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"""
This program tests the correct addition and removal of components to the InstalledComponentsDB,
as well as the components
CLI functions are used to ensure the test is as similar as possible to a real user-to-cli interaction
This test assumes that there is a DIRAC master server running on the local machine
This test... | fstagni/DIRAC | tests/Integration/Framework/NotRun_Test_ComponentInstallUninstall.py | Python | gpl-3.0 | 8,990 | [
"DIRAC"
] | 0c00b9a619b229509df941a9ca4ae699049b1e545278cba0a38cf16b0dbe01f2 |
# -*- coding: utf-8 -*-
"""
pySEBAL_3.4.0
@author: Tim Hessels, Jonna van Opstal, Patricia Trambauer, Wim Bastiaanssen, Mohamed Faouzi Smiej, Yasir Mohamed, and Ahmed Er-Raji
UNESCO-IHE
June 2018
"""
import sys
import os
import shutil
import numpy as np
import osr
import gdal
from math import sin, c... | wateraccounting/SEBAL | pySEBAL/pySEBAL_code.py | Python | apache-2.0 | 129,049 | [
"ADF"
] | d70dd6e216315c8439ed76cb9df5caeef1735fc60991402ed0ea39f0d9c23f36 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Sat Sep 29 21:55:06 2018
@author: leandrodemarcovedelago
"""
import numpy as np
import numpy.matlib as npmatlib
import math
import Utils
class Acor:
def __init__(self, alg_variant, uses_log):
"""
* alg_variant should be one of the ... | leandrodemarcovedelago/thesis-aco | informe/ACOR.py | Python | gpl-3.0 | 7,338 | [
"Gaussian"
] | 1ecdcd9b04a206bc60912b0d12bda10d571f5efe66c59eb219b9ea5f1876cdc8 |
# -*- coding: utf-8 -*-
# Copyright (c) Vispy Development Team. All Rights Reserved.
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
import numpy as np
from os import path as op
from numpy.testing import assert_allclose, assert_array_equal
from vispy.io import write_mesh, read_mesh, load_data... | Eric89GXL/vispy | vispy/io/tests/test_io.py | Python | bsd-3-clause | 4,228 | [
"VTK"
] | 2b7aeabd1241f053e63cd1f06cc3875b0dd040bc3842275b32ec28a0e1385525 |
# (c) 2012-2017, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/tests/main/test_views.py | Python | apache-2.0 | 1,718 | [
"Galaxy"
] | 9efbf73def989efb65a93aa82336d3fa6203ce7cadb93100f6de74ff826ab652 |
# proxy module
from __future__ import absolute_import
from mayavi.core.file_data_source import *
| enthought/etsproxy | enthought/mayavi/core/file_data_source.py | Python | bsd-3-clause | 97 | [
"Mayavi"
] | c88be1105eeb98fa116174b3444a7b7d6dc20004ffd6bc2ba5593478f87c37fe |
"""
Copyright (c) 2017 Sam Witte
Created on Jan 19, 2017
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any late... | SamWitte/Codds_DarkMatter | src/Data/3BinXe2.py | Python | gpl-2.0 | 2,545 | [
"Gaussian"
] | 44fce778221c44153f7265cfa0ca0efd8477eb8d857bfb9285dfd950f96772be |
# -*- coding: utf-8 -*-
'''
Copyright (C) 2011-2021 Maximilian Maahn, U Leipzig
maximilian.maahn_AT_uni-leipzig.de
example script for converting mrrRaw data to netcdf using IMProToos
'''
from __future__ import print_function
import sys
import numpy as np
import glob
import os
import datetime
import IMProToo
import g... | aronnem/IMProToo | examples/batch_convert_rawData.py | Python | gpl-3.0 | 3,538 | [
"NetCDF"
] | 3e9bda5ae9431604d48ba241639424a6805fdb0fbb810aa82d6c50741f50be54 |
# -*- coding: utf-8 -*-
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This package defines the astrophysics-specific units. They are also
available in the `astropy.units` namespace.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
... | tbabej/astropy | astropy/units/astrophys.py | Python | bsd-3-clause | 6,881 | [
"Dalton"
] | 3faa81935a7a4ef5dd36ba92746a3afd0a535bbc10d8db99e2b4406c5fbdd4ed |
from sympy import (meijerg, I, S, integrate, Integral, oo, gamma,
hyperexpand, exp, simplify, sqrt, pi, erf, sin, cos,
exp_polar, polar_lift, polygamma, hyper, log)
from sympy.integrals.meijerint import (_rewrite_single, _rewrite1,
meijerint_indefinite, _inflate_g, _create... | ichuang/sympy | sympy/integrals/tests/test_meijerint.py | Python | bsd-3-clause | 26,696 | [
"Gaussian"
] | 51106bf4fbae88fc6ee6f664c6f6c87f10054e29df48ac8af4b6357cc5bc8859 |
from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.io import write
# Find the initial and final states for the reaction.
# Set up a (3 x 3) two layer slab of Ru:
a = 2.70
c = 1.59 * a
sqrt3 = 3. ** .5
bulk = Atoms('2Cu', [(0., 0... | misdoro/python-ase | doc/tutorials/N2Ru-Dissociation1.py | Python | gpl-2.0 | 1,333 | [
"ASE"
] | 108a855b6fa001fc4fa450f806b898abd7e79550d08e40274053ce66574281db |
#!/usr/bin/env python
#
# Copyright 2002-2003 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.
"""
Bio.DocSQL: easy access to DB API databases.
>>> import os... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/DocSQL.py | Python | gpl-2.0 | 5,991 | [
"Biopython"
] | ce8803776ec3aa73eb19bb526e79c0e6aa7e335508ae7bbabcc8cd3f6777fa89 |
from django.db import models
from edc_base.model.fields import OtherCharField
from edc_constants.choices import YES_NO, YES_NO_NA
from edc_code_lists.models import WcsDxAdult
from td_list.models import MaternalDiagnoses
class DiagnosesMixin(models.Model):
"""Base Model for forms with diagnosis questions i.e Ma... | botswana-harvard/tshilo-dikotla | td_maternal/models/diagnoses_mixin.py | Python | gpl-2.0 | 1,465 | [
"VisIt"
] | 8496e637384e062199cf39a17d20bbf90056f2345ebf8174e37d8b56135cb415 |
# -*- coding: utf-8 -*-
'''
Master Reborn Add-on
Copyright (C) 2017 Master Reborn
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... | TheWardoctor/Wardoctors-repo | plugin.video.master.reborn/resources/lib/sources/__init__.py | Python | apache-2.0 | 52,029 | [
"ADF"
] | 19713e508d6a025bf670817fccf09c70f9a6e3385a528aacca362b32730ce68b |
from rdkit import Chem
from rdkit import rdBase
from rdkit import RDConfig
import os
from rdkit.Chem import rdMolDescriptors as rdMD
from rdkit.Chem import AllChem
haveDescrs3D = hasattr(rdMD, 'CalcAUTOCORR3D')
import time, unittest
def _gen3D(m, is3d, calculator):
if not is3d:
m = Chem.AddHs(m)
ps = All... | ptosco/rdkit | Code/GraphMol/Descriptors/Wrap/test3D.py | Python | bsd-3-clause | 5,546 | [
"RDKit"
] | 541c4a27a34d07c4da7df8acb7bcafb72de49160f5bbbfc9609dc72284402216 |
import os
import numpy as np
from os.path import join as pjoin
from dipy.viz import actor, window, widget, fvtk
from dipy.data import DATA_DIR
from dipy.data import fetch_viz_icons, read_viz_icons
import numpy.testing as npt
from dipy.testing.decorators import xvfb_it
use_xvfb = os.environ.get('TEST_WITH_XVFB', False... | villalonreina/dipy | dipy/viz/tests/test_fvtk_widgets.py | Python | bsd-3-clause | 6,791 | [
"VTK"
] | 458877fb78099b5d5c46f5e2d84c522902610b5e3c59941434836b0052878e85 |
"""This module holds classes for image loading and manipulation."""
import copy
import io
import pathlib
from collections import Counter, Iterable
from datetime import datetime
from io import BytesIO, BufferedReader
import re
import os.path as osp
import os
from typing import Union, Sequence, List, Any, Tuple, Optional... | jrkerns/pylinac | pylinac/core/image.py | Python | mit | 39,827 | [
"Gaussian"
] | 17f935ad3049400cc1f73b19edb26a88fa333351d4e917a8c8bf59e15a71fb0e |
"""
Loadable.Loadable subclass
"""
# This file is part of Munin.
# Munin is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
# Munin is... | munin/munin | deprecated/longtel.py | Python | gpl-2.0 | 3,525 | [
"Galaxy"
] | a034b0128553d529e2e9441dfd4ed651085f55e4c26c2bcbbb27479e47cecdd6 |
import numpy as np
import pandas as pd
import mdtraj as md
from mixtape.utils import iterobjects, assign
import mixtape.ghmm, mixtape.featurizer
import sklearn.hmm
import os
name = "tica"
json_filename = "./%s.jsonlines" % name
feature_filename = "./%s.pkl" % name
featurizer = mixtape.featurizer.load(feature_filename... | hainm/MSMs | attic/src/code/hmsm/plot_assign.py | Python | gpl-2.0 | 1,331 | [
"MDTraj"
] | d2024dfa56dc1f9e27bb8beda79e04274d7e33ef0371ce98298a5b6acd1ae14f |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""Integration tests for regridding."""
# Import iris.tests first so that some things can be initialised before
# importing an... | ocefpaf/iris | lib/iris/tests/integration/test_regridding.py | Python | lgpl-3.0 | 9,065 | [
"NetCDF"
] | 97ba1552b4ed14f6532d17980b3ab9ecd6d5285179af5749975af3165e766643 |
import logging
from galaxy.web.form_builder import SelectField
log = logging.getLogger( __name__ )
REPOSITORY_DEPENDENCY_DEFINITION_FILENAME = 'repository_dependencies.xml'
REPOSITORY_SUITE_DEFINITION = 'repository_suite_definition'
TOOL_DEPENDENCY_DEFINITION = 'tool_dependency_definition'
TOOL_DEPENDENCY_DEFINITION_... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/repository_types/util.py | Python | gpl-3.0 | 2,985 | [
"Galaxy"
] | a13eaac3d6ba070b955077032ce6761ae4390ad8c445eb56c716ae04e567a784 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_GetDefaultStretchMode.py | Python | gpl-3.0 | 913 | [
"ORCA"
] | bb86feef9bf3fe55d3e99e75351e7f93f071fd15615ca8e0265d10c1ce1b35ee |
import numpy
import scipy.special
def gauss(hyp, y=None, mu=None, s2=None, inf=None, hi=None, nargout=None):
"""
Gaussian likelihood function for regression. The expression for the
likelihood is
likGauss(t) = exp(-(t-y)^2/2*sn^2) / sqrt(2*pi*sn^2),
where y is the mean and sn is the standard deviation.
... | depet/scikit-learn | sklearn/gpml/lik.py | Python | bsd-3-clause | 14,213 | [
"Gaussian"
] | 9c34f7588779898ac0dbce3fc1728f76aa9bd62b40b5bbea65fc7da503b6b075 |
# coding: utf-8
import os, sys, time, re
from Crypto.Cipher import AES
import crypt
import pwd
from binascii import b2a_hex, a2b_hex
import hashlib
import datetime
import random
import subprocess
import uuid
import json
import logging
from settings import *
from django.core.paginator import Paginator, EmptyPage, Inva... | 786951355/jumpserver | jumpserver/api.py | Python | gpl-2.0 | 14,614 | [
"VisIt"
] | df5ef54e0fd9e782b763748b7b697057754b8e6d59194386290c9abd44d5f21d |
def visit_Call(self, node):
"""
The visit of a call node.
Ignores all calls except for those we need to modify.
:param node: A call node
"""
name = self.__find_call_name(node)
if name in ATOMIC_SOURCES:
id = self.__get_id()
self.__replace_c... | Betaboxguugi/P6 | documentation/presentation/code/visit_call.py | Python | gpl-3.0 | 655 | [
"VisIt"
] | 1ad654f7e138197a818fe1e80073e1d5e3e36c9a45d5381b3deef9096a132be5 |
# -*- coding:utf-8 -*-
# Copyright (c) 2015, Galaxy Authors. All Rights Reserved
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
#
# Author: wangtaize@baidu.com
# Date: 2015-04-01
from django.conf import urls
urlpatterns = urls.patterns("console.cluster.views",
... | fxsjy/galaxy | console/backend/src/console/cluster/urls.py | Python | bsd-3-clause | 355 | [
"Galaxy"
] | 789c32ac2b7f4bf1b061a70669d7d88c9944f91b4ad62b45543d3e993ab22fbf |
"""
Command-line interface for model evaluation
@author Siddharth Reddy <sgr45@cornell.edu>
"""
from __future__ import division
import click
import logging
import math
import pickle
import os
import pandas as pd
import numpy as np
from lentil import datatools
from lentil import models
from lentil import est
from l... | rddy/lentil | scripts/lse_eval.py | Python | apache-2.0 | 7,567 | [
"Gaussian"
] | a1317fee94c290e86ef8cd9138a1dbd3e013c4514716b8a9f00e1dfe0304d368 |
# -*- coding: utf-8 -*-
"""
This script opens data files and extracts relevant data. Then, using a sklearn
gaussian process package, fits a gaussian to the crosswind (1d) temperature
measurements and interpolates temparture values (relative, not absolute) at a
2 mm interval.
TODO: make gaussian process it's own scrip... | isomerase/GP-temperature-interpolation | gptempdata-2d.py | Python | mit | 3,799 | [
"Gaussian"
] | c57967fffbf09dc971d54d9d791dc26ee1fd7a1b3c981f9e662cb468bd5dff9e |
__author__ = 'Christo Robison'
from spectral import *
import numpy as np
#import tensorflow as tf
import h5py
import pylab
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from scipy import fftpack
import time
from skimage import io, exposure, img_as_uint, img_as_float
import png
io.use_plugin('... | Crobisaur/HyperSpec | Python/final_tests.py | Python | gpl-3.0 | 4,173 | [
"Gaussian"
] | 49d3f765150536f6cb66677c16a9ba765c4813896713759ed3fe2db6d7a38be5 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | gph82/PyEMMA | pyemma/coordinates/data/featurization/angles.py | Python | lgpl-3.0 | 8,442 | [
"MDTraj"
] | a0dfaf8b53f150c1591c38f75a6472574d9669c867fc407e5e470da8d234fab0 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'XtalxplorerMainWindowUI.ui'
#
# Created: Tue Feb 3 00:17:01 2015
# by: PyQt4 UI code generator 4.11.3
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUt... | jamasi/Xtal-xplore-R | gui/XtalxplorerMainWindowUI.py | Python | agpl-3.0 | 25,560 | [
"CRYSTAL"
] | 832ae67ec99f037e6d075d3019b99dff9b8ef1547e002227528942d42be6d29c |
# coding=utf-8
import argparse
import json
from selenium import webdriver, common
from common.config import Config
from common.proxy import Proxy
class Anime():
RANDOM_PROXY = -1
NO_PROXY = -2
def __init__(self):
pass
def fetch_anime(self, url, proxy_idx=NO_PROXY):
exec_path = Confi... | lchloride/bilibili_bangumi | anime/parser.py | Python | apache-2.0 | 10,500 | [
"VisIt"
] | 1fe914e75b9a52baa6d57c2cd2f35f4362f4b65b605229454933c3775cc05f05 |
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | graemian/ami-mooc-pilot | modules/dashboard/dashboard.py | Python | apache-2.0 | 29,317 | [
"VisIt"
] | c5ad63b33b79c4a29799fd2ce8ea3606db40839a974102d033bd3e4c47dfc0a0 |
from cefpython3 import cefpython as cef
import re, os, platform
import sys
import json
from threading import Thread
from subprocess import Popen, PIPE
def get_python_path():
return os.path.split(os.path.abspath(os.path.dirname(os.__file__)))[
0] + "/python"
def get_application_path(target=None):
... | McGill-DMaS/Kam1n0-Plugin-IDA-Pro | ida-plugin/Kam1n0/utilities/RequestPage.py | Python | apache-2.0 | 6,740 | [
"VisIt"
] | 7eca72ba851daae8785957137d9db7b7580ff4a9f73f034f9f80c99f5e0339f8 |
# original from
# http://tech.octopus.energy/news/2016/01/21/testing-for-missing-migrations-in-django.html
from io import StringIO
from django.core.management import call_command
from django.test import TestCase, override_settings
class MigrationTestCase(TestCase):
@override_settings(MIGRATION_MODULES={})
d... | webu/django-filer | tests/test_migrations.py | Python | bsd-3-clause | 885 | [
"Octopus"
] | 7f17b12f882f804ec7d9c577c886daf3d224d58d2ad31cd57489d330d6c8fc0a |
"""
Rewrite of rgFastQC.py for Version 0.11.2 of FastQC.
Changes implemented from tmcgowan at
https://testtoolshed.g2.bx.psu.edu/view/tmcgowan/fastqc
and iuc at https://toolshed.g2.bx.psu.edu/view/iuc/fastqc
with minor changes and bug fixes
SYNOPSIS
rgFastQC.py -i input_file -j input_file.name -o output_html_fil... | yhoogstrate/tools-iuc | tools/fastqc/rgFastQC.py | Python | mit | 6,425 | [
"Galaxy"
] | 695ccaceff09549b23b2f8d741e6b3e71075db3c7b8a9b314dc3b8093ce97eb0 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Craig J. Anderson
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Matt Keenan (matt.keenan@... | pmghalvorsen/gramps_branch | gramps/plugins/textreport/descendreport.py | Python | gpl-2.0 | 17,729 | [
"Brian"
] | a07a90986a12809473ddbb1fc515ba994cc15428a745dbf1e58a0b932392ce44 |
# Copyright 2018 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... | ghchinoy/tensorflow | tensorflow/tools/compatibility/update/generate_v2_renames_map.py | Python | apache-2.0 | 7,196 | [
"VisIt"
] | e855d4a34aaf2b413ee4e8fb4396b3d1cddb034ce94d650e9f66522948066e71 |
#!/bin/env python
"""
List the number of requests in the caches of all the ReqProxyies
"""
import DIRAC
from DIRAC.Core.Base.Script import Script
@Script()
def main():
Script.registerSwitch("", "Full", " Print full list of requests")
Script.parseCommandLine()
from DIRAC.RequestManagementSystem.Client.Re... | DIRACGrid/DIRAC | src/DIRAC/RequestManagementSystem/scripts/dirac_rms_list_req_cache.py | Python | gpl-3.0 | 1,203 | [
"DIRAC"
] | 53c1d2e5b3e4a25caeb1ba9481c950f2b16734344ed9d4c07c1c5d8127bac4cb |
#!/usr/bin/env python3
import os
import sys
import gzip
## files from NCBI BLAST tabular format
filename_A = sys.argv[1]
filename_B = sys.argv[2]
def read_tbl(filename):
rv = dict()
f = open(filename,'r')
if filename.endsiwth('.gz'):
f = gzip.open(filename,'rt')
for line in f:
if line.... | taejoonlab/taejoonlab-toolbox | align/bp_tbl-to-reciprocal_best.py | Python | gpl-3.0 | 986 | [
"BLAST"
] | 05a036adc29e1fa28ad774a5a71d2583b8f51f35f9aff76aa5d2021214258a60 |
# -*- coding:Utf-8 -*-
"""
.. currentmodule:: pylayers.util.geomutil
"""
from __future__ import print_function
import shapely.geometry as sh
import scipy.linalg as la
import pdb
import logging
import networkx as nx
import doctest
import os
#import mayavi.mlab as mlab
import matplotlib.pyplot as plt
import numpy as np... | dialounke/pylayers | pylayers/util/geomutil.py | Python | mit | 167,030 | [
"Mayavi"
] | 720e3d654b271aa310aa567a768e37ccd709da80f1c92ae408980ba66d5fa248 |
# Copyright (C) 2011-2012 Mark Burnett
#
# 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 prog... | mark-burnett/filament-dynamics | actin_dynamics/fitting_controller.py | Python | gpl-3.0 | 14,927 | [
"Gaussian"
] | c6ab78d7c6db2aa5d6dbaf981a30a052e1f33e7c9c88594170318e98c8592390 |
#!/usr/bin/env python
"check build refs"
#
# Copyright (C) 2011-2021 ABINIT Group (Yann Pouillon)
#
# This file is part of the ABINIT software package. For license information,
# please see the COPYING file in the top-level directory of the ABINIT source
# distribution.
#
from __future__ import unicode_literals, divisi... | abinit/abinit | abichecks/scripts/check-build-refs.py | Python | gpl-3.0 | 2,656 | [
"ABINIT"
] | feeacb24f78e5a00c280781ec3e0f13a1c7900d8c0ee3c538ff549c7029acf3a |
import numpy as np
import pylab as pl
import matplotlib
import matplotlib.pyplot as plt
from collections import defaultdict
import glob
import readline # otherwise the wrong readline is imported by rpy2
SAGE_XPS = 11
SAGE = 12
EAGE = 31
N_MONTHS = EAGE-SAGE+1
#TYPES = ["basic", "single-context", "topics"]
#TYPES = ["b... | SnippyHolloW/contextual_word_segmentation | src/plot_AGs_results.py | Python | mit | 18,834 | [
"Gaussian"
] | 742c307bd97ab11476f8dbf82a83dfd13d7ca9b83f1c9576e2d0067535c4c8da |
import sys
sys.path.append("../")
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
import neuroseries as nts
# def softma... | gviejo/ThalamusPhysio | python/pyfigures/main_article_old_fig_mouse12.py | Python | gpl-3.0 | 17,980 | [
"NEURON"
] | 7290bb894c5835e1e7be3baa3903ab075309911a1f636cfd8830c00cb0860e42 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('mantis_actionables', '0023_auto_20150310_1419'),
]
operations = [
migrations.AddField(
model_name='status',
... | siemens/django-mantis-actionables | mantis_actionables/migrations/0024_auto_20150311_1335.py | Python | gpl-2.0 | 903 | [
"Amber"
] | 91d8f5510b13db70881eba4fb7de9f4021d7d863998a56a8d6cf3cf8523524ac |
#!/usr/bin/env python
##########################################################################
#
# Copyright 2008 Tungsten Graphics, Inc., Cedar Park, Texas.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files ... | aYukiSekiguchi/ACCESS-Chromium | third_party/mesa/MesaLib/src/gallium/tests/python/retrace/model.py | Python | bsd-3-clause | 5,631 | [
"VisIt"
] | bd6974c427fc372721d10e99862623492c00ccd0335c859cc551391d869c73a0 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module define a WulffShape class to generate the Wulff shape from
a lattice, a list of indices and their corresponding surface energies,
and the total area and volume of the wulff shape,the weighted surface energy,
th... | vorwerkc/pymatgen | pymatgen/analysis/wulff.py | Python | mit | 27,746 | [
"pymatgen"
] | e3e034207642e1ceb817f0214573b0e80d895a6f9094d1f595096007fca8de12 |
#
# Copyright 2018 Analytics Zoo 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 applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/chronos/model/tcn.py | Python | apache-2.0 | 7,620 | [
"ORCA"
] | 112f617f4809fbfe2dbfb03cddc7cce505ac89600a3548a0bdedf62a4d55b2c3 |
"""Contains the MoveIn transition class."""
# move_in.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 time
import pygame
from mpf.system.timing i... | jabdoa2/mpf | mpf/media_controller/transitions/move_in.py | Python | mit | 4,014 | [
"Brian"
] | bae8b159a4125f683b5ac2556bf2efa1c2476b67d9064247bf0a249d238cb8cc |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011-2016 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | prculley/gramps | gramps/gen/plug/report/_book.py | Python | gpl-2.0 | 25,807 | [
"Brian"
] | 720a4d6b9b7570c76a88c4ff268921f0d8621493abd39f46d0f89978f1f28f9d |
# -*- 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/__init__.py | Python | gpl-2.0 | 7,425 | [
"Amber",
"CHARMM",
"Gromacs",
"LAMMPS",
"MDAnalysis",
"NAMD"
] | f4cc206f8a5dc0701fc7e027e63bbe19d912debc91b4be2ab185993d4172910a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import logging
import os
from monty.io import zopen
from monty.json import MSONable
from .utils import read_table_pattern, read_pattern
"""
Classes for reading/manipulating/writing QChem ouput files... | czhengsci/pymatgen | pymatgen/io/qchem_io/outputs.py | Python | mit | 9,412 | [
"Q-Chem",
"pymatgen"
] | 2e5f85e3ed2ff5851fe73273c6714a838d1cb439d65771c2f7045b50051df488 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The fusion module provides higher-level interfaces to some of the operations
that can be performed with the seg_LabFusion command-line program.
"""
import os
import warnings
from nipype.interfa... | fprados/nipype | nipype/interfaces/niftyseg/steps.py | Python | bsd-3-clause | 5,022 | [
"Gaussian"
] | e31567a30a8106039f6d623f9a59716fdd7ce8f05cfbf097f14d2cb7bd5ce953 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import os
import warnings
from string import Template
import numpy as np
from monty.io import zopen
from pymatgen.core.structure import Molecule, Structure
from monty.json import MSONable
from pym... | fraricci/pymatgen | pymatgen/io/nwchem.py | Python | mit | 35,922 | [
"Gaussian",
"NWChem",
"pymatgen"
] | 7c6a362daf6b62e14aba6b5ef42fc41d6ff76ac7ed01f5a15e79e1c79ecf0f86 |
'''
Created on Jul 21, 2011
@author: mkiyer
'''
'''
Created on Jun 4, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published ... | tectronics/chimerascan | chimerascan/deprecated/nominate_chimeras_v0.4.1.py | Python | gpl-3.0 | 8,443 | [
"pysam"
] | 2d330529eb4d8c966340890cc65beaf075091ef4b61cb4904314ad6b1e633df4 |
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Honeybee is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | samuto/Honeybee | src/Honeybee_Simulation Control.py | Python | gpl-3.0 | 4,014 | [
"EPW"
] | 2a99f7fab866856e643f3562617ed65aa41c0b334f7f27ba02bb4417d4915e76 |
# Copyright 2018 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | tensorflow/moonlight | moonlight/score_processors.py | Python | apache-2.0 | 1,382 | [
"VisIt"
] | 31439d36a30e7248155267849bff6af954ddbdd3898e3e7b902b54058742a477 |
#!/usr/bin/env python
"""
From lammps logs file(s), finds key output such as system energy and temperature
"""
from __future__ import print_function
import argparse
import os
import sys
import re
from md_utils.md_common import (InvalidDataError, warning, file_rows_to_list, IO_ERROR, GOOD_RET, INPUT_ERROR,
... | team-mayes/md_utils | md_utils/lammps_log_proc.py | Python | bsd-3-clause | 5,922 | [
"LAMMPS"
] | 90d158388f56ce3acd6be4805c0d8bfd5d67bc97529573e936945354a0712ee3 |
#-*- coding: utf-8 -*-
#! /usr/bin/env python
'''
#------------------------------------------------------------
filename: lab10_runTCcheckReLu_spiraldata.py
To check effect of Relu activation function over
Deep neural networks.
This script wants to see Relu activation can mitigate
Gradient Vanishin... | jwkanggist/EveryBodyTensorFlow | lab10_runTFcheckReLu_spiraldata.py | Python | unlicense | 14,810 | [
"NEURON"
] | c0fb020959ff578483ccc6e0ccbdb8607f71d9671f83c39762ea400ca25563fb |
# Copyright (c) 2015-2016 Cara Vinson <ceridwenv@gmail.com>
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Licensed under the LGPL: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html
# For details: https://github.com/PyCQA/astroid/blob/master/COPYING.LESSER
from __future__ import print_func... | lucidmotifs/auto-aoc | .venv/lib/python3.5/site-packages/astroid/tests/unittest_transforms.py | Python | mit | 8,122 | [
"VisIt"
] | 5767391f5f24eec28953f71b55a882730beebcdd7b5d2c6b4bd84ce527af2f5c |
import pathlib
import numpy as np
import pytest
from util import full
from loprop.core import penalty_function, AU2ANG, pairs
from loprop.dalton import MolFragDalton
from .common import LoPropTestCase
from . import h2o_rot_data as ref
thisdir = pathlib.Path(__file__).parent
case = "h2o_rot"
tmpdir = thisdir / case ... | vahtras/loprop | tests/test_h2o_rot.py | Python | gpl-3.0 | 18,025 | [
"Dalton"
] | e70bfa3f20d34a117cf74dd1218ff0136b4c1eab85be4feb60f0d1a4f980b1f0 |
import scipy.linalg
import numpy as np
import matplotlib.pyplot as pl
def eta(x, threshold):
return np.sign(x) * np.fmax(np.abs(x) - threshold, 0)
def etaprime(x, threshold):
return (x > threshold) + (x < -threshold)
def largestElement(x, n):
lenx = len(x)
if (n > lenx):
n = lenx-1
if (n ... | aasensio/pyiacsun | pyiacsun/sparse/damp.py | Python | mit | 3,311 | [
"Gaussian"
] | 05024f7fc0eacd708c3f2a9e72b02635df38cda2e8175520ce3e21141da45337 |
"""
QAPI event generator
Copyright (c) 2014 Wenchao Xia
Copyright (c) 2015-2018 Red Hat Inc.
Authors:
Wenchao Xia <wenchaoqemu@gmail.com>
Markus Armbruster <armbru@redhat.com>
This work is licensed under the terms of the GNU GPL, version 2.
See the COPYING file in the top-level directory.
"""
from qapi.common imp... | dslutz/qemu | scripts/qapi/events.py | Python | gpl-2.0 | 6,148 | [
"VisIt"
] | 88a4f9422d5d2f1b0add22ef140e4619b07020eaa048e0e1d22a16c4ccabe275 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A. Beauchamp, TJ Lane, Jo... | hainm/mdtraj | mdtraj/core/trajectory.py | Python | lgpl-2.1 | 66,597 | [
"Amber",
"CHARMM",
"Desmond",
"Gromacs",
"LAMMPS",
"MDTraj",
"NAMD",
"NetCDF",
"OpenMM"
] | c335e22901ed42b01822a14f396066f577b15e150446f9d5e54bd39c4d9d798f |
import os
import os.path as osp
from setuptools import setup, find_packages
from setuptools.command.test import test as TestCommand
import sys
if os.getenv("READTHEDOCS") == "True":
# to make versioneer working, we need to unshallow this repo
# because RTD does a checkout with --depth 50
import subprocess... | Chilipp/psy-simple | setup.py | Python | gpl-2.0 | 2,916 | [
"NetCDF"
] | db1db4e8ad675c7af4c8d6a02022bcefe4380d3226f8ec794e23f54b5ac55e25 |
import os
import shutil
import tempfile
import unittest
from collections import Iterable
from PIL import Image
import numpy
from mayavi.sources.vtk_data_source import VTKDataSource
from mayavi.modules.iso_surface import IsoSurface
from mayavi.modules.text3d import Text3D
from mayavi.tests import datasets
from mayavi... | simphony/simphony-mayavi | simphony_mayavi/tests/test_restore_scene.py | Python | bsd-2-clause | 7,067 | [
"Mayavi"
] | b8c48b5b44c1f3e43209a21a27ff40b4394924f0be309824b824f030d62aea95 |
"""
example script to show the detector parameter determination for area detectors
from images recorded in the primary beam and at known symmetric coplanar Bragg
reflections of a reference crystal
"""
import os
import numpy
import xrayutilities as xu
Si = xu.materials.Si
datadir = 'data'
specfile = "si_align.spec"
... | dkriegner/xrayutilities | doc/source/example_xu_ccd_parameter_hkl.py | Python | gpl-2.0 | 4,109 | [
"CRYSTAL"
] | 5c2d3868f4c5db588192848d12d82e79854257817cbfd49d03db4961107d83a3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (c) 2013 Spotify AB
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | BeifeiZhou/annoy | setup.py | Python | apache-2.0 | 2,123 | [
"VisIt"
] | a84af307064c38c5bbab1a93494b071cfac1caefe1f42d03d6bf8fc5df2bef55 |
from __future__ import print_function
import queue
import cancat
import struct
from cancat.J1939db import *
from cancat import *
from cancat.vstruct.bitfield import *
PF_RQST = 0xea
PF_TP_DT = 0xeb
PF_TP_CM = 0xec
PF_ADDRCLAIM = 0xee
PF_PROPRIETRY= 0xef
PF_KWP1 = 0xdb
PF_KWP2 = 0xda
PF_... | atlas0fd00m/CanCat | cancat/j1939.py | Python | bsd-2-clause | 37,051 | [
"COLUMBUS"
] | 929263b1ab66278ce224d65bfe3460674bab51907d13f5c5967688831f58e3cf |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | cdegroc/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 34,977 | [
"Brian"
] | 3c10492f3755f0e77c1fc55233e8a0f76d105c1828bc6afd6cb94ec82abae59e |
# PSTH experiments
#
# Copyright (C) 2010-2012 Huang Xin
#
# See LICENSE.TXT that came with this file.
from __future__ import division
import os
import sys
import time
import Pyro.core
import subprocess
from Experiment import ExperimentConfig,Experiment
class PSTHExperiment(Experiment):
PSTH_SERVER_PROCESS = None... | chrox/RealTimeElectrophy | Experimenter/Experiments/PSTHExperiment.py | Python | bsd-2-clause | 13,693 | [
"Gaussian"
] | b5e70b4974a85c70f3514b2276ca27aad5eb1d8f93776e2cdfdcdef8c9b91d0e |
import numpy as np
from numpy.dual import svd
from scipy.spatial.distance import pdist, squareform, cdist
from StringGPy.utilities.gpy_kernels import StringGPKern, string_cov
import sys
from multiprocessing import Pool, cpu_count
'''
Computes the (unconditional) covariance matrix between two vectors.
'''
def covMatrix... | YLnKS/StringGPy | StringGPy/utilities/other_goodies.py | Python | bsd-3-clause | 11,053 | [
"Gaussian"
] | a2a6ad0230d862e11259cc047d8c60ea5405ce7aa9ac6104c8346056798faa38 |
from DIRAC import gLogger, S_OK
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.StorageManagementSystem.Client.StorageManagerClient import StorageManagerClient
from DIRAC.Resources.Storage.StorageElement import StorageElement
from DIRAC.StorageManagementSystem.DB.StorageManagementDB import THROTTLING_ST... | DIRACGrid/DIRAC | src/DIRAC/StorageManagementSystem/Agent/StageRequestAgent.py | Python | gpl-3.0 | 24,958 | [
"DIRAC"
] | 7d7d4c8c264f7e661798e80d654bf0d8ebb739ee9b028c7ebce449c47a30c364 |
# -*- coding: utf-8 -*-
'''
Created on 28 Nov 2013
@author: Kimon Tsitsikas
Copyright © 2012-2013 Kimon Tsitsikas, Delmic
This file is part of Odemis.
Odemis is free software: you can redistribute it and/or modify it under the terms
of the GNU General Public License version 2 as published by the Free Software
Fou... | delmic/odemis | src/odemis/acq/align/test/coordinates_test.py | Python | gpl-2.0 | 19,482 | [
"Gaussian"
] | df20a56b91d6e4e96e117a20466fd80a13ab08dfb835b50e299b59e81f1a97f8 |
###############################################################################
# #
# 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 #
... | dparks1134/biolib | biolib/blast_parser.py | Python | gpl-3.0 | 5,252 | [
"BLAST"
] | 20d1c10739f75cb4d5b390d68445fd6435d236c887056dc3bb32a5a73d094c2a |
import numpy
import numpy.linalg
import scipy.linalg
import scipy.interpolate
from scipy.signal import wiener, filtfilt, butter, gaussian
from scipy.ndimage import filters
from matplotlib import pyplot as plt
plt.style.use('classic')
from assimulo.solvers import IDA
from assimulo.problem import Implicit_Problem
fro... | matthewpklein/battsimpy | tests/dae_genPart.py | Python | gpl-3.0 | 59,229 | [
"Gaussian"
] | 2a9fc896ae8822b3b45135ca7e637c430c63e8e7f4fd4c332365e22e5794f799 |
""" FileReport module defines the FileReport class, to report file status to the transformation DB
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import copy
from DIRAC import S_OK
from DIRAC.Core.Utilities import DEncode
from DIRAC.TransformationSyste... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Client/FileReport.py | Python | gpl-3.0 | 2,597 | [
"DIRAC"
] | 37aff056408001bc7e51dcc119aab28f1769f423c5de4b1181574b51a34ea7bc |
import numpy as np
import time
from astrometry.util.ttime import Time
from astrometry.util.resample import resample_with_wcs, OverlapError
from astrometry.util.fits import fits_table
from astrometry.util.plotutils import dimshow
from tractor import Tractor, PointSource, Image, Catalog, Patch, Galaxy
from tractor.gala... | legacysurvey/legacypipe | py/legacypipe/oneblob.py | Python | bsd-3-clause | 102,118 | [
"Galaxy"
] | 2f68d5e59e47673c37ad7e3a11740153236317159f0cfc5211314df492bff638 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.uk/wiki... | acsis-project/emissions | emissions/python/periodic_1960/regrid_CO_emissions_n96e_360d_1960.py | Python | gpl-3.0 | 7,011 | [
"NetCDF"
] | fc5f314596d51023aee5675f4210b5a0c78da4e2b5e3ef81b96878afe408e3f9 |
# sql/expression.py
# Copyright (C) 2005-2013 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Defines the base components of SQL expression trees.
All components are derived ... | gujiawen/flask_web | venv/lib/python2.7/site-packages/sqlalchemy/sql/expression.py | Python | mit | 222,486 | [
"VisIt"
] | 7c750f376070127410e22450f20f9d5e1fa2a94d41e16f41e747c9f2983bbbf8 |
# 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 u... | nusdbsystem/incubator-singa | python/singa/tensor.py | Python | apache-2.0 | 43,493 | [
"Gaussian"
] | 5f0354ee44d0c10fb19eb81c0b0c5203455a179eab97a0ed46b1755ddc1fe4b4 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
from odoo.tests.common import SavepointCase, TransactionCase, HttpCase
class TransactionCaseWithUserDemo(TransactionCase):
def setUp(self):
super(TransactionCaseWithUserDemo, self).setUp()
self.en... | ddico/odoo | odoo/addons/base/tests/common.py | Python | agpl-3.0 | 8,468 | [
"Amber"
] | 8faef9197b1f8d9275db4c3722076a5d2c37c01f7c592945373fce26d715263b |
# -*- coding: utf-8 -*-
"""
This is a Python implementation of the fast algorithm developed by
Vincent Mazet and Nicolas Chopin
(see http://miv.u-strasbg.fr/mazet/rtnorm/).
The version this code is based on is the Matlab implementation from 2012.
Created on Mon Aug 12 13:48:22 2013
Update on 11/27/2014: Added `erf` f... | nick-youngblut/SIPSim | SIPSim/rtnorm.py | Python | mit | 203,109 | [
"Gaussian"
] | 3090bf5dc13edbb4f194b35e63b8faea428a7103917ad1dc94f8119422075868 |
# special hop classes that have not been moved into MDAnalysis.analysis.density
# Already changed msg --> logger and various other bits and pieces.
import numpy # need v >= 1.0
import sys
import os,os.path,errno
import cPickle
import warnings
from gridData import Grid, OpenDX # http://github.com/orbeckst/GridData... | iwelland/hop | hop/density_newmda.py | Python | lgpl-3.0 | 13,736 | [
"MDAnalysis",
"VMD"
] | 557ccd7ed122856b9e33c0533aa7eb559e58b6431c5bd049f789f5879c340c2b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Run this test like so:
# vtkpython TestParallelCoordinatesColors.py -D $VTK_DATA_ROOT \
# -B $VTK_DATA_ROOT/Baseline/Charts/
import os
import vtk
import vtk.test.Testing
import math
class TestParallelCoordinatesColors(vtk.test.Testing.vtkTest):
def testLinePlot(se... | aashish24/VTK-old | Charts/Core/Testing/Python/TestParallelCoordinatesColors.py | Python | bsd-3-clause | 3,087 | [
"VTK"
] | 7c70736b87f006b60c0a5324faed58410af18633133b18280da8c83b3a45c3e9 |
import unittest
# https://www.interviewcake.com/question/python3/mesh-message
# MeshMessage problem from InterviewCake.
# Essentially a breath-first search that keeps track of previous parent.
from collections import deque
def get_path(graph, start_node, end_node):
if start_node not in graph:
raise Exce... | jackchi/interview-prep | graph/graph-shortest-path.py | Python | mit | 2,958 | [
"VisIt"
] | 6e097a3ab56e825cf8d38f5b65e11314f0a392d3f321f1034f39dbaca9b50795 |
"""
Code for managing the implementation cache.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
import os
from logging import debug, info, warn
from zeroinstall.support import basedir
from zeroinstall import SafeException, support
c... | pombredanne/zero-install | zeroinstall/zerostore/__init__.py | Python | lgpl-2.1 | 10,114 | [
"VisIt"
] | 5ae1a93d1c93dfcf50128949f67bc8e4e1f67cd285cd407d075c52b2b627f60f |
"""Module symbol-table generator"""
from compiler import ast
from compiler.consts import SC_LOCAL, SC_GLOBAL_IMPLICIT, SC_GLOBAL_EXPLICT, \
SC_FREE, SC_CELL, SC_UNKNOWN
from compiler.misc import mangle
import types
import sys
MANGLE_LEN = 256
class Scope:
# XXX how much information do I need ... | ktan2020/legacy-automation | win/Lib/compiler/symbols.py | Python | mit | 14,949 | [
"VisIt"
] | ec5146c044ebbd07b2f7b83fd95b6bd9487cf5d419468a71aa93e8af89ecbcda |
# -*- coding: utf-8 -*-
""" Laplacian segmentation """
# Code source: Brian McFee
# License: ISC
from collections import defaultdict
import numpy as np
import scipy
import sklearn.cluster
import librosa
def embed_beats(A_rep, A_loc, config):
R = librosa.segment.recurrence_matrix(A_rep, width=config["rec_widt... | urinieto/msaf | msaf/algorithms/scluster/main2.py | Python | mit | 4,321 | [
"Brian"
] | 4e5285e5a4accc4db16fdff101bdfc988862ae538d203a5bca9ba903b7eab43a |
from unittest import mock
import numpy as np
import pytest
import hyperspy.api as hs
from hyperspy.misc.utils import slugify
from hyperspy.decorators import lazifyTestClass
from hyperspy.misc.test_utils import ignore_warning
RTOL = 1E-6
class TestModelJacobians:
def setup_method(self, method):
s = hs... | sem-geologist/hyperspy | hyperspy/tests/model/test_model.py | Python | gpl-3.0 | 45,608 | [
"Gaussian"
] | ff46a00e846313115e34c677e9adb06e812c10af555a8ea4b4c0c6d52361441b |
import pytest
import numpy as np
import elfi
def simple_gaussian_model(true_param, seed, n_summaries=10):
"""The simple gaussian model that has been used as a toy example in the LFIRE paper."""
def power(x, y):
return x**y
m = elfi.ElfiModel()
mu = elfi.Prior('uniform', -5, 10, model=m, na... | elfi-dev/elfi | tests/unit/test_bolfire_unit.py | Python | bsd-3-clause | 1,654 | [
"Gaussian"
] | 818258680d0567afd8ed4b790297b544a0f76f6cc570bec9dd464a587fbb1e65 |
#
# Copyright 2015 LinkedIn Corp. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | thomas-young-2013/wherehowsX | metadata-etl/src/main/resources/jython/CodeSearchLoad.py | Python | apache-2.0 | 6,633 | [
"ESPResSo"
] | 6c8ec7225d8118f370a3308653fbf3242f7d24c12ddc3de5426e8a0e51b96eed |
# -*- coding: utf-8 -*-
#
# -----------------------------------------------------------------------------------
# Copyright (c) Microsoft Open Technologies (Shanghai) Co. Ltd. All rights reserved.
#
# The MIT License (MIT)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this softw... | xunxunzgq/open-hackathon-bak_01 | open-hackathon-server/src/hackathon/docker/hosted_docker.py | Python | mit | 24,562 | [
"VisIt"
] | 3aacb61c9d879ea58ed6808783ea654368c5551fa96590b4e87269053e6f3563 |
from ase.data.molecules import molecule
from ase.visualize import view
from gpaw import GPAW
from gpaw.wannier import Wannier
calc = GPAW(nbands=4)
atoms = molecule('H2O')
atoms.center(vacuum=3.)
atoms.set_calculator(calc)
atoms.get_potential_energy()
# Initialize the Wannier class
w = Wannier(calc)
w.localize()
cen... | qsnake/gpaw | doc/exercises/wannier/wannier-h2o.py | Python | gpl-3.0 | 397 | [
"ASE",
"GPAW"
] | 42c8fdce4b828b778f084a0941bcf7dadffbd6f542bedb7e0a76a78877f70948 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | doc/sphinxman/source/psi4doc/ext/__init__.py | Python | lgpl-3.0 | 978 | [
"Psi4"
] | 785dd09fdca20a408283535bd3eeddbbdfe3991bc9dc79a82929f8bb60e8704e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | vmanoria/bluemix-hue-filebrowser | hue-3.8.1-bluemix/apps/useradmin/src/useradmin/tests.py | Python | gpl-2.0 | 37,802 | [
"MOE"
] | a10296ea3b576e6c831fa0ef296d4b30c3990cb9417d86fe7638f524d191686c |
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.conf.urls.i18n import i18n_patterns
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpatterns = [
#... | manax-dojo/cashflow | config/urls.py | Python | bsd-3-clause | 1,829 | [
"VisIt"
] | c2710bcb615576e8bbaf76b62d21a8faff15018795571ea0fcb07136c6272c79 |
import numpy as np
from GPy.core import Param
from GPy.kern.src.grid_kerns import GridRBF
from GPy.kern.src.psi_comp import PSICOMP_RBF, PSICOMP_RBF_GPU
from GPy.kern.src.stationary import Stationary
from paramz.transformations import Logexp
class CausalRBF(Stationary):
"""
Radial Basis Function kernel, aka s... | neildhir/DCBO | src/bayes_opt/causal_kernels.py | Python | mit | 6,617 | [
"Gaussian"
] | 535e9381c3e72e0f8c6ba62e487f8bf01d352e8ebc7f4985e43c20d880896ae3 |
__author__ = 'Daan Wierstra and Tom Schaul'
from itertools import chain
from scipy import zeros
from pybrain.structure.networks.feedforward import FeedForwardNetwork
from pybrain.structure.networks.recurrent import RecurrentNetwork
from pybrain.structure.modules.neuronlayer import NeuronLayer
from pybrain.structure.... | hassaanm/stock-trading | src/pybrain/structure/networks/neurondecomposable.py | Python | apache-2.0 | 4,335 | [
"NEURON"
] | 037373e8a0658abb5451046c49ccbe16a93f770f5dbc7ed22099ef58482355a5 |
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