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# coding: utf-8
# In[5]:
from __future__ import division
from sys import stdout
import numpy as np
import sys
import networkx as nx
import numpy as np
import networkx as nx
import sklearn.metrics as met
import sklearn.manifold as man
import matplotlib.pyplot as plt
MIN_EXPANSION_SIZE = 10
#function to generate ... | DavidMcDonald1993/ghsom | ghsom.py | Python | gpl-2.0 | 19,300 | [
"NEURON",
"VisIt"
] | 77b259794440bf3c463b1cd47cc43228c2b6f70102fa6134f76f6576d57a0d69 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
... | harterj/moose | python/chigger/tests/utils/test_animate.py | Python | lgpl-2.1 | 1,087 | [
"MOOSE"
] | b2fc44931d68c0b6e268f7fe336b9f2f6507f6dbde30d811980ffb6ac20be269 |
# encoding: utf-8
# Class which creates "Calculator" objects that uses the EMT() model to calculate the quantities used in the ErrorFunction script in order to optimize the value of the seven parameters used in the EMT() model.
# Written by: Rasmus E. Christiansen
# Imported Packages
import numpy
from asap3.EMT2013 ... | auag92/n2dm | Asap-3.8.4/Python/asap3/Tools/ParameterOptimization/Rasmus2011/QuantityCalculatorEMT.py | Python | mit | 31,380 | [
"ASE",
"CRYSTAL"
] | f07383e7fd04575aaa459e8f9d2095f53b960b33ba9fc5f3c054d85eb59adc2c |
##############################################################################
# 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/r-dnacopy/package.py | Python | lgpl-2.1 | 1,704 | [
"Bioconductor"
] | 793c1b0aae90fdb271e702b2afe97be40b844dc3a8b7585a23c38ea6b24c6072 |
import numpy as np
from ase.units import Hartree
from weakref import proxy
hbar=0.02342178
class LinearlyPolarizedLaser:
""" Class for laser potential. """
def __init__(self,energy,flux,polarization,phase=0.0):
""" Laser parameters.
electrostatic potential=-E0*sin(omega*t+phase)*dot(polariza... | pekkosk/hotbit | hotbit/environment.py | Python | gpl-2.0 | 2,077 | [
"ASE"
] | 1704d31aef6f7c3d10bbb164127648f3e37340f3abb1032e53818e4dfa45df3a |
#
# Copyright 2016 The BigDL 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 law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/data/test_pandas_backend.py | Python | apache-2.0 | 15,558 | [
"ORCA"
] | f444e48c2a66f3616a8769c2c113b724881d1e63bb2e14c6df162d5df47ee859 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Autocompletion config for YouCompleteMe in Chromium.
#
# USAGE:
#
# 1. Install YCM [https://github.com/Valloric/YouCompleteMe]
# (Googlers s... | geminy/aidear | oss/qt/qt-everywhere-opensource-src-5.9.0/qtwebengine/src/3rdparty/chromium/tools/vim/chromium.ycm_extra_conf.py | Python | gpl-3.0 | 12,264 | [
"VisIt"
] | 7c25b72657e9c4a0301e3edd0cf0b02260b55ee3b8f3cc1a271698ecc7831530 |
#!/usr/bin/python
import json,datetime,sys,os,code,random,collections
from optparse import make_option
import openpyxl as xl
#Django Imports
from django.contrib.auth.models import User
from django.db.models import Max
from django.core.management import ManagementUtility
from django.core.management.base import BaseComm... | tperrier/mwachx | utils/management/commands/reset_demo.py | Python | apache-2.0 | 5,688 | [
"VisIt"
] | b21bffcc0a1d4bdab7d89c873d21f902f748d0360e0558ed06f0f9ad38deadcd |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | adityacs/ansible | lib/ansible/modules/network/avi/avi_pool.py | Python | gpl-3.0 | 16,763 | [
"VisIt"
] | cd533968a399085a7bb42bd0282192680762166c07617f536d0d9dd39013329d |
from ConfigObjects import Recipe, Enchantment, ItemStack, Factory, CraftedRecipe
from ParseConfig import ParseConfig
coeffs={}
gMod=1
mMod=0.1
def main():
print 'Running....'
ItemStack.importMaterials()
Enchantment.importEnchantments()
createConfigFile()
def createConfigFile():
config={}
... | ProgrammerDan/FactoryMod | Config Scripts/GenerateConfig.py | Python | bsd-3-clause | 16,879 | [
"BLAST"
] | 9cd3b3114e2a9c34d07c0b7f9b94020a473a783b64b297628b18ae9084b10ca3 |
import numpy as np
###############
## Class for univariate gaussian
## p(x) = 1/sqrt(2*pi*simga^2) * e ^ - (x-miu)^2/2*sigma^2
## Where miu is the gaussian mean, and sigma^2 is the gaussian variance
################
class Gaussian():
def __init__(self,mean,variance):
self.mean = mean;
self.varia... | oplatek/lxmls-toolkit | lxmls/distributions/gaussian.py | Python | mit | 677 | [
"Gaussian"
] | 626f259efd29df95a81e56b1dc697bc422bd91b2e82fddacdbbd1fb68795248f |
# Copyright 2016 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import copy
import json
import unittest
from dashboard import bisect_report
from dashboard.common import testing_common
from dashboard.models import try_job... | sahiljain/catapult | dashboard/dashboard/bisect_report_test.py | Python | bsd-3-clause | 32,498 | [
"VisIt"
] | 615af7f1c151965ef373ed407326af268fa2e21c54fdbdf7ddc53013779369f7 |
# -*- coding: utf-8 -*-
import numpy as np
import numpy.linalg as lin
from gp_kernels import kernel_gp, kernel_gaussian
def gp_loglik(K_test, K_test_train, K_train, test_t, train_t, sig2, beta):
"""Gaussian process log-likelihood calculation."""
# Kernel transformation
A = kernel_gp(K_train, sig2, beta)... | aaskov/nsp | gp/gp_loglik.py | Python | mit | 750 | [
"Gaussian"
] | 834ab3bbd38428f190f0604e2808cf34ee340a5a02dae34797461adbf37cd483 |
#!/usr/bin/env python
# Python example script that uses the vtkRIinterface to create an instance of the
# R interpreter and pass it some data, modify the data in R, and pass the result
# back to VTK.
# VTK must be built with VTK_USE_GNU_R turned on for this example to work!
from vtk import *
import math
if __name__... | msmolens/VTK | Examples/Infovis/Python/Rinterface.py | Python | bsd-3-clause | 1,841 | [
"VTK"
] | 481b075cdce52cc2610179a7dad81c6476d7dc998ac8abbf7ee6ed0494983888 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RStatmod(RPackage):
"""Statistical Modeling
A collection of algorithms and functions ... | LLNL/spack | var/spack/repos/builtin/packages/r-statmod/package.py | Python | lgpl-2.1 | 1,321 | [
"Gaussian"
] | e7dd01307b0d96de4204dbd163a9bc25d94a4cb718d1f91db7f478861e44d44b |
"""
=================================
Gaussian Mixture Model Selection
=================================
This example shows that model selection can be performed with
Gaussian Mixture Models using information-theoretic criteria (BIC).
Model selection concerns both the covariance type
and the number of components in th... | walterreade/scikit-learn | examples/mixture/plot_gmm_selection.py | Python | bsd-3-clause | 3,271 | [
"Gaussian"
] | 4f13008dd343a8ae90eba67c9cd6f1cde4df25ec65275c740bf45e98a03762fa |
#coding:utf-8
## Spark Application - execute with spark-submit
## Imports
import csv
import os
import time
import numpy as np
import pandas as pd
import statsmodels.api as sm
import statsmodels.tsa.stattools as sts
from StringIO import StringIO
from pyspark import SparkConf, SparkContext, SQLContext
## Module Consta... | lionelliang/PairTradingSpark | checkpairtradingSpark.py | Python | gpl-2.0 | 10,134 | [
"ADF"
] | 2cd684953dcc0b7ab245a26b027d99f0d3cb2dbc654963575fb859e0e00e4722 |
# $HeadURL: $
'''
:mod: RssConfiguration
Module that collects utility functions.
'''
from DIRAC import S_OK
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.Helpers.Operations import Operations
from DIRAC.Reso... | arrabito/DIRAC | ResourceStatusSystem/Utilities/RssConfiguration.py | Python | gpl-3.0 | 4,088 | [
"DIRAC"
] | 4b1d821db08eb841c74643d38f4494ea6983d974fee4d8a53ec40ff1d85093b7 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
from eh... | ReilySiegel/ehs_esports | config/urls.py | Python | mit | 1,685 | [
"VisIt"
] | 4f9553a37d57fb37ea8adf762916719fcf0ddd018543d78cbe58ec8effda3cd9 |
#!/usr/bin/env python
""" This script instantiate a DFC client against a given service,
and hammers it with read request (listDirectory) for a given time.
It produces two files : time.txt and clock.txt which contain time measurement,
using time.time and time.clock (see respective doc)
It assumes that th... | DIRACGrid/DIRAC | tests/Performance/DFCPerformance/readPerf.py | Python | gpl-3.0 | 2,409 | [
"DIRAC"
] | 168e850278ff3fa2ebcfd1f4a37ede51d0adfda25f5e47c26cb4abbdbd882cac |
import bge
from mouse import *
from keyboard import *
from building import *
from civilisation import *
from ressource import *
import random
class Game():
def __init__(self, players):
"""param: self, number of players"""
self.players = players
self.civilisations = []
... | folkrav/rts-b51 | src/projectX/game.py | Python | gpl-3.0 | 2,449 | [
"CRYSTAL"
] | b950c64dc8702fc9bd32c78c95abc21d5fa9d8cc9c73f129bc478f4ff2d75937 |
from . import base
from .. import stats
from .. import items
from .. import dialogue
from .. import context
from .. import spells
from .. import invocations
from .. import effects
from .. import animobs
from .. import targetarea
from .. import aibrain
import random
from . import animals
from . import undead
from .. imp... | jwvhewitt/dmeternal | old_game/monsters/people.py | Python | gpl-2.0 | 17,995 | [
"BLAST"
] | 0029dd023d82851e497fe252c52d861f1b006c9dab4e9a5acb07bfd6a423ebe1 |
# -*- coding: utf-8 -*-
"""
Created on Fri May 29 11:23:17 2015
Sellemeier coefficients and nonlinear parameter for PPLN
This file is part of pyNLO.
pyNLO is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundati... | ycasg/PyNLO | src/pynlo/media/crystals/XTAL_PPLN.py | Python | gpl-3.0 | 6,036 | [
"CRYSTAL"
] | 90db38a9bb6079e20b483348a320ad3c1b6b77ee345999242c92b97e2e10c873 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Gaussian Mixture Model Class:
contains the basic fields and methods of GMMs
The class GMM _old uses C bindings which are
computationally and memory efficient.
Author : Bertrand Thirion, 2006-2009
"""
... | bthirion/nipy | nipy/algorithms/clustering/gmm.py | Python | bsd-3-clause | 29,373 | [
"Gaussian"
] | b45ba4c6705d6bb19fb8a30817150e4d1079a025096c2efb1cc38c5a4d52f7b0 |
# S.D. Peckham
# Sept 2014 (new version to use netCDF4)
# June 2010 (streamlined a bit more)
# December 2, 2009 (updated open_new_file to use "info")
# October 13, 2009
import os
import sys
import time
import numpy as np
import bov_files
import file_utils
import rti_files
import netCDF4 as nc
#--------------------... | mdpiper/topoflow | topoflow/utils/ncgs_files.py | Python | mit | 19,007 | [
"NetCDF"
] | 720076c7ec2159bdadd98ef8488e17efdc51d2d0cf90395137c0004cbb052f05 |
# -*- coding: utf-8 -*-
"""The config functions."""
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
import atexit
from functools import partial
import json
import os
import os.path as op
import platform
import shutil
import sys
import tempfile
import re
import numpy as np
from .check impor... | pravsripad/mne-python | mne/utils/config.py | Python | bsd-3-clause | 21,324 | [
"Mayavi",
"VTK"
] | 9a54928ae5753f94342243e750a0e324ac7ddcfe05a7987bcfb54d31b36bed98 |
# -*- coding: utf-8 -*-
import re
import sublime
from sublime_plugin import TextCommand, WindowCommand
from .SublimeBoo import server, get_code, convert_hint
from .BooHints import format_type, format_method, find_open_paren
MEMBER_REGEX = re.compile(r'[\w\)\]]\.$')
WORD_REGEX = re.compile(r'^\w+$')
class BooDotCom... | drslump/sublime-boo | commands.py | Python | mit | 20,206 | [
"VisIt"
] | d6a9a605f5008555e51a99586ceab17dd683222e84e4af4f8cdaef5fa4b27c23 |
#!/usr/bin/env python
# from nltk.classify.megam import config_megam, call_megam
#from nltk.classify.weka import WekaClassifier, config_weka
from datetime import time
from nltk import ELEProbDist
from nltk.classify.naivebayes import NaiveBayesClassifier
from nltk.classify.positivenaivebayes import PositiveNaiveBayesCl... | xflows/tf_core | tf_core/nltoolkit/lib/classification.py | Python | mit | 8,140 | [
"Gaussian"
] | 7955156643c356ef39f6fc2777f9c199f00234292ae41f8a8ed8fb447c6170dc |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# math2html: convert LaTeX equations to HTML output.
#
# Copyright (C) 2009-2011 Alex Fernández
#
# Released under the terms of the `2-Clause BSD license'_, in short:
# Copying and distribution of this file, with or without modification,
# are permitted in any m... | Soya93/Extract-Refactoring | python/helpers/py3only/docutils/utils/math/math2html.py | Python | apache-2.0 | 171,688 | [
"Bowtie"
] | d9787e9ad7f53e94ec07e34dc9bddff47020e790f024ccc9b91451618b95cac5 |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'castep'
tab.settings['Output file name'] = 'phonon.castep'
#
# SettingsTab
#
tab = self.notebook.settingsTab
tab.settings['Eckart flag'] = False
tab.settings['Neutral Born charges'] = False
tab.settings['Sigma value'] = 5
tab.settings['Mass definition... | JohnKendrick/PDielec | Examples/Castep/Na2SO42/script.py | Python | mit | 2,005 | [
"CASTEP"
] | 1f882e3474086bf98e05427ffabeb26b4510f21e5a8b7c91c9e3ff22af3c20cf |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_h5md.py | Python | gpl-3.0 | 977 | [
"ESPResSo"
] | a12c7a08a5b85763d7f402b1dc0188c18e82448217354ba3a444e0d5a7625360 |
from ANNarchy import *
# Compulsory to allow structural plasticity
setup(structural_plasticity=True)
# Simple neuron type
LeakyIntegratorNeuron = Neuron(
parameters="""
tau = 10.0 : population
baseline = 0.0
""",
equations = """
tau * dr/dt + r = baseline + sum(exc) : min=0.0
"... | ANNarchy/ANNarchy | examples/structural_plasticity/StructuralPlasticity.py | Python | gpl-2.0 | 1,923 | [
"NEURON"
] | e1c2ff81542d97cf995ef025177e6363630a7901e280f53d592f7edd0bf89055 |
# Orca
#
# Copyright (C) 2010-2011 The Orca Team
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; e... | GNOME/orca | src/orca/scripts/toolkits/WebKitGtk/script.py | Python | lgpl-2.1 | 24,873 | [
"ORCA"
] | f8dabb923a0594f9c69eea883f40c913dcad5fc9ef24b133349159ff3da39df7 |
from polychartQuery.expr import ExprTreeVisitor
from polychartQuery.utils import isNumber
# GENERAL SHARED FUNCTIONS
QUOTE = "'" # note: double quote does not work in postgres!
def escape(str): return str # TODO: implement
def quote(str): return QUOTE+escape(str)+QUOTE
def unquote(str):
if str[0] == QUOTE and str[-1... | Polychart/builder | server/polychartQuery/sql/expr.py | Python | agpl-3.0 | 5,886 | [
"VisIt"
] | 89dfd5cb45557bd50343b6620d9ce95e05d6e7f2511dde511de8b7399f1d2985 |
from benchbuild.utils.wrapping import wrap
from benchbuild.projects.benchbuild.group import BenchBuildGroup
from benchbuild.utils.compiler import lt_clang_cxx
from benchbuild.utils.downloader import Git
from benchbuild.utils.run import run
from benchbuild.utils.versions import get_version_from_cache_dir
from plumbum i... | simbuerg/benchbuild | benchbuild/projects/benchbuild/lammps.py | Python | mit | 1,566 | [
"LAMMPS"
] | cb60332e053a4881c8b39645bb0c6e17069aa679b61c03961a565edc55547a61 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# utils.py
#
# Copyright 2014 Gary Dalton <gary@ggis.biz>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licen... | gary-dalton/Twenty47 | twenty47/utils.py | Python | mit | 19,151 | [
"Dalton"
] | 1662cfac97d79e16af7cea32e3f4c91e660178cba0d9bd3d0f007bf704c768c2 |
import atexit
import contextlib
import fnmatch
import importlib.util
import itertools
import os
import shutil
import sys
import uuid
import warnings
from enum import Enum
from functools import partial
from os.path import expanduser
from os.path import expandvars
from os.path import isabs
from os.path import sep
from po... | TeamSPoon/logicmoo_workspace | packs_web/butterfly/lib/python3.7/site-packages/_pytest/pathlib.py | Python | mit | 20,034 | [
"VisIt"
] | caaa607b1decb33402ad43f78a4eef33a8c7718846271db6037fb102110eaf7f |
"""
Cardiac image multi-atlas segmentation pipeline
Author: Wenjia Bai
First created: 2015.03.31
Last modified: 2016.11.21 by wbai
"""
import os
def segment_data(image_name, landmarks_name, output_dir, atlas_root, atlas_list, template_dir, par_dir, remove_temp=True):
# Check files
if not os.path.exists(imag... | baiwenjia/CIMAS | cimas.py | Python | apache-2.0 | 15,158 | [
"VTK"
] | ab8fe050024c4faab69f0f108fdb4bd0b3f01f6f2710fa43861f3b15f18447b1 |
import pytest
class TestHasCheckedFiled:
@pytest.fixture(autouse=True)
def setup_session(self, session):
session.visit("/form")
def test_is_true_if_a_checked_field_is_on_the_page(self, session):
assert session.has_checked_field("gender_female")
assert session.has_checked_field("Ha... | elliterate/capybara.py | capybara/tests/session/test_has_checked_field.py | Python | mit | 4,316 | [
"VisIt"
] | 11240a39ebc00be0b8999870648fc5705f33516ece128b5426e5473d3736a26a |
from __future__ import division
from iotbx.pdb.multimer_reconstruction import multimer
import iotbx.pdb
import mmtbx.f_model
from cctbx import xray
import scitbx.lbfgs
import getpass
import os
import sys
from scitbx.array_family import flex
ncs_1_copy="""\
MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1
M... | youdar/work | work/NCS/test_files/run_03.py | Python | mit | 14,976 | [
"PyMOL"
] | 510aa5f3459964895457dc2b4921204770a577be6ea9fd3f77cd67ab55ed822e |
from ase import Atoms
from ase.db import connect
from ase.structure import molecule
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms, FixBondLength
for name in ['y2.json', 'y2.db']:
c = connect(name)
print(name, c)
id = c.reserve(abc=7)
c.delete([d.id for d in c.select(abc=7)]... | PHOTOX/fuase | ase/ase/test/db2.py | Python | gpl-2.0 | 979 | [
"ASE"
] | 037260eef955b20464ccc535399f4a0cb85de4e93c66e04654bea24589206d50 |
# Copyright 2009 Lee Harr
#
# This file is part of pybotwar.
#
# Pybotwar 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.
#
# Pybotwar ... | CodingRobots/CodingRobots | world.py | Python | gpl-3.0 | 20,209 | [
"BLAST"
] | a377b3d76965fee90d388577853ba069b8d75b898542c945c98dfd128ed91c48 |
#-*- coding:utf-8 -*-
"""sslfetch.connections.py
Python Lib for ssl connection downloads.
Complete with:
optional timestamp file to load
Headers:
'User-Agent'
'If-Modified-Since',
'last-modified'
custom
proxies
Copyright (C) 2013 Brian Dolbec <dolsen@gentoo.org>
Distrib... | dol-sen/ssl-fetch | sslfetch/connections.py | Python | gpl-2.0 | 14,171 | [
"Brian"
] | 1f7acdd20b74b0dc3b84d9fba3989e3ce7082e6d19d932bb39fe67a1e35cd771 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/jobfolder/jobfolder.py | Python | gpl-3.0 | 19,629 | [
"CRYSTAL",
"VASP"
] | 104e27371f25aec9c307e1ce0e55e671996591d94daab9ca513a1138b535d5e9 |
# The help text for various thresholding options whose code resides here is in modules/identify.py
from __future__ import absolute_import
from __future__ import division
import inspect
import math
import numpy as np
import scipy.ndimage
import scipy.sparse
import scipy.interpolate
from .otsu import otsu, entropy, ot... | CellProfiler/centrosome | centrosome/threshold.py | Python | bsd-3-clause | 33,646 | [
"Gaussian"
] | e5a42466ab5c8717d8f8013b6e176e246271df457f59a6cb5a1e0a60535439ab |
import os
import unittest
from datetime import timedelta
import numpy as np
import netCDF4
from pyaxiom.netcdf import EnhancedDataset
from pyaxiom.netcdf.sensors import TimeSeries, get_dataframe_from_variable
import logging
from pyaxiom import logger
logger.level = logging.INFO
logger.addHandler(logging.StreamHandle... | ocefpaf/pyaxiom | pyaxiom/tests/test_timeseries.py | Python | mit | 25,516 | [
"NetCDF"
] | adfcd3ca77d3451f3668207545a02a9d454a8b869efa93e49c657cca20d70788 |
#!/usr/bin/env python
#
# This file is part of OpenDrift.
#
# OpenDrift 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, version 2
#
# OpenDrift is distributed in the hope that it will be useful,
# but WITHOU... | knutfrode/opendrift | opendrift/scripts/hodograph.py | Python | gpl-2.0 | 3,847 | [
"NetCDF"
] | 5e58b6e9c760b657989098e2748f24ae0dd41e2ff4ee7740baf6adef643c7306 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/distributions/python/ops/bijectors/real_nvp.py | Python | apache-2.0 | 12,026 | [
"Gaussian"
] | bb6c9cd7510517660b4aaf895654807e87a29a3190ee1f7b80cae75b6240422c |
# coding: utf8
"""Livestreamer extracts streams from various services.
The main compontent of Livestreamer is a command-line utility that
launches the streams in a video player.
An API is also provided that allows direct access to stream data.
Full documentation is available at http://docs.livestreamer.io/.
"""
_... | mrquim/mrquimrepo | script.module.livestreamer/lib/livestreamer/__init__.py | Python | gpl-2.0 | 1,974 | [
"Brian"
] | c2bddc66ce817e4f90fcc7fce1378f19310808c82704d4359255b22270da0398 |
#
# Copyright 2012 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... | memorydump85/cardamon | moneyplot/oauth2.py | Python | mit | 12,190 | [
"VisIt"
] | 6d0cc68a62d77bd3156efe682a124cfb6a0bca83eaea59810378a2a78fc3d59a |
#! /usr/bin/env python
# -*- coding:utf-8 -*-
#
# Application to demonstrate the use of the MeshToolkit library
#
# External dependencies
import argparse
import sys
import numpy as np
import MeshToolkit as mtk
# Initialisation
input_mesh = None
# Create a command line argument parser
parser = argparse.ArgumentParser... | microy/MeshToolkit | meshtoolkit.py | Python | mit | 4,117 | [
"Gaussian"
] | f2e227b53faabb4720c39519cdd7d056d5ec3f4037ed2dbd75dba990fb538659 |
# -*- 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.
from PyQt4 import QtGui, QtCore
class Qt4Progress(QtGui.QProgressDialog):
def __init__(self, title, parent=None):
... | cclib/cclib | cclib/progress/qt4progress.py | Python | bsd-3-clause | 1,013 | [
"cclib"
] | c663b30ec9984bccf151229be418a9181ba8069895ae5d912b9dcde9c21c90b5 |
#
# packages.py: package management - mainly package installation
#
# Copyright (C) 2001, 2002, 2003, 2004, 2005, 2006 Red Hat, Inc.
# All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software... | icomfort/anaconda | packages.py | Python | gpl-2.0 | 14,576 | [
"VisIt"
] | fef5f81c3287cf674783f70083dcad854afc2e9900321e20e3e139b936379714 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# 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)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/core/util.py | Python | gpl-2.0 | 25,240 | [
"MDAnalysis"
] | 22323b163e505df2b148d01dd5f8754e928abc97be5352b3da7b83ee1f820de2 |
# This wizard contributed by Ezequiel "Zac" Panepucci 011114
# modified by Warren L. DeLano
from pymol.wizard import Wizard
from pymol import cmd
import pymol
from chempy.models import Indexed
from chempy import Atom,Bond
from chempy.cpv import add, sub, cross_product, scale, dot_product
from chempy.cpv import normali... | gratefulfrog/lib | python/pymol/wizard/box.py | Python | gpl-2.0 | 15,266 | [
"ChemPy",
"PyMOL"
] | 7498becd660bd15c713c873cdc9da29894a52c4658b81fe89ffa1333c3e4c0f5 |
# -*- coding: utf-8 -*-
"""
ast
~~~
The `ast` module helps Python applications to process trees of the Python
abstract syntax grammar. The abstract syntax itself might change with
each Python release; this module helps to find out programmatically what
the current grammar looks like an... | codendev/rapidwsgi | src/mako/_ast_util.py | Python | gpl-3.0 | 26,249 | [
"VisIt"
] | a6a56f1107c68a9439cfe345e248afe3dce9785872d169f0b193acee0aa5dc6b |
# Copyright 2014 by Kevin Wu.
# Revisions copyright 2014 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Provides code to access the REST-style KEGG online AP... | zjuchenyuan/BioWeb | Lib/Bio/KEGG/REST.py | Python | mit | 10,820 | [
"Biopython"
] | 865facb891c85ddc0faca9a2309e1b862b3349698e2fb9ba0620e7a7d47a5b35 |
"""
Ze Neek Player
- A CLI-based internet radio stream player for neeks
- Play internet radio from your command line C:
- Geek + Nerd = Neek. Get it?
- Made in Python 2.7
- Requires PyGst (Gstreamer Python Bindings)
- Requires Gstreamer, its plugins and the development files
for Gstreamer as well.
License: GNU GPLv... | mister-raindrop/neek-player | neekPlayer.py | Python | gpl-3.0 | 1,295 | [
"VisIt"
] | cf7382421f56bde6cbb2a622ba39eb9e922cb5400be472fd39f67cec24f83365 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# 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.
# ---------------------... | JWDebelius/scikit-bio | skbio/util/tests/test_misc.py | Python | bsd-3-clause | 4,255 | [
"scikit-bio"
] | 990c8544f9bc33ffb4ae7405136c6f445e34f8a480ff35c4569f4f12f8e80c1f |
# flake8: noqa: E241
from tests.core import mock
from trakt import Trakt
from httmock import HTTMock
def test_movie():
with HTTMock(mock.fixtures, mock.unknown):
movies = Trakt['movies'].popular()
assert [(m.title, m.year) for m in movies] == [
("Deadpool", 2016),
("The Dark Knight"... | fuzeman/trakt.py | tests/test_popular.py | Python | mit | 1,088 | [
"Galaxy"
] | 54e2d352daff72630f5d8921a51601d1434950d529091cf446b4fcf502112cfc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Extract fasta sequences that are above a minimal length.
Usage:
%program <input_file> <min_length> <output_file>"""
import sys
import re
try:
from Bio import SeqIO
except:
print("This program requires the Biopython library")
sys.exit(0)
try:
fast... | enormandeau/Scripts | fasta_extract_min_length.py | Python | gpl-3.0 | 737 | [
"Biopython"
] | c483b4e5398071da5368661dbee59218c827f4ec5955bafe36409b6a37c83c5b |
import os
import Forge.core.System
def createRenderHierarchy( path, sceneName, frames ):
"""create the render folder hierarchy"""
'@parameter path (string) Path of the environement.'
'@parameter sceneName (string) Name of the scene.'
'@parameter frames (array of int) Frames to render.'
folders = ... | Black-Cog/Forge | core/rendermanRib.py | Python | bsd-3-clause | 25,735 | [
"Gaussian"
] | ea18ac718f6fc5c752f5577a7c823dc1df862616a781bcb39d4580f4e4d4afef |
"""Test the PhyML executable.
https://github.com/biopython/biopython/blob/master/Tests/test_phyml_tool.py
"""
import sys
import os
import unittest
from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline
from Bio import MissingExternalDependencyError
class PhymlTest(unittest.TestCase):
... | datasnakes/Datasnakes-Scripts | OrthoEvol/Orthologs/Phylogenetics/PhyML/phyml_test/phyml_test.py | Python | mit | 2,300 | [
"Biopython"
] | 62187af817cfc5bd8155b3f430befb9e5debac53781003d7e7905602071541bc |
import os
from dirac.lib.base import *
from DIRAC import gConfig, gLogger, rootPath
from dirac.lib.diset import getRPCClient
from dirac.lib.credentials import getUserDN, getUsername
from dirac.lib.credentials import getSelectedGroup, checkUserCredentials
from DIRAC.FrameworkSystem.Client.UserProfileClient import UserP... | DIRACGrid/DIRACWeb | dirac/controllers/web/External.py | Python | gpl-3.0 | 2,298 | [
"DIRAC"
] | 9ae9ac66d5b94a044a10ffec6509106408a1ece6a3d9ad66e0e905e27982363f |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014, 2015 CERN.
#
# INSPIRE 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... | Dziolas/inspire-next | inspire/modules/forms/views.py | Python | gpl-2.0 | 3,060 | [
"VisIt"
] | 821401e77bb5d57b948525c7fb04ce195766eecbbf67cad84dfbb4edd6b88836 |
# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit for the Earth and Planetary Sciences
# Copyright (C) 2012 - 2015 by the BurnMan team, released under the GNU
# GPL v2 or later.
from __future__ import absolute_import
from os import path
import numpy as np
import scipy.optimize as opt
try:
... | geodynamics/burnman | burnman/eos/dks_liquid.py | Python | gpl-2.0 | 24,441 | [
"Avogadro",
"DIRAC"
] | 977e7b1886ab9d6a2d036936240c78ca208eb632c535c9f5fed4edba314073f4 |
#!/usr/bin/env python
'''
ooiservices.manage
Manage script for specific services related tasks
'''
from flask.ext.script import Manager
from ooiservices import app
from ooiservices.util.erddap_catalog import ERDDAPCatalog, ERDDAPCatalogEntry
import os
manager = Manager(app)
def add_to_catalog(catalog_path, dataset... | ednad/ooi-ui-services | ooiservices/generate_catalog.py | Python | apache-2.0 | 1,064 | [
"NetCDF"
] | 02385190330388b7ad9966c00f4e55ef2941188d0bc9c289ec85eddc7f9cede9 |
# Orca
#
# Copyright 2007-2009 Sun Microsystems Inc. and Joanmarie Diggs
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any lat... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/acroread/script.py | Python | gpl-3.0 | 27,288 | [
"ORCA"
] | 0b3ee5895a824fedddf1b3e1a3508b12d0c45f0fbd42cacf25af15326aef2b40 |
"""
Utilities to execute a function with a given proxy.
executeWithUserProxy decorator example usage::
@executeWithUserProxy
def testFcn( x, i, kw = 'qwerty' ):
print "args", x, i
print "kwargs", kw
print os.environ.get( 'X509_USER_PROXY' )
return S_OK()
...
result = testFcn( 1.0, 1, kw = '... | hgiemza/DIRAC | Core/Utilities/Proxy.py | Python | gpl-3.0 | 6,847 | [
"DIRAC"
] | a45adcc1191feab9371b2c16bb93ffb40aa73e9e628276963bbcd5329811e299 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/diversity/_util.py | Python | bsd-3-clause | 5,494 | [
"scikit-bio"
] | 35fc79021ff22404f2a3f1e56bad16da1338373b9967a4ebab5949b1299096a1 |
# coding: utf8
{
' (leave empty to detach account)': ' (leave empty to detach account)',
' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages using SMS & Email to various groups and individuals before, during and after a disaster.': ' Module is the main communicatio... | ptressel/sahana-eden-madpub | languages/vi.py | Python | mit | 259,181 | [
"VisIt"
] | 7b50f734bae97857af072c19d6a18cf41891829ea403f368066c8e7596901a99 |
#!/usr/bin/env python
#**************************************************************************
# Tintwizard
#
# Copyright (C) 2009 Euan Freeman <euan04@gmail.com>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License version 3
# as published ... | krnlyng/tint2 | src/tint2conf/tintwizard.py | Python | gpl-2.0 | 107,754 | [
"VisIt"
] | b31c5de6d457e76a0af4d374e58218adbf6fea4f7b07e1e5961c4116243ad91e |
"""
:copyright: Copyright 2006-2016 by the PyNN team, see AUTHORS.
:license: CeCILL, see LICENSE for details.
"""
import numpy
from pyNN import recording
from pyNN.neuron import simulator
import re
from neuron import h
recordable_pattern = re.compile(r'((?P<section>\w+)(\((?P<location>[-+]?[0-9]*\.?[0-9]+)\))?\.)?(... | anupkdas-nus/global_synapses | pyNN-dispackgaes/neuron/recording.py | Python | gpl-3.0 | 4,605 | [
"NEURON"
] | d59293a090560e79599f49ade84adcfb359c947944a37f83f89a9a467ae20274 |
# -*- coding: utf-8 -*-
from collections import defaultdict
import os
import numpy as np
from pyfr.shapes import BaseShape
from pyfr.util import subclass_where
from pyfr.writers import BaseWriter
class VTKWriter(BaseWriter):
# Supported file types and extensions
name = 'vtk'
extn = ['.vtu', '.pvtu']
... | iyer-arvind/PyFR | pyfr/writers/vtk.py | Python | bsd-3-clause | 14,930 | [
"VTK"
] | 04d7448a8e712112d9bdd9c3384452db6a3c88336ab6b25dd492dffc49970b80 |
"""This module provides support for Fourier transforms. It calculates
the bilateral Fourier transform using:
S(f) = \int_{-\infty}^{\infty} s(t) e^{-j * 2 * \pi * t} dt
It also allows functions that strictly do not have a Fourier transform
by using Dirac deltas. For example, a, cos(a * t), sin(a * t), exp(j
* a ... | mph-/lcapy | lcapy/fourier.py | Python | lgpl-2.1 | 12,994 | [
"DIRAC"
] | 607da2b330a47e8a65e7f803a0af2ea28dde2574f540cd70290767d955dcfd43 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 5.0.4.
Change directory to p... | iglpdc/nipype | nipype/interfaces/fsl/epi.py | Python | bsd-3-clause | 38,169 | [
"Gaussian"
] | 2d429a090dabe00191bdda8ce032d1c20306442cf83e56e07def7b969e1eb405 |
#!/usr/bin/env python
import platform
import time
import numpy
from pyscf import lib
from pyscf.dft import rks
from mpi4pyscf.lib import logger
from mpi4pyscf.scf import hf as mpi_hf
from mpi4pyscf.tools import mpi
comm = mpi.comm
rank = mpi.rank
@mpi.parallel_call(skip_args=[1, 2, 3, 4], skip_kwargs=['dm_last', '... | sunqm/mpi4pyscf | mpi4pyscf/dft/rks.py | Python | gpl-3.0 | 4,942 | [
"PySCF"
] | e8cf083238871cff48ca2b7985893459ae113db9f8e6ffa9b8004c7232fed1f9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | lothian/psi4 | psi4/driver/procrouting/sapt/sapt_mp2_terms.py | Python | lgpl-3.0 | 11,036 | [
"Psi4"
] | 0e02c318025b597df87db7ae302fcc60e8e7b67c6c42f7f5e3b5c077cc535181 |
##############################################################################
# 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-affyqcreport/package.py | Python | lgpl-2.1 | 2,211 | [
"Bioconductor"
] | 31958dda4c671c63b813fd40739b0b2ca6e76a90d03cd927b62c4a48a8deb37f |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/des/des_meds.py | Python | gpl-3.0 | 20,128 | [
"Galaxy"
] | 0734a852658a9244ac5d7d80de13156b1dc65fa2b9ff00375120bd3e2951beba |
################################################################################
# #
# Copyright (C) 2010-2017 The ESPResSo project #
# ... | KonradBreitsprecher/espresso | doc/tutorials/06-active_matter/EXERCISES/flow_field.py | Python | gpl-3.0 | 5,592 | [
"ESPResSo",
"ParaView",
"VTK"
] | cbf0b56d08527db9d3410b6a89e35bd55a956f24f273df4ea00686a28551523e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from datetime import datetime
import os
from django.utils import html
from django.utils._os import upath
from django.utils.encoding import force_text
from django.utils.unittest import TestCase
class TestUtilsHtml(TestCase):
def check_output(self, ... | atruberg/django-custom | tests/utils_tests/test_html.py | Python | bsd-3-clause | 8,672 | [
"ADF"
] | 43815c75b4f989c97b456c48156ec1f40809ef4de852ec377c6818b5ff15b8e6 |
# Network class.
from scipy.special import expit
import numpy as np
import pyperclip
import screenPixel
import pyautogui as pg
import random
import re
import os
'''
inp nodes hidden nodes exit nodes
100 20 2
'''
class network:
def mutate(self,x):
if(np.random.rand() < self.mutationRate)... | Chrisr850/Snake.io-player | testnetwork.py | Python | mit | 4,943 | [
"NEURON"
] | 40eeebab988494ec14e2a269ce7bda8081a0e50dfb892551adea004adb5f0f8b |
data = [
'East Los Angeles',34.0238889,-118.1711111,
'Los Angeles',34.0522222,-118.2427778,
'San Diego',32.7152778,-117.1563889,
'San Francisco',37.7750000,-122.4183333,
'San Jose',37.3394444,-121.8938889,
'Chicago', 41.8500000, -87.6500000,
'New York',40.7141667,... | nesl/mercury | Web/filter_city.py | Python | gpl-2.0 | 2,824 | [
"COLUMBUS"
] | c4a097b43844449d3a5a3ebd61e4a1ab436c3a401845dcd5a4f6f4adcf76d18d |
from rdkit import Chem
class SubstructureSet:
def __init__(self):
self.substructures = dict()
def add_substructure(self, smiles, value):
if smiles in self.substructures:
self.substructures[smiles].add_occurrence(value)
else:
self.substructures[smiles] = Substr... | patrick-winter-knime/mol-struct-nets | molstructnets/steps/interpretation/extractsaliencymapsubstructures2d/substructure_set.py | Python | gpl-3.0 | 1,024 | [
"RDKit"
] | 9a2c4786e2db67af6f9ea1d79bbfe1731b584d875cae102a38b1fddabad781de |
#this python script first creates a neighborlist of atoms using Periodic CKDTree search
#next one can get the Qn distribution of a Si-O-Al network or Si-O-Si network using this script
#this version can also find the coordination of Si and Al and NBO statistics
#Author: Mohammad Rafat Sadat, Dept. of CEEM University of ... | msadat/python-scripts | Qn_coord_periodic_kdtree_V1.0.py | Python | gpl-3.0 | 12,337 | [
"LAMMPS"
] | 4e501d75bdf1a637a163d7cd2212091d99c246e2ccce4a9f4ef84b4f4c5c3f34 |
#!/usr/bin/env python
####################################################################################
### Copyright (C) 2015-2019 by ABLIFE
####################################################################################
####################################################################################
###... | ablifedev/ABLIRC | ABLIRC/bin/ablib/utils/distribution.py | Python | mit | 26,148 | [
"HTSeq"
] | 866b4feaf02a6c481cad023c592d6200318ef9b7a546af7d557b797ce87750d1 |
"""
This module implements :class:`Group`, which represents a subset of the
channels in an :class:`AnalogSignal` or :class:`IrregularlySampledSignal`.
It replaces and extends the grouping function of the former :class:`ChannelIndex`
and :class:`Unit`.
"""
from os import close
from neo.core.container import Container
... | JuliaSprenger/python-neo | neo/core/group.py | Python | bsd-3-clause | 3,012 | [
"NEURON"
] | 335369a66bafa3f51ba4f7904a61a43a38320a14148238c15d05063c3437bede |
# -*- coding: utf-8 -*-
#!/usr/bin/env python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
# Copyright... | prculley/gramps | gramps/gen/plug/docgen/graphdoc.py | Python | gpl-2.0 | 41,093 | [
"Brian"
] | a2de670824f2c99c1785258eff3be84993e6a54f773606a72575c0422b4c69ac |
#!/usr/bin/env python
"""Test script to check for required functionality.
Execute this code at the command line by typing:
python swc-installation-test-2.py
Run the script and follow the instructions it prints at the end.
This script requires at least Python 2.6. You can check the version
of Python that you hav... | selimnairb/2014-02-25-swctest | setup/swc-installation-test-2.py | Python | bsd-2-clause | 34,853 | [
"Mayavi"
] | 1154dbe5c5e3a838fae8bfaf1a414abb7caad5a7dde31cb27634e1b4bc8fd1e6 |
# -*- coding: latin-1 -*-
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later ... | FedoraScientific/salome-hexablock | doc/test_doc/replace_hexa/replace_hexa.py | Python | lgpl-2.1 | 2,479 | [
"VTK"
] | dac358884476a746809c268a9edfa142447b3f192e40619df01af57e465aa3dc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
## Copyright 2015 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## 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 ... | scholer/nascent | nascent/nucleotides.py | Python | agpl-3.0 | 29,920 | [
"MDAnalysis",
"Mayavi"
] | d7ced376be93a815345390fba84a5f73427c25d2054fe652c13d9f36b6491f73 |
# -*- coding: utf-8 -*-
import numpy as np
from PIL import Image
# /////////////// Corruption Helpers ///////////////
import skimage as sk
from skimage.filters import gaussian
from io import BytesIO
from wand.image import Image as WandImage
from wand.api import library as wandlibrary
import wand.color as WandColor
i... | hendrycks/robustness | ImageNet-C/imagenet_c/imagenet_c/corruptions.py | Python | apache-2.0 | 14,857 | [
"Gaussian"
] | fb962115845e0a7ceaf5a6e3cda17f4aab07c66e3c367c219cafc7032c4a43fb |
from coalib.bearlib.abstractions.Linter import linter
from coalib.bears.requirements.DistributionRequirement import (
DistributionRequirement)
@linter(executable='verilator',
output_format='regex',
use_stderr=True,
output_regex=r'\%(?:(?P<severity>Error|Warning.*?).*?):'
... | SanketDG/coala-bears | bears/verilog/VerilogLintBear.py | Python | agpl-3.0 | 1,474 | [
"VisIt"
] | b840885b57da73425f0bd8db3a52d596ac1d6d2e1e9419fdf503bf5a47ed049d |
"""
=================
Drop Shadow Frame
=================
A widget providing a drop shadow (gaussian blur effect) around another
widget.
"""
from AnyQt.QtWidgets import (
QWidget, QGraphicsScene, QGraphicsRectItem, QGraphicsDropShadowEffect,
QStyleOption, QAbstractScrollArea, QToolBar
)
from AnyQt.QtGui impo... | cheral/orange3 | Orange/canvas/gui/dropshadow.py | Python | bsd-2-clause | 13,319 | [
"Gaussian"
] | 6f46fd315e038ab0bf859fc0adf6470e228bbceba1e6bf88a4aaac950f5ca2fc |
# -*- coding: utf-8 -*-
{
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for the area.": 'この地域を地理的に指定するロケーション。これはロケーションの階層構造のうちの一つか、ロケーショングループの一つか、この地域の境界に面するロケーションです。',
"Acronym of the organ... | flavour/ifrc_qa | languages/ja.py | Python | mit | 353,257 | [
"VisIt"
] | 9eee2afc37a69e8dae8267d942501ac235ff64e799c8d9ecbcd7e09af61ab487 |
"""
@name: Modules.Entertainment.sharp
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2017 by D. Brian Kimmel
@note: Created on Jul 12, 2016
@license: MIT License
@summary:
192.168.1.92
pink
poppy
10002
"""
__updated__ = '2019-12-30'
# ## END DBK
| DBrianKimmel/PyHouse | Project/src/Modules/House/Entertainment/Sharp/sharp.py | Python | mit | 304 | [
"Brian"
] | 1813f624b349d55fe1627ee86a454e355b40ca364d936dd32a67c76e76e04340 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | jralls/gramps | gramps/plugins/docgen/svgdrawdoc.py | Python | gpl-2.0 | 13,465 | [
"Brian"
] | 5bb8dd57492ad9291644afc4195517975dc3c1f890bc09866a49711c650e62e7 |
#!/usr/bin/env python
'''
This example shows how to use pseudo spectral integrals in SCF calculation.
'''
from pyscf import gto
from pyscf import scf
from pyscf import sgx
mol = gto.M(
atom='''O 0. 0. 0.
H 0. -0.757 0.587
H 0. 0.757 0.587
''',
basis = 'ccp... | gkc1000/pyscf | examples/sgx/00-simple_sgx.py | Python | apache-2.0 | 484 | [
"PySCF"
] | 5b506c556d11808ec266ce32fbc59a14611eb679270dfc0b7069f01b053f0ddc |
# -*- coding: utf-8 -*-
# SPDX-FileCopyrightText: 2016-2019 The Atlite Authors
#
# SPDX-License-Identifier: GPL-3.0-or-later
"""
Management of data retrieval and structure.
"""
import pandas as pd
import xarray as xr
import os
from numpy import atleast_1d
from tempfile import mkstemp, mkdtemp
from shutil import rmtr... | FRESNA/atlite | atlite/data.py | Python | gpl-3.0 | 5,883 | [
"NetCDF"
] | de4116aa05e7b0486a758a479c3ff6cc318f561ce83bfbf307ad1b4d09b48950 |
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