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from django.test import TestCase
from django.contrib.auth import get_user_model
from experiments.models import Experiment, ENABLED_STATE
from experiments.signals import user_enrolled
from experiments.utils import participant
EXPERIMENT_NAME = 'backgroundcolor'
class WatchSignal(object):
def __init__(self, signa... | squamous/django-experiments | experiments/tests/test_signals.py | Python | mit | 1,400 | [
"Brian"
] | 38a5868a5fd378cf1d32cdb33c871c9ab0a9e6d9a63ea378e5a6eddd3a807659 |
"""
The image module supports basic image loading, rescaling and display
operations.
"""
from __future__ import division
import os, warnings
import numpy as np
from numpy import ma
from matplotlib import rcParams
import matplotlib.artist as martist
from matplotlib.artist import allow_rasterization
import matplotlib.... | SpaceKatt/CSPLN | apps/scaffolding/mac/web2py/web2py.app/Contents/Resources/lib/python2.7/matplotlib/image.py | Python | gpl-3.0 | 46,614 | [
"Gaussian"
] | 11cef616d3453b519809fc4a5db78d26afc0f8e33bbf229e921b61285c451e5d |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/auxiliary/test_xvg.py | Python | gpl-2.0 | 4,340 | [
"MDAnalysis"
] | 67d4f6f64ab81afa864482122b49c5280031f6bcfeaaa0492daee6e084323467 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the Opera browser history parsers."""
import unittest
from plaso.parsers import opera
from tests.parsers import test_lib
class OperaTypedParserTest(test_lib.ParserTestCase):
"""Tests for the Opera Typed History parser."""
def testParse(self):
"""... | joachimmetz/plaso | tests/parsers/opera.py | Python | apache-2.0 | 3,302 | [
"VisIt"
] | 95a23f87b7ab30d36624656993be01e76b12a6956f7761dbf29197bd64518ce2 |
# -*- coding: utf-8 -*-
"""
Copyright 2013-2014 Olivier Cortès <oc@1flow.io>
This file is part of the 1flow project.
1flow 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 versio... | EliotBerriot/1flow | oneflow/core/models/nonrel/read.py | Python | agpl-3.0 | 42,501 | [
"exciting"
] | 28d232ea215633d0a209b89dd69a41dc9813d5812bf38aab370035fff468337d |
# stdlib imports
from functools import reduce
import collections
import datetime
import json
import operator
import time
import urllib.parse
# django imports
from django.conf import settings
from django.contrib.auth import get_user_model
from django.contrib.auth.decorators import login_required
from django.contrib.auth... | cmu-db/dbdb.io | dbdb/core/views.py | Python | apache-2.0 | 57,692 | [
"VisIt"
] | 70384e7665ca733b5aa2b29ba253462a8cba1b3ad357bec6092ac18ce3a27db5 |
# 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... | apache/incubator-singa | python/singa/layer.py | Python | apache-2.0 | 58,103 | [
"Gaussian"
] | 777151b49600ae1962056d47c09fb3e6c86023cf476b01e2a4de9a236b4a6ccf |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | JWDebelius/scikit-bio | skbio/stats/_misc.py | Python | bsd-3-clause | 1,470 | [
"scikit-bio"
] | e779e9e8f82c811ef0ce16c9f3c2176e2bbe95147aa1214456f97c25abc54846 |
'''
# This script is an example of calculation of long range interactions (Coulomb interaction) using
# the Ewald summation method.
#
# The initial data file is 'ewald.espressopp'. It contains initial information about
# the system: the box size, particle id, position and charge.
#
# File 'ewald_result.dat' con... | capoe/espressopp.soap | examples/ewald/ewald.py | Python | gpl-3.0 | 6,691 | [
"ESPResSo"
] | 4f7ddf0ef27814e09a2da7f6d6cd64446574a5fc5a60f83b9c1f6ded62551f1d |
# Define a CloudFormation template to host a tiny ElasticSearch stack:
# 1 ElasticSearch server
# 1 Logstash indexing server
# 1 Kibana server
#
# Template Parameters (provided at templat creation time):
# - name
# Name of the stack, of course. Required.
# - description
# Description of the stack. Please provide on... | mccormickmichael/laurel | app/elk/tiny_template.py | Python | unlicense | 14,862 | [
"Elk"
] | 2b1d87caba4fbebc4195a0c96ed86a115310d1fa2f4956ee8c12fca531d32ddd |
import numpy as np
import torch
from torch.autograd import Variable
import torch.nn as nn
from rllab.misc.overrides import overrides
from pytorchrl.core.parameterized import Parameterized
from pytorchrl.distributions.diagonal_gaussian import DiagonalGaussian
from pytorchrl.policies.base import StochasticPolicy
clas... | nosyndicate/pytorchrl | pytorchrl/policies/gaussian_mlp_policy.py | Python | mit | 10,812 | [
"Gaussian"
] | 8b10a87fb022c0f7f2d521e86f9755427a6a6fc2ce431137461d49e9a8374d42 |
from __future__ import print_function
import argparse
import os
import random
from collections import defaultdict
import pysam
import mirtop.libs.logger as mylog
import mirtop.libs.do as runner
def _read_fasta(fa, size):
source = dict()
with open(fa) as inh:
for line in inh:
if line.sta... | miRTop/mirtop | scripts/make_spikeins.py | Python | mit | 3,822 | [
"pysam"
] | 4ec1a3d6cd8a16f3fb1842c6af2a91150a02fe02ce01a3c81f8e436b72f1ddc1 |
def sextract(filter):
from config_bonn import appendix, cluster, tag, arc, filter_root
import utilities
import os, re, bashreader, sys, string
from glob import glob
from copy import copy
dict = bashreader.parseFile('progs.ini')
for key in dict.keys():
os.environ[key] = str(dict[key]... | deapplegate/wtgpipeline | non_essentials/calc_test/calc_tmp.save2.py | Python | mit | 30,619 | [
"Galaxy"
] | 6c01a19e70fd96a8cf38619e9c17b8515e4f4656124f7848e3cecb74e675252a |
# Copyright 2009-2014 Ram Rachum.
# This program is distributed under the MIT license.
from __future__ import with_statement
import os.path, sys
sys.path += [
os.path.dirname(__file__),
os.path.join(os.path.dirname(__file__), 'third_party.zip'),
]
import bisect
import re
import inspect
import logging
imp... | cool-RR/cute-wing-stuff | scripts/implicit_getattr_to_explicit.py | Python | mit | 2,509 | [
"VisIt"
] | c5a1b9dcda809aa1c5aafeb7c3010830d837f1ee654b115104222a8c896b42ad |
#
# mainTab
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'vasp'
tab.settings['Output file name'] = 'OUTCAR'
#
# Handle the special case of the first scenario
#
self.notebook.switchScenario(0,scenarioType="Single crystal")
#
#
#
tab = self.notebook.mainTab
tab.settings['Program'] = 'vasp'
tab.settings['Output... | JohnKendrick/PDielec | Examples/SingleCrystal/Bi2Se3/script.py | Python | mit | 1,880 | [
"CRYSTAL",
"VASP"
] | 91f790c8fa6ed4d3ea0501d1935b42bb81752e139ffcfdb54ab8b0780e016a80 |
#!/usr/bin/env python
from __future__ import division
__author__ = "Jai Ram Rideout"
__copyright__ = "Copyright 2012, The QIIME project"
__credits__ = ["Jai Ram Rideout", "Jose Antonio Navas Molina"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Jai Ram Rideout"
__email__ = "jai.rideout@gmail.com"
f... | josenavas/qiime | qiime/parallel/blast.py | Python | gpl-2.0 | 4,254 | [
"BLAST"
] | c3b4d7daba291465bfab3d0985914008d43e5e690c9eb7a5aea140975d3ef9f9 |
import numpy
import itertools
import random
import math
def convert_spike_list_to_timed_spikes(spike_list, min_idx, max_idx, tmin, tmax, tstep):
times = numpy.array(range(tmin, tmax, tstep))
spike_ids = sorted(spike_list)
possible_neurons = range(min_idx, max_idx)
spikeArray = dict([(neuron, times) for... | dhgarcia/babelModules | pynnModules/Network/spike_file_to_spike_array.py | Python | gpl-3.0 | 8,559 | [
"NEURON"
] | 66c971b7b41b36c39f815de93e86aebe99a06a5bac46f0f7f0f9f629d9046bad |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to
# submit large numbers of jobs on supercomputers. It provides a python interface to physical input,
# ... | pylada/pylada-light | tests/espresso/test_structure.py | Python | gpl-3.0 | 6,911 | [
"CRYSTAL",
"ESPResSo",
"VASP"
] | e88ebce100d051d0226aaf439d8185d0e0ea723a98941be1bd9a1769698122c0 |
#!/usr/bin/env python
import cv2
from datetime import datetime
from dateutil.tz import tzlocal
import numpy as np
import pyqtgraph as pg
import scipy
import os
from pyqtgraph import FileDialog
from pyqtgraph.Qt import QtGui
from pyqtgraph.parametertree import Parameter, ParameterTree
from scipy.sparse import csc_matri... | agiovann/Constrained_NMF | bin/caiman_gui.py | Python | gpl-2.0 | 24,280 | [
"NEURON"
] | bebc0d8dda08200c0fec6e83b846e25ae28a528e766f8536de5421b08b56ce7a |
# -*- coding: utf-8 -*-
#!/usr/bin/python
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Thom Sturgill
# Copyright (C) 2007-2009 Brian G. Matherly
# Copyright (C) 2008-2011 Rob G. Healey <robhealey1@gmail.com>
# Copyright (C) 2008 Jason Simanek
# Copyright (C) 2010 Jakim Friant
... | dermoth/gramps | gramps/plugins/webreport/webcal.py | Python | gpl-2.0 | 85,396 | [
"Brian"
] | f18ac3ab7886222841e061e89dce63ab1219537841beda4fb3b2b35326ce6996 |
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("mapfile", help="filename of mapfile")
args = parser.parse_args()
import cogent.parse.bowtie
data = cogent.parse.bowtie.BowtieOutputParser( args.mapfile )
count = 0
for row in data:
print row
count += 1
if count > 20:
br... | humberto-ortiz/dmel-ercc | cogent-test.py | Python | gpl-3.0 | 327 | [
"Bowtie"
] | bca0a4d89880d0226bcba689ea0ae92fe966388d1a8e187bff92aad408e9df47 |
# =============================================================================
# File: firenzecard.py
# Author: Io Flament
# Created: July 2017
# Last Modified: October 2017
# Description: Runs Exploratory Analysis of Firenzecard data
# =========================================================... | DSSG2017/florence | src/features/firenzecard.py | Python | mit | 22,572 | [
"VisIt"
] | 549b2b95a324e3410b04daee5df0b288d35f98112284eb3db25d3f4669164204 |
from __future__ import print_function
##############################################################################
#
# Author: Alejandro Molina-Sanchez
# Run real-time simulations with Yambo
#
# Warning: Real-time simulations requires several data folders for running
# properly. Before using these scripts compulsivel... | alexmoratalla/yambopy | scripts/realtime/rt-pulse.py | Python | bsd-3-clause | 8,650 | [
"Yambo"
] | dcdcf54f5ca3368413654d24e610b872666b1d6c634cac5c31ee7390e4876f22 |
# freeseer - vga/presentation capture software
#
# Copyright (C) 2011, 2013 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# 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 Foundati... | Freeseer/freeseer | src/freeseer/plugins/output/ogg_icecast/__init__.py | Python | gpl-3.0 | 8,804 | [
"VisIt"
] | 6bac858ff9c6a1aaecc9142fd2b928edc549c275ae2db601d4eb860c10c221fc |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | hmc_swindles/targets/probit_regression.py | Python | apache-2.0 | 3,954 | [
"Gaussian"
] | bacd26ca608e1de9c6f03dfb179800f13c16702887f4d537bbec98e0f3d733f4 |
# -*- coding: utf-8 -*-
import pytest
from io import StringIO
from trapp.log import Log
from trapp.importer import Importer
from trapp.import_game import ImporterGames
from trapp.import_goal import ImporterGoals
from trapp.import_lineup import ImporterLineups
from trapp.import_player import ImporterPlayers
def test_i... | matt-bernhardt/trapp | tests/test_importer.py | Python | gpl-2.0 | 12,458 | [
"COLUMBUS"
] | 0e8fc49c2502e6d536a627e9eca92dd4a9af80133241f35d813b2b24869abc41 |
"""
Views for the verification flow
"""
import datetime
import decimal
import json
import logging
import urllib
from pytz import UTC
from ipware.ip import get_ip
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.core.mail import send_mail
from django.core.urlresolv... | inares/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 58,975 | [
"VisIt"
] | 40900e6ac510097f12525393043b7594744efe2c02a0509b13679b133250c7a7 |
# -*- coding: utf-8 -*-
#
import os
import warnings
from tempfile import TemporaryDirectory
import numpy
from dolfin import (
Constant,
DirichletBC,
Expression,
FacetNormal,
FiniteElement,
Function,
FunctionSpace,
Mesh,
MeshFunction,
MixedElement,
SubDomain,
SubMesh,
... | nschloe/maelstrom | examples/problems/crucible.py | Python | mit | 18,298 | [
"CRYSTAL"
] | 7e394dda246cc7261006ec919eeeb7f52b607428ea0a03bdc5555142a13db943 |
from django.db import models, transaction
# from django.db.models import get_model
from edc_appointment.models import AppointmentMixin
# from edc_base.audit_trail import AuditTrail
from edc_base.model.models import BaseUuidModel
from edc_base.model.validators import (datetime_not_before_study_start, datetime_not_futur... | botswana-harvard/tshilo-dikotla | td_maternal/models/postnatal_enrollment.py | Python | gpl-2.0 | 7,617 | [
"VisIt"
] | 7150bba7b96ba3a5c1ecb7dac7cd4b8863908a4f2b52f7c734474755d6ccf93d |
from ase import Atoms
from gpaw import GPAW, PW
a = 2.87
m = 2.2
fe = Atoms('Fe2',
scaled_positions=[(0, 0, 0),
(0.5, 0.5, 0.5)],
magmoms=[m, -m],
cell=(a, a, a),
pbc=True)
calc = GPAW(mode=PW(350),
kpts=(6, 6, 6),
txt='... | robwarm/gpaw-symm | doc/exercises/iron/anti.py | Python | gpl-3.0 | 409 | [
"ASE",
"GPAW"
] | 8c165f8602a6e537923835bf966fbcf3e73273968ee706110675cebb2e40449a |
# FermiLib plugin to interface with Psi4
#
# Copyright (C) 2017 ProjectQ-Framework (www.projectq.ch)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
... | ProjectQ-Framework/FermiLib-Plugin-Psi4 | fermilibpluginpsi4/_psi4_conversion_functions.py | Python | lgpl-3.0 | 9,265 | [
"Psi4"
] | 36b8f2ea7be06e7e486df007e74b5d8b27feb4940f97a35cee0fbce6523f8573 |
"""Config flow for Elk-M1 Control integration."""
import logging
from urllib.parse import urlparse
import elkm1_lib as elkm1
import voluptuous as vol
from homeassistant import config_entries, exceptions
from homeassistant.const import (
CONF_ADDRESS,
CONF_HOST,
CONF_PASSWORD,
CONF_PROTOCOL,
CONF_T... | tchellomello/home-assistant | homeassistant/components/elkm1/config_flow.py | Python | apache-2.0 | 5,265 | [
"Elk"
] | dd8d385d7866fc82bdfa2e25c9b9fd14cec68859ecc42f4ad944374e107bcc27 |
#!/usr/bin/env python
# -*- coding: latin-1 -*-
"""
Geo functions for distances, bearings, speeds, latitudes and longitudes
"""
from math import radians, degrees, sin, cos, tan, asin, atan2
from math import sqrt, pi, log
from time import strftime
def km_h(speed_in_m_s):
"""km_h(10) = 36 <=> 10 m/s = 36 km/h"""
... | Green-Elk/kajgps | kajgeo.py | Python | gpl-3.0 | 9,364 | [
"Elk"
] | c497d069f2038a246b5e38cdf4825deba7a725447cf39e9d51a2935c48c92543 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2016, Ansible RedHat, Inc
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | ilpianista/ansible | lib/ansible/modules/utilities/logic/set_stats.py | Python | gpl-3.0 | 1,930 | [
"Brian"
] | b0198409580ab211ba36179920ced74e0e6da877d1e619c631bf329bb22fa79b |
"""
Run some VASP tests to ensure that the VASP calculator works. This
is conditional on the existence of the VASP_COMMAND or VASP_SCRIPT
environment variables
"""
from ase.test.vasp import installed
assert installed()
from ase import Atoms
from ase.io import write
from ase.calculators.vasp import Vasp
import numpy... | grhawk/ASE | tools/ase/test/vasp/vasp_co.py | Python | gpl-2.0 | 1,698 | [
"ASE",
"VASP"
] | 6c2a3511a5b7d57c776c10c8ddf0470883d131811277eb4f30e14abd2659309c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001 Jesper Zedlitz
# Copyright (C) 2004-2006 Donald Allingham
# Copyright (C) 2007 Johan Gonqvist <johan.gronqvist@gmail.com>
# Copyright (C) 2008,2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013-2014 ... | beernarrd/gramps | gramps/plugins/textreport/numberofancestorsreport.py | Python | gpl-2.0 | 9,325 | [
"Brian"
] | 0d6f19c4ac2d8966fe574b198cc828e2493b638c06422207e48be332660df0ed |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
from monty.serialization import loadfn
from pymatgen.analysis.defects.core import DefectEntry
from pymatgen.analysis.defects.thermodynamics import DefectPhaseDiagram
from pymatgen.core i... | vorwerkc/pymatgen | pymatgen/analysis/defects/tests/test_thermodynamics.py | Python | mit | 5,831 | [
"pymatgen"
] | 4ede8fdc21b5ebdfc2ff4c792f0ceb91662ab088af78ddd2f61720f0f74c8ecf |
from sympy import (meijerg, I, S, integrate, Integral, oo, gamma, cosh,
hyperexpand, exp, simplify, sqrt, pi, erf, sin, cos,
exp_polar, polygamma, hyper, log, expand_func)
from sympy.integrals.meijerint import (_rewrite_single, _rewrite1,
meijerint_indefinite, _inflate_g, _... | ga7g08/sympy | sympy/integrals/tests/test_meijerint.py | Python | bsd-3-clause | 27,483 | [
"Gaussian"
] | 9bebb60dd01b1564e3abde3da47e86159996614c01d1338d75c3e1adb459bcb1 |
import pytest
from pytest_bdd import scenario, given, when, then
from webapp.apprunner import start, stop
@pytest.yield_fixture
def app():
yield start()
stop()
@scenario('website.feature', 'I visit the website')
def test_website():
pass
@given("The server is running")
def server(app):
""" start se... | bitterjug/munger | tests/functional/setup/test_website.py | Python | gpl-2.0 | 609 | [
"VisIt"
] | 4c241c3fbb7398cbbb524f53649af81081547cd87fd98b262226d275dabb1248 |
"""A generic client for creating and managing transformations.
See the information about transformation parameters below.
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
import six
import json
from DIRAC import gLogger, gConfig, S_OK, S_ERROR
from DIR... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Client/Transformation.py | Python | gpl-3.0 | 26,973 | [
"DIRAC"
] | e585569f63b6dc723f9b1c3fa2e7722ba29f015a9d812b3ed3221dd94172d75e |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import datetime
import math
import random
import os
import sys
import pickle
import gzip
import ovdgenerators as gens
def drawLine(myscreen, pt1, pt2, lineColor):
myscreen.addActor(ovdvtk.Line(p1=(pt1.x, pt1.y, 0), p2=(pt2.x, pt2.y, 0), color=lineColo... | aewallin/openvoronoi | python_examples/polygon_interior_1.py | Python | lgpl-2.1 | 4,111 | [
"VTK"
] | 3a7e5d2f3c83e05eca540256374f5c8bf8005ab8a5f1b9695b430d9ade8184ba |
#!/usr/bin/python
#
# Copyright 2014 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 b... | cctaylor/googleads-python-lib | examples/adwords/v201409/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,880 | [
"VisIt"
] | 3af6968db43db869584309371087d8128cba6c1e1b7bb6a301057b8c3f608d45 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2010 Radim Rehurek <radimrehurek@seznam.cz>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Module for Latent Semantic Analysis (aka Latent Semantic Indexing) in Python.
Implements fast truncated SVD (Singular Value Decomp... | cngo-github/gensim | gensim/models/lsimodel.py | Python | gpl-3.0 | 34,984 | [
"Gaussian"
] | 760f27aba77525012871bceb723007b08fd1f2d2f64104367a1ea0c57b50ac30 |
# $Id$
#
# Copyright (C) 2001-2008 Greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" Automatic search for quantization bounds
This uses the expected informational gain to determine where quantization bounds should
lie.
**Notes**:
- bounds are less than, so if the bounds are [1.,2.],
[0.9,... | rvianello/rdkit | rdkit/ML/Data/Quantize.py | Python | bsd-3-clause | 10,529 | [
"RDKit"
] | da59c9cd6004a2ffac4859cad7db1f534bb8f4dbd287c81c21fd094dda0d19cd |
#!/usr/bin/env python
import os
from Bio import SeqIO
import sys
from Initial_functions import Uniq
from Bio.Blast import NCBIXML
def BWA_analysis(sra_name,additional_file,database,mapping_mode,file_mode,z):
global fliC_option
global fljB_option
global family_c_list
global family_b_list
global ... | denglab/SeqSero | libs/BWA_analysis_H_update_new_family_dependent.py | Python | gpl-2.0 | 19,874 | [
"BLAST",
"BWA"
] | 738a5d6d4163eb8c8478c7fbf12ec98d516e112c443287372af1c4e4d83328f4 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for set manage target of biz feature
"""
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from . import (
SUPER_USER_INFO, PLATFORMER_USER_INFO, PLAT_COMPANY_NAME, PLAT_COMPANY_CODE,
GaccoBizTestMixin,
)
from ...pages.biz.ga_achievem... | nttks/edx-platform | common/test/acceptance/tests/biz/test_ga_set_manage_target.py | Python | agpl-3.0 | 14,958 | [
"VisIt"
] | 5f01870030ef15e509ace852d2f9f150057ee7c98f54e5a1c4960e6b058bcfa6 |
from aiida.parsers.exceptions import OutputParsingError
from aiida.orm.data.array.trajectory import TrajectoryData
from aiida.parsers.plugins.vasp.instruction import BaseInstruction
import numpy as np
import mmap
def read_VASP_XDATCAR(file_name, time_step,
limit_number_steps=10000000,
... | abelcarreras/aiida_extensions | plugins/parsers/vasp/instruction/data/trajectory_data_parser.py | Python | mit | 4,127 | [
"VASP"
] | 7058504f2be3f0219eeb3b32775c29a6faaeba0d37cbc3f2a72950f37bb061b2 |
# being a bit too dynamic
# pylint: disable=E1101
from __future__ import division
import warnings
import re
from collections import namedtuple
from distutils.version import LooseVersion
import numpy as np
from pandas.util._decorators import cache_readonly, Appender
from pandas.compat import range, lrange, map, zip, ... | harisbal/pandas | pandas/plotting/_core.py | Python | bsd-3-clause | 128,319 | [
"Gaussian"
] | 9c8e499361eb7c8b995e8b236780c79dbdcdfd4a6f78ea7296ffd6384d0c2e6a |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright (c) 2015--, The Horizomer Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------... | biocore/WGS-HGT | horizomer/benchmark/parse_output.py | Python | bsd-3-clause | 11,853 | [
"scikit-bio"
] | 1c6fdaad78bca11e1210e70e8d6c957a9dbfbfbbeeab5dcc4185ba7dfb146406 |
from DIRAC import S_OK, S_ERROR
from DIRAC.AccountingSystem.Client.Types.Pilot import Pilot
from DIRAC.AccountingSystem.private.Plotters.BaseReporter import BaseReporter
class PilotPlotter( BaseReporter ):
_typeName = "Pilot"
_typeKeyFields = [ dF[0] for dF in Pilot().definitionKeyFields ]
def _reportCumulati... | Sbalbp/DIRAC | AccountingSystem/private/Plotters/PilotPlotter.py | Python | gpl-3.0 | 11,095 | [
"DIRAC"
] | 581d99f8e2af617fcdd3ca96fc1ba96d460742e4d9e6381de6f87c4aff3f3b7f |
import requests
import xmltodict
import DateTime
from tkinter.tix import *
screen_width = 950
screen_height = 700
def get_vertrektijden(station='ut'):
"""
Input: stationscode
Aanroepen database,
Output: dict met vertrektijden vanuit de stations
"""
auth_details = ('philip.vanexel@... | Flipje666/Actuele_vertrektijden | final gui + api.py | Python | mit | 10,519 | [
"Elk"
] | 7422a0b5e08b8d4fb914321f98148343fa862a5c06d64394a6ccfc6293bf692e |
# -*- coding: utf-8 -*-
import csv
import copy
import datetime
import logging
import io
import json
import re
import time
import zipfile
import codecs
from collections import defaultdict, deque, OrderedDict
from django.contrib import messages
from django.contrib.auth.decorators import login_required, user_passes_test
f... | lingdb/CoBL-public | ielex/views.py | Python | bsd-2-clause | 157,549 | [
"VisIt"
] | 5c6395ae051028d8c9bf15f50dbac5bda0be303680ca3316e07755143a52ed32 |
import os, sys, re, inspect, types, errno, pprint, subprocess, io, shutil, time, copy
import path_tool
path_tool.activate_module('FactorySystem')
path_tool.activate_module('argparse')
from ParseGetPot import ParseGetPot
from socket import gethostname
#from options import *
from util import *
from RunParallel import R... | katyhuff/moose | python/TestHarness/TestHarness.py | Python | lgpl-2.1 | 44,147 | [
"MOOSE",
"VTK"
] | 8099fc8e557db937f9c92b80dd0d4199a940178a1c934a5e7a92e9c369fa0419 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageGradientMagnitude(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkImageGradientMagnitude.py | Python | bsd-3-clause | 507 | [
"VTK"
] | 7cc6699cf7d95b0d1e022211dfefe356c9a283e7f2649806145fa4613e0309f8 |
from __future__ import absolute_import
from __future__ import print_function
from __future__ import division
import unittest
import os
import numpy as np
from pymatgen.analysis.ferroelectricity.polarization import *
from pymatgen.core.structure import Structure
from pymatgen.io.vasp.outputs import Outcar
from pymatge... | xhqu1981/pymatgen | pymatgen/analysis/ferroelectricity/tests/test_polarization.py | Python | mit | 9,344 | [
"VASP",
"pymatgen"
] | d7b6342fe8acc016cbd45e9e1a56bab567f4b818847d0cfb90d70bdb87af160b |
#! /usr/bin/env python3
from vasppy.poscar import Poscar
import math
import argparse
def parse_command_line_arguments():
parser = argparse.ArgumentParser( description='Rotates the cell lattice in VASP POSCAR files' )
parser.add_argument( 'poscar', help="filename of the VASP POSCAR to be processed" )
parse... | bjmorgan/vasppy | vasppy/scripts/rotate_poscar.py | Python | mit | 834 | [
"VASP"
] | f0ae190251174f22c82d65828f933e4803716e479a17f7ea8623e1df52d0aa20 |
../../../../share/pyshared/orca/orca_i18n.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/orca_i18n.py | Python | gpl-3.0 | 44 | [
"ORCA"
] | 7f1ae9be8838eb41962cd444c8c5a8d89b56c4bcbbde8261d5a39db6f7eeba07 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
import numpy as np
from monty.dev import deprecated
from pymatgen.core.periodic_table import Element
"""
Utilities for generating nicer plots.
""... | setten/pymatgen | pymatgen/util/plotting.py | Python | mit | 13,979 | [
"pymatgen"
] | 07f9068d4f0ef08dc6abfe01fa47d5a3903cd8bbe3fb2d48c0354d1b72dcde97 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
=========================================================
Principal components analysis (PCA)
=========================================================
These figures aid in illustrating how a point cloud
can be very flat in one direction--which is where PCA
comes in to ch... | pdedumast/ShapeVariationAnalyzer | src/py/generatelib/generate_polys.py | Python | apache-2.0 | 10,177 | [
"VTK"
] | 899c81511cfe1cea870bd9e34684c3c702caf02c4df2d87b8d9bf47a977779d0 |
from electrum.util import print_error
import httplib, urllib
import socket
import threading
import hashlib
import json
from urlparse import urlparse, parse_qs
try:
import PyQt4
except Exception:
sys.exit("Error: Could not import PyQt4 on Linux systems, you may try 'sudo apt-get install python-qt4'")
from PyQt... | spasmilo/electrum | plugins/labels.py | Python | gpl-3.0 | 9,305 | [
"VisIt"
] | 4e14891190813e5c1fb8a75d686b70f3c71c9b3aa16d431f021a38e1d574fcba |
import data
from galaxy import util
from galaxy.datatypes.sniff import *
from galaxy.web import url_for
from tabular import Tabular
from galaxy.datatypes import metadata
from galaxy.datatypes.metadata import MetadataElement
class ChromInfo( Tabular ):
file_ext = "len"
MetadataElement( name="chrom", default=1,... | dbcls/dbcls-galaxy | lib/galaxy/datatypes/chrominfo.py | Python | mit | 482 | [
"Galaxy"
] | 16241ebea06226af2112389dcddc79cbdc3fdb124ed664e3f0d079966cbb63eb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Example script for calculations inside the nc2map module
This script is part of the nc2map Python module, version 0.0b.
It shall introduce you into the data management within the nc2map module
and show you how per efficiently perform arithmetics and visualization at
the... | Chilipp/nc2map | demo/calculation_demo.py | Python | gpl-2.0 | 3,608 | [
"NetCDF"
] | 72c2fc056723c7ec7198ff159306c4795d8d4ca577ddfaeb5e0907e9325ac5f4 |
"""K-means clustering with weights"""
__author__ = 'sylvain'
import warnings
import numpy as np
import scipy.sparse as sp
# from sklearn.base import BaseEstimator, ClusterMixin, TransformerMixin
from sklearn.metrics.pairwise import euclidean_distances
from sklearn.utils.extmath import row_norms, squared_norm
# from ... | thorwhalen/ut | ml/cluster/w_kmeans.py | Python | mit | 39,462 | [
"Gaussian"
] | db9dc579e850dbf0005ddabaf63fcadc87dbdcb2965c905ce4cca6cb43f1f7dd |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Lice... | Lukc/ospace-lukc | client-pygame/lib/osci/res.py | Python | gpl-2.0 | 13,877 | [
"Galaxy"
] | a7d74278198c92909e99cd7963ad8baad63a713c3c4749ca2bf18740c152ee69 |
'''This file is part of AeoLiS.
AeoLiS 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.
AeoLiS is distributed in the hope that it will... | openearth/aeolis-python | aeolis/__init__.py | Python | gpl-3.0 | 1,881 | [
"NetCDF"
] | 781b2904b2cdcd2509d2bd877e4926ac20f5f5da16c0f06272d0ddebe61a526e |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import time
import threading
from DIRAC import gLogger, S_ERROR
from DIRAC.Core.Utilities.ThreadScheduler import gThreadScheduler
class TransportPool(object):
def __init__(self, logger=False):
if ... | ic-hep/DIRAC | src/DIRAC/Core/DISET/private/TransportPool.py | Python | gpl-3.0 | 4,891 | [
"DIRAC"
] | a55f81a46b81d047828713767540115e9d762c9961b35447436c1d998d769110 |
import numpy as np
from scipy.stats import multivariate_normal
from menpofit.math.fft_utils import pad, crop
def centered_meshgrid(shape):
r"""
Method that generates a centered meshgrid.
Parameters
----------
shape : (`int`, `int`)
The desired meshgrid shape.
Returns
-------
... | nontas/trafficsignrecognition | trafficsignrecognition/correlationfilter/utils.py | Python | bsd-3-clause | 3,062 | [
"Gaussian"
] | f3ad673bf5e2825bf622e147a600a6f68a3b83d579ce6b6337d5a8ab4d054925 |
# coding: utf-8
import unittest
import os
from pymatgen import Molecule
from pymatgen.io.fiesta import FiestaInput, FiestaOutput
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", 'test_files')
class FiestaInputTest(unittest.TestCase):
def setUp(self):
coords = [[0.000000, 0.000000, ... | gVallverdu/pymatgen | pymatgen/io/tests/test_fiesta.py | Python | mit | 3,999 | [
"pymatgen"
] | 31d4601068bc4f736cc9b889fca5c2b0d279377b367485098be0882a23e78202 |
"""Support for Konnected devices."""
import copy
import hmac
import json
import logging
from aiohttp.hdrs import AUTHORIZATION
from aiohttp.web import Request, Response
import voluptuous as vol
from homeassistant import config_entries
from homeassistant.components.binary_sensor import DEVICE_CLASSES_SCHEMA
from homea... | Danielhiversen/home-assistant | homeassistant/components/konnected/__init__.py | Python | apache-2.0 | 14,300 | [
"VisIt"
] | 474e28b23e88b0b8a37f7441943105bf4755333d1343dec6365f2c5063dc332c |
# -*- coding: utf-8 -*-
"""
sphinx.pycode
~~~~~~~~~~~~~
Utilities parsing and analyzing Python code.
:copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from os import path
from sphinx import package_dir
from sphinx.errors import PycodeErr... | superdesk/Live-Blog | documentor/libraries/Sphinx-1.1.3-py3.2/sphinx/pycode/__init__.py | Python | agpl-3.0 | 12,891 | [
"VisIt"
] | 63b5a848195a1afe46c4dbe47003dd2d5e8f8da0be6b7a228856664dac7657e0 |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM 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
#
# ... | CiscoSystems/nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 131,638 | [
"FEFF"
] | 27df6e5ced6c883ec08eda2993d4eca306a925b7bd78b42f6395184a0118aa7b |
##############################################################################
##############################################################################
# Example code for
# quasi-Newton particle Metropolis-Hastings
# for a linear Gaussian state space model
#
# Please cite:
#
# J. Dahlin, F. Lindsten, T. B. Sch\"{... | compops/qpmh2-sysid2015 | para/pmh.py | Python | gpl-3.0 | 19,261 | [
"Gaussian"
] | cc129ec6ed7889d3790b9afb94e8ed228eed04d16c77feb4ab7b2a3b70bfd544 |
import pytest
import numpy as np
import json
import pandas.util.testing as tm
from pandas import compat, Index, DataFrame
from pandas.io.json import json_normalize
from pandas.io.json.normalize import nested_to_record
@pytest.fixture
def deep_nested():
# deeply nested data
return [{'country': 'USA',
... | louispotok/pandas | pandas/tests/io/json/test_normalize.py | Python | bsd-3-clause | 16,104 | [
"COLUMBUS"
] | fba875c57e9b3d0e4a4237d7d6c2efcc6768fc77ee09eadef403a79a836c6ae3 |
# Copyright 2016 United States Government as represented by the Administrator
# of the National Aeronautics and Space Administration. All Rights Reserved.
#
# Portion of this code is Copyright Geoscience Australia, Licensed under the
# Apache License, Version 2.0 (the "License"); you may not use this file
# except in c... | ceos-seo/data_cube_ui | apps/data_cube_manager/forms/ingestion.py | Python | apache-2.0 | 22,231 | [
"NetCDF"
] | 1364cf1808c0c5a43a9d3fc1853054891173e9256d00974aaa436247a7c216fa |
# Copyright 2014 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""WebsiteTest testing class."""
import logging
import time
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common... | axinging/chromium-crosswalk | components/test/data/password_manager/automated_tests/websitetest.py | Python | bsd-3-clause | 12,521 | [
"VisIt"
] | 83332e7bc9809217bbd5749bc8eba299cffaee8e2f9923f0fd5c0fa5bbded641 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistri... | ashutoshvt/psi4 | psi4/share/psi4/basis/primitives/diff_gbs.py | Python | lgpl-3.0 | 4,597 | [
"Psi4"
] | 9348668487059faa972c997652759b1177cf686be2d8355286de3dcf5ebe90d2 |
from ..errors import AngrExitError
from . import ExplorationTechnique
import logging
l = logging.getLogger(name=__name__)
class Slicecutor(ExplorationTechnique):
"""
The Slicecutor is an exploration that executes provided code slices.
"""
def __init__(self, annotated_cfg, force_taking_exit=False, fo... | angr/angr | angr/exploration_techniques/slicecutor.py | Python | bsd-2-clause | 5,141 | [
"MOE"
] | f9c397ea091b461ed494cf7f5ddfd5e2af5d03fb4b1ccd4027687ad0b707fdaa |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
# Read the image.
readerFactory = vtk.vtkImageReader2Factory()
reader = readerFactory.CreateImageReader2(fileName)
reader.SetFileName(fileName)
reader.Update()
ff... | lorensen/VTKExamples | src/Python/ImageProcessing/VTKSpectrum.py | Python | apache-2.0 | 3,417 | [
"VTK"
] | 741dc56ac57fd6e169063dec99c8c7fc275482c9bf79c1da8b5e65f576e717a5 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/bsseeker2/package.py | Python | lgpl-2.1 | 2,193 | [
"Galaxy",
"pysam"
] | f1e428ce779096c94507637bee2097a15e67deb5afbfc57be7bcd6e9fd1ec113 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | kastnerkyle/kastnerkyle.github.io-nikola | blogsite/conf.py | Python | bsd-3-clause | 41,286 | [
"VisIt"
] | 7000aab75a32ce9a7413926faa133554e4e75e03ee3144f8e522c6f4bf5132a1 |
"""
========================================================================
Concentration Prior Type Analysis of Variation Bayesian Gaussian Mixture
========================================================================
This example plots the ellipsoids obtained from a toy dataset (mixture of three
Gaussians) fitte... | RPGOne/Skynet | scikit-learn-0.18.1/examples/mixture/plot_concentration_prior.py | Python | bsd-3-clause | 5,631 | [
"Gaussian"
] | 3aab4dc566025395dc01a4c34f9d0e2e1ffa087ff7870b58972f6f5e75cbac4e |
# 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
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0134_h2o_rhf_rpa_pb.py | Python | apache-2.0 | 1,545 | [
"PySCF"
] | 1be8a5fbc159d887462037fca60d2eb22cd32657339c1d397350454e4f69123d |
def printHSP(hsp, indent=''):
for attr in ['bits', 'expect', 'frame', 'query_end', 'query_start',
'sbjct', 'query', 'sbjct_end', 'sbjct_start']:
print('%s%s: %s' % (indent, attr, hsp[attr]))
def normalizeHSP(hsp, readLen, blastApplication):
"""
Examine an HSP and return informatio... | terrycojones/dark-matter | dark/blast/hsp.py | Python | mit | 7,637 | [
"BLAST",
"Biopython"
] | c65f5cb76180d577f38a375e20e1ff4859939f5e661e830edfb0919805cbf9a7 |
# -*- coding: utf-8 -*-
###############################################################################
#
# This source file is part of the tomviz project.
#
# Copyright Kitware, Inc.
#
# This source code is released under the New BSD License, (the "License").
#
# Unless required by applicable law or agreed to in ... | mathturtle/tomviz | tomviz/python/tomviz/io/__init__.py | Python | bsd-3-clause | 2,175 | [
"VTK"
] | de2f571ea4a0d8208607299cb1385d60d3e836862d85be003e60f27417b94643 |
import types
from datetime import datetime
import numpy as np
import chianti
import chianti.data as chdata
import chianti.constants as const
import chianti.filters as chfilters
import chianti.util as util
#
defaults = chdata.Defaults
class spectrum:
'''Calculate the emission spectrum as a function of temperature a... | wkerzendorf/chiantipy | chiantipy/chianti/core/Spectrum.py | Python | gpl-3.0 | 11,764 | [
"Gaussian"
] | 86d9dc2c5ddf34d9027e4bfd090889495f174f44a808abafb664d692d531db19 |
# Copyright (C) 2014 Karl R. Wurst
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in ... | kwurst/grading-scripts | test_assignment.py | Python | gpl-3.0 | 2,053 | [
"VisIt"
] | 44d21728e7aeaedf0d77e5de9781a28cccc35c04131b2b87a341872095fe9bd8 |
import os
import yaml
import pytest
import moldesign as mdt
from moldesign.compute import packages
from .molecule_fixtures import *
__PYTEST_MARK__ = ['internal', 'config']
# mark all tests in this module with this label (see ./conftest.py)
@pytest.fixture(scope='function')
def tempconfigfile(tmpdir):
tmpdir = ... | Autodesk/molecular-design-toolkit | moldesign/_tests/test_config.py | Python | apache-2.0 | 3,146 | [
"NWChem",
"OpenMM"
] | ed76d1e1d0801ca6cdc806e739b3f2e3e29f4262af0b682739d21fadba3fe879 |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
Defines the Interface(extends class Slab) and
Ligand(extends class Molecule) classes
"""
from six.moves import range
import sys
... | henniggroup/MPInterfaces | mpinterfaces/interface.py | Python | mit | 31,649 | [
"ASE",
"VASP",
"pymatgen"
] | fbc4dfcf5065a0281cbe73f83bd6b0ad13db35d6e2002cb4f94ac00750a28c4d |
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm
from keras.datasets import mnist
from keras.optimizers import RMSprop
from vae import VariationalAutoEncoder
# set parameters
batch_size = 100
latent_dim = 2
nr_epochs = 30
layers = [256, 128]
optimizer = RMSprop(lr=1e-3)
# get MNIST digi... | DKaravolos/variational_autoencoder | train_vae_mnist.py | Python | mit | 2,230 | [
"Gaussian"
] | b6c489c86167c842a04b81b756c16e9a185dba72b01bc2a250a2d54eb050e045 |
# Global settings for core project.
import os
# PATH CONFIGURATION
PROJECT_DIR = os.path.dirname(os.path.dirname(__file__))
PUBLIC_DIR = os.path.join(PROJECT_DIR, 'public')
# Python dotted path to the WSGI application used by Django's runserver.
WSGI_APPLICATION = 'plugin_manager.core.wsgi.application'
# END PATH CON... | ahharu/plugin-manager | plugin_manager/core/settings/base.py | Python | mit | 7,856 | [
"Elk"
] | 1abc41f3d5ba012cc6c20c855d62343c761801c015c1b1df5983a0cb6e025c1c |
''' ResourceManagementHandler
Module that allows users to access the ResourceManagementDB remotely.
'''
from DIRAC import gConfig, S_OK, gLogger
from DIRAC.Core.DISET.RequestHandler import RequestHandler
from DIRAC.ResourceStatusSystem.Utilities import Synchronizer
from DIRAC.ResourceStatusSystem.Service.ResourceSt... | andresailer/DIRAC | ResourceStatusSystem/Service/ResourceManagementHandler.py | Python | gpl-3.0 | 6,815 | [
"DIRAC"
] | f7bc62e9ff68b245251a7fa7c09f9a1f39b100914ed7a8a6884d9f409f99fa8c |
#! /usr/bin/env python
#
# see also http://docs.openstack.org/cli/quick-start/content/nova-cli-reference.html
#
from __future__ import print_function
import inspect
import requests
from datetime import datetime, timedelta
import iso8601
import base64
import httplib
import json
import os
import ast
from pprint import ... | rajpushkar83/cloudmesh | cloudmesh/iaas/openstack/cm_compute.py | Python | apache-2.0 | 55,386 | [
"NEURON"
] | 5375520e70a6c4549edfb2140408bc7862bf19aefc7aff641f0c86331146226b |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/ferret/package.py | Python | lgpl-2.1 | 4,430 | [
"NetCDF"
] | 250923c45c52a41da6d87ca7f3649144fe8884194aa3ec9c3c37644cedc002a7 |
import logging
import os
import shutil
import tempfile
import unittest
from Bio import SeqIO
from phylotyper.config import PhylotyperOptions
from phylotyper.run import build_pipeline, check_gene_names
from phylotyper.subtypes_index import SubtypeConfig
from phylotyper.tree.seq import SeqDict
from phylotyper.tree.seqal... | superphy/insilico-subtyping | phylotyper/test/test_new.py | Python | apache-2.0 | 15,768 | [
"BLAST"
] | 931c87385d09dfead16002e834a63daaba4e940212eedf6ea6b660192bde0798 |
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | src/formattedcode/writers.py | Python | apache-2.0 | 9,472 | [
"VisIt"
] | 23cb831b0c8baee93c88dae7b7e4e3fe1c4f5e4a49c34b0205841a145655e364 |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import, division, print_function
import ast
import errno
import itertools
import imp
import marshal
import os
import re
import six
import string
import struct
import sys
import types
import atomicwrites
import py
from _pytest.a... | davidszotten/pytest | src/_pytest/assertion/rewrite.py | Python | mit | 39,382 | [
"VisIt"
] | 7febd236b550bd5edef6b093e121e68e3620405490db486209632806d2f46692 |
# ======================================================================
# Given vtu/pvtu file(s) resulting from an MVR elasticity simulation
# (the solution files hence contain three scalar valued arrays named
# 'u0', 'u1' and 'u2' as PointData), this vtk-based python script
# warps the initial/original mesh geometr... | CognitionGuidedSurgery/msml | src/msml/ext/vonMisesStressComputation_mvrPostProcessingAnalytics.py | Python | gpl-3.0 | 6,424 | [
"VTK"
] | afb050edb8f1f534c9bfa52ee1303345771ed429f6958b84f36dd1a5f5470c67 |
import unittest
from emmail.objects.clusterer import Clusterer
from emmail.tests.test_data import *
# Single BLAST output file
clusterer = Clusterer(blastOutputFile=test_blast_product,
output_stream="stdout",
output_type="short",
head... | Andre-Tan/EmMAIL | emmail/tests/test_clusterer.py | Python | gpl-3.0 | 1,404 | [
"BLAST"
] | 22bebebca564e0d663dcf660906d4cc9460ea75d041346b53c1f374235742fc4 |
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2016 msto <mstone5@mgh.harvard.edu>
#
# Distributed under terms of the MIT license.
"""
Simple venn diagrams.
"""
import matplotlib.pyplot as plt
import matplotlib.patches as patches
def venn4(subsets,
set_labels=('A', 'B', 'C', 'D'),
# s... | msto/svplot | svplot/venn.py | Python | mit | 8,650 | [
"Amber"
] | 017345cfde78f401a370fdd7bf707945aea5d981027c84fab36416efcd643b2d |
#http://www.netinstructions.com/how-to-make-a-web-crawler-in-under-50-lines-of-python-code/
from html.parser import HTMLParser
from urllib.request import urlopen
from urllib import parse
# We are going to create a class called LinkParser that inherits some
# methods from HTMLParser which is why it is passed into ... | HeyIamJames/Crawlers | crawler.py | Python | mit | 3,721 | [
"VisIt"
] | 3cbb41dd97fa3b6b87f4afedd0e64a65c5b938b34d0bcd06558f7186f6d1e987 |
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