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#(c) 2012 Massachusetts Institute of Technology. All Rights Reserved
# Code written by: Maksim Imakaev (imakaev@mit.edu)
import numpy
import numexpr
import mirnylib.numutils
class gradientDescentDomains:
"""
A strange class to find domains by finning exponential model.
Domains are fitted to the formula
... | bxlab/HiFive_Paper | Scripts/HiCLib/mirnylab-hiclib-460c3fbc0f72/src/hiclib/domainSearch.py | Python | bsd-3-clause | 5,581 | [
"MOE"
] | bc4b8d988802268a19afad01c0bcb5b50edc00cb00615450ee7d9570c3488460 |
"""
Tests for the Course Outline view and supporting views.
"""
import datetime
import json
import re
from completion import waffle
from completion.models import BlockCompletion
from completion.test_utils import CompletionWaffleTestMixin
from django.contrib.sites.models import Site
from django.urls import reverse
from... | Stanford-Online/edx-platform | openedx/features/course_experience/tests/views/test_course_outline.py | Python | agpl-3.0 | 27,047 | [
"VisIt"
] | 4cb28165c70b4b62c13240cbbb746b1dbc9f89aa5a8153b1684153bdc4f2e4cf |
# From: Bayesian Models for Astrophysical Data, Cambridge Univ. Press
# (c) 2017, Joseph M. Hilbe, Rafael S. de Souza and Emille E. O. Ishida
#
# you are kindly asked to include the complete citation if you used this
# material in a publication
#
#Code 10.6 Multivariate Gaussian mixed model in Python, using Stan,
... | astrobayes/BMAD | chapter_10/code_10.6.py | Python | gpl-3.0 | 3,085 | [
"Gaussian"
] | b143cdeb7170297bae3bc5b134a7b68167a9e7df8365079dc722b9eac9d54bc3 |
# -*- coding: utf-8 -*-
import os
import re
import sys
import json
import types
import logging
import requests
import ssl
from requests.exceptions import ConnectionError
from requests.packages.urllib3.exceptions import ProtocolError
from .decorators import *
from requests_oauthlib import OAuth1, OAuth1Session
if s... | edsu/twarc | twarc/client.py | Python | mit | 34,597 | [
"VisIt"
] | 2d352972903c3a5ac282f65c8fb891c3a4af598a465ea6b8c31579b7bcec4bfc |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
import tempfile
import subprocess
from subprocess import check_call
import os
from os import path
import sys
import shutil
from ZIBMolPy.ui import userchoice, userinput, Option, OptionsList
from ZIBMolPy.io.topology import Topology, preprocess
options_desc = OptionsList... | CMD-at-ZIB/ZIBMolPy | tools/gromacs_topology_merger.py | Python | lgpl-3.0 | 4,818 | [
"Gromacs"
] | dccba259fbcb3ece58bd5a1a5b6aa29278b24637b36915ad0fd89fda0053e477 |
"""
Galaxy root package -- this is a namespace package.
"""
# Starting somewhere in 2.5.x, Python on Mac became broken - despite being fat,
# the machine portion of the platform is not set to 'fat'.
#
# For more, see:
#
# http://bugs.python.org/setuptools/issue19
#
import os, sys
from distutils.sysconfig import get_co... | volpino/Yeps-EURAC | lib/galaxy/__init__.py | Python | mit | 1,129 | [
"Galaxy"
] | 73d395e8ca9ad641d2254b8ec4a4aa7c093fe7015378a84db9b4611297198453 |
from six import iteritems
import numpy as np
from numpy import zeros, array, cross, amax, amin
from numpy.linalg import norm
import vtk
from vtk import vtkQuad
from pyNastran.converters.shabp.shabp import SHABP
from pyNastran.gui.gui_objects.gui_result import GuiResult
is_shabp = True
class ShabpIO(object):
de... | saullocastro/pyNastran | pyNastran/converters/shabp/shabp_io.py | Python | lgpl-3.0 | 10,196 | [
"VTK"
] | d4c87a709c968095d9b041c65e104d198b31372ab497667a742599abcedb46a6 |
import modeller
import modeller.scripts
import IMP
import IMP.test
import IMP.modeller
import IMP.core
class Tests(IMP.test.TestCase):
def get_environ(self):
"""Get a Modeller environ object"""
if not hasattr(self, '_modeller_environ'):
# Speed tests up a little by only creating this ... | shanot/imp | modules/modeller/test/test_load_model_atoms.py | Python | gpl-3.0 | 5,038 | [
"CHARMM"
] | 2272a28b42926d28acb3285147911eb542f0ed69dbbe6b86579f149c45a925fb |
"""
This example demonstrates the use of caches
"""
from flask import Flask, render_template_string, redirect, current_app
from sqlalchemy import create_engine, MetaData
from flask_login import UserMixin, LoginManager, login_user, logout_user, current_user
from flask_blogging import SQLAStorage, BloggingEngine
from fla... | gouthambs/Flask-Blogging | example/blog_cache.py | Python | mit | 2,754 | [
"DIRAC"
] | 17b6f58aa79597a983d6d2d8551f0df645861f313b8af7af6e5abd0aaac452b2 |
# coding=utf-8
import sys
reload(sys)
sys.setdefaultencoding('utf-8')
import requests
import logging
import time
import json
import lxml.html
import traceback
import urllib
import re
import os
from constant import my_headers, my_proxies
date = time.strftime("%Y-%m-%d", time.localtime())
import random
def randHeade... | chuncaohenli/clp_project | spider_jd/newspider.py | Python | mit | 5,669 | [
"Galaxy"
] | 773207022df37866432eaba772682582231894857302c39b18ad7d2c40240e0c |
# -*- coding: utf-8 -*-
#
# This hook sends episode updates to monthly.moe and marks them as watched.
#
# To use, copy this file to ~/.trackma/hooks/ and fill in the access token.
ACCESS_TOKEN = ""
if not ACCESS_TOKEN:
raise Exception("You must provide the Monthly.moe HTTP API access token..")
import urllib.pars... | MadeOfMagicAndWires/trackma | hooks/monthly.py | Python | gpl-3.0 | 1,293 | [
"MOE"
] | 3383b0cb336bdd4d0ed06c944d8b54f53474324141b9376275ca2351a7d0866d |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | symbolic_functionals/syfes/dataset/dataset.py | Python | apache-2.0 | 28,244 | [
"PySCF",
"pymatgen"
] | 9ace6dd8cd223757a9b9d18c812d73c5911a72b280d63d89b0ba2e3417c4f7a7 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import json
from datetime import datetime, timedelta
import ddt
from openedx.core.lib.tests import attr
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.common.auto_auth import AutoAuthPage
from ...pages.common.logout import ... | ahmedaljazzar/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 36,063 | [
"VisIt"
] | 5b5e4f44f50577101e4ac63a1eb2f8c30eee130fa42904211f1e6b06c0a46bbe |
# -*- coding: utf-8 -*-
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2016 Brian Langenberger
#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 ver... | tuffy/python-audio-tools | docs/programming/source/conf.py | Python | gpl-2.0 | 7,303 | [
"Brian"
] | 543c26bfa7ee90883a856e8df3c4e229cd0f3ccaf093c367cabe7d363a0e8280 |
import numpy as np
from astropy.modeling.models import custom_model
'''This class is just 2* Gaussian + constant.
Can be removed once astropy supports fitting of composite models.
Also (known bug, but not fixed yet), fitting does not work with bounds.
However, without bounds the fit will just put the gauss in the... | hamogu/TWHya | utils.py | Python | gpl-2.0 | 6,405 | [
"Gaussian"
] | 4dfef02a42806580654b6f97cc9ed30acf761eda856d58764690c617d3b90b5c |
""" Contains the Flasher parent class. """
# flasher.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
from mpf.system.device import Device
class Flasher(D... | spierepf/mpf | mpf/devices/flasher.py | Python | mit | 2,808 | [
"Brian"
] | ae9656d1e24126644d28876fbff427ebf815fff1eb19e96b90f172cd1772eabd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import json
import os
import unittest
from pymatgen.core.composition import Composition
from pymatgen.analysis.structure_prediction.substitution_probability import (
SubstitutionPredictor,
Substitutio... | gmatteo/pymatgen | pymatgen/analysis/structure_prediction/tests/test_substitution_probability.py | Python | mit | 3,710 | [
"pymatgen"
] | fc3447a317d441cc524105ceea9294d8ab3d3ef3244aabb10929d6497fea92b1 |
#!/usr/bin/env python3
#alphabetical constants
__a = 65
__z = 90
__A = 97
__Z = 122
#constants for user input options in text_step and word_step functions
__ENTER = ''
__W_NEXT_INST = '>'
__W_PREV_INST = '<'
__INSTRUCTIONS = 'qa'
__YES = __NEXT_LINE = 1
__NO = __QUIT = __FIRST = 0
__NOMOVE = -1
"""
Karl Toby Rosenbe... | KTRosenberg/Text-Analyzer-and-Step-through-Viewer | old/Text_Analyzer_ver_2_9_main.py | Python | mit | 52,013 | [
"VisIt"
] | 74ec83b799b6a29ad5f14136d23cf24abe0bc897deb4cf3a797cb451d41e1036 |
#!/usr/bin/env python3
##########################################################################
#
# Copyright 2012 Jose Fonseca
# All Rights Reserved.
#
# 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 t... | apitrace/apitrace | scripts/unpickle.py | Python | mit | 9,124 | [
"VisIt"
] | f4e4be637bb3dd474ca54d8f8f9aeb26019c8187d241ac5c63707d46c9c891f7 |
# coding: utf-8
from __future__ import unicode_literals
import unittest
import os
import json
from pymatgen.core.periodic_table import Specie
from pymatgen.core.composition import Composition
from pymatgen.structure_prediction.substitutor import Substitutor
def get_table():
"""
Loads a lightweight lambda t... | Dioptas/pymatgen | pymatgen/structure_prediction/tests/test_substitutor.py | Python | mit | 1,524 | [
"pymatgen"
] | f06b1648e4afad4e376aa05e5eb7cae003402be9dff57369a63d340a8b6466c7 |
"""
Contains an abstract base class that supports chemically aware data splits.
"""
from __future__ import division
from __future__ import unicode_literals
import random
__author__ = "Bharath Ramsundar, Aneesh Pappu "
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import tempfile
import nu... | ktaneishi/deepchem | deepchem/splits/splitters.py | Python | mit | 36,106 | [
"RDKit"
] | 820b9d77fdc4e3d584ec710301ffba010880a9dd64920ed3bbd093c0887d2214 |
import os
from setuptools import setup, find_packages
setup(name='pychiptools',
version='0.0.1',
packages=find_packages(),
description='pychiptools is a Python module to analyze ChIP-seq NGS data',
author='Patrick Lombard',
author_email='ptk.lmb55@gmail.com',
# packages=['pychiptools... | pdl30/pychiptools | setup.py | Python | gpl-2.0 | 1,191 | [
"pysam"
] | d5489102da5baf2c66df6fa0a9a3d3cc62d50256af6baeb6531f229d3b37acba |
"""
Two-dimensional pattern generators drawing from various random
distributions.
"""
import warnings
import numpy as np
import param
from param.parameterized import ParamOverrides
from holoviews.core import SheetCoordinateSystem
from .patterngenerator import PatternGenerator
from imagen import Composite, Gaussian
f... | ioam/imagen | imagen/random.py | Python | bsd-3-clause | 24,422 | [
"Gaussian"
] | f1e0daec8b26f6e5dd24e73257755628bd88f48d7ebd1fe903e3984929339e21 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
The dwi module of niftyfit, which wraps the fitting methods in NiftyFit.
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath(... | mick-d/nipype | nipype/interfaces/niftyfit/dwi.py | Python | bsd-3-clause | 21,609 | [
"Gaussian"
] | 32c98f9a3c172ca591159f68dff28e0dba6851ffaca311c59b20b6468006f62c |
{
"name" : "Database Auto-Backup & Backup Auto-Transfer to FTP server",
"version" : "6.1.1",
"author" : "Emipro Technologies",
"website" : "http://www.emiprotechnologies.com",
"category" : "Generic Modules",
"description": """
Key feature of this module includes,
--... | odoousers2014/LibrERP | db_backup_ept/__openerp__.py | Python | agpl-3.0 | 1,661 | [
"VisIt"
] | 5270460f5b659e83b0a3b92696ffe2d733cdc8b68f13d9d695a2da93902c5ae8 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlp... | chadgates/locmaster | config/urls.py | Python | bsd-3-clause | 1,584 | [
"VisIt"
] | 3badb75d9cccfb45b0e1221c39f0a0a8bea69591475200bb2a721e3a6b6c5ccb |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/plan_county.py | Python | apache-2.0 | 12,724 | [
"VisIt"
] | 9788469487436b7fea08cbb8204228a3386497656c96609092026a69784bd1da |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | tlksio/tlksio | env/lib/python3.4/site-packages/pylint/checkers/variables.py | Python | mit | 25,427 | [
"VisIt"
] | adfa321876e9025cbf7f80e9b883b31414823a1cdbcd4d205bae0ec7b78bceb9 |
class Solution(object):
# [....... [........ [.. [.. [..[....... [.. .. [..[.. [..[........
# [.. [.. [.. [.. [..[.. [..[.. [.. [.. [..[.. [.. [.. [..
# [.. [.. [.. [.. [.. [..[.. [.. [.. [.. [.. [.. [..
# [. [.. ... | TanakritBenz/leetcode-adventure | kth-smallest-in-bst.py | Python | gpl-2.0 | 3,214 | [
"VisIt"
] | fe38d04cd9ba6795e5a208dd66ccedf41d6254265c1bb9d74c079f94e5087dc5 |
import matplotlib.pyplot as plt
from sunpy import map
import numpy as np
import os
import copy
from skimage.feature import canny
from scipy import ndimage
def mask_sun(array,pxval):
#This function will apply a centered filled circular mask
#of radius rad and pxval values to the input array
r=172 #Empirical... | kkozarev/mwacme | src/lasco/lasco_find_shocks_bdiff.py | Python | gpl-2.0 | 2,708 | [
"Gaussian"
] | 916ee5d637c6d55fdc2d4e5257e937afff7e8f859b36c0475a18c3c5c958ce7a |
import netCDF4 as nc4
import numpy as np
import time as tm
import datetime as dt
def writeBasicNetcdf(ncname,types,deepcoszero,shallowconvmin,minZdiff,truncZconvthres,
dBZformaxconvradius,weakechothres,backgrndradius,maxConvRadius,
minsize,startslope,maxsize,title,institution,... | swpowell/raintype_python | uw_raintype/netcdf_io.py | Python | gpl-3.0 | 19,400 | [
"NetCDF"
] | cb646bed1aa5866672f51b741d293e6bb5e530d69b318bd1b27c9fc13a138fd2 |
from datetime import time
import brian
from perceptchoice.model.monitor import WTAMonitor
brian.set_global_preferences(useweave=True,openmp=True,useweave_linear_diffeq =True,
gcc_options = ['-ffast-math','-march=native'],usecodegenweave = True,
usecodegenres... | jbonaiuto/perceptual-choice-hysteresis | src/python/perceptchoice/model/network.py | Python | gpl-3.0 | 16,647 | [
"Brian",
"NEURON"
] | f2f40cd80460a8abc2aeeb1cc1c1771508a94c42012436c7e57391b3a34e7e21 |
"""Py-Phished v1.0
Ben Floyd, License: BSD-3 Clause
Py-Phished is a python-based webserver/email client for internal phishing campaigns.
The goal is to test company training efficacy and email safety and assess the overall response
rate to malicious phishing attempts. The emailer can be controlled via the site w... | pwna5aurus/py-phished | pyphish.py | Python | bsd-3-clause | 8,804 | [
"VisIt"
] | 7e6850fb8eae6c0813e6674bd37f35c891f055470884777b06f2f6c4db830353 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/Zero.py | Python | gpl-3.0 | 7,206 | [
"ESPResSo"
] | 8e35142086ccc2574734bc13aaf8ec9e6dc6b32531c16cac51dc3897891aed65 |
#!/usr/bin/env python
# encoding: utf-8
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2009-2011 by the RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of thi... | enochd/RMG-Py | rmgpy/reaction.py | Python | mit | 55,491 | [
"RDKit"
] | 6ce80462e45010c0787dc4c054b90521d5b0b65ceabd726892ef76b01e31506f |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Wed Nov 19 00:18:55 2014
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
(at your option) any later version.
... | SamWitte/Codds_DarkMatter | src/Data/PICASSO.py | Python | gpl-2.0 | 2,403 | [
"DIRAC"
] | 8e2dce37e6f3915957545e519ac3d461d295347a1b98369878896f8a5238d224 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (gregory_r_warnes@groton.pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
###################... | intip/da-apps | plugins/da_centrallogin/modules/soappy/SOAPpy/NS.py | Python | gpl-2.0 | 3,735 | [
"Brian"
] | 49777d4cf079054f801b36f7f70d24903e8f4698eb6361c176478c2aa9a9e772 |
"""Test automatically write out of restart files"""
import os
from glob import glob
from gpaw import GPAW
from ase import Atom, Atoms
from gpaw.test import equal
restart = 'gpaw-restart'
result = 'gpaw-result'
# H atom:
H = Atoms([Atom('H')])
H.center(vacuum=3.0)
calc = GPAW(gpts=(32, 32, 32), nbands=1)
calc.attac... | ajylee/gpaw-rtxs | gpaw/test/restart2.py | Python | gpl-3.0 | 1,140 | [
"ASE",
"GPAW"
] | 8936f4391da96abb44fbe9b707e440bf0305ac00a9090549d95bf3fd4d42faf2 |
# -*- coding: utf-8 -*-
"""
Gaussian Model of Point-like Sources
====================================
Simple class to do Gaussian Fitting to a spot.
:requires: NumPy, astropy
Created on Thu Apr 20 16:42:47 2017
:author: Ruyman Azzollini
"""
# IMPORT STUFF
from pdb import set_trace as stop
import numpy as np
f... | ruymanengithub/vison | vison/point/gauss.py | Python | gpl-3.0 | 2,569 | [
"Gaussian"
] | 56617eaf4857291938c85c653fbb87740497bc7b755f3100373b88733dca745c |
"""
The iHMPSession module allows users to easily establish a connection
to an Open Science Data Framwork (OSDF) instance operated for the
Integrative Human Microbiome Project (iHMP).
"""
import importlib
import logging
from osdf import OSDF
from cutlass.Util import *
class iHMPSession(object):
"""
The iHMP S... | ihmpdcc/cutlass | cutlass/iHMPSession.py | Python | mit | 9,706 | [
"VisIt"
] | 9ede1aac626721281fd8b098edb4f0d6d489a5c36aad650a7e7d3bcd0d530250 |
# -*- coding: utf-8 -*-
import json
from io import StringIO
from operator import itemgetter
from django.shortcuts import get_object_or_404
from guardian.shortcuts import assign_perm
from catmaid.control.authentication import (can_edit_all_or_fail,
can_edit_or_fail, PermissionError)
from catmaid.control.common i... | tomka/CATMAID | django/applications/catmaid/tests/apis/test_treenodes.py | Python | gpl-3.0 | 59,687 | [
"NEURON"
] | cf6e978e7c02e39b4d3a0975e71a484f72862a3eb3c8da189562aee76fa106ee |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Version: Sat 4 Jan 2014
# Based on notebook cutouts.ipynb.
#
"""
Create cutouts around a point in the sky.
"""
# from __future__ import unicode_literals # Some numpy functionality crashes,
# from __future__ import print_function
import os
import datetime as dt
impo... | xidus/ted | ted/sdss/cutouts/__init__.py | Python | bsd-3-clause | 87,489 | [
"Galaxy",
"Gaussian"
] | 44e47fadaabfcf0477648ca20359461bc3614cb3df3261ddfe4b4d9f2552b44b |
# $Id$
# Hop --- a framework to analyze solvation dynamics from MD simulations
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
#
# 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... | Becksteinlab/hop | hop/constants.py | Python | gpl-3.0 | 2,552 | [
"MDAnalysis"
] | 69f56a418e38751db6992edb52f0b59db2ad4e664a5f79801a81ba9eb24c45f7 |
# Copyright (C) 2021 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/python-graphs | python_graphs/program_graph.py | Python | apache-2.0 | 35,260 | [
"VisIt"
] | 6e0ec546112583267ba95d364fe22a4f096cf88ebc6305c763137a0e5e05ed1d |
#! /usr/bin/env python
"""
Module with frame/cube filtering functionalities
"""
from __future__ import division
__author__ = 'C. Gomez @ ULg'
__all__ = ['frame_filter_highpass',
'frame_filter_lowpass',
'cube_filter_highpass',
'cube_filter_iuwt',
'frame_filter_gaussian2d',
... | henry-ngo/VIP | vip_hci/var/filters.py | Python | mit | 12,968 | [
"Gaussian"
] | f9470fde982b8ff5995a7a1b8f870d06156f616b20b04e77d1f00b6cd98b4c85 |
import PythonQt
from PythonQt import QtCore, QtGui
import director.objectmodel as om
import director.visualization as vis
from director import affordanceitems
from director import lcmUtils
from director import callbacks
from director import cameracontrol
from director import splinewidget
from director import transformU... | RobotLocomotion/director | src/python/director/robotviewbehaviors.py | Python | bsd-3-clause | 22,537 | [
"VTK"
] | f2ac105ef5202cf6e30bdf51d7b62f75cab883fbc78fa4599eaa9d318021502e |
import numpy as np
def linear(r):
return -r
def thin_plate_spline(r):
if r == 0:
return 0.0
else:
return r**2*np.log(r)
def cubic(r):
return r**3
def quintic(r):
return -r**5
def multiquadric(r):
return -np.sqrt(r**2 + 1)
def inverse_multiquadric(r):
return 1/np.s... | anntzer/scipy | scipy/interpolate/_rbfinterp_pythran.py | Python | bsd-3-clause | 6,242 | [
"Gaussian"
] | 3c30425550c4548ade4c98d9f66ed93a241515ad72e7efe308ab023945aca246 |
#
# Copyright (C) 2013,2014 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... | KonradBreitsprecher/espresso | testsuite/wang_landau_reaction_ensemble.py | Python | gpl-3.0 | 5,305 | [
"ESPResSo"
] | 2212023bc141874a87ab13d4a3b68b6bb79189569dae66cf611d48d6976cd5b1 |
from __future__ import print_function
import os
import sys
sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..", ".."))
from pattern.graph.commonsense import Commonsense
# A semantic network is a graph in which each node represents a concept
# (e.g., flower, red, rose) and each edge represents a relation b... | shubhangiKishore/pattern | examples/06-graph/06-commonsense.py | Python | bsd-3-clause | 2,521 | [
"Octopus"
] | 15c0f98b3d65d9dc307693917ca030df885d6bc42bd24613d91063ec9f870fcc |
#!/usr/bin/python
""" Main routine to derive glacier geometry from velocity and elevation data
"""
from __future__ import division, print_function
import os, sys, copy, warnings
import datetime
import numpy as np
import matplotlib.pyplot as plt
import dimarray.geo as da
from dimarray.compat.basemap import interp
fro... | perrette/webglacier1d | outletglacierapp/models/mesh.py | Python | mit | 25,755 | [
"Gaussian",
"NetCDF"
] | 0776bf7de07a1887e63258daeb27e9d8b113be7387a80c0ce4e52ab7002d3e42 |
"""
Routines for creating summaries fro user interfaces of some core agents
"""
__licenses__ = """
This file is part of RAPD
Copyright (C) 2011-2018, 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 pub... | RAPD/RAPD | src/plugins/subcontractors/summary.py | Python | agpl-3.0 | 85,198 | [
"CRYSTAL",
"Jmol"
] | 4d186e3842881027ba6d6fb86446abf099834cf3158b53b2a94d67bbbed4fae0 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkExtractGrid(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vt... | nagyistoce/devide | modules/vtk_basic/vtkExtractGrid.py | Python | bsd-3-clause | 495 | [
"VTK"
] | 7bf13a97f4366ca69340a417589813c2137d7aebe48249051b12816d0b353db9 |
from typing import List, TypeVar
from Firefly import logging
from Firefly.const import EVENT_ACTION_ANY, EVENT_ACTON_TYPE, SOURCE_LOCATION, SOURCE_TRIGGER, TIME
from Firefly.helpers.events import Event
from Firefly.helpers.subscribers import verify_event_action, verify_event_action_time
"""
An individual trigger shou... | Firefly-Automation/Firefly | Firefly/automation/triggers.py | Python | apache-2.0 | 13,877 | [
"Firefly"
] | 0c45d2b2e2343e2a4c3cfb42d55de27af21610246f533f2776a426070c3aa8bd |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# 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 ... | shakamunyi/ansible | v2/ansible/cli/galaxy.py | Python | gpl-3.0 | 21,564 | [
"Galaxy"
] | d202f765084be9fb36d987eb2aefc7bf92abada85254159b399ca09524dc4eda |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/common/tables.py | Python | gpl-3.0 | 2,218 | [
"Brian"
] | 729a4d314b0ba97b937a3f502b6e16ad9bf579a99eeeca72dbc121abd3a5e6b4 |
# Copyright 2016 The TensorFlow 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 applica... | zasdfgbnm/tensorflow | tensorflow/contrib/py2tf/converters/side_effect_guards.py | Python | apache-2.0 | 7,005 | [
"VisIt"
] | 837285df39ae61d2c7efed2387b5ee7b53d58013bf811ae6800ae68ce4bc5195 |
# coding: utf-8
# Copyright (c) 2009-2021 The Regents of the University of Michigan
# This file is part of the HOOMD-blue project, released under the BSD 3-Clause
# License.
# Maintainer: joaander / All Developers are free to add commands for new
# features
from hoomd.md import _md
import hoomd
from hoomd.integrate ... | joaander/hoomd-blue | hoomd/minimize/fire.py | Python | bsd-3-clause | 8,315 | [
"HOOMD-blue"
] | f72fa729640d2983da2684b33f4119414e04e2a075992782d474e0edb18ef028 |
import sys
import os
import deepchem
import tempfile, shutil
from bace_datasets import load_bace
from deepchem.hyper import HyperparamOpt
from sklearn.ensemble import RandomForestRegressor
from sklearn.ensemble import RandomForestClassifier
from deepchem.models.sklearn_models import SklearnModel
from deepchem import me... | bowenliu16/deepchem | examples/bace/bace_rf.py | Python | gpl-3.0 | 4,656 | [
"CRYSTAL"
] | 7aead467059613b9b0c7e259e9b3052b5716a55b0e3e0d8a6e93d0dce940693c |
#!/usr/bin/env python
import vtk
def main():
fileName, dataPoint = get_program_parameters()
colors = vtk.vtkNamedColors()
thickness = list()
displacement = list()
for i in range(0, 10):
thickness.append('thickness' + str(i))
displacement.append('displacement' + str(i))
read... | lorensen/VTKExamples | src/Python/Visualization/Blow.py | Python | apache-2.0 | 5,773 | [
"VTK"
] | a907ce6378a6a573d913183cb8d6e476cce2ccec6f5f54649fc5468f9b79a3b6 |
''' <h1>Library for combined x-ray and neutrons simulations.</h1>
<p>The neutron simulations is capable of handling non-magnetic,
magnetic non-spin flip as well as neutron spin-flip reflectivity. </p>
<h2>Classes</h2>
<h3>Layer</h3>
<code> Layer(b = 0.0, d = 0.0, f = 0.0+0.0J, dens = 1.0, magn_ang = 0.0, magn = 0.0, s... | joshp123/genx | models/spec_nx.py | Python | gpl-3.0 | 19,561 | [
"Gaussian"
] | 0a36bc52a04abcd39eb1448e87185630638f9fe122e6c582c66fe60eb8ae608a |
# Copyright (c) 2014-2015 Bruno Daniel <bruno.daniel@blue-yonder.com>
# Copyright (c) 2015-2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2016-2019 Ashley Whetter <ashley@awhetter.co.uk>
# Copyright (c) 2016 Derek Gustafson <degustaf@gmail.com>
# Copyright (c) 2016 Glenn Matthews <glenn@e-dad.net>
# Copyrigh... | ruchee/vimrc | vimfiles/bundle/vim-python/submodules/pylint/tests/extensions/test_check_docs.py | Python | mit | 69,815 | [
"VisIt"
] | 937a5c15e04842b70480f24b042212e1c368efe76816bf7d5e9b6aff7fca5e4a |
if __name__ == "__main__":
import sys,os
append_path = os.path.abspath(sys.argv[0])[:-20]
print "Append to PYTHONPATH: %s" % (append_path)
sys.path.append(append_path)
import re
import math
import Tools.web as web
from Tools.BetterFile import BetterFile
import ChemicalInfo
from Geometry import Scan,IRC... | mtthwflst/terse | Parsers/Gaussian.py | Python | mit | 35,634 | [
"Amber",
"Gaussian",
"Jmol"
] | 606bcbbd3c26b667f207d66adde2915e296dc1f3004b376062808f9c2db48c3e |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'ArticleSummary.author_list_str'
db.delete_column('neuroelectro_articlesummary', 'author_li... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0046_auto__del_field_articlesummary_author_list_str.py | Python | gpl-2.0 | 25,753 | [
"NEURON"
] | 9fb5fea7d2d4c3ae24526dde8c0ddbe6e894264f91142b6a57dd7c0fbea071e8 |
import os
os.environ['DJANGO_SETTINGS_MODULE'] = 'galaxy.settings.custom'
from galaxy.wsgi import application # noqa
| chouseknecht/galaxy | config/wsgi.py | Python | apache-2.0 | 120 | [
"Galaxy"
] | 9aca088cb1048493944d60f2701568bcc421ef4bd243fe2a93549a88d74fb319 |
# global imports
import numpy as np
import itertools
import scipy
import scipy.special
import scipy.stats
import collections
from numba import jit
def get_states(N):
"""return all possible states as arrays for N binary units"""
return np.array([np.array(x) for x in itertools.product([0, 1], repeat=N)])
def ... | jakobj/binary_network | helper.py | Python | bsd-2-clause | 25,348 | [
"NEURON"
] | 863e0000be9f3eee4989e0438e4bdb12b85b89f37c686aec2aefa79310480090 |
#!/usr/bin/env python3
#
# Copyright (c) 2012 Brian Yi ZHANG <brianlions at gmail dot com>
#
# This file is part of pynebula.
#
# pynebula 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 th... | brianlions/python-nebula | nebula/debug_info.py | Python | gpl-3.0 | 6,089 | [
"Brian"
] | 6b98ed1e4af4047de06c5c72c2fa523f5e6c54a541473d2aaac9d6aefda31712 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006 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/database/test/test_database.py | Python | gpl-2.0 | 2,424 | [
"VisIt"
] | 4bde4d040b80719d3498a8a47e23ab0c2abd719b06dd061dbd4857ea1ab25a38 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/Community-Zenpacks | ZenPacks.community.WMIFilesMonitor/setup.py | Python | gpl-2.0 | 3,312 | [
"VisIt"
] | a0f51de73d3fbf0ec4e5b64ef654b6b6936703d3aa0afbd5d053be7a6f6895a3 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Bayesian Blocks for Time Series Analysis
========================================
Dynamic programming algorithm for solving a piecewise-constant model for
various datasets. This is based on the algorithm presented in Scargle
et al 2012 [1]_. This cod... | stargaser/astropy | astropy/stats/bayesian_blocks.py | Python | bsd-3-clause | 17,959 | [
"Gaussian"
] | 5b59e595a5969d4a5567d51b4e4be2e892ff0c7d34f799da83ec6fd2fdaad272 |
import base64
import os
import re
import shutil
import subprocess
import tempfile
import urllib
from contextlib import contextmanager
from datetime import timedelta
from typing import (
Any,
Callable,
Collection,
Dict,
Iterable,
Iterator,
List,
Mapping,
Optional,
Sequence,
Se... | eeshangarg/zulip | zerver/lib/test_classes.py | Python | apache-2.0 | 69,499 | [
"VisIt"
] | 3b9d9f183d4cc2477808fec994c9eebf7523fdb847a77ae07b8371952738d0d5 |
'''
Created on 2015-05-11
@author: zhangxulong
'''
"""
TODO
"""
import numpy
from theano import function, shared
from theano import tensor as TT
import theano
import theano.scalar
sharedX = (lambda X, name:
shared(numpy.asarray(X, dtype=theano.config.floatX), name=name))
def kinetic_energy(vel):
""... | daleloogn/deeplearning-turtorial | hmc/hmc.py | Python | gpl-2.0 | 15,185 | [
"Gaussian"
] | 87d85bf9cb2afbd49f24fc8f20cf2cd282c5e8024d2ad24ebc9a718cd8a93c61 |
# jsonfile
# (C) Dalton Serey - UFCG
"""
# usage
Use it as a simple dict with a save method that saves the data to the file. If
the file exists it will be read at instantiation. If you create more than one
object for the same filename, the same object will be returned by the
constructor (it is a singleton). See the e... | daltonserey/tst | tst/jsonfile.py | Python | agpl-3.0 | 3,536 | [
"Dalton"
] | 049460878fb4fb9d8b7491ab7cf52b298c49afe31d2fbbff7fa860d0900f0cfe |
# Copyright (c) 2012-2016 The ANTLR Project. All rights reserved.
# Use of this file is governed by the BSD 3-clause license that
# can be found in the LICENSE.txt file in the project root.
#/
# The basic notion of a tree has a parent, a payload, and a list of children.
# It is the most abstract interface for all th... | kuckaogh/csclpp | csclpp/src/csclpp/dts/antlr4/tree/Tree.py | Python | gpl-3.0 | 4,140 | [
"VisIt"
] | c2da46350f1f7f655b2f690df575b39541568004f693fe07ff98907efb60b46a |
# Copyright 2021, Kay Hayen, mailto:kay.hayen@gmail.com
#
# Part of "Nuitka", an optimizing Python compiler that is compatible and
# integrates with CPython, but also works on its own.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in complianc... | kayhayen/Nuitka | nuitka/plugins/standard/ImplicitImports.py | Python | apache-2.0 | 57,716 | [
"VTK"
] | e8e6afd1ccd5b7a37138dd1c73de47eb688343266da4dd06f8c8156b477dfb0d |
# -*- coding: utf-8 -*-
r'''
*******************************************************************
* File: writeSBML.py
* Description:
* Author: HarshaRani
* E-mail: hrani@ncbs.res.in
********************************************************************/
/*********************************... | BhallaLab/moose-core | python/moose/SBML/writeSBML.py | Python | gpl-3.0 | 67,215 | [
"MOOSE"
] | 7cdf8e1b8f5299b0e469ab41c195f924682ce567f2585adda48b1de54e0d7890 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008-2009 Brian G. Matherly
# Copyright (C) 2009 Rob G. Healey <robhealey1@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General P... | pmghalvorsen/gramps_branch | gramps/plugins/lib/libholiday.py | Python | gpl-2.0 | 18,531 | [
"Brian"
] | b2ded173659ace274dd410086b2baa664cc0541e2947ecc64ee9b8980ecab517 |
from django import forms
from django.forms.models import ModelForm
from edc_constants.constants import NO, YES
from microbiome.apps.mb.constants import MODIFIED, DISCONTINUED, NEVER_STARTED
from edc_constants.constants import UNKNOWN, NOT_APPLICABLE
from ..models import InfantArvProph, InfantArvProphMod, InfantBir... | botswana-harvard/microbiome | microbiome/apps/mb_infant/forms/infant_arv_proph_form.py | Python | gpl-2.0 | 5,126 | [
"VisIt"
] | 36e45f2f41b4b3f662dde898dd2a038225daaaaec45c0152286d3b553973e69f |
# -*- coding: utf-8 -*-
import getpass
import threading
import thread
import time
import datetime
import sys
import tools
from editor import Editor
import config
def preloaderPause(fn, *args, **kwargs):
def wrapped(*args, **kwargs):
if not preloader.isLaunch:
return fn(*args, **kwargs)
... | Xunius/txt2evernote | lib/geeknote/out.py | Python | gpl-3.0 | 7,928 | [
"VisIt"
] | 4b09ec99297adf8f3c50e80976df470d557815ed5e01e2ca0b5c3115ed956178 |
#
# @@ 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.
#
import doctest
import unittest
from rdkit.Chem import inchi
from rdkit.TestRunner import redirect... | ptosco/rdkit | rdkit/Chem/MolKey/UnitTestMolKey.py | Python | bsd-3-clause | 5,245 | [
"RDKit"
] | aab7f48092d47f88e27f82012376d93aa3f10bd42a15261e84660efb49a5284b |
# TODO#!/usr/bin/env python
"""
Install.py tool to download, compile, and setup the pace library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_help... | rbberger/lammps | lib/pace/Install.py | Python | gpl-2.0 | 3,346 | [
"LAMMPS"
] | 601e83fbb20c9b391875d3537d8131f758ccb712ac8591db7c3a30e14bac0823 |
# vim: set fileencoding=utf8 :
"""Align, register and fuse frames specified on the command line using the
DTCWT fusion algorithm.
Usage:
fusevideo [options] -o <output> <frames>...
fusevideo (-h | --help)
Options:
-n, --normalise Re-normalise input frames to lie on the
... | rjw57/dtcwtfusion | dtcwtfusion/fusevideo.py | Python | bsd-2-clause | 18,558 | [
"Gaussian"
] | a97862ce102c9e0fda40a1ee3979ee0c20f66b782a51c616ebfad62343838925 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
"""
Miscellaneous tools used by OpenERP.
"""
from functools import wraps
import cPickle
import cProfile
from contextlib import contextmanager
import subprocess
import logging
import os
import passlib.utils
import socke... | AyoubZahid/odoo | openerp/tools/misc.py | Python | gpl-3.0 | 39,402 | [
"VisIt"
] | 9e5347880b09abe2ab963d91abd63d1053132e56ed5c9dd018368f510f0aab15 |
import os, string, cStringIO, gc
from Ft.Lib import Uri, UriException
from Ft.Xml import XInclude, Domlette, cDomlette
from Ft.Xml import ReaderException, XIncludeException
from Ft.Xml.Lib import TreeCompare
READER = Domlette.NonvalidatingReader
BASE_URI = Uri.OsPathToUri(os.path.abspath(__file__), attemptAbsolute=T... | Pikecillo/genna | external/4Suite-XML-1.0.2/test/Xml/Core/test_xinclude.py | Python | gpl-2.0 | 25,598 | [
"FEFF"
] | 5fbb00aecf6440b306c1fcb5276a9899730981e3750da41afcd7eab763d3a262 |
lines = """
Afsondering Clinic Eastern Cape Alfred Nzo District Municipality
Amadiba Clinic Eastern Cape Alfred Nzo District Municipality
Amandengane Clinic Eastern Cape Alfred Nzo District Municipality
Amantshangase Clinic Eastern Cape Alfred Nzo District Municipality
Baleni Clinic Eastern Cape Alfred Nzo District Mun... | Code4SA/healthe-forms | facilities.py | Python | mit | 197,062 | [
"CRYSTAL"
] | 5eb1d6d24cea868e7af966481497bcfafc66f01e716feeed4ac5513ed9d07b8d |
#!/usr/bin/env python
# this file is a behavoir that we have created to to run a robot in full autonomous mode
# to do that we are using a stat machine created using the smach class of python
# using the smach is the main reasen we are using the python
# the robot will try to explore the it's global costmap by pickin... | SajadAzami/communication_node | src/aut_exploration/scripts/exploration_client.py | Python | bsd-3-clause | 47,595 | [
"VisIt"
] | 79d898fc4333abba343504f92a1598ec2e46f6bb6b5e0271aad7493a63fc468a |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <markdowncell>
# [The Real BART API | bart.gov](http://www.bart.gov/schedules/developers/api)
#
# [BART - API Documentation](http://api.bart.gov/docs/overview/index.aspx)
#
# Two options for use of key
#
# * use the public key: `MW9S-E7SL-26DU-VV8V`
#
# * get y... | rdhyee/consuming-apis-with-python | BART.py | Python | apache-2.0 | 12,824 | [
"Brian"
] | af9e94cc5e18fead5b81d7c339a779b04cda39e130b3f9954716173380e3de04 |
#! /usr/bin/env python
"""testLangevin.py - test the Langevin dynamics.
Usage: python testLangevin.py
Tests Langevin dynamics using the EMT Copper potential.
"""
import sys, time
from numpy import *
import asap3
from asap3.testtools import ReportTest
from asap3.md.langevin import Langevin
from asap3.md.verlet impor... | auag92/n2dm | Asap-3.8.4/Test/parallel/parallelLangevin.py | Python | mit | 3,439 | [
"ASE"
] | c76dc02ee18570a77e2b196200acfbc616c42e4afcbc7f1bdc7774bf0fc82cdf |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkProgrammableFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkProgrammableFilter.py | Python | bsd-3-clause | 495 | [
"VTK"
] | 3a935d3ff6271b2a3638719ac8074780ecf69113b339e8645cb0c828a8e0950b |
# ipr.model
import random
import os
import sys
import time
import tempfile
import itertools
import multiprocessing as mp
import subprocess
import numpy as np
import csv
from utils import *
from config import *
from data import *
from collections import defaultdict
#from analysis import *
def gulp_call(bundle):
or... | wolverton-research-group/fitpot | fitpot/optimizer.py | Python | mit | 12,657 | [
"GULP"
] | 7fee34aa5cd60a4a7615dd6ddbdab0faf083e7477f475786cc6a6f4df22d374c |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
from django.contrib.auth.decorators import login_required
from django.views.decorators.http import require_POST
from django.utils.translation imp... | kamalx/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 26,014 | [
"VisIt"
] | eb6418db68bdd2add1a87eaab0b9543a81d55247b304248125abe00e1b185b1d |
from setuptools import setup, find_packages
from Cython.Build import cythonize
import versioneer
versioneer.versionfile_source = 'vdjalign/_version.py'
versioneer.versionfile_build = 'vdjalign/_version.py'
versioneer.tag_prefix = '' # tags are like 1.2.0
versioneer.parentdir_prefix = 'vdjalign-' # dirname like 'mypro... | cmccoy/ighutil | python/setup.py | Python | gpl-3.0 | 903 | [
"pysam"
] | 7771fcd1935b380ef2e1c2fd0fa819cfc802cdad9596691f7b684bc0f0e652ad |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Transposome(PerlPackage):
"""A toolkit for annotation of transposable element families fro... | LLNL/spack | var/spack/repos/builtin/packages/transposome/package.py | Python | lgpl-2.1 | 626 | [
"BLAST"
] | 9ce9c19215c8b22a4891ff8ae959d493b217a0d9a0b9579fb51960db59119133 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/client/tabs/campaign.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# not... | hdemeyer/king-phisher | king_phisher/client/tabs/campaign.py | Python | bsd-3-clause | 27,197 | [
"VisIt"
] | b2ce53b7721efbf1fa40cc94333bacae5902ec66789d11cfee6446addcc4c455 |
from Sire.IO import *
from Sire.Squire import *
from Sire.Units import *
from Sire.Qt import *
water = PDB().readMolecule("test/io/sb2.pdb")
qmff = QMFF()
mopac = Mopac()
print(mopac.chargeCommandFile(water), "\n")
qmff.setQuantumProgram( mopac )
qmff.add(water)
print(qmff.energyCommandFile(), "\n")
t = QTime... | chryswoods/SireTests | unittests/Squire/mopac.py | Python | gpl-2.0 | 588 | [
"MOPAC"
] | b714231e954e9137bd358d563bd61090703719b01a002e49530670b2923e3287 |
"""
#;+
#; NAME:
#; cos_halos
#; Version 1.0
#;
#; PURPOSE:
#; Module for COS-Halos analysis
#; 29-Nov-2014 by JXP
#;-
#;------------------------------------------------------------------------------
"""
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as np
impo... | nhmc/xastropy | xastropy/cgm/cos_halos.py | Python | bsd-3-clause | 11,767 | [
"Galaxy"
] | bb6afe8cb0c80af8de5c1c05ddbc187293c8340f5cca768ba63053d3a8c6b740 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen.analysis.structure_prediction.volume_predictor import DLSVolumePredictor, \
RLSVolumePredictor
from pymatgen.util.testing import PymatgenTest
from pymatgen.core impor... | gpetretto/pymatgen | pymatgen/analysis/structure_prediction/tests/test_volume_predictor.py | Python | mit | 4,699 | [
"pymatgen"
] | 1b2c7a370975b47f154320485a71c6141f07562a5c873e8f9904f01a4423343e |
#!/usr/bin/env python
# Copyright 2014 the V8 project authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# This script retrieves the history of all V8 branches and
# their corresponding Chromium revisions.
# Requires a chromium checkout ... | weolar/miniblink49 | v8_5_1/tools/release/releases.py | Python | apache-2.0 | 19,589 | [
"VisIt"
] | f92087aa91a77f5754e89a74e2ef1eeb115729a2eb173f18e140a3908000aa83 |
#!/usr/local/bin/env python
"""
Test YANK using simple models.
DESCRIPTION
This test suite generates a number of simple models to test the 'Yank' facility.
COPYRIGHT
Written by John D. Chodera <jchodera@gmail.com> while at the University of California Berkeley.
LICENSE
This code is licensed under the latest avai... | choderalab/brokenyank | tests/yank-tests.py | Python | lgpl-3.0 | 8,266 | [
"NetCDF",
"OpenMM"
] | 1ff1f14629f99579e7ad7fcbd7af059fa262997d07a1e3e1f9ee100f8720f810 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.atat import Mcsqs
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files', "atat")
... | Bismarrck/pymatgen | pymatgen/io/tests/test_atat.py | Python | mit | 2,646 | [
"pymatgen"
] | 72557f485142d3086427c08468d03ab2f5140feb4c518231ee1fe531c4676797 |
# err-dnsutils: Run common DNS utils: host, dig, nslookup
# Copyright (C) 2012 Nick 'zoni' Groenen <zoni@zoni.nl>
#
# 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 L... | zoni/err-dnsutils | dnsutils.py | Python | gpl-3.0 | 3,651 | [
"VisIt"
] | 88cb2018bcaafb45beb72d23e55e11fa086978bf248299ff457292309df6b7d4 |
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