text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
#! /usr/bin/env python
#
# The purpose of this script is to create a moltemplate lt file for the oplsaa.
# forcefield. This will assist researchers in building complex simulations using
# this OPLS-UA and the OPLS-AA forcefields.
__author__="Jason Lambert"
# (some additional corrections by Miguel Gonzalez, Yue Chun C... | andeplane/lammps | tools/moltemplate/src/moltemplate_scripts_depreciated/oplsaa_moltemplate.py | Python | gpl-2.0 | 17,448 | [
"LAMMPS",
"TINKER"
] | 90eb971daff1fe3925af4a903e6e2a3a261365b4b156ea587c42d96cab320478 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | src/extractcode/libarchive2.py | Python | apache-2.0 | 30,608 | [
"VisIt"
] | 1f04eee00aca19dbed3743f9cd11871d555e73882fd5ffceaa87f2ad4b07331a |
import unittest
from nose.plugins.attrib import attr
import rscraper
from rscraper.getRepoMetadata import *
from rscraper.dbutil import *
import json
import os
import inspect
import rscraper.crossref
import rscraperTesting
class RscraperTesting(rscraperTesting.RscraperTesting):
@attr("integration", "internet")
... | cbogart/rscraper | tests/test_integration.py | Python | apache-2.0 | 6,793 | [
"Bioconductor"
] | 4188aa5315a489116ea8f43effb639b629301fbd152e67d921aad26006b0e507 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | racemidev/WMI_cmd | pysamba/twisted/__init__.py | Python | gpl-2.0 | 521 | [
"VisIt"
] | 79859b6198db387f3b2c40c35b9ca50ab84540e32077806ef2e1d0d18020a136 |
###################################################################################################
# Plot utilities
###################################################################################################
import ch.psi.pshell.plot.LinePlotSeries as LinePlotSeries
import ch.psi.pshell.plot.LinePlotErrorSer... | paulscherrerinstitute/pshell | src/main/assembly/script/Lib/plotutils.py | Python | gpl-3.0 | 4,131 | [
"Gaussian"
] | 45f49011802a450244f3250c7225f3af3edfe1e68978716c17b42a6070812ee5 |
"""Read all matched data and make some plotting
"""
import os
import re
from glob import glob
import numpy as np
from matchobject_io import (readCaliopImagerMatchObj,
DataObject,
CloudsatImagerTrackObject,
readCloudsatImagerMatchObj,
... | adybbroe/atrain_match | atrain_match/reshaped_files_scr/plot_ctth_bias_distributions.py | Python | gpl-3.0 | 36,611 | [
"Gaussian"
] | b32f875a66fa5511eaae2b97c61c4a2f1664cdb7b2e001bfb32a651c18c7e5ba |
#!/usr/bin/env python
# Produce density of states from CP2K MOLog file
# Usage: cp2k-dos.py cp2k.out
import argparse
import asetk.format.cp2k as cp2k
import numpy as np
import os
# Define command line parser
parser = argparse.ArgumentParser(
description='Produce density of states from CP2K output or .MOLog file')... | ltalirz/asetk | scripts/cp2k-dos.py | Python | mit | 3,400 | [
"CP2K",
"Gaussian"
] | d76238507a52cba118308047441c0371411fea44d0756e32ecad5ac7b92b2885 |
#!/bin/env python
"""
Module openmm.unit
Contains classes Unit and ScaledUnit.
This is part of the OpenMM molecular simulation toolkit originating from
Simbios, the NIH National Center for Physics-Based Simulation of
Biological Structures at Stanford, funded under the NIH Roadmap for
Medical Research, grant U54 GM072... | mdtraj/mdtraj | mdtraj/utils/unit/unit.py | Python | lgpl-2.1 | 26,390 | [
"OpenMM"
] | 64059131ab36651cbf2b49d2baa9ba0e1736ee37a3e07bf0ffa9004fdff72c5f |
import numpy as np
import tensorflow as tf
import elbow.util as util
class AbstractMVGaussian(object):
def __init__(self, d):
self.d = d
def log_p(self, x):
raise Exception("not implemented")
def entropy(self):
return self._entropy
def mean(self):
return self._mean... | davmre/bayesflow | elbow/gaussian_messages.py | Python | bsd-3-clause | 6,906 | [
"Gaussian"
] | 630275737de58c4d76ff9ebb55df1862d324c8cde0c1202f872ffeb884c1803f |
# coding: utf8
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '\ " update\ " - необязательное выражение как \ " field1=\'newvalue\'\ ". нельзя изменить или удалить результаты соединения',
'# of International Staff': '# международного персонала',
'# ... | waidyanatha/sambro-eden | languages/ru.py | Python | mit | 373,263 | [
"VisIt"
] | 43cc83d0e13cf02799ead438b6ff903d7c781eaff25b09a94c380558ce392b65 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-08-10 06:52:28
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-08-10 06:53:57
from __future__ import print_function, division, absolute_import
import os
from invoke imp... | havok2063/SciScript-Python | tasks.py | Python | apache-2.0 | 1,178 | [
"Brian"
] | e118a54d06588e84199e640df8b3e1e0668d70eb99290f6a31fc4599441e7d30 |
'''
Created on 07/31/2014
@Ronak Shah
'''
import argparse
import sys
import time
import os.path
import stat
from subprocess import Popen
import shlex
import shutil
from datetime import date
def main():
parser = argparse.ArgumentParser(prog='Run_Pindel.py', description='Run Pindel for Long Indels & MNPS (32bp-350b... | rhshah/Exome-Pipeline | bin/Run_Pindel.py | Python | apache-2.0 | 8,144 | [
"BWA"
] | 2f090c8c3bbb9c5d84347c162a1828589e83658b7e0975e5e62e4032fcb5b60a |
from __future__ import print_function, absolute_import, division
import os
import shutil
import tempfile
import numpy as np
from mdtraj.testing import get_fn
from nose.tools import assert_raises, assert_raises_regexp
from sklearn.externals.joblib import Parallel, delayed
from msmbuilder.dataset import dataset
from .... | mpharrigan/mixtape | msmbuilder/tests/test_dataset.py | Python | lgpl-2.1 | 6,441 | [
"MDTraj"
] | ee28a8475a52bb2300a4e607c639dc44ce5796fba742b5d09ab40065f8d503ca |
#!/usr/bin/env python3
# Coptyright 2016 (c) Brian McKean
'''
File name: instprobes.py
Author: Brian McKean
Date created: 08/31/2016
Date last modified: 09/02/2016
Python Version: 3.5
Gets a list of IPs and dns names for a set of ec2 instances
input: a string that the program will use t... | co-bri/quevedo | v1_scripts/deployq.py | Python | mit | 894 | [
"Brian"
] | 0e68986908e570b4406ae382404598aec8cbc6003f9b3d5f4c0a79eee57e519b |
# Copyright: (c) 2017, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2018, 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 argparse
from operator import attrget... | 2ndQuadrant/ansible | lib/ansible/cli/inventory.py | Python | gpl-3.0 | 16,314 | [
"Brian"
] | 7ffffc32e690d3726cdfb6e70ad934da67c444693930da02a77e60b9d551e2a8 |
#!/usr/bin/python
import subprocess as sp, argparse
parser=argparse.ArgumentParser()
parser.add_argument('--mei',nargs='*')
parser.add_argument('--option_tag',nargs='*')
parser.add_argument('--path',nargs='*')
args=parser.parse_args()
insertME=''.join(args.mei)
option_tag=''.join(args.option_tag)
path_current=''.joi... | JXing-Lab/ME-SCAN-SVA | modules/JW_producing_fixed_insertion_with_ind_info.py | Python | gpl-3.0 | 3,329 | [
"BLAST"
] | 0a6550f30466b15c1fb4d109e0191d556d3c3b06b6459f19be7acb48773e8300 |
# -*- coding: utf-8 -*-
from __future__ import division, with_statement, print_function
from collections import OrderedDict
import numpy as np
import six
import time
from six.moves import range
import acq4.util.ptime as ptime
from acq4.devices.Camera import Camera
from acq4.util import micromanager
from acq4.util.Mu... | acq4/acq4 | acq4/devices/MicroManagerCamera/mmcamera.py | Python | mit | 17,600 | [
"ORCA"
] | 2f04ad4c7bf65aa4f94b968efccfd083f13f5843f218fb02887b23f3d42eda48 |
# coding=utf-8
from __future__ import unicode_literals
import json
import pytz
from datetime import datetime, date
from django.core.urlresolvers import reverse
from django.conf import settings
from django.utils import timezone
from mock import patch
from smartmin.tests import _CRUDLTest
from smartmin.csv_imports.mode... | praekelt/rapidpro | temba/contacts/tests.py | Python | agpl-3.0 | 111,277 | [
"VisIt"
] | 018d96f8566295bda183b35aa5fa4ea78906809e2cc1357dcd639d6d0c260155 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | ahaldane/numpy | numpy/core/_add_newdocs.py | Python | bsd-3-clause | 202,188 | [
"Brian"
] | e4da7ed360e7b16a687c3c5d2ca637ba9a41ee48be2bc00971eafdb9ce776d4e |
# lots to do:
# __ native drawLines
# __ add native drawCurve method
# __ native rectangle/round rect method
# __ native drawEllipse
# __ native drawArc
# __ drawImage support (work on Pyart side of things)
from __future__ import print_function
import pyart
from rdkit.sping.pid import *
from rdkit.sping... | rvianello/rdkit | rdkit/sping/Pyart/pidPyart.py | Python | bsd-3-clause | 8,316 | [
"RDKit"
] | a0ac3ef66cceb8d225691a7694fe10044db1259bb37f4f3d4378d4fa1c365bfe |
""" :mod: GFAL2_SRM2Storage
=================
.. module: python
:synopsis: SRM2 module based on the GFAL2_StorageBase class.
"""
from types import StringType, ListType
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
fro... | vmendez/DIRAC | Resources/Storage/GFAL2_SRM2Storage.py | Python | gpl-3.0 | 7,963 | [
"DIRAC"
] | 6e777da8c9f486c02e7a5d23cf8461cf28cb38d4b85ac999b850c62a2d3bdf51 |
"""A GTK dialog which displays a list of Zero Install applications in the menu."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, gobject
import os, sys
import gtk, pango
import subprocess
from zeroinstall import support
from zeroinstal... | res2k/0install | zeroinstall/gtkui/applistbox.py | Python | lgpl-2.1 | 12,066 | [
"VisIt"
] | 228b65acc6267e62bd080ea9272bedb2ca9fa86af962eabd41c189d6b9b0661f |
from distutils.core import setup
#, Extension
#import os
import sys
import subprocess
# see also http://docs.python.org/distutils/setupscript.html
def which(prog):
"""make sure prog is in PATH
"""
try:
subprocess.call([prog],
stderr=subprocess.PIPE,
... | CSB5/vipr | setup.py | Python | gpl-2.0 | 1,809 | [
"BWA"
] | 345554106cc03f429d2f30adb82b69a10c2ccabf11cf831f99241da04d2a9b5f |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..utils import (
ExtractorError,
float_or_none,
int_or_none,
parse_duration,
parse_iso8601,
unescapeHTML,
)
from ..compat import (
compat_etree_fromstring,
compat_HTTPError,
)
cla... | Thor77/youtube-dl | youtube_dl/extractor/bbc.py | Python | unlicense | 47,282 | [
"VisIt"
] | 9b797b30a31b8cb3bbf36da76fa5a431d3fac2ef8e2b4a291e8dc5b8ca97320a |
"""
The B{0install} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _, logger
import os, sys
from optparse import OptionParser
import logging
from zeroinstall import SafeEx... | pombredanne/0install | zeroinstall/cmd/__init__.py | Python | lgpl-2.1 | 4,597 | [
"VisIt"
] | c3b494df038dd2803539fc762ac4d63ed8ecb51d15c65fcdd196d74d198c24d3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/database/models.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# n... | zigitax/king-phisher | king_phisher/server/database/models.py | Python | bsd-3-clause | 12,482 | [
"VisIt"
] | 4a1e8aca1de496cb3df41958ba142ac7a64abfd47d86055aadb7ca16fe960c07 |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, inc... | moses-palmer/slimit | src/slimit/visitors/minvisitor.py | Python | mit | 14,581 | [
"VisIt"
] | f3e9b2961ef2610b9f43b9ae062b00973271a7daa9a6f9008d3b5737c4f2698f |
"""Contains the Attract class which is the attract mode in a pinball machine.
"""
# attract.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging... | spierepf/mpf | mpf/modes/attract/code/attract.py | Python | mit | 5,170 | [
"Brian"
] | cde7d370c5cc86720bd8d3f4d13421618592c012a845c8133ebf0c39ae5fb35f |
import numpy as np
import math
import itertools
import sys
import time
import os
import random
import h5py
import logging
import pandas as pd
import csv
mydir = os.path.dirname(__file__)
sys.path.append(os.path.join(mydir, '.'))
from cudamat import gnumpy as gp
class Unbuffered:
def __init__(s... | gomyway/deeplink | common.py | Python | gpl-3.0 | 18,687 | [
"Gaussian"
] | f42f78833b7998517a3de5423dc80535abd65a84f67a5b594f67a5b592259c10 |
# -*- coding: utf-8 -*-
"""
Tests of neo.io.exampleio
"""
# needed for python 3 compatibility
from __future__ import absolute_import, division
import warnings
import unittest
import quantities as pq
import numpy as np
from neo.io.nestio import ColumnIO
from neo.io.nestio import NestIO
from neo.test.iotest.common_io... | rgerkin/python-neo | neo/test/iotest/test_nestio.py | Python | bsd-3-clause | 34,009 | [
"NEURON"
] | 125a5e30d6b3f51f1985cae89e3c0a21f0c80d2cace47b62bf47dad6e2c8230e |
from rdkit import Chem
from molpher.core import MolpherMol, MolpherAtom, ExplorationTree as ETree
from molpher.core.morphing.operators import MorphingOperator
from molpher.random_numbers import get_random_number
class AddFragment(MorphingOperator):
def __init__(self, fragment, open_atoms_frag, oper_name):
... | lich-uct/molpher-lib | src/python/molpher/examples/morphing_opers.py | Python | gpl-3.0 | 2,370 | [
"RDKit"
] | 9b712ceeb693c1ac802dab30b5c525ba166c8b59450eb599edb94b762420ea2c |
import os
import logging
from galaxy.util.submodules import submodules
import galaxy.jobs.runners.state_handlers
log = logging.getLogger(__name__)
def build_state_handlers():
return _get_state_handlers_dict()
def _get_state_handlers_dict():
state_handlers = {}
for module in submodules(galaxy.jobs.runn... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/jobs/runners/state_handler_factory.py | Python | gpl-3.0 | 641 | [
"Galaxy"
] | 145a9997f26210f51ad83a1e836f4411c9d713e3102da70b328f42dd56c587bb |
import sys
print 'running the test script with args', sys.argv
if len(sys.argv) != 2:
print 'need to pass in the test directory location'
sys.exit(1)
# the velocity is [y*t, 0, 0] and the time step length is 0.018
# the beginning x-location for the seeds is 1
# the y location for the seeds are [1, 11.5, 22,... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Examples/Catalyst/CxxParticlePathExample/TestScripts/verifyparticlepath.py | Python | gpl-3.0 | 3,192 | [
"ParaView"
] | 2370f661be942354d7de2a28d20c954591a8796dac14094ecdcf56f73ccc1fd5 |
# Copyright 2013 Pau Haro Negre
# based on C++ code by Carl Staelin Copyright 2009-2011
#
# See the NOTICE file distributed with this work for additional information
# regarding copyright ownership.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with... | pauh/neuron | run_experiment.py | Python | apache-2.0 | 5,390 | [
"NEURON"
] | 9973426df1d7b460ddcfc7015ac2f25813e1b52d32d95fd15f26d8f579ff3198 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | RyanSkraba/beam | sdks/python/apache_beam/runners/interactive/pipeline_instrument.py | Python | apache-2.0 | 24,452 | [
"VisIt"
] | 6895de2ff18045f0605574ac52ee6208f3b494d4a98fc3d4729fa1389f46bb8b |
# -*- coding: utf-8 -*-
# standard
import os
import tempfile
import copy
import string
import re
import struct
import ctypes
import urllib
# 3rd party
import yaml
from PyQt4 import QtGui, QtCore
# local
import legacy.popeye
import legacy.chess
import options
import model
import pbm
import pdf
import xfen2img
import... | tectronics/olive-gui | gui.py | Python | gpl-3.0 | 91,394 | [
"VisIt"
] | 5c7efc5cb3d4968bf22ca990e7920b62ddd84ce7e8264511ce68b4ac14c76590 |
from __future__ import print_function
"""Modules for calculating thermochemical information from computational
outputs."""
import os
import sys
import numpy as np
from ase import units
def rotationalinertia(atoms):
"""Calculates the three principle moments of inertia for an ASE atoms
object. This uses the a... | suttond/MODOI | ase/thermochemistry.py | Python | lgpl-3.0 | 20,377 | [
"ASE"
] | 2a651af47e8c62effee65e1dc7792c48be23f9b8d82fb7e0c549495a5a5eb74d |
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
from django.views import defaults as default_views
from waiter.dashboards.views import DashboardView
from waiter.errors.vi... | ivanistheone/waiter | config/urls.py | Python | mit | 2,504 | [
"VisIt"
] | fd044d4139bf5c07d06db0104874dcde7b1af47187467fe328d941972e0595d9 |
"""
Workflow class is the main container of Steps and Modules
"""
import os, re, types
import xml.sax
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Workflow.Module import *
from DIRAC.Core.Workflow.Step import *
from DIRAC.Core.Workflow.Utility import *
from DIRAC import S_OK, S_ERROR
__RCSID__ = "$... | Andrew-McNab-UK/DIRAC | Core/Workflow/Workflow.py | Python | gpl-3.0 | 14,682 | [
"DIRAC"
] | f7eff7b389ca4897fd6e13d5ac400a1afde9ec7ac55e87b835b22bb4ba2e0818 |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test command-line interface.
"""
#===================================================... | sonyahanson/yank | Yank/tests/test_cli.py | Python | lgpl-3.0 | 2,163 | [
"Amber"
] | 83ba3a7c09e118ebc925c310e0ba7e50f66abfc6f7c1af524f630631294174c2 |
"""Unpacking archives of various formats."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import os, subprocess
import shutil
import glob
import traceback
from tempfile import mkdtemp, mkstemp
import re
from logging import debug, warn
... | timdiels/zeroinstall | zeroinstall/zerostore/unpack.py | Python | lgpl-2.1 | 18,936 | [
"VisIt"
] | 7971f9d9019d6e65c29adf8ee30fef070931d6219fc575efcfb2e1b49915d551 |
#
# Model of E. coli
#
# Spatial Scale: 1 micron
# Simulation Engine: Nucleus
#
import pymel.core as pm
import maya.cmds as mc
import maya.mel as mel
pm_parts = pm.nParticle( p=[(0, 0, -6), (0, 0, 6)], n="parts")
# protects against multiple objects called "parts"
parts_nm = pm_parts[1].name()
p_shape = mc.select(p... | bbartoldson/wetware-studio | models/cells/ecoli.model.py | Python | mit | 4,224 | [
"Brian"
] | ee0a567be4bf42a1656639de660916ca06f4cf2559d8b86bc5028494832e2359 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/p4util/fchk.py | Python | lgpl-3.0 | 4,737 | [
"Psi4"
] | 9230e73f172f529fa5c616e4bdd161ac08ccb13b0c79f4af0196b9848836b700 |
"""
Definitions for the Dynamics. Dynamics derives from 2 other mixin
classes, which provide functionality for hierachical components and for local
components definitions of interface and dynamics
:copyright: Copyright 2010-2017 by the NineML Python team, see AUTHORS.
:license: BSD-3, see LICENSE for details.
"""
from... | INCF/lib9ML | nineml/abstraction/dynamics/base.py | Python | bsd-3-clause | 22,523 | [
"VisIt"
] | 332ba793158d18d3902187e44d498183831072c4de577c5c335b07a77f42f0e1 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Bayesian Blocks for Time Series Analysis
========================================
Dynamic programming algorithm for solving a piecewise-constant model for
various datasets. This is based on the algorithm presented in Scargle
et al 2012 [1]_. This cod... | tbabej/astropy | astropy/stats/bayesian_blocks.py | Python | bsd-3-clause | 18,663 | [
"Gaussian"
] | b38cbfcea9ce51e2fbffc804c0a74b8212ade088973026d0eac1152d7b966a7f |
import re
from datetime import datetime
import pytz
from django import forms
from django.conf import settings
from django.test import TestCase
import vendor.timezones.forms
import vendor.timezones.timezones_tests.models as test_models
from vendor.timezones.utilities import localtime_for_timezone, adjust_datetime_t... | samuelclay/NewsBlur | vendor/timezones/timezones_tests/tests.py | Python | mit | 6,356 | [
"Brian"
] | 570a4fcb99f7b8faa689252c08a07e20e8d127cc40a7ae6bc218b00cb053d4e6 |
"""Actions for the help menu """
# Copyright (C) 2009-2010, Ecole Polytechnique Federale de Lausanne (EPFL) and
# University Hospital Center and University of Lausanne (UNIL-CHUV)
#
# Modified BSD License
# Enthought library imports
from pyface.action.api import Action
from traitsui.api import auto_close_message
from ... | LTS5/connectomeviewer | cviewer/action/help.py | Python | bsd-3-clause | 3,301 | [
"Mayavi"
] | 45d4b288db25a0baf366d6bfa7bd9ceb8b3ab3ad5e4b5ebe69bef6dba6c98129 |
colours = [("cloudy blue","#acc2d9"),
("dark pastel green","#56ae57"),
("dust","#b2996e"),
("electric lime","#a8ff04"),
("fresh green","#69d84f"),
("light eggplant","#894585"),
("nasty green","#70b23f"),
("really light blue","#d4ffff"),
... | TreeFrogBandit/Project-Codenames | libraries/xkcd_colours.py | Python | gpl-3.0 | 35,377 | [
"Amber"
] | 2c74981d3cffd20301392d68d6752b59bd55d1827c7e8e065f970cdf39f1e572 |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/r-simpleaffy/package.py | Python | lgpl-2.1 | 2,156 | [
"Bioconductor"
] | 2c0de2d87a50eba2b2978c28958b1e2cf32ad06119141fb97a55dc727c231af9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""LFPy setuptools file
"""
from distutils.spawn import spawn
import os
import sys
import shutil
d = {}
exec(open(os.path.join('LFPy', 'version.py')).read(), None, d)
version = d['version']
try:
from setuptools import setup, Extension
except ImportError as ie:
r... | espenhgn/LFPy | setup.py | Python | gpl-3.0 | 4,010 | [
"NEURON"
] | 92536ba86788053b17f32575b5b50d4832cd702a7a7e49fe58d211b965225315 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/util/__init__.py | Python | gpl-2.0 | 948 | [
"Psi4"
] | 613e66a957ef0f3269df991bb62f03e931eee0c8db5d5ec78132257055a619c9 |
#!/usr/bin/env python3
from . import conf
from .utils import PheWebError
import sys, json
import os
import importlib
import functools
import math
from typing import List,Dict,Callable
if sys.platform.startswith('win'):
raise Exception("PheWeb doesn't support Windows, because pysam doesn't support windows.")
if ... | statgen/pheweb | pheweb/command_line.py | Python | agpl-3.0 | 4,469 | [
"pysam"
] | fd88f846044696935876ad50e7c0eb647e0f260abc721bc1089977b184ca5796 |
"""CATMAID to Blender Import Script.
Connects to CATMAID servers and retrieves skeleton data.
Copyright (C) Philipp Schlegel, 2014.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 o... | schlegelp/CATMAID-to-Blender | CATMAIDImport.py | Python | gpl-3.0 | 105,532 | [
"NEURON"
] | 8d4de49cd5be4d3078d297ce718444e14446306315b323817b782f1d4db92ff2 |
#!/usr/bin/env python
import sys
#parse_blastx2Sprot by DJ Barshis
#this script takes an -7 text outformat blast output from a blastx against sprot
#and extracts the top uniprot ID for each hit
#usage is parse_blastx2Sprot.py sprotblastoutput.txt outfilename.txt
INFILE = open(sys.argv[1], 'r') #Input file 1 is your... | cuttlefishh/papers | vibrio-fischeri-transcriptomics/code/python/parse_blastx2Sprot.py | Python | mit | 778 | [
"BLAST"
] | fcfec11cc05c9dc92964f4e7c73ac52aa5b856086b66e8f270f5fbeffc4ea961 |
"""Next gen sequence alignments with Bowtie2.
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
"""
import os
from itertools import ifilter
import pysam
from bcbio.pipeline import config_utils
from bcbio.utils import file_exists
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance impo... | hjanime/bcbio-nextgen | bcbio/ngsalign/bowtie2.py | Python | mit | 5,716 | [
"Bowtie",
"Galaxy",
"pysam"
] | 839ad2e48e87ff28e3cc765f0a24b90299f95fef431e9848afc08f2e9da5d904 |
import os, sys
from scipy.optimize import fminbound
import numpy
import math
## These functions calcualte the the pseudo_lhd and pseudo_gradient,
## that is they calculate the derivative through G^-1
##
## this doesn't work because the likelihood is not a good measure of
## model fit.
#import symbolic
#(calc_pseud... | daler/idr | idr/optimization.py | Python | gpl-2.0 | 16,460 | [
"Gaussian"
] | 0afdae4de4ca8d16dafebc6147fe2880b3549442dc346d526091afd83c36cbf5 |
"""Class to compute richness/redshifts for a set of ra/dec/z positions.
"""
import fitsio
import numpy as np
import esutil
from .cluster import ClusterCatalog
from .background import Background
from .mask import HPMask
from .galaxy import GalaxyCatalog
from .cluster import Cluster
from .cluster import ClusterCatalog
f... | erykoff/redmapper | redmapper/runcat.py | Python | apache-2.0 | 6,308 | [
"Galaxy"
] | f26f08c5ffc541b3fec30a2c56ef9c0733541bb0fe7f9d523b711ebe95c5f5d2 |
from distutils.core import setup
from Cython.Build import cythonize
from distutils.extension import Extension
import numpy as np
import mpi4py as mpi4py
import sys
import platform
import subprocess as sp
import os.path
import string
# Now get include paths from relevant python modules
include_path = [mpi4py.get_inclu... | sally-xiyue/pycles | setup.py | Python | gpl-3.0 | 13,988 | [
"NetCDF"
] | 5e59d78644e607fba2d5365fafedae3c53aa7f8334a2b1909c7a1b56e3420d5b |
# coding: utf-8
import unittest
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.testing import PymatgenTest
from pymatgen.util.coord_utils import in_coord_list
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.analysis.wulff import WulffS... | xhqu1981/pymatgen | pymatgen/analysis/tests/test_wulff.py | Python | mit | 7,178 | [
"pymatgen"
] | e652962b3a5ea723af05dbce95322e4294e527ebd3632a5ac15660401688ce99 |
# Copyright (c) 2017, Henrique Miranda
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from math import sqrt
from time import time
max_exp = 50
min_exp =-100.
def abs2(x):
return x.real**2 + x.imag**2
def lorentzian(x,x0,g):
height=1./(np.pi*g)
return height*(... | henriquemiranda/yambopy | yambopy/dbs/dipolesdb.py | Python | bsd-3-clause | 9,873 | [
"Gaussian"
] | 044906eb1a920ef5eeccfea2522926bbb382377a5a85f5588f03b2f8f1353131 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import sys
import shlex
import subprocess
import collections
import os.path
import json
import getpass
def exec_command(command, **kwargs):
shell = kwargs.get("shell", False)
stdin = kwargs.get("stdin", None)
stdout = kwargs.get("stdout", None)
stderr = k... | jsstd/js-task-paths | scripts/tasks/main.py | Python | mit | 6,314 | [
"GULP"
] | 336259e96098920930e8e585e0412a99b7ad50ba32733c38794618fa8a60e793 |
"""
Plots the synaptic matrix of a given model
Example:
run synapticMatricesPlot.py 101 LH
"""
import matplotlib.pyplot as py
import numpy as np
import sys
modelname = sys.argv[1]
figurename = sys.argv[2]
c1 = np.load(modelname+'.dat')
py.imshow(c1, interpolation='none',origin='lower')
py.title(figurename)
py.xlabel(... | kalfasyan/DA224x | code/eigens/synapticMatricesPlot.py | Python | gpl-2.0 | 416 | [
"NEURON"
] | 7d06dc3017239356bee7c4168ce37e3525265f09a9ae2288f439fe3ed42e97cb |
'''
Created on Feb 5, 2017
@author: Jake
'''
from Species import *
from Individual import *
from Neuron import *
from Connection import *
from Data_Extract import *
from time import time
from collections import defaultdict
import numpy as np
POPULATION_SIZE = 100
MUTATION_VALUE = 5
MUTATION_WE... | JakeShulman/G-Neat | Population.py | Python | apache-2.0 | 5,213 | [
"NEURON"
] | 5f5dd28625d19c13de12133339c32a3ad906ea071cee0efd2d3c7ac35f281e8a |
# encoding:utf-8
"""
:synopsis: views diplaying and processing main content post forms
This module contains views that allow adding, editing, and deleting main textual content.
"""
import datetime
import logging
import os
import os.path
import random
import sys
import tempfile
import time
from django.core.files.storag... | rosihorrorshow/askbot-devel | askbot/views/writers.py | Python | gpl-3.0 | 28,254 | [
"VisIt"
] | fc10432e5333e2d29a0cc3333e6ac14a1b7e51a5360d94896f11994bd37b2cc0 |
# Copyright (C) 2018 The HDF Group
#
# This examaple creates several HDF5 long string(>netCDF java limit 32767) datasets and attributes.
#
#
import h5py
import numpy as np
from random import choice
from string import lowercase
#
# Create a new file using defaut properties.
#
n = 32768
sca_big_str="".join(choice(lowerca... | OPENDAP/hdf5_handler | data/src/t_big_str.py | Python | lgpl-2.1 | 1,080 | [
"NetCDF"
] | 3920d7caeaeb896d4dc275d3b3f05e966fcfd55baad8f0209eae98ff56066ab4 |
import typing
import numpy as np
import measurement_stats as mstats
from measurement_stats.distributions.kernels import gaussians
class Kernel(typing.NamedTuple):
"""Data structure for Kernel objects."""
single: typing.Callable[[float, 'mstats.ValueUncertainty', float], float]
many: typing.Callable[[fl... | sernst/RefinedStatistics | measurement_stats/distributions/kernels/__init__.py | Python | mit | 1,304 | [
"Gaussian"
] | 2157d10ccc8cf6a1978c82faf02e94d861257357f5eb80498d8132328c7ddc32 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/diversity/alpha/_lladser.py | Python | bsd-3-clause | 17,533 | [
"scikit-bio"
] | 4f091577bf209c4df1e4b4314366965b2352f5bdd9cbebbd894aedc151f6e227 |
#!/usr/bin/python
import logging, os
import functools
import fnmatch
from PyQt4.QtGui import QMainWindow, QSizePolicy, QWidget, QVBoxLayout, QAction,\
QKeySequence, QLabel, QItemSelectionModel, QMessageBox, QFileDialog, QFrame, \
QDockWidget, QProgressBar
from PyQt4.QtCore import SIGNAL, QSettings, QSiz... | bitmingw/FindYourSister | sloth/sloth/gui/labeltool.py | Python | bsd-2-clause | 17,231 | [
"VisIt"
] | aefaebfac660f19f75ab686c201901d43c7d8b22eb17ce100d3e296e2d617866 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | mlperf/training_results_v0.5 | v0.5.0/google/research_v3.32/gnmt-tpuv3-32/code/gnmt/model/t2t/tensor2tensor/models/research/rl.py | Python | apache-2.0 | 14,542 | [
"Gaussian"
] | 5b134ca00470aa11c17ac6970b650c95f570734b971f48425d3bf1468e267cd4 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis Engemann <denis.engemann@gmail.com>
# Andrew Dykstra <andrew.r.dykstra@gmail.com>
# Teon Brooks <teon.brooks@gmail.com>
#
# License: BSD (3-clause)
import os
... | wronk/mne-python | mne/channels/channels.py | Python | bsd-3-clause | 31,888 | [
"Mayavi"
] | 2624a260b8de1bf2b2a947a1e40504ba5b7f7c4fd4ba256572526d85830c4804 |
import vtk
#renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName("F:/ass3/SMRX.vtk")
reader.UpdateWholeExtent()
#outline (color: white)
outline = vtk.vtk... | stablum/scientific-visualization | ass3/streamtracer.py | Python | gpl-3.0 | 2,320 | [
"VTK"
] | a65b560ae3760a1ee5e9d0090a788fa1ad382507d53e2fdb12892827a744cbe6 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/ui/wizard.py | Python | gpl-2.0 | 13,643 | [
"Brian"
] | 2a766adc90663c33870b19ac93bd7ac6858a7bca22ab8a6baf85507d05cefffd |
#!@WHICHPYTHON@
"""
Displays the Jmol input page
"""
print 'Content-type: text/html\n\n'
__date__ = "18 June 2008"
__author__ = "Samir Unni"
__version__ = "0.0.1"
from src.aconf import *
import cgi, cgitb, pickle, urllib, os, glob
cgitb.enable()
form = cgi.FieldStorage()
def initVars():
#global serviceURL
... | MonZop/BioBlender | bin/pdb2pqr-1.6/visualize.py | Python | bsd-2-clause | 5,755 | [
"Jmol",
"VMD"
] | ac8231f68ea36d3b200db77c0b7afdae133d0e6fba91f19dec4357c3d7efb2af |
"""
This module contains code for detection of doors.
"""
import freenect
import cv2
import numpy as np
import time
import serial
import math
import matplotlib.mlab as mlab
from matplotlib import pyplot as plt
import sys
sys.path.append('/usr/lib/python2.7/dist-packages')
__name__ = "Kinect"
DOOR_FLAG = False
DOOR_COUN... | amirajdhawan/eYSIP_2015_Depth_Mapping_Kinect | Application/Python_code/Final Code/Kinect.py | Python | cc0-1.0 | 39,365 | [
"Gaussian"
] | 8f723196506ca56d6e019a99a59f7a6a06f6c0aa3bcbef9b746c56a1a7f3a558 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""PYStructure
Usage:
pystructure.py SRC_PATH [-o FILE | --output=FILE]
Options:
-o FILE --output=FILE Save result to output file.
-h --help Show help information.
--version Show version.
"""
import os
from colle... | hanks/pystructure | pystructure/pystructure.py | Python | mit | 11,895 | [
"VisIt"
] | 06b603e1e84d7b74b8c5ca9c6676ea16a302b458527a03c6dcb376cc344eff10 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from distutils.core import setup
import py2app
import os, glob
def data_files(dirname = 'xml'):
"""Figure out the sugar structure and massage it into data_files format."""
def data_file(component):
return (os.path.join('..', '..', component),
glob.glob(os.pa... | mkhl/bash.sugar | setup.py | Python | mit | 1,591 | [
"ESPResSo"
] | 9623a2826784c19a2f18775667b4068bd69247686320a71aa3401c7a3a6b6db7 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import random
from pymatgen.core.lattice import Lattice
from pymatgen.util.coord import *
from pymatgen.util.testing import PymatgenTest
class CoordUtilsTest(PymatgenTest):
def test_get_linear_interpolated_value(self):... | vorwerkc/pymatgen | pymatgen/util/tests/test_coord.py | Python | mit | 13,229 | [
"pymatgen"
] | 0bf4efbacc6714cba1c3ba0e9462c907131f998db054f2b2bea4661893f6343d |
# #
# Copyright 2013-2020 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 (... | pescobar/easybuild-framework | test/framework/options.py | Python | gpl-2.0 | 245,424 | [
"NetCDF"
] | 5d4d1e63bcc6cdd1fded797df4e0859620ab2a3d3137f01be2c005e5e1e7a308 |
#!/usr/bin/python
"""Frequency response in an EM reverberation chamber
Visit http://imagetheorymodel.manuamador.fr/ for the
latest version and more information
"""
__author__ = "Emmanuel Amador (emmanuel.amador@insa-rennes.fr)"
__version__ = "$Revision: 0.1 $"
__date__ = "$Date: 2011/06/12$"
__copyright__ = "Copyrigh... | manuamador/Misc | PostDoc_python/RC/ExampleFRvect.py | Python | agpl-3.0 | 7,459 | [
"VisIt"
] | b1a29ddda0f4fe4484c14e64c56ea94fa3066eea6a094ac633e1ecd485dd202c |
"""Functions that assert conditions for use in pytest tests.
The AgentOptionsTest can be used to check consistency of options for Agents.
"""
import inspect
import importlib
import logging
import os
from pprint import pformat
from mock import patch, call, MagicMock as Mock
import DIRAC
from DIRAC.Core.Utilities.C... | arrabito/DIRAC | tests/Utilities/assertingUtils.py | Python | gpl-3.0 | 7,277 | [
"DIRAC"
] | 40292864e2c21ee53cc7640aadc796881923a604da79cec9b6ea44d262c63b20 |
# Copyright (C) 2013-2017 Paulo V. C. Medeiros
# This file is part of BandUP: Band Unfolding code for Plane-wave based calculations.
#
# BandUP 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 ... | band-unfolding/bandup | src/python_interface/bandupy/runners.py | Python | gpl-3.0 | 3,226 | [
"ABINIT",
"CASTEP",
"VASP"
] | 32a2ea86d831a3e0de76382a70bd7f421022662bac6aec8fdc78a41c0f70f2cb |
#
# -*- coding: utf-8 -*-
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008 Raphael Ackermann
# 2002-2003 Donald A. Peterson
# 2003 Alex Roitman
# 200... | SNoiraud/gramps | gramps/plugins/docgen/latexdoc.py | Python | gpl-2.0 | 49,389 | [
"Brian"
] | 7f34ce4b59971f814aa08440e43869e7a0432a04359fbcdf65d1aac8f67a172f |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | napkindrawing/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 104,376 | [
"VisIt"
] | e871b4cf0a24627dad8b5cea06696071d6e2feac13942faf36abfc321b0ec4b6 |
#!/usr/bin/env python
from __future__ import unicode_literals, division, print_function, absolute_import
import re
import os
import sys
re_markers = re.compile("^(<<<<<<< TREE|=======|>>>>>>> MERGE-SOURCE)$")
re_fbktop = re.compile("fallbacks$")
re_fbkdir = re.compile("(exports|sources|stamps)")
re_tmpdir = re.com... | jmbeuken/abinit | abichecks/scripts/check-conflict-markers.py | Python | gpl-3.0 | 3,135 | [
"ABINIT"
] | 73e4a578a162734101a78c41729f33dc41dfb1625345289606d9345c728b9cd5 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import petrarch_ud, PETRglobals, PETRreader, utilities, codecs, PETRgraph
import sys
import csv
# Get the Output File Name
file_out = sys.argv[1]
outfile = open(file_out, 'wb')
fout_report = csv.writer(outfile)
config = utilities._get_data('data/config/', 'PETR_config.... | openeventdata/UniversalPetrarch | Test Suite/test_script_ud.py | Python | mit | 845,915 | [
"VisIt"
] | a1a5730df856dd1cc12e0611a5859ea7f676100c16ab2ae104296f5e8a8ae5e0 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# 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 requ... | GarethNelson/rl-glue-ext | projects/codecs/Python/src/tests/test_taskspec.py | Python | apache-2.0 | 3,347 | [
"Brian"
] | 1956435cfed7502ff785a52df8dff166559c8ade004376216f5dd414122cb6c3 |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | eddiejessup/pizza | src/patch.py | Python | gpl-2.0 | 60,310 | [
"LAMMPS"
] | efa8bd7600d898d26459e571ade35fb78aa95279f4a088f14d414155664204a8 |
# Copyright (C) 2014,2015 Nippon Telegraph and Telephone Corporation.
#
# 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 ... | ramrunner/gobgp | tools/pyang_plugins/bgpyang2golang.py | Python | apache-2.0 | 23,376 | [
"VisIt"
] | cae54110811e5e9785aaad0329f3be12d460a5ce2672d19e0fa0e705914eff79 |
# Copyright (C) 2012,2013,2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms... | fedepad/espressopp | src/tools/decomp.py | Python | gpl-3.0 | 6,161 | [
"ESPResSo"
] | c26e120321ccd90ef1d6369d04ccd52ea0aa17528535d4721ff939d1ef494a94 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
"""
Module is used for visualization of segmentation stored in pkl file.
"""
import sys
import os.path
path_to_script = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.join(path_to_script, "../extern/dicom2fem/src"))
from loguru import logger
# logge... | mjirik/lisa | lisa/show_segmentation.py | Python | bsd-3-clause | 4,338 | [
"VTK"
] | a6bb9e4730d12b9a1a5cdc397fd2594b3b85dd352b32f3a973762be328bdf9d3 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
# pylint: disable=invalid-name
import types
import warnings
import pytest
import numpy as np
from numpy.testing import assert_allclose
from numpy.random import default_rng
from astropy.modeling.core import Fittable1DModel
from astropy.modeling.parameter... | pllim/astropy | astropy/modeling/tests/test_constraints.py | Python | bsd-3-clause | 22,852 | [
"Gaussian"
] | 2dbb0d55941d8f06647679ccf57096fffdbff93d233e404ad12314f54ddcc55c |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Calculation of Mayer's bond orders based on data parsed by cclib."""
import random
import numpy
from cc... | cclib/cclib | cclib/method/mbo.py | Python | bsd-3-clause | 4,093 | [
"cclib"
] | 5b7eb2ec9d8fef0c90ba3bd80c97bd4249a97cecdea138ee95806fe9e54e0776 |
import warnings
import matplotlib.pyplot as plt
import numpy as np
from sklearn.preprocessing import normalize
class RandomWalk2D:
''' Class for q-learning random walk '''
def __init__(self, grid_size=3, end_states=[(0,0)], rewards=[1], \
exploration=.1, move_cost=0, alpha=.3, gamma=.9):
sel... | rahulsrma26/code-gems | RL/randomWalk/qLearning.py | Python | mit | 5,044 | [
"VisIt"
] | 072ea50e2326c067a29be22422f76532abe419ca5055ec4b94c1edf057c85776 |
import numpy as np
import random
import common
def es_mutate_steps(steps, p):
steps_size = len(steps)
new_steps = []
t1 = np.sqrt(2 * steps_size) ** -1
t2 = np.sqrt(2 * np.sqrt(steps_size)) ** -1
for idx,step in enumerate(steps):
new_step = step * np.exp( (t1 * common.gaussian(0,1))
... | VictorRodriguez/personal | GP_tutorial/homework3/mutation.py | Python | apache-2.0 | 1,149 | [
"Gaussian"
] | e53c42ed5c768180c68c70a19b478264c5c547d78453d97eb416997e3de89741 |
#!/usr/bin/env python2.5
#
# Copyright 2008 the Melange authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applic... | MatthewWilkes/mw4068-packaging | src/melange/src/soc/views/models/document.py | Python | apache-2.0 | 8,189 | [
"VisIt"
] | d207f196e68a1ecc9bc99357a119eb42a1f755a2042bae554ca75db04420387f |
import json
import orca
import pandas as pd
import pandas.util.testing as pdt
import pytest
from .. import server
@pytest.fixture
def tapp():
server.app.config['TESTING'] = True
return server.app.test_client()
@pytest.fixture(scope='module')
def dfa():
return pd.DataFrame(
{'a': [100, 200, 300... | SANDAG/orca | orca/server/tests/test_server.py | Python | bsd-3-clause | 10,586 | [
"ORCA"
] | 57384d0402a6158a80a6550125eeaf94f656e06d810ff5f05656f2d051902089 |
#!/usr/bin/env python2
#
# Copyright (c) 2013 Insollo Entertainment, LLC. All rights reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without li... | krattai/noo-ebs | ref_code/nanomsg/doc/diag.py | Python | bsd-2-clause | 10,280 | [
"VisIt"
] | 3bf73b506d9a83fe885c11e6d3ea8eeb0a4cb8d946f4b55d56d0ca4eabd62497 |
#!/usr/bin/env python
# Dan Blankenberg
from __future__ import print_function
import base64
import datetime
import logging
import optparse
import os
import shutil
import subprocess
import tempfile
from json import (
dumps,
loads
)
from os.path import basename
from xml.etree.ElementTree import tostring
try:
... | Delphine-L/tools-iuc | data_managers/data_manager_rsync_g2/data_manager/data_manager_rsync.py | Python | mit | 17,444 | [
"Galaxy"
] | 3fafd2df72d6284f83618fa6e4a4631185adbd61bc698d3efc26a43090e8d3a6 |
########################################################################
# $HeadURL $
# File: ReTransfer.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 14:24:21
########################################################################
""" :mod: ReTransfer
================
.. module: ReTransfer... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/ReTransfer.py | Python | gpl-3.0 | 5,805 | [
"DIRAC"
] | 48b92dad9a61c31626b5ea3529d7ad63c8fe3761daecd60c2eda0722c2338d95 |
"""
:math:`I_GP_GT_G` Colourspace
=============================
Defines the :math:`I_GP_GT_G` colourspace transformations:
- :func:`colour.XYZ_to_IgPgTg`
- :func:`colour.IgPgTg_to_XYZ`
References
----------
- :cite:`Hellwig2020` : Hellwig, L., & Fairchild, M. D. (2020). Using
Gaussian Spectra to Derive a H... | colour-science/colour | colour/models/igpgtg.py | Python | bsd-3-clause | 5,424 | [
"Gaussian"
] | ec4f36d002b548f5648e67234fdaa4695502c4c08513441d5db44d5dd3be15da |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.