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from flask.ext.testing import TestCase
from flask.ext.login import current_user
from flask import current_app, url_for, session
from adsws.core import db, user_manipulator
from adsws.testsuite import make_test_suite, run_test_suite
from adsws import accounts
from adsws.accounts import utils
from adsws.accounts.emails ... | jonnybazookatone/adsws | adsws/tests/test_accounts.py | Python | gpl-2.0 | 29,422 | [
"VisIt"
] | 8acf1f6ee6f6b9ef81f88e2d71d923f41643217bbeb1b4d53a89985e182ef818 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/lib/mediaitem.py | Python | gpl-2.0 | 26,601 | [
"Brian"
] | 8dc4417ca8838433825cdaa743d6e35d8c430779e4b5530b8e54912777f0c83a |
# version code ef5291f09f60+
coursera = 1
# Please fill out this stencil and submit using the provided submission script.
## 1: (Task 1) Minutes in a Week
minutes_in_week = ...
## 2: (Task 2) Remainder
#For this task, your expression must use //
remainder_without_mod = ...
## 3: (Task 3) Divisibility
divisib... | tjctw/PythonNote | matrix/src_from_web/python_lab.py | Python | cc0-1.0 | 6,267 | [
"MOE"
] | 0ef9422f241b107337d0ebfc71ae55eb1642fd958b4680ed2f723d372b056ec3 |
#
# Copyright (C) 2013-2018 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... | hmenke/espresso | testsuite/python/interactions_non-bonded.py | Python | gpl-3.0 | 23,510 | [
"ESPResSo",
"Gaussian"
] | 2659400f1730d3da36972f0fb76ed00e90e197aec6e349af4e11be88a17eef9b |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | angstwad/ansible | lib/ansible/plugins/cache/jsonfile.py | Python | gpl-3.0 | 5,651 | [
"Brian"
] | 14cc8b14e8cc6264ca0be0b7e68cc1f3f3997c75b3ab778945f4c481d4440330 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for Student's Profile Page.
"""
from flaky import flaky
from contextlib import contextmanager
from datetime import datetime
from bok_choy.web_app_test import WebAppTest
from nose.plugins.attrib import attr
from ...pages.common.logout import LogoutPage
from ...pages.lms.acc... | martynovp/edx-platform | common/test/acceptance/tests/lms/test_learner_profile.py | Python | agpl-3.0 | 31,744 | [
"VisIt"
] | fc71d8dca27b8cbd535b654ef1f3619a074cd16713e7d0be5788da3f028c6afb |
# Sebastian Raschka, 2015 (http://sebastianraschka.com)
# Python Machine Learning - Code Examples
#
# Chapter 2 - Training Machine Learning Algorithms for Classification
#
# S. Raschka. Python Machine Learning. Packt Publishing Ltd., 2015.
# GitHub Repo: https://github.com/rasbt/python-machine-learning-book
#
# License... | rasbt/python-machine-learning-book | code/optional-py-scripts/ch02.py | Python | mit | 11,798 | [
"NEURON"
] | eb8895314b73542d30f2683aaaa11208dabae3b9ba000d2d18e4b3bb4be31aa7 |
# -*- 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 t... | MDAnalysis/mdanalysis | package/MDAnalysis/core/__init__.py | Python | gpl-2.0 | 2,105 | [
"MDAnalysis"
] | 955cac3c23c447b340dba9ae6bea1700849e62f1a9046323de88bca9ef829497 |
"""
This script tests the implementation of
the spherically symmetric nonlinear
Fokker-Planck equation with a spherically
symmetric Gaussian source term. The script
can be used to investigate how the source
rate and the source width affect the evolution
of the distribution function.
"""
import matplotlib.pyplot as ... | ehirvijo/fokker-planck-fenics | python/spherically_symmetric_backward_euler_stepping.py | Python | gpl-3.0 | 4,366 | [
"Gaussian"
] | 57ccac802bb662782a34cbd6495dbc75bbf019fc83c117ea8c706e5c6ccfef40 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module provides tools for making a simulated image for tests.
"""
from astropy.io import fits
import numpy as np
from ..geometry import EllipseGeometry
from ...datasets import make_noise_image
def make_test_image(nx=512, ny=512, x0=None, y0=No... | astropy/photutils | photutils/isophote/tests/make_test_data.py | Python | bsd-3-clause | 3,779 | [
"Galaxy",
"Gaussian"
] | d03d27cd38ce2a154461ae7d80efe47dcbf0590ece0288f0cd5a2cd4e6e26c6a |
# coding: utf-8
import os
basedir = os.path.abspath(os.path.dirname(__file__))
class Config:
SECRET_KEY = os.environ.get('SECRET_KEY') or '\xa1\xcc5\x8f\xe1\xc7\xa0!\xe8\xec\x8bG\xefv\x89i{+\xae\xa5\x8d\xc7\x08"\xba\x0e\x11\xc3\xcb\xdd\xd6'
SQLALCHEMY_COMMIT_ON_TEARDOWN = True
SQLALCHEMY_TRACK_MODIFICATI... | LokiSharp/Sharloki-Blog | config.py | Python | mit | 2,196 | [
"MOE"
] | c152d464c1c4b5426c7bd4e68d00aa3a711fa2b942b18f2bdab4fbfcd96701dd |
"""
==========================================
Outlier detection with several methods.
==========================================
When the amount of contamination is known, this example illustrates two
different ways of performing :ref:`outlier_detection`:
- based on a robust estimator of covariance, which is assumin... | depet/scikit-learn | examples/covariance/plot_outlier_detection.py | Python | bsd-3-clause | 3,878 | [
"Gaussian"
] | f6025f167b27128dc6736bbc06557508b2fc2761c0e926d552dba1e7de5b17e0 |
''' Crawls the network using Breadth First Search algorithm pattern, by first starting with a manually entered root node, and then building an adjacency list based of the neighbors of the root, and the neighbors of the neighbors of the root, etc.
Besides getting each device's neighbors, we get some data about ea... | plucena24/network_discovery | inventory/gather_inventory.py | Python | apache-2.0 | 8,500 | [
"VisIt"
] | ae0386a733ec9f25750f1909d5fcd6386b805f45c9f6b2fd78999b5dfd5db476 |
import tweepy
import json,re,sys
# Authentication details. To obtain these visit dev.twitter.com
consumer_key = 'ufulV3imKoYNzdh58LotTC1YD'
consumer_secret = '2A781ma736HTenAXXYn9tRIelQYJkbCqY0GLi7W71ZwwDmNU59'
access_token = '2564905075-MY9osfHabaRnonQVHHhHeA1vCLSOhuHWjBNBiIY'
access_token_secret = 'JsD8Woc7i... | manglakaran/TrafficKarmaSent | src/traffickarmasent/test.py | Python | mit | 2,759 | [
"VisIt"
] | 6c0624916cd4ce23ed3cdc32eb85b8a20f9b8b6174e646126383c1a76f611989 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#############################################################################
# Copyright 2016 Konrad Sakowski
#
# 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 c... | ghkonrad/bublus | gui.py | Python | apache-2.0 | 48,547 | [
"Galaxy"
] | 7a7544cbf070da2300518e91c48e51df20911ed0acf53bca2975e610c1813514 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
#
# 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 Fre... | arunkgupta/gramps | gramps/gen/filters/rules/source/_hasgallery.py | Python | gpl-2.0 | 1,792 | [
"Brian"
] | 026d458cfe2dd09700d32ac9e1b9642529f1807e7446f4984d95b3f3921c5c31 |
# -*- coding: utf-8 -*-
""" ChemconnectUtil.py Some of the command function are written """
__author__ = "Harsha Rani"
__copyright__ = "Copyright 2017, Harsha Rani and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintainer... | dilawar/moose-core | python/moose/chemUtil/chemConnectUtil.py | Python | gpl-3.0 | 12,674 | [
"MOOSE"
] | 0e7d7a83b18c9006ba433c9f6bb0f40815a820363fdfb9f230e4e2147404b260 |
import py
from rpython.rlib.parsing.parsing import PackratParser, Rule
from rpython.rlib.parsing.tree import Nonterminal
from rpython.rlib.parsing.regex import StringExpression, RangeExpression
from rpython.rlib.parsing.lexer import Lexer, DummyLexer
from rpython.rlib.parsing.deterministic import compress_char_set, DFA... | jptomo/rpython-lang-scheme | rpython/rlib/parsing/regexparse.py | Python | mit | 76,213 | [
"VisIt"
] | 696234987ce29736a970091e15aee58e80fb51b6e5c3a007938f6bb8ce548761 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from random import shuffle
from time import sleep
from json import load, dump
from re import compile as regexcompile
from os.path import splitext
from urllib import urlopen, urlretrieve
from locale import setlocale, LC_ALL
from os.path import exists
from os import mkdir, listd... | Feneric/PocketInstaller | Installers/ifstories.py | Python | mit | 29,776 | [
"Galaxy",
"VisIt"
] | ba8f99a61e140eb64bacc7a3347fe57ba3fb2838d45e77d5b346fed00b626c83 |
# Load, filter, prep RNAseq data for baseline analyses
# Note: This code is deprecated - use the Matlab version prep_rnaseq.m
from load_patient_data import load_per_visit_data
import numpy as np
import pandas as pd
import csv
import cmsgpack
import scipy.io as sio
# Flags for intermediate processing
load_data = False... | xpspectre/multiple-myeloma | prep_rnaseq_data.py | Python | mit | 4,144 | [
"VisIt"
] | c563114d97e9c0b56684063f72ba4ccc37efdd3b1a82398e919c0869b4772668 |
def connect(node1, node2):
node1.connect(node2)
class BaseNode(object):
'''Something that can be connected to something else.'''
def __init__(self, nin, nout, id=None):
self.nin = nin
self.nout = nout
self.nextnode = None
self.previousnode = None
self.id = id
... | sergiopasra/connectsim | conectsim/optics/basenodes.py | Python | gpl-3.0 | 2,220 | [
"VisIt"
] | 1d0d70c697406c9d8f8cf17b368046b7b2d29ff6e6629006711b469e10c18018 |
"""
This file is part of RAPD
Copyright (C) 2012-2018, Cornell University
All rights reserved.
RAPD 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, version 3.
RAPD is distributed in the hope that it will... | RAPD/RAPD | src/old_agents/rapd_agent_anom.py | Python | agpl-3.0 | 89,114 | [
"CRYSTAL"
] | f3db831b04b976765510d574e1642e4e5bb823aff78d29573dca9a95b1dec1de |
"""Bowtie abstract component classes.
All visual and control components inherit these.
"""
from typing import Any, Callable, Optional, ClassVar, Tuple # pylint: disable=unused-import
from abc import ABCMeta, abstractmethod
import string
from functools import wraps
import json
from datetime import datetime, date, tim... | jwkvam/bowtie | bowtie/_component.py | Python | mit | 10,337 | [
"Bowtie"
] | 9c336b00726e84051c142fa86c16447d7f994e37e2aa233ee3d43921e9ed36e4 |
# $HeadURL: $
''' AlwaysActivePolicy module
'''
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
__RCSID__ = '$Id: $'
class AlwaysActivePolicy( PolicyBase ):
'''
The AlwaysActivePolicy is a dummy module that can be ... | Sbalbp/DIRAC | ResourceStatusSystem/Policy/AlwaysActivePolicy.py | Python | gpl-3.0 | 895 | [
"DIRAC"
] | 3c70647b529aee412d97394e89fc769637a7bce7d8f1cf71f5f54f4619bbbf89 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/qcdb/molpro2.py | Python | lgpl-3.0 | 27,516 | [
"CFOUR",
"Psi4"
] | aa278f42cb9f2623985d19a8ebf2992e8db4fa34d1e15f4e5429ad60ac7b6ee8 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from datetime import datetime
from unittest import skip
from bok_choy.page_object import XSS_INJECTION
from nose.plugins.attrib import attr
from pytz import timezone, utc
from common.test.acceptance.pages.lms.account_settings import Accou... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 19,625 | [
"VisIt"
] | f58b98d420bb4ced65935fb2be9b4c5c32e23c6821372300275bd43560703de0 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Use selected CI as the active space solver for CASSCF (New in PySCF-1.3)
'''
from pyscf import gto, scf, mcscf, fci
b = 1.2
mol = gto.M(
atom = 'N 0 0 0; N 0 0 %f'%b,
basis = 'cc-pvdz',
)
mf = scf.RHF(mol).run()
mc = mcscf.CASSCF(mf, 8... | gkc1000/pyscf | examples/mcscf/50-casscf_with_selected_ci.py | Python | apache-2.0 | 449 | [
"PySCF"
] | ea7ed7d3b552c319856af7f09b42c0b3962b11fa78d3cb45c0d9f2d9b16a3a3c |
r"""*Custom errors for* ``sphobjinv``.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
5 Nov 2017
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
https://github.com/bskinn/sphobjin... | bskinn/sphobjinv | src/sphobjinv/error.py | Python | mit | 804 | [
"Brian"
] | f28b75e2c65282728845d38540db8cec0c140e73df9f81287b8d334b0cf20538 |
#
# 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 us... | alec-heif/MIT-Thesis | spark-bin/python/pyspark/mllib/clustering.py | Python | mit | 36,931 | [
"Gaussian"
] | fed8bdd062fe485c4232d89c6e5995c14c960d556fe600c9ea186394b268c4a2 |
import vtk
import numpy as np
import os
def post_proc_cfd(dir_path, vtu_input, cell_type="point",
vtu_output_1="calc_test_node.vtu",
vtu_output_2="calc_test_node_stats.vtu", N_peak=3):
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(os.path.join(dir_path, vt... | kayarre/Tools | vtk/post_proc_cfd.py | Python | bsd-2-clause | 10,052 | [
"VTK"
] | db36f59b7f220127d1ef823bdcf13280d89ce7ff233ee541ee2297cf7cfd20fb |
# Copyright 2016 Massachusetts Open Cloud
#
# 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... | CCI-MOC/moc-openstack-tools | reset-password.py | Python | apache-2.0 | 4,091 | [
"VisIt"
] | 17f33981488d14aaaa1371863db4d9f209ffbbd40c7c79fcc697bc192e009deb |
from __future__ import division
from functools import partial
import numpy as np
from scipy.stats import multivariate_normal
from menpo.feature import normalize_norm
from menpo.shape import PointCloud
from menpo.image import Image
from menpo.base import name_of_callable
from menpofit.base import build_grid
from menpo... | yuxiang-zhou/menpofit | menpofit/clm/expert/ensemble.py | Python | bsd-3-clause | 18,242 | [
"Gaussian"
] | 4e1d83c286ec502378ac556d30422fff3ea50c608152d904b91b738bfc1e199a |
# Copyright 2000-2001 by Andrew Dalke.
# Revisions copyright 2008 by Peter Cock.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import sys
# Add path to Bio
sys.path.append('... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Alphabet/IUPAC.py | Python | gpl-2.0 | 3,244 | [
"Biopython"
] | 32c44668729f195f81ead3fad52df6f187548b2ce40fd93582fa12ec360ffcc0 |
from InputParameters import InputParameters
import os, sys, shutil
# Get the real path of cluster_launcher
if(os.path.islink(sys.argv[0])):
pathname = os.path.dirname(os.path.realpath(sys.argv[0]))
else:
pathname = os.path.dirname(sys.argv[0])
pathname = os.path.abspath(pathname)
# Add the utilities/python_getp... | gleicher27/Tardigrade | moose/framework/scripts/ClusterLauncher/Job.py | Python | lgpl-2.1 | 1,896 | [
"MOOSE"
] | f3fd84c49b945d30256ae25ad44d816fc9594aba60cd45cfe78c344a35595201 |
import re
import copy
import inspect
import functools
import collections.abc
from itertools import chain
from textwrap import indent, dedent
from collections.abc import Iterable, Collection
import numpy as np
import pandas as pd
from .utils import make_args_iterable, IsNull, NotNull
from .client import inject_client
... | connectome-neuprint/neuprint-python | neuprint/neuroncriteria.py | Python | bsd-3-clause | 37,486 | [
"NEURON"
] | d4b310ea9863d4b639a9f27c99894780617f3cdb16c8477db22555892213c4ce |
# Chapter 7 Combining Different Models for Ensemble Learning
# Learning with ensembles
from scipy.misc import comb
import math
def ensemble_error(n_classifier, error):
k_start = math.ceil(n_classifier / 2.0)
probs = [comb(n_classifier, k) * error**k * (1- error) ** (n_classifier - k)
for k in range... | wei-Z/Python-Machine-Learning | self_practice/Chapter 7 Combining Different Models for Ensemble Learning part I.py | Python | mit | 15,350 | [
"exciting"
] | 2b88a3f3bd895260c580fffb768831b393bc45eba4d1ce8d2de34e899125c1ab |
from firefly_common import *
from firefly_syntaxhl import *
class TextWidget(QTextEdit):
def __init__(self, parent, syntax=False):
super(TextWidget, self).__init__(parent)
self.syntax = syntax
if syntax == "python":
hl = PythonHL(self)
#option = self.document().def... | opennx/nx.client | dlg_texteditor.py | Python | gpl-3.0 | 4,288 | [
"Firefly"
] | 43c65f2ae22320ef33bafe8e44f8ac98f17ac1a5966eab8e3617e55fca222434 |
import re, os, sys, time
from Tester import Tester
from RunParallel import RunParallel # For TIMEOUT value
class RunApp(Tester):
@staticmethod
def validParams():
params = Tester.validParams()
params.addRequiredParam('input', "The input file to use for this test.")
params.addParam('test_name', ... | jhbradley/moose | python/TestHarness/testers/RunApp.py | Python | lgpl-2.1 | 14,951 | [
"MOOSE"
] | 4279a2827c5a97cb9301ffedac3597c1f760c3d5046b30e52be4fd579f5a031b |
# -*- coding: utf-8 -*-
# Copyright 2017 Luc Saffre
# License: BSD (see file COPYING for details)
"""Test some functionalities-
This module is part of the Lino test suite. You can test only this
module by issuing either::
$ go mti
$ python manage.py test
$ python manage.py test tests.test_misc.QuickTest
or::
... | khchine5/book | lino_book/projects/mti/tests/test_misc.py | Python | bsd-2-clause | 11,820 | [
"VisIt"
] | 7ce9b8ed5abc410976e5b07c999898c51393e7f2019149aafd0b5067efdb19c7 |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/peacock/tests/input_tab/InputFileEditorWithMesh/test_InputFileEditorWithMesh.py | Python | lgpl-2.1 | 13,434 | [
"MOOSE"
] | fc4765f98850240159266e7314bd870a7b7eacae25e25ceb3733d71acf506e11 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | JackNokia/robotframework | src/robot/result/resultbuilder.py | Python | apache-2.0 | 7,130 | [
"VisIt"
] | f17fd277e9beed74b4592846aaf5a43e0f6e07ba2491ecaae3d63102909628e7 |
import numpy, os
import matplotlib.pyplot as plt
from labutil.plugins.pwscf import run_qe_pwscf, PWscf_inparam, parse_qe_pwscf_output
from labutil.objects import Struc, Dir, ase2struc, Kpoints, Constraint, PseudoPotential
from ase.io import write
from ase import Atoms
def make_struc(alat, displacement=0):
"""
... | bkoz37/labutil | samples/lab3_samples/Pbtio_sample.py | Python | mit | 3,102 | [
"ASE",
"CRYSTAL"
] | 0ead61a27c64dae31b8f05c8a2d8b627316b3b3f3f6e95524dc70d5d9236999d |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) IPython Development Team.
# Distributed under the terms of the Modified BSD License.
from __future__ import print_function
#-----------------------------------------------------------------------------
# Minimal Python version sanity check
#---------------------... | ellisonbg/vegaexplore | setup.py | Python | bsd-3-clause | 7,089 | [
"Brian"
] | e616c4da51ee70c7344905e076526d6b3edfb4a8ebeef7d0a73b4a3e2daa815a |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to convert a LAMMPS datafile into a PDB file
using a conversion dictionary or a template PDB file
Example:
lmp_data2pdb.py data.128dopc_kalp23 -o 128dopc_kalp23_initial.pdb -d 0:wat 1-128:dop 129:kalp23_leap.pdb
"""
import argparse
import os
import sy... | SGenheden/Scripts | Lammps/lmp_data2pdb.py | Python | mit | 6,725 | [
"LAMMPS"
] | b6c5a92212e6df62e29fe861d87f4867f6cced62808076d71ce1032f4569290c |
import subprocess
import os
def cat_files(file_ext, direc=False, output="cat_combination.txt",galaxy=False):
""" concatenates files together """
#cwd = os.getcwd()
try:
if direc:
os.chdir(direc)
cmd = "cat *.{} > {}".format(file_ext,output)
else:
cmd = "c... | TAMU-CPT/galaxy-tools | tools/efetch/helperFunctions.py | Python | gpl-3.0 | 1,307 | [
"Galaxy"
] | a07825d3ebb624c1ac6401984f8ede05719400fb141d8efd33950c3768b62050 |
########################################################################
# This example illustrates how a function can be used to control a reaction
# rate. This kind of calculation is appropriate when we need to link
# different kinds of physical processses with chemical reactions, for
# example, membrane curvature... | upibhalla/moose-core | tests/alpha/ex7.6_func_controls_reac_rate.py | Python | gpl-3.0 | 2,504 | [
"MOOSE"
] | dbfe610f560918055acf559aff6557cb99c87cafe3cbb674f776cd57708ce83f |
# Revisions copyright 2009 by Peter Cock. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import unittest
from Bio import SeqIO
from Bio.Sequencing import Phd
class PhdTestOne... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Phd.py | Python | gpl-2.0 | 19,847 | [
"Biopython"
] | c758e38dcca15653a1c3cfe7ea310ab2fa5edcfb5c56df87fa602760287a450d |
# gearwheel_macro.py
# the macro to generate a gearwheel.
# created by charlyoleg on 2013/06/19
#
# (C) Copyright 2013 charlyoleg
#
# This file is part of the Cnc25D Python package.
#
# Cnc25D is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by... | charlyoleg/Cnc25D | cnc25d/tests/gearwheel_macro.py | Python | gpl-3.0 | 8,047 | [
"VisIt"
] | d8d3c21d714a638253889ea9c2aef1f191c698b3c5a2d0e950ef19b56e0ad169 |
"""
This module contains helper methods for accessing operational attributes or parameters of DMS objects
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Clien... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/Utilities/DMSHelpers.py | Python | gpl-3.0 | 18,084 | [
"DIRAC"
] | bbf1292ae5fcce2cf7596dfbc4332db4b322049b0c1ab627ed6e846c69e02b2d |
#* 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 ... | nuclear-wizard/moose | python/peacock/utils/TextSubWindow.py | Python | lgpl-2.1 | 1,236 | [
"MOOSE"
] | 94af40329287226792808065b6dc340f08b80792565b3bf51a99b021a2607935 |
#!/usr/bin/env python
#JSON {"lot": "RHF/cc-pvtz",
#JSON "scf": "PlainSCFSolver",
#JSON "linalg": "DenseLinalgFactory",
#JSON "difficulty": 1,
#JSON "description": "Basic RHF example with dense matrices, includes export of Hamiltonian"}
from horton import *
import numpy as np
# DFT calculation
# ----------------... | crisely09/horton | data/examples/ftoccs/ft_optocc_dft.py | Python | gpl-3.0 | 6,041 | [
"Gaussian"
] | 44347eb0432857fed992f901a9021f2d41a39a946e0324999a4298398fd54375 |
# $HeadURL$
__RCSID__ = "$Id$"
import threading
import thread
import time
import random
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.Client.PathFinder import getGatewayURLs
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilit... | rajanandakumar/DIRAC | ConfigurationSystem/private/Refresher.py | Python | gpl-3.0 | 6,422 | [
"DIRAC"
] | fe205f880abd8621bc00b9a1a57daebe672ccb666bfb9c28e9f9e349a69bfaf3 |
# Copyright 2018 The Oppia Authors. 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 ... | oppia/oppia | core/domain/story_services.py | Python | apache-2.0 | 31,315 | [
"VisIt"
] | 3e72d9e1cb18f96d7230dd62808fb3f50fb0f02d0771c82b3a062f6ec3c91619 |
"""Call HLA alleles with assembly methods implemented in bwakit.
https://github.com/lh3/bwa/blob/master/README-alt.md#hla-typing
https://github.com/lh3/bwa/tree/master/bwakit
"""
import csv
import glob
import os
import toolz as tz
from bcbio import utils
from bcbio.distributed.transaction import file_transaction
fro... | guillermo-carrasco/bcbio-nextgen | bcbio/hla/bwakit.py | Python | mit | 3,898 | [
"BWA"
] | 287dcc8f9292e662b16c289fb8a222b99f773d665d7895672ff22a02c551b8bc |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# importusers - Import users from XML file in provided URL
# Copyright (C) 2003-2009 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 Ge... | heromod/migrid | mig/server/importusers.py | Python | gpl-2.0 | 5,614 | [
"Brian"
] | 0f3be8b88dc4c8881e8f04670d7e035a0f2df4699bd0af5486468857897d1def |
"""
Functions to calculate differential functions.
These functions can be used to calculate for example
luminosity functions, stellar and dark matter halo
functions etc.
:requires: NumPy
:version: 0.17
:author: Sami-Matias Niemi
:contact: niemi@stsci.edu
"""
import numpy as N
def diffFunctionLogBinning(data, colum... | sniemi/SamPy | astronomy/differentialfunctions.py | Python | bsd-2-clause | 8,514 | [
"Galaxy"
] | c5c48ab747e25892573ea1003934fc989debdace39e5406f4bee57c97b8b84ed |
from ...common import RTOL, ATOL, pandas
from ...cg.kdtree import KDTree
from ..util import get_points_array
from ... import cg
from ... import weights
from .. import Distance as d, Contiguity as c
from ...io import geotable as pdio
from ...io.FileIO import FileIO as psopen
import numpy as np
from ... import examples ... | sjsrey/pysal_core | pysal_core/weights/tests/test_Distance.py | Python | bsd-3-clause | 11,190 | [
"COLUMBUS",
"Gaussian"
] | 5613f9af6b42a21b93ae4fbda5715ac457a576717063c4b6911c7bfe4680af44 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function
# from future import standard_library
# standard_library.install_aliases()
from builtins import zip
from builtins import next
from past.builtins import basestring
from past.builtins import str
from builtins ... | psychopy/versions | psychopy/data/staircase.py | Python | gpl-3.0 | 86,280 | [
"Gaussian"
] | 10aa0a7e628f5c77f51fa63d672b5acb82c70f75504c29c165655d175dd84f49 |
"""
The plot module handles plotting ZPF boundaries and provides a user-facing
function `binplot` for users to plot binary phase diagrams with a similar API
as `equilibrium`.
"""
import pycalphad.variables as v
import matplotlib.pyplot as plt
from pycalphad.plot.eqplot import _axis_label
from pycalphad.plot.utils impo... | tkphd/pycalphad | pycalphad/plot/binary/plot.py | Python | mit | 4,590 | [
"pycalphad"
] | 4120596021fd692f61927c96673af9c9918a05745795355f7e82002e95b48f2b |
#! test fragment decomposition + to/from_dict
import numpy as np
import psi4
from psi4.driver import qcdb
psi4.set_output_file("output.dat", False)
def test_chgmult(expected, cgmpdict, label):
rc, rfc, rm, rfm = expected
qcdb.compare_integers(rc, cgmpdict['molecular_charge'], label + ': c')
qcdb.compare_... | amjames/psi4 | tests/python/mints13/input.py | Python | lgpl-3.0 | 4,134 | [
"Psi4"
] | 44ebaa7e279273bfbffb630ef2f3026efdb9fe8aad8a381f621b8b3e998743a9 |
import os
import pytest
import phonopy
import phono3py
current_dir = os.path.dirname(os.path.abspath(__file__))
@pytest.fixture(scope='session')
def si_pbesol():
yaml_filename = os.path.join(current_dir, "phono3py_si_pbesol.yaml")
forces_fc3_filename = os.path.join(current_dir, "FORCES_FC3_si_pbesol")
re... | atztogo/phono3py | test/conftest.py | Python | bsd-3-clause | 1,112 | [
"phonopy"
] | a31c0f0db0bc828b17574ae89d661b724eb9d4a9b20cc6bbef873961240add60 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | andrebellafronte/stoq | stoqlib/gui/widgets/searchentry.py | Python | gpl-2.0 | 10,577 | [
"VisIt"
] | 92531f14e43ccc8a9609dd8b22b121706280cbe165b2e8928e99b160d6144f7d |
# shrunk - Rutgers University URL Shortener
"""Flask application for the link server."""
from flask import Flask, render_template, request, redirect, g
import shrunk.client
import shrunk.util
# Create application
app = Flask(__name__)
# Import settings in config.py
app.config.from_pyfile("config.py", silent=True)... | ksuarz/shrunk | shrunk/linkserver.py | Python | mit | 1,630 | [
"VisIt"
] | 99ad77a97466c70e0dba1484a34cbc945141a3a8afddb941749fe0374052ad1a |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-delete
# Author : Stuart Paterson
########################################################################
"""
Reschedule the given DIRAC job
"""
__RCSID__ = "$Id$"
import DIRAC
from D... | andresailer/DIRAC | Interfaces/scripts/dirac-wms-job-reschedule.py | Python | gpl-3.0 | 1,260 | [
"DIRAC"
] | d7ee7c5d5aac2b067605ae650a04880a3bc5e1fb1dac85f5c8a049cb14a4d65f |
#!/usr/bin/python
# -*- coding: iso-8859-15 -*-
"""
Activation functions common API wrappers for caffe frameowrk.
"""
from __future__ import absolute_import
from __future__ import print_function
from caffe.net_spec import NetSpec, to_proto
from caffe import layers as L
from caffe import params as P
# sigmoid
def si... | deepnn/coffee | covfefe/frameworks/caffe/activations.py | Python | mit | 4,592 | [
"NEURON"
] | 6ee02ca04f404fb29852edc9390a408b5122776500cd827de60aed690402cded |
"""
===========================
Random projection benchmark
===========================
Benchmarks for random projections.
"""
import gc
import sys
import optparse
from datetime import datetime
import collections
import numpy as np
import scipy.sparse as sp
from sklearn import clone
from sklearn.random_projection i... | huzq/scikit-learn | benchmarks/bench_random_projections.py | Python | bsd-3-clause | 8,567 | [
"Gaussian"
] | 5030f18b90725d503dcf771c7c6f08901d3287567159808218aee018f34beec3 |
from django import forms
from django.core.exceptions import ObjectDoesNotExist
from django.contrib.admin.widgets import AdminRadioSelect, AdminRadioFieldRenderer
from edc_base.form.old_forms import BaseModelForm
from edc_constants.constants import ON_STUDY
from edc_visit_tracking.forms import VisitFormMixin
from td_m... | botswana-harvard/tshilo-dikotla | td_maternal/forms/maternal_visit_form.py | Python | gpl-2.0 | 5,743 | [
"VisIt"
] | c6fa481a8905f3f3469bf331f336ed85e8839b3582749a5bb1da310b2bb4e777 |
"""Module to skim the PDB for similar unit cells"""
from __future__ import division
__author__ = "Adam Simpkin & Felix Simkovic"
__date__ = "30 Jun 2017"
__version__ = "1.0"
import ast
import datetime
import glob
import logging
import numpy as np
import os
from simbad.core.lattice_score import LatticeSearchResult
i... | rigdenlab/SIMBAD | simbad/lattice/lattice_search.py | Python | bsd-3-clause | 11,678 | [
"CRYSTAL"
] | 057cb3649a1ac83b3717c5f280dfad7211bc946e525f12c13118d56b4301c2a3 |
# I2C PROGRAMMER FOR RTD2660 FROM RASPBERRY PI
# Optimized for PCB800099 and PCB800661 cards. This software programs the flash memory connected to RTD2660.
# Github: https://github.com/raparram/Programador-I2C-RTD2660-Rpi3
# Code base: https://github.com/mushketer888/pyrtd2660i2c
# Please! Visit this.
from smbus imp... | raparram/Programador-I2C-RTD2660-Rpi3 | prog.py | Python | unlicense | 10,810 | [
"VisIt"
] | 76b438cb3c1bae20f6e25e31503a0221a8c4992f4e135f247039b27b86dfb277 |
import numpy as np
from dftCode.geometry import gen_r_G_G2
def gaussian(sig,coeff,x):
""" Defining Gaussian charge distribution at point x in 3D space.
Args:
inputs:
sig => sigmas for each Gaussian.
coeff => coefficients for each gaussian funtion.
Note: All th... | nycmouli/PYDFT | dftCode/charge_dis.py | Python | mit | 1,694 | [
"Gaussian"
] | 0a5fa4cc647d916a51fa239f038e9c792861532f4e21d62a19daa866168bcd1d |
from fabric.api import run, env, cd, sudo
env.use_ssh_config = True
env.hosts = ["Oxygen"]
# Container used to compile the assets
NODE_CONTAINER = 'c-nodejs-tcampeu'
def deploy():
with cd('/home/projects/wordpress/www/wp-mu/wp-content/themes/tcampeu-theme'):
sudo('git pull git@github.com:openstate/tcampe... | openstate/tcampeu-theme | fabfile.py | Python | mit | 677 | [
"GULP"
] | 0f59a833b4f32e8e298fe12ee27411fa18920bee1dcb17516e65492083213bc6 |
import itertools
import pddl_types
import f_expression
import tasks
def parse_condition(alist):
condition = parse_condition_aux(alist, False)
return condition
def parse_condition_aux(alist, negated):
"""Parse a PDDL condition. The condition is translated into NNF on the fly."""
tag = alist[0]
if... | thierry1985/project-1022 | MISC/tempo-sat-temporal-fast-downward/translate/pddl/conditions.py | Python | mit | 22,170 | [
"VisIt"
] | a69e1aff2a80e5aa1e1b254a0496bf0808af878b799460f39e2e42b063c529a7 |
"""Minimal Python 2 & 3 shim around all Qt bindings
DOCUMENTATION
Qt.py was born in the film and visual effects industry to address
the growing need for the development of software capable of running
with more than one flavour of the Qt bindings for Python - PySide,
PySide2, PyQt4 and PyQt5.
1. Bu... | pyblish/pyblish-maya | pyblish_maya/vendor/Qt.py | Python | lgpl-3.0 | 65,426 | [
"VisIt"
] | 32f12c5dff42c74a9398bdcef00efb1bdf6f92cf92ec27a62b81c3644e7205b2 |
# -*- encoding: utf-8 -*-
"""
Haiku.py
Based on Twitter API
(Japanese) http://watcher.moe-nifty.com/memo/docs/twitterAPI13.txt
(Original) http://apiwiki.twitter.com/REST+API+Documentation
"""
__author__="ymotongpoo <ymotongpoo@gmail.com>"
__date__ ="$2008/11/22 09:57:30$"
__version__="$Revision: 0.10"
__credi... | ymotongpoo/restroom | 0x7d8/wisesaw/Haiku.py | Python | apache-2.0 | 11,883 | [
"MOE"
] | 52a23040302e887e6e090bf4fffa16a9565b6805af3035589243da966f49dc87 |
# GetSailfishCountInfo/GetSailfishCountInfo.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called GetSailfishCountInfo
# User admin@galaxy.org at 06/05/2015 08:32:13
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
#... | myoshimura080822/tools_of_preanalysis_on_docker_galaxy | GetQuantityCountInfo/GetQuantityCountInfo.py | Python | mit | 32,618 | [
"Galaxy"
] | f696616ff4c9e284f80f9ae23d938c096aededf7eb44e4ea6da506056e1e1171 |
#!/usr/bin/env python3
#* 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/lgp... | harterj/moose | python/mooseutils/jsondiff.py | Python | lgpl-2.1 | 2,127 | [
"MOOSE"
] | 20fc7dbb05a183f4e6e7ed834c21db1a568ff2115a64f87c48ccc67574bddb0e |
#!/usr/bin/env python
# encoding: utf-8
import re
import sys
import gzip
import pysam
import argparse
import itertools
from pypgen.misc import helpers
from pypgen.fstats import fstats
from collections import OrderedDict, defaultdict
def default_args():
"""Parse sys.argv"""
parser = argparse.ArgumentParser(fo... | ngcrawford/pypgen | pypgen/parser/VCF.py | Python | bsd-3-clause | 22,567 | [
"pysam"
] | 86d2fdae149229393ba19c55701261ddf453d608c7deafadc31a71f528354129 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
TSP solver using Concorde or OR-tools. This is much faster than the LP-formulation in
algorithms.lpsolve.tsp(). See also:
https://developers.google.com/optimization/routing/tsp
"""
import os.path as op
import os
import logging
import shutil
import numpy as np
from col... | tanghaibao/jcvi | jcvi/algorithms/tsp.py | Python | bsd-2-clause | 12,653 | [
"VisIt"
] | f41598f11090894b7e179beef7e36989dfa7ddac29c78da30ea6878657c2cd9f |
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# License: MIT License (See LICENSE.md)
# Copyright (c) 2013
# All rights reserved.
"""
lttree_check.py
The original template file format supports any variable types or file names.
However if you plan to process template files using lttree.py to c... | smsaladi/moltemplate | moltemplate/lttree_check.py | Python | bsd-3-clause | 145,656 | [
"LAMMPS"
] | e0685cd52973077ccf49815da0ab98d68293674b538f7cb90a51034d50289c1b |
# ========================================================================
#
# Imports
#
# ========================================================================
import sys
import re
import numpy as np
import copy
import dg1d.basis as basis
import dg1d.enhance as enhance
import dg1d.advection_physics as advection_ph... | marchdf/dg1d | dg1d/solution.py | Python | apache-2.0 | 19,768 | [
"Gaussian"
] | 8de2d5c1e6a2c6b410ca7bc578096ffb55efaec2f3404dbce450d9dacd712475 |
# $HeadURL$
__RCSID__ = "$Id$"
import time
import copy
import os
import os.path
import tempfile
import GSI
from DIRAC.Core.Utilities.ReturnValues import S_ERROR, S_OK
from DIRAC.Core.Utilities.Network import checkHostsMatch
from DIRAC.Core.Utilities.LockRing import LockRing
from DIRAC.FrameworkSystem.Client.Logger imp... | fstagni/DIRAC | Core/DISET/private/Transports/SSL/pygsi/SocketInfo.py | Python | gpl-3.0 | 13,365 | [
"DIRAC"
] | ee269936c5521c797ad1f20319ad25771028566c4c952eed8bc716c8a3306b0f |
""" ProxyRepository class is a front-end to the proxy repository Database
"""
__RCSID__ = "$Id$"
import time
import random
import types
import hashlib
import urllib
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Base.DB import DB
from DIRAC.Core.Security.X5... | fstagni/DIRAC | FrameworkSystem/DB/ProxyDB.py | Python | gpl-3.0 | 45,953 | [
"DIRAC"
] | bbb1db3bc9ffeffa1e44101a47f114fc075b096a89836e45c55b544fefb7875a |
"""
PySCeS - Python Simulator for Cellular Systems (http://pysces.sourceforge.net)
Copyright (C) 2004-2020 B.G. Olivier, J.M. Rohwer, J.-H.S Hofmeyr all rights reserved,
Brett G. Olivier (bgoli@users.sourceforge.net)
Triple-J Group for Molecular Cell Physiology
Stellenbosch University, South Africa.
Permission to us... | bgoli/pysces | pysces/kraken/KrakenDataTools.py | Python | bsd-3-clause | 6,758 | [
"Mayavi",
"PySCeS",
"VTK"
] | 62c783533e52ad6a8a69160cf0ca71eaf30116e6bb3fbb69744419c93ce89900 |
# Copyright 2018 Amazon.com, Inc. or its affiliates. All Rights Reserved.
# SPDX-License-Identifier: Apache-2.0
import numpy as np
from scipy import special
# some variables
sq2 = np.sqrt(2)
eps = np.finfo(np.float32).eps
l2p = np.log(2) + np.log(np.pi)
def joint_min(mu: np.ndarray, var: np.ndarray, with_derivativ... | EmuKit/emukit | emukit/bayesian_optimization/epmgp.py | Python | apache-2.0 | 7,593 | [
"Gaussian"
] | edeb72eaf6e99bda56f59d9d0a16fe2c764fc2eebd87b822ccd1e862d5648b7d |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
Calibration module:
This module contains the classes for
1. Calibrate: Base class for specifying the parameters for
calibration a... | joshgabriel/MPInterfaces | mpinterfaces/calibrate.py | Python | mit | 60,446 | [
"VASP",
"pymatgen"
] | b15f201edd0d25a3837e42cbce52b5d943a12cddb5befc3fb06746b58d4bceab |
# -*- coding: ascii -*-
# ^ Ascii chars are the norm in Python 2.x source code.
# This'll make a 3.x interpreter panic when any unicode sneaks in.
from lib import moddb
def populate_catalog(mod_db):
mod_info = moddb.ModInfo()
mod_info.set_title( "A Strange New Galaxy" )
mod_info.set_author( "Metzelmax" )... | Grognak/Grognaks-Mod-Manager | lib/default_moddb.py | Python | gpl-3.0 | 127,641 | [
"Amber",
"BLAST",
"CRYSTAL",
"Firefly",
"Galaxy"
] | 07a73e68dade9c5b7144110611c7b3f72b164700c8e38a0e24adebfbdf61962e |
"""
Note Snatcher: a simple notes organizer
Copyright (C) 2015 Brian Ratliff
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
... | brianratliff/notesnatcher | setup.py | Python | gpl-3.0 | 845 | [
"Brian"
] | 72950ac7b743a2c1b2e1495b16eec104dff38af4cc9b138fe08e1ff1d48394f2 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | yugangzhang/scikit-beam | skbeam/core/fitting/__init__.py | Python | bsd-3-clause | 3,590 | [
"Gaussian"
] | f7cd1bed86c8ff107c46c251c25258e1c692355df9668a9e8bffa38dc30a7e16 |
try:
from django.urls import reverse
except ImportError:
from django.core.urlresolvers import reverse
from tastypie import authorization
from tastypie.authentication import MultiAuthentication
from crits.certificates.certificate import Certificate
from crits.certificates.handlers import handle_cert_file
from c... | Magicked/crits | crits/certificates/api.py | Python | mit | 4,269 | [
"Amber"
] | a22b1ab29a6f6f2638efa526701d2d4572f7235d168a9b71705b91b1c04cec47 |
"""Database schemas, examples, and tools"""
import copy
from warnings import warn
from cerberus import Validator
from .sorters import POSITION_LEVELS
SORTED_POSITION = sorted(POSITION_LEVELS.keys(), key=POSITION_LEVELS.get)
ACTIVITIES_TYPE = ["teaching", "research"]
AGENCIES = ["nsf", "doe"]
APPOINTMENTS_TYPE = ["g... | scopatz/regolith | regolith/schemas.py | Python | cc0-1.0 | 178,726 | [
"Brian",
"VisIt"
] | 06e97da058f122cb2cd96d5e550ed77bfb7bcc8dea5f2814d67ed8f83a14e5d7 |
# Script to show walking a WarTune character around in a circle
# NobodyCam@gmail.com 10.5.2013
from splinter import *
from Tkinter import *
from pymouse import PyMouse
from pykeyboard import PyKeyboard
from gi.repository import Gtk
from gi.repository import Wnck
import time
# define the steps for WarTune
def WarT... | NoBodyCam/WarTuneLogin | WarTuneAutomation.py | Python | apache-2.0 | 5,295 | [
"VisIt"
] | 25b4af35cdf825c325478cfd077480e81ae8a4bc53ad13c9d95b1a15fae552d6 |
# -*- 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 publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/generic/generic_GetIPAddressV4.py | Python | gpl-3.0 | 4,542 | [
"ORCA"
] | cb1dfb63b4c15bd06f8a0de78a678aa62fb7d1d57192c92c5449ba2e21d86272 |
import os
from MooseMarkdown import MooseMarkdown
from markdown.util import etree
def get_collection_items(info_objects, show_hidden=False):
"""
Returns li html elements for each object in a system.
Input:
info_objects: A list of MooseInfoBase objects to collect.
"""
items = []
# Alphabe... | backmari/moose | python/MooseDocs/extensions/__init__.py | Python | lgpl-2.1 | 3,261 | [
"MOOSE"
] | db2aa3b9d65de4602dcd10a2be04cc388e28931efd9fe8103996eb6c2b4d8350 |
# Run: python vtuToTxt.py <filename.vtu> <meshfile.k> <matsfile.k> <bone_offset>
# Ex: python vtuToTxt.py material_mapped_mesh.vtu meshfile.k matsfile.k 10000000
# Reads in an anstructured grid in vtu format and returns a mesh file containing elements and nodes, and mats file
# containg parts and materials in LS-DYNA f... | araex/mitk-gem | Scripts/VtuToKfile_example.py | Python | gpl-3.0 | 3,154 | [
"VTK"
] | c15ad7fe86796d5dc72f4f05f95f4bf17762f09bf7ff124b4d94440fe9ef59d6 |
# Test to make sure CLONEs were packaged correctly using short MD simulations.
#
# John D. Chodera <choderaj@mskcc.org> - 27 Mar 2013
#
# PREREQUISITES
#
# * OpenMM
# http://simtk.org/home/openmm
# PARAMETERS
import sys
from ast import literal_eval
# XXX NOTE: process_only_these_targets is not used in this script. I... | choderalab/Ensembler2 | scripts/attic/test-openmm-project.py | Python | gpl-2.0 | 4,974 | [
"OpenMM"
] | 6b02c1fa2265743f189e9419b9ef46ae9f1a07867a768318a0074aa3b97dfd96 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2005-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012 Gary Burton
# Copyright (C) 2... | dermoth/gramps | gramps/gui/viewmanager.py | Python | gpl-2.0 | 67,656 | [
"Brian"
] | 42691d73b564807bb4998dd7ef173f105cc842752dda59b41ecb298f11c10798 |
#################################################################################
##____ ___ _ _ ____ ___ _____ ____ ___
#| _ \_ _| \ | | __ ) / _ \_ _| |___ \ / _ \
#| |_) | || \| | _ \| | | || | __) || | | |
#| __/| || |\ | |_) | |_| ... | Curbfeeler/PinbotFromES | attract.py | Python | mit | 25,138 | [
"Brian"
] | 39bac8a3ecd875c5768c9b103e4c0ae981baf3fd54ea3b2afa827399ddd32569 |
from __future__ import division, print_function
import unittest
import inspect
import sympy
from sympy import symbols
import numpy as np
from symfit.api import Variable, Parameter, Fit, FitResults, Maximize, Minimize, exp, Likelihood, ln, log, variables, parameters
from symfit.functions import Gaussian, Exp
import scip... | Eljee/symfit | symfit/tests/tests.py | Python | gpl-2.0 | 23,874 | [
"Gaussian"
] | 4d25a915908ed3b4ebb64d7aa66b71be99324dabf027e1a00fd9bd448e1ede58 |
##
# Copyright 2012-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | torbjoernk/easybuild-framework | test/framework/modules.py | Python | gpl-2.0 | 18,269 | [
"NetCDF"
] | ef365eb1cc1d3bd190ee8b841c8db42a5c1f3cb8db2170be5d570b38d2f5c31f |
import ast
import builtins
import io
import tokenize
import unicodedata
import uuid
class IntegerDivisionWrapper(ast.NodeTransformer):
"""Wrap all int divisions in a call to :class:`~fractions.Fraction`."""
def visit_BinOp(self, node):
def is_integer(x):
if isinstance(x, ast.Num) and isin... | diofant/diofant | diofant/interactive/session.py | Python | bsd-3-clause | 3,809 | [
"VisIt"
] | d1960e4fdb77b3786fbdb50eea2e410f70e9ee50aee2fb92365fbf04910164ea |
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