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# Copyright (C) 2016 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the ... | pannarale/pycbc | pycbc/events/stat.py | Python | gpl-3.0 | 24,539 | [
"Gaussian"
] | 1079765c48433279f8916304191eac8d6d235955f77599eafd270321a47efdd0 |
########################################################################
# $HeadURL$
########################################################################
""" CurveGraph represents simple line graphs with markers.
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Pro... | arrabito/DIRAC | Core/Utilities/Graphs/CurveGraph.py | Python | gpl-3.0 | 4,781 | [
"DIRAC"
] | 26294b2bf23ddc6b06a1ce40611bb5c0276a2b580097f43ab8b36334561aebc8 |
#A minimum example illustrating how to use a
#Gaussian Processes for binary classification
import numpy as np
import matplotlib.pyplot as plt
from scipy.stats import norm
from sklearn.preprocessing import normalize
n = 1000
def stochProcess(x, a, b):
return np.exp(a*x) * np.cos(b*x)
def fx(processes, x):
sam... | KHP-Informatics/sleepsight-analytics | scarp.py | Python | apache-2.0 | 1,058 | [
"Gaussian"
] | dbe31156e4e0a220eec43d3f1405c73a41143a57887241888db7b171cce89f4d |
#!/usr/bin/env python
'''
author: zhuh
date: 2013.10.30
version: 0.0.1
'''
import sys
import os
import re
import math
import getopt
import numpy as np
import MDAnalysis
import MDAnalysis.core.qcprot as qcp
import time as Time
K= 1.3806504e-23
'''It's the Boltzmann constant'''
HBA = 1.05457148e-34
H = 6.62606957e-3... | zhuhong/HECMD | HECMD.py | Python | gpl-2.0 | 15,909 | [
"Gromacs",
"MDAnalysis"
] | b5fbdadbbc9f99d11119c0237dcc4c33af035098eb0c2c6d1b6488d12c6377da |
#!/usr/bin/env python
# This example demonstrates how to use 2D Delaunay triangulation.
# We create a fancy image of a 2D Delaunay triangulation. Points are
# randomly generated.
# Copyright 2008 Dan Collins
# This is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public... | badbytes/pymeg | meg/plotvtk.py | Python | gpl-3.0 | 9,973 | [
"VTK"
] | 9ca26353115488aee9e3e7c565c9c137c31a756a8b06f191136dd9e8c05c3d08 |
#!/usr/bin/env python
"""
Convert from pileup file to interval index file.
usage: %prog <options> in_file out_file
"""
from __future__ import division
import optparse
from galaxy import eggs
eggs.require( "bx-python" )
from bx.interval_index_file import Indexes
def main():
# Read options, args.
parser = o... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/datatypes/converters/pileup_to_interval_index_converter.py | Python | gpl-3.0 | 802 | [
"Galaxy"
] | fe42cfc5c4fce63a753d4472ca8ddfca5314c71ee879b51456293593205b5027 |
"""This source manages a CitcomS Hdf file given to it.
"""
# Author: Martin Weier
# Copyright (c) 2006, California Institute of Technology
# License: GPL Style
# Enthought library imports.
from enthought.traits import Trait, TraitPrefixList, Instance, Int, Str, Button
from enthought.traits.ui import View, Group, Ite... | geodynamics/citcoms | visual/Mayavi2/original_plugins/plugins/CitcomS_hdf_file_reader.py | Python | gpl-2.0 | 11,659 | [
"Mayavi",
"VTK"
] | 6cf5c7925c57bef97173133c272f17a5b700d731e86bb2e2a1ebacf90ff431ac |
"""
Test code for phasing a single view
"""
import numpy as np
from odin.potential import Potential
from thor import scatter
class CdiPotential(Potential):
"""
Simple gaussian-error evaluator for CDI image
"""
def __init__(self, intensities, qxyz, sigma, force_no_gpu=False):
"""
... | tjlane/odin | src/python/cdi.py | Python | gpl-2.0 | 1,899 | [
"Gaussian"
] | 2b21e13529a662ac87446f5d1bb5db66bd25c82e2eabe7543e404ecab2fe147e |
# -*- coding: utf-8 -*-
"""Factories for the OSF models, including an abstract ModularOdmFactory.
Example usage: ::
>>> from tests.factories import UserFactory
>>> user1 = UserFactory()
>>> user1.username
fred0@example.com
>>> user2 = UserFactory()
fred1@example.com
Factory boy docs: http://f... | samanehsan/osf.io | tests/factories.py | Python | apache-2.0 | 18,375 | [
"Brian"
] | 02ba52f903809d50e3fc5463bd30c1a48ff4b86167c3d1bb2504ae8717d9d5a2 |
import numpy as np
from sdcit.hsic import HSIC
from sdcit.utils import rbf_kernel_median, residual_kernel, residualize, columnwise_normalizes
def FCIT_noniid_K(Kx, Ky, cond_Kx, cond_Ky, Kz=None, seed=None):
if seed is not None:
np.random.seed(seed)
RX1 = residual_kernel(Kx, cond_Kx)
RY1 = residu... | sanghack81/SDCIT | sdcit/flaxman.py | Python | mit | 2,280 | [
"Gaussian"
] | 5343072abfc0b329ed890d341c9a8f0d0bde1d9c2df986de6dc643242fca9aa7 |
from models.distributions import Distribution
from collections import defaultdict
from utils.boxcox import BoxCox
from mcerp import *
import functools
import logging
# Get yield rate based on Possion model.
def get_yield(size, a, d):
return (1 + size * d / a) ** (-1 * a)
# Pollack's rule.
def get_pollack(size):
... | UCSBarchlab/Archrisk | models/uncertainty_models.py | Python | bsd-3-clause | 5,217 | [
"Gaussian"
] | e289ef85c38234f00628cc7cb2490a7cdf6877714c008e0ee86e5f6e9f2fb264 |
""" The CS! (Configuration Service)
Modified to work with Tornado
Encode data in base64 because of JSON limitations
In client side you must use a specific client
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from base64 import b6... | ic-hep/DIRAC | src/DIRAC/ConfigurationSystem/Service/TornadoConfigurationHandler.py | Python | gpl-3.0 | 4,394 | [
"DIRAC"
] | bd553d5d345859a749a3e39f8cb8d9472da60e8643cf3e8a93d4bbe7699cf8a8 |
"""Clean an input BAM file to work with downstream pipelines.
GATK and Picard based pipelines have specific requirements for
chromosome order, run group information and other BAM formatting.
This provides a pipeline to prepare and resort an input.
"""
import os
import sys
import pysam
from bcbio import bam, broad, u... | a113n/bcbio-nextgen | bcbio/pipeline/cleanbam.py | Python | mit | 8,337 | [
"pysam"
] | 283aae8b5bdfecdcdaa1169f557de9a31c833aec30544209d4b4f16114aad0db |
from typing import Any, Dict, Tuple
################################################################
# Zulip Server settings.
#
# This file controls settings that affect the whole Zulip server.
# See our documentation at:
# https://zulip.readthedocs.io/en/latest/production/settings.html
#
# For developer documentati... | showell/zulip | zproject/prod_settings_template.py | Python | apache-2.0 | 27,801 | [
"VisIt"
] | b133f6d605269312604c1ceeb46624a0f178ddb7f826d7af346786bdf4276270 |
#!/usr/bin/python
#
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
#
# 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/LICE... | nouiz/fredericbastien-ipaddr-py-speed-up | tags/2.1.5/ipaddr_test.py | Python | apache-2.0 | 46,325 | [
"FEFF"
] | efd1f586f2e348526edeca375e221ef692895de2c96c01e1dc985ed3d9e277b3 |
#!/usr/bin/env python
import argparse, os
import math
import numpy as np
import pickle
import random
import utils
script_dir = os.path.dirname(os.path.realpath(__file__))
output_dir = os.path.join(script_dir, '..', 'data/random')
parser = argparse.ArgumentParser("Generate object, options: ")
parser.add_argument('--... | schinmayee/bayesian-object-tracking | src/simulate.py | Python | mit | 15,492 | [
"Gaussian"
] | 29bfca8f59648d992c12a3e906b7f82f938d57f4ff17b90a634fab226d32f8b5 |
# 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 RAltcdfenvs(RPackage):
"""alternative CDF environments (aka probeset mappings)
Con... | LLNL/spack | var/spack/repos/builtin/packages/r-altcdfenvs/package.py | Python | lgpl-2.1 | 1,395 | [
"Bioconductor"
] | c5ddb9ee1ad1456fc682976141fc12d33783995770f9d90b2a45a21b8034f1b1 |
"""This demo illustrates how to use of DOLFIN for solving a nonlinear
PDE, in this case a nonlinear variant of Poisson's equation,
- div (1 + u^2) grad u(x, y) = f(x, y)
on the unit square with source f given by
f(x, y) = x*sin(y)
and boundary conditions given by
u(x, y) = 1 for x = 0
du/dn... | alogg/dolfin | demo/undocumented/nonlinear-poisson/python/demo_nonlinear-poisson.py | Python | gpl-3.0 | 2,377 | [
"VTK"
] | 85993c2150915b4e8adbb7146debc2465b20f7a4899bcc851cdb609d7f0ae167 |
# -*- coding: utf-8 -*-
# Copyright 2012 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from .fake_webapp import EXAMPLE_APP
class SlowlyTypeTest:
def test_simple_type(self):
"should provide a away to change fi... | cobrateam/splinter | tests/type.py | Python | bsd-3-clause | 2,398 | [
"VisIt"
] | 78095a51ef514322c3645d3ed42402767ebb24ede190e10b79fc2bb77729b49e |
import base64
import hashlib
import logging
import os
import re
from uuid import uuid4
from django.conf import settings
from watson import search as watson
from auditlog.registry import auditlog
from django.contrib import admin
from django.contrib.auth import get_user_model
from django.urls import reverse
from django.c... | OWASP/django-DefectDojo | dojo/models.py | Python | bsd-3-clause | 105,489 | [
"VisIt"
] | 1903233f9cbc4853cf2d47b36860e66a821f9564a533bc2ebad823c2f557e020 |
__author__ = 'stephen'
import numpy as np
import scipy.io
import scipy.sparse
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
import matplotlib.pylab as pylab
from .utils import get_subindices
import matplotlib.ticker as mtick
from collections import Counter
from s... | stephenliu1989/HK_DataMiner | hkdataminer/utils/plot_ (stephen-desktop-linux's conflicted copy 2019-08-24).py | Python | apache-2.0 | 23,284 | [
"Gaussian"
] | 9617a0db7f291b72784c6724e5a116786f67c6aeaf9e72b2c87bdda241cd89df |
""" A test DB in DIRAC, using MySQL as backend
"""
from DIRAC.Core.Base.DB import DB
class AtomDB(DB):
def __init__(self):
DB.__init__(self, 'AtomDB', 'Test/AtomDB', 10)
retVal = self.__initializeDB()
if not retVal['OK']:
raise Exception("Can't create tables: %s" % retVal['Message'])
def __in... | arrabito/DIRAC | docs/source/DeveloperGuide/AddingNewComponents/DevelopingDatabases/AtomDB.py | Python | gpl-3.0 | 921 | [
"DIRAC"
] | 0d6decaebbc8702cbfc14869b047c299ac76852a9ab64f2fa5732795b8018a01 |
r"""
Empirical Power Estimation (:mod:`skbio.stats.power`)
=====================================================
.. currentmodule:: skbio.stats.power
The purpose of this module is to provide empirical, post-hoc power estimation
of normally and non-normally distributed data. It also provides support to
subsample data ... | jwdebelius/Machiavellian | machivellian/power.py | Python | bsd-3-clause | 15,760 | [
"scikit-bio"
] | 72f25221d0447512b7828b7945ca90059ce94c8e310cf29ac4e5dde44f405ecc |
import tornado
from tornado.options import define, options
from types import StringType
import torndb
import redis
from scinet3.model import (Document, Keyword)
################
# Mysql, Redis config
#################
define("port", default=8000, help="run on the given port", type=int)
define("mysql_port", default=... | xiaohan2012/rl-search | cmdapp.py | Python | mit | 14,004 | [
"NEURON"
] | 5680d1934de3d053eda6443be505e116d94559dd6dce8ef214bfed3ef29d2913 |
from PythonQt import QtCore, QtGui
from director import uipanel
from director import pointpicker
from director import applogic
from director import objectmodel as om
from director import vieweventfilter
from director import visualization as vis
from director import vtkAll as vtk
from director.debugVis import DebugData... | patmarion/director | src/python/director/measurementpanel.py | Python | bsd-3-clause | 7,107 | [
"VTK"
] | 8463dc99ae099b62085e3580b2ccc1ef84f3d4d81f7f9bf105e45a2b72b72290 |
from pysimm import system, lmps, forcefield
# from pysimm import amber
def run(test=False):
try:
ethanol = system.read_pubchem_smiles('CCO')
except:
import os
ethanol = system.read_mol(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'CCO.mol'))
try:
acetone = syste... | polysimtools/pysimm | Examples/08_ethanol_acetone_mixture/run.py | Python | mit | 2,562 | [
"Amber"
] | 613502ddd0e4e46d2e4d0436be71687ff5f463bf5f35e99694d5534b0eefe4c3 |
##############################################################################
##############################################################################
# Estimating the volatility of coffee futures
# using a stochastic volatility (SV) model with alpha-stable log-returns.
#
# The SV model is inferred using th... | compops/gpo-abc2015 | scripts-paper/example2-pmhabc.py | Python | mit | 5,215 | [
"Gaussian"
] | 7694de5ac82a31fbcd3b807cf9c88e9d0caf41293e24de1290ed059aad1cb584 |
import os
import shutil
import numpy
from vtk_xml_serial_unstructured import *
from _gfrd import Sphere, Cylinder, Box, Plane
from multi import Multi
from utils import crossproduct, INF
class VTKLogger:
"""
"""
def __init__(self, sim, dir='vtkdata', buffer_size=None, show_shells=True,
ex... | ecell/epdp | visualization/vtklogger.py | Python | gpl-2.0 | 20,028 | [
"ParaView",
"VTK"
] | 708838c719a8e4628a402af059523cf7cb1f042521e5d511c097e4fd73a9f968 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/MooseDocs/test/common/test_parse_settings.py | Python | lgpl-2.1 | 2,528 | [
"MOOSE"
] | c2affaa68601e481ad11060be74d900d11a9f4bb56b54b10f1a1a6ee8d552472 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2022, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
import numpy as np
from unittest import TestCase
from exatomic.va import GenInput as gi, gen_delta
from exatomic.gaussian import Fchk
from exatomic.adf import Output
from exatomic.ba... | exa-analytics/exatomic | exatomic/va/tests/test_inputs.py | Python | apache-2.0 | 3,702 | [
"ADF",
"Gaussian"
] | 4e72894f3cc00ec8b2817632f9ca4b18b171a4fd78cb5fd7f86c9d83601faad7 |
'''A system for parallel, remote execution of multiple arbitrary tasks.
Much of this, both in concept and execution, was inspired by (and in some
cases based heavily on) the ``concurrent.futures`` package from Python 3.2,
with some simplifications and adaptations (thanks to Brian Quinlan and his
futures implementatio... | westpa/westpa | lib/wwmgr/work_managers/__init__.py | Python | mit | 1,500 | [
"Brian"
] | a83f050c4a9318cbf03b36155b500617c4b72acb76d85034949ad7dc97298608 |
#! /usr/bin/python
'''pysam - a python module for reading, manipulating and writing
genomic data sets.
pysam is a lightweight wrapper of the htslib C-API and provides
facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ
files as well as access to the command line functionality of the
samtools and bcft... | pysam-developers/pysam | setup.py | Python | mit | 19,717 | [
"pysam"
] | 5010006ad92da829912de5e9612177a99aeccc9d181903c47d70fd9d9a0301f9 |
# Copyright (c) 2012, CyberPoint International, LLC
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this lis... | ririw/libpgm | libpgm/CPDtypes/lg.py | Python | bsd-3-clause | 4,376 | [
"Gaussian"
] | b900beed781f5537add8fea37c9eaeb8b8f2c3bc52299ba71d5621b596f7b24a |
# Copyright 2013-2020 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 PyPyscf(PythonPackage):
"""PySCF is a collection of electronic structure programs powered... | rspavel/spack | var/spack/repos/builtin/packages/py-pyscf/package.py | Python | lgpl-2.1 | 1,481 | [
"PySCF"
] | b4df23662ed1640e047a6d3655fcc1a1c610d606f802eb6c8f20803ebe59c41d |
# The OARN Relief Nursery Database
# Copyright (C) 2015 Oregon Association of Relief Nurseries
#
# This program 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 of the
# License, or (at... | wire-rabbit/oarn-database | oarn/oarndb/models/__init__.py | Python | agpl-3.0 | 8,295 | [
"VisIt"
] | 0ca2753bed9b6becc9e038e77173a83e957edd2fb8aeefae3234f6329c73fc0c |
"""
====================
Module **tools.py**
====================
Binding for some sequence mapping tools amongst others.
"""
# Internal modules #
from pyrotrfid.cmd import command
################################################################################
@command
def sam_to_bam(sam_filename, bam_filename):
... | xapple/pyrotrfid | pyrotrfid/tools.py | Python | gpl-3.0 | 1,819 | [
"BWA"
] | 05d0dc5c271b8044700b9871ed4f38a0202187bacbe8209de1f5e26b480a3b5a |
# Copyright 1999 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import os
import unittest
from Bio.ExPASy import Enzyme
class TestEnzyme(unittest.Test... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Enzyme.py | Python | gpl-2.0 | 4,592 | [
"Biopython"
] | d649094ca0288a234ad8c78e04e8bdac01d9225510603538d5be5ec5f522897f |
"""Forest of trees-based ensemble methods
Those methods include random forests and extremely randomized trees.
The module structure is the following:
- The ``BaseForest`` base class implements a common ``fit`` method for all
the estimators in the module. The ``fit`` method of the base ``Forest``
class calls the ... | Achuth17/scikit-learn | sklearn/ensemble/forest.py | Python | bsd-3-clause | 61,610 | [
"Brian"
] | c2f2398118616cb6d7e4f33c9ffde02b9521a06a71505d6d4ba1855910b5cb9d |
try: paraview.simple
except: from paraview.simple import *
from paraview import coprocessing
#--------------------------------------------------------------
# Code generated from cpstate.py to create the CoProcessor.
# ----------------------- CoProcessor definition -----------------------
def CreateCoProcessor()... | mathstuf/ParaViewCatalystExampleCode | CxxOverlappingAMRExample/SampleScripts/feslicescript.py | Python | bsd-3-clause | 3,128 | [
"ParaView"
] | 3cbf3d035d898b365f2596e9614d0402be7d5659a0caaf0d524423414d386c5e |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
"""
Versioneer 2
============
* Like a rocketeer, but for versions!
* Based on https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* Edited by Ryan Dwyer
This is a... | ryanpdwyer/sigutils | versioneer.py | Python | mit | 37,837 | [
"Brian"
] | a733c2f06d26093517cc3895aca7a9687a70b1b8e2ccda5e430e71c305fac3ae |
# Copyright (C) 2009 Google Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the f... | teamfx/openjfx-9-dev-rt | modules/javafx.web/src/main/native/Tools/Scripts/webkitpy/common/config/committers_unittest.py | Python | gpl-2.0 | 20,160 | [
"Brian"
] | a1af8c0dfc5b7646c5f52dc96cbaca1536eed09630b6f87fa90775d983bf6b35 |
import speclite.filters as spec_filters
import astropy.units as astro_units
import numpy as np
import astropy.constants as constants
from threeML.utils.interval import IntervalSet
class NotASpeclikeFilter(RuntimeError):
pass
class FilterSet(object):
def __init__(self, filter, mask=None):
"""
... | volodymyrss/3ML | threeML/plugins/photometry/filter_set.py | Python | bsd-3-clause | 5,556 | [
"Gaussian"
] | f100aef5a5a4bf91b6fd460e8586982b27a2ca49ab9d71b37141a96f310ecb9a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright (c) 2016 Jérémie DECOCK (http://www.jdhp.org)
# This script is provided under the terms and conditions of the MIT license:
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (th... | jdhp-sap/data-pipeline-standalone-scripts | datapipe/denoising/wavelets_mrfilter.py | Python | mit | 31,150 | [
"Gaussian"
] | c72834667e9011e2fe281a33427db05eb5eae775d7873bfee9736d2e1bce21b9 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
""" Ban one or more Storage Elements for usage
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base im... | calancha/DIRAC | DataManagementSystem/scripts/dirac-admin-ban-se.py | Python | gpl-3.0 | 7,040 | [
"DIRAC"
] | 5946c5198b85e54193bc752f0ef4dd2e2c2188439253beb8d19d6d9d4faa53a9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
TODO:
-Still assumes individual elements have their own chempots
in a molecular adsorbate instead of considering a single
chempot for a single molecular adsorbate. E.g. for an OH
... | johnson1228/pymatgen | pymatgen/analysis/surface_analysis.py | Python | mit | 53,621 | [
"pymatgen"
] | 85f0bd572a88167509a05e73b231c94937e66d6334663d1d81a077bded9b052f |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-org-policy | scripts/fixup_orgpolicy_v2_keywords.py | Python | apache-2.0 | 6,245 | [
"VisIt"
] | 5325e13b3bdaa8469ea876f42188c1273f201cb8fcc08d6233a89550a0726d22 |
#!/usr/bin/env python3
########################################################################
# Solves problem 323 from projectEuler.net.
# Calculates the average number of tries you need to get the 32 bits
# in 1 using or operations with random numbers.
# Copyright (C) 2011 Santiago Alessandri
#
# This p... | sanSS/programming-contests | project-euler/problem323.py | Python | gpl-3.0 | 2,010 | [
"VisIt"
] | 22f97d3b54a159e152f12bd5d1b75a44d84f497be471c84aeae9ba8cee79ada6 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/server_rpc.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice... | hdemeyer/king-phisher | king_phisher/server/server_rpc.py | Python | bsd-3-clause | 32,013 | [
"VisIt"
] | f9ff541482872ba75cf507c60039cf0ef7653d0cd94360f2e9501e60e2cfffef |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string, optparse, subprocess
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','desc... | titanium-forks/benbahrenburg.Ti.SevenSwitch | build.py | Python | mit | 8,771 | [
"VisIt"
] | 6db6d37b3c4684dc5aee6d04d787e1083c34fce5a4a5aedf5afe3cc117afa73d |
#!/usr/bin/env python
##
## See COPYING file distributed along with the ncanda-data-integration package
## for the copyright and license terms
##
"""
Check Missing Scans
===================
- Take as input a csv file containing subject id, visit, and validation type.
- Then query redcap to see if scan information is... | kipohl/ncanda-data-integration | scripts/redcap/check_missing_scans.py | Python | bsd-3-clause | 3,654 | [
"VisIt"
] | 90f4d3e8a3c3dd33dc7252e8cb61c8f6476322a8ce0b8babe2f7279e1459dfb9 |
# -*- coding: utf-8 -*-
"""
Created on Sun May 10 12:39:33 2015
Author: Josef Perktold
License: BSD-3
"""
import warnings
import pytest
import numpy as np
from numpy.testing import assert_allclose, assert_equal
from statsmodels.discrete.discrete_model import Poisson, Logit, Probit
from statsmodels.genmod.generalized... | jseabold/statsmodels | statsmodels/base/tests/test_penalized.py | Python | bsd-3-clause | 24,844 | [
"Gaussian"
] | effd001ca76c64d103dce1b47d4480094139b6dfe80188b662aa0bf10d0c1b3d |
import math
from itertools import izip_longest
class NeuronConnection(object):
def __init__(self, parent, child, weight=0.4):
self.parent = parent
self.child = child
self.weight = weight
class Neuron(object):
def __init__(self, input=None, output=None, is_bias=False):
self... | dev-coop/neural-net-hacking-examples | python/Part 3/neural_network_with_connections.py | Python | mit | 4,284 | [
"NEURON"
] | c19c2e9374d8ba184ade8602cd68cab954814f75f7c9a106da1ca2bd9b3a63e4 |
"""
This module implements basic kinds of jobs for Nwchem runs.
"""
import shutil
import subprocess
from monty.io import zopen
from monty.shutil import gzip_dir
from custodian.custodian import Job
__author__ = "Shyue Ping Ong"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "ongsp@ucsd.edu"
__stat... | materialsproject/custodian | custodian/nwchem/jobs.py | Python | mit | 2,234 | [
"NWChem"
] | e8fed0fc10872620481f14dcd00439790cda2835883e295ac0e9809f4819ab60 |
#
# Copyright (C) 2010-2019 The ESPResSo project
# Copyright (C) 2002,2003,2004,2005,2006,2007,2008,2009,2010
# Max-Planck-Institute for Polymer Research, Theory Group
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public... | KaiSzuttor/espresso | doc/tutorials/02-charged_system/scripts/nacl_units_confined.py | Python | gpl-3.0 | 6,204 | [
"ESPResSo"
] | 96fec7224176673adbc780b52c06482a76fa06ca2895c25374152bed17c676d9 |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
##!/mnt/lustre_fs/users/mjmcc/apps/python2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
import sys
import numpy as np
from numpy.linalg import *
import MDAnalysis
from distance_fun... | rbdavid/Distance_matrix | matrix_calc.py | Python | gpl-3.0 | 1,896 | [
"MDAnalysis"
] | eae064e94b9c7fd4cceec9fe723a79eb675ed37a3788c96c93bc47893bbffcea |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import abel
import scipy
from scipy.special import eval_legendre
from scipy import ndimage
###################################... | rth/PyAbel | abel/linbasex.py | Python | mit | 15,652 | [
"Gaussian"
] | de566b5de4227e5d890569cc84c6344521a81d16a6b4b45829009c116bbf1fe5 |
#
# @file TestASTNode.py
# @brief ASTNode unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id: TestASTNode.py 11526 2010-07-22 00:35:38Z mhucka $
# $HeadURL: https://sbml.svn.sourceforge.net/svnroot/sbml/trunk/libsbml/src/bindings/python/test/math/TestASTNode.py $
#
# ======... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/math/TestASTNode.py | Python | gpl-3.0 | 44,808 | [
"VisIt"
] | 9b2b73d731aebaff18ef14a553ecf08bed1fcfa5789b69cff39d1e4f715153fd |
#!/usr/bin/env python
"""
Generate the images and rst files for gallery of SfePy examples.
The following steps need to be made to regenerate the documentation with the
updated example files:
1. Generate the files:
- for sfepy.org deployment::
$ ./script/gen_gallery.py -l ../doc-devel
- for local test bu... | RexFuzzle/sfepy | script/gen_gallery.py | Python | bsd-3-clause | 20,332 | [
"VTK"
] | 9b9b41b0ff65a6392b1da8ac44df96d26f85144581a1bc8b06f235834bdd7768 |
#!/home/andriy/anaconda3/envs/python2/bin/python
#!/usr/bin/python
import getopt
import sys
from Bio import SeqIO
import time
import os
import shutil
import pandas
__author__ = "Andriy Sheremet"
#Helper functions definitions
def parse_contigs_ind(f_name):
"""
Returns sequences index from the input files(s... | nyirock/mg_blast_wrapper | mg_blast_wrapper_v1.7_anaconda.py | Python | mit | 15,957 | [
"BLAST"
] | 9bd4a5d13220594ab2f077286309a3325bc00c8e2da2191bd4bf2e194621dd08 |
import unittest
from test import test_support
from itertools import *
import weakref
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = test_support.MAX_Py_ssize_t
minsize = -maxsize-1
def onearg(x):
'... | wang1352083/pythontool | python-2.7.12-lib/test/test_itertools.py | Python | mit | 69,418 | [
"GULP"
] | d8f575e3068d06b1befbcd1f02e3f98f07b5b2a53eb388a548268ffda0de0c82 |
#!/usr/bin/env python
### LAMMPS replica trajectory reorder by temperature
### coded by TS (partly adapated from sim.traj.lammps.py by MSS)
import os, sys, numpy as np, argparse, time, cPickle as pickle
from tqdm import tqdm, trange
import cStringIO as StringIO, gzip
from mpi4py import MPI
import pymbar, whamlib
# ... | tanmoy7989/mysim | reorderLammpsREMD.py | Python | gpl-3.0 | 9,873 | [
"LAMMPS"
] | 4606ddd0c1d31dc55b8766de71d9a2142e3c474645a0b34e6dfd11a925256108 |
from ovito import *
from ovito.io import *
from ovito.modifiers import *
import numpy
node = import_file("../../files/LAMMPS/animation.dump.gz")
node.modifiers.append(AssignColorModifier(color = (0,1,0)))
assert((node.compute().particle_properties.color.array[0] == numpy.array([0,1,0])).all())
| srinath-chakravarthy/ovito | tests/scripts/test_suite/assign_color_modifier.py | Python | gpl-3.0 | 298 | [
"LAMMPS",
"OVITO"
] | 6a63fe4ab9dea5c52ae8a2030d0cc754805ca81b50beb34a8219ba9d659557f4 |
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the... | karrtikr/ete | ete3/treeview/qt4_render.py | Python | gpl-3.0 | 44,795 | [
"VisIt"
] | 5599c217843f94b7306d552bc2b79ca062353be6f89cf793763a6038865ac874 |
"""
Tests for common utility functions
"""
from __future__ import (absolute_import, division, print_function, unicode_literals)
try:
from builtins import * # pylint: disable=unused-wildcard-import,redefined-builtin,wildcard-import
except ImportError:
import sys
print("WARNING: Cannot Load builtins for py3 ... | rgant/saas-api-boilerplate | tests/common/test_utilities.py | Python | gpl-3.0 | 5,189 | [
"Brian"
] | 178b8f3d52a0b4dcdc80f44e63f18c35d96b536c669e16274870906b2975cd58 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# editor - Online editor back end
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | heromod/migrid | mig/shared/functionality/editor.py | Python | gpl-2.0 | 17,105 | [
"Brian"
] | 9ed6f54a63ea357ad07262cf2a980d6ab57801b90f3aedebbae1699f789c2e68 |
###############################################################################
# Copyright 2017-2021 - Climate Research Division
# Environment and Climate Change Canada
#
# This file is part of the "fstd2nc" package.
#
# "fstd2nc" is free software: you can redistribute it and/or modify
# it under... | neishm/fstd2nc | fstd2nc/mixins/xycoords.py | Python | lgpl-3.0 | 30,069 | [
"NetCDF"
] | e5497022bd1881b141d0428be206464011ad3d76536289983d16b7fe40c16577 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
u"""
Copyright (c) 2016 Masaru Morita
This software is released under the MIT License.
See LICENSE file included in this repository.
"""
import random
import sys
sys.path.append('../')
from util.ActivationFunction import Step
from util.GaussianDistribution import GaussianDi... | MoriKen254/DeepLearningWithPython | SingleLayerNeuralNetworks/Perceptrons.py | Python | mit | 6,099 | [
"Gaussian"
] | d1a884631758c1a7b9b7739fdccadc46a0bfc9c278b273c47064d6a2019ecda8 |
#
# Copyright (c) 2017 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... | yasharmaster/scancode-toolkit | src/scancode/api.py | Python | apache-2.0 | 9,085 | [
"VisIt"
] | 667bb9518ba6adc42a456b12d0bb970e1e112441b336e1cbe560a073693cb624 |
from gpaw.upf import UPFSetupData, upfplot
from gpaw.pseudopotential import pseudoplot, PseudoPotential
def get(fname):
s = UPFSetupData(fname)
return s
s = get('O.pz-hgh.UPF')
#upfplot(s.data, show=True)
bfs = s.create_basis_functions()
pp = PseudoPotential(s, bfs)
import numpy as np
x = np.linspace(0.0, 5.... | robwarm/gpaw-symm | gpaw/test/pseudopotential/upf_h2o.py | Python | gpl-3.0 | 2,021 | [
"ASE",
"GPAW"
] | 9412b987274160e0b9edbdc10fad6401f8d6f83386af781133768f42cbac5299 |
# -*- coding: utf-8 -*-
''' Provides user IO to FAS '''
#
# Copyright © 2008 Ricky Zhou
# Copyright © 2008-2014 Red Hat, Inc.
# Copyright © 2012 Patrick Uiterwijk
#
# 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... | fedora-infra/fas | fas/user.py | Python | gpl-2.0 | 72,972 | [
"VisIt",
"exciting"
] | b47277a0edc0444a3dec3a00f28d9af86d3e6a0ecfdc4d1dbad8d53b90eca986 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
import unittest
from pymatgen.io.abinit.launcher import ScriptEditor
class ScriptEditorTest(unittest.TestCase):
def test_base(self):
... | matk86/pymatgen | pymatgen/io/abinit/tests/test_launcher.py | Python | mit | 669 | [
"ABINIT",
"pymatgen"
] | e7e326e352c4abf913a55ce3363a709ab413708bd21b3a5b1486d8b37d237b34 |
#
# 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/scancode/test_interrupt.py | Python | apache-2.0 | 2,755 | [
"VisIt"
] | ce9526ff4d79eb4ce705c3451d8e558a30d2329a96884c57afc3df4b7a110363 |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/remindor-qt | remindor_qt/TimeDialog.py | Python | gpl-3.0 | 6,218 | [
"Brian"
] | 94472a7542a8de74bb0f5c8e8e61e61e1e071cc49893cf610cda811eace29455 |
from __future__ import absolute_import
__author__ = 'ross'
import unittest
'''
* Version 7.75 Marker denoting start of set-up parameters
CO2 Heating device name (see Calibration file)
145-hole Sample holder file
0 Timed delay before beginning multiple-runs
30 Timed delay between runs
3 Number of unknowns between blan... | UManPychron/pychron | test/experiment/mult_runs_sequence.py | Python | apache-2.0 | 4,749 | [
"CRYSTAL"
] | dd595c48e56fe193f574eab5e188800318406b188b1fe98236d38b50a56e2ae7 |
#Copyright (C) 2013 Alex Nitz
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the h... | stevereyes01/pycbc | pycbc/strain/strain.py | Python | gpl-3.0 | 79,437 | [
"Gaussian"
] | 53ad1b813764eaf97fb6613c1e8a7ea1ee3903582ea25734c996d763c0a19350 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division, print_function
# Imports
import numpy as np
# Plotting
import matplotlib.pyplot as pl
import seaborn; seaborn.set_style('ticks')
from scipy import interpolate
import pandas as pd
def main():
# GRB111117A L_B
MB_star = -21.83 # F... | jselsing/GRB111117A | py/LB_observability.py | Python | mit | 2,266 | [
"Galaxy"
] | c6a42f037a42a470e6e75fbde7f69ce263914747919162a7bf8e11a7cc94e2ad |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit http://feedparser.org/ for the latest version
Visit http://feedparser.org/docs/ for the latest documentation
Required: Python 2.1 or later
Recommended: Python 2.3 or... | freevo/freevo1 | src/util/feedparser.py | Python | gpl-2.0 | 154,269 | [
"NetCDF",
"VisIt"
] | aca49f20c3d4660469cbb16401b1aff2ccd6caa820d2fb391b125670593d4a43 |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | hmenke/espresso | testsuite/python/exclusions.py | Python | gpl-3.0 | 6,741 | [
"ESPResSo"
] | 23975d0f95fe5cf064dd7307d1d9a4a6090f1ddf861f0cb336d8c49799584740 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006,2007,2012,2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public v... | ghutchis/cclib | test/data/testSPun.py | Python | lgpl-2.1 | 6,651 | [
"Dalton",
"Jaguar",
"Molpro",
"ORCA",
"cclib"
] | 43517cc7c2c189c8d405bcf4c4511aa9d75c8ddf4c2da9d8fe64a21ef46bd334 |
# 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 following conditions are ... | wizmer/NeuroM | neurom/core/population.py | Python | bsd-3-clause | 2,886 | [
"NEURON"
] | d799f33f72ca6ffc5c5dbcfa5a6a66b9c3f59e1fd78b5641de147208e9889817 |
from edc_dashboard.subject import RegisteredSubjectDashboard
from edc_registration.models import RegisteredSubject
from microbiome.apps.mb.constants import INFANT
from microbiome.apps.mb_infant.models import InfantVisit, InfantBirth
from microbiome.apps.mb_lab.models import InfantRequisition
from microbiome.apps.mb_ma... | botswana-harvard/microbiome | microbiome/apps/mb_dashboard/classes/infant_dashboard.py | Python | gpl-2.0 | 4,778 | [
"VisIt"
] | 4678e3a3bfecb637064de8ec52c33962846b412eb105bd16f1b9d2e2fd3203cc |
"""Simple test for the ImageDataProbe filter.
"""
# Author: Prabhu Ramachandran <prabhu [at] aero . iitb . ac . in>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# Standard library imports.
from os.path import abspath
from StringIO import StringIO
import copy
# Local imports.
from common import TestCas... | liulion/mayavi | integrationtests/mayavi/test_labels.py | Python | bsd-3-clause | 4,124 | [
"Mayavi",
"VTK"
] | cced572ce05043454daa7dcd9dde8b1958f84fea2a3056f296412e16478c5c4e |
#!/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... | sunqm/pyscf | pyscf/soscf/test/test_newton_ah.py | Python | apache-2.0 | 10,202 | [
"PySCF"
] | 8f7c3a65ff60bfacf86959ce34180fd422230d632556e4800c552c620eb66911 |
# $Id: nodes.py 7788 2015-02-16 22:10:52Z milde $
# Author: David Goodger <goodger@python.org>
# Maintainer: docutils-develop@lists.sourceforge.net
# Copyright: This module has been placed in the public domain.
"""
Docutils document tree element class library.
Classes in CamelCase are abstract base classes or auxilia... | lmregus/Portfolio | python/design_patterns/env/lib/python3.7/site-packages/docutils/nodes.py | Python | mit | 77,200 | [
"VisIt"
] | 46be40c05ec2e8c5baa0ffdac3e8daf8d9bbda2aa9210e5b02122a1f9a9cded5 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/encore/clustering/cluster.py | Python | gpl-2.0 | 9,587 | [
"MDAnalysis"
] | cfdbc90d2a00b6c8ebba4848ca1228ff6aa80f923438311d46b4b251581cb84a |
import random
#import matplotlib.pyplot as plt
#http://matplotlib.org/api/pyplot_api.html
import numpy as np
#
# this modified version of the scipy.stats.kde.gaussian_kde() relies
# only on numpy. simply using "import numpy as np" will enable any script
# to use this class.
#
class gaussian_kde(object):
"""
... | gpfinder/gpfinder | GPFinder/gaussian_kde.py | Python | gpl-3.0 | 5,153 | [
"Gaussian"
] | 590f7ed504f31b6be2475687ceb6fd50c84a3df9ec15cce9fbe6bd21eba29e12 |
#!/bin/env python
"""
Create and put 'PutAndRegister' request with a single local file
warning: make sure the file you want to put is accessible from DIRAC production hosts,
i.e. put file on network fs (AFS or NFS), otherwise operation will fail!!!
Usage:
dirac-dms-put-and-register-request [options] re... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_put_and_register_request.py | Python | gpl-3.0 | 2,802 | [
"DIRAC"
] | 4c75d25e8ec5906e4f5555fb54b7be9f8f5411e0bb4c119a36d174344ccd1397 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
The transfer functions (actually classes) define simple transformations, from incoming ROS values to the injected
live spikes or from observed spikes in ROS live output.
The base classes do all the work, so all you do here is inherit from them and define their behavi... | reiths/ros_spinnaker_interface | ros_spinnaker_interface/transfer_functions.py | Python | mit | 9,701 | [
"NEURON"
] | 564af797f859c44cbdd6c5c5a81fa8d53b001eed95327e0e0be66e07dd7e1f94 |
# -----------------------------------------------------------------------------
# User configuration
# -----------------------------------------------------------------------------
dataset_destination_path = '/Users/seb/Desktop/diskout_volume_%s'
file_path = '/Users/seb/Downloads/ParaViewData-3.98.1/Data/disk_out_ref.... | Kitware/arctic-viewer | scripts/examples/vtk/samples/diskout-volume.py | Python | bsd-3-clause | 3,922 | [
"VTK"
] | 65e381ad6739c67d1de90f60291a626de5b25847c6592a04c451356d7011ab95 |
#!/bin/env python
"""
Cascade decomposition
=====================
This example script shows how to compute and plot the cascade decompositon of
a single radar precipitation field in pysteps.
"""
from matplotlib import cm, pyplot as plt
import numpy as np
import os
from pprint import pprint
from pysteps.cascade.band... | pySTEPS/pysteps | examples/plot_cascade_decomposition.py | Python | bsd-3-clause | 4,576 | [
"Gaussian"
] | 29d4f65631e91ff9f39755c5342d8ae7dcc54fb67963b779b3331e3b891a1b24 |
# This file is part of Androguard.
#
# Copyright (C) 2014 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
... | yang-guangliang/android_guard | androguard/decompiler/dad/ast.py | Python | apache-2.0 | 24,226 | [
"VisIt"
] | ae3c2099f374a0bab76b65d4a933148a878cad972f4ca286910d79362f905cf3 |
from xml.etree import ElementTree;
e = ElementTree.parse('./json.xml').getroot();
stations = [];
for child in e:
station = {};
station['code'] = child.find('Code').text;
station['type'] = child.find('Type').text;
station['land'] = child.find('Land').text;
station['namen'] = [];
for naam in ch... | AtlasDev/TICT-V1PROG-15 | les-8/final.py | Python | mit | 1,015 | [
"Elk"
] | b919c46d569029f6d4899ac4b8168b4645016e1f7beaf1ede557eb31c96f81f5 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of blast-python.
#
# blast-python 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)
# ... | crs4/blast-python | test/all_tests.py | Python | gpl-3.0 | 1,089 | [
"BLAST"
] | ae16ab6816101477165bb201859b30aa5f57e80f9211823249960589499450e0 |
import unittest
from test import test_support
from itertools import *
import weakref
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
maxsize = test_support.MAX_Py_ssize_t
minsize = -maxsize-1
def onearg(x):
'... | jlspyaozhongkai/Uter | third_party_build/Python-2.7.9/lib/python2.7/test/test_itertools.py | Python | gpl-3.0 | 68,229 | [
"GULP"
] | 1197421564aa8e966b47353c650cb775235d7ca0081837c10249261a5cacb3cf |
"""
Original code from John Schulman for CS294 Deep Reinforcement Learning Spring 2017
Adapted for CS294-112 Fall 2017 by Abhishek Gupta and Joshua Achiam
Adapted for CS294-112 Fall 2018 by Michael Chang and Soroush Nasiriany
"""
import numpy as np
import tensorflow as tf
import gym
import logz
import os
import time
im... | berkeleydeeprlcourse/homework | hw2/train_pg_f18.py | Python | mit | 29,999 | [
"Gaussian"
] | ff2e20d4373bcb6eb739e7be6694b0b1bbf8b018ba736f1875ac0ba61f69cad0 |
import functools
import multiprocessing
import multiprocessing.queues
import os
import pysam
import msgpack
from ..transcripts.transcriptchecker import TranscriptChecker
from .. import exceptions
from ..transcripts import Transcript
from ..utilities.log_utils import create_null_logger, create_queue_logger
import loggin... | lucventurini/mikado | Mikado/preparation/checking.py | Python | lgpl-3.0 | 14,046 | [
"pysam"
] | 1da507ba20f937f5726995eb94406ff67947dc637a0103dc2eaf947e33ed6916 |
#!/usr/bin/python
from collections import defaultdict
from SymbolTable import SymbolTable, FunctionSymbol, VariableSymbol
import AST
types_table = defaultdict(lambda: defaultdict(lambda: defaultdict(lambda: None)))
for op in ['+', '-', '*', '/', '%', '<', '>', '<<', '>>', '|', '&', '^', '<=', '>=', '==', '!=']:
t... | salceson/kompilatory | lab4/TypeChecker.py | Python | mit | 11,078 | [
"VisIt"
] | 45ab0c9359df7c1f20383b641d52dff05c12a503e9393f8122d0214be8e01e16 |
#!/usr/bin/env python3
import sys
import os
import time
#alphabetic constants
_a = 65
_z = 90
_A = 97
_Z = 122
#constants for user input options in text_step and word_step functions
ENTER = ''
W_NEXT_INST = '>'
W_PREV_INST = '<'
INSTRUCTIONS = 'qa'
YES = NEXT_LINE = 1
NO = QUIT = FIRST = 0
NOMOVE = -1
"""
Karl Toby... | KTRosenberg/Text-Analyzer-and-Step-through-Viewer | old_summer_2016/Text_Analyzer_Step_through_Viewer_main_2.py | Python | mit | 48,902 | [
"VisIt"
] | c65a730a8c95ffef7b354b0c9c814203b1cbb17c54a892fbfd00b6a1ad582985 |
#!/usr/bin/env python
import csv
import pysam
import textwrap
import sys
import argparse
parser = argparse.ArgumentParser(description="Given a BED file of repeat regions, extract the appropriate sequence from a fasta file. The output is written to the screen, so the user is advised to use redirection.")
parser.add_arg... | dpryan79/SE-MEI | bed2fasta.py | Python | gpl-2.0 | 843 | [
"pysam"
] | 082117cde0d8008975e645ed2168f7d1a4061c0bfa98bf3f4b946d260131d1b9 |
#!/usr/bin/env python
"""
align.py
NCBI Hackathon, RNA-seq team
January 5, 2015
Created by Abhi Nellore
Aligns RNA-seq FASTQs specified by a manifest file, each of whose lines has the
following format:
SRA accession number <TAB> sample group <TAB> sample name
Outputs BAM files. Each filename is in the following for... | NCBI-Hackathons/hackathon_v001_rnaseq | align.py | Python | cc0-1.0 | 16,397 | [
"BLAST"
] | 12867d007c339e5a7d428550a0ba9dc3d3c2b3145c9c530a49f2378b21f2b139 |
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