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### clustering.py
#Copyright 2005-2008 J. David Gladstone Institutes, San Francisco California
#Author Nathan Salomonis - nsalomonis@gmail.com
#Permission is hereby granted, free of charge, to any person obtaining a copy
#of this software and associated documentation files (the "Software"), to deal
#in the Software ... | wuxue/altanalyze | clustering_ICGS.py | Python | apache-2.0 | 150,537 | [
"Bioconductor"
] | 1edbbf76f6d86f3250fe00012e68f455186d5459a487fc250fd4e94f801e0704 |
# FIXME: to bring back to life
from DIRAC.Resources.Catalog.FileCatalogClient import FileCatalogClient
import cmd
import sys
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.AbstractFileSystem import DFCFileSystem
from DIRAC.DataManagementSystem.Client.CmdDirCompletion.DirectoryCompletion import DirectoryComp... | DIRACGrid/DIRAC | tests/Integration/DataManagementSystem/FIXME_dfc_dir_completion.py | Python | gpl-3.0 | 1,327 | [
"DIRAC"
] | 160da808287cbbec94749a0ab505317a567d8270e8f220e10106c028b9fe384e |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | output/Brian2/brian2_benchmark_COBAHH_clocksyn_hidens_0001/brian2_benchmark_COBAHH_clocksyn_hidens_0001.py | Python | gpl-3.0 | 3,792 | [
"Brian"
] | 0034628625a23e0fe5d3c1c6535d2d680b385ae5513e71b31553020a35e7e4ac |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/examples/example_genetic_tsp.py | Python | apache-2.0 | 4,015 | [
"VisIt"
] | 88b623c694621b6b44938ae755902e71f1328cd6098618f753f4a345a782498b |
#
# 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/h5md.py | Python | gpl-3.0 | 8,047 | [
"ESPResSo"
] | ae6c9f8907cf2b64d57968b7decd86a2c4d03b808884d476a5047476aabf4dc3 |
"""
Unit tests for the `bent_plume_model` module of ``TAMOC``
Provides testing of the classes, methods and functions defined in the
`bent_plume_model` module of ``TAMOC``. These tests check the behavior of the
object, the results of the simulations, and the read/write algorithms.
The ambient data used here are from t... | socolofs/tamoc | tamoc/test/test_bpm.py | Python | mit | 23,041 | [
"NetCDF"
] | 6780a27d356d68481c7c58a7bec9539d33b4e7b6d5ee54837cf6cf2b6343f609 |
#!/usr/bin/env python
#coding:utf-8
"""
Author: --<> Purpose: Created: 2015/3/12
"""
import splinter
import time
browser=splinter.Browser('firefox')
assert isinstance(browser,splinter.driver.webdriver.firefox.WebDriver)
browser.visit('https://kyfw.12306.cn/otn/login/init')
time.sleep(1)
browser.find_by_id('username... | sangdan/securities-trade | p4.py | Python | gpl-3.0 | 983 | [
"VisIt"
] | 5ec6fb2d25b1532633010cf7e236673603f4624f74dee23f6718f238ae45c196 |
import sys
import re
import pandas as pd
from StringIO import StringIO
from glob import glob
import shutil
import tables as tb
import ctypes as ct
import numpy as np
import cPickle as cp
import tempfile
data_dir = '/scratch/midway/jumper/'
from mpi4py import MPI
world = MPI.COMM_WORLD
rank,size = world.rank, world.s... | John-Jumper/Upside-MD | py/sidechain_interaction.py | Python | gpl-2.0 | 16,474 | [
"Gaussian"
] | 2b5a17dfb97b7e8a164e6abad93dd25cbc727359aad8eaa6dfbf89745b98353b |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import datetime
import random
import re
import string
from lxml import html
from urllib2 import urlopen
from urlparse import urljoin
from urlparse import urlparse
from werkzeug import url_encode
from odoo import models... | chienlieu2017/it_management | odoo/addons/link_tracker/models/link_tracker.py | Python | gpl-3.0 | 10,106 | [
"VisIt"
] | 6f62de4b147ebf0e323e53ba555220d26456a490e197bb4283b6251be8a1f8c6 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/procrouting/findif_response_utils/data_collection_helper.py | Python | lgpl-3.0 | 4,102 | [
"Psi4"
] | fd18b10e138318770fd9426e55d05152849b0c84027dac70ed7b3b6053beedaa |
import unittest, os, sys, time
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_glm, h2o_hosts, h2o_browse as h2b, h2o_import as h2i, h2o_exec
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_for_errors()
@classmethod
def setUpClass(cls):
localhost = h2o.decid... | woobe/h2o | py/testdir_multi_jvm/test_allstate_claim_prediction.py | Python | apache-2.0 | 2,318 | [
"Gaussian"
] | 855aab13bffb520fc9b29f02e4103a6f4200cd97904192e4edaaba0e957466b3 |
"""Provide the Subreddit class."""
# pylint: disable=too-many-lines
from copy import deepcopy
from json import dumps, loads
from os.path import basename, dirname, join
from urllib.parse import urljoin
from prawcore import Redirect
import websocket
from ...const import API_PATH, JPEG_HEADER
from ...exceptions import A... | leviroth/praw | praw/models/reddit/subreddit.py | Python | bsd-2-clause | 101,559 | [
"VisIt"
] | 343c96f17e894ba37a70c606b3803dfd489eeb18ee4c81bf3ca5684ba4c4bb7b |
# Todd Miller jmiller@stsci.edu
from __future__ import division, print_function
import os, sys, math
import os.path
import Tkinter as Tk, FileDialog
# Paint image to Tk photo blitter extension
import matplotlib.backends.tkagg as tkagg
from matplotlib.backends.backend_agg import FigureCanvasAgg
import matplotlib.... | cactusbin/nyt | matplotlib/lib/matplotlib/backends/backend_tkagg.py | Python | unlicense | 35,145 | [
"FLEUR"
] | b5e68aa180bf441496278c15977224e4d9511ee6b7da4b13476aa440579208a1 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/ncbi-rmblastn/package.py | Python | lgpl-2.1 | 1,585 | [
"BLAST"
] | b5ee98e643e3d3af1211409bf2c928612a333b45c6a27ea5b6bb2a46135b9b3a |
from collections import Counter
from kademlia.log import Logger
from kademlia.utils import deferredDict
from kademlia.node import Node, NodeHeap
class SpiderCrawl(object):
"""
Crawl the network and look for given 160-bit keys.
"""
def __init__(self, protocol, node, peers, ksize, alpha):
"""
... | pldubouilh/maidsafe | kademlia/kademlia/crawling.py | Python | gpl-2.0 | 6,145 | [
"exciting"
] | 14188164cea4408ede7a742cd926774e83f53be891d2d0f8cfb92efd62db5740 |
'''
Merges two fasta files into one, adding a prefix to the name of each sequence
(different prefix for each of the two files)
Usage:
%% python generate_combined_cds.py <fasta1.fasta> <prefix1> <fasta2.fasta> <prefix2> <output.fasta>
Requirements: Biopython must be installed
'''
import sys
from Bio.Seq import Seq
fr... | DworkinLab/ChandlerChariTackDworkin2014 | expression_scripts/dge/generate_combined_cds.py | Python | mit | 1,172 | [
"BWA",
"Biopython"
] | 0c19ea90e6e8ec53b7b5849538a45bc4698b817bb4eb799f0af64b1b1bd327b5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
The initial version of this module was based on a similar implementation
present in FireWorks (https://pypi.python.org/pypi/FireWorks).
Work done by D. Waroquiers, A. Jain, and M. Kocher.
The main differenc... | Bismarrck/pymatgen | pymatgen/io/abinit/qadapters.py | Python | mit | 83,425 | [
"ABINIT",
"pymatgen"
] | 26887a3e3d70e62079c7350c419a27f797851cf75861daa3ec735f95f203e06b |
# Author: Gael Varoquaux <gael _dot_ varoquaux _at_ normalesup _dot_ org>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import Instance
from tvtk.api import tvtk
# Local imports
from mayavi.filters.filter_base import FilterBase
from mayavi.core.pipeline_info ... | dmsurti/mayavi | mayavi/filters/elevation_filter.py | Python | bsd-3-clause | 1,148 | [
"Mayavi"
] | 62c5d55f435c3b5c7c218c3e86bf3b4a8e37a0163faf07d01664090f2a66d8e2 |
tests=[
("python","UnitTestChem.py",{}),
("python","UnitTestChemv2.py",{}),
("python","UnitTestChemAtom.py",{}),
("python","UnitTestChemBond.py",{}),
("python","UnitTestChemSmarts.py",{}),
("python","UnitTestFragmentDescriptors.py",{}),
("python","UnitTestGraphDescriptors.2.py",{}),
("python","UnitTest... | rdkit/rdkit-orig | rdkit/Chem/test_list.py | Python | bsd-3-clause | 1,947 | [
"RDKit"
] | feae58510b10871604920a986f8e52014b791078b4fe97bdf3a1cc3b6041f754 |
#! /usr/bin/python
import __main__
#__main__.pymol_argv = ['pymol','-qc']
__main__.pymol_argv = ['pymol','']
import sys,time,os
import pymol
pymol.finish_launching()
pymol.cmd.feedback("disable","all","actions")
pymol.cmd.feedback("disable","all","results")
sys.path.append("/home/scratch/software/Pymol-script-repo-m... | demharters/git_scripts | calc_elbow_tcr_single.py | Python | apache-2.0 | 799 | [
"PyMOL"
] | 4f6a7428c4bef63be8e63d89021099c74465a4be0da2616b69079b02fb3e26c2 |
import sys
from ase import view, Atoms
from ase.data.s22 import data, s22
from ase.calculators.vdwcorrection import vdWTkatchenko09prl
from ase.parallel import parprint
from gpaw import GPAW, FermiDirac
from gpaw.cluster import Cluster
from gpaw.analyse.hirshfeld import HirshfeldDensity, HirshfeldPartitioning
from gp... | qsnake/gpaw | gpaw/test/big/vdw/adenine-thymine_complex_stack.py | Python | gpl-3.0 | 1,729 | [
"ASE",
"GPAW"
] | 878be56def413bb3270b4010308c7f49e64e6c2ca650c0849cfb8395630103f6 |
# $Id: nodes.py 6293 2010-03-26 08:37:17Z milde $
# Author: David Goodger <goodger@python.org>
# Copyright: This module has been placed in the public domain.
"""
Docutils document tree element class library.
Classes in CamelCase are abstract base classes or auxiliary classes. The one
exception is `Text`, for a text (... | rpdillon/wikid | wikid/docutils/nodes.py | Python | gpl-3.0 | 64,828 | [
"VisIt"
] | 8e8ebd70d3099773d133268cdc1b90930927f9ac75254c4290c2d0e68b783ad4 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.FrameworkSystem.private.monitoring.ColorGenerator import ColorGenerator
def test_getHexColor():
cg = ColorGenerator()
for i in range(2):
assert cg.getHexColor() == "0000FF"
... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/private/monitoring/test/Test_ColorGenerator.py | Python | gpl-3.0 | 2,097 | [
"DIRAC"
] | 2c8bea17772379fa14fdcf4e2918b9e47f5a673229345b0800287eeda7b54e7b |
# (C) British Crown Copyright 2010 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | jkettleb/iris | lib/iris/tests/test_grib_load.py | Python | lgpl-3.0 | 28,638 | [
"Gaussian"
] | 5d2e3e742dd5dd8e54536ebc3290ac8971d2d90225d8d2509a80e7b798cc7ee7 |
"""
Miscellaneous utility functions.
"""
import sys
import os
import re
import shutil
import tempfile
import urllib2
import string
from Bio import SeqIO
from django.conf import settings
# Number of characters that snpeff requires per line of the genbank file
SNPEFF_MIN_LINE_LEN = 20
def make_temp_file(label, extens... | woodymit/millstone | genome_designer/utils/__init__.py | Python | mit | 4,056 | [
"Biopython"
] | 87e01a9e16b339b8f5aa07ad36a1c9ac9cdee2a4c17ef25a0c2b229eedc055b1 |
#
# The Python Imaging Library.
# $Id$
#
# the Image class wrapper
#
# partial release history:
# 1995-09-09 fl Created
# 1996-03-11 fl PIL release 0.0 (proof of concept)
# 1996-04-30 fl PIL release 0.1b1
# 1999-07-28 fl PIL release 1.0 final
# 2000-06-07 fl PIL release 1.1
# 2000-10-20 fl PIL release 1.1.1... | ruibarreira/linuxtrail | usr/lib/python2.7/dist-packages/PIL/Image.py | Python | gpl-3.0 | 80,423 | [
"Gaussian"
] | 63d6e3df216378f40c4ab2b91ecac75bd215b4b43b3c1e83fe8d24b9ec94805b |
#encoding:utf-8
# Some utils can be useful.
from utils import get_url
from utils import SupplyResult
# Write here subreddit name. Like this one for /r/jokes.
subreddit = 'jokes'
# This is for your public telegram channel.
t_channel = '@r_jokes'
def send_post(submission, r2t):
# Check what is inside this submis... | nsiregar/reddit2telegram | channels/r_jokes/app.py | Python | mit | 1,516 | [
"VisIt"
] | 72f3151e76e7c8ede72c958320f721609523b3b11faee25939f51bf8f9797663 |
# Copyright (C) 2012-2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 the GNU General... | espressopp/espressopp | src/integrator/LBInitPopUniform.py | Python | gpl-3.0 | 1,955 | [
"ESPResSo"
] | 213f3cdc9f8af2dc4d63ce295fbacd55578b9e3d541149a935cc39a20a2efa46 |
#!/usr/bin/python
#-*- coding: utf-8 -*-
# Copyright (C) 2015, Nikolai Chernikov <nikolai.chernikov.ru@gmail.com>
#
# "convert2ugrid" is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License v3+. "convert2ugrid" is distributed in the
# hope that it will be use... | cdd1969/convert2ugrid | lib/process_davit_ncdf.py | Python | gpl-3.0 | 47,591 | [
"NetCDF"
] | a43f3cb1194b9438708e3fa524544ee7f6e2060dcd2c066663ef0d091a87c955 |
#!/usr/bin/env python
# vim: fileencoding=utf-8 et ts=4 sts=4 sw=4 tw=0 fdm=marker fmr=#{,#}
"""A simple RPC server that show how to run multiple RPC services."""
#-----------------------------------------------------------------------------
# Copyright (C) 2012-2014. Brian Granger, Min Ragan-Kelley, Alexander Glyzo... | srault95/netcall | examples/tornado/server_tornado.py | Python | bsd-3-clause | 2,548 | [
"Brian"
] | ae858906edcea24c54022f30a1c34ad1991ce6ab5ac24b38cade01c397f0e506 |
# -*- coding: utf-8 -*-
"""
Description:
Input: event / site data previously analyzed by photostim
Output:
- per-event probability of being direct / evoked / spont
- per-site probability of having evoked / direct input
- per-cell measurements of direct and presynaptic area
Whereas photostim largely o... | hiuwo/acq4 | acq4/analysis/modules/MapAnalyzer/MapAnalyzer.py | Python | mit | 42,613 | [
"Gaussian"
] | e489e14fb2333e560defa5127b998404f84bb2edd72233843ff3fdff0c68bf78 |
# -*- coding: utf-8 -*-
# (c) 2016-2017 Andreas Motl <andreas@getkotori.org>
import re
import json
import types
import mimetypes
import pymongo
from six import BytesIO
from copy import deepcopy
from urlparse import urlparse
from bunch import bunchify, Bunch
from collections import OrderedDict
from twisted.application.s... | zerotired/kotori | kotori/io/protocol/http.py | Python | agpl-3.0 | 26,537 | [
"NetCDF"
] | 26ce9a4942d1e565ff6066db4723b0b0e277a03ccc81fdcfb68a58186dbb3163 |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-get-queue-cpu-time.py
# Author : Federico Stagni
########################################################################
"""
Report CPU length of queue, in seconds
This script is used by the dirac-pilo... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/scripts/dirac_wms_get_queue_cpu_time.py | Python | gpl-3.0 | 1,107 | [
"DIRAC"
] | 46f349d6616939c89dc097f5a78228565dab73337ad820fb491509ad1d089db4 |
""" Tests of the molecule utilities
:Author: Jonathan Karr <jonrkarr@gmail.com>
:Date: 2017-04-12
:Copyright: 2017, Karr Lab
:License: MIT
"""
from datanator.util import molecule_util
from datanator.util import warning_util
from wc_utils.util.types import assert_value_equal
import numpy
import pybel
import unittest
... | KarrLab/kinetic_datanator | tests/util/test_molecule_util.py | Python | mit | 8,055 | [
"Pybel"
] | 7329a063051d1ffaca7b178a907204871e22996e9e78fae40aec397a115e7f38 |
# -*- encoding: utf-8 -*-
# Yuuno - IPython + VapourSynth
# Copyright (C) 2017 StuxCrystal (Roland Netzsch <stuxcrystal@encode.moe>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, eit... | stuxcrystal/yuuno | yuuno_ipython/ipython/utils.py | Python | lgpl-3.0 | 3,106 | [
"MOE"
] | 57e75ea0d71fef5a1c809c6b0660ad76768d83ccedaccc4bbeed42615dd5e8c2 |
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 02 14:01:17 2018
@author: car72
Contains all necessary functions for analysis of NPoM darkfield and photoluminescence spectra
Best used in conjunction with Condense_Fit_DF control script
"""
from __future__ import division
from __future__ import print_function
from buil... | nanophotonics/nplab | nplab/analysis/NPoM_DF_Analysis/DF_Multipeakfit.py | Python | gpl-3.0 | 150,504 | [
"Gaussian"
] | 2e6622ed65c71dd7bc6ab01c97e3d5553677947644186a9f03ad00f8868ea6e3 |
from basebot import BaseBot
# Example responses:
#
# Move forwards:
# return {'ACTION': 'MOVE', 'WHERE': 1}
#
# Move backwards:
# return {'ACTION': 'MOVE', 'WHERE': -1}
#
# Shooting projectile:
# return {'ACTION': 'SHOOT', 'VEL': 100, 'ANGLE': 35}
# # 'VEL' should be a value x, 0 < x < 150
# # 'ANGLE' should... | Onapsis/pywars | example_data/bots/bot1/script.py | Python | mit | 1,486 | [
"VisIt"
] | 1d90c3b76c14ae6cf947d954762af3f0c89877a82a312831c8a04ba1940537c8 |
from setuptools import setup, find_packages
setup(
name='tinker',
version='0.1',
classifiers=[
"Programming Language :: Python",
"Framework :: Pylons",
"Topic :: Internet :: WWW/HTTP",
"Topic :: Internet :: WWW/HTTP :: WSGI :: Application",
],
author='James Arthur',
... | thruflo/tinker | setup.py | Python | unlicense | 1,343 | [
"TINKER"
] | 1126bf10ef8d1c0fb2ecdd3121bb9ee38e2d95d82382caa8f21a761a21c6e8ea |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import os
import tempfile
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinit.abiinspect import *
_test_dir = os.path.join(... | matk86/pymatgen | pymatgen/io/abinit/tests/test_abiinspect.py | Python | mit | 3,870 | [
"ABINIT",
"pymatgen"
] | 79d755fea0ae3356d925b9cdf1a759d0788ad631ff3447e5eb54f7249626d308 |
import numpy as np
from StringIO import StringIO
import tokenize
import ast
# import the logging library
import logging
# Get an instance of a logger
logger = logging.getLogger(__name__)
class CallCollector(ast.NodeVisitor):
def __init__(self):
self.calls = []
self.current = None
def visit_C... | nanchenchen/script-analysis | pyanalysis/apps/enhance/tokenizers.py | Python | mit | 7,748 | [
"VisIt"
] | bfa233f66a55f3f4ebc1f482024943ab3b2323f83d65679ea8da40f1e5833a7e |
#http://virantha.com/2013/11/14/starting-a-simple-flask-app-with-heroku/
import json
import os
import re
from datetime import datetime, timedelta, date
from flask import Flask
from flask.templating import render_template
import gflags
import httplib2
from apiclient.discovery import build
from oauth2client.client impor... | ryanprater/calendar_graph | calendar_graph.py | Python | mit | 8,669 | [
"VisIt"
] | fd3bf27f9af02bd6172b3e21b8979400e6da29db5aa1b0ae9079b43282b00f62 |
from Firefly.const import (CONTACT, CONTACT_CLOSED, CONTACT_OPEN, EVENT_ACTION_OFF, EVENT_ACTION_ON, MOTION, MOTION_ACTIVE, MOTION_INACTIVE, NOT_PRESENT, PRESENCE, PRESENT, SENSOR_DRY, SENSOR_WET,
WATER)
from Firefly.helpers.device import *
def metaDimmer(min=0, max=100, command=True, requ... | Firefly-Automation/Firefly | Firefly/helpers/metadata/metadata.py | Python | apache-2.0 | 15,952 | [
"Firefly"
] | c4c6360877b745ab75015b7bf21971a4248f33d10e1c48e7d92ca5d8223c2d75 |
#!/usr/bin/python
import sys, os, traceback, optparse
import time
import networkx as nx
import pandas as pd
import numpy as np
from collections import deque, defaultdict
import random
import itertools, math
from pprint import pprint
import matplotlib
matplotlib.use('pdf')
import matplotlib.pyplot as plt
from datetime ... | abitofalchemy/hrg_nets | hrgs_karate_chop.py | Python | gpl-3.0 | 19,789 | [
"VisIt"
] | 3379e820f09ce56940e4fe8b1a5d54ec0f30da67a63c70b9fc1b37366d167819 |
from datetime import datetime
import logging
log = logging.getLogger(__name__)
import numpy
from box import BoundingBox
from mclevelbase import exhaust
import materials
from entity import Entity, TileEntity
from copy import deepcopy
def convertBlocks(destLevel, sourceLevel, blocks, blockData):
return materials.... | fhfuih/MCEdit-Unified | pymclevel/block_copy.py | Python | isc | 7,243 | [
"VisIt"
] | ad59a09539a42d216c02439e60375594a976c8dcae152ebb75d03b3e91377cdc |
from __future__ import absolute_import
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU Gener... | fmaguire/ete | ete3/treeview/qt4_render.py | Python | gpl-3.0 | 44,834 | [
"VisIt"
] | 9e8418de8ed0cc35967bb90dca9d909dd85ea7c84ddbd573d1e04e50479a5073 |
# 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/zip_county_bulk.py | Python | apache-2.0 | 14,150 | [
"VisIt"
] | b4e0480501abb2426eb6417b3501d1b610fa0e44193b63da745547f497565c1b |
#from Tkinter import *
import PIL
import numpy
from numpy import newaxis
from scipy import *
from pylab import *
from skimage.morphology import label
from skimage.measure import regionprops
from scipy.ndimage.morphology import binary_fill_holes
from RSF import *
from subprocess import call
import time
import ctypes
fr... | stephenplaza/NeuTu | neurolabi/python/stackImageProcess.py | Python | bsd-3-clause | 54,829 | [
"DIRAC",
"Gaussian",
"NEURON"
] | 1c46e0cfb5243ecfced7ee23e37947e2e51b6a4d1477595c1e7cee0f52d353b3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2009 Timothée Lecomte
# This file is part of Friture.
#
# Friture is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as published by
# the Free Software Foundation.
#
# Friture is distri... | tlecomte/friture | sandbox/delay.py | Python | gpl-3.0 | 7,559 | [
"Gaussian"
] | 2d72a9d0cad219e1c97d49c873089eea9100be46262a8e8205e942106421ddea |
"""
Acceptance tests for Studio related to course reruns.
"""
import random
from bok_choy.promise import EmptyPromise
from nose.tools import assert_in
from ...pages.studio.index import DashboardPage
from ...pages.studio.course_rerun import CourseRerunPage
from ...pages.studio.overview import CourseOutlinePage
from ..... | ahmadiga/min_edx | common/test/acceptance/tests/studio/test_studio_rerun.py | Python | agpl-3.0 | 4,166 | [
"VisIt"
] | 991803cc28c565bbca41e553819e2448a7b8b76401b856679b4f1d240ae80490 |
import os
import pickle
import math
from ase.io import write
import numpy as np
from scipy.integrate import quad
from geometricmd.geometry import convert_vector_to_atoms
def get_times(curve):
t = [0.0]
mass_matrix = np.diag(np.dstack((curve.configuration['molecule'].get_masses(),)
... | suttond/GeometricMD | geometricmd/animation.py | Python | lgpl-3.0 | 2,952 | [
"ASE",
"Jmol"
] | 68b4693da860b73a8facddc8ac23c02cc1d0d0f43c8faabe1531f5131cbba9c6 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-08-06 22:12:44
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-08-30 15:10:16
from __future__ import print_function, division, absolute_import
from functools import wra... | havok2063/SciScript-Python | python/sciserver/utils.py | Python | apache-2.0 | 5,867 | [
"Brian"
] | 4f93d9364cacd7f006eae4eaddff4d4ea97e3cee269d22afcc6b2188f46cc8bc |
'''
Created on 16/03/2010
@author: jose
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of project.
# franklin 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... | JoseBlanca/franklin | test/backbone/annotation_test.py | Python | agpl-3.0 | 29,196 | [
"BLAST"
] | 84ab06f6d707db397a1729fa1e3d77aea125fa3e206e0d54f28863ae8fc793dd |
import math
import copy
import numpy
from . import zpickle
from numpy import exp,array
from .Struct import Struct
def hdf5_load_images(fname):
import h5py,os
if not os.path.exists(fname):
raise ValueError("File does not exist: %s" % fname)
f=h5py.File(fname,'r')
var={}
var['im_scale_sh... | bblais/plasticity | plasticity/utils.py | Python | mit | 15,529 | [
"Gaussian"
] | 688b8796f54b1a0aa155da17613dc94ce32150669423594eebbda9d55aece814 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Plugin Project Create Script
#
import os, sys, shutil, string, uuid, re, zipfile, glob
from string import capitalize
from StringIO import StringIO
# template_dir simply points to the directory that this file lives in on disk
template_dir = os.path.abspath(os.path.dir... | gianina-ingenuity/titanium-branch-deep-linking | testbed/x/mobilesdk/osx/5.5.1.GA/plugin/plugin.py | Python | mit | 4,032 | [
"VisIt"
] | a20cc4d15cbd9ffc543e9085820ae12064dc07096545380255f6be68ad2532e2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# 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.
... | dmillington/ansible-modules-core | windows/win_lineinfile.py | Python | gpl-3.0 | 6,480 | [
"Brian"
] | 4301906c3d32c6f55cfdf93aeb42b55b7c5e91b7701a616c45fd1a4f1e6d65d5 |
"""\
MINDO3.py: Dewar's MINDO/3 Semiempirical Method
This program is part of the PyQuante quantum chemistry program suite.
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
license. Please see the file LICENSE that is part of this
distrib... | berquist/PyQuante | PyQuante/MINDO3.py | Python | bsd-3-clause | 28,409 | [
"MOPAC"
] | 7dad876b3ef966651efdeaf7e2248077595d2433f19b8bac7f977838ca0e7296 |
# Copyright 2018 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | tensorflow/transform | tensorflow_transform/beam/analysis_graph_builder.py | Python | apache-2.0 | 26,760 | [
"VisIt"
] | 2451ea7996064cab8b7d1a058322308c76bd6510f63236ebe8b3dac68e0f0f00 |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import step, world
from lettuce.django import django_url
@step('I visit the courseware URL$')
def i_visit_the_course_info_url(step):
url = django_url('/courses/MITx/6.002x/2012_Fall/courseware')
world.browser.visit(url)
| ahmedaljazzar/edx-platform | lms/djangoapps/courseware/features/courseware.py | Python | agpl-3.0 | 319 | [
"VisIt"
] | 51fc421990da8eb78434eb240389cd0e027bf19ebfd014b57c5f04adab6a8152 |
#!/usr/bin/env python
########################################################################
# File : dirac-dms-add-file
# Author : Stuart Paterson
########################################################################
"""
Upload a file to the grid storage and register it in the File Catalog
Usage:
dirac-dms... | ic-hep/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_add_file.py | Python | gpl-3.0 | 3,620 | [
"DIRAC"
] | 003ec2e084e73469ce2cf907961e43d66aa2179a029b1dbb266d3e6214fa1bb2 |
from pypipe.tools.toolsconfig import Bwa
from pypipe.utils import tool, check_if_program_exists
check_if_program_exists('bwa')
@tool
def mem():
return Bwa.mem()
@tool
def aln():
return Bwa.aln()
@tool
def samse():
return Bwa.samse()
@tool
def sampe():
return Bwa.sampe()
@tool
def bwasw():
... | ctlab/pypipe | pypipe-core/pypipe/tools/bwa.py | Python | mit | 341 | [
"BWA"
] | dcf6d1f8106e1209d7ce4f9d3010abe5cae5128b39161bc6c53f53683e797d20 |
# -*- coding: utf-8 -*-
"""
L7 Introducing Osmnx for working with OpenStreetMap and routing.
Created on Tue Dec 5 15:48:04 2017
@author: Henrikki Tenkanen
"""
# Working with OpenStreetMap data
# ===============================
# OpenStreetMap (OSM) is a global crowd-sourced dataset that contains a lot of informat... | Automating-GIS-processes/2017 | source/codes/L7/osmnx_L7_intro.py | Python | mit | 5,560 | [
"exciting"
] | a2be9edcaf4a0335fe2940ca92bc9fb1e7850beb7d304d93dda4a79580b59ee5 |
#!/usr/bin/env python
import os.path
import vtk
def get_program_parameters():
import argparse
description = 'Decimate polydata.'
epilogue = '''
This is an example using vtkDecimatePro to decimate input polydata, if provided, or a sphere otherwise.
'''
parser = argparse.ArgumentParser(descrip... | lorensen/VTKExamples | src/Python/Meshes/Decimation.py | Python | apache-2.0 | 5,683 | [
"VTK"
] | 08c2b7ffbf0d4e446510132ec04d314fb0fb244606cbf3224dc3cff1ec8446ff |
#!/usr/bin/env python
'''
Boys localization, Edmiston-Ruedenberg localization and Pipek-Mezey
localization
'''
import numpy
from pyscf import gto, scf
from pyscf import lo
from pyscf.tools import molden
mol = gto.M(
atom = '''
C 0.000000000000 1.398696930758 0.000000000000
C 0.000000000000 -1.39... | gkc1000/pyscf | examples/local_orb/03-split_localization.py | Python | apache-2.0 | 1,340 | [
"PySCF"
] | ebb2b8f8f6b9a3d11b6cf626dafbcaff30a7668473c56fa092e76c25d643d691 |
# -*- coding: utf-8 -*-
"""Observation untilities."""
import csv
import io
import json
# from plogger.debug import plogger.debug
import logging
import os
import shutil
from datetime import datetime, timedelta
import pandas
import requests
import xmltodict
from confy import env
from dateutil import parser
from django.c... | parksandwildlife/wastd | wastd/observations/utils.py | Python | mit | 200,499 | [
"ORCA",
"VisIt"
] | 356e57ee67dc6fc7d610591124b17b6ac6058d64c08a49bc11ca9651bbd9642b |
"""
Mappings from file extensions to biopython types
"""
import bz2
import gzip
import os.path
import sys
# Define mappings in a dictionary with extension : BioPython_file_type.
EXTENSION_TO_TYPE = {'.aln': 'clustal',
'.afa': 'fasta',
'.fa': 'fasta',
'.faa... | theboocock/ancient_dna_pipeline | src/seqmagick/seqmagick/fileformat.py | Python | mit | 2,292 | [
"Biopython"
] | 15f024e5e0baa06c64e576e7b3b1c1c93c41f34eba09dd64a7df638ecf14c7dd |
#!/usr/bin/python
#
# Copyright (C) 2014, Jaguar Land Rover
#
# This program is licensed under the terms and conditions of the
# Mozilla Public License, version 2.0. The full text of the
# Mozilla Public License is at https://www.mozilla.org/MPL/2.0/
#
#
# Simple RVI service caller
#
import sys
from rvilib impor... | PDXostc/rvi_mobile_unlock | raspi/rvi_call.py | Python | mpl-2.0 | 1,637 | [
"Jaguar"
] | 146b0953db32ac4844d33d9b909392a63a1e01223891dfa6e42adc7e1bc92710 |
import pytest
import re
from capybara.exceptions import ElementNotFound
from capybara.tests.helpers import extract_results
class ClickButtonTestCase:
@pytest.fixture(autouse=True)
def setup_session(self, session):
session.visit("/form")
class TestClickButton(ClickButtonTestCase):
@pytest.mark.r... | elliterate/capybara.py | capybara/tests/session/test_click_button.py | Python | mit | 13,033 | [
"VisIt"
] | 941742755ebbcd92ded5ee17c26d4f4b81c85f0993335953e05ed84eeae539ca |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christopher M. Bruns
# Contributors: Peter Eastman, Robert McG... | casawa/mdtraj | mdtraj/formats/pdb/pdbstructure.py | Python | lgpl-2.1 | 37,185 | [
"CRYSTAL",
"Gromacs",
"MDTraj",
"OpenMM",
"VMD"
] | d71e0334fba6439a1f88558f40d212b7c6aac1b88eec1560516f748493e4841e |
"""
poses.py
-----------
Find stable orientations of meshes.
"""
import numpy as np
from .triangles import points_to_barycentric
try:
import networkx as nx
except BaseException as E:
# create a dummy module which will raise the ImportError
# or other exception only when someone tries to use networkx
... | dajusc/trimesh | trimesh/poses.py | Python | mit | 10,162 | [
"Gaussian"
] | 2f21ea7992153262feb55de9e4d2a29f9369930560b2e1b4bc0575b3d86e74c4 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/py-spglib/package.py | Python | lgpl-2.1 | 1,822 | [
"CRYSTAL"
] | d3da9d66a35953d09577b5b7bb2e7f6f783b071810718fd8551b145a0d4b9086 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, print_function
from compliance_checker.base import BaseCheck, BaseNCCheck, Result, TestCtx
from compliance_checker.cf.appendix_d import (dimless_vertical_coordinates,
no_missing... | DanielJMaher/compliance-checker | compliance_checker/cf/cf.py | Python | apache-2.0 | 152,934 | [
"NetCDF"
] | 7800ca5a76d88b3b48e5425492590f168b8da2eac5b172a42992614396f04f80 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | pie/settings_global.py | Python | gpl-3.0 | 4,264 | [
"Brian"
] | ce9be78884f51d891ff85d8e7eb11184f16832a7c9296ac1b2bf4fed62751b6b |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create a rendering window and renderer
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
renWin.StereoCapableWindowOn()
iren = vtk.vtkRenderWindowInte... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/EnSight/Testing/Python/EnSightGoldElementsBin.py | Python | gpl-3.0 | 1,366 | [
"VTK"
] | 940a3a79ca1862191380cfce5929c69766d17df7830c6622684ff08ca07b9ade |
# Copyright (C) 2015 Philipp Baumgaertel
# All rights reserved.
#
# This software may be modified and distributed under the terms
# of the BSD license. See the LICENSE.txt file for details.
import numpy as np
from .UncertaintyPropagation import UncertaintyPropagationExact, UncertaintyPropagationApprox
from .Utilitie... | snphbaum/scikit-gpuppy | skgpuppy/InverseUncertaintyPropagation.py | Python | bsd-3-clause | 5,799 | [
"Gaussian"
] | 1dd0f10d4ebb66b94f1a2baaeabed339b1599186d070f1abbf065c9a5bafed47 |
__author__ = 'sibirrer'
from astrofunc.LensingProfiles.flexion import Flexion
import numpy as np
import numpy.testing as npt
import pytest
class TestExternalShear(object):
"""
tests the Gaussian methods
"""
def setup(self):
self.flex = Flexion()
g1, g2, g3, g4 = 0.01, 0.01, 0.01, 0... | sibirrer/astrofunc | test/test_flexion.py | Python | mit | 2,353 | [
"Gaussian"
] | 27cc51bfefb0601925b2bcb57b2ce0caee7949db3b327ab8fc5c8ce5a92cc391 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/mdi_engine.py | Python | lgpl-3.0 | 15,746 | [
"Psi4"
] | 852976b29ffa7e52350ca56f2fde1e579dd033b782dc48e5099af18cd68a5202 |
#!/usr/bin/env python
"""
Utilities for using M2Crypto SSL with DIRAC.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import tempfile
from M2Crypto import SSL, m2, X509
from DIRAC.Core.DISET import DEFAULT_SSL_CIPHERS, DEFAULT_SSL_METHODS
fro... | ic-hep/DIRAC | src/DIRAC/Core/DISET/private/Transports/SSL/M2Utils.py | Python | gpl-3.0 | 8,620 | [
"DIRAC"
] | 261fc89e31aa6b40a2a4fb87dd51faed8d4c7512aed09927cb7a6eb3c2123a8a |
"""
The code module ssd.py was developed to accompany the book
Signals and Systems for Dummies published by Wiley Publishing.
Copyright 2012, 2013 Mark Wickert, mwickert@uccs.edu
v 1.0
Notes
-----
The primary purpose of this function library is to support the book Signals and Systems for Dummies. Beyond that it shou... | BMJHayward/soundgen | utils/tenbandeq.py | Python | gpl-3.0 | 88,302 | [
"Gaussian"
] | f5c7164e71e27ff452a33d23f05c059b29ccd9bf6a4610bcf55aa9eac35bb2c2 |
import datetime
import math
import os
import random
import statistics
from collections import defaultdict
from functools import lru_cache
import matplotlib as mpl
import matplotlib.cm as cm
import matplotlib.colors as colors
import matplotlib.pyplot as plt
import numpy as np
from opensfm import io, multiview
from open... | oscarlorentzon/OpenSfM | opensfm/stats.py | Python | bsd-2-clause | 28,704 | [
"Gaussian"
] | ecfe65430a9aa63986e5837c0d53ab91aad004d973a2220618913d29cc496036 |
########################################################################
# File : StatesAccountingAgent.py
# Author : A.T.
########################################################################
""" StatesAccountingAgent sends periodically numbers of jobs in various states for various
sites to the Monitorin... | andresailer/DIRAC | WorkloadManagementSystem/Agent/StatesAccountingAgent.py | Python | gpl-3.0 | 5,407 | [
"DIRAC"
] | 7ff74ad85ad0bda2599d0b0aecad95205c98fa7205a26d42d870323acc928f5a |
from neural_network import NeuralNetwork
from formulae import calculate_average_error, seed_random_number_generator
from video import generate_writer, annotate_frame, take_still
import parameters
class TrainingExample():
def __init__(self, inputs, output):
self.inputs = inputs
self.output = output... | paladin74/neural-network-animation | main.py | Python | mit | 2,589 | [
"NEURON"
] | 1adcb369842187302c3faa8d3f753eaed16d48560e9cc8f3e99040f1bbb1baa0 |
"""Stateful programmatic WWW navigation, after Perl's WWW::Mechanize.
Copyright 2003-2006 John J. Lee <jjl@pobox.com>
Copyright 2003 Andy Lester (original Perl code)
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file COPYING.txt
included w... | ppizarror/korektor | bin/mechanize/_mechanize.py | Python | gpl-2.0 | 24,967 | [
"VisIt"
] | c12488f546891769ba1e3635ddcd4c166db89de1e5315732750945f03d533525 |
# -*- coding: utf-8 -*-
# -*- coding: utf-8 -*-
'''
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.
Preamble
The GNU General ... | CuonDeveloper/cuon | cuon_client/cuon/bin/cuon/bin/Cuon.py | Python | gpl-3.0 | 78,868 | [
"VTK"
] | db8c8147f18d7bfcdeaa16dc769f889d7fd263463b0749580bda9991a22253e4 |
#!/usr/bin/env python2
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
import sys
from functools import partial
from PyQt5.Qt import (
QMainWi... | songfj/calibre | src/calibre/gui2/tweak_book/editor/image.py | Python | gpl-3.0 | 11,219 | [
"Gaussian"
] | ae39b40f80be591451d5068fdd2e07453eda5125afccf9557568563f8fb3b0d6 |
from contextlib import contextmanager
class Base(object):
""" The base class for drivers used by sessions. """
@property
def needs_server(self):
""" bool: Whether this driver needs to communicate with a real HTTP server. """
return False
@property
def current_url(self):
"... | elliterate/capybara.py | capybara/driver/base.py | Python | mit | 7,193 | [
"VisIt"
] | 18fb5da40795688cacdecc3866528677ff9692d073d24b8e58aa8c7dea9653d1 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import collections
import numbers
import string
from itertools import combinations_with_replacement, product
import os
import six
import re
from collections ... | czhengsci/pymatgen | pymatgen/core/composition.py | Python | mit | 43,461 | [
"pymatgen"
] | e687520cce00a5b7b81554049c9f512f42617dd99451acb47df51862979510e1 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/pytest/utils.py | Python | lgpl-3.0 | 1,848 | [
"Psi4"
] | 5f101415da8e61094255d672fcbcb7a75f5bba25368059df65a241f17f2b476d |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import logging
from math import ceil
import sys
import numpy as np
import tensorflow as tf
DEPTH_MEAN = [127.5, 127.5, 127.5]
class FCN8VGG:
def __init__(self, vgg16_npy_path=None):
if... | jpapon/minimal_ros_nodes | cnn_classifier/src/cnn_classifier/tensorflow_fcn/fcn8_vgg_depth.py | Python | bsd-3-clause | 20,469 | [
"Gaussian"
] | f71df063d5fb1085f3a9dda71f3045e62c715ec4fd2336e454eeeb349888a7bd |
#!/usr/bin/env python
"""
Get rid of lines containing duplicate bonded nbody interactions in the
corresponding section of a LAMMPS data file (such as bonds, angles,
dihedrals and impropers). Duplicate lines which occur later are
preserved and the earlier lines are erased.
(This program reads from sys.s... | yidongxiainl/lammps | tools/moltemplate/moltemplate/remove_duplicates_nbody.py | Python | gpl-2.0 | 1,633 | [
"LAMMPS"
] | 0daa8c99bffe66851dcb7b35a2d2f02b2c8fb843605ff8158807294f8835e262 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetR... | ashray/VTK-EVM | Filters/Core/Testing/Python/combStreamers.py | Python | bsd-3-clause | 2,465 | [
"VTK"
] | 7147bd372591aa71b9fbebc6986833b6775de53041f8d04bd78da8d482bf6d4d |
import pytest
import numpy as np
from numpy.testing import assert_allclose
from .... import units
from ....tests.helper import assert_quantity_allclose
from .. import LombScargle
ALL_METHODS = LombScargle.available_methods
ALL_METHODS_NO_AUTO = [method for method in ALL_METHODS if method != 'auto']
FAST_METHODS = [m... | kelle/astropy | astropy/stats/lombscargle/tests/test_lombscargle.py | Python | bsd-3-clause | 16,935 | [
"Gaussian"
] | e85429d7c15f7d771e30573c16f8dbe3ef1bede9a450a36f7ffa09e2bbb7310d |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2007, 2008, 2009, 2010, 2011 CERN.
#
# Invenio 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 (a... | crepererum/invenio | invenio/legacy/webjournal/config.py | Python | gpl-2.0 | 19,872 | [
"VisIt"
] | 92d454a52b3e4168b77917e562a58a8da51f3505cf392d3d9547c03a1f86d703 |
# -*- coding: utf-8 -*-
#
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Pub... | jchodera/cclib | src/cclib/parser/logfileparser.py | Python | lgpl-2.1 | 17,626 | [
"ADF",
"Avogadro",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | c35c8b1de760ce0564b6cdd9709178bea262cd8c8713eab342a1173cf6a9ca87 |
"""Classes to describe the volume limit mask.
"""
import fitsio
import healpy as hp
import numpy as np
import esutil
import os
import healsparse
from .catalog import Catalog, Entry
from .depthmap import DepthMap
from .redsequence import RedSequenceColorPar
from .utilities import astro_to_sphere, get_healsparse_subpix_... | erykoff/redmapper | redmapper/volumelimit.py | Python | apache-2.0 | 14,010 | [
"Galaxy"
] | 919c312365d5bb0742743d14893384628a4d1466984dd6855cbd2db3daab2408 |
'''oscaar v2.0
Module for differential photometry
Developed by Brett Morris, 2011-2013'''
import numpy as np
from numpy import linalg as LA
import pyfits
from matplotlib import pyplot as plt
import matplotlib.cm as cm
from scipy import ndimage, optimize
from time import sleep
import shutil
from glob import glob
... | bluegod/OSCAAR | oscaar/astrometry/trackSmooth.py | Python | mit | 8,586 | [
"Gaussian"
] | f662eb5085524ed259e404c37f6e818b445fa20364c0dde888b920e64ad367d7 |
# 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/StillingerWeberPairTerm.py | Python | gpl-3.0 | 7,738 | [
"ESPResSo"
] | 55da18c6287a45afa41d677c9e50a817e18d7e194bb5de691ae4a5187dbe1f55 |
'''
MIT License
Copyright (c) 2016 Yuhui Li
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, dist... | yuhuili/capriccio | capriccio.py | Python | mit | 11,776 | [
"CRYSTAL"
] | 8175376486bfe3060770c226ba7b71db8329694f7136bfb92b2cf8f296d9b34e |
"""NWAlign.py
Implementation of the Needleman-Wunsch global alignment algorithm.
This algorithm calculates the optimal aligment between two sequences
allowing gaps.
The algorithm is O(nm) for both time and space.
classes:
NWAlign
"""
# standard modules
import array
# Biopython classes
from Bio import Alphabet
from... | kaspermunch/MultiPurpose | MultiPurpose/NWAlign/NWAlign.py | Python | gpl-2.0 | 9,135 | [
"Biopython"
] | 54bcee1a463cb2de80ced6b63583fe586d02e92984c7e544bc9030888a5ca274 |
# Natural Language Toolkit: Maximum Entropy Classifiers
#
# Copyright (C) 2001-2017 NLTK Project
# Author: Edward Loper <edloper@gmail.com>
# Dmitry Chichkov <dchichkov@gmail.com> (TypedMaxentFeatureEncoding)
# URL: <http://nltk.org/>
# For license information, see LICENSE.TXT
"""
A classifier model based on m... | arju88nair/projectCulminate | venv/lib/python3.5/site-packages/nltk/classify/maxent.py | Python | apache-2.0 | 59,244 | [
"Gaussian"
] | 63b19962b3edac9e7b6a931ccecd9ce3c6190147d6af0f5f693fd6026e474c86 |
"""
Functionality that you wish was on :mod:`os` and :mod:`os.path`.
And some that you don't!
Members
=======
"""
import binascii as _binascii
import contextlib as _contextlib
import errno as _errno
import fnmatch as _fnmatch
import ntpath
import os as _os
import shutil as _shutil
import stat as _stat
import tempfile... | rgalanakis/brennivin | brennivin/osutils.py | Python | mit | 5,157 | [
"MOE"
] | 24436487945d7f6b1e3a2c1763e7e8b36e1fdab88480022cb884245e13aa3ee5 |
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