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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Thurs Oct 05 07:36:55 2017
@author: michellemorales
"""
#!/usr/bin/python
import sys
import os
from Tkinter import *
import FeatureExtract
import json
import tkMessageBox
def run():
global pars
ibm_pass = str(pars["IBM_PASSWORD"])
ibm_un = s... | michellemorales/OpenMM | scripts/gui.py | Python | gpl-2.0 | 1,276 | [
"OpenMM"
] | 2b19a722b86547f27301d0865e3cdbd3e91b571a09196c29c6d21e35fc03e971 |
#!/usr/bin/env python
# pylint: disable-msg=C0103
##***** BEGIN LICENSE BLOCK *****
##Version: MPL 1.1
##
##The contents of this file are subject to the Mozilla Public License Version
##1.1 (the "License"); you may not use this file except in compliance with
##the License. You may obtain a copy of the License at
##htt... | mpetyx/pychatbot | SemanticWebApproach/RoboWriter/allegrordf-1.0.1/franz/openrdf/query/commonlogic.py | Python | apache-2.0 | 112,429 | [
"VisIt"
] | 027955197838351ef091f7137818c9c0e59600ab882aa1e54071c82e132273d3 |
import imp
import os
import marshal
import struct
import sys
from cStringIO import StringIO
is_jython = sys.platform.startswith('java')
from compiler import ast, parse, walk, syntax
from compiler import misc, future, symbols
from compiler.consts import SC_LOCAL, SC_GLOBAL, SC_FREE, SC_CELL
from compiler.consts import ... | zephyrplugins/zephyr | zephyr.plugin.jython/jython2.5.2rc3/Lib/compiler/pycodegen.py | Python | epl-1.0 | 47,446 | [
"VisIt"
] | 08bca6776c4826af946b640750f15cba125b9813757f0ad1bcbe66f492b33cd6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | qrkourier/ansible | lib/ansible/modules/network/lenovo/cnos_conditional_command.py | Python | gpl-3.0 | 7,085 | [
"VisIt"
] | f5faccbc26f513f4f9ff300c539587aa0bb49ed766befb4db95538f6205116a0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
"""
Error handlers for errors originating from the Submission systems.
"""
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/abinit/scheduler_error_parsers.py | Python | mit | 13,858 | [
"pymatgen"
] | 988bd3b11d330b08727b69dde1f5cfa2cdbd2d0bb06bce7d5eba00668f472752 |
#!/usr/bin/env python
# ----------------------------------------------------------------------
# Copyright (C) 2014-2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you ca... | BoltzmannBrain/NAB | run.py | Python | agpl-3.0 | 7,503 | [
"Gaussian"
] | 43a16ae95613bbb66dbb2e47a00246bbdba5a7465f7b952eae2fb032a24de27c |
#pylint: disable=invalid-name
# File: ReduceSCD_Parallel.py
#
# Version 2.0, modified to work with Mantid's new python interface.
#
# This script will run multiple instances of the script ReduceSCD_OneRun.py
# in parallel, using either local processes or a slurm partition. After
# using the ReduceSCD_OneRun script to... | dymkowsk/mantid | scripts/SCD_Reduction/ReduceSCD_Parallel.py | Python | gpl-3.0 | 14,307 | [
"CRYSTAL"
] | 94ffcf307dc69af4bca0a2ca80ebec7447936bc5f7672b01d0d9e60a5bcbba75 |
""" Example showing how to pick data on a surface, going all the way back
to the index in the numpy arrays.
In this example, two views of the same data are shown. One with the data
on a sphere, the other with the data flat.
We use the 'on_mouse_pick' method of the scene to register a callback on
clicking on the spher... | dmsurti/mayavi | examples/mayavi/data_interaction/pick_on_surface.py | Python | bsd-3-clause | 2,477 | [
"Mayavi",
"VTK"
] | 2f818efa284ca289bd2f7f4e7d5eaaec6c287392eb75302112a624ee53ab1561 |
#! python
'''Hangman'''
import random, string
HANGMANPICS = ['''
+---+
|
|
|
|
|
==========''', '''
+---+
| |
|
|
|
|
==========''', '''
+---+
| |
O |
|
|
|
==========''', ''... | deshmukhmayur/python-projects | hangman.py | Python | gpl-3.0 | 4,501 | [
"MOOSE"
] | c0507c7f5ab4899422835d154b735b586c81ffb1f1e04d84e029283d341274c3 |
#!/usr/bin/env python
"""
Functions for data IO for neural network training.
"""
from __future__ import print_function
import argparse
import sys
import os
import time
from operator import add
import math
import numpy as np
from scipy.io import netcdf
import theano
import theano.tensor as T
import lasagne
theano.c... | vanessajurtz/lasagne4bio | peptide_MHCII/scripts/data_io_func.py | Python | gpl-3.0 | 47,255 | [
"NetCDF"
] | 98f0b855d0d0f5e3b63f6038c268f440ec1da2c9a90c6a2c5fe484614659e6f1 |
# rall64_graphic.py ---
#
# Filename: rall64_graphic.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Thu May 29 13:18:12 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
... | BhallaLab/moose-examples | rall_1964/rall64_graphic.py | Python | gpl-2.0 | 4,690 | [
"MOOSE"
] | f63ab7fe880fbe67985e9ca48c5a417bfcbb5afb0cd6bdaad516ed980b2ced72 |
# -*- coding: utf-8 -*-
"""features for collecting abstract protocol costs"""
from ast import *
from tasty.tastyc import bases
from tasty.tastyc.bases import (CALL_TYPE_CTOR, CALL_TYPE_CONVERSION, CALL_TYPE_METHOD,
CALL_TYPE_TASTY_FUNC_CTOR, CALL_TYPE_TASTY_FUNC_CALL)
from tasty.types... | tastyproject/tasty | tasty/tastyc/analyze_costs.py | Python | gpl-3.0 | 8,274 | [
"VisIt"
] | a72cfa5d51543b9ab5554420a623988eb0e6ccf54b617df71e4c522f51e289bf |
from db_functions.compute_field_summaries import computeNeuronEphysSummariesAll, computeEphysPropSummaries, \
computeEphysPropValueSummaries, computeNeuronSummaries, computeArticleSummaries, assign_stat_object_to_data_tables
__author__ = 'stripathy'
def update_summary_fields():
"""Updates database summary f... | neuroelectro/neuroelectro_org | scripts/update_db_summary_fields.py | Python | gpl-2.0 | 723 | [
"NEURON"
] | d2b3c0186adf9ba37917914bcbab89fbb5e953f6e3af12590e2ae0e2bbdfa56f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import json
import warnings
from pymatgen.electronic_structure.bandstructure import BandStructure
from pymatgen.electronic_structure.boltztrap import BoltztrapAnalyzer, \
Boltztra... | mbkumar/pymatgen | pymatgen/electronic_structure/tests/test_boltztrap.py | Python | mit | 16,990 | [
"ASE",
"BoltzTrap",
"pymatgen"
] | 5fbc6de29d3e81feda6d98ee60f78a1d755f72751df1ebf8ab70cdc682a49704 |
import itertools
import logging
import re
import time
import urllib
from collections import defaultdict
from datetime import datetime, timedelta, timezone
from decimal import Decimal
from typing import Any, Callable, Dict, List, Optional, Sequence, Set, Tuple, Type, Union
import pytz
from django.conf import settings
f... | brainwane/zulip | analytics/views.py | Python | apache-2.0 | 56,863 | [
"VisIt"
] | 3af7b35da34ca1c1e15e86a2021914c227d025d8e3b9f56b4319c0a98f94e7fa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes representing non-periodic and periodic sites.
"""
import collections
import numpy as np
from monty.json import MSONable
from monty.dev import deprecated
from pymatgen.core.lat... | tschaume/pymatgen | pymatgen/core/sites.py | Python | mit | 21,743 | [
"pymatgen"
] | 08b3656f7b612b46e673d092f8f3b520a7704948bb6aadc6a82704e007cacfd4 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/MooseDocs/test/commands/test_generate.py | Python | lgpl-2.1 | 2,292 | [
"MOOSE"
] | 57807bc1c3aaf2eec32438c25f39d2065ac4b9b2124c859eddc5d4d3bb221728 |
# -*- coding: utf-8 -*-
from typing import Tuple, Dict, Set
from pyramids import trees
from pyramids.categorization import Property, Category
from pyramids.rules import branch
TraversableElement = 'Union[trees.Parse, trees.ParseTree, trees.TreeNodeInterface]'
class LanguageContentHandler:
"""A content handler ... | hosford42/pyramids | pyramids/traversal.py | Python | mit | 8,556 | [
"VisIt"
] | 1075001793cfe1f57ca63e2344ee40b653bdc178c184b553404a4ca8c157e327 |
# (C) British Crown Copyright 2010 - 2016, 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... | jswanljung/iris | lib/iris/util.py | Python | lgpl-3.0 | 54,362 | [
"NetCDF"
] | 9ba19bac1495c09995e7a46ca16cbfc4d6f1e3ea9954fcd8a8787ee02097522c |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free ... | supertom/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 32,096 | [
"Galaxy"
] | 05a18f843b7eee8cdcbf1b3bcb84aaec507b93b6a9019d961913ca06263f4f99 |
"""setuptools.command.bdist_egg
Build .egg distributions"""
from distutils.errors import DistutilsSetupError
from distutils.dir_util import remove_tree, mkpath
from distutils import log
from types import CodeType
import sys
import os
import textwrap
import marshal
from setuptools.extern import six
from pkg_resource... | wildchildyn/autism-website | yanni_env/lib/python3.6/site-packages/setuptools/command/bdist_egg.py | Python | gpl-3.0 | 17,178 | [
"VisIt"
] | 5c36a6bbaf9c7f262ba9debb606439816a3ed1cf24b96aa43f2d6f6297ec031c |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Tests for online Entrez access.
This file include tests for accessing the online Entre... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Entrez_online.py | Python | gpl-2.0 | 6,875 | [
"Biopython"
] | 71dd85b69b3716fdbaa78875071574a30caca57360db911e27b97f9d05616e80 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/custom/lib/customxmlhandler.py | Python | gpl-2.0 | 6,009 | [
"Brian"
] | b490f90e75270b4a2ae71b4eb499f9b79d5981e20d4430bb461c60f8d51d9f3d |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | iemejia/incubator-beam | sdks/python/apache_beam/runners/interactive/pipeline_fragment.py | Python | apache-2.0 | 9,582 | [
"VisIt"
] | d3b3420877ca913d2f7d29afa55cc76d9ff8c8a5e4951d68179217359c067251 |
from data.Element import Element
from data import Msg
class Test(Element):
"""description of class"""
def __init__(self, path, name, depth=0, parent=''):
super().__init__(path, name, depth, parent)
self.diffs = {}
self.empty_files = []
def accept(self, visitor):
visitor.... | Sildra/PyTester | PyTester/data/Test.py | Python | apache-2.0 | 471 | [
"VisIt"
] | beac9b80bfccfcded2f997899ae05681c77921cd52bff7def3b315658cd2ae83 |
#===============================================================================
#
# OpenMPTemplates.py
#
# This file is part of ANNarchy.
#
# Copyright (C) 2016-2021 Julien Vitay <julien.vitay@gmail.com>,
# Helge Uelo Dinkelbach <helge.dinkelbach@gmail.com>
#
# This program is free software: you c... | vitay/ANNarchy | ANNarchy/generator/Population/OpenMPTemplates.py | Python | gpl-2.0 | 14,627 | [
"NEURON"
] | 7f66951b5ed5ddd2033b4891a74afb59ff5f1ff2d51f80c805445b3302b87d91 |
#!/usr/bin/env python
import fileinput
import sys
import os
import re
import math
import json
import numpy as np
import subprocess
from optparse import OptionParser
# These kernels have guaranteed correct Jacobians
whitelisted_kernels = ['Diffusion', 'TimeDerivative']
# regular expressions to parse the PETSc debug... | mellis13/moose | python/jacobiandebug/analyzejacobian.py | Python | lgpl-2.1 | 12,108 | [
"MOOSE"
] | 4932c04e08beb89c3ba08478369ad6ecd5b80c526f5bffde1b86b999e6f10c99 |
from __future__ import absolute_import
from __future__ import print_function
from six import iteritems
from builtins import range
import os
import re
from glob import glob
from os import path
import numpy as np
from netCDF4 import Dataset
from pyproj import Proj
from pyproj import transform
from shyft import api
from... | felixmatt/shyft | shyft/repository/netcdf/arome_data_repository.py | Python | lgpl-3.0 | 24,389 | [
"NetCDF"
] | aa7383f5aa715ba8a0b29084b1c855715b7c80ae422e255410ad0884deb6f7cc |
#!/usr/bin/env python2
"""
rdio-history-csv.py
~~~~~~~~~~~~~~~~~~~
Simple script for parsing the output of
https://www.rdio.com/api/1/getHistoryForUser
The way I made this happen was:
#. login to rdio.com in chrome,
#. visit https://www.rdio.com/people/tylercipriani/history/ with devtools
open
#.... | thcipriani/rdio-shit | bin/rdio-history-csv.py | Python | gpl-2.0 | 1,498 | [
"VisIt"
] | c0840e61091ae016da0b8f8640dcf27ae79fe58314bd388473c68beb6c773f3a |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import uuid
class Migration(migrations.Migration):
dependencies = [
('visit', '0061_visit_insights'),
]
operations = [
migrations.CreateModel(
name='RequestedService',
... | koebbe/homeworks | visit/migrations/0062_auto_20150816_0035.py | Python | mit | 1,319 | [
"VisIt"
] | 38fafce789a353eb5fe17adc3da2c3db9848746eacc2776c2435407a676f5d63 |
# ======================================================================
#
# Cosmograil: cosmograil.tools.sextractor
#
# sextractor module.
#
# Author: Laurent Le Guillou <laurentl@ster.kuleuven.ac.be>
#
# $Id: sextractor.py,v 1.2 2005/07/06 21:40:43 hack Exp $
#
# ======================================================... | wschoenell/chimera_imported_googlecode | src/chimera/util/sextractor.py | Python | gpl-2.0 | 18,823 | [
"Galaxy"
] | da19b911f71e4f4bde6c01ba36ed66e90e46beea4dbcd131341f7b036758f16f |
# -*- coding: utf-8 -*-
import sys
sys.path.append('../')
from browser_interface.queue.QueueFactory import QueueFactory
from browser_interface.field.FieldFactory import FieldFactory
from browser_interface.browser.BrowserFactory import BrowserFactory
from browser_interface.log.Logging import Logging
from common import ... | xtuyaowu/jtyd_python_spider | feng_huang_net/fh_producer.py | Python | mit | 2,301 | [
"VisIt"
] | 313784242de981eb65a9e9e1d1859558b4b5f92b65cb51624c87b31bc60af7fd |
#!/usr/bin/env python
"""
Runs checkTransformationIntegrity from ValidateOutputDataAgent on selected Tranformation
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
__RCSID__ = "$Id$"
import sys
from DIRAC.Core.Utilities.DIRACScript import DIRACScript a... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/scripts/dirac_transformation_verify_outputdata.py | Python | gpl-3.0 | 1,147 | [
"DIRAC"
] | 5ec6e290054c052f11a92203a118d42b40d19615041792113d1832341e5d7a05 |
from math import sqrt
from ase import Atoms, Atom
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import BFGS, QuasiNewton
from ase.neb import NEB
# Distance between Cu atoms on a (111) surface:
a = 3.6
d = a / sqrt(2)
fcc111 = Atoms(symbols='Cu',
cell=[(d, 0, ... | JConwayAWT/PGSS14CC | lib/python/multimetallics/ase/test/COCu111.py | Python | gpl-2.0 | 2,010 | [
"ASE"
] | 5053dc55d13d046b38b5f1d559d226a41e22b3266220d688b2e8f62715309f52 |
#!/usr/bin/env python
from __future__ import absolute_import, print_function, division
import functools
import numpy as np
import matplotlib.pylab as plt
from scipy.optimize import curve_fit
import lsst.daf.persistence as dp
import lsst.afw.image as afw_image
from lsst.afw.fits.fitsLib import FitsError
from desc.twinkl... | LSSTDESC/Twinkles | bin/plot_point_mags.py | Python | mit | 6,238 | [
"VisIt"
] | 54b7cf61bce4596f6ae1eb502dbcd15b8697dc84676704c323c056a0ca0084ad |
# Orca
#
# Copyright 2010 Joanmarie Diggs.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library i... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/Thunderbird/script_utilities.py | Python | gpl-3.0 | 4,077 | [
"ORCA"
] | 8f06f6d6f6016af4b5fa73e8f77d8cf8fe1f455a5ed743aff917d71cd99d6840 |
# Created on 09/18/11 14:14:57
from math import *
from random import *
from UnitCommands import *
def CreateScenario(SM):
SM.SetScenarioDescription("""Backfires and Condors\nVersion 2.0 of 2010/06/24\n\nA scenario for Global Conflicts 2.\n\nWritten by Ralf Koelbach.\nrkoelbach@yahoo.com\n\nBackfires and Condors i... | gcblue/gcblue | scenarios/SinglePlayer/ColdWar/Backfires.py | Python | bsd-3-clause | 149,535 | [
"COLUMBUS"
] | 1bfa7b6f9ccc86e28d1b79f186ccda87eda7f4ee1081eb8bb2c502a03187fdf6 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/flat_review.py | Python | gpl-3.0 | 76,473 | [
"ORCA"
] | d23d6bd1eec573c2ed990fd8a9b696544183b6a47a02bb1f26c90f1e9abb0d70 |
import numpy as np
import scipy as sp
from scipy.optimize import minimize
from abc import ABC, abstractmethod
###################
#Gaussian processes
###################
class GP(ABC):
'''
General class to hold parameters common to both GPR and GPC.
'''
def __init__(self,kernel):
self.kernel =... | mark-r-anderson/GaussianProcesses | GPs/GP.py | Python | mit | 18,385 | [
"Gaussian"
] | bff0afc6adec19fb26dda44a48c878951bd2cd1d91be275b55ffe78f300d8ac1 |
import pandas as pd
import nmrpystar
import mdtraj as md
stride = 100
t0 = md.load(["./Trajectories_ff99sbnmr/1am7_%d.dcd" % i for i in range(10)], top="./1am7_fixed.pdb")[::stride]
t1 = md.load(["./Trajectories/1am7_%d.dcd" % i for i in range(15)], top="./1am7_fixed.pdb")[::stride]
#full_prediction0 = md.nmr.chemi... | choderalab/open-forcefield-group | nmr/code/compare_shifts_compare_forcefields.py | Python | gpl-2.0 | 1,878 | [
"MDTraj"
] | 5dff9a606c471b402c8c0b5ca1aee3aef5a1e864a2af5eb8b1282e459281160b |
# Copyright 2007-2010 by Peter Cock. All rights reserved.
# Revisions copyright 2010 by Uri Laserson. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# This code is NOT intend... | LyonsLab/coge | bin/last_wrapper/Bio/GenBank/Scanner.py | Python | bsd-2-clause | 81,886 | [
"Biopython"
] | 60f370071cf85ad73243ba8516f71e33acba3beba06af12bc43850bab03de6c2 |
import numpy
from Bio import Phylo
from sys import argv
def to_adjacency_matrix(tree):
"""Create an adjacency matrix (NumPy array) from clades/branches in tree.
Also returns a list of all clades in tree ("all_clades"), where the position
of each clade in the list corresponds to a row and column of the n... | YnkDK/AiBToS-Project2 | bin/parser3.py | Python | mit | 2,222 | [
"Biopython"
] | fc2f655ce3c6c24cdf561fa06f555f517e931bc51ab8408871480eb7ff8cfa56 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.community.HPBladeChassis | ZenPacks/community/HPBladeChassis/parsers/HPBladeChassis/BladeStatus.py | Python | gpl-2.0 | 1,759 | [
"VisIt"
] | fd41911c659ad8788a850513c987beba4923d609a9c18fd5b9ab1bc71fa6a4d6 |
#!/usr/bin/env python
import argparse
from Bio import AlignIO
# A simple converter from Nexus to Phylip format using BioPython.
# Matt Gitzendanner
# University of Florida
parser = argparse.ArgumentParser()
parser.add_argument("-i", help="input file")
parser.add_argument("-o", help="output file")
args = parser.pars... | Cactusolo/ToolBox | nex_to_phy.py | Python | mit | 612 | [
"Biopython"
] | 750e58fcfcef259728000e26ad638941ea07c0653a23205bea6204f60eec496f |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of t... | mozts2005/OuterSpace | server/lib/ige/ospace/ISystem.py | Python | gpl-2.0 | 44,480 | [
"Galaxy"
] | f3dbf6c20c85bddec5fd1fc9fb2064c1ec5a186b004033144f546460897df615 |
# Jython Database Specification API 2.0
#
# $Id: zxtest.py 2281 2003-04-10 20:17:43Z bzimmer $
#
# Copyright (c) 2001 brian zimmer <bzimmer@ziclix.com>
from com.ziclix.python.sql import zxJDBC
from java.util import Calendar, Date as JDate
import tempfile, os, time, runner
class zxCoreTestCase(runner.SQL... | DarioGT/OMS-PluginXML | org.modelsphere.sms/lib/jython-2.2.1/Lib/test/zxjdbc/zxtest.py | Python | gpl-3.0 | 39,389 | [
"Brian"
] | f3171f74354b4433cd1e19edaa67065e53aba19d53534929b9b179ab2a39d05e |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 1000
n = 2000
testMehrotra = True
testIPF... | birm/Elemental | examples/interface/QPDirectDense.py | Python | bsd-3-clause | 3,319 | [
"Gaussian"
] | 0c80223de5b062bb9b61bdea9ee60395a7d8e522dc2294eb32c3af8be888aba7 |
from math import sqrt, pi, sin
import random
import numpy
import matplotlib.pyplot as plt
neurons = 10
acceptable_error = .0001 #stops updating if the average squared error is less than this
max_iter = 100000 #stops updating if this number of iterations is reached
updates = 5 #number of times to calculate the average ... | bbartoldson/examples | hacker_ANN/net.py | Python | mit | 2,364 | [
"NEURON"
] | b52a6f8b38f5cb0d6ee5117d36285bc28a2c45ce81022087fccb2d4d1185885a |
from compiler import *
ui_strings = [
("music_volume", "Music Volume:"),
("sound_volume", "Sound Volume:"),
("mouse_sensitivity", "Mouse Sensitivity:"),
("invert_mouse_y_axis", "Invert Mouse Y Axis"),
("enabled", "Enabled"),
("disabled", "Disabled"),
("damage_to_player", "Damage to Player:... | Sw4T/Warband-Development | mb_warband_module_system_1166/Module_system 1.166/DISABLED_module_ui_strings.py | Python | mit | 37,731 | [
"VisIt"
] | e257908a46c297d917d57639eebaad1ac86faaa3f5001707faa4190f9f770a30 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | beernarrd/gramps | gramps/plugins/textreport/ancestorreport.py | Python | gpl-2.0 | 14,185 | [
"Brian"
] | 6fa8f657406eeedcac70a08807d28e3660271cf80701e8818755a77a70648337 |
# Copyright (C) 2009-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library ... | FedoraScientific/salome-hexablock | doc/pyplots/test_make_elmts_transform.py | Python | lgpl-2.1 | 1,689 | [
"VTK"
] | ff366e630e9d32bd5e8c6f685c9c185e2183d09598c7969fd0aa7bf70907f8c2 |
#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# simple.py
# Purpose: mimic operation of examples/COUPLE/simple/simple.cpp via Python
# Serial syntax: simple.py in.lammps
# in.lammps = LAMMPS input script
# Parallel syntax: mpirun -np 4 simple.py in.lammps
# ... | aurix/lammps-induced-dipole-polarization-pair-style | python/examples/simple.py | Python | gpl-2.0 | 2,238 | [
"LAMMPS"
] | ad4085a65866936331e6e7d3c6642443946ab809f4d8003f7c4b83797fffdcf0 |
# coding=utf-8
from __future__ import unicode_literals
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_nam... | Nebucatnetzer/tamagotchi | pygame/lib/python3.4/site-packages/faker/providers/person/dk_DK/__init__.py | Python | gpl-2.0 | 7,622 | [
"Brian"
] | 4f824e04d88b16be46a926c03aacd7571b692f068de2449100b9a191acdfbdd9 |
################################################################################
# Copyright (c) 2014, Lee-Ping Wang and the Authors
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# 1. Redistrib... | rmcgibbo/qchem-utils | qchem_utils/qchem.py | Python | gpl-2.0 | 40,007 | [
"Gaussian",
"Q-Chem"
] | 393c1de26b51fc8c0288e3d487cd6de87cd032b8e5e9fde1124c519abb9f14ed |
#!/usr/bin/env python
# encoding: utf-8
import os
import sys
import itk
from possum import pos_itk_core
from possum import pos_itk_transforms
from possum.pos_common import r
"""
.. note::
Some of the non-cruical, optional functions in this module require vtk
module to be installed. If it is not available t... | pmajka/poSSum | possum/utils/pos_util_midpoints.py | Python | mit | 12,120 | [
"VTK"
] | a86a98520d4606232da945d1addd9283964184ad390161ba12fad74d5682df2b |
import numpy as np
from ase.lattice import bulk
from ase.dft.kpoints import monkhorst_pack
from ase.parallel import paropen
from gpaw import GPAW, PW
from gpaw.mpi import size, rank, world, serial_comm
from gpaw.xc.tools import vxc
from gpaw.xc.hybridg import HybridXC
mgo = bulk('MgO', 'rocksalt', a=4.189)
if rank <... | robwarm/gpaw-symm | gpaw/test/pw/mgo_hybrids.py | Python | gpl-3.0 | 2,057 | [
"ASE",
"GPAW"
] | 7e2910e3519115f6443f2ba8eff9071d74f11fe4523bd236d44973e0de760781 |
"""Tests for the DIRAC.Core.Utilities.Extensions module"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import pytest
import six
import DIRAC
from DIRAC.Core.Utilities.Extensions import (
findSystems,
findAgents,
findExecutors,
findServic... | yujikato/DIRAC | src/DIRAC/Core/Utilities/test/Test_Extensions.py | Python | gpl-3.0 | 1,244 | [
"DIRAC"
] | a7c6db839cc4da3f32e9d9d4bb537c2af503c092754f1102b80953e002743b7d |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/magic/sky/skysubtractor.py | Python | mit | 37,310 | [
"Galaxy"
] | 3cbdb3fc286026b61bc7ee725319800023e4dfe17627ef3b85c5c412d77ee68e |
from collections import defaultdict
import networkx as nx
__all__ = ["check_planarity", "PlanarEmbedding"]
def check_planarity(G, counterexample=False):
"""Check if a graph is planar and return a counterexample or an embedding.
A graph is planar iff it can be drawn in a plane without
any edge intersecti... | sserrot/champion_relationships | venv/Lib/site-packages/networkx/algorithms/planarity.py | Python | mit | 38,152 | [
"VisIt"
] | f48659ce11ea276adfe718af0e5652672bc4e561e435e67bbb41f50a6c508aff |
# -*- coding: utf-8 -*-
# Copyright (c) 2015, ESS LLP and contributors
# For license information, please see license.txt
from __future__ import unicode_literals
import frappe
from frappe.model.document import Document
from frappe import throw, _
from frappe.utils import cstr
from erpnext.accounts.party import validate... | ovresko/erpnext | erpnext/healthcare/doctype/healthcare_practitioner/healthcare_practitioner.py | Python | gpl-3.0 | 3,781 | [
"VisIt"
] | c34b03d81696b001c293f316365718b0449fb0386d315452eb03c76fa0633cb7 |
# 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... | sebrandon1/neutron | neutron/tests/unit/agent/linux/test_iptables_firewall.py | Python | apache-2.0 | 86,686 | [
"FEFF"
] | 40202d53f024e4de5c8950fbee0bb11efcfa7117f87482da4bbf1fee4d40ed7a |
#!/usr/bin/env python
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the fol... | mgeplf/NeuroM | examples/radius_of_gyration.py | Python | bsd-3-clause | 4,691 | [
"NEURON"
] | 46f277521bf187a3ad3e73493edc95d7e3112c75677e507e3c57e4191f56dbc8 |
from ase.atoms import Atoms
def write_ascii(fileobj, images):
if isinstance(fileobj, str):
fileobj = open(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
fileobj.write('atoms = ')
else:
fileobj.write('images = [')
symbols = images[0].get_chem... | grhawk/ASE | tools/ase/io/ascii.py | Python | gpl-2.0 | 567 | [
"ASE"
] | bd6627fc0121907f350fc6661ee34536c28133bec70c07b1247f5787dcfa681f |
# coding: utf-8
from __future__ import division, unicode_literals
import unittest
from pymatgen.analysis.hhi.hhi import HHIModel
class HHIModelTest(unittest.TestCase):
def test_hhi(self):
hhi = HHIModel()
self.assertEqual(hhi.get_hhi("He"), (3200, 3900))
self.assertEqual(hhi.get_hhi_produ... | rousseab/pymatgen | pymatgen/analysis/hhi/tests/test_hhi.py | Python | mit | 849 | [
"pymatgen"
] | 1cbcd0a8ec3ed5136450f2c43e5f9cc6d524352fd0a8bef4a90507bb5150e610 |
import numpy as np
from gpaw.response.bse import BSE
w_grid = np.linspace(0, 15, 1001)
# It stores the four-points kernel used for building the two-particles
# Hamiltonian in LiF_W_qGG.
bse = BSE('LiF_fulldiag.gpw',
w=w_grid,
q=np.array([0.0001, 0., 0.]),
optical_limit=True,
ec... | robwarm/gpaw-symm | doc/exercises/bse/LiF_BSE.py | Python | gpl-3.0 | 540 | [
"GPAW"
] | a48d04332a52141dac6c6a69ab5aa1899fd31675604d82d7dc50dcd1e6479456 |
from textwrap import dedent
import _pytest._code
import py
import pytest
from _pytest.config import PytestPluginManager
from _pytest.main import EXIT_NOTESTSCOLLECTED, EXIT_USAGEERROR
@pytest.fixture(scope="module", params=["global", "inpackage"])
def basedir(request, tmpdir_factory):
from _pytest.tmpdir import ... | hpk42/pytest | testing/test_conftest.py | Python | mit | 14,608 | [
"VisIt"
] | cda1e6a54150a4e4388d8a6256d5edf962ca83584df70e8b2a155ca73129512c |
"""Make or load test datasets."""
import numpy as np
from functools import partial
from numpy.random import random_integers
from sklearn.preprocessing import scale
import simfMRI.noise as noisefns
from simfMRI.expclass import Exp
from simBehave.trials import event_random
from simfMRI.misc import process_prng
class ... | parenthetical-e/wheelerdata | load/simulated.py | Python | bsd-2-clause | 16,089 | [
"Gaussian"
] | 6e7cbd8854e187e18c0c31be11535b57dd301d25ebd382065e86740ae49460b2 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005, 2006 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 Soft... | andrebellafronte/stoq | stoqlib/gui/slaves/clientslave.py | Python | gpl-2.0 | 4,949 | [
"VisIt"
] | 62a1c1a656532d645204df5e2fa814e8147c40741586bdba4f63a3c5149b590a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
test_ddlgenerator
----------------------------------
Tests for `ddlgenerator` module.
"""
import glob
import unittest
import pymongo
import os.path
from collections import namedtuple, OrderedDict
try:
from ddlgenerator.ddlgenerator import Table
except ImportError:... | catherinedevlin/ddl-generator | tests/test_ddlgenerator.py | Python | mit | 4,872 | [
"Brian"
] | fdeb4b737b9afb29c20c935abf6ab3500f390d183a5070182edc76c4275cc40e |
"""
ex20170307_Model_REG2.py
Build Model REG2. Second Version of Model REG from Godley & Lavoie (Chapter 6)
Uses the model builder from the sfc_models.gl_book sub-package.
Copyright 2017 Brian Romanchuk
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance wi... | brianr747/SFC_models | sfc_models/examples/scripts/ex20170307_Model_REG2.py | Python | apache-2.0 | 1,828 | [
"Brian"
] | 1723e3904db2c16b81ad3011ec5b3bff29ccb2dbeb73a10e750af19e1de76b56 |
# Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain ... | microsoft/DiscoFaceGAN | training/loss.py | Python | mit | 10,648 | [
"VisIt"
] | 21e917a0ea0572a5e39780431444dd4ce9bb03327a147707bf23b5391905a175 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | anksp21/Community-Zenpacks | ZenPacks.AndreaConsadori.UbiquitiNanostation/ZenPacks/AndreaConsadori/UbiquitiNanostation/modeler/plugins/UbiquitiDeviceMap.py | Python | gpl-2.0 | 1,334 | [
"VisIt"
] | ac089ae0407d680b174e84762eb7204ea478b42b9da15a95dfd0fe8bfc6b32c7 |
from copy import deepcopy
import logging
from PyQt5.QtCore import (QCoreApplication, QPoint, QRectF, Qt)
from PyQt5.QtGui import (QColor, QTransform)
from PyQt5.QtWidgets import (QAbstractItemView, QAction, QApplication, QGraphicsScene, QGraphicsView, QHBoxLayout,
QMessageBox, QPlainTextEdi... | CNR-Engineering/PyTelTools | pyteltools/workflow/multi_gui.py | Python | gpl-3.0 | 32,948 | [
"VTK",
"VisIt"
] | d03b8389e665ba129cb73fe7fa100cc95f9c79fdf2fcb9e6d7ad8eccee5fab32 |
from ase.calculators.interface import Calculator
import os, sys
import shutil, shlex
from subprocess import Popen, PIPE
from tempfile import mkdtemp, NamedTemporaryFile
import numpy as np
import unitconversion
from bonds import Bonds
from ffdata import FFData, SequenceType, ImproperType
from multiasecalc.lammps.io.lamm... | csmm/multiase | multiasecalc/lammps/lammpsbase.py | Python | gpl-2.0 | 26,101 | [
"ASE",
"LAMMPS"
] | 20a01516f64bbe3adcdd202118e9e37f7052ae70634a80cb64e2377981624a6c |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | tests/func_tests/test_generic.py | Python | lgpl-3.0 | 4,139 | [
"VisIt"
] | a4a5bae93cff62fd7a18d1584ea1864e5b73ca7b0fc69903630dd7382ed98103 |
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 22 10:18:45 2017
@author: a002028
"""
#import numpy as np
import os
import pandas as pd
import json
import codecs
import pickle
#import netcdf
"""
#==============================================================================
#========================================... | ekostat/ekostat_calculator | core/load.py | Python | mit | 13,247 | [
"NetCDF"
] | b7053822f882ff4e05b08e8aa182795ce7c09b6b5e40bec4a6446e423fd81ca2 |
dali_file = "dali.txt"
pdb_dir = "dali_pdb"
max_pairs = 10
def fetch_pdb(pdbCode,outFile):
import urllib
import gzip
import os
import string
remoteCode = string.upper(pdbCode)
if not os.path.exists(pdb_dir):
os.mkdir(pdb_dir)
if not os.path.exists(outFile):
try:
... | gratefulfrog/lib | python/pymol/pymol_path/examples/cookbook/dali.py | Python | gpl-2.0 | 2,564 | [
"PyMOL"
] | 9150ab57951c67b7afbaa7d2389f31f64e3ea1311c223b3a060cfb7ea53fa259 |
"""
Define steps for bulk email acceptance test.
"""
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from lettuce.django import mail
from nose.tools import assert_in, assert_equal
from django.core.management import call_command
from django.conf import setting... | solashirai/edx-platform | lms/djangoapps/instructor/features/bulk_email.py | Python | agpl-3.0 | 6,776 | [
"VisIt"
] | fb7896f7468cd2de1fbcff97406751943b6c2f96f9d5479a58edc54e179db365 |
#!/usr/bin/env python
from __future__ import print_function
from future import standard_library
standard_library.install_aliases()
import urllib.request, urllib.parse, urllib.error
import json
import os
import sys
import psycopg2
import urlparse
import emoji
from flask import Flask
from flask import request, render_t... | Swapratim/marvin-test | context.py | Python | apache-2.0 | 100,371 | [
"VisIt"
] | db5bcc3a8e2162b963084fc12f037dcaf38cc9fa2fef1859bca8d1cbe2c0abe0 |
"""Perform GATK based filtering, perferring variant quality score recalibration.
Performs hard filtering when VQSR fails on smaller sets of variant calls.
"""
import os
import toolz as tz
from bcbio import broad, utils
from bcbio.distributed.transaction import file_transaction
from bcbio.log import logger
from bcbio... | Cyberbio-Lab/bcbio-nextgen | bcbio/variation/gatkfilter.py | Python | mit | 9,778 | [
"BWA"
] | e4976b63137c60641d539b643bb16ba4706c043d35ee97a81ae460516758ee33 |
##############################################################################
# MSIBI: A package for optimizing coarse-grained force fields using multistate
# iterative Boltzmann inversion.
# Copyright (c) 2017 Vanderbilt University and the Authors
#
# Authors: Christoph Klein, Timothy C. Moore
# Contributors: Davy ... | mosdef-hub/msibi | msibi/state.py | Python | mit | 4,215 | [
"MDTraj"
] | f71f4badf3731d67e71f594c43f69292100ef9e469fa0943c8403fa8dfc3bc65 |
#!/usr/bin/python
#
# @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 program is free software; you can redistribute it and/or modify
# it ... | andysim/psi4 | doc/sphinxman/document_plugins.py | Python | gpl-2.0 | 15,256 | [
"Psi4"
] | 64aee7ba79dbca05c5e069f89e16f0c7b87863c2ba941f653cfcfe3558ed6b99 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | adityacs/ansible | lib/ansible/modules/network/avi/avi_role.py | Python | gpl-3.0 | 3,201 | [
"VisIt"
] | a47c704f9c9e612e603462ca3d09c54e7113d1845b3462c63f0888420df87dba |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
A master convenience script with many tools for vasp and structure analysis.
"""
import argparse
import itertools
import sys
from tabulate import tabulate, tabulate_formats
from pym... | davidwaroquiers/pymatgen | pymatgen/cli/pmg.py | Python | mit | 13,307 | [
"VASP",
"pymatgen"
] | 838f081f2af72a3baa816c4f5923e869c6f5f23dd7767ae13f777c66b8f6ec3b |
#
# Parse tree nodes for expressions
#
from __future__ import absolute_import
import cython
cython.declare(error=object, warning=object, warn_once=object, InternalError=object,
CompileError=object, UtilityCode=object, TempitaUtilityCode=object,
StringEncoding=object, operator=object,
... | jos4uke/getSeqFlankBlatHit | lib/python2.7/site-packages/Cython/Compiler/ExprNodes.py | Python | gpl-2.0 | 469,145 | [
"VisIt"
] | e17a6b83921b4ea7f488219459f5cf9400b29e468399bf7e2505d1d6171febe8 |
"""
Courseware views functions
"""
import logging
import json
import textwrap
import urllib
from collections import OrderedDict
from datetime import datetime
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions... | shurihell/testasia | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 65,149 | [
"VisIt"
] | 046fe7be0472254e782e5aea3e4bda0a33b5b8a7f2a640884fcdbbfceb2df3d8 |
import os
import sys
import yaml
import unittest
import luigi
import logging
import yaml
import ratatosk
from ratatosk.config import get_config, get_custom_config, RatatoskConfigParser
from ratatosk import interface, backend
import ratatosk.lib.align.bwa
import ratatosk.lib.files.fastq
import ratatosk.lib.tools.gatk
im... | percyfal/ratatosk | test/test_config.py | Python | apache-2.0 | 9,636 | [
"BWA"
] | a6cb330108f21a5f8fad0c1e5632646d83563152ca1324897beabd47730e577e |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 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 redistri... | psi4/psi4 | psi4/share/psi4/basis/primitives/dunning_prepend_and_checknew.py | Python | lgpl-3.0 | 2,192 | [
"Molpro",
"Psi4"
] | 4c2419fbe7e4d9bdd566836f2425018002d2258c89e42408e222e3da10d6ad9c |
"""
======================================
Decision Tree Regression with AdaBoost
======================================
A decision tree is boosted using the AdaBoost.R2 [1] algorithm on a 1D
sinusoidal dataset with a small amount of Gaussian noise.
299 boosts (300 decision trees) is compared with a single decision tr... | treycausey/scikit-learn | examples/ensemble/plot_adaboost_regression.py | Python | bsd-3-clause | 1,425 | [
"Gaussian"
] | e5f6ff56d534af285526dde8892721af14bd97d368bd54a0ff1d101722c04447 |
#
# Copyright (C) 2010-2019 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public... | KaiSzuttor/espresso | doc/tutorials/02-charged_system/scripts/nacl_units_confined_vis.py | Python | gpl-3.0 | 5,696 | [
"ESPResSo"
] | a482de1c640253e18a32355235c52afefa29c31b3fda275d2ce892a4df688ad1 |
#
# 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... | retrography/scancode-toolkit | tests/licensedcode/test_performance.py | Python | apache-2.0 | 4,566 | [
"VisIt"
] | ef54e5dc32863f2e8a4d57af6e21610592746228c9749783b1012fe2c3d78646 |
import cgi
import os
import os.path
import sys
import pgdb
import cStringIO
class http_response(object):
def __init__(self, environ, start_response):
import cStringIO
self.buffer = cStringIO.StringIO()
self.environ = environ
self.start_response = start_response
self.status = '200 OK'
self.headers = [('Co... | barneydesmond/qqc | qqc_view.py | Python | mit | 9,170 | [
"Desmond"
] | b59ef2c6f2e888def18b209515899d970260ff31c9387aafbab6bc371fb7a28e |
#!/usr/bin/env python
""""
Simple implementation of http://arxiv.org/pdf/1502.04623v2.pdf in TensorFlow
Example Usage:
python draw.py --data_dir=/tmp/draw --read_attn=True --write_attn=True
Author: Eric Jang
"""
import tensorflow as tf
from tensorflow.examples.tutorials import mnist
import numpy as np
import os
... | HaydenFaulkner/phd | tensorflow_code/external_libraries/draw-ericjang/draw.py | Python | mit | 8,395 | [
"Gaussian"
] | 49ae937241b70a3bb06bfd2c0a8f02b1191045c540f33fa5f018971ac42f4892 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | WangWenjun559/Weiss | summary/sumy/sklearn/tree/tree.py | Python | apache-2.0 | 34,561 | [
"Brian"
] | cc325638b76d77d8cb50b21dacf332e72694bb90cf47df88627f8d2f0e423e27 |
import re
from openelex.models import Contest, Candidate, Office, Result
import logging
import time
import os
# if not os.path.isdir("logs"):
# os.makedirs("logs")
# logging.basicConfig(filename=time.strftime("logs/%Y%m%d-%H%M%S-validate.log"),level=logging.DEBUG)
# Generic validation helpers
def _validate_can... | openelections/openelections-core | openelex/us/vt/validate/validates.py | Python | mit | 8,951 | [
"Brian"
] | b9da8cd685829336345a01002fbb16925983b7f6b61801066ba2ff33a02ed7b6 |
# Copyright (c) 2017 Brian Ginsburg, Julie Rutherford-Fields
# This work is available under the "3-clause ('new') BSD License”.
# Please see the file COPYING in this distribution
# for license terms.
import nltk
from nltk import CFG
from nltk.corpus import stopwords
from nltk.parse.generate import generate
from nltk.t... | thuselem/teergrube | app/email/grammars.py | Python | bsd-3-clause | 5,113 | [
"Brian"
] | 1e2eb5f01a236ba773b5b61219fcd8c9d6f8d222f73fdcf215bd13862bfb6d30 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
import sys
@process
def source(chan_out):
for i in range(10):
chan_out("Hello... | runefriborg/pycsp | examples/TerminationRacePoison.py | Python | mit | 548 | [
"Brian"
] | 37ac823089583b9908e9ac64ecea01c2138a517431f347fb92d34d630baa14a1 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
#... | kannon92/psi4 | psi4/share/psi4/fsapt/copy_pymol.py | Python | gpl-2.0 | 1,373 | [
"Psi4",
"PyMOL"
] | 83ac4c099cb6633f0272ae11a30633aad7d2b46a1cabf22aaf20ce9ec2e36b30 |
#!/usr/bin/env python
#
# Author: Oliver J. Backhouse <olbackhouse@gmail.com>
# George H. Booth <george.booth@kcl.ac.uk>
#
'''
Use a converged AGF2 calculation to build the full photoemission (quasiparticle) spectrum
Default AGF2 corresponds to the AGF2(1,0) method outlined in the papers:
- O. J. Backhouse,... | sunqm/pyscf | examples/agf2/03-photoemission_spectra.py | Python | apache-2.0 | 1,438 | [
"PySCF"
] | ada80af6b50d26f8537e57f0be28edc635542293d9334f33fdc53bbab8b14238 |
from collections import OrderedDict
from marshmallow_jsonapi import Schema, fields
from tornado import gen
from tornado_rest_jsonapi import exceptions
from tornado_rest_jsonapi.data_layers.base import BaseDataLayer
from tornado_rest_jsonapi.resource import ResourceDetails, ResourceList
class WorkingDataLayer(BaseDa... | force-h2020/tornado-rest-jsonapi | tornado_rest_jsonapi/tests/resource_handlers.py | Python | bsd-3-clause | 7,040 | [
"Octopus"
] | 288dcafeee575c788c0374427184ea172560d51c5f7b3ada8e8a40de35e63dd2 |
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