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#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
"""
test_parsing
~~~~~~~~~~~~~~
Test parsing of basis set data from raw EMSL BSE downloads.
"""
import json
import sys
import unittest
from src.EMSL_dump import EMSL_dump
class ParserTestCa... | mattbernst/ebsel | tests/test_parsing.py | Python | mit | 12,896 | [
"GAMESS",
"NWChem"
] | e1fe6e6967b03e2ce80304aaf1aae1452869df8e03b08c9bf55995fd1f9d0b5e |
### INSTRUCTIONS ###
'''
Today, as you were browsing for flights to visit the San Francisco office, you discovered that all flights were on sale for $10. Being a curious developer, you discovered that the bug giving the $10 tickets allows you to pick any number of airports for layovers as long as you don't repeat any s... | SelvorWhim/competitive | Bloomberg_codecon/2016_Qualifiers/travel_to_the_west.py | Python | unlicense | 1,885 | [
"VisIt"
] | 6107c77aed566f3419f50de15ba222eff9a5897caaf0c9f49406f91865cbd2de |
#!/usr/bin/env python
#coding: utf-8
### Functions ###
def header(string):
"""
Display header
"""
timeInfo = time.strftime("%Y-%m-%d %H:%M")
print '\n', timeInfo, "****", string, "****"
def average_read_len(bam, sampleSize):
"""
Compute the average read length based on a subset o... | brguez/TEIBA | src/python/germlineMEI4bkpAssembly.py | Python | gpl-3.0 | 5,543 | [
"pysam"
] | c64a0914fdfc7e5b9877e0527b4d0e1fa7dfd05045115624096d8fa8191fe9ff |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# PMDA
# Copyright (c) 2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the GNU Public Licence, v2 or any higher ve... | MDAnalysis/pmda | pmda/contacts.py | Python | gpl-2.0 | 12,291 | [
"CRYSTAL",
"MDAnalysis"
] | f68196f542e04cfbb82fdeb7befba7cf23fa2a4243b878968bfb08a88f57cdf7 |
# (c) Nelen & Schuurmans. GPL licensed, see LICENSE.rst.
# Base Django settings, suitable for production.
# Imported (and partly overridden) by developmentsettings.py which also
# imports localsettings.py (which isn't stored in svn). Buildout takes care
# of using the correct one.
# So: "DEBUG = TRUE" goes into devel... | lizardsystem/lizard-efcis | lizard_efcis/settings.py | Python | gpl-3.0 | 7,621 | [
"BLAST"
] | 7141f20a9f93077b804ac2fd2e1933ea0b2440b2f4b315bcfeaad0e71921a507 |
# $HeadURL$
__RCSID__ = "$Id$"
import threading
import thread
import time
import random
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.Client.PathFinder import getGatewayURLs
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilit... | Andrew-McNab-UK/DIRAC | ConfigurationSystem/private/Refresher.py | Python | gpl-3.0 | 6,790 | [
"DIRAC"
] | 0a786deab2ebca52e60d37a1cb15b3f3d681de0773b46b79db8e6eb9318c6025 |
#!/usr/bin/env python
"""
RS 2014/02/03: Wrapper class for marginalizing over E(B-V) and R_V
"""
# ----------------------------------------------------------------------------
# Dependencies
# ----------------------------------------------------------------------------
import numpy a... | rscalzo/pyBoloSN | SNMCMC/SNMCMC_EBMVwRV.py | Python | mit | 8,952 | [
"Galaxy"
] | deebbdbcf9c25366de4373a03513906861c1330d9dedb3a2eb0b440f76c2d7d1 |
from custom_io import get_remote_data, custom_io_constants
from parsing_tools import get_model_component_from_varname, lists
import os
from scipy.io import netcdf
import cdo
CDO = cdo.Cdo()
GLOBAL_DEBUG = False
class bcolors:
HEADER = '\033[95m'
OKBLUE = '\033[94m'
OKGREEN = '\033[92m'
WARNING = '\0... | AWI-Paleodyn/Python_Helpers | simulation_tools/__init__.py | Python | gpl-2.0 | 12,603 | [
"NetCDF"
] | dd8c3040e54d264ba3240261630ed2e540c802a88bd806a98ec35aa88ecbff48 |
tests=[
("python","testFeatures.py",{})
]
longTests=[]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestRunner.RunScript('test_list.py',0,1)
sys.exit(len(failed))
| soerendip42/rdkit | Code/ChemicalFeatures/Wrap/test_list.py | Python | bsd-3-clause | 215 | [
"RDKit"
] | c7c9df96422668328c349408e82c6a1402d1229298af946b8137b3cd2e79bc12 |
# encoding: utf-8
"""
Export (not only) geometry to various formats.
"""
from yade.wrapper import *
from yade import utils,Matrix3,Vector3
#textExt===============================================================
def textExt(filename, format='x_y_z_r', comment='',mask=-1):
"""Save sphere coordinates and other paramete... | ThomasSweijen/yadesolute2 | py/export.py | Python | gpl-2.0 | 31,320 | [
"VTK"
] | fc1dbee6e033fe448c9ebb4311d46d652a59fb6fc43f1a5269bcab99dd666452 |
import re
to_canonical = {
'BOND': ['bond'],
'ANGLE': ['angle'],
'UB': ['angle','urey_bradley'],
'DIHED': ['proper'],
'IMP': ['improper'],
'CMAP': ['cmap'],
'HBOND': ['h-bond'],
'VDWAALS': ['vdw_total'],
'1-4 VDW': ['vdw_14'],
'EEL': ['coulomb_total'],
'1-4 EEL': ['coul... | dgasmith/EEX_scratch | eex/translators/amber/amber_metadata.py | Python | bsd-3-clause | 8,561 | [
"Amber",
"LAMMPS"
] | 0eedb27c1c48878737c7e109ab354b29d8a38628a8cbdc08c147432ad808164b |
from plotly.basewidget import BaseFigureWidget
class FigureWidget(BaseFigureWidget):
def __init__(
self, data=None, layout=None, frames=None, skip_invalid=False, **kwargs
):
"""
Create a new :class:FigureWidget instance
Parameters
----------
data
... | plotly/python-api | packages/python/plotly/plotly/graph_objs/_figurewidget.py | Python | mit | 802,932 | [
"Gaussian",
"VisIt"
] | 9c18c348a945dacaa0a7729e80649d8068e6b2297ddbbb8e6aeffaa2489d8b8e |
########################################################################
# File : ComputingElement.py
# Author : Stuart Paterson, A.T.
########################################################################
""" The Computing Element class is a base class for all the various
types CEs. It serves several purpos... | DIRACGrid/DIRAC | src/DIRAC/Resources/Computing/ComputingElement.py | Python | gpl-3.0 | 21,966 | [
"DIRAC"
] | 4cc6fead1a2a530d08b5578c49b044104e0be4c8be9da90b68f9b822d0f89a6a |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/r-iranges/package.py | Python | lgpl-2.1 | 2,092 | [
"Bioconductor"
] | 9452e3c3b7a5d698ed4f3eefe2714a3e47a8fe43c0593ee6e6d415bed09af01a |
from typing import Callable, List, Tuple, Union
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from mpl_toolkits.mplot3d import Axes3D # NOQA
from . import hilbert
try:
from mayavi import mlab
maya_imported = True
except ImportError:
maya_imported = False
print("Could not im... | natl/fractaldna | fractaldna/structure_models/voxelisation.py | Python | mit | 20,447 | [
"Mayavi"
] | 5864c2fbbbc3dcf86b090c62f4302503827b4cbb449382e9230028d2faaaa0a7 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | mhlechner/psi4 | psi4/driver/qcdb/basislistdunning.py | Python | gpl-2.0 | 31,438 | [
"Psi4"
] | 242abde292a1c099c94fb6ae42510a5a615ab629e738c9a7f6627b963b801331 |
""" A collection of mutations that can be used. """
import numpy as np
from random import random, randrange
from math import ceil, cos, sin, pi
from ase.ga.utilities import atoms_too_close
from ase.ga.utilities import atoms_too_close_two_sets
from ase.ga.offspring_creator import OffspringCreator
from ase import Atoms
... | suttond/MODOI | ase/ga/standardmutations.py | Python | lgpl-3.0 | 8,833 | [
"ASE",
"Dalton"
] | 75a51441ba9cb589a8f8ed65091e3f0677970c7df70d4b2d77eed72a0fd1a8e1 |
# Chinese / 中文 - Translations - Python 3 Only!
from seleniumbase import BaseCase
from seleniumbase import MasterQA
class 硒测试用例(BaseCase): # noqa
def __init__(self, *args, **kwargs):
super(硒测试用例, self).__init__(*args, **kwargs)
self._language = "Chinese"
def 开启(self, *args, **kwargs):
... | mdmintz/SeleniumBase | seleniumbase/translate/chinese.py | Python | mit | 20,517 | [
"VisIt"
] | c563e6c23535636f5a7e7faa57677e10b64805fba65673368f1ecf46ec0551b5 |
# -*- coding: utf-8 -*-
"""
Created on Sun Jul 05 22:14:07 2015
plot ONE EDGE of ONE CELL, run the commented lines below main block to
generate the distributions first
@author: sweel
"""
# pylint: disable=C0103
import matplotlib.pyplot as plt
import seaborn as sns
import numpy as np
import cPickle as pickle
sns.set_con... | moosekaka/sweepython | tubule_het/plt_lineseries/Dist_DY_OneEdgeCell.py | Python | mit | 4,023 | [
"VTK"
] | 0e786ab98132eeffa3b2ab13edb87d3e3292b2d12864cd68be0b8a19298a91d3 |
# Copyright (c) 2014, Georgios Is. Detorakis (gdetor@gmail.com) and
# Nicolas P. Rougier (nicolas.rougier@inria.fr)
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redis... | gdetor/SI-RF-Structure | Statistics/protocols.py | Python | gpl-3.0 | 6,518 | [
"Gaussian"
] | 3e0ffaf58eee8033d0e43eae5a028d3724ec8489f2c0dfaa05f14629f83086a2 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/orthomcl/package.py | Python | lgpl-2.1 | 2,025 | [
"BLAST"
] | 18aecf48c2809b85d38c43db5951e4d9ea1a632e79de396f59d0b927a514d83f |
# from builtins import range
# from builtins import object
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input... | d-li14/CS231n-Assignments | assignment2/cs231n/classifiers/fc_net.py | Python | gpl-3.0 | 16,265 | [
"Gaussian"
] | e751d2ace4fc000b5839572f36f30ca436466e1d7cd5a6e20cd647da9b6050d7 |
#!/usr/bin/env python
__description__ = \
"""
Parse the output from diehdral-recorder.tcl and make it pretty and R-readable.
"""
__author__ = "Michael J. Harms"
__usage__ = "parse-dihedral.py diehdral-output"
__date__ = "110413"
import sys
class WaterError(Exception):
"""
General error class for this module.
... | harmsm/md-analysis-tools | frustration/parse-water.py | Python | unlicense | 1,211 | [
"VMD"
] | 5c76b517838b4984590515035d3f67954a186824e5bdcf813d547d54486e9150 |
import asyncio, discord, aiohttp
import re, io, random, datetime
from discord.ext import commands
from utils import checks
from mods.cog import Cog
code = "```py\n{0}\n```"
class Moderation(Cog):
def __init__(self, bot):
super().__init__(bot)
self.cursor = bot.mysql.cursor
self.discord_path = bot.path.discord
... | NotSoSuper/NotSoBot | mods/Moderation.py | Python | mit | 42,036 | [
"MOE"
] | 64685ccf41f9b22a45287a64aeed520d9fb530e88f3084417e8bb7ecd9659fdf |
from octopus.runtime import *
v = variable(0, "v", "v")
s = sequence(
loop_while(v < 5, sequence(
log("v = " + v),
set(v, v + 1)
)),
set(v, 0),
loop_while(v < 2, sequence(
log("v = " + v),
set(v, v + 1)
), min_calls = 5),
log("Done")
)
run(s)
| rasata/octopus | examples/test_while.py | Python | mit | 261 | [
"Octopus"
] | 49b57ff859119583366a827791cb771d478d334eb56340282e4a9da2cd57dfe3 |
# (C) British Crown Copyright 2010 - 2013, 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... | kwilliams-mo/iris | lib/iris/tests/test_grib_save.py | Python | gpl-3.0 | 10,295 | [
"NetCDF"
] | 575b0e759e93b02e3de4d4b57c94c23ebbf128fd4b0ae3c2b54d37577b6c6de9 |
import logging
from autotest.client.shared import error
@error.context_aware
def run_win_disk_write(test, params, env):
"""
KVM virtio viostor heavy random write load:
1) Log into a guest
2) Install Crystal Disk Mark [1]
3) Start Crystal Disk Mark with heavy write load
@param test: QEMU test... | sathnaga/virt-test | qemu/tests/win_disk_write.py | Python | gpl-2.0 | 1,559 | [
"CRYSTAL"
] | 464d55284934561234c2bc70ee9751f4a3f09c79e798dfe4f987191ae42cb91c |
import itertools
import os
import random
from datetime import datetime
from typing import Any, Callable, Dict, List, Mapping, Sequence, Tuple
import bmemcached
import orjson
from django.conf import settings
from django.contrib.sessions.models import Session
from django.core.management import call_command
from django.c... | brainwane/zulip | zilencer/management/commands/populate_db.py | Python | apache-2.0 | 38,985 | [
"Amber",
"Galaxy"
] | 95914cd305ece328584d4908ce4c4c093180423d7ed6f263165249991a6a4e0a |
# ============================================================================
#
# 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/proxy/queryproxy.py | Python | gpl-2.0 | 14,457 | [
"VisIt"
] | 806873ecc23ad6103920b5e6e75cffbf149c1744de3a16f1dea413c655828014 |
# This file is part of cclib (http://cclib.sf.net), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. Yo... | Clyde-fare/cclib_bak | src/cclib/method/mpa.py | Python | lgpl-2.1 | 4,568 | [
"cclib"
] | 617c523050c06b0319876d0de019cc4ce217f0347130f55072aed93712c6bfcc |
"""
Corrupt known signal with point spread
======================================
The aim of this tutorial is to demonstrate how to put a known signal at a
desired location(s) in a :class:`mne.SourceEstimate` and then corrupt the
signal with point-spread by applying a forward and inverse solution.
"""
# %%
import os... | bloyl/mne-python | tutorials/simulation/70_point_spread.py | Python | bsd-3-clause | 6,403 | [
"Gaussian"
] | 14a2b4146749b3cb44026e3acfd8a955f769a9d931da21924c9b67bb4c3883ea |
#! /usr/bin/env python
from __future__ import print_function
import openturns as ot
#from openturns.viewer import PlotSensitivity
ot.TESTPREAMBLE()
ot.RandomGenerator.SetSeed(0)
try:
input_dimension = 3
output_dimension = 1
formula = [
'sin(_pi*X1)+7*sin(_pi*X2)*sin(_pi*X2)+0.1*((_pi*X3)*(_pi*X3... | aurelieladier/openturns | python/test/t_SobolIndicesAlgorithm_std.py | Python | lgpl-3.0 | 3,478 | [
"Gaussian"
] | 421f3826e3def1ddde700bfe8d0c5a958d87407abc3c5464239937bb1603dc0e |
"""
This module defines common methods used in simulator specific build modules
@author Tom Close
"""
##########################################################################
#
# Copyright 2011 Okinawa Institute of Science and Technology (OIST), Okinawa
#
###################################################... | tclose/PyPe9 | pype9/simulate/common/code_gen/base.py | Python | mit | 19,174 | [
"NEURON"
] | 1dec512ea281c593cfa527be595dc15ef0ead84734328053a95d9689fe84e945 |
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, around, unique, asarray,
zeros, arange, sort, amin, amax, any, atleast_1d,
sqrt, ceil, floor, array, compress,
pi, exp, ravel, count_nonzero, ... | person142/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 117,580 | [
"Gaussian"
] | a8d7f0deb9980ef951968eae13632efb0bfc325100cca1a8489bd3ccb19f7f61 |
tests = [
("testExecs/testTransforms.exe", "", {}),
("testExecs/testGrid.exe", "", {}),
]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| rvianello/rdkit | Code/Geometry/test_list.py | Python | bsd-3-clause | 267 | [
"RDKit"
] | bbf6b5d6a355942fac77191340038a1563817f0da42e6368362bf8967f414309 |
import numpy as np
import pymc3 as pm
class MultiArmedBandit(object):
"""
A Multi-armed Bandit
"""
def __init__(self, k):
self.k = k
self.action_values = np.zeros(k)
self.optimal = 0
def reset(self):
self.action_values = np.zeros(self.k)
self.optimal = 0
... | bgalbraith/bandits | bandits/bandit.py | Python | apache-2.0 | 3,035 | [
"Gaussian"
] | ba18cbdd81794d122b5c775b2061e05942ccef0b3d71c259d072ae5df466b73d |
from functools import wraps
from .utils import smart_decorator, combine_alternatives
from .tree import Tree
from .exceptions import VisitError, GrammarError
from .lexer import Token
###{standalone
from inspect import getmembers, getmro
class Discard(Exception):
"""When raising the Discard exception in a transfo... | erezsh/lark | lark/visitors.py | Python | mit | 15,756 | [
"VisIt"
] | eac14526d819a65902f689e885a8a9fd4ad26c3a6f8317c0e2717cc11b76811c |
from django.test import TestCase
from flexible_permissions.agents import normalize_agent
from flexible_permissions.shortcuts import NULL
from tests.models import User, Group, Exhibit
from tests.utils import create_test_models
class AgentsTestCase(TestCase):
def setUp(self):
create_test_models()
def ... | staab/django-flexible-permissions | tests/test_agents.py | Python | mit | 1,124 | [
"VisIt"
] | 4435673af062eb638f0d00b8b29a602987e04cd4ec6fc5b45d56c5f1913426d4 |
########################################################################
# $HeadURL $
# File: OperationHandlerBase.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/03/13 13:48:52
########################################################################
""" :mod: OperationHandlerBase
=========================... | calancha/DIRAC | RequestManagementSystem/private/OperationHandlerBase.py | Python | gpl-3.0 | 8,755 | [
"DIRAC"
] | d91d5782710b34e29be2ee015b3cade77756e8233958318b996131dfb14d3e9b |
# -*- coding: utf-8 -*-
# -*- coding: utf-8 -*-
# Copyright (c) 2020 Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
import pytest
from ansible import context
from ansibl... | azaghal/ansible | test/units/cli/galaxy/test_execute_list.py | Python | gpl-3.0 | 1,734 | [
"Galaxy"
] | 9afa50373bc75763b1c9ad64a7abbdde30be81e3a09b57f1c218a5f7631c90f6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import re
import itertools
import warnings
import logging
import math
import glob
import six
import numpy as np
from numpy.linalg import det
from co... | setten/pymatgen | pymatgen/io/vasp/inputs.py | Python | mit | 73,261 | [
"VASP",
"pymatgen"
] | ddd081c455dd8395f06aa74096645dc8811ac60d53275dd36f4dd9d9f4ad4257 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_backup.py | Python | gpl-3.0 | 4,617 | [
"VisIt"
] | f613bdcb218ed768b58aad9a2ccc1d6e0434b27a82b6a0c60a153707891d7f8e |
"""
This module contains a list of movies and logic to trigger opening the
Fresh Tomatoes Movie Trailer page.
"""
#------------------------------------------------------------------------------
#
# Developer Notes:
#
# Even though media.Movie only requires some arguments, I have included all
# optional arguments (kwar... | hessler/udacity-movie-trailer-website | movie_trailer_website/entertainment_center.py | Python | mit | 18,440 | [
"CASINO"
] | 5d8544dd6e6313a0aa958e8e78e3ab9a368e4bcfa3d05b241277c4fe85d68837 |
# glcellloader.py ---
#
# Filename: loadcell.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Thu Feb 4 20:34:34 2010 (+0530)
# Version:
# Last-Updated: Tue Jul 13 11:35:28 2010 (+0530)
# By: Subhasis Ray
# Update #: 112
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/gl/glcellloader.py | Python | lgpl-2.1 | 3,607 | [
"MOOSE"
] | 3d46328ad57e75f6810497d6fa646a205a93cdb4daa850541d7a6abf259671e7 |
"""
Integration tests for singletask vector feature models.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "GPL"
import os
import unittest
import temp... | bowenliu16/deepchem | deepchem/models/tests/test_api.py | Python | gpl-3.0 | 6,426 | [
"RDKit"
] | 9419d7c70e3e8867588e5a2506843034041033a257f8fa953bf99d20e4ad7fbd |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under ... | MDAnalysis/mdanalysis | package/MDAnalysis/selections/gromacs.py | Python | gpl-2.0 | 1,911 | [
"Gromacs",
"MDAnalysis"
] | 5241c1a469f45500f3dc7392c171d5c7497fa151ff4ba53bd690dd80aa451587 |
"""Copyright 2008 Phidgets Inc.
This work is licensed under the Creative Commons Attribution 2.5 Canada License.
To view a copy of this license, visit http://creativecommons.org/licenses/by/2.5/ca/
"""
__author__ = 'Adam Stelmack'
__version__ = '2.1.4'
__date__ = 'May 02 2008'
from threading import *
from ... | jantman/tuxostat | fs_backup/home/tuxostat/devel/PhidgetsPython/Phidgets/Devices/PHSensor.py | Python | gpl-3.0 | 8,111 | [
"VisIt"
] | 39ca86a57c11be1a43a8653588feeaaed1bf9bf69dc910d446ec3b130376a40c |
# -*- coding: utf-8 -*-
import datetime
from django.conf import settings
from django.contrib.contenttypes.models import ContentType
from django.contrib.sites.models import Site
from django.http import HttpResponse
from django.test import TestCase, override_settings
from django.utils.timezone import now as timezone_now
... | Galexrt/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 105,080 | [
"VisIt"
] | d531fd4241d1a262b2cde551eaea8b4cf75ff8b963f419dc0f8e03ca32d45161 |
##
# Copyright 2012-2017 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... | migueldiascosta/easybuild-framework | test/framework/module_generator.py | Python | gpl-2.0 | 36,370 | [
"NetCDF"
] | bc6ccb70ba1d209f8cf40afab57ce708498094bc6e4902ead03a9e87bea6fc72 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/Input/BlockTree.py | Python | lgpl-2.1 | 15,198 | [
"MOOSE"
] | 52bda5422e6d1b8df3df2810b04da3d11b1d86e70639bb75280a3d291de4d612 |
import numpy as np, SimPEG as simpeg, vtk
import vtk.util.numpy_support as npsup
# sys.path.append('/home/gudni/Dropbox/code/python/vtkTools/')
from polydata import convertToImplicitPolyDataDistance
# Clip and extrude the topo
def clipDataSetWithPolygon(vtkDataSet,vtkPoly,returnImpDist=False,insideOut=True,extractBoun... | grosenkj/telluricpy | telluricpy/vtkTools/extraction.py | Python | mit | 6,929 | [
"VTK"
] | 304d1b35f4658e4801a8c9efa63e71707dbc22321b0a9826097e760c8fb5f877 |
from __future__ import unicode_literals
import unittest
from nose.tools import *
from py_stringmatching.tokenizer.alphabetic_tokenizer import AlphabeticTokenizer
from py_stringmatching.tokenizer.alphanumeric_tokenizer import AlphanumericTokenizer
from py_stringmatching.tokenizer.delimiter_tokenizer import DelimiterTo... | Anson-Doan/py_stringmatching | py_stringmatching/tests/test_tokenizers.py | Python | bsd-3-clause | 13,083 | [
"ASE"
] | 5a5e47dbe4bee82481dda454fe92c8182a1e3bbab3b8b85029f0eea06a6721dd |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
CIS excited state density with TDA amplitudes
'''
import numpy as np
from pyscf import gto, dft, tdscf
mol = gto.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = '631g',
)
mf = dft.RKS(mol)
mf.xc = 'b3lyp'
mf.kernel()
mytd = tdscf.TDA(mf).run... | gkc1000/pyscf | examples/tddft/22-density.py | Python | apache-2.0 | 1,497 | [
"Jmol",
"PySCF"
] | 6359b3ac292ff9445465857b20196693e06e8b6d6241b9e9c3ca7c59d81658d9 |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName1, fileName2 = get_program_parameters()
# Here we read data from a annular combustor. A combustor burns fuel and air
# in a gas turbine (e.g., a jet engine) and the hot gas eventually makes its
# way to ... | lorensen/VTKExamples | src/Python/VisualizationAlgorithms/WarpCombustor.py | Python | apache-2.0 | 3,722 | [
"VTK"
] | b2b87df58588b9ce639920bab5bbf1b82d68a587a40472019be78a49dcc5e796 |
import numpy as np
import pytest
from .utils import *
from .addons import using_dftd3
import psi4
@pytest.fixture
def dft_bench_systems():
ang = np.array([
[ -1.551007, -0.114520, 0.000000],
[ -1.934259, 0.762503, 0.000000],
[ -0.599677, 0.040712, 0.000000]])
oldang = ang * 0.... | CDSherrill/psi4 | tests/pytests/test_dft_benchmarks.py | Python | lgpl-3.0 | 19,605 | [
"ORCA",
"Psi4",
"Q-Chem"
] | 0cdc1a4358b0624b301d7555faab76d836764d2d0e3a102eaf9539a9daa496e9 |
#
# Copyright 2018 Red Hat | Ansible
#
# 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.
#
# ... | alxgu/ansible | lib/ansible/plugins/lookup/k8s.py | Python | gpl-3.0 | 11,371 | [
"Galaxy",
"VisIt"
] | 8e256ace34bb264bdc0c7cef8476d466155957d938e72f715b0fe7998624abf2 |
#!/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/Openwebif | plugin/controllers/views/web/timeradd.py | Python | gpl-2.0 | 5,213 | [
"VisIt"
] | d6066a2fe87e8423375234239b18a6d90fab4b3d937d6c937e3e2bd2fe00c66b |
#
# @file TestTrigger.py
# @brief SBML Trigger unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located a... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestTrigger.py | Python | bsd-3-clause | 4,624 | [
"VisIt"
] | c5352d9e535f14ae53284e0b6b6e268b93b3683a83318dc80be62691e99eaac2 |
#!/usr/bin/python3
# -*- coding: UTF-8 -*-
## buggygame.py
#############################################################################
# Copyright (C) Labomedia 2011:2015
#
# This file is part of Buggy.
#
# Buggy is free software: you can redistribute it and/or modify
# it under the terms of the GNU Genera... | sergeLabo/Buggy | game/BuggyServer/buggygame.py | Python | gpl-2.0 | 12,195 | [
"Brian"
] | 1c04f8cb8591d59882fd3a2bda92364df787c7347e922847f0a6ec607dd3ccc0 |
########################################################################
# File : EndpointFactory.py
# Author : Andrei Tsaregorodtsev
########################################################################
""" The Cloud Endpoint Factory has one method that instantiates a given Cloud Endpoint
"""
from DIRAC ... | atsareg/VMDIRAC | VMDIRAC/Resources/Cloud/EndpointFactory.py | Python | gpl-3.0 | 2,128 | [
"DIRAC"
] | c9ef53d6186736a4f78f9637f75c474fbcfff4a2c7c1fed6a40223966490281c |
import time
import argparse
import numpy as np
import tensorflow as tf
import reader
import model
import pickle
import os
def parsing_args():
parser = argparse.ArgumentParser()
parser.add_argument('--mode', type=str, default='train',
help='train or test')
parser.add_argument('--i... | darongliu/Lstm_Turing_LM_tf | exp_diff_dropout_position/attention_LSTM/run.py | Python | mit | 13,140 | [
"NEURON"
] | 879f3a374cec29134d8eaaf08ed7b0bc0b4372609f79a280f7feb12ace2d67fc |
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 2 2015
Library for MG_Synth. Defines functions for reading motifs, generating
synthetic DNA sequences, computing likelihoods, etc
@author: ivanerill
"""
#The following code assumes that Biopython is installed
from Bio.Seq import Seq
from Bio import motifs
from Bio.Alph... | ErillLab/MGtest | MG_synth_lib.py | Python | gpl-2.0 | 16,250 | [
"Biopython"
] | c8a6243eb02fb5eb4af00e9fa443da03ceb65ab5d5c5d7cd036de4a37425deac |
# -*- coding: utf-8 -*-
"""Tests for collapse functions."""
import unittest
from pybel import BELGraph
from pybel.constants import DIRECTLY_INCREASES
from pybel.dsl import gene, mirna, pathology, pmod, protein, rna
from pybel.struct.mutation.collapse import (
collapse_all_variants,
collapse_nodes,
collap... | pybel/pybel | tests/test_struct/test_transformations/test_collapse.py | Python | mit | 4,313 | [
"Pybel"
] | ede6ea0fe591469f3126812ef5d613f9c31c5ad6912eabfce62608a52829fc70 |
"""
Generate a list of NC ids of the phages and their hosts for the CRISPR
searches. We accept two different parameters, the number of mismatches
and the BLAST output file. Note that we expect the blast output file
to incldue qlen slen as the last two columns
"""
import rob
import sys
import os
import re
try:
mm... | linsalrob/PhageHosts | code/crispr_mismatches_counts.py | Python | mit | 1,909 | [
"BLAST"
] | 0f34621ac02d4709acdfee590dfdf32ee106b48b23e1a8408e6bd46cbdf1c398 |
#!/usr/bin/env python
# Useful functions for reaction coordinate optimization
import sys,os,math
from numpy import *
from scipy import optimize
def gaussian(param,x):
# gaussian function of x with parameters mu, sigma and height
mu = param[0]
sigma = param[1]
height = param[2]
gauss = height*exp(-((x-mu)/sigma)... | daviddesancho/rc_ptp | rc_lib.py | Python | gpl-2.0 | 4,954 | [
"Gaussian"
] | 2015de02488cd037056b36d117aa296573ad55d8eba2ec581d0d9c431538f426 |
# Test data for convolution
convolutionDefinition = """
name : "ConvolutionTest"
input : "data"
input_shape {dim:1 dim :3 dim :5 dim :5}
layer {
name : "convolution"
type : "Convolution"
bottom : "data"
top : "convolution"
convolution_param {
num_output : 4
kernel_size: 2
weight_filler {
type: "xavier"
}... | yiheng/BigDL | pyspark/test/bigdl/caffe/caffe_layers.py | Python | apache-2.0 | 12,168 | [
"Gaussian"
] | b1fcb174e075a1afe99ad24795ba4f80a1920fb1d791cd1f8515c6a5aadaf34f |
#!/usr/bin/env python
# Copyright (c) 2005-2010 ActiveState Software Inc.
"""eol -- a tool for working with EOLs in text files
Usage:
eol FILE... # list EOL-style of file(s)
eol -c NAME FILE... # convert file(s) to given EOL-style
eol -f NAME FILE... # find files with the given EOL-style... | msduketown/SublimeKodi | libs/eol/eol.py | Python | gpl-3.0 | 29,069 | [
"VisIt"
] | 32d022f6bb363f83c4b36b4bddb54128cc63961ea05e58750c9ced471f1877d9 |
import pandas as pd
import numpy as np
import xgboost as xgb
from sklearn.base import BaseEstimator,TransformerMixin, ClassifierMixin
from sklearn.preprocessing import LabelEncoder
from sklearn.linear_model import ElasticNetCV, LassoLarsCV
from sklearn.ensemble import GradientBoostingRegressor
from sklearn.pi... | ArkadeepAdhikari/Predicting-Car-Testing-Time | apps/xgboostmodel.py | Python | apache-2.0 | 5,181 | [
"Gaussian"
] | 81190f8dd6b1858dad33451fad74858c13265157aa61e9b973cb06755750daad |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Copyright (C) 2020 Stoq Tecnologia <http://www.stoq.com.br>
# All rights reserved
#
# This program 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;... | stoq/stoq-server | stoqserver/api/resources/client.py | Python | gpl-2.0 | 7,924 | [
"VisIt"
] | 9a5a534ba0f6c43481dd524d73b1ae9dd03d2af6d08c24a48de638e592bf29e3 |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# 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 w... | JWDebelius/scikit-bio | skbio/io/_registry.py | Python | bsd-3-clause | 25,832 | [
"scikit-bio"
] | 27dd5d82dd134ca3076caf77e5d48117602b3674037b173c2c7d9ef1d4b8dc74 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-get-jdl
# Author : Stuart Paterson
########################################################################
"""
Retrieve the current JDL of a DIRAC job
"""
__RCSID__ = "$Id$"
import DI... | sposs/DIRAC | Interfaces/scripts/dirac-wms-job-get-jdl.py | Python | gpl-3.0 | 1,172 | [
"DIRAC"
] | bfa97be789a7ab95a9444bb2f2aa8d00ae9b6ce4834e14cfb0ac077541803a87 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkVoxelModeller(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | nagyistoce/devide | modules/vtk_basic/vtkVoxelModeller.py | Python | bsd-3-clause | 487 | [
"VTK"
] | 9685f5a41dc1e92e1ee64130735bd33c0af126135a333e9c30d4c4a01bc7f1ef |
# Copyright 2016 Google Inc. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | JavaRabbit/CS496_capstone | appengine/standard/ndb/property_subclasses/snippets.py | Python | apache-2.0 | 1,896 | [
"COLUMBUS"
] | 0129fe9698030b2c81a2dfc89fe41ebe2dfece65ccbb6a18cedfc95d12ad5256 |
#!/usr/bin/env python
import sys
import pysam
import argparse
import random
import subprocess
import os
import bamsurgeon.replacereads as rr
import bamsurgeon.aligners as aligners
import bamsurgeon.mutation as mutation
import traceback
from bamsurgeon.common import *
from uuid import uuid4
from re import sub
from shu... | MischaLundberg/bamsurgeon | bin/addindel.py | Python | mit | 18,248 | [
"BWA",
"pysam"
] | d0fdf415b57989c1fe88cfe21177c6f188219afec0c716e039251d3e8c16fd1d |
'''
Copyright (C) 2013-2014 Robert Powers
This file is part of MikeNetGUI.
MikeNetGUI 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.
Mike... | bopowers/MikenetGUI | lib/tabs.py | Python | gpl-3.0 | 63,418 | [
"Gaussian"
] | d4d1db9b560a43afc7e49a98b2cafe665d138f4d7267f845c2c81db09a8bb8f2 |
import json
import requests
import sys
''' Disable Warnings when using verify=False'''
'''requests.packages.urllib3.disable_warnings()'''
def get_reqistry_request(url, username=None, password=None, ssl=False):
req = None
if ssl==True:
proto="https://"
else:
proto="http://"
url_endpoint = proto + url
s =... | windperson/private-docker-registry | cli/browser.py | Python | apache-2.0 | 6,820 | [
"VisIt"
] | 1b863a816a34fe1286abc21ea0bcecbda756a4ee3db7bcf4ab105125c90f32af |
"""Implementation of feedforward network, including Gauss-Newton approximation
for use in Hessian-free optimization.
.. codeauthor:: Daniel Rasmussen <daniel.rasmussen@appliedbrainresearch.com>
Based on
Martens, J. (2010). Deep learning via Hessian-free optimization. In Proceedings
of the 27th International Conferenc... | drasmuss/hessianfree | hessianfree/ffnet.py | Python | bsd-2-clause | 34,715 | [
"Gaussian",
"NEURON"
] | 1971614e4dc0b248bffcf5dc9cf0baebe18a5101209a39cb340f76692ce21624 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free So... | fdupoux/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 9,321 | [
"Firefly"
] | 1c1fca830ed25f3e8e3d6cd3c6549945c5b39993f9c274ea4cf68f958d855a6f |
"""
Python interface to GnuPG.
This module is used to invoke GnuPG to check the digital signatures on interfaces.
@see: L{iface_cache.PendingFeed}
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import subprocess
import base64, re
i... | pombredanne/zero-install | zeroinstall/injector/gpg.py | Python | lgpl-2.1 | 10,836 | [
"VisIt"
] | e86a656f75f5c04a1946fbb1a6083cfdd648f96f95bed89cf7e5cd9f3e3b7f3c |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | tersmitten/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 51,831 | [
"VisIt"
] | fb3ed9c0ca1c26ef383c2b363a04e4b299cffb36be4c643ce6d51e37553db09c |
# -*- coding: utf-8 -*-
# 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... | sem-geologist/hyperspy | hyperspy/drawing/utils.py | Python | gpl-3.0 | 57,794 | [
"ADF"
] | b7e9ee650bcb1037cd5593c83eaa6e45adc6e5549a797fbf6119fd28b7c29806 |
# Copyright (C) 2010-2018 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... | mkuron/espresso | samples/visualization_npt.py | Python | gpl-3.0 | 2,646 | [
"ESPResSo"
] | 08ee793610d31189f2878fbe8665a930895202ea65c46802fb4fb6ef6f953c3e |
# $HeadURL: $
''' DIRACAccountingCommand
The DIRACAccountingCommand class is a command class to
interrogate the DIRAC Accounting.
'''
from datetime import datetime, timedelta
from DIRAC import S_OK, S_ERROR
from DIRAC.AccountingSystem.Client.ReportsClien... | Sbalbp/DIRAC | ResourceStatusSystem/Command/DIRACAccountingCommand.py | Python | gpl-3.0 | 10,672 | [
"DIRAC"
] | eb538a0b24a99e7ff7ba2d21319a4ea2cbcf4802c1b14053d1d353007d3bfd38 |
"""
Copyright (c) 2013-2014 Benedicte Ofstad
Distributed under the GNU Lesser General Public License v3.0.
For full terms see the file LICENSE.md.
"""
import unittest
import abavib as av
import read_input as ri
import numpy as np
import sys
class abavib_test(unittest.TestCase):
def setUp(self):
... | Benedicte/vibrational_motion | abavib_unittester.py | Python | lgpl-3.0 | 34,585 | [
"Dalton"
] | e3d9dacc1582afc2c860d724e3f686813483b4eb076af39a7e2a57b4c45e4f83 |
#!/usr/bin/env python3
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, e... | espressopp/espressopp | testsuite/pickle_potential/warmup/testWarmup.py | Python | gpl-3.0 | 2,173 | [
"ESPResSo"
] | 8a383b1d432a49e097e2ef253f4467deb138af6f9d8dee8f6f04f0e1723fe2ff |
import argparse
from pathlib import Path
import sys
import textwrap
import h5py
import matplotlib
from matplotlib.animation import FuncAnimation
from matplotlib.patches import Rectangle
import matplotlib.image as mpimg
import matplotlib.pyplot as plt
import numpy as np
from scipy.interpolate import splrep, splev
from... | eljost/pysisyphus | pysisyphus/plot.py | Python | gpl-3.0 | 30,829 | [
"Gaussian",
"Jmol"
] | 3e911c5874ff1fc622fff323102748b16e0372b92b51d3aa269f34c763ca9e94 |
""" ArgumentReadOnce counts the usages of each argument of each function. """
from pythran.analyses.aliases import Aliases
from pythran.analyses.global_declarations import GlobalDeclarations
from pythran.passmanager import ModuleAnalysis
from pythran.tables import MODULES
import pythran.intrinsic as intrinsic
import ... | pbrunet/pythran | pythran/analyses/argument_read_once.py | Python | bsd-3-clause | 8,643 | [
"VisIt"
] | 4c617040278916ae73303d1c0498f05c91db35b7e286b52738f0239f44068009 |
"""
Provides methods for collecting inputs and argments needed by functions
that are 'managed'. Managed here refers to functions and global variables
that are registered within, and called by, some type of orchestration
framework rather than called directly.
This is an extension of (and heavily influenced by) the vari... | bridwell/orca_sandbox | orca_sandbox/collector.py | Python | mit | 3,663 | [
"ORCA"
] | d2ab19ae0f962133da1912db71f4540c886ba06a1225daff10a4d16f53ef9edf |
# -*- coding: utf-8 -*-
# test_nsdf.py ---
# Changed from nsdf.py from
# https://github.com/BhallaLab/moose-examples/snippets/nsdf.py
from __future__ import print_function
import numpy as np
from datetime import datetime
import getpass
import os
# Use in-repo moose to install.
import moose
print('using moose from: %s... | upibhalla/moose-core | tests/python/test_nsdf.py | Python | gpl-3.0 | 3,682 | [
"MOOSE"
] | 0635d9e1702c5fb387c5a21a671b51eacd8c7515615c447534454e0cf674db10 |
#!/usr/bin/python
from PyQt4 import QtCore, QtGui
import glob
import os
import sys
import datetime
import re
import subprocess
dirSelf = os.path.dirname(os.path.realpath(__file__))
print(dirSelf)
sys.path.append(dirSelf.rstrip(os.sep).rstrip("guiBin").rstrip(os.sep) + os.sep + "lib")
scb = "selectCheckBox.py"
selec... | shrinidhi666/rbhus | rbhusUI/guiBin/rbhusSubmit.py | Python | gpl-3.0 | 17,866 | [
"DIRAC"
] | 2bc1e0ee647e4db79117bbef9f1cf52ae46ff6a1a4ab6ba0e6aa29e555bee9a9 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Methods for selecting the bin width of histograms
Ported from the astroML project: http://astroml.org/
"""
import numpy as np
from . import bayesian_blocks
__all__ = ['histogram', 'scott_bin_width', 'freedman_bin_width',
'knuth_bin_width... | stargaser/astropy | astropy/stats/histogram.py | Python | bsd-3-clause | 12,607 | [
"Gaussian"
] | ce66edb0c7816f15c1e4115e3799048b6a9a337141009f4551fdfeb63c42dcf5 |
# -*- coding: utf-8 -*-
"""
Created on Wed May 11 08:08:52 2016
@author: tkc
"""
import re
from collections import defaultdict
import pandas as pd
import numpy as np
import scipy
import scipy.stats
from scipy import optimize
from math import factorial # used by Savgol matrix
from scipy.optimize import cu... | tkcroat/Augerquant | Development/Auger_integquant_functions_11Nov16backup.py | Python | mit | 64,350 | [
"Gaussian"
] | f60430a08cff78dabba5052a2e64d99f48ba5a51f404fe2b0873349f5e382ded |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
import numpy as np
from scipy import linalg
from copy import deepcopy
import re
from .cov import read_cov, _get_whitener_data
from .io.constants import FIFF
from .io.pic... | dgwakeman/mne-python | mne/dipole.py | Python | bsd-3-clause | 22,795 | [
"Mayavi"
] | cb551b8a520aec65c8966c84b2a09433a1e6f29f0731d1d6f70fe1ed1e1c46cf |
import os
import subprocess
import sys
import time
from typing import List
import py.path
import _pytest.pytester as pytester
import pytest
from _pytest.config import ExitCode
from _pytest.config import PytestPluginManager
from _pytest.pytester import CwdSnapshot
from _pytest.pytester import HookRecorder
from _pytest... | JoelMarcey/buck | third-party/py/pytest/testing/test_pytester.py | Python | apache-2.0 | 25,763 | [
"Brian"
] | 3377fb1fb9126b09dee0cf78ad37527f5e0c7ae1242f60a1013b6f713b0e7c35 |
#
# Copyright Amazon.com, Inc. or its affiliates. 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.
# A copy of the License is located at
#
# http://aws.amazon.com/apache2.0
#
# or in the "license" file accompanyi... | alexeblee/s2n | tests/integration/s2n_test_constants.py | Python | apache-2.0 | 22,336 | [
"Octopus"
] | d9b0e956a4fe519030fb8028941b7d67b11355c9d6fb1dd13f9ce49540bad61c |
# Copyright 2016 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
import ast
import inspect
import itertools
import sys
import typing
from abc import ABC, abstractmethod
from dataclasses import dataclass
from typing import Callable, Dict, List, Optional,... | tdyas/pants | src/python/pants/engine/rules.py | Python | apache-2.0 | 18,089 | [
"VisIt"
] | 9464d54bb84129a997f44c6ed3fe70dd16b16014396ca4243ae59e31fc818ec4 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | mhlechner/psi4 | psi4/driver/qcdb/basislistother.py | Python | gpl-2.0 | 22,464 | [
"Psi4"
] | 425ed700a0c3b217d8adbf823714c113da33de60dede7a80a6d526cc9c917f46 |
import numpy as np
from ase.structure import molecule
from gpaw import GPAW
unitcell = np.array([6.5, 6.6, 9.])
gridrefinement = 2
for formula in ('Na', 'Cl', 'NaCl',):
calc = GPAW(xc='PBE',
nbands=-5,
h=0.18,
convergence={'eigenstates':1E-8},
txt=... | ajylee/gpaw-rtxs | doc/tutorials/all-electron/NaCl.py | Python | gpl-3.0 | 835 | [
"ASE",
"GPAW"
] | 98f14a57e730d2c12fac634868634b53115c7f1112e0cdbd86af26c2f56673d4 |
"""
Spatial Error Models with regimes module
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
import multiprocessing as mp
import regimes as REGI
import user_output as USER
import summary_output as SUMMARY
from pysal import lag_spatial
from ols import BaseOLS... | TaylorOshan/pysal | pysal/spreg/error_sp_regimes.py | Python | bsd-3-clause | 62,938 | [
"COLUMBUS"
] | 9e66ad352feb5679d85e3f5cec59fb217962c4aff47287ca7a7ad308d616de33 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
A function to generate synthetic flat field images for 3D projection data normalisation
@author: Daniil Kazantsev
"""
from scipy.special import spherical_yn
from scipy.special import y1
from scipy.ndimage.filters import gaussian_filter
from scipy.ndimage.i... | dkazanc/TomoPhantom | Wrappers/Python/tomophantom/supp/flatsgen.py | Python | apache-2.0 | 5,121 | [
"Gaussian"
] | 8e5efc0265bff0ddb9a76a154b127a578432348fec668b7ff277d9c387120e4e |
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