils
from ddapp.timercallback import TimerCallback
from ddapp.asynctaskqueue import AsyncTaskQueue
from ddapp import objectmo... | RussTedrake/director | src/python/ddapp/surprisetask.py | Python | bsd-3-clause | 10,703 | [
"VTK"
] | b2a751459049a711c8378bb8d612df864f627b0af8387027bd822591b8ca5d7a |
"""
Numba-specific errors and warnings.
"""
import abc
import contextlib
import os
import sys
import warnings
import numba.core.config
import numpy as np
from collections import defaultdict
from numba.core.utils import (chain_exception, use_old_style_errors,
use_new_style_errors)
from fu... | seibert/numba | numba/core/errors.py | Python | bsd-2-clause | 24,652 | [
"VisIt"
] | f9fe5545bc5f0dda9857a6de226e78b0c117fb221ed14952a54ea514908fbb54 |
#!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, ei... | govarguz/espressopp | examples/adress/hadress_tetraliquid/hadress_tetraliquid_KTI/hadressKTI.py | Python | gpl-3.0 | 11,990 | [
"CRYSTAL",
"ESPResSo"
] | 61fb2402209a0aeafd26578676ff3ad43218b5f2fe5e16a45ef86e9963d1be28 |
# Load CosmoMC format .dataset files with lensing likelihood data
# AL July 2014
# note this is not well tested with final published versions of likelihoods
# Does not handle calibration parameter
from __future__ import absolute_import
from __future__ import print_function
from matplotlib import pyplot as plt
import os... | ClaudioNahmad/Servicio-Social | Parametros/CosmoMC/CosmoMC-master/python/CMBlikes.py | Python | gpl-3.0 | 12,103 | [
"Gaussian"
] | e5e3bb36087fdb988a5939ad9b09a54518cb9264c19ef35c9ef05c8c52b625cb |
import random
from lib.keras_utils import *
from lib.utils import *
from parameters import *
from skimage.transform import ProjectiveTransform
EPS = 1e-10 # Epsilon
MIN_CP = -2. # Minimum power index of c
MAX_CP = 2. # Maximum power index of c
SCORE_THRES = 0.99 # Softmax score threshold to consider success of ... | chawins/aml | lib/OptTranLane.py | Python | mit | 19,306 | [
"Gaussian"
] | 192a500cb1813c9c98180c4639f61bcd916942ce2626335c255c40d707bb24af |
# -----------------------------------------------------------------------------
# Copyright (c) 2015 Ralph Hempel <rhempel@hempeldesigngroup.com>
# Copyright (c) 2015 Anton Vanhoucke <antonvh@gmail.com>
# Copyright (c) 2015 Denis Demidov <dennis.demidov@gmail.com>
# Copyright (c) 2015 Eric Pascual <eric@pobot.org>
#
# ... | dwalton76/ev3dev-lang-python | ev3dev2/sound.py | Python | mit | 25,650 | [
"Galaxy"
] | 9183ec98ca53282b2fc5a7a8281559966898bef8af474a450c7db2be62fd907b |
import vtk
class Scene:
def __init__(self):
render_window = vtk.vtkRenderWindow()
self.renderer = vtk.vtkRenderer()
render_window.AddRenderer(self.renderer)
self.interactor = vtk.vtkRenderWindowInteractor()
self.interactor.SetRenderWindow(render_window)
camera = ... | RodericDay/CIF-characterize | vtk_tools.py | Python | mit | 2,925 | [
"VTK"
] | 1534a1c114b0613a6e53339cac4fa948d95eafde0354a4a6e8fff746cc640ad3 |
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime
import dateutil.parser
from lazy import lazy
from xmodule.seq_module import SequenceDescriptor, Seque... | nicky-ji/edx-nicky | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 48,311 | [
"VisIt"
] | 6e6fe6ffee3c0e33950ca46b25ce04002824b82116518bc396dae83abd07c612 |
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundati... | Freeseer/freeseer | src/freeseer/plugins/output/videopreview/__init__.py | Python | gpl-3.0 | 4,047 | [
"VisIt"
] | 6fffd2184f490ec39a5993eb2d6388186478c5777c020064759590f9fda39c9c |
#!/usr/bin/env python
# GOAL: measure completeness of 24um scans
#
# PROCEDURE:
# - run sextractor on image to create segmentation map
# - place artificial sources in areas where there is not existing source
# - rerun sextractor to detect artificial images
#
#
#
from pylab import *
# run sextractor
#... | rfinn/LCS | paper1code/LCScompleteness24.py | Python | gpl-3.0 | 14,141 | [
"Galaxy"
] | 06dfc505b566eaec47baaea44f751000f4d61a05632405497891264059525f7b |
import tomviz.operators
class LabelObjectAttributes(tomviz.operators.CancelableOperator):
def transform_scalars(self, dataset):
"""Computes certain attributes of labeled objects, including surface
area, volume, surface-area-to-volume ratio, and centroid.
"""
# Initial progress
... | cryos/tomviz | tomviz/python/LabelObjectAttributes.py | Python | bsd-3-clause | 2,976 | [
"VTK"
] | b8744b1a97f516e6ed2788429948b32c83ddc168f69e3cd6418332a6b8d5ce55 |
import llvm
import llvm.core
import sys
from functools import reduce
from llvmpy import api
from collections import defaultdict, namedtuple
from .Analysis import Analysis
from .Function import Function
from .Subtask import Subtask
from .AtomicBasicBlock import S, E, ControlFlowEdge
import logging
from .common import No... | danceos/dosek | generator/analysis/LLVMPYAnalysis.py | Python | lgpl-3.0 | 15,053 | [
"VisIt"
] | c7c23ae63e35c727c27be2cf9428e28e334fc7ad77a1d0ac30c58cc7a406a850 |
#
# This file is part of jetflows.
#
# Copyright (C) 2014, Henry O. Jacobs (hoj201@gmail.com), Stefan Sommer (sommer@di.ku.dk)
# https://github.com/nefan/jetflows.git
#
# jetflows 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... | stefansommer/dpca | code/landmarks/kernels/pyGaussian.py | Python | gpl-3.0 | 6,717 | [
"Gaussian"
] | bcf134b807f23f0c034718c871d5098202a328773ce837fe90cc4a8f723dcf4a |
# -*- coding: utf-8 -*-
"""
Create an initial ATP Profile for an ECs Mesh and write it out as .vtp.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the GenerateATPMap script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__... | BlueFern/DBiharMesher | meshes/c8064/Generate8064ATPMapV2.py | Python | gpl-2.0 | 1,119 | [
"VTK"
] | 510f786a8cfa96a7c492df38e9b3a79241d59e7eaf9bfe82b2163c351fd8c5c5 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2016, 2016, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | olpaw/mx | mx_microbench.py | Python | gpl-2.0 | 3,958 | [
"VisIt"
] | 759b8b57e60646b83f6446212b4f4ccc86a2d262e0c1d370e2d8212d25a1870c |
#
# Copyright 2014, 2020 James Kermode (Warwick U.)
# 2019 James Brixey (Warwick U.)
# 2015 Punit Patel (Warwick U.)
# 2014 Lars Pastewka (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software:... | libAtoms/matscipy | matscipy/surface.py | Python | lgpl-2.1 | 8,658 | [
"Matscipy"
] | 8721793ca0aac01c7bb5e063cffecfe90c4cb44e4b286a1279fc63054b8d5988 |
#!/usr/bin/env python3
# Copyright 2021 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | GoogleCloudPlatform/hadoop-discovery-tool | code_release.py | Python | apache-2.0 | 1,099 | [
"VisIt"
] | f2c83933b3ed7cb1ac4ca5329187df390a78ed7b5c36da2c04e9a0a49acae3c5 |
# -*- coding: utf-8 -*-
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# Karaage documentation build configuration file, created by
# sphinx-quickstart on Thu Jan 16 14:28:57 2014.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that n... | brianmay/karaage | docs/admin/conf.py | Python | gpl-3.0 | 9,208 | [
"Brian"
] | a75af3d5aff7ab86d21da0c3030fb45abe5214a0028362efcbe9b3a456a9e991 |
# coding=utf-8
# Copyright 2022 The ML Fairness Gym 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 applicab... | google/ml-fairness-gym | distributions.py | Python | apache-2.0 | 3,400 | [
"Gaussian"
] | 96383b06362e0eaeda28b5b3da644c573776306fa40fc87d632f74b6c717b917 |
"""
An efficient implementation of the triple-plane view showing 3 cut planes
on volumetric data, and side views showing each cut, with a cursor to
move the other cuts.
This is an example of complex callback interaction. It builds on the
:ref:`example_volume_slicer` but has more complex logic. You should try
to unders... | dmsurti/mayavi | examples/mayavi/interactive/volume_slicer_advanced.py | Python | bsd-3-clause | 11,548 | [
"Mayavi",
"VTK"
] | 3afb28f52bb3156d369d461d74825e8362611e147efd02fc20ae238327ff0909 |
import tempfile
from pele.systems import AtomicCluster
from pele.potentials import LJ
from pele.utils.xyz import write_xyz
__all__ = ["LJCluster"]
class LJCluster(AtomicCluster):
"""
define the System class for a Lennard-Jones cluster
Parameters
----------
natoms : int
See Also
... | cjforman/pele | pele/systems/ljcluster.py | Python | gpl-3.0 | 4,080 | [
"PyMOL"
] | 928e8ac6dd1a41b4933343f21f4813fed57ea46d4d232e9f4295a6f9ec0db60d |
#! /usr/bin/env python
"""
Get Pilots Logging for specific Pilot UUID or Job ID.
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC import S_OK
from DIRAC.Core.Base import Script
from DIRAC.WorkloadManagementSystem.Client.PilotsLoggingClient import PilotsLoggingClient
from DIRAC.WorkloadManagementSystem.DB.PilotAgentsDB... | arrabito/DIRAC | WorkloadManagementSystem/scripts/dirac-admin-pilot-logging-info.py | Python | gpl-3.0 | 2,194 | [
"DIRAC"
] | 499c40a20bed735c704c13b7901a23ecf6790dd1d192a8af29efa2cca78b1cc5 |
#from logging import info
import multiprocessing
from scipy.stats import rankdata
from logging import info
import numpy
import itertools
import pysam
import array
from .fileParser import parse_file_by_strand
BIN = 1000
def estimate_shiftsizes(parameter):
''' the root function for estimating the shiftsizes'''
... | shawnzhangyx/PePr | PePr/pre_processing/shiftSize.py | Python | gpl-3.0 | 3,784 | [
"pysam"
] | dc8ebcefc800f2cc95af3d1dec42704cffe67cdbc65dd6ca55d61e419c6ca6a9 |
#
# 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... | WindCanDie/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 49,801 | [
"Gaussian"
] | ff9878cb71682bc90d36c3b3f9abf1f379b3cf7e220a8fc6082abbe552e1d84d |
#! /usr/bin/env python
# This file is part of python-misp.
#
# Copyright 2015 Nicolas Bareil <nicolas.bareil@airbus.com>
# while at Airbus Group CERT <http://www.airbus.com>
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance wi... | nbareil/python-misp | misp_test.py | Python | apache-2.0 | 18,323 | [
"Galaxy"
] | 1ee661c2a1a8b7df4cb9349f2b82303929853397fbcbc652fcc28943890062d5 |
# Copyright 2006, 2007 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SeqIO support for the "clustal" (aka ClustalW) file format.
You are expected to u... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SeqIO/ClustalIO.py | Python | apache-2.0 | 12,544 | [
"BioPerl",
"Biopython"
] | 97ca203ecbe8e668b9dce505fbc153bc07138bac3eac4223eea9e732057115ca |
#!/usr/bin/env python
# encoding: utf-8
"""Traverse a directory tree.
"""
import os
import os.path
import pprint
def visit(arg, dirname, names):
print dirname, arg
for name in names:
subname = os.path.join(dirname, name)
if os.path.isdir(subname):
print ' %s/' % name
els... | Akagi201/learning-python | ospath/ospath_walk.py | Python | mit | 590 | [
"VisIt"
] | 2c485e09ceaa877bc5cd95c2dd74c45dfe6c62f4c2d109ab93223a27c8ce2ce4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import json
import warnings
import numpy as np
from pymatgen import Lattice, Structure, Specie, Molecule
from pymatgen.transformations.standard_transformations import \
OxidationS... | fraricci/pymatgen | pymatgen/transformations/tests/test_advanced_transformations.py | Python | mit | 32,310 | [
"VASP",
"pymatgen"
] | 241784c62eab228712c7546a0c0b6a21954133aa9ea25c5e5d01cbf34b411f6a |
"""
Extract the reads from a fastq file that are not in the bam file
"""
import os
import sys
import argparse
import pysam
from roblib import stream_fastq
def reads_from_bam(bamf, verbose=False):
"""
Read the reads in a bam file
:param bamf: bam file
:param verbose: more output
:return: a set of r... | linsalrob/crAssphage | bin/bam/fastq_not_in_bam.py | Python | mit | 1,673 | [
"pysam"
] | 6dc8d77784ab10d45e9a15f541caa53ecc09723d9ad24e428eb2b6d139b22d77 |
# -*- coding: utf-8 -*-
""" GIS Module
@requires: U{B{I{gluon}} <http://web2py.com>}
@requires: U{B{I{shapely}} <http://trac.gispython.org/lab/wiki/Shapely>}
@copyright: (c) 2010-2012 Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaini... | vgupta6/Project-2 | modules/s3/s3gis.py | Python | mit | 313,191 | [
"Amber"
] | a28fa46cdc94f8246e2285cb99b6926ba075736412b4fa0e2f70ff041ffca6de |
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