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"""Vimdoc plugin management."""
from collections import OrderedDict
import json
import os
import warnings
import vimdoc
from vimdoc import error
from vimdoc import parser
from vimdoc import regex
from vimdoc.block import Block
# Plugin subdirectories that should be crawled by vimdoc.
DOC_SUBDIRS = [
'plugin',
... | malcolmr/vimdoc | vimdoc/module.py | Python | apache-2.0 | 17,433 | [
"VisIt"
] | b00b3182194a9a12d342934eb3b6b7947a630fed4106bc61757e501650479b39 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/widgets.py | Python | gpl-3.0 | 990 | [
"Brian"
] | 1c51243d2fbadf2931a3417395250371b8b6cd5117b18d1e85f1a6ba4c1e74ae |
# Copyright (c) 2006-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2011-2014 Google, Inc.
# Copyright (c) 2013-2016 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Michal Nowikowski <godfryd@gmail.com>
# Copyright (c) 2015 Radu Ciorba <radu@devrandom.ro>
# Copyright (c) 2015 Dmitry Pr... | rogalski/pylint | pylint/checkers/variables.py | Python | gpl-2.0 | 57,018 | [
"VisIt"
] | 02b9ec30bff833c21256d5cf4ac8f56502e88650f919a6366c6f9c4d3a4002d1 |
import os
import re
import sys
import uuid
import requests
from ast import literal_eval
from subprocess import call
conf = {} # populated by given command line arguments via start()
def request(context, flow):
request = flow.request
if(request.host == "feelinsonice-hrd.appspot.com" and request.path == '/bq/blob'):
... | thebradbain/snapception | snapception/mitmdump_input.py | Python | mit | 1,693 | [
"VisIt"
] | d8a5d61a619dcb8f16956d83cca13ba5e9f1aa03b450421c74b4b3df0f5c2179 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
""" Generation tools for NNGT """
import logging
import numpy as np
import scipy.sparse as ssp
from scipy.spatial.distance import cdist
from numpy.random import randint
import nngt
from nngt.lib import InvalidArgument, nonstring_container
from nngt.lib.logger import _log_... | Silmathoron/NNGT | nngt/lib/connect_tools.py | Python | gpl-3.0 | 12,235 | [
"Gaussian"
] | 06a1eed7a64d988b2722e65ddb8055f9f6027493046616a6ae34e0d2cec4d9f1 |
'''
Created on Nov 7, 2010
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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... | genome-vendor/chimerascan | chimerascan/pipeline/merge_spanning_alignments.py | Python | gpl-3.0 | 10,791 | [
"pysam"
] | 86b6f39d1c608059d4e47345bc1c571e2f761004e9e0fb285455d75c0aa04437 |
# Placeholder because parallel moved
# Remove this in version 1.0
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(("parallel has moved to MDAnalysis.lib.parallel "
"and will be removed from here in release 1.0"),
... | alejob/mdanalysis | package/MDAnalysis/core/parallel.py | Python | gpl-2.0 | 375 | [
"MDAnalysis"
] | d04be92cf9bbc0fa8791d7d040541f5c8ecd3b0f2480fba1c825b6f0f875d595 |
#!/usr/bin/python
###############################################################################
#
# Prepares histograms for individual rings of channel atoms based on a user-
# -defined column of the channel atom datafiles.
#
# Example: For 14-column data with this type (described elsewhere):
#
# 1 7.0 0.413 0.373 0.... | cing/ChannelAnalysis | ChannelAnalysis/PoreAnalysis/Histograms.py | Python | mit | 6,160 | [
"MDAnalysis"
] | 885b7b4538229c40b4f46113f1902386d2311518d9c63a8b70d464896adcec58 |
from datetime import date, timedelta
from ..core import WesternCalendar
from ..core import SUN, MON, TUE, THU, SAT
from ..registry_tools import iso_register
@iso_register('US')
class UnitedStates(WesternCalendar):
"United States of America"
FIXED_HOLIDAYS = WesternCalendar.FIXED_HOLIDAYS + (
(7, 4, ... | novafloss/workalendar | workalendar/usa/core.py | Python | mit | 11,414 | [
"COLUMBUS"
] | d45bf8f0bbbae02c9bbc91f2fc7a776619dd20d6069949b134a7632d920a3171 |
# TODO#!/usr/bin/env python
"""
Install.py tool to download, compile, and setup the pace library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, subprocess
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import f... | jeremiahyan/lammps | lib/pace/Install.py | Python | gpl-2.0 | 3,322 | [
"LAMMPS"
] | 0a2e0515659750756fefecfd14f26e6e4af13cfc4023d5563e6faaaa23ea173f |
# -*- coding: UTF-8 -*-
# Copyright 2017-2019 Rumma & Ko Ltd
# License: GNU Affero General Public License v3 (see file COPYING for details)
from lino.api import rt, _
from lino.utils.mldbc import babel_named as named
def objects():
Group = rt.models.groups.Group
User = rt.models.users.User
UserTypes = rt... | lino-framework/xl | lino_xl/lib/groups/fixtures/demo.py | Python | bsd-2-clause | 722 | [
"Galaxy"
] | 8ff0d0cd48ee50a6e4633e535d1979083d37f959684eb680e2ec60cbfb1521d8 |
# Copyright 2012 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 ... | CSavvy/coursebuilder | modules/dashboard/dashboard.py | Python | apache-2.0 | 29,214 | [
"VisIt"
] | ca9d83dc208d46de843478f722139f3daecae9a76c795af6d06150613019e6c8 |
import numpy as np
import random
import nest
import nest.voltage_trace as plot
import nest.raster_plot
import matplotlib.pyplot as plt
import pylab as pl
nest.ResetKernel()
nest.SetKernelStatus(
{'overwrite_files': True }) # set to True to permit overwriting
delay = 1. # the delay in ms
w_ex = 45.
g = 3.83
w_i... | research-team/NEUCOGAR | NEST/cube/noradrenaline/tests/test_sero.py | Python | gpl-2.0 | 2,782 | [
"NEURON"
] | bbe6bff4ba8ea29178d699e382e825a022e7253ee88f5a4558e7b0f9819c9a95 |
"""
Topological fingerprints for macromolecular structures.
"""
import numpy as np
import logging
import itertools
from deepchem.utils.hash_utils import hash_ecfp
from deepchem.feat import ComplexFeaturizer
from deepchem.utils.rdkit_utils import load_complex
from deepchem.utils.hash_utils import vectorize
from deepchem... | peastman/deepchem | deepchem/feat/complex_featurizers/contact_fingerprints.py | Python | mit | 9,618 | [
"RDKit"
] | 5d05b79c999f02d198adbfece570889b00cd47065960b7c1519d21e27db2293c |
# Copyright (C) 2012 Alex Nitz
# 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
# self.option) any later version.
#
# This program is distributed in ... | soumide1102/pycbc | pycbc/events/events.py | Python | gpl-3.0 | 32,584 | [
"Gaussian"
] | 8875549d97abd445bc95bd0c83d2bb26f3458fd527070c8a1894e00b7f0c8bbf |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('client', '0001_initial'),
]
operations = [
migrations.CreateModel(
name='Visit',
fields=[
... | dwagon/Scheduler | scheduler/visit/migrations/0001_initial.py | Python | gpl-2.0 | 945 | [
"VisIt"
] | 5eb51a27eaf72ec8252cd494ba3f40fef42d7f2adafa3adec9e9fcc2fbf14c8d |
from owmeta_core.bundle import Bundle
from owmeta_core.context import Context
from owmeta.neuron import Neuron
from owmeta.worm import Worm
with Bundle('openworm/owmeta-data') as bnd:
ctx = bnd(Context)(ident="http://openworm.org/data").stored
# Extract the network object from the worm object.
net = ctx(W... | openworm/PyOpenWorm | examples/list_conns.py | Python | mit | 1,002 | [
"NEURON"
] | 11682f3e177b0843f8ad6e61fc8988a19751f72776623af4593752dc882dcc93 |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from decimal import Decimal
import analytics
import pytz
import logging
import smtplib
import StringIO
import csv
from courseware.courses import get_course_by_id
from boto.exception import ... | wwj718/ANALYSE | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 65,389 | [
"VisIt"
] | fa13c3a680eb025ad5f2cc297a936badc81f7bdb48cd3e4904b838be8950c1c4 |
import yaml
import re
from collections import Counter
class Calculation:
"""
class describing a single VASP calculation
"""
def __init__( self, title, energy, stoichiometry ):
"""
Initialise a Calculation object
Args:
title (Str): The title string for this calc... | bjmorgan/vasppy | vasppy/calculation.py | Python | mit | 5,642 | [
"VASP"
] | 727edb36d16d4fb8de07b02c7b24abecceae4aa4594ff2119be80daf36a128a5 |
import contact_angle as cnt
import mdtraj as md
import numpy as np
from contact_angle.utils.general import get_fn
def test_flipped():
"""Same trajectory, but rotated around x-axis - should give same contact angle
"""
traj = md.load(get_fn('chol-tail-original.dcd'),
top=get_fn('chol-wetting.ho... | tcmoore3/contact_angle | contact_angle/tests/test_above-below.py | Python | mit | 968 | [
"MDTraj"
] | a4242b1b91e36ca10d80847ce61b6a52e169d986f397a8cb159806d9dcd6849a |
import copy
import logging
import os.path
import re
from spitfire.compiler.ast import *
from spitfire.compiler.analyzer import *
from spitfire.compiler.visitor import print_tree
from spitfire.compiler.walker import flatten_tree
import __builtin__
builtin_names = vars(__builtin__)
class _BaseAnalyzer(object):
def _... | eklitzke/spitfire | spitfire/compiler/optimizer.py | Python | bsd-3-clause | 30,190 | [
"VisIt"
] | 38d9aef7c58e8500e9b91def8906ac34b67140dc5e32f5a9a15c643bded0d7bf |
#!/usr/bin/env python3
from setuptools import setup, find_packages
import setuptools.command.build_py
from coalib import assert_supported_version
assert_supported_version()
from coalib.misc.BuildManPage import BuildManPage
from coalib.output.dbus.BuildDbusService import BuildDbusService
from coalib.misc.Constants imp... | Tanmay28/coala | setup.py | Python | agpl-3.0 | 4,386 | [
"VisIt"
] | 686ff75b24065d6dd584c77198afbd695645adf639d4bc4745a5e66e9356b916 |
# -*- encoding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
import os
import traceback
import h2o
from h2o.base import Keyed
from h2o.exceptions import H2OValueError
from h2o.job import H2OJob
from h2o.model.extensions import has_extension
from h2o.plot import decorate... | h2oai/h2o-3 | h2o-py/h2o/model/model_base.py | Python | apache-2.0 | 88,728 | [
"Gaussian"
] | 45ce53d1e50c092b5d141bb96dd135b5ffaa64bb571cc2b88cf58fe76a45c38c |
import os
import sys
import glob
import re
import livereload
import multiprocessing
import logging
import shutil
import MooseDocs
import build
log = logging.getLogger(__name__)
def serve_options(parser, subparser):
"""
Command-line options for serve command.
"""
serve_parser = subparser.add_parser('se... | backmari/moose | python/MooseDocs/commands/serve.py | Python | lgpl-2.1 | 2,695 | [
"MOOSE"
] | a74de31b76acadfcde53afadca43de8eca5efddee5cea0e7a3d65f77c1142b53 |
###############################################################################
# #
# This library is free software; you can redistribute it and/or #
# modify it under the terms of the GNU Lesser General Public #
... | wwood/BamM | bamm/tests/test_bamFilter.py | Python | lgpl-3.0 | 7,042 | [
"pysam"
] | e289c70a022e98bb4c6ac2b76d0b386005655954d6a48b1330e50fb9d6f530d6 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Provides an interface to communicate with the device via the adb command.
Assumes adb binary is currently on system path.
"""
import collections
imp... | wangscript/libjingle-1 | trunk/build/android/pylib/android_commands.py | Python | bsd-3-clause | 49,727 | [
"Galaxy"
] | cca6c071991443e4e12712fa1ec0b9239e132000aecbcebf4f2c266fb1b17734 |
#
# Copyright (C) 2010 Gianluca Sforna
#
# 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.
import math
class CanvasBase:
"""Base class for specialized ... | rvianello/rdkit | rdkit/Chem/Draw/canvasbase.py | Python | bsd-3-clause | 2,571 | [
"RDKit"
] | c54e12427d753d44e40dc649ee0351fe728bdca90f6eaf9f2ea3a6bfd37d9b8a |
r"""
=====================================================================
The Johnson-Lindenstrauss bound for embedding with random projections
=====================================================================
The `Johnson-Lindenstrauss lemma`_ states that any high dimensional
dataset can be randomly projected i... | sergeyf/scikit-learn | examples/miscellaneous/plot_johnson_lindenstrauss_bound.py | Python | bsd-3-clause | 7,773 | [
"Gaussian"
] | 8623cfcc4bda5c9400c4375d0f287b7ebb1048d7214e3835c1558ec8578bb258 |
# Copyright Bruno da Silva de Oliveira 2003. Use, modification and
# distribution is subject to the Boost Software License, Version 1.0.
# (See accompanying file LICENSE_1_0.txt or copy at
# http://www.boost.org/LICENSE_1_0.txt)
"""
Pyste version %s
Usage:
pyste [options] interface-files
where optio... | alexa-infra/negine | thirdparty/boost-python/libs/python/pyste/src/Pyste/pyste.py | Python | mit | 14,446 | [
"VisIt"
] | cd9d27216ab605573ad0eeaad6d34d3f3592de027fed43917d03874842d4663d |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright 2011 OpenStack LLC.
# 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/... | tylertian/Openstack | openstack F/cinder/cinder/tests/api/openstack/test_xmlutil.py | Python | apache-2.0 | 25,721 | [
"VisIt"
] | 4556bc78536abf25f5bf05b2199eb37318d5246352720ea4eb66bf9febfeda8b |
"""
Plots the 2D vorticity field from a IBAMR simulation at saved time-steps using
the visualization software VisIt.
"""
from snake.ibamr.simulation import IBAMRSimulation
simulation = IBAMRSimulation()
body_name = 'flyingSnake2dAoA35ds004filledInside' # file name (no extension)
simulation.plot_field_contours_visi... | barbagroup/cuIBM | external/snake-0.3/examples/ibamr/plotVorticity.py | Python | mit | 590 | [
"VisIt"
] | b2606fba2bccb4432752b1c967e2d73fd7cab5a93dd93c7041ea7d5e467b7789 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
:py:mod:`gp.py` - Gaussian Processes
------------------------------------
Routines for optimizing the GP hyperparameters for a given light curve.
'''
from __future__ import division, print_function, absolute_import, \
unicode_literals
from .mathutils import Chun... | rodluger/everest | everest/gp.py | Python | mit | 8,337 | [
"Gaussian"
] | ecbd88156b69af29d098ddfb75045ea6cc04931dedad4ad01472f6e4c37cec9b |
import numpy as np
import pele.utils.readAmberParam as readAmb
import ambgmin_ as GMIN
import pele.potentials.gminpotential as gminpot
import pele.basinhopping as bh
from pele.storage import savenlowest
from pele.NEB import NEB
from pele.takestep import displace
class molSystem:
def __init__(self):
self.... | kjs73/pele | playground/amber/metenk/run_gui.py | Python | gpl-3.0 | 2,407 | [
"Amber"
] | d86f15f16b8c8c45201bf66e94b0215ab851342a0690d88fcf977232edb0c868 |
"""
BLAST+6 format (:mod:`skbio.io.format.blast6`)
==============================================
.. currentmodule:: skbio.io.format.blast6
The BLAST+6 format (``blast+6``) stores the results of a BLAST [1]_ database
search. The results are stored in a simple tabular format with no column
headers. Values are separate... | anderspitman/scikit-bio | skbio/io/format/blast6.py | Python | bsd-3-clause | 12,758 | [
"BLAST",
"scikit-bio"
] | a84835f79a6acccfdef9db87cfda17412074644b07a10885f19890241c58ada1 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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... | tiagocardosos/stoq | stoqlib/gui/test/test_account_transaction_editor.py | Python | gpl-2.0 | 3,202 | [
"VisIt"
] | 24b0e3d16fb5ceec46ed1f6c6943924c9db443ac0098ffedbbdbe59041af6742 |
#! /bin/python
# $Id
# -----------------------------------------------------------------------------
# CppAD: C++ Algorithmic Differentiation: Copyright (C) 2003-16 Bradley M. Bell
#
# CppAD is distributed under multiple licenses. This distribution is under
# the terms of the
# Eclipse Public Licens... | wegamekinglc/CppAD | bin/push_git2svn.py | Python | epl-1.0 | 11,193 | [
"VisIt"
] | 262a450f28725eb3b8d246bd2899cf44ba58ccbd6536743ef79c4b95b444fbcb |
# Copyright 2018 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | google/differentiable-atomistic-potentials | dap/tests/test_tf_hook.py | Python | apache-2.0 | 2,166 | [
"ASE"
] | 1e361c3c71b5fbafffba1c02965c1f5b185d5e31cbb5b70dbd17db2bc884cc69 |
'''\
a piddle wrapper for wxPython DeviceContexts
piddleWxDc.py
By Paul and Kevin Jacobs
History -
1.0 Many fixes and the rest of required piddle functionality added.
0.5 Much work done by Jeffrey Kunce on image support and code factoring.
PiddleWxDc adds Piddle-compatible methods to any wxPython DeviceCont... | bp-kelley/rdkit | rdkit/sping/WX/pidWxDc.py | Python | bsd-3-clause | 8,748 | [
"RDKit"
] | 36256bf2bb1889dd911e46d195a184afa2413bb83c90332fe3d7d862387c7ada |
from js_ast import *
from js_process_ast import *
from js_cc import js_parse
from js_global import Glob, glob
from js_typed_classes import resolve_type
import os, sys, os.path, struct, imp, shutil, time, random, math
"""
okay. basic data model of typed objects:
each object compiles to an array of typed arrays, ... | joeedh/webblender | tools/extjs_cc/js_typed_class_generator.py | Python | apache-2.0 | 8,860 | [
"VisIt"
] | 6c12b9a0d9f00f9d36d359f1f159c58d5d4a7806d88a7ec7aaae627c6a1d70b1 |
"""
sentry.web.frontend.accounts
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:copyright: (c) 2012 by the Sentry Team, see AUTHORS for more details.
:license: BSD, see LICENSE for more details.
"""
from __future__ import absolute_import
import six
from django.conf import settings
from django.contrib import messages
from django.cont... | zenefits/sentry | src/sentry/web/frontend/accounts.py | Python | bsd-3-clause | 15,937 | [
"VisIt"
] | 5f9a30962a4115c83a2cc4f53db64b0f1981a12c7b93b0226b0fd46203e3a871 |
from ase.all import *
from ase.calculators.morse import MorsePotential
atoms = Atoms('H7',
positions=[(0, 0, 0),
(1, 0, 0),
(0, 1, 0),
(1, 1, 0),
(0, 2, 0),
(1, 2, 0),
... | suttond/MODOI | ase/test/example.py | Python | lgpl-3.0 | 682 | [
"ASE"
] | 47d6d411630a6961341564790e9795a9490940342298114ee4c5cb89a19ff986 |
# -*- coding: utf-8 -*-
import os
import codecs
import tempfile
import unittest
from StringIO import StringIO
from yalign.datatypes import Sentence
from yalign.input_conversion import tokenize, text_to_document, \
html_to_document, parallel_corpus_to_documents, tmx_file_to_documents, \
srt_to_document
base... | pombredanne/yalign | tests/test_input_conversion.py | Python | bsd-3-clause | 11,043 | [
"VisIt"
] | d8ed48e4b7715caf75d833a0786d2743efa8170590e1d13b1ac76dbe25d63868 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#######################################################################
#
# MetrixWeatherSetup for Enigma2
# Coded by Sinthex IT-Solutions (c) 2014
# www.open-store.net
#
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-Shar... | idrogeno/IdroMips | lib/python/Screens/OMMetrixWeatherSetup.py | Python | gpl-2.0 | 3,249 | [
"VisIt"
] | 220d35c8f07536cac657ad7c2cef0bd90c0d1969ddbd8991b8127f7d3cb7588f |
#
# @file TestParameterRule.py
# @brief ParameterRule unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by co... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestParameterRule.py | Python | gpl-3.0 | 3,753 | [
"VisIt"
] | 02732933a978b8d4c63b22c47d15676d435d1e12a302873e228519e97c484799 |
# Default Django settings. Override these with settings in the module
# pointed-to by the DJANGO_SETTINGS_MODULE environment variable.
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
gettext_noop = lambda s: s
#################... | jhoos/django | django/conf/global_settings.py | Python | bsd-3-clause | 22,662 | [
"VisIt"
] | c33ff9a26eb8751cf2d618417141cd1bee600397db36438a4ef7dd36afeffdde |
# Copyright 2015 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... | sbc100/yapf | yapf/yapflib/subtype_assigner.py | Python | apache-2.0 | 17,304 | [
"VisIt"
] | e36bc1634d9a5fbaf9b22608410c984ecab4f6c9b374051e10d011f61bf6be96 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
from zeroinstall import support
def get_fetch_info(policy, impl):
"""Get the text for a Fetch column."""
if impl is None:
return ""
elif policy.get_cached(impl):
if impl.local_path:
... | timdiels/zeroinstall | zeroinstall/0launch-gui/utils.py | Python | lgpl-2.1 | 577 | [
"VisIt"
] | 012e12199ebce6f0d18f4c960bbe2bb633fa3e2536cd1b38c4a89c9978df851c |
import unittest
import numpy as np
import pysal
from pysal.spreg.twosls_sp_regimes import GM_Lag_Regimes
from pysal.spreg import utils
from pysal.spreg.twosls_sp import GM_Lag
from pysal.common import RTOL
class TestGMLag_Regimes(unittest.TestCase):
def setUp(self):
self.w = pysal.queen_from_shapefile(pysa... | TaylorOshan/pysal | pysal/spreg/tests/test_twosls_sp_regimes.py | Python | bsd-3-clause | 15,918 | [
"COLUMBUS"
] | cd8434f467f663af182d1cc5e9780c349be27bc1a33f6c443aafa498eb146286 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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 Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/gui/editors/creditcheckhistoryeditor.py | Python | gpl-2.0 | 3,510 | [
"VisIt"
] | 490f5d2bc7e1064549982ce3693289c61c9df1e10696ae9cd2983142d2319d05 |
""" The Matcher service provides an interface for matching jobs to pilots
It uses a Matcher and a Limiter object that encapsulates the matching logic.
It connects to JobDB, TaskQueueDB, JobLoggingDB, and PilotAgentsDB.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ i... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Service/MatcherHandler.py | Python | gpl-3.0 | 5,080 | [
"DIRAC"
] | b0f1dfc3b68b5d179bd4b0148e832c9f20d76aaa04032f92d3ab4b0cd98e527a |
#!/usr/bin/python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test command-line interface.
"""
#===================================================... | andrrizzi/yank | Yank/tests/test_cli.py | Python | mit | 4,237 | [
"Amber"
] | fee44b4898db2e0fbbdc08a358b86ce17b83914c241095224835548b43c4a080 |
import os
import sys
import math
import vtk
import colorsys
import time
import functools
import traceback
import PythonQt
from PythonQt import QtCore, QtGui
import ddapp.applogic as app
from ddapp import objectmodel as om
from ddapp import perception
from ddapp import lcmUtils
from ddapp import roboturdf
from ddapp imp... | RussTedrake/director | src/python/ddapp/segmentation.py | Python | bsd-3-clause | 161,203 | [
"VTK"
] | be8ef3fe4dd9522b27c98c58a624fc4937f4c0afc3a256a86cd473d5638c58da |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Mar 19, 2012
"""
__author__ = "Shyue Ping Ong, Stephen Dacek"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__ma... | aykol/pymatgen | pymatgen/entries/tests/test_compatibility.py | Python | mit | 36,806 | [
"pymatgen"
] | 3f27e71dfcda71ed5937907e7509dd37efae0b6b6dc55cfe6b57557c8465a4ad |
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
#
# all rights reserved
# Licensed under the LGPL
# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
... | myoshimura080822/galaxy-mytools_ToolFactory | rgToolFactory.py | Python | mit | 32,318 | [
"Galaxy"
] | 2f90a5586d0b1cf11a953871f8cfba8306d20a135892b2222f840099b9359e53 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen import Structure, Lattice, Specie, DummySpecie
import numpy as np
"""
Classes for reading/writing mcsqs files following the rndstr.in format.
"""
__author__ = "Matthew Horton"
__copyright__ = "C... | fraricci/pymatgen | pymatgen/io/atat.py | Python | mit | 4,449 | [
"CRYSTAL",
"pymatgen"
] | 82e80b2190fdaf9e127996107bacde4a24f98edc8919e9edf6b1db4fb67c63fe |
import numpy as np
filename = 'tomography_model.xyz'
ftop = open(filename,'r')
dummy = ftop.readline() # x,y,z min; x,y,z max
dummy = ftop.readline() # dx dy dz
numdim = ftop.readline() # num elements x,y,z
numdim = numdim.split()
numpoints = int(numdim[0])*int(numdim[1])*int(numdim[2])
dummy = ftop.readline() # min/m... | alanschiemenz/specfem_FWI_workflow | libraries/xyztovtk.py | Python | gpl-3.0 | 1,012 | [
"VTK"
] | 9858c3988668253b9d3e235955df197efd074d702493c19d8716188eb4fedfce |
import os
import sys
import pickle
import matplotlib
matplotlib.use('Agg')
import numpy as np
from ase.atoms import Atoms
from ase.utils import devnull
from ase.data import atomic_numbers, atomic_names, covalent_radii
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters
from gpaw... | qsnake/gpaw | doc/setups/make_setup_pages_data.py | Python | gpl-3.0 | 7,442 | [
"ASE",
"GPAW"
] | 70edc6c61e789d9d4edfd6c2e9134d8a7df9c5c86e8010db22cadf126f0ab149 |
# $HeadURL$
"""
Context
This module contains the helpers needed to fetch the contextualisation setup
configuration. The usage is always the same. Instance a new ContextConfig object,
and it will make sure is the right one.
This module provides Context helpers for the contextualisation methods:
* cloud... | vmendez/VMDIRAC | WorkloadManagementSystem/Utilities/Context.py | Python | gpl-3.0 | 7,046 | [
"DIRAC"
] | 43adeec0e171ac7c79de800cdc6055454fef7e3ae5f74559fe5cf5fc5842e028 |
# -*- coding: utf-8 -*-
import ntpath
import egads
import os
import inspect
import logging
from PyQt5 import QtWidgets, QtCore, QtGui
from other_functions import check_compatibility_netcdf
from algorithm_window_functions import MyAlgorithmDisplay
def gui_position(self):
logging.debug('gui - gui_functions.py - gu... | eufarn7sp/egads-gui | functions/gui_functions.py | Python | gpl-3.0 | 32,231 | [
"NetCDF"
] | 1eea2560df359cfba3a9c08b9732e6202e8a599134e024a973bfeafa5b41ee1e |
from context import blast
from context import pytest
import os
import glob
def test_make_BLAST_database(tmpdir):
"""
Test the make_BLAST_database() function
Function signature::
make_BLAST_database(fasta_file)
"""
fasta = os.path.abspath("../../example/Antibiotic_markers.fa")
tmpdir = st... | nbenzakour/SeqFindR | tests/unittests/test_blast.py | Python | apache-2.0 | 1,075 | [
"BLAST"
] | 46cc152e8c502d57d9957208921a762d513591df53af27048d4acc973cf19d94 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.core.units import Ry_to_eV
from pymatgen.electronic_structure.core import Spin
from pymatgen.io.lmto import LMTOCopl, L... | vorwerkc/pymatgen | pymatgen/io/tests/test_lmto.py | Python | mit | 3,983 | [
"pymatgen"
] | 70342583ae24dc96aef30538c5312c9bfdb9d4b86c8e71628bb2b5dbbb9c9d1a |
#!/usr/bin/env python
# Copyright 2014-2020 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
#
# U... | sunqm/pyscf | pyscf/x2c/sfx2c1e_grad.py | Python | apache-2.0 | 10,187 | [
"PySCF"
] | 6e09e2fed6aa8ec31155526038fa042ab604b4d2e7f65d09be54bdee314240ca |
"""Wrappers for ast.Name nodes."""
from __future__ import division
from __future__ import absolute_import
from __future__ import print_function
from __future__ import unicode_literals
import ast
from ..asttools import references as reftools
from ..asttools import name as nametools
from ..asttools import scope as sco... | kevinconway/pycc | pycc/astwrappers/name.py | Python | apache-2.0 | 5,032 | [
"VisIt"
] | 4d2bef27306a90447d441bca4211b5d8df7df2e603cb44dfd1fd12d5ac66e213 |
from __future__ import absolute_import, division, print_function
from examples.helpers import authenticate
from trakt import Trakt
from pprint import pprint
import logging
import os
import time
logging.basicConfig(level=logging.DEBUG)
if __name__ == '__main__':
# Configure
Trakt.configuration.defaults.clie... | fuzeman/trakt.py | examples/scrobbler.py | Python | mit | 1,585 | [
"Galaxy"
] | 346664e7e0d2c1235f651f454ddacc70ea6fba0a92c05dc5317548e68e876cb7 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Unit tests for the PhyloXML and PhyloXMLIO modules.
"""
import os
import tempfile
im... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_PhyloXML.py | Python | gpl-2.0 | 30,329 | [
"Biopython",
"Octopus"
] | 19d57a0b4458cc11e29b553cd09b079a0eec9fd707866a4f25a31d63cdd0b736 |
import numpy as np
from matplotlib import pyplot
import rft1d
#(0) Set parameters:
np.random.seed(0)
nTestStatFields = 3
nNodes = 101
nIterations = 10000
FWHM = 10.0
### initialize RFT calculator:
rftcalc = rft1d.prob.RFTCalculator(STAT='Z', nodes=nNodes, FWHM=FWHM, n=nTestStatField... | 0todd0000/rft1d | rft1d/examples/val_conj_0_gauss.py | Python | gpl-3.0 | 1,159 | [
"Gaussian"
] | 9895dac88abb2afcb0bb0b5650f1bb12bb465aac0ed2b5855ae8b992a83f86e0 |
# $Id: HDF.py,v 1.3 2005-07-14 01:36:41 gosselin_a Exp $
# $Log: not supported by cvs2svn $
# Revision 1.2 2004/08/02 15:36:04 gosselin
# pyhdf-0.7-1
#
# Revision 1.1 2004/08/02 15:22:59 gosselin
# Initial revision
#
# Author: Andre Gosselin
# Maurice-Lamontagne Institute
# gosselina@dfo-mpo.gc.ca
... | ryfeus/lambda-packs | HDF4_H5_NETCDF/source2.7/pyhdf/HDF.py | Python | mit | 10,551 | [
"NetCDF"
] | 8e53dc1d1c9b90f638d200a49c4dd1960e166eb6e2cfd194100ddeed828345b5 |
#!/usr/bin/env python
import numpy as np
import scipy.interpolate as interp
from qharv.reel import ascii_out
def get_dsk_amat(floc):
""" extract A matrix from qmcfinitesize output
k->0 behavior of 3D structure factor S(k) is fitted to a Gaussian
S(k) = k^... | Paul-St-Young/solid_hydrogen | qmcpack_fs_reader.py | Python | mit | 6,461 | [
"Gaussian",
"QMCPACK"
] | dc4d2a7aae216124f6b85470fd536a1d802ef8f79fecd0c2ad139ce7ac832379 |
# Copyright 2012, Nachi Ueno, NTT MCL, 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
#
# Unles... | bigswitch/neutron | neutron/tests/unit/agent/linux/test_iptables_firewall.py | Python | apache-2.0 | 85,885 | [
"FEFF"
] | edba7db50de50644d6c06fce734373b7888643fdeda773562032e910ae8f9c3e |
from __future__ import print_function
from django.http import HttpResponse
from django.shortcuts import render
from django.views.decorators.csrf import csrf_exempt
import json
import string
import random
import pickle
from time import time
from sys import maxsize
from DBNlogic.nets import DBN, RBM
from DBNlogic.sets ... | ggiuffre/DBNsim | DBNsite/DBNtrain/views.py | Python | mit | 7,977 | [
"NEURON"
] | a77f3812ac786b1ba56db033675129f9664c2e0b45c7c82b177644169019e562 |
#!/usr/bin/env python3
#
# Copyright (C) 2011, 2012, 2014, 2015, 2016, 2017, 2018, 2019, 2020 David Maxwell and Constantine Khroulev
#
# This file is part of PISM.
#
# PISM 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
# ... | pism/pism | examples/python/sia_forward.py | Python | gpl-3.0 | 3,592 | [
"NetCDF"
] | be45a880f32fc9c2dbb0602aed4cb19f9d9b0c039be0422dae085ceeec533074 |
#!/homes/dthybert/software/Python-2.7.5/python
import pysam
import scipy.stats
import sys
import argparse
import math
def Z_score(val, mean,std):
return (float(val)-float(mean))/float(std)
def isGoodRead(read,threshold_pval,dicoStats,bamFile):
if read.alignment.is_reverse ==read.alignment.mate_is_rever... | tk2/assembly-eval | consistent/GetRegionWellAssembled_v20150722.py | Python | mit | 10,308 | [
"pysam"
] | 0fcb318df843b15d5aec6c17a994fb23bd2a311c1a88bac46900d477be156f18 |
from __future__ import print_function
import re
import argparse
import os.path
import io
parser = argparse.ArgumentParser()
parser.add_argument('version', help='file version')
parser.add_argument('outfile', help='outfile with extension .c/.h')
parser.add_argument('inputs', nargs='*', action='store', help='input filena... | joyhope/open62541 | tools/amalgamate.py | Python | lgpl-3.0 | 2,785 | [
"VisIt"
] | 5de490a49ef06a53813a5bf6ca6b846b7d1f7ef460d7132e0945a213ae796c76 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2007 Philippe LAWRENCE
#
# This file is part of pyBar.
# pyBar 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 Licen... | Philippe-Lawrence/pyBar | pyBar.py | Python | gpl-3.0 | 101,841 | [
"FLEUR"
] | 37d3f64d505130fcf0c1eea8779de4cddccae61d59eb45a1da143ab1e8b83bd9 |
# -----------------------------------------------------------------------------
# Download data:
# - Browser:
# http://midas3.kitware.com/midas/folder/10409 => VisibleMale/vm_head_frozenct.mha
# - Terminal
# curl "http://midas3.kitware.com/midas/download?folders=&items=235235" -o vm_head_frozenct.mha
# ----... | Kitware/tonic-data-generator | scripts/vtk/medical/head-ct-volume-step-func.py | Python | bsd-3-clause | 4,130 | [
"VTK"
] | fe87ee6e98f9def48a12a3680fd934996c9fd24a205c66b9083dfa430f33d626 |
# -*- coding: utf-8 -*-
"""
Created on Mon Oct 2 03:58:30 2017
This file contains multiple functions that contribute to userinput
@author: Simon Moe Sørensen, moe.simon@gmail.com
"""
import numpy as np
def inputStr(prompt):
"""
Userinput that only allows strings
INPUT:
prompt: String
OUTPU... | danmark2312/Project-Electricity | functions/userinput.py | Python | gpl-3.0 | 1,617 | [
"MOE"
] | cdedc9389e0d3ec1238e2f94b861f5a11a9e78d2948e5eda54a08bcfacc778d0 |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
QAD Quantum Aided Design plugin ok
classe per la gestione delle quote
-------------------
begin : 2014-02-20
copyright : iiiii
... | gam17/QAD | qad_dim.py | Python | gpl-3.0 | 317,606 | [
"ESPResSo"
] | 544bfa8c12d4cdd58146e60871c0167694e9108251caff8ebd9ce8cf69a2a813 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | wjiangjay/origin | vendor/k8s.io/kubernetes/cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 44,441 | [
"CDK"
] | 11325ca23d9b98fd90e1084556a893527ca13c362b56f27d5a27003fbd0350dd |
# Copyright (C) 2017 Matthew C. Zwier and Lillian T. Chong
#
# This file is part of WESTPA.
#
# WESTPA 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... | ajoshpratt/westpa | lib/west_tools/w_fluxanl.py | Python | gpl-3.0 | 16,409 | [
"Gaussian"
] | 6ea6cf1f9f066a69ed28185ed023cf4179bdf607df3dfb8d5f300b80640703cc |
# This component calculates the humidity ratio from the ladybug weather file import parameters
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <chris@mackeyarchitecture.com>
# Ladybug is free s... | boris-p/ladybug | src/Ladybug_Humidity Ratio Calculator.py | Python | gpl-3.0 | 7,319 | [
"EPW"
] | d557dbe61bafdba770304a17485bd94404750aea2c34be561d7d1623747c2562 |
import datetime
import re
import smtplib
import time
import urllib
from typing import Any, List, Optional, Sequence
from unittest.mock import MagicMock, patch
from urllib.parse import urlencode
import orjson
from django.conf import settings
from django.contrib.auth.views import INTERNAL_RESET_URL_TOKEN
from django.con... | showell/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 203,718 | [
"VisIt"
] | 34a3006bbd83e442b5463749c68f6938a9bfcd31e7e7fb89d126aed6fb4a3716 |
import seaborn # noqa
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
from tqdm import tqdm
from sklearn.preprocessing import MinMaxScaler, Normalizer
num_vecs = 100000
# num_num_dims = 10
# dim_stride = 10
num_radii = 20
num_dims_list = [2, 4, 8, 18, 32, 64, 128] # list(range(0, num_num_dim... | totalgood/nlpia | src/nlpia/book/examples/ch_app_h.py | Python | mit | 3,097 | [
"Gaussian"
] | 6848451543663dee5158a8116d98e3269fb6b2472684cbebc1b85f355dda281c |
from __future__ import absolute_import
import numpy as np
import pandas as pd
import random
import scipy
import copy
from pysurvival import utils
from pysurvival.models import BaseModel
# %matplotlib inline
# List of Survival Distributions
DISTRIBUTIONS = ['Exponential',
'Weibull',
'G... | square/pysurvival | pysurvival/models/simulations.py | Python | apache-2.0 | 16,325 | [
"Gaussian"
] | f512606c14220a18cf830090c751bb5078bdacd5cfb30f8e461383200f844466 |
"""
This script screens genes against a reference database using megaBLAST for every input FASTA file.
Specifically, it takes as input a list of FASTA files and searches every DNA sequence against the reference database. Obviously,
it performs a targeted analysis for input sets of DNA sequences.
For example, you may wa... | wanyuac/BINF_toolkit | screen_genes_blast.py | Python | gpl-3.0 | 4,849 | [
"BLAST"
] | 93d9d2277877969ffaaaa9613ad7c70582fec10d893e0c0b9ee0f977345676fc |
""" pytest for WorkflowTasks
"""
# pylint: disable=protected-access,missing-docstring,invalid-name
from mock import MagicMock
import pytest
from DIRAC.Interfaces.API.Job import Job
# sut
from DIRAC.TransformationSystem.Client.TaskManager import WorkflowTasks
mockTransClient = MagicMock()
mockTransClient.setTaskS... | arrabito/DIRAC | TransformationSystem/Client/test/Test_Client_WorkflowTasks.py | Python | gpl-3.0 | 4,449 | [
"DIRAC"
] | e17d523acdc9e4d40bbcd940ac505a7048d890c6c2d1f1bb7a030250a0091c82 |
# -*- coding: utf-8 -*-
# @Author: Maria Elena Villalobos Ponte
# @Date: 2016-12-14 22:10:04
# @Last Modified by: Maria Elena Villalobos Ponte
# @Last Modified time: 2016-12-15 12:07:46
import rpy2
import rpy2.robjects.numpy2ri
import rpy2.robjects.pandas2ri
import numpy as np
from rpy2.robjects.packages import imp... | mvp291/dsga1005 | code/r_independence.py | Python | apache-2.0 | 1,104 | [
"Gaussian"
] | 28d697ff65e0a67b804d8819b07cb86a1a003f167f6684f27b144a458ecca16e |
##
## Look up application name via package name
##
## 0. Searching app name other metadata by package name
## ex:python LookUPAppName 0 packageName.txt output.csv
## The input file contains app package names which are separated by \n
## com.asus.email
## com.asus.todo
## com.asus.launcher
##
## 1. Searching popular app... | ChengFeiwen/mypython | LookupAppName4.py | Python | apache-2.0 | 5,988 | [
"VisIt"
] | 2277df5d9675ea6928525056060d6f141810b2a23dd7d9d4ac432cee03a7efeb |
# Filename: setup.py
import os
import sys
from os.path import join as pjoin
import pyeda
try:
from setuptools import setup, Extension
except ImportError:
from distutils.core import setup, Extension
NAME = pyeda.__name__
VERSION = pyeda.__version__
AUTHOR = "Chris Drake"
AUTHOR_EMAIL = "cjdrake AT gmail D... | karissa/pyeda | setup.py | Python | bsd-2-clause | 6,351 | [
"ESPResSo"
] | aaaa80db2dbc69b29095300ef6434fe2167f3debadfd4e5a73f735a520e08f6c |
from __future__ import print_function, division
from typing import Union, Optional, List, Iterable, Dict, Any
from collections import defaultdict
from abc import ABCMeta
import copy
import re
import string
import math
import logging
import sys
import numpy as np
from sympy import (MatMul, MatAdd, Basic, MatrixExpr,... | jna29/SymGP | symgp/utils/utils.py | Python | mit | 115,211 | [
"VisIt"
] | 2bf2d1007118aca6cec3dacc7fae4f2120223121537964726b9f953272c39ab7 |
# Copyright (C) 2011-2020 Free Software Foundation, Inc.
# 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.
#
# This progr... | mattstock/binutils-bexkat1 | gdb/system-gdbinit/elinos.py | Python | gpl-2.0 | 3,080 | [
"CDK"
] | 604eaec2fb7fa49e8daa0088dba98b53404d33105dd8e6f5fd82685c51f2ec1c |
""" Base classes for classification """
import numpy
import os
import cPickle
import warnings
import logging
import timeit
# base class
from pySPACE.missions.nodes.base_node import BaseNode
# representation of the linear classification vector
from pySPACE.resources.data_types.feature_vector import FeatureVector
# th... | Crespo911/pyspace | pySPACE/missions/nodes/classification/base.py | Python | gpl-3.0 | 21,922 | [
"Gaussian"
] | 4698ead4933d9cbe9a4a14682ba540258d89781f680957d8526e1fcd4f746829 |
#
# Copyright (c) 2015 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... | vinodpanicker/scancode-toolkit | src/extractcode/uncompress.py | Python | apache-2.0 | 4,180 | [
"VisIt"
] | 4cd64fb5b5d0c3301329e86af837c06227d5fb4ce65730f8605e8100119875b1 |
"""
Copyright 2017 Google Inc.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software
dis... | conversationai/wikidetox | experimental/extract_pov_edits/ingester_test.py | Python | apache-2.0 | 3,644 | [
"TINKER"
] | 3468b5f16fc40e280515f87cf31d517695f3fe13b866ef1d03ce57a38bb25499 |
"""CSShellCmd class emulates the behaviour of a shell to edit the CS config.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
import cmd
import os
from DIRAC.Core.Base.CLI import CLI, colorize
from DIRAC.ConfigurationSystem.Client.Co... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Client/CSShellCLI.py | Python | gpl-3.0 | 7,156 | [
"DIRAC"
] | 57c401c34fdf89cd36b172cdd209557fcdc0e1298adcd2201be78bd0f7333b07 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
import procmemory
def drawVertices(myscreen, weave, vertexType, vertexRadius, vertexColor):
pts = weave.getVertices( vertexType )
print " got ",len(pts)," of type ", vertexType
for p in pts:
myscreen.addActor( camvtk.Sphere... | JohnyEngine/CNC | opencamlib/scripts/fiber/fiber_16_weave2_STL.py | Python | apache-2.0 | 4,845 | [
"VTK"
] | c535739735962c55a2e00ad95bfddb8898d67e7b6c820d3a53a9febfa97eb352 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# textarea - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/cgi-bin/textarea.py | Python | gpl-2.0 | 1,104 | [
"Brian"
] | 3910098bcc138a450e553418ac15c42b7a4ec309431c341ea1e3ba849de6364f |
#!/usr/bin/env python
#
# Electrum - lightweight Bitcoin client
# Copyright (C) 2011 thomasv@gitorious
#
# 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... | thirdkey-solutions/granary | granary/electrum_v1_mnemonic.py | Python | mit | 18,829 | [
"CRYSTAL",
"VisIt"
] | 7f8dd430b4725d34cfbc3dc860e35748e9ec4632333626c5f166f3be3bcf402c |
#!/usr/bin/env python3
# (C) 2016, Markus Wildi, wildi.markus@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
# ... | jstrobl/rts2 | scripts/u_point/u_model.py | Python | lgpl-3.0 | 25,850 | [
"Gaussian",
"VisIt"
] | ae3c81239e7aaf9758dba6e70e86238670edd8db42119d6f0bd5eb7ad24f6a89 |
from basesynapse import BaseSynapse
import numpy as np
import pycuda.gpuarray as garray
from pycuda.tools import dtype_to_ctype
import pycuda.driver as cuda
from pycuda.compiler import SourceModule
cuda_src = """
__global__ void dummy_synapse(
%(type)s *buffer,
int buffer_ld,
int buffer_curr,
int buf... | cerrno/neurokernel | neurokernel/LPU/synapses/DummySynapse.py | Python | bsd-3-clause | 2,755 | [
"NEURON"
] | ea98e27dd5106c81cb906941f13f80532547b6427f0ce4bcbe42eae640b28eec |
from __future__ import print_function
import numpy as np
from ase import Atom, Atoms
from ase.calculators.calculator import Calculator
from ase.optimize import FIRE, BFGS
from ase.data import atomic_numbers
from ase.data.vdw import vdw_radii
class RepulsivePotential(Calculator):
"""Purely repulsive potential (Gau... | grhawk/ASE | tools/ase/utils/voids.py | Python | gpl-2.0 | 3,344 | [
"ASE",
"Gaussian"
] | 9bf8bf50581c534ea3f5c0138b9d3686970080043cbd771337e1063c106998ef |
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