text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#! /usr/bin/python3
# -*- coding: utf-8 -*-
'''
Webfirewall filters. Filter http connect, request, response header, response, and html.
Requirements
* tor
* pymiproxy
* goodcrypto webfirewall
Certificate authority file is written to ca_file, specified below.
Import the cert file in... | goodcrypto/goodcrypto-web | goodcrypto/webfirewall/filters.py | Python | gpl-3.0 | 39,990 | [
"VisIt"
] | 0fa656243baf2e2a81f08e26466904af9a59948001c813b4449e1edb1783ed29 |
import os
from setuptools import setup
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
version = 'undefined'
for line in open(os.path.join('helperlibs', '__init__.py'), 'r'):
if line.startswith('version'):
exec(line.strip())
short_description = "A collection of bi... | kblin/bioinf-helperlibs | setup.py | Python | gpl-3.0 | 1,552 | [
"Biopython"
] | 33af271316a463c5da338ba9075ed2facf5a0068669b71edb72e9cec94a7680b |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/modeltree.py | Python | gpl-2.0 | 3,809 | [
"VisIt"
] | 492fb338be031f7dc566b6e92f3a9e84a3878a2061d0de36b066a76a3b6708b3 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-show-task-queues
# Author : Ricardo Graciani
########################################################################
"""
Show details of currently active Task Queues
"""
from __future__ import pri... | petricm/DIRAC | WorkloadManagementSystem/scripts/dirac-admin-show-task-queues.py | Python | gpl-3.0 | 2,815 | [
"DIRAC"
] | 39aeb1d0f2b52ed832fb4128fbbcd6f6f47d60f1a9fbfa627f03b9eb25866061 |
'''
Created on 23/11/2009
@author: Brian Thorne
@author: Allan McInnes
'''
import logging
from numpy import linspace
from scipysim import Source, Actor, Event, LastEvent
import time, random # These are used to test the async
class Ramp(Source):
'''
A ramp source
'''
def __init__(self, out, amplitude... | mm318/scipysim-nogui | scipysim/actors/signal/ramp.py | Python | gpl-3.0 | 1,547 | [
"Brian"
] | f1c8c68d0845e4687854e0159412fbc5f6fc81cacb12320fedc071c4641e9e2a |
#!/bin/env python
"""
Copyright (C) 2012 by Adam Ewing (adam.ewing@gmail.com)
Released under the MIT license, see LICENSE.txt
"""
import pysam, sys, re
def uniqann(annList):
uniq = {}
for ann in annList:
uniq[ann] = 1
return uniq.keys()
def checkfile(fname):
try:
open(fname)
e... | adamewing/discord-retro | lib/annotate.py | Python | mit | 2,349 | [
"pysam"
] | 1d8c2ef30bdcab356d621ee212d342b82c14ab6be25a14fe1aa11cbec445d74a |
'''
This module contains the one-parameter exponential families used
for fitting GLMs and GAMs.
These families are described in
P. McCullagh and J. A. Nelder. "Generalized linear models."
Monographs on Statistics and Applied Probability.
Chapman & Hall, London, 1983.
'''
#from statsmodels.family.family im... | phobson/statsmodels | statsmodels/genmod/families/__init__.py | Python | bsd-3-clause | 523 | [
"Gaussian"
] | 57a18561f537f570eedd8bfdc9023d937e68058eff44ec340e041d8420abe535 |
# $HeadURL$
__RCSID__ = "$Id$"
import datetime, time
import types
import threading
import random
from DIRAC.Core.Base.DB import DB
from DIRAC import S_OK, S_ERROR, gMonitor, gConfig
from DIRAC.Core.Utilities import List, ThreadSafe, Time, DEncode
from DIRAC.AccountingSystem.private.ObjectLoader import loadObjects
from... | avedaee/DIRAC | AccountingSystem/DB/AccountingDB.py | Python | gpl-3.0 | 74,606 | [
"DIRAC"
] | 0260226151563445d467a631e7539736e6a1d973f2fe9e4d29bd9fefd9ad43d5 |
# Copyright 2013 by Nate Sutton. All rights reserved.
# Based on test_Clustalw_tool.py by Peter Cock.
# Example code used from Biopython's Phylo cookbook by Eric Talevich.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_Fasttree_tool.py | Python | gpl-2.0 | 6,595 | [
"Biopython"
] | 36e3237f2b96d20dd4a3ac827e28bf601d030e37ea6fefe5e836e9248aca4752 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Evaluate the defect concentration based on composition, temperature,
and defect energies using "Dilute Solution Model"
Reference: Phys Rev B, 63, 094103, 2001,
"Density of constitutional and thermal point d... | gmatteo/pymatgen | pymatgen/analysis/defects/dilute_solution_model.py | Python | mit | 52,908 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | e6811f1dd5ac289791ad215d54c6a249f52022a35e8545a1ed1304c311797825 |
# -*- coding: utf-8 -*-
# crossComptSimpleReac.py
#
# Filename:crossComptSimpleReac.py
# Author: Upinder S. Bhalla
# Maintainer:
# Created: Oct 12 16:26:05 2014 (+0530)
# Version:
# Last-Updated: May 16 2017
# By: Upinder S. Bhalla
# Update #:Dec 14 2021
# By: HarshaRani G.V
# URL:
# Keywords:... | BhallaLab/moose-examples | snippets/crossComptSimpleReac.py | Python | gpl-2.0 | 5,626 | [
"MOOSE"
] | 4e987e8f950459d4368dd7575a5234574de959ed9b02735ca4294a09bbc7f7c8 |
###############################################################################
#
#
# Package: RoadNarrows Robotics Laelaps Robotic Mobile Platform ROS Package
#
# Link: https://github.com/roadnarrows-robotics/laelaps
#
# ROS Node: laelaps_*
#
# File: Gauge.py
#
## \file
##
## $LastChangedDate$
## $Rev$
#... | roadnarrows-robotics/laelaps | laelaps_control/src/laelaps_control/Gauge.py | Python | mit | 39,493 | [
"Amber"
] | 47230a90d5b9a86413a6edd19b9ea7d66f8a3658da6b0fc63666a50fd688f09f |
"""
==========================================================================
Illustration of prior and posterior Gaussian process for different kernels
==========================================================================
This example illustrates the prior and posterior of a GPR with different
kernels. Mean, st... | vortex-ape/scikit-learn | examples/gaussian_process/plot_gpr_prior_posterior.py | Python | bsd-3-clause | 2,900 | [
"Gaussian"
] | 55d67bf8e8ab27b69e1516efaf9f7926435d28a806694a5f32f695318a185e5b |
"""Module with MPI-empowered classes for parallel VTK file types."""
__copyright__ = "Copyright © 2018-2022 Lucas Frérot"
__license__ = "SPDX-License-Identifier: MIT"
import functools
from os import PathLike
from os.path import splitext, basename
from mpi4py import MPI
from . import writer
from . import vtk_files
... | prs513rosewood/uvw | uvw/parallel.py | Python | mit | 6,816 | [
"VTK"
] | 178f2d3e1de1134d83af838887c4da6ed5b53488338013f1c66b3fd1cab166bc |
import numpy as np
# mathtext fails to create title with matplotlib 0.99 on el6
import matplotlib
matplotlib.rc('text', usetex=True)
import matplotlib.pyplot as plt
from ase.units import Bohr
from gpaw import GPAW
rs = 5.0 * Bohr
calc = GPAW('surface.gpw', txt=None)
density = calc.get_pseudo_density()[0, 0]
h = 0.2
a =... | robwarm/gpaw-symm | doc/tutorials/jellium/fig2.py | Python | gpl-3.0 | 1,010 | [
"ASE",
"GPAW"
] | 381816b64bcb83c93b9ae026dd96635eef6893b11c8842ad472ea2cdb99376e1 |
__author__ = 'bptripp'
import numpy as np
from scipy.optimize import curve_fit
import matplotlib.pyplot as plt
from sklearn.cluster import KMeans
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis
from keras.models import Sequential
from keras.layers.core import Dense, Activation, Flatten
from keras.... | bptripp/grasp-convnet | py/cninit.py | Python | mit | 7,083 | [
"Gaussian"
] | e7ecc47ed720d24590615160f6b76b59c82b192394277fe23bb6046af57ff56a |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 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/agui | agui/backends/pyside/widgets/time_picker.py | Python | gpl-3.0 | 1,513 | [
"Brian"
] | df8b71ee8b7ae2a12154b45b732faab82cd841a6adeb654a10b1cab32ac9afb6 |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2016, Shoop Commerce Ltd. All rights reserved.
#
# This source code is licensed under the AGPLv3 license found in the
# LICENSE file in the root directory of this source tree.
import os
import pytest
from django.core.urlresolvers import rever... | suutari/shoop | shuup_tests/browser/front/test_checkout_with_login_and_register.py | Python | agpl-3.0 | 12,125 | [
"VisIt"
] | 1419ca740b6616b343ef24e4659e89c571948e5f0e37b9bd6242a42f64b707b3 |
00000 0 output/gaussian.py.err
00000 0 output/gaussian.py.out
| Conedy/Conedy | testing/random/expected/sum_gaussian.py | Python | gpl-2.0 | 70 | [
"Gaussian"
] | ece5f5a5a946908406cdd0f58011171baa9e19ea6f8a8adfb4659a25e63ef38a |
import ast
from pyflakes import messages
import __builtin__
allowed_before_future = (ast.Module, ast.ImportFrom, ast.Expr, ast.Str)
defined_names = set(('__file__', '__builtins__'))
class Binding(object):
"""
@ivar used: pair of (L{Scope}, line-number) indicating the scope and
line number tha... | wimac/projects | dotfiles/.vim/ftplugin/python/pyflakes/pyflakes/checker.py | Python | gpl-2.0 | 13,179 | [
"VisIt"
] | af6bff98ff698d05c9a91c90eb39778c6c8e5dadb53c184d1ae88a8038885405 |
#########################################################################################
# LSF.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" LSF.py is a DIRAC independent class representing LSF batch system.
LSF objects are used as bac... | arrabito/DIRAC | Resources/Computing/BatchSystems/LSF.py | Python | gpl-3.0 | 5,593 | [
"DIRAC"
] | f7aeeac4656e433a158959c4f4b775f9363b5fd8f17949cfcfb125bcadf41126 |
#!/usr/bin/python
import sys, os, getopt, string, ConfigParser
import pyfits
import astropy
import aplpy
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
import skimage.io as io
from skimage import exposure
class ArgumentError(Exception):
pass
def main(argv):
config_file=None
list_file=No... | astroCV/astroCV | tools/color_image/make_rgb_image.py | Python | bsd-2-clause | 13,468 | [
"Gaussian"
] | 76c7102e0bfe7b20aaea00c7c7e82eaad8c5b1edd1ab6dd05e5a57e3369370e4 |
#!/usr/bin/env python
import os
import sys
import sqlite3
from collections import defaultdict, namedtuple
import atexit
import json
import subprocess
import tempfile
import numpy as np
from scipy.stats import mode
import pysam
import cyvcf2 as vcf
from gemini.annotations import annotations_in_region, annotations... | xuzetan/gemini | gemini/gemini_annotate.py | Python | mit | 13,686 | [
"pysam"
] | 41edac24200ac9cb6980409e4fef4871844de753579ff220b5eadc52dc9ca523 |
# -*- coding: utf-8 -*-
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope tha... | remicollet/bodhi | bodhi/tests/functional/test_updates.py | Python | gpl-2.0 | 88,972 | [
"VisIt"
] | 2a9c6ca045f9b122e4ce2dadf29f87bdeb42fa72ff75e64a794837621a447f01 |
#!/usr/bin/env/python
"""
catalyst-pubmed.py -- identify pubmed papers for author using catalyst
service
"""
__author__ = "Michael Conlon"
__copyright__ = "Copyright 2013, University of Florida"
__license__ = "BSD 3-Clause license"
from Bio import Entrez # tools for using NLM... | indera/vivo-pump | uf_examples/publications/catalyst_pubs.py | Python | bsd-2-clause | 1,793 | [
"Biopython"
] | 76dd54f6d86562cb2bb67533a2f7c5a9c6133ca38b5111160a3eefad31530301 |
from scipy.odr import odrpack as odr
from scipy.odr import models
import numpy as np
def gaussian(B, x):
''' Returns the gaussian function for B=m,stdev,max,offset '''
return B[3] + B[2] / (B[1] * np.sqrt(2 * np.pi)) * \
np.exp(- ((x - B[0]) ** 2 / (2 * B[1] ** 2)))
def double_gaussian(B, x):
""... | M1kol4j/helita | helita/utils/fitting.py | Python | bsd-3-clause | 11,317 | [
"Gaussian"
] | c5e7aab5d979034b657bc88ec9aded7c3fd4e2bb67d176d095cad4dd5b2c4663 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to identify optimal substrates for film growth
"""
import warnings
from pymatgen.analysis.interfaces import ZSLGenerator, SubstrateAnalyzer # noqa
__author__ = "Shyam Dwarak... | gmatteo/pymatgen | pymatgen/analysis/substrate_analyzer.py | Python | mit | 723 | [
"pymatgen"
] | 5001aefdc7ffc18d4fac82278a4ae3a40849e36a18829dbcb8895cf97ff3b78b |
from __future__ import division, print_function
import warnings
import numpy as np
try:
import numba
except ImportError:
numba = None
else:
from ._numba_tools import _gaussian_grid_numba_1D
def nufftfreqs(M, df=1):
"""Compute the frequency range used in nufft for M frequency bins"""
return df * n... | hadim/spindle_tracker | spindle_tracker/signal/nufft.py | Python | bsd-3-clause | 5,039 | [
"Gaussian"
] | 9c83fea937638da93946cd93506faeb6e4afdfec178459c9d928cbf215e37248 |
#!/usr/bin/env python
'''
File name: main_ripp_mod.py
Author: Guillaume Viejo
Date created: 16/08/2017
Python Version: 3.5.2
'''
import sys
import numpy as np
import pandas as pd
import scipy.io
from functions import *
# from pylab import *
# import ipyparallel
from multiprocessing import Pool
imp... | gviejo/ThalamusPhysio | python/main_test_ISI_ISOMAP.py | Python | gpl-3.0 | 5,063 | [
"Gaussian"
] | a0812d7ed64d130c0bfc47e0833a9091afcd82ee8a5676449811ed85e65b4723 |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
"""
Oak Barrel Winecraft
Kolsch Ale
Used by permission of Oak Barrel Winecraft. All rights reserved.
You can purchase this kit at their store:
- http://oakbarrel.com/
Original Stats:
OG: 1.045
FG: 1.008 - 1.012
ADF: 72 % - 78 %
IBU:
Color:
Alcohol: 4.3... | chrisgilmerproj/brewday | examples/oak_barrel_winecraft/kolsch_ale_dict.py | Python | mit | 1,839 | [
"ADF",
"CRYSTAL"
] | 97eb00cf3476aced1e477de17a1ffaac4997ec2f2179d0e1dfe8cd65ba21712e |
"""
Rayleigh Optical Depth - Scattering in the Atmosphere
=====================================================
Implements *Rayleigh* scattering / optical depth in the atmosphere computation:
- :func:`colour.scattering_cross_section`
- :func:`colour.phenomena.rayleigh_optical_depth`
- :func:`colour.rayleigh_sca... | colour-science/colour | colour/phenomena/rayleigh.py | Python | bsd-3-clause | 48,000 | [
"Avogadro"
] | cced72165b5c8c12ebc03746d9abedcf01049c896312ab0d28af85075c1fc61b |
''' This is to postprocess a folder full of wavefunctions. '''
import glob
import numpy as np
import os
import pandas as pd
import pickle
from argparse import ArgumentParser
from quantumpropagator import calculate_stuffs_on_WF, readWholeH5toDict, err, calculate_dipole_fast_wrapper, warning
import quantumpropagator as... | acuzzio/GridQuantumPropagator | Scripts/CreateOutputFilesFromWF.py | Python | gpl-3.0 | 12,480 | [
"Gaussian"
] | ed5076c6b750402b2f98455d71f3405e2b3f7633a2ba18fcdcb272397f50ab3c |
'''
Spatial Two Stages Least Squares
'''
__author__ = "Luc Anselin luc.anselin@asu.edu, David C. Folch david.folch@asu.edu"
import copy
import numpy as np
import pysal
import numpy.linalg as la
import twosls as TSLS
import robust as ROBUST
import user_output as USER
import summary_output as SUMMARY
from utils import ... | spreg-git/pysal | pysal/spreg/twosls_sp.py | Python | bsd-3-clause | 21,796 | [
"COLUMBUS"
] | f2fbee0ef8fc51c003ade6fe3e051d96fbf7909e61094fedd0a9629017a99973 |
#!/usr/bin/env python3
from PIL import Image
import sys
import os
import numpy as np
import argparse
parser = argparse.ArgumentParser(
description="Convert image to grayscale HDF5 or NetCDF.")
parser.add_argument(
'input', help="Input filename")
parser.add_argument(
'-f', '--format', action='... | abrupt-climate/hyper-canny | scripts/convert_image.py | Python | apache-2.0 | 1,600 | [
"NetCDF"
] | 6b0cbecabfad82013d91fbcedb1e85375fdad40ec5dff7b3d6f7628d7f1b18c0 |
# -*- test-case-name: twisted.conch.test.test_recvline -*-
# Copyright (c) Twisted Matrix Laboratories.
# See LICENSE for details.
"""
Tests for L{twisted.conch.recvline} and fixtures for testing related
functionality.
"""
import os
import sys
from twisted.conch.insults import insults
from twisted.conch import recvl... | whitehorse-io/encarnia | pyenv/lib/python2.7/site-packages/twisted/conch/test/test_recvline.py | Python | mit | 25,406 | [
"VisIt"
] | f35cca609058a31c0f76bf0c9bfc945cc811e2aca454655a222b431ad2b4a545 |
import os
from ase.units import Hartree
from gpaw.lrtddft import LrTDDFT
from gpaw.lrtddft.spectrum import spectrum
def check_convergence(lr, # LrTDDFT object
dirname='conv', # directory name to store the files
title=None, # title for gnuplot
... | qsnake/gpaw | gpaw/lrtddft/convergence.py | Python | gpl-3.0 | 4,664 | [
"ASE",
"GPAW"
] | 0dad15dedeea6b6270c98b05c1abd7829a4fd8312a1c61b111e08cd3d10bf6f6 |
#! /usr/bin/python
"""versioneer.py
(like a rocketeer, but for versions)
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Version: 0.7+
This file helps distutils-based projects manage their version number by just
creating version-control tags.
For developers who work from a V... | sahat/bokeh | versioneer.py | Python | bsd-3-clause | 25,525 | [
"Brian"
] | 3bb2895c3298800b60b2aba423f326dec5e906c5ff96d4c031e7429b6b8c9a99 |
# -*- encoding: utf-8
from sqlalchemy.testing import eq_, engines
from sqlalchemy import *
from sqlalchemy import exc
from sqlalchemy.dialects.mssql import pyodbc, pymssql, adodbapi
from sqlalchemy.engine import url
from sqlalchemy.testing import fixtures
from sqlalchemy import testing
from sqlalchemy.testing import as... | robin900/sqlalchemy | test/dialect/mssql/test_engine.py | Python | mit | 9,522 | [
"ASE"
] | 262bf2b0b2705d8845321cb96ebc074283cabbd25396c39e5a8d226d971e3f1a |
from django.utils.translation import ugettext_lazy as _
from corehq.apps.app_manager import id_strings
from corehq.apps.app_manager.const import (
SCHEDULE_DATE_CASE_OPENED,
SCHEDULE_GLOBAL_NEXT_VISIT_DATE,
SCHEDULE_LAST_VISIT,
SCHEDULE_LAST_VISIT_DATE,
SCHEDULE_NEXT_DUE,
)
from corehq.apps.app_man... | dimagi/commcare-hq | corehq/apps/app_manager/suite_xml/features/scheduler.py | Python | bsd-3-clause | 5,732 | [
"VisIt"
] | f49f8473d44baa15de328180de017972ed3d7f3491a8caa01766b1cb96ea7447 |
"""
FROWNS LICENSE
Copyright (c) 2001-2003, Brian Kelley
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... | ubccr/pinky | pinky/mol/idgen.py | Python | bsd-2-clause | 2,263 | [
"Brian"
] | 3849e4ddd6f48aba4bcb3b8c1151c74c11f8e1d8f5052c402440b18a44bc7d87 |
# -*- coding: UTF-8 -*-
from sys import exit
from random import randint
class Scene(object):
def enter(self):
print "This scene is not yet configured. Subclass it and implement enter()."
exit(1)
class Death(Scene):
quips = ["You died. You kinda suck at this.",
"Your mom would be proud... | Hyyyyyyyyyy/acm | PythonTest/t43_Final.py | Python | mit | 3,600 | [
"BLAST"
] | 75b4b547235200179e33ff4977c8377bc8aba3768d3672a856567b5b757ff45e |
#!/usr/bin/env python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# BornProfiler --- A package to calculate electrostatic free energies with APBS
# Written by Kaihsu Tai, Lennard van der Feltz, and Oliver Beckstein
# Released under th... | Becksteinlab/BornProfiler | bornprofiler/run_setup.py | Python | gpl-3.0 | 6,809 | [
"MDAnalysis"
] | bfd97645c1d246d21fc1576871fcc0e200e9987ebf08358abc0210c8ad5cc133 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/example/tfpark/keras/keras_dataset.py | Python | apache-2.0 | 4,352 | [
"ORCA"
] | d81dfae2c53ab5a7557f0bd956ee9487bf2f4ce14cf87044abdb6c04e9966d57 |
"""
PackageKit integration.
"""
# Copyright (C) 2010, Aleksey Lim
# See the README file for details, or visit http://0install.net.
import os, sys
import locale
import logging
from zeroinstall import _, SafeException
from zeroinstall.support import tasks, unicode
from zeroinstall.injector import download, model
_log... | timdiels/0install | zeroinstall/injector/packagekit.py | Python | lgpl-2.1 | 12,840 | [
"VisIt"
] | d9ea441b4a8a340aff389dc202d8cc535d559939310d14b8449a182c4da347b4 |
# 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... | espressopp/espressopp | src/analysis/Velocities.py | Python | gpl-3.0 | 2,331 | [
"ESPResSo"
] | 3d71450b33fafc44759cf154fcee8a9d71fde4254d23a19283de54b4fbd9f612 |
"""
Filename: kalman.py
Reference: http://quant-econ.net/py/kalman.html
Implements the Kalman filter for a linear Gaussian state space model.
"""
from textwrap import dedent
import numpy as np
from numpy import dot
from scipy.linalg import inv
from quantecon.matrix_eqn import solve_discrete_riccati
class Kalman(obj... | gxxjjj/QuantEcon.py | quantecon/kalman.py | Python | bsd-3-clause | 6,830 | [
"Gaussian"
] | 91e95dfc921fd89e8693618430d08b01090897987f3de95597dc380fc7eeacac |
#
# Copyright (c) 2015 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... | lach76/scancode-toolkit | tests/licensedcode/test_models.py | Python | apache-2.0 | 6,313 | [
"VisIt"
] | 8bb3fc0dfde2a482afdba709906568d88099b0354cd9f661003938cb65d39e89 |
"""A Python module for fitting, characterising and simulating rhodopsin photocurrents."""
#__doc__ =
# Main module file for PyRhO
import platform
import os
#from pkg_resources import get_distribution, DistributionNotFound
import logging
import pkg_resources
# Necessary?
import matplotlib as mpl
import matplotlib.pyp... | ProjectPyRhO/PyRhO | pyrho/__init__.py | Python | bsd-3-clause | 6,612 | [
"Brian",
"NEURON"
] | d36649bdbedf3b2ac69887fb2b397c03601b23ce740c4b7a44985ff780d89ac5 |
'''
Copyright 2009, 2010 Brian S. Eastwood.
This file is part of Synctus.
Synctus 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.
Synctus ... | beastwood/synctity | testqt.py | Python | gpl-3.0 | 2,505 | [
"Brian"
] | 509bde5a4cb9a5ce86f0b51c1a369a6485b44a55a4813f80e7b0d76a2dc1d1a6 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | rmcgibbo/mdtraj | mdtraj/formats/hdf5.py | Python | lgpl-2.1 | 40,767 | [
"MDTraj",
"OpenMM"
] | e7723c1eb6ae9efc76c0953751a18f30d53e0d8816cbf04f30e380b8a9117833 |
################################################################################
# Copyright (C) 2015 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Unit tests for `gamma` module.
"""
import numpy as np
from scipy... | jluttine/bayespy | bayespy/inference/vmp/nodes/tests/test_gamma.py | Python | mit | 5,599 | [
"Gaussian"
] | 5c34f7f912b4ceb79ab4630761847e0d8bd6cb1f7c43ffc0d48554a116f5098e |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import Directive
from docutils.statemachine import ViewList
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.directives import CodeBlock
fr... | georgemarshall/django | docs/_ext/djangodocs.py | Python | bsd-3-clause | 13,489 | [
"VisIt"
] | f05f2c413b41ad6781a201f5c61798fc5cf3681222b1dbb73619c457f799f505 |
# This file is part of Invenio.
# Copyright (C) 2008, 2009, 2010, 2011, 2012, 2013 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any l... | jmacmahon/invenio | modules/miscutil/lib/dbquery.py | Python | gpl-2.0 | 20,180 | [
"BLAST"
] | e628845aca5d5131a7065335f966cfbda70a1af7b1d5404e4ea74d5337f1a443 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to handle the calculation of the IR spectra
This implementation is adapted from Abipy
https://github.com/abinit/abipy
where it was originally done by Guido Petretto and Matteo Gi... | mbkumar/pymatgen | pymatgen/phonon/ir_spectra.py | Python | mit | 8,248 | [
"ABINIT",
"pymatgen"
] | 3f050afbcc0d467626de9a5b55045325498c699b7d03392120c09fbbbce77ea5 |
#!/usr/bin/env python
"""Wrap fasta sequences to a given length (60 characters by default).
Usage:
%program <input_file> <output_file> [line_length]"""
import sys
try:
from Bio import SeqIO
except:
print "This program requires the Biopython library"
sys.exit(0)
try:
in_file = open(sys.argv[1], ... | wkh124/wkh124 | fasta_wrap.py | Python | gpl-3.0 | 883 | [
"Biopython"
] | 7c83f3af9d6053ec9ef1179d89169d046d873d9f693bf64054556449f051079e |
from __future__ import print_function
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetTempDir
VTK_TEMP_DIR = vtkGetTempDir()
contr = vtk.vtkMultiProcessController.GetGlobalController()
if not contr:
nranks = 1
rank = 0
else:
nranks = contr.GetNumberOfProcesses()
rank = contr.Ge... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/ParallelXML/Testing/Python/testParallelXMLWriters.py | Python | gpl-3.0 | 4,378 | [
"VTK"
] | 394b668eacccab3e44b6c97f28be61521eb6b5fef15add4385a9c5eab62d05f2 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | andreaso/ansible | lib/ansible/modules/network/avi/avi_vsdatascriptset.py | Python | gpl-3.0 | 4,437 | [
"VisIt"
] | 4f2cc14814958ca9fb52780c8521118372d1fe2acc8f64e6dbee3705ec2bf7ee |
from setuptools import setup, find_packages
version = '0.0.0'
setup(
name='ipytube',
version=version,
description='IPython youtube search embed',
author='Brian McFee',
author_email='brian.mcfee@nyu.edu',
url='http://github.com/bmcfee/ipytube',
download_url='http://github.com/bmcfee/ipytube... | bmcfee/ipytube | setup.py | Python | mit | 1,018 | [
"Brian"
] | 939eadc3f0e36c84322b979bb881081222d6a1b17d91ce69abad48bcea9f969d |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# test_fix_map.py
"""
Test if fix_map and dorr yield the same results.
"""
import unittest
import numpy as np
from .. import dorr
class TestFixMap(unittest.TestCase):
def setUp(self):
vec_i_js = np.array([[1, 2, 3],
[-1, -0.... | derNarr/synchronicity | synchronicity/tests/test_fix_map.py | Python | mit | 1,500 | [
"Gaussian"
] | 25836e8e4c7a401fabee3f9b82a88356bb693989542acbd4ca9764ebfbf60916 |
""" Bokeh is a Python interactive visualization library that targets modern
web browsers for presentation.
Its goal is to provide elegant, concise construction of novel graphics in the
style of d3.js, but also deliver this capability with high-performance
interactivity over very large or streaming datasets. Bokeh can ... | muku42/bokeh | bokeh/__init__.py | Python | bsd-3-clause | 967 | [
"VisIt"
] | 2c98d070aeb809b2519a5c235cc4f7c98424ee8c0f72153d6e4ec90c0a6712ea |
"""
demo3.py
Getting an I-V relation by voltage clamp simulation
"""
import neuron
# neuron.load_mechanisms('.')
from neuron import h, gui
h.load_file("stdrun.hoc") # load init(), run(), etc.
# Creating a cell
soma = h.Section(name="soma")
soma.insert("ml")
soma.diam = 15
soma.L = 15
# soma.betaw_ml = 0
# Addi... | shhong/a310_cns_2017 | Practice_3/demo3.py | Python | gpl-3.0 | 1,236 | [
"NEURON"
] | 8095c1f74ed6f0ce6f094f57706c68e5ccc04796982827e9c9d0369c00884784 |
#!/usr/bin/env python
# Copyright 2014-2021 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/cc/qcisd.py | Python | apache-2.0 | 17,710 | [
"PySCF"
] | e52582cf859ea1a3199d666b5ce97609038d44a4df2698f5303e02cf508e8d9a |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/geometry/tests/test_order.py | Python | lgpl-2.1 | 3,883 | [
"MDTraj"
] | d6b7666f167a820e6eab07744ab4aae6c2814dd3a3aa97385a32154a8b2ba375 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/share/psi4/databases/S22by5.py | Python | lgpl-3.0 | 176,348 | [
"Psi4"
] | 8fa67bdbc2c835e07e11c950912ba640051fa8a0cd87b928a0ccae279337610e |
"""
Compute statistics from linear traces of embryos. The most basic
statistic is min/max, but others will be compiled here.
"""
import numpy as np
from scipy import ndimage as nd
def min_max(tr):
"""Return the ratio of minimum to maximum of a trace.
Parameters
----------
tr : 1D array of float
... | jni/lesion | lesion/stats.py | Python | bsd-3-clause | 2,791 | [
"Gaussian"
] | 79db92f3b9f32c06d568e12f196b7ac6d417b5a4e0cccb3b6a1fa8c783bb4fe6 |
#!/usr/bin/env python
"""
Copyright 2016 Brian Quach
Licensed under MIT (https://github.com/brianquach/udacity-nano-fullstack-conference/blob/master/LICENSE) # noqa
"""
from collections import Counter
import endpoints
import json
import random
from google.appengine.api import taskqueue
from google.appengine.ext impor... | brianquach/udacity-nano-fullstack-game | game.py | Python | mit | 26,812 | [
"Brian"
] | f0a7e26af853ac22c2a465b8fa017b79eda11257cf43dae705ec9620e5b23c26 |
'''
Created on 23.05.2013
@author: Johannes Rieke
potentials in mV
conductances in mS
capacitances in muF
currents in muA
lengths in mum
concentrations in mM
literature:
Hodgkin / Huxley (1952): A quantitative description of membrane current and its application to conduction and excitation in nerve
Destexhe / Mainen... | jrieke/NeuroSim | src/Neuron.py | Python | mit | 29,385 | [
"NEURON"
] | 2c44a24b7beaf67ce3eb89982802e954950c2360b669ddd693d426fce449a4ec |
# Generated by Django 2.2.12 on 2020-09-24 09:42
import django.core.validators
from django.db import migrations, models
import registration.models
class Migration(migrations.Migration):
dependencies = [
('registration', '0017_betatestapplication_hero_cover_image'),
]
operations = [
migr... | open-craft/opencraft | registration/migrations/0018_0018_hardcode_basedomain_and_add_error_codes.py | Python | agpl-3.0 | 2,435 | [
"VisIt"
] | 0258cada930e368ad3481cd663d204fe58b5320cfc4879ca3c59f30b1b9bfa4c |
#!/usr/bin/env pvbatch
try: paraview.simple
except: from paraview.simple import *
from numpy import linspace
import pviz
import sys
if __name__== '__vtkconsole__' : sys.argv=['dummy.py','-i','1'] # for interactive sessions only
oviz = pviz.viz(sys.argv) # Instantiate a new visualisation
isocontour=FindSource('i... | ruizanthony/pviz | examples/advanced/pvsm_sweepQcrit.py | Python | lgpl-3.0 | 722 | [
"ParaView"
] | 8e205cd88ccb1d4572e0ad9fdba02822433b9e1016dd0980de5029f06a7146a2 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | kevin-coder/tensorflow-fork | tensorflow/python/autograph/converters/control_flow.py | Python | apache-2.0 | 19,258 | [
"VisIt"
] | 6e1bee1756b7c11044fb2ea5228939631b72ea64dfda8adfa67ef8fab4d23651 |
# Copyright (c) 2014 Universidade Federal Fluminense (UFF)
# Copyright (c) 2014 Polytechnic Institute of New York University.
# This file is part of noWorkflow.
# Please, consult the license terms in the LICENSE file.
from __future__ import (absolute_import, print_function,
division, unicode_li... | paopao74cn/noworkflow | capture/noworkflow/now/prov_definition/slicing_visitor.py | Python | mit | 10,881 | [
"VisIt"
] | f9f7ca579e9273468b9bd22d6d0a77310df496787f0be8f9fd78f23fb04bfc7f |
from sfepy.base.base import *
import sfepy.base.la as la
from meshio import MeshIO
import os.path as op
##
# 28.05.2007, c
def make_point_cells( indx, dim ):
conn = nm.zeros( (indx.shape[0], dim + 1), dtype = nm.int32 )
for ii in range( 0, dim + 1 ):
conn[:,ii] = indx
return conn
##
# 23.05.2007,... | certik/sfepy | sfepy/fem/mesh.py | Python | bsd-3-clause | 17,779 | [
"VTK"
] | bd05a68dcdd1e7c7430938a999c6df75027ab77fdaa2ae719a80c8204d19d8d7 |
# -*- coding: utf-8 -*-
""" Example of using the Gaussian Process (GP) for function approximations.
In this scipt, we will ...
"""
import numpy as np
import matplotlib.pyplot as plt
from gp.gp_kernels import kernel
from gp.gp_loglik import gp_loglik
from data.data_sunspot import get_sunspot, data_split
#%%
if __name_... | aaskov/nsp | example_gp.py | Python | mit | 4,300 | [
"Gaussian"
] | 8be8f561670eb55cc89d97dfcc6a618237213d95ee94835741ad44dad93ac65d |
# -*- coding: utf-8 -*-
#
#
# This source file is part of the FabSim software toolkit, which is distributed under the BSD 3-Clause license.
# Please refer to LICENSE for detailed information regarding the licensing.
#
# fab.py contains general-purpose FabSim routines.
from templates import *
from machines import *
... | UCL-CCS/FabSim | deploy/fab.py | Python | bsd-3-clause | 17,405 | [
"LAMMPS"
] | 6109950ae5b696fd4d1ebae4d8092aad1bd24d02585b3200305263c9939534a9 |
import locale
import logging
import os
import subprocess
import sys
from collections.abc import Sequence
from shutil import rmtree
from tempfile import mkdtemp
from pelican import Pelican
from pelican.generators import StaticGenerator
from pelican.settings import read_settings
from pelican.tests.support import (Logged... | farseerfc/pelican | pelican/tests/test_pelican.py | Python | agpl-3.0 | 10,904 | [
"exciting"
] | 41b2c19e924f3df084d3fb4c9179da63ae498d88abc8f500e0ec63d39a57bedb |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | VisTrails/VisTrails | vistrails/gui/shell.py | Python | bsd-3-clause | 6,873 | [
"VisIt"
] | 8ed5eca4c44c80be9f13e4753452a7834a98a533507d94003abaf3e1fbc68da6 |
#!/usr/bin/env python
import argparse
from QuadraticLayer import QuadraticLayer
from IzhikevichLayer import IzhikevichLayer
from NetworkSimulator import simulate
from NeuronNetwork import NeuronNetwork
from Plotters import plot_show, plot_membrane_potentials, plot_firings
neuron_models = {"quadratic": QuadraticLaye... | lawrencejones/neuro | iz/NetworkDemo.py | Python | gpl-3.0 | 1,259 | [
"NEURON"
] | 6212ed2a9371cd7afd9d3550fd06bed971d3fcf7059b0c1bcb5bb297f9c7d713 |
"""
awot.io.flight
==============
Routines for reading flight data from file
"""
from __future__ import absolute_import, print_function
import os
import numpy as np
from datetime import datetime
from netCDF4 import Dataset, num2date, date2num
from . import common
from ..io.name_maps_flight import get_name_map
#####... | nguy/AWOT | awot/io/flight.py | Python | gpl-2.0 | 15,620 | [
"NetCDF"
] | 2d4b561ea5c4cbb00bb637d0c740ba907f88ea27e882f53c56167a5194ceb5fd |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Features/multiple_features/best_kNN_PC/cross_validate_objects_kNN_PC_BMED_8813_HAP_scaled_method_II_area_shape.py | Python | mit | 4,401 | [
"Mayavi"
] | 59b4a5921df89f35b8cf820b300ede392faca7f17591eda1210500fdd30d48f2 |
"""
Assign geographically density value to a points.
"""
from scipy.spatial import KDTree
from scipy.spatial.distance import cdist
from scipy.stats import norm
from scipy.optimize import minimize
import numpy as np
def general_density_assignation(locs, parameters, values=None, locs2=None):
"Density assignation ... | tgquintela/Mscthesis | FirmsLocations/Retrieve/density_assignation.py | Python | mit | 9,368 | [
"Gaussian"
] | f69ce0643b2e23311790a7ab2afae23900c2f952c2461f690857e79b2a91f95b |
# -*- coding: utf-8 -*-
#
# hl_api_models.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, ... | HBPNeurorobotics/nest-simulator | pynest/nest/lib/hl_api_models.py | Python | gpl-2.0 | 5,112 | [
"NEURON"
] | daf3f962beb7879638fbeaa9256913af0218e82962e00e137960536a547d8e84 |
#!/usr/bin/env python
from vtk import *
source = vtkRandomGraphSource()
source.SetNumberOfVertices(15)
source.SetStartWithTree(True)
source.SetIncludeEdgeWeights(True)
bfs = vtkBoostBreadthFirstSearch()
bfs.AddInputConnection(source.GetOutputPort())
bfs.SetOriginVertex(0)
view = vtkGraphLayoutView()
vie... | hlzz/dotfiles | graphics/VTK-7.0.0/Examples/Infovis/Python/boost_bfs.py | Python | bsd-3-clause | 911 | [
"VTK"
] | 573f09a28e1194a58c405f32999a1e85e0817ece4eb203bce26deb98ce480d34 |
# codes.py
code_dict1 = {'Arsenal' : 'ARS','Aston Villa': 'AVL','Burnley': 'BUR','Chelsea': 'CHE','Crystal Palace': 'CRY',
'Everton': 'EVE','Hull City':'HUL','Leicester City':'LEI','Liverpool': 'LIV','Manchester City':'MCI',
'Manchester United':'MUN','Newcastle United':'NEW','Queens Park Rangers':'QPR',
'Southampto... | supercr7/foot-fixtures | codes.py | Python | mit | 1,785 | [
"CRYSTAL"
] | ff73d9d9e4c9e1633c7a25b108b8ea503ade2416359b057a42e8d9b122ba999b |
# Copyright (c) 2015, Scott J Maddox. All rights reserved.
# Use of this source code is governed by the BSD-3-Clause
# license that can be found in the LICENSE file.
import os
import sys
fpath = os.path.abspath(os.path.join(os.path.dirname(__file__),
'../fdint/gfd.pyx'))
with open(... | scott-maddox/fdint | scripts/gen_gfd_pyx.py | Python | bsd-3-clause | 1,359 | [
"DIRAC"
] | e6892e579ebffe830d2ce01125e9fad43c125866a35fe152d2ee49ef196cdd13 |
#!/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... | gianina-ingenuity/titanium-branch-deep-linking | testbed/x/mobilesdk/osx/5.5.1.GA/module/iphone/templates/build.py | Python | mit | 8,783 | [
"VisIt"
] | 2f809bc72d483ee811a8e420bd700c37f7d8594e9337a4a716805bd1b1e778fc |
#! /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-domains | scripts/fixup_domains_v1beta1_keywords.py | Python | apache-2.0 | 7,070 | [
"VisIt"
] | 9a14d7ffa489a59865681c10165340e20eea3a97a191f26461cbc124bb34c4b4 |
from django.db import models
from mkt.site.models import ModelBase
class DeployBuildId(ModelBase):
"""
After deployments are completely finished to all the webheads, build IDs
that are generated from our frontend builds (marketplace-gulp) and written
to src/build_id.txt are stored in this table, keye... | ingenioustechie/zamboni | mkt/commonplace/models.py | Python | bsd-3-clause | 726 | [
"GULP"
] | a31bf7363b7b9bec1e4ff5ac74b18eb85673d9303ea254f57828de80d0df6c25 |
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plot
import sys,os
import ROOT
import numpy as np
from matplotlib.colors import LogNorm
__author__ ="pkopka"
#Script plot line of response
# input file generate aplication analusis made by Pawel Kowalski
# python jplot.py <inputfile>
def main(argv):... | JPETTomography/j-pet-gate-tools | jplot/jplot.py | Python | apache-2.0 | 8,506 | [
"CRYSTAL"
] | b84d74e559da3a345c3e66fa3fbeb52d1ed1816f98079f2a9ba0cc66f74d3639 |
import sys
import os
from readability import xauth
from httplib2 import ServerNotFoundError
from workflow import Workflow, PasswordNotFound
import argparse
from helpers import get_client
def execute(wf):
try:
wf.get_password('readability_oauth_token')
wf.get_password('readability_oauth_token_secre... | fniephaus/alfred-readability | src/readability_launcher.py | Python | mit | 3,328 | [
"VisIt"
] | fc543c38ed786e5385637a8596121faa2b60152d385e025d8ab823698dfbd2d4 |
"""Methods for smoothing data over a grid."""
import numpy
from scipy.ndimage.filters import generic_filter
from gewittergefahr.gg_utils import grids
from gewittergefahr.gg_utils import error_checking
TOLERANCE = 1e-6
EFOLDING_TO_CUTOFF_RADIUS_DEFAULT = 3.
def _get_distances_from_center_point(
grid_spacing_... | thunderhoser/GewitterGefahr | gewittergefahr/gg_utils/grid_smoothing_2d.py | Python | mit | 7,691 | [
"Gaussian"
] | 0bdfb9111ced0ea732283d045c0421d6050d43ae02802806c01413eefd405fa4 |
from flask import Blueprint
from flask import request
from flask import render_template
from bson import json_util
from main import app,db,security
from models.models import MongoTestModel
test_api = Blueprint('test_api', __name__)
@test_api.route("/api/tests/email/<_sender>", methods=['GET'])
def test_send_email(... | tedsunnyday/SE-Server | controllers/test_controller.py | Python | apache-2.0 | 2,432 | [
"VisIt"
] | 687492737e19738d03425bdc940d6d9f285c0e23d548d79c9da8a2d8a3d75b93 |
import datetime
import os
from unittest import mock
from django.conf import settings
from django.contrib.auth.models import Group, Permission
from django.core import mail
from django.core.files.base import ContentFile
from django.http import HttpRequest, HttpResponse
from django.test import TestCase, modify_settings,... | zerolab/wagtail | wagtail/admin/tests/pages/test_edit_page.py | Python | bsd-3-clause | 113,334 | [
"VisIt"
] | 34df9143451c3f149b9a6ff11e674527ba9550c152196e03956807c2895efc99 |
# Author: Travis Oliphant 2001
# Author: Nathan Woods 2013 (nquad &c)
from __future__ import division, print_function, absolute_import
import sys
import warnings
from functools import partial
from . import _quadpack
import numpy
from numpy import Inf
__all__ = ['quad', 'dblquad', 'tplquad', 'nquad', 'quad_explain',
... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/integrate/quadpack.py | Python | apache-2.0 | 30,797 | [
"Gaussian"
] | ba01cc7faf6bcd09d1de8185fa2ca9c56dae00a3144f36343ecad685b4e26749 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''plotting/analysis routines on output of example_parallel_network.py
Copyright (C) 2018 Computational Neuroscience Group, NMBU.
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 ... | LFPy/LFPy | examples/bioRxiv281717/figure_7_8/example_parallel_network_plotting.py | Python | gpl-3.0 | 25,819 | [
"NEURON"
] | 73b1169e14062f59b1a8008c689bd1b18b5087eb63ce7b1591d79af8a93ad3a5 |
"""Pipeline code to run alignments and prepare BAM files.
This works as part of the lane/flowcell process step of the pipeline.
"""
from collections import namedtuple
import glob
import os
import toolz as tz
from bcbio import bam, utils
from bcbio.bam import cram
from bcbio.ngsalign import (bbmap, bowtie, bwa, topha... | a113n/bcbio-nextgen | bcbio/pipeline/alignment.py | Python | mit | 7,783 | [
"BWA",
"Bowtie",
"Galaxy"
] | 85276e55ce939fd54f56be03169b654fce013eefe9852cfad92b74a930c9e7b4 |
import numpy as np
import matplotlib.pyplot as plt
class FVGrid(object):
def __init__(self, nx, ng, xmin=0.0, xmax=1.0):
self.xmin = xmin
self.xmax = xmax
self.ng = ng
self.nx = nx
# python is zero-based. Make easy intergers to know where the
# real data lives
... | zingale/hydro_examples | advection/fv_mol.py | Python | bsd-3-clause | 5,693 | [
"Gaussian"
] | 04ff23a55d6163553b74a9ebd5fa38c901b23b147bb1a32a1b0579706020fe53 |
"""
Another module for converting bamtofastq, defaults to writing gzfiles
Accepts only one input file
Includes class for converting paired-end sequencing files to two fastq pipes
Supports SAM, BAM
"""
from argparse import ArgumentParser
from gzip import GzipFile
from os import mkfifo, getcwd, devnull
import os
from o... | benjschiller/seriesoftubes | seriesoftubes/converters/bamtofastq2.py | Python | artistic-2.0 | 6,616 | [
"pysam"
] | 682824ec93838add6c8ac96ceaf28f17ea0a2f8472bce1ade25495efda90aca4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import, print_function
from builtins import * # noqa pylint: disable=unused-import, redefined-builtin
from past.builtins import basestring
import logging
import re
import time
from datetime import datetime, timedelta
from dateutil.pa... | drwyrm/Flexget | flexget/plugins/internal/api_trakt.py | Python | mit | 49,010 | [
"VisIt"
] | 8d7a09bdb4c7144e8c09ac921c8a93761ff2e0cc679b740d00a0b3155ca2bf80 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | fabian-paul/PyEMMA | pyemma/coordinates/tests/test_featurizer.py | Python | lgpl-3.0 | 53,261 | [
"MDTraj"
] | 929e71f7b070bfe35eae6900c3cf56853495afdedbb70fb21cda750fa13a5dca |
#!/usr/bin/env python
"""
Populates the database with the current installations of components
This script assumes that the InstalledComponentsDB, the
ComponentMonitoring service and the Notification service are installed and running
"""
from datetime import datetime
from DIRAC import exit as DIRACexit
from DIRAC imp... | Andrew-McNab-UK/DIRAC | FrameworkSystem/scripts/dirac-populate-component-db.py | Python | gpl-3.0 | 7,401 | [
"DIRAC"
] | 498e94d76969aa07cc88b6ced8fee1b3c306c0e04d44f5aeabe42aeca384e70b |
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