text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | ngoix/OCRF | sklearn/tree/tree.py | Python | bsd-3-clause | 40,464 | [
"Brian"
] | 09e834d412c796bf4b0bdf2677c99b5be656fb80c0e835b0cfba12c47e1922c9 |
'''
Script to run station location quality assurance for stations in netCDF database.
'''
from twx.db import StationDataDb
from twx.db.obs_por import build_por_mask
from twx.qa.qa_location import LocQA
from twx.utils import StatusCheck
from twx.utils.config import TwxConfig
import numpy as np
import os
if __name__ ==... | jaredwo/topowx | scripts/step06_qa_stn_loc.py | Python | gpl-3.0 | 2,780 | [
"NetCDF"
] | 0ca50e8ce7c0ca5a527a10434abfbdb6af7af504c3d173bc22ef6bb50c9f7a45 |
# -*- coding: utf-8 -*-
import json
import urllib.request
import urllib.parse
import re
class countries:
def __init__(self, core, client):
core.addCommandHandler("pais", self, chelp="Muestra información de un país. Uso: pais <código del país>",
alias=["país", "country"])
def pais(self, bot, ... | irc-CoBot/pyCoBot | modules/countries/countries.py | Python | mit | 43,558 | [
"BWA"
] | 3571a6fe5b44796fd1494b6b25952590ab143cbd5d90f9cb916e471d15a1697c |
# 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.
"""Collections of various bits of useful biological data."""
| zjuchenyuan/BioWeb | Lib/Bio/Data/__init__.py | Python | mit | 230 | [
"Biopython"
] | 2210451473d51ecc77fd9f794d8dd83ac304e06835af34327c80e41858242ee1 |
import pytest
from stellar_sdk import (
AiohttpClient,
Asset,
MuxedAccount,
Network,
ServerAsync,
TransactionEnvelope,
)
from stellar_sdk.account import Thresholds
from stellar_sdk.call_builder.call_builder_async import *
@pytest.mark.slow
@pytest.mark.asyncio
class TestServerAsync:
async... | StellarCN/py-stellar-base | tests/test_server_async.py | Python | apache-2.0 | 7,152 | [
"MOE"
] | bd55cd3c376874f1d3e6ce82a804c1d945d2d71e241487c9fd5ccfef44a52978 |
import gc
from math import cos, fabs, pi, radians, sin
import numpy
from numpy import array, array_equal, concatenate, copy, diag, dot, identity, logical_and, outer, vstack, zeros, float32
from operator import itemgetter, attrgetter
from os import listdir
from os.path import basename, dirname, exists, join, normpath, s... | Marginal/OverlayEditor | clutterdef.py | Python | gpl-2.0 | 80,966 | [
"BLAST"
] | cad2403d056618c376e5f81e98b1cf509eaa8e682a1b4278817a7329cf8b2d5f |
import numpy as np
from utils import learning_rules as rules
class PermutationParityMachine(object):
"""Permutation Parity Machine (PPM)
Used in Neural Cryptography to generate a key of size K*N via its weights. Weights consists of 0s and 1s.
"""
def __init__(self, K, N):
"""Initializes the ... | johnsbuck/neural_cryptography | parity_machine/ppm.py | Python | mit | 2,153 | [
"NEURON"
] | c2fecddab4f85f0686fc415a199f35caf768e366f53f030a3516a100903e4eed |
"""
==========
Model Grid
==========
Fit a line based on parameters output from a grid of models
"""
import numpy as np
from pyspeckit.mpfit import mpfit
import matplotlib.cbook as mpcb
import copy
try:
import scipy.interpolate
import scipy.ndimage
scipyOK = True
except ImportError:
scipyOK=False
def g... | vlas-sokolov/pyspeckit | pyspeckit/spectrum/models/modelgrid.py | Python | mit | 2,013 | [
"Gaussian"
] | 07ae893fc16ae731dcb88bd0d7b129feb13b56b3345a784dc761dba6dcbf88f0 |
from splinter import Browser
browser = Browser('phantomjs')
browser.visit('http://dev.usv.com')
if browser.status_code == 200:
print("success") | ktrumble/prmai | tests.py | Python | gpl-3.0 | 146 | [
"VisIt"
] | 32c00c0acdc506727cdbef523d35dede2b23c960cd0f673e669e90460b2f40c8 |
"""Functions to plot M/EEG data on topo (one axes per channel)
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eri... | ARudiuk/mne-python | mne/viz/topo.py | Python | bsd-3-clause | 28,610 | [
"Gaussian"
] | d5335a06a526f11435d7e77c00f5edd2bb733a7ed8a54b46124307c5efb89897 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Functional tests using WebTest."""
import datetime as dt
import httplib as http
import logging
import unittest
import markupsafe
import mock
import pytest
from nose.tools import * # flake8: noqa (PEP8 asserts)
import re
from addons.wiki.utils import to_mongo_key
from ... | sloria/osf.io | tests/test_webtests.py | Python | apache-2.0 | 45,154 | [
"VisIt"
] | 72697ba59166222c2561f2e25be4e85703f8544f97c55f941d130402a2dd090b |
# coding: utf-8
import logging
import urllib
import time
from collections import defaultdict
from lxml import html
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolvers import reverse
from django.contrib.auth... | XiaodunServerGroup/xiaodun-platform | lms/djangoapps/wechat/views.py | Python | agpl-3.0 | 54,747 | [
"VisIt"
] | 3ca56ea58e273ac311ed0cfa9c9145aa09333b09ebe1ff997fd5576be4ac1b52 |
# Copyright 2020 Tensorforce Team. 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 la... | reinforceio/tensorforce | tensorforce/agents/tensorforce.py | Python | apache-2.0 | 40,790 | [
"Gaussian"
] | 4692f3f8864973307c28f820606709c9febe549f3520f00eced1b018f74418d4 |
"""
Python bindings for the `webkit-server <https://github.com/niklasb/webkit-server/>`_
"""
import sys, os
import subprocess
import re
import socket
import atexit
import json
# path to the `webkit_server` executable
SERVER_EXEC = os.path.abspath(os.path.join(os.path.dirname(__file__),
... | Elbandi/webkit-server | webkit_server.py | Python | mit | 17,539 | [
"VisIt"
] | 84e8d26a2b131343adbe6fa9ba3b14fabbe23c3264b5b18b8e42cb65ce06e15f |
'''
################################################################################
# James Clough 2015
# jrc309@ic.ac.uk
# 2016 Complexity & Networks course
#
# log_bin.py v1.3
# 14/01/2016
#
# Usage instructions for log binning:
#
# to import the log_bin functions:
# from log_bin import *
#
# to use the log_bin fu... | zraxon/Oslo-Model | log_bin.py | Python | gpl-3.0 | 9,777 | [
"TINKER"
] | a510521d870e590685acc89f71c9a5a690370ca70ef8fb9568531307894fb736 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2010, Monash e-Research Centre
# (Monash University, Australia)
# Copyright (c) 2010, VeRSI Consortium
# (Victorian eResearch Strategic Initiative, Australia)
# All rights reserved.
# Redistribution and use in source and binary forms, with or without
# modification, are pe... | grischa/mytardis-mrtardis | tardis/tardis_portal/forms.py | Python | bsd-3-clause | 28,650 | [
"CRYSTAL"
] | 3bca160dc82cbf1d94ac5f3bf7dc2c1f2e5caf4969c407f4d20dee67a4b88491 |
"""
Module simplifying manipulation of XML described at
http://libvirt.org/formatdomain.html
"""
import logging
from avocado.utils import process
from .. import xml_utils
from ..libvirt_xml import base, accessors, xcepts
from ..libvirt_xml.devices import librarian
class VMXMLDevices(list):
"""
List of dev... | PandaWei/avocado-vt | virttest/libvirt_xml/vm_xml.py | Python | gpl-2.0 | 84,223 | [
"VisIt"
] | e70146545e83bbcd3b42a633a30432b32d6cb23d22c75d2fe0bf85af3e959000 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, 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.
"""Parser for DALTON output files"""
import re
import numpy
from cclib.parser import logfileparser
from cclib.parser i... | berquist/cclib | cclib/parser/daltonparser.py | Python | bsd-3-clause | 59,720 | [
"Dalton",
"Gaussian",
"cclib"
] | 41599a5a5493830a56b023a9a2b8fdeb3c11cb6a6247c8f89f71f11cb7042c44 |
#!/usr/bin/env python
import numpy as np
def read_vibra_vectors(fname=None):
""" Reads siesta.vectors file --- output of VIBRA utility """
from io import StringIO # StringIO behaves like a file object
if fname is None: fname = 'siesta.vectors'
with open(fname, 'r') as content_file: content = content_file.re... | gkc1000/pyscf | pyscf/nao/m_phonons.py | Python | apache-2.0 | 3,246 | [
"PySCF",
"SIESTA"
] | a826e1a52ef3a52ba3486962661d2a1ab1cd2c2e0335c8f8e0a7692582ad8041 |
from openzwave.network import ZWaveNode
from Firefly import logging
from Firefly.components.zwave.zwave_device import ZwaveDevice
from Firefly.const import CONTACT, CONTACT_CLOSED, CONTACT_OPEN, DEVICE_TYPE_SWITCH, STATE
from Firefly.helpers.metadata.metadata import metaWaterLevel
TITLE = 'Aeotec Zwave ZW097 Dry Cona... | Firefly-Automation/Firefly | Firefly/components/zwave/zwave_aeotec_zw097_dry_contact.py | Python | apache-2.0 | 2,915 | [
"Firefly"
] | d13ccbba2f73f017686b61a6de056428f3f4718ef64acdb44c4b63d2518fdb81 |
from __future__ import print_function
from json import dumps
from getpass import getuser
from .base.base_drmaa import BaseDrmaaManager
from .util.sudo import sudo_popen
from ..managers import status
try:
from galaxy.tools.deps.commands import which
except ImportError:
from galaxy.tool_util.deps.commands impor... | natefoo/pulsar | pulsar/managers/queued_external_drmaa.py | Python | apache-2.0 | 4,656 | [
"Galaxy"
] | d36fc33f566419d29bb7afdbad9fda9646bef05381f20735e7e6cbcac2bbadc3 |
#!/usr/bin/env python
"""
midi.py -- MIDI classes and parser in Python
Placed into the public domain in December 2001 by Will Ware
Python MIDI classes: meaningful data structures that represent MIDI events
and other objects. You can read MIDI files to create such objects, or
generate a collection of objects and use ... | jiedo/piano_ear | midi.py | Python | gpl-3.0 | 17,391 | [
"CRYSTAL"
] | 7ead1537de8d7b01d83be2b2c104da478d4512175f620f4fdf730712c6f539a6 |
from sqlalchemy import *
from migrate import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import *
import logging
log = logging.getLogger( __name__ )
metadata = MetaData()
def display_migration_details():
prin... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/model/migrate/versions/0050_drop_cloud_tables.py | Python | gpl-3.0 | 6,064 | [
"Galaxy"
] | 5f7216ea46c932697723bfa99741248ef589b45fe561ec05aad00d97b677b08d |
#!/usr/bin/env python
#Dan Blankenberg
import sys
import os
import tempfile
import optparse
import subprocess
from galaxy.util.json import from_json_string, to_json_string
CHUNK_SIZE = 2**20
ONE_GB = 2**30
DEFAULT_DATA_TABLE_NAME = "sailfish_indexes"
def get_id_name( params, dbkey, fasta_description=None):
#T... | mr-c/tools-iuc | data_managers/data_manager_sailfish_index_builder/data_manager/bwa_index_builder.py | Python | mit | 4,643 | [
"BWA",
"Galaxy"
] | c9758e2bee850e1b226f00aff5b237f9f1f8439dad03f018d22781ad980f69ba |
#!/usr/bin/env python
################################################################################
#
# qnex2nexafs.py
#
# Version 1.0
#
# Usage qnex2nexafs.py SEED
#
# Converts the series of xspectra outputs (in the form of .qnex files from Kane's
# BASH script) to the .nexafs format created by nexspec, for use wit... | HSINWEI/physics | python/qnex2nexafs.py | Python | gpl-3.0 | 2,735 | [
"Quantum ESPRESSO"
] | a54eed11336d5e006b5a6aa92bb6c61c96f894cf4e6a48db11fa27925e2b3432 |
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import ThreadScheduler
from DIRAC.Core.Base.ExecutorMindHandler import ExecutorMindHandler
from DIRAC.WorkloadManagementSystem.Client.JobState.JobState import JobState
from DIRAC.WorkloadManagementSystem.Client.JobState.CachedJobState import... | andresailer/DIRAC | WorkloadManagementSystem/Service/OptimizationMindHandler.py | Python | gpl-3.0 | 6,796 | [
"DIRAC"
] | f989b0a9002080af6e49a1cdda31e856cc060621ca97eb2d9b8eef6a76da5ad9 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyBiomine(PythonPackage):
"""Bioinformatics data-mining."""
homepage = "https://githu... | rspavel/spack | var/spack/repos/builtin/packages/py-biomine/package.py | Python | lgpl-2.1 | 729 | [
"pysam"
] | 38658fd2f6ccac800c21ce6d4ce56576b16239d5eca2b6a40bc8d737510dc6fb |
"""Adding icons and menu items using the freedesktop.org system.
(xdg = X Desktop Group)
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import shutil, os, tempfile
from zeroinstall import SafeException
from zeroinstall.suppor... | afb/0install | zeroinstall/gtkui/xdgutils.py | Python | lgpl-2.1 | 2,907 | [
"VisIt"
] | 979a42aa364ca5a5c2dc8b2d9abdc2c576b9150945a47488cdca3b42af487a2e |
# Copyright 2010 by Tiago Antao. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This class provides code to parse BIG GenePop files.
The difference between this class and ... | bryback/quickseq | genescript/Bio/PopGen/GenePop/FileParser.py | Python | mit | 11,381 | [
"Biopython"
] | e29b9b1ac1b262f54835108f94eaf8abc402ae4725ec05c1b7efbc2d3eb67859 |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify it
# u... | graalvm/mx | mx_urlrewrites.py | Python | gpl-2.0 | 7,464 | [
"VisIt"
] | dfc68e6af7a538704bb2c5abe1a177a7cee81baee85d9fdebf6ed7d234f11f2f |
# -*- coding: utf-8 -*-
"""
Aperture Photometry of point-like objects
=========================================
Simple class to do aperture photometry on a stamp of a point-source.
:requires: NumPy
Created on Thu Apr 20 14:37:46 2017
:author: Ruyman Azzollini
"""
# IMPORT STUFF
from pdb import set_trace as sto... | ruymanengithub/vison | vison/point/photom.py | Python | gpl-3.0 | 4,905 | [
"Gaussian"
] | 3c1561f986c9571181e0048f4896e3c346f21dbf4719d7b2801683452b93adc6 |
import numpy as np
from gpaw.test import wrap_pylab
wrap_pylab()
import pylab as pl
def plot_EELS(head):
# plot EELS spectra
pl.figure(figsize=(4,7))
d = np.loadtxt(head + '_q_list')
q = d[:,0]
ndata = q.shape[0] + 1
w = np.zeros(ndata)
w2 = np.zeros(ndata)
for i in range(1,ndata):
... | qsnake/gpaw | gpaw/test/big/response/plot_spectra.py | Python | gpl-3.0 | 1,486 | [
"GPAW"
] | 00fe4e5f977fbcd0135702cb31a0f83ccce5ef8029d30261184e793f953efd60 |
"""
This is the heart of the algorithm. Implements the objective function and mu
and sigma estimators for a Gaussian diffusion probabilistic model
"""
import numpy as np
import theano
import theano.tensor as T
from blocks.bricks import application, Initializable, Random
import regression
import util
class Diffusion... | Sohl-Dickstein/Diffusion-Probabilistic-Models | model.py | Python | mit | 15,153 | [
"Gaussian"
] | fcc404f6884affea476b595d00992fc20037d476f7a5032536018fec3af09567 |
# copies.py - copy detection for Mercurial
#
# Copyright 2008 Matt Mackall <mpm@selenic.com>
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
import util
import heapq
def _nonoverlap(d1, d2, d3):
"Return list of elements in d1... | vmg/hg-stable | mercurial/copies.py | Python | gpl-2.0 | 12,819 | [
"VisIt"
] | d29ab33690666e530f04eb31a6ea08510e356173a8891c291615db92840e4d31 |
"""
==============================
Pediatric Profiles:
==============================
The following is an example of tractometry for pediatric bundles.
.. note::
This example and resulting pyAFQ support for pediatric bundles was
inspired by and largely due to the work of Grotheer et al. [Grotheer2021]_.
This ... | arokem/pyAFQ | examples/plot_baby_afq.py | Python | bsd-2-clause | 3,339 | [
"Brian"
] | fc2fa85c716abea06d9cd04d38a522752ff6fe55a68efb3fb54169211447c002 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import traceback
import re
from omero_version import omero_version
from webclient.webclient_gateway import OmeroWebGateway
logger = logging.getLogger(__name__)
def upgradeCheck():
# upgrade check:
# -------------
# On each startup OMERO.web che... | mtbc/openmicroscopy | components/tools/OmeroWeb/omeroweb/webadmin/webadmin_utils.py | Python | gpl-2.0 | 1,608 | [
"VisIt"
] | 9c5aafbee06767fa57e25c6478d964c4d01f36f0c5b9a31d5e4e4eca518a8e33 |
#
# @file TestCVTerms.py
# @brief CVTerms unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# s... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/annotation/TestCVTerms.py | Python | bsd-3-clause | 5,431 | [
"VisIt"
] | ce856f6f73d2f255cf8251c40ec058670bc8c615c030ee4876132faf5f5cf753 |
# -*- coding: utf-8 -*-
#
# network.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
# (... | lekshmideepu/nest-simulator | pynest/examples/Potjans_2014/network.py | Python | gpl-2.0 | 21,367 | [
"NEURON"
] | e53a5ca1418118024f7f8bf604f72c0f14b05abbd5057f12a41fa47a4d443586 |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free ... | andmos/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 41,223 | [
"Galaxy"
] | e3202fe5cdca1cfd7edffaaac8a271475df9fe0f801129e984c4f9aa32d68a60 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_network_size.py | Python | apache-2.0 | 9,997 | [
"VisIt"
] | e7e2d6d9be19cb7443d78fb6c2c7da15192145eb1338b5cc7d3adc6ea070fda3 |
#! /usr/bin/env python
from __future__ import print_function, division
from collections import namedtuple
"""
Copyright (C) 2016 Wesley Fraser (westhefras@gmail.com, @wtfastro)
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
t... | fraserw/trippy | trippy/psf.py | Python | gpl-3.0 | 52,236 | [
"Gaussian"
] | b5fa3424ee939a8dd7add6f7f59b3659c0c4fcc4a34eed0490c206b42ea69bd4 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | yipenggao/moose | python/chigger/tests/displacement/displacement_mag.py | Python | lgpl-2.1 | 1,373 | [
"MOOSE"
] | 7fac754ba6576111d346db9d7c44346ba1c434d937d782c4cba5849554013720 |
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
# in this test, I compare H2O HGLM runs with and without stating starting values.
def test_HGLM_R():
h2o_data = h2o.import_file(path=pyunit_ut... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_PUBDEV_6876_HGLM_initial_values.py | Python | apache-2.0 | 2,153 | [
"Gaussian"
] | 25474db248df7e795cdf849f967487712960c2777d917242535b9a6655fb35ad |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module defines classes for point defects
"""
import os
import abc
import json
from bisect import bisect_left
from pymatgen.core.periodic_table import Specie, Element
from pymatgen.core.sites import PeriodicSite
from pymatgen.symmetry.analyze... | Dioptas/pymatgen | pymatgen/analysis/defects/point_defects.py | Python | mit | 53,108 | [
"GULP",
"pymatgen"
] | c568d3b01a2f4479a15060a8e52d0ca24b7685a8a87ac9b38ad645d475348144 |
'''
Extractors that operate primarily or exclusively on Video stimuli.
'''
import numpy as np
from pliers.stimuli.video import VideoStim
from pliers.extractors.base import Extractor, ExtractorResult
from pliers.utils import attempt_to_import, verify_dependencies
cv2 = attempt_to_import('cv2')
class VideoExtractor(... | tyarkoni/pliers | pliers/extractors/video.py | Python | bsd-3-clause | 3,783 | [
"Gaussian"
] | 7370ece76afbf9b6602ba8fee5c4db033e8aac8d058979f93fd3e59f7ae68087 |
# coding: utf8
"""Streamlink extracts streams from various services.
The main compontent of Streamlink is a command-line utility that
launches the streams in a video player.
An API is also provided that allows direct access to stream data.
Full documentation is available at https://streamlink.github.io.
"""
import ... | javiercantero/streamlink | src/streamlink/__init__.py | Python | bsd-2-clause | 2,509 | [
"Brian"
] | c6f01d1024c71ec80508431624f35d995062dc5c6737ead94dbad9188737cdd6 |
from __main__ import vtk, qt, ctk, slicer
import numpy as np
from collections import OrderedDict
class ParenchymalVolume:
def __init__(self, parenchymaLabelmapArray, sphereWithoutTumorLabelmapArray, spacing, keysToAnalyze=None):
""" Parenchymal volume study.
Compare each ones of the different label... | acil-bwh/SlicerCIP | Scripted/CIP_LesionModel/FeatureExtractionLib/ParenchymalVolume.py | Python | bsd-3-clause | 3,862 | [
"VTK"
] | f1f41fccf49ce02b4d37fe87ca6057452c6e82a508e771e3aaa0f38296f5743a |
# Copyright (C) 2011-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/ek_eof_one_species_x.py | Python | gpl-3.0 | 1,384 | [
"ESPResSo"
] | 957fa0339f9a4ead8c18fdf9c50ff704d94d2ea701b41c448de4f5620a269f40 |
# -*- coding: utf-8 -*-
# This script is modified version of GraupnerBrunel2012 model by Aditya Gilra.
# Modification is following:
# - Added global seed.
# - Removed some messages.
# - Added assertion.
#
# NOTE: This script is used for testing random number generators on various
# platform. This should not be use... | upibhalla/moose-core | tests/python/test_GraupnerBrunel2012_STDPfromCaPlasticity.py | Python | gpl-3.0 | 7,889 | [
"MOOSE",
"NEURON"
] | 23a2b5cb3759c42e112d27c64dcf2a026bd23394d97972cbf587b8c0a9abf4b1 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import diaper
import fauxfactory
import hashlib
import iso8601
import random
import re
import command
import yaml
from contextlib import closing
from django.core.cache import cache
from django.core.exceptions import ObjectDoesNotExist
from django.core.mail... | quarckster/cfme_tests | sprout/appliances/tasks.py | Python | gpl-2.0 | 87,237 | [
"VisIt"
] | 7d7e054cec592e0318abe8e08c859df0638d2d2b7e3fa340b7576129689f063f |
# Copyright (C) 2012 Brian Parma
#
# 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 later version.
#
# This program is distributed in th... | eri-trabiccolo/exaile | plugins/ipconsole/ipython_view/__init__.py | Python | gpl-2.0 | 1,771 | [
"Brian"
] | 8bdc0dc1dc2a7dab83aad6ef36a3cdbe7bb18d8af7759c15f6b4af012af99b22 |
#!/usr/bin/env python3
from utils import filename, save2pdf, setup, rcparams, to_inches
from utils.plots_helper import sensors
import matplotlib
from matplotlib import pyplot
from matplotlib.backends.backend_pdf import PdfPages
import itertools
matplotlib.rcParams['text.latex.preamble'] = [r"\usepackage{siunitx}"]
... | cpitclaudel/dBoost | graphics/scalability.pdf.py | Python | gpl-3.0 | 2,629 | [
"Gaussian"
] | 46c8277539eb6e97fc1aff6ad1975d8ea5f144aacee77bf7d4ab0a6256cd5064 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to define everything related to band structures.
"""
import collections
import itertools
import math
import re
import warnings
import numpy as np
from monty.json import MSONab... | davidwaroquiers/pymatgen | pymatgen/electronic_structure/bandstructure.py | Python | mit | 45,082 | [
"CRYSTAL",
"pymatgen"
] | 1b1b9bca567809ce14d7a524ea0b85447e0dd6a37d192e94700b4a883268095e |
# -*- 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 ... | MDAnalysis/mdanalysis | package/MDAnalysis/topology/DMSParser.py | Python | gpl-2.0 | 7,334 | [
"MDAnalysis"
] | 7dc3ddda9af0c4a235f9bcc699d9b350eadfd6769272a915769c3ad4476f68a3 |
"""Tests for pdfs"""
from copy import copy, deepcopy
from math import e, erf, exp, log, pi, sqrt
import numpy as np
import pybayes as pb
from support import PbTestCase, stochastic
class TestRVComp(PbTestCase):
"""Test random variable component"""
def test_init(self):
rvcomp = pb.RVComp(123, "prett... | strohel/PyBayes | pybayes/tests/test_pdfs.py | Python | gpl-2.0 | 48,659 | [
"Gaussian"
] | df51e57e669a3f5067c1586c994e6a69bc86187468d6ed643c6b898c83b36afa |
# coding=utf-8
"""Functions for adding NetCDF files to the modelmeta database.
The root function is `index_netcdf_file`, which causes a NetCDF file to be
added or updated in the modelmeta database.
`index_netcdf_file` uses a set of database manipulation functions to handle
finding or inserting the objects (records) ... | pacificclimate/modelmeta | mm_cataloguer/index_netcdf.py | Python | gpl-3.0 | 49,033 | [
"NetCDF"
] | 527828f834d7cade2c1827bed477dc6776e58113cdabdfadb447524bd702b61c |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# math2html: convert LaTeX equations to HTML output.
#
# Copyright (C) 2009-2011 Alex Fernández
#
# Released under the terms of the `2-Clause BSD license'_, in short:
# Copying and distribution of this file, with or without modification,
# are permitted in any m... | bgris/ODL_bgris | lib/python3.5/site-packages/docutils/utils/math/math2html.py | Python | gpl-3.0 | 178,952 | [
"Bowtie"
] | d5e97d973f4173467924a2e6b0327886047e4b9ec8870cfa4a73216df141220b |
import pytest
import os
from fontTools.ttLib import TTFont
from fontbakery.checkrunner import (DEBUG, INFO, WARN, ERROR,
SKIP, PASS, FAIL, ENDCHECK)
from fontbakery.codetesting import (assert_results_contain,
assert_PASS,
... | googlefonts/fontbakery | tests/profiles/googlefonts_test.py | Python | apache-2.0 | 173,857 | [
"Galaxy"
] | e529e4bfd20d63f10264d101fadfd46100172df595625f92be0444ff325ad961 |
# Example_ZnS-CationMutation.py by J. M. Skelton
# -------
# Imports
# -------
# Import routines from Transformer.
from Transformer.IO.StructureIO import ReadStructure;
from Transformer.Framework.BatchIO import ExportResultSet;
from Transformer.Framework.Core import AtomicSubstitutions;
from Transformer.Utilities... | JMSkelton/Transformer | Examples/Example_ZnS-CationMutation.py | Python | gpl-3.0 | 1,842 | [
"VASP"
] | f15087a93a07577f47e028d687fdb0a61f49b7db89f4e28d5986db9a1ff84720 |
'''The core Python FlickrAPI module.
This module contains most of the FlickrAPI code. It is well tested and
documented.
'''
from __future__ import print_function
import logging
import six
import functools
from .tokencache import SimpleTokenCache, OAuthTokenCache
from .auth import OAuthFlickrInterface, FlickrAccessT... | onitu/onitu | drivers/flickr/onitu_flickr/flickrapi/core.py | Python | mit | 29,347 | [
"VisIt"
] | 50547caf6469bf741971819ad1eac3f837a65be66c971fc108e3d445b0c03776 |
# -*- coding: utf-8 -*-
#
# test_current_recording_generators.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 versio... | terhorstd/nest-simulator | pynest/nest/tests/test_current_recording_generators.py | Python | gpl-2.0 | 9,213 | [
"NEURON"
] | 92cf8e8dc454be0c8a9a42f53991f0a54a41511018681b96d5f205befb06d85a |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 ... | pwillworth/galaxyharvester | html/udEmail.py | Python | gpl-3.0 | 5,204 | [
"Galaxy"
] | a3787dac2e7a9633b1f7844b131338c5c37faaf70b974e0e96acd741b02f9e24 |
#!/usr/bin/python3
import sys
sys.path.append('./..')
import deep_feedback_learning
import numpy as np
import matplotlib.pyplot as plt
print("testICOWithFilters")
with open('test_bp_filt_py.csv', 'wb') as csvfile:
csvfile.close()
with open('test_bp_filt_py.csv', 'ab') as csvfile:
# two input neurons, ... | nlholdem/icodoom | ICO1/deep_feedback_learning/tests_py/test_ico_learning_with_filters.py | Python | gpl-3.0 | 1,945 | [
"NEURON"
] | c1437f06cc0e20ead9f683c36be9a13d03eb61aad65bbc474e70ccb52c9b8a34 |
import unittest
from jamenson.runtime.atypes import *
from jamenson.runtime.atypes.ptypes import *
class TestPTypes(unittest.TestCase):
def chkt(self, tp, op):
self.failUnless(typep(op, tp), "%r is not of type %s" % (op, tp))
def chkf(self, tp, op):
self.failIf(typep(op, tp), "%r is of ty... | matthagy/Jamenson | jamenson/tests/runtime/atypes/ptypes.py | Python | apache-2.0 | 2,373 | [
"ADF"
] | 5778b84efb4701c3db3c392bf10a9907185776647d8a097747c5667591621953 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
"""
function for calculating the convergence of an x, y data set
main api:
test_conv(xs, ys, name, tol)
tries to fit multiple functions to th... | sonium0/pymatgen | pymatgen/util/convergence.py | Python | mit | 14,376 | [
"pymatgen"
] | 2d4fecf0ef2eb065045ea0fac4a3e3d5f20e51ea78ece5135451a4d744ce8642 |
#!/usr/bin/env python
"""Provide plots summarizing recalibration of quality scores.
Usage:
analyze_quality_recal.py <recal_bam> <input_fastq1> <input_fastq2>
--chunk_size=25 --input_format=fastq-illumina
--dbdir=/tmp/chapmanb
<recal_bam> is a BAM alignment file containing recalibrarted quality scores
... | Cyberbio-Lab/bcbio-nextgen | scripts/utils/analyze_quality_recal.py | Python | mit | 13,178 | [
"Biopython",
"pysam"
] | 0252f68f052349992d6630639528787df4f4bc1c8e571208d85fd135d322fd5f |
"""Create and put Requests to move files.
List of operations:
#. ReplicateAndRegister LFNs
#. Check for Migration
#. Remove all other replicas for these files
"""
import os
import DIRAC
from DIRAC import gLogger
from DIRAC.Core.Base import Script
from DIRAC.Core.Utilities.List import breakListIntoChunks
from DIRA... | fstagni/DIRAC | DataManagementSystem/scripts/dirac-dms-create-moving-request.py | Python | gpl-3.0 | 10,763 | [
"DIRAC"
] | dffe33d800b4558a574a231114e42ca10cd061f1d6635ae728a4ee63ade1c41a |
from django.conf.urls import patterns, url
from sensordatainterface.views import edit_views
urlpatterns = patterns('',
# Site create/update/delete
url(r'^sites/create-site/(?:(?P<site_id>\d+)/)?$', edit_views.edit_site, name='create_site'),
url(r'^sites/delete-site/(?P<site_id>\d+)/$', edit_vie... | UCHIC/ODM2Sensor | src/sensordatainterface/urls/edit_urls.py | Python | bsd-3-clause | 5,318 | [
"VisIt"
] | 1a6ae4fc62187c3441ac72a9ff70a5f92f71944880bc254bcbf34db9246b6436 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
# Copyright (C) 2012 Michiel D. Nauta
#
# This program is free software; you can redistri... | pmghalvorsen/gramps_branch | gramps/plugins/tool/check.py | Python | gpl-2.0 | 113,447 | [
"Brian"
] | f69a732213b6735724421df34a9ece91b6093caf4a8252f5945bf6494f573d10 |
#!/usr/bin/env python
import os, sys, re, shutil
from optparse import OptionParser, OptionGroup, Values
# Determine the MOOSE Directory
MOOSE_PYTHON_DIR = None
if os.environ.has_key('MOOSE_DIR'):
MOOSE_PYTHON_DIR = os.path.join(os.environ['MOOSE_DIR'], 'python')
else:
MOOSE_PYTHON_DIR = os.path.join(os.path.split(... | jhbradley/moose | scripts/cluster_launcher.py | Python | lgpl-2.1 | 5,493 | [
"MOOSE"
] | 037d7cce81a4d8aac42b06f4f5f9bcec3bd22e9654634399e0525e0465424f55 |
# -*- coding: utf-8 -*-
"""
A toolbox for reading dust opacities in every shape and form.
Author: R. Lombaert
"""
import os
import numpy as np
from numpy import array
from scipy.interpolate import InterpolatedUnivariateSpline as spline1d
from scipy.interpolate import interp1d
from astropy import units as u
import c... | robinlombaert/ComboCode | cc/tools/readers/KappaReader.py | Python | gpl-3.0 | 7,619 | [
"MOPAC"
] | a3bc2f6b689ae3d3acdb09065946c6d09c47ba05e8829ff290ea985ec8691415 |
class BinaryTreeNode(object):
def __init__(self,value=None):
self.left = None
self.right = None
self.value = value
self.visited = False
def get_value(self):
return self.value
def set_value(self, value):
self.value = value
def set_lef... | lzamparo/practice | data_structs/binary_tree_node.py | Python | mit | 633 | [
"VisIt"
] | 19f71591ea282eca14c6b12551b0599597ea6f04cfd38e93013207f1a259eeca |
# -----------------------------------------------------------------------------
# User configuration
# -----------------------------------------------------------------------------
outputDir = '/Users/seb/Desktop/float-image/'
# -----------------------------------------------------------------------------
from paravie... | Kitware/arctic-viewer | scripts/examples/paraview/samples/composite-wavelet.py | Python | bsd-3-clause | 2,130 | [
"ParaView",
"VTK"
] | 5bc1e9af33d0cbcf06998a2fb60af4686a8c50e45af0a165b7e666c0b49d133f |
import os, string
import unittest
import vtk, qt, ctk, slicer
import numpy as np
from slicer.ScriptedLoadableModule import *
#
# CompareVolumes
#
class VolumeProbe(ScriptedLoadableModule):
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
parent.title = "Volume Probe"
... | acil-bwh/SlicerCIP | Scripted/VolumeProbe/VolumeProbe.py | Python | bsd-3-clause | 30,050 | [
"VTK"
] | 8334350d24e3e5570901f6e2ea05bcfc5c630d9bfd98fe065acad69e3d400a94 |
import gspread
import vissim_v8 as vissim
from oauth2client.service_account import ServiceAccountCredentials
import numpy as np
scope = ['https://spreadsheets.google.com/feeds']
credentials = (ServiceAccountCredentials.from_json_keyfile_name(
'/Users/brian/.ssh//GoogleOAuth.json', scope))
gc = gspread.... | brianhuey/vissim | vissim_v8/sheet_to_vissim.py | Python | mit | 1,222 | [
"Brian"
] | ededbc8b7d18029a938a871f8c585dec3547f254575c98f0a250251b043b757a |
__version__ = '1.9.3'
import g2clib
import struct
import string
import math
import warnings
import operator
from datetime import datetime
try:
from StringIO import StringIO
except ImportError:
from io import BytesIO as StringIO
import numpy as np
from numpy import ma
try:
import pyproj
except ImportError:
... | erdc-cm/pygrib | ncepgrib2.py | Python | isc | 59,495 | [
"Gaussian"
] | 1658e62548e60d9dffd0572bd83a06c25a0e6bd46e19c2e4a1e49f9b3107a193 |
#
# Author: Alejandro Molina-Sanchez
#
# Example of YamboQPDB Class
#
from qepy import *
from yambopy import *
import matplotlib.pyplot as plt
# Define path in reduced coordinates using Class Path
npoints = 10
path = Path([ [[ 0.0, 0.0, 0.0],'$\Gamma$'],
[[ 0.5, 0.0, 0.0],'M'],
[[1.... | alexmoratalla/yambopy | tutorial/bn/plot-qp.py | Python | bsd-3-clause | 2,054 | [
"Yambo"
] | c2aaac39dd7c9b5d38cff6ce21e6e14e8984d3f95cd93af283d75ea8116f503b |
"""
.. _sfm-reconst:
==============================================
Reconstruction with the Sparse Fascicle Model
==============================================
In this example, we will use the Sparse Fascicle Model [Rokem2015]_, to
reconstruct the fiber orientation distribution function (fODF) in every voxel.
First... | StongeEtienne/dipy | doc/examples/sfm_reconst.py | Python | bsd-3-clause | 5,815 | [
"Brian"
] | 298e04649420f7d406278c961780a6efc518634608987769e6cdfee33b3d6563 |
# Eidolon Biomedical Framework
# Copyright (C) 2016-8 Eric Kerfoot, King's College London, all rights reserved
#
# This file is part of Eidolon.
#
# Eidolon 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, eith... | ericspod/Eidolon | eidolon/Utils.py | Python | gpl-3.0 | 101,436 | [
"VisIt"
] | d490380cc10a5a344c14ef13cb55e387eccb39ccbc6efaa4c6044fd616bdc81a |
import numpy
from scipy.optimize import curve_fit
import echidna.core.scale as scale
from echidna.core.config import SpectraConfig
import echidna.core.spectra as spectra
import unittest
class TestScale(unittest.TestCase):
def gaussian(self, x, *p):
""" A gaussian used for fitting.
Args:
... | ashleyrback/echidna | echidna/test/test_scale.py | Python | mit | 3,907 | [
"Gaussian"
] | abb49fab8e973581cdee6e4f1acccf165ddc35394322198f0eb25be6d013dd2c |
#!/usr/bin/env python
__author__ = 'waroquiers'
import unittest
import os
import numpy as np
from pymatgen.util.testing import PymatgenTest
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
from pymatgen.analysis.chemenv.coordination_environments.coordi... | czhengsci/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_coordination_geometry_finder.py | Python | mit | 11,778 | [
"pymatgen"
] | 268cc1753511996f3a6d4801c491aba8b75d3bf73a59fe5689b514fe5d0a720d |
from __future__ import absolute_import
from __future__ import print_function
import unittest
import rdflib as R
import six
import warnings
from PyOpenWorm.data import DataUser
from PyOpenWorm.dataObject import DataObject, DatatypeProperty, _partial_property
from PyOpenWorm.neuron import Neuron
from PyOpenWorm.connecti... | gsarma/PyOpenWorm | tests/DataObjectTest.py | Python | mit | 4,624 | [
"NEURON"
] | c9b421dccf4d9bb98e17278d25d4b6229f08a820aa28bb81828c06ae9d02c2ee |
"""
======================================================
Bayesian Gaussian Mixture Concentration Prior Analysis
======================================================
Plot the resulting ellipsoids of a mixture of three Gaussians with
variational Bayesian Gaussian Mixture for three different values on the
prior the d... | PatrickOReilly/scikit-learn | examples/mixture/plot_bayesian_gaussian_mixture.py | Python | bsd-3-clause | 4,427 | [
"Gaussian"
] | a80faf2ae10cb3ac673d7ca258e98c04483b43d3d6e560732b219c10e9fc195c |
import random
import itertools
import string
import os
import tempfile
import logging
import subprocess
import functools
from pkg_resources import resource_filename
import contextlib
import shutil
import warnings
import mdtraj as md
from mdtraj.utils import enter_temp_directory
from mdtraj.utils.delay_import import imp... | choderalab/openmoltools | openmoltools/utils.py | Python | mit | 19,231 | [
"Amber",
"Gromacs",
"MDTraj",
"OpenMM",
"RDKit"
] | 51ffd107035de7ad5db9c1eac3fa05b265831e18eb7ba49866f3fedb951f6b01 |
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 7 14:38:46 2011
Plot pca test error vs train error
@author: -
"""
# Computes the gaussian gradients on a boxm_alpha_scene
import os;
import optparse;
import time;
import sys;
import plot_pca_functions;
import numpy as np
import matplotlib.pyplot as plt
import math
if _... | mirestrepo/voxels-at-lems | bvpl/bvpl_octree/pca_test_vs_train.py | Python | bsd-2-clause | 1,887 | [
"Gaussian"
] | bed566c05d4bd31f06f6aac11bf42204dbd1624c84e9dcdf30cd0c6739d7298e |
""" Base class for MyProxy and VOMS
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import tempfile
import DIRAC
from DIRAC import gConfig, S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.X509... | ic-hep/DIRAC | src/DIRAC/Core/Security/BaseSecurity.py | Python | gpl-3.0 | 3,211 | [
"DIRAC"
] | 31bf7b6d5605103d645e5e57c025f986ccb347ab29447db7b135bb37ff879ef8 |
import numpy.lib.stride_tricks
import numpy as np
from scipy.fft import rfftn, irfftn
from numpy import ma
from tqdm import tqdm
from openpiv.pyprocess import get_field_shape, find_first_peak
"""This module contains a pure python implementation of the basic
cross-correlation algorithm for PIV image processing."""
__l... | OpenPIV/openpiv-python | openpiv/pyprocess3D.py | Python | gpl-3.0 | 23,069 | [
"Gaussian"
] | b62706fa1c221457c1869a19e29cf221dde0879044678e8a2a99f54e124c8d77 |
# Copyright 2020 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | google/qkeras | experimental/lo/optimizer.py | Python | apache-2.0 | 9,825 | [
"ESPResSo"
] | 683b45041fe4c325df39d45e1c287aa4973573f057bd89909c4663f94c0a8f19 |
import numpy as np
tol = 1e-8
a = np.eye(3, dtype=complex)
a[1:, 0] = 0.01j
w0 = [0.98585786, 1.0, 1.01414214]
# NumPy's Diagonalize
from numpy.linalg import eigh
w = eigh(a)[0]
print w
assert abs(w - w0).max() < tol
# LAPACK's QR Diagonalize
from gpaw.utilities.lapack import diagonalize
diagonalize(a.copy(), w)
print ... | qsnake/gpaw | gpaw/test/eigh.py | Python | gpl-3.0 | 566 | [
"GPAW"
] | 2afbf812443d96f8454741c35e32e855e5fc37d3cf774a93c3f8518f57500eec |
r"""
Format biological sequences (:mod:`skbio.format.sequences`)
===========================================================
.. currentmodule:: skbio.format.sequences
This module provides functions for writing sequence files in a variety of
different formats, the available formatters are listed below.
Functions
----... | Kleptobismol/scikit-bio | skbio/format/sequences/__init__.py | Python | bsd-3-clause | 1,054 | [
"scikit-bio"
] | 3d7d36757479e62488a45a1f1e949e2aa40f0f7eb92cdc3684db46f3d9d4beb3 |
"""Bayesian hyperparameter optimization (hyperopt) is very modern and useful
technique to optimize the hyperparameters of a non-differentiable loss function.
We make use of the scikit-optimize package, which contains a Gaussian Process
hyperopt method.
"""
import argparse
import cPickle as pkl
import os
import sys
imp... | deworrall92/harmonicConvolutions | BSD500/bayesian_optimization.py | Python | mit | 2,616 | [
"Gaussian"
] | 60c68786a01ae23ba8528111a6400940d20339db629136e445318aad49f51b0d |
import logging
import json
import time
import datetime
import re
import pytricia
from pprint import pprint
TLP = "amber"
GROUP = "everyone"
RE_IPV4 = re.compile("^(?:(?:25[0-5]|2[0-4][0-9]|[01]?[0-9][0-9]?)\.){3}")
RE_FQDN = re.compile("^(?:[0-9a-zA-Z-]{1,63}\.)+[a-zA-Z]{2,63}$")
RE_URL = re.compile("^(http|https|smt... | csirtgadgets/cif-sdk-py | cifsdk/observable.py | Python | lgpl-3.0 | 4,695 | [
"Amber"
] | efa8edd402a28f6c783682fbb48df61919eefb6b7d135eda238cff2b06932cd1 |
from bs4 import BeautifulSoup
from urllib.parse import urlparse
from urllib.parse import urljoin
import requests
class Crawler:
"""Simple crawler to get all internal links from a website."""
def __init__(self, base_uri):
"""Initialize local data."""
self.base_uri = base_uri
self.base_... | rudaporto/simple_sitemap | crawler.py | Python | gpl-3.0 | 2,493 | [
"VisIt"
] | 0ab141971b676295d996b424e34d88c02845b089fb53a5ba9df6b054b978c332 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Implements ProcessPoolExecutor.
The follow diagram and text describe the data-flow through the system:
|======================= In-process =====================|== Out-of-process ==|
+----------+ +----------... | ychen820/microblog | y/google-cloud-sdk/platform/google_appengine/lib/concurrent/concurrent/futures/process.py | Python | bsd-3-clause | 14,309 | [
"Brian"
] | 600a439c9048bd5f819c11746dcba4569c1941db90dc071fc126b1679959c197 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/cc/gccsd_lambda.py | Python | apache-2.0 | 8,403 | [
"PySCF"
] | 48672ec0cff0a2407479309b259eec50b776871c535b438618e2af4a805e2a24 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the CCX dashboard.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.tests.helpers import UniqueCourseTest, EventsTestMixin
from common.test.acceptance.pages.lms.auto_auth import AutoAut... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/lms/test_ccx.py | Python | agpl-3.0 | 2,224 | [
"VisIt"
] | 95ed6518d976dadfdb0d743842064b8cf6e09544720c2067b71738ccf53994b5 |
import operator
import numpy as np
from numpy.core.multiarray import normalize_axis_index
from scipy.linalg import (get_lapack_funcs, LinAlgError,
cholesky_banded, cho_solve_banded,
solve, solve_banded)
from . import _bspl
from . import _fitpack_impl
from . import _f... | tylerjereddy/scipy | scipy/interpolate/_bsplines.py | Python | bsd-3-clause | 51,751 | [
"Brian"
] | 6e3efe294ceb9ef20bc3d09ec11212b6b2f37e26a5249ba43742a59f52c18e66 |
#
# 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... | mbroadst/debian-qpid-cpp-old | tests/python/proton_tests/messenger.py | Python | apache-2.0 | 28,107 | [
"Galaxy"
] | 67f15bf972013b17c0810b70a56ebaadc77a7dbbb5d8f302550481f3e44175d0 |
#####################################################################################
# $HeadURL$
#####################################################################################
"""Collection of DIRAC useful file related modules.
.. warning::
By default on Error they return None.
"""
__RCSID__ = "$Id$"
impo... | Sbalbp/DIRAC | Core/Utilities/File.py | Python | gpl-3.0 | 5,406 | [
"DIRAC"
] | ad74695b889ec363ae5fc450ba713d84db1e44aadfb40f46f476960bacf93be6 |
# Import of the relevant tools
import time
import numpy as np
import theano
import theano.tensor as T
from theano import pp, config
from plotly.tools import FigureFactory as FF
import plotly.graph_objs as go
from .surfaces import Surface
class SurfacesManifold :
"""
Encapsulates a few useful io + type conversio... | jeanfeydy/lddmm-ot | LDDMM_Python/lddmm_python/modules/manifolds/surfaces_manifold.py | Python | mit | 5,529 | [
"DIRAC"
] | c9774b687850fa7389a3b498eec66c025f584e9fb35546367fceba726864f5ec |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.