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"""
specs/utils.py
Helper functions for high-level specifications
Contributors: salvador dura@gmail.com
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install... | thekerrlab/netpyne | netpyne/specs/utils.py | Python | mit | 1,785 | [
"NEURON"
] | d9db4967d6e673382b4f02a6b304f9873cbc50caae6b9492c01ea9978061c4a7 |
# -*- coding: utf-8 -*-
#
# Copyright © 2016 Mark Wolf
#
# This file is part of scimap.
#
# Scimap 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 lat... | m3wolf/scimap | scimap/peakfitting.py | Python | gpl-3.0 | 16,766 | [
"Gaussian"
] | 95ab59515f31aadc59fd28449faeee338a5064e11e69b363612f91c64794458b |
import math
import warnings
from operator import itemgetter
import itertools
import numpy as np
from numpy import ma
import matplotlib
import collections
from functools import reduce
rcParams = matplotlib.rcParams
import matplotlib.artist as martist
from matplotlib.artist import allow_rasterization
import matplotli... | alephu5/Soundbyte | environment/lib/python3.3/site-packages/matplotlib/axes.py | Python | gpl-3.0 | 334,618 | [
"Gaussian"
] | 4525c9b233b6eedd71e1e5f2ce596cca078d1cf2d9642ba75a5685f92016a31b |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Final_Comparison_Variable_Length/Force_Motion/hmm_crossvalidation_force_motion.py | Python | mit | 24,480 | [
"Gaussian",
"Mayavi"
] | 58d6a9c11e96271d8a1bbb08b41c28b762f6d80236e229810882e0fa9349ac7c |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('show_repository')
@click.argument("toolShed_id", type=str)
@pass_context
@custom_exception
@json_output
def cli(ctx, toolShed_id):
"""Get details of a given Tool Shed repository... | galaxy-iuc/parsec | parsec/commands/toolShed/show_repository.py | Python | apache-2.0 | 875 | [
"Galaxy"
] | 1c9354f21201b76e06dafdb58db3662b8abc280646c4efd45697640d698a6ad6 |
#!/usr/bin/python2.4
# Copyright (c) 2006-2008 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.
'''Exception types for GRIT.
'''
class Base(Exception):
'''A base exception that uses the class's docstring in addition to a... | meego-tablet-ux/meego-app-browser | tools/grit/grit/exception.py | Python | bsd-3-clause | 3,989 | [
"xTB"
] | b745154d03f47ff0d1f812072db26ce91f5cf2fce508d32df411c4b45a3ce5e9 |
#!/usr/bin/env python
from optparse import OptionParser
import os
import glob
import sfepy
from sfepy.base.base import pause, output, nm
from sfepy.postprocess import Viewer, get_data_ranges, create_file_source
from sfepy.solvers.ts import get_print_info
usage = """%prog [options] filename
This is a script for quick... | olivierverdier/sfepy | postproc.py | Python | bsd-3-clause | 12,479 | [
"Mayavi",
"VTK"
] | 9fa5cfc076b9a3e201a70e8964c2c18677603bc34f4f6862ccad9f5c527b7c93 |
# -*- coding: ascii -*-
# $Id: CNCCanvas.py,v 1.7 2014/10/15 15:04:06 bnv Exp $
#
# Author: vvlachoudis@gmail.com
# Date: 24-Aug-2014
import math
import time
import bmath
try:
from Tkinter import *
import Tkinter
except ImportError:
from tkinter import *
import tkinter as Tkinter
from CNC import Tab, CNC
im... | carlosgs/bCNC | CNCCanvas.py | Python | gpl-2.0 | 70,971 | [
"FLEUR"
] | 6ed21ffe7a7186f3e2982328737e50f9ea58ecbcda827d94ea99ec07fa07d885 |
# -*- coding: utf-8 -*-
# Copyright 2013 Mirantis, 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 requi... | nebril/fuel-web | nailgun/nailgun/rpc/receiver.py | Python | apache-2.0 | 44,251 | [
"VisIt"
] | ad25d62f3b371fe6f4817c9d47dd59ff5b35a3d58afcb3680c67f7cdb39ca83c |
# #############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors: Carlos Xavier Hernandez
#
# MDTraj i... | casawa/mdtraj | mdtraj/tests/test_selection.py | Python | lgpl-2.1 | 10,083 | [
"MDTraj"
] | 283c9278d6ab5323e87a8ba17dd5210adb50d3e6fd04cf4382efbc27b591cab3 |
from .. import Provider as MiscProvider
class Provider(MiscProvider):
"""
Provider for miscellaneous data for en_PH locale
This class also houses all other provider methods that would have otherwise been weird to place in another provider.
"""
gemstone_names = (
"Agate",
"Amber",... | joke2k/faker | faker/providers/misc/en_PH/__init__.py | Python | mit | 4,398 | [
"Amber",
"Galaxy"
] | 9ecc107ea273b488e81e692dff8d8a1caa9e13c5e90b9415afeed201314c16b9 |
# spud - keep track of photos
# Copyright (C) 2008-2013 Brian May
#
# 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.
#
# ... | brianmay/spud | spud/managers.py | Python | gpl-3.0 | 19,791 | [
"Brian"
] | 8203d07c361cdfcec0ee483d7b804dfa646abeee4b810a6440e94e47a16bbabc |
from __future__ import print_function
import h2o
import sys
sys.path.insert(1,"../../../") # allow us to run this standalone
from tests import pyunit_utils
from h2o.estimators.gbm import H2OGradientBoostingEstimator
from h2o.estimators.random_forest import H2ORandomForestEstimator
from h2o.estimators.deeplearning impo... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/stackedensemble/pyunit_stackedensemble_regression.py | Python | apache-2.0 | 7,845 | [
"Gaussian"
] | af5af8248142ba203eceaf002d1c5da47b118294df370dbe7a6f52d7bc7f794d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | julio-menendez/django-rest-angular-project-template | project_name/config/urls.py | Python | mit | 1,086 | [
"VisIt"
] | c6536fc2824d57296401d0b6fb46f3f5be9547b0b5d07afda1188502bf4054db |
#!/usr/bin/env python
from psqlgraph import Node, Edge
from gdcdatamodel import models as md
CACHE_EDGES = {
Node.get_subclass_named(edge.__src_class__): edge
for edge in Edge.get_subclasses()
if 'RelatesToCase' in edge.__name__
}
LEVEL_1_SQL = """
INSERT INTO {cache_edge_table} (src_id, dst_id, _prop... | NCI-GDC/gdcdatamodel | migrations/update_case_cache_append_only.py | Python | apache-2.0 | 5,901 | [
"VisIt"
] | 197dcc76834e16377c6cbbc516abbb0b6f664ccf51723f2c6cb13381211cb675 |
# GetFastQCRawDataFiles/GetFastQCRawDataFiles.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called GetFastQCRawDataFiles
# User admin@galaxy.org at 04/05/2015 11:29:50
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#... | myoshimura080822/tools_of_preanalysis_on_docker_galaxy | GetFastQCRawDataFiles/GetFastQCRawDataFiles.py | Python | mit | 32,557 | [
"Galaxy"
] | 291294b46e9155cd99d4d541181023891d451c49a442e8e9eae540d0cfffa5c4 |
#! /usr/bin/env python
#David Shean
#dshean@gmail.com
#This script uses ASP correlator to produce disparity maps from two inputs
#Input data should be orthorectified/mapped in the same projected coordinate system
#Run disp2v.py to convert to surface velocities
import sys
import os
import argparse
import subprocess
f... | dshean/vmap | vmap/vmap.py | Python | mit | 24,631 | [
"Gaussian"
] | 9e0c16caee08d7a0bab584c79099a00fbb2ea0946fccc6539cb06e8ca8b32676 |
from ...rl import Plant
import warnings
import numpy as np
class CollisionAvoidanceFrontal(Plant):
"""Plant for ePuck to realize collision avoidance. The state
consists of the three frontal infrared sensors. The reward is
negative, if one of the three frontal sensors reads a proximity
lower than ``thet... | igsor/HDPy | HDPy/epuck/plant/plants.py | Python | bsd-3-clause | 6,383 | [
"Gaussian"
] | 1c5bba246519e60bbcac19ea49ec6df8d6d4201d2cec062d5e649559ad47c433 |
# verify.py - verify Mercurial revisions
#
# Copyright 2014 Facebook.
#
# This software may be used and distributed according to the terms
# of the GNU General Public License, incorporated herein by reference.
import stat
from dulwich import diff_tree
from dulwich.objects import S_IFGITLINK, Commit
from edenscm.mercu... | facebookexperimental/eden | eden/hg-server/edenscm/hgext/hggit/verify.py | Python | gpl-2.0 | 3,244 | [
"Octopus"
] | 858c9d2eb4fee53f63abf6462755abb7af5dae6e2af656c329c49d26d8ddd24f |
# -*- coding: utf-8 -*-
"""
Created on Sat Jul 25 16:13:56 2015
@author: ckirst
"""
##############################################################################
# Test Alignment
##############################################################################
import os;
from iDISCO.Parameter import *
from iDISCO.Ru... | ChristophKirst/ClearMap | ClearMap/Test/test_chain_data.py | Python | gpl-3.0 | 21,201 | [
"VTK"
] | 9934be852619a91fe2c18f5e036c72cac7b979c82318d493a60b49f76d0f5c19 |
import pytest
from capybara.node.document import Document
class TestCurrentScope:
@pytest.fixture(autouse=True)
def setup_session(self, session):
session.visit("/with_scope")
def test_returns_the_document_when_outside_of_a_scope(self, session):
assert isinstance(session.current_scope, Do... | elliterate/capybara.py | capybara/tests/session/test_current_scope.py | Python | mit | 765 | [
"VisIt"
] | 647c0f4ce2de3055fb893dcbda896c821ba883c582309a808f67f9e51e885ace |
#!/usr/bin/env python
# Based heavily on the Bowtie 2 data manager wrapper script by Dan Blankenberg
from __future__ import print_function
import argparse
import os
import subprocess
import sys
from json import dumps, loads
DEFAULT_DATA_TABLE_NAME = "kallisto_indexes"
def get_id_name( params, dbkey, fasta_descripti... | mblue9/tools-iuc | data_managers/data_manager_kallisto_index_builder/data_manager/kallisto_index_builder.py | Python | mit | 3,498 | [
"Bowtie"
] | e592dce00207beeda01a284a9e60388ae2bbe5cb550b320249464232b19a8533 |
# -*- coding: utf-8 -*-
from optparse import OptionParser
import sys,os,platform,time,traceback,getpass
from troubleshooting.framework.variable.variable import *
from troubleshooting.framework.modules.builder import BuilderFactory
from troubleshooting.framework.version.version import VERSION
from troubleshooting.frame... | gaoxiaofeng/troubleShooting | src/troubleshooting/framework/running/args.py | Python | apache-2.0 | 11,967 | [
"VisIt"
] | 9b1899cb14994b4eb2cf239f5f0d601875a84acd28f6f01f8c384d3b099d982d |
# -*- coding: utf-8 -*-
__author__ = 'isparks'
import unittest
from rwslib.extras.audit_event import parser
import datetime
class ParserTestCaseBase(unittest.TestCase):
def setUp(self):
class EventReporter(object):
"""Parser that will collect data"""
def __init__(self):
... | Oli76/rwslib | rwslib/extras/audit_event/test_parser.py | Python | mit | 20,407 | [
"VisIt"
] | 359867c112e34e2a0aedb30a64e1d71290810aeafa4121d4b60bffb43117b54c |
#!/usr/bin/env python
"""
Module for target objects. A target carries the physical information
about a target (ra, dec, distance, density profile, etc.) and
interfaces with the `jcalc` module to calculate the l.o.s. integral at
a given sky position. Classes inherit from the `Target` baseclass and
can be created with th... | kadrlica/dmsky | dmsky/targets.py | Python | mit | 26,539 | [
"Galaxy"
] | e8b627aff84d73eb80b20f8834b8ab3a9968779b762046957e85ec0606536b3e |
# -*- 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/awidgets/color_chooser.py | Python | gpl-3.0 | 1,357 | [
"Brian"
] | 3bd25f4ad80c44d6ed7d8b45736d4d50fb5e7334cf05e9c7331ec4449461f72f |
# Copyright 2016 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... | sjperkins/tensorflow | tensorflow/contrib/learn/python/learn/learn_io/graph_io.py | Python | apache-2.0 | 34,466 | [
"VisIt"
] | 31b868c2b28c5cefb52589771029e9e0a7d5891f4a49ba2f4813f5d2a39c09cb |
#/*
# *
# * TuneIn Radio for XBMC.
# *
# * Copyright (C) 2013 Brian Hornsby
# *
# * 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... | sshnaidm/ru | plugin.audio.tuneinradio/resources/lib/tunein.py | Python | gpl-2.0 | 40,322 | [
"Brian"
] | ea97ede82bab89bdcb1dcf690900ffad9f0a50447922d779f286c4944c977422 |
# -*- coding: utf-8 -*-
"""
sphinx.writers.texinfo
~~~~~~~~~~~~~~~~~~~~~~
Custom docutils writer for Texinfo.
:copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
import textwrap
from os import path
import warnings
from six import... | axbaretto/beam | sdks/python/.tox/docs/lib/python2.7/site-packages/sphinx/writers/texinfo.py | Python | apache-2.0 | 47,057 | [
"VisIt"
] | 24745715c56058a7f5b85d7e40ce95aa59621842639c3fef6861c79340dc6b91 |
from os import scandir, strerror
from os.path import join, islink, isdir, dirname, basename
from errno import ENOENT
def walk(top, topdown=True, onerror=None, followlinks=False, skiplinks=False):
onerror = onerror or (lambda err : None)
if isdir(top):
yield from _walk(top, topdown, onerror, followlink... | WHenderson/HashDb | hashdb2/walk.py | Python | apache-2.0 | 4,276 | [
"VisIt"
] | 28efac477c132362223912e8b02db56d16eb617d9423bf11ef45d39d515800bd |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Adjust CCSD DIIS
'''
from pyscf import gto, scf, cc
mol = gto.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = 'ccpvdz')
mf = scf.RHF(mol).run()
#
# Increase the DIIS space to improve convergence
#
mycc = cc.CCSD(mf)
mycc.diis_space = 10
mycc... | gkc1000/pyscf | examples/cc/14-ccsd_diis.py | Python | apache-2.0 | 695 | [
"PySCF"
] | 0f47baf584f4e6ad4bbb4573d11faeff9b51b941c169b2e1b1235b6cb49d77a2 |
################################################################################
# SCFGP: Sparsely Correlated Fourier Features Based Gaussian Process
# Github: https://github.com/MaxInGaussian/SCFGP
# Author: Max W. Y. Lam (maxingaussian@gmail.com)
####################################################################... | MaxInGaussian/SCFGP | experiments/kin8nm/kin8nm.py | Python | bsd-3-clause | 4,991 | [
"Gaussian"
] | e9529bd135cf35107f8481ea57deefb2db715648b04edb12ad2bb3e4c85af804 |
#! /usr/bin/env pvpython
#
#
# usage: ./paraviewpython-example.py alpha_kernel.pvsm [2]
#
# creates jpg: image*.jpg
import os
import sys
import fileinput
import string
from paraview import servermanager
number = ""
## input:
if len(sys.argv) == 2:
filename = str(sys.argv[1])
else :
if len(sys.argv) == 3:
fil... | geodynamics/specfem3d_globe | EXAMPLES/regional_MiddleEast/paraviewpython-example.py | Python | gpl-3.0 | 1,073 | [
"ParaView"
] | 3b7c835685e98d510de3a14e3e20f045f0221d5e3484dc115810502072156006 |
# sql/elements.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Core SQL expression elements, including :class:`.ClauseElement`,
:class:`.ColumnE... | adamwwt/chvac | venv/lib/python2.7/site-packages/sqlalchemy/sql/elements.py | Python | mit | 121,621 | [
"VisIt"
] | faea6f7e7bfb652dbd1b5dda887846e64054a2b7826e2f9abd79fc5d88ac26ac |
import random
import unittest
from SDWLE.agents.basic_agents import PredictableAgent, DoNothingAgent
from testsSDW.agents.testing_agents import OneCardPlayingAgent, EnemySpellTestingAgent, \
CardTestingAgent, EnemyMinionSpellTestingAgent, PlayAndAttackAgent, HeroPowerAndCardPlayingAgent
from SDWLE.constants import... | jomyhuang/sdwle | testsSDW__copy/card_tests/warlock_tests.py | Python | mit | 35,039 | [
"BLAST",
"CRYSTAL"
] | 96e6440dadb43b7c29c92f8f81a6c9d7d7d105b9f98c0e0c899dcba0631c8bab |
"""
A script to automate installation of tool repositories from a Galaxy Tool Shed
into an instance of Galaxy.
Galaxy instance details and the installed tools can be provided in YAML
format in a separate file (see ``tool_list.yaml.sample`` for a sample of
such file) or on the command line as script options (see the us... | natefoo/ansible-tools | files/install_tool_shed_tools.py | Python | mit | 24,377 | [
"Galaxy"
] | ea8b41d8177d40ba6f09513642de596ec43f26fe43d53add353c2c8699bdff8d |
"""
Acceptance tests for Studio related to the container page.
"""
from nose.plugins.attrib import attr
from ..pages.studio.overview import CourseOutlinePage
from ..fixtures.course import XBlockFixtureDesc
from ..pages.studio.component_editor import ComponentEditorView
from ..pages.studio.utils import add_discussion
... | carsongee/edx-platform | common/test/acceptance/tests/test_studio_container.py | Python | agpl-3.0 | 15,557 | [
"VisIt"
] | 9f87717d1a83292fba966c0177104dec3f5d377456c66e7b869eca628955471d |
__author__ = 'dalton'
import random
import items, world
class Player():
def __init__(self):
self.inventory = [items.Gold(15), items.Rock()]
self.hp = 100
self.location_x, self.location_y = world.starting_position
self.victory = False
def is_alive(self):
return self.hp... | dalrrard/text-adventure-tut | adventuretutorial/player.py | Python | mit | 1,803 | [
"Dalton"
] | 14ba8ac107d317dcf2398eea58fba85288e94196546ad387f8cb9e8166e94671 |
#!/usr/bin/env python
__author__ = 'Alexander Ponomarev'
import sys
import re
import os
import subprocess
import tempfile
import pickle
import hashlib
from os import path
from ev import Mutators, Initializators
from optparse import OptionParser, OptionGroup
from pyevolve import G1DList, GSimpleGA, Consts, Selectors
... | lamerman/gatool | gatool.py | Python | bsd-3-clause | 10,765 | [
"Gaussian"
] | a248407f2271d1fbcfcb9b366cb88aeed090274f6feb0f2d48caa2317790522a |
# $Id$
#
# Copyright (C) 2000-2006 greg Landrum
#
# @@ 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.
#
""" Matrix operations which may or may not come ... | rdkit/rdkit-orig | rdkit/ML/MatOps.py | Python | bsd-3-clause | 765 | [
"RDKit"
] | 802f69c06f0be18d9dc02c71da373a6f753c708eb90d04c1d11e7f27db87cbe6 |
import logging
from dirac.lib.base import *
from dirac.lib.credentials import authorizeAction
log = logging.getLogger(__name__)
class ControlController(BaseController):
def index(self):
return render( '/web/environment.mako' )
| DIRACGrid/DIRACWeb | dirac/controllers/web/control.py | Python | gpl-3.0 | 238 | [
"DIRAC"
] | 4243e714bc38d0c2dc7a4219d626e46b577671057a89226d5e288d8eef50b26b |
from __future__ import unicode_literals
import re
import json
import os
from .common import InfoExtractor
from ..compat import (
compat_urlparse,
compat_urllib_parse_urlencode,
compat_urllib_parse_urlparse,
compat_str,
)
from ..utils import (
unified_strdate,
determine_ext,
int_or_none,
... | mxamin/youtube-dl | youtube_dl/extractor/nhl.py | Python | unlicense | 12,601 | [
"Brian"
] | 8db27fa77fbb345d282b3fb1055ec61c62c65d6be613dfd27d15575d7c714da0 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
import tempfile
import shutil
import numpy as np
import pytest
from datetime import datetime
import os
from urllib.parse import urlparse
import re
from unittest.mock import Mock, MagicMock, patch
from astropy import coordinates
from astropy import units a... | ceb8/astroquery | astroquery/alma/tests/test_alma_remote.py | Python | bsd-3-clause | 27,769 | [
"Galaxy"
] | 0d3648bf4bb877524e0872aaf1e866823cd92ce774414cd0b6128a5ba557f369 |
"""
Utilities for ComponentMonitoring features
"""
import datetime
from DIRAC import gConfig
from DIRAC.FrameworkSystem.Client.ComponentMonitoringClient import ComponentMonitoringClient
def monitorInstallation( componentType, system, component, module = None, cpu = None, hostname = None ):
"""
Register the instal... | marcelovilaca/DIRAC | FrameworkSystem/Utilities/MonitoringUtilities.py | Python | gpl-3.0 | 2,662 | [
"DIRAC"
] | 9f1c5de336f6e12b16839da66cd5eabc71dc841fac2c922d7174d20de81eb73d |
from gast.astn import AstToGAst, GAstToAst
import gast
import ast
import sys
class Ast3ToGAst(AstToGAst):
def visit_Name(self, node):
new_node = gast.Name(
self._visit(node.id),
self._visit(node.ctx),
None,
)
return ast.copy_location(new_node, node)
... | ryfeus/lambda-packs | Tensorflow_Pandas_Numpy/source3.6/gast/ast3.py | Python | mit | 6,678 | [
"VisIt"
] | da83432af4ab4ee49aa56ce07983a1210a6303de07de0ca5ce126985a95cde5a |
"""
This is used to test the ElasticSearchDB module. It is used to discover all possible changes of Elasticsearch api.
If you modify the test data, you have to update the test cases...
"""
import unittest
import sys
import datetime
import time
from DIRAC import gLogger
from DIRAC.Core.Utilities.ElasticSearchDB import... | petricm/DIRAC | tests/Integration/Test_ElasticsearchDB.py | Python | gpl-3.0 | 24,568 | [
"DIRAC"
] | 34ecafcdbaadc20a4f280bb1dd9fdfaacff8ef27e83e3da6c79a37c55723e3db |
#!/usr/bin/env python
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "Li... | guozhangwang/kafka | release.py | Python | apache-2.0 | 34,951 | [
"VisIt"
] | 097d1eb5502a920df871afa5eb39a9be825ddbee4bd4124a02db44b29f3d04b4 |
# Portions of this code are adapted from MDTraj and are released under the
# following license.
##############################################################################
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by... | ctk3b/mbuild | mbuild/utils/io.py | Python | mit | 4,343 | [
"Bioconda",
"MDTraj"
] | c536bef3c3e8fbfe5c98d24f4225b3b7c37ea3c0f42d82c224f05b086d693b17 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/lib/sofimport.py | Python | gpl-2.0 | 19,317 | [
"Brian"
] | fd491b40659ebb37281e06ce6372ea94324ca4a735f168f29916f72959add780 |
# Orca
#
# Copyright (C) 2010 Joanmarie Diggs
#
# Author: Joanmarie Diggs <joanied@gnome.org>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/toolkits/WebKitGtk/structural_navigation.py | Python | gpl-3.0 | 2,983 | [
"ORCA"
] | 3da8cb3bb1b08a48948557c8a820f49f0dbc8a004c7dcf0cf637a60d9c675cef |
""" DIRAC FileCatalog component representing a directory tree with simple nodes
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
from DIRAC import S_OK, S_ERROR
from DIRAC.DataManagementSystem.DB.FileCatalogComponents.Direct... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/DirectoryManager/DirectoryNodeTree.py | Python | gpl-3.0 | 5,248 | [
"DIRAC"
] | d52fc1209af17ec83fa5d309ffac8231c3a54243b93589a4f70e7774ea39b816 |
"""
Defines a GenericModule which is a collection of mayavi
filters/components put together. This is very convenient and useful to
create new modules.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from t... | dmsurti/mayavi | mayavi/modules/generic_module.py | Python | bsd-3-clause | 9,695 | [
"Mayavi"
] | c371b7c7fdd5076922303b17afc4d0e986bf4ee24b9e843628c6ed3b727590e9 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors: Tim Moore
#
# MDTraj is free s... | rmcgibbo/mdtraj | mdtraj/geometry/order.py | Python | lgpl-2.1 | 12,587 | [
"MDTraj"
] | f648d97a81f47419e35bb3c509b921fa0bcf8824e45ecfef7d5291281b75157b |
# Authors: Peter Prettenhofer <peter.prettenhofer@gmail.com> (main author)
# Mathieu Blondel (partial_fit support)
#
# License: BSD 3 clause
"""Classification, regression and One-Class SVM using Stochastic Gradient
Descent (SGD).
"""
import numpy as np
import warnings
from abc import ABCMeta, abstractmethod
... | shyamalschandra/scikit-learn | sklearn/linear_model/_stochastic_gradient.py | Python | bsd-3-clause | 83,599 | [
"Gaussian"
] | 05255b0d6159e0a223ba7246ed105d934c8af6a60ae1b5a1d712caf84bd71c9b |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import os
import itertools
from django.core.urlresolvers import reverse, NoReverseMatch
from django.template import TemplateSyntaxError, Context, Template
from django.tes... | szopu/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 65,767 | [
"VisIt"
] | 2251019bc7f2a2c1988d579421dde8386b873f0251fd3e62bcb21ca8b8346dba |
# A Minimal Example of the Neural Engineering Framework
#
# The NEF is a method for building large-scale neural models using realistic
# neurons. It is a neural compiler: you specify the high-level computations
# the model needs to compute, and the properties of the neurons themselves,
# and the NEF determines the ... | printedheart/opennars | nars_gui/src/main/python/nef_minimal/nef_minimal.py | Python | agpl-3.0 | 10,003 | [
"NEURON"
] | 8aba5daee1459a1194b4c76bdba8e3cdc9a035035c8bcada8c2a6f5ca72b1a58 |
# pylint: disable=C0111
from lettuce import world, step
from nose.tools import assert_less
from xmodule.modulestore import Location
from contentstore.utils import get_modulestore
from selenium.webdriver.common.keys import Keys
VIDEO_BUTTONS = {
'CC': '.hide-subtitles',
'volume': '.volume',
'play': '.video... | torchingloom/edx-platform | cms/djangoapps/contentstore/features/video.py | Python | agpl-3.0 | 8,727 | [
"VisIt"
] | e4561a3b349f6d14dfc880d60d4d46fc0261245e667bae141e1ed205a55a4963 |
# Copyright 2016 Brian Innes
#
# 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, ... | brianinnes/vPiP | python/test3.py | Python | apache-2.0 | 1,506 | [
"Brian"
] | b9ab44ac289dbdcb6abccc975976a290b450dde3c2998004adf5738a397318e9 |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and,cint
from frappe import _
from frappe.model.mapper import g... | suyashphadtare/test | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 17,773 | [
"VisIt"
] | fbe4bd0a1a4f28581a4942765f799416bf93d72b6723bd9797fd61eeba2a1010 |
#!/usr/bin/env python
"""
Create a DIRAC RemoveReplica|RemoveFile request to be executed by the RMS
"""
import os
from hashlib import md5
import time
from DIRAC.Core.Base.Script import Script
from DIRAC.Core.Utilities.List import breakListIntoChunks
@Script()
def main():
# Registering arguments will automaticall... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_create_removal_request.py | Python | gpl-3.0 | 3,539 | [
"DIRAC"
] | 976cd920e6ee36bce90d7834020ff898b40a4242335d5dbfe162726af6422d34 |
########################################################################
# $HeadURL$
# File: RequestValidator.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/09/18 07:55:16
########################################################################
""" :mod: RequestValidator
======================
.. mo... | hgiemza/DIRAC | RequestManagementSystem/private/RequestValidator.py | Python | gpl-3.0 | 9,733 | [
"DIRAC"
] | bdce18a14bc440fa85a9cbc4bea61d115add2987028242b4795c1332857aab8c |
import os
from tornado.escape import json_decode
import test.base
import test.factories
from models import User, Sharedfile, Sourcefile, Subscription, Notification, Comment, Shake
import lib.utilities
class AccountTests(test.base.BaseAsyncTestCase):
def setUp(self):
super(AccountTests, self).setUp()
... | spaceninja/mltshp | test/functional/account_tests.py | Python | mpl-2.0 | 4,896 | [
"VisIt"
] | 1465e7ce163949fc0ce73f3a45708f03410b633a5a596164b9ddc605906fbc3b |
import numpy as np
from ase import Atoms
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.visualize import view
from ase.optimize.fire import FIRE as QuasiNewton
from ase.lattice.surface import surface
from ase.lattice.cubic import FaceCenteredCubic
#set the num... | misdoro/python-ase | doc/tutorials/neb/idpp3.py | Python | gpl-2.0 | 2,050 | [
"ASE"
] | 8e684bf221cc701480556014b69bc0bf72f0e456d057c0d612aa5a146ed3521e |
""" DIRAC Graphs package provides tools for creation of various plots to provide
graphical representation of the DIRAC Monitoring and Accounting data
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be added>
"""
from __future__ import print_func... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/Graphs/__init__.py | Python | gpl-3.0 | 6,163 | [
"DIRAC"
] | 84cebbcb88331547ade66ac09290eeab041f79c8e21dab0ac765a05e89f720b4 |
"""
Define a pure lightcurve
"""
from util import *
import numpy as np
import pylab as py
import scipy.ndimage as nd
class PureLightCurve:
"""
This class generate a discret hypothetic quasar light curve. At this time we can generate it by:
1. a random walk
2. a law noise generator
(see the funtion descripti... | COSMOGRAIL/PyCS | pycs/sim/old/PureLightCurve.py | Python | gpl-3.0 | 5,376 | [
"Gaussian"
] | c2abc63e6e030f38dfc9c5171b276d9b601af3d035f8e52aad1c3c9953b82ea2 |
#!/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... | gkc1000/pyscf | pyscf/pbc/scf/addons.py | Python | apache-2.0 | 18,133 | [
"DIRAC",
"Gaussian",
"PySCF",
"VASP"
] | 1b5ac5e95dceec8c982516faacbaac5b862e711937f6cc1a535ea57bedb9c63f |
#
# 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... | yashdsaraf/scancode-toolkit | src/textcode/analysis.py | Python | apache-2.0 | 6,839 | [
"VisIt"
] | 780c05e88bf7702f0432746214f20604fa4140737afe4bea44a1e07802daa42f |
#!/usr/bin/env python
"""
Generate the images and rst files for gallery of SfePy examples.
The following steps need to be made to regenerate the documentation with the
updated example files:
1. remove doc/examples/*::
$ rm -rf doc/examples/*
2. generate the files:
$ ./script/gen_gallery.py
3. regenerate the... | sfepy/sfepy | script/gen_gallery.py | Python | bsd-3-clause | 19,012 | [
"VTK"
] | 88cf87b76086ff0b6ba3768cc630cd50b8d4d70a568287d8ccfc672f302419d4 |
# Config class for use when reading lammps dump files. Basic atom properties
# are stored in list of Atom objects. Statistical analysis is performed on
# whole configuration
# UPDATE 6/01/2014
# Now includes a data object for storing data sets and performing averages,
# variance etc.
from numpy import matrix
from ... | JMuscatello/python-lammps-tools | config_dump.py | Python | gpl-3.0 | 87,825 | [
"LAMMPS"
] | cc230337abf933dd0fcd0936327e0b89f67c2ab97b76d1ff3babdfbaa8945d69 |
"""
DragonPy - Dragon 32 emulator in Python
=======================================
information from:
http://dragon32.info/info/memmap.html - Dragon 32/64 Memory Map (with CoCo refs)
http://dragon32.info/info/romref.html - Dragon 32/64 ROM Reference guide
AUTHOR: Graham E. Kinns
ot... | jedie/DragonPy | dragonpy/Dragon32/mem_info.py | Python | gpl-3.0 | 46,478 | [
"FEFF"
] | 46c2c2204ef3cccf717a351a1f6f4303937ebd70e13dc35ef6f935d95a5f225c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""Module provides some code scaffolding to simplify use of built dictionary for constructing BoW vectors.
Notes
-----
Text corpora usually reside on disk, as text files in one format or another ... | piskvorky/gensim | gensim/corpora/textcorpus.py | Python | lgpl-2.1 | 25,356 | [
"VisIt"
] | 84743292998a3c30d57ee9333a03094030257ff75ac62435066518db57e91154 |
# 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)
import os
class Gromacs(CMakePackage):
"""GROMACS (GROningen MAchine for Chemical Simulations) is a molecular
dy... | LLNL/spack | var/spack/repos/builtin/packages/gromacs/package.py | Python | lgpl-2.1 | 20,761 | [
"Gromacs"
] | 3aa1a09f349236af571ae6889535c34fd74fbb7f997843bcca5e5f08749d6f6e |
import pyspeckit
# load a FITS-compliant spectrum
spec = pyspeckit.Spectrum('10074-190_HCOp.fits')
# The units are originally frequency (check this by printing spec.xarr.units).
# I want to know the velocity. Convert!
# Note that this only works because the reference frequency is set in the header
spec.xarr.convert_t... | jpinedaf/pyspeckit | docs/example_hcop.py | Python | mit | 1,377 | [
"Gaussian"
] | 02531f21db4c828360a76a3821634db4fa2caabfda6bf20628123129dc3407be |
# GromacsWrapper: test_example.py
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
from __future__ import division, absolute_import, print_function
import os.path
import pytest
from numpy.testing import a... | jandom/GromacsWrapper | gromacs/tests/test_setup.py | Python | gpl-3.0 | 1,021 | [
"Gromacs"
] | a34a76286f72f175ac43f455872b1c2ddf64a49ee4d41f00bd5491d497f9dc39 |
# -*- coding: utf-8 -*-
"""
This file contains settings required to make ICs for the dust settling test
of Price & Laibe (2015) (see section 4.4 Dust settling in a protoplanetary disc)
This uses a stretched cubic grid with a gaussian vertical density profile as
a starting point (similar to Price & Laibe's hexagonal gri... | ibackus/testdust | src/examples/settling-ICgen/settings_cubic_grid.py | Python | mit | 1,727 | [
"Gaussian"
] | e67c6dfb2540a72cc0df4e673933bea3b937aeb7dbb11b95a5ae125a5297750b |
"""Top down operator precedence parser.
This is an implementation of Vaughan R. Pratt's
"Top Down Operator Precedence" parser.
(http://dl.acm.org/citation.cfm?doid=512927.512931).
These are some additional resources that help explain the
general idea behind a Pratt parser:
* http://effbot.org/zone/simple-top-down-pa... | lightslife/aliyun-cli | aliyuncli/jmespath/parser.py | Python | apache-2.0 | 18,275 | [
"VisIt"
] | 7fa77b23439c61338d04d65e7dd4c213087ede23434c8605315be1437eb70dc8 |
from __future__ import print_function
import numpy as np
try:
import vtk
from vtk.util.numpy_support import vtk_to_numpy
except:
pass
def calculate_vtk_max_pointwise_difference(file1,file2,tol=1e-6):
arrays = [0]*2
reader = vtk.vtkStructuredPointsReader()
for i, fname in enumerate([file1, file... | lahnerml/espresso | testsuite/python/tests_common.py | Python | gpl-3.0 | 3,027 | [
"VTK"
] | 2159b01b1d3736b6b3580a68a8c72102d5dcf2249668658eda3994c18ec3a2ff |
"""Gaussian processes classification."""
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve
from scipy.optimize import fmin_l_bfgs_b
from scipy.special import erf... | BiaDarkia/scikit-learn | sklearn/gaussian_process/gpc.py | Python | bsd-3-clause | 32,306 | [
"Gaussian"
] | e7e9e23c379fa8be17ca10069150a5a737133b1b1bc8f21ffe896a1658f3f453 |
# (C) British Crown Copyright 2017 - 2018, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | LukeC92/iris | lib/iris/_lazy_data.py | Python | lgpl-3.0 | 7,032 | [
"NetCDF"
] | abaa9de46445d9fa3b7502c1a2901fe74293c5fca15ead440dbf41ee79b52940 |
import os
import sys
import platform
def GetInstallationPaths(echo=False):
path = os.path.dirname(os.path.dirname(__file__))
PYTHONPATH = path
###### MAC ######
if 'darwin' in platform.system().lower():
# MAC OS INSTALL
print('We are assuming you are on Mac OS:')
PV_PLUGIN_PAT... | banesullivan/ParaViewGeophysics | PVGeo/__main__.py | Python | bsd-3-clause | 3,003 | [
"ParaView"
] | 16e9b022d58c9f4bdb993c3cba05436311162e95f66a36d17658a906e0fd697c |
# -*- coding: utf-8 -*-#
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright © 2014, 2019 Dave Hocker
#
# 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 Fo... | dhocker/athomepowerlineserver | disclaimer/Disclaimer.py | Python | gpl-3.0 | 1,292 | [
"xTB"
] | 2e4c96c582382900e7154cee4571474c7672c45531521492f834ae67f9760b6a |
# Naive Bayes
import os
import cv2
import numpy as np
from scipy import stats
def naive_bayes(imgdir, maskdir, outfile, mkplots=False):
"""Naive Bayes training function
Inputs:
imgdir = Path to a directory of original 8-bit RGB images.
maskdir = Path to a directory of binary mask images. Mask imag... | jshoyer/plantcv | plantcv/learn/naive_bayes.py | Python | mit | 8,979 | [
"Gaussian"
] | 9d2ff2a758011a5c2f6d55facf186150f5d5994309a70350752fa14c28474c2a |
# modified mexican hat wavelet test.py
# spectral analysis for RADAR and WRF patterns
import os, shutil
import time
import pickle
import numpy as np
from scipy import signal, ndimage
import matplotlib.pyplot as plt
from armor import defaultParameters as dp
from armor import pattern
from armor import objects4 as ob
... | yaukwankiu/armor | tests/modifiedMexicanHatTest2.py | Python | cc0-1.0 | 4,032 | [
"Gaussian"
] | 71f1debe44067b046ab9896c795f05ef34eb05ea0331bcb1d67f8f13c1b07f05 |
import numpy as np
import paraBEM
from paraBEM.pan2d import vortex_2, vortex_2_v
from paraBEM.vtk_export import VtkWriter
from paraBEM.utils import check_path
source = paraBEM.Vector2(0, 0)
direction = paraBEM.Vector2(1, 0)
n = 20
a = np.linspace(-10, 10, n).tolist()
b = [paraBEM.Vector2(i, j) for i in a for j in a]
... | looooo/paraBEM | examples/vtk/vtk_vortex_2.py | Python | gpl-3.0 | 775 | [
"VTK"
] | 3229259689be853691842dc0d90cd83bb8b06d648261985bc09d31da0d486b55 |
import fnmatch
import os
import posixpath
import re
import sys
from ast import AST, Attribute, iter_fields, Name
if sys.version_info[0] == 3:
string_types = (str,)
else:
string_types = (basestring,) # noqa
IGNORED_DIRS = [
'*.egg-info',
'.bzr',
'.cache',
'.git',
'.hg',
'.idea',
'.... | taedori81/shoop | _misc/sanity_utils.py | Python | agpl-3.0 | 4,901 | [
"VisIt"
] | fe542915d7fb93bf055d5d781af77d2a9e97a51e30884503fb559ecb886bdb52 |
"""
Notes:
- Make possible to bypass the multiple input/output and make it only one input / one output to run faster.
- Check the possibility of using the AER format instead of my own or at least to develop a converter node or a option
where it is possible to choose the format (mine or AER).
- Check the possibility of... | ricardodeazambuja/BrianConnectUDP | brian_multiprocess_udp_using_setitimer.py | Python | cc0-1.0 | 40,474 | [
"Brian",
"NEURON"
] | 79490f8002ad640f760cc35c00326432e4bff91d6b9510c9b8e0c33124c36a0c |
"""
specs/simConfig.py
SimConfig class includes simulation configuration parameters and methods
Contributors: salvadordura@gmail.com
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
# required to make json saving ... | thekerrlab/netpyne | netpyne/specs/simConfig.py | Python | mit | 6,594 | [
"NEURON"
] | ea2234aee9d7a62c5321272e3945563622dbb09f5b31a87284357d3500d3dabe |
#!/usr/bin/env python3
"""
Filter hetero. genotype based on sample minor reads ratio.
Minor-read ratio (MRR), which was defined as the ratio of reads for the less
covered allele (reference or variant allele) over the total number of reads
covering the position at which the variant was called. (Only ap... | wavefancy/BIDMC-PYTHON | Exome/VCFHetroMinorReadsRatioFilter/VCFHetroMinorReadsRatioFilter.py | Python | mit | 4,421 | [
"pysam"
] | 19a27eb92d769fc33ccbbb2d5ed790e2aa5fd412c0a710aa41fd524f39d30c6a |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import sys
import gtk
from dialog import Template
from zeroinstall import _
from zeroinstall.gtkui import help_box
from zeroinstall.injector.model import network_levels
from zeroinstall.injector import trust, gpg
from... | timdiels/0install | zeroinstall/0launch-gui/preferences.py | Python | lgpl-2.1 | 7,715 | [
"VisIt"
] | 49b636e69e99b73ed48eb8172a7b7b5739144beaf8ed51f155f6dd5bc045df10 |
#!/usr/bin/env python
"""
MultiQC is a tool to aggregate bioinformatics results across many samples into a single report. It is written in Python and contains modules for a large number of common bioinformatics tools.
You can install MultiQC from PyPI as follows::
pip install multiqc
Then it's just a case of goi... | ewels/MultiQC | setup.py | Python | gpl-3.0 | 11,730 | [
"HTSeq"
] | 52061ff748224c7818372a493420bd05dbde5933a73e946d7bb3e9017e5fcb4e |
#/*
# *
# * TuneIn Radio for XBMC.
# *
# * Copyright (C) 2013 Brian Hornsby
# *
# * 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... | xmbcrios/riostv | plugin.audio.tuneinradio/resources/lib/tunein.py | Python | gpl-2.0 | 40,339 | [
"Brian"
] | 67e3498469cdf96aad8908ebbf299ce687fdbbfca8a0c82ff25d3d0f8160c1df |
from __future__ import division, absolute_import, print_function
import warnings
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns, assert_no_warnings, assert_array_equal,
assert_array_almost_equal, suppress_warnings)
f... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/numpy/random/tests/test_random.py | Python | mit | 64,445 | [
"Gaussian"
] | 3124d05f0c876d2f671941e5d1f25b4b74d44085760b481ac3ec0413f75ab2d9 |
import sys
import os
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
import matplotlib.path as mpath
import matplotlib.patches as mpatches
import pdb
import imp
from scipy.io import netcdf
import glob
import datetime
import socket
import urllib
sys.path.append('../swig/')
import forefire
... | forefireAPI/firefront | test/simpleExample_HeatFluxFromobsModel.py | Python | gpl-2.0 | 4,098 | [
"NetCDF"
] | 6ae3b7a6b0c0a7f4a75e2f34e9d9113e36aa01796c9bb6b877f37ae74b4b80c9 |
# -*- coding: utf8 -*-
import os.path
import os
import numpy as np
import copy
import PDielec.Calculator as Calculator
from PyQt5.QtWidgets import QPushButton, QWidget
from PyQt5.QtWidgets import QComboBox, QLabel, QLineEdit, QListWidget
from PyQt5.QtWidgets import QApplication
from PyQ... | JohnKendrick/PDielec | PDielec/GUI/SingleCrystalScenarioTab.py | Python | mit | 28,480 | [
"CRYSTAL"
] | 43dd024cdca258644763965c84b1dbb545ef6f103b0e7c1314a2a520bdba75c3 |
# porcelain.py -- Porcelain-like layer on top of Dulwich
# Copyright (C) 2013 Jelmer Vernooij <jelmer@jelmer.uk>
#
# Dulwich is dual-licensed under the Apache License, Version 2.0 and the GNU
# General Public License as public by the Free Software Foundation; version 2.0
# or (at your option) any later version. You can... | sonntagsgesicht/regtest | .aux/venv/lib/python3.9/site-packages/dulwich/porcelain.py | Python | apache-2.0 | 57,662 | [
"VisIt"
] | bd87088d70890ad58498ed8be23292b232e08198e9a92186df63901518f9ba2e |
import os, sys
lib_path = os.path.abspath('../../helpers')
sys.path.append(lib_path)
lib_path = os.path.abspath('../')
sys.path.append(lib_path)
import math
import MetalicsSolver
import random
import copy
import json
from NanoClass import genParticle
from ase.md.nvtberendsen import NVTBerendsen
from ase.md.... | JConwayAWT/PGSS14CC | lib/python/multimetallics/solvers/SimulatedAnnealingNanoparticles.py | Python | gpl-2.0 | 3,318 | [
"ASE"
] | 449b07ed08f31f2784b8764926ce105f3e61cabe4afce2e7ea1e902e90f72abf |
import unittest
from noaaclass import noaaclass
from datetime import datetime
import time
class TestGvarimg(unittest.TestCase):
def remove_all_in_server(self):
sub_data = self.noaa.subscribe.gvar_img.get()
ids = [d['id'] for d in sub_data if '[auto]' in d['name']]
if len(ids):
... | scottlittle/noaaclass | tests/gvarimg_test.py | Python | mit | 6,608 | [
"NetCDF"
] | 197179a5f3ade636ca9ca54b3c4947b9e51c94e8e0dd7d622c8e9991fdc0ea9f |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/qcdb/libmintsgshell.py | Python | lgpl-3.0 | 15,031 | [
"GAMESS",
"Psi4"
] | 787d89e4d5ffd6c3da0483042892864e209a40dd5379360e80290955089ba6c3 |
import numpy as np
from perceptron import Perceptron
class Adaline(Perceptron):
"""
Implementation of an Adaptive Linear Neuron, that can be abstracted to
various input sizes or dimensions. Displays using pyplot.
"""
ETA = 1
def __init__(self, grph, eta, max_t):
Perceptron.__init__(se... | cbporch/perceptron | adaline.py | Python | mit | 1,193 | [
"NEURON"
] | eb28653c043f6e4a2e90d5596745efd3f11dcd167c49409cda3e23b636bf951b |
########################################################################
# $HeadURL $
# File: PhysicalRemoval.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 11:56:10
########################################################################
""" :mod: PhysicalRemoval
=====================
.. modul... | vmendez/DIRAC | DataManagementSystem/Agent/RequestOperations/PhysicalRemoval.py | Python | gpl-3.0 | 6,584 | [
"DIRAC"
] | 37a1fe662942b9d7eebeb597e006b091699da3ad62c68c23a1359943761b3d71 |
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