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'''
User Job class. Used to define (guess what?) user jobs!
@author: Stephane Poss
'''
from Interfaces.API.Job import Job
from Interfaces.API.Dirac import Dirac
from DIRAC.Core.Security.ProxyInfo import getProxyInfo
from DIRAC.Configura... | sposs/DIRACInterfaceDoc | code/Interfaces/API/UserJob.py | Python | gpl-2.0 | 8,468 | [
"DIRAC"
] | b55a7fdc167e66911772450d8729c79140ddd864f6bb60774791a9fdaa142458 |
import sys
from PyQt4.QtGui import QIntValidator, QDoubleValidator, QApplication, QSizePolicy
from Orange.widgets import widget, gui
from Orange.widgets.settings import Setting
from Orange.data import Table, Domain, ContinuousVariable
import numpy as np
#try:
# from ..tools.xoppy_calc import xoppy_doc
#except Impor... | srio/Orange-XOPPY | devel/glossary/BC_PerfectCrystal.py | Python | bsd-2-clause | 6,835 | [
"CRYSTAL"
] | 314c3aeee54cf9ff365a67de1bc981dff5ca781209866275bf1b2d2077e656aa |
# Copyright 2008, 2009 CAMd
# (see accompanying license files for details).
"""Atomic Simulation Environment."""
from ase.atom import Atom
from ase.atoms import Atoms
_deprecate_things_from_ase_module = True
# Some day in the future, we will uncomment this line:
#__all__ = ['Atoms', 'Atom']
from ase.units impor... | slabanja/ase | ase/__init__.py | Python | gpl-2.0 | 2,475 | [
"ASE",
"SIESTA",
"TURBOMOLE",
"VASP"
] | 6a8c1a1c7f01348a650aac1d8b0e5f2e4bb63ada994578f5743a8d5758badd3a |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#... | nuclear-wizard/moose | python/parameters/test/test_Parameter.py | Python | lgpl-2.1 | 8,270 | [
"MOOSE"
] | c10dcaede565eab833912e04987bc0e5f56cc8de5a9f285954af860ded99b804 |
import sys
sys.path.append('/usr/lib/python/')
sys.path.append('/usr/lib/python/site-packages/Numeric')
# generate the data.
try:
from Numeric import *
except:
print 'No Numeric installed'
#import mayavi
import time
#import pyvtk
#import vtk
import os
class test:
def __init__(self):
pass
... | CuonDeveloper/cuon | cuon_client/cuon_newclient/bin/cuon/VTK/test.py | Python | gpl-3.0 | 4,144 | [
"Mayavi",
"VTK"
] | 20ed4ab224a4022a9b032876996b86cb93f5207da80785513665c48821751215 |
from __future__ import division, print_function
import numpy as np
import sys
from scipy.integrate import simps
from collections import OrderedDict
from ...shared import flatten, filter_indices
from .functions import (rpm2radps, radps2rpm, compare_data,
find_omega2g, find_omega2g_dec, find_omega2g_fh, readrpms_f... | bmcage/centrifuge-1d | centrifuge1d/modules/shared/measurements.py | Python | gpl-2.0 | 65,263 | [
"Gaussian"
] | 4839f1381cda742a3d1fea595cc57edb9f71d189a31e713895ad58ccedd1631b |
from pyhull.voronoi import VoronoiTess
from pyhull.delaunay import DelaunayTri
from pymatgen.transformations.transformation_abc import AbstractTransformation
from pymatgen.core.sites import PeriodicSite
from pymatgen.util.coord_utils import barycentric_coords
from pymatgen.analysis.structure_analyzer import solid_angle... | tchen0965/structural_descriptors_repo | voronoi.py | Python | mit | 11,136 | [
"pymatgen"
] | df6852ab814f232d53deab9e3d76ccbc8a7de0c9cb225302b7e8c55ced9c65ea |
from engine.constants.run_type import HADOOP, LOCAL, INLINE
from engine.engine import Engine
from datahandler.image.image_data_handler import ImageDataHandler
from algorithms.image.gaussian_filter_factory import GaussianFilterFactory
from skimage import io as skio
if __name__ == '__main__':
print("=== G... | xapharius/mrEnsemble | Engine/src/examples/learning_on_images.py | Python | mit | 1,072 | [
"Gaussian"
] | f24a2612ad59b13745754ec9c02901c16ac49e3abe6db369ad06422fa2609141 |
"""
This class brings together a L{solve.Solver} to choose a set of implmentations, a
L{fetch.Fetcher} to download additional components, and the user's configuration
settings.
@since: 0.53
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall impor... | timdiels/zeroinstall | zeroinstall/injector/driver.py | Python | lgpl-2.1 | 7,396 | [
"VisIt"
] | 68388176496907ab8e7f3de13b4c2c22ec3edbecbb5d1134e878bba6332cc88c |
##
# Copyright 2009-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/s/siesta.py | Python | gpl-2.0 | 14,349 | [
"NetCDF",
"SIESTA"
] | 9eff61a840da33eb44bcec35c7a67df6bd68a8e58e0ecfdf3623b2d245aa3c11 |
from django.conf import settings
try:
from acceptance_tests import auth
except ImportError:
# Avoid pylint errors when auth doesn't exist
auth = None
class LoginMixin:
"""Mixin used for log in through a cookie."""
def login(self, superuser=False):
"""Craft cookie to fake a login."""
... | edx/credentials | acceptance_tests/mixins.py | Python | agpl-3.0 | 939 | [
"VisIt"
] | c0eec5fa3c2210fe6d73f9f501d583b4b8f0c8c6207ea1d341959a53a341bf16 |
#! /usr/bin/env python
# Hi There!
# You may be wondering what this giant blob of binary data here is, you might
# even be worried that we're up to something nefarious (good for you for being
# paranoid!). This is a base64 encoding of a zip file, this zip file contains
# a fully functional basic pytest script.
#
# Pyt... | sportsy/sports-stats | runtests.py | Python | mit | 236,333 | [
"ASE"
] | 5ff261d89c4dc277cd5d384f51c242ba2bdfe951d17152b5fb7341e8cf838680 |
import warnings
import numpy as np
import os
# choose from netcdf4, scientificio, scipyio
cdf_lib = 'netcdf4'
#cdf_lib = 'scipyio'
#use_scientificio = False
# Set the path here. This path will be used to find your experiments.
if os.getenv("LOC") == "standard":
# For now, the same behaviour as other locations
hom... | willo12/spacegrids | spacegrids/_config.py | Python | bsd-3-clause | 2,815 | [
"NetCDF"
] | b17616d4db1c01e2090cb571b0150a5b145515fa7b48b962aa0d98587e439dd1 |
# Copyright 2014 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | GrandmasterK/XScheduler | venv/lib/python2.7/site-packages/oauth2client/tools.py | Python | mit | 8,931 | [
"VisIt"
] | 3e598a2d4ad785e2f3f45ef81a60803b05f3792fd927154714155fb75f87bd93 |
import itertools
import sys
import ast
import types
class TreeWalker(object):
'''Class that will walk an ast and call registered functions for each node found.
To use this class, register functions in the visit_functions and
leave_functions dictionaries. The key for a callback sound be the class of
... | ajalt/eece6083-compiler | ececompiler/syntaxtree.py | Python | mit | 8,660 | [
"VisIt"
] | 1f9ed8ba79c15e332c0256980f023ab7a3a21b1d7d12deb02411f9b1ddaecd44 |
from ase.structure import bulk
from sys import argv
from ase.dft.kpoints import ibz_points, get_bandpath
from gpaw import *
from ase import *
from gpaw.test import gen
from gpaw import setup_paths
import os
"""This calculation has the following structure.
1) Calculate the ground state of Diamond.
2) Calculate the ban... | ajylee/gpaw-rtxs | gpaw/test/diamond_gllb.py | Python | gpl-3.0 | 2,143 | [
"ASE",
"GPAW"
] | e42e34ae702bd32bee203cd035a32ddd686e470074012578f739a696a0628ea4 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""Main gpaw module."""
import os
import sys
try:
from distutils.util import get_platform
except ImportError:
modulepath = os.environ.get('GPAW_GET_PLATFORM')
if modulepath is None:
errmsg = ('Error: Cou... | ajylee/gpaw-rtxs | gpaw/__init__.py | Python | gpl-3.0 | 8,772 | [
"GPAW"
] | 3b9e94cb2be1984825642b1c980aaf5c95eb34a38deb98b650618f87c62f3d62 |
# -*- coding: utf-8 -*-
import math
from operator import add
from functools import reduce
import pytest
from chempy import Substance
from chempy.units import (
allclose,
units_library,
default_constants,
Backend,
to_unitless,
SI_base_registry,
default_units as u,
)
from ..testing import r... | bjodah/chempy | chempy/util/tests/test_expr.py | Python | bsd-2-clause | 18,801 | [
"ChemPy"
] | 23b77468191eca791b576f5700bd0c956ebfefaccc0b283acf0a779a7d43a1de |
from . import common
from . import chess
def provides():
return ['Unsound', 'Shortmate', 'Cooked', 'Has duals']
# todo: h#*.5 with setplay
def check(problem, board, solution):
retval = common.retval(provides)
for twin in solution.siblings:
twin.make(board)
if 'intended-solutions' in pr... | dturevski/olive-gui | legacy/soundness.py | Python | gpl-3.0 | 3,505 | [
"VisIt"
] | a75cb352fdcca0864b902c65300bcc34ae969a46c8fadafedb798b2d3b75711a |
#
# 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... | kaiping/incubator-singa | python/singa/autograd.py | Python | apache-2.0 | 48,530 | [
"Gaussian"
] | 22d0c639a13307d2c8afec67aa5faa98808994089ae9f824b5039b20722cce61 |
"""Generalized linear mixed model"""
import warnings
import re
import numpy as np
import pandas as pd
from sklearn.base import BaseEstimator
from sklearn.utils.random import check_random_state
from category_encoders.ordinal import OrdinalEncoder
import category_encoders.utils as util
import statsmodels.formula.api as s... | wdm0006/categorical_encoding | category_encoders/glmm.py | Python | bsd-3-clause | 13,244 | [
"Gaussian"
] | 399f7b5d0a9accc84ca433f5275039c48acdc3d24ca3053bab33e5b0c158065d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | henryfjordan/django_beginnings | config/urls.py | Python | bsd-3-clause | 1,317 | [
"VisIt"
] | 9562d0441fdacb5e12af7122a13dc9c3dc098d3de227d6944d0fa6e3fc789fe0 |
# 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)
import os
from spack import *
class Siesta(Package):
"""SIESTA performs electronic structure calculations and ab i... | LLNL/spack | var/spack/repos/builtin/packages/siesta/package.py | Python | lgpl-2.1 | 3,671 | [
"NetCDF",
"SIESTA"
] | 152e938e5e260507bf19f71e69db34eb042e9cd8d1fc3d603dc4f53557b40877 |
# mako/pyparser.py
# Copyright 2006-2019 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Handles parsing of Python code.
Parsing to AST is done via _ast on Python > 2.5, otherwise the co... | endlessm/chromium-browser | third_party/mako/mako/pyparser.py | Python | bsd-3-clause | 7,789 | [
"VisIt"
] | 9a8825a7ed74ec421d200e9b315b7aa07bd998f6c444957c89e232854499eaf3 |
#!/usr/bin/env python2
# vim:fileencoding=UTF-8:ts=4:sw=4:sta:et:sts=4:ai
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2011, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
from calibre ... | elssar/calibre | src/calibre/web/jsbrowser/login.py | Python | gpl-3.0 | 1,738 | [
"VisIt"
] | 4d615f13cd0dea995ad503969290d0ef7fa7662d7c8e364d47efb902d829aac6 |
#!/usr/bin/env python
#
# @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
#... | kannon92/psi4 | psi4/share/psi4/fsapt/fsapt.py | Python | gpl-2.0 | 24,551 | [
"Psi4"
] | 179d31ab9ab085315de92d14b813495043a7860657cc5980d18c5d15bc9b33b7 |
import re
from galaxy import util
from ..instrumenters import InstrumentPlugin
from ...metrics import formatting
import logging
log = logging.getLogger( __name__ )
PROCESSOR_LINE = re.compile(r"processor\s*\:\s*(\d+)")
class CpuInfoFormatter( formatting.JobMetricFormatter ):
def format( self, key, value ):
... | jmchilton/lwr | galaxy/jobs/metrics/instrumenters/cpuinfo.py | Python | apache-2.0 | 2,090 | [
"Galaxy"
] | 579e8c7ecffce6b3c5ab9ac9385f2f24a488d3c0d7d39f9777d69b0b924bc890 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either vers... | marscher/PyEMMA | pyemma/coordinates/data/util/reader_utils.py | Python | lgpl-3.0 | 10,316 | [
"MDTraj"
] | 902f51a97de384898f67865fc92b8d297cdc498876433ce702ef646e82943028 |
""" KeystoneClient class encapsulates the work with the keystone service interface
"""
import requests
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.Time import fromString, dateTime
class KeystoneClient(object):
def __init__(self, url, parameters):
self.log = gLogger.getSubLogger("Ke... | DIRACGrid/DIRAC | src/DIRAC/Resources/Cloud/KeystoneClient.py | Python | gpl-3.0 | 10,059 | [
"DIRAC"
] | 9c08613c44adf041ec8256a5ec195d249856f969dfbb3e75c062658209ae00fe |
"""
Script creates pvsm file with colors and video and screenshot.
All is based on recentely created vtk file in ~/lisa_data. All vtk files with the same beginning of file name are
concidered.
Use:
Paraview -> View -> Python Shell -> Run Script
Paraview -> Tools -> Python Shell -> Run Script
"""
import sys
import os.... | mjirik/lisa | lisa/paraview_skript_lisa_auto.py | Python | bsd-3-clause | 20,853 | [
"ParaView",
"VTK"
] | e896f795fdd1281883e307a5693ffe3dbb1f5e9b8dbc5a424bff187205c19913 |
# A translation of calc_fitness.pl into python! For analysis of Tn-Seq.
# This script requires BioPython, which in turn has a good number of dependencies (some optional but very helpful).
# How to install BioPython and a list of its dependencies can be found here: http://biopython.org/DIST/docs/install/Installation.htm... | jsa-aerial/aerobio | Scripts/calc-loess-fitness.py | Python | mit | 47,499 | [
"Biopython",
"Bowtie"
] | 7f9d91b0bf2807fe128eb60b8a062d96ff089e2300f90d65c9515c73e76591d6 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/alerts/alertsplugin.py | Python | gpl-2.0 | 8,792 | [
"Brian"
] | 679bfd460a332a2374e35c186ea42d87df25aad7f02603688d287be320d78863 |
# Copyright 2012 Dorival de Moraes Pedroso. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from os.path import exists, normpath
from os import mkdir, remove
from glob import glob
from numpy import sqrt
class Vtu:
def __init__(se... | cpmech/tlfem | tlfem/vtu.py | Python | bsd-3-clause | 11,757 | [
"ParaView",
"VTK"
] | c53f884921eae35f3578f06768415081a815f57da9cb52242378e3274ba8b816 |
#!/usr/bin/env python
import matplotlib.pyplot as plt
import scipy.interpolate as scinterp
import scipy.signal
from scipy.ndimage import filters
import numpy as np
import peak_original
import sys
import random
import os
def moving_average(series, sigma=0.7):
b = scipy.signal.gaussian(39, sigma)
average = filte... | tayebzaidi/snova_analysis | Miscellaneous/SNANAanalysis_all.py | Python | gpl-3.0 | 4,110 | [
"Gaussian"
] | 33ae056b53713706ea0710ee8be025e1e05e77a4146a2a3d743fd03a0ce509a7 |
# List Splunk Indexes
# For use with Munk - Maltego for Splunk
# Author: Brian Warehime @nulltr0n
# 9/6/2014
# Importing various modules
from MaltegoTransform import *
import subprocess
import sys
import re
import ConfigParser
import os
# Configuration Parser to grab necessary options.
def getLocalConfPath():
path... | brianwarehime/munk | transforms/listindex.py | Python | gpl-2.0 | 2,893 | [
"Brian"
] | af76fc391e1280916d68561f9d2e5b4931e00f3394ef84ef3f908ae31589b768 |
#!/usr/bin/env python
from scipy import interpolate
from netCDF4 import Dataset
import os
import numpy as np
import shutil
import f90nml
from wrfpy.config import config
from wrfpy import utils
from datetime import datetime
class wrfda_interpolate(config):
def __init__(self, itype='rural'):
if itype not in ['ru... | rvanharen/wrfpy | wrfpy/scale.py | Python | apache-2.0 | 6,461 | [
"NetCDF"
] | eb8f149e2d0935e2504c42457977181dbaf25f3c89890357b1f5d2a526c36933 |
"""
Process an input dataset into a format suitable for machine learning.
"""
from __future__ import division
from __future__ import unicode_literals
import os
import gzip
import pandas as pd
import numpy as np
import csv
import numbers
import tempfile
import time
import sys
from deepchem.utils.save import log
from dee... | ktaneishi/deepchem | deepchem/data/data_loader.py | Python | mit | 13,764 | [
"RDKit"
] | 62901fcbd651c19db1c8d7c2a61ec2942bd8ffa0c6c6e1fbcda66b90a3dd01ce |
import os
import pytest
import re
import shutil
import capybara
from capybara.tests.compat import patch
@pytest.mark.requires("screenshot")
class TestSaveScreenshot:
@pytest.fixture
def alternative_path(self):
return os.path.join(os.getcwd(), "save_screenshot_tmp")
@pytest.fixture(autouse=True)
... | elliterate/capybara.py | capybara/tests/session/test_save_screenshot.py | Python | mit | 2,518 | [
"VisIt"
] | 9fa3375cb257b62c316fefd65ec0ab88e053e8bc3a37b4ca9276fb2aac056f8c |
#!/usr/bin/env python
# coding=utf-8
import unittest
import time
from ct.crypto import cert
from ct.crypto import error
from ct.crypto.asn1 import oid
from ct.crypto.asn1 import x509_common
from ct.crypto.asn1 import x509_extension as x509_ext
from ct.crypto.asn1 import x509_name
from ct.crypto.asn1 import x509
from ... | mozmark/tls-observatory | vendor/github.com/google/certificate-transparency/python/ct/crypto/cert_test.py | Python | mpl-2.0 | 31,484 | [
"VisIt"
] | dd3c23fd8154c2480682ed578bb4fe400aa7aeed57454953b5429b88a884df41 |
#!/usr/bin/env python3
# coding=utf-8
"""
agps3.py is a Python 2.7-3.5 GPSD interface (http://www.catb.org/gpsd)
Defaults host='127.0.0.1', port=2947, gpsd_protocol='json' in two classes.
1) 'GPSDSocket' creates a GPSD socket connection & request/retrieve GPSD output.
2) 'DataStream' unpacks the streamed gpsd data int... | wadda/gps3 | gps3/agps3.py | Python | mit | 9,115 | [
"MOE"
] | 7b27a8eedbfb29b1381f14e841375cfcf0158b1ac099a68ac059f24a5639a04d |
# structures.py
# Author: Ben Names
"""
This module contains a library of classes devoted to structural analysis.
The primary purpose of this library is to fascilitate the ROM (reduced order
modeling) of structures that can simplified to beams. The real power of this
library comes from it's the XSect class. This class... | bennames/AeroComBAT-Project | AeroComBAT/Structures.py | Python | mit | 237,082 | [
"Mayavi"
] | b250eaa7ea3f5627ec75ef53e0dfe5547597014e78ffdb878158fdb5814d829b |
"""
Courseware views functions
"""
import logging
import urllib
import json
from datetime import datetime
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolve... | hamzehd/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 56,770 | [
"VisIt"
] | dd62c54af56f85d2e87e704d7bc2586c88046f2ce464335cc1bd547633e3d3c1 |
#!/usr/bin/env python
import pprint
import re
import os, sys
import unittest
sys.path[0:0] = ['.', '..']
from pycparser import c_parser
from pycparser.c_ast import *
from pycparser.c_parser import CParser, Coord, ParseError
_c_parser = c_parser.CParser(
lex_optimize=False,
yacc_debug... | CtheSky/pycparser | tests/test_c_parser.py | Python | bsd-3-clause | 69,710 | [
"MOE",
"VisIt"
] | 75e3276a307145577bf2b39f962e746507c5eab96173106ad3e32bde93cecebb |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/delegates/virtualaddressdelegate.py | Python | gpl-2.0 | 2,612 | [
"VisIt"
] | 34752f2f0111fca677f9b90ad1c39df0a876acfdf2c99247459cb1c34bbdfb3d |
#!/usr/bin/env python3
from collections import defaultdict, namedtuple
from esipy import App, EsiSecurity, EsiClient
import codecs
FILE='refresh.code'
ESI = namedtuple('ESI', ['app', 'security', 'client'])
def init_esi():
esi_app = App.create('https://esi.evetech.net/_latest/swagger.json?datasource=tranquility... | eve-val/market-site | esi_load.py | Python | mit | 2,731 | [
"VisIt"
] | de9aa778ff559ca66d2f5099d69c2812dfac40af05f4ec3c87a37c21a89e0db4 |
#!/usr/bin/env python
import os, pickle, random, time
try:
os.remove('my_gp_module.pyc')
except OSError:
pass
import scipy as sp
from scipy.linalg import eigh
from my_gp_module import GaussianProcess
import matplotlib.pyplot as plt
# --------------------------------------------
# WHAT IT DOES:
# Given Nfixed ... | marcocaccin/MarcoGP | swipe_nteach.py | Python | apache-2.0 | 4,205 | [
"Gaussian"
] | 87e8f181089e909b0493b24a59d7b094bb38688b0ced133a57f3a67154dda17b |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of t... | aristanetworks/arista-ovs-nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 88,973 | [
"FEFF"
] | cfdeace40c05339a1fbc8a791af16f9a6da808d0fe6e42699c9d1257712b20ab |
from .metadata_wrapper import DeletedInvalidMetadata
class MetadataWrappers:
"""A class that generates a collection of MetadataWrapper objects, e.g. CRF
or REQUISITION, from a queryset of metadata objects.
See classes Crf, Requisition in edc_visit_schedule.
"""
metadata_getter_cls = None
me... | botswana-harvard/edc-meta-data | edc_metadata/metadata_wrappers/metadata_wrappers.py | Python | gpl-2.0 | 1,037 | [
"VisIt"
] | 7f27b0488a5b9b74590867e42d1227c9b95a8bdfc9149582a2fd6d3ebcbe1d12 |
"""
Atomic coordinate featurizer.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Joseph Gomes and Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "LGPL v2.1+"
import numpy as np
from deepchem.utils.... | rbharath/deepchem | deepchem/feat/atomic_coordinates.py | Python | mit | 9,305 | [
"MDTraj",
"RDKit"
] | fb7d994aae15d92732ee67279124422568d7f6fcc5455aa0f2018bdabdf723e7 |
# Lint as: python3
"""Mechanistic models for forecasting epidemics."""
import abc
import collections
import dataclasses
from typing import Callable, Mapping, Text, Union
from epi_forecast_stat_mech import utils
from epi_forecast_stat_mech.statistical_models import probability as stat_prob
from flax.deprecated import n... | HopkinsIDD/EpiForecastStatMech | epi_forecast_stat_mech/mechanistic_models/mechanistic_models.py | Python | apache-2.0 | 53,894 | [
"Gaussian"
] | 36cfc99116751043f1ecbb3d568b8dc6329ca9f2e9a2f99f603f64971fe97035 |
#!/usr/bin/env python
# Copyright (C) 2014 Open Data ("Open Data" refers to
# one or more of the following companies: Open Data Partners LLC,
# Open Data Research LLC, or Open Data Capital LLC.)
#
# This file is part of Hadrian.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this... | opendatagroup/hadrian | titus/titus/pmml/version_3_2.py | Python | apache-2.0 | 80,914 | [
"NEURON"
] | e4fbfe49d4ae0d8f333228065d25966190c271534acd19baf87f59b083c08f59 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | arunkgupta/gramps | gramps/gen/plug/menu/_person.py | Python | gpl-2.0 | 1,791 | [
"Brian"
] | 217df6a4aacc87e88f9f62cf009cfc3e569f0cf557bc9f56aef69220ac54312f |
"""
Class for making requests to a ComponentMonitoring Service
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client import Client
class ComponentMonitoringClient( Client ):
def __init__( self, **kwargs ):
"""
Constructor function
"""
Client.__init__( self, **kwargs )
self.setServer( 'Framework/... | arrabito/DIRAC | FrameworkSystem/Client/ComponentMonitoringClient.py | Python | gpl-3.0 | 343 | [
"DIRAC"
] | 6a29960b40505e5e37cf1898a2d555dcef8486061ee73fdf6d49491ebfbeb8f0 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | liuwenf/moose | python/chigger/tests/exodus/blocks/combo.py | Python | lgpl-2.1 | 1,416 | [
"MOOSE",
"VTK"
] | 66942f2b1c7ea154f90ea6eda1826ab2f8043f0bff17540e45e70539b88cab75 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | wshallum/ansible | lib/ansible/modules/cloud/amazon/elasticache.py | Python | gpl-3.0 | 21,767 | [
"Dalton"
] | 1b6a4814e6e1daa2fd91fc175ec51389da8cb516653000a92e47397150524812 |
# -*- coding: utf-8 -*-
#
# test_rate_neuron_communication.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2... | terhorstd/nest-simulator | pynest/nest/tests/test_rate_neuron_communication.py | Python | gpl-2.0 | 9,241 | [
"NEURON"
] | 58e5421a480b22dd6c66a3c53203190996e099332118ff5f72d91268ef8e78cc |
# Symmetry can only be used in EELS spectra calculations for GPAW svn 6305 above.
# Refer to A. Rubio and V. Olevano, et.al, Physical Review B 69, 245419 (2004)
# for comparision of results
import os
import sys
from math import sqrt
import numpy as np
from ase import Atoms
from ase.units import Bohr
from ase.parallel... | ajylee/gpaw-rtxs | gpaw/test/big/response/graphite_EELS.py | Python | gpl-3.0 | 1,978 | [
"ASE",
"GPAW"
] | e6519528c5c33e519d6e7c15d9029ac53ed9a6c8feaa97c5db096e6532e7b6d3 |
from __future__ import print_function
import vigra
from vigra import graphs
from vigra import numpy
import pylab
# parameter
filepath = '12003.jpg' # input image path
sigmaGradMag = 2.0 # sigma Gaussian gradient
superpixelDiameter = 10 # super-pixel size
slicWeight = 10.0 # SLIC color - spatial weight
beta ... | dstoe/vigra | vigranumpy/examples/merge_graph.py | Python | mit | 1,698 | [
"Gaussian"
] | f635f0a79ca476d7a1d49974307cc4ea0464994efeb3677d230e9606a8d6d655 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import warnings
import six
import ruamel.yaml as yaml
import os
"""
This module provides classes to perform topological analyses of structures.
"""
__author_... | matk86/pymatgen | pymatgen/analysis/structure_analyzer.py | Python | mit | 88,389 | [
"CRYSTAL",
"Gaussian",
"Jmol",
"pymatgen"
] | b8f581bcfd7cf092804084d9985c423f6d80d443d47b8c11a8f9e14c67acd772 |
# Copyright (c) 2003-2012 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | yorvic/.vim | bundle/python-mode/pylibs/pylama/checkers/pylint/checkers/design_analysis.py | Python | gpl-3.0 | 16,295 | [
"VisIt"
] | 4214f8c97b6eaef3883949921a02bcd3d32e2adf4372aafcc7d59a156b3716ad |
"""Global variables associated to the test suite."""
#: List of CPP variables that should be defined in config.h in order to enable this suite.
need_cpp_vars = [
"HAVE_NETCDF",
]
#: List of keywords that are automatically added to all the tests of this suite.
keywords = [
"netcdf"
]
#: List of input files
inp_files ... | abinit/abinit | tests/etsf_io/__init__.py | Python | gpl-3.0 | 448 | [
"NetCDF"
] | 3b687bd98d611ff01f2baf0aa9a177d8d18ae464773a7068102d4230d2ae8831 |
#!/usr/bin/env python3
import logging
import random
import re
import time
from uuid import uuid4
from telegram import InlineQueryResultArticle, InputTextMessageContent
from telegram.ext import Updater, CommandHandler, InlineQueryHandler
def start(bot, update):
update.message.reply_text("""Returns a random value.... | DanAmador/telegram-dice-bot | dice.py | Python | mit | 2,992 | [
"VisIt"
] | 61dedb154ed5bebb498e14d3f547d297f84e7d34f10cf8396ba9b1620417878b |
""" SandboxMetadataDB class is a front-end to the metadata for sandboxes
"""
__RCSID__ = "$Id$"
import types
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Utilities import List
from DIRAC.Core.Security import Properties, CS
class SandboxMetadataDB( DB ):
def __init__(... | calancha/DIRAC | WorkloadManagementSystem/DB/SandboxMetadataDB.py | Python | gpl-3.0 | 16,994 | [
"DIRAC"
] | 1706d9b9b8a8ddc960b05093be78e3d2eca3a29eab12ac5acbefb71e6630e916 |
# -*- coding: utf-8 -*-
#
# gap_junctions_inhibitory_network.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version... | hesam-setareh/nest-simulator | pynest/examples/gap_junctions_inhibitory_network.py | Python | gpl-2.0 | 5,513 | [
"NEURON"
] | d70c3f79fd1b46dd1c24ebc372fc55e6fa51195f268dceb513cf3824719cd522 |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | spirrello/spirrello-pynet-work | applied_python/lib/python2.7/site-packages/pylint/lint.py | Python | gpl-3.0 | 58,105 | [
"VisIt"
] | 7ffa0b799575dc0a5b71c41c344bd36e6632b8610696ffed22445c291ed4bf3a |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
# Octopus! sounds goood :-)
''' * Re-encodes mp3 and wav * '''
import os
import re
import sys
import time
import json
import random
import multiprocessing
from subprocess import Popen, PIPE, TimeoutExpired
from clint.textui import progress
import taglib
# *** Configs ***... | timkofu/octopus | octopus.py | Python | mit | 5,750 | [
"Octopus"
] | 3f09d941109ca17219877693b0db25cbf33b89d17c6828cb88aadbde24367dc3 |
import collections
import datetime as dt
import pandas as pd
from pandas.util.testing import assert_index_equal
from ..util import multi_mode_write, get_mono_line_copyright_message, to_buffer
WEEK_DAYS = ("Sunday", "Monday", "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday")
INSTANTS_COLUMNS = (
"year",... | Openergy/oplus | oplus/weather_data/weather_data.py | Python | mpl-2.0 | 16,548 | [
"EPW"
] | 47820512b2f69a14a8dad2774324c63f23523ef587ef7cd9e828681db805efaa |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import numpy as np
from pymatgen.analysis.defects.core import (
DefectEntry,
Interstitial,
Substitution,
Vacancy,
create_saturated_interstitial_structure,
)
from pymatgen.core i... | vorwerkc/pymatgen | pymatgen/analysis/defects/tests/test_core.py | Python | mit | 16,270 | [
"pymatgen"
] | 501b9eeec3392400ee0f6433560eeec0e3a8a3c240c42a1cc4cc8ba7678d7459 |
from ANNarchy import *
# ###########################################
# Configuration
# ###########################################
setup(dt=0.1)
# ###########################################
# Network parameters
# ###########################################
NE = 8000 # Number of excitatory cells
NI = NE/4 ... | vitay/ANNarchy | benchmarks/brunel/ANNarchy-STDP.py | Python | gpl-2.0 | 3,078 | [
"NEURON"
] | 3bbffdb559ab0f26492ba87394f7ea9368c64a981049ad87fa9e6bc89443edcf |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/ajax/channels.py | Python | gpl-2.0 | 18,606 | [
"VisIt"
] | 4e5d547dbfc96e2fa2964008fd1a5b050933e2667ec95b14d703442bcc0653cd |
from sklearn.naive_bayes import GaussianNB
import pandas as pd
import numpy as np
# you can type the data by yourself in a dictionary and then make it into data frame
# d = {'Gender' : ['male', 'male', 'male', 'male', 'female', 'female', 'female', 'female']
# , 'height' : [6, 5.92, 5.58, 5.92, 5, 5.5, 5.42, 5.75]
#... | tangsttw/python-machine-learning-practice | Naive-Bayes/naive-bayes.py | Python | mit | 915 | [
"Gaussian"
] | a53bef4d1daa403634d1cb5ed2db28a35ce39d28cd1bcec36e8962d08a850180 |
#!/usr/bin/env python
"""
A front-end module to run a compiled kMC model. The actual model is
imported in kmc_model.so and all parameters are stored in kmc_settings.py.
The model can be used directly like so::
from kmos.model import KMC_Model
model = KMC_Model()
model.parameters.T = 500
model.do_step... | mieand/kmos | kmos/run/__init__.py | Python | gpl-3.0 | 76,904 | [
"ASE"
] | 0fd3bc0df1f455e896499774b69006ed867c401e7a78c8e65b77a7c7bd1c7957 |
##Run Add-On Pack Installer
import urllib,urllib2,re,xbmcplugin,xbmcgui,xbmc,xbmcaddon,os,sys,downloader,extract,time,shutil,subprocess
from resources.modules import main
addon_id='script.pack.installer'; AddonTitle='Add-on Pack Installer';
wizardUrl='https://raw.githubusercontent.com/Josh5/addon-packs/master/'; #... | Josh5/Add-on-Pack-Installer | script.pack.installer/default.py | Python | gpl-2.0 | 13,216 | [
"VisIt"
] | 2dce9e0e82bec3b03266d78ad7722bd31b0768a477c79600db6de4a08ec3a473 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.ext.jhu import get_kpoints
from pymatgen.io.vasp.inputs import Incar
__... | matk86/pymatgen | pymatgen/ext/tests/test_jhu.py | Python | mit | 903 | [
"VASP",
"pymatgen"
] | bc585ad226cdeaca9d61aa60ea9a647f22bae98a7ccf858ff2dedf0198ac0daa |
import numpy as np
import pylab
import ase.transport.stm as stm
# Parameters for a simple model.
#
#
# * eps_a
# v_ts / \ v_a2
# ... * * * * * * * * * ...
# \/ \/
# t1 ... | grhawk/ASE | tools/ase/transport/stm_test.py | Python | gpl-2.0 | 1,715 | [
"ASE"
] | 664866853c26650b0d3653c7981e12c8079ec9d1befb6fd686b5d11f7c788dbe |
# Copyright 2010 CAMd
# (see accompanying license files for details).
from optparse import OptionParser
import numpy as np
from ase.lattice.surface import fcc111, hcp0001, bcc110, bcc100, diamond111, \
add_adsorbate
from ase.structure import estimate_lattice_constant
from ase.data import reference_states, atomi... | grhawk/ASE | tools/ase/utils/adsorb.py | Python | gpl-2.0 | 6,505 | [
"ASE",
"CRYSTAL"
] | 55a104316ee6a19e89f05e7e555d8c850f72dde8b42d4665a2bf27ad39fd74b0 |
"""
Author: Willem Wybo
Date: 18/08/2015
Place: BBP, Geneva
"""
import matplotlib.pyplot as pl
import numpy as np
import copy
import pickle
from multiprocessing import Pool
from mpl_toolkits.axes_grid1 import ImageGrid
import morphologyReader as morphR
import neuronModels as neurM
save = True
overwrite = True
def... | WillemWybo/SGF_formalism | fig2_axon.py | Python | mit | 16,920 | [
"NEURON"
] | 0929403a716172073239b8d05132badb33b3ff09c5c168d411d39babd703f33d |
import json
import numpy
from heroes import HEROES
__author__ = 'yanbo'
import io
import os
from smoke.io.wrap import demo as io_wrap_demo
from smoke.replay import demo as replay_demo
from smoke.replay.const import Data
import pylab
import matplotlib
import matplotlib.image
import scipy.ndimage
import cPickle
from map... | Morijarti/dota-2-heatmap | heatmap_generator.py | Python | mit | 10,141 | [
"Gaussian"
] | b0288399e986dfcd6fd75f9d8aff6d3bc48edc210dae93c3f4fe66f8dd0d341f |
import functools
import gym
from math import log
import numpy as np
import tree # pip install dm_tree
from typing import Optional
from ray.rllib.models.action_dist import ActionDistribution
from ray.rllib.models.torch.torch_modelv2 import TorchModelV2
from ray.rllib.utils.annotations import override, DeveloperAPI, Ex... | ray-project/ray | rllib/models/torch/torch_action_dist.py | Python | apache-2.0 | 23,924 | [
"Gaussian"
] | e09d5551592b47231f91b8167b12dca8f557e995203a57f9c9e2801a5c006ee6 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_loanwizard.py | Python | gpl-2.0 | 6,632 | [
"VisIt"
] | e23cd9da24a6f3fcd64676c99f261c117452dc7cc78a696893b863b3c6374d23 |
# (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... | scollis/iris | lib/iris/tests/test_grib_load.py | Python | gpl-3.0 | 27,803 | [
"Gaussian"
] | 5de3483f7c09e631f3886f06dcaa20ef72999fdeba7e4a3e522bf81d06c34765 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. You s... | ghutchis/cclib | test/parser/testutils.py | Python | lgpl-2.1 | 2,297 | [
"cclib"
] | 4937add3e50768bc6b496eda6231f686ac415a2a077af82b4406beeb89d9ccec |
# This test is partly based from:
# https://www.argpar.se/posts/programming/testing-django-admin/
from urllib.parse import urljoin
import json
from bs4 import BeautifulSoup
from django import forms
from django.contrib.admin import ACTION_CHECKBOX_NAME
from django.contrib.admin.sites import AdminSite
from django.c... | seanballais/botos | tests/test_admin.py | Python | gpl-3.0 | 95,577 | [
"VisIt"
] | 39448ff5b7675b62616348bf5bc54b8c955739b2fc6d990416a489a147a0f979 |
#!/usr/bin/env python
"""
Modal analysis of a linear elastic block in 2D or 3D.
The dimension of the problem is determined by the length of the vector
in ``--dims`` option.
Optionally, a mesh file name can be given as a positional argument. In that
case, the mesh generation options are ignored.
The default material ... | lokik/sfepy | examples/linear_elasticity/modal_analysis.py | Python | bsd-3-clause | 12,393 | [
"VTK"
] | 257bd74afb27daffb178d4bc857aa82ea49388fe7ccbbb9a9c6bf2c0fc54f57c |
"""
@name: PyHouse/src/Modules/Famlies/UPB/_test/test_UPB_Pim.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Apr 8, 2013
@summary: Test the UPB controller.
Passed all 30 tests - DBK - 2015-08-15
"""
... | DBrianKimmel/PyHouse | Project/src/Modules/House/Family/Upb/_test/test_UPB_Pim.py | Python | mit | 6,366 | [
"Brian"
] | d64119c1f9f0336009b9a47652dadb6ad6697f1b2ce53f7dee558d92f8a13994 |
import numpy as np
import pytest
from dftCode.geometry import _M, _N, gen_r_G_G2
from dftCode.charge_dis import gaussian,charge_dis
def test_gaussian():
""" Tests the gaussian charge distribution routine in charge_dis.py
"""
assert np.allclose(gaussian([0.75,0.5],[1,-1],np.linspace(0,1,10)),np.array([-0.3... | nycmouli/PYDFT | tests/test_charge_dis.py | Python | mit | 1,089 | [
"Gaussian"
] | 4ee7d1c9e47940fe5d7c877ba5f0181b45632cdae3d1e40a80c4830ba0b2e87b |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 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 y... | jat255/hyperspy | hyperspy/_components/gaussian2d.py | Python | gpl-3.0 | 5,242 | [
"Gaussian"
] | 3bc476f7a06a0381398f58e3837391a01739edff68a0074cd52e042a00285c54 |
#!/usr/bin/env python
"""
boundary.py
ROMS boundary utilities
Written by Brian Powell on 01/15/14
Copyright (c)2010--2021 University of Hawaii under the MIT-License.
"""
import seapy
import numpy as np
import netCDF4
import textwrap
from collections import namedtuple
from rich.progress import track
# Defin... | powellb/seapy | seapy/roms/boundary.py | Python | mit | 40,579 | [
"Brian",
"NetCDF"
] | a596acefe043da6f5c471f33ba934b5b51639d549f399002e5d55566365ea9c9 |
import hashlib
import numpy as np
from cryspy import numbers as nb
from cryspy import geo as geo
from cryspy import blockprint as bp
from cryspy import tables
class Drawable():
def __init__(self, name, pos):
assert isinstance(name, str), \
"First argument of crystal.Drawable.__init__(...) must ... | cryspy-team/cryspy | cryspy/crystal.py | Python | gpl-3.0 | 19,865 | [
"CRYSTAL"
] | 6df14860fb6abd1d5a6d2a8442d19cbb6319ae50e3494872ae2e5eaafd4ba4f0 |
#!/usr/bin/env python
"""
Extract genomic signal label sequences from the genome sequence and annotation file.
Transcription Start Site[tss],
Translational Initiation Site[tis],
Splice Sites [don, acc],
Transcription Stop Site[cleave]
Translation Stop Site [cdsstop]
the resulting label sequ... | vipints/genomeutils | signal_labels/fetch_signal_seq_examples.py | Python | bsd-3-clause | 60,843 | [
"Biopython"
] | b34711a1ed356355a9b7a6abbdc73f684a3daf6fdd36a4a3d57c760c0c73e19d |
from PyQt4 import QtGui, Qt, QtCore
from PyQt4.QtGui import QLabel
from PyQt4.QtGui import QWidget
from PyQt4.QtGui import QToolBar
from PyQt4.QtGui import QPushButton
from PyQt4.QtGui import QGridLayout
from PyQt4.QtGui import QTextEdit
from PyQt4.QtCore import QMimeData
from PyQt4.QtGui import QDrag
from PyQt4.QtGui ... | dilawar/moose-full | moose-gui/plugins/NeuroKitVisualizer.py | Python | gpl-2.0 | 5,434 | [
"MOOSE"
] | 9736e2cc23dad93c448c096316f4f33d1837b7e587d88ffce136e5e32f3e4801 |
import ast
class IndentGetter(ast.NodeVisitor):
@classmethod
def get_lines(cls, text_or_node):
if isinstance(text_or_node,str):
node = ast.parse(text_or_node)
else:
node = text_or_node
parser = cls()
return parser.process_text(node)
def process_text(... | furbrain/tested | tested/scopes/indents.py | Python | gpl-3.0 | 862 | [
"VisIt"
] | 9035939fdc0cbf794ee7a8c2224208444ee7419f3758ab55bb8a4f629d66dd7f |
""" This module implements the ResNet34 CNN archiecture. The implementation is vase don the implementation
provided within examples of Keras library: https://github.com/fchollet/keras/blob/master/keras/applications/resnet50.py.
"""
# Keras
from keras.layers import Convolution2D, Activation, Dense, Flatten, Input, merg... | kcyu2014/ml_project2 | project2/model/resnet.py | Python | mit | 5,709 | [
"NEURON"
] | 1b27fe10daf19c42160f9f04744f56aa676b1bd8afb59b7fa31979d456b2ef9e |
r"""
Laplace equation in 1D with a variable coefficient.
Because the mesh is trivial in 1D, it is generated by :func:`mesh_hook()`, and
registered using :class:`UserMeshIO <sfepy.discrete.fem.meshio.UserMeshIO>`.
Find :math:`t` such that:
.. math::
\int_{\Omega} c(x) \tdiff{s}{x} \tdiff{t}{x}
= 0
\;, \qu... | rc/sfepy | examples/diffusion/laplace_1d.py | Python | bsd-3-clause | 2,313 | [
"VTK"
] | 02c5f210edb9dd4720a30b493809d3aca6a1916e9e8b04f3fc6e927779c4859b |
import unittest
from python.src.neural_networks.neural_network_utils import NeuralNetworkUtils
from python.src.neural_networks.feed_forward import FeedForwardNN
class NeuralNetworkUtilsTest(unittest.TestCase):
def test_output_breadth_traversal(self):
network = FeedForwardNN(structure = [1, 3, 5, 4, 2])
... | DomenicD/dom_ml_playground | python/test/neural_networks/neural_network_utils_test.py | Python | mit | 559 | [
"NEURON"
] | 1507838a308b5838b752400a2a91982b2ae41d108cd2d68d23a77884b41293c7 |
# -*- encoding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
# noinspection PyUnresolvedReferences
from h2o.utils.compatibility import * # NOQA
from h2o.exceptions import H2OValueError
from h2o.model.extensions import has_extension
from h2o.model.model_base import Model... | michalkurka/h2o-3 | h2o-py/h2o/model/regression.py | Python | apache-2.0 | 5,205 | [
"Gaussian"
] | e7bdf8dcc6a8eab9dbb7cd3ffc305d81ba38025aef05310a36967fc132937507 |
# This file is part of Radler.
#
# Radler 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.
#
# Radler is distributed in the hope that it... | SRI-CSL/radler | radler/radlr/ros/roscmake.py | Python | gpl-3.0 | 6,273 | [
"VisIt"
] | 71524bf8f6ba3b723a15982d8b4e465239aa9b827d21dcb1468a2752cf4e4f13 |
"""
netParams.py
High-level specifications for M1 network model using NetPyNE
Contributors: salvadordura@gmail.com
"""
from netpyne import specs
import pickle, json
netParams = specs.NetParams() # object of class NetParams to store the network parameters
netParams.version = 49
try:
from __main__ import cfg ... | thekerrlab/netpyne | examples/M1detailed/netParams.py | Python | mit | 36,624 | [
"Elk"
] | 413e038b507698b826fee2125639ab374e33245567c1e3ee5c4536585c85b374 |
"""Different python compatible f2py subroutines."""
import ase.dftd.dftd_native
from ase.dftd.dftd_interface import d3_pbc
from ase.dftd.dftd_interface import d2_pbc
| alexei-matveev/ase-local | ase/dftd/__init__.py | Python | gpl-2.0 | 169 | [
"ASE"
] | 8b8fd65a077959812e7e06b35975a59580bbbd7d1e846b6f3760aa10f9be2a4f |
import numpy as np
from scipy.optimize import least_squares
import mol_io as io
def read_ref(refname):
with open(refname,'r') as f:
data = list(f)
mol = np.empty(len(data))
ref = np.empty(len(data))
for i,line in enumerate(data):
tmp = line.split()
mol[i] = float(i)
ref... | jmargraf/agrippa | DFfit/DFfit.py | Python | gpl-3.0 | 3,665 | [
"ORCA"
] | f26f73e93c11638d9249424050ef0eb00db92e433812b3c60c2730951394964d |
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