text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
"""
The MIT License (MIT)
Copyright (c) 2017 SML
Permission is hereby granted, free of charge, to any person obtaining a
copy of this software and associated documentation files (the "Software"),
to deal in the Software without restriction, including without limitation
the rights to use, copy... | Dino0631/RedRain-Bot | cogs/notinusecogs/misc2.py | Python | gpl-3.0 | 49,471 | [
"CASINO"
] | 958176997d96c61427a3d33d102c810b684a546af77cb56c8f2599a0d7206cdc |
## INFO ########################################################################
## ##
## plastey ##
## ======= ... | kitchenbudapest/vr | main.py | Python | gpl-3.0 | 27,035 | [
"VisIt"
] | 4dd4f021f0e95ae1fd9c608a6212e1b5f18b5823fd00353b88706139ccda70e8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#Usage: MultiLane.py folder/ video.avi data.npz interpolated_lanes.pickle
from ArgParser import parse_args
from GPSReader import GPSReader
from GPSTransforms import IMUTransforms
from MultiLaneGenerator import MultiLane
from Q50_config import LoadParameters
from VtkRenderer im... | sameeptandon/sail-car-log | process/MultiLane.py | Python | bsd-2-clause | 7,094 | [
"VTK"
] | 928acd94c2a4ec8ad68bc69dfe3e73e7a67d17e7a251392758c95734b6f10be3 |
"""Fallaxy (ansible-galaxy) plugin for integration tests."""
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import os
import uuid
from . import (
CloudProvider,
CloudEnvironment,
CloudEnvironmentConfig,
)
from ..util import (
find_executable,
display,
)
f... | azaghal/ansible | test/lib/ansible_test/_internal/cloud/fallaxy.py | Python | gpl-3.0 | 5,719 | [
"Galaxy"
] | 50351a92207173c7cb69a183eb180c6d17fa32471df8cb72df4e284036a70a4a |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2018, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Calculation of Mulliken population analysis (MPA) based on data parsed by cclib."""
import random
import n... | cclib/cclib | cclib/method/mpa.py | Python | bsd-3-clause | 3,953 | [
"cclib"
] | 16c4343f183a78ea63fca38fd5393ec8874fec11abc14ff6a7a54e9df206952e |
#!/usr/bin/python
##############################################################
# SpineML to GENN platform independent wrapper #
# Alex Cope 2017 #
# #
# convert_script_s2g is used to manage passing a ... | genn-team/genn | bin/convert_script_s2g.py | Python | gpl-2.0 | 9,593 | [
"NEURON"
] | 18e2e8295841047f735fc8841b36f493bb45a468228952054b7c62acf7ca894b |
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also implements
RFC 2047 encoded w... | batermj/algorithm-challenger | code-analysis/programming_anguage/python/source_codes/Python3.8.0/Python-3.8.0/Lib/email/_header_value_parser.py | Python | apache-2.0 | 106,086 | [
"CRYSTAL"
] | ccc40efa801902ec7b2ad226a2e33e3e50a74d544fc315667dc5fe0c4174ea5b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
TODO-0: If just the space group is selected and not the cell:
try to find the proper cell if it is not ambigous
(like P21212, P2122,,,),
TODO-1: Add in the CORRECT summary the Rmrgd-F, and total
overloaded refl.
TODO-2: Start multiple COLS... | jsburg/xdsme | XDS/XDS.py | Python | bsd-3-clause | 73,694 | [
"CRYSTAL"
] | eb60c2274781c28ac3acf2c1f53099231f672e4da498ce1086bf4288d07d0aaf |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import random
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getpass,
compat_... | Dunkas12/BeepBoopBot | lib/youtube_dl/extractor/common.py | Python | gpl-3.0 | 114,911 | [
"VisIt"
] | 23457e58782876f3a1926c136abd432a9ef256eee2b45fa35914972b0c065235 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | liuwenf/moose | python/MooseDocs/tests/template/test_template.py | Python | lgpl-2.1 | 4,058 | [
"MOOSE"
] | b7d64fdf3589dc7eb708f8202a4ae39a4aec31e33e8c096aeedc401f516b3150 |
##Built-In Libraries##
import time
import csv
import string
##Third-Party Libraries##
import numpy as np
from PIL import Image,ImageTk
import wolframalpha
##Other TP Files##
import mnist_training as mnist #See File for Citations
import unpackData as unpack #See File for Citations
class Network(object):... | josephwkim/mathnotes | neuralNet.py | Python | mit | 35,008 | [
"NEURON"
] | 5725dcbfaca7eefd6f93ffb8a6697ed533964b0aea255ee0c4a2d94a484ec9c8 |
# -*- coding: utf-8 -*-
from pyaxiom.netcdf import CFDataset
class IncompleteMultidimensionalTimeseriesProfile(CFDataset):
@classmethod
def is_mine(cls, dsg):
try:
assert dsg.featureType.lower() == 'timeseriesprofile'
assert len(dsg.t_axes()) >= 1
assert len(dsg.x_... | axiom-data-science/pyaxiom | pyaxiom/netcdf/sensors/dsg/timeseriesProfile/im.py | Python | mit | 1,478 | [
"NetCDF"
] | 533af11ac9ebe039de044d51fc4d8186c96cd15280dc3fa73a2da192680a8100 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# functional - functionality backend helpers
# 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 L... | heromod/migrid | mig/shared/functional.py | Python | gpl-2.0 | 6,295 | [
"Brian"
] | fa5469fa7dbad77fc33bb11750f1cc2aab647f95ad3afca99f40cbc2c581b8a3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Rendering/OpenGL/Testing/Python/TestFreetypeTextMapperBigger.py | Python | gpl-3.0 | 3,056 | [
"VTK"
] | 7cf4c143d148453d8098892a42ec47234bbe207bd35daa8fb2f8cf6c27884f87 |
from __future__ import absolute_import
import numpy as np
import os
import shutil
import tempfile
import matplotlib
matplotlib.use('Agg', warn=False)
from matplotlib.pyplot import Artist, savefig, clf, cm
from matplotlib.testing.noseclasses import ImageComparisonFailure
from matplotlib.testing.compare import compare_... | perrygeo/geopandas | tests/test_plotting.py | Python | bsd-3-clause | 4,605 | [
"COLUMBUS"
] | 79128b4208a2f6b8ef0e3a0be562259f71954cc2568466a957886a4f4c1692af |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import datetime
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from mock import patch
from zerver.lib.test_helpers import MockLDAP
from confirmation.models import Confirmation
from zilencer.models i... | amyliu345/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 50,543 | [
"VisIt"
] | bedb559f13cc2096e9fdb2d069260c2444332233e8fe7c324d73f12db954c70c |
#
# Copyright 2021 Lars Pastewka (U. Freiburg)
# 2020 Thomas Reichenbach (Fraunhofer IWM)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Pub... | libAtoms/matscipy | examples/pressure_coupling/equilibrate_pressure.py | Python | lgpl-2.1 | 3,869 | [
"ASE",
"Matscipy"
] | 9db2c635ed3509905bffbf27d2e3fedbe44269b763a0185ee50ae43d8bd82bab |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | sxjscience/tvm | tests/python/relay/test_type_functor.py | Python | apache-2.0 | 2,826 | [
"VisIt"
] | e3992c81043f0114ba712d3f257f5b3b71e15f05d5bf03fcb5e6270d8a0379e6 |
#!/usr/bin/env python
##
## @file validateSBML.py
## @brief Validates one or more SBML files
## @author Akiya Jouraku (translated from libSBML C++ examples)
## @author Ben Bornstein
## @author Michael Hucka
##
## $Id$
## $HeadURL$
##
## This file is part of libSBML. Please visit http://sbml.org for more
## in... | ejfresch/qdc | validateSBML.py | Python | gpl-3.0 | 4,671 | [
"VisIt"
] | 4534de227c8256ac7551d98eafc63b29516c79e6e05e06c28f8aa28f8cfd583f |
# -*- coding: utf-8 -*-
#
# Picard, the next-generation MusicBrainz tagger
# Copyright (C) 2006-2007 Lukáš Lalinský
# Copyright (C) 2007 Javier Kohen
# Copyright (C) 2008 Philipp Wolfer
#
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as... | mineo/picard | picard/script.py | Python | gpl-2.0 | 28,202 | [
"Brian"
] | 77202aaa411a014c0a879dd06a5a76bf0626db2ccc2b634dc85ebf1ca5ff61ff |
import os
import copy
import math
import functools
import numpy as np
from ddapp import transformUtils
from ddapp.asynctaskqueue import AsyncTaskQueue
from ddapp import objectmodel as om
from ddapp import visualization as vis
from ddapp import robotstate
from ddapp import segmentation
from ddapp import planplayback
f... | edowson/director | src/python/ddapp/mappingdemo.py | Python | bsd-3-clause | 24,062 | [
"VTK"
] | db4110b7c67127a30e7dc6c0b79ee7ade9a0044396b95b2c78baed284f689f49 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/driver/procrouting/proc.py | Python | lgpl-3.0 | 192,397 | [
"Psi4"
] | c3d52da0a6414aa684083766a6e5fd4ba18a314fe0a48586316c9f20cf1387c5 |
# Copyright (C) 2018-2020 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU Affero General Public License version 3, or any later version
# See top-level LICENSE file for more information
from copy import deepcopy
from datetime import timedelta
impo... | SoftwareHeritage/swh-web-ui | swh/web/tests/data.py | Python | agpl-3.0 | 15,484 | [
"VisIt"
] | 519c744724118458218e176a6add46bfdd3034a4aa31110291cd937a3bdc53d5 |
#
# Copyright (C) 2015 Greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
from rdkit import Chem
from rdkit.Chem import AllChem
import nu... | rvianello/rdkit | Contrib/PBF/pbf.py | Python | bsd-3-clause | 1,745 | [
"RDKit"
] | 1f598facc77cd13cf0c1b1d2c5dfdd636af05ea574354be6a0a68fac2f527d01 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/wizard/pages/update_entities_page.py | Python | gpl-2.0 | 2,533 | [
"VisIt"
] | e4848e0ba2b1c6dce88229508bb119761a5f4387baa3828e6d6e5e2def5a05e2 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/vasp/nlep/nlep.py | Python | gpl-3.0 | 6,815 | [
"CRYSTAL",
"VASP"
] | fe90e31afdead9a5cbf8664557a7dff883ac9b0e7b1551309668c63ee8e7bb55 |
from p5 import *
def setup():
size(640, 360)
background(255)
def draw():
# Get a gaussian number w/ mean of 0 and standard deviation of 1.0
xloc = randomGaussian()
sd = 60
mean = width/2
xloc = (xloc * sd) + mean
noStroke()
fill(0, 10)
ellipse(xloc, height/2, 16, 16)
run()
| croach/natureofcode.py | introduction/noc_i_4_gaussian.py | Python | mit | 320 | [
"Gaussian"
] | e7aa54cdc52c0c3332f10e75dd9ce8cc4d1694104dd54e0c665c866bb6cc2795 |
import numpy as np
import histomicstk.utils as htk_utls
def reg_edge(im_input, im_phi, well='double', sigma=1.5, dt=1.0, mu=0.2,
lamda=1, alpha=-3, epsilon=1.5, iter=100):
"""Distance-regularized edge-based level sets.
Distance-regularization is used in this edge-based level set implementation
... | DigitalSlideArchive/HistomicsTK | histomicstk/segmentation/level_set/reg_edge.py | Python | apache-2.0 | 5,602 | [
"DIRAC"
] | d89b64feeccf75b89b0bf02afa11be4d5a3d6c44282eed87f18a20296b2c8cf9 |
# coding: utf-8
"""Parser for KumaScript used in compatibility data.
KumaScript is a macro system used on MDN:
https://github.com/mozilla/kumascript
KumaScript uses a JS-like syntax. The source is stored as pages on MDN:
https://developer.mozilla.org/en-US/docs/Template:SpecName
KumaScript can query the database,... | jwhitlock/web-platform-compat | mdn/kumascript.py | Python | mpl-2.0 | 38,117 | [
"VisIt"
] | ce932df802017404e502071a3bfc7fe32641d5bd4130519319e7f9d2d6835d23 |
#!/usr/bin/env python
import numpy as np
import argparse
import random
import ray
from ray import tune
from ray.tune.schedulers import PopulationBasedTraining
class PBTBenchmarkExample(tune.Trainable):
"""Toy PBT problem for benchmarking adaptive learning rate.
The goal is to optimize this trainable's accu... | ray-project/ray | python/ray/tune/examples/pbt_example.py | Python | apache-2.0 | 4,406 | [
"Gaussian"
] | 43fc2b126db9b8f05dbfff1578cc61f978253202cca02701cca18a2092fc26d5 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
import vtk
from vtk.wx.wxVTKRenderWindowInteractor import wxVTKRenderWindowInteractor
import wx
from module_kits.wx_kit import utils as wxutils
import wx.lib.agw.aui as aui
wx.aui = aui
from wx.html import HtmlWindow
class ... | nagyistoce/devide | interfaces/wx_interface/main_frame.py | Python | bsd-3-clause | 15,352 | [
"VTK"
] | 9e158a488434dac4028b9a62d14a8509fc3b4cab49b09c28d847c97c00e66538 |
praatscripts = {
'formants.praat':"""
form Variables
sentence filename
real nformants
real ceiling
endform
Read from file... 'filename$'
To Formant (burg)... 0 'nformants' 'ceiling' 0.025 50
frames = Get number of frames
output$ = "time"+tab$+"F1"+tab$+"B... | mmcauliffe/linguistic-helper-functions | linghelper/phonetics/praat/scripts.py | Python | gpl-3.0 | 4,319 | [
"Gaussian"
] | aa85d84cba0b907a6821b600d7c926379e15a0ce3454f0c79f79ba1f3e2ffd49 |
import numpy, mlpy, time, scipy, os
import audioFeatureExtraction as aF
import audioTrainTest as aT
import audioBasicIO
import matplotlib.pyplot as plt
from scipy.spatial import distance
import matplotlib.pyplot as plt
import matplotlib.cm as cm
from sklearn.lda import LDA
import csv, os.path, sklearn, sklearn.hmm, cPi... | bossjones/pyAudioAnalysis | audioSegmentation.py | Python | apache-2.0 | 38,084 | [
"Gaussian"
] | fa508d556be97dcc197c0c79b2e24ac69b4e37388e294d36580d15783a6419a9 |
"""
Unit tests for enrollment methods in views.py
"""
import ddt
from mock import patch
from django.test.utils import override_settings
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse
from courseware.tests.helpers import LoginEnrollmentTestCase
from courseware.tests.modulesto... | wwj718/ANALYSE | lms/djangoapps/instructor/tests/test_legacy_enrollment.py | Python | agpl-3.0 | 15,172 | [
"VisIt"
] | f0d9937cd67099a2e07ec2447e40ae4447bb82729d87bed1a9ee4895596936d9 |
# coding: utf-8
"""
MINDBODY Public API
No description provided (generated by Swagger Codegen https://github.com/swagger-api/swagger-codegen) # noqa: E501
OpenAPI spec version: v6
Generated by: https://github.com/swagger-api/swagger-codegen.git
"""
import pprint
import re # noqa: F401
impor... | mindbody/API-Examples | SDKs/Python/swagger_client/models/get_client_visits_response.py | Python | bsd-2-clause | 4,569 | [
"VisIt"
] | 7a94f2a9857353bb0b9bb77c9a2dd209d02fed3af7d318acf75d31aac43b6676 |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('get_common_problems')
@click.argument("job_id", type=str)
@pass_context
@custom_exception
@json_output
def cli(ctx, job_id):
"""Query inputs and jobs for common potential proble... | galaxy-iuc/parsec | parsec/commands/jobs/get_common_problems.py | Python | apache-2.0 | 557 | [
"Galaxy"
] | 436fa497f9e6a97ff1be67273d12fc7887a280a436892e3b936086b18b044d6d |
#Written by ChocolateBubbles,edited by RobertABT 2014
#I strongly believe the .whatever format should be universal...
import region
from mayavi import mlab
from pylab import imread
from scipy.ndimage import gaussian_filter
from stl_tools import numpy2stl
print 'Format required is as HP40 not hp40'
usrselectedcoords = ... | RobertABT/heightmap | editedstlwrite.py | Python | mit | 781 | [
"Mayavi"
] | 4f3316f7d0b615bfc200bcfe6930d5b2e7db6b7774ddad2eda741b363c8f1976 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | ramondelafuente/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 86,695 | [
"VisIt"
] | d2bd42f1a3ad797dd69cab805e7fb591a628b498a3bb240b36d361308eb5278a |
"""
=======================================
Signal processing (:mod:`scipy.signal`)
=======================================
Convolution
===========
.. autosummary::
:toctree: generated/
convolve -- N-dimensional convolution.
correlate -- N-dimensional correlation.
fftconvolve -- N-dimensional convol... | jlcarmic/producthunt_simulator | venv/lib/python2.7/site-packages/scipy/signal/__init__.py | Python | mit | 11,403 | [
"Gaussian"
] | 52d4bda46d823d19b2d06fc0ef27547a5633a25eaccafc2dca21e91b36df6e8c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def main():
colors = vtk.vtkNamedColors()
colors.SetColor("BkgColor", [26, 51, 102, 255])
parametricObjects = list()
parametricObjects.append(vtk.vtkParametricBohemianDome())
parametricObjects[-1].SetA(5.0)
parametricObjects[-1].SetB(... | lorensen/VTKExamples | src/Python/Deprecated/GeometricObjects/ParametricObjectsDemo2.py | Python | apache-2.0 | 4,159 | [
"VTK"
] | ffb29f4e4c40ab5dde4b8bef368b86a6cd2d18dd2296212df7fc68630a343ea2 |
#
# Copyright (C) 2001,2002 greg Landrum and Rational Discovery LLC
#
""" Various bits and pieces for calculating descriptors
"""
from __future__ import print_function
from rdkit import RDConfig
class DescriptorCalculator:
""" abstract base class for descriptor calculators
"""
#------------
# methods u... | strets123/rdkit | rdkit/ML/Descriptors/Descriptors.py | Python | bsd-3-clause | 1,456 | [
"RDKit"
] | 203cd10f8ce522e22e0b594bcf835c2b6e8f2a14cf42749ed982bc2c23ce0f21 |
#
# Author: Henrique Pereira Coutada Miranda
# Run a GW calculation using Yambo
#
from __future__ import print_function
from yambopy import *
from qepy import *
yambo = 'yambo'
if not os.path.isdir('database'):
os.mkdir('database')
#check if the nscf cycle is present
if os.path.isdir('nscf/bn.save'):
print(... | henriquemiranda/yambopy | tutorial/bn/gw_bn.py | Python | bsd-3-clause | 1,066 | [
"Yambo"
] | 69b46858ff37a756ce4738920421ef69b69ee840baed1de6740d4551e6324fc7 |
import math
import pickle
import six
from rdkit import Chem
from numpy.testing import assert_almost_equal
from mordred import Calculator, descriptors
from nose.tools import eq_
from mordred.error import MissingValueBase
def test_pickle_calculator():
orig = Calculator(descriptors)
d0 = orig.descriptors[0]
... | mordred-descriptor/mordred | mordred/tests/test_pickle.py | Python | bsd-3-clause | 1,052 | [
"RDKit"
] | fa46227bb4ae280db17105c69d66cf7f1d935b1d7cec15a989a0c40f8923f777 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/actions/Notifications.py | Python | gpl-3.0 | 8,123 | [
"ORCA"
] | 7f2647e966210096bd2c6c80c66ef68705aeb5a6c1d9f9264cf7c07202210ae3 |
# Copyright 2013 Julian Metzler
"""
This program 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, or
(at your option) any later version.
This program is distributed in the ... | tytek2012/TweetPony | examples/_common.py | Python | agpl-3.0 | 2,207 | [
"VisIt"
] | e6da01aed55b06b103741142ddf8b39f8334955b2dd59674643e7e742978eebf |
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCRequestHandler
class.
A list of possible usage patterns follows:
1. Install functions:
server = SimpleXMLRPCServer(("l... | Yinxiaoli/iros2015_folding | src/folding_control/src/xmlrpclib-1.0.1/SimpleXMLRPCServer.py | Python | mit | 8,882 | [
"Brian"
] | 2e58d86bc8df62d9aec66d537e7d8141f9a9134658129e980a2d5f73c8d89574 |
# -*- coding: utf-8 -*-
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
import sys, os... | SymbiFlow/symbiflow-docs | source/conf.py | Python | isc | 10,732 | [
"Amber"
] | fa15b8fc4d5b31c66f3df0d7fd4453eb8eaafded560102f41d489114857285df |
"""Used to generate polarization functions for atomic basis sets."""
import sys
import math
import traceback
import numpy as np
from ase import Atom, Atoms
from ase.data import molecules as g2
from gpaw import Calculator
from gpaw.kpoint import KPoint
from gpaw.grid_descriptor import GridDescriptor
from gpaw.spline ... | qsnake/gpaw | gpaw/atom/polarization.py | Python | gpl-3.0 | 27,154 | [
"ASE",
"GPAW",
"Gaussian"
] | 8b1a8699d16820d5091290e5d43dd05b152cfeb1395dd260665d06c10d226ad8 |
""" Contains unit tests of NetworkAgent module
"""
import DIRAC.AccountingSystem.Agent.NetworkAgent as module
import unittest
from mock.mock import MagicMock
__RCSID__ = "$Id$"
MQURI1 = 'mq.dirac.net::Topic::perfsonar.summary.packet-loss-rate'
MQURI2 = 'mq.dirac.net::Queue::perfsonar.summary.histogram-owdelay'
ROO... | Andrew-McNab-UK/DIRAC | AccountingSystem/Agent/test/Test_NetworkAgent.py | Python | gpl-3.0 | 3,707 | [
"DIRAC"
] | ffca2adb8ead450208c51cd96443a6234dd4f0587f19b4ef1d017673d84a1d06 |
import numpy as np
tiny = 1e-10
import logging, sys
import myio
import pickle
'''
Copyright (c) UWM, Ali Dashti 2016 (original matlab version)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Copyright (c) Columbia University Hstau Liao 2018 (python version)
'''
#_logger = logging.getLogger(__nam... | hstau/covar-cryo | covariance/util.py | Python | gpl-2.0 | 6,217 | [
"Gaussian"
] | 0639c15853cf72b117f07e34064c8e33f4a598cb8b29eda70964bc6eefa72cf7 |
#!/usr/bin/env python
import sys
from Bio.Blast.NCBIXML import parse
def get_query_ids(blast_file_handle):
parser = parse(blast_file_handle)
records = [i for i in parser]
return [i.query for i in records if len(i.alignments)]
if __name__=='__main__':
for i in sys.argv[1:]:
with open(i) as f:... | Serpens/small_bioinfo | blastxml_nonzero_queries.py | Python | gpl-3.0 | 388 | [
"BLAST"
] | 84f4985460f2a0be007afae7d1f22a94a3a3eb133efe81a7cbfa8a41d7f7796e |
#!/usr/bin/env python3
from pysisyphus.calculators.Gaussian16 import Gaussian16
from pysisyphus.helpers import geom_from_library, geom_from_xyz_file, do_final_hessian
# from pysisyphus.optimizers.ANCOptimizer import ANCOptimizer
from pysisyphus.optimizers.NCOptimizer import NCOptimizer
# geom = geom_from_library("az... | eljost/pysisyphus | tests_staging/test_ancopt/test_ncopt.py | Python | gpl-3.0 | 1,357 | [
"xTB"
] | e319706c91865eefd4115da49af3ac307b538a0150699a293af7c702f53c158c |
"""
Tests for serial.py.
"""
import cPickle
from cStringIO import StringIO
import gzip
import shutil
import tempfile
import unittest
from rdkit import Chem
from rdkit.Chem import AllChem
from vs_utils.utils.rdkit_utils import conformers, serial
class TestMolIO(unittest.TestCase):
"""
Base test class for mol... | rbharath/vs-utils | vs_utils/utils/rdkit_utils/tests/test_serial.py | Python | gpl-3.0 | 25,593 | [
"RDKit"
] | 4bc619b10a7018ef8bed1caf7259cf3dd7778e5eb420e04d4e61da350944cdd9 |
# -*- coding: utf-8 -*-
# Copyright (c) 2006-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2012-2015 Google, Inc.
# Copyright (c) 2013 moxian <aleftmail@inbox.ru>
# Copyright (c) 2014 Brett Cannon <brett@python.org>
# Copyright (c) 2014 frost-nzcr4 <frost.nzcr4@jagmort.com>
# Copyright (c) 2014... | axbaretto/beam | sdks/python/.tox/lint/lib/python2.7/site-packages/pylint/checkers/format.py | Python | apache-2.0 | 41,989 | [
"VisIt"
] | 6d83b11836c3e59d22489a784a04b08d22980fd0337f12732aaff6b9a957b508 |
from numpy import array, arange, frombuffer, load, asarray, random, \
fromstring, expand_dims, unravel_index, prod
try:
buffer
except NameError:
buffer = memoryview
from ..utils import check_spark, check_options
spark = check_spark()
def fromrdd(rdd, nrecords=None, shape=None, index=None, labels=None, d... | alexandonian/lightning | lightning/series/readers.py | Python | apache-2.0 | 14,558 | [
"Gaussian"
] | d5fd2e658de86859bad38d0c004d3fa9a11dfa5ecc8779207d0e2be94e6285b9 |
# -*- coding: utf-8 -*-
"""Utilities for the PyBEL database manager."""
from typing import Dict, Mapping, Optional, Tuple, Union
from ..utils import parse_datetime
def extract_shared_required(config, definition_header: str = "Namespace"):
"""Get the required annotations shared by BEL namespace and annotation r... | pybel/pybel | src/pybel/manager/utils.py | Python | mit | 2,492 | [
"Pybel"
] | 7cd23955b03f4c3eeae3dd843562508b4f6b9f1f9198bf24853650deb3120dcd |
#######################################################################
#
#
# Volume Text Renderer for Dreambox/Enigma-2
# Coded by Vali (c)2010
# Support: www.dreambox-tools.info
#
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view ... | openatv/enigma2 | lib/python/Components/Renderer/VVolumeText.py | Python | gpl-2.0 | 1,574 | [
"VisIt"
] | c8f8edf0f2c1b0baf69f0a7f3ff09811b3b4ea9e9a984340d108b35672655333 |
#pylint: disable=C0111
#pylint: disable=W0621
from lettuce import world
import time
from urllib import quote_plus
from selenium.common.exceptions import WebDriverException, StaleElementReferenceException
from selenium.webdriver.support import expected_conditions as EC
from selenium.webdriver.common.by import By
from s... | elimence/edx-platform | common/djangoapps/terrain/ui_helpers.py | Python | agpl-3.0 | 4,151 | [
"VisIt"
] | df548a5912fc57f6ec9637c5b25fc2341b0dda4f260bc02067786ebeb510cc18 |
from trustbutverify import analyzers
import mdtraj as md
import pandas as pd
analyzer = analyzers.ChemicalShiftAnalyzer("1am7", "/home/kyleb/src/choderalab/ForcefieldData/nmr/bacteriophage_lysozyme/16664.str")
expt = analyzer.load_expt()
analyzer = analyzers.ScalarCouplingAnalyzer("1am7", "/home/kyleb/src/choderalab... | choderalab/TrustButVerify | scripts/test_analyzer.py | Python | gpl-2.0 | 593 | [
"MDTraj"
] | 0a95b71108d2c639f713f1bdcdde1be748dd0ae18591040b369a40c422aace0c |
########################################################################
# File : CPUNormalization.py
# Author : Ricardo Graciani
########################################################################
""" DIRAC Workload Management System Client module that encapsulates all the
methods necessary to handle CPU... | andresailer/DIRAC | WorkloadManagementSystem/Client/CPUNormalization.py | Python | gpl-3.0 | 8,966 | [
"DIRAC"
] | 4db82fba2b3158d74a748c29281ef15c2b3958f568612251d9fcbb48eadb01c8 |
"""**Class projection**
"""
from osgeo import osr
# The projection string depends on the gdal version
DEFAULT_PROJECTION = '+proj=longlat +datum=WGS84 +no_defs'
class Projection:
"""Represents projections associated with layers
"""
def __init__(self, p):
"""Constructor for Projection.
... | takmid/inasafe | safe/storage/projection.py | Python | gpl-3.0 | 4,330 | [
"NetCDF"
] | 3f60267f54703cc7595c6cb20b20f604cde672fb8ed398e90321ad4d69b2b609 |
import ast
code = """
x = 1
y = 2
z = x + y
x, y, z
"""
module = ast.parse(code)
module.body
ast.dump(module, annotate_fields=False, include_attributes=False)
# "Module([Assign([Name('x', Store())], Num(1)), Assign([Name('y', Store())], Num(2)), Assign([Name('z', Store())], BinOp(Name('x', Load()), Add(), Name(... | satishgoda/programmingusingpython | docs/library/language/ast/ast_NodeVisitor_subclass1.py | Python | gpl-2.0 | 1,984 | [
"VisIt"
] | 65868e16f8ac5affca42fc91a1568b53b0611b53bd2f884bd51f43d9cb78be14 |
"""
An isogram is a word that has no repeating letters, consecutive or non-consecutive. Implement a function that determines whether a string that contains only letters is an isogram. Assume the empty string is an isogram. Ignore letter case.
is_isogram("Dermatoglyphics" ) == true
is_isogram("aba" ) == false
is_isogra... | aadithpm/code-a-day | py/Isograms.py | Python | unlicense | 479 | [
"MOOSE"
] | 1a372298db5795b0355d152227633ffe86d63be693747bc4b903a3d008ad4fad |
# -*- coding: utf-8 -*-
#
# test_quantal_stp_synapse.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of th... | HBPNeurorobotics/nest-simulator | pynest/nest/tests/test_quantal_stp_synapse.py | Python | gpl-2.0 | 4,353 | [
"NEURON"
] | 06a31eec37f9d1551d380ddb45ba97ea42461db7ab597cdbd914102a0bca4d64 |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/ensemble/forest.py | Python | mit | 64,801 | [
"Brian"
] | 0a74af56114846db39a5643eb37773fd199356e0a1e551ca7c521ff1e867deff |
# Python test set -- part 1, grammar.
# This just tests whether the parser accepts them all.
# NOTE: When you run this test as a script from the command line, you
# get warnings about certain hex/oct constants. Since those are
# issued by the parser, you can't suppress them by adding a
# filterwarnings() call to this... | xbmc/atv2 | xbmc/lib/libPython/Python/Lib/test/test_grammar.py | Python | gpl-2.0 | 19,154 | [
"GULP"
] | 0e6c9826b95a3b53bf3addb2e4df1ee4e72da4adfbef0eb12819d5c92fabc3be |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | susilehtola/psi4 | psi4/driver/procrouting/findif_response_utils/data_collection_helper.py | Python | lgpl-3.0 | 4,102 | [
"Psi4"
] | a316e6674f68358160450cd74e32c2b433116963e44b902950f94d70eec49932 |
#!/usr/bin/env python3
# Tests check_format.py. This must be run in a context where the clang
# version and settings are compatible with the one in the Envoy
# docker. Normally this is run via check_format_test.sh, which
# executes it in under docker.
from __future__ import print_function
from run_command import run... | envoyproxy/envoy | tools/code_format/check_format_test_helper.py | Python | apache-2.0 | 16,423 | [
"VisIt"
] | 7f47e95965af0bc597f445a51008cf2569ecce438bd3ad991bf5145eb40ea166 |
"""
:Author: Pierre Barbier de Reuille <pierre.barbierdereuille@gmail.com>
Module implementing non-parametric regressions using kernel smoothing methods.
"""
#from __future__ import division, absolute_import, print_function
from scipy import stats
from scipy.linalg import sqrtm, solve
import scipy
import numpy as np
... | jtcb/regress-plan | astar/pyqt_fit/kernel_smoothing.py | Python | gpl-2.0 | 25,276 | [
"Gaussian"
] | b84bf6287a1ca106b882f67d6a4849d49e3f59b77158980be9a753fc3034aec5 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | noroutine/ansible | lib/ansible/modules/network/avi/avi_networkprofile.py | Python | gpl-3.0 | 3,894 | [
"VisIt"
] | baf20537e5001eac491476eceb88fbd875d53e4206ceafc1a9af4867efe71ac5 |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2011'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
'''
Contains class for common routines for loading all CANON data
Mike McCann
MBARI 22 April 2012
@undocumented: __doc__ parser
@status: production
@license: GPL
'''
import os
i... | stoqs/stoqs | stoqs/loaders/CANON/__init__.py | Python | gpl-3.0 | 88,295 | [
"NetCDF"
] | 26c59baaed1583abba6e8ff2c1bb89a7da6d9495564af7693caab1b1f32bb1c4 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <mainak@neuro.hut.fi>
# Mark Wronkiewicz <wronk.mark@gmail.c... | wronk/mne-python | mne/viz/tests/test_3d.py | Python | bsd-3-clause | 9,172 | [
"Mayavi"
] | bd5a3346252f96dee800aa154f60eaea8c5706ae3b42b4700a4b9c59d72c1068 |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from datetime import date, timedelta
from workalendar.core import WesternCalendar, ChristianMixin
from workalendar.core import SUN, MON, TUE, WED, FRI, SAT
class Brazil(WesternCalendar... | sirk390/workalendar | workalendar/america.py | Python | mit | 7,348 | [
"COLUMBUS"
] | df3d0369cedafbb30d79424a353c68d20f48e89c51f68533ffc57021c1ff7438 |
#!/usr/bin/env python3
# The MIT License (MIT)
#
# Copyright © 2015 Glenn Fitzpatrick
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation th... | gfitzp/kindle-clipper | kindle-clipper.py | Python | mit | 8,941 | [
"CASINO"
] | c7acee64dc7ab8deb0e606ecbbf2576924b8e117c7a71d5266078648ff7323b8 |
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
from ambhas.copula import Copula
from scipy import stats
input1 = pd.read_excel("Input_Data.xlsx", sheetname="Oil Call Option Prices")
input2 = pd.read_excel("Input_Data.xlsx", sheetname="FX Call Option Prices")
input3 = pd.read_excel("Inpu... | GauthamGoli/quantify-2016 | Modelling Joint Distributions/source_code.py | Python | mit | 5,896 | [
"Gaussian"
] | d3edeef00b885c2343aa90887bf7cf5699860e05815ba0ef2abe2cb089174914 |
"""Implements tools for computing performance profiles.
This module implements tools for computing
the Dolan and More performance profiles for
a set of solvers on a given set of test
problems. For the definition of performance
profiles, see
E.D. Dolan and J.J. More, Benchmarking optimization
software with perfor... | tbs1980/otkpp | pyotk/pyotk/perfprof.py | Python | gpl-3.0 | 4,857 | [
"Gaussian"
] | de535ee3ba068f26504ea8bba0e19207c63482f1fa91b73f6a8ee631e6eb6acd |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | harterj/moose | python/peacock/base/TabbedPreferences.py | Python | lgpl-2.1 | 2,204 | [
"MOOSE"
] | 949a7d01726b7a7c754e7b777a00c1b70e5ed53c977e44dfdef353e99c0c7651 |
"""
Utilities for cleaning HTML code.
"""
def clean_html(*args, **kwargs):
raise ImportError("clean_html requires html5lib or pytidylib")
def sanitize_html(*args, **kwargs):
raise ImportError("sanitize_html requires html5lib")
def clean_html5lib(input):
"""
Takes an HTML fragment and processes it usi... | luiscarlosgph/nas | env/lib/python2.7/site-packages/django_wysiwyg/utils.py | Python | mit | 2,416 | [
"ADF"
] | 03c9b44138179e29144728ccc8bc6a40f36def1b25b4b1e3b0c6a6ac5973affe |
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Honeybee is free software; you can redistribute it and/or modify
# it under the terms of the GNU Ge... | samuto/Honeybee | src/Honeybee_Generate Climate Based Sky.py | Python | gpl-3.0 | 7,211 | [
"EPW"
] | 75bcfb6f415691f576c086a7ca64c284d16e086b19aed454b2d18185bdaa71ce |
"""
Given a n*n adjacency array.
it will give you a maximum flow.
This version use DFS to search path.
Assume the first is the source and the last is the sink.
Time complexity - O(Ef)
example
graph = [[0, 16, 13, 0, 0, 0],
[0, 0, 10, 12, 0, 0],
[0, 4, 0, 0, 14, 0],
[0, 0, 9, 0, 0, 20],
... | keon/algorithms | algorithms/graph/maximum_flow_dfs.py | Python | mit | 2,038 | [
"VisIt"
] | 38c72597e00740ad0ab5946760e2644b962c4c3ef3b13f26277c8fec5f8fc1c1 |
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | hjanime/VisTrails | vistrails/packages/vtk/__init__.py | Python | bsd-3-clause | 3,026 | [
"VTK"
] | d72123f2d89f8cca8879d3f1a9f534ab1ec38829b16b618fbc362d6e7c90fc4d |
#!/usr/bin/env python
## /*=========================================================================
## Program: Visualization Toolkit
## Module: HeaderTesting.py
## Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
## All rights reserved.
## See Copyright.txt or http://www.kitware.com/Copyright... | naucoin/VTKSlicerWidgets | Common/Testing/HeaderTesting.py | Python | bsd-3-clause | 16,639 | [
"VTK"
] | 154e3a86d47af6a9f5989fbcc82727e40f90add1103ca56317afa997b43371a5 |
# (C) British Crown Copyright 2010 - 2013, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | kwilliams-mo/iris | lib/iris/fileformats/netcdf.py | Python | gpl-3.0 | 49,965 | [
"NetCDF"
] | 1dec12d4d2204304a5aabf7047c218270074cce7b0a190a633f7d070cf6f1725 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/stats/ordination/tests/test_ordination_results.py | Python | bsd-3-clause | 12,214 | [
"scikit-bio"
] | a3b6b76903748290e8d989cc01e4c139167f30fdc4db321fd09ccdea70c98b66 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import re
import os
import warnings
from string import Template
from six import string_types
from six.moves import zip
import numpy as np
from monty.io impo... | nisse3000/pymatgen | pymatgen/io/nwchem.py | Python | mit | 36,074 | [
"Gaussian",
"NWChem",
"pymatgen"
] | e2144b094fe47af2e4a400073114701636bd1723a0d19ea1fa9401c6686772ba |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alxgu/ansible | lib/ansible/modules/network/avi/avi_gslbservice.py | Python | gpl-3.0 | 9,674 | [
"VisIt"
] | 7569d7b24a4ab511e8e689426632f74d1b0478e93cbdafc63dae66e64a323549 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2003-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | pmghalvorsen/gramps_branch | gramps/plugins/gramplet/eval.py | Python | gpl-2.0 | 4,212 | [
"Brian"
] | ad2cf1f1fadae6e15f89c658a1d59508d61d65f61e80e11dd6b688c51e6ccc97 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2017 Stanford University and the Authors
#
# Authors: Matthew Harrigan
# Contributors:
#
# MDTraj is free software: ... | leeping/mdtraj | tests/conftest.py | Python | lgpl-2.1 | 1,234 | [
"MDTraj"
] | 4dac104a52354dac4fe57c00cec8aa5cb5c451c9489eb09bc6174b336f0c63e1 |
#!/usr/bin/env python
import os
from ase.io import read,write
from ase.optimize import QuasiNewton
# Turbomole input coordinates must be in the file 'coord'.
# The coordinates are updated to the file 'coord' during the minimization.
test = read('coord')
test.set_calculator(Turbomole())
dyn = QuasiNewton(test, traj... | alexei-matveev/ase-local | doc/ase/calculators/turbomole_ex1_relax.py | Python | gpl-2.0 | 393 | [
"ASE",
"TURBOMOLE"
] | c4196e37f89e439b239cefaa2a9e0626e29995404ca81a1459e0542d0a7aca64 |
#!/bin/env python
# -*- coding: utf-8 -*-
# pylint: disable=line-too-long,invalid-name
"""
| This file is part of the web2py Web Framework
| Copyrighted by Massimo Di Pierro <mdipierro@cs.depaul.edu>
| License: BSD
| Thanks to ga2arch for help with IS_IN_DB and IS_NOT_IN_DB on GAE
Validators
-----------
"""
import os... | web2py/pydal | pydal/validators.py | Python | bsd-3-clause | 158,798 | [
"CASINO",
"Jaguar",
"MOE"
] | 19c9fe3710b49fa89a1e466cd96511a55b6f1e7deb8244abdd8986376ea123d1 |
'''
Reads, processes, and writes flat data types using the FeedReader, FeedWriter, and DataProcessor classes.
Visit their documentation for example configuration files.
Execution:
python feed_driver.py -c config.json
by Bereket Abraham
'''
from reader import *
from processor import *
from writer import *
import argp... | babraham123/rpw | feed_driver.py | Python | mit | 2,110 | [
"VisIt"
] | f95c7e60d337c80018d0791e33ba8f7a3fa4d8d3e71f845e59729071c7ca3a4f |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | espressomd/espresso | testsuite/python/dawaanr-and-dds-gpu.py | Python | gpl-3.0 | 4,900 | [
"ESPResSo"
] | 057d9d07edbce31776f817a757e43483a506d3af556d71b0368e773a9e236593 |
import os
import shutil
import logging
import unittest
import tempfile
import deepchem as dc
import numpy as np
from sklearn.ensemble import RandomForestClassifier
logger = logging.getLogger(__name__)
class TestDrop(unittest.TestCase):
"""
Test how loading of malformed compounds is handled.
Called TestDrop si... | miaecle/deepchem | deepchem/data/tests/test_drop.py | Python | mit | 1,153 | [
"RDKit"
] | f595eb889034dfd55a92579add6266915def68855e2aa7d0899b696255aa87b8 |
# -*- coding: utf-8 -*-
# Copyright (C) 2004-2019 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
#
# Authors: Aric Hagberg (aric.hagberg@gmail.com)
# Pieter Swart (swart@lanl.gov)
# Dan Sch... | sserrot/champion_relationships | venv/Lib/site-packages/networkx/generators/degree_seq.py | Python | mit | 30,646 | [
"Brian"
] | 26a34dbc8f2d997216f41376ce50dd4f5ddf6f3ffc199ca52c3345b65df9125e |
import urllib
import bleach
import ssl
import socket
import re
import datetime, time
from OpenSSL import SSL
from django.db import models
from django.forms import ModelForm
from django.template.defaultfilters import slugify
from django.conf import settings
from django.core.urlresolvers import reverse
# Us... | haoqili/MozSecWorld | apps/msw/models.py | Python | bsd-3-clause | 15,142 | [
"VisIt"
] | be12816a27019ffad993bcedc11f9f423a1c8a999173fdbecb8fb5223579ad1c |
import chainerx
from chainerx import _docs
def set_docs():
_docs_creation()
_docs_indexing()
_docs_linalg()
_docs_logic()
_docs_manipulation()
_docs_math()
_docs_sorting()
_docs_statistics()
_docs_connection()
_docs_normalization()
_docs_pooling()
def _docs_creation():
... | okuta/chainer | chainerx/_docs/routines.py | Python | mit | 76,765 | [
"Gaussian"
] | 2b455d13101af7232c3c5cf0fbdc4ba5a21b9d0182aebb9526d57cf372a5b2fb |
"""An NNTP client class based on:
- RFC 977: Network News Transfer Protocol
- RFC 2980: Common NNTP Extensions
- RFC 3977: Network News Transfer Protocol (version 2)
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print('Group', name, 'ha... | Herkemer/pynab | lib/nntplib.py | Python | gpl-2.0 | 47,585 | [
"Brian"
] | 2d5d8eeb9998fec7730584aad10b08fa91f5651f6cd306f5a22bd001f1ff04f6 |
# (c) 2017, Florian P. Bayer <f.bayer@tum.de>
#
# sequences.py is part of the PyOmics project.
# It contains all kinds of Sequence objects that provide useful functionality.
# Import standard library modules
import re
import math
import warnings
from collections import Counter
import random
# Import from other non-s... | FloBay/PyOmics | PyOmics/Sequence/sequences.py | Python | bsd-3-clause | 82,389 | [
"Dalton"
] | 1b72cdcff2ecbac940f5fcd1e83dbd203b14f553e604c4c8746ef4d50f4e153b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
# Copyright INRIA
# Contributors: Nicolas P. Rougier (Nicolas.Rougier@inria.fr)
#
# DANA is a computing framework for the simulation of distributed,
# asynchronous, numerical and adaptive models... | rougier/dana | examples/sigmapi.py | Python | bsd-3-clause | 3,695 | [
"Gaussian"
] | 86b69b7642bfe18f388bdeb1b3a4dbd29e7251e4fe0f35769192c069b7fbaca5 |
#!/usr/bin/python
# coding: utf-8
import os
from django.conf import settings
from django.test import LiveServerTestCase
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from sauceclient import SauceClient
from selenium import webdriver
class ProcurementTestCase(StaticLiveServerTestCase):
... | marshalc/guerdon | guerdon/holiday/tests/test_ui.py | Python | gpl-2.0 | 3,098 | [
"VisIt"
] | 3b4655fb56f215af32061bc045fad4843c69381cdc84976fc1522d0be3ef5c57 |
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