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# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------
# Copyright (c) 2009-2015 Jendrik Seipp
#
# RedNotebook 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... | Isendir/rednotebook | rednotebook/info.py | Python | gpl-2.0 | 24,256 | [
"VisIt"
] | 36a963746485577bde3dbe67923718a6f453e0f98a03526ffc6e9ec92d3021e1 |
# -*- coding: utf-8 -*-
"""upload_docs
Implements a Distutils 'upload_docs' subcommand (upload documentation to
PyPI's pythonhosted.org).
"""
from base64 import standard_b64encode
from distutils import log
from distutils.errors import DistutilsOptionError
import os
import socket
import zipfile
import tempfile
import ... | google/material-design-icons | update/venv/lib/python3.9/site-packages/setuptools/command/upload_docs.py | Python | apache-2.0 | 7,315 | [
"VisIt"
] | 3b5dfb6cdf5db7fb042debdfe2fc2ec16464a201dfe1b3d773e8cd4715506a2c |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# mal
# ------------------------------------------------------------
# Proveedor de información de MyAnimeList mediante la API Jikan v3
# Utilizado para obtener datos de animes para la videoteca
# del addon, infoLabels y también par... | alfa-addon/addon | plugin.video.alfa/core/mal.py | Python | gpl-3.0 | 37,049 | [
"MOE"
] | af104003b940046a43ba3df4c59a8c96c915b81616227645811d99dca12e1cdf |
""" Expose the model metadata module as a datatype module also,
allowing it to live in galaxy.model means the model module doesn't
have any dependencies on th datatypes module. This module will need
to remain here for datatypes living in the tool shed so we might as
well keep and use this interface from the datatypes m... | icaoberg/cellorganizer-galaxy-tools | datatypes/metadata.py | Python | gpl-3.0 | 1,195 | [
"Galaxy"
] | 65abdf42773a2b50ceb984ced62a37188cb07d9a4793982942bbe2d7b0542f89 |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
import pyglet
import cocos
from cocos.director import director
from cocos.actions import *
from cocos.layer import *
from cocos.particle_systems import *
cl... | adamwiggins/cocos2d | test/test_particle_smoke.py | Python | bsd-3-clause | 858 | [
"Galaxy"
] | d8bb0c28f35d6d28ec738c1329815128ae0803f51155d88cfa2f78ef3c818ed3 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/Variable_Stiffness_Variable_Velocity/HMM/with padding 1.2s/hmm_crossvalidation_force_20_states.py | Python | mit | 29,306 | [
"Mayavi"
] | 938014607dec3e6d3580edaba92e3d16c9f67cb320066a4e23afbdfe29cad17d |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-get-jdl
# Author : Stuart Paterson
########################################################################
"""
Retrieve the current JDL of a DIRAC job
"""
__RCSID__ = "$Id$"
import DI... | coberger/DIRAC | Interfaces/scripts/dirac-wms-job-get-jdl.py | Python | gpl-3.0 | 1,394 | [
"DIRAC"
] | 915da359d39d3424d17ff135cc52267eb9e26a66f096ab8dfdba03533ab4c460 |
## Copyright (C) 2005-2006 Graham I Cummins
## 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 dist... | gic888/MIEN | interface/modelbuilder.py | Python | gpl-2.0 | 25,254 | [
"NEURON"
] | 53acf7358e9989a4f70df9fdcf1ced4d58ecb35b59cfa21ea97f67f84b236ead |
# 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... | drpngx/tensorflow | tensorflow/contrib/autograph/converters/asserts.py | Python | apache-2.0 | 1,737 | [
"VisIt"
] | 4fc56ed591a5fb4899a8d994622e65a0af2346396cff5d63e4bfbc869420ea93 |
# -*- coding: utf-8 -*-
"""Testing functions."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
#
# License: BSD-3-Clause
from contextlib import contextmanager
from functools import partial, wraps
import os
import inspect
from io import StringIO
from shutil import rmtree
import sys
import tempfile
import ... | mne-tools/mne-python | mne/utils/_testing.py | Python | bsd-3-clause | 16,406 | [
"VTK"
] | 6a0e77c90bb0eaa4eff36f0814049388f637d98032c89034464823ecf8154d90 |
""" Definitions of a standard set of pilot commands
Each commands is represented by a class inheriting CommandBase class.
The command class constructor takes PilotParams object which is a data
structure which keeps common parameters across all the pilot commands.
The constructor must call the supercla... | arrabito/DIRAC | WorkloadManagementSystem/PilotAgent/pilotCommands.py | Python | gpl-3.0 | 38,374 | [
"DIRAC"
] | 87e76412090fb2fa6cd842ee60fdccd1c9373c1a948dc9088d6c23a1556b044a |
import pysam
import argparse
import sys
import logging
from collections import OrderedDict
DEBUG = True
NOT_DEBUG= not DEBUG
parser = argparse.ArgumentParser(description="Get read count in chromosomes",
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-i',... | shengqh/ngsperl | lib/Alignment/bamReference.py | Python | apache-2.0 | 1,447 | [
"pysam"
] | f91310f73a4ede164087d31d2791afb3bfd9666e854c3b7b8cae8fa2e157270a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Name: update_cfg_file.py
# Purpose: Module to manipulate distro specific and main config files.
# Authors: Sundar
# Licence: This file is a part of multibootusb package. You can redistribute it or modify
# under the terms of GNU General Public License, v.2 or abov... | mbusb/multibootusb | scripts/update_cfg_file.py | Python | gpl-2.0 | 64,603 | [
"VisIt"
] | e62f2b5098c61d1ccd328f59d9b969c7327998d230ee39abcfce770f158f760e |
import os
import unittest
import vtk, qt, ctk, slicer
import math
import sys
#
# AstroPVDiagramSelfTest
#
class AstroPVDiagramSelfTest:
def __init__(self, parent):
parent.title = "Astro PVDiagram SelfTest"
parent.categories = ["Testing.TestCases"]
parent.dependencies = ["AstroVolume"]
parent.contrib... | Punzo/SlicerAstro | AstroPVDiagram/Testing/Python/AstroPVDiagramSelfTest.py | Python | bsd-3-clause | 6,002 | [
"VTK"
] | a13fa5ffce75cfa753f530231c8d1b80185cd7d57fa09e0b23d1b049b80a3bdf |
"""
Taken from ProDy
(http://www.csb.pitt.edu/prody/_modules/prody/proteins/blastpdb.html)
"""
import re
import time
import urllib2
import xml.etree.cElementTree as etree
from urllib import urlencode
def blast_pdb(sequence, nhits=250, expect=1e-10, timeout=60, pause=1):
query = {
'DATABASE': 'pdb',
... | platinhom/CADDHom | python/bioinformatics/blastp.py | Python | gpl-2.0 | 4,365 | [
"BLAST"
] | 9a01b2459dd186a6dad43d5968bdad9de6083fb6eec3e081d9132a5b3c502320 |
#!/usr/bin/env python
# File: montage.py
# Created on: Mon Mar 18 10:08:05 2013
# Last Change: Tue Aug 13 14:06:18 2013
# Purpose of script: <+INSERT+>
# Author: Steven Boada
import img_scale
import pyfits as pyf
import pylab as pyl
from mpl_toolkits.axes_grid1 import axes_grid
#from mk_galaxy_struc import mk_galaxy_s... | boada/ICD | sandbox/legacy_plot_code/plot_icd_z_montage.py | Python | mit | 2,741 | [
"Galaxy"
] | bfa0089efefd7d5b1cfdf1da4b500c458e13684e30b29684138e672ccc01844e |
'''
Created on Jul 15, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
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 ... | tectronics/chimerascan | chimerascan/deprecated/chimeras_to_breakpoints_v2.py | Python | gpl-3.0 | 20,400 | [
"pysam"
] | 45c247852fb0e18c5a989ffcae84e9d06d8340cae3673208bdb46aa65ed609cb |
from nltk.stem import WordNetLemmatizer
input_words = ['liked', 'idol', 'wanna', 'happiness', 'death', 'hormone', 'secretion', 'addition', 'better', 'looking', 'exciting', 'best', 'kcal', 'is', 'CO2']
lemmatizer = WordNetLemmatizer()
lemmatizer_names = ['NOUN LEMMATIZER', 'VERB LEMMATIZER']
formatted_text = '{:>24}... | heeyong97/2017sejongAI | Week9/lemmatizer.py | Python | gpl-3.0 | 603 | [
"exciting"
] | b599109fcaf89146713d4fa8d144a2613115344212b887caf8f87b96dbfe9d16 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Created on 24/09/14 13:38
@author: Carlos Eduardo Barbosa
Program to load templates from the MILES library for pPXF use.
"""
import os
import numpy as np
import pyfits as pf
import ppxf_util as util
from config import *
def load_templates_regul(velscale):
""" Loa... | kadubarbosa/hydra1 | load_templates.py | Python | gpl-2.0 | 8,293 | [
"Galaxy"
] | a6cf57aca1d31916cbe76b9b8edd0efbe2daa67a4acd45a7107bc7c3d72bd929 |
__author__ = 'tylin'
__version__ = '1.0.1'
# Interface for accessing the Microsoft COCO dataset.
# Microsoft COCO is a large image dataset designed for object detection,
# segmentation, and caption generation. pycocotools is a Python API that
# assists in loading, parsing and visualizing the annotations in COCO.
# Ple... | chenfsjz/coco | PythonAPI/pycocotools/coco.py | Python | bsd-2-clause | 14,801 | [
"VisIt"
] | 26212cc53bff675002dcc6eba12f0459e786e060bb3f6e8ceb89c24be09f6eb1 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_OC_biomass_emissions_n96e_greg.py | Python | gpl-3.0 | 19,112 | [
"NetCDF"
] | 5e81b803ef1547b304e0f928df0d0446ebc7ccf3489810e3b0152709cf3a413f |
import os
import glob
from pypers.core.step import CmdLineStep
class VariantRecalibrator(CmdLineStep):
spec = {
"name": "VariantRecalibrator",
"version": "2.3-9",
"descr": [
"Runs gatk vcf VariantRecalibrator,",
"generating recal and tranches files to be used by App... | frankosan/pypers | pypers/steps/gatk/variantrecalibrator.py | Python | gpl-3.0 | 4,753 | [
"Gaussian"
] | 907c4403d4eb368514bb6ad276604655c4f6f89fea491f778bb79dd8210ba56d |
#!/usr/bin/env python
"""
Functions to generate ROMS netcdf files
Written by Brian Powell on 04/26/13
Copyright (c)2017 University of Hawaii under the MIT-License.
"""
import os
import re
import netCDF4
import numpy as np
from datetime import datetime
from seapy.lib import default_epoch
from seapy.cdl_parser i... | ocefpaf/seapy | seapy/roms/ncgen.py | Python | mit | 38,868 | [
"Brian",
"NetCDF"
] | 0fd10d653710c4f40bce781f28c8daa38e7b450d28dfae67d94a8ea5e4ee3307 |
#!/usr/bin/env python
import argparse
import pysam
import numpy
import timeit
import re
import networkx as nx
start = timeit.default_timer()
## EXAMPLE COMMAND LINE
# python correct_bam_barcodes_21.11.2016.py --infile PATH/TO/test.bam --outfile PATH/TO/corrected.test.bam --barcodes BOTH
# Function to get the amoun... | imgag/megSAP | src/NGS/barcode_correction.py | Python | gpl-3.0 | 25,086 | [
"pysam"
] | 44f6904da96f3f68597ac2b003a10c9d7d3cc84e30619e40feb9218281cacc77 |
# Copyright 2012 Google Inc.
#
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any late... | JetChars/vim | vim/bundle/python-mode/pymode/libs/pylint/checkers/stdlib.py | Python | apache-2.0 | 8,282 | [
"VisIt"
] | bc182f76edd3a80b671b8050d5a69b72478ff385010a41120f05b568e42d3b4e |
from __future__ import absolute_import, division, print_function
from jaspyx.visitor import BaseVisitor
class Delete(BaseVisitor):
def visit_Delete(self, node):
for target in node.targets:
self.indent()
self.output('delete ')
self.visit(target)
self.finish()... | ztane/jaspyx | jaspyx/visitor/delete.py | Python | mit | 321 | [
"VisIt"
] | 1dbb08b248e56250121c1be34605da04e14bf70887bc6861f7e8b750fbea7e7e |
#! /usr/bin/python
# $Id$
# -----------------------------------------------------------------------------
# CppAD: C++ Algorithmic Differentiation: Copyright (C) 2003-12 Bradley M. Bell
#
# CppAD is distributed under multiple licenses. This distribution is under
# the terms of the
# Eclipse Public... | utke1/cppad | bin/epl_html2txt.py | Python | epl-1.0 | 2,514 | [
"VisIt"
] | 87a3d62f7415a336edbb8b04a83a2a73f6ea278ce6b4ebab115cff2d4a300ab6 |
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not use ... | samuelchong/libcloud | libcloud/security.py | Python | apache-2.0 | 2,950 | [
"VisIt"
] | c1bf1a0451b32ffba7b3c7356cf7a70e9a06cf055d0e5dd0189c175eb9e7cbf0 |
# -*- coding: utf-8 -*-
############################################################################
#
# Copyright (C) 2008-2015
# Christian Kohlöffel
# Vinzenz Schulz
#
# This file is part of DXF2GCODE.
#
# DXF2GCODE is free software: you can redistribute it and/or modify
# it under the terms... | Poofjunior/dxf2gcode | dxfimport/geoent_spline.py | Python | gpl-3.0 | 7,412 | [
"Gaussian"
] | 228fd1aa870ab6e3f94e9b431243f4245722ec34d162849eb769fa9a9a1ce125 |
from __future__ import division
import random, sys, pygame, asteroid, explosion, player
from random import randint
class Game(object):
width, height = 800, 600
asteroids = pygame.sprite.Group()
shoots = pygame.sprite.Group()
explosions = []
points = 0
level = 5
levelAsteroidFrequency = {
... | sollidsnake/galaxy-destroyer | game.py | Python | gpl-2.0 | 7,638 | [
"Galaxy"
] | a5d7a85ea783e6c7b5a0deef15c087a6533327fdfa0eb23dbdcb746ac75f3cda |
# read_cm1.py
class readcm1(object): ####################################################################################
'''
The binary output option in cm1 returns files in a very unusable and inconvenient
output structure, unlike some nicer output options such as netCDF. This class is
desi... | vandegu/umich | read_cm1.py | Python | mit | 14,904 | [
"NetCDF"
] | e3d31da5da5b8d76eaa10bc12d27329c6ea5e1f7a3564b48a5c6e13e79b27ab8 |
# Copyright 2021 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 required by applicable law or agreed to in... | google-research/crafty | observe.py | Python | apache-2.0 | 23,915 | [
"Gaussian"
] | 81e24a307b53d61517acba6f885cbc15c94db2c6162a9e3b05e2e4b955fbefef |
import sys, os
sys.path.insert(1, os.path.join("..",".."))
import h2o
from tests import pyunit_utils
from h2o.estimators.deeplearning import H2ODeepLearningEstimator
def weights_and_distributions():
htable = h2o.upload_file(pyunit_utils.locate("smalldata/gbm_test/moppe.csv"))
htable["premiekl"] = htable["premiek... | madmax983/h2o-3 | h2o-py/tests/testdir_algos/deeplearning/pyunit_weights_and_distributions_deeplearning.py | Python | apache-2.0 | 1,284 | [
"Gaussian"
] | a6c772e7400548c10a04c8ab5f871188116b3f13f5497a4e6b515cc60a8c21dd |
#
# Copyright 2017 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... | google/joint_vae | experiments/vae_imagination_eval.py | Python | apache-2.0 | 30,719 | [
"Gaussian"
] | 22f6ff167666a16dc269c7e79085a56372ad80ae133b7dd71b789e753affac20 |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | KaiSzuttor/espresso | testsuite/python/observables.py | Python | gpl-3.0 | 9,091 | [
"ESPResSo"
] | 929f9da72c459be00783849081af79c12576d4425ff8bebe58f0d83ec14897f1 |
#-------------------------------------------------------------------------------
# Name: module1
# Purpose:
#
# Author: David
#
# Created: 13/03/2017
# Copyright: (c) David 2017
# Licence: <your licence>
#-------------------------------------------------------------------------------
import cv2
i... | davidvdp/CVFilterOverview | Portrait.py | Python | apache-2.0 | 7,688 | [
"Gaussian"
] | 5a1302be39c7ce0b8643f71867cc2e6d91fc11b3fbf0759ffd374ef85eaf5b64 |
"""
View for Courseware Index
"""
# pylint: disable=attribute-defined-outside-init
from datetime import datetime
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.core.context_processors import csrf
from django.core.urlreso... | synergeticsedx/deployment-wipro | lms/djangoapps/courseware/views/index.py | Python | agpl-3.0 | 22,684 | [
"VisIt"
] | b298f10cbb65d8281cdc02c61fbead7166d5f75ca1bfbdb8df996befbbdfefd8 |
"""Options manager for :class:`Poly` and public API functions. """
from __future__ import print_function, division
__all__ = ["Options"]
from sympy.core import S, Basic, sympify
from sympy.core.compatibility import string_types, with_metaclass
from sympy.utilities import numbered_symbols, topological_sort, public
fr... | wxgeo/geophar | wxgeometrie/sympy/polys/polyoptions.py | Python | gpl-2.0 | 21,096 | [
"Gaussian"
] | 4e1c96f58d57abcc723c4807778e703941d190e930bf0c7efcba111675b59a96 |
# Include the Dropbox SDK libraries
from dropbox import client, rest, session
# Get your app key and secret from the Dropbox developer website
APP_KEY = #removed for security reasons
APP_SECRET = #removed for security reasons
# ACCESS_TYPE should be 'dropbox' or 'app_folder' as configured for your app
ACCESS_TYPE = '... | levibostian/VSAS | docs/Risk assessment/dropbox_requestToken.py | Python | mit | 1,044 | [
"VisIt"
] | 020e19f1c522775dbabcb29bdc0b855ce0d406bcaa42f531c12ee11f7de363f3 |
import numpy as np
from .util import spatial_frequencies
import scipy.ndimage
from skimage.filters import gaussian
import matplotlib.pyplot as plt
import warnings
def MTF_a(k,a1,a2,a3,a4):
return (a1 - a2)/(1 + (k/(2*a3))**np.abs(a4)) + a2
def detect(img,sampling,dose=None,MTF_param=None,MTF_func=None,blur=No... | jacobjma/PyQSTEM | pyqstem/detection.py | Python | gpl-3.0 | 1,407 | [
"Gaussian"
] | 0821be9a87d6ac5581632ebbaa7e2cde080c902e09d17c176edbe674526a28dc |
"""The WaveBlocks Project
Thie file contains code for a sparsity oracle looking
at the Gaussian integral of both packets.
@author: R. Bourquin
@copyright: Copyright (C) 2013, 2014 R. Bourquin
@license: Modified BSD License
"""
from WaveBlocksND.SparsityOracle import SparsityOracle
from WaveBlocksND.GaussianIntegral ... | WaveBlocks/WaveBlocksND | WaveBlocksND/SparsityOracleGIHAWP.py | Python | bsd-3-clause | 2,260 | [
"Gaussian"
] | d832481eb96272f6d0949bbd811d90ce5a44d1059cafa378e3d0e0fcd00fbaa4 |
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#
# Okinawa Institute of Science and Technology, Japan.
#
# This script runs on STEPS 2.x http://steps.sourceforge.net
#
# H Anwar, I Hepburn, H Nedelescu, W Chen and E De Schutter
# Stochastic calcium mechanisms cause dendritic calcium spike... | CNS-OIST/STEPS_Example | publication_models/API_1/Anwar_J Neurosci_2013/HybridCaburst_stochCaP.py | Python | gpl-2.0 | 29,332 | [
"Avogadro"
] | 52e51b25c44ffc9ef0694a8df13c0fb80ee57fd4b4d34acaefc006a3312c610a |
import numpy as np
def multiple_2d_circ_gauss_func(p_guess):
def f(p, fjac=None, data=None, err=None,return_models=False):
#p[0] = background
#p[1] = amplitude
#p[2] = x_offset
#p[3] = y_offset
#p[4] = sigma for both x and y
#And so on for the 2nd and 3rd gaussian... | bmazin/ARCONS-pipeline | util/fitFunctions.py | Python | gpl-2.0 | 10,022 | [
"Gaussian"
] | e6457e65eacfedfd7716dfec40f6e61fbe5ba0826489933f76ddb8252d61da71 |
##
# TRACK 4
# CALL & RESPONSE
# Brian Foo (brianfoo.com)
# This file builds the sequence file for use with ChucK from the data supplied
##
# Library dependancies
import csv
import json
import math
import os
import time
# Config
BPM = 60 # Beats per minute, e.g. 60, 75, 100, 120, 150
DIVISIONS_PER_BEAT = 16 # e.g. 4 ... | shawngraham/music-lab-scripts | 04_dating/dating.py | Python | mit | 12,150 | [
"Brian"
] | 906a3dcd60dba4c21883b3b8fe1080baf0c166b7f00e993a8aa22134da79214f |
import os
import PythonQt
from PythonQt import QtCore, QtGui
from ddapp import callbacks
import ddapp.applogic as app
import ddapp.objectmodel as om
import ddapp.visualization as vis
import ddapp.vtkAll as vtk
from ddapp import jointcontrol
from ddapp import getDRCBaseDir
from ddapp import lcmUtils
from ddapp import fi... | gizatt/director | src/python/ddapp/roboturdf.py | Python | bsd-3-clause | 18,377 | [
"VTK"
] | d0535c0bb2b801c1d210b3af939c3dca332bcca8a662f7182df5e36071ffcb70 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tensorflow | tensorflow/python/kernel_tests/signal/spectral_ops_test.py | Python | apache-2.0 | 15,849 | [
"Gaussian"
] | 4b8680cdd21f6dde05a8dac0c24dc10530ececb21f34313b023fcdba3a47c9da |
#!/home/user/anaconda2/bin/python
## Modified from Daniel Buscombe's starter script at https://github.com/dbuscombe-usgs/pyhum
## Supply .DAT file using -i and SON folder using -s
## OR cd into a directory with both .DAT/SON and process all using 'humall' (~/bin/humall)
import sys, getopt
from Tkinter import Tk
from... | iannesbitt/sidescantools | hummap.py | Python | mit | 2,643 | [
"Gaussian"
] | 850b344d839744e449e82571cf5dc12e8ee6641984b8d89c4beec67667b6c22d |
import numpy as np
import scipy.optimize as opt
from wavelets import Morlet
import pylab as plb
class Wavenet():
def __init__(self, wavelet, ncount, x, y):
"""Create wavenet.
Args:
cn: int: Number of neurons
Returns:
net: Wavenet
Attributes:
param: dict:... | abalckin/wavenet | wavenet.py | Python | lgpl-3.0 | 6,671 | [
"NEURON"
] | 52f06037266587c98d6ec562bc06dcf24ddfb0548c3eacdc3bbfd02dda665683 |
import unittest
import pylab as pl
import matplotlib as mpl
import itertools
import sys
import math
import timeit
import copy
import time
import struct
import scipy.stats.mstats as stats
import ConfigParser
import os.path
import getopt
import h5py
from gmm_specializer.gmm import *
MINVALUEFORMINUSLOG = -1000.0
class... | RedHenLab/Audio | GSoC2015/Speaker_Dia_RedHen/pycasp/cluster.py | Python | gpl-2.0 | 26,523 | [
"Gaussian"
] | e5207d0b8f68d3447e15bd528e11d89e8ad132fa758f7ce60d02b61dc92d3fc3 |
import os
import os.path
import sys
import xml.sax.handler
import xml.sax
#---------------------------------------------------------------------------
class ClassExtractor(xml.sax.handler.ContentHandler):
"""This class is essentially a callback. It is used to parse the xml files.
It searches for "class" attr... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Utilities/MinimalBuildTools/ParseXMLResources.py | Python | gpl-3.0 | 2,361 | [
"VTK"
] | 8010826ef964edbd067fe7b32901dbfcd1b60f4b9ef86fc9d1a22936d3d1fddf |
#!/usr/bin/env python
'''
MakeMagneticContours.py:
This script will create a magnetic field map using
equipartition estimates from a spectral index fits
file. Please edit the global constants as needed.
For more information about the magnetic field
equipartition estimates, please consult the standard
... | mpbusch/LOFAR-ForegroundGalaxyCollaboration | MakeMagneticContours.py | Python | mit | 3,346 | [
"Galaxy"
] | f4489795e4b569b47b358e84507012af0d202e6c21a568c671e67889db8dbd83 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License
"""
Module for reading Lobster output files. For more information
on LOBSTER see www.cohp.de.
"""
import itertools
import os
import warnings
from typing import Any, Dict, List, Optional
import numpy as np
import spglib
from m... | materialsproject/pymatgen | pymatgen/io/lobster/inputs.py | Python | mit | 33,885 | [
"VASP",
"pymatgen"
] | 6e65a23f8eba710773e7e54e3d49b6fa2d762089616db2ceaa4be30fc1c7b610 |
import os, pdb, platform, time, warnings
import ctypes as ct
import numpy as np
MAX_ONES = 1024*256
if platform.system() == 'Windows' or platform.system().startswith('CYGWIN_NT'):
mydir = os.path.dirname(__file__)
os.environ['PATH'] += ";" + mydir
_cudamat = ct.cdll.LoadLibrary('libcudamat.dll')
else:
... | gomyway/deeplink | cudamat/cudamat.py | Python | gpl-3.0 | 57,243 | [
"Gaussian"
] | 8aa88de50fae60bf44ca8076da30a29a71896c496ce027f5806099a218d05bd0 |
# Copyright 2013 The Swarming Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0 that
# can be found in the LICENSE file.
"""OAuth2 related utilities and implementation of browser based login flow."""
# pylint: disable=W0613
import base64
import BaseHTTPServer
i... | Teamxrtc/webrtc-streaming-node | third_party/webrtc/src/chromium/src/tools/swarming_client/utils/oauth.py | Python | mit | 21,103 | [
"VisIt"
] | f54b022b6cd7be2aba1e2d266438da956990d86409b82def2da938edf0408604 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Dtf(AutotoolsPackage):
"""DTF (Data Transfer Framework) is a general I/O arbitration
m... | LLNL/spack | var/spack/repos/builtin/packages/dtf/package.py | Python | lgpl-2.1 | 2,275 | [
"NetCDF"
] | 2b4a21bda88679ce5f646d7207a13296a3bbfaacf667c211f9fb26d1d7d2c7ff |
#!/usr/bin/env python
# coding: utf-8
# Features
# ============================
#
# Features within PHOEBE are anything that can be "attached" to a component or a dataset to inform how to compute the forward-model. These currently include spots and gaussian processes - but the framework is flexible enough to handle ... | phoebe-project/phoebe2-docs | development/tutorials/features.py | Python | gpl-3.0 | 2,424 | [
"Gaussian"
] | 46bb1ff7c67d4ff73a06a65fed09ef13fce72ab5fc259273129eed125fed6411 |
"""
ftpwalk -- Walk a hierarchy of files using FTP (Adapted from os.walk()).
"""
def ftpwalk(ftp, top, topdown=True, onerror=None):
"""
Generator that yields tuples of (root, dirs, nondirs).
"""
# Make the FTP object's current directory to the top dir.
ftp.cwd(top)
# We may not have read permi... | ActiveState/code | recipes/Python/499334_Remove_FTP_directory_walk/recipe-499334.py | Python | mit | 3,322 | [
"VisIt"
] | 2f6425ee138894f6f492e728f6561620a78794859aeaac9a45772c9393d6a77d |
# The MIT License (MIT)
#
# Copyright (c) 2015 Brian Wray (brian@wrocket.org)
#
# 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
# ... | wrocket/Tulip-Chess | tests/basic-tests/test_evaluate.py | Python | mit | 9,199 | [
"Brian"
] | 6180e02825ed0937e5b98701b1e7b8ef902d56b42b705fa5b4886108f4af108d |
#!/usr/bin/env python
#|
#| Downweight bases that are cytosines
#|
#|
#| Works to perform a C->T transition
#| and a G->A transition
#|
#| @author James Boocock
#| @date 12/09/2014
#|
from Bio import SeqIO
import argparse
def check_c_2_t(base):
"""
C to T checker
"""
if base == 'T':
retur... | smilefreak/NGaDNAP | scripts/ancient_filter.py | Python | mit | 4,221 | [
"pysam"
] | a3eb7bbf3b9fda5432ed9f2a1e5a23b5ad93dd2414aed65ac15e571b26207b41 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
Created on Mar 15, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | migueldiascosta/pymatgen | pymatgen/transformations/tests/test_site_transformations.py | Python | mit | 9,414 | [
"pymatgen"
] | e5572bf227250eaeac6abc5878e9a2065a9cc7449f3d78c796c98d095b6de0e2 |
#brain on drops
import os
import numpy as np
import nibabel as nib
from collections import OrderedDict
from mayavi import mlab
from boyle.nifti.roi import get_rois_centers_of_mass
def test_quiver3d():
x, y, z = np.mgrid[-2:3, -2:3, -2:3]
r = np.sqrt(x ** 2 + y ** 2 + z... | Neurita/cajal | cajal/connectivity.py | Python | bsd-3-clause | 6,547 | [
"Mayavi"
] | 597f8ab6d751bc0b00748b8ac85fb69b8555d7dafec673ebe594033423e6584d |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkHyperOctreeSampleFunction(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkHyperOctreeSampleFunction.py | Python | bsd-3-clause | 500 | [
"VTK"
] | abfd95093a9d9ecbd30558fc73eec1193ff9ed374e05d9c63b682b63eb55a0d9 |
#!/usr/bin/env python
import math
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Image pipeline
reader = vtk.vtkPNGReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/fullhead15.png")
# Take the gradient in X, and smooth in Y
# Create a s... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/TestSeparableFilter.py | Python | bsd-3-clause | 1,144 | [
"Gaussian",
"VTK"
] | a4c26840585ba05f5f7a3cd5abb30d7664fea9e09b2eadaf5b13c38590b7df43 |
"""Compatibility fixes for older versions of libraries
If you add content to this file, please give the version of the package
at which the fix is no longer needed.
# originally copied from scikit-learn
"""
# Authors: Emmanuelle Gouillart <emmanuelle.gouillart@normalesup.org>
# Gael Varoquaux <gael.varoquau... | kambysese/mne-python | mne/fixes.py | Python | bsd-3-clause | 37,120 | [
"Gaussian",
"Mayavi"
] | 5749eedc3aaa4d5079596eed1aa245a58137f8c2bab75bd4a7d6083015aac323 |
""" JobStateUpdateHandler is the implementation of the Job State updating
service in the DISET framework
The following methods are available in the Service interface
setJobStatus()
"""
from __future__ import absolute_import
import six
from six.moves import range
__RCSID__ = "$Id$"
import time
from DI... | chaen/DIRAC | WorkloadManagementSystem/Service/JobStateUpdateHandler.py | Python | gpl-3.0 | 12,909 | [
"DIRAC"
] | 23ff978efd0d67935a66f6d8022dde0fdeaa2ccac3d4c38aa28f066c826fc637 |
#!/usr/bin/env python
# pywws - Python software for USB Wireless Weather Stations
# http://github.com/jim-easterbrook/pywws
# Copyright (C) 2008-15 pywws contributors
# 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 Fr... | miguelalonso/pywws | src/pywws/toservice.py | Python | gpl-2.0 | 22,250 | [
"VisIt"
] | 345de33f9bc43fe102b84305c21fee5bf3944f417f93271e714086c6d68cd77e |
import os, sys
from distutils.core import setup
from setuptools import find_packages
def readme():
with open('README.md') as f:
return f.read()
setup(name='SeqSero2',
version=open("version.py").readlines()[-1].split()[-1].strip("\"'"),
description='Salmonella serotyping',
long_description=read... | denglab/SeqSero2 | setup.py | Python | gpl-2.0 | 1,265 | [
"Biopython"
] | 8f2a06b0e375e6db859207a49f8c6c984d3c0201722be9708ad0b8d8d9b36506 |
# Copyright (c) 2010 Howard Hughes Medical Institute.
# All rights reserved.
# Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms.
# http://license.janelia.org/license/jfrc_copyright_1_1.html
"""
A custom centrality script for the C. elegans network.
"""
import networkx
# Load th... | JaneliaSciComp/Neuroptikon | Source/Scripts/C. elegans/Centrality.py | Python | bsd-3-clause | 2,516 | [
"NEURON"
] | 7420e85a1fc62b0ce1bdce8d1bc52f6ddbe88b32beb5dd8b7ff5ab1fa427b001 |
#!/usr/bin/env python
#Copyright 2013 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive license for use of this work by or on behalf of the U.S. Government. Export of this program may require a license from the United States Government.
from mpi4py import MPI
import pymongo
... | sandialabs/grandmaster | processing/updatePUPCmodel.py | Python | apache-2.0 | 4,638 | [
"VTK"
] | c9ad6eb9c4915dc46903dbdad75f869ea0d44fec1be3e2ab4b7703c81ea5eee6 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parser for PDB files."""
from __future__ import print_function
import warnings
try:... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/PDB/PDBParser.py | Python | gpl-2.0 | 13,243 | [
"Biopython"
] | 738ca6a3159b057ef3118948228ff106f225c98207643ecd6c9746668c0df33a |
""" Class that contains client access to the job monitoring handler. """
from __future__ import absolute_import
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client import Client, createClient
@createClient('WorkloadManagement/JobMonitoring')
class JobMonitoringClient(Client):
def __init__(self, **kwargs):
super... | petricm/DIRAC | WorkloadManagementSystem/Client/JobMonitoringClient.py | Python | gpl-3.0 | 800 | [
"DIRAC"
] | b7bf641a1df445837989cbf99837a76f360c8794cca0ce8147ba2334e016122e |
from __future__ import absolute_import
import cython
cython.declare(PyrexTypes=object, Naming=object, ExprNodes=object, Nodes=object,
Options=object, UtilNodes=object, LetNode=object,
LetRefNode=object, TreeFragment=object, EncodedString=object,
error=object, warning=object... | c-blake/cython | Cython/Compiler/ParseTreeTransforms.py | Python | apache-2.0 | 121,925 | [
"VisIt"
] | db92a389f97e19f06eafa97b3f3b6c1a444117f24344d4b4ada5ea83b70c7020 |
import numpy as np
from gym.spaces import Box
from metaworld.envs import reward_utils
from metaworld.envs.asset_path_utils import full_v2_path_for
from metaworld.envs.mujoco.sawyer_xyz.sawyer_xyz_env import SawyerXYZEnv, _assert_task_is_set
class SawyerDrawerCloseEnvV2(SawyerXYZEnv):
_TARGET_RADIUS = 0.04
de... | rlworkgroup/metaworld | metaworld/envs/mujoco/sawyer_xyz/v2/sawyer_drawer_close_v2.py | Python | mit | 4,612 | [
"Gaussian"
] | 006207fb67b2d8f3b7238f6fb28e33fd9977d84d12d308cc9d4d29f25373571c |
# $Id$
#
# Copyright (c) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" utility functionality for fingerpri... | soerendip42/rdkit | rdkit/Chem/Fingerprints/FingerprintMols.py | Python | bsd-3-clause | 17,794 | [
"RDKit"
] | 2ca81a67d8dc015ce500c2afec0fec497ca46afa2772217aeb17dd8131b02ea8 |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | sbc100/yapf | yapftests/reformatter_buganizer_test.py | Python | apache-2.0 | 73,591 | [
"Firefly"
] | 9ef89ada202e244e96964fdbe1179345a2f48a08a230a93700230fc9df95ca93 |
# Copyright (c) 2004 Canonical Limited
# Author: Robert Collins <robert.collins@canonical.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at y... | zarboz/XBMC-PVR-mac | tools/darwin/depends/samba/samba-3.6.6/lib/subunit/python/subunit/tests/TestUtil.py | Python | gpl-2.0 | 2,788 | [
"VisIt"
] | 489973e9b5caee4063426bb2b5e53d76dbffa8568d7ae2286536fa771adbda88 |
"""Test check utilities."""
# Authors: MNE Developers
# Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#
# License: BSD-3-Clause
import os
import os.path as op
import sys
import numpy as np
import pytest
from pathlib import Path
import mne
from mne import read_vectorview_selection
from mne.datasets import t... | mne-tools/mne-python | mne/utils/tests/test_check.py | Python | bsd-3-clause | 11,295 | [
"VTK"
] | 65b7bb2d7c00ae200f5858bde7f0edfd7f97e5837fb1b8d260846c95cd2360b2 |
"""
Set of routines to interface with MULTI (1D or _3D)
"""
import numpy as np
import os
class Multi_3dOut:
def __init__(self, outfile=None, basedir='.', atmosid='', length=4,
verbose=False, readall=False):
""" Class that reads and deals with output from multi_3d """
self.verbose ... | M1kol4j/helita | helita/sim/multi.py | Python | bsd-3-clause | 16,939 | [
"NetCDF"
] | b0984b34347a0158f7bdc31c7ad628d08d1bede27f6ce70cfdad3597616f14ab |
"""Synthetic datasets for vector-field learning."""
from numpy import arange, sqrt, meshgrid, pi, exp, gradient, floor, hstack
# pylint: disable=C0103
def _gaussian(x_mesh, y_mesh, x_mesh_mean, y_mesh_mean, scale=1):
"""Generate a gaussian.
Parameters
----------
x_mesh : array, shape = [n_samples, ... | operalib/operalib | operalib/datasets/vectorfield.py | Python | bsd-3-clause | 7,798 | [
"Gaussian"
] | e3c1b1851215d59be586cffe7bc7e293419b76505da1a9154a458be8695356a3 |
# $HeadURL$
"""
Encoding and decoding for dirac, Ids:
i -> int
I -> long
f -> float
b -> bool
s -> string
z -> datetime
n -> none
l -> list
t -> tuple
d -> dictionary
"""
__RCSID__ = "$Id$"
import types
import datetime
_dateTimeObject = datetime.datetime.utcnow()
_dateTimeType = type( _dateTimeObject )
_dat... | avedaee/DIRAC | Core/Utilities/DEncode.py | Python | gpl-3.0 | 6,959 | [
"DIRAC"
] | e5074eaefe86ab15a87e23d9e081467e9725b9c63f5f0ae330017c847e8e195e |
"""
Genetics Module of the CAB Sugarscape simulation.
Encapsulates all aspects of the agent genetics.
Credit to David Grotzky.
"""
__author__ = 'Michael Wagner'
__version__ = '1.0'
from cab.util.rng import get_RNG
# TODO: Implement proper immune system.
class Chromosome:
"""
This class handles all biologica... | Micutio/CAB_Simulations | SugarScape/abm/ss_genetics.py | Python | mit | 8,545 | [
"Gaussian"
] | 1cb8b74c24899bd30dfa8626ba7899ff7197edcc2c6110811f41714a538a10c5 |
# $Id$
#
# Copyright (C) 2006 Greg Landrum
#
import unittest, os, sys
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import Chem
from rdkit import DataStructs
from rdkit.Chem import MolCatalog
class TestCase(unittest.TestCase):
def test1(self):
cat = MolCatalog.CreateMolCatalog()
... | jandom/rdkit | Code/GraphMol/MolCatalog/Wrap/rough_test.py | Python | bsd-3-clause | 1,303 | [
"RDKit"
] | 3a92f260b8ffd2cea2792490cfc51c99620acb769bf46c74398713b8ddf9e3d3 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | ashutoshvt/psi4 | psi4/share/psi4/databases/RSE42.py | Python | lgpl-3.0 | 77,097 | [
"Psi4"
] | 2b347ea756ece66b5421e650d56666925dace04e258a4c9e88baaefba7895373 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, Matthew Har... | leeping/mdtraj | tests/test_topology.py | Python | lgpl-2.1 | 9,078 | [
"MDTraj",
"OpenMM"
] | 622d95724aaff0489b1de32c256dc18ff379a6a2b120576a1e3cf9642b3f23cc |
"""Django forms for hs_core module."""
import copy
from models import Party, Creator, Contributor, validate_user_url, Relation, Source, Identifier, \
FundingAgency, Description
from django.forms import ModelForm, BaseFormSet
from django.contrib.admin.widgets import forms
from django.utils.safestring import mark_s... | ResearchSoftwareInstitute/MyHPOM | hs_core/forms.py | Python | bsd-3-clause | 46,995 | [
"NetCDF"
] | cdb1dc114cbc76ee701ec923e5420e14949a768b7cf76894df6794d2e2b28a9d |
#!/usr/bin/env python
'''
Phillip Kuznetsov
2017
'''
from __future__ import print_function
import os, sys
os.environ['GLOG_minloglevel'] = '2' # suprress Caffe verbose prints
import re
import settings
sys.path.insert(0, settings.caffe_root)
import caffe
import numpy as np
from numpy.linalg import norm
import scipy.... | philkuz/ppgn | sampling_all_losses.py | Python | mit | 12,411 | [
"NEURON"
] | 8ae6de728a039f075116768d15de908fcfeafc2706e545bf75478690d4c607c0 |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
from vmtk import vtkvmtk
import argparse
import itertools
import os
import copy
# map the average crossectional area to the boundary reference info
def Execute(args):
print("evaluate centerlines")
reader_ctr = vmtkscripts.v... | kayarre/Tools | vmtk/clip_outlets_subset.py | Python | bsd-2-clause | 2,097 | [
"VTK"
] | 2c0d18cd4a479c7077f28779bcc14b1d70926302c84afb9ad783680d2a57ca60 |
""" The SGE TimeLeft utility interrogates the SGE batch system for the
current CPU consumed, as well as its limit.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import os
import re
import time
import socket
from DIRAC import S_... | yujikato/DIRAC | src/DIRAC/Resources/Computing/BatchSystems/TimeLeft/SGEResourceUsage.py | Python | gpl-3.0 | 4,360 | [
"DIRAC"
] | 4401182489b1828c8f9fce639a7a9c5c27bea9f0b2109ec9dfbe6fd1ca8c8845 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/input_tab/OutputNames/test_OutputNames.py | Python | lgpl-2.1 | 4,243 | [
"MOOSE"
] | 1a536ecaa03693cebd8827b1adebac57cb46e839097dc02303801134d6d6f9a2 |
from rest_framework import serializers
from cocomapapp.models import Tag, Topic, Post, Relation, Vote, Visit
from django.contrib.auth.models import User
from rest_framework_bulk import (BulkListSerializer, BulkSerializerMixin)
class RelationSerializer(serializers.ModelSerializer):
class Meta:
model = Relat... | bounswe/bounswe2016group11 | cocomapapp/serializers.py | Python | apache-2.0 | 3,232 | [
"VisIt"
] | 33b7c10b3f19ca710b0fd726101e327fbc9120be143a528697b284165400f685 |
# -*- coding: utf-8 -*-
"""Tests for the HTML summary assembler."""
import os
import tempfile
import unittest
from pybel.examples import sialic_acid_graph
try:
import bio2bel_hgnc
import bio2bel_entrez
except ImportError:
bio2bel_hgnc = None
bio2bel_entrez = None
class TestSummaryAssembler(unittes... | pybel/pybel-tools | tests/test_assemblers/test_summary_html.py | Python | mit | 1,535 | [
"Pybel"
] | 5a74d6265717fda0d9f056734b51f2136f45784caafa7e274b3de28bcbc1a58b |
# Copyright 2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
import sys
import os
import re
import csv
import copy
import warnings
from optparse import OptionParser
from gnuradio import filter
try:
import numpy as np
except ImportError:
... | trabucayre/gnuradio | gr-filter/python/filter/design/filter_design.py | Python | gpl-3.0 | 90,858 | [
"Gaussian"
] | 6267ebd9c311c1e75ad283e0fb91cb962d6cd03c15385c36e00d5ff82fc17aab |
# Variables used throughout
# Think of them as 'Global-ish'
# Settings
settings_list = []
SFX = 0
MUSIC = 1
PARTICLES = 2
WORLD_UNLOCKED = 3
SENSITIVITY = 4
SETTING_FULLSCREEN = 5
# MUSIC
MENU_MUSIC = 0
WORLD_ONE = 1
WORLD_TWO = 2
WORLD_THREE = 3
BOSS_MUSIC = 4
# Screen resolution stuff here
SCREEN_WIDTH = 1024
SCR... | JoshuaSkelly/TroubleInCloudLand | utils/settings.py | Python | mit | 2,861 | [
"ESPResSo"
] | 18cd42d9d8c36b469cfb8b4dc61859ed9077559a70b9bdccef6fe07e107eea19 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
import logging
import shutil
import subprocess
import tempfile
import textwrap
import filecmp
import pytest
from unittest import TestCase, skip, TestLoader, TextTestRunner
from urllib.parse import urlparse
from uuid import uuid4
import os, sys
import argparse
import collectio... | ekg/vg | vgci/vgci.py | Python | mit | 69,869 | [
"BWA"
] | f70ee577fe600c6f775cd520f7d07c7aef9f17d0068d6f3ceb8dcfde3518db90 |
"""Class to generate redmagic randoms"""
import os
import copy
import numpy as np
import healsparse
from ..configuration import Configuration
from ..catalog import Catalog
from ..galaxy import GalaxyCatalog
from ..volumelimit import VolumeLimitMask
class RedmagicGenerateRandoms(object):
"""
Class to generate ... | erykoff/redmapper | redmapper/redmagic/redmagic_randoms.py | Python | apache-2.0 | 4,548 | [
"Galaxy"
] | 5e9af54650b451235cfddb51253af4564198a01e60472e84ef31b7c5e0581ac1 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | dilwaria/thoughtconcert | config/urls.py | Python | mit | 1,610 | [
"VisIt"
] | b8fbc705e85f2f8763e3b6ca94b3bfd34f72387ca3a7ff38f3f25b19148bf938 |
#!/usr/bin/env python
# Copyright (C) 2014. Ben Pruitt & Nick Conway
# See LICENSE for full GPLv2 license.
#
# 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
... | Wyss/mascpcr | setup.py | Python | gpl-2.0 | 2,882 | [
"Biopython"
] | c40a20cc933d388ec570bcf49bb1d49f70a7f9c7b3507ca8a09c23e7187b47f6 |
import math
import time
import random
import struct
import numpy as np
from numba import jit
from ibex.utilities import dataIO
from ibex.utilities.constants import *
from ibex.graphs.biological.util import CreateDirectoryStructure, ExtractExample, GenerateExamplesArray, ScaleFeature
@jit(nopython=True)
def Extra... | bmatejek/ibex | graphs/biological/edge_generation.py | Python | mit | 18,935 | [
"NEURON"
] | 16619ca7daa4ca72108e8b671e932ab153e385c1fb780c1d17452d670f5c7178 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
##from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
##import hrl_lib.mayavi2_util as mu
import hrl_lib.vi... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/multivariate_gaussian_emissions/hmm_crossvalidation_force_motion_10_states_scaled_wrt_all_data.py | Python | mit | 18,213 | [
"Gaussian",
"Mayavi"
] | d6ccae5c3e80101f44545a18fabb645024215f12429411dc596b6c9c5527798f |
import sys
import vtk
import ca_smoothing
stl = vtk.vtkSTLReader()
stl.SetFileName(sys.argv[1])
stl.Update()
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(stl.GetOutputPort())
normals.ComputeCellNormalsOn()
normals.Update()
clean = vtk.vtkCleanPolyData()
clean.SetInputConnection(normals.GetOutputPor... | tfmoraes/python-casmoothing | test_python_wrapper.py | Python | gpl-2.0 | 523 | [
"VTK"
] | 41bb1c2b0c6851db40cc32e73aa75ecd7228b39c751c75596c2bd9e729b247d0 |
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