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"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import functools
import re
import warnings
i... | ahaldane/numpy | numpy/lib/polynomial.py | Python | bsd-3-clause | 40,727 | [
"Gaussian"
] | 43ace17c21f8ddb836a0a76d7da21016b6f128b2abb25084347761febe70559c |
import pytest
import numpy as np
from numpy.testing import assert_allclose
from astroML.fourier import (FT_continuous,
IFT_continuous,
PSD_continuous,
sinegauss,
sinegauss_FT)
@pytest.mark.parametrize('... | astroML/astroML | astroML/tests/test_fourier.py | Python | bsd-2-clause | 3,325 | [
"Gaussian"
] | 801907c723ccec1ab25fb74ad9d132681a03846eda950f2d4797046c23303d92 |
import pytest
import time
from xpath import dsl as x
import capybara
from capybara.exceptions import Ambiguous, ElementNotFound, FrozenInTime
from capybara.selector import add_selector, remove_selector
from capybara.tests.compat import patch
class FindTestCase:
@pytest.fixture(autouse=True)
def setup_session... | elliterate/capybara.py | capybara/tests/session/test_find.py | Python | mit | 12,779 | [
"VisIt"
] | 2ccd856ee32d65025f39febc4869cae3d61659e2f7e4eef764866d7f69ae689f |
"""
Brian T. Bailey
ITM 513 - MP3
2Dooz GUI Class Module
"""
import tkFont
from Tkinter import *
from tkMessageBox import *
import datautils
from Task import PRIORITY_CODE
from Task import PRIORITY_COLOR
from Task import PRIORITY_VALUE
from Task import Task
class AppGui(object):
"""2Dooz GUI Components Class.
... | briantbailey/ITM-513 | mp3/src/domain/gui.py | Python | mit | 20,775 | [
"Brian"
] | 0f1dcc66e373680695ac678e5541797d0187c586219f44a61aa9780815f629ed |
#!/usr/bin/env python
"""
"""
import vtk
def main():
colors = vtk.vtkNamedColors()
fileName = get_program_parameters()
colors.SetColor("SkinColor", [255, 125, 64, 255])
colors.SetColor("BkgColor", [51, 77, 102, 255])
# Create the renderer, the render window, and the interactor. The renderer
... | lorensen/VTKExamples | src/Python/Medical/MedicalDemo1.py | Python | apache-2.0 | 3,793 | [
"VTK"
] | b024edf360f3b07bf756713d31c42766f0c20179fde83bab3d895eb328db821c |
"""Support for package tracking sensors from 17track.net."""
from datetime import timedelta
import logging
from py17track import Client as SeventeenTrackClient
from py17track.errors import SeventeenTrackError
import voluptuous as vol
from homeassistant.components.sensor import PLATFORM_SCHEMA, SensorEntity
from homea... | adrienbrault/home-assistant | homeassistant/components/seventeentrack/sensor.py | Python | apache-2.0 | 11,446 | [
"VisIt"
] | 10fbba29d0eeb5488526fc180c79ca9f419c158ccd68816c54dd4fbe816855e6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Copyright (C) 2012 Computational Neuroscience Group, NMBU.
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 you... | LFPy/LFPy | LFPy/test/test_eegmegcalc.py | Python | gpl-3.0 | 33,528 | [
"NEURON"
] | f7e37b434a2f51a6bf3bdce2f49335251ad90c1738621c6f2b0be79ed1b125e0 |
#
# commands.py - the GraalVM specific commands
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2012, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free ... | lewurm/graal | mx/mx_graal.py | Python | gpl-2.0 | 97,101 | [
"VisIt"
] | 994080c98bcfa39352fa2c695dbe41609e9f3d26e9d3693a4712333b6b5c8476 |
# 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.
# Copyright Iddo Friedberg idoerg@cc.huji.ac.il
"""A class to handle frequency tables
Methods to read a letter frequency or a letter count file:
Exampl... | zjuchenyuan/BioWeb | Lib/Bio/SubsMat/FreqTable.py | Python | mit | 2,524 | [
"Biopython"
] | 5db5143d6dc6eb1f733190d5c74727e763b2dd5f748e008ff78a8aebbbb5e402 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Appcelerator Titanium Mobile
# Copyright (c) 2011-2012 by Appcelerator, Inc. All Rights Reserved.
# Licensed under the terms of the Apache Public License
# Please see the LICENSE included with this distribution for details.
#
# Android Application Script
#
import os, s... | xissy/titanium-mobile-sdk | android/android.py | Python | apache-2.0 | 13,996 | [
"VisIt"
] | 5ac56d9343a401620931cc47dd5fc51fb83df5361864bdfc439a2980ebfb4a12 |
"""
This is a comment
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
# $Source: /tmp/libdirac/tmp.stZoy15380/dirac/DIRAC3/DIRAC/Core/Workflow/test/JobSamples.py,v $
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Wor... | yujikato/DIRAC | src/DIRAC/Core/Workflow/test/JobSamples.py | Python | gpl-3.0 | 18,981 | [
"DIRAC"
] | 4b3df0aae88f6e250b2cd6c08ecf40441bf53c5c8429781541827bfe2e856c97 |
#!/usr/bin/env python
'''Convert your alignment files in BAM format into coverage files in bigWig format
Usage:
bam_to_bigwig.py BAM_FILE [BAM_FILE ...]
[-o, --bigwig_filename=<output file name>
-t, --tempfile
-k, --keep-tempfile
-s, --ignore-secondary
-q, --ignore-qc-fail
-d, --ignore... | hotdogee/bam_to_bigwig | bam_to_bigwig.py | Python | gpl-3.0 | 14,100 | [
"pysam"
] | 7083ef16c61d28b50a581d729104d4d9933582558021eed164ef442c00bc885b |
import os
import glob
import time
import numpy as np
from skimage import io
from random import choice
import matplotlib.pyplot as plt
from skimage import color
from skimage.util import img_as_float
from skimage.segmentation import find_boundaries
from skimage.morphology import skeletonize
from skimage.filters impo... | imaluengo/SMURFS-Superpixels | pysmurfs/misc.py | Python | mit | 6,718 | [
"Gaussian"
] | 8402193c3bd5c09152816f6e8cfa056dfcc093a8568ca4e887d21bbb04ba0381 |
#!/usr/bin/env python3
import evdev
import ev3dev.ev3 as ev3
from ev3dev.ev3 import Leds
from ev3dev.ev3 import MediumMotor
import threading
from time import sleep
from output.motor_control import MotorControl
from output.led_control import LedControl
SPEED_MAX = 100
STICK_MAX = 255
STICK_MIN = 0
POLARIZATION = -1
FO... | alriedel/ev3-control | ps3_control.py | Python | mit | 5,369 | [
"Amber"
] | bc1a5a174ee551dd4dd6b667345e232a80c574e6d24a60ed57d60aef24eae11f |
import sys
import unittest
# Run from the root dir
sys.path.insert(0, '.')
from pycparser import c_parser, c_generator, c_ast
_c_parser = c_parser.CParser(
lex_optimize=False,
yacc_debug=True,
yacc_optimize=False,
yacctab='yacctab')
def compare_asts(a... | sideeffects/pycparser | tests/test_c_generator.py | Python | bsd-3-clause | 6,440 | [
"VisIt"
] | e99e891ab34bc462d235a008459fdbb7e80d9f0528c4017acb734138fde1ec07 |
import os
import sys
import glob
try:
import numpy
except ImportError:
print "You need to have numpy installed on your system to run setup.py. Sorry!"
sys.exit()
try:
from Cython.Distutils import build_ext
except ImportError:
print "You need to have Cython installed on your system to run setup.py.... | caglar10ur/anvio | setup.py | Python | gpl-3.0 | 2,549 | [
"pysam"
] | 7fb071c791afc52cadbae162fc3938b20c5a266598612716386436d2851805a7 |
# Copyright (c) 2012 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.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | markYoungH/chromium.src | PRESUBMIT.py | Python | bsd-3-clause | 61,378 | [
"VisIt"
] | 650887ccf44d3cc69dafd98642adfd3e5f5602b864397d797707c03780f146e7 |
#!/usr/bin/env python
import sys
from pvconnect import pvserver_process
if len(sys.argv) < 5:
print 'Incorrect usage'
print ('pververlauncher.py server_port user@host' +
' remote_paraview_location mpi_num_tasks')
sys.exit(0)
data_host = sys.argv[2]
data_dir = '.'
job_ntasks = sys.argv[4]
parav... | zenotech/ParaViewConnect | scripts/pvserver_vslauncher.py | Python | bsd-3-clause | 626 | [
"ParaView"
] | 2885718d89dccbd5fdf6cf6563e90b3b2a0253a0d3cb11969812bf51ca90e730 |
#!/usr/bin/env python
#filename: tsne.py
import os
import sys
import argparse
import mdtraj as md
import numpy as np
from sklearn.metrics import euclidean_distances
from sklearn.manifold import TSNE
from lib.write_plot import write_plots, write_pcs, write_fig
from lib.traj_info import trajectory_info, get_internal_coor... | RUBi-ZA/MODE-TASK | tsne.py | Python | gpl-3.0 | 7,778 | [
"MDTraj"
] | db71f5ba4db0b3c0ffbc6f82d0f1726ab1ed45f6b34e3adb163f600a6c45995e |
# -*- coding: utf-8 -*-
"""
This will DESTROY ALL YOUR DATA.....
looks for netCDF files - and then trys to 'clean' them...
INPLACE...
WITHOUT BACKUPS...
Created on Sat Jul 26 19:47:19 2014
@author: ran110
"""
'change me to whatever is the error'
magicErrorNumber = -1.401298464324817e-45
import netCDF4
import glob
... | terryrankine/scripting | netcdf-ga/magic-cleanup.py | Python | apache-2.0 | 1,895 | [
"NetCDF"
] | ed173b47396925d02d090757bd0ad9ecd9dae80209c8285ce769d18f422e812f |
import cStringIO
try:
from DIRAC.Core.Utilities.Graphs import barGraph, lineGraph, pieGraph, cumulativeGraph, qualityGraph, textGraph
except Exception, plotException:
raise Exception( "Missing plotting lib: %s" % str( plotException ) )
from DIRAC import S_OK, S_ERROR
def checkMetadata( metadata ):
if 'span' in ... | avedaee/DIRAC | AccountingSystem/private/Plots.py | Python | gpl-3.0 | 2,980 | [
"DIRAC"
] | 15a5e6b0f9e13be6907a771b06a1f1acb61096d1750f10b92f946e286186ac2a |
"""Conformer generation.
Author: Seth Axen
E-mail: seth.axen@gmail.com
"""
import logging
import numpy as np
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import PropertyMol
from .util import add_conformer_energies_to_mol
# Heavily modified by Seth Axen from code under the following license
... | keiserlab/e3fp | e3fp/conformer/generator.py | Python | lgpl-3.0 | 13,890 | [
"RDKit"
] | 98a90931606c83a76eff6e7bc9e2c0898b2bbef2d780e67ea0d6d3d44e4c3f94 |
#
# Copyright (C) University College London, 2007-2012, all rights reserved.
#
# This file is part of HemeLB and is provided to you under the terms of
# the GNU LGPL. Please see LICENSE in the top level directory for full
# details.
#
"""Define a filter to add the data in a HemeLB extracted property file to the geo... | jenshnielsen/hemelb | Tools/hemeTools/converters/ExtractedPropertyUnstructuredGridReader.py | Python | lgpl-3.0 | 10,326 | [
"VTK"
] | 339a867ec49acdddf4426183db6490213d9dd305c951eba6a94971877fa6f21e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
""" Test context-sensitive Parser registry.
"""
from os import pardir
from os.path import join
from unittest import main, TestCase
#logging.basicConfig(level=logging.DEBUG)
from module_test import *
from sneakylang import *
from sneakylang.document import DocumentNode
... | andrejtokarcik/python-sneakylang | sneakylang/test/test_treebuilder.py | Python | bsd-3-clause | 7,216 | [
"VisIt"
] | f35c22846f8ecb97f6ccb59aa2525ad4f7f1220e5108975ea09cba4c97a03eac |
# -*- coding: utf-8 -*-
u"""Hellweg execution template.
:copyright: Copyright (c) 2017 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkio
from pykern.pkcollections import PKDict
fro... | mrakitin/sirepo | sirepo/template/hellweg.py | Python | apache-2.0 | 14,507 | [
"Gaussian"
] | 90f287969bc01cbdbde5fb908655f5f598c4befd56f69b54755c18018ffedb3d |
# -*- coding: utf-8 -*-
import configuracion
try:
from urlparse import parse_qsl
except:
from cgi import parse_qsl
import webbrowser
import oauth2 as oauth
REQUEST_TOKEN_URL = 'https://api.twitter.com/oauth/request_token'
ACCESS_TOKEN_URL = 'https://api.twitter.com/oauth/access_token'
AUTHORIZATION_URL = 'h... | pilotopirx/pirxconnect | obtenertoken.py | Python | unlicense | 2,649 | [
"VisIt"
] | 8ae161183a57379f3de7bb5f5ca7d5fcc78deb6332f364a4765cda29b8e03d65 |
'''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/model.py | Python | gpl-3.0 | 59,606 | [
"NetCDF"
] | 367dde031d6dce08470385640244279cfeeebac9d76ad431c9ffac3eeca14403 |
../../../../share/pyshared/orca/event_manager.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/event_manager.py | Python | gpl-3.0 | 48 | [
"ORCA"
] | 5fed3595b7a46ffe990c691fb339857f77b37351e33905bd78c2c6d60da732f9 |
#!/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... | orhankislal/madlib | src/madpack/madpack.py | Python | apache-2.0 | 63,925 | [
"ORCA"
] | d320821f94d11a170ab8ec0802286a47a9eb1eaaa6e67d6b0af15c6d030438da |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
import numpy as np
import warni... | sgenoud/scikit-learn | sklearn/mixture/gmm.py | Python | bsd-3-clause | 28,544 | [
"Gaussian"
] | 6625a272e6972967125ddb64c0b3e98e4c4f54fe05af39ca4982cd3a93de6394 |
#!/usr/bin/env python
from __future__ import print_function
from mdtools.rms_tools import fit, centroid, kabsch, rmsd, superpose
from tqdm import tqdm
import mdtraj as md
import numpy as np
import scipy.linalg
import sys
import os
#
# script for performing Principal component analysis (PCA) for MD trajectory
# perfor... | TaizoAyase/mdtools | pca/pca.py | Python | gpl-2.0 | 5,507 | [
"MDTraj"
] | 0deaf352908a60b0ba640b52592907a6d3a215c1e0b59a455f627d93bf4dbb3a |
import tempfile
import numpy as np
from pele.systems import AtomicCluster
from pele.potentials import LJ
from pele.utils.xyz import write_xyz
__all__ = ["LJCluster"]
class LJCluster(AtomicCluster):
"""
define the System class for a Lennard-Jones cluster
Parameters
----------
natoms : int
... | js850/pele | pele/systems/ljcluster.py | Python | gpl-3.0 | 4,492 | [
"PyMOL"
] | 962f0a421fe2a2a3b5f2729ceef1bd44b9b162343f7704438e47c362641fdb25 |
from collections import Counter, defaultdict
WORD_LIST = [ # hidden variable in this kata on CodeWars
'a', 'ability', 'able', 'about', 'above', 'absence', 'absolutely',
'academic', 'accept', 'access', 'accident', 'accompany', 'according',
'account', 'achieve', 'achievement', 'acid', 'acquire', 'across', '... | the-zebulan/CodeWars | katas/beta/special_scores_for_words.py | Python | mit | 19,615 | [
"VisIt"
] | 183ab458b83cdf60cdb4630b2a6e4183fa3dc2ae6354d05fb01d5ab89785bf5c |
from rdflib.namespace import Namespace
import csv
from owmeta_core.datasource import Informational
from owmeta_core.data_trans.csv_ds import CSVDataSource, CSVDataTranslator
import re
import traceback
from .. import CONTEXT
from ..utils import normalize_cell_name
from ..channel import Channel, ExpressionPattern
from ... | openworm/PyOpenWorm | owmeta/data_trans/wormbase.py | Python | mit | 8,518 | [
"NEURON"
] | ef21cdb6120098a40bee39b7a3b1686eca9149ed7a2c7ab475416f3b6032fdf5 |
""" Module to test exec_bowtie member methods.
This module contains unit tests for exec_bowtie.py.
"""
import os
import unittest
import shutil
from src import exec_bowtie
__author__ = "YiDing Fang"
__maintainer__ = "YiDing Fang"
__email__ = "yif017@eng.ucsd.edu"
__status__ = "prototype"
# input file contents. F... | ucsd-ccbb/jupyter-genomics | src/microbiome/test/test_exec_bowtie.py | Python | mit | 19,830 | [
"Bowtie"
] | d04236e9e08702503ac2abd2cf13f2ca495128a6eed8ce5a29f2063b1ac12814 |
FEEDAPP_ICON = 'icon'
FEEDAPP_IMAGE = 'image'
FEEDAPP_DESC = 'description'
FEEDAPP_QUOTE = 'quote'
FEEDAPP_PREVIEW = 'preview'
FEEDAPP_TYPES = (
FEEDAPP_ICON,
FEEDAPP_IMAGE,
FEEDAPP_DESC,
FEEDAPP_QUOTE,
FEEDAPP_PREVIEW,
)
FEEDAPP_TYPE_CHOICES = [(c, c) for c in FEEDAPP_TYPES]
# Editorial Brand type... | andymckay/zamboni | mkt/feed/constants.py | Python | bsd-3-clause | 2,643 | [
"Amber"
] | 488a97d5f37cbab0414a73a1a7fb4fcab4c2e6dfeee4e151bd3a7bfe3727c725 |
#!/bin/env python
""" create and put 'ReplicateAndRegister' request """
__RCSID__ = "$Id: $"
import os
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__,
'Usage:',
' %s [option|cfgfile] requestName LFNs targetSE1 [ta... | andresailer/DIRAC | DataManagementSystem/scripts/dirac-dms-replicate-and-register-request.py | Python | gpl-3.0 | 4,566 | [
"DIRAC"
] | ab264a5e67862543a11a05c2ccb22b4a895247bff8b3bb108348675928f9f76a |
import dropbox
import sys, os, json, re
APP_KEY = ''
APP_SECRET = ''
ACCESS_TYPE = 'app_folder'
STATE_FILE = 'copy_between_accounts.json'
def main():
if APP_KEY == '' or APP_SECRET == '':
sys.stderr.write("ERROR: Set your APP_KEY and APP_SECRET at the top of %r.\n" % __file__)
sys.exit(1)
pr... | calvdee/dropbox_python_sdk | example/copy_between_accounts.py | Python | mit | 4,689 | [
"VisIt"
] | 26a12aed776f705fd2276bf0f6d7a18ba7e1ed8a887234b19fa5ff1128e4b0ef |
# -*- coding: utf-8 -*-
import moose
import numpy as np
import matplotlib.pyplot as plt
import chan_proto
import param_chan
from params import *
def linoid(x, param):
# plt.figure()
# plt.plot(x,(param[2]+np.exp((V+param[3])/param[4])))
den = (param[2] + np.exp((V + param[3]) / param[4]))
nom = (param... | dharmasam9/moose-core | tests/python/test_difshells.py | Python | gpl-3.0 | 6,182 | [
"MOOSE"
] | 182362af76f8048d2d9c5a6fe8d3a074c0c23932a803feb73b72b7016a849353 |
# 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.
#
"""Represent Neural Networks.
This module contains classes to represent Generic Neural Networks that
can be trained.
Many of the ideas in this and ... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/NeuralNetwork/BackPropagation/Network.py | Python | gpl-2.0 | 4,238 | [
"Biopython"
] | 76e5bedaf5a5c92bcde63e6e8622af6a607dcf9c089cdef1d61566be6f1b4307 |
# Authors: Jan Cholasta <jcholast@redhat.com>
#
# Copyright (C) 2014 Red Hat
# see file 'COPYING' for use and warranty information
#
# 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 versi... | msimacek/freeipa | ipaserver/install/ipa_cacert_manage.py | Python | gpl-3.0 | 13,559 | [
"VisIt"
] | 383cb573f04a009c600773020b4651fbaaae849498553e4a814877e34ebf413d |
# -*- coding: utf-8 -*-
# vim: tabstop=4 shiftwidth=4 softtabstop=4
#
# Copyright (C) 2021 GEM Foundation
#
# OpenQuake is free software: you can redistribute it and/or modify it
# under the terms of the GNU Affero General Public License as published
# by the Free Software Foundation, either version 3 of the License, o... | gem/oq-engine | openquake/calculators/event_based_damage.py | Python | agpl-3.0 | 10,374 | [
"ADF"
] | 49adfbfe5ff08c9829bc4cd0ae73684d05c4f015cf52dda417c8d06d8ae4e0ed |
#-------------------------------------------------------------------------------
# . File : GaussianOutputFile.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#------------------------------------------... | mfx9/MolarisTools | MolarisTools/Parser/GaussianOutputFile.py | Python | gpl-3.0 | 22,594 | [
"Gaussian"
] | 7c182e5fd3c3be577fcfe6c372df231d17e26bc85249a2555499bc87bdb2c049 |
# Copyright (C) 2014
# Jakub Krajniak
# Copyright (C) 2012,2013,2015
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistr... | capoe/espressopp.soap | src/FixedQuadrupleListAdress.py | Python | gpl-3.0 | 3,209 | [
"ESPResSo"
] | 31628f20521953a81f4214789e0d515186f04a98ae715899195f554ce8c2cadc |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | ninotoshi/tensorflow | tensorflow/contrib/distributions/python/ops/gaussian_conjugate_posteriors.py | Python | apache-2.0 | 5,563 | [
"Gaussian"
] | 8f3141332cfdaf4d546c8e142f4a0b0715b2866b44ce9251d0e422f85f9681fb |
"""This conftest is here to allow for checking garbage collection and
memory leaks for all plotting tests
"""
import gc
import pytest
import pyvista
# these are set here because we only need them for plotting tests
pyvista.global_theme.load_theme(pyvista.themes._TestingTheme())
pyvista.OFF_SCREEN = True
def pytest... | akaszynski/vtkInterface | tests/plotting/conftest.py | Python | mit | 1,121 | [
"VTK"
] | cde27b9fee07992b81e0602118b9cb458971d43ea0b8237d884a0de076aa1efb |
'''
Created on Jun 8, 2012
@author: mkiyer
'''
import sys
import logging
import argparse
import os
# local imports
import chimerascan.pysam as pysam
from chimerascan.lib import config
from chimerascan.lib.base import imin2
from chimerascan.lib.sam import parse_pe_reads, copy_read
from chimerascan.lib.feature import T... | tectronics/chimerascan | chimerascan/deprecated/filter_transcriptome_multihits_v1.py | Python | gpl-3.0 | 3,886 | [
"pysam"
] | 1951cf7b7749c5ab6ea041f84b35fc32157177351e93227e04817fc33af622af |
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
ImageConstantPad()
| jeromevelut/Peavip | Testing/ImageConstantPad.py | Python | gpl-3.0 | 129 | [
"ParaView"
] | f84b108eb41b9def2b737354f8b6aaa5ec6e23c8d1cf8208647d489076d56904 |
#!/usr/bin/env python
# framework to start a simulated vehicle and connect it to MAVProxy
# Peter Barker, April 2016
# based on sim_vehicle.sh by Andrew Tridgell, October 2011
import optparse
import sys
import atexit
import os
import os.path
import subprocess
import tempfile
import getpass
import time
import signal
... | chapman/ardupilot | Tools/autotest/sim_vehicle.py | Python | gpl-3.0 | 28,183 | [
"Firefly"
] | d42cecff295ede7127f77609afa492687775ba6d609977676be70dc79a09c849 |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of line navigation output of Firefox on GNOME bugzilla's form
for entering bugs.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wait for the focus to be on a ... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/line_nav_enter_bug.py | Python | lgpl-2.1 | 19,583 | [
"ORCA"
] | 40a3782c58a29ed504a11fd8a3499d20cf8bdabca87aacfbae6c40ecbeed834b |
import numpy as np
from matplotlib import pyplot as plt
from sklearn.gaussian_process import GaussianProcessRegressor
from sklearn.gaussian_process.kernels import RBF, ConstantKernel
from scipy import optimize
from copy import deepcopy
import time
import matplotlib.cm as cm
np.random.seed(1)
class GP:
def __init... | iagapov/ocelot | optimizer/GP/gaussian_process.py | Python | gpl-3.0 | 10,119 | [
"Gaussian"
] | 7cb2e589522e17a2986b84dd3bb23d7a64c925f5d86d8d242410eac96c1b9241 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
import numpy as np
class Neuron():
"""
docstring for Neuron.
"""
def __init__(self, inputs):
self.inputs = np.array(inputs) # entradas
self.weights = 0 # pe... | aulusdiniz/neuron | neuropy/neuron.py | Python | mit | 1,727 | [
"NEURON"
] | e32f8cc5b02f9f2d910f85b9050b4adac33da06ca9e7ee8e3fb6671cc0f6a090 |
#!/usr/bin/env python
"""Provide plots summarizing recalibration of quality scores.
Usage:
analyze_quality_recal.py <recal_bam> <input_fastq1> <input_fastq2>
--chunk_size=25 --input_format=fastq-illumina
--dbdir=/tmp/chapmanb
<recal_bam> is a BAM alignment file containing recalibrarted quality scores
... | a113n/bcbio-nextgen | scripts/utils/analyze_quality_recal.py | Python | mit | 13,176 | [
"Biopython",
"pysam"
] | 14e0595acade778f42ce72400e9fc727289fc5baaec8a09d3e84bb8999159ec6 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
class HoomdBlue(CMakePackage):
"""HOOMD-blue is a general-purpose particle simulation ... | iulian787/spack | var/spack/repos/builtin/packages/hoomd-blue/package.py | Python | lgpl-2.1 | 3,923 | [
"HOOMD-blue"
] | 3b00c5b10045a4a4f6be5c9b632a59bd8c614b7090699d18fb3c37eb40b918c6 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser Gen... | ghutchis/cclib | src/cclib/parser/adfparser.py | Python | lgpl-2.1 | 49,080 | [
"ADF",
"cclib"
] | 4a189d8e72d13d05f662cd0a57d09b78a932f9f8e136885a70db1a3278cc3613 |
import pylab as pyl
from astLib import astStats
import cPickle as pickle
from scipy import stats
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.ston_I >10., galaxies)
f = pyl.figure(1, figsize=(6,4))
f1s1 = f.add_subplot(111)
icd = pyl.asarray([galaxy.ICD_IH*100 for gala... | boada/ICD | sandbox/lowerSN/plot_icd_color.py | Python | mit | 925 | [
"Galaxy"
] | f6acf9d345cafd787a8a3738a820d148312ed4a1a9683a05236c650ea90df7a8 |
from six.moves import zip, range
import errno
import MDAnalysis as mda
from MDAnalysis.coordinates.base import Timestep
import numpy as np
import os
import shutil
import warnings
from nose.plugins.attrib import attr
from numpy.testing import (assert_equal, assert_array_almost_equal, dec,
as... | alejob/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_xdr.py | Python | gpl-2.0 | 30,746 | [
"Amber",
"Gromacs",
"MDAnalysis",
"NetCDF"
] | 020f0f0324524f34198eaa60d4134b458a4d02fbc437f6ae2a5f584eca8ab0ea |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
@author: R. Patrick Xian, L. Rettig
"""
# =========================
# Sections:
# 1. Utility functions
# 2. File I/O and parsing
# 3. Data transformation
# =========================
from __future__ import print_function, division
from .base import Fi... | RealPolitiX/mpes | mpes/fprocessing.py | Python | mit | 123,114 | [
"Gaussian"
] | c7d93e65190ebea42645007fabaaf2e73c5776ca789fa65f3c94858f084b8414 |
# Orca
#
# Copyright 2006-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gnome-search-tool/__init__.py | Python | gpl-3.0 | 853 | [
"ORCA"
] | 393cf742a00327d2ea1b2656fc558a27577ed551c34ec724a83ddea2ff851bfe |
import os
import glob
from setuptools import setup, find_packages
SETUP_PTH = os.path.dirname(os.path.abspath(__file__))
def readme():
with open('README.rst') as f:
return f.read()
setup(
name="pydii",
packages=find_packages(),
version="1.0.0",
install_requires=["pymatgen... | mbkumar/pydii | setup.py | Python | mit | 2,363 | [
"pymatgen"
] | 4649ed6475ce872c811aa91999b674768e9162adfb233161fc06bea35e42cebd |
#
# WengoSCons, a high-level library for SCons
#
# Copyright (C) 2004-2005 Wengo
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any lat... | erikge/iOS_trick | shell/build_webrtc_audio/Env/environment.py | Python | gpl-3.0 | 46,840 | [
"VisIt"
] | 683884f924a80ab1b5093dc077371fba8f21dff26f1257e365e79a038cc72a86 |
# -*- 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... | alejob/mdanalysis | package/MDAnalysis/analysis/polymer.py | Python | gpl-2.0 | 5,460 | [
"MDAnalysis"
] | 506598fc4f5c99997ff8e10c1bc83d5f6a3ff0d5b3c3978d9788e1907de9c61d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import itertools
import numpy as np
import math
from . import coord_cython as cuc
"""
Utilities for manipulating coordinates or list of coordinates, under periodic
boundary conditions or otherwise. Many of th... | dongsenfo/pymatgen | pymatgen/util/coord.py | Python | mit | 15,663 | [
"pymatgen"
] | 917d38949e5e69196dff6c17d7aa1d3f7789d42ec409fd451281495e8af80fc2 |
"""
Reads in a number of .vtp ATP files and writes them to hdf5 files. Each time-step
exists as a dataset within the hdf5 file for the particular branch of the input
geometry.
"""
import h5py
import os
import vtk
import glob
originalTimeStep = 0.01
timeStep = 0.01
taskMeshIn = ''
atpMeshPattern = ''
axialQuads = 0
cir... | BlueFern/DBiharMesher | util/DumpATPSeriesToHdf5.py | Python | gpl-2.0 | 6,165 | [
"VTK"
] | 25e8a8f1d5c802acfdad8e8b75c99d2dcc1f412fcb7865e5fcaf84a06d37820d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##
# derived_models.py: Models that decorate and extend other models.
##
# © 2012 Chris Ferrie (csferrie@gmail.com) and
# Christopher E. Granade (cgranade@gmail.com)
#
# This file is a part of the Qinfer project.
# Licensed under the AGPL version 3.
##
# This progra... | MichalKononenko/python-qinfer | src/qinfer/derived_models.py | Python | agpl-3.0 | 35,703 | [
"Gaussian"
] | ee14ac59cc798ebebe4f2f0aa9b29b20eaa8a93817f4796938ebda69e96aa4e2 |
# -*- coding: utf-8 -*-
#
# clopath_synapse_spike_pairing.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 ... | SepehrMN/nest-simulator | pynest/examples/clopath_synapse_spike_pairing.py | Python | gpl-2.0 | 5,804 | [
"NEURON"
] | 3d0054cdc8c5788a25907ce564df1ae4229e1da11b954e602a463654d878cd6d |
# Generated from NestedLists.g4 by ANTLR 4.5.2
from antlr4 import *
if __name__ is not None and "." in __name__:
from .NestedListsParser import NestedListsParser
else:
from NestedListsParser import NestedListsParser
# This class defines a complete generic visitor for a parse tree produced by NestedListsParser.... | arminnh/c-to-p-compiler | resources/antlr-introduction/NestedListsVisitor.py | Python | mit | 878 | [
"VisIt"
] | fbd9a551636fbb54ab463e20e55894dc3597c06d1be62d48d559d8f1205a7601 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: contactxjw@gmail.com
# Created at 2016-12-04
from __future__ import absolute_import, unicode_literals
CARD_TYPE = {
'CC': '信用卡',
'DC': '储蓄卡',
}
BANK_INFO = {
'ABC': '中国农业银行',
'ARCU': '安徽省农村信用社',
'ASCB': '鞍山银行',
'AYCB': '安阳银行',
'BANK... | xjw0914/bank-card | bank_card/static.py | Python | apache-2.0 | 5,872 | [
"xTB"
] | 25d4d4452828d9bef02f63abed2560d34488da3fbc6d65ae875a8ee5b64046e6 |
"""
Test courseware search
"""
import os
import json
from ..helpers import remove_file
from ...pages.common.logout import LogoutPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.lms.courseware_search import CoursewareSearchPage
from ...pages.lms.staff_view import StaffPage
from ...fixtures.cour... | tiagochiavericosta/edx-platform | common/test/acceptance/tests/lms/test_lms_cohorted_courseware_search.py | Python | agpl-3.0 | 13,915 | [
"VisIt"
] | af75215b9ec1141cde5d00abdc8adff1c347dfa33fc1e07f83c503ef82f4cbb7 |
#!python
# coding=utf-8
import math
from datetime import datetime
from collections import namedtuple
import pytz
import numpy as np
import pandas as pd
import netCDF4 as nc4
from pygc import great_distance
from shapely.geometry import Point, LineString
from pyaxiom.utils import unique_justseen, normalize_array, get_f... | axiom-data-science/pyaxiom | pyaxiom/netcdf/sensors/dsg/trajectoryProfile/cr.py | Python | mit | 10,454 | [
"NetCDF"
] | 0804c83b9670360369ac8435d97d1417bd1fc113d5ec0a26ccaf57f7070008d4 |
#!/usr/bin/env python
# Copyright 2014-2019 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/geomopt/addons.py | Python | apache-2.0 | 3,024 | [
"PySCF"
] | 5c7fa900d17efc02c2313cea042a5de71dfca98eab4fa9ca133527773a3ab1e7 |
# (C) 2011, Alexander Korsunsky
# (C) 2011-2015 Elke Schaper
"""
:synopsis: The Repeat Class.
.. moduleauthor:: Elke Schaper <elke.schaper@isb-sib.ch>
"""
from collections import defaultdict
from copy import deepcopy
import logging
import numpy as np
import pickle
import re
from tral.repeat import repeat_sc... | elkeschaper/tral | tral/repeat/repeat.py | Python | gpl-2.0 | 32,230 | [
"Biopython"
] | 64ebe2815dcec1ac48c559f0e40f0c06a0ae914b765fe97488fad92903c74ebd |
########################################################################
# $HeadURL$
# File : Optimizer.py
# Author : Stuart Paterson
########################################################################
"""
The Optimizer base class is an agent that polls for jobs with a specific
status and minor status pair. ... | vmendez/DIRAC | WorkloadManagementSystem/Agent/OptimizerModule.py | Python | gpl-3.0 | 12,157 | [
"DIRAC"
] | c32ef593eac1fa641049bd0b080cf266c632425a9ef4b3446de9b605a10694b4 |
#!/usr/bin/env python
"""Starts an interactive JIRA session in an ipython terminal.
Script arguments support changing the server and a persistent authentication
over HTTP BASIC or Kerberos.
"""
from __future__ import print_function
try:
import configparser
except ImportError:
from six.moves import configpars... | dwmarshall/pycontribs-jira | jira/jirashell.py | Python | bsd-2-clause | 11,617 | [
"VisIt"
] | 978cbb10cd32ebcae2f29865367a078ce828018934f7e58cd0c53dcab7481f33 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLHierarchicalBoxDataReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkXMLHierarchicalBoxDataReader.py | Python | bsd-3-clause | 540 | [
"VTK"
] | 0af0c02cd68c7f3ded8f1a3d7a46abc91b778694e7a77f310cca53d9aba45469 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#----------------------------------------------------------------------------
# Copyright 2017 Marcel Paffrath (Ruhr-Universitaet Bochum, Germany)
#
# This file is part of ActiveSeismoPick3D
#----------------------------------------------------------------------------
... | seismology-RUB/ASP3D | asp3d/util/fmtomoUtils.py | Python | gpl-3.0 | 39,541 | [
"ParaView",
"VTK"
] | 5f69577cc9fdc65a22728516d508432bfd2c518cb00a0a5350fc34292d9315ca |
import operator, os
from datetime import datetime, timedelta
from galaxy.webapps.reports.base.controller import *
import pkg_resources
pkg_resources.require( "SQLAlchemy >= 0.4" )
from sqlalchemy.orm import eagerload
from sqlalchemy import desc
import logging
log = logging.getLogger( __name__ )
class System( BaseContr... | volpino/Yeps-EURAC | lib/galaxy/webapps/reports/controllers/system.py | Python | mit | 8,760 | [
"Galaxy"
] | 52d10f6692fffb9345854a4703f46a3d72e655a252e1bbf96b4938b760aff2a1 |
# coding:utf-8
import random
import matplotlib.pyplot as plt
import numpy as np
from scipy.stats import multivariate_normal
from mla.base import BaseEstimator
from mla.kmeans import KMeans
class GaussianMixture(BaseEstimator):
"""Gaussian Mixture Model: clusters with Gaussian prior.
Finds clusters by repe... | rushter/MLAlgorithms | mla/gaussian_mixture.py | Python | mit | 6,750 | [
"Gaussian"
] | 430a1b31e2513e89cee372fad70d3adae5f459aca236dcd2c4ce9ae9a78c6d61 |
import sys
import copy
"""
Harmony 3 is an iOS game that prompts the user to
reproduce a certain configuration of color blocks,
given an exact number of required swaps per block,
between blocks directly inline with each other,
horizontally and vertically.
For more information, visit:
https://itunes.apple.com/us/app/h... | rmwu/harmony-solver | harmony.py | Python | mit | 19,055 | [
"VisIt"
] | a9a6bf39756589427988a4aeee494178dda8227125e74b5b60763829791fa93c |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap(src_... | kshedstrom/pyroms | examples/Arctic_GLORYS/remap.py | Python | bsd-3-clause | 6,635 | [
"NetCDF"
] | d3f3dbbeb188e8ee6d490cdf4ec71f33ae3428562c6da4024d05cfc565c24106 |
# Copyright 2016 Netherlands eScience Center
#
# Licensed under the Apache License, Version 2.0 (the 'License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | 3D-e-Chem/python-modified-tanimoto | kripodb/webservice/client.py | Python | apache-2.0 | 6,701 | [
"RDKit"
] | 59d765e3a6eba4d5fd6968b79c57563d8a43c8d96427077e6107cd2b63d3d11d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# in nomine Patri
import requests
import psycopg2
from bs4 import BeautifulSoup, Tag
BADSEEDS = list('''?!//\\.,{}|[](){}[]]().,:;\"“”〈〈〉〉¹²⁴''')
BADSEEDS.append('\xb7')
BADSEEDS.append("'")
connect_manu = psycopg2.connect("dbname=manu_tironis user=quellen password=quel... | Winnetou/ManuTironis | utils/vocabul_scrapper.py | Python | cc0-1.0 | 3,815 | [
"VisIt"
] | 26a8086f7cce0d896d08408f74b3c76568f47931ab20a05b25aac56016f3a8dd |
# This file is part of Shyft. Copyright 2015-2018 SiH, JFB, OS, YAS, Statkraft AS
# See file COPYING for more details **/
# questions: f.n.matt@geo.uio.no, sven.decker@geo.uio.no
import os
import numpy as np
from netCDF4 import Dataset
from shyft import api
from shyft import shyftdata_dir
from .. import interfaces
from... | jfburkhart/shyft | shyft/repository/netcdf/senorge_data_repository.py | Python | lgpl-3.0 | 16,993 | [
"NetCDF"
] | d13ba45bc5772908769d01bf1a6ff574cbf546862d6bd281892180d5a9dc1ad5 |
#Copyright ReportLab Europe Ltd. 2000-2004
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__=''' $Id: paraparser.py 3250 2008-08-18 16:13:05Z rgbecker $ '''
import string
import re
from types import Tupl... | jwheare/digest | lib/reportlab/platypus/paraparser.py | Python | bsd-3-clause | 38,446 | [
"VisIt"
] | 96e0ff761b1c1813db2ee92843185b7dccfc9ebbad92211e12711ff292b34c12 |
# pylint: disable=protected-access, unused-argument
# pylint: disable=no-value-for-parameter
__copyright__ = "Copyright 2020, http://radical.rutgers.edu"
__license__ = "MIT"
from unittest import TestCase
import os
import radical.utils as ru
from radical.repex.replica import Replica
from radical.entk import Pipeli... | radical-cybertools/radical.repex | tests/unittests/test_replica.py | Python | mit | 8,157 | [
"Gromacs"
] | a46dd17aa8e649810215798c1e6bd2df96e1ffd8fc1738c2f920ea643b881382 |
import numpy as np
from ase.units import Bohr
from gpaw import debug
from gpaw.mpi import world
#from gpaw.utilities.dscftools import mpi_debug
mpi_debug = lambda x, ordered=True: None # silenced
from gpaw.overlap import Overlap
from gpaw.utilities import unpack
from gpaw.lfc import NewLocalizedFunctionsCollection as... | qsnake/gpaw | gpaw/pair_overlap.py | Python | gpl-3.0 | 20,641 | [
"ASE",
"GPAW"
] | 1e4a1cd0e059c66c16535ac4b5776de71de658873cb7c09b5af6fbfa8fbd939f |
"""
Module to set up run time parameters for Clawpack -- AMRClaw code.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
# Topography files can be found in a tar file posted at:
# http://faculty.washington.edu... | xinshengqin/tsunami_benchmarks | nthmp_currents_2015/problem2/from_japan1/setrun.py | Python | bsd-3-clause | 16,361 | [
"NetCDF"
] | e7393395fa637558d473c4f0931b99b1319b868e45ef5204d7fb78809c9f093f |
#! coding: utf-8
# pylint: disable-msg=W0311
# Make this unique, and don't share it with anybody.
SECRET_KEY = '<replace with a secret key>'
DEBUG = False
PRIMARY_DOMAIN = 'play.jupo.com'
EMAIL_REPLY_TO_DOMAIN = 'reply.jupo.com'
MONGOD_SERVERS = "127.0.0.1:27017"
ELASTICSEARCH_SERVER = '127.0.0.1:9200'
MEMCAC... | juposocial/jupo | src/settings.example.py | Python | agpl-3.0 | 2,159 | [
"VisIt"
] | ba6fefc134650bd69f79635464be0a41a2c073bfcfae30e32921b4c96489a6e3 |
from ase.structure import molecule
from ase.visualize import view
from gpaw import GPAW
from gpaw.wannier import Wannier
calc = GPAW(nbands=4)
atoms = molecule('H2O')
atoms.center(vacuum=3.)
atoms.set_calculator(calc)
atoms.get_potential_energy()
# Initialize the Wannier class
w = Wannier(calc)
w.localize()
centers ... | robwarm/gpaw-symm | doc/exercises/wannier/wannier-h2o.py | Python | gpl-3.0 | 392 | [
"ASE",
"GPAW"
] | 8f16da21b75ea8c2a4db01904bd6f6e6ad9b24205edc54e8972b5a8ddba6fef9 |
# Copyright 2014-2019 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... | sunqm/pyscf | pyscf/adc/__init__.py | Python | apache-2.0 | 2,566 | [
"PySCF"
] | 69211a9d8368ebe111ce8c1893d4783e1619b7e5c504b54fbd45cd4a1fcbe71f |
"""Deals with the socket communication between the PIMD and driver code.
Copyright (C) 2013, Joshua More and Michele Ceriotti
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 ... | quang-ha/lammps | tools/i-pi/ipi/interfaces/sockets.py | Python | gpl-2.0 | 29,683 | [
"LAMMPS"
] | d1d4d2c1ec22e4e7c52384a81294f66492a3f2bac5bcfd8fa66bb4c782292f56 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under ... | MDAnalysis/mdanalysis | package/MDAnalysis/selections/pymol.py | Python | gpl-2.0 | 2,094 | [
"MDAnalysis",
"PyMOL"
] | 9938712e3035a724986d9c677880e34f2586a31a4347282badeeec99027d115a |
#!/usr/bin/env python
# PythonJS to Go Translator
# by Brett Hartshorn - copyright 2014
# License: "New BSD"
import os, sys, itertools
import ast
import pythonjs_to_go
go_types = 'bool string int float64'.split()
rust_hacks = ('__rust__array__', '__rust__arrayfixed__', '__rust__map__', '__rust__func__')
go_hacks = ('_... | kustomzone/Rusthon | pythonjs/pythonjs_to_rust.py | Python | bsd-3-clause | 116,443 | [
"VisIt"
] | 5afb179e4d3ecd89be1a31845be095cdbdc02ccfbdf8d77a1ace1e5a3ed62ce2 |
#!/usr/bin/env python
import unittest
import numpy
import os
from pyscf import lib
from pyscf.pbc import gto, dft, scf, df
from pyscf.pbc.gw import kugw_ac
cell = gto.Cell()
cell.build(
unit = 'B',
a = [[ 0., 6.74027466, 6.74027466],
[ 6.74027466, 0., 6.74027466],
[ 6.740... | sunqm/pyscf | pyscf/pbc/gw/test/test_kugw.py | Python | apache-2.0 | 2,497 | [
"PySCF"
] | d22f76a72cf94bcbe0cb953d1aee01b1482f8733c8a5b83246d747c74d67a026 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2009-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | ghutchis/cclib | src/cclib/parser/ccio.py | Python | lgpl-2.1 | 6,286 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 3435576b88224b7e0a5bc9bc1db087cc474023c6e5b094fb173ce5b1fedcf635 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2010 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; either version 2 of the License, or
# (at your optio... | beernarrd/gramps | gramps/gui/user.py | Python | gpl-2.0 | 5,939 | [
"Brian"
] | 96adc3663e985bdeae7e91974a35ad16d6ecc2c85feec5c59af3ac7ab1943d0d |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/share/psi4/databases/CORE.py | Python | gpl-2.0 | 23,837 | [
"Psi4"
] | 07215b176ea063ae5cb07733fb36312da7e3faa8a8d976345ceaf6e7faedeeee |
import unittest
import math
import torch
import tempfile
import shutil
from glob import glob
import os
import pyprob
from pyprob import util, Model
from pyprob.distributions import Normal, Uniform
from pyprob.nn import OfflineDataset
import pyprob.diagnostics
class DatasetTestCase(unittest.TestCase):
def __init_... | probprog/pyprob | tests/test_dataset.py | Python | bsd-2-clause | 7,468 | [
"Gaussian"
] | 536ebdb2d9cb1d6157c23ea7ab8adf9b8e8521efd1c6452870ba608e834889f2 |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import functools
import io
import json
import random
import shutil
import tempfile
import ddt
import pytz
from django.conf import settings
from django.contrib.auth.models import User
from django.core import mail
from django.core.fil... | Lektorium-LLC/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 227,175 | [
"VisIt"
] | 440cc3e701d3ec227487cc7859302260ccc0325b6188d0c7be3244cc50583e27 |
from __future__ import print_function
from builtins import range
"""
SECTION 1 : Load and setup data for training
the datasets separated in two files from originai datasets:
iris_train.csv = datasets for training purpose, 80% from the original data
iris_test.csv = datasets for testing purpose, 20% from the original ... | rianrajagede/simplesamplecode | Tensorflow/iris_tf_v1.py | Python | mit | 3,582 | [
"NEURON"
] | 79827c884743a3d918c1553d064c300a22cd1ec6e90c99f24bd143f60a1a64fc |
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