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#!/usr/bin/env python3
from __future__ import unicode_literals
import json
import time
from urllib.parse import urlencode
from xml.dom import minidom
import requests
from bs4 import BeautifulSoup
from . import database_tasks, report_tasks, alg_utils
CREDIBLE_USERNAME = alg_utils.get_secret('credible', 'username')
C... | jkcubeta/algernon | src/overwatch/src/overwatch/alg_tasks/credible_tasks.py | Python | apache-2.0 | 23,349 | [
"VisIt"
] | 8f519a092efcf7176278a2b4dec914f9185dd5b0926e24233a9ac3247f5acbac |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Bowtie(MakefilePackage):
"""Bowtie is an ultrafast, memory-efficient short read aligner
... | LLNL/spack | var/spack/repos/builtin/packages/bowtie/package.py | Python | lgpl-2.1 | 3,221 | [
"Bowtie"
] | 5414b925e18257b7a32349a3f51eab7abc31592dc9834bb6576d389a7fce143d |
"""
Gaussian foreground simultaion
Simulate gaussian foregrounds, in particular those in the style of Santos, Cooray and Knox [1]_.
These are foregrounds that can be represented with a covariance
function that seperates with angle and frequency.
References
----------
.. [1] http://arxiv.org/abs/astro-ph/0408515
"""
... | radiocosmology/cora | cora/foreground/gaussianfg.py | Python | mit | 5,626 | [
"Gaussian"
] | 9a5a8b6e6c114b24a1ca6f25dbafaabfd9c3352ffa3225d4022f23c18c7888a8 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
#
# Copyright (C) 2015 Bitergia
#
# 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 later ve... | sanacl/GrimoireELK | grimoire/elk/telegram.py | Python | gpl-3.0 | 5,129 | [
"Elk"
] | 6d9deecba7cf1c3fd976e26df9f0306c4466087d61adf648c5f37d048be9575f |
#!/usr/bin/env python
# fig 3b processing
# description: set up reads for allele-specific ATAC (quasar) calls
# data: /srv/scratch/dskim89/ggr/ggr.atac.2019-06-06.ase
import os
import glob
import pandas as pd
import numpy as np
def filter_bam_file(in_bam, out_bam):
""" filter bam file
"""
# make header... | vervacity/ggr-project | figs/fig_2.modelling/fig_3-b.1a.process.py | Python | mit | 7,702 | [
"ASE"
] | 1087694ec72d21c97001eefe62e931e057baff978fa761bb9ad8577baff673b9 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | kevin-intel/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 51,132 | [
"Gaussian"
] | 12595aee76faff77db5b6248f0819da33b1ebb680ecde8169b1ee47a735af6b5 |
from agpy import convolve,smooth
from pylab import *
test_image = zeros([512,512])
# point
test_image[204,204] = 1
# box
test_image[280:297,280:297] = 1/256.
shiftest_image = zeros([300,320])
shiftest_image[100:120,180:220]=1.0
print "Testing for a shift"
figure(11)
clf()
smoothed,kernel = smooth(shiftest_image,retu... | jcesardasilva/agpy | tests/test_smooth.py | Python | mit | 4,734 | [
"Gaussian"
] | ae6385334163293d4a921e9f16ac7aa5f027c7896f0febd01e840a28d945ddc1 |
from __future__ import print_function
__author__ = """Alex "O." Holcombe, Charles Ludowici, """ ## double-quotes will be silently removed, single quotes will be left, eg, O'Connor
import time, sys, platform, os
from math import atan, atan2, pi, cos, sin, sqrt, ceil, radians, degrees
import numpy as np
import psychopy, ... | alexholcombe/dot-jump | dataRaw/Fixed Cue/test_dot-jump25Oct2016_11-42.py | Python | gpl-3.0 | 25,593 | [
"Gaussian"
] | cbf37047c5f8f000d1743cf8e827eb24d1eca671cb253509fccb5c3b67c6fcd8 |
# Copyright (c) 2001 Autonomous Zone Industries
# Copyright (c) 2003 Bryce "Zooko" Wilcox-O'Hearn
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
__revision__ = "$Id: Conversation.py,v 1.19 2003/03/09 18:54:57 zooko E... | zooko/egtp_new | egtp/Conversation.py | Python | lgpl-2.1 | 25,617 | [
"VisIt"
] | 1c33b4e82e54e0eec9e9154e5ce588b97845998b7660ccc3610df5f9b28eeea7 |
########################################################################
# File: Request.py
# Date: 2012/07/16 13:43:45
########################################################################
"""
:mod: Request
.. module: Request
:synopsis: request implementation
request implementation
"""
# Disable invalid names w... | vmendez/DIRAC | RequestManagementSystem/Client/Request.py | Python | gpl-3.0 | 17,938 | [
"DIRAC"
] | dcc0b67f72bd62387b14dccaea4db593572043915f2ac2c75079258c935f3424 |
import urllib.request
import sys
import json
import time
import difflib
# List of countries which we want appear to be coming from - list below selected based on top 20 countries by GDP
# Add/remove per your requirements - second field is ISO_3166 country code
# Country codes can be obtained from: https://en.wikipedi... | adamkramer/shape_shift | shape_shift.py | Python | gpl-3.0 | 11,221 | [
"Galaxy"
] | e6eb3ae9556e5b783b70aacecdbb30ffbde35733ffca99011f2a9306b9d2f922 |
import math
import numpy as np
import pysam
import clodius.tiles.bigwig as ctbw
def abs2genomic(chromsizes, start_pos, end_pos):
abs_chrom_offsets = np.r_[0, np.cumsum(chromsizes)]
cid_lo, cid_hi = (
np.searchsorted(abs_chrom_offsets, [start_pos, end_pos], side="right") - 1
)
rel_pos_lo = star... | hms-dbmi/clodius | clodius/tiles/bam.py | Python | mit | 6,802 | [
"pysam"
] | af643255900873b9b0ff009cb3fbeb31dfe8c2c60783a887cadd02dbacf381d8 |
#!/usr/bin/env python
"""
Print list of users with proxies.
Example:
$ dirac-admin-users-with-proxy
* vhamar
DN : /O=GRID-FR/C=FR/O=CNRS/OU=CPPM/CN=Vanessa Hamar
group : dirac_admin
not after : 2011-06-29 12:04:25
persistent : False
-
DN : /O=GRID-FR/C=FR/O=CNRS/OU=CPPM/CN=Vanessa... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_admin_users_with_proxy.py | Python | gpl-3.0 | 2,701 | [
"DIRAC"
] | 080239ae148250dfa7f72e3d9cd3617e8bed7cf4a558c03391bbabf51b8e03bd |
#
# 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... | vinodpanicker/scancode-toolkit | src/cluecode/copyrights.py | Python | apache-2.0 | 35,651 | [
"VisIt"
] | f6d00d3b7289b3ff7743d3899db98c2f74efb57d8975198235b226ed16464dc2 |
# Disable the AST optimizer on this module
__fatoptimizer__ = {'enabled': False}
import ast
import fatoptimizer.convert_const
import fatoptimizer.namespace
import fatoptimizer.optimizer
import fatoptimizer.tools
import io
import re
import sys
from fatoptimizer.tools import UNSET
import textwrap
import unittest
from un... | haypo/fatoptimizer | test_fatoptimizer.py | Python | mit | 95,707 | [
"VisIt"
] | 06da45e18f18360dcb899bd0445650f5b5a3398861add1d858213645f149556f |
# -*- coding: utf-8 -*-
from pygsp import utils
from . import Filter # prevent circular import in Python < 3.5
class Gabor(Filter):
r"""Design a filter bank with a kernel centered at each frequency.
Design a filter bank from translated versions of a mother filter.
The mother filter is translated to eac... | epfl-lts2/pygsp | pygsp/filters/gabor.py | Python | bsd-3-clause | 3,450 | [
"Gaussian"
] | 7b5d9958d3d3a7c3659db4eb7f5d6de4b21b8a5cb63af8bcc815f1e0b0d73ae8 |
#!/usr/bin/env python
import vtk, os
from pymicro.crystal.lattice import Crystal
from pymicro.view.scene3d import Scene3D
from pymicro.view.vtk_utils import *
from vtk.util.colors import gold
'''
Create a 3d scene with a unit cells of primitive tetragonal crystal
lattice. The basis associated consist of one Au atom a... | heprom/pymicro | examples/3d_visualisation/AuCu_crystal.py | Python | mit | 1,319 | [
"CRYSTAL",
"VTK"
] | be8babe69c6595a3d04f7f67171bbc3ed8aad056ea7e3a04b887e5a6d88ef729 |
import argparse
import os
import shutil
import struct
import sys
import tempfile
import time
from twisted.internet import reactor
from twisted.web.server import Site
from twisted.web.static import File
from twisted.python import log
import mhef.n3ds
import proxy
def make_quests(path, cipher, language, quest_files)... | svanheulen/mhqs | mh4u_proxy.py | Python | gpl-3.0 | 7,086 | [
"VisIt"
] | 43c77f3f596f0bb2b07e555e021ae1245b32e71f52e2da6dc543afb2b968867a |
import types
class SeqioFilter( list ):
"""This class is to allow filtering of the Biopython SeqIO record
SeqIO.parse returns a generator object so anytime you want to perform
an action on it, you must iterate through the entire list. This
class add the ability to filter and return only a subset of t... | linsalrob/EdwardsLab | roblib/seqio_filter.py | Python | mit | 2,355 | [
"Biopython"
] | 29c3554077ec5f32851af5355bb9daeb30b4f0eb4b63c3f10fe9d4bd870aa7bb |
from rdkit.Chem.rdMolDescriptors import CalcNumRotatableBonds
from ._base import Descriptor
from .BondCount import BondCount
__all__ = ("RotatableBondsCount", "RotatableBondsRatio")
class RotatableBondsBase(Descriptor):
__slots__ = ()
explicit_hydrogens = False
@classmethod
def preset(cls, version)... | mordred-descriptor/mordred | mordred/RotatableBond.py | Python | bsd-3-clause | 1,368 | [
"RDKit"
] | ec93e2194c20f96879a5fd20fe046a54deea3be5a5b5bc5cb35f7dff21565ddd |
# Copyright 2014-2016 The ODL development group
#
# This file is part of ODL.
#
# ODL 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.
... | bgris/ODL_bgris | lib/python3.5/site-packages/odl/space/fspace.py | Python | gpl-3.0 | 43,234 | [
"Gaussian"
] | 5b82e699073b0dc5d32d54c19ca959fec73de1405f161c35a43a37ed5421ea4e |
"""
Module for utilities related to simulation
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from builtins import next
from builtins import dict
from builtins import map
from builtins import str
try:
base... | Neurosim-lab/netpyne | netpyne/sim/utils.py | Python | mit | 28,991 | [
"NEURON"
] | f991b135a581bf4080b12d843169ac286b879583cd9355a80cf827a2915944fd |
"""Axis binary sensor platform tests."""
from unittest.mock import Mock
from homeassistant import config_entries
from homeassistant.components import axis
import homeassistant.components.binary_sensor as binary_sensor
from homeassistant.setup import async_setup_component
EVENTS = [
{
"operation": "Initia... | leppa/home-assistant | tests/components/axis/test_binary_sensor.py | Python | apache-2.0 | 3,072 | [
"VMD"
] | 4a318f0bb285a7a2e3d5f119b1702fb50b1e657dd4b71763b190e245ccf9c23a |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free ... | levenlabs/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 32,139 | [
"Galaxy"
] | 7752510af303aaae678ebea932f00ae69a0cd68631d4a55b42fc7cae8256af73 |
"""
Class encapsulating the management of repositories installed into Galaxy from the Tool Shed.
"""
import copy
import logging
import os
from galaxy import util
from tool_shed.util import common_util
from tool_shed.util import container_util
from tool_shed.util import shed_util_common as suc
from tool_shed.util import... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py | Python | gpl-3.0 | 77,968 | [
"BWA",
"Galaxy"
] | 2e3f8b29e9ccfd225d7cb4d8bbbc22346441faee5bd515e06adfc35e54e69a22 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2017 Łukasz Rogalski <rogalski.91@gmail.com>
# Copyright (c) 2018 ssolanki <sushobhitsolanki@gmail.com>
# Copyright (c) 2018 Ville Skyttä <ville.skytta@upcloud.com>
# Licensed under the GPL: https://www.gnu.org/licen... | kczapla/pylint | pylint/pyreverse/inspector.py | Python | gpl-2.0 | 12,352 | [
"VisIt"
] | 85f09d7c7be7ffa833f652cefb2c09b5b6322836cde5ec37ddcd313a47315934 |
__author__ = 'mnowotka'
from django.conf import settings
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Draw
from rdkit import RDLogger
from pybel import ob, readstring
from indigoWrapper import *
import requests
from django.utils.http import urlquote
from rdkit.Chem import InchiToInchiKe... | thesgc/chembiohub_ws | chembl_business_model/utils.py | Python | gpl-3.0 | 26,780 | [
"Open Babel",
"Pybel",
"RDKit"
] | 42ae02584e768760f90519549b98eafb8246221f638596e9863e9acad79de4d9 |
import ast
import hashlib
import json
import unittest
from io import BytesIO
from oceannavigator import create_app
from plotting.scriptGenerator import generatePython, generateR
class TestScriptGenerator(unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.app = create_app()
def test_genera... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | tests/test_scriptGen.py | Python | gpl-3.0 | 5,458 | [
"Gaussian"
] | d2ee8d7e319849af697ea4539273a31bc8434a20190f17236add2c7dd928101b |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
QtCore.QString = str
except ImportError:
raise ImportError("Cannot load either PyQt or PySide... | Chuban/moose | gui/vtk/MeshRenderWidget.py | Python | lgpl-2.1 | 22,884 | [
"VTK"
] | 2b75837946ed239401d7fd6adf0215366878b507f1d070aa17dc75428835609e |
##
# Copyright 2012-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | pneerincx/easybuild-framework | test/framework/modules.py | Python | gpl-2.0 | 14,748 | [
"NetCDF"
] | 16d275301c49bad4f5726f1e6126018ff569e738fe4069fda81c2633be884258 |
"""
test views
"""
import datetime
import json
import re
import pytz
import ddt
import urlparse
from mock import patch, MagicMock
from nose.plugins.attrib import attr
from capa.tests.response_xml_factory import StringResponseXMLFactory
from courseware.courses import get_course_by_id
from courseware.tests.factories imp... | simbs/edx-platform | lms/djangoapps/ccx/tests/test_views.py | Python | agpl-3.0 | 39,324 | [
"VisIt"
] | b7fa4d397fd7647ce4f01065e3d481e5f03f11c70c3a218eec93649404dbd616 |
import re
import json
import requests
from functools import update_wrapper
from django import forms
from django.conf import settings
from django.views.generic import View
from django.core.urlresolvers import reverse
from django.http import HttpResponse, HttpResponseRedirect
from django.shortcuts import render
from djan... | getsentry/sentry-hipchat-ac | sentry_hipchat_ac/views.py | Python | apache-2.0 | 20,481 | [
"VisIt"
] | 80cd3407a893259f42b875ad521175263c9ada51b8e4d25507ee6209168aed9f |
import numpy as np
import scipy.sparse
from scipy.io.netcdf import NetCDFFile
from aston.trace.Trace import AstonFrame, AstonSeries
from aston.tracefile.TraceFile import TraceFile
class NetCDF(TraceFile):
ext = 'CDF'
mgc = '4344'
traces = ['#ms']
def total_trace(self, twin=None):
f = NetCDFFi... | molliewebb/aston | aston/tracefile/NetCDF.py | Python | gpl-3.0 | 3,291 | [
"NetCDF"
] | ddf456628d03ede5405e0611e3d1dfc1e8be62729e1536cea11e62c64d37c2d8 |
"""Model input/output tools."""
# (c) Copyright 2016 Andrew Dawson.
#
# 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 later version.
#
... | ajdawson/python_for_climate_scientists | course_content/barotropic-model/barotropic/io.py | Python | gpl-3.0 | 5,379 | [
"NetCDF"
] | 4f30d09899f0a5befe46910dfb95fdcb8b6a52cac6dd6d2ad6d85a19dffaef80 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
#
# This file is part of the NNGT project to generate and analyze
# neuronal networks and their activity.
# Copyright (C) 2015-2019 Tanguy Fardet
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | Silmathoron/NNGT | nngt/generation/mpi_connect.py | Python | gpl-3.0 | 13,750 | [
"Gaussian"
] | fa96913795309c31f713e3b5db0d2b5284e1e61c4b862d2ad7ff86acbe393fbe |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/qcdb/dashparam.py | Python | gpl-2.0 | 15,141 | [
"Psi4",
"TURBOMOLE"
] | f730a37090a286a977b263e26b0b2a557be4996e0e3fe1b8307d2557c4e23243 |
# creates: fcc100.png fcc110.png bcc100.png fcc111.png bcc110.png bcc111.png hcp0001.png fcc111o.png bcc110o.png bcc111o.png hcp0001o.png ontop-site.png hollow-site.png fcc-site.png hcp-site.png bridge-site.png
import os
from ase import *
from ase.lattice.surface import *
ortho = 'fcc100 fcc110 bcc100'.split()
hex = '... | freephys/python_ase | doc/ase/surface.py | Python | gpl-3.0 | 1,427 | [
"ASE"
] | a6616bb83721d01b3dc197b4ac9a6f0b55c62312461827d7d5c85f043fa9cc38 |
# -*- coding: utf-8 -*-
"""
Created on Sun Nov 9 00:06:24 2014
@author: kristian
"""
from skumleskogen import *
import time
################## OPTIONS ##################
debug_on = True
write_to_file = True
hukommelse = {}
sti_totalt = ["inn"]
noder_med_lås = set()
forrige_retning = []
file = None
try:
del ... | krissrex/python_projects | Projects/Oving10-itgk/main.py | Python | mit | 6,889 | [
"exciting"
] | 52c367741ae1c1f9abca2b74c37a3a252e437b35b5d1e837dce936f2fecb0374 |
"""
=======================================
Signal processing (:mod:`scipy.signal`)
=======================================
Convolution
===========
.. autosummary::
:toctree: generated/
convolve -- N-dimensional convolution.
correlate -- N-dimensional correlation.
fftconvolve --... | Eric89GXL/scipy | scipy/signal/__init__.py | Python | bsd-3-clause | 14,598 | [
"Gaussian"
] | 0088797b201f8093a3f9a4a3b4c450568f7ddc515da508266dbf9f75ef6f1cb6 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Daniel Strohmeier <daniel.strohmeier@tu-ilmenau.de>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import copy
import warnings
import numpy as np
from ..io.pick import pick_channels_cov
from ..forwar... | wronk/mne-python | mne/simulation/evoked.py | Python | bsd-3-clause | 4,699 | [
"Gaussian"
] | a371cb55eb292728f15aec4ecd2931d14cbf405a08f7b533b0a8726c4bc26635 |
import collections
import dataclasses
import random
import itertools
from . import machines
from . import syntax
from . import operations
from . import runs
from . import trees
__all__ = ['Grammar', 'from_grammar', 'to_grammar', 'any_parse', 'only_parse', 'all_parses']
class Grammar:
"""A string-rewriting grammar... | ND-CSE-30151/tock | tock/grammars.py | Python | mit | 26,741 | [
"VisIt"
] | 90427fe0cea0937f23b3b1011060f4a29a5e453e3430a4a997afc15f628b9736 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/interface_gcp.py | Python | gpl-2.0 | 11,924 | [
"Psi4"
] | 7fa7e70ebf3837b5b11c87b5882c33d5f343a15af15db6c8c1bd04de82461f08 |
from __future__ import annotations
from math import sqrt
import pytest
from scitbx import matrix
class Model:
def __init__(self, test_nave_model=False):
# Set up experimental models with regular geometry
from dxtbx.model import BeamFactory, DetectorFactory, GoniometerFactory
# Beam alo... | dials/dials | tests/algorithms/spot_prediction/test_stills_reflection_predictor.py | Python | bsd-3-clause | 5,664 | [
"CRYSTAL"
] | 1ba384583c6572eab4c61cf3cf41ded650d9daab4b792c35bc6fee9747ae5f3e |
import numpy as np
import scipy.signal
import torch
from math import ceil
from torch import nn as nn
# from .module import Module
from torch.nn import Parameter
from torch.nn import functional as F
from torch.nn.init import xavier_normal
from torch.nn.modules.utils import _pair
from torch.utils.data import DataLoader
f... | eywalker/attorch | attorch/layers.py | Python | mit | 46,852 | [
"Gaussian"
] | 6f24e064918f5bc9867c55beac5212258b538449d4bd091ab7cb90e246e20840 |
# (C) British Crown Copyright 2010 - 2014, Met Office
#
# This file is part of Iris.
#
# Iris 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 3 of the License, or
# (at your option) any l... | bblay/iris | lib/iris/tests/test_analysis.py | Python | gpl-3.0 | 54,747 | [
"NetCDF"
] | 95cd97cb8f55451f7cb81cd5ae76d6aaaaabb6d3ebf8f74d1135084c1090a7a8 |
#********************************************************************************
#
# 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)... | bpkeene/pythonPlayground | GUI_Template.py | Python | gpl-3.0 | 16,981 | [
"Brian"
] | 9a04f4af3fd76831a9c9d59223cd21bacc66d88968a40faba7b4c8f0e6965e21 |
#!/usr/bin/env python3
"""The influence of windowing of lin. sweep signals when using a
Kaiser Window by fixing beta (=7) and fade_in (=0).
fstart = 100 Hz
fstop = 5000 Hz
Deconvolution: Unwindowed
"""
import sys
sys.path.append('..')
import measurement_chain
import plotting
import calculation
import g... | spatialaudio/sweep | lin_sweep_kaiser_window_bandlimited_script6/lin_sweep_kaiser_window_bandlimited_script6_1.py | Python | mit | 2,208 | [
"DIRAC"
] | f70520af4434b7c59d8e628fbaa8c4be1dc30a3472d0a92a2ff748de63603937 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides so-called "strategies" to determine the coordination environments of an atom in a structure.
Some strategies can favour larger or smaller environments. Some strategies uniquely identifies the environm... | vorwerkc/pymatgen | pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py | Python | mit | 119,637 | [
"pymatgen"
] | 0ef3597b80699185706673541b720684b89d317f41844c36139be617a0632349 |
# Copyright (C) 2017 Zhixian MA <zxma_sjtu@qqq.com>
"""
A script to preprocess the raw data fetched from Chandra Data Archive (CDA)
The processing steps are as follows
1. Get field of view (FOV) from the fov1.fits file, the CCD_ID is set as 7 as the default
2. Get evt2_sub.fits by dmcopying from the evt2.fits accordi... | myinxd/cavdet | cnn/utils_pre.py | Python | mit | 8,416 | [
"Galaxy"
] | 652272d8f778f0c04b832a8f6ed2a5c9cabffcc6e213406ffc1a6d0f68f1fa91 |
# -*- 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-compute | tests/unit/gapic/compute_v1/test_region_health_checks.py | Python | apache-2.0 | 117,533 | [
"Octopus"
] | 8d3d42e96b0000f758784efdf96aeddf5f8055c264573c4646ef21a30f2be81c |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-cpu-normalization
# Author : Andrew McNab
########################################################################
"""
Determine Normalization for current CPU.
The main users of this script are the... | arrabito/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-cpu-normalization.py | Python | gpl-3.0 | 3,218 | [
"DIRAC"
] | 22ea9017512fe70da8c96d8d51cec56de0066bb29e5e9afe6d02a00a6a21e579 |
# Standard Library
from builtins import str
from builtins import range
import random
import string
# Third Party Stuff
from django.conf import settings
from django.contrib import messages, auth
from django.contrib.auth import authenticate, login, logout
from django.contrib.auth.decorators import login_required
from dj... | Spoken-tutorial/spoken-website | cms/views.py | Python | gpl-3.0 | 19,636 | [
"VisIt"
] | 4b0e6b93e66a79ac773bbca13224b057c7967cba0d2742ccc679085f47c1d395 |
"""Factor Analysis.
A latent linear variable model.
FactorAnalysis is similar to probabilistic PCA implemented by PCA.score
While PCA assumes Gaussian noise with the same variance for each
feature, the FactorAnalysis model assumes different variances for
each of them.
This implementation is based on David Barber's B... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/decomposition/factor_analysis.py | Python | gpl-2.0 | 11,946 | [
"Gaussian"
] | fec248df62649015a64123ee1b5c54d2ef3deb9d742f250ba2661629a5d39fdc |
#!/bin/env python
# -*- coding: utf-8 -*-
from Sire.IO import *
from Sire.System import *
from Sire.Mol import *
from Sire.MM import *
from Sire.FF import *
from Sire.CAS import *
from Sire.Maths import *
from Sire.Analysis import *
from Sire.System import *
from Sire.Base import *
from Sire.Units import *
import Sir... | michellab/Sire | wrapper/Tools/LSRC.py | Python | gpl-2.0 | 95,590 | [
"Amber"
] | 89bf70949025944ed05df8982742e0246e68a65f9ed7a4468c8bb590e68c3192 |
#
# 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... | pgandhi999/spark | python/pyspark/mllib/util.py | Python | apache-2.0 | 19,611 | [
"Gaussian"
] | e385176d62fc65e56e7bd61bdb93e36b7afab6826cf4fe2c2d19312287bd52e8 |
from osp.conf.settings import *
# Unique key used for salting passwords
SECRET_KEY = 'Chac-8#haCa_Ra-e?-e+ucrur=gEFRasejayasaC?meMe!AC-a'
# DEBUG should be False in production, True in development
DEBUG = True
# Expire session cookie when user quits the browser session if set
# to True. (This will also log the user ... | mariajosefrancolugo/osp | deploy/osp_settings.py | Python | lgpl-3.0 | 7,115 | [
"VisIt"
] | 0235d897dece5c4b93511fad6cbee43b0b5c714d99ec1e69c4923d800051c38b |
#!/usr/bin/env python
# generate Python Manifest for the OpenEmbedded build system
# (C) 2002-2010 Michael 'Mickey' Lauer <mlauer@vanille-media.de>
# (C) 2007 Jeremy Laine
# licensed under MIT, see COPYING.MIT
import os
import sys
import time
VERSION = "2.6.4"
__author__ = "Michael 'Mickey' Lauer <mlauer@vanille-me... | Martix/Eonos | contrib/python/generate-manifest-2.6.py | Python | mit | 14,988 | [
"VisIt"
] | a73697739c6238d76dc3b5af6e9edf9d451bee58e631dec53e0cc7a3406e511a |
""" Test class for JobWrapper
"""
# pylint: disable=protected-access, invalid-name
# imports
from __future__ import print_function
import unittest
import importlib
import os
import shutil
from mock import MagicMock, patch
from DIRAC import gLogger
from DIRAC.DataManagementSystem.Client.test.mock_DM import dm_mock
... | chaen/DIRAC | WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py | Python | gpl-3.0 | 4,284 | [
"DIRAC"
] | a54beaa6efd39dc712cf79428fd75f14986508106cf20aa2646b8472a984f374 |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" unit testing code f... | jandom/rdkit | rdkit/DataStructs/UnitTestcBitVect.py | Python | bsd-3-clause | 11,080 | [
"RDKit"
] | b565ec4c394087218c14fd7e530673e187ae99f9383cea4e70821e8dc8d4ec9a |
#! /usr/bin/python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner (modified by Florian Wilhelm)
* License: Public Domain
* Version: 0.8+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
Fo... | uwekamper/django-url-counter | versioneer.py | Python | bsd-3-clause | 28,459 | [
"Brian"
] | 21069e867ca5c260e43b39956455598f653a6c9df87264e68d85dc4cad7cafb0 |
# Copyright 2016-2017 Capital One Services, LLC
# Copyright The Cloud Custodian Authors.
# SPDX-License-Identifier: Apache-2.0
import csv
import json
import pickle
import os
import tempfile
import vcr
from urllib.request import urlopen
from .common import BaseTest, ACCOUNT_ID, Bag
from .test_s3 import destroyBucket
f... | capitalone/cloud-custodian | tests/test_resolver.py | Python | apache-2.0 | 6,910 | [
"Galaxy",
"MOOSE"
] | 22ab0e6ae9e8967490b68cbd16ebcb50be4cbca22c0c1d689d0fc50ce21eabf2 |
"""This source manages a VTK dataset given to it. When this source is
pickled or persisted, it saves the data given to it in the form of a
gzipped string.
"""
# Author: Prabhu Ramachandran <prabhu_r@users.sf.net>
# Copyright (c) 2005-2015, Enthought, Inc.
# License: BSD Style.
import sys
import os
import tempfile
# ... | dmsurti/mayavi | mayavi/sources/vtk_data_source.py | Python | bsd-3-clause | 14,464 | [
"Mayavi",
"VTK"
] | e05016dee60b3560d774b9902875ee4f48ed1aeec48e86a91a4692289e11249a |
#!/usr/bin/env python
"""
Start DIRAC component using runsvctrl utility
"""
__RCSID__ = "$Id$"
#
from DIRAC.Core.Base import Script
Script.disableCS()
Script.setUsageMessage( '\n'.join( [ __doc__.split( '\n' )[1],
'Usage:',
' %s [option|cfgfile]... | andresailer/DIRAC | FrameworkSystem/scripts/dirac-start-component.py | Python | gpl-3.0 | 1,220 | [
"DIRAC"
] | e3a599d82b9973e57f4c31d1f3db782341df51209b776492c2d0bf205e0c2844 |
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# 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.
#
#################################################################... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Restriction/RanaConfig.py | Python | gpl-2.0 | 3,025 | [
"Biopython"
] | 620a4bd957b0ccbe534ee3009e8bd5a81e88933f5d64b64ade9114fa2411fc1f |
#!/usr/bin/env python
import os
import shutil
import subprocess
import sys
from time import sleep
import json
from Bio import SeqIO
from store import update_job
def run_cmd(cmd, wdir=None, ignore_error=False):
"""
Run a command line command
Returns True or False based on the exit code
"""
if wdi... | combogenomics/contiguator-webapp | tasks.py | Python | mit | 11,579 | [
"BLAST"
] | af173c49af3250239bc2f62b95b80b32d1c765e632862c9d3573bee66daca018 |
"""
An object to register callbacks and dispatch event wiring mouse clicks
on a scene to picking.
"""
# ETS imports
from traits.api import HasTraits, Dict, Instance, \
Enum, Int, Callable, on_trait_change, List, Tuple, WeakRef
from mayavi.core.scene import Scene
from tvtk.api import tvtk
VTK_VERSION = ... | liulion/mayavi | mayavi/core/mouse_pick_dispatcher.py | Python | bsd-3-clause | 7,481 | [
"Mayavi",
"VTK"
] | 70b965c49f8f837e497a8af215cea30274ac943f9f6aaded4a05ed432f297867 |
import sys
import os
import pysam
import difflib
import gzip
import inspect
import tempfile
IS_PYTHON3 = sys.version_info[0] >= 3
if IS_PYTHON3:
from itertools import zip_longest
from urllib.request import urlopen
else:
from itertools import izip as zip_longest
from urllib2 import urlopen
if IS_PYTH... | bioinformed/pysam | tests/TestUtils.py | Python | mit | 4,775 | [
"pysam"
] | cb510ec94896daa01e939c5062f7dff0b570abb30a4319705e88843e1775c9cf |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015-2016 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
#... | NervanaSystems/deepspeech | speech/train.py | Python | apache-2.0 | 5,087 | [
"Gaussian"
] | 04a05bd509c83dcfc66c271e8c7bd923f0c102d325e3cba6507cd5374aabade6 |
# Copyright (C) 2013-2019 2ndQuadrant Ltd
#
# Client Utilities for Barman, Backup and Recovery Manager for PostgreSQL
#
# Barman 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,... | 2ndquadrant-it/barman-cli | tests/test_barman_wal_archive.py | Python | gpl-3.0 | 11,295 | [
"BWA"
] | c138a2758c9144713097792b8c86426ece30840b221770f96a2ed7d7c62cdd8f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the ... | pmghalvorsen/gramps_branch | gramps/gen/filters/rules/family/_hassourcecount.py | Python | gpl-2.0 | 1,808 | [
"Brian"
] | c2537af08d11fac59c433f7a6a7dc3e5b8ab0786a325aa0cfd484a46f5d08ae8 |
# Look at sdf_example.py in the examples/ directory for more detail
from sdfpy import load_sdf
from thingking import loadtxt
import vtk
import numpy as np
def dist(r1, r2):
d = r2-r1
return np.sqrt(np.dot(d,d))
def glyphMapper(pts, sclrs):
points = vtk.vtkPoints()
for pt in pts:
points.Insert... | ryanpbrewster/SciVis-2015 | src/animateHalo.py | Python | mit | 5,758 | [
"VTK"
] | d70f716febf0aee4f630334b1008015bb1de0d2e65dc4b8e5a00d25fc6ff1ceb |
import shutil
import os
import mdtraj as md
from openmoltools.utils import import_, enter_temp_directory, run_antechamber, create_ffxml_file
import logging
logger = logging.getLogger(__name__)
logging.basicConfig(level=logging.DEBUG, format="LOG: %(message)s")
# Note: We recommend having every function return *copie... | kyleabeauchamp/openmoltools | openmoltools/openeye.py | Python | gpl-2.0 | 14,737 | [
"MDTraj",
"OpenMM"
] | e0f20de4dc7b27a8fae71253500ada70c7f2f40c0cd93efffc9a76190c12d68f |
#
# ANNarchy - SimpleSTDP
#
# A simple model showing the STDP learning on a single neuron.
#
# Model adapted from Song, Miller and Abbott (2000) and Song and Abbott (2001)
#
# Code adapted from the Brian example: http://brian.readthedocs.org/en/1.4.1/examples-plasticity_STDP1.html
#
# authors: Helge Uelo Dink... | vitay/ANNarchy | examples/simple_stdp/SimpleSTDPModel.py | Python | gpl-2.0 | 2,208 | [
"Brian",
"NEURON"
] | 1150762d1f6f440455fcb27c2afe528146c8141ad2e3188d93784bbaec7bc660 |
import mimetypes
import re
from optparse import make_option
from urllib.parse import urlparse
from . import InventoryCommand
from inventory.models import Dataset, Distribution
mimetypes.init()
class Command(InventoryCommand):
help = 'Normalizes property values'
option_list = InventoryCommand.option_list + ... | opennorth/inventory | inventory/management/commands/normalize.py | Python | mit | 42,922 | [
"NetCDF"
] | f47f70b3ffec72a4daa6559df4abdb9b6c278c1af384f844cc162e4047f59d24 |
"""A setuptools based setup module"""
#Always prefer setuptools over distutils
from setuptools import setup, find_packages
#To use a consistent encoding
from codecs import open
from os import path,system
here = path.abspath(path.dirname(__file__))
#Get the long description from the README file
with open(path.join(he... | thekerrlab/netpyne | setup.py | Python | mit | 4,303 | [
"NEURON"
] | 496b3399fb75238ce5f82a7c5b323a0e1e7a95f7bf86b9ff9dd1791e1299c8ce |
'''
@author: Victor Barrera
Description: This scripts makes use of the siq module to obtain the methylation value for each CpG island region.
'''
import sys
import pysam
import re
from siq import *
# Obtain the CpG island sequence file,
# the sam-file and the minimum read filter
cpgi_sec_path=sys.argv[1]
sam_path=sys... | vbarrera/thesis | Genomic_Evaluation_of_individual_CpG_Methylation/Python/CpGMethStatus.py | Python | gpl-2.0 | 1,440 | [
"pysam"
] | 1ffe6fb97d08294bd08ff7e4a458dd0585d0aef2e42fe2ca6bc8264c9af88049 |
__author__ = 'mjsul_000'
import pysam
import sys
import subprocess
class variation:
def __init__(self, chrom, pos, ref, alt, qual):
self.chrom = chrom
self.pos = int(pos)
self.ref = ref
self.alt = alt
self.qual = qual
def groupflow(samfile, vcffile, outfile, minreadsvar=... | mjsull/HapFlow | groupFlows.py | Python | gpl-3.0 | 20,669 | [
"pysam"
] | 57588c3efe89ec2969cf4b146d51f2ab5e797b0094ecdd4eb37ab40ebabe8581 |
#!/usr/bin/env python
#
# Copyright (C) 2014
# Brian Caswell <bmc@lungetech.com>
# Narf Industries <info@narfindustries.com>
#
# 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 res... | f0rki/cb-multios | original-challenges/SIGSEGV/support/old/overflow/overflow.py | Python | mit | 2,207 | [
"Brian"
] | 26621007550e2eb821be519e90be2f6069f74c6fba7efb6a75242bedad8d5c33 |
#!/usr/bin/env python
from __future__ import print_function
import json
import optparse
import os.path
import sys
from load_db import create_table
from query_db import describe_tables, get_connection, run_query
"""
JSON config:
{ tables : [
{ file_path : '/home/galaxy/dataset_101.dat',
table_name :... | mvdbeek/tools-iuc | tools/query_tabular/query_tabular.py | Python | mit | 6,993 | [
"Galaxy"
] | c24193d131f5fe947cd1abe7931b00502ae01339a92f0821946968f53ee4e936 |
"""
Note Snatcher: a simple notes organizer
Copyright (C) 2015 Brian Ratliff
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 later version.
... | brianratliff/notesnatcher | edittags.py | Python | gpl-3.0 | 8,588 | [
"Brian"
] | ca20105984e9fe509aa94cea8129044d6afdf78dde65dfe76dab2f3eb0fe9eb9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
cc_plugin_ncei/ncei_point.py
'''
from compliance_checker.base import BaseCheck
from cc_plugin_ncei.ncei_base import TestCtx, NCEI1_1Check, NCEI2_0Check
from cc_plugin_ncei import util
class NCEIPointBase(BaseCheck):
_cc_spec = 'ncei-point'
valid_feature_types... | ioos/cc-plugin-ncei | cc_plugin_ncei/ncei_point.py | Python | apache-2.0 | 5,599 | [
"NetCDF"
] | 2230c5358120be66eeca7c2d8ba28a1e32990b522624cbe85ad6cd8b9029cc3e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <briancoca+ansible@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_ve... | hryamzik/ansible | lib/ansible/modules/system/debconf.py | Python | gpl-3.0 | 5,176 | [
"Brian"
] | dd1562be5e78105b1c5e7607acb58aed674947f055fd2d4f6958ea9d161c6fa5 |
import utils
import numpy as np
from scipy import ndimage
from matplotlib import pylab as plt
from PIL import Image
import cv2
#TODO: Load image into an array
raw_img = np.fromfile('LENA256.RAW', dtype=np.uint8, sep="")
img_array = raw_img.reshape((256, 256))
Image.fromarray(img_array).save('Lena.jpg')
# raw_img = np.... | mrnameless123/advance-image-processing-class | main.py | Python | gpl-3.0 | 2,561 | [
"Gaussian"
] | 6acaa1dad3cd91020ebd7c75f5e6ed9cfb2eb3b3fbef81649ef7f248e6e553b5 |
import binascii
import copy
import json
import re
from base64 import b64encode
import django.core.exceptions
from captcha.audio import AudioCaptcha
from captcha.image import ImageCaptcha
from django.contrib.auth.password_validation import validate_password
from django.core.validators import MinValueValidator
from djan... | desec-io/desec-stack | api/desecapi/serializers.py | Python | mit | 34,993 | [
"TINKER"
] | e8278ba3d175da5dc3afcf18e1756e9275a558689635f8bc2aaf532b1a1f249c |
""" Threaded implementation of services
"""
import os
import time
import re
import threading
import zipfile
import zlib
import DIRAC
from DIRAC.Core.Utilities.File import mkDir
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData, ConfigurationData
from DIRAC.ConfigurationSystem.private.R... | Andrew-McNab-UK/DIRAC | ConfigurationSystem/private/ServiceInterface.py | Python | gpl-3.0 | 11,836 | [
"DIRAC"
] | 36ebe85400fc2d618b00452344bf7eb45b7ab1b53f09d387840d40aa4dcf4e00 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# In this example, an image is centered at (0,0,0) before a
# rotation is applied to ensure that the rotation occurs about
# the center of the image.
reader = vtk.vtkPNGReader()
reade... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestChangeInformation.py | Python | gpl-3.0 | 1,250 | [
"VTK"
] | 5413b2c04a2c14f3114a023653def1f15dbf8f6a7c800fd1511b946325d482bf |
#!/usr/bin/python
#----------------------------------------------------------------------------#
# #
# ozz-animation is hosted at http://github.com/guillaumeblanc/ozz-animation #
# and distributed under the MIT License (MIT). ... | mgdesign-fr/ozz-animation | build-helper.py | Python | mit | 12,126 | [
"VisIt"
] | bf09c97f5e68794a4babfd08ad46af27442652c4ba80c976ee93ab42f7e42a7a |
# coding=utf-8
# main codes, call functions at stokes_flow.py
# Zhang Ji, 20160410
import sys
import petsc4py
petsc4py.init(sys.argv)
# import warnings
# from memory_profiler import profile
import numpy as np
from src import stokes_flow as sf
# import stokes_flow as sf
from src.stokes_flow import problem_dic, obj_dic... | pcmagic/stokes_flow | sphere/sphere_rs.py | Python | mit | 20,947 | [
"VTK"
] | c716593bae7d3dcbce5cd7f319815d73575934d88edb9fe7a9fb0669bb275902 |
import numpy as np
import numbers
from scipy import sparse
from scipy import linalg
import scipy.sparse.linalg as spla
from mesh import Vertex, Interval, HalfEdge, QuadCell, convert_to_array
from function import Map, Nodal, Constant
from fem import parse_derivative_info, Basis
from inspect import signature
import... | hvanwyk/quadmesh | src/assembler.py | Python | mit | 130,191 | [
"Gaussian"
] | dd6099fa0c8e9c528d1c5c186d8fee1493d41d66328888a36e9234f4ce8f62ee |
"""
Acceptance tests for Studio related to the split_test module.
"""
import math
from unittest import skip
from nose.plugins.attrib import attr
from selenium.webdriver.support.ui import Select
from xmodule.partitions.partitions import Group
from bok_choy.promise import Promise, EmptyPromise
from common.test.accepta... | naresh21/synergetics-edx-platform | common/test/acceptance/tests/studio/test_studio_split_test.py | Python | agpl-3.0 | 48,100 | [
"VisIt"
] | ff07317907d6e5d73cdff00b97bae6b23dd5042539e0594cc3be2becbdd5e603 |
# encoding: utf-8
"""
Global exception classes for IPython.core.
Authors:
* Brian Granger
* Fernando Perez
* Min Ragan-Kelley
Notes
-----
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008 The IPython Development Team
#
# Distributed under the terms of the BSD ... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/core/error.py | Python | apache-2.0 | 1,534 | [
"Brian"
] | f31631b6fb92fc48903c15cab018edec5901f6447567ec5ddadcfe7ac13e9c8d |
#!/usr/bin/env python
#
# Copyright 2013 by Leighton Pritchard. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
""" Tests for general functionality of the KGML parser and pathwa... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_KGML_nographics.py | Python | gpl-2.0 | 4,772 | [
"Biopython"
] | 4a6974415ec35d44f61fa5c96ca343c551956e566187f7ef856fc9884496d969 |
#!/usr/bin/env python
"""
@package ion.processes.event
@file ion/processes/event/notification_sent_scanner.py
@author Brian McKenna <bmckenna@asascience.com>
@brief NotificationSentScanner plugin. An EventPersister plugin scanning for, and keeping state(count) of, NotificationEvent's
"""
import time
from datetime imp... | ooici/coi-services | ion/processes/event/notification_sent_scanner.py | Python | bsd-2-clause | 5,398 | [
"Brian"
] | 19f31ec03366bdc1cf0179c071a17efe12dcb73b55a872b2140bd98eb6e4ca3a |
"""
Numerical python functions written for compatability with matlab(TM)
commands with the same names.
Matlab(TM) compatible functions
-------------------------------
:func:`cohere`
Coherence (normalized cross spectral density)
:func:`csd`
Cross spectral density uing Welch's average periodogram
:func:`detrend`... | runt18/nupic | external/linux32/lib/python2.6/site-packages/matplotlib/mlab.py | Python | agpl-3.0 | 104,342 | [
"Gaussian"
] | 3c42a5b83fec48b1027ac64484c9244ad5fa5c19afdf2ed424141ccd25064bf8 |
# -*- coding: utf-8 -*-
"""
This file is a part of python_translate package
(c) Adam Zieliński <adam@symfony2.guru>
For the full copyright and license information, please view the LICENSE and LICENSE_SYMFONY_TRANSLATION
files that were distributed with this source code.
"""
import ast
import codegen
from python_trans... | adamziel/python_translate | python_translate/extractors/python.py | Python | mit | 6,128 | [
"VisIt"
] | dbef96b9142ab48ec0602f32a13df96c10a2e9ca9d665c114d10e025ad72f6b6 |
# -*- coding: UTF-8 -*-
"""
``blast_old`` :sup:`*` - Old module. Use ``blast`` instead
-----------------------------------------------------------------
:Authors: Menachem Sklarz
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
A class... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/main_NSF_classes/searching/blast_old.py | Python | gpl-3.0 | 16,504 | [
"BLAST"
] | 982d113465149c664a62c965ab2c2cace54147a7d31d25debea65b8fad6b122f |
"""
Routines for handling 'Projects' in Python.
"""
import ast
import imp
import os
import sys
import tarfile
import token
import traceback
from ConfigParser import SafeConfigParser
from cStringIO import StringIO
from threading import RLock
from tokenize import generate_tokens
# from pkg_resources import get_distribu... | DailyActie/Surrogate-Model | 01-codes/OpenMDAO-Framework-dev/openmdao.main/src/openmdao/main/project.py | Python | mit | 23,432 | [
"VisIt"
] | 4598782f5dd96e2632cbe272283bc0a28d3becbfcc5399998c8463a2419ed85d |
# coding: utf-8
# # Using Python to Access NEXRAD Level 2 Data from Unidata THREDDS Server
# This is a modified version of Ryan May's notebook here:
# http://nbviewer.jupyter.org/gist/dopplershift/356f2e14832e9b676207
#
# The TDS provides a mechanism to query for available data files, as well as provides access to ... | rsignell-usgs/notebook | NEXRAD/THREDDS_NEXRAD.py | Python | mit | 7,648 | [
"NetCDF"
] | 054bdae1152bffe46aa135246a5de2c1e4652994519ec75b7fcf373a5acba153 |
"""
Utilities to create replication transformations
"""
from DIRAC.TransformationSystem.Client.Transformation import Transformation
from DIRAC.TransformationSystem.Client.TransformationClient import TransformationClient
from DIRAC import gLogger, S_OK, S_ERROR
def createDataTransformation(flavour, targetSE, sourceSE... | arrabito/DIRAC | TransformationSystem/Utilities/ReplicationTransformation.py | Python | gpl-3.0 | 3,648 | [
"DIRAC"
] | c4021ccac66445a3c797034750b4e2b069fbfca6358656e23212292ba66f5b2b |
"""
select
"""
from __future__ import absolute_import, division, print_function, unicode_literals
import logging
from PySide import QtGui
from mcedit2.editortools import EditorTool
from mcedit2.util.bresenham import bresenham
from mcedit2.util.load_ui import load_ui
log = logging.getLogger(__name__)
class Sel... | Rubisk/mcedit2 | src/mcedit2/editortools/select_entity.py | Python | bsd-3-clause | 3,391 | [
"VisIt"
] | 4e4d3544924c5be4eb86232d5455e00b0c6d084bf51101d1ac01b620f136f107 |
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