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#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.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 So... | alxgu/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 15,039 | [
"Firefly"
] | f4b3f546e4d6dbfb4864183bc94b5b9fa764791a28476be4298d0e242bf3d897 |
#
# 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
import time
m = 4000
n = 2000
display = True
... | sg0/Elemental | examples/interface/LAV.py | Python | bsd-3-clause | 2,431 | [
"Gaussian"
] | 235f040bb6a54e0ed1588eeec4774a4428054a0bd36ed304b80b415256857f2e |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import random
import pytz
import io
import json
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.core import m... | jbassen/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 218,148 | [
"VisIt"
] | bc0b5ec12cc05ab6be788f53e01b3abcec8aa973504f820e9a265afa1b01f0a3 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to represent the phonon density of states, etc.
"""
import numpy as np
import scipy.constants as const
from pymatgen.core.structure import Structure
from pymatgen.util.coord im... | gVallverdu/pymatgen | pymatgen/phonon/dos.py | Python | mit | 13,642 | [
"Avogadro",
"Gaussian",
"pymatgen"
] | d6be9723e9b8978d5981d43cb25bb1cd81102254d06e3579cb3d46426a0ab174 |
# -*- coding: utf-8 -*-
import os
import sys
from setuptools import setup, find_packages
here = os.path.abspath(os.path.dirname(__file__))
README = open(os.path.join(here, 'README.rst')).read()
# Pandas on Python 3.5 will attempt to install `numpy==1.20.1`,
# which will bail out on aarch64 with `RuntimeError: Python ... | daq-tools/kotori | setup.py | Python | agpl-3.0 | 7,184 | [
"NetCDF"
] | 5e7befbe711e13048a80a2be9c68e582ab46ad5bac21583dd7d296cee83f939b |
#!/usr/bin/python
#
# SAVI Portal to take GENI certs and create SAVI users from them
#
# Use Flask as the REST server
#
from flask import Flask, request, render_template
#
# Crypto libraries to read the certs. OpenSSL.crypto has a richer interface
# but M2Crypto.X509 has simpler verification, whch is what we use now
#... | rickmcgeer/GENI_SAVI | SAVIFrontEnd/frontEnd.py | Python | mit | 10,482 | [
"VisIt"
] | 10f0c11055019638600fb1da9342af9f25ea10dd46523a2f1ba299a3ee7f69f9 |
""" An utility to load modules and objects in DIRAC and extensions, being sure that the extensions are considered
"""
__RCSID__ = "$Id$"
import re
import imp
import pkgutil
import collections
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import List, DIRACSingleton
from DIRAC.ConfigurationSystem.... | arrabito/DIRAC | Core/Utilities/ObjectLoader.py | Python | gpl-3.0 | 7,791 | [
"DIRAC"
] | 5ca30f98bbdc71f8447cd1b323a0d65602588cae0e6bc8ff748753d5e3a19656 |
from collections import defaultdict
# word_list is a hidden variable in this CodeWars kata
word_list = [
'a', 'ability', 'able', 'about', 'above', 'absence', 'absolutely',
'academic', 'accept', 'access', 'accident', 'accompany', 'according',
'account', 'achieve', 'achievement', 'acid', 'acquire', 'across',... | the-zebulan/CodeWars | katas/kyu_7/lorraine_wants_to_win_tv_contest.py | Python | mit | 19,461 | [
"VisIt"
] | 47603cbaf879ae91089d883dc3fe28017273b6b676b5fdeb5e9a4852399b7287 |
# iCraft is Copyright 2010 both
#
# The Archives team:
# <Adam Guy> adam@adam-guy.com AKA "Adam01"
# <Andrew Godwin> andrew@aeracode.org AKA "Aera"
# <Dylan Lukes> lukes.dylan@gmail.com AKA "revenant"
# <Gareth Coles> colesgareth2@hotmail.com... | TheArchives/Nexus | core/entities/borg.py | Python | bsd-2-clause | 6,539 | [
"VisIt"
] | 101d1946498acc3d5b75b82a159aff303707865cb004e18a4392ac3b83086571 |
# Orca
#
# Copyright 2004-2008 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... | pvagner/orca | src/orca/scripts/apps/gedit/script.py | Python | lgpl-2.1 | 5,930 | [
"ORCA"
] | d2d8c8765352b903094495ad7697006303fa80db95116da06917dfcd04b1d106 |
# /*******************************************************************
# * File: pymoose.py
# * Description: This is a wrapper over moose.py and apart from
# * exposing the functions thereof, it adds some
# * utility functions.
# * Author1: Subhasis Ra... | BhallaLab/moose-thalamocortical | python/moose/utils.py | Python | lgpl-2.1 | 24,979 | [
"MOOSE",
"NEURON"
] | 856dfabd2238069951d9601e575e9a6718cf1347e842064d0d44485299b7a82e |
from .utils import *
vcf_filter = os.path.join(dir_path,
"test_data",
"vcf_filter_test.vcf.gz")
gnomad = os.path.join(dir_path, "test_data", "gnomadTest.vcf.gz")
dbsnp = os.path.join(dir_path, "test_data", "dbSnpTest.vcf.gz")
multichrom = os.path.join(dir_path, "test... | gantzgraf/vape | test/test_vcf_filters.py | Python | gpl-3.0 | 6,882 | [
"pysam"
] | d4eb9e3c8fb2d55f5f55a307459de6f167755639d3ce861e3edaf1ebdd9d7b6a |
#
# Copyright (C) 2005-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import argparse
import re
import os
from rd... | bp-kelley/rdkit | rdkit/Chem/FeatFinderCLI.py | Python | bsd-3-clause | 3,328 | [
"RDKit"
] | 6619e0fcaa5e70545ec59d404778d77db7998ba38e1aae6d74be5ffe623e6a7f |
#
# 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,
... | slonik-az/cython | Cython/Compiler/ExprNodes.py | Python | apache-2.0 | 485,870 | [
"VisIt"
] | 2f34db606a76e8063b28a4b033269b1e418c6736e791087932115c072044dbe4 |
import numpy as np
import pdb
import warnings
import random
import math
from operator import xor
from inspect import isfunction
class UncertainParameter(object):
'''Base Class for handling uncertain parameters in optimization under
uncertainty problems using horsetail matching. If this class is used, a
c... | lwcook/horsetail-matching | horsetailmatching/parameters.py | Python | mit | 7,776 | [
"Gaussian"
] | 9cb49506df75b9f344fc4722db2c89c63e6d3dfdee5b120beb77c7917c48fc55 |
"""
Qualityscore class
"""
import data
import logging
from galaxy.datatypes.sniff import *
from galaxy import util
log = logging.getLogger(__name__)
class QualityScoreSOLiD ( data.Text ):
"""
until we know more about quality score formats
"""
file_ext = "qualsolid"
def sniff( self, filename ):
... | volpino/Yeps-EURAC | lib/galaxy/datatypes/qualityscore.py | Python | mit | 3,331 | [
"Galaxy"
] | c39ff9ddee80b95631782b4965bd38b887bdb9563cabfb141e1cc809535b4ddb |
import openvoronoi as ovd
import ovdvtk
import truetypetracer as ttt # https://github.com/aewallin/truetype-tracer
import time
import vtk
import math
import offset2vtk
def insert_polygon_points(vd, polygon):
pts = []
for p in polygon:
pts.append(ovd.Point(p[0], p[1]))
id_list = []
print "in... | aewallin/openvoronoi | python_examples/ma-offset/ma-offset_1.py | Python | lgpl-2.1 | 4,226 | [
"VTK"
] | 584d852756339d32112a0c702edc8523b06cc58b2e955115d61a48cbf3a355d2 |
#!/usr/bin/env python
#-------------------------------------------------------------------------------
# Name: module1
# Purpose:
#
# Author: BreaShare
#
# Created: 21/05/2013
# Copyright: (c) user 2013
# Licence: <your licence>
#--------------------------------------------------------------------... | Jianlong-Peng/pytools | PMF/bin2/gen_pmf_fingerB.py | Python | gpl-2.0 | 3,427 | [
"Pybel"
] | e7b79a638a69ed232a7b5e02db3fc52c42add79090cd06ba718fece3dbc5ced0 |
# -*- coding: utf-8 -*-
#
# SPIDAL Tutorial: MDAnalysis with Midas documentation build configuration file, created by
# sphinx-quickstart on Sat Feb 4 03:35:42 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in t... | Becksteinlab/SPIDAL-MDAnalysis-Midas-tutorial | docs/sphinx/conf.py | Python | bsd-3-clause | 7,390 | [
"MDAnalysis"
] | 7cc7c103166b24bb459eeb7a243239ac7961f4258d2f9d9d66d6e8e7a35cff70 |
"""Defines the option parser from proteus's parun script"""
import os
import optparse
import sys
from proteus import Profiling
log = Profiling.logEvent
def get_prog_opts(args, usage=""):
"""Returns options and unused args from command line arg list.
usage - optional argurment for help option.
"""
... | IgnitionProject/ignition | ignition/utils/proteus/optparser.py | Python | bsd-3-clause | 6,577 | [
"VTK"
] | f3fdf1e08303f2ea572b9582119007434025fcc88ca11e1755f8ca2749df7234 |
""" codecs -- Python Codec Registry, API and helpers.
Written by Marc-Andre Lemburg (mal@lemburg.com).
(c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
"""#"
import builtins, sys
### Registry and builtin stateless codec functions
try:
from _codecs import *
except ImportError as why:
... | prefetchnta/questlab | bin/x64bin/python/36/Lib/codecs.py | Python | lgpl-2.1 | 37,389 | [
"FEFF"
] | 479c2ba7a3a454dffeac13ba729f317e717f353533d75054486e20b1adb2352f |
"""
Derived module from filehandler.py to handle Vtk files.
"""
import numpy as np
import scipy.io as sio
import ezyrb.filehandler as fh
import vtk
import vtk.util.numpy_support as ns
class VtkHandler(fh.FileHandler):
"""
Vtk format file handler class
:cvar string infile: name of the input file to be processed.
... | fsalmoir/EZyRB | ezyrb/vtkhandler.py | Python | mit | 3,884 | [
"VTK"
] | 9b61242fa0a3367e7aab917548c3a6e1024fbad7efa8a04550f210c457db8cf4 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/ajax/screenshot.py | Python | gpl-2.0 | 9,697 | [
"VisIt"
] | 6bf0065a1d37dd6d2313b0faf66b12b5ba7bc70a9c719c26bb07c3c88347b0d6 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | ravibhure/ansible | lib/ansible/modules/network/avi/avi_serviceenginegroup.py | Python | gpl-3.0 | 36,906 | [
"VisIt"
] | 93a030665196af319587fa08b069d0daa9f814c8e457e527c031456c13b8a4e8 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/scancode/cache.py | Python | apache-2.0 | 12,814 | [
"VisIt"
] | f8f1047d977fa64af82a3a88ecd659bb8b31589a9e3d3d6cb61c4c65a5dd8fe6 |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2013, The Deblur Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# --------------------------... | josenavas/deblur | setup.py | Python | bsd-3-clause | 2,347 | [
"scikit-bio"
] | 1df05106b23e4c55b4d29a83f23b762578ecb443ef055210dd1fda9464bd9a76 |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | motion2015/a3 | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 57,078 | [
"VisIt"
] | f9a068b2c085c5c5fef8831d9f26ac22f7e4dddac698d5e495a3ae1cfa07e996 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Visit.sender'
db.add_column(u'clinics_visit', 'sender',
... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0031_auto__add_field_visit_sender.py | Python | bsd-2-clause | 11,526 | [
"VisIt"
] | 66c771d16b1dc26c8ffd38434fafbccf6dd61960986664165f0a08a1c4599cb6 |
"""Test of PBLAS Level 2 & 3 : rk, r2k, gemv, gemm.
The test generates random matrices A0, B0, X0, etc. on a
1-by-1 BLACS grid. They are redistributed to a mprocs-by-nprocs
BLACS grid, BLAS operations are performed in parallel, and
results are compared against BLAS.
"""
import sys
import numpy as np
from gpaw.mpi ... | qsnake/gpaw | gpaw/test/parallel/pblas.py | Python | gpl-3.0 | 5,366 | [
"GPAW"
] | 3ba3987a6c129d40e0881faf003912cf63a4436a0b6edf3f2ca06cc4bdd274e9 |
# python
from chempy import io
from chempy import protein
from chempy import protein_mmff
from chempy import bond_mmff
#
#print 'normal'
#protein_mmff.check_sum(protein_mmff.normal)
#print 'n_terminal'
#protein_mmff.check_sum(protein_mmff.n_terminal)
#print 'c_terminal'
#protein_mmff.check_sum(protein_mmff.c_terminal... | gratefulfrog/lib | python/pymol/pymol_path/examples/chempy/generate_mmff.py | Python | gpl-2.0 | 757 | [
"ChemPy"
] | f9be1750cbc212e2cf2d327c593b3e6b954841456b0c85de28f2deb6ffe89b22 |
# -*- coding: utf-8 -*-
# This file is part of h5py, a Python interface to the HDF5 library.
#
# http://www.h5py.org
#
# Copyright 2008-2013 Andrew Collette and contributors
#
# License: Standard 3-clause BSD; see "license.txt" for full license terms
# and contributor agreement.
"""
Group test module.
... | Weihonghao/ECM | Vpy34/lib/python3.5/site-packages/h5py/tests/old/test_group.py | Python | agpl-3.0 | 33,722 | [
"VisIt"
] | 84d09f35df4e89b12037e1c27379854961eb01e184b6698a3a3b3927098ba8cf |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | vismartltd/edx-platform | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 59,037 | [
"VisIt"
] | 6e3628d9a0e6504fcf02e4d9793c2c024af5225293dc21d1938d0dfc8a506d6f |
"""Contains the Player class which represents a player in a pinball game.
"""
# player.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
cl... | spierepf/mpf | mpf/system/player.py | Python | mit | 6,397 | [
"Brian"
] | 02ee172d92cbcaa19882eda19421a042ea35cd965979be64850712ff1e06a223 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | Vimos/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 30,823 | [
"Gaussian"
] | 933585ff7c8e5e5b35286db73c0e633802c0223cb652c7173b0189580c92914d |
# $Id$
#
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors as rdMD, Descriptors
from rdkit.Chem import AllChem
from rdkit import DataStructs
from rdkit import RDConfig
from rdkit.Geometry import rdGeometry as rdG
import unittest
haveBCUT = hasattr(rdMD, 'BCUT2D')
def feq(v1, v2, tol=1.e-4):
return ab... | ptosco/rdkit | Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py | Python | bsd-3-clause | 29,006 | [
"RDKit"
] | bc941e09c8f221bba92c9edc908525edc411e06564042c156b90828af7d0acf6 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Contains all writers for standard chemical representations."""
from cclib.io.cjsonreader import CJSON as CJSONReader
f... | langner/cclib | cclib/io/__init__.py | Python | bsd-3-clause | 955 | [
"cclib"
] | 72b9c99991a8c29d0fc7aeb815ef1cd62501275ffbc71ede85d5bbd40f219be9 |
# -*- coding: utf-8 -*-
"""
pyradarmet.geometry
===================
Functions to calculate radar geometry characteristics.
References
----------
Rinehart (1997), Radar for Meteorologists.
Battan (1973), Radar Observations of the Atmosphere.
Bech et al. (2003; JAOT), The Sensitivity of Single Polarization Weather Rada... | nguy/PyRadarMet | pyradarmet/geometry.py | Python | gpl-2.0 | 6,281 | [
"Gaussian"
] | 32e4ac7acae0806decb5e969349ac90f7c361599ed4bcf38877e4262698fc917 |
#!/usr/bin/env python
'''
BibTex parser.
'''
import sys
import string
import cStringIO
import json
import unicodedata
import re
class BibTexParser(object):
def __init__(self, fileobj):
data = fileobj.read()
# On some sample data files, the character encoding detection simply hangs
... | jasonzou/MyPapers | parserscrapers_plugins/bibtex.py | Python | mit | 97,622 | [
"Bowtie"
] | 80af3df457e40c2797af6b067ea498f78b9943fe41807699eae4806186027dec |
import unittest
from splinter import Browser
from fake_webapp import EXAMPLE_APP
from base import WebDriverTests
class PhantomJSBrowserTest(WebDriverTests, unittest.TestCase):
@classmethod
def setUpClass(cls):
cls.browser = Browser("phantomjs")
@classmethod
def tearDownClass(cls):
cl... | bubenkoff/splinter | tests/test_webdriver_phantomjs.py | Python | bsd-3-clause | 1,734 | [
"VisIt"
] | de255aac80985899cb4cf354abab99a991e8527e4b8aec82f15fcdace5d09d3e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/encore/clustering/ClusterCollection.py | Python | gpl-2.0 | 8,217 | [
"MDAnalysis"
] | 418ecd2909a3114a893ebd91e09e0d7618784bd057d210a4ddacbc4b24c6589d |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | uncertainty_baselines/datasets/diabetic_retinopathy_severity_shift_mild.py | Python | apache-2.0 | 15,528 | [
"Gaussian"
] | 6fb2f536db2ccd3c285d4dc6da7431ed78d7afc0ff3f528c3d76f053a79f435a |
import package_with_folder
package_with_folder.nested_folder_with_init.moose.fast()
| python-security/pyt | examples/import_test_project/test_package_with_folder.py | Python | gpl-2.0 | 85 | [
"MOOSE"
] | 3ed77974425ec13ee287fd4de31e214934e0afefa03dfb41c7d17f7adcfbfe20 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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
#
# Unle... | zhengguoyong/kubernetes | hack/verify-flags-underscore.py | Python | apache-2.0 | 8,870 | [
"VisIt"
] | 2fb57bfc781f014bfd4c4697a0f3e7ea154149db8e834040609ceaba0dbaf5d8 |
import numpy as np
import itertools
class RBM:
def __init__(self, num_hidden, learning_rate,max_epochs, num_visible=10):
self.num_hidden = num_hidden
self.num_visible = num_visible
self.learning_rate = learning_rate
# Agirlik matrisi W'yi yarat (buyukluk num_visible x num_hidden),
# bunun icin... | burakbayramli/dersblog | stat/stat_165_rbm/rbm.py | Python | gpl-3.0 | 4,119 | [
"Gaussian"
] | d494a58737a839dc5d3a08c66d13545e13984e89926f7e28127e8e9244a26ce7 |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2008 Raik Gruenberg & Johan Leckner
##
## 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 v... | ostrokach/biskit | Biskit/AmberLeap.py | Python | gpl-3.0 | 7,856 | [
"Amber"
] | 93b2d185fed36831727a20832437b07d3818354b08ef94fad96ae99d4024215b |
# $Id$
#
# Copyright (C) 2004-2005 Rational Discovery LLC.
# All Rights Reserved
#
""" handles doing cross validation with naive bayes models
and evaluation of individual models
"""
from rdkit.ML.Data import SplitData
from rdkit.ML.NaiveBayes.ClassificationModel import NaiveBayesClassifier
try:
from rdkit.ML.F... | bp-kelley/rdkit | rdkit/ML/NaiveBayes/CrossValidate.py | Python | bsd-3-clause | 2,660 | [
"RDKit"
] | bb6662757f8f84fe5f0e2b2933eb770c15c9125b2dd797335948d4256067fe53 |
""" Definitions relating to the simulated DM distribution of FRBs.
To use this code, please download the asymmetric_kde package from
https://github.com/tillahoffmann/asymmetric_kde [Hoffman and Jones, 2015] """
from asymmetric_kde import ProperGammaEstimator
from frb.dm import igm
import numpy as np
import scipy as sp... | FRBs/FRB | frb/dm_kde/dm_frb_sim.py | Python | bsd-3-clause | 6,348 | [
"Gaussian"
] | 134175924dba2c219c5d8866ecfbe5ca5525b4b858312495b3855c44cafb8eb1 |
# Orca
#
# Copyright 2004-2008 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... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gedit/script.py | Python | gpl-3.0 | 23,205 | [
"ORCA"
] | 13e0769b096112473b4b4361c094a564c5faa5f42b6d13e553b7d216a2bcbaba |
"""
PropagationCommand module
This command gets all the elements that exist under a given site and applies the following logic:
if even one element is 'Active' for the given site then it marks the site as 'Active', if all elements
are set in a different status (like banned or error) then it marks the site as 'Banned'
"... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Command/PropagationCommand.py | Python | gpl-3.0 | 1,990 | [
"DIRAC"
] | 9162d3216aad757cdfea7559efd24ab113a3c2006444198dac8c936e680b5de0 |
########################################################################
# $HeadURL$
# File : InstallTools.py
# Author : Ricardo Graciani
########################################################################
"""
Collection of Tools for installation of DIRAC components:
MySQL, DB's, Services's, Agents
It only ... | sposs/DIRAC | Core/Utilities/InstallTools.py | Python | gpl-3.0 | 87,366 | [
"DIRAC"
] | 444915d4ada30471818ffcfea372f11e3872bbc25bea4a30bb398b746e791cb5 |
### Download the data, if not already on disk #################################
import os
if not os.path.exists('MRbrain.tar.gz'):
# Download the data
import urllib
print "Downloading data, Please Wait (7.8MB)"
opener = urllib.urlopen(
'http://graphics.stanford.edu/data/voldata/MRbrain.t... | kayarre/dicomwrangle | mri.py | Python | bsd-2-clause | 3,100 | [
"Mayavi"
] | 6af1b8137d300b16769ec1056861f9ecc16aa5f6f26fbcc2f097680ee7fab48c |
# synapse_tutorial.py ---
#
# Filename: synapse_tutorial.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Fri Jan 17 09:43:51 2014 (+0530)
# Version:
# Last-Updated: Thu Oct 2 11:27:05 IST 2014
# By: Upi
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#... | dilawar/moose-full | moose-examples/snippets/synapse_tutorial.py | Python | gpl-2.0 | 4,892 | [
"MOOSE"
] | aaed4def027800b0bbecd9afb37b7bc1e5852a6a62d3a2863e1cd7946d49e786 |
from aiida import load_dbenv
load_dbenv()
from aiida.orm import Code, DataFactory, WorkflowFactory
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
import numpy as np
import os
import pymatgen
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
##########################
struc... | abelcarreras/aiida_extensions | workflows/launcher/launch_phonon_vasp_mp.py | Python | mit | 6,532 | [
"CRYSTAL",
"VASP",
"phonopy",
"pymatgen"
] | 0dae10df238eb08218ce981a8220675273833feaabd28cf174ad0c8c7490039c |
# -*- coding: utf-8 -*-
# Copyright 2013 by Petra Kubincova
import read_maf as preprocessing
import seq_structures as seq
import bgzf_tool as bgzftool
#import mapping
import sys
import os
def parse_mapping_input(args):
try:
import optparse
parser = optparse.OptionParser()
parser.add_optio... | kpetra/maptool | preprocessing/maptool.py | Python | mit | 13,144 | [
"Biopython"
] | ec3de84515daee306e7d4d8592ea3e65102dccc434a52f404044ff526705efab |
from ase.asec.command import Command
from ase.visualize import view
class ViewCommand(Command):
@classmethod
def add_parser(cls, subparser):
parser = subparser.add_parser('view', help='ag ...')
def run(self, atoms, name):
view(atoms)
| conwayje/ase-python | ase/asec/view.py | Python | gpl-2.0 | 273 | [
"ASE"
] | 70ff2dc0dce0e76099613378515b2150773af3b7f85edd561a1306d98988aaf5 |
''' Significant lifting from https://jmetzen.github.io/2015-11-27/vae.html '''
import time
import numpy as np
import tensorflow as tf
from tensorflow.python.ops import rnn
import random
import matplotlib.pyplot as plt
import re, string
from sklearn.feature_extraction.text import CountVectorizer
from collections impo... | dricciardelli/vae2vec | def_def_oh_ctc.py | Python | mit | 37,360 | [
"Gaussian"
] | 3f2c265d529638fe897fd04f52caac58af053ec2e79fd3177b0d790fc3df062f |
import numpy as np
from scipy.stats import multivariate_normal
def gaussian_PSFs():
'''Provide a simple set of PSFs and image for testing and example.
Returns
-------
psfbase : np.array
Three Gaussians with different width and covariance as PSF base
functions.
image, image2 : np.ar... | hamogu/psfsubtraction | psfsubtraction/data.py | Python | mit | 1,195 | [
"Gaussian"
] | d7c9051e49564ad48388b7fa6f0059b4754cf0fcd4abd49f487bdb6f0bb95708 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | nuclear-wizard/moose | python/peacock/PostprocessorViewer/PostprocessorDataWidget.py | Python | lgpl-2.1 | 2,317 | [
"MOOSE"
] | ddc82993697962f6eafc8540d48c6a3ea6e8e005a11137ea5df3c405754c947e |
#######################################
# Copyright 2019 PMP SA. #
# SPDX-License-Identifier: Apache-2.0 #
#######################################
import os
import pytest
import json
from unittest import mock
from unittest.mock import patch
from rpackutils.config import Config
from rpackutils.reposconfig ... | sgubianpm/RPackUtils | tests/test_reposconfig.py | Python | gpl-2.0 | 6,857 | [
"Bioconductor"
] | ff402c27fb44bce112c4fe272d9d40fd33af9da7ed609a80133aad18f9201862 |
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# bu... | jdufresne/validatorcrawler | validatorcrawler/crawler.py | Python | gpl-3.0 | 3,309 | [
"VisIt"
] | 54caffa1f028a1c107d3577d9b935928edfe48aaa1d11125fa763d9d2e1e1b0c |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | aevum/moonstone | src/moonstone/gui/qt/component/mscreen.py | Python | lgpl-3.0 | 20,338 | [
"VTK"
] | c0d59ae6f30eabc4b0072c38430d2207d5f52598f2a060433cdfe317afe1ca39 |
# -*- coding: utf-8 -*-
"""
jinja2.compiler
~~~~~~~~~~~~~~~
Compiles nodes into python code.
:copyright: (c) 2010 by the Jinja Team.
:license: BSD, see LICENSE for more details.
"""
from itertools import chain
from copy import deepcopy
from keyword import iskeyword as is_python_keyword
from jinja2... | 8l/libfirm | scripts/jinja2/compiler.py | Python | lgpl-2.1 | 62,561 | [
"VisIt"
] | ccb3f34ced0dca0184be84a89b973facff73cf60966e3e4520457ea90ca97f50 |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2015 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permiss... | asttra/pysces | pysces/PyscesTest.py | Python | bsd-3-clause | 28,898 | [
"PySCeS"
] | 3871dfd62d1ed88d6a61a3882a0e0030be97a52cf11a832a822ce3e6e4481ce8 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2013, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | runt18/nupic | src/nupic/swarming/permutationhelpers.py | Python | agpl-3.0 | 26,130 | [
"Gaussian"
] | b8da4df77a9a1feff3da714c25f3ac2331506ccb42e8c5922ec3e88fcd36c4b6 |
# -*- coding: utf-8 -*-
# pylint: disable=C,R,W
"""This module contains the 'Viz' objects
These objects represent the backend of all the visualizations that
Superset can render.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unico... | dmigo/incubator-superset | superset/viz.py | Python | apache-2.0 | 85,206 | [
"VisIt"
] | 85c3538bc76af5520ef180467a3131f4b583e87e4d850373a78f3894955ae36f |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the G... | espressopp/espressopp | src/interaction/StillingerWeberTripleTerm.py | Python | gpl-3.0 | 8,110 | [
"ESPResSo"
] | e6537600db07fbdabc9301ba19abf4dcd80f10a51980854f3f45f57c69f66207 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
""" Module: geometry
================
"""
from __future__ import print_function
import numpy as np
from scipy import stats
from MDAnalysis.core.groups import Atom, AtomGroup, Residue, Resi... | Marcello-Sega/pytim | pytim/observables/local_frame.py | Python | gpl-3.0 | 9,326 | [
"Gaussian",
"MDAnalysis"
] | 59cddef6db68c8d2b8de9bdd70cb6024317970668d86e4ce7d8ee107597018d1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
from collections import defaultdict
from math import isnan
import numpy as np
from pymatgen.core.composition import Composition
from pymatgen.analysis.reaction_calculator impo... | davidwaroquiers/pymatgen | pymatgen/analysis/tests/test_reaction_calculator.py | Python | mit | 21,502 | [
"pymatgen"
] | 5fb3047e3a5a9903cf9bc4c48fd0f80d58a8d1a9fbbdaf597646794206308d4c |
#
# co_co_variable_once_per_scope.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at... | kperun/nestml | pynestml/cocos/co_co_variable_once_per_scope.py | Python | gpl-2.0 | 3,649 | [
"NEURON"
] | 2d564145e1e7b23d9746a88a17f66f1547b17cae33275bb7c35334e03aa8eab8 |
################################################################################
# Copyright (c) 2012, Dougal J. Sutherland (dsutherl@cs.cmu.edu). #
# All rights reserved. #
# ... | dougalsutherland/sdm | python/sdm/wrappers.py | Python | bsd-3-clause | 17,059 | [
"Gaussian"
] | 9ff89de0c434e7cb1fd1a3a0f008cba2ec673ac3ff51f6aefe23e335f5fc298b |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/streamsubservices.py | Python | gpl-2.0 | 5,526 | [
"VisIt"
] | 9270be060772f015d11e3afbc10fc037ac6ec7bf15827bb7c29ef6eb02cefbd1 |
# -*- coding: utf-8 -*-
# $Id: manpage.py 8116 2017-06-18 19:09:40Z milde $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module is put into the public domain.
"""
Simple man page writer for reStructuredText.
Man pages (short for "manual pages") contain system documentation on unix-like... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/docutils/writers/manpage.py | Python | mit | 35,720 | [
"VisIt"
] | 71b876c762862e3dad720c8d6aeebef3b54b995d1ce879367e7f9a3fbe278b1c |
#! A test of the basis specification. A benzene atom is defined using a ZMatrix containing dummy atoms
#! and various basis sets are assigned to different atoms. The symmetry of the molecule is automatically
#! lowered to account for the different basis sets.
import psi4
refnuc = 204.01995737868003 #TEST
refscf = -... | rmcgibbo/psi4public | tests/python/mints2/input.py | Python | lgpl-3.0 | 4,144 | [
"Psi4"
] | 0969e174943fcdb015656a10e9ad6021a392572ae46cd710e754877244cea3aa |
"""
NOTE:
the below code is to be maintained Python 2.x-compatible
as the whole Cookiecutter Django project initialization
can potentially be run in Python 2.x environment
(at least so we presume in `pre_gen_project.py`).
TODO: ? restrict Cookiecutter Django project initialization to Python 3.x environm... | nunchaks/cookiecutter-django | hooks/post_gen_project.py | Python | bsd-3-clause | 7,904 | [
"GULP"
] | 23f68efd590d52939f496b80788345ffd3748724a6a7aa620eeb2e3f04786c5b |
# Copyright 2020 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... | tensorflow/examples | tensorflow_examples/lite/model_maker/core/task/model_spec/audio_spec.py | Python | apache-2.0 | 23,830 | [
"Gaussian"
] | 9c3f682461e074c5093e7d690c1ea12f3a912b5180fd04cd56c4b366eec6d7f5 |
from builtins import range
from builtins import object
import numpy as np
from cs231n.layers import *
from cs231n.layer_utils import *
class TwoLayerNet(object):
"""
A two-layer fully-connected neural network with ReLU nonlinearity and
softmax loss that uses a modular layer design. We assume an input dim... | kabrapratik28/Stanford_courses | cs231n/assignment2/cs231n/classifiers/fc_net.py | Python | apache-2.0 | 19,266 | [
"Gaussian"
] | 47fcd506ad5674583ee65438dfd47f0fd9e9da160af39872f460f5f2b9109d9c |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall.injector.namespaces import XMLNS_IFACE
from xml.dom import Node, XMLNS_NAMESPACE, XML_NAMESPACE
class Namespace(object):
def __init__(self):
self.namespace_prefixes = {} # Namespace -> prefix
de... | 0install/0repo | repo/namespace.py | Python | lgpl-2.1 | 2,668 | [
"VisIt"
] | f5d5727f4d89875fdb51a42bbeaec040081eb3918636339b6206b63b15063f1b |
"""
Set of objects to manage triggers streams.
A trigger is an audio signal with a value of 1 surrounded by 0s.
TrigXXX objects use this kind of signal to generate different
processes with sampling rate time accuracy.
"""
"""
Copyright 2010 Olivier Belanger
This file is part of pyo, a python module to help digita... | xyproto/gosignal | pyo/pyolib/triggers.py | Python | gpl-3.0 | 95,913 | [
"Gaussian"
] | 25ca11456639801f4641a70f9dcbe92f6fc26f0c79013e562aaebb7b72f2a4d6 |
#!/usr/bin/env python
# $HeadURL$
"""
Perform initial sanity checks on WN, installs and configures DIRAC and runs
Job Agent to execute pending workload on WMS.
It requires dirac-install script to be sitting in the same directory.
"""
__RCSID__ = "$Id$"
import os
import sys
import getopt
import urllib2
import stat
i... | miloszz/DIRAC | WorkloadManagementSystem/PilotAgent/dirac-pilot_1.py | Python | gpl-3.0 | 27,920 | [
"DIRAC"
] | 0e1035983c087fb1e0259012a4c43b208203f9ee9de6e93d42f1245aa1e0932e |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/plugins/kgapplications/tests/test_commands.py | Python | gpl-3.0 | 1,234 | [
"Brian"
] | 82837415b93046089747eadcc4ddfbd3b364dfc977ac017d21cdae1b3254604b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2013 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the L... | iwm911/plaso | plaso/parsers/opera_test.py | Python | apache-2.0 | 4,285 | [
"VisIt"
] | 14ecb449d78e50b43a408a13e8b32db88d964305d037393562900d07d8a861de |
from __future__ import division, print_function, unicode_literals
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particl... | google-code-export/los-cocos | test/test_particle_fireworks.py | Python | bsd-3-clause | 981 | [
"Galaxy"
] | db030c7e8e3daf4199160140efeb2f9163e77bcc5a69bdcfc2370660f53ba6fd |
# -*- coding: utf-8 -*-
{
"'Sounds-like' name search allowing search even the spelling of the name is not known exactly": "'Sounds-like'名稱搜尋或搜尋,即使名稱的拼字不完全",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that ha... | code-for-india/sahana_shelter_worldbank | languages/zh-tw.py | Python | mit | 338,502 | [
"VisIt"
] | ab7b54aa09e3f734d65668c35524f01a1bd93af5a2ab9c6dcd6bb78524de0b63 |
#!/usr/bin/env python3
import ipaddress
import json
# This could all be in one script but that would take more Time and Effort, so this works for now:
#
# $ ansible-playbook -i env/admintraining/inventory env/admintraining/jetstream.yml
# In a venv w/ `openstack` installed:
# $ openstack server list --name 'gat-.*' -f... | galaxyproject/infrastructure-playbook | env/admintraining/route53.py | Python | mit | 1,744 | [
"Galaxy"
] | 5d6cf183313124e0905bce02ffa9a95829ddc85cc532a0470c8c3bea4a47c348 |
"""
Custom AST NodeVisitor classes uses for Python xss linting.
"""
from __future__ import absolute_import
import ast
import re
from xsslint.reporting import ExpressionRuleViolation
from xsslint.rules import RuleSet
from xsslint.utils import Expression, ParseString, StringLines
ruleset = RuleSet(
python_concat_h... | ESOedX/edx-platform | scripts/xsslint/xsslint/visitors.py | Python | agpl-3.0 | 12,675 | [
"VisIt"
] | cc4333596353d04248bf70233aa5e37dbeff6e840e9ff7d7f2a1b787c42affd0 |
"""
===========================
Formaldehyde cm-line fitter
===========================
This is a formaldehyde 1_11-1_10 / 2_12-2_11 fitter. It includes hyperfine
components of the formaldehyde lines and has both LTE and RADEX LVG based
models
"""
from __future__ import print_function
import numpy as np
from ...mpfit... | vlas-sokolov/pyspeckit | pyspeckit/spectrum/models/formaldehyde.py | Python | mit | 23,626 | [
"Gaussian"
] | 6b669206a653f59141f6e6fa1feb4b135b75950db5400087d669f442d60a4cda |
"Definition of a univariate parameter."
from equadratures.distributions.gaussian import Gaussian
from equadratures.distributions.uniform import Uniform
from equadratures.distributions.chebyshev import Chebyshev
from equadratures.distributions.beta import Beta
from equadratures.distributions.cauchy import Cauchy
from eq... | psesh/Effective-Quadratures | equadratures/parameter.py | Python | mit | 20,260 | [
"Gaussian"
] | 76670d5d62d6b4829cc362aa5a5db907628b69342d73be6b0e1da000587f03f9 |
#!/usr/bin/env python
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the h... | hbp-sanncs/pyscm | find_parameters.py | Python | gpl-3.0 | 1,303 | [
"NEURON"
] | 84c4e8530aa3ec8bc24abffaad1c9c62ef10a86f4ee197d35e8e05bf5297d24e |
# Copyright 2021 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... | petewarden/tensorflow | tensorflow/python/util/nest.py | Python | apache-2.0 | 64,165 | [
"VisIt"
] | 237e99d1e4858294376a67ef8389d0a6cfd170c595bcc8c75dc6c29d4c14a2b1 |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import os
import random
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def milsong_checkpoint():
milsong_train = h2o.upload_file(pyunit_utils.locate("bigdata/laptop/milsongs/milsongs-train.csv.gz"))
milsong_valid = h2... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_milsongs_large_gbm.py | Python | apache-2.0 | 2,798 | [
"Gaussian"
] | a42ab86b7e2e124cd5bc788ca05112d646b4b3c459f2f95e3532ae6ff58d3a55 |
# Copyright 2009 Yusuf Simonson
# This file is part of Snowball.
#
# Snowball is free software: you can redistribute it and/or modify it under the
# terms of the GNU Affero General Public License as published by the Free
# Software Foundation, either version 3 of the License, or (at your option) any
# later version.
#
... | heliumpigs/snowball | web/engine.py | Python | agpl-3.0 | 9,029 | [
"VisIt"
] | d5cf827522d9dbab946fb745b063e2fac5f672714173be2afec0620671cf6c41 |
"""
Perform Levenberg-Marquardt least-squares minimization, based on MINPACK-1.
AUTHORS
=======
The original version of this software, called LMFIT, was written in FORTRAN
as part of the MINPACK-1 package by Jorge More, Danny Sorenson, Burton Garbow
and Kenneth Hillstrom.
Craig Markwardt converted the FORTRAN code to... | erh3cq/hyperspy | hyperspy/external/mpfit/mpfit.py | Python | gpl-3.0 | 80,224 | [
"Gaussian"
] | 70db1a0a5b473dca85e6a66cba6d59e1587f54ea1e0cd1283d755f85f42ea540 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# http://lammps.sandia.gov, Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE... | sy0302/lammps_qtb | python/lammps.py | Python | gpl-2.0 | 6,759 | [
"LAMMPS"
] | e568407865ee5ebc3f76a92800e2b26939b8452f055cb41539944baebd259701 |
# -*- coding: utf-8 -*-
"""The check functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD (3-clause)
from difflib import get_close_matches
from distutils.version import LooseVersion
import operator
import os
import os.path as op
import sys
from pathlib import Path
import numpy as... | Teekuningas/mne-python | mne/utils/check.py | Python | bsd-3-clause | 24,925 | [
"Mayavi"
] | f18e741725e13408f8362544b1e05a69823f2ff88b0aa0618f09766cadf0212c |
# vim: fdm=marker
'''
author: Fabio Zanini
date: 08/12/14
content: Plot tree of haplotypes.
'''
# Modules
from __future__ import print_function
import os
import argparse
import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
# Functions
def tree_from_json(json_file):
'''Convert JS... | davidrglass/antidengue | src/treeviewer.py | Python | mit | 16,220 | [
"Biopython"
] | 725ac8758d7c4e3361ed39835bdd1d79497446ef0b239c1909bb402a09109684 |
#
# Copyright (c) 2010 Brian E. Granger
#
# This file is part of pyzmq.
#
# pyzmq is free software; you can redistribute it and/or modify it under
# the terms of the Lesser GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option)... | svpcom/pyzmq-ctypes | zmq/tests/test_multipart.py | Python | lgpl-3.0 | 1,561 | [
"Brian"
] | f72157e897219d16b10dd5ef47f10173c6d23f2cbbf6370ad3717c5d1f5f6f75 |
#
# Copyright 2013 Quantopian, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | erikness/AlephOne | tests/test_perf_tracking.py | Python | apache-2.0 | 60,968 | [
"COLUMBUS"
] | fc50d2f2fc357f7f67bbe17659d6144db60cdf99c3150818997c90db511c9cb7 |
from bluebottle.test.utils import BluebottleTestCase
from django.core.urlresolvers import reverse
from django.core import mail
from rest_framework import status
from bluebottle.utils.tests.test_unit import UserTestsMixin
from bluebottle.test.factory_models.wallposts import TextWallpostFactory
from bluebottle.test.fact... | jfterpstra/bluebottle | bluebottle/wallposts/tests/test_api.py | Python | bsd-3-clause | 20,881 | [
"BLAST"
] | b40d7f2a07714534656615e8c2cdaa541dbd7e84f60cf82b88478cd8d4007c33 |
#
# Copyright 2002 by Michael Hoffman. 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.
"""
Access to General Feature Format databases created with Bio::DB:GFF
based on documen... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/GFF/__init__.py | Python | apache-2.0 | 14,163 | [
"Biopython"
] | 7cb5210a88261b5c166752ffc1ec00ece4f4cf310f9bd1b87f5199f3255ce43b |
#!/usr/bin/env python
import argparse
import glob
import os
import re
import sys
RE_INPUT = ('\s+Search initialized with\s+(?P<num>\d+)\s+structures from the '
'input structure file')
RE_TOTAL = ('\s+Total number of structures processed =\s+(?P<num>\d+)')
def count_steps(direc):
filenames = glob.glob(... | Q2MM/q2mm | tools/count_steps.py | Python | mit | 3,226 | [
"MacroModel"
] | f8ef374dad234610af4ffb5867ade2cda7edaaced2c0b278c3576a027f18a45a |
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