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"""
This example demonstrates using Mayavi as a component of a large Qt
application.
For this use, Mayavi is embedded in a QWidget. To understand this
example, please read section :ref:`builing-applications`.
"""
# First, and before importing any Enthought packages, set the ETS_TOOLKIT
# environment variable to qt4, ... | zinka/arraytool_gui | misc/test.py | Python | bsd-3-clause | 3,931 | [
"Mayavi",
"VTK"
] | dd6dedb04084073ddef2dd00b4335b94f94181609946165f7e6733c6c0f9e844 |
import numpy as np
import numpy.linalg as linalg
import matplotlib.pyplot as plt
import sys, os
import glob2
import os, sys
from tabulate import tabulate
# Information specific to this computation.
hr_filename = 'NiO_hr.dat'
out_suffix = '_hamiltonian.txt'
Efermi = 14.0853
# This reads the hamiltonian elements for a... | ZGainsforth/QEScripts | Wannier/ComputeWannierHamiltonians.py | Python | mpl-2.0 | 3,938 | [
"Wannier90"
] | 667c34c20cdc553bb5de8478781b19a49a3445a3491677a986d2f8123e532720 |
"""
Created on 6/05/2013
@author: thom
"""
import logging
import string
from rdkit.Chem import AllChem as Chem
from evaluator import Evaluator
from molecular_population import MolecularPopulation
from molecule import Molecule
class EvaluatorSummary(Evaluator):
def get_result_titles(self):
return ["N... | th0mmeke/toyworld | evaluators/evaluator_summary.py | Python | gpl-3.0 | 5,124 | [
"RDKit"
] | 842b917ad93a379dd4e8cdda6e621433b4baf3988f59d08b9df0662b056eeaa0 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import django.core.validators
class Migration(migrations.Migration):
dependencies = [
('tracking', '0012_create_link_to_clinic'),
]
operations = [
migrations.CreateModel(
... | Heteroskedastic/Dr-referral-tracker | tracking/migrations/0013_auto_20160412_1228.py | Python | mit | 1,914 | [
"VisIt"
] | 1470ad4feb0940805ccea8de335daaeada6397889b8fb550d89765b380ef31ce |
#!/usr/bin/env python
# Copyright 2014-2020 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... | sunqm/pyscf | pyscf/eph/uks.py | Python | apache-2.0 | 10,792 | [
"PySCF"
] | 2f4d295b248bb718675b7edd223dfdd9e3caa069aab8d0031157d134a37884cf |
from __future__ import annotations
import math
import random
import pytest
from dxtbx.model import ExperimentList
from scitbx import matrix
from dials.algorithms.profile_model.gaussian_rs import (
BBoxCalculator3D,
CoordinateSystem,
transform,
)
from dials.array_family import flex
def evaluate_gaussia... | dials/dials | tests/algorithms/reflection_basis/test_transform.py | Python | bsd-3-clause | 16,940 | [
"Gaussian"
] | a1c8a712e70b9d003b7352ab1eabb85fe6524722ca27f1bb95ddf6ea5c536c58 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Cubesphere-like netcdf saving benchmarks.
Where possible benchmarks should be parameterised for two sizes of input data:
... | SciTools/iris | benchmarks/benchmarks/netcdf_save.py | Python | lgpl-3.0 | 2,201 | [
"NetCDF"
] | 0d0b8ce48524a59ff488055fb54cb073e95fa2e630eb8a3b9a192a72bc067b14 |
import unittest
from pymatgen.util.plotting import periodic_table_heatmap, van_arkel_triangle
from pymatgen.util.testing import PymatgenTest
import matplotlib
class FuncTestCase(PymatgenTest):
def test_plot_periodic_heatmap(self):
random_data = {'Te': 0.11083818874391202, 'Au': 0.7575629917425387,
... | dongsenfo/pymatgen | pymatgen/util/tests/test_plotting.py | Python | mit | 872 | [
"pymatgen"
] | 5b891422f704abab5eedca9d30132fd7db37cef5b5bc9e466df3ca6d88e31617 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2015 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any pe... | haggi/appleseed-maya | module/shaders/src/compile_shaders.py | Python | mit | 2,330 | [
"VisIt"
] | 703aa49b17aabd3ebe510a8ac2503b4bd92d73a77b50c2d1f28da81d3c87b15c |
config = {
# environment this app is running on: localhost, testing, production
'environment': "localhost",
# webapp2 sessions
'webapp2_extras.sessions' : {'secret_key': '_PUT_KEY_HERE_YOUR_SECRET_KEY_'},
# webapp2 authentication
'webapp2_extras.auth' : {'user_model': 'boilerplate.models.User',
... | rittersport3/CityWatchers | config/localhost.py | Python | lgpl-3.0 | 4,064 | [
"VisIt"
] | a2c320dcf0201c70bbf41f395b3895d13b42ccd3c8aa7822c77942f6da2263be |
"""
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... | wwj718/edx-platform | lms/djangoapps/verify_student/views.py | Python | agpl-3.0 | 59,314 | [
"VisIt"
] | a9de5496446e43f9d46a94a5d50f80cd8d640715a7b34e9e4cf987b9cc2d1cd0 |
from contextlib import contextmanager
import os
import sys
import unittest
from rdkit import Chem
from rdkit import RDConfig
from rdkit.Chem.ChemUtils.SDFToCSV import Convert, initParser
from io import StringIO
class TestCase(unittest.TestCase):
def test1(self):
fName = os.path.join(RDConfig.RDDataDir, ... | bp-kelley/rdkit | rdkit/Chem/ChemUtils/UnitTestSDFToCSV.py | Python | bsd-3-clause | 2,817 | [
"RDKit"
] | bff420244220ef4988d9565002cc5744eb53153f37de46cb136127d440b88b56 |
#!/usr/bin/python
"""
prepare_data - auxiliary script aiming to prepare the data structure to
reconstruct a number of gene trees i.e. a phylome
Copyright (C) 2016 - Salvador Capella-Gutierrez, Toni Gabaldon
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Ge... | Gabaldonlab/phylomizer | source/prepare_data.py | Python | gpl-3.0 | 10,555 | [
"BLAST"
] | f02dd2a6a22fa4d07442e6f23c07e277e36163de48816b9e6ded64635f08e07e |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
"""Consumer class that builds a Structure object.
This is used by the PDBParser and MMC... | bryback/quickseq | genescript/Bio/PDB/StructureBuilder.py | Python | mit | 10,408 | [
"Biopython"
] | cc6e5cb5bbfb190890dd0e0da0a053e5b83a71c568e2070bd600af734cdaaa1d |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/r-gtrellis/package.py | Python | lgpl-2.1 | 2,224 | [
"Bioconductor"
] | 58554cee863752814abd57fbd7bdb589e4bde4e57b2014e12cafe40802a88ea6 |
"""
@created_at 2014-07-17
@author Exequiel Fuentes <efulet@gmail.com>
@author Brian Keith <briankeithn@gmail.com>
Basado en el trabajo de Juan Bekios-Calfa <juan.bekios@ucn.cl>
"""
# Se recomienda seguir los siguientes estandares:
# 1. Para codificacion: PEP 8 - Style Guide for Python Code (http://legacy.python.or... | efulet/pca | pca/lib/naive_bayes_classifier.py | Python | mit | 4,417 | [
"Brian"
] | 9574c089fa70b012127e35e5f4a14abf7bb940cc0241014fe9ac8ba8297835d1 |
# -*- coding: utf-8 -*-
"""
Created on Fri Feb 6 12:45:40 2015
@author: miles
"""
import numpy as np
from utils import *
from cochlea_model import *
from brian.hears import LinearFilterbank
from brian.stdunits import kHz, Hz, ms
def LowPass_filter_(fc,fs):
TWOPI = 2*np.pi
c = 2.0 * fs
c1LP = ... | pabloriera/pycochlea | pycochlea/periphery.py | Python | gpl-2.0 | 5,668 | [
"Brian"
] | 0f7f43cd2c258e12985c48d7d49125216004118a9cf999a29f150888530920df |
# #
# Copyright 2013-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (... | akesandgren/easybuild-framework | test/framework/options.py | Python | gpl-2.0 | 296,951 | [
"NetCDF",
"SIESTA"
] | 660d2fed7e5bd07621ebd93d11678e8c35b49a366fabe77a01ccdf8cb74d9b65 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | bgrant0607/kubernetes | cluster/juju/layers/kubernetes-master/reactive/kubernetes_master.py | Python | apache-2.0 | 36,298 | [
"CDK"
] | 91255537c68f49129eb918da951d2e4bc4562ae180fbce5362b5cf6e1b4076bf |
#!/usr/bin/env python
"""
Sensor handler for color ball detection
"""
from socket import *
import sys, struct, time, os
import array as pyarray
class sensorHandler:
def __init__(self, proj, shared_data):
"""
Opens socket, subscribes to multicast group, and calculates
local vs. Vicon clo... | jadecastro/LTLMoP | src/lib/handlers/deprecated/sensor/colorBallSensor.py | Python | gpl-3.0 | 4,087 | [
"ORCA"
] | 83ffcf1a3b2d84841ce6238c140c687d421536fcd0c57a863939fc0561d0b1e1 |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
import os, sys
def fn_name(): return sys._getframe(1).f_code.co_name
try:
import gi
except ImportError:
raise ImportError("Gtk3 backend requires pygobject to be installed.")
try:
gi.re... | unnikrishnankgs/va | venv/lib/python3.5/site-packages/matplotlib/backends/backend_gtk3.py | Python | bsd-2-clause | 33,857 | [
"FLEUR"
] | 21868f896a7d119d3f04b0dace2e44da0f949baf08d3e958ae132b3f5d34bba4 |
""" Data Dictionary CSV Validator
@author: Victor Meyerson
"""
import os
import csv
# Header columns for data dictionary
FIELD_NAME = "Variable / Field Name"
FORM = "Form Name"
FIELD_TYPE = "Field Type"
FIELD_LABEL = "Field Label"
CHOICES = "Choices, Calculations, OR Slider Labels"
TEXT_TYPE = "Text Validation Type ... | victorSRI/redcap_rdf | redcap_rdf/datadict_validator.py | Python | bsd-3-clause | 7,209 | [
"VisIt"
] | ae00434ddd60f4575198d2b27e7e4045f0520d4e559d7b899d8ea20a1892f0d1 |
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Mathieu Blondel <mathieu@mblondel.org>
# Olivier Grisel <olivier.grisel@ensta.org>
# Andreas Mueller <amueller@ais.uni-bonn.de>
# Eric Martin <eric@ericmart.in>
# Giorgio Patrini <giorgio.patrini@anu.edu.au>
# ... | manhhomienbienthuy/scikit-learn | sklearn/preprocessing/_data.py | Python | bsd-3-clause | 118,565 | [
"Gaussian"
] | f6dc6a8ab5835ebcfbf62854aa1cceb4abddb51e8fc3fb9745dce55427671554 |
#!/usr/bin/env python
''' buildCodeDOC
It accepts as argument the DIRAC version ( or branch name )
'''
# defined on DIRACDocs/source/Tools/fakeEnvironment
import fakeEnvironment
import DIRAC
import os
import pkgutil
import sys
import tempfile
DOCMODULES = [ 'API', 'Client', 'Service', 'Utilities' ]
def getTm... | andresailer/DIRAC | docs/Tools/buildCodeDOC.py | Python | gpl-3.0 | 7,191 | [
"DIRAC"
] | 40e5e0a587dc585c924e4bc6d880f32cbfd6e813650affbf7a6e6c2204243952 |
# -*- coding: utf-8 -*-
"""
[Python 2.7 (Mayavi is not yet compatible with Python 3+)]
Created on Wed Dec 16 22:44:15 2015
@author: Ryan Stauffer
https://github.com/ryanpstauffer/market-vis
[This module referenced http://www.theodor.io/scraping-google-finance-data-using-pandas/]
Market Visualization Prototype
Quotes M... | ryanpstauffer/market-vis | marketvis/quotes.py | Python | mit | 5,030 | [
"Mayavi"
] | cb7af044733bc4cddb91d309248eb034c00cac6102a6e52af23b0b9dbe952aef |
# Copyright 2012 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of ngs_crumbs.
# ngs_crumbs 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, ... | JoseBlanca/ngs_crumbs | crumbs/seq/trim.py | Python | gpl-3.0 | 17,144 | [
"BLAST",
"BWA"
] | c1ae050bc1ac2dd52b5594f407a16f583d6c706a72d0f4eca4d4539e06be8c9f |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# 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)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/auxiliary/core.py | Python | gpl-2.0 | 3,638 | [
"MDAnalysis"
] | a7bfa52c3984277e3f3c67290cf6b2592414e44a099356b8ec202d40be437e45 |
#!/usr/bin/env python
"""CSP Commstime benchmark.
See F.R.M. Barnes (2006) Compiling CSP. In Proceedings of
Communicating Process Architectures 2006.
Code adapted from PyCSP by John Markus Bjorndalen, available:
http://www.cs.uit.no/~johnm/code/PyCSP/
PyCSP - Communicating Sequential Processes for Python. John Mark... | bjlittle/python-csp | benchmark/commstime/commstime.py | Python | gpl-2.0 | 1,672 | [
"Brian"
] | 6ccacc3e155d4c4c7b9e1ff1b034f5f026dc1d60a58cdd702147a400a5918817 |
import numpy as np
from scipy import signal
def find_sideband(ft_data, which=+1, copy=True):
"""Find the side band position of a hologram
The hologram is Fourier-transformed and the side band
is determined by finding the maximum amplitude in
Fourier space.
Parameters
----------
ft_data: ... | RI-imaging/qpimage | qpimage/holo.py | Python | mit | 9,555 | [
"Gaussian"
] | 350938947c1cc4e4f5707c1c3962459462305ca784510b97e792b9232d790f21 |
"""
Acceptance tests for Studio.
"""
from unittest import expectedFailure
from bok_choy.web_app_test import WebAppTest
from ..pages.studio.asset_index import AssetIndexPage
from ..pages.studio.auto_auth import AutoAuthPage
from ..pages.studio.checklists import ChecklistsPage
from ..pages.studio.course_import import I... | XiaodunServerGroup/xiaodun-platform | common/test/acceptance/tests/test_studio.py | Python | agpl-3.0 | 8,703 | [
"VisIt"
] | 7bdaf5a909fc59ca48355c993b6cc4babbc81a84679f35f3f88ff3b9fa4451f1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements an XRD pattern calculator.
"""
import os
import json
from math import sin, cos, asin, pi, degrees, radians
import numpy as np
from pymatgen.symmetry.analyzer import SpacegroupAnaly... | gVallverdu/pymatgen | pymatgen/analysis/diffraction/xrd.py | Python | mit | 11,340 | [
"CRYSTAL",
"pymatgen"
] | 4fcd69d4d3b61433154a0dba7df3655a90809d0abc04c1acef800f1865efd72a |
# -*- coding: utf-8 -*-
from __future__ import division
import numpy as np
from scipy.linalg import pascal, invpascal, toeplitz
from scipy.special import legendre
from scipy.interpolate import PPoly, UnivariateSpline
try:
from functools import cache
except ImportError: # no functools in Python 2
def cache(fun... | PyAbel/PyAbel | abel/tools/polynomial.py | Python | mit | 32,017 | [
"Gaussian"
] | 279d745c1114ad7a96a6461645aacd87ee7e969d80b1066d12dd1a5927805294 |
#!/usr/bin/env python
"""Read in two csv files and check that the float contents are the same"""
from __future__ import print_function
import sys
from termcolor import colored
from openpyxl import load_workbook
global threshold
def main():
# Start processing the directories
if len(sys.argv) <= 1 :
pr... | JohnKendrick/PDielec | PDielec/checkexcel.py | Python | mit | 5,880 | [
"CRYSTAL"
] | 88d28f07514433153d1fece7211a19028036da5426541fbc6ff663d6e727bdb3 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/lib/settingsmanager.py | Python | gpl-2.0 | 3,318 | [
"Brian"
] | 545cb1e53fce011d616b0022a6e8a982c351c731119c7f645554cd6c0100947c |
##
# Copyright 2015-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | torbjoernk/easybuild-easyblocks | easybuild/easyblocks/m/molpro.py | Python | gpl-2.0 | 8,111 | [
"Molpro"
] | 98e396349909deb5f6b9a0639582f8f169fbae186d32d417fe2e3dfd8b1d4023 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/util/_testing.py | Python | bsd-3-clause | 13,826 | [
"scikit-bio"
] | c6b40e0254ac827ac30f0ea1c76d4fd749a7c22aa1faea9f98e78934457206ba |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | Forage/Gramps | gramps/plugins/quickview/onthisday.py | Python | gpl-2.0 | 5,069 | [
"Brian"
] | c854ddb062cad169e7a90c814e5cd4a942265018591b1e4f042e302d8a8464a3 |
from AritLexer import AritLexer
from AritParser import AritParser
# from AritVisitor import AritVisitor
from MyAritVisitor import MyAritVisitor, UnknownIdentifier
from antlr4 import InputStream, CommonTokenStream
import sys
# example of use of visitors to parse arithmetic expressions.
# stops when the first SyntaxErr... | lauregonnord/cap-labs | TP03/arith-visitor/arit.py | Python | gpl-3.0 | 747 | [
"VisIt"
] | 5e4130dba91705a0a49478d6e9e6635a5ef7a52719a141f3034c8c3ba653881f |
# -*- encoding: utf-8 -*-
from __future__ import print_function
import json
import time
from builtins import str as text
import pytest
from django.contrib.auth.models import User
from django.utils.translation import gettext_lazy as _
from model_bakery import baker
from multiseek import logic
from multiseek.logic impo... | mpasternak/django-multiseek | test_project/test_app/tests.py | Python | mit | 25,528 | [
"VisIt"
] | 8473bcbf061ec9ecd8b71f78ab433f43e8567916984dc92f5eaa601b44ddf454 |
"""The config flow tests for the forked_daapd media player platform."""
import pytest
from homeassistant import data_entry_flow
from homeassistant.components.forked_daapd.const import (
CONF_LIBRESPOT_JAVA_PORT,
CONF_MAX_PLAYLISTS,
CONF_TTS_PAUSE_TIME,
CONF_TTS_VOLUME,
DOMAIN,
)
from homeassistant.... | tchellomello/home-assistant | tests/components/forked_daapd/test_config_flow.py | Python | apache-2.0 | 8,044 | [
"Firefly"
] | 5d5cd70ee3eb17faa2ded6ca0e8456891c6f9807020c643ee5bc6384c6154f41 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from ase import
| jochym/ase-qe | ase-qe/__init__.py | Python | gpl-3.0 | 62 | [
"ASE"
] | 84b4e4b3c3103dcca0c70097fa1c1fedcb6db44ccec132010b0816bc29700da7 |
import os
import re
import uuid
import requests
import json
import logging
logging.basicConfig(level=logging.DEBUG)
logging.getLogger("urllib3").setLevel(logging.WARNING)
from django.core.management.base import BaseCommand
from account.models import Team
from django.conf import settings
from django.utils import timezo... | galaxy-ctf/milky-way | milkyway/management/commands/rancher_sync.py | Python | agpl-3.0 | 13,486 | [
"Galaxy"
] | eac0e1df2de833f29460c3b438bf93193cdb3a263e811475b2122b276180d3bb |
#!/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/tools/molden.py | Python | apache-2.0 | 17,740 | [
"PySCF"
] | 9dd1da05fcd2c62378db5f1f19879c17962a0710c3fb39fada02fbaeff568c0c |
#!/usr/bin/env python3
from __future__ import print_function
from glob import glob
from argparse import ArgumentParser
import os, re, sys
parser = ArgumentParser(prog='check-packages.py',
description="Check package table completeness")
parser.add_argument("-v", "--verbose",
... | pastewka/lammps | doc/utils/check-packages.py | Python | gpl-2.0 | 2,743 | [
"LAMMPS"
] | daf0806b45f7e18334b4946abef16ea757c3a12bd1dce1a070311bf954f87b0f |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# grid_monitor - Monitor page generator
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public Licens... | heromod/migrid | mig/server/grid_monitor.py | Python | gpl-2.0 | 28,123 | [
"Brian"
] | cdf765e8dac6258ab6294e78c9a00d388759db0f80d949476e24d27700a67efa |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | gdooper/scipy | scipy/special/add_newdocs.py | Python | bsd-3-clause | 154,618 | [
"Gaussian"
] | d034452b3148837754e323d4a1138ffdea6fe0cf6814e4f6172e1407977d83e2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
use leaf alogrithm to remove redundancy
this algorithm is published in this following paper
1. Bull, S. C., Muldoon, M. R. & Doig, A. J. Maximising the Size of Non-Redundant Protein Datasets Using Graph Theory. PLoS One 8, (2013).
Simon Bull gives an implementation for ... | lituan/tools | leaf_seq.py | Python | cc0-1.0 | 7,347 | [
"Biopython"
] | 48a0d61e51ea651ea2614e45de582da7487d63d5c37a9476f332dac4902948ac |
#!/usr/bin/python3
import sys, os
import time
import argparse
import json
import curses
import logging
import configparser
import subprocess
import urllib
from urllib.request import urlopen
from urllib.parse import quote_plus
import gettext
from monitor import Colors
from monitor import WarningWindow
from monitor imp... | aserebryakov/godville-monitor-console | pygod.py | Python | gpl-2.0 | 14,394 | [
"VisIt"
] | 80bf59c919ed9c8a6ca270bd3d59584149fb7c8ef70d49ef0d38c765e9289c11 |
import numpy as np
import pandas as pd
from statsmodels.sandbox.stats.multicomp import multipletests
import regreg.api as rr
from ...api import (randomization,
glm_group_lasso,
multiple_queries)
from ...tests.instance import (gaussian_instance,
lo... | selective-inference/selective-inference | selectinf/randomized/tests/sandbox/test_cv.py | Python | bsd-3-clause | 6,370 | [
"Gaussian"
] | bd37fcf32b60f737b5af2fc63c2d9bd367a12daa3b39f671e28b2f596db0ba17 |
from __future__ import absolute_import, division, print_function
import sys, os
import argparse
import time
import warnings
import numpy as np
from scipy.constants import speed_of_light
from scipy.stats import cauchy
from astropy.table import Table,Column
import astropy.io.fits as pyfits
import multiprocessing
import... | desihub/desisim | py/desisim/scripts/quickquasars.py | Python | bsd-3-clause | 41,683 | [
"Gaussian"
] | 54ac955d84030bc93c8ec936d3f023d88e05553b3445b07d4a5e34db33dac2b3 |
# Copyright 2012 Patrick Varilly, Stefano Angioletti-Uberti
#
# 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... | patvarilly/DNACC | examples/ssDNA_tethers/ssDNA_tethers.py | Python | gpl-3.0 | 8,404 | [
"Gaussian"
] | d36fdef23abe538c18e5714232ca4f3ab419f1e9c3896256a59e2f978a9cc08c |
import os
import numpy as np
import h5py
import time
from pyscf import gto, scf, mp, cc, ci, fci, ao2mo
from pyscf.cc import ccsd_rdm
from frankenstein.be.sd import SD
from frankenstein.tools.tensor_utils import get_symm_mat_pow
from frankenstein.be.sd import schmidt_decomposition, schmidt_decomposition_new
from fran... | hongzhouye/frankenstein | pyscf_be/pysd.py | Python | bsd-3-clause | 35,392 | [
"PyMOL",
"PySCF"
] | 6390286230b730ac046c2139262bb49b7f75466110342b998e30c9f40fb8bdd3 |
from __future__ import with_statement
import unittest
from repoze.bfg import testing
from karl import testing as karltesting
from zope.testing.cleanup import cleanUp
class TestAdminView(unittest.TestCase):
def setUp(self):
cleanUp()
def tearDown(self):
cleanUp()
def test_it(self):
... | boothead/karl | karl/views/tests/test_admin.py | Python | gpl-2.0 | 40,372 | [
"exciting"
] | c511520e24476b8a6c09717b0f00f717a54548fa7741e560102d27cc9e05f7ea |
# Copyright: (c) 2013, James Cammarata <jcammarata@ansible.com>
# Copyright: (c) 2018, Ansible Project
# 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
import os.path
import re
import sh... | amenonsen/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 57,910 | [
"Galaxy"
] | 056773abea2cbf4af1a3c21c11341729205ee1d35587cac1204b0c50eb09b70e |
#
# QAPI command marshaller generator
#
# Copyright IBM, Corp. 2011
#
# Authors:
# Anthony Liguori <aliguori@us.ibm.com>
# Michael Roth <mdroth@linux.vnet.ibm.com>
#
# This work is licensed under the terms of the GNU GPLv2.
# See the COPYING.LIB file in the top-level directory.
from ordereddict import OrderedDict... | Aaron0927/qemu | scripts/qapi-commands.py | Python | gpl-2.0 | 9,831 | [
"VisIt"
] | 208835bcbb3967345e7e4fd49cd36d866cf9321bc6157310037851d65badc6ef |
import jinja2
import json
import os
import subprocess
import cclib
# For atomic number -> atomic symbol, and num valence electrons
from mendeleev import element
import openchemistry as oc
def run_calculation(geometry_file, output_file, params, scratch_dir):
# Read in the geometry from the geometry file
# Thi... | OpenChemistry/mongochemdeploy | docker/cp2k/src/run.py | Python | bsd-3-clause | 5,911 | [
"CP2K",
"cclib"
] | 48e6a6d1fa8c9daf43b55c3c3002f79e58de3a4591f451b9a5daf72b919fdb58 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""This module provides functions and classes related to Task objects."""
from __future__ import division, print_function, unicode_literals, absolute_import
import os
import time
import datetime
import shutil
i... | setten/pymatgen | pymatgen/io/abinit/tasks.py | Python | mit | 173,421 | [
"ABINIT",
"NetCDF",
"Wannier90",
"pymatgen"
] | 44efeabdb866a65e2ed055b4066f04c40f56023a258c9b150052add15ed258ce |
# Copyright (C) 2006-2016 Music Technology Group - Universitat Pompeu Fabra
#
# This file is part of Essentia
#
# Essentia 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 (FSF), either version 3 of the ... | carthach/essentia | src/python/essentia/extractor/highlevel.py | Python | agpl-3.0 | 3,989 | [
"exciting"
] | 9ef12ecce240175039749bc740f82ad56e582965221897ad0583af3fe2dfc709 |
#!/bin/env python
# -*- coding: utf-8 -*-
#
#Created on 31.03.17
#
#Created for pymepps-streaming
#
#@author: Tobias Sebastian Finn, tobias.sebastian.finn@studium.uni-hamburg.de
#
# Copyright (C) {2017} {Tobias Sebastian Finn}
#
# This program is free software: you can redistribute it and/or modify
# it under... | maestrotf/pymepps-streaming | pymeppsstream/streams/ncsubset.py | Python | gpl-3.0 | 5,787 | [
"NetCDF"
] | 32c9ed54ccbef432803edddf036e97e16dce1efc0d47fa9149060e5b9a9cd1da |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | vmanoria/bluemix-hue-filebrowser | hue-3.8.1-bluemix/apps/useradmin/src/useradmin/test_ldap_deprecated.py | Python | gpl-2.0 | 32,107 | [
"MOE"
] | d79634870ae201ee0379726156deb36128f1ccdacdd56481eb2043eb859152f7 |
"""
Filename: arma.py
Authors: Doc-Jin Jang, Jerry Choi, Thomas Sargent, John Stachurski
Provides functions for working with and visualizing scalar ARMA processes.
"""
import numpy as np
from numpy import conj, pi
import matplotlib.pyplot as plt
from scipy.signal import dimpulse, freqz, dlsim
# == Ignore unnecessary... | gxxjjj/QuantEcon.py | quantecon/arma.py | Python | bsd-3-clause | 9,906 | [
"Gaussian"
] | 9cbbc52eae5ed8041e73d4eee98b7266c4a987cc0919efeb838408c00775ddc4 |
from ase import *
from gpaw import GPAW
from gpaw.utilities import equal
a = 5.0
H = Atoms('H', [(a/2, a/2, a/2)], magmoms=[1],
pbc=False,
cell=(a, a, a))
H.set_calculator(GPAW(h=0.1, setups='ae', fixmom=True))
e1 = H.get_potential_energy()
c = a / 2.0
d = 0.74
s = d / 2 / 3**0.5
H2 = Atoms('H2',... | qsnake/gpaw | oldtest/ae-calculation.py | Python | gpl-3.0 | 584 | [
"ASE",
"GPAW"
] | f085f4d92fec6dc6dc57bbab29d8082a10e8b47b927fe34b88b86c09ee43812f |
from unittest import TestCase
import brainrnaseq as brs
import pandas as pd
class BrainRNASeqTest(TestCase):
def test_mapping_data(self):
items = {
'Homo sapiens': ['A1BG', 'A1B|ABG|GAB|HYST2477', '16S rRNA', '-'],
'Mus musculus': ['Pzp', 'A1m|A2m|AI893533|MAM', 'ND2', '-'],
... | white-lab/pyproteome | tests/brainrnaseq_test.py | Python | bsd-2-clause | 7,370 | [
"NEURON"
] | bc11507dd6b77da6c7a0663a45b421b57d590d0ce5b87535e8b3bab92c072cc8 |
"""
Tests for user authorization password-related functionality.
"""
import json
import logging
import re
from datetime import datetime, timedelta
from unittest.mock import Mock, patch
import pytest
import ddt
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core import mail
... | EDUlib/edx-platform | openedx/core/djangoapps/user_authn/views/tests/test_password.py | Python | agpl-3.0 | 12,929 | [
"VisIt"
] | 2a9e1e8f50e00251014b77ab0b7b5e09eba5b9aa9ef206bad8b3725a63fee2d7 |
import pkg_resources
import string
import random
import os
from biomaj.mongo_connector import MongoConnector
from biomaj_core.config import BiomajConfig
from biomaj_core.utils import Utils
import logging
class SchemaVersion(object):
"""
BioMAJ database schema version. This package can be used to make some s... | horkko/biomaj | biomaj/schema_version.py | Python | agpl-3.0 | 5,031 | [
"BLAST"
] | a7a54b3673633dfc290007269ed17e587d17a708e931640e6c6bd0128b7ed7cb |
# Copyright iris-grib contributors
#
# This file is part of iris-grib and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Unit tests for `iris_grib.message.Section`.
"""
# Import iris_grib.tests first so that some things can be initi... | SciTools/iris-grib | iris_grib/tests/unit/message/test_Section.py | Python | lgpl-3.0 | 2,906 | [
"Gaussian"
] | 14e4fd90b5cb143a0bc5c58a797449a2348dbbac87fcd04d800d50503a930874 |
from chemfiles import Trajectory, UnitCell, Atom, Topology, Frame, Selection
name = "nt12.opt"
a = 24.2
# Read the frame
frame = Trajectory(name+".xyz").read()
# Set the topology
topo = Trajectory("topology.pdb").read()
frame.set_topology(topo.topology())
# Get the positions
positions = frame.positions()
# Set the... | lscalfi/imogolite | 2-Isotherms/0-UnitCell/create.py | Python | mit | 6,723 | [
"Chemfiles"
] | 50972aa5ca094fcb726f1ccb60b1b517c07c18676414fddd2bc35f32d507e807 |
#!/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/prop/efg/test/test_dhf.py | Python | apache-2.0 | 1,224 | [
"PySCF"
] | e81725adcb89aa5c158200db0560fe81c128d87da20bc6ef16f7ac9b050c011a |
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Free University
# Berlin, 14195 Berlin, Germany.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of source... | arokem/PyEMMA | pyemma/coordinates/api.py | Python | bsd-2-clause | 59,936 | [
"Amber",
"CHARMM",
"Gromacs",
"LAMMPS",
"MDTraj",
"NAMD",
"NetCDF",
"TINKER"
] | 6e9bc450bd44b6e8624686b268fdf207f56c9e38fbd03b210495afd094cbf29b |
# coding: utf-8
#!/usr/bin/env python
"""
A convenience script engine to read Gaussian output in a directory tree.
"""
from __future__ import division, print_function
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.0"
__maintainer__ = "Shyue Ping Ong"
__email__ ... | rousseab/pymatgen | scripts/gaussian_analyzer.py | Python | mit | 3,689 | [
"Gaussian",
"pymatgen"
] | 889c8f801593b8f281be4076cfbbe1b9fe9e8c6342708294a7e4c412adb19539 |
'''
diacamma.condominium tests package
@author: Laurent GAY
@organization: sd-libre.fr
@contact: info@sd-libre.fr
@copyright: 2015 sd-libre.fr
@license: This file is part of Lucterios.
Lucterios is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published b... | Diacamma2/syndic | diacamma/condominium/tests_callfunds.py | Python | gpl-3.0 | 117,010 | [
"Dalton"
] | 61ab34525f10c9102259e3f7f48956b915ba18f03882502a0d47d2ae541381f5 |
from __future__ import division
import numpy as np
import matplotlib
matplotlib.use("Agg")
import matplotlib.pyplot as plt
import matplotlib.animation as animation
import matplotlib.patches as patches
import matplotlib.path as path
import subprocess
plt.style.use('classic')
# Parameters for animation
aL=4
cH=0.25
lam... | letsgoexploring/signalingAnimation | code/signalingAnimationSeparatingLowType.py | Python | mit | 4,284 | [
"Brian"
] | 47828f09b93a4b7627b5f6d6c558570a1c9babb124d0dbd2b54ea8d9fde66f63 |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import, division, print_function
import ast
import _ast
import errno
import itertools
import imp
import marshal
import os
import re
import struct
import sys
import types
import py
from _pytest.assertion import util
# pytest ca... | hoehnp/navit_test | lib/python2.7/site-packages/_pytest/assertion/rewrite.py | Python | gpl-2.0 | 36,252 | [
"VisIt"
] | 244194b301d6acae5259c25ca05493695b8e8cce328b77605f13c95d3ef10562 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all Worden's CN13ID Western Flyer cruise in October 2013
CN13ID: CANON 2013 Interdisciplinary
Mike McCann
MBARI 23 ... | google-code-export/stoqs | loaders/CANON/loadCN13ID_october2013.py | Python | gpl-3.0 | 11,369 | [
"NetCDF"
] | a34c76950f8dd3b14218f32914f71027eeb1ab87f3078c75a6780f95d73f9532 |
from math import *
from random import *
import pickle
import pygame
import inspect
__author__ = 'Max Chiang'
from ChiangObjectives import *
import time
import sys
path = sys.path[0]
if not path: path = sys.path[1]
def STAB(PokeType,PokeType2,AttType):
if PokeType==AttType or PokeType2==AttType:
... | chen-charles/PyPokemon | PokemonFinalProjectV1/Combinedv2.py | Python | gpl-3.0 | 114,361 | [
"BLAST"
] | 03a1b863918233b91a545d106e14677bc03b11b20196c5d465e3f3e0f49153f5 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Copyright (C) 2020 Stoq Tecnologia <http://www.stoq.com.br>
# All rights reserved
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation;... | stoq/stoq-server | stoqserver/__init__.py | Python | gpl-2.0 | 2,477 | [
"VisIt"
] | 69e78d7341ddc11a4ce6a875ee9806901cdcd0d7aadc129ff3ea402bfb3ca9b9 |
#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Antonio Gonzalez Pena"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Justin Kuczynski", "Rob Knight", "Antonio Gonzalez Pena",
"Catherine Lozupone", "Jose Antonio Navas Molina"]
__lice... | josenavas/qiime | scripts/principal_coordinates.py | Python | gpl-2.0 | 4,906 | [
"scikit-bio"
] | cd5660f3641b46a73511e1ffbf3ae3d70e269dc62713bfdf13d1e6d8890780be |
# -*- coding: utf-8 -*-
"""
Unit tests for the OBSolve class.
Thomas Ogden <t@ogden.eu>
"""
import os
import unittest
import numpy as np
from maxwellbloch import ob_solve, t_funcs
# Absolute path of tests/json directory, so that tests can be called from
# different directories.
JSON_DIR = os.path.abspath(os.path... | tommyogden/maxwellbloch | maxwellbloch/tests/test_ob_solve.py | Python | mit | 10,518 | [
"Gaussian"
] | e983fb6af514811c115d0d7bbe6b9f1f70590814edef154729c88ae6d51fc01e |
from __future__ import absolute_import
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, warning=object... | ryfeus/lambda-packs | HDF4_H5_NETCDF/source2.7/Cython/Compiler/ParseTreeTransforms.py | Python | mit | 135,741 | [
"VisIt"
] | c664f658d6084933699e18edc23af95013c7ebae4d9e9f55604d269c8ad1663a |
import mayavi.mlab as mlab
from pylayers.gis.layout import *
from pylayers.simul.link import *
L = Layout('Luebbers.ini')
#L.showG('st',aw=True,labels=True,nodelist=L.ldiffout)
#f,lax= plt.subplots(2,2)
#L.showG('s',aw=True,labels=True,fig=f,ax=lax[0][0])
#lax[0][0].set_title('Gs',fontsize=18)
#L.showG('st',aw=True,la... | buguen/pylayers | pylayers/gis/test/test_luebbers.py | Python | lgpl-3.0 | 830 | [
"Mayavi"
] | 564090264cd55c02c799b55ba5e4fb808ccaadefc3117422cbff1a51206cf408 |
"""
Unit tests for the JPER API class
"""
from octopus.modules.es.testindex import ESTestCase
from octopus.lib import http, paths
from octopus.core import app
from service.tests import fixtures
from service import api, models
from octopus.modules.store import store
import os
class MockResponse(object):
def __init... | JiscPER/jper | service/tests/unit/test_api.py | Python | apache-2.0 | 8,162 | [
"Octopus"
] | c75f88626cbf8a81b6e9e267053de0724fc7e24bfb7e695a8330a6e46bcfac79 |
#!/usr/bin/env python
import sys
import re
import os.path
import numpy as N
import sgmllib
from pprint import pprint
PTG_NUMS=[1, 2, 3, 6, 10, 16, 25, 47, 75, 81, 83, 89, 99, 111,
123, 143, 147, 149, 156, 162, 168, 174, 175, 177, 183, 189, 191, 195, 200, 207, 215, 221]
ptg_names = [
["C1" , "1"],
["Ci"... | abinit/abinit | src/43_ptgroups/ptg.py | Python | gpl-3.0 | 42,905 | [
"ABINIT"
] | 8e220095a13cef14298c20e334a3befd8a865c81bc4d429059b7786d5fcaf9ec |
#!/usr/bin/env python
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
# Main Madpack installation executable.
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
import sys
import getpass
import re
import os
import glob
import traceback
import subprocess
import datetime
import tempfile
import shutil... | rashmi815/incubator-madlib | src/madpack/madpack.py | Python | apache-2.0 | 62,969 | [
"ORCA"
] | faecb8f299ae07dba36294579e65510ccf79c407c76d2e5405e43fa661e1a026 |
# -*- coding: utf-8 -*-
from __future__ import print_function
"""test_streamer.py:
Test script for Streamer class.
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2016, Dilawar Singh"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"... | dilawar/moose-core | tests/core/test_streamer.py | Python | gpl-3.0 | 3,284 | [
"MOOSE"
] | 90b24bd18b1b96230363505cfc1cb1c2e7607f8b453d909d9b9cca21f030ec20 |
from __future__ import annotations
from dials.array_family import flex
from dials.array_family.flex import Binner
from dials.util.report import Array, Report, Table
def flex_ios(val, var):
"""
Compute I/sigma or return zero for each element.
"""
assert len(val) == len(var)
result = flex.double(le... | dials/dials | algorithms/integration/report.py | Python | bsd-3-clause | 21,120 | [
"CRYSTAL"
] | d096661c9f1d0cbc3d9f94bed489fa2f745666c52ad7df5b639bb631a1d29385 |
"""
============================
Neural Coding Reward Example
============================
A demonstration to use Spykes' functionality to reproduce Ramkumar et al's
"Premotor and Motor Cortices Encode Reward."
"""
# Authors: Mayank Agrawal <mayankagrawal96@gmail.com>
#
# License: MIT
###############################... | codekansas/spykes | examples/plot_neural_coding_reward_example.py | Python | mit | 8,919 | [
"NEURON"
] | cc17f471338a6a30c7f98c557fba875b60a6141ded60cbd6ded946397abec675 |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/accounts/admin.py | Python | apache-2.0 | 8,011 | [
"Galaxy"
] | b8d4cc0aa5ffd3eb7e898ef18b98c3284e4775a1195be8508715554966e67d8c |
"""utils.py
Some general utilities used in various testing routines.
(C) 2016 The Baccus Lab
"""
import os
import numpy as np
from pyret.filtertools import _gaussian_function
from pyret import spiketools
def get_default_filter_size():
"""Return the default x, y, and temporal size of a spatiotemporal filter."""... | baccuslab/pyret | tests/utils.py | Python | mit | 3,002 | [
"Gaussian"
] | 7d740ec1c7e2d167cd3ab4b80818fac3e31571dddcab84fbc8a8c0425f2e7dcc |
from rdkit.Chem import MolSurf
from rdkit.Chem.EState import EState_VSA as RDKit_EState_VSA
from ._base import Descriptor
__all__ = ("LabuteASA", "PEOE_VSA", "SMR_VSA", "SlogP_VSA", "EState_VSA", "VSA_EState")
class LabuteASA(Descriptor):
r"""Labute's Approximate Surface Area descriptor(rdkit wrapper)."""
... | mordred-descriptor/mordred | mordred/MoeType.py | Python | bsd-3-clause | 2,718 | [
"MOE",
"RDKit"
] | 8ead0ae1c3814f0ba84d1bbdb3adb1194a429e5876fbf183cbf540ee9668c262 |
# Copyright (c) 2021, Google Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and t... | google/deepconsensus | deepconsensus/preprocess/utils.py | Python | bsd-3-clause | 33,756 | [
"pysam"
] | 3e17fa5dbd03bf5d0ba08cea84343ea0b2b37bcd285768a6b2060eea27c19281 |
"""
DIRAC Times module
Support for basic Date and Time operations
based on system datetime module.
It provides common interface to UTC timestamps,
converter to string types and back.
The following datetime classes are used in the returned objects:
- dateTime = datetime.datetime
- date = datetime.date
- t... | yujikato/DIRAC | src/DIRAC/Core/Utilities/Time.py | Python | gpl-3.0 | 9,140 | [
"DIRAC"
] | fc49e643db17d58a2d708b9f5e6cca913b5d760208f1d0013c221790f5c2f69b |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu Jun 1 15:32:10 2017
@author: mschull
"""
import numpy as np
import math
from astropy.convolution import convolve
from astropy.convolution import Gaussian2DKernel, Box2DKernel
# script imports
# imports
def to_jd(datetime):
"""
Converts a ... | bucricket/projectMAS | pydisalexi/TSEB_utils_usda.py | Python | bsd-3-clause | 21,861 | [
"Gaussian"
] | e78d7ba57685d7baf7838997853c0a2afa43901a8c04f72055e8dd737b9ee18d |
# init.py ---
#
# Filename: init.py
# Description:
# Author:
# Maintainer:
# Created: Wed May 23 21:24:11 2012 (+0530)
# Version:
# Last-Updated: Sat Aug 6 14:35:20 2016 (-0400)
# By: subha
# Update #: 75
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Initialize model prototypes
... | BhallaLab/moose-examples | traub_2005/py/channelinit.py | Python | gpl-2.0 | 1,279 | [
"MOOSE"
] | ed0fee15d521b12fb1823bea11ee5712473a054e29dbb96e26ab0f1ad034b46b |
from django.conf.urls import url
from django.contrib.auth.decorators import login_required
from django.views.decorators.csrf import ensure_csrf_cookie
from django.views.generic import TemplateView
import django.contrib.auth.views as djauth
# For adding explicit grouping resource endpoints in API documentation.
from r... | catsop/CATMAID | django/applications/catmaid/urls.py | Python | gpl-3.0 | 28,809 | [
"NEURON"
] | 24e2c4ae4029bbcdf53f186df73907f9ddfd3d4b2a1668b2cd2751230d3728c6 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines the abstract base classes for battery-related classes.
Regardless of the kind of electrode, conversion or insertion, there are many
common definitions and properties, e.g., average volt... | richardtran415/pymatgen | pymatgen/apps/battery/battery_abc.py | Python | mit | 16,560 | [
"pymatgen"
] | d4e4f2d49ce618c73680c43de3fcb55ece20ee0893e4108617748637f9d3c5a7 |
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import matplotlib.cm as cm
import os
import matplotlib.gridspec as gridspec
... | gviejo/ThalamusPhysio | python/main_search_examples_fig3.py | Python | gpl-3.0 | 7,499 | [
"Gaussian"
] | ed85772963709dde390593345c099a1458c69e541f27133f58e0b805b583a6c4 |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy import array
from numpy.testing import (assert_array_almost_equal, assert_array_equal,
assert_, run_module_suite)
from scipy import signal
window_funcs = [
('boxcar', ()),
('triang', ())... | ogrisel/scipy | scipy/signal/tests/test_windows.py | Python | bsd-3-clause | 4,508 | [
"Gaussian"
] | fb776070b3defdec90386247cd3db0247eba0a22a31e60ac044b33ac1d5733a2 |
"""
=======================================
Robust vs Empirical covariance estimate
=======================================
The usual covariance maximum likelihood estimate is very sensitive to the
presence of outliers in the data set. In such a case, it would be better to
use a robust estimator of covariance to guara... | loli/sklearn-ensembletrees | examples/covariance/plot_robust_vs_empirical_covariance.py | Python | bsd-3-clause | 6,309 | [
"Gaussian"
] | 58df2d7a6962b2900c72e07894f52f437bb366cf8354fa697dbe3afd39094d9f |
# Copyright (c) Charl P. Botha, TU Delft.
# All rights reserved.
# See COPYRIGHT for details.
class BMPReader:
kits = ['vtk_kit']
cats = ['Readers']
help = """Reads a series of BMP files.
Set the file pattern by making use of the file browsing dialog. Replace
the increasing index by a %d format s... | nagyistoce/devide | modules/readers/module_index.py | Python | bsd-3-clause | 4,768 | [
"VTK"
] | 55324d2c811a126ef52bb62d4105fc0733d450f512f1b29aefa5254c2d74f3a7 |
#!/usr/bin/env python
import sys, os, re, shutil, commands, scipy.stats
from pyrna.parsers import to_fasta
from pyrna.features import DNA
from pyrna.computations import Tool, Blast
from pyrna import utils
from pymongo import MongoClient
from pandas import DataFrame
from Bio import AlignIO
from bson import ObjectId
""... | JossinetLab/CAAGLE | scripts/search_orthologs.py | Python | mit | 22,430 | [
"BLAST"
] | 3e0b1a0a5232463d6a5974ee9d412a9ed5da4440030aa597073166fd421c4dbd |
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