text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""
# Copyright (c) 05 2015 | surya
# 06/05/15 nanang.ask@kubuskotak.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 2
# of the License, or (at your option) any later ve... | suryakencana/niimanga | niimanga/tests/test_context/test_insert_anime.py | Python | lgpl-3.0 | 8,321 | [
"BLAST",
"Octopus"
] | 6a68157dffc0c1baa3c66065ea6d989cdb78ab5516a6003d0d66c50766df7ad6 |
"""
This module provides functions for running verification checks on small
models and to create reports about them.
"""
from __future__ import print_function
from collections import defaultdict
import ConfigParser
import argparse
import csv
import datetime
import json
import logging
import os
import glob
import math
... | nens/threedi-verification | threedi_verification/verification.py | Python | gpl-3.0 | 41,292 | [
"NetCDF"
] | 521ff602936aa11c06aac4942e69b7da8973d1be760fd6c7001a8761561ac7d3 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | simonwydooghe/ansible | lib/ansible/modules/network/avi/avi_scheduler.py | Python | gpl-3.0 | 5,284 | [
"VisIt"
] | 2ca5b4e3980c7fdf8e906aa687838d04f7b59c26a392e227c67601f711dca89f |
"""
Analysis of a single session, single subject fMRI dataset
=========================================================
In this tutorial, we compare the fMRI signal during periods of auditory
stimulation versus periods of rest, using a General Linear Model (GLM).
The dataset comes from an experiment conducted at the ... | bthirion/nistats | examples/01_tutorials/plot_single_subject_single_run.py | Python | bsd-3-clause | 14,185 | [
"Gaussian"
] | e460385096adb6a35211bc0ab7f8dde832e2326878f8a104014270449ddec130 |
#
# 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... | akopich/spark | python/pyspark/ml/clustering.py | Python | apache-2.0 | 41,736 | [
"Gaussian"
] | b1a3a3f667db79986c044a671af338a0d7f0761694ead220e9f0983a374b1b06 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/dbwrap.py | Python | lgpl-3.0 | 174,568 | [
"Gaussian",
"Psi4",
"PyMOL"
] | 1b425bc695bcc60804c8ebe967972dfc196fe0e22d05d2621e8cd528e9ee0a5d |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_compiled_4000.py | Python | gpl-3.0 | 3,912 | [
"Brian"
] | a39f7dbfd4aac09c006719614bb97704bc8c1286d4323355186d2d140d1fee1b |
"""
Copyright (c) 2014 Brian Muller
Copyright (c) 2015 OpenBazaar
"""
import heapq
from operator import itemgetter
from protos import objects
class Node(object):
def __init__(self, node_id, ip=None, port=None, signed_pubkey=None,
vendor=False):
self.id = node_id
self.ip = ip
... | the9ull/OpenBazaar-Server | dht/node.py | Python | mit | 3,782 | [
"Brian"
] | c369888b51b42c4c8d8f8f26cf5639026f8c386332a5d2ed03aed892c7d3485a |
"""
Manage tool data tables, which store (at the application level) data that is
used by tools, for example in the generation of dynamic options. Tables are
loaded and stored by names which tools use to refer to them. This allows
users to configure data tables for a local Galaxy instance without needing
to modify the t... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/data/__init__.py | Python | gpl-3.0 | 25,532 | [
"Galaxy"
] | 46f6bf36f20f5beb3651a37243ddc6d86eca8e045c7b59698dc178e829940d4f |
from __future__ import annotations
import os
from dxtbx.model import Crystal
from rstbx.cftbx.coordinate_frame_helpers import align_reference_frame
from scitbx import matrix
def dump(experiments, directory):
"""
Dump the experiments in mosflm format
:param experiments: The experiments to dump
:para... | dials/dials | util/mosflm.py | Python | bsd-3-clause | 3,905 | [
"CRYSTAL"
] | 0ae44afd5d2783e6f85c80b9abbf0a579bc62a79a3280971d8c7b5e3b2221ebd |
import numpy as np
import pandas as pd
import scipy as sp
import pickle
from scipy import fft
from time import localtime, strftime
import matplotlib.pyplot as plt
from skimage.morphology import disk,remove_small_objects
from skimage.filter import rank
from skimage.util import img_as_ubyte
import wave
#############... | jonathanwoodard/MLSP_2013 | 1_pattern_extraction.py | Python | mit | 10,429 | [
"Gaussian"
] | 1b76a2f6894ba8cf6c296a64dd12c1e50b3b461fbe687ca2644aaf1d61ccb3a0 |
# -*- coding: utf-8 -*-
# Copyright (c) 2010-2016 OpenStack Foundation
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | swiftstack/swift | test/unit/proxy/test_server.py | Python | apache-2.0 | 506,879 | [
"MOOSE"
] | 8a546d5890c143200795a88f07167518b0005525492a70dd3b858273b6efcfbe |
#!/usr/bin/env python
# Fat-free Python3 to Javascript/ES6 compiler attempt.
# see https://github.com/ahmedaliadeel/bulbul
import ast
import astor # pip install astor
import json
import os
import simplejson as json
import sys
#x = ast.parse(open("dec4.py").read())
#from bs4 import BeautifulSoup
#import bs4
# see ht... | mdornseif/bulbul | bulbul.py | Python | lgpl-3.0 | 8,682 | [
"VisIt"
] | 2d3ca35451b13ef379184b625fd6e71832462c8109aa343f2174e584b52d1f60 |
#
# Copyright (C) 2015 Jerome Kelleher <jerome.kelleher@well.ox.ac.uk>
#
# 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 of the License, or
# (at your option) any later version.... | jeromekelleher/ancestral-waves | src/simulations.py | Python | gpl-3.0 | 56,496 | [
"Gaussian"
] | 3f522c20b80f5312d6ca6ef56130061e1f1c38bc920e09825903e209c032b576 |
#!/usr/bin/env python
# encoding: utf-8
"""
vcf2phylip.py
Created by Nick Crawford on 2011-11-18.
Copyright (c) 2011
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 of the License, ... | ngcrawford/pypgen | scripts/vcf2fasta_alignment.py | Python | bsd-3-clause | 10,419 | [
"pysam"
] | 244e921b1c9b9c9b4459e72786e3aaf070499ac4cf4856873f233c44af243032 |
# LIBTBX_SET_DISPATCHER_NAME dev.dials.make_sphinx_html
from __future__ import annotations
import os
import sys
from optparse import SUPPRESS_HELP, OptionParser
import procrunner
import py
import dials.util
@dials.util.show_mail_handle_errors()
def run(args=None):
dials_dir = py.path.local(dials.__file__).dir... | dials/dials | command_line/make_sphinx_html.py | Python | bsd-3-clause | 3,965 | [
"Biopython"
] | f32901d07f8003ba91616769e489e18afca2d316587c694f494c00443ade4800 |
"""Rewrite assertion AST to produce nice error messages."""
import ast
import errno
import functools
import importlib.abc
import importlib.machinery
import importlib.util
import io
import itertools
import marshal
import os
import struct
import sys
import tokenize
import types
from pathlib import Path
from pathlib impor... | pytest-dev/pytest | src/_pytest/assertion/rewrite.py | Python | mit | 43,855 | [
"VisIt"
] | cb29b6935955e87a133726f0ce9d777f71827efe950ff0c777562de1bb36633a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import print_function
import urllib,urllib2,re,xbmcplugin,xbmcgui,sys,xbmcaddon,base64,socket
import CommonFunctions, urlparse, os
try:
import StorageServer
except:
import storageserverdummy as StorageServer
cache = StorageServer.StorageServer("cinemassacre_... | Kr0nZ/plugin.video.cinemassacre_com | default.py | Python | gpl-2.0 | 16,101 | [
"BLAST"
] | 6a4113f326cd10d0c9c48943ffe7676a7d21c062d34b671b92b938e446c93f9f |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | vidartf/hyperspy | hyperspy/models/model1d.py | Python | gpl-3.0 | 30,579 | [
"Gaussian"
] | eb3bba2e1e9975512ce72024a60172bed4fa612fbdf3e34d4bb6156b5b1f1f6f |
import logging
import os
import sqlite3
import sys
from collections import OrderedDict, defaultdict
from functools import wraps
from warnings import warn
import numpy as np
import pyproj
import regex
from cf_units import Unit
from compliance_checker import cfutil
from compliance_checker.base import BaseCheck, BaseN... | ioos/compliance-checker | compliance_checker/cf/cf_1_7.py | Python | apache-2.0 | 34,165 | [
"NetCDF"
] | 0e9817d3c90284202df565568aeb52de75c8a4832efc295de47cd43e13f51782 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import itertools
import os
from django.contrib.auth.models import User
from django.contrib.auth.signals import user_logged_in, user_logged_out
from django.http import Htt... | filias/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 63,582 | [
"VisIt"
] | 21b3e204855551e496bfe7a989ffd81e1fa9a361780b194d7963e130460210ef |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# MCT - Mini Cliente Torrent
# ------------------------------------------------------------
import os
import re
import tempfile
import urllib
import urllib2
import platform
import sys
import traceback
import xbmc
imp... | alfa-jor/addon | plugin.video.alfa/platformcode/mct.py | Python | gpl-3.0 | 40,280 | [
"ADF"
] | 2664a9c87bd90292b1854f37768481b438ee65019b7896268449163fed64891f |
"""
Deprecating this in favor of parser.py
"""
import imp
import ast
import inspect
from operator import add
from string import maketrans, translate
from collections import OrderedDict, Iterable
from coretypes import Integer, TypeVar, Record, Enum, Type, DataShape, \
Range, Either, Fixed
syntax_error = """
Fil... | davidcoallier/blaze | blaze/datashape/parse.py | Python | bsd-2-clause | 4,984 | [
"VisIt"
] | dc56fc738df5ef8291341d414b44ddaca3b311c51d814c7489df06a6457a53c4 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | testsuite/python/lb_poiseuille_cylinder.py | Python | gpl-3.0 | 7,173 | [
"ESPResSo"
] | 45f30a3c35e19ac84662f3c02c735f063c438f768ec8c2de188a450a11241800 |
#! /usr/bin/env python
from __future__ import print_function
from openturns import *
TESTPREAMBLE()
RandomGenerator.SetSeed(0)
try:
# this analitycal example is taken from "Bayesian Modeling Using WinBUGS" - Ioannis Ntzoufras
# 1.5.3: Inference for the mean or normal data with known variance
# Variable... | aurelieladier/openturns | python/test/t_RandomWalkMetropolisHastings_std.py | Python | lgpl-3.0 | 3,113 | [
"DIRAC"
] | 717df9caa32835e93065e144d5ec966bc6b2e239b5b99021e23b3bc408352955 |
import datetime
from sqlalchemy import (
JSON,
Boolean,
Column,
DateTime,
Enum,
ForeignKey,
Index,
Integer,
String,
UniqueConstraint,
func,
select,
)
from sqlalchemy.dialects.postgresql import JSONB, aggregate_order_by
from sqlalchemy.ext.hybrid import hybrid_property
fr... | psi4/DatenQM | qcfractal/storage_sockets/models/results_models.py | Python | bsd-3-clause | 17,462 | [
"RDKit"
] | 26d77fb98719c04c1432d72d84f950cd3764f2d383ab08bbd928f8b4f779804f |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy as np
node = import_file("../../files/CFG/shear.void.120.cfg")
modifier = CentroSymmetryModifier()
node.modifiers.append(modifier)
print("Parameter defaults:")
print(" num_neighbors: {}".format(modifier.num_neighbors))
modifier.n... | srinath-chakravarthy/ovito | tests/scripts/test_suite/centrosymmetry_modifier.py | Python | gpl-3.0 | 446 | [
"OVITO"
] | 8ee402d6471b35c3b3bea9696141c7921c05594446c14ed0efc453bab3fa6f49 |
#!/usr/bin/env python
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This prog... | d7415/merlin | excalibur.py | Python | gpl-2.0 | 95,164 | [
"Galaxy"
] | 5546c7a70355177113bab2a22c22b87c557df342b0456e9be5628d040892c275 |
'''
Created on May 5, 2015
@author: julian
'''
import math
import random
import matplotlib.pyplot as plt
from Chromosome import *
REGION_SIZE = 100.0
NUMBER_OF_CITIES = 10
NUMBER_OF_CHROMOSOMES = 100
NUMBER_OF_EPOCHS = 100
MUTATION_PROBABILITY = 0.25
RANDOM_SEED = 9876
cities = {}
def plot_citi... | jjbunn/PyGeneticAlgorithm | TravellingSalesmanGA.py | Python | apache-2.0 | 4,203 | [
"VisIt"
] | e252ed238ccf5d50f947f757b43d071bce138985a6b4f954d848cb4b72d69d85 |
"""
Recommendation Steps
Steps file for recommendation.feature
"""
import environment
import json
import requests
from app import server
from behave import *
from os import getenv
from compare import expect, ensure
from selenium import webdriver
from selenium.webdriver.common.by import By
from selenium.webdriver.supp... | devopsdelta/recommendations | features/steps/recommendations_steps.py | Python | apache-2.0 | 8,199 | [
"VisIt"
] | 90f3cf196bed71dd6060adbe5a75625ca5237a84fb5cf7e1f3d7809f6ac4a723 |
"""Screen aggregate geometries with respect to similarity.
This subsubmodule is part of ManipulateAggregates.energyscan. It implements the
third step of the 3-step procedure that creates low energy aggregate geometries.
Parallelization is only supported for the determination of pointgroups.
"""
# This file is part o... | razziel89/ManipulateAggregates | ManipulateAggregates/energyscan/similarityscreening.py | Python | gpl-3.0 | 30,196 | [
"Pybel"
] | 5f362a7872416baa51f6eb8c600c31cb15adb12527f6b69bddf56f222d5778dd |
##############################################################################
# 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... | mfherbst/spack | var/spack/repos/builtin/packages/r-affyilm/package.py | Python | lgpl-2.1 | 2,014 | [
"Bioconductor"
] | 09d5218c53512a143a4f622443c5f3c35f8792dd47babfa181acf93c7f02e5b7 |
# Copyright (c) 2012, Cloudscaling
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable... | NetApp/manila | manila/hacking/checks.py | Python | apache-2.0 | 13,099 | [
"VisIt"
] | ceb705fa7c10d9612d02db7a77b66200d475d1a3fc97472c865e0cbd31c6c3d7 |
"""
cluster.py
This module contains functions for creating and manipulating
clusterings/partitionings.
"""
import os
import sys
from rasmus import graph
from rasmus import util
from compbio import blast
# TODO: update function name styles
##############################################
# comparing c... | wutron/compbio | rasmus/cluster.py | Python | mit | 3,561 | [
"BLAST"
] | 88fad043eeebf866b10d44b59ad0478c0521c55c09e90b1f2e07cdc74a839321 |
# test_gc.py ---
#
# Filename: test_gc.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Mon May 19 10:25:13 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This program... | subhacom/moose-core | tests/python/test_gc.py | Python | gpl-3.0 | 3,727 | [
"MOOSE"
] | 258ba220d58f99ff50aeb9edce1c802900a850b0d8e5522a3a0dc03fac3b3c3d |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | classification/Classification_with_kNN/Single_Contact_Classification/Time_Window/test11_cross_validate_objects_400ms.py | Python | mit | 4,621 | [
"Mayavi"
] | ef3822e864413cf94ff8b3f49d89a6acbe28c69b3f7f986e021ebe5b7d08f6d6 |
from splinter import Browser
import config
import time
def firstwizard(b, name):
b.visit( config.serverurl + name )
b.find_by_css('a.button-large').click()
b.find_by_css('#dbname').fill( name )
b.find_by_css('#uname').fill( config.dbuser )
b.find_by_css('#pwd').fill( config.dbpass )
b.find_by_c... | kkarpieszuk/setwp | libraries/brwsr.py | Python | mit | 2,920 | [
"VisIt"
] | 86fc169c52918a12de51bad91461901302fcc795568d5bae1994ee8856eb3dff |
#!/usr/bin/env python
"""
This script regenerates the enum values in pymatgen.core.libxc_func.py.
It requires in input the path of the `libxc_docs.txt` file contained in libxc/src
The script parses this file, creates a new json file inside pymatgen.core
and update the enum values declared in LibxcFunc.
The script must ... | johnson1228/pymatgen | dev_scripts/regen_libxcfunc.py | Python | mit | 3,433 | [
"pymatgen"
] | 80359c5ff4b89a4f90ee8ee071829432afb8c8bd56d64202bf93311a17b9c8ca |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from .fake_webapp import EXAMPLE_APP
class SlowlyTypeTest(object):
def test_simple_type(self):
"should provide a away to ... | gjvis/splinter | tests/type.py | Python | bsd-3-clause | 2,407 | [
"VisIt"
] | 927fcca5e8a782d17913413370587797f39995c4b2c17cf34806b206bf3bbb91 |
from tigershark.facade import CompositeAccess
from tigershark.facade import ElementAccess
from tigershark.facade import ElementSequenceAccess
from tigershark.facade import Facade
from tigershark.facade import Money
from tigershark.facade import SegmentAccess
from tigershark.facade import SegmentConversion
from tigersha... | jdavisp3/TigerShark | tigershark/facade/f271.py | Python | bsd-3-clause | 17,122 | [
"VisIt"
] | 04b37f4ffb38d7bfb25954b0b005503a21bc6f3174624e6480980db751357716 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import sys
i... | nuclear-wizard/moose | python/TestHarness/__init__.py | Python | lgpl-2.1 | 585 | [
"MOOSE"
] | 24128015aa77395d2b68cb00438379d1ecb3018d7b1af5f90222a7da0a95fb5d |
# multiComptSigNeur.py ---
# Upi Bhalla NCBS Bangalore 2013.
# Commentary:
# A toy compartmental neuronal + chemical model. The neuronal model is in
# a dendrite and five dendritic spines. The chemical model is in three
# compartments: one for the dendrite,
# one for the spine head, and one for the postsynaptic dens... | dilawar/moose-full | moose-examples/snippets/multiComptSigNeur.py | Python | gpl-2.0 | 21,008 | [
"MOOSE"
] | a78064953c4a3ea7fe6f3dbd5d2d92dde84ac2017cd1f6d0b29fc50c60865d4a |
"""
===============================================
:mod:`ec` -- Evolutionary computation framework
===============================================
This module provides the framework for creating evolutionary computations.
.. Copyright 2012 Inspired Intelligence Initiative
..... | phantomas1234/inspyred | inspyred/ec/ec.py | Python | gpl-3.0 | 36,219 | [
"Gaussian"
] | d31c897f90656e489916df6671b4464d51ee034195274cf8711b0b28723fac48 |
# Copyright 2021, OpenCensus 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 w... | census-ecosystem/opencensus-python-extensions-azure | examples/functions_requests.py | Python | apache-2.0 | 3,120 | [
"VisIt"
] | 4123ae30a7555d405d4701b50b1ed0f81c478fbbe2d67cdf3bed174a24e4507e |
#!/usr/bin/env python
"""
Send an email via Gmail either as a text or as an HTML.
# from jabbapylib.mail import gmail_send
"""
import os
import smtplib
from email.MIMEMultipart import MIMEMultipart
from email.MIMEBase import MIMEBase
from email.MIMEText import MIMEText
from email import Encoders
def mail_text(send... | jabbalaci/jabbapylib | jabbapylib/mail/gmail_send.py | Python | gpl-3.0 | 3,426 | [
"VisIt"
] | e40bd06e2ffddccc3cbb22a250042b795a39f79b79ddc5163aa439059bd0abaa |
# -*- coding: utf-8 -*-
#
# test_parrot_neuron_ps.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the L... | sdiazpier/nest-simulator | testsuite/pytests/test_parrot_neuron_ps.py | Python | gpl-2.0 | 10,591 | [
"NEURON"
] | 0fa48a9fb2f3cb967301d59ed1e5da5efbb2b8da6942e3e07bbd6f6489f6dd64 |
import os
import numpy as np
import pyfits as pyf
try:
import cPickle as pickle
except ImportError:
import pickle
class galaxy:
__module__ = os.path.splitext(os.path.basename(__file__))[0]
def __init__(self,
ID=-1,
RA=-1,
DEC=-1,
Imag=-1,
Zmag=-1,
Jmag=-1... | boada/ICD | sandbox/legacy_plot_code/mk_galaxy_struc_fortable.py | Python | mit | 9,825 | [
"Galaxy"
] | 32f3eb168c06161d2e61b34d5f44d527a70c311b65f187f5a66a996ea0af4f1c |
import matplotlib.pylab as plt
from patch import PolygonPatch
from matplotlib.collections import PatchCollection
from matplotlib import cm
from os import path
from shyft.repository.service.gis_location_service import GisLocationService
from shyft.repository.netcdf.arome_data_repository import AromeDataRepository
from ... | felixmatt/shyft | shyft/tests/demo_statkraft_stuff.py | Python | lgpl-3.0 | 7,055 | [
"NetCDF"
] | 514e2c8d8283b1a39415fb8258048df1866b99c25b9c49292a64e6f384b97fca |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Jason Swails
# Contributors:
#
# MDTraj is free software: you ... | rmcgibbo/mdtraj | mdtraj/formats/psf.py | Python | lgpl-2.1 | 9,757 | [
"CHARMM",
"Dalton",
"MDTraj",
"OpenMM"
] | 0a917650acbe858e9d94b8ee2d5e9a0457e8c395ef20b0f19bdabf53da558af8 |
#!/usr/bin/python2.4
#
# Copyright 2007 The Python-Twitter Developers
#
# 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... | theZacAttacks/python-tcler | get_access_token.py | Python | bsd-2-clause | 4,316 | [
"VisIt"
] | d3613ea270fb789bb1022c1f47d5b6f0cacb00de96d0581566764df62464fcca |
# Copyright (c) 2018 PaddlePaddle 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 appli... | PaddlePaddle/Paddle | python/paddle/fluid/layers/nn.py | Python | apache-2.0 | 613,109 | [
"Gaussian",
"NEURON"
] | c0b87b8c7f8d83aa2b1b4a02dccee5871549ccdb5df49e327d4c6605fbf750b1 |
# -*- coding: utf-8 -*-
# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry
# and reaction kinetics.
# Copyright (C) 2008-2012 Toon Verstraelen <Toon.Verstraelen@UGent.be>, An Ghysels
# <An.Ghysels@UGent.be> and Matthias Vandichel <Matthias.Vandichel@UGent.be>
# Center for Molecular Modeling... | molmod/tamkin | tamkin/io/qchem.py | Python | gpl-3.0 | 6,083 | [
"Avogadro",
"Q-Chem"
] | 117bc5a39c09721a998968775398f5e4dd693bb34aad7ccc00c0cea4e3c758ee |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | andreaso/ansible | lib/ansible/modules/network/avi/avi_pool.py | Python | gpl-3.0 | 18,173 | [
"VisIt"
] | 6bd20928069109bd303717f1724a48e88070e22b9639f31a95ff737259658e49 |
from xstruct import pack
from objects import Object
class Galaxy(Object):
"""\
The Galaxy is a container for a large group of close star systems, like the Milky Way.
The Galaxy contains no extra data.
"""
subtype = 1
substruct = ""
def __init__(self, sequence, \
id, type, name, \
size, \
posx, posy... | thousandparsec/libtpproto-py | tp/netlib/objects/ObjectExtra/Galaxy.py | Python | lgpl-2.1 | 627 | [
"Galaxy"
] | b46b0712115c86a06ab94709c098dbc0a821c7eaee7ac2eeba903c83319a0dac |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import logging
import numpy as np
from monty.json import MSONable
from scipy.spatial import HalfspaceIntersection
from scipy.optimize import bisect
from itertools import chain
from pymatgen.electronic_structur... | dongsenfo/pymatgen | pymatgen/analysis/defects/thermodynamics.py | Python | mit | 30,394 | [
"pymatgen"
] | 31d0f6133acac7893c10654df458cc944dcfbc43c205056370ea73afcde91570 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | HuaweiSwitch/ansible | lib/ansible/modules/network/lenovo/cnos_interface.py | Python | gpl-3.0 | 26,955 | [
"VisIt"
] | 145c1eee3ad41d7d6b4b61b7a78e3b94418fa7946fdcd9e65d920641767b3719 |
# -*- coding: utf-8 -*-
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
from __future__ import unicode_literals
import copy
import os
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from django.conf import settings
... | synasius/django | tests/cache/tests.py | Python | bsd-3-clause | 85,392 | [
"Brian"
] | d865c877f2996a66ebb90c1190b919e0e40116f1abd3dca4808a2a228c804add |
# 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... | npuichigo/ttsflow | third_party/tensorflow/tensorflow/contrib/timeseries/python/timeseries/ar_model.py | Python | apache-2.0 | 32,793 | [
"Gaussian"
] | e58fdbb2aa861bdcde9a4933f8536f55f96b1a4599d2bf721170cd768650d339 |
#!/usr/bin/python2.5
# Copyright (C) 2007 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 la... | google/transitfeed | schedule_viewer.py | Python | apache-2.0 | 19,533 | [
"VisIt"
] | 8924f93bb598518492832043414b60e7e6b5716f43bd57991631ef34e5926199 |
#!/usr/bin/env python
# Copyright (c) 2011-2018-2017, wradlib developers.
# Distributed under the MIT License. See LICENSE.txt for more info.
import unittest
import tempfile
import wradlib.georef as georef
import wradlib.zonalstats as zonalstats
import wradlib.util as util
import numpy as np
from osgeo import osr
np... | heistermann/wradlib | wradlib/tests/test_zonalstats.py | Python | mit | 24,331 | [
"NetCDF"
] | 5889aa7c230715712d264473312000836b0d6113bb56200007d98718fc1f1d42 |
import os
import random
import datetime
from django.db import models
from django.contrib.auth.models import User, Group
from django.forms import ModelForm, Textarea, TextInput
from django.forms.extras.widgets import SelectDateWidget
from .settings import *
from django.db import transaction
from itertools import chain
... | dparizek/newecosystems | newecosystems/apps/core/models.py | Python | mit | 8,070 | [
"Firefly"
] | 1be8586186e230ffb877bdec09ddc718f1ba418089b490be033ccee817d762b1 |
## INFO ########################################################################
## ##
## COUBLET ##
## ======= ... | petervaro/coublet | views/stream.py | Python | mit | 3,574 | [
"VisIt"
] | dc670d1af51cba149ce7a743e4c94695f5512f3f0807d26db089d56325bf12c1 |
"""
Courseware views functions
"""
import logging
import urllib
import json
from datetime import datetime
from collections import defaultdict
from django.utils import translation
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from d... | adlnet-archive/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 41,049 | [
"VisIt"
] | 87680671a61e577406ab25abf0a11c7a9c59d8948b98ce5853ac028d0d3570b2 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/analysis/test_rms.py | Python | gpl-2.0 | 12,496 | [
"MDAnalysis"
] | c3b1bdd27b7413d9c7a3af95a58b26d3796a5a28c7a6d45700df98dc17951996 |
# -*- coding: utf-8 -*-
from twisted.plugin import IPlugin
from pymoronbot.moduleinterface import IModule, ignore
from pymoronbot.modules.commandinterface import BotCommand
from zope.interface import implementer
import random
import datetime
import re
from six import iteritems
from pymoronbot.message import IRCMessa... | MatthewCox/PyMoronBot | pymoronbot/modules/automatic/Responses.py | Python | mit | 29,919 | [
"Octopus"
] | 819a7684639a85517eb9dfecc7123cd22db99515bfce82264e30bbbeaac507c2 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | sunqm/pyscf | pyscf/pbc/df/test/test_band.py | Python | apache-2.0 | 3,476 | [
"PySCF"
] | c303a1a571d364357934b63a3cf563380b1bba3e9eb3187ff9f75afad67cd584 |
from __future__ import division
from warnings import warn
import numpy as np
binary_erosion = None # expensive, from scipy.ndimage
binary_dilation = None # expensive, from scipy.ndimage
from menpo.base import MenpoDeprecationWarning
from menpo.transform import Translation
from menpo.visualize.base import ImageViewe... | yuxiang-zhou/menpo | menpo/image/masked.py | Python | bsd-3-clause | 60,116 | [
"Gaussian"
] | 77f5be015e2f59ade22f76ca821fd6b0fd57fd9bcf7675465c6d25564a030258 |
import gc
import sys
import unittest
import weakref
from test import support
class FinalizationTest(unittest.TestCase):
def test_frame_resurrect(self):
# A generator frame can be resurrected by a generator's finalization.
def gen():
nonlocal frame
try:
... | Orav/kbengine | kbe/src/lib/python/Lib/test/test_generators.py | Python | lgpl-3.0 | 52,850 | [
"VisIt"
] | 3fe7ff3221c3e8d433945d779f201527f91a0a75dc46bbaca7e1ad1fc235d76f |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/magic/sources/trainedfinder.py | Python | mit | 20,607 | [
"Galaxy"
] | e5b8a54fda6f7338695edb1e89aa2ca57ca4c7ba052b4da11344b5baf8ae159b |
"""
Bok-choy tests for the Studio Accessibility Feedback page.
"""
import ddt
from common.test.acceptance.pages.studio.index import AccessibilityPage
from common.test.acceptance.tests.helpers import AcceptanceTest
@ddt.ddt
class AccessibilityPageTest(AcceptanceTest):
"""
Test that a user can access the page ... | hastexo/edx-platform | common/test/acceptance/tests/studio/test_studio_accessibility_form.py | Python | agpl-3.0 | 2,577 | [
"VisIt"
] | 4201971af32d72bd4a29d5662954d239a526f9089cc3edb1ce7e43f3cf8fa43e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
################################################################################
#
# ChemPy - A chemistry toolkit for Python
#
# Copyright (c) 2010 by Joshua W. Allen (jwallen@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# co... | chasquiwan/CoCoPy | modules/analysis/element.py | Python | mit | 11,928 | [
"ChemPy"
] | 33a4066aa2d3567a5bd468ee8fa9c3114baa3fcaed7b036788a3d02cc4e0b3e6 |
########################################################################
# $HeadURL$
# File : WatchdogFactory.py
# Author : Stuart Paterson
########################################################################
""" The Watchdog Factory instantiates a given Watchdog based on a quick
determination of the local... | Sbalbp/DIRAC | WorkloadManagementSystem/JobWrapper/WatchdogFactory.py | Python | gpl-3.0 | 2,208 | [
"DIRAC"
] | 6da6bc34f62945a2a84f6797f9300dfca0e0377fb55881b061e14229c26f84c6 |
# -*- coding: utf-8 -*-
""" Software Management Core Library
This module provides the core library for Software Management.
(c) 2015, 2016 - Jaguar Land Rover.
Mozilla Public License 2.0
"""
import dbus
import traceback
import settings
import logging
logger = logging.getLogger(settings.LOGGER)
# enum implementati... | rstreif/genivi_software_management | common/swm.py | Python | mpl-2.0 | 3,421 | [
"Jaguar"
] | 2198c4a8142ae8df33b141a344c081496fbdd939187761e915e66af2dc49ed3b |
"""
Deep Deterministic Policy Gradients
Make Actor and Critic subclasses of a NNet class? Not sure ... for now, I'll
put everything here but that might take a lot.
"""
import gym
import numpy as np
import sys
import tensorflow as tf
import tensorflow.contrib.layers as layers
import time
from replay_buffer import Rep... | DanielTakeshi/rl_algorithms | ddpg/ddpg.py | Python | mit | 17,541 | [
"Gaussian"
] | 7867e8d05936df58cff4f01c478fd3876d5f05a9eb4b48be207f7d2e728258e1 |
""" This script submits a test prodJobuction with filter
"""
# pylint: disable=wrong-import-position, protected-access
import time
import os
import json
from DIRAC.Core.Base.Script import Script
Script.setUsageMessage("\n".join([__doc__.split("\n")[1], "Usage:", " %s test directory" % Script.scriptName]))
Script.re... | DIRACGrid/DIRAC | tests/System/dirac-test-production.py | Python | gpl-3.0 | 4,516 | [
"DIRAC"
] | 843c361b82339882a658129c1a8b70a3e576f511502e97f16ea4cb4b9f84b19d |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code... | rdkit/rdkit-orig | rdkit/Chem/Suppliers/UnitTestSDMolSupplier.py | Python | bsd-3-clause | 4,271 | [
"RDKit"
] | e904b38a242ce14af23dbd5bddc1a4b2b621a93d935084b1fdbb7a217449cdc7 |
# Visualize difference between KL(p,q) and KL(q,p) where p is a mix of two
# 2d Gaussians, and q is a single 2d Gaussian
# Author: animesh-007
import superimport
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import multivariate_normal
mu = np.array([[-1,-1],[1,1]])
Sigma = np.zeros((2,2,2))
... | probml/pyprobml | scripts/KLfwdReverseMixGauss.py | Python | mit | 1,402 | [
"Gaussian"
] | d813b5ea346c06f17249f93480ed05ffc3b5891ee8760b21a57c39026cc4eb1d |
#!/usr/bin/env python
# coding: utf-8
# Distributions
# ============================
#
# Distributions are mostly useful when using samplers (which we'll see in the next tutorial on [solving the inverse problem](./solver.ipynb)) - but can also be useful to propagate any set of distributions (whether those be uncertai... | phoebe-project/phoebe2-docs | development/tutorials/distributions.py | Python | gpl-3.0 | 7,335 | [
"Gaussian"
] | 9253902bbe81339b43c7fdda7ef1d0e25e07d0b201737cc0ac52debce762f7a5 |
##############################################################################
# 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-affyio/package.py | Python | lgpl-2.1 | 1,817 | [
"Bioconductor"
] | ecf20ac81c7a5aa60aceff010e8a0ab26b5b43c52a65ecb57105fbbd0c482ab1 |
import logging
import calendar
import copy
import dateutil
import numpy
import datetime
from dimagi.ext.couchdbkit import Document, DocumentSchema, StringProperty, IntegerProperty, DateTimeProperty
from casexml.apps.case.models import CommCareCase
from corehq.apps.crud.models import AdminCRUDDocumentMixin
from corehq.a... | qedsoftware/commcare-hq | corehq/apps/indicators/models.py | Python | bsd-3-clause | 37,214 | [
"VisIt"
] | 94ccd21cfe336959a212f86a5d2b7367075253da735d1dc7d40ace969ce0bb29 |
# (c) 2016, Adrian Likins <alikins@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later vers... | rosmo/ansible | test/units/cli/test_galaxy.py | Python | gpl-3.0 | 19,876 | [
"Galaxy"
] | 2e45d8f19396f36bddaeab026f105bddaaaec7bdecbb85c2144bf162ddbec34a |
"""Perform validation of final calls against known reference materials.
Automates the process of checking pipeline results against known valid calls
to identify discordant variants. This provides a baseline for ensuring the
validity of pipeline updates and algorithm changes.
"""
import collections
import contextlib
im... | vladsaveliev/bcbio-nextgen | bcbio/variation/validate.py | Python | mit | 34,989 | [
"pysam"
] | 58a23ee8321c9181d5816a6ae44e253bc223fa5166c5be28fb7b090aa95e0d69 |
# -*- coding: utf-8 -*-
"""
Cosmic Rays
===========
This scripts derives simple cosmic ray statististics from Gaia BAM data.
Note that the Gaia BAM data are binned 4 x 1 leading to pixel geometries
that are 120 x 10 microns. One can derive a statistical correction to
take into account the binning. Further corrections ... | sniemi/EuclidVisibleInstrument | analysis/analyseGaiaBAMCosmicRayData.py | Python | bsd-2-clause | 19,247 | [
"Gaussian"
] | 0b8c7962e4291897886f201df64cf231a06ca7518e2c8d783a987120c86f4d58 |
# coding: utf-8
import scipy.stats
import numpy as np
from math import ceil
from .. import img_as_float
from ..restoration._denoise_cy import _denoise_bilateral, _denoise_tv_bregman
from .._shared.utils import skimage_deprecation, warn
import pywt
def denoise_bilateral(image, win_size=None, sigma_color=None, sigma_sp... | rjeli/scikit-image | skimage/restoration/_denoise.py | Python | bsd-3-clause | 21,667 | [
"Gaussian"
] | 91bce46ff75b0cee68c170c5ce08d5a9a61b64c577d406e85b5f61e49fdbf02f |
"""Module for working with mBuild Compounds."""
__all__ = ["clone", "Compound", "Particle"]
import itertools
import os
import tempfile
from collections import OrderedDict
from collections.abc import Iterable
from copy import deepcopy
from warnings import warn
import ele
import numpy as np
from ele.element import Elem... | iModels/mbuild | mbuild/compound.py | Python | mit | 90,955 | [
"Amber",
"LAMMPS",
"MDTraj",
"Open Babel",
"OpenMM",
"Pybel"
] | 66e66a7a61afd8b7f1dc45cff12df328dd0f70ee360f9f97b59a7071462d4b84 |
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 18 11:27:46 2016
@author:
Maximilian N. Guenther
Battcock Centre for Experimental Astrophysics,
Cavendish Laboratory,
JJ Thomson Avenue
Cambridge CB3 0HE
Email: mg719@cam.ac.uk
"""
#import warnings
import numpy as np
import matplotlib.pyplot as plt
#from astropy.modeling... | DJArmstrong/autovet | Features/old/Centroiding/scripts/stacked_images.py | Python | gpl-3.0 | 12,874 | [
"Gaussian"
] | 7d65deb6bcc723a9e8f323d6a5c815df41a05cefc034c33847ec9f28c874b7a6 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | dgasmith/psi4 | psi4/driver/diatomic.py | Python | lgpl-3.0 | 11,372 | [
"Psi4"
] | 987e31455b86c8ce73fcc0c76553669a13575938079412ffed4c552d37f616cc |
#Using Scrapy with Selenium to scape a rendered page [Updated]
from scrapy.contrib.spiders.init import InitSpider
from scrapy.http import Request, FormRequest
from scrapy.contrib.linkextractors.sgml import SgmlLinkExtractor
from scrapy.contrib.spiders import CrawlSpider, Rule
from scrapy.spider import BaseSpider... | InfiniteRandomVariable/hello-world | tutorial/tutorial/spiders/guardian1.py | Python | apache-2.0 | 3,894 | [
"VisIt"
] | 7b75fb13b56bcd8fb2913d8ccd21d1a9b3883d3212737fc45fc0111c762c7ba1 |
#!/usr/bin/env python
'''
GAEUnit: Google App Engine Unit Test Framework
Usage:
1. Put gaeunit.py into your application directory. Modify 'app.yaml' by
adding the following mapping below the 'handlers:' section:
- url: /test.*
script: gaeunit.py
2. Write your own test cases by extending unittest.TestCas... | arjunsatyapal/lantern | demo1-test/gaeunit/gaeunit.py | Python | apache-2.0 | 21,847 | [
"VisIt"
] | 26a83927ffa4756d452519f5e9c07a8245f417f34a770a3a02bf40507d890cdd |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | kvar/ansible | lib/ansible/modules/network/avi/avi_ipaddrgroup.py | Python | gpl-3.0 | 4,996 | [
"VisIt"
] | 285fc4b4e72712ce433d34451d85ca759f6ee95aee7c744e98451b72ae15dcc6 |
#
# This file is a part of KNOSSOS.
#
# (C) Copyright 2007-2011
# Max-Planck-Gesellschaft zur Foerderung der Wissenschaften e.V.
#
# KNOSSOS is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 2 of
# the License as published by the Free So... | thorbenk/knossos-svn | tools/configknossos_ui.py | Python | gpl-2.0 | 7,997 | [
"VisIt"
] | 746d5723901e640bab0c65dc960f06004a2b519cc99d7b8b44064382afbc2500 |
#in this version i have removed the seq, as it serves no purpose for what i am doing now
import math
class Homolog:
"""This is a class that will hold the values that i wish to store about homologs"""
#def __init__(self, Accession, Organism, Locus, Gene, Predicted_gene, Synonyms, Eval, Percent_ident, Bits_score... | reamdc1/gene_block_evolution_old | homolog2.py | Python | gpl-3.0 | 8,897 | [
"BLAST"
] | 253a595d561851dde3bd9d0e62df44588e38c4c2d82dff8a6884eeafd2fa134d |
from __future__ import division, absolute_import, print_function
import os
import sys
import types
import re
import warnings
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import ndarray, ufunc, asarray
import numpy as np
# getargspec and formatargspec were removed in Python... | gfyoung/numpy | numpy/lib/utils.py | Python | bsd-3-clause | 36,308 | [
"VisIt"
] | 9a1b896f937560089c335a1681263efc2ec55600ece9604b353041ffafbff5ab |
# Code from Chapter 6 of Machine Learning: An Algorithmic Perspective (2nd Edition)
# by Stephen Marsland (http://stephenmonika.net)
# You are free to use, change, or redistribute the code in any way you wish for
# non-commercial purposes, but please maintain the name of the original author.
# This code comes with no... | Anderson-Lab/anderson-lab.github.io | csc_466_2021_spring/MLCode/Ch6/kernelpca.py | Python | mit | 2,005 | [
"Gaussian"
] | 6480f9358cfda861ac8f666a7c6f8ac380538c6ed5448956f45a41cda4aaea00 |
#
# alm_opt.py
#
# This is an example to run ALM in the fitting mode.
#
import h5py
from alm import ALM
import numpy as np
def get_inputs(num_snapshots):
lavec = [[9.3329999969514006, 0.0000000000000000, 0.0000000000000000],
[-4.6664999984757003, 8.0826150908799992, 0.0000000000000000],
... | ttadano/ALM | example/AlN/AlN-lasso.py | Python | mit | 8,012 | [
"CRYSTAL"
] | 29e8dc88d90ff7ce92c4292397788991d3f81086cfbc4827ea54367b4d01afb7 |
# -*- coding: utf-8 -*-
# Copyright (C) 2008 CSC Scientific Computing Ltd.
# Please see the accompanying LICENSE file for further information.
"""This module defines an Overlap operator.
The module defines an overlap operator and implements overlap-related
functions.
"""
import sys
import numpy as np
from gpaw.uti... | robwarm/gpaw-symm | gpaw/overlap.py | Python | gpl-3.0 | 5,010 | [
"GPAW"
] | a2185bf80f75bb89fed7f55b5b09ff83dd02fe6c1465e385b3e21809235f4dae |
#!/usr/bin/env python3
# This file is part of SunlightDPD - a home for open source software
# related to the dissipative particle dynamics (DPD) simulation
# method.
# Copyright (c) 2009-2018 Unilever UK Central Resources Ltd
# (Registered in England & Wales, Company No 29140; Registered
# Office: Unilever House, Bla... | patrickbwarren/SunlightHNC | urpm_oneoff.py | Python | gpl-2.0 | 8,872 | [
"Gaussian"
] | 1e990ccfa04653df99e9f9f77e78ef79176cfd75596faf2507946cae97b3dc80 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2014 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_workordersearch.py | Python | gpl-2.0 | 3,656 | [
"VisIt"
] | adc45fb991d84bd48cb01a8873dc6fb4c1a3fb7dbb23e0b0156c51301d4e75fd |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | samples/gibbs_ensemble_socket.py | Python | gpl-3.0 | 14,928 | [
"ESPResSo"
] | 95877d6bb4db297b72ef3bcd45f5067f074042ec5cec8ac46eaa0a45288bfcd9 |
# Copyright (c) 2013, GlaxoSmithKline Research & Development Ltd.
# All rights reserved.
#
# 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
# ... | bp-kelley/rdkit | Contrib/mmpa/search_mmp_db.py | Python | bsd-3-clause | 16,256 | [
"RDKit"
] | 4827791c1f7d940f841ee8aff39934694f24a12a1de2cab399a0d33744303f9b |
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