text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
import glob
import os
import mdtraj as md
import fah
def make_path(filename):
try:
path = os.path.split(filename)[0]
os.makedirs(path)
except OSError:
pass
def get_num_runs_clones(path):
"""Get the number of runs and clones.
Parameters
----------
path : str
... | kyleabeauchamp/FAHMunge | FAHMunge/automation.py | Python | lgpl-2.1 | 2,989 | [
"MDTraj"
] | 1794e3746d4f420aa37867871ecf82c64f93627ccb69bb54aa4e25c102271dac |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module implements abstract base classes for post-processing entries.
Any class which modifies entries should inherit these classes.
"""
import six
_... | matk86/pymatgen | pymatgen/entries/post_processors_abc.py | Python | mit | 1,471 | [
"pymatgen"
] | 2b6a0d2b0cd2a7188f95fe2ab36b5ff4e37207e164251cf1782477cf46fc2057 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | ravibhure/ansible | lib/ansible/modules/network/avi/avi_virtualservice.py | Python | gpl-3.0 | 26,455 | [
"VisIt"
] | cadfa77ae6a5f053b63ce5052454569c6b6f3fba6523d620293ff4afacdeff44 |
###############################################################################
# Name: ed_menu.py #
# Purpose: Editra's Menubar and Menu related classes #
# Author: Cody Precord <cprecord@editra.org> #
... | ezequielpereira/Time-Line | libs/wx/tools/Editra/src/ed_menu.py | Python | gpl-3.0 | 46,756 | [
"VisIt"
] | 19fa780c1fc2a1abc9fdfcca2e54278839e394225fa216b106f0723e56f47ec7 |
# break out of code on keyboard interrupt -------------------------------------
import os, signal, sys
def signalHandler(signal, frame):
os._exit(1)
signal.signal(signal.SIGINT, signalHandler)
# imports ---------------------------------------------------------------------
from glob import glob
from omf import f... | dpinney/omf | omf/scratch/disaggDataGeneration/regression/code/generateDissagData.py | Python | gpl-2.0 | 16,265 | [
"Gaussian"
] | 85c00d391abe5aa818444343705baacb990febb3990b8231f6a567238261f906 |
"""
Sasview model constructor.
Given a module defining an OpenCL kernel such as sasmodels.models.cylinder,
create a sasview model class to run that kernel as follows::
from sasmodels.sasview_model import load_custom_model
CylinderModel = load_custom_model('sasmodels/models/cylinder.py')
"""
from __future__ im... | SasView/sasmodels | sasmodels/sasview_model.py | Python | bsd-3-clause | 36,967 | [
"Gaussian"
] | 659578561b49f935054dec8362890878ceab00b97606fc7acb2cc1dbd3dede41 |
#!/usr/bin/env python
__author__ = 'Mike McCann,Duane Edgington,Reiko Michisaki'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all Worden's CN13ID Western Flyer cruise in October 2013
CN13ID: CANON 2013 Interdisciplinary
Mike McCann
MBARI 23 ... | stoqs/stoqs | stoqs/loaders/CANON/loadCN13ID_october2013.py | Python | gpl-3.0 | 11,697 | [
"NetCDF"
] | efdac5a0604162cc656561fc72f4d7c21ccf6f3290bc9bc8b74382d487ec8f0f |
"""
=============================
Generic SpectralModel wrapper
=============================
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
Module API
^^^^^^^^^^
"""
import numpy as np
from pyspeckit.mpfit import mpfit,mpfitException
from pyspeckit.spectrum.parinfo import ParinfoList,Parinfo
import copy
... | pyspeckit/pyspeckit | pyspeckit/spectrum/models/model.py | Python | mit | 49,120 | [
"Gaussian"
] | 5b37d34c291bf39496d70e7f084466a4d231f62b7ee1030c3d723f8e83a51bc9 |
#Schrodinger 1D equation solved by finding eigenvectors for a gaussian potential
import numpy as np
import scipy
import scipy.integrate
import scipy.linalg
import scipy.misc
import scipy.special
import pylab as plt
l=10
N=1024
def v(x):
return np.exp(-x*x)
m=1
w=1
hbar=1
X, dx=np.linspace(-l, l, N, retstep=True)
H=... | StanczakDominik/NumericalSchrodinger | SchrodingerEigenvectorsGaussianPotential.py | Python | mit | 1,212 | [
"Gaussian"
] | 55096e0f59a0a75276405356bfdeaabb2fa1bfd20843346ed20e779a7030e023 |
#! /usr/bin/python
"""CAnonicalize N-Triples
Options:
--verbose -v Print what you are doing as you go
--help -h Print this message and exit
--from=uri -f uri Specify an input file (or web resource)
--diff=uri -d uri Specify a difference file
Can have any number of --from <file> p... | vdimarco/Open-Data-Linker | ETL/cannon_Nt3_graph.py | Python | apache-2.0 | 12,100 | [
"Brian"
] | 01e021fd10833903b2d29ea44de61ef6bc00290b9d9e8df64715e1ba2514a1b5 |
"""Class for managing, downloading and extracting features from genbank files."""
# Standard Library
import os
import shutil
from pathlib import Path
# BioPython
from BioSQL import BioSeqDatabase
from Bio import SeqIO
# OrthoEvol
from OrthoEvol.Tools.logit import LogIt
from OrthoEvol.Orthologs.Blast import OrthoBlastN
... | datasnakes/Datasnakes-Scripts | OrthoEvol/Orthologs/GenBank/genbank.py | Python | mit | 26,973 | [
"BLAST",
"Biopython"
] | cefbb777b505a7dc925e50e257d21dec1d57d04c7e51ef967fed193ff9f5e754 |
# Module for XML, HTML and CGI output
# jaxml
# (C) Jerome Alet <alet@librelogiciel.com> 2000-2002
# You're welcome to redistribute this software under the
# terms of the GNU General Public Licence version 2.0
# or, at your option, any higher version.
#
# You can read the complete GNU GPL in the file COPYING
# which sh... | denys-duchier/Scolar | config/softs/jaxml-3.01/jaxml.py | Python | gpl-2.0 | 49,250 | [
"VisIt"
] | 7c821ed33114e00d62a3efdc419ebfcb5e51f0effa69eaadd62395dca24a541d |
quantity_qualifier = {
"01": "Discrete Quantity",
"02": "Cumulative Quantity",
"03": "Discreet Quantity - Rejected Material",
"04": "Discrete Quantity - Rejected Material: Disposition Replacement",
"05": "Discrete Quantity - Rejected Material: Disposition Credit",
"06": "Discrete Quantity - Reje... | sbuss/TigerShark | tigershark/facade/enums/common.py | Python | bsd-3-clause | 146,273 | [
"ADF",
"VisIt"
] | 5f4d14bf04013dfd457adac1808170549f5fe2b757d6815cdc6d31884c186c6c |
import warnings
import numpy as np
import tensorflow as tf
from sklearn.decomposition import NMF, TruncatedSVD
from tqdm import trange
from . import utils, warp
from .regularizers import curvature, l2
class TWPCA(object):
def __init__(self, data, n_components,
sess=None,
shared... | ganguli-lab/twpca | twpca/model.py | Python | mit | 21,822 | [
"NEURON"
] | 762f38e0477fe0a149c42a0ccb8a301ee3d14c306f54fa2add30afc0a8b68c6f |
# -*- coding: utf-8 -*-
"""SendGmailSimplified API is a API that is based on the currently existing official Gmail API with
which you can connect a Google Gmail Account with secure keys without using your real Google
Password. It is hosted on Github: https://github.com/AnonymerNiklasistanonym/SendGmailSimplified
"""
... | AnonymerNiklasistanonym/SendGmailSimplified | SendGmailSimplified.py | Python | mit | 22,353 | [
"VisIt"
] | 8a62e4d94d2e29fcc7c116a86b843332e0ac078ee2711439d3d2ec07ebdd1e3d |
#! /usr/bin/env python2
# Copyright (C) 2011 Sebastian Pipping <sebastian@pipping.org>
# Copyright (C) 2013 Brian dolbec <dolsen@gentoo.org>
# Licensed under GPL v2 or later
import os
import re
import sys
import textwrap
_pattern_arch_generic = re.compile('^class arch_([a-z0-9_.-]+)\\(generic_([a-z0-9_.-]+)\\):')
_... | elitak/catalyst | doc/make_subarch_table_guidexml.py | Python | gpl-2.0 | 3,405 | [
"Brian"
] | 01688128f4b9de46064f316caa1d00fafdc3c7b002fbaa160db4e64cdd251fcd |
from flask import Flask, render_template_string, redirect
from sqlalchemy import create_engine, MetaData
from flask.ext.login import UserMixin, LoginManager, login_user, logout_user
from flask.ext.blogging import SQLAStorage, BloggingEngine
app = Flask(__name__)
app.config["SECRET_KEY"] = "secret" # for WTF-forms and... | wdm0006/Flask-Blogging | example/main.py | Python | mit | 1,822 | [
"DIRAC"
] | 826dbba398658d5e7c1a08aa18c39a39d56a3a8c55bb738c2bddecdfebc01b6c |
from __future__ import absolute_import
from typing import Any, Tuple
from django.db import models
from django.conf import settings
from django.contrib.auth.models import AbstractBaseUser, UserManager, \
PermissionsMixin
from django.dispatch import receiver
from zerver.lib.cache import cache_with_key, flush_user_pr... | peiwei/zulip | zerver/models.py | Python | apache-2.0 | 54,193 | [
"VisIt"
] | 78feef3c69cd9ee3cc240ce94b05a39fd229adebe17e850e4bb5c01e81d06a27 |
#!/usr/bin/env python3
""" Various utilities/tools for BLAST """
from __future__ import print_function
__all__ = ["safe_exec", "update_blast_version"]
import os
import subprocess
import platform
import unittest
import tempfile
import re
def safe_exec(cmd):
""" Executes a command and checks its return value, thr... | kyungtaekLIM/PSI-BLASTexB | src/ncbi-blast-2.5.0+/c++/scripts/projects/magicblast/post_build/blast_utils.py | Python | lgpl-3.0 | 3,956 | [
"BLAST"
] | 7782dd051021f7174a3bfbc3fb99a19d811b179e27f15f318e84a1f40f5185a9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | kain88-de/mdanalysis | package/MDAnalysis/analysis/hbonds/__init__.py | Python | gpl-2.0 | 1,223 | [
"MDAnalysis"
] | 697e77e69f781f6c2d0ea1eec1006aec69aa8dfe3165252b4ee922350ff65ae1 |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
def main():
myscreen = camvtk.VTKScreen()
focal = cam.Point(5, 5, 0)
r = 30
theta = (float(45)/360)*2*math.pi
fi=45
campos = cam.Point( r*math.sin(theta)*math.cos(fi), r*math.sin(theta)*math.sin(f... | tectronics/opencamlib | scripts/kdtree_debug_0.py | Python | gpl-3.0 | 3,677 | [
"VTK"
] | 6db7a2d80c232f3e6846e871eab3e43fe51551f5c33c38227041756ead0a8a0a |
#!/usr/bin/env python
"""
Wrapper classes for providing a minimal consistent interface to cheminformatics toolkits
Currently supported toolkits:
* The `OpenEye Toolkit <https://docs.eyesopen.com/toolkits/python/quickstart-python/index.html>`_
* The `RDKit <http://www.rdkit.org/>`_
* `AmberTools <http://ambermd.org/Am... | open-forcefield-group/openforcefield | openff/toolkit/utils/toolkits.py | Python | mit | 229,097 | [
"Amber",
"MOPAC",
"OpenFF Toolkit",
"RDKit"
] | c0248f4fc181996049b0ab7dc1fb669cf6b0b02dd6a1cb31741b6a54601638ad |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.CloudStack | ZenPacks/zenoss/CloudStack/parsers/CloudStack.py | Python | gpl-2.0 | 2,039 | [
"VisIt"
] | aee9b63aefe7c434c2838a06eb637a06648fd02dbb2b6dab3d4c24932acc782b |
from datetime import date
from ..core import WesternCalendar, MON, TUE, WED, FRI
from ..registry_tools import iso_register
@iso_register('CL')
class Chile(WesternCalendar):
"Chile"
FIXED_HOLIDAYS = WesternCalendar.FIXED_HOLIDAYS + (
(5, 21, "Navy Day"),
(6, 29, "Saint Peter and Saint Paul"),
... | jaraco/calendra | calendra/america/chile.py | Python | mit | 1,443 | [
"COLUMBUS"
] | 1b13e4c4a5916b72ccd0612204c14295a830bb05c1cea5feaa0ed92d1e1aff76 |
#: vim set encoding=utf-8 :
##
# TwoStep Plugin
# Protects the server from malicious users.
#
# author William F., Henry Jeff
# version 0.41
# copyright MIT
##
# Imports
import PluginAPI as api
import discord
import json
import requests
import threading
from random import randint
from bottle import route, post,... | 10c8/pixelbot | plugins/TwoStep.py | Python | mit | 8,217 | [
"VisIt"
] | c123b7a3bd8516205211ab07488cef11dc9e19343fe99b5fe6c33b82d3ffdb48 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Hamilton Kibbe <ham@hamiltonkib.be>
import pytest
from ..cam import CamFile, FileSettings
def test_filesettings_defaults():
""" Test FileSettings default values
"""
fs = FileSettings()
assert fs.format == (2, 5)
assert fs.notation == "abs... | curtacircuitos/pcb-tools | gerber/tests/test_cam.py | Python | apache-2.0 | 4,335 | [
"Octopus"
] | 35e341b5392a62196875576bf8488c92e1a1036245cc3ad92ad0f8c1941b19d8 |
import vtk
def get_program_parameters():
import argparse
description = 'Generate a triangle with colored points and write it to a .vtp file.'
epilogue = '''
'''
parser = argparse.ArgumentParser(description=description, epilog=epilogue)
parser.add_argument('filename', help='A required vtp filenam... | lorensen/VTKExamples | src/Python/PolyData/TriangleColoredPoints.py | Python | apache-2.0 | 1,684 | [
"VTK"
] | 148097491313734a9393eaed7f4438b3f2c538d189ecfa09d27061cd6c874132 |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/n/ncl.py | Python | mit | 7,247 | [
"NetCDF"
] | 200421573b561f5f3053acd77cfab54137bcc4febafb2f07c211fde11ab91852 |
import warnings
import numpy as np
from numpy.testing import (
assert_, assert_raises, assert_equal, assert_warns,
assert_no_warnings, assert_array_equal, assert_array_almost_equal,
suppress_warnings
)
from numpy import random
import sys
class TestSeed:
def test_scalar(self):
... | WarrenWeckesser/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 67,069 | [
"Gaussian"
] | 23e899f0ef26d1100785cdda4b2f51a1f864fee05e8758219eea3bfba6fdacb2 |
# 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)
import os
import sys
from spack import *
class Vtk(CMakePackage):
"""The Visualization Toolkit (VTK) is an open-so... | LLNL/spack | var/spack/repos/builtin/packages/vtk/package.py | Python | lgpl-2.1 | 17,008 | [
"NetCDF",
"VTK",
"VisIt"
] | 6cd4a9167c8549d36255587babbde3cfb8ba77f25685ecb7a30f54e363ce79af |
# Copyright 2012, SIL International
# All rights reserved.
#
# This 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 the Free Software Foundation; either version 2.1 of License, or
# (at your option) any lat... | silnrsi/graide | lib/graide/testlist.py | Python | lgpl-2.1 | 27,700 | [
"VisIt"
] | 3e89ad68d43596260344d07003a45f52aa25498df9a9d1d9338ccd3935f76d15 |
from typing import Type
from types import ModuleType
from octopus.blocktopus.workspace import Block
from twisted.logger import Logger
log = Logger()
block_types = {}
exclude = set([Block])
processed = set()
def register_builtin_blocks():
from octopus.blocktopus import blocks
import importlib
for ... | richardingham/octopus | octopus/blocktopus/block_registry.py | Python | mit | 1,679 | [
"Octopus"
] | c6dfe8cec54eff780e04e5e408e0429ed3c28d5f8b548706742c5f2f7fe1ceaf |
"""K-means clustering"""
# Authors: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Thomas Rueckstiess <ruecksti@in.tum.de>
# James Bergstra <james.bergstra@umontreal.ca>
# Jan Schlueter <scikit-learn@jan-schlueter.de>
# Nelle Varoquaux
# Peter Prettenhofer <peter.prettenh... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/sklearn/cluster/k_means_.py | Python | mit | 60,896 | [
"Gaussian"
] | 4102754c9af4b25bf915a89cb0aaf7984ea60a4b22ec19a20b1f66e62c0faa2c |
from __future__ import division
import glob
import numpy as NP
from functools import reduce
import numpy.ma as MA
import progressbar as PGB
import h5py
import healpy as HP
import warnings
import copy
import astropy.cosmology as CP
from astropy.time import Time, TimeDelta
from astropy.io import fits
from astropy import ... | nithyanandan/PRISim | prisim/bispectrum_phase.py | Python | mit | 309,270 | [
"Gaussian"
] | 4141db8b4b51d25b8bf1aa0d95af67182cb130a0179fcafa35a5166189aa99a7 |
"""
http://neuralnetworksanddeeplearning.com/chap1.html#implementing_our_network_to_classify_digits
http://numericinsight.com/uploads/A_Gentle_Introduction_to_Backpropagation.pdf
https://ayearofai.com/rohan-lenny-1-neural-networks-the-backpropagation-algorithm-explained-abf4609d4f9d
"""
#### Libraries
# Standard libr... | nitish-tripathi/Simplery | ANN/Odin_10/Network.py | Python | mit | 12,776 | [
"Gaussian",
"NEURON"
] | 4ff7c333f211d10fc91e03a523174a25fbba0cb3fb22512a2c21c51870073d7f |
# 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 RAffyqcreport(RPackage):
"""QC Report Generation for affyBatch objects.
This packa... | iulian787/spack | var/spack/repos/builtin/packages/r-affyqcreport/package.py | Python | lgpl-2.1 | 1,427 | [
"Bioconductor"
] | 5437da0709d8d820ab8776a9631ffa00d7ac05f458fbe586cb716f329745bc96 |
#
# Copyright (c) 2005-2006 by Lee Braiden. Released under the GNU General Public
# License, version 2 or later. Please see the included LICENSE.txt file for details.
# Legally, that file should have been included with this one. If not, please contact
# Lee Braiden (email leebraid@gmail.com) for a copy.
#
import sys... | lee-b/katchtv | code/KTVHTMLPart.py | Python | gpl-2.0 | 25,357 | [
"VisIt"
] | 09c6dbd58b7605d7cb46af2d88ee940ac584505e2db1bc7cd61c9c46fa69c713 |
#!/usr/bin/env python
# Based on codepy's setup.py (see http://mathema.tician.de/software/codepy)
import distribute_setup
import gmm_specializer
distribute_setup.use_setuptools()
from setuptools import setup
import glob
setup(name="gmm_specializer",
version=gmm_specializer.__version__,
description="This... | hcook/gmm | setup.py | Python | bsd-3-clause | 1,434 | [
"Gaussian"
] | d5ff5c8cf25a23eab476c6eadaaccb13bcd9483f6e9835c2d546faf30e17bb77 |
#!/usr/bin/env python
import blastbesties as bb
import argparse
def mainArgs():
### Argument handling.
parser = argparse.ArgumentParser(description='Finds reciprocal best blast pairs from BLAST output format 6 (tabular). Where hits are sorted by query name then descending match quality.')
parser.add_argument('-v', ... | Adamtaranto/blast-besties | blastbesties/cmd_rbb.py | Python | mit | 1,632 | [
"BLAST"
] | 4af850123b5a9e14112831177424b249cae0dcc730bc5be077415c4cb247243e |
""" test File Plugin
"""
import mock
import unittest
import tempfile
import os
import shutil
import errno
from DIRAC import S_OK
from DIRAC.Resources.Storage.StorageElement import StorageElementItem
def mock_StorageFactory_getConfigStorageName(storageName, referenceType, seConfigPath=None):
resolvedName = stora... | DIRACGrid/DIRAC | src/DIRAC/Resources/Storage/test/Test_FilePlugin.py | Python | gpl-3.0 | 18,507 | [
"DIRAC"
] | b987b462f639721fe5c6adfef3b8c894470c2605e018dedc5a4f92ffd0afdd6d |
# -*- coding: utf-8 -*-
"""
Created on Mon May 23 11:13:53 2011
.. module:: statistics
:synopsis: Several functions for data fitting (regression) and analysis,
e.g. DFA
.. moduleauthor: Moritz Maus <moritz@hm10.net>
"""
import numpy as np
import numpy.random as rnd
from pylab import (svd, pinv, dot, diag... | MMaus/mutils | mutils/statistics.py | Python | gpl-2.0 | 19,048 | [
"Gaussian"
] | ec886f0602d4d2e5c87808cac472f0482e2a280867a29e93597299e2528629e8 |
""" Utility for loading plotting types.
Works both for Accounting and Monitoring.
"""
import re
from DIRAC.Core.Utilities import DIRACSingleton
from DIRAC.Core.Utilities.Plotting.ObjectLoader import loadObjects
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
from DIRAC.Monit... | arrabito/DIRAC | Core/Utilities/Plotting/TypeLoader.py | Python | gpl-3.0 | 1,724 | [
"DIRAC"
] | 613faee76bf166e207ca3341c5537b1780967c4c98264b9f2d5050d483b71c2a |
#
# Copyright (c) 2017 Intel Corporation
# SPDX-License-Identifier: BSD-2-Clause
#
from __future__ import print_function, absolute_import
import numpy
import types as pytypes
import collections
import operator
import warnings
from llvmlite import ir as lir
import numba
from numba.six import exec_
from numba import ... | jriehl/numba | numba/ir_utils.py | Python | bsd-2-clause | 77,341 | [
"VisIt"
] | 672343d5f5a9d1b34663b21febfed436a1470a2f2707237d0c0b724ed944a877 |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licens... | tuffy/python-audio-tools | audiotools/cdtoc.py | Python | gpl-2.0 | 9,455 | [
"Brian"
] | 2e2bab6733d827d260bb9ed6df2e7f2d8a1eb5edd0214332d09cd78970cd4d12 |
#!/usr/bin/env python
#
# Optimize the marching cubes table for wireframe.
#
# MC gives a list of triangles. We can draw the wireframe by drawing three
# edges for every triangle, but since each edge (except at the boundary region)
# is shared between two triangles, we'd draw each edge twice.
# The most efficient solut... | uglymol/uglymol | tools/isolut.py | Python | mit | 15,055 | [
"PyMOL"
] | 44d0bb21e75f591c98196ed3eae89f785daae6c4dd61eb92c186bb05f9c3b33f |
#!/usr/bin/env python
#
# Copyright (c) 2002 Bryce "Zooko" Wilcox-O'Hearn
# portions Copyright (c) 2001 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
__cvsid = '$Id: Node.py,v 1.5 2002/07... | zooko/egtp | Node.py | Python | agpl-3.0 | 3,439 | [
"VisIt"
] | afb30d282b42e706dd3adc448c9680e761bb85c7c4cf9d3185cbd0bf27400c5c |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | brianmay/karaage | karaage/plugins/__init__.py | Python | gpl-3.0 | 1,031 | [
"Brian"
] | 7cf515a1730569d7961ebd393d4a6dc055e33a753f4afa00d466a79a08b92e20 |
# -*- coding: utf8 -*-
# $Id: __init__.py 6269 2010-03-18 22:27:53Z milde $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributions from several people include... | rpdillon/wikid | wikid/docutils/writers/latex2e/__init__.py | Python | gpl-3.0 | 105,037 | [
"VisIt"
] | f83a931559590f832923cecb335e1008c685ebe479624b67d8ac7ff0ed4c5f0c |
#!/usr/bin/env python
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
import sys
sys.path.append("../")
from functions import *
from pylab import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import neuroseries as nts
import os
import hsluv
da... | gviejo/ThalamusPhysio | python/figure_talk/main_talk_v4_fig1.py | Python | gpl-3.0 | 16,177 | [
"Gaussian"
] | 5460b520963e5ab700d070a2d2ccd29de418b590125dae066a9c9e71a204945c |
import argparse
import collections
import concurrent.futures
from functools import partial
from math import ceil
import os
import pickle
import re
import shutil
import matplotlib
matplotlib.use('Agg', force=True)
import matplotlib.pyplot as plt
from matplotlib.ticker import MaxNLocator
import numpy as np
import pand... | nanoporetech/pomoxis | pomoxis/assess_homopolymers.py | Python | mpl-2.0 | 22,740 | [
"pysam"
] | b1b09ddd977ffdf7f1f786fcb2da8ab282d61784bcae7190e5abce01565881f2 |
# Copyright (c) 2013, Hansel Dunlop.
# License, see LICENSE for details
import os
import select
import socket
class SocketConnection(object):
def __init__(self, socket, address):
self._socket = socket
self.address = address
def __unicode__(self):
return 'Client Connection from %s' % ... | aychedee/octopus | octopus/server.py | Python | isc | 3,094 | [
"Octopus"
] | 1a5036d46f49067efb512a6d883a4d7c519b05d5550abac031d6279d510cf81f |
#!/usr/local/bin/env python
# =============================================================================================
# Analyze datafiles produced by YANK.
# =============================================================================================
# ==========================================================... | andrrizzi/yank | Yank/analyze.py | Python | mit | 27,206 | [
"MDTraj",
"NetCDF",
"OpenMM"
] | 745ebf2b6ac8e1b0850b53b82811be0b1060ec4173b4bc6c2bd39ff449a9d6a2 |
"""Wrappers for interacting with ``git``"""
import asyncio
import atexit
import logging
import os
import re
import tempfile
import subprocess
from typing import List, Union
import git
import yaml
from . import utils
logger = logging.getLogger(__name__) # pylint: disable=invalid-name
def install_gpg_key(key) -> ... | bioconda/bioconda-utils | bioconda_utils/githandler.py | Python | mit | 25,126 | [
"BLAST",
"Bioconda"
] | bb0b0f1afd7a896b079d1f79f08dc0680210dc3980f67de28d346a32140a7e8f |
""" PolicyBase
The Policy class is a simple base class for all the policies.
"""
from DIRAC.ResourceStatusSystem.Command.Command import Command
class PolicyBase:
"""Base class for all the policies. Do not instantiate directly.
To use, you should call `setCommand` on the real policy instance.
"""
... | ic-hep/DIRAC | src/DIRAC/ResourceStatusSystem/PolicySystem/PolicyBase.py | Python | gpl-3.0 | 1,211 | [
"DIRAC"
] | db9904bfedb05aff1b23caf797e05ac1e1e93cef6ce4e7164a01de4affbc2489 |
# Recurrent Neural Networks
[Overview video](https://www.youtube.com/watch?v=SEnXr6v2ifU&ab_channel=AlexanderAmini).
See also lecture on Thursday October 22 and examples from [week 42](https://compphysics.github.io/MachineLearning/doc/pub/week42/html/week42.html).
[IN5400 at UiO Lecture](https://www.uio.no/studier/em... | CompPhysics/MachineLearning | doc/src/LectureNotes/_build/jupyter_execute/chapter10.py | Python | cc0-1.0 | 103,230 | [
"NEURON"
] | ca1bbc53b3c65ee87cbcae8d5d25a3499d6687a5a84090fbe4c6547a1216f612 |
"""This module provides ParaView equivalents to several ParFlow
pftools algorithms; these are implemented using VTKPythonAlgorithmBase
subclasses and demonstrate how to access both surface and subsurface
computational grids within a single filter."""
from paraview.util.vtkAlgorithm import *
import numpy as np
class p... | Kitware/HPCCloud | pvw-dependencies/pv-flow/flow/plugins/parflow.py | Python | apache-2.0 | 22,541 | [
"ParaView",
"VTK"
] | c5e24181eda9c3266396b2e11dd59846abf83295a6f444fd2ca78e74515db670 |
#!/usr/bin/env python3
# encoding: utf-8
# Copyright (C) 2019 Space Science and Engineering Center (SSEC),
# University of Wisconsin-Madison.
#
# 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 F... | davidh-ssec/polar2grid | polar2grid/readers/viirs_edr_active_fires.py | Python | gpl-3.0 | 4,009 | [
"NetCDF"
] | 3a9181283d063fa225c987a4b0e929f2678e388a1e92edeb266c775a7126ddf5 |
# -*- coding: utf-8 -*-
'''
Copyright (c) 2015 by Tobias Houska
This file is part of Statistical Parameter Estimation Tool (SPOTPY).
:author: Tobias Houska and Alejandro Chamorro-Chavez
This class holds the Simulated Annealing (SA) algorithm based on Kirkpatrick et al. (1983):
Kirkpatrick, S., Gelatt, C. D., Vecchi... | p-lauer/spotpy | spotpy/algorithms/sa.py | Python | mit | 6,367 | [
"Gaussian"
] | 4bde5ab8b74b1afd44681917f573fd992fd698bed2849ca2367632d53e02e651 |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as ... | CopyChat/Plotting | Downscaling/bias.TCC.GCMs.py | Python | gpl-3.0 | 4,182 | [
"NetCDF"
] | dd3b38b3f5ba45440e453f72185c812bf867b96531cb5d1d2a4def7661f5034c |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | baselines/mnist/variational_inference.py | Python | apache-2.0 | 18,849 | [
"Gaussian"
] | 4742cd6887fb9b45685d85cafee5261d33b47952e44cd4acbc15558302efed42 |
# Copyright 2007, Michael J. Harms
# This program is distributed under General Public License v. 3. See the file
# COPYING for a copy of the license.
__description__ = \
"""
gen_input.py
A module containing functions to generate a hbuild.inp file for input into
CHARMM.
"""
__author__ = "Michael J. Harms"
__date__ ... | harmslab/pdbtools | pdbtools/charmm/gen_input.py | Python | gpl-3.0 | 9,111 | [
"CHARMM"
] | dbb5721b5d36c0e858dfbad52e7fe9cf39d7f112178a4a7f55cef7e41a6a357e |
"""
Project 2 - stochastic resonance
"""
from __future__ import division
import sys
from PyDSTool import *
from common_lib import *
from Ch9_HH_red import *
# default
gentype='dopri'
# Parameter An = noise amplitude
# As = sine wave amplitude
# f = frequency, should be >= 50 Hz
par_args = {'tau_v'... | robclewley/compneuro | Ch9_stoch_res_project.py | Python | bsd-3-clause | 3,645 | [
"NEURON"
] | a1eb1a90ad4393074ff7f0be599d679003f5b27be829ab0a0f0491fd8174d716 |
from datetime import datetime
import re
import traceback
import warnings
import numpy as np
import pandas as pd
from collections import defaultdict
from pandas.tslib import OutOfBoundsDatetime
from .core import indexing, ops, utils
from .core.formatting import format_timestamp, first_n_items
from .core.variable impor... | drewokane/xray | xarray/conventions.py | Python | apache-2.0 | 36,727 | [
"NetCDF"
] | 775c372b166017507f8dc6433c5e03c11e4f6feab5637c16e41b36589fd61723 |
#! /usr/bin/python
'''
Gaussian smoothing with Python.
'''
import cv2
import numpy as np
import math
from scipy.signal import sepfir2d
def gaussian_filter(sigma, filter_length=None):
'''
Given a sigma, return a 1-D Gaussian filter.
@param sigma: float, defining the width of the filter
@pa... | mandar2812/python-dev | vision/assignment1/mandar-smoothing1.py | Python | gpl-2.0 | 2,819 | [
"Gaussian"
] | aecdb106efdec1440ebdb4e2b434531a81134022c212fef906067e5dddd9121a |
# coding=utf-8
"""Object for calculating PMV comfort from DataCollections."""
from __future__ import division
from ladybug_geometry.geometry2d.pointvector import Point2D, Vector2D
from ladybug_geometry.geometry2d.line import LineSegment2D
from ladybug_geometry.geometry2d.polyline import Polyline2D
from ladybug_geometr... | ladybug-analysis-tools/ladybug-core | ladybug/psychchart.py | Python | gpl-3.0 | 42,221 | [
"EPW"
] | a832e1e6b95f05d8afa4dc01049fa0364190b29d85d542912341e552614d0a57 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001 David R. Hampton
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | SNoiraud/gramps | gramps/gui/plug/report/__init__.py | Python | gpl-2.0 | 1,163 | [
"Brian"
] | e031e6c390609b7abf13d5b9e9ead79dc437409e577ca8b44b088a88d044ed39 |
# 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 the G... | kkreis/espressopp | src/analysis/XDensity.py | Python | gpl-3.0 | 1,807 | [
"ESPResSo"
] | 093a420dc2221b9ce7f076a5f2c31a13bc6fb192be0aa435213ff119083a9d9a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
=========================================================================
Program: Visualization Toolkit
Module: TestNamedColorsIntegration.py
Copyright (c) Ken Martin, Will Schroeder, Bill Lorensen
All rights reserved.
See Copyright.txt or http://www.... | ashray/VTK-EVM | Rendering/OpenGL/Testing/Python/TestFreetypeTextMapperBigger.py | Python | bsd-3-clause | 3,070 | [
"VTK"
] | a128d2924d6964612a4132ec45922c9e23ff454df28a03f37bfdc2da3368d5d2 |
#
# Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons Foundation
#
# 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... | frew/simpleproto | scons-local-1.1.0/SCons/Taskmaster.py | Python | bsd-2-clause | 30,023 | [
"VisIt"
] | 3d9a9385a13738358632b2ec57f6433a3de5bcde10e922fe0beb58fc6d1d12c9 |
from random import randint
from string import Template
svg_init = """<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
<!--
Created by Marcos 'Feirlane' López <feirlane@gmail.com>
This work is licensed under the Creative Commons A... | Feirlane/RadioFM | utils/svg_bars_generator.py | Python | bsd-2-clause | 1,646 | [
"VisIt"
] | 52554c34ca033399f38f2d0199553337bfb1f545b396b6c4bc75d75c0eda6768 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.matrixlib.defmatrix import matrix, asmatrix
# need * as we're copying the numpy namespace
from numpy import *
__version__ = np.__version__
__all__ = np.__all__[:] # copy numpy namespace
__all__ += ['rand', 'randn', 'repmat... | LumPenPacK/NetworkExtractionFromImages | win_build/nefi2_win_amd64_msvc_2015/site-packages/numpy/matlib.py | Python | bsd-2-clause | 9,584 | [
"Gaussian"
] | ccbc5af1268363a479f8bc18f11fb02ea1a9af2ca9df293f8149c95ac5dde4e8 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#####################################################################################
# BAYESIAN MODEL SELECTION FOR ACTIVATION DETECTION ON FMRI GROUP DATA
# Merlin Keller, 2009
import numpy as np
import ... | nipy/nipy-labs | nipy/labs/group/spatial_relaxation_onesample.py | Python | bsd-3-clause | 47,827 | [
"Gaussian"
] | 56f16d9f5334f377a1808bc7b7c070cd6ef2ded15eab2168c0e4e5bef4d8e6d1 |
#!/usr/bin/env python
"""
vg_mapeval.py: Compare alignment positions from gam or bam to a truth set
that was created with vg sim --gam
"""
import argparse, sys, os, os.path, errno, random, subprocess, shutil, itertools, glob, tarfile
import doctest, re, json, collections, time, timeit
import logging, logging.handlers... | vgteam/toil-vg | src/toil_vg/vg_mapeval.py | Python | apache-2.0 | 147,207 | [
"BWA",
"pysam"
] | da5cb745957f80ed30f569c13378aefb2f8de86e9793a3b40cf774bbbc858064 |
# compartmental_neuron.py ---
#
# Filename: compartmental_neuron.py
# Description:
# Author:Subhasis Ray
# Maintainer:
# Created: Tue Aug 7 10:27:26 2012 (+0530)
# Version:
# Last-Updated: Tue Dec 29 12:40:48 2015 (-0500)
# By: Subhasis Ray
# Update #: 86
# URL:
# Keywords:
# Compatibility:
#
#
# Commen... | BhallaLab/moose-examples | snippets/compartmental_neuron.py | Python | gpl-2.0 | 4,371 | [
"MOOSE",
"NEURON"
] | 8a02bf7c70d26769d82d399b58ccc2f61b9c094df563e757a91f4082327d4610 |
# ex02.py
#
# Functions and data useful in exercise 2 of the Plant and Pathogen
# Bioinformatics course at EMBL
from matplotlib.colors import LogNorm
from Bio import SeqIO
import matplotlib # to get version
import matplotlib.pyplot as plt
import pandas as pd
import os
# GLOBALS
datadir = "pseudomonas_blastp/rbbh... | widdowquinn/Notebooks-Bioinformatics | helpers/rbbh.py | Python | mit | 8,454 | [
"BLAST"
] | e532274def0889054cc3d178eefdd5544b260b64f10604b1fd0f2a41daa8d835 |
""" test
"""
import unittest
import types
import importlib
import itertools
from mock import MagicMock
from DIRAC import S_OK, gLogger
from DIRAC.RequestManagementSystem.Client.Request import Request
from DIRAC.TransformationSystem.Client.TaskManager import TaskBase, WorkflowTasks, RequestTask... | marcelovilaca/DIRAC | TransformationSystem/Client/test/Test_Client.py | Python | gpl-3.0 | 27,659 | [
"DIRAC"
] | cbdea14602089a0876777db30b847beeae1e1578d8bd2808951c534660854bb7 |
# Copyright 2014-2015 Novartis Institutes for Biomedical Research
# 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 applic... | Novartis/railroadtracks | src/model/simulate.py | Python | apache-2.0 | 24,767 | [
"BWA"
] | d7f7dee063cbf4ed578a06073036599f66f95ef5918c8924d6947f94a781a0dd |
"""
Unit tests for the stem.util.enum class and functions.
"""
import unittest
import stem.util.enum
class TestEnum(unittest.TestCase):
def test_enum_examples(self):
"""
Checks that the pydoc examples are accurate.
"""
insects = stem.util.enum.Enum('ANT', 'WASP', 'LADYBUG', 'FIREFLY')
self.as... | tetravision/Test | test/unit/util/enum.py | Python | lgpl-3.0 | 1,437 | [
"Firefly"
] | 26c7ad7c1d0507782502e2a305dc534bc97b0ab6535e946b4a9f621964f955a7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2009 Douglas S. Blank
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as p... | pmghalvorsen/gramps_branch | gramps/plugins/quickview/samesurnames.py | Python | gpl-2.0 | 7,208 | [
"Brian"
] | 9c3483fc5a62be7b5d62b173938367907b242c141f04a97647beb45a4d31360d |
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Brian Coca <brian.coca+dev@gmail.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
DOCUMENTATION = '''
---
module: getent
short_descrip... | mattclay/ansible | lib/ansible/modules/getent.py | Python | gpl-3.0 | 5,681 | [
"Brian"
] | 7fc25d23e52bea0134239e5f1c2a8923926761a46ae747ed4dfd80f7da36dd21 |
# (c) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.... | CitizenB/ansible | lib/ansible/plugins/lookup/url.py | Python | gpl-3.0 | 2,020 | [
"Brian"
] | d9d9a1acdaaa492a162f00ee4efb9da07effb6affa49082acc8b54ebafad833d |
# Autodetecting setup.py script for building the Python extensions
#
import sys, os, importlib.machinery, re, optparse
from glob import glob
import importlib._bootstrap
import importlib.util
import sysconfig
from distutils import log
from distutils.errors import *
from distutils.core import Extension, setup
from dist... | mi-schindler/M3_Container | oss_packages/src/Python-3.6.1/setup.py | Python | gpl-2.0 | 101,386 | [
"VisIt"
] | 5f5bcf456b30415f9730d66fe3d088247d99aa1993301ca0b2aa49a059348d9f |
import numpy as np
import matplotlib
import os
import pandas as pd
from astropy.io import fits
import subprocess
import cosmics
import shlex
import sys
import matplotlib.pyplot as plt
# --------
"""
python pisco_pipeline/pisco_combine_v2.py ut170624/ SDSS603 'twilight'
#v2: scamp only a pair of exposure map for eac... | leogulus/pisco_pipeline | pisco_combine_v2.py | Python | mit | 17,794 | [
"Brian"
] | 2e14cdb0467541e33d1291d8d54e9b664eb52785821b219a39eb6ec359175328 |
#!/usr/bin/env python
import copy
import numpy as np
import os
import subprocess
BASE_DIR = os.path.dirname(os.path.dirname(__file__))
INPUT_FOLDER = os.path.join(BASE_DIR, "dat/amber/")
def write_amber_in(calc_type, in_name, *args):
"""Writes an Amber input file for a desired type of calculation
pass any ar... | eduardoftoliveira/qt_scripts | omg/amber.py | Python | gpl-3.0 | 17,850 | [
"Amber"
] | ac1044dc6b47d27d43d4b5540365c9c6a54061514ad87f11d2cc9b708360184f |
# 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/features/tests/test_get_features.py | Python | bsd-3-clause | 33,662 | [
"NEURON"
] | 9d82b51b7878b57fd940c5a4540f1114fc927471ae101b0e610deea193d682c9 |
'''
Created on 06/04/2011
@author: jose
'''
from __future__ import division
import re
from Bio.pairwise2 import align
from franklin.seq.alignment_result import (get_alignment_parser,
filter_alignments,
_fix_matches)
from franklin.... | JoseBlanca/franklin | franklin/seq/alignment.py | Python | agpl-3.0 | 10,387 | [
"BLAST",
"Biopython"
] | ad7c67291f516aa236bbf0ba2f2c43b4b0ae9c64150ea0440b27b0e7ac5b49e9 |
# -*- coding: utf-8 -*-
from io import StringIO
import json
import platform
import re
from typing import Any, Dict
from unittest import skipIf
from urllib.parse import urlencode
from django.db import connection, transaction
from django.shortcuts import get_object_or_404
from guardian.shortcuts import assign_perm
fro... | catmaid/CATMAID | django/applications/catmaid/tests/apis/test_skeletons.py | Python | gpl-3.0 | 89,897 | [
"NEURON"
] | cd4df11fb8bac88bee551c4ec912a0f0b2ed96893008f33a6621725928fee9ab |
#!/usr/bin/env python
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Softwar... | ostrokach/biskit | scripts/Mod/model_for_docking.py | Python | gpl-3.0 | 6,576 | [
"BLAST"
] | 5a8c454b8e0b2c0b874dc76e726379fd14c7bcc8837622680186ce833e323a70 |
"""
A print function that pretty prints sympy Basic objects.
:moduleauthor: Brian Granger
Usage
=====
Once the extension is loaded, Sympy Basic objects are automatically
pretty-printed.
As of SymPy 0.7.2, maintenance of this extension has moved to SymPy under
sympy.interactive.ipythonprinting, any modifications to ... | mattvonrocketstein/smash | smashlib/ipy3x/extensions/sympyprinting.py | Python | mit | 5,638 | [
"Brian"
] | 43fdb968a7bebaa59b5c6f252a63df7e1a87c8b00305d61f7acf6db0d96b8db5 |
"""neural network model."""
import math
import tensorflow as tf
import numpy as np
import inputs
#########################################
# FLAGS
#########################################
FLAGS = tf.app.flags.FLAGS
tf.app.flags.DEFINE_boolean('top_unlabel', True,
"whether to use unlabele... | yuhui-lin/web_page_classification | model.py | Python | mit | 30,961 | [
"Gaussian"
] | 8630235e8e0cd0e215593d717ff16f617ec57b4772669f8acf2602434e70dab7 |
"""
These tests exposes lower level functions than needed -- see test_convenience for simpler constructions
"""
from __future__ import print_function
import numpy as np, pandas as pd
from scipy.stats import norm as ndist
import regreg.api as rr
from ...tests.decorators import wait_for_return_value, register_report
im... | selective-inference/selective-inference | selectinf/randomized/tests/sandbox/test_Mest.py | Python | bsd-3-clause | 10,116 | [
"Gaussian"
] | 5b6a8d439b0b9df43b0359ab03ae569daa23781ec97dd6f9edd6d858afb22c53 |
# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | arokem/scipy | scipy/special/tests/test_basic.py | Python | bsd-3-clause | 132,918 | [
"Elk"
] | adf7bc16408b501f99e4cd9dc22341e3695c8270f3974cf8565627560d936fac |
"""
3D data rendering using Mayavi.
"""
# Copyright (C) 2009-2011 University of Edinburgh
#
# This file is part of IMUSim.
#
# IMUSim 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 Lic... | martinling/imusim | imusim/visualisation/rendering.py | Python | gpl-3.0 | 8,990 | [
"Mayavi"
] | e73e3cc848fe57b415056a5757d75b6f0f908a51becdf44da7817c7b966fd050 |
"""
Histogram-related functions
"""
from __future__ import division, absolute_import, print_function
import contextlib
import functools
import operator
import warnings
import numpy as np
from numpy.compat.py3k import basestring
from numpy.core import overrides
__all__ = ['histogram', 'histogramdd', 'histogram_bin_ed... | jorisvandenbossche/numpy | numpy/lib/histograms.py | Python | bsd-3-clause | 39,967 | [
"Gaussian"
] | cd26244644df5ffdcfb0321dcdaad38a6542845c4aa283f15742d83a495d63a8 |
import time
import myalgorithm as alg
'''Result Format: A list for every neuron. Each spike time is a entry.
'''
def read_data(filename='all.txt'):
fin=open(filename,'r')
res=[]
for line in fin:
l=line.split(' ');
for i in range(len(l)):
l[i]=float(l[i]);
res.append(l);
fin.close();
return res;
def writ... | yanxiangtianji/Neuron | dataAnalysis/process_base.py | Python | gpl-2.0 | 5,385 | [
"NEURON"
] | 1c30249cf771decacf5a63f44671ead592314a92c141f85349235d2843eff9ef |
#!/usr/bin/python
# -*- coding: utf-8 -*-
import time
import socket
import sys
import os
import serial
import Axon
from Kamaelia.Chassis.Pipeline import Pipeline
from Kamaelia.Chassis.Graphline import Graphline
from Kamaelia.Chassis.ConnectedServer import ServerCore
from Kamaelia.UI.Pygame.Image import Image
from Kam... | sparkslabs/kamaelia | Sketches/MPS/ArduinoRelated/OuijaCube.py | Python | apache-2.0 | 13,205 | [
"Galaxy"
] | f968c30f2e3b7b33ee9dbf2d7ff58ac74cb6066bbe43e19ec52f8237ac8396a8 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 5.0.4.
Change directory to p... | mick-d/nipype_source | nipype/interfaces/fsl/epi.py | Python | bsd-3-clause | 25,929 | [
"Gaussian"
] | e8d57aa4d4a6a9d3119b5aebf3069636c6948c979cc9ee9230dd94b1e8724b87 |
from ase import *
from ase import io
from ase.cluster.icosahedron import Icosahedron
from ase.optimize import *
from espresso import espresso
# read in the cluster
name = 'PtCu13'
atoms = io.read('cluster.traj')
#espresso calculator setup
calc = espresso(pw=500, #plane-wave cutoff
dw=5000, ... | chemeng444/chemeng444.github.io | ASE/Getting_Started/run_cluster.py | Python | gpl-2.0 | 1,371 | [
"ASE",
"ESPResSo",
"Quantum ESPRESSO"
] | bbc67a68f8bfe7ff692fc8933a762ce8a391dba3d846784d8e858bbb9c9a3b16 |
import matplotlib.pyplot as plt
from sunpy import map
import numpy as np
import os
import copy
from skimage.feature import canny
from scipy import ndimage
def mask_sun(array,pxval):
#This function will apply a centered filled circular mask
#of radius rad and pxval values to the input array
r=172 #Empirical... | kkozarev/mwacme | src/lasco/lasco_find_shocks_rdiff.py | Python | gpl-2.0 | 2,487 | [
"Gaussian"
] | 8951313546616fa2ef9d0833818c189827f50e0025b89a368f3f3739072f145e |
"""
The MIT License (MIT)
(c) Juergen Simon 2014 (juergen.simon@uni-bonn.de)
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, c... | meteo-ubonn/meanie3D | python/meanie3D/app/utils.py | Python | mit | 9,799 | [
"NetCDF",
"VisIt"
] | bb5fb3f2b5b242f86697b3e34f68dbddb7581dfaf60a424ed0c5fb43d1a22044 |
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