text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# Copyright (c) 2010-2012 OpenStack Foundation
#
# 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 agree... | openstack/swift | swift/obj/updater.py | Python | apache-2.0 | 33,568 | [
"BLAST"
] | 9c77a055971cc63c29bacef316753c84d26d6c4ae7c3f35c21fe8a11eb6b1cf0 |
# match.py - filename matching
#
# Copyright 2008, 2009 Olivia Mackall <olivia@selenic.com> and others
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
from __future__ import absolute_import, print_function
import bisect
import c... | smmribeiro/intellij-community | plugins/hg4idea/testData/bin/mercurial/match.py | Python | apache-2.0 | 53,313 | [
"VisIt"
] | e71d1ed0739d829c56dc656e54981b7a12a601fdd423e8d44280200ba3d2413a |
#!/usr/bin/python
######################################################################
# Autor: Andrés Herrera Poyatos
# Universidad de Granada, January, 2015
# Breadth-First Search for Shortest Path Problem in Graph Theory
#######################################################################
# This program read ... | andreshp/Algorithms | Graphs/ShortestPath/BreadthFirstSearch/BreadthFirstSearch.py | Python | gpl-2.0 | 5,870 | [
"VisIt"
] | e71ebe603a784c21e7f62c2dc12c120efcbb1cb3fc83d0a2157e8955e3993949 |
#importing some packages
import matplotlib.pyplot as plt
import matplotlib.image as mpimg
import numpy as np
import cv2
import math
import os
# Import everything needed to edit/save/watch video clips
from moviepy.editor import VideoFileClip
def grayscale(img):
"""Applies the Grayscale transform
Th... | tranlyvu/autonomous-vehicle-projects | Finding Lane Lines/src/finding_lane_lines.py | Python | apache-2.0 | 6,734 | [
"Gaussian"
] | 48a87a48a2860a29b09acebc0b03b36ed39f24e3ea75a8ca61f125d6eda0f2a4 |
"""Utilities used by AIM
"""
import os, sys
from math import sqrt, pi, sin, cos, acos
from subprocess import Popen, PIPE
from config import update_marker, tephra_output_dir, fall3d_distro
import numpy
import logging
import time
import string
from Scientific.IO.NetCDF import NetCDFFile
def run(cmd,
stdout=No... | GeoscienceAustralia/PF3D | source/aim/utilities.py | Python | gpl-3.0 | 39,189 | [
"NetCDF"
] | cd65c7b1d44b828b48db495292a372568524f2adb17c8ad884dc997b8e7196fa |
# Copyright (c) 2000-2008 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... | dbbhattacharya/kitsune | vendor/packages/pylint/test/unittest_pyreverse_writer.py | Python | bsd-3-clause | 2,652 | [
"VisIt"
] | 451c59a5390fb46a18a6699b5a5ec3dbe1fff4fc8f10faf882f76e612dfa7d04 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | galsim/optics.py | Python | gpl-3.0 | 49,279 | [
"Galaxy"
] | 7427435084f5524fad027023ad91bc32e0f2075cb384df2efb1ce8d2ef8c9276 |
# Copyright (C) 2013, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os, subprocess
from os.path import join, dirname, abspath
from zeroinstall import SafeException
from repo import scm
topdir = dirname(dirname(dirname(abspath(__file__))... | bastianeicher/0repo | repo/cmd/create.py | Python | lgpl-2.1 | 2,001 | [
"VisIt"
] | eed2e476b0c9a3f565e989503159ef732262619dfc7c52b43fa9b6e9d4675faf |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides plotting capabilities for battery related applications.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ =... | gVallverdu/pymatgen | pymatgen/apps/battery/plotter.py | Python | mit | 3,550 | [
"pymatgen"
] | 0ea287ea03bc5e07682c05bc33293ec245cd16e277040b59ef3b78e49105aa27 |
import imgaug as ia
from imgaug import augmenters as iaa
import os
import cv2
import numpy as np
DATASET_DIR = '/media/meerkat/Data/datasets/docs_crlv_plate_augmented'
NUM_AUG_IMAGES = 10
NUM_SCALES = 3
MAX_SCALE = 1.6
IM_HEIGHT = 64
alphabet = '0123456789abcdefghijklmnopqrstuvwxyz/'
# Sometimes(0.5, ...) applies... | meerkat-cv/annotator-supreme | annotator_supreme/plugins/export_crlv_plate_augmentation.py | Python | mit | 9,056 | [
"Gaussian"
] | dcd995400261a74e2d8f2e7785c9b04cd36f0b274b2eb0ecf45107ed8036b26b |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Cancel' will indicate an asset log entry did not occur",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that has a boundary for... | code-for-india/sahana_shelter_worldbank | languages/sv.py | Python | mit | 403,965 | [
"VisIt"
] | a9adc002bc84f637c2cc4c4e457bb6ab4ea1126e8936719de947a683e9b3058b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/qcdb/qchem.py | Python | lgpl-3.0 | 18,475 | [
"CFOUR",
"Psi4",
"Q-Chem"
] | 0baa13a55ebd7b3d29de8f253f7d911a91013d0e0664a499b31ec7b93779c427 |
"""Support for creating packages of data.
Ambry creates packages of data that simplify the process of finding,
cleaning, transforming and loading popular datasets. The data bundle format,
tools and management processes are designed to make common public data sets easy
to use and share, while allowing users to audit ho... | CivicKnowledge/ambry | ambry/__init__.py | Python | bsd-2-clause | 1,391 | [
"VisIt"
] | df5ec87fedb094d85bccf6979dc5f9a6495276248cfa344bcd20998959c2af5f |
'''A set of utilities to interact with gromacs'''
# Need to add a parser to insert this contrib script
# $ chemlab gromacs energy
# it should show a little interface to view the energy
# Let's launch the program and determine what happens
from chemlab.io import datafile
from pylab import *
from chemlab.molsim.analys... | GabrielNicolasAvellaneda/chemlab | chemlab/contrib/gromacs.py | Python | gpl-3.0 | 3,251 | [
"Gromacs"
] | 8f926999158b8244fdd2e215a159e6d2ab2cc9948f8bea6700ef8e93f5d25d1e |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Teng Lin
#
# MDTraj is free so... | ctk3b/mdtraj | mdtraj/tests/test_dtr.py | Python | lgpl-2.1 | 10,946 | [
"MDTraj"
] | 02b9746f56b899f5e012abf3e65d23b3e0c7070e2dceca86861694f8033a1d10 |
"""
Otsu's binarization
uses parameter retVal
global thresholding -- uses arbitrary value for threshold (trial and error)
bimodal image (histogram has 2 peaks) - can approximately take value between the 2 peaks as threshold
- Otsu binarization - automatically calculates threshold value from image histogram for bimodal... | SSG-DRD-IOT/commercial-iot-security-system | opencv/tutorials/imageProcessing/thresholding/otsu_binarization.py | Python | mit | 2,182 | [
"Gaussian"
] | 63a4a0582f53f577cf27f7b5b39ced709f08886f5156dfd94f334dba547f829c |
# This program computes the delay between the different gene segments using the
# convolved Gaussian process framework for RNA pol-II dynamics
#
# Ciira wa Maina, 2013
# Dedan Kimathi University of Technology.
# Nyeri-Kenya
import sys
import numpy as np
import pylab as pb
import conv_gp_funcs as cgf
import scipy a... | ciiram/PyPol_II | PyPolII.py | Python | bsd-3-clause | 5,281 | [
"Gaussian"
] | 19df8641f1fe470811aa27f0933f0511055520a4c0800225d289025ecbb27872 |
import sys
import hashlib
import pytest
import numpy as np
from numpy.linalg import LinAlgError
from numpy.testing import (
assert_, assert_raises, assert_equal, assert_allclose,
assert_warns, assert_no_warnings, assert_array_equal,
assert_array_almost_equal, suppress_warnings)
from numpy.random import G... | simongibbons/numpy | numpy/random/tests/test_generator_mt19937.py | Python | bsd-3-clause | 109,525 | [
"Gaussian"
] | d5d906e33f77cd8866cc3080a0b885e90616d09d0ef4a956880503fbbb98dc4e |
""" Unit Test of Workflow Modules
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import unittest
import itertools
import os
import copy
import shutil
from mock import MagicMock as Mock
from DIRAC import gLogger
class ModulesTestCase(unittest.TestCas... | yujikato/DIRAC | src/DIRAC/Workflow/Modules/test/Test_Modules.py | Python | gpl-3.0 | 31,932 | [
"DIRAC"
] | 0d65bf898316b5fc0ae8938c179a8a54f746aabac2592d20ccf760989f420cd7 |
#!/usr/bin/env python
"""
crate_anon/anonymise/eponyms.py
===============================================================================
Copyright (C) 2015-2021 Rudolf Cardinal (rudolf@pobox.com).
This file is part of CRATE.
CRATE is free software: you can redistribute it and/or modify
it under th... | RudolfCardinal/crate | crate_anon/anonymise/eponyms.py | Python | gpl-3.0 | 53,538 | [
"Brian"
] | f86798a5fc01c7a1bdd53a66d4b58da5cec31b23c8ef33a3fb4a9477985485c1 |
# -*- coding: utf-8 -*-
# options.py
# Global options file
# Copyright 2006 Giuseppe Venturini
# This file is part of the ahkab simulator.
#
# Ahkab 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, version 2 o... | ahkab/ahkab | ahkab/options.py | Python | gpl-2.0 | 7,088 | [
"Gaussian"
] | 04127cdf0b347e60e24916650833ffa82712fa68fadae4e9e0d7eded27ff89d8 |
"""Backscraper for Supreme Court of Maine 2013
CourtID: me
Court Short Name: Me.
Author: Brian W. Carver
Date created: June 20, 2014
"""
from datetime import date
from datetime import datetime
from lxml import html
from juriscraper.OpinionSite import OpinionSite
from juriscraper.opinions.united_states.state import me... | brianwc/juriscraper | opinions/united_states_backscrapers/state/me_2013.py | Python | bsd-2-clause | 548 | [
"Brian"
] | 671da93643dd5fe53d9be5f7d19cc44c15d3aa7ec48f4d0ec7209ded41e7a7a6 |
"""
Blueprint which provides the RESTful web API for JPER
"""
from flask import Blueprint, make_response, url_for, request, abort, redirect, current_app
from flask import stream_with_context, Response
import json, csv
from octopus.core import app
from octopus.lib import webapp, dates
from flask.ext.login import login_u... | JiscPER/jper | service/views/webapi.py | Python | apache-2.0 | 13,902 | [
"Octopus"
] | 1ac4bda890abb683585248c9063cbb9ba5aacc8b50701f5423ae69ed63a8e61b |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particles, Sun"
import pyglet
import summa
from summa.director import dir... | shackra/thomas-aquinas | tests/test_particle_sun.py | Python | bsd-3-clause | 1,236 | [
"Galaxy"
] | ae8d36dc2372ca944460ff2991b60828fd46b47bcff4a2448507f2cd3900ae6a |
import numpy as np
from matplotlib import pyplot
from spm1d import rft1d
eps = np.finfo(float).eps #smallest float
#(0) Set parameters:
np.random.seed(0)
nResponses = 12
nNodes = 101
nIterations = 2000
FWHM = 8.5
interp = True
wrap = True
heights = [2.0, 2.2, 2.4]
c ... | 0todd0000/spm1d | spm1d/rft1d/examples/val_upx_1_t_set.py | Python | gpl-3.0 | 1,698 | [
"Gaussian"
] | 225fc069002fffb90ff47e2ba7d4d1d405624862f08a30510b6f0d424de1fee3 |
"""
SLSClient class is a client for the SLS DB, looking for Status of a given Service.
"""
import socket
import urllib2
from xml.dom import minidom
from DIRAC import S_OK, S_ERROR
def getAvailabilityStatus( sls_id, timeout = None ):
"""
Return actual SLS availability status of entity in sls_id.
Use SLS API: fa... | vmendez/DIRAC | Core/LCG/SLSClient.py | Python | gpl-3.0 | 1,533 | [
"DIRAC"
] | 39932ad0ed206ad54f729de86fb7ae9fbe820ba3be3b16fd8ed3fbb09a4c21cc |
#!/usr/bin/python3
LICENSE= """
/* VECTORBLOX ORCA
*
* Copyright (C) 2012-2018 VectorBlox Computing Inc., Vancouver, British Columbia, Canada.
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:... | VectorBlox/risc-v | tools/riscv-toolchain/opcodes-lve.py | Python | bsd-3-clause | 11,209 | [
"ORCA"
] | be12a45b2cd90723b9c0d98bfcf15f15459ea0adadd3923c49fa7acffa9ce4f4 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkJPEGReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | chrisidefix/devide | modules/vtk_basic/vtkJPEGReader.py | Python | bsd-3-clause | 468 | [
"VTK"
] | f486fa2b544b2ca21aa8549bc1a9b25b7554e14aaa409a220cd4c695591e7e29 |
# -*- coding: utf-8 -*-
# Copyright © 2014 Casey Dahlin
#
# this file is part of foobar.
#
# foobar 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 la... | sadmac7000/Scratchwire.com | scratchwire/app_forms.py | Python | gpl-3.0 | 5,131 | [
"exciting"
] | 122315ee9a35d26f50aa0d85eecb2eafcd99800292118ad7ab5111efb0b13747 |
from __future__ import absolute_import
from .Errors import error, message
from . import ExprNodes
from . import Nodes
from . import Builtin
from . import PyrexTypes
from .. import Utils
from .PyrexTypes import py_object_type, unspecified_type
from .Visitor import CythonTransform, EnvTransform
class TypedExprNode(Exp... | jos4uke/getSeqFlankBlatHit | lib/python2.7/site-packages/Cython/Compiler/TypeInference.py | Python | gpl-2.0 | 20,899 | [
"VisIt"
] | a87d51b1a43c006c893980bcd942a7bf996acda0952b45571617e4f707fa08e4 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Test the Hirshfeld Method in cclib"""
import sys
import os
import logging
import unittest
import numpy
from cclib.me... | ATenderholt/cclib | test/method/testhirshfeld.py | Python | bsd-3-clause | 5,023 | [
"Psi4",
"cclib"
] | 5f6724ffb6c4dc44976f6c8e44404a6f33b8aad205eb0ecb413ae13cf958721e |
# -*- coding: utf-8 -*-
# This file is part of MOOSE simulator: http://moose.ncbs.res.in.
# MOOSE 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 lat... | dharmasam9/moose-core | python/setup.py | Python | gpl-3.0 | 2,269 | [
"MOOSE"
] | edc1791e50aea84680c3faf32323467a72fcac0bcff5909442c9b46619a052fd |
import numpy as np
import matplotlib.pyplot as plt
import mpl_toolkits.axes_grid1
import utils
import scipy.sparse
import tensorflow as tf
# Global parameters
dataset_name = 'standard'
patch_size = (32, 32) # (patch_height, patch_width)
compression_percent = 60
# Data acquisition
# Generate original images
utils.g... | mdeff/ntds_2016 | project/reports/compressed_sensing/main.py | Python | mit | 5,839 | [
"Gaussian"
] | b124de1832f8e8caddc35b13721431b7c141407e01ec366dc85e6949cb121c74 |
import os
import logging
import unittest
import deepchem as dc
logger = logging.getLogger(__name__)
class TestDrop(unittest.TestCase):
"""
Test how loading of malformed compounds is handled.
Called TestDrop since these compounds were silently and erroneously dropped.
"""
def test_drop(self):
"""Test ... | deepchem/deepchem | deepchem/data/tests/test_drop.py | Python | mit | 982 | [
"RDKit"
] | 9fe94eb55d4d55484a2ea2527f09f120d197a335c8316f0e9742ce6594daef83 |
# coding: utf-8
# In[ ]:
#!/bin/env python
"""
This solves for the terms common scalar phase, tec, and complex gain using MH algorithm.
author: Joshua Albert
albert@strw.leidenuniv.nl
"""
import numpy as np
import pylab as plt
from dask import delayed
def phase_unwrapp1d(theta):
'''the difference between two ... | Joshuaalbert/RadioAstronomyThings | src/rathings/notebooks/tec_solver.py | Python | apache-2.0 | 27,398 | [
"Gaussian"
] | aa79c4075432f2b2682582a2c2d3a61ab24743e14e11a01c9f56f4400e267347 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
# @file gd_algorithm.py
# @brief
# @author QRS
# @blog qrsforever.github.io
# @version 1.0
# @date 2019-09-23 11:25:05
################################ jupyter-vim #######################################
# https://github.com/qrsforever/vim/blob/master/bundle/.configs/jupyte... | qrsforever/workspace | ML/ai/gd_algorithm.py | Python | mit | 22,271 | [
"Gaussian"
] | 4a5a0b4dc731f76c0a3749699d9b301d2c9e647c0fdda3e282ef8561062dfecd |
"""
.. module:: utilities
:platform: Unix
:synopsis: Helpful function for ScatterBrane
.. moduleauthor:: Katherine Rosenfeld <krosenf@gmail.com>
.. moduleauthor:: Michael Johnson
"""
from __future__ import print_function
import numpy as np
from scipy.interpolate import RectBivariateSpline
from scipy.ndimage... | krosenfeld/scatterbrane | scatterbrane/utilities.py | Python | mit | 6,159 | [
"Gaussian"
] | d60a6912070b799491adbaa8a63ecdf241f8bb991d439754c0f40ab4d40eb51b |
import numpy as np
from ..antechamber.atomtype import atomtype
import math
def pdb(molecule, ff='amber', fn='cnt.pdb', save_dir='.'):
"""Creates a .pdb (protein data bank) type list for use with molecular dynamics packages.
pdb_lines returns list holding every line of .pdb file."""
amber_2_opls = {"CA": "... | ajkerr0/kappa | kappa/md/generate.py | Python | mit | 13,545 | [
"Amber",
"Gromacs",
"LAMMPS"
] | 300ed0f225ea9e51dbfcb43fc5a821cb309f62623003276bed08fb578cf69ffc |
# Copyright 2017 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# TODO(https://crbug.com/1262296): Update this after Python2 trybots retire.
# pylint: disable=deprecated-module
import optparse
import threading
import py_... | catapult-project/catapult | systrace/systrace/tracing_agents/walt_agent.py | Python | bsd-3-clause | 4,648 | [
"VisIt"
] | 87b2612c9ea0b24b56c642f78669488c13eaa227f103bf546a01138aa1d13948 |
from __future__ import division
from Bio.Blast import NCBIXML
from utils_parse_BLAST import *
from utils_analysis import *
import pysam
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from numpy import *
import rpy2.robjects as ro
from rpy2.robjects import r
from rpy2.robjects.numpy2ri import numpy2ri
impor... | oicr-ibc/riser | bin/analysis_BLAST.py | Python | gpl-3.0 | 13,325 | [
"BLAST",
"pysam"
] | 48f53ff96a2fd834f20fa72a93fa9ea74c86cc6e4a9d0de9ca864da5a24ae531 |
#!/usr/bin/env python
# CREATED:2013-03-11 18:14:30 by Brian McFee <brm2132@columbia.edu>
# unit tests for librosa.beat
from __future__ import print_function
# Disable cache
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except:
pass
import pytest
import numpy as np
import scipy.stats
import librosa
f... | carlthome/librosa | tests/test_beat.py | Python | isc | 8,484 | [
"Brian"
] | 6b1302dc0b71ecb8f8ada9f3048bb96cd1895cd0b8abe02614676c0e7e54b0ed |
"""
Quatfit routines for PDB2PQR
This module is used to find the coordinates of a new
atom based on a reference set of
coordinates and a definition set of coordinates.
Original Code by David J. Heisterberg
The Ohio Supercomputer Center
1224 Kinnear Rd.
Columbus, OH 43212-1163
(614... | dmnfarrell/peat | Protool/quatfit.py | Python | mit | 14,790 | [
"COLUMBUS"
] | c13e260ced31224966343da85f7dd3e2608f1a2648f0e801bf12eb70e216a6ed |
from __future__ import print_function
import mdtraj as md
from mdtraj.testing import get_fn, eq, DocStringFormatTester, skipif
from mdtraj.utils import six
import os
import shutil
import tarfile
import tempfile
from fahmunge import fah
def test_fah_core17_1():
filename = get_fn('frame0.xtc')
tempdir = tempfile... | steven-albanese/FAHMunge | FAHMunge/tests/test_fah.py | Python | lgpl-2.1 | 1,251 | [
"MDTraj"
] | 26d7b88e94f3d1884b97786ec58d54f2adccf00191cb706b9ceadc687f8dd45d |
""" An utility to load modules and objects in DIRAC and extensions, being sure that the extensions are considered
"""
import collections
import os
import re
import pkgutil
import DIRAC
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import List
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/ObjectLoader.py | Python | gpl-3.0 | 9,279 | [
"DIRAC"
] | 9ef381741ce0c040bc3955c30b371b38678a5e1b5fd81af19c77e910c5a6fc56 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import random
import unittest
from collections import Counter
import numpy as np
from pymatgen.analysis.defects.utils import (
ChargeDensityAnalyzer,
ChargeInsertionAnalyzer,
QModel,
... | gmatteo/pymatgen | pymatgen/analysis/defects/tests/test_utils.py | Python | mit | 15,780 | [
"VASP",
"pymatgen"
] | c897fb8095004024e84f426d420ef6bdace3090d78400cc100f4dab12e05ae5a |
# Copyright (c) 2015-2016 Claudiu Popa <pcmanticore@gmail.com>
# Licensed under the LGPL: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.en.html
# For details: https://github.com/PyCQA/astroid/blob/master/COPYING.LESSER
import contextlib
import unittest
import astroid
from astroid import extract_node
from astro... | lucidmotifs/auto-aoc | .venv/lib/python3.5/site-packages/astroid/tests/unittest_protocols.py | Python | mit | 7,587 | [
"VisIt"
] | 2d8d8ae0d3c3158a09a3bce08235396193ed67421274e7667a1080e6b0d35a7f |
########################################################################
# $HeadURL$
# File : InputDataAgent.py
########################################################################
"""
The Input Data Agent queries the file catalog for specified job input data and adds the
relevant information to the job opti... | Sbalbp/DIRAC | WorkloadManagementSystem/Executor/InputDataValidation.py | Python | gpl-3.0 | 13,219 | [
"DIRAC"
] | c23f4ac6877fc8cdfe27b882fc3bc3d266f7b897bfe7706e309b58c239a54ee9 |
import os
import pdb
import numpy
import netCDF4
import sys
import pandas
import logging
import plot
import constants
import pygeoutil.util as util
import pygeoutil.rgeo as rgeo
import tempfile
# TODO: Clean up output paths, currently windows specific
# TODO: Check if creating butler map is working (not high priorit... | ritviksahajpal/LUH2 | LUH2/GLM/shifting_cult.py | Python | mit | 18,333 | [
"NetCDF"
] | 0a765a6cfab51ba544c8e73e487efb544d13e67f67cc6fef40326ff40533fb0c |
#!/usr/bin/env python3
#
# Data manager for reference data for the 'mothur_toolsuite' Galaxy tools
import io
import json
import optparse
import os
import shutil
import sys
import tarfile
import tempfile
import urllib.error
import urllib.parse
import urllib.request
import zipfile
from functools import reduce
# When ext... | galaxyproject/tools-iuc | data_managers/data_manager_mothur_toolsuite/data_manager/fetch_mothur_reference_data.py | Python | mit | 20,605 | [
"Galaxy"
] | bcf69114809bdf879311492c1a905ea3dd766d9be39f0d0877d84bda18ac7208 |
#!/usr/bin/python
#
# Copyright 2015 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 b... | wubr2000/googleads-python-lib | examples/adwords/v201502/campaign_management/validate_text_ad.py | Python | apache-2.0 | 2,766 | [
"VisIt"
] | b576366710a8431661f8d3252c035df462a7eccab6e1504f097ba0b1b8e4e28e |
r"""
Homology :mod:`homology`
========================
Tools for "symmetrizing" a period matrix.
There exists a symplectic transformation on the period matrix of a real curve
such that the corresponding a- and b-cycles have certain transformation
properties until the anti-holomorphic involution on said Riemann surfac... | cswiercz/abelfunctions | abelfunctions/homology.py | Python | bsd-3-clause | 14,848 | [
"Gaussian"
] | bc9bdfcfa80512b0fdc6585d4ff7da17e5ad3b55fc3c9123a5bbea4fdb2d14b7 |
########################################################################
# File : CPUNormalization.py
# Author : Ricardo Graciani
########################################################################
""" DIRAC Workload Management System Client module that encapsulates all the
methods necessary to handle CPU... | marcelovilaca/DIRAC | WorkloadManagementSystem/Client/CPUNormalization.py | Python | gpl-3.0 | 6,590 | [
"DIRAC"
] | 69b132e25cac2410d6cb6c8a14bdc6a16e72e5d039dee090bfb8ce3eb66be88e |
# $Id$
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
# @@ 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.
#
""" unit testing code f... | soerendip42/rdkit | rdkit/DataStructs/UnitTestcBitVect.py | Python | bsd-3-clause | 10,981 | [
"RDKit"
] | b8b98a4270349e66f2b61176eb2eb322bbed4bba1d65497bb40b5353c5fc3347 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# File: ponies.py
# by Arzaroth Lekva
# lekva@arzaroth.com
#
from collections import OrderedDict
PONY_LIST = OrderedDict([
('Pony_Ace', 'Ace'),
('Pony_Action_Shot', 'Action Shot'),
('Pony_AKYearling', 'AKYearling'),
('Pony_Aloe', 'Aloe'),
('Pony_Appl... | Arzaroth/CelestiaSunrise | celestia/utility/ponies.py | Python | bsd-2-clause | 10,899 | [
"FLEUR"
] | 4ca211c8fa345eae3950b15c17bea42c56be6b2efa664cde5a580e0693f8e0d5 |
#!/usr/bin/env python
# encoding: utf-8
"""PGEM test configuration model.
Default connect to configuration.db which save the test items settings.
"""
__version__ = "0.1"
__author__ = "@fanmuzhi, @boqiling"
__all__ = ["PGEMConfig", "TestItem"]
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy imp... | hardanimal/UFT_UPGEM | src/UFT/backend/configuration.py | Python | gpl-3.0 | 3,635 | [
"CRYSTAL"
] | b48f8a4584146ffac3fd1c3b5f88a7b0787347ce17b8717857759817e793349e |
# (c) 2013-2016, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.com>
# Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under t... | eerorika/ansible | lib/ansible/plugins/action/assemble.py | Python | gpl-3.0 | 6,427 | [
"Brian"
] | 653b8615fa6d7726d5b929858d152b08327a9b5abc2775a0abae3c1774965bc0 |
# encoding: 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):
# Adding field 'MessageType.clinic'
db.add_column('core_messagetype', 'clinic', self.gf('django.db.models.... | praekelt/txtalert | txtalert/core/migrations/0018_auto__add_field_messagetype_clinic__chg_field_messagetype_group.py | Python | gpl-3.0 | 16,298 | [
"VisIt"
] | 1d015b1b897de2d8cb2fc3b6e3820eaa0209da1f0fe11c0fa5d24e3c5507dc7b |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('refactor_workflow')
@click.argument("workflow_id", type=str)
@click.option("--actions", type=str, multiple=True, required=True)
@click.option(
"--dry_run",
help="When true, ... | galaxy-iuc/parsec | parsec/commands/workflows/refactor_workflow.py | Python | apache-2.0 | 859 | [
"Galaxy"
] | 8c55e0a4de07c7e0d5c5e877366262b1cd6844d1241737d0f7728b65e83a16c0 |
import Tools.HTML
if __name__ == "__main__":
import sys,os
append_path = os.path.abspath(sys.argv[0])[:-15]
print("Append to PYTHONPATH: %s" % (append_path))
sys.path.append(append_path)
import re
import Tools.web as web
from Tools.file2 import file2
from Geometry import Scan,IRC,Geom,ListGeoms
import... | talipovm/terse | terse/Interface/Orca.py | Python | mit | 14,537 | [
"Gaussian",
"Jmol",
"ORCA"
] | ca60c71f83ebbb8cfffbdbbd4150cf90ef6a7b3cb9b493b5bd366ce8e79c858a |
# -*- coding: utf-8 -*-
#
# Copyright 2015-2016 - Gabriel Acosta <acostadariogabriel@gmail.com>
#
# This file is part of Pireal.
#
# Pireal 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 t... | centaurialpha/pireal | src/pireal/interpreter/parser.py | Python | gpl-3.0 | 11,042 | [
"VisIt"
] | 9e30968f58becd25b2ec9e0582717bac18ff47b78cd2c173638cdcb561840737 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 ... | nuclear-wizard/moose | python/peacock/Input/MeshBlockSelectorWidget.py | Python | lgpl-2.1 | 2,568 | [
"MOOSE",
"VTK"
] | d55b8452cd8351085b6dca23e33dfa02ff6cbc409eee52d07a0a12dd64a25cae |
"""
Django settings for homeworks project.
Generated by 'django-admin startproject' using Django 1.8.
For more information on this file, see
https://docs.djangoproject.com/en/1.8/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.8/ref/settings/
"""
# Build path... | koebbe/homeworks | homeworks/settings.py | Python | mit | 3,306 | [
"Brian",
"VisIt"
] | c09a9dcda48f0b7c971ade441debd56ee90093705ddba3ece2baca00e3cb45ff |
from model_mommy import mommy
# def test_simple(timbrowser):
# timbrowser.visit(timbrowser.url)
# assert timbrowser.is_text_present('Timtec')
def test_login(timbrowser, user):
b = timbrowser
b.visit(b.url)
b.find_by_xpath('//a[normalize-space(text())="Entrar"]').click()
assert b.is_element_p... | mupi/tecsaladeaula | tests/test_fullstack.py | Python | agpl-3.0 | 802 | [
"VisIt"
] | 1e3b32d40aaac555269af2a4450890522849807e9dfd519b21b8e652c4657df9 |
# Copyright (c) 2013, ReMake Electric ehf
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice,
# this list of conditions... | remakeelectric/mqtt-malaria | beem/msgs.py | Python | bsd-2-clause | 3,699 | [
"Gaussian"
] | ce8f66c37617a95ad1501e87b9870479f38968e27452504f3fd929297db7878b |
#
# Copyright 2001 - 2006 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space 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 Lice... | Lukc/ospace-lukc | server/lib/ige/ospace/ISystem.py | Python | gpl-2.0 | 35,859 | [
"Galaxy"
] | b332ac7d0eda7084e03e4bae63c2237f579026517ce65c1e09ac15b616ea1374 |
# leaves.py
# DNF plugin for listing installed packages not required by any other
# installed package.
#
# Copyright (C) 2015 Emil Renner Berthing
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public ... | esmil/dnf-plugins-extras | plugins/leaves.py | Python | gpl-2.0 | 4,887 | [
"VisIt"
] | 35f5009b8e9da0290808812c2ed3380301f7f394b5201c354ec4e12b389cc07d |
#!/usr/bin/env python
'''
GW calculation with exact frequency integration
'''
from pyscf import gto, dft, gw
mol = gto.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = 'ccpvdz')
mf = dft.RKS(mol)
mf.xc = 'pbe'
mf.kernel()
nocc = mol.nelectron//2
gw = gw.GW(mf, freq_int='exact')
gw.kernel()
print(gw.mo_energy)
| sunqm/pyscf | examples/gw/02-gw_exact.py | Python | apache-2.0 | 315 | [
"PySCF"
] | ad382b6adf7c1151619d85220d625acea1185ed929230ae1bf2b330257f9496a |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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 v... | graik/biskit | biskit/tools.py | Python | gpl-3.0 | 33,854 | [
"PyMOL"
] | e6fd57d0688304e67236b7bccffefdaacf5bfb4bf9c540176af957be732e86c1 |
""" RHEAS module for retrieving maximum and minimum
temperature from the NCEP Reanalysis stored at the IRI Data Library.
.. module:: ncep
:synopsis: Retrieve NCEP meteorological data
.. moduleauthor:: Kostas Andreadis <kandread@jpl.nasa.gov>
"""
import numpy as np
import datasets
from decorators import netcdf
fr... | nasa/RHEAS | src/datasets/ncep.py | Python | mit | 2,291 | [
"NetCDF"
] | 9420a573e5cc24dbda0b0d9b9db882acd69eb7e391b8a79dab0ccebba49f8c92 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkAVSucdReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.v... | nagyistoce/devide | modules/vtk_basic/vtkAVSucdReader.py | Python | bsd-3-clause | 476 | [
"VTK"
] | 6b3d3fb1f85ca25b85e9d7e4fd364fe2630490f9f05f6197d5452ad1b4b89bb9 |
# encoding: utf-8
"Module for homogeneous deformation and calculations of elastic constants."
import gtk
from ase.gui.simulation import Simulation
from ase.gui.minimize import MinimizeMixin
from ase.gui.energyforces import OutputFieldMixin
from ase.gui.widgets import oops, pack, AseGuiCancelException
import ase
impor... | slabanja/ase | ase/gui/scaling.py | Python | gpl-2.0 | 18,083 | [
"ASE"
] | 48401915d4c0487395d662c7fde084d43a3f524682cd361433d4e7b59a95aa71 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
This module has been moved pymatgen.io.gaussian. This sub module will
be removed in pymatgen 4.0.
"""
__author__ = 'Shyue Ping Ong'
... | migueldiascosta/pymatgen | pymatgen/io/gaussianio.py | Python | mit | 662 | [
"Gaussian",
"pymatgen"
] | e19b29c26f02edd41530df487af26a455f3e7f7a8e98e670e23ccf440f3a592f |
# Released under The MIT License (MIT)
# http://opensource.org/licenses/MIT
# Copyright (c) 2013-2015 SCoT Development Team
import unittest
import numpy as np
from numpy.testing import assert_allclose
from scot.varbase import VARBase as VAR
from scot.datatools import acm
epsilon = 1e-10
class TestVAR(unittest.Tes... | scot-dev/scot | scot/tests/test_var.py | Python | mit | 3,293 | [
"Gaussian"
] | eab7901d1d5b202a7a3faea0648b4a43c9836cd925b38bd4575301f0c5d54437 |
from __future__ import print_function
import os
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
from astropy.io import fits
from astropy.time import Time
from PyAstronomy import pyasl
from scipy import ndimage
import pandas as pd
import gaussfitter as gf
from cycler impo... | savvytruffle/cauldron | rvs/BF_functions.py | Python | mit | 17,121 | [
"Gaussian"
] | e5f270e4561d995ae74ef6bce7fa1311908b10b9bb285a3610126e0ee2854d00 |
# Tests that multiple views can render and save images correctly in batch.
from paraview import smtesting
smtesting.ProcessCommandLineArguments()
from paraview.simple import *
v1 = CreateRenderView()
Sphere()
Show()
Render()
from paraview.vtk.vtkTestingRendering import vtkTesting
import os.path
prefix, ext = os.pat... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/ParaViewCore/ServerManager/Default/Testing/Python/MultiView.py | Python | gpl-3.0 | 1,316 | [
"ParaView",
"VTK"
] | 421e4d45ba64b948e1bb3a3a97bd33e54f839226516c6e687708b9aad28d676b |
import os, time
from wslink import register as exportRpc
from paraview import simple, servermanager
from paraview.web import protocols as pv_protocols
from vtkmodules.vtkCommonCore import vtkUnsignedCharArray, vtkCollection
from vtkmodules.vtkCommonDataModel import vtkImageData
from vtkmodules.vtkPVClientServerCoreR... | Kitware/HPCCloud | pvw-dependencies/pv-lite/lite_protocols.py | Python | apache-2.0 | 5,489 | [
"ParaView",
"VTK"
] | 19a788398fcd7388854323944451925e87d1d4822e3392f0666e9fdf376baff8 |
#!/usr/bin/env python
""" Mission 7-Detect and Deliver
1. Random walk with gaussian at center of map until station position is acquired
2. loiter around until correct face seen
3. if symbol seen, move towards symbol perpendicularly
4. if close enough, do move_base aiming
task 7:
-----------------
Created by ... | ron1818/Singaboat_RobotX2016 | robotx_nav/nodes/mc_deliver.py | Python | gpl-3.0 | 8,318 | [
"Gaussian"
] | abc7649bb9bfe8bca72d15c3b5b4a1fb596fe58be612ed608dd1255b823d8be1 |
import maya.cmds as cmds
import os
from datetime import datetime
###############################
###jsLookdevAssistant DEV #####
###############################
#Author: Joseph Szokoli
#Website: cargocollective.com/josephSzokoli
#Help:
#To create a shelf icon, move jsLookdevAssistant.py to your scripts folder and a... | jszokoli/jsTK | Misc/jsLookdevAssistant.py | Python | gpl-3.0 | 67,262 | [
"exciting"
] | c81e04e19f7048473121fb695ff616eecae6738a09f2b7ada9ac561356406ad0 |
# Gaussian Process Classifier demo
# Author: Drishtii@
# Based on
# https://github.com/probml/pmtk3/blob/master/demos/gpcDemo2d.m
# See also gpc_demo_2d_pytorch for a Gpytorch version of this demo.
import superimport
import pyprobml_utils as pml
import numpy as np
import matplotlib.pyplot as plt
from sklearn.gaussia... | probml/pyprobml | scripts/gpc_demo_2d_sklearn.py | Python | mit | 1,888 | [
"Gaussian"
] | db43135819c3a333112e9ec9711e3280831d9dbbdbd440671ab6fa52b754ae20 |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""Extract information from alignment objects.
In order to try and avoid huge alignment objects with tons of functions,
functions which return sum... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Align/AlignInfo.py | Python | gpl-2.0 | 30,803 | [
"Biopython"
] | 1fff7cae2b158b124714c0252538fe9b05326990671149c40d57f7c744c65b30 |
#!/usr/bin/python -O
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
#################################################... | INNUENDOWEB/INNUca | src/SPAdes-3.9.0-Linux/share/spades/spades_pipeline/corrector_logic.py | Python | gpl-3.0 | 2,370 | [
"BWA"
] | 4916cdfd035068aa0dd2175bc49e6070376ec4c5ffab1f702885f5619e63120e |
#!/usr/bin/env python
# Copyright (c) 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
# Copyright (C) 2008 Evan Martin <martine@danga.com>
"""A git-command for integrating reviews on Rietveld and Gerrit."""
from __f... | Shouqun/node-gn | tools/depot_tools/git_cl.py | Python | mit | 225,299 | [
"VisIt"
] | e230671946e96c329091bbccca0c02f921c448741572726dbe54aa7b5461f576 |
#._cv_part guppy.heapy.View
class Horizon:
def __init__(self, mod):
self.mod = mod
self._hiding_tag_ = mod._hiding_tag_
# Make preallocations of things that will be needed for news()
self.retset = self.mod.retset
self.hv = mod.hv
self.exc_info = self.mod._root.sys.exc_info
self.iso = self.mod.iso
str(self.... | vmanoria/bluemix-hue-filebrowser | hue-3.8.1-bluemix/desktop/core/ext-py/guppy-0.1.10/guppy/heapy/View.py | Python | gpl-2.0 | 15,803 | [
"VisIt"
] | bcfdce2c8280a7ea6da030ba6fb1b2bf2ab17a85776cfc36c91716b12741ee4f |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yashdsaraf/scancode-toolkit | tests/packagedcode/test_package_models.py | Python | apache-2.0 | 5,875 | [
"VisIt"
] | 9fd4da740547b96187cda572bf4f95e3b6cef55175b18b8979eac6b0c67b512c |
from __future__ import absolute_import
from __future__ import print_function
from __future__ import division
import unittest
import os
import numpy as np
from pymatgen.analysis.elasticity.elastic import *
from pymatgen.analysis.elasticity.strain import Strain, Deformation
from pymatgen.analysis.elasticity.stress imp... | setten/pymatgen | pymatgen/analysis/elasticity/tests/test_elastic.py | Python | mit | 21,160 | [
"pymatgen"
] | 82fb49fa82f646997a8501489e4031c45fff426b2ddbb6e10a3826c2efbf33a7 |
# Copyright 2022 The Magenta 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 applicable law or agreed to in ... | magenta/magenta | magenta/models/svg_vae/glyphazzn.py | Python | apache-2.0 | 10,793 | [
"Gaussian"
] | 293de5f41151d004b6de58df9335e095247ac92efb724b0000b3873c7d5c33fc |
#!/usr/bin/env python
"""
write_spec_files.py:
This script generates spec file for various distributions.
Last modified: Mon Aug 10 22:28:30 2015
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, Dilawar Singh and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]... | BhallaLab/moose-full | OBS/home:moose/moogli/write_spec_files.py | Python | gpl-2.0 | 3,279 | [
"MOOSE"
] | dba3ba5caa6dc423e07b3a71c24aaaa650fec6cb4800d0e05e3acbd13bee9cdd |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
import warnings
import numpy as... | olologin/scikit-learn | sklearn/mixture/gmm.py | Python | bsd-3-clause | 31,376 | [
"Gaussian"
] | 06e2fa8270c76130feba2d862937e39bb5291ef586f52a1255f31ab642f75699 |
from libs.graph.DLinkedList import Queue, DoubledLinkedList as List
from libs.graph.PriorityQueue import PriorityQueueBinary as PriorityQueue
from libs.graph.Tree import *
#it is better to use a DoubledLinkedList to operate with a great efficiency on
#the lists those will be used in the graph representation
class Node... | IA-MP/KnightTour | libs/graph/Graph.py | Python | mit | 11,556 | [
"VisIt"
] | 453423fcfc3e6495cb6fab9f76df887ec5d5392e5f4e15f20f0f67e79d75fd14 |
import SloppyCell.Collections as Collections
expt = Collections.Experiment('RasGreen1NGF')
expt.longname = 'NGF Stimulation 50 ng/ml - Qiu and Green 1994'
expt.comments = """REF: M-S. Qiu and S. H. Green, Neuron (1991) 7, 937-946
CELLTYPE: PC12
MEAS: GTP binding by Ras in response to NGF at 50 ng/ml
UNITS: Ra... | GutenkunstLab/SloppyCell | Example/PC12/Experiments/RasGreen1NGF.py | Python | bsd-3-clause | 946 | [
"NEURON"
] | 643bbc19041b2b9ecdd5a3ae3b5f0eee7757a4dfe803f614d8790c74d585f9f6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Modified parameters file for the Hybrid LFP scheme, applying the methodology with
the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (... | espenhgn/hybridLFPy | examples/Hagen_et_al_2016_cercor/cellsim16popsParams_modified_ac_exc.py | Python | gpl-3.0 | 39,720 | [
"Gaussian",
"NEURON"
] | c9333004f5790f864c7be1112bb83c5922d26b3f238a03bb7a415bb4f5f85394 |
# -*- coding: utf-8 -*-
"""
===================================================================
Determining and plotting the altitude/azimuth of a celestial object
===================================================================
This example demonstrates coordinate transformations and the creation of
visibility cur... | pllim/astropy | examples/coordinates/plot_obs-planning.py | Python | bsd-3-clause | 6,289 | [
"VisIt"
] | 12bef7dc219d41692d2cbc9fe75a49900ea1f0df6e831e5d70e413d075a0fb12 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/authUser.py | Python | gpl-3.0 | 4,311 | [
"Galaxy"
] | c752c6b6074c7a9d00def465275ac21226bc5a2314f6413f49aee0ecbe1c8d5a |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Convert a qual (qv) file to several BinnedArray files for fast seek.
This script takes approximately 4 seconds per 1 million base pairs.
The input format is fasta style quality -- fasta headers followed by
whitespace separated integers.
usage: %prog qual_file output_file... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/qv_to_bqv.py | Python | bsd-3-clause | 2,126 | [
"Galaxy"
] | 36ee50fb5a8586892adcef27fc8629b61688509f97924c1eae45ec43c118df7d |
#!/usr/bin/env python
import copy
import json
import os
import os.path
import re
import sys
from collections import OrderedDict
from CTDopts.CTDopts import (
_Choices,
_FileFormat,
_InFile,
_Null,
_NumericRange,
_OutFile,
_OutPrefix,
ModelError,
ParameterGroup
)
from lxml import etr... | WorkflowConversion/CTDConverter | ctdconverter/galaxy/converter.py | Python | gpl-3.0 | 95,121 | [
"Galaxy",
"OpenMS"
] | 57d482a4b020ff44676360befdb75122dc04bad8c02fc0b517d05ee720e26617 |
__author__ = 'sebastians'
# The function provided here can be used if you get no image output with cmd.png (can be no or a black picture).
# Can be also used if you experience segmentation faults with cmd.ray
from pymol import cmd
import os
def png_workaround(filepath, width=1024, height=768):
"""Workaround for... | ssalentin/pymol-animations | special-topics/workaround-png.py | Python | mit | 923 | [
"PyMOL"
] | 1b3428834feeebc8fd6c20c5049c8624a95296d8df8ed602c7428b21ccecb11b |
import numpy
from VirtualObservatoryCatalog import VirtualObservatoryCatalog
class GBMBurstCatalog(VirtualObservatoryCatalog):
def __init__(self):
super(GBMBurstCatalog, self).__init__('fermigbrst',
'http://heasarc.gsfc.nasa.gov/cgi-bin/vo/cone/coneGet.pl?table=fe... | sybenzvi/3ML | threeML/catalogs/Fermi.py | Python | bsd-3-clause | 2,590 | [
"Galaxy"
] | 0c61ff7ff1153a92e727f7f3484c2ac911b7675b45222cfe95653f6f0c882ca9 |
import pytest
import re
from time import sleep
import capybara
from capybara.exceptions import ReadOnlyElementError
from capybara.node.element import Element
from capybara.tests.helpers import extract_results, isfirefox, ismarionette, ismarionettelt
class NodeTestCase:
@pytest.fixture(autouse=True)
def setup... | elliterate/capybara.py | capybara/tests/session/test_node.py | Python | mit | 22,594 | [
"VisIt"
] | adeb4a7e889aeb6cba4a5605da2913f89e362e8350def7cc4f05fadc3b55057a |
#
# @file TestValidASTNode.py
# @brief Test the isWellFormedASTNode function
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/math/TestValidASTNode.py | Python | bsd-3-clause | 8,581 | [
"VisIt"
] | de6d9218c72aeb3c2924aa761889a8d3cefcb9430c530cd8ae428c5a1009a09c |
# -*- coding: utf-8 -*-
# Copyright (C) 2008 Murphy Lab
# Carnegie Mellon University
#
# Written by Luis Pedro Coelho <luis@luispedro.org>
#
# 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; eit... | luispedro/readmagick | setup.py | Python | gpl-3.0 | 3,112 | [
"VisIt"
] | 4f291b849b2a7fb6adff1e5647370f1dc1eb95aff0e45fc7bfe9169bf96c19df |
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