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import pdb
import numpy as np
import matplotlib.pyplot as plt
import math
######################################################################
#
# Learning algorithms and helpers
#
######################################################################
# Ordinary least squares regression
# X is an n x d matrix
# Y i... | LYZhelloworld/Courses | 50.021/08/learn/learn.py | Python | mit | 12,634 | [
"Gaussian"
] | 68dbb73ee3f21f31bb0498c27df45069a2b6cac7a70116d3ceea527c8c36d70a |
#!/usr/bin/env python
# polarizer.py - add Drude oscillators to LAMMPS data file.
# Agilio Padua <agilio.padua@univ-bpclermont.fr>
# Alain Dequidt <alain.dequidt@univ-bpclermont.fr>
# version 2015/07/17
import sys
import argparse
import random
from copy import deepcopy
usage = """Add Drude oscillators to LAMMPS data ... | crtrott/lammps | tools/drude/polarizer.py | Python | gpl-2.0 | 27,657 | [
"LAMMPS"
] | 96c6762061c0edf3f9ea0d0476527133e9269e366f79ed0a80c68a202ddf6baa |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | valtandor/easybuild-easyblocks | easybuild/easyblocks/o/openfoam.py | Python | gpl-2.0 | 18,234 | [
"ParaView"
] | f8cacde257d269ab1efc059b7728145c075536d27c5378b8121877a85a9d97ff |
"""
Provides mapping between extensions and datatypes, mime-types, etc.
"""
import os
import sys
import tempfile
import threading
import logging
import imp
import data
import tabular
import interval
import images
import sequence
import qualityscore
import genetics
import xml
import coverage
import tracks
import chromin... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/registry.py | Python | gpl-3.0 | 51,559 | [
"BLAST",
"Galaxy"
] | d9783b0d6f0604f01adf375152b595c53e0af7c1c08e0babd0c0e84ae62d582e |
# encoding: utf-8
import ckan.plugins.toolkit as tk
import ckan.logic
from owslib.wms import WebMapService
import requests
import json
import ckan.lib.helpers as h
import ckan.logic as logic
from ckan.model import (PACKAGE_NAME_MIN_LENGTH, PACKAGE_NAME_MAX_LENGTH)
from dateutil.relativedelta import relativedelta
from ... | ccca-dc/ckanext-thredds | ckanext/thredds/logic/action.py | Python | gpl-3.0 | 49,216 | [
"NetCDF"
] | 1fe4f607094ea2649b6b30c0502e3689b9ad8cfe5a059d1d3913bc1eea16582d |
import os
import math
def ReadRestart(file_header, step_init):
# Open the restart file, and read all the lines. Store only the contents of the sections named
# CELL and COORD for further parsing of the system.
# Open the file, based on the selected case
if step_init == 0:
wit... | rasolercrespo/GO_job_submission_script | job_funcs.py | Python | gpl-2.0 | 21,121 | [
"CP2K"
] | 6627f835179b9bd25db9d029566d99ac4fb089211107440297d3b562f5703d4b |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2022, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | qiime2/q2-feature-table | q2_feature_table/_summarize/_visualizer.py | Python | bsd-3-clause | 11,912 | [
"BLAST"
] | 97555a171fee21fc6192473b1837c90d6b182dc04fabb0474d75749cca2b81f6 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'ExpFactConceptMap'
db.create_table(u'neuroelectro_expfact... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0081_auto__add_expfactconceptmap__add_field_neuronephysdatamap_exp_fact_con.py | Python | gpl-2.0 | 37,869 | [
"NEURON"
] | 957fdaee7ed2ff500e8e58af00ba07de2c857b548a2e5289e642c43e3b45797a |
import sys
from ase.atoms import string2symbols
from asap3 import EMT
from asap3.Tools.ParameterOptimization import ParameterPerformance
from asap3.Tools.ParameterOptimization.EMT import *
from asap3.Tools.MaterialProperties import MaterialPropertiesData
def get_parameters(file, number=2):
file = open(file)
t... | auag92/n2dm | Asap-3.8.4/Projects/ParameterOptimization/performance_EMTclassic.py | Python | mit | 2,192 | [
"ASE"
] | 0959bfb657d4b9d5464864a08af2513eead2ae292e09b1dcaa86d90fd8faf6a6 |
# drizzle/base.py
# Copyright (C) 2005-2012 the SQLAlchemy authors and contributors <see AUTHORS file>
# Copyright (C) 2010-2011 Monty Taylor <mordred@inaugust.com>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Support for the Driz... | SohKai/ChronoLogger | web/flask/lib/python2.7/site-packages/sqlalchemy/dialects/drizzle/base.py | Python | mit | 15,314 | [
"VisIt"
] | f358903e655749d37e92ab45f3a6a93c600f963f23d8bead63b560fbf1891394 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import os
import random
from collections import OrderedDict
import gzip
import json
import numpy as np
... | nisse3000/pymatgen | pymatgen/io/lammps/tests/test_data.py | Python | mit | 37,731 | [
"LAMMPS",
"pymatgen"
] | 897f12ebfd2762e23870b52b9afa09ab31ced43ecf88363fb5661cbc86357501 |
#/usr/bin/env python2
# Copyright (C) 2013,2014,2015,2016 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 Licens... | Marcello-Sega/espresso | tools/blockfile2pickle.py | Python | gpl-3.0 | 9,779 | [
"ESPResSo"
] | 022d38b3c58a3b7bffd166080e3c9db2c8bb26ebe40bb08918913da9fd5c51ca |
from util import format_number
from vector3 import Vector3
from math import sin, cos, tan, sqrt, pi, radians
from copy import deepcopy
from array import array
#import psyco
#psyco.full()
class Matrix44Error(Exception):
"""Matrix44 Exception class"""
def __init__(self, description):
... | guoxiaoyong/simple-useful | simpleopengl/gameobjects/matrix44.py | Python | cc0-1.0 | 32,041 | [
"ADF"
] | 4fb69b59af48604708022ff23467ecd2061a4fe72282df905f8525a310fe9030 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from bok_choy.web_app_test import WebAppTest
from ..helpers import (
UniqueCourseTest,
Even... | rue89-tech/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 40,437 | [
"VisIt"
] | 1f607caa9bf5c15e66cd6f725befd1d397591dc6071d900596af2c7c4d67ce33 |
import tweepy # This is a Twitter API helper library.
import time
# You should get the following keys and authentication codes for your Twitter account
# Visit apps.twitter.com
consumer_key = 'consumer_key'
consumer_secret = 'consumer_secret'
access_token = 'access_token'
access_token_secret = 'access_token_secret'
... | Logan1x/Python-Scripts | bin/twitter_retweet_bot.py | Python | mit | 992 | [
"VisIt"
] | ab0fe799d5ff4362a04cc220912c5d8aedabcb43cb49238f91993ee654efd3da |
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
import sys
from PIL import Image
import numpy as np
import math
import argparse
def getMatrix(image):
data = list(image.getdata())
width, height = image.size
matrix = np.array(data).reshape(height,width)
return matrix
def getData(matrix):
data = lis... | apeyrard/sjtu-work | DIP/exercises/ex3/ex3.py | Python | mit | 3,652 | [
"Gaussian"
] | 755f06a4dcec6f26db45ea2561823860c762ff306c201f9b3e5ad042d1aa4f35 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for Entrance exams in the LMS
"""
from textwrap import dedent
from ..helpers import UniqueCourseTest
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.lms.courseware import CoursewarePage
from ...pages.lms.problem import ProblemPage
from ...fixtures.... | ahmadiga/min_edx | common/test/acceptance/tests/lms/test_lms_entrance_exams.py | Python | agpl-3.0 | 4,073 | [
"VisIt"
] | ca19fd7cd5ca9fa16ff906fa6f113c1955453b0539ca04eda020a93e126dd335 |
import abc
import argparse
import re
import pickle
import numpy as np
import pandas as pd
BASE_ATTR = """
Parameters
----------
filename : str
The path and the name of the file.
sample_regex : str
A regex string for isolating sample columns.
ptm_type : str, None
... | pambot/cbio-proteomics | ms2cbioportal.py | Python | mit | 17,234 | [
"Avogadro"
] | 8614e07b08b5bb2212cca624ad56baefbda48c04a2ab3b7424b3a98fc649734f |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/editors/fileeditor.py | Python | gpl-2.0 | 7,417 | [
"VisIt"
] | 04ca0e16e73e4e759854d738e4f6d1b13db3c686dedcd54e53218b3e253bd319 |
"""This module tests various ways how to set up the provisioning using the provisioning dialog."""
import re
from datetime import datetime
from datetime import timedelta
import fauxfactory
import pytest
from widgetastic.utils import partial_match
from widgetastic_patternfly import CheckableBootstrapTreeview as CbTree
... | nachandr/cfme_tests | cfme/tests/infrastructure/test_provisioning_dialog.py | Python | gpl-2.0 | 20,125 | [
"VisIt"
] | 3f46f8c80cf511f263da6adb157692561b5510a016c4da589463051ba569ced4 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/visualization/streamlines_3D.py | Python | gpl-2.0 | 26,376 | [
"Gromacs",
"MDAnalysis",
"Mayavi"
] | 1750f1667491c85446a785372aea48ad3df107ea16004e72af6abada42c7254c |
# 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 version.
#
# This program is distributed in the hop... | UltrasoundSam/metaArray | metaArray/misc.py | Python | gpl-2.0 | 43,149 | [
"Gaussian"
] | 0bc1954a9bf64fb6e0bad19dc29f4dacc4e543cf5473e970f607b86b53ed7316 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
from __future__ import absolute_import, division, print_function
import os
import copy
import yaml
import numpy as np
from fermipy import utils
def get_function_par_names(name):
"""Get the list of parameters associated with a function.
Parameter... | jefemagril/fermipy | fermipy/model_utils.py | Python | bsd-3-clause | 5,901 | [
"Gaussian"
] | a0bf31a6e543515acbe7593964964417e439a7ff5aca946cb54a60ecdfdf33b1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Perform fragmentation of molecules.
"""
import copy
import logging
from monty.json import MSONable
from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
from pymatgen.analysis.local_env ... | richardtran415/pymatgen | pymatgen/analysis/fragmenter.py | Python | mit | 17,600 | [
"pymatgen"
] | 9fe02d4f062786ddee47248342d8f3563469c715e8eec711d4cc2404554e2d7d |
"""
Topological sort.
From Tim Peters, see:
http://mail.python.org/pipermail/python-list/1999-July/006660.html
topsort takes a list of pairs, where each pair (x, y) is taken to
mean that x <= y wrt some abstract partial ordering. The return
value is a list, representing a total ordering that respects all
the inpu... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/util/topsort.py | Python | gpl-3.0 | 7,495 | [
"Galaxy"
] | 994732ca7d6131c0b22be42d193953b51cb0bf9449c7b882dfed283485242c05 |
#
# Copyright (C) 2015-2017 University of Oxford
#
# This file is part of msprime.
#
# msprime 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... | ashander/msprime | msprime/simulations.py | Python | gpl-3.0 | 47,258 | [
"DIRAC"
] | 4409cbd54a76d1bb35779c63ee9dda4cf86b8ba021b6df2203dc398f8d15ed74 |
from chiplotle.core.visitor import Visitor
class AffixFormatVisitor(Visitor):
'''Hard-sets formatters defined in Groups onto the drawable _Shapes.
This cannot be undone!
Useful as an operation previous to splitting a shape tree to avoid
loosing the implied formating information across grou... | drepetto/chiplotle | chiplotle/geometry/core/affixformatvisitor.py | Python | gpl-3.0 | 918 | [
"VisIt"
] | 3fc227a2af2d78b742cddb20988c2ff6b67cba6fe2840b6f5aaa8618258a5bb8 |
"""
This module operates on the AST before any checks are made.
It's sole goal is to remove purely syntactic sugar and to replace it with a
semantically equivalent AST.
"""
import ast
from typy.exceptions import NotYetSupported
# TODO
# x.__len__() <==> len(x)
# x.__delitem__(y) <==> del x[y]
# x.__delslice__(i, j)... | Procrat/typy | typy/insuline.py | Python | mit | 3,898 | [
"VisIt"
] | 244a9c82a93853b4686d37ab8462d7aa6703d44fec9da1016997387b6c6d22a8 |
import unittest
from itertools import combinations_with_replacement
from phevaluator.tables import CHOOSE, DP, SUITS
class TestSuitsTable(unittest.TestCase):
DP = [0] * len(SUITS)
@classmethod
def setUpClass(cls):
for k in [5, 6, 7, 8, 9]:
cls.update_k(cls.DP, k)
@staticmethod
... | HenryRLee/PokerHandEvaluator | python/tests/table_tests/test_dptables.py | Python | apache-2.0 | 3,604 | [
"VisIt"
] | e763e03563474d49fba5d20917cb03f5b14d681f2770064e06a808c936fcc3a8 |
# 05.06.2007, c
# last revision: 05.06.2007
input_name = '../examples/navier_stokes/stokes.py'
output_name = 'test_stokes.vtk'
from testsBasic import TestInput
class Test( TestInput ):
pass
| olivierverdier/sfepy | tests/test_input_stokes.py | Python | bsd-3-clause | 196 | [
"VTK"
] | 0eebc5517f2b714aa27968c1e57044e00d5cb08deabaac0ea3fc10706e8277f3 |
"""Dump a days worth of output to file."""
# stdlib
import os
import datetime
from multiprocessing import Pool
import sys
# third party
import numpy as np
import pandas as pd
from tqdm import tqdm
import geopandas as gpd
from rasterstats import zonal_stats
from affine import Affine
from pyiem import dep as dep_utils
f... | akrherz/dep | scripts/RT/env2csv.py | Python | mit | 6,820 | [
"GULP"
] | c86ab26f6b806e0de904a780665d22aa723e8c393f387a31d60119e8f342cc74 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import warnings
from numbers import Number
from pathlib import Path
from collections import OrderedDict
import json
from monty.json import MontyEncoder, MontyDecoder
import numpy as np
from pymatge... | vorwerkc/pymatgen | pymatgen/analysis/tests/test_phase_diagram.py | Python | mit | 31,485 | [
"pymatgen"
] | 988969fc8d21c0ebc9a8c5eba31b28ffc5ccd43b431328a1d8f7bce2bc5f53c8 |
"""
Featurizes proposed binding pockets.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2017, Stanford University"
__license__ = "MIT"
import numpy as np
import mdtraj as md
from deepchem.uti... | joegomes/deepchem | deepchem/feat/binding_pocket_features.py | Python | mit | 1,806 | [
"MDTraj"
] | 50dc9f95d940265d00ad9cee5c1a75b331ca857bfc458ce01128ca998dc2cc98 |
################
# data classes #
################
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import relationship
from sqlalchemy.orm.session import Session # provides object_session()
from sqlalchemy.schema import ForeignKey
Base = declarative_base()
from sqlalchemy import Table, Col... | hdetering/discomark | discomark/models.py | Python | gpl-2.0 | 9,168 | [
"BLAST"
] | 9d99215f3d21b25efa6afb8eae249d59b8e84686256fe6a67ce404f3f2df6346 |
"""
Monitoring Type for Data Operation
"""
from DIRAC.MonitoringSystem.Client.Types.BaseType import BaseType
class DataOperation(BaseType):
def __init__(self):
super().__init__()
self.keyFields = [
"OperationType",
"User",
"ExecutionSite",
"Source... | DIRACGrid/DIRAC | src/DIRAC/MonitoringSystem/Client/Types/DataOperation.py | Python | gpl-3.0 | 1,509 | [
"DIRAC"
] | e740c804c9131ada6da96a9569a93b6d5b30c03ca50667dafb309c44867ff85b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#################################################################################
# LAYMAN ACTIONS
#################################################################################
# File: cli.py
#
# Handles layman actions via the command line interface.
#
# C... | gentoo/layman | layman/cli.py | Python | gpl-2.0 | 13,954 | [
"Brian"
] | aac7ecc6c6a7974c330f74fa4a09f70dda260aa12682ce8ffae41ffbc8c0889e |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Examples for transform_ci function to transform FCI wave functions with
respect to the change of orbital space:
1. Transform wavefunction wrt orbital rotation/transformation.
2. Transfer a FCI wave function from a smaller orbital space to the wa... | gkc1000/pyscf | examples/fci/33-rotate_wfn.py | Python | apache-2.0 | 3,745 | [
"PySCF"
] | e8d6b112d097da813dfec364e6a24adf809e5f56ea4c35dc090372f94b3bca43 |
#!/usr/bin/env python3
# Copyright 2021, 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or a... | GoogleCloudPlatform/firestore-migration-tooling | dynamodb-firestore/streaming-replication/cdk/app.py | Python | apache-2.0 | 1,554 | [
"CDK"
] | a7f3afba68a98d5ce1626cd33c1d7f9fcc939627a677604b68d5e67361437a73 |
# Author: Robert Kern <robert.kern@enthought.com>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance
from tvtk.api import tvtk
# Local imports
from mayavi.filters.filter_base import FilterBase
from mayavi.core.pipeline_info import PipelineInfo
##... | dmsurti/mayavi | mayavi/filters/triangle_filter.py | Python | bsd-3-clause | 1,310 | [
"Mayavi"
] | 452290c622127f1c18acaeda145bef2ba801fba1ee35a4f35157aad4d16253d9 |
"""Generate the StageIV climatology file."""
import datetime
import os
import numpy as np
from pyiem.util import ncopen, logger
LOG = logger()
BASEDIR = "/mesonet/data/stage4"
def init_year(ts):
"""Create a new NetCDF file for a year of our specification!"""
# Get existing stageIV netcdf file to copy its co... | akrherz/iem | scripts/iemre/init_stage4_dailyc.py | Python | mit | 2,527 | [
"NetCDF"
] | bbff43c01135bc5f3c9c0f427aafe49da0d9f10ddffd18354bd1d1953932821c |
#!/usr/bin/env python
# File: plot_icd_mass.py
# Created on: Tue Jun 4 11:31:32 2013
# Last Change: Mon Aug 12 14:09:04 2013
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import pylab as pyl
import cPickle as pickle
def plot_icd_vs_mass():
galaxies = pickle.load(open('galaxies.pickle','rb'))
arrow_... | boada/ICD | sandbox/legacy_plot_code/plot_icd_z_box.py | Python | mit | 4,933 | [
"Galaxy"
] | f50d3606919e8e9196cd9260adb7f3e55e5c1f3cef28611d127877b9cd710f13 |
# Copyright 2001 by Katharine Lindner. 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.
"""Martel based parser to read SAF formatted files.
This is a huge regular regular expres... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Saf/saf_format.py | Python | apache-2.0 | 2,399 | [
"Biopython"
] | 609746cef5c4808a4f146ee53958001a81ffc0532e87c46d62df98384c3ad141 |
#!/usr/bin/python
# encoding: utf-8
# === IMPORTANT ====
# NOTE: In order to support no-ASCII file names,
# your system's locale MUST be set to 'utf-8'
# CAVEAT: DOESN'T work with proxy, the underlying reason being
# the 'requests' package used for http communication doesn't seem
# to work prope... | wangjun/bypy | bypy.py | Python | gpl-3.0 | 80,410 | [
"VisIt"
] | 345e3231fe4a4cf3470056798da4281ff890ef4541178fa41b90f62f50ee7b5c |
"""
Data conversion utility for NetworkX
=====================================
Convert cytoscape.js style graphs from/to NetworkX object.
https://networkx.github.io/
"""
import networkx as nx
# Special Keys
ID = 'id'
NAME = 'name'
DATA = 'data'
ELEMENTS = 'elements'
NODES = 'nodes'
EDGES = 'edges'
SOURCE = 'sour... | scholer/py2cytoscape | py2cytoscape/util/util_networkx.py | Python | mit | 3,292 | [
"Cytoscape"
] | a41382212111a4e2360c9a4c3e87e739e8cb50f135576e13a1a023f92dc27922 |
"""Orca Screen Reader"""
__copyright__ = "Copyright (c) 2005-2006 Sun Microsystems Inc."
__license__ = "LGPL"
| ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/__init__.py | Python | gpl-3.0 | 115 | [
"ORCA"
] | 31b8dafe110e1dd80c790a5dad1bfe79ef360df5fc1b2eee1ad17a3d09c80cbf |
"""
Test functions for multivariate normal distributions.
"""
from __future__ import division, print_function, absolute_import
import pickle
from numpy.testing import (assert_allclose, assert_almost_equal,
assert_array_almost_equal, assert_equal,
assert_array_les... | jakevdp/scipy | scipy/stats/tests/test_multivariate.py | Python | bsd-3-clause | 56,569 | [
"Gaussian"
] | f6051c03e8779812e7c9a9de0233f9e7ca3ef343b1845a66527a628ad377b1b9 |
#-----------------------------------------------------------------
# casescore: casescore.py
#
# Given a C (c99) code, this package classifies the identifiers
# by naming style into different groups and computes the
# frequency distribution of each group.
#
# Copyright (C) 2014, Arun Saha
# License: BSD
#-------------... | arunksaha/casescore | casescore.py | Python | bsd-3-clause | 5,161 | [
"VisIt"
] | 890872143b60baf07119f619c255159bf5126132b0f5d477e63736fc42ae2f09 |
#!/usr/bin/python
#########################################################################################################################
#This script was written by Nathan Whelan.
# THIS SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF... | NathanWhelan/autormate-PAML-codeml | codemlScript.py | Python | mit | 2,202 | [
"Biopython"
] | e7c353720a61be638d7343264e0a07a47f6915cada1a567014aff6454922318b |
"""
Version 2012/08/20, Torsten Kerber
Contributors:
Torsten Kerber, Ecole normale superieure de Lyon:
Paul Fleurat-Lessard, Ecole normale superieure de Lyon
based on a script by Rosa Bulo, Ecole normale superieure de Lyon
This work is supported by Award No. UK-C0017, made by King Abdullah
University of Science... | suttond/MODOI | ase/calculators/mopac.py | Python | lgpl-3.0 | 8,322 | [
"ASE",
"MOPAC"
] | c936f7bca34220f46a6de66c714c94c3216de7e275bbcdb9b41b705b5b13352e |
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 08 15:09:49 2016
@author: tih
"""
import numpy as np
import os
import scipy.interpolate
import gdal
from openpyxl import load_workbook
import osr
from datetime import datetime, timedelta
import pandas as pd
import shutil
import glob
from netCDF4 import Dataset
import warn... | wateraccounting/SEBAL | PreSEBAL/preSEBAL_new2.py | Python | apache-2.0 | 110,149 | [
"NetCDF"
] | ce50a816df3d7e79cc5b9f252dd7ccc50604a55af053ddbb607feaeac2da9bcb |
from django.urls import reverse
from mainapp.tests.live.chromedriver_test_case import ChromeDriverTestCase
class HistoryTest(ChromeDriverTestCase):
fixtures = ["initdata"]
def test_revision_button(self):
self.visit(reverse("paper", args=[1]))
self.assertTextIsNotPresent("Revisions")
... | meine-stadt-transparent/meine-stadt-transparent | mainapp/tests/live/test_history.py | Python | mit | 798 | [
"VisIt"
] | 3df1f585a57369fa9072946cc3ae0af4dc851c7f8a86d9a85c363f7035127939 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose | moose-examples/snippets/changeFuncExpression.py | Python | gpl-3.0 | 4,465 | [
"MOOSE"
] | 098ca1bf3fdafc70a51ff18bfe1a22ce1bea113d0e7ff8e573421fb7ea68c41c |
from .moose import *
| BhallaLab/moose-thalamocortical | python/moose/__init__.py | Python | lgpl-2.1 | 21 | [
"MOOSE"
] | ff796e69990a61b334ecbaeb4c544da13230ba6d6e3c923c04f11e21221e95bc |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Kleptobismol/scikit-bio | skbio/stats/ordination/_base.py | Python | bsd-3-clause | 18,694 | [
"scikit-bio"
] | 94aa4d4df492e4bc96b4cf5bb13490b7f829773fc6ee39370f099a51803125ed |
import numpy as np
import astropy.convolution
import skimage.filters
import warnings
from functools import partial
convolve = partial(
astropy.convolution.convolve,
nan_treatment='fill',
normalize_kernel=False,
)
convolve_fft = partial(
astropy.convolution.convolve,
nan_treatment='fill',
nor... | tudo-astroparticlephysics/starry_night | starry_night/image_kernels.py | Python | mit | 1,977 | [
"Gaussian"
] | 02a2dcbf0eee1fad09cd418c7b169b9b73ac9921410a288db639a768988206cd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
| matk86/pymatgen | pymatgen/util/tests/test_decorators.py | Python | mit | 152 | [
"pymatgen"
] | 4b795930c6dee11343662ca3923bc8924e6625a8cf020b6d362b5cbdbba4e5eb |
## INFO ########################################################################
## ##
## pickolo ##
## ======= ... | petervaro/pickolo | pickolo/app.py | Python | gpl-3.0 | 11,924 | [
"VisIt"
] | 9c4f1d7093630928e8292d9c3afc5d8a898d5ad8e36d5574b7ccbd81278c325d |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_clm(... | dcherian/pyroms | examples/Arctic_HYCOM/remap_clm.py | Python | bsd-3-clause | 5,003 | [
"NetCDF"
] | 6de57bcf06db1099b73b72e4de7f79021b5528a343de6b31ada442a8b17bbcc0 |
import os
import numpy
import math
from scipy import interpolate
from decimal import *
import string
import pickle
import time
TWOPLACES = Decimal(10) ** -2 # same as Decimal('0.01')
FOURPLACES = Decimal(10) ** -4 # same as Decimal('0.0001')
SIXPLACES = Decimal(10) ** -6 # same as Decimal('0.000001')... | BradGreig/21CMMC | 21CMMC_SourceCode/Programs/21CMMC.py | Python | gpl-2.0 | 49,681 | [
"Gaussian"
] | 58a911541b3c29d3a5ca51e81e4c91d2d6ee12ac6a9cdb9c96a20dcbee6bc688 |
from __future__ import print_function
import copy
import warnings
from neatsociety.statistics import get_species_sizes
try:
import graphviz
except ImportError:
graphviz = None
warnings.warn('Could not import optional dependency graphviz.')
try:
import matplotlib.pyplot as plt
except ImportError:
... | machinebrains/neat-python | neatsociety/visualize.py | Python | bsd-3-clause | 5,868 | [
"NEURON"
] | 5be1ce8ca3f3ba36271d290967ec38679325a34b62e71ed4095010eaf7ac6913 |
# 4BitVerticalBargraph2x.py
#
# A DEMO 4 bit slow analogue bargraph generator in colour for STANDARD Python 2.6.x and Linux...
# This is a vertical version of the horizontal one also given away by myself.
# It is written so that anyone can understand how it works.
#
# (Original copyright, (C)2011, B.Walker, G0LCU.)
# I... | ActiveState/code | recipes/Python/577675_Four_Bit_Vertical_Coloured_Analogue_Bar_Graph/recipe-577675.py | Python | mit | 5,615 | [
"Amber"
] | b7bbe5f860fbd10f94f13e246b8c87e728a02fa7f8a44f1a622e3bcb32a0c0a5 |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | kjung/scikit-learn | sklearn/cluster/k_means_.py | Python | bsd-3-clause | 55,794 | [
"Gaussian"
] | c96073558c4b261f15794fcc9add912f30f0021d2c3cc9c8a49dcc1cd6700c0a |
# Copyright 2017 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | tombstone/models | research/lfads/distributions.py | Python | apache-2.0 | 17,394 | [
"Gaussian"
] | 015ea7bbf281bfb8d61e3b13cb63fa2419b99dcd44ae5fadad52ea5846db5110 |
# Copyright (c) 2011-2018, wradlib developers.
# Distributed under the MIT License. See LICENSE.txt for more info.
import unittest
import wradlib as wrl
from wradlib.io import radolan
from wradlib.io import rainbow
from subprocess import check_call
import numpy as np
import zlib
import gzip
import tempfile
... | heistermann/wradlib | wradlib/tests/test_io.py | Python | mit | 44,344 | [
"NetCDF"
] | a50eb24be88197007b4b7a45f8c441b18d77cfa3d99cbee7416603fc4ed919f2 |
import numpy
import sys
#import random
## cgkit comes from: http://cgkit.sourceforge.net
#from cgkit.noise import noise
print "# vtk DataFile Version 2.0"
print
print "ASCII"
print "DATASET UNSTRUCTURED_GRID"
from pylab import *
import random
maxY = 256.0
minY = -270.0
Ysubdivisions = 16.
deltaY = (maxY - minY... | mfassler/jaivis | data/Maps/BeachSunset/generators/coastline-generator.py | Python | gpl-2.0 | 2,259 | [
"VTK"
] | e27e21f5672fd3de90a323ce5f244e2fe290e5fdc63ebfe3407539b6e6a1f039 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'pyqt_filter.ui'
#
# Created: Thu Mar 17 10:51:17 2011
# by: PyQt4 UI code generator 4.7.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
class Ui_MainWindow(object):
def setupUi(self, Main... | atzengin/OCC | oc-utils/python/utils/pyqt_filter.py | Python | gpl-3.0 | 32,755 | [
"Gaussian"
] | bfca6b13ba2d97fe3f9a10e7701e8cf717437ad070ae9cdf14214435cd74dc0a |
# Set up a basic scene for rendering.
from paraview.simple import *
import sys
script = """
import vtk
def setup_data(view):
# Don't actually need any data
pass
def render(view, width, height):
canvas = vtk.vtkImageCanvasSource2D()
canvas.SetExtent(0, width-1, 0, height-1, 0, 0)
canvas.SetNumberOfScalarCom... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Applications/ParaView/Testing/Python/TestPythonViewScript.py | Python | gpl-3.0 | 1,397 | [
"ParaView",
"VTK"
] | 4de38b4780534a36e80e649e6224024189589d6cf648669bbfa6c6cc727ba3e4 |
import numpy as np
import theano
import theano.tensor as T
from theano import pp, config
from pyvtk import VtkData, PolyData, Vectors, PointData, Scalars # Will be useful to export the control points
import scipy.misc
#from .images import Image
class ImagesManifold :
"""
Class which handles all the image-speci... | jeanfeydy/lddmm-ot | LDDMM_Python/lddmm_python/modules/manifolds/images_manifold.py | Python | mit | 4,880 | [
"VTK"
] | 4ec7478147a1bc3bfc1bcb7b33d46edb35687e5664c313c8e462a61a4b8efa21 |
'''
For blastn searches we are going to calculate the percent coverage of the phage genome and score the longest coverage as the best hit. It doesn't matter where the hits are on the bacterial genome.
We are going to use a cutoff of 0.001 E value
'''
import sys,os,re
from phage import Phage
phage=Phage()
try:
b... | linsalrob/PhageHosts | code/tabulate_blastn.py | Python | mit | 1,762 | [
"BLAST"
] | 2ebff484ad877fc6ed17a2534e801cb88836f019336fb5c76b7bd616b357b784 |
from person import Person
from job import Job
jobprefers = {
'sunday': ['amber', 'lisa', 'ana','matt', 'rob', 'kyle', 'kevin', 'abi', 'amy', 'jack', 'hope', 'mike'],
'monday': ['abi', 'kevin', 'rob', 'matt','amy', 'amber', 'lisa', 'kyle', 'jack','ana', 'hope', 'mike'],
'tuesday': ['rob', 'hope', 'abi', 'matt','lis... | vmlane/jobMatcher | testClasses.py | Python | mit | 2,565 | [
"Amber"
] | dbc126297a34984ff737e404990d4c5c30e9083a7fc02b2ac92f071c39fe344a |
import os
import bpy
from io_scene_cs.utilities import rnaType, rnaOperator, B2CS
from io_scene_cs.utilities import RemovePanels, RestorePanels
from io_scene_cs.io import Export
class csSettingsPanel():
bl_space_type = "PROPERTIES"
bl_region_type = "WINDOW"
bl_context = "render"
b2cs_context = "render"
b... | baoboa/Crystal-Space | scripts/blender/io_scene_cs/ui/settings.py | Python | lgpl-2.1 | 4,224 | [
"CRYSTAL"
] | a53c389e3973b085291464ce3a34186c82f701fc36280a5c3dc4f48c3049bf52 |
import os
from numpy import array,dot,pi
from numpy.linalg import inv,norm
from generic import obj
from periodic_table import periodic_table
from physical_system import PhysicalSystem
from simulation import Simulation
from qmcpack_input import QmcpackInput,generate_qmcpack_input
from qmcpack_input import BundledQmcpac... | habanero-rice/hclib | test/performance-regression/full-apps/qmcpack/nexus/library/qmcpack.py | Python | bsd-3-clause | 19,534 | [
"QMCPACK"
] | 3c10b519598c11f9dc23b5c8cfbe3f6d9b2d4f3585db74a0c2a216158a7ff48b |
# encoding: utf-8
"""
An embedded IPython shell.
Authors:
* Brian Granger
* Fernando Perez
Notes
-----
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/frontend/terminal/embed.py | Python | lgpl-3.0 | 10,945 | [
"Brian"
] | 129e781b7c75859041612dfbb99802be11bdc55d1be6b25c9f90b88faf2d83d7 |
"""
Caffe network visualization: draw the NetParameter protobuffer.
.. note::
This requires pydot>=1.0.2, which is not included in requirements.txt since
it requires graphviz and other prerequisites outside the scope of the
Caffe.
"""
from caffe.proto import caffe_pb2
"""
pydot is not supported under p... | menglin0320/resnet_try | python/caffe/draw.py | Python | mit | 7,633 | [
"NEURON"
] | ed802544e0f784345b2d292aa7d21f9041773db8a0304b5019d9ce702959be05 |
#
# Copyright (C) 2013-2021 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... | espressomd/espresso | samples/gibbs_ensemble/gibbs_ensemble.py | Python | gpl-3.0 | 5,410 | [
"ESPResSo"
] | 0b75dc8689b2ab4c816a669a54af06e1f584569945085cefa8248150a2edab04 |
# coding: utf-8
from __future__ import unicode_literals
import base64
import binascii
import collections
import ctypes
import email
import getpass
import io
import itertools
import optparse
import os
import platform
import re
import shlex
import shutil
import socket
import struct
import subprocess
import sys
import xm... | rrooij/youtube-dl | youtube_dl/compat.py | Python | unlicense | 92,961 | [
"Bowtie"
] | f1e6c05b8163206ac6897bdeef29af64078aaa0085a782ef3e048c6bb162301d |
#============================================================================
#
# Copyright (c) Kitware 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... | matthieuheitz/VesselView | Modules/Scripted/Welcome/Welcome.py | Python | apache-2.0 | 3,470 | [
"VTK"
] | 5358f91872fa21e920d9abc0843e8cd7b65fb4b679ffe78abe2fe854e8e4c92b |
# -*- coding: utf-8 -*-
# Copyright (c) 2007, 2008, Benoît Chesneau
# Copyright (c) 2007 Simon Willison, original work on django-openid
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# ... | tvenkat/askbot-devel | askbot/deps/django_authopenid/views.py | Python | gpl-3.0 | 48,584 | [
"VisIt"
] | 4e77c479089388dcf35f2ef755fa205a9aad5f073b501fedf515f1c6af556c54 |
# $HeadURL: $
''' GGUSTicketsCommand
The GGUSTickets_Command class is a command class to know about
the number of active present opened tickets.
'''
import urllib2
from DIRAC import S_ERROR, S_OK
from DIRAC.Core.LCG.GGUSTicketsClient ... | vmendez/DIRAC | ResourceStatusSystem/Command/GGUSTicketsCommand.py | Python | gpl-3.0 | 5,602 | [
"DIRAC"
] | 08d59cabb77c474ab84f0022082eb5b4189673707d09122fd1a6b55df9010478 |
#!/usr/bin/env python3
import numpy as np
"""This module contains MISMIP constants and parameters, as well as functions
computing theoretical steady state profiles corresponding to various MISMIP
experiments.
It should not be cluttered with plotting or NetCDF output code.
"""
def secpera():
"Number of seconds p... | pism/pism | examples/mismip/mismip2d/MISMIP.py | Python | gpl-3.0 | 9,438 | [
"NetCDF"
] | 2891e190c09ef4ca325ddf4977304875f2294e4544a2614fd9657d9592edfa53 |
import shutil
import os
import unittest
import extract_msg
TEST_FILE = "example-msg-files/unicode.msg"
class TestCase(unittest.TestCase):
def setUp(self):
shutil.rmtree("raw", ignore_errors=True)
for name in os.listdir('.'):
if os.path.isdir(name) and name.startswith('2013-11-18_102... | mattgwwalker/msg-extractor | tests.py | Python | gpl-3.0 | 1,662 | [
"Brian"
] | 03e6f1df1cb2a2300ab43ded0b0238a0a2c9a5cd05c676dd6ea4140b1ebddb72 |
# -*- coding: utf-8 -*-
"""An implementation of the CausalR algorithm described by [Bradley2017]_.
.. [Bradley2017] Bradley, G., & Barrett, S. J. (2017). `CausalR - extracting mechanistic sense from genome scale
data <https://doi.org/10.1093/bioinformatics/btx425>`_. Bioinformatics, (June), 1–3.
"""
... | pybel/pybel-tools | src/pybel_tools/analysis/causalr.py | Python | mit | 8,115 | [
"Pybel"
] | c00d0add59666b8aea6cbf5af5e73aa522ff3b9d20f1b200b128d4252662d3d1 |
# sybase/base.py
# Copyright (C) 2010-2014 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG http://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is par... | skycucumber/Messaging-Gateway | webapp/venv/lib/python2.7/site-packages/sqlalchemy/dialects/sybase/base.py | Python | gpl-2.0 | 28,629 | [
"ASE"
] | 02b38264122d5c4ba9ca5ba5c41ce3afd67cd6cb74e998067eab5f2c912ead61 |
#!/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
... | nuclear-wizard/moose | python/chigger/tests/speed/speed.py | Python | lgpl-2.1 | 1,611 | [
"MOOSE"
] | 7a0b636079ff2471011adca3da7c09cc63f7e04a3cf1549598f2de0de17b79e5 |
# Copyright 2019 DeepMind Technologies Limited. 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 ... | deepmind/tree | tree/tree_test.py | Python | apache-2.0 | 47,249 | [
"VisIt"
] | 76acf38dfca661dee2b40f5a773e147d156251dba6ec33b6cac364ffabe656fd |
"""rbf - Radial basis functions for interpolation/smoothing scattered Nd data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Permission to use, modify, and distrib... | mortonjt/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 9,100 | [
"Gaussian"
] | ca739fe6a5b9af02cb1b511e420b18ddcff4601835399319a691b760b1199feb |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import os
from collections import OrderedDict
from mpinterfaces import get_struct_from_mp
from mpinterfaces.lammps import CalibrateLa... | henniggroup/MPInterfaces | examples/lammps_jobs.py | Python | mit | 1,957 | [
"LAMMPS"
] | 9629061d591520c3f19f3531a0fdcc5854787e11829464aa7475350e5cc0d725 |
#!/bin/env python2.7
# encoding: utf-8
# from __future__ import print_function
from __future__ import division
import os
import sys
from collections import defaultdict
from collections import Iterable
from collections import namedtuple
import logging
log = logging.getLogger(os.path.basename(__file__))
# log.disabled =... | amethyst-asuka/GCModeller | GCModeller/python/NCBI_taxonomy_tree-master/ncbiTaxonomyTree.py | Python | gpl-3.0 | 13,790 | [
"VisIt"
] | 07e38f71a57432edd3a6977489ed17aeea859695642fdce8568743f9c69225c6 |
# -*- coding: utf-8 -*-
"""Testing for CX and NDEx import/export."""
import os
import tempfile
from pybel import BELGraph, from_cx, from_cx_file, to_cx, to_cx_file
from pybel.examples import braf_graph, egf_graph, sialic_acid_graph, statin_graph
from tests.test_io.test_cx.cases import TestCase
from tests.test_io.tes... | pybel/pybel | tests/test_io/test_cx/test_import.py | Python | mit | 2,035 | [
"Pybel"
] | 95534764f76407f74fb2c7133611d5819aa0e96a58d8fda1f674e027448799cf |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Mozilla Firefox history database plugin."""
import collections
import unittest
from plaso.lib import definitions
from plaso.parsers.sqlite_plugins import firefox_history
from tests.parsers.sqlite_plugins import test_lib
class FirefoxHistoryPluginTest(... | log2timeline/plaso | tests/parsers/sqlite_plugins/firefox_history.py | Python | apache-2.0 | 6,326 | [
"VisIt"
] | ef7163468910a8fbc518dfd56603319627bfe6c99cda126b3e0e5983fc733572 |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
chargepairs_by_type.py reads a LAMMPS data file (or an exce... | jag1g13/lammps | tools/moltemplate/src/chargepairs_by_type.py | Python | gpl-2.0 | 17,075 | [
"LAMMPS"
] | 338533fc95c16cd757d500f97061565612ffe07c83d85fb730da17d80e0cebb9 |
# 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 RMatrixgenerics(RPackage):
"""S4 Generic Summary Statistic Functions that Operate on Matri... | LLNL/spack | var/spack/repos/builtin/packages/r-matrixgenerics/package.py | Python | lgpl-2.1 | 1,059 | [
"Bioconductor"
] | 718e4ff2239810c1fec4562079b2d9c9906acf4c17a012256bdb0ff3d81e3c64 |
# stimtable.py ---
#
# Filename: stimtable.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed May 8 18:51:07 2013 (+0530)
# Version:
# Last-Updated: Mon May 27 21:15:36 2013 (+0530)
# By: subha
# Update #: 124
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log... | BhallaLab/moose-examples | snippets/stimtable.py | Python | gpl-2.0 | 3,666 | [
"MOOSE"
] | 19a2b89deb81283cc7ce9230affc820b52ce88489f4007f2f380d40edf4c0315 |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/typecode/contenttype.py | Python | apache-2.0 | 20,108 | [
"VisIt"
] | bd676e41b06b7f55047a806b56a6378e2157cc5b6a8ad1ddc1139d31a47c3f65 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2017, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | ywcui1990/nupic.research | htmresearch/frameworks/poirazi_neuron_model/neuron_model.py | Python | agpl-3.0 | 9,343 | [
"NEURON"
] | 162a3f277960d42b01b40606399ef879ce0d98efaac7fb6dd8c482e4124c03f8 |
# 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... | Xeralux/tensorflow | tensorflow/contrib/py2tf/converters/single_return.py | Python | apache-2.0 | 11,035 | [
"VisIt"
] | 11d23b6359c6720b7dcd0f60e5d19890baebf8485bc9486e2caca47509150fc4 |
# Copyright (c) 2015-2017 Cisco Systems, Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to
# deal in the Software without restriction, including without limitation the
# rights to use, copy, modify, merge... | retr0h/maquina | molecule/config.py | Python | mit | 10,983 | [
"Galaxy"
] | 69cb1dab6f9e14a6954b607e6f83e98b13def6c0021421e9d4d4410aea715cb1 |
import numpy as np
from scipy.stats import poisson, uniform
NPTS = 100
LENGTH_OF_DAY = 7*60
N_DOCS = 3
N_ITERATIONS = 500
T_SCALE = 5
MIN_VISIT_TIME = 5
MAX_VISIT_TIME = 20
n_clients = np.empty(N_ITERATIONS, dtype=int)
n_wait = np.empty(N_ITERATIONS, dtype=int)
av_wait_time = np.empty(N_ITERATIONS, dtype=float)
close... | amaggi/bda | chapter_01/ex_09.py | Python | gpl-2.0 | 2,845 | [
"VisIt"
] | 987a1f54d3abd1a59c69ff1db6496a71ab168f787e35d3b82d3cd8d82f1fdad1 |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011 CERN.
##
## Invenio 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) a... | cul-it/Invenio | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 99,220 | [
"ADF"
] | cbd900ed0a0a4eef65f566ecb5dfbd7fe3bd53c8907a39a4a1557b3f8b314f26 |
#!/usr/bin/env python
# Copyright 2012 Google Inc. All Rights Reserved.
"""Tests for grr.lib.objectfilter."""
import unittest
from grr.lib import objectfilter
attr1 = "Backup"
attr2 = "Archive"
hash1 = "123abc"
hash2 = "456def"
filename = "boot.ini"
class DummyObject(object):
def __init__(self, key, value):... | statik/grr | lib/objectfilter_test.py | Python | apache-2.0 | 19,241 | [
"Desmond"
] | 534f61c8566fcb0f8f1c8f000d2b1669cb284e4cfeea894e6158664f4716c63d |
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