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#!/usr/bin/env python3
from collections import namedtuple
# Read the challenge input
with open("input.txt", 'r') as input_file:
puzzle_input = input_file.read()
# Tuple to use as dictionary key
Location = namedtuple('Location', ['x', 'y'])
# Start dictionary with Santa's starting location
presents_delivered = {Lo... | joseph-roque/advent-of-code | day_03/p2_robo.py | Python | mit | 1,197 | [
"VisIt"
] | fdea909e370130253b7fa9232e15638bd792086ff15d5ab1563298f4635674e3 |
import itertools
import numpy as np
from functools import reduce
from pyscf import lib
from pyscf.pbc.lib import kpts_helper
einsum = lib.einsum
#FIXME: the dtype of each intermediates. When the khf is at gamma point, the
# dtype is inconsistent between intermediates and t amplitudes
def make_tau(cc, t2, t1, t1p, f... | gkc1000/pyscf | pyscf/pbc/cc/kintermediates_uhf.py | Python | apache-2.0 | 59,610 | [
"PySCF"
] | 2ba167c5b9afb5f5eb5aeb8916c43637292938a68f22f294aed68a6785faf338 |
# -*- coding: utf-8 -*-
"""
http://www.astroml.org/sklearn_tutorial/dimensionality_reduction.html
"""
print (__doc__)
import numpy as np
import copy
import matplotlib
import matplotlib.mlab
import matplotlib.pyplot as plt
from matplotlib import gridspec
import nslkdd.preprocessing as preprocessing
import sugarbee.re... | zedoul/AnomalyDetection | test_discretization/test_distance.py | Python | mit | 782 | [
"Gaussian"
] | 9fc6771f02091fd3d1dad77fd0eed3631f350fe527854e1db8bd35bf06e9ca76 |
"""
Dispersed Phases
================
Create several objects and functions to manipulate dispersed phase particles
The `single_bubble_model`, `stratified_plume_model`, and `bent_plume_model`
all must handle dispersed phase particles in several different ways. This
module defines several particle classes that provi... | socolofs/tamoc | tamoc/dispersed_phases.py | Python | mit | 59,836 | [
"Gaussian",
"NetCDF"
] | 16bc2940606da738f7f64b8b940690952fe3e971690db87ebe203e40ad624ed0 |
# Copyright 2021 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | keras-team/keras | keras/engine/functional_utils.py | Python | apache-2.0 | 10,492 | [
"VisIt"
] | 019fbff137b14e9d271277542fb2831df16929d20fdd1d0905a41f7532484584 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Intel-Corporation/tensorflow | tensorflow/python/ops/linalg/linalg_impl.py | Python | apache-2.0 | 65,569 | [
"Gaussian"
] | 68df3f20fc0b686b1ec48388bcd5c644a5e4d8ee0b5cbb2c14012ddd2b438619 |
import unittest
from nose.tools import (assert_is_not_none, assert_raises, assert_equal)
import scipy.sparse
from sknn.mlp import BaseMLP
class TestInputDataTypes(unittest.TestCase):
def setUp(self):
self.nn = BaseMLP(layers=[("Gaussian",)], n_iter=1)
def test_FitSciPySparse(self):
X, y = s... | capitancambio/scikit-neuralnetwork | sknn/tests/test_types.py | Python | bsd-3-clause | 587 | [
"Gaussian"
] | 4ff08d903603baa5491844ad1456cd0f252cb79d55459f6f949f27cc9f44c09f |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# ... | DougFirErickson/neon | tests/serialization/alexnet.py | Python | apache-2.0 | 3,992 | [
"Gaussian"
] | df5c09a8dfbfa05e45287f43602837d8ed2a073180774c77f92de90aa560e590 |
#!/usr/bin/env python
#MIT License
#Copyright (c) 2017 Massimiliano Patacchiola
#
#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
#t... | mpatacchiola/dissecting-reinforcement-learning | src/3/temporal_differencing_control_sarsa.py | Python | mit | 9,331 | [
"VisIt"
] | 406e662c242c81d8e1a2a381183b535f0da49e2dd8258bd4efd3a719a94092bf |
"""
Copyright (c) 2014, Guillermo A. Perez, Universite Libre de Bruxelles
This file is part of the AbsSynthe tool.
AbsSynthe 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
(a... | osankur/abssynthe | algos.py | Python | gpl-3.0 | 4,244 | [
"VisIt"
] | 84ba2de384308c85aeaad15e824118fdbdf1a8d0f0dc3589b771c2e4e5ea7b50 |
#!/usr/bin/env python
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the fol... | wizmer/NeuroM | neurom/check/runner.py | Python | bsd-3-clause | 6,398 | [
"NEURON"
] | 2b77b0c2329951c688a1cc8737348757fb9f78721ac262faff7fc91892cd4de3 |
##############################################################################
# Copyright (c) 2013-2017, 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... | lgarren/spack | var/spack/repos/builtin/packages/r-biostrings/package.py | Python | lgpl-2.1 | 1,948 | [
"Bioconductor"
] | 99a1d072055c2beff2e64d39ed969e4947885d45a54f10aa9ec4d49a92b1bce1 |
# -*- coding: utf-8 -*-
from collections import OrderedDict
import os
import sys
import time
try:
from cStringIO import StringIO
except ImportError:
from StringIO import StringIO
from .bamsam import convert_bam_file
from .bed import convert_bed_file
from .chain import CHAIN_STRING, ChainFile, ChainIter, Chai... | everestial/g2gtools | g2gtools/g2g.py | Python | gpl-3.0 | 42,880 | [
"pysam"
] | bd3621ea2b3f2dc596584a67fce3835d1160a2aa1467c9a686093e2bbcf65292 |
""" NOTA BENE: This agent should NOT be run alone. Instead, it serves as a base class for extensions.
The TaskManagerAgentBase is the base class to submit tasks to external systems,
monitor and update the tasks and file status in the transformation DB.
This agent is extended in WorkflowTaskAgent and Reque... | DIRACGrid/DIRAC | src/DIRAC/TransformationSystem/Agent/TaskManagerAgentBase.py | Python | gpl-3.0 | 31,985 | [
"DIRAC"
] | 6f751afa924e5603373f4eaa36d3d2caa71f98c7d0197879c8566fee77e4c63d |
##########################################################################
# This file is part of ssm.
#
# ssm 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
# ... | ntncmch/ssm | src/Ccoder.py | Python | gpl-3.0 | 42,947 | [
"Gaussian"
] | 28e31ba4c769100361d51166000c4c9eb2036bb13d82f2fd2d184c6ccf415180 |
"""
Description of the video:
Mimic of Star Wars' opening title. A text with a (false)
perspective effect goes towards the end of space, on a
background made of stars. Slight fading effect on the text.
"""
import numpy as np
from moviepy.editor import *
from moviepy.video.tools.drawing import color_gradient
from ski... | kerstin/moviepy | examples/star_worms.py | Python | mit | 5,225 | [
"Galaxy"
] | 06bc57d518a81d0f7c05b855da6bdf7bffe27ecb832f5c582804bb9e0f6bb02e |
"""Move files to local Galaxy upload directory and add to Galaxy Data Libraries.
Required configurable variables in upload:
dir
"""
from __future__ import print_function
import collections
import os
import shutil
import time
from bcbio import utils
from bcbio.log import logger
from bcbio.upload import filesystem
fr... | brainstorm/bcbio-nextgen | bcbio/upload/galaxy.py | Python | mit | 8,148 | [
"Galaxy"
] | fd7f63bb0e0b75c7ffb54ce4cb2be469c625d9e4c98fb63725fecf0b02ef3370 |
from argparse import ArgumentParser, RawDescriptionHelpFormatter
from copy import deepcopy
import os
import subprocess
import pysam
import random
# DO NOT SEED
#random.seed("3337")
def parse_options(description, epilog):
parser = ArgumentParser(description=description, formatter_class=RawDescriptionHelpFormatter,... | broadinstitute/hellbender | scripts/unsupported/reheader_bam/reheader_bam.py | Python | bsd-3-clause | 3,842 | [
"pysam"
] | 541593744fc0a55f75e5d01295c5377ec4e12c296b2848f464acf758f06328ba |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
One-dimensional Gamma-Gaussian mixture density classes : Given a set
of points the algo provides approcumate maximum likelihood estimates
of the mixture distribution using an EM algorithm.
Author: Bert... | ellisdg/3DUnetCNN | unet3d/utils/nipy/ggmixture.py | Python | mit | 20,840 | [
"Gaussian"
] | 64b1ad101a0cc9cee7751fb36b5d2216676d591158e0e7e22c242ff5b18a0529 |
from ase.lattice import bulk
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
from gpaw.xc.exx import EXX
from ase.parallel import paropen
resultfile = paropen('si.pbe+exx.results.txt', 'a')
# Plane wave cutoff
pwcutoff = 600.0
# NxNxN k-point sampling, gamma-centred grid
k = 8
# Si lattice constant
alat... | robwarm/gpaw-symm | doc/exercises/rpa/si.pbe+exx.py | Python | gpl-3.0 | 1,101 | [
"ASE",
"GPAW"
] | 683d257b1e48a8b4b249ca5c8f937d40c06228a1b69cc9d8e089500e315ed5d3 |
# howtoplay.py -- a basic help screen for angrydd
# Copyright 2004 Joe Wreschnig <piman@sacredchao.net>
# Released under the terms of the GNU GPL v2.
__revision__ = "$Id: howtoplay.py 286 2004-09-04 03:51:59Z piman $"
import pygame; from pygame import transform
import characters; from characters import Character
impo... | joshuacronemeyer/Angry-Drunken-Programmers | howtoplay.py | Python | gpl-2.0 | 9,742 | [
"CRYSTAL"
] | c9265a7810ce6a1da5612e4c39a22429f54287530b89cb4758e9ab1372409278 |
# https://scikit-learn.org/stable/auto_examples/gaussian_process/plot_compare_gpr_krr.html
import numpy as np
import matplotlib.pyplot as plt
import pyprobml_utils as pml
import time
import numpy as np
import matplotlib.pyplot as plt
from sklearn.kernel_ridge import KernelRidge
from sklearn.model_selection import ... | probml/pyprobml | scripts/krr_vs_gpr.py | Python | mit | 2,543 | [
"Gaussian"
] | b3bbed0b9fe06efdcb9c82bec0d2c70282d3a18287e09d35f4570f6ae9b7794c |
# Copyright (c) 2013, Web Notes Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and
from frappe import _
from frappe.model.mapper import get_map... | Tejal011089/digitales_erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | agpl-3.0 | 16,661 | [
"VisIt"
] | c609c7039bd2da19bbb3d03c82c6d8ee2616f08904367795084831ce8d0aaa0d |
# Copyright (c) 2001-2014, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility and open public tr... | kadhikari/navitia | source/jormungandr/jormungandr/utils.py | Python | agpl-3.0 | 19,997 | [
"VisIt"
] | 28c230fc6334aee10f54d7ad138706696e0e6adf5107a0f9d4c7d041a513f067 |
""" DIRAC.TransformationSystem.Agent package """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
| yujikato/DIRAC | src/DIRAC/TransformationSystem/Agent/__init__.py | Python | gpl-3.0 | 158 | [
"DIRAC"
] | 5b771454a5ec736cf3e14a76791cafde931c15ab422e4687ab765c7b80014921 |
# copyright (c) 2003 Clark Evans
# You may copy this under the terms of any open source license.
#
# Documentation:
#
# A YPath expression is split into a recurisve combination of
# two sorts of items: path segments and predicates.
#
#
#
#
from types import ListType, StringType, IntType, DictType, InstanceType... | ystk/tools-yocto1-rpm | syck/ext/python/ypath.py | Python | lgpl-2.1 | 15,230 | [
"VisIt"
] | a93eba686113eb2d5c981ef7d3ef4b673b5efb86913aeb5affebf47eb8043b99 |
#!/usr/bin/python
"""
phylomizer - automated phylogenetic reconstruction pipeline - it resembles the
steps followed by a phylogenetist to build a gene family tree with error-
control of every step
Copyright (C) 2014-2016 - Salvador Capella-Gutierrez, Toni Gabaldon
This program is free software: you can redi... | Gabaldonlab/phylomizer | source/phylomizer.py | Python | gpl-3.0 | 12,704 | [
"BLAST"
] | 88c5c2437075af9f07ae3f3553380b73942aeb549d9c5853cf2c1d66f74e10ae |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import datetime
import re
from HTMLParser import HTMLParser
from sqlalchemy import or_, orm
from sqlalchemy.dialects.postgresql import JSONB
from app import db
from app import logger
import page
from util import NoDoiException
from util import clean_doi
from util import is_d... | Impactstory/oadoi | pmh_record.py | Python | mit | 18,129 | [
"MOOSE"
] | 7934363d112ac73f7475d1cb04627efb9bdfee482d1f16c2dec6e7f60e388506 |
# 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/integrator/VelocityVerletOnRadius.py | Python | gpl-3.0 | 1,817 | [
"ESPResSo"
] | e00e2e0a55d75906bfb7118c5ac0b6bc00ac89cc0ef7aa92aecd05df7716e96a |
# Copyright 2014 Cloudera Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, so... | glenioborges/ibis | ibis/sql/compiler.py | Python | apache-2.0 | 43,537 | [
"VisIt"
] | ea415545cff6a2a34e66bfbc5e8bfe513223e3ca6d7199ccea7d6a3aeb1545ad |
from optparse import OptionParser
import statsmodels.api as sm
import scipy as sp
from scipy import linalg
from scipy import stats
docstr = """
Demonstrates l1 regularization for likelihood models.
Use different models by setting mode = mnlogit, logit, or probit.
Examples
-------
$ python demo.py --get_l1_slsqp_resu... | statsmodels/statsmodels | statsmodels/examples/l1_demo/demo.py | Python | bsd-3-clause | 13,470 | [
"Gaussian"
] | 9a6e36b1400cfcb7bd24a8bb09bf57e506a4efb12b9ed25e0b178523b5ec4963 |
"""
Cubes
=====
Tools to deal with spectroscopic data cubes.
Some features in Cubes require additional packages:
* smoothing - requires agpy_\'s smooth and parallel_map routines
* `pyregion <git://github.com/astropy/pyregion.git>`_
The 'grunt work' is performed by the :py:mod:`cubes` module
"""
from __futu... | low-sky/pyspeckit | pyspeckit/cubes/SpectralCube.py | Python | mit | 72,624 | [
"Gaussian"
] | c5b0567beb978d0cfeb5b938183e713a62f4007c875c9565a98bcd37ac43cefc |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | Microvellum/Fluid-Designer | win64-vc/2.78/Python/lib/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 85,919 | [
"VisIt"
] | 941c950219db3e4e678c234f8fefe54686eebd02baf4751ac0f66f565a179b04 |
from textwrap import dedent
import py, pytest
from _pytest.config import PytestPluginManager
@pytest.fixture(scope="module", params=["global", "inpackage"])
def basedir(request):
from _pytest.tmpdir import tmpdir
tmpdir = tmpdir(request)
tmpdir.ensure("adir/conftest.py").write("a=1 ; Directory = 3")
t... | Carreau/pytest | testing/test_conftest.py | Python | mit | 12,459 | [
"VisIt"
] | 794a38035b93efe3dcf2a884174134d6753cdc758d3d25d6d12df9e770b7ad07 |
# tcr.py ---
#
# Filename: tcr.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Fri Oct 16 10:14:07 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 17:14:04 2011 (+0530)
# By: Subhasis Ray
# Update #: 60
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary: This is a redoing... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/tcr.py | Python | lgpl-2.1 | 5,750 | [
"MOOSE",
"NEURON"
] | b1aadfd5b6d6dcd081029c495d67e40aca43f24413335ddb07052c6d86300ac6 |
import math
import heapq
import htslibWrapper
import pysam
#
# TODO:
#
# Current algorithm lumps reads from all read groups together
#
#########################################################################################
#
# Some math functions
#
#################################################################... | andyrimmer/Platypus | src/python/lowcov.py | Python | gpl-3.0 | 29,375 | [
"pysam"
] | 73765c5e2fd0e163c60c2d3e831c3455cb54089730c5dd89777c84310113a5ba |
"""Test for the PLOT3D reader and its multiblock capabilities. This
also tests the SelectOutput filter.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Prabhu Ramachandran
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from io import BytesIO... | dmsurti/mayavi | integrationtests/mayavi/test_plot3d_mb_reader.py | Python | bsd-3-clause | 2,946 | [
"Mayavi"
] | e1a6ee4402b551b550978d920bf3d89c9f9448cc8770a61c971d4dc8c1573e2e |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | sxjscience/tvm | tests/python/relay/test_pass_annotation.py | Python | apache-2.0 | 23,469 | [
"VisIt"
] | 7e0886a231fb0a76693f1e3268f20bebcae955e66e10a078d40668128d420ae8 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | SHASHANKB/spark | examples/src/main/python/sql/datasource.py | Python | apache-2.0 | 7,838 | [
"COLUMBUS"
] | 7423a0a5d5162f0f9fc1d711ad10435456ad416d8fa227f86d0f570b53b821fb |
# This is the code that visits the warehouse.
from Pyro5.api import Proxy
from person import Person
uri = input("Enter the uri of the warehouse: ").strip()
warehouse = Proxy(uri)
janet = Person("Janet")
henry = Person("Henry")
janet.visit(warehouse)
henry.visit(warehouse)
| irmen/Pyro5 | examples/warehouse/phase2/visit.py | Python | mit | 275 | [
"VisIt"
] | e0d8afbe85730b3063db3e08379cb7fff7bbcb5aefc2bf45739f770f95937613 |
from flask import Blueprint, g, current_app, request, jsonify, abort, Response, url_for
from flask_restful import Resource, Api
from pwnedapi import db
from pwnedapi.decorators import token_auth_required, roles_required, validate_json, csrf_protect
from pwnedapi.utils import CsrfToken, encode_jwt, get_bearer_token, sen... | lanmaster53/PwnedHub | pwnedapi/views/api.py | Python | gpl-3.0 | 21,246 | [
"VisIt"
] | d2b7fa7687a260bace73009d7d3b14249a67c65813d880f0f160aba0284b06d1 |
import sys
import os
import numpy as np
import h5py
import multiprocessing
import cPickle
import matplotlib.pyplot as plt
import itertools
from scipy.stats import sigmaclip
from sklearn.gaussian_process import GaussianProcess
fMapper = {
"apcp_sfc" : "Total_precipitation",
"dlwrf_sfc" : "Downward_Long-Wave_Rad... | acbecker/solar | gp2/gp2.py | Python | mit | 8,811 | [
"Gaussian"
] | 8fe38dc71f013e7cdc1b4c00530a21e963efa61e9ab542f3283e868f9af56e87 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Hc(MakefilePackage):
"""HC is a global mantle circulation solver following Hager & O'Conne... | LLNL/spack | var/spack/repos/builtin/packages/hc/package.py | Python | lgpl-2.1 | 1,392 | [
"NetCDF"
] | bbae91ab1855638579ff95c58da9e7a1f1648c55363bf2cfce20ae4013e45529 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2009 Jan Decaluwe
#
# The myhdl library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License as
# published by t... | jmgc/myhdl-numeric | myhdl/_Waiter.py | Python | lgpl-2.1 | 8,214 | [
"VisIt"
] | 533499245683195f9f0c4443f41f8191f9860260526ccc5a3fd66d5ed00ded06 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | do/modeling/plot_truncated.py | Python | agpl-3.0 | 3,068 | [
"Galaxy"
] | 2cac0fc2a3e1cc1d665a46c4635aca762694c3ec3f9f1a8eaabb5e2a4c468792 |
import collections
import itertools
import os
import re
def parseModuleFile(modulefile):
''' Function to parse module file.
Args:
modulefile (str)- Path to tab-delimited file containing module data.
The first and second columns are required and are the program and
the progr... | adam-rabinowitz/ngs_python | scripts/RNASeq_Pipeline_EMBL/EMBL_RNASeq_Functions.py | Python | gpl-2.0 | 16,201 | [
"HTSeq"
] | 50a64cf150d13e7e46c9c99841bb8b8bdfc270c915f0f2ca6ac72775b57c7d8e |
import os
import glob
import pandas
import bisect
from MooseDataFrame import MooseDataFrame
import message
class VectorPostprocessorReader(object):
"""
A Reader for MOOSE VectorPostprocessor data.
Args:
pattern[str]: A pattern of files (for use with glob) for loading.
MOOSE outputs VectorPost... | Chuban/moose | python/mooseutils/VectorPostprocessorReader.py | Python | lgpl-2.1 | 7,773 | [
"MOOSE"
] | a3f7f7f5fb062e1c1378a4612dd7696c07b994274f64d6e9db8cf0d416d1bae6 |
# Copyright (c) 2014 Intel Corporation.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# * Redistributions of works must retain the original copyright notice, this list
# of conditions and the following disclaimer.... | xiaojunwu/crosswalk-test-suite | tools/atip/atip/web/web.py | Python | bsd-3-clause | 11,607 | [
"VisIt"
] | 6a6555d0509ee31f5c949fe66d5c333949a72950b11b02da66215a8e65c1ed63 |
#!/usr/bin/env python
# Emacs: treat this as -*- python -*-
import os
import sys
from optparse import OptionParser
def build_parser():
usage = '%prog [OPTION] [BASIS]...'
parser = OptionParser(usage=usage, version='%prog 1.0')
parser.add_option('-f', '--files', action='store_true',
d... | qsnake/gpaw | gpaw/lcao/analyse_basis.py | Python | gpl-3.0 | 1,912 | [
"GPAW"
] | 8ad06ba67184e7cfa4e876b24c28af7d26fc95f13ae13ad5b921f670777d8a2a |
"""
Filename: lss.py
Reference: http://quant-econ.net/py/linear_models.html
Computes quantities associated with the Gaussian linear state space model.
"""
from textwrap import dedent
import numpy as np
from numpy.random import multivariate_normal
from scipy.linalg import solve
#-Check if Numba is Available-#
from .u... | agutieda/QuantEcon.py | quantecon/lss.py | Python | bsd-3-clause | 11,000 | [
"Gaussian"
] | be363b493e366ca1ccf21fd95442fc77bd9428787e3a378fa3600d4ac819bea5 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 11 14:36:29 2017
@author: derek
"""
import os
import tensorflow as tf
import numpy as np
def _parse_function(example_proto):
"""Reads tfrecords with features {shape: (height,width,depth) of cube data,
label: (malignancy, lobulation, spicul... | dereknewman/cancer_detection | train_rms_cubes_3d.py | Python | mit | 13,192 | [
"Gaussian"
] | 3beb7474e7abef251e1298788c4d7feaa9ffe24693bb44276157b685bffb6542 |
import pytest
import warnings
import numpy as np
import astropy.units as u
# from astropy.modeling import models, fitting
from ..analysis_utilities import stack_spectra, fourier_shift
from .utilities import generate_gaussian_cube, gaussian
from ..utils import BadVelocitiesWarning
def test_shift():
amp = 1
v... | jzuhone/spectral-cube | spectral_cube/tests/test_analysis_functions.py | Python | bsd-3-clause | 11,793 | [
"Gaussian"
] | 96536632b458d6aa09810787f88f2e4f9d369da396594cad8e62497622332ed3 |
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License, Version 2.0 (the "Li... | bbc/kamaelia | Code/Python/Bindings/Dirac-0.6.0/setup.py | Python | apache-2.0 | 1,931 | [
"DIRAC"
] | d3e499fec2f80e715f010077017f82922ea4439d1e2c0f20d7573cc504a685c5 |
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
from __future__ import unicode_literals
import os
import xml.etree.ElementTree
from xml.etree.cElementTree import ElementTree, fromstring
from .Database import Database
class XMLConfigLoader:
def __init__... | cnvogelg/fs-uae-gles | launcher/fs_uae_launcher/XMLConfigLoader.py | Python | gpl-2.0 | 10,017 | [
"ADF"
] | 737978590c29897f6ed9ab072a86edcd51c02a4c624587d8727956bcfcdb8d25 |
import os
import json
import configparser
import better_exceptions
from datetime import datetime
from operator import itemgetter
from jinja2 import Environment, FileSystemLoader
better_exceptions.MAX_LENGTH = None
THIS_DIR = os.path.dirname(os.path.abspath(__file__))
def atom_date(timestamp):
# Convert timestam... | sugrocks/website | dllist.py | Python | mit | 11,902 | [
"CRYSTAL"
] | 3027659ef55ae55511d5403c26d803d2c178351fc387c19e8c186809b2a1fdc6 |
#!/usr/bin/env python
# Author : Pierre Schnizer
"""
Wrapper for the ode solver of gsl. This solver wraps all features as descirbed
in Chapter 25 of the gsl documentation.
The _odeiv file provides the low level wrapper. Direct usage at your special
own risk.
Here is the pythonic version of the example from the gsl d... | juhnowski/FishingRod | production/pygsl-0.9.5/pygsl/odeiv.py | Python | mit | 15,809 | [
"Gaussian"
] | 23965fe2731b6c252c0950629dd51116b00f74f9bbb3df801783623c1cbb4fb2 |
"""This module contains all of the important meta-information for
Hypatia such as the author's name, the copyright and license, status,
and so on.
"""
__author__ = "Lillian Lemmer"
__copyright__ = "Copyright 2015 Lillian Lemmer"
__credits__ = ["Lillian Lemmer"]
__license__ = "MIT"
__maintainer__ = __author__
__site__... | brechin/hypatia | hypatia/__init__.py | Python | mit | 706 | [
"Brian"
] | 3263f1471a341935fa18a5b5e5b7d6cbcc4ccd484e99af0f11adefdc60e10acf |
"""
Visualization of ARGs (Ancestral Recombination Graphs)
"""
# python imports
from itertools import chain, izip
import random
from math import *
# rasmus imports
from rasmus import util, treelib, stats, sets
# compbio imports
from compbio import arglib
# summon imports
import summon
from summon import sumtr... | mdrasmus/compbio | compbio/vis/argvis.py | Python | mit | 29,840 | [
"VisIt"
] | 38ee40830c968a44a7269b414f67185caf6877cfd603d87f36b48744be6105a1 |
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | dnjohnstone/hyperspy | hyperspy/tests/model/test_model.py | Python | gpl-3.0 | 28,010 | [
"Gaussian"
] | 5c436a3c2279a70a83d734ac222c870ef55b0ab67d265c15f668c3c5ef7e42b6 |
# disable missing docstring
# pylint: disable=missing-docstring
import json
from lettuce import world, step
from nose.tools import assert_equal, assert_true # pylint: disable=no-name-in-module
from common import type_in_codemirror, open_new_course
from advanced_settings import change_value, ADVANCED_MODULES_KEY
from ... | ahmadiga/min_edx | cms/djangoapps/contentstore/features/problem-editor.py | Python | agpl-3.0 | 12,757 | [
"VisIt"
] | b74447e2c36dfd36dea980def5d93cb3694833b183998e776783692d9cc61e78 |
from typing import (
AbstractSet,
Any,
Callable,
Dict,
Iterable,
List,
Mapping,
MutableMapping,
Optional,
Sequence,
Set,
Tuple,
Union,
cast,
)
import django.db.utils
from django.conf import settings
from django.contrib.contenttypes.models import ContentType
from ... | shubhamdhama/zulip | zerver/lib/actions.py | Python | apache-2.0 | 251,567 | [
"Octopus"
] | 08b43619b44d265c14f0d311c7bde51e5f0e1ccebdad0289f8b2262cab19eb22 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2013 Michael Rabbitt, Roberto Alsina
#
# 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... | servalproject/nikola | nikola/plugins/compile_markdown/mdx_podcast.py | Python | mit | 3,143 | [
"Brian"
] | 782e5ee6dae95936321060109f37b165ad715446be4aca127f3f1f3e59e25256 |
def attribute_data_observable(data):
return {'type': 'artifact', 'payload_bin': data}
def attribute_data_pattern(data):
return "artifact:payload_bin = '{}'".format(data)
def define_address_type(address):
if ':' in address:
return 'ipv6-addr'
return 'ipv4-addr'
def observable_as(_, attribute_v... | FIRSTdotorg/MISP | app/files/scripts/stix2/misp2stix2_mapping.py | Python | agpl-3.0 | 24,281 | [
"Amber"
] | 0fdc14ee59476cbe4aff3505b87e1aed219c31c688eea5bd8816d580ffff6faa |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals
"""
This package implements modules test the input and output modules for QChem
""" | gpetretto/pymatgen | pymatgen/io/qchem_io/tests/__init__.py | Python | mit | 234 | [
"pymatgen"
] | 077934ba45dffefae8a750113052458beb3d067eac20600e6657771cad34b796 |
#!/usr/bin/env python
from compliance_checker.cf import CFBaseCheck, BaseCheck, dimless_vertical_coordinates
from compliance_checker.cf.util import is_vertical_coordinate, is_time_variable, units_convertible
from compliance_checker.base import DSPair
from wicken.netcdf_dogma import NetCDFDogma
from netCDF4 import Data... | webtrike/compliance-checker | compliance_checker/tests/test_cf.py | Python | apache-2.0 | 31,772 | [
"NetCDF"
] | 405f6c785f598b247729afb7093bc50b41b4cb0978a4f09f8aba76bbd4daf030 |
import requests
"""
Communications library for commercial (COTS) USB weather stations:
https://github.com/jim-easterbrook/pywws/
Docs on adding your weather station to openweathermap.org:
http://openweathermap.org/stations
"""
def fetch_IP_geodata():
"""
Retrieve geo data keyed by our IP address from ip-api.... | Sonophoto/PythonNotes | weatherLookup/weatherLookup.py | Python | bsd-2-clause | 3,359 | [
"VisIt"
] | 552d5df6f6ac3543a79dcb0619132d0697c1d64cc3ef5e195615ab9c6a916061 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
import itk
import module_kits.itk_kit as itk_kit
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
class levelSetMotionRegistration(ScriptedConfigModuleMixin, ModuleBase):
def __init__... | nagyistoce/devide | modules/insight/levelSetMotionRegistration.py | Python | bsd-3-clause | 5,044 | [
"Gaussian"
] | 513b0bbb5adda810739edfb0bf40d7a5fb610b76b574bb89f3fd2015d9755da7 |
"""Reads the GloVe word embeddings
Visit: https://nlp.stanford.edu/projects/glove/"""
import os
import numpy as np
import anna.data.utils as utils
DESTINATION = "glove"
NAME = "glove.840B.300d"
TXT_NAME = NAME + ".txt"
ZIP_NAME = NAME + ".zip"
URL = "http://nlp.stanford.edu/data/" + ZIP_NAME
def fetch_and_parse(da... | jpbottaro/anna | anna/data/dataset/glove.py | Python | mit | 2,177 | [
"VisIt"
] | cadc7ec1638433fa16550677ad9ab1be51f80874521e9d1f77c77fb5b7d766d0 |
"""
example script for running a RNA-seq analysis
python rnaseq_pipeline.py rnaseq_pipeline.yaml
you will have to write a couple of functions to group the input
data in useful ways
"""
from cluster_helper.cluster import cluster_view
import sys
import yaml
from bipy.log import setup_logging, logger
from bcbio.utils i... | roryk/bipy | examples/rnaseq/rnaseq_pipeline.py | Python | mit | 7,478 | [
"HTSeq"
] | 2c3cac3920085b4a89156c1ac835253655fd73cc2df7cd4ff1ef3a6be215388f |
from __future__ import division, print_function, absolute_import
import numpy as np
import itertools as itr
import amitgroup as ag
from pnet.layer import Layer
import pnet
import pnet.matrix
from scipy import linalg
from sklearn.utils.extmath import logsumexp, pinvh
def _log_multivariate_normal_density_diag(X, means... | jiajunshen/partsNet | pnet/oriented_gaussian_parts_layer.py | Python | bsd-3-clause | 30,760 | [
"Gaussian"
] | 447516162813791702ed693bb53a709bcbb56cf45ce75c1a409f6ed8ac39c6a9 |
# -*- coding: latin-1 -*-
#
# Copyright (c) 2015-2016 Paul Bomke
# Distributed under the GNU GPL v2.
#
# This file is part of monkeyprint.
#
# monkeyprint 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... | robotsinthesun/monkeyprint | monkeyprintGui.py | Python | gpl-2.0 | 60,767 | [
"VTK"
] | 57f6549c9d22a712df65ff65206ed4b7f67d0a934b676010d060bf40351d66ff |
# This file is part of the Fluggo Media Library for high-quality
# video and audio processing.
#
# Copyright 2010 Brian J. Crowell <brian@fluggo.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Founda... | fluggo/Canvas | fluggo/editor/graph/audio.py | Python | gpl-3.0 | 4,204 | [
"Brian"
] | 19e6c72802db6291494511b750bc3b4bf9db00a486a3b346f0c50c4be777b322 |
# SCDEwrapper/SCDEwrapper.py - a self annotated version of rgToolFactory.py generated by running rgToolFactory.py
# to make a new Galaxy tool called SCDEwrapper
# User admin@galaxy.org at 16/04/2015 10:09:46
# rgToolFactory.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# copyright ross lazarus (ro... | myoshimura080822/tools_of_rnaseq_on_docker_galaxy | SCDE_Wrapper/SCDEwrapper.py | Python | mit | 32,783 | [
"Galaxy"
] | a1be52be0b6b2b74b0f229d9cf623a37b268eeffa2e02f808750182839baefe3 |
def countup(n):
if n >= 10:
print "Blast off"
else:
print n
countup(n + 1)
def main():
countup(0)
countup(1)
countup(-20)
return
main()
| suay1936/suay1936-cmis-cs2 | countup.py | Python | cc0-1.0 | 190 | [
"BLAST"
] | 714d1891b8e1795cf4727da8c8b812c39f4bef78282ff870784d6ddd8f17b76c |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/prop/gtensor/__init__.py | Python | apache-2.0 | 783 | [
"PySCF"
] | 7534bee9ccd8043e7264e61e71921378f31e154d7c3cec6b3cc8c30b3f6942f3 |
# Copyright: (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Copyright: (c) 2016, Toshio Kuratomi <tkuratomi@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import ... | thnee/ansible | lib/ansible/cli/__init__.py | Python | gpl-3.0 | 22,791 | [
"Galaxy"
] | 2fa3ecb8e206e93c507195709b5fa3966dc90a43bda7d6d71c40b5cfb2ace3e1 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Variable_Stiffness_Variable_Velocity/HMM/with 0.8s/hmm_crossvalidation_force_motion_20_states_scaled_wrt_all_data.py | Python | mit | 41,532 | [
"Mayavi"
] | 52404e00a659ecbb96944e23e6fd9f1edd90b4f9993eb3b4ac3e92ce0da9ecf5 |
__author__="Marina Wahl"
"""
In the MVC paradigm, models are the database interface
"""
from datetime import datetime
import hashlib
# Werkzeug's security module implements secure password hashing
# through these two functions
from werkzeug.security import generate_password_hash, check_password_hash
# for hash... | bt3gl/The-Anti-Social-Network | app/models.py | Python | mit | 15,070 | [
"VisIt"
] | aa605f10388a8334154a27d4ac5db3fa1c560cbe50fcf74f1809b6574bdbcad3 |
"""
=================
Confidence Levels
=================
When setting the sigma levels for ChainConsumer, we need to be careful
if we are talking about 1D or 2D Gaussians. For 1D Gaussians, 1 and 2 :math:`\sigma` correspond
to 68% and 95% confidence levels. However, for a a 2D Gaussian, integrating over 1 and 2 :math... | Samreay/ChainConsumer | examples/customisations/plot_confidence_levels.py | Python | mit | 1,673 | [
"Gaussian"
] | 034f11487b92734375843fd66e6cdcaebf70e09410f4056ec32e72ef1bdae9a8 |
#!/usr/bin/python
#
# Copyright (C) 2015 by Markus Meinert
# This file is distributed under the terms of the GNU General Public License.
# See the file COPYING for license details.
#
# http://elk.sourceforge.net/
#
# elk-optics.py v1.0
#
# This script comes with no warranty. Check the results
# carefully for production... | rohkeaID/elk-w90-improved | utilities/elk-optics/elk-optics.py | Python | gpl-3.0 | 3,765 | [
"Elk"
] | 23d29f2b7fcdaae8bf0b4d6d78ec2a80083c15a6cd03e4b57016dd096f29f4fb |
#! /usr/bin/env python
# ======================================================================
# matscipy - Python materials science tools
# https://github.com/libAtoms/matscipy
#
# Copyright (2014) James Kermode, King's College London
# Lars Pastewka, Karlsruhe Institute of Technology
#
# This progr... | marcocaccin/crack2Dglass | make_crack.py | Python | gpl-2.0 | 6,220 | [
"ASE",
"Matscipy"
] | e4bd37f8de20c84ebb17f6afb229c801a7f1f6490916b24b4b55b7ac61dde619 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Generally, the CASSCF solver does NOT return the natural orbitals.
1. Attribute .natorb controls whether the active space orbitals are transformed
to natural orbitals in the results.
2. When .natorb is set, the natural orbitals may NOT be sort... | gkc1000/pyscf | examples/mcscf/03-natural_orbital.py | Python | apache-2.0 | 1,286 | [
"PySCF"
] | 07862f819ed8e23d8289d84b2397c27016e13a7ea1ca21501756362d1ff8651b |
#!/usr/bin/env python
"""tree_cable.py: A depth 10 binary tree like cable with following properties.
Depth Number Length (microns) Diameter (microns)
==========================================================================
0 1 32.0 16.0
1 2 25.4 10.08
2 4 20.16 6.35
3 8 16.0 4.0
4 16 12.7 2.52... | subhacom/moose-core | tests/python/Rallpacks/rallpacks_tree_cable.py | Python | gpl-3.0 | 8,348 | [
"MOOSE"
] | cf56b67b05833940da1456d4d1a7f45f23f948531e97d69ff668fa1463f3bb81 |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical s... | loli/sklearn-ensembletrees | sklearn/hmm.py | Python | bsd-3-clause | 48,577 | [
"Gaussian"
] | d207545da86c2e93cd98b11902f700454d4f6c74a793287adeaa437530f94773 |
"""Identify program versions used for analysis, reporting in structured table.
Catalogs the full list of programs used in analysis, enabling reproduction of
results and tracking of provenance in output files.
"""
import os
import contextlib
import subprocess
import sys
import yaml
import toolz as tz
from bcbio import... | guillermo-carrasco/bcbio-nextgen | bcbio/provenance/programs.py | Python | mit | 12,250 | [
"BWA",
"Galaxy",
"HTSeq"
] | 0ea083d7c70201699288c541bc2b54556909710373383046f524afd216a26348 |
###########################################################################
#
# Copyright 2020 Google LLC
#
# 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
#
# https://www.apache.org/l... | google/starthinker | dags/salesforce_to_bigquery_dag.py | Python | apache-2.0 | 5,630 | [
"VisIt"
] | 1a5d5bf6a2330020a7d7985169ab3d67c8c9ceafdf4cb98ff7f9a9c021e13528 |
"""
Mind: Specify path for your bader executable in main with the needed options
"""
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.analysis.energy_models import EnergyModel
from pymatgen.analysis.ewald import EwaldSummation
from pymatgen.io.vaspio import Chgcar, Potcar
from mpinterfa... | joshgabriel/MPInterfaces | dev_scripts/coulomb_summer_test.py | Python | mit | 9,086 | [
"pymatgen"
] | cf18995f2deefe4483f929cec9a242de7a3d0562886489bee7d17bc184243941 |
import sys, string
import export
import math
import random
import copy
import os
import os.path
import unique
import traceback
R_present=True
try:
### If file is present use this location
loc = unique.filepath('Config/R_location.txt')
s = open(loc,'r')
useStaticLocation=s.read()
#pr... | nsalomonis/AltAnalyze | R_interface.py | Python | apache-2.0 | 55,242 | [
"Bioconductor"
] | 105694ea3d7abc39019df49f86b752b67b3d19455ae6aeb21a8ebdcf1ae72903 |
# Copyright 2012 by Wibowo Arindrarto. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SearchIO parser for HMMER table output format."""
from itertools import chain
imp... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/SearchIO/HmmerIO/hmmer3_tab.py | Python | gpl-2.0 | 12,592 | [
"Biopython"
] | 28c793853ae6341f853f3accb9320e20b8a27aa3d392d8f991e486bf95ef24f4 |
""" This script submits a test production
"""
# pylint: disable=wrong-import-position, protected-access
import os
import json
from DIRAC.Core.Base.Script import Script
Script.parseCommandLine()
# from DIRAC
from DIRAC import gLogger
from DIRAC.ProductionSystem.Client.ProductionClient import ProductionClient
from DI... | DIRACGrid/DIRAC | tests/System/dirac-test-prod-sys.py | Python | gpl-3.0 | 5,148 | [
"DIRAC"
] | b6a6f66ad87587e8dbee668940efb186436869a0b63cecff27071f1535a00995 |
"""
Base class for Gaussian process latent variable models
This is really not ready for release yet but is used by the gpasso model
"""
import sys
sys.path.append('./../..')
from pygp.gp import GP
import pdb
from pygp.optimize.optimize_base import opt_hyper
import scipy as SP
import scipy.linalg as linalg
def PCA(Y... | PMBio/pygp | pygp/gp/gplvm.py | Python | gpl-2.0 | 7,170 | [
"Gaussian"
] | e8ed0277aed3c464ab2a713b21696c304f65f8ce3f0c9c5c62be488c4b902e82 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | marscher/mdtraj | MDTraj/geometry/tests/test_hbonds.py | Python | lgpl-2.1 | 4,586 | [
"MDTraj",
"PyMOL"
] | 15513a2fe948f5b0b68ec161cdcab92f000ae4eafa8a978712a1b0b83f1c65ad |
# -*- coding: utf-8 -*-
'''model.py: underlying model of photo data.'''
__author__ = 'drseergio@gmail.com (Sergey Pisarenko)'
import logging
import os
import sys
from PyQt4 import QtCore, QtGui
try:
from gi.repository import GExiv2
except ImportError:
print ('You must have GExiv2 installed, please visit:\n'
... | drseergio/qeytaks | qeytaks/model.py | Python | gpl-3.0 | 4,137 | [
"VisIt"
] | 2b31b1e55c62d9230d8d9c972b824547bfe81a792a25ef54c6c5e5283090181b |
import math
import operator
import os
#
from .memory import MemoryTree
from .optics import *
from . import abcd
import numpy as np
#
from numpy import pi, conj
from collections import OrderedDict as OD
#
def mode_overlap_q(q1, q2, lam=0.001552):
"""
Mode overlap (power transmission) between two coaxial Gaussian... | XueshiGuo/Gau-modematching | modematching/gaussian_beam.py | Python | mit | 8,677 | [
"Gaussian"
] | 1bbbaf7c03969466dd47c031c47f320abcaa31cd06f663a22f8271094e4d25ed |
from django.shortcuts import render, render_to_response
from django.http import HttpResponse, HttpResponseRedirect
from django.template import RequestContext
from django.contrib.auth import authenticate, login, logout
from django.contrib.auth.decorators import login_required
from datetime import datetime
# Import the ... | bjing/tango_with_jango_project | rango/views.py | Python | gpl-3.0 | 4,884 | [
"VisIt"
] | b599f0c447084733dd1a7d108af9588a8babfdb5d8be646417e8ad70125be4e5 |
import sys,os
sys.path.insert(0,os.path.join(sys.path[0],'..'))
from xenoGI import parameters,blast,genomes,xenoGI
# Identifies xenoGI proteins with significant similarity to a provided
# protein multifasta, printing their xenoGI gene names to
# standard out, one per line. Expects to be run in a xenoGI working
# direc... | ecbush/xenoGI | misc/getProteinsWithBlastHitsVsMultifasta.py | Python | gpl-3.0 | 2,242 | [
"BLAST"
] | 0e5f6dcd95d3515ca3fa983ce9ea0ca70805806af9e2c9be0942eeba5b210f64 |
import sys
import subprocess
from .exceptions import PyperclipException
EXCEPT_MSG = """
Pyperclip could not find a copy/paste mechanism for your system.
For more information, please visit https://pyperclip.readthedocs.org """
PY2 = sys.version_info[0] == 2
text_type = unicode if PY2 else str # noqa
def ini... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/pandas/io/clipboard/clipboards.py | Python | mit | 4,047 | [
"VisIt"
] | 7736496e790f3080724488e657469887442b1721c9be208b89c419d253944527 |
"""
API for initiating and tracking requests for credit from a provider.
"""
import datetime
import logging
import uuid
import pytz
from django.db import transaction
from lms.djangoapps.django_comment_client.utils import JsonResponse
from openedx.core.djangoapps.credit.exceptions import (
UserIsNotEligible,
... | simbs/edx-platform | openedx/core/djangoapps/credit/api/provider.py | Python | agpl-3.0 | 15,608 | [
"VisIt"
] | a24b1fd841d4f50347df08a6ec445e3db5534900a9a8d6f6f24579cb59345cbc |
#!/usr/bin/env python
import sys
import numpy
import _hmm
class HMM:
"""A simple HMM implementation with dependency only on numpy able to handle discrete and gaussian-mixture HMMs."""
def __init__(self, num_states=2, num_distributions=1, transitions=None, pi=None, distributions=None, seed=None):
"""... | bxlab/hifive | hifive/libraries/hmm.py | Python | mit | 9,699 | [
"Gaussian"
] | 9e17fc749bb5735478b624478cb84c9d5fde9485d4f2d3cf4d85d9b2e89477b5 |
# $Id: docutils_xml.py 7315 2012-01-18 10:16:20Z milde $
# Author: David Goodger, Paul Tremblay, Guenter Milde
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""
Simple document tree Writer, writes Docutils XML according to
http://docutils.sourceforg... | ddd332/presto | presto-docs/target/sphinx/docutils/writers/docutils_xml.py | Python | apache-2.0 | 6,271 | [
"VisIt"
] | 1d11159b161f45a341ad8dfa2003d88c4ceb15b90b5b78728db574043cce4b3b |
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