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# -*- coding: utf-8 -*-
"""This file contains a parser for the Mozilla Firefox history."""
import sqlite3
from plaso.events import time_events
from plaso.lib import event
from plaso.lib import eventdata
from plaso.parsers import sqlite
from plaso.parsers.sqlite_plugins import interface
# Check SQlite version, bail ... | jorik041/plaso | plaso/parsers/sqlite_plugins/firefox.py | Python | apache-2.0 | 15,322 | [
"VisIt"
] | ca9a9a55d281cfc86b4f22c18e2ce9bd125499d30588f20236c008f1f7bf1a42 |
#
# Copyright 2011-2013 Blender Foundation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... | Passtechsoft/TPEAlpGen | blender/intern/cycles/blender/addon/properties.py | Python | gpl-3.0 | 41,098 | [
"Gaussian"
] | 7dc65d27c9e51d41fcf8ed51f19d5212d046adef84898342eaa9296a4acffa4f |
#!/usr/bin/env python
from pymatgen.core.periodic_table import all_symbols, Element
import urllib
def get_nist_data(element):
url = "http://physics.nist.gov/cgi-bin/Elements/elInfo.pl?element=%d&context=text"
lines = urllib.urlopen(url % element.Z).read().split('\n')
data = {}
for line in lines:
... | ldamewood/figures | scripts/periodic_table.py | Python | mit | 591 | [
"pymatgen"
] | 6583a2c309b7def7926557e83ed6aa209a98de8d8e904b0e71f42d4e195e188e |
import os
import unittest
import numpy as np
import tensorflow as tf
from pymatgen.core import Structure
from megnet.data.crystal import (CrystalGraph, CrystalGraphDisordered,
CrystalGraphWithBondTypes,
get_elemental_embeddings)
from megnet.data.graph ... | materialsvirtuallab/megnet | megnet/data/tests/test_crystal.py | Python | bsd-3-clause | 3,152 | [
"CRYSTAL",
"pymatgen"
] | 6159716b7b6dbaea7ba8b40381f3aa29a2a064b025d8ac79e438b774b52b1bb6 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/network_comparison_response.py | Python | apache-2.0 | 13,134 | [
"VisIt"
] | b043509fde9fb0751a3951ed5f557ea9482b9abe11a420930a12369615b6a7b3 |
from paraview.simple import *
import os
import sys
import numpy as np
path = os.getcwd() + "/"
file_name = sys.argv[1] + ".e"
csv_name = sys.argv[2] + ".csv"
offset = int(sys.argv[3])
reader = ExodusIIReader(FileName=path+file_name)
tsteps = reader.TimestepValues
writer = CreateWriter(path + csv_name , reader)
write... | jhaase1/zapdos | problems/Schottky_emission/transient/no_ballast/parametric/extra/toCSV2.py | Python | lgpl-2.1 | 556 | [
"ParaView"
] | 181f3e22acac6b89e9e63d9e5b62cad009420b54ffaf6cfb1f37e8d3b27a090c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''
Python wrapper for librfn.
Copyright © 2015 Thomas Unterthiner
Licensed under GPL, version 2 or a later (see LICENSE.txt)
'''
import os
import time
import ctypes as ct
import numpy as np
import matplotlib.pyplot as plt
import warnings
import sys
if sys.version_info < (... | Tamme/mutationalsignaturesNCSUT | RFN/rfn.py | Python | gpl-3.0 | 6,855 | [
"Gaussian"
] | 5718f824aff26a5d224e12a45e2c03e3a1ecf28b9395cb04770c5cdd2a2c5e1e |
#
# 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 | tests/textcode/test_strings.py | Python | apache-2.0 | 6,592 | [
"VisIt"
] | 6e28dde27faaf71a7f92ecaa63fffa9857479d9f75433bec1f3a6652f870974f |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vt... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/clipPyramid.py | Python | bsd-3-clause | 5,443 | [
"VTK"
] | 401f1ab7fb4ee13253300c517da40edc2fd332e689dea186fa7a2a146f9202ba |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2007-2009 Gary Burton <gary.burton@zen.co.uk>
# Copyright (C) 2007-2009 Stephane Charet... | sam-m888/gramps | gramps/plugins/webreport/family.py | Python | gpl-2.0 | 17,542 | [
"Brian"
] | a9f9e878907d0975cb517b64e9581e5ad86719ce6f257aec17c9529236bb030b |
import sys
sys.path.append('../../../vmdgadgets')
import vmdutil
from vmdutil import vmddef
def avoid_collision1(vmd):
center = vmdutil.str_to_b('センター')
right_arm = vmdutil.str_to_b('右腕')
right_elb = vmdutil.str_to_b('右ひじ')
#1032 追加
c_1032 = vmddef.BONE_SAMPLE._replace(
frame=1032, name=cen... | Hashi4/vmdgadgets | sample/lookat/sm31942771/minor_adjust.py | Python | apache-2.0 | 4,178 | [
"VMD"
] | e6f427f2f96cfb783dca861a4911f4d7dac803c44ecc7b8f74cdc9d64a6d7a8c |
# Bioclimatic Chart
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Abraham Yezioro <ayez@ar.technion.ac.il>
# Ladybug is free software; you can redistribute it and/or modify
# it under the terms of the GN... | samuto/ladybug | src/Ladybug_Bioclimatic Chart.py | Python | gpl-3.0 | 83,572 | [
"EPW"
] | d5297a84bdbcd32351192cc05792514e7eb1b4c66aafed5f2374085ad89bd787 |
''' Generate a reference for alignment
This |spi| batch file (`spi-reference`) generates a properly filtered and scaled reference for alignment.
Tips
====
#. The volumes do not have to be in SPIDER format (automatic conversion is attempted). However,
:option:`--data-ext` must be used to set the appropriate SPI... | ezralanglois/arachnid | arachnid/pyspider/reference.py | Python | gpl-2.0 | 12,115 | [
"Gaussian"
] | 41b50b4f1e6ff1db61380ae79148848a97deea1fccfde85675aa5543a74e82d9 |
from django.core.management.base import BaseCommand
from django.conf import settings
from django.db import connection
from collections import defaultdict
import os
from datetime import datetime, timedelta
from common.utils import Date
from schools.models import (
School, Boundary)
from stories.models import (
... | klpdotorg/dubdubdub | apps/stories/management/commands/generate_sms_report.py | Python | mit | 17,179 | [
"VisIt"
] | 83df2da148cdcc76c6934db4db7a78e3d77c4744acaa37183458c0055648644c |
# -*- coding: utf-8 -*-
import datetime
import json
import os
import shutil
from django.conf import settings
from django.core.files.storage import default_storage as storage
from django.core.urlresolvers import reverse
import mock
from nose.tools import eq_, ok_
from pyquery import PyQuery as pq
import mkt
from mkt.... | clouserw/zamboni | mkt/submit/tests/test_views.py | Python | bsd-3-clause | 38,827 | [
"exciting"
] | 89680f2bc0bfa2390c2cc11fb41dde7482ac00133ec85f5a0e8e60bc9b6a81db |
# -*- coding: utf-8 -*-
# Copyright (C) 2017 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., University of Heidelberg, and University of
# of Connecticut School of Medicine.
# All rights reserved.
# Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
# Properties, Inc., Universit... | jonasfoe/COPASI | copasi/bindings/python/unittests/Test_CCopasiObjectName.py | Python | artistic-2.0 | 2,523 | [
"COPASI"
] | dffc6ec29610bd8e4b7a478cf45e0fb99079699449c41a1860d9551bf6f891ec |
"""
This script is used to design the design matrix for our linear regression.
We explore the influence of linear and quadratic drifts on the model
performance.
Script for the filtered data.
Run with:
python noise-pca_filtered_script.py
from this directory
"""
from __future__ import print_function, division
im... | ye-zhi/project-epsilon | code/utils/scripts/noise-pca_filtered_script.py | Python | bsd-3-clause | 14,797 | [
"Gaussian"
] | f0d1e48df3e76da2a0962f1c74316d73f5d5be5f6d8943249bdc2506016cb5a9 |
# -*- coding: utf-8 -*-
"""
Django settings for echo_seeds project.
For more information on this file, see
https://docs.djangoproject.com/en/dev/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/dev/ref/settings/
"""
# Build paths inside the project like this: os.... | briandant/echo-seeds | echo_seeds/config/common.py | Python | bsd-3-clause | 8,943 | [
"Brian"
] | 42827adf9252966a4499a04cf6e79c62ab57205c89e3193f4a95521fc5143668 |
'''
Created on 2013 mai 24
@author: peio
'''
import subprocess
import os
from tempfile import NamedTemporaryFile
from Bio import SeqIO
from Bio.Seq import Seq
class IsIndelError(Exception):
pass
class OutsideAlignment(Exception):
pass
class BetweenSegments(Exception):
pass
class SeqCoords(object):... | JoseBlanca/vcf_crumbs | vcf_crumbs/prot_change.py | Python | gpl-3.0 | 10,257 | [
"Biopython"
] | 8c29496d60888c492918b0c445988a7b9e2312fde71b5b2a4f91e3d928bf4613 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be use... | tikan/rmock | tests/func_tests/test_start_stop_server.py | Python | lgpl-3.0 | 2,709 | [
"VisIt"
] | 5d5e364665ba28fb04c2a44dc9380028a3321b1518b04abdced864f067c364c4 |
from __pyosshell__ import *
from __molecules__ import *
from __qmshell__ import *
import xml.dom.minidom as xml
def WriteSystemXml(name,gro,xyz,xml = 'system.xml'):
mol = SingleMoleculeFromGro(gro)[0]
mol.fragment()
mol.make_dict()
mol.name = name
es,xyz = e_xyz_from_xyz(xyz)
# CHECK CONGRUENCY
for atm, e, x... | 12AngryMen/votca-scripts | lib/Carlstuff/evaporation/__votca_ctp__.py | Python | apache-2.0 | 23,221 | [
"Gaussian"
] | 52b91164c7c466df916cf53ee1f549e982f6ef7a8cde3acae2622c5e9469d6c3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This file is part of the SPORCO package. Details of the copyright
# and user license can be found in the 'LICENSE.txt' file distributed
# with the package.
"""
Greyscale ℓ2-TV Denoising
=========================
This example demonstrates the use of class :class:`.tvl2.T... | bwohlberg/sporco | examples/scripts/tv/tvl2den_gry.py | Python | bsd-3-clause | 2,718 | [
"Gaussian"
] | dd5f2ea877bcf4bcd0a9b9935b105fec3713ba3fc6f2a7ffe73e870ee7d4b81b |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. currentmodule:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules.
.. seealso::
`scipy.special.cython_s... | lhilt/scipy | scipy/special/__init__.py | Python | bsd-3-clause | 27,314 | [
"Gaussian"
] | 71865e408e75c70ba5a3658eac5517bdaa7e4ef301505432d93c28c4b38b7dd4 |
"""
Open Babel utilities.
"""
__author__ = "Steven Kearnes"
__copyright__ = "Copyright 2014, Stanford University"
__license__ = "BSD 3-clause"
from StringIO import StringIO
import subprocess
from rdkit import Chem
from rdkit_utils import serial
from vs_utils.utils import image_utils
class Ionizer(object):
"""... | rbharath/pande-gas | vs_utils/utils/ob_utils.py | Python | bsd-3-clause | 4,834 | [
"Open Babel",
"RDKit"
] | e0c2dbec2eb9e40fe9f43b3b54cf53e8768eb2988e17eae8d78a8351cf19bdfc |
from Bio.PDB import Selection, PDBParser
from Bio.PDB.NeighborSearch import NeighborSearch
from contactnetwork.interaction import *
from contactnetwork.pdb import *
from contactnetwork.models import *
from io import StringIO
from protein.models import ProteinConformation
from structure.models import Structure
from ... | cmunk/protwis | contactnetwork/cube.py | Python | apache-2.0 | 12,696 | [
"Biopython"
] | 4cecb3b1d09475a204c68ae11aa770feafd518015286425279885a8d01c6c7aa |
# 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... | xodus7/tensorflow | tensorflow/python/autograph/pyct/static_analysis/activity.py | Python | apache-2.0 | 13,600 | [
"VisIt"
] | 2303cce48ac2557d8e6ffddae22226d8deb1b76717431a033c1e8d38f6dace86 |
# Copyright 2018 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... | mlperf/training_results_v0.7 | Google/benchmarks/transformer/implementations/transformer-research-TF-tpu-v4-512/lingvo/core/layers_with_attention.py | Python | apache-2.0 | 85,989 | [
"Gaussian"
] | d352f3c32233430ddd270f727fbc142f7e9898ee0e9cb178bcf82e3b0c4b8c02 |
from rpython.rtyper.lltypesystem.lltype import (Struct, Array, FixedSizeArray,
FuncType, typeOf, GcStruct, GcArray, RttiStruct, ContainerType, parentlink,
Void, OpaqueType, Float, RuntimeTypeInfo, getRuntimeTypeInfo, Char,
_subarray)
from rpython.rtyper.lltypesystem import llmemory, llgroup
from rpython.tra... | jptomo/rpython-lang-scheme | rpython/translator/c/node.py | Python | mit | 38,642 | [
"VisIt"
] | 7984dc11df831622fbc5d28abd37adf2c6db3e47490067da6639c794f24f01fb |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ... | francisco-dlp/hyperspy | hyperspy/tests/signal/test_eels.py | Python | gpl-3.0 | 10,558 | [
"Gaussian"
] | 4fd0cba058d49f29d4ac51b1dd3837d47e84347c1cda1f9e3d0037ab7536228f |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | espressomd/espresso | testsuite/python/cellsystem.py | Python | gpl-3.0 | 1,941 | [
"ESPResSo"
] | 7f45545cd59fae170b5ce4ad29b8f78d5c7698bfc55f6c617e9aef324e327f7a |
# -*- coding: utf-8 -*-
"""Single-dipole functions and classes."""
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
from copy import deepcopy
from functools import partial
import re
import numpy as np
from scipy impor... | adykstra/mne-python | mne/dipole.py | Python | bsd-3-clause | 52,898 | [
"Mayavi"
] | b1fc1c2f003eb97d49a2bc7568fb87001d0038b3e9e20bbd9fda08d365cf1652 |
import os
from zombie.compat import TestCase, PY3
if PY3:
from socketserver import UnixStreamServer, StreamRequestHandler
else:
from SocketServer import UnixStreamServer, StreamRequestHandler
import threading
try:
from json import loads, dumps
except ImportError:
from simplejson import loads, dumps # ... | ryanpetrello/python-zombie | zombie/tests/test_client.py | Python | mit | 4,899 | [
"VisIt"
] | 6c96dc371589a9a91ace524710452d1901d6b1a388e32c67b3e7fca035394c00 |
import os, re, time, shutil, json
import dendropy
from seq_util import *
from date_util import *
from virus_stability import virus_stability
import rethinkdb as r
import hashlib
class tree_stability(object):
'''
Goes back through all virus objects, looks up their calculated ddg from outgroup. Virus_stability d... | blab/stability | augur/src/tree_stability.py | Python | agpl-3.0 | 9,594 | [
"FoldX"
] | 84d17a0778b46ef46814c02e3222a246bf8199549cbb5585119da79f8b754966 |
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
import logging
allcg = AllCoordinationGeometries()
lgf = LocalGeometryFinder()
logging.basi... | vorwerkc/pymatgen | dev_scripts/chemenv/check_new_coordination_geometry.py | Python | mit | 1,080 | [
"pymatgen"
] | 61324ec0868dc3327548e00ff91917d2c825a1606235ca217fb8b4554450edef |
# iCraft is Copyright 2010 both
#
# The Archives team:
# <Adam Guy> adam@adam-guy.com AKA "Adam01"
# <Andrew Godwin> andrew@aeracode.org AKA "Aera"
# <Dylan Lukes> lukes.dylan@gmail.com AKA "revenant"
# <Gareth Coles> colesgareth2@hotmail.com... | TheArchives/Nexus | core/entities/mrt.py | Python | bsd-2-clause | 6,657 | [
"Brian",
"VisIt"
] | 3b1bba3c13e793c6e5563b2005d000f13fc058ac8b5649fc4a1dca7d10a6636e |
import logging
import numpy as np
import pytest
import nengo
from neurons import AdaptiveLIF
from nengo.utils.numpy import rms
logger = logging.getLogger(__name__)
def test_alif_neuron(Simulator, plt):
"""Test that the adaptive LIF dynamic model matches the predicted rates
Tests a single neuron across mult... | fragapanagos/adaptive_lif | test_neurons.py | Python | mit | 4,689 | [
"NEURON"
] | 61fd7ea29d30cd592336e88f1e5a28fb634af9925224b17dad1037c93ebab373 |
'''
Utilities for tests.
'''
from six.moves import zip
import numpy as np
import astropy.units as u
from astropy.io import fits
from astropy.utils import NumpyRNGContext
from ..spectral_cube import SpectralCube
def generate_header(pixel_scale, spec_scale, beamfwhm, imshape, v0):
header = {'CDELT1': -(pixel_s... | jzuhone/spectral-cube | spectral_cube/tests/utilities.py | Python | bsd-3-clause | 3,524 | [
"Gaussian"
] | 6d09cbf3e4ba26802982a45ca57165d030031faa217f1f064f2f63a94123b8f9 |
# -*- coding: utf-8 -*-
import sys
import math
from pylab import *
try:
import moose
except ImportError:
print("ERROR: Could not import moose. Please add the directory containing moose.py in your PYTHONPATH")
import sys
sys.exit(1)
from moose.utils import * # for BSplineFill
class GluSyn_STG(moose.... | BhallaLab/moose-examples | neuroml/lobster_pyloric/synapses/GluSyn_STG.py | Python | gpl-2.0 | 2,442 | [
"MOOSE"
] | ff0527035c1c8792577135dbc240a535b1e9ca1caf42b3688ca332d57931ec20 |
from __future__ import absolute_import
from __future__ import unicode_literals
import logging
from functools import reduce
from docker.errors import APIError
from docker.errors import NotFound
from .config import ConfigurationError
from .config import get_service_name_from_net
from .const import DEFAULT_TIMEOUT
from... | KevinGreene/compose | compose/project.py | Python | apache-2.0 | 15,116 | [
"VisIt"
] | 0006bdd5fdd8e867a83f2775a64d0c2a5d27d3f71e621972605b2428f7cf4e90 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/xianci/xianci.py | Python | apache-2.0 | 4,002 | [
"PySCF"
] | 091062fc180987ef85ef47efd59ab97233a2d70c8439f5f2f12bbfbfc1c8b062 |
#!/usr/bin/env python
"""
roms.interp
Methods to interpolate ROMS fields onto other grids
Written by Brian Powell on 11/02/13
Copyright (c)2017 University of Hawaii under the MIT-License.
"""
import numpy as np
import netCDF4
import os
import seapy
from seapy.timeout import timeout, TimeoutError
from joblib... | ocefpaf/seapy | seapy/roms/interp.py | Python | mit | 33,035 | [
"Brian",
"NetCDF"
] | faafebeaa7636f81d7470c62753635fb0dfc1df26189ada9c4cc4785a0f302eb |
#!/usr/bin/env python
import os
import urllib2
import gzip
import time
import numpy as np
import pandas as pd
from itertools import izip
from StringIO import StringIO
from collections import defaultdict
from biom import Table
from lxml import etree
from skbio.parse.sequences import parse_fastq, parse_fasta
import ... | biocore/American-Gut | americangut/util.py | Python | bsd-3-clause | 19,771 | [
"ADF"
] | 8f43ed4341aeab17ee4c53826fd3966a9031df9568e91ed8b6a5c33db120b58e |
"""Tests of tools for setting up interactive IPython sessions."""
import ast
from diofant.interactive.session import IntegerDivisionWrapper
__all__ = ()
def test_IntegerDivisionWrapper():
tree = ast.parse('1/3')
tree2 = ast.parse('Rational(1, 3)')
dump = ast.dump(tree2)
tree_new = IntegerDivisionW... | skirpichev/omg | diofant/tests/interactive/test_ipython.py | Python | bsd-3-clause | 1,238 | [
"VisIt"
] | 9e66c0d3a58953e499b61adbce6228534d8f4470c51e2b23ea2540c3c8955500 |
"""
@name: PyHouse/src/Modules/Computer/Communication/_test/test_communication.py
@author: D. Brian Kimmel
@contact: d.briankimmel@gmail.com
@copyright: 2016-2017 by D. Brian Kimmel
@date: Created on May 30, 2016
@licencse: MIT License
@summary:
Passed all 5 tests - DBK - 2017-01-19
"""
__updat... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Communication/_test/test_communication.py | Python | mit | 2,303 | [
"Brian"
] | 5b0b05bc5329e0372bede08633bff5321077805b40761e19c3c3f0a299ad5c2c |
from future import standard_library
standard_library.install_aliases()
import sst
import sst.actions
from urllib.parse import urlparse
sst.actions.set_base_url('http://localhost:%s/' % sst.DEVSERVER_PORT)
# haven't visited a url yet, so all assert_url* fail
sst.actions.fails(
sst.actions.assert_url, 'http://loca... | DramaFever/sst | src/sst/selftests/assert_urls.py | Python | apache-2.0 | 2,179 | [
"VisIt"
] | a8181dfc3128bd8b450c9bfbf7a3e66d7bcac49b8bfd36f062b3215116e07b75 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'PatientInformation.notes'
db.add_column('patient_patientinformation', 'notes',
... | aazhbd/medical_info01 | patient/migrations/0032_auto__add_field_patientinformation_notes.py | Python | bsd-3-clause | 30,204 | [
"VisIt"
] | d6d64808a6e74ba7e0c0c6dc2e4d424afd295eaa1ee9cf3381cfd85acbfb348b |
# list Map scans from saved 1mm data
from scipy.io import netcdf
from glob import glob
from datetime import datetime, timedelta
import numpy as np
files = glob('/data_lmt/vlbi1mm/vlbi1mm_2016-*.nc')
for fname in sorted(files):
try:
nc = netcdf.netcdf_file(fname)
v = nc.variables
pgm = ''.join(v['Header.Dcs.Ob... | sao-eht/lmtscripts | 2017/list2016maps.py | Python | mit | 976 | [
"NetCDF"
] | 29abe5c191076c3514de4a30ffba27e8dc52a647ccb3f78d4f13d2dd8bbfae06 |
#!/usr/bin/env python
# Copyright 2017-2021 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/cc/kccsd.py | Python | apache-2.0 | 35,158 | [
"PySCF"
] | edc3e2d0c7e858d609267f1810bf7c744f05a8f079cc5bf6c8b0a10588b294d0 |
'''
Created on Jun 2, 2011
@author: mkiyer
'''
import logging
import collections
import os
import sys
import argparse
from chimerascan import pysam
from chimerascan.bx.cluster import ClusterTree
from chimerascan.lib import config
from chimerascan.lib.base import LibraryTypes, imin2
from chimerascan.lib.sam import pa... | Alwnikrotikz/chimerascan | chimerascan/deprecated/find_discordant_reads_v5.0.0a.py | Python | gpl-3.0 | 14,265 | [
"pysam"
] | 4cb7a84f56d71f25df2d0f0de726baba3eec9476dc53b4427302f64d840b105d |
"""Reproduce results from Fig. 2 of `bib.raanes2014ext`."""
import numpy as np
import dapper.mods as modelling
from dapper.mods.LA import Fmat, sinusoidal_sample
from dapper.mods.Lorenz96 import LPs
from dapper.tools.linalg import tsvd
# Burn-in allows damp*x and x+noise balance out
tseq = modelling.Chronology(dt=1,... | nansencenter/DAPPER | dapper/mods/LA/raanes2015.py | Python | mit | 2,659 | [
"Gaussian"
] | fe5404c83e351704ab4ec15423add8a46bf95a48b96aef54211679dd7cb8409c |
# Copyright 2016 Brian Innes
#
# 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, ... | brianinnes/pycupi | python/border.py | Python | apache-2.0 | 1,270 | [
"Brian"
] | 289d1be87e76277dd7232bac30570690563dac7989f241de0020dcfa4cd361e9 |
"""
Supercell class
Class to store supercells of crystals. A supercell is a lattice model of a crystal, with
periodically repeating unit cells. In that framework we can
1. add/remove/substitute atoms
2. find the transformation map between two different representations of the same supercell
3. output POSCAR format (po... | DallasTrinkle/Onsager | onsager/supercell.py | Python | mit | 22,765 | [
"CRYSTAL",
"VASP"
] | b82ece69acb4fd41c275e6c59cb39d159cb6eb8d141f61af7a0dfa95b92b7b59 |
################################
# Author : septicmk
# Date : 2015/09/05 16:57:57
# FileName : visualization.py
################################
from vtkpython import *
import math
import pandas as pd
from random import random
class vtkTimerCallback():
def __init__(self):
self.timer_count... | septicmk/MEHI | MEHI/utils/visualization.py | Python | bsd-3-clause | 4,115 | [
"VTK"
] | 7343a45764f11ddbd953c840258377d35368f04c3dd319123d5ec9dec452b566 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
# vim:fdm=marker
#
# =============================================================
# Copyright © 2018 Daniel Santiago <dpelaez@cicese.edu.mx>
# Distributed under terms of the GNU/GPL license.
# ============================================================... | dspelaez/tools | tools/bomm.py | Python | gpl-3.0 | 35,771 | [
"NetCDF"
] | 533e58b1cc4ffc6c3a56583ea1a8848e854eb2b0c2ff30aef19eaf161d100d20 |
# -*- coding: utf-8 -*-
""" Sahana Eden Incident Reporting Model
@copyright: 2009-2014 (c) Sahana Software Foundation
@license: MIT
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 Sof... | devinbalkind/eden | modules/s3db/irs.py | Python | mit | 56,474 | [
"VisIt"
] | 01ef7b4b0893e645712274456837fc61774daaf1099870ea44fc1fbcbd77756c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008-2009 Gary Burton
# Copyright (C) 2008 Robert Cheramy <robert@cheramy.net>
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2010 Nick Ha... | pmghalvorsen/gramps_branch | gramps/plugins/export/exportgedcom.py | Python | gpl-2.0 | 55,775 | [
"Brian"
] | 7a4bfe7e34fe46c9b11df3d09646a2225cf0976341badb047e93b7a45ac81782 |
# -*- coding: utf-8 -*-
import vtk
import xc_base
import xc
from miscUtils import LogMessages as lmsg
import create_array_set_data
__author__= "Luis C. Pérez Tato (LCPT) Ana Ortega (AO_O)"
__copyright__= "Copyright 2015, LCPT AO_O"
__license__= "GPL"
__version__= "3.0"
__email__= "l.pereztato@ciccp.es ana.Ortega@cicc... | lcpt/xc | python_modules/postprocess/xcVtk/cad_mesh.py | Python | gpl-3.0 | 4,973 | [
"VTK"
] | de5c572fbcf124bd7b00cc391aa12026d2b1139afba45e5ee46a30ddea66be21 |
"""
@name: Modules/House/Family/Replink/_test/test_core.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2020-2020 by D. Brian Kimmel
@note: Created on Feb 2, 2020
@license: MIT License
@summary: This
Passed all 1 tests - DBK - 2019-12-29
"""
__updated__ = '2020-02-02'... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Reolink/_test/test_reolink_device.py | Python | mit | 881 | [
"Brian"
] | e341f25ea16a0794c6e52b4026568cb0e093615325f29bdc12cc196e726bbc35 |
import math
from ClimateUtilities import * #To get the math methods routines
#
#All units are mks units
#
#ToDo:
# * Add conversion factors (calories to joule,Megatons, etc.)
# * Unit conversion calculating object
# * Database of interesting constants (e.g energy and C
# content of coal)
# ... | aymeric-spiga/planets | reserve/phys.py | Python | gpl-2.0 | 23,846 | [
"Avogadro"
] | 5a44c0dd47ba128dc772bc987df17d62992363c414987dfc189c6bc5dc6595e5 |
from datetime import datetime
from turbogears.database import PackageHub
from sqlobject import *
from turbogears import identity
sqlhub.processConnection = connectionForURI("postgres://sweetter:sweetter@localhost/sweetter")
# class YourDataClass(SQLObject):
# pass
# identity models.
class Visit(SQLObject):
... | danigm/sweetter | sweetter/s2_to_s3/s2model.py | Python | agpl-3.0 | 7,917 | [
"VisIt"
] | 2b8edddd23d2bce33c593dc8dd8d41f17286e7ba352a0f9b21a0f706c10bb665 |
from Bio import ExPASy
from Bio import SeqIO
import numpy as np
import csv
AA_LETTERS = sorted("ACEDGFIHKMLNQPSRTWVY")
# list all proteins in ecoli by uniprot_ID - aprse from .txt file
def download_aa_dist_per_gene(UPID_list_fname, cutoff):
UPID_list = []
for row in open(UPID_list_fname, 'r'):
if row:
... | eladnoor/proteomaps | src/amino_acid_distribution/download_aa_sequences.py | Python | mit | 4,068 | [
"Biopython"
] | 10a30ec9b648c0d787af1f9731188268d60325016dc787500861f9ce49987ae9 |
################################################################################
##
## Pythonc--Python to C++ translator
##
## Copyright 2013 Zach Wegner, Matt Craighead
##
## This file is part of Pythonc.
##
## Pythonc is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Pub... | zwegner/pythonc | transform.py | Python | gpl-3.0 | 17,388 | [
"VisIt"
] | af399d42c3da82e89a17768d38910f046db1eca0843528e83cde60de84fc083f |
#!/usr/bin/python2
# vim: ts=4 : sts=4 : sw=4 : et :
import sqlite3
import datetime
import os.path
import sys
import wx
from wx.lib.mixins.listctrl import ListCtrlAutoWidthMixin
from wx.lib.mixins.listctrl import ColumnSorterMixin
import version
import survey
import data
import about
galaxy_names = [
"Thustra's... | pizzasgood/galactiscan | gui.py | Python | gpl-3.0 | 22,558 | [
"Galaxy"
] | 5e21048435b5e88b7a7355998f35d07985259468b79ad2c8f2fd7d673b0a9f93 |
# cmdutil.py - help for command processing in mercurial
#
# Copyright 2005-2007 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from node import hex, nullid, nullrev, short
from i18n import _
import ... | spraints/for-example | mercurial/cmdutil.py | Python | gpl-2.0 | 80,076 | [
"VisIt"
] | 296d766851cff8d127f259673cb18544aa4af79c42b6048ea8ebafe27dab937e |
# 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 | tunas/controller_test.py | Python | apache-2.0 | 11,472 | [
"VisIt"
] | 83cdb3056ac553a61487d2bc2e741d107985b4a0f95d7e9997a4ad6b282a4f7c |
# import h5py
import numpy as np
# from pprint import pprint
# from termcolor import colored as c, cprint
# from IPython.display import FileLink
# from IPython import display
# from tqdm import tqdm
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
color_palette = ['#507ba6', '#f08e39', '#e0595... | kinshuk4/MoocX | misc/deep_learning_notes/Proj_Centroid_Loss_LeNet/LeNet_plus_centerloss/analysis.py | Python | mit | 3,979 | [
"NEURON"
] | 160a2d9fdac477c4af4e2530a0acf01fe8f6ee3b3e3ef338bd6881f52d55b4bc |
#Some functions to help analysing DUT-8
import numpy as np
import sys
from ase import Atoms, neighborlist
import os
import pickle
def buildNL(mol, path='./', radii=None, save=True):
#create nl
if radii is None:
radii = {}
radii[ 'H'] = 0.30
radii[ 'C'] = 0.77
radii[ 'N'] = 0.70
... | patrickmelix/Python4ChemistryTools | moffunctions.py | Python | mit | 5,110 | [
"ASE"
] | 47546c5daeac3a03f84120bc0ddece4a2046247563164f7065c416f28fe696bc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Zappa CLI
Deploy arbitrary Python programs as serverless Zappa applications.
"""
from __future__ import unicode_literals
from __future__ import division
import argcomplete
import argparse
import base64
import pkgutil
import botocore
import click
import collections... | parroyo/Zappa | zappa/cli.py | Python | mit | 87,982 | [
"VisIt"
] | 710c0823e03a4e6abc0a776da06a52b42cc6fc581b10446344905b97600979bd |
r"""
:mod:`~matplotlib.mathtext` is a module for parsing a subset of the
TeX math syntax and drawing them to a matplotlib backend.
For a tutorial of its usage see :ref:`sphx_glr_tutorials_text_mathtext.py`. This
document is primarily concerned with implementation details.
The module uses pyparsing_ to parse the TeX ... | jonyroda97/redbot-amigosprovaveis | lib/matplotlib/mathtext.py | Python | gpl-3.0 | 122,856 | [
"Bowtie"
] | 108e56b237b55eb6d3c1bf89d9056235ab914dc0e4ccf733b48325f44b852aff |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | samples/visualization_interactive.py | Python | gpl-3.0 | 2,788 | [
"ESPResSo"
] | 71afcc87fc1e7212b9fa9260f54001e2315875c0a7203dbcc2779b3b6050e1c3 |
# (C) British Crown Copyright 2014 - 2016, Met Office
#
# This file is part of iris-grib.
#
# iris-grib 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 opt... | pp-mo/iris-grib | iris_grib/tests/unit/message/test_Section.py | Python | lgpl-3.0 | 3,573 | [
"Gaussian"
] | dc4a81bf595ecf834f989e7ff989b0cf2c7f7a3002dab3a2ae52e37da05af1e3 |
"""Tests related to prerun part of the linter."""
import os
import subprocess
from typing import List
import pytest
from _pytest.monkeypatch import MonkeyPatch
from flaky import flaky
from ansiblelint import prerun
from ansiblelint.constants import INVALID_PREREQUISITES_RC
from ansiblelint.testing import run_ansible_... | ansible/ansible-lint | test/test_prerun.py | Python | mit | 6,088 | [
"Galaxy"
] | 001d3a83e45d18fa277b4b9c191c9d11295591229b5e9b74d2b1379a426dc6c9 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from __future__ import absolute_import
import time
from logging import getLogger
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from lettuce import step, world
from lettuce.django import django_url
f... | proversity-org/edx-platform | lms/djangoapps/courseware/features/common.py | Python | agpl-3.0 | 7,864 | [
"VisIt"
] | 6b6bc70c083f47b5aaa01592b94f6388f47b087d65f4c9e4d487a72198c1de3e |
# Copyright 2003-2008 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.
#
# Contact: Leighton Pritchard, Scottish Crop Research Institute,
# ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Graphics/GenomeDiagram/_FeatureSet.py | Python | gpl-2.0 | 8,994 | [
"Biopython"
] | 5f8666ba884a35b339ccdf38ce49f2d4c7b7f6e7e561b7f949d68b8779eecbd0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2014, 2015 Abhay Devasthale and Martin Raspaud
# Author(s):
# Martin Raspaud <martin.raspaud@smhi.se>
# Adam Dybbroe <adam.dybbroe@smhi.se>
# Sajid Pareeth <sajid.pareeth@fmach.it>
# This program is free software: you can redistribute it and/or mod... | mraspaud/mpop | mpop/satin/ascat_nc.py | Python | gpl-3.0 | 2,879 | [
"NetCDF"
] | 3336db7f26cae3cc8f956409649f88c08da0a8a04a2d2dd1dd34f9a5da1270ba |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
from oauth2client.file import Storage
from oauth2client.client import flow_from_clientsecrets
from oauth2client.tools import run_flow
from apiclient.discovery import build
from gdcmdtools.base import BASE_INFO
import httplib2
import pprint
import shutil
impor... | tienfuc/gdcmdtools | gdcmdtools/auth.py | Python | bsd-2-clause | 4,840 | [
"VisIt"
] | 08bf06e46972be0a8f667aabad411ce8f966b2d161accd6d6ff0964613a98f50 |
import itertools
import argparse
import sys
import os
import errno
import subprocess
import winbrew
import winbrew.util
class InstallException(Exception):
pass
class InstallPlan:
"""
Executes a topological sort to determine the order in which to install
packages.
"""
def __init__(self, formul... | mfichman/winbrew | winbrew/execute.py | Python | mit | 9,401 | [
"VisIt"
] | 809db27e4aedc786efee77170afa746ff93cf7db192f0dc18cae00db4815e02b |
import sys, itertools, optparse
optParser = optparse.OptionParser(
usage = "python %prog [options] <flattened_gff_file> <sam_file> <output_file>",
description=
"This script counts how many reads in <sam_file> fall onto each exonic " +
"part given in <flattened_gff_file> and outputs a list of... | jhl667/quick_scripts | dexseq_count.py | Python | gpl-2.0 | 6,001 | [
"Bioconductor",
"HTSeq"
] | ea4ea8b40e1b2bba8057bbc9a517dfd6e5015a71c8b91d34f6f4f4fce4b0f346 |
# Copyright 2008 by Michiel de Hoon. 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.
"""Parser for XML results returned by NCBI's Entrez Utilities. This
parser is used by the re... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Entrez/Parser.py | Python | gpl-2.0 | 20,827 | [
"Biopython"
] | 8288b865d01f2e70f0ad6463bc133aa28cb80311a9fd758686f51b214f68b9fe |
#coding= utf-8
class PhoneticAlgorithms():
'''
This script implements the Double Metaphone algorithm (c) 1998, 1999 by Lawrence Philips
it was translated to Python from the C source written by Kevin Atkinson (http://aspell.net/metaphone/)
By Andrew Collins - January 12, 2007 who claims no rights to... | amsqr/k-Met | phonetic_algorithms.py | Python | gpl-3.0 | 21,699 | [
"Brian"
] | ca04bf02a6f97c6a85a174765f81af6b3adfb09d7125f8eae66bf11298fe2de7 |
import unittest
from hamcrest import *
from cis.data_io.products.NCAR_NetCDF_RAF import NCAR_NetCDF_RAF
from cis.test.integration.test_io.test_products.test_data_products import ProductTests
from cis.test.integration_test_data import cis_test_files
class TestNCAR_NetCDF_RAF(ProductTests, unittest.TestCase):
def... | cedadev/cis | cis/test/integration/test_io/test_products/test_ncar_raf.py | Python | lgpl-3.0 | 4,482 | [
"NetCDF"
] | 82f281dbdc615a9c32c9d2c913e868357f69d1b9c5fed2c1802b2dc2cfcd1ebc |
'''
PipelineLncRNA.py - functions and classes for use with the lincRNA pipeline
===========================================================================
'''
import re
import sys
import os
import CGAT.GTF as GTF
import CGAT.IOTools as IOTools
import gzip
import collections
import CGAT.IndexedGenome as IndexedGenome... | CGATOxford/CGATPipelines | obsolete/PipelineLncRNA.py | Python | mit | 100,312 | [
"Galaxy"
] | 0d11493c36124ac0988b4365f1725d51f8fec611e850d58f1f76211c3868cb36 |
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import with_statement
__license__ = 'GPL 3'
__copyright__ = '2009, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
from itertools import izip
from calibre.customize import Plugin as _Plugin
FONT_SIZES = [('xx-small', 1),
... | sss/calibre-at-bzr | src/calibre/customize/profiles.py | Python | gpl-3.0 | 25,766 | [
"Galaxy"
] | 331363d05f7792ffa6e66f2f8ba7589f59faa07fdeddb0036ff1bcc4996d89d5 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011 CERN.
##
## 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 (at your option) a... | robk5uj/invenio | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 99,247 | [
"ADF"
] | fb57e4f7b214b71ed7f50fd59cf1c3d5c6042113cd824ee728052d22648446fb |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/binmeshtranslator.py | Python | mit | 7,523 | [
"VisIt"
] | 62b90ea684f2a4e53f4e4e71f9ffd956895e2760d8648d8017f1577be1918e43 |
# Copyright (C) 2020
# Max Planck Institute for Polymer Research & JGU Mainz
# Copyright (C) 2012,2013,2015,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ... | govarguz/espressopp | src/VerletList.py | Python | gpl-3.0 | 3,985 | [
"ESPResSo"
] | c3b13c55888a10ef6604455b13366bf73593f6d929ed3209a901f89b89dcd0e7 |
#-*- coding:UTF-8 -*-
#! /usr/bin/python
import getpass,sys
from spider import renrenspider
version = "0.3"
if __name__ == "__main__":
email=raw_input('请输入用户名：')
password=getpass.getpass('请输入密码：')
renrenspider=renrenspider(email,password)
renrenspider.login()
mode=999
while(mode!='000'):
mode=raw_input('请输入... | jamesliu96/renren | main.py | Python | mit | 667 | [
"VisIt"
] | 7773c0221435d18f64a21bb228efc87509044e0edc5cc74e89b9a4bc93d26628 |
from django.db import transaction
from django.db.models.signals import post_save
from django.dispatch import receiver
from django.utils import timezone
from edc_registration.models import RegisteredSubject
from edc_appointment.models import Appointment
from edc_constants.constants import (
FEMALE, SCHEDULED, SCREE... | TshepangRas/tshilo-dikotla | td_maternal/models/signals.py | Python | gpl-2.0 | 13,723 | [
"VisIt"
] | 0a6771b1be3d50b0f6e91901a3dba56445dbb9a68ca4936963b47e3b2ec0a046 |
# -*- coding: utf-8 -*-
import sys
import math
from pylab import *
try:
import moose
except ImportError:
print("ERROR: Could not import moose. Please add the directory containing moose.py in your PYTHONPATH")
import sys
sys.exit(1)
from moose.utils import * # for BSplineFill
class AchSyn_STG(moose.... | BhallaLab/moose-examples | neuroml/lobster_pyloric/synapses/AchSyn_STG.py | Python | gpl-2.0 | 2,461 | [
"MOOSE"
] | 03e4f701aa82b182aab47a6e01c16956395589398e603fcad72b2cfd1da5f182 |
#!/usr/env/python
"""
rock_weathering.py
CellLab-CTS model that simulates the weathering of rock to saprolite around
a network of fractures.
Created (and translated from earlier code by) by Greg Tucker, Jul 2015
"""
from __future__ import print_function
import time
import numpy as np
from landlab import RasterModel... | decvalts/landlab | landlab/components/cellular_automata/examples/rock_weathering.py | Python | mit | 5,558 | [
"NetCDF"
] | b0a2aecacbbb07ea42c462b7a68243473a81d9f580d065ff9768d2c4eabdf18a |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/util/_misc.py | Python | bsd-3-clause | 5,575 | [
"scikit-bio"
] | 5a51c810f798e1d0b6fcd90f137dd3586158da236c00fa8c22bde18f17bbe4b1 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | Shaswat27/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 74,473 | [
"Gaussian"
] | 1501cf4f0ed7a28ccf93326976a4becce0dd1931c0fa038910868f9d05eca9ee |
'''
sbclearn (c) University of Manchester 2017
sbclearn is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=no-member
# pylint: disable=ungrouped-imports
import sys
import numpy a... | neilswainston/development-py | synbiochemdev/sbclearn/ccs/ccs_learn.py | Python | mit | 879 | [
"VisIt"
] | 7ab384eb9a84278c96f8c3ffdb23b62af46dbcceca192174833551714081417c |
#######################################
# pyGPGO examples
# hyperpost: shows posterior distribution of hyperparameters
# for a Gaussian Process example
#######################################
import numpy as np
from pyGPGO.surrogates.GaussianProcessMCMC import GaussianProcessMCMC
from pyGPGO.covfunc import matern32
... | hawk31/pyGPGO | examples/hyperpost.py | Python | mit | 570 | [
"Gaussian"
] | 8c8c3c1a57c93ab689ccbca37962af665842fb1f59bcfed53b110872846232bf |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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
#... | psi4/psi4 | psi4/share/psi4/databases/HTBH.py | Python | lgpl-3.0 | 38,476 | [
"Psi4"
] | 4aeb5d604659f87df3055e2f3220d09fa00e52261285c84341e21b8e49deef3c |
"""
local path implementation.
"""
from __future__ import with_statement
from contextlib import contextmanager
import sys, os, re, atexit, io
import py
from py._path import common
from py._path.common import iswin32, fspath
from stat import S_ISLNK, S_ISDIR, S_ISREG
from os.path import abspath, normcase, ... | cvegaj/ElectriCERT | venv3/lib/python3.6/site-packages/py/_path/local.py | Python | gpl-3.0 | 33,568 | [
"VisIt"
] | 868c013b7ba2377ece21834286fb5165fd571a86e080ab71038e3ad160b41592 |
from __future__ import print_function
import random
import time
from numpy import random as nprand
import moose
def make_network():
size = 1024
timestep = 0.2
runtime = 100.0
delayMin = timestep
delayMax = 4
weightMax = 0.02
Vmax = 1.0
thresh = 0.2
tau = 1 # Range of tau
tau0 = 0.5 # minimum tau
refr = 0... | subhacom/moose-core | tests/python/mpi/recurrentIntFire.py | Python | gpl-3.0 | 2,818 | [
"MOOSE",
"NEURON"
] | 18e8976ed824a5c9f86b35936321a52699b0a7bd0581c75e889e8d3566e3b70d |
#!/usr/bin/env python
import numpy
import scipy.io.wavfile
import scipy.fftpack
import scipy.signal
import defs
WINDOWSIZE = defs.ZEROPADDING_FACTOR * defs.BUFFER_WINDOWSIZE
### convenience functions
def amplitude2db(power):
return 20.0 * scipy.log10( power )
def db2amplitude(db):
return 10.0**(db/20.0)
d... | gperciva/artifastring | research/mode-detect/stft.py | Python | gpl-3.0 | 2,992 | [
"Gaussian"
] | 01aef76705b0d6f9177b6276e7f27afccaae13d3a2d56e1e449d2421ce9c53af |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-admin-get-job-pilots
# Author : Stuart Paterson
########################################################################
"""
Retrieve info about pilots that have matched a given Job
"""
__RCSI... | Sbalbp/DIRAC | Interfaces/scripts/dirac-admin-get-job-pilots.py | Python | gpl-3.0 | 1,367 | [
"DIRAC"
] | d31f7860f163cb57fc9b6cb58cfc052824f7643f1ccc58cb5eda97e18de37eb3 |
# -*- coding: utf-8 -*-
from __future__ import division, print_function, absolute_import
"""
ZNCC using Pyramids
"""
__author__ = "Per-Erik Forssén"
__copyright__ = "Copyright 2013, Per-Erik Forssén"
__license__ = "GPL"
__email__ = "perfo@isy.liu.se"
import logging
logger = logging.getLogger()
import numpy as np
d... | spillai/crisp | crisp/znccpyr.py | Python | gpl-3.0 | 7,934 | [
"Gaussian"
] | cc4fe3741522a97c11ace4f098c5ff7b4bf2fa5c49145f524685981bd59c5128 |
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