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from __future__ import division, print_function, absolute_import
import sys
from random import randint, random, shuffle
from turtle import TurtleScreen, RawTurtle, TK
from contextlib import contextmanager
if sys.version_info[0] < 3:
from Tkinter import Tk, mainloop
else:
from tkinter import Tk
mainloop =... | AllTheWayDown/turtlepower | turtlepower/world.py | Python | mit | 6,489 | [
"Gaussian"
] | bdfa75073ea2fa53be21d4d575e435e86dacdb0e7299c0751a61d6fb234f383c |
#!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICU... | cigani/NEST | L5_TTPC1_cADpyr232_1/run_RmpRiTau.py | Python | mit | 7,100 | [
"NEURON",
"VisIt"
] | 5a624841d76bf75ff8b219cefcb6c527597beceec46ab4889fb85910ba0e05c0 |
__author__ = 'Ahmed Hani Ibrahim'
import abc
class LearningAlgorithm(object):
# __metaclass__ = abc.ABCMeta
@abc.abstractmethod
def learn(self, learningRate, input, output, network):
"""
:param learningRate: double
:param input: list
:param output: list
:param netwo... | AhmedHani/Python-Neural-Networks-API | OptimizationAlgorithms/LearningAlgorithm.py | Python | mit | 390 | [
"NEURON"
] | afaa744f25ff5037c8e86530d6df47d563d32c007a14f3d5094a2415094cb0d4 |
# -*- coding: utf-8 -*-
"""
Created on Thu Jul 16 01:26:31 2015
Plot the rms of 'gradient' of two intensity edges/vectors shifted by a lag k
@author: sweel
"""
import matplotlib.pyplot as plt
import os
import cPickle as pickle
import seaborn as sns
import pandas as pd
from collections import defaultdict
from tubule_het... | moosekaka/sweepython | tubule_het/rfp_analysis/lagsplotrfp.py | Python | mit | 4,064 | [
"VTK"
] | f6b05fb88dc598ced1b87aeb3e69b79154de8a22aaeb5a4306f9dc765d60490f |
#!/usr/bin/python
# Author: Ary Pablo Batista <arypbatista@gmail.com>
"""
This file is part of JSGobstones.
JSGobstones 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 Licen... | lalo73/JSGobstones | compile.py | Python | gpl-3.0 | 7,657 | [
"GULP"
] | 1dd9543bea83f209ce70349c6baf02a9270142a28b770b40f6a37a2b7ca5d5a3 |
# This file is part of OpenHatch.
# Copyright (C) 2010 Parker Phinney
# Copyright (C) 2010 Jack Grigg
# Copyright (C) 2009, 2010 OpenHatch, Inc.
# Copyright (C) 2010 Jessica McKellar
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as... | jledbetter/openhatch | mysite/search/tests.py | Python | agpl-3.0 | 66,967 | [
"VisIt"
] | dbbe2b3100b756ce4da1b3ed0549ff0dce94634819aacb717f1fb4c008eaf8b5 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Christopher M. Bruns
# Contributors: Robert McGibbon, Jason Sw... | casawa/mdtraj | mdtraj/core/element.py | Python | lgpl-2.1 | 15,631 | [
"MDTraj",
"OpenMM"
] | ee91a3ffc21c7a06e42ea6a4845c0d892f31fb29dcf1fe8583a7b999d8d06430 |
#!/usr/bin/env python
"""
An example of how to modify the data visualized via an interactive dialog.
A dialog is created via `TraitsUI
<http://code.enthought.com/projects/traits/>`_ from an object (MyModel).
Some attributes of the objects are represented on the dialog: first a
Mayavi scene, that will host our visuali... | dmsurti/mayavi | examples/mayavi/interactive/mlab_interactive_dialog.py | Python | bsd-3-clause | 2,716 | [
"Mayavi"
] | 5e7bfd13064b69d6d1cd3e636fb7df00e624509b00008f06187dd9a5e72d1aa2 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# 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 l... | fingeronthebutton/RIDE | src/robotide/lib/robot/model/tagstatistics.py | Python | apache-2.0 | 5,149 | [
"VisIt"
] | b57d669e675e49f97d321a3339cdae420eb4405bcd0bb087bd9bf9f22829d0d4 |
print('Will plot single galaxy luminosity density profiles')
import astropy.table as table
from defcuts import *
from def_get_mags import *
from my_def_plots import *
from defflags import many_flags
import matplotlib.pyplot as plt
indir='/Users/amandanewmark/repositories/galaxy_dark_matter/GAH/'
outdir='/Users/ama... | anewmark/galaxy_dark_matter | not currently in use/call_get_mags.py | Python | mit | 2,488 | [
"Galaxy"
] | f33dd84b7f585ea14655ae34e6a4ef7f60729ea6fc315a8045b7a4d50690b50a |
NEW_REQUEST_EMAIL_TEXT="""
Hello LiPAD Admins,
A new {} request has been submitted. You can view the request using the following link:
{}
"""
NEW_REQUEST_EMAIL_HTML="""
<p>Hello LiPAD Admins,</p>
<p>A new {} request has been submitted. You can view the request using the following link:</p>
... | PhilLidar-DAD/geonode | geonode/datarequests/email_utils.py | Python | gpl-3.0 | 9,512 | [
"VisIt"
] | ce988d91919c0754621058d486811aa3b0962bff7482fde94ca4dd33d0746679 |
input_name = '../examples/navier_stokes/navier_stokes2d.py'
output_name = 'test_navier_stokes2d.vtk'
from tests_basic import TestInput
class Test(TestInput):
pass
| RexFuzzle/sfepy | tests/test_input_navier_stokes2d.py | Python | bsd-3-clause | 168 | [
"VTK"
] | c2ec8011d57d289601045b1d7da51a4580a2287c051885276e7509d4f638131d |
import os
import pathlib
import tempfile
import time
import tracemalloc
import dufte
import matplotlib.pyplot as plt
import meshzoo
import numpy as np
import meshio
def generate_triangular_mesh():
p = pathlib.Path("sphere.xdmf")
if pathlib.Path.is_file(p):
mesh = meshio.read(p)
else:
poi... | nschloe/meshio | tests/performance.py | Python | mit | 11,085 | [
"VTK"
] | 6407bc1edd04fc0ea685a88a0eb8affbc334ca1e2f95d8b2d6cd8f68a74eca07 |
import random
import numpy as np
import matplotlib.pyplot as plt
import sklearn
import cv2
import re, os, glob, pickle, shutil
import random
import Config
class POM_room(object):
#def __init__(self,pom_file_path,parts_root_folder,img_index_list,n_parts,resize_pom = 4,cameras_list = range(7),HW_grid = (-1,-1),... | pierrebaque/DeepOcclusion | pom_room.py | Python | gpl-3.0 | 10,978 | [
"Gaussian"
] | fcb78ab3f36f3886737473355f81150d4294be5554cd1a9157baf84d20fb4a73 |
"""
==========================
FastICA on 2D point clouds
==========================
Illustrate visually the results of :ref:`ICA` vs :ref:`PCA` in the
feature space.
Representing ICA in the feature space gives the view of 'geometric ICA':
ICA is an algorithm that finds directions in the feature space
corresponding t... | cdegroc/scikit-learn | examples/decomposition/plot_ica_vs_pca.py | Python | bsd-3-clause | 3,177 | [
"Gaussian"
] | f05d6bd1a30e4e8bcb1bc26d1fa81d1606a87449f221b004353d80e1214d196c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Run the script for details of the licence
# or refer to the notice section later in the file.
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#!<^DATA
#!<^CON... | janosgyerik/gtd-cli-py | ikog.py | Python | gpl-3.0 | 101,858 | [
"VisIt"
] | d8d8919f3f987043af09279b17c7a081e6f058e2de7204dd09efee632a317041 |
""" Contains the ModeController class."""
# mode_controller.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
# Documentation and more info at http://missionpinball.com/mpf
import logging
import os
from collections impo... | qcapen/mpf | mpf/system/mode_controller.py | Python | mit | 13,060 | [
"Brian"
] | f8d2c229faef888b10b1e2cee781ca8c2ebaccc03ba8de2be9679da1c26f2fcc |
# coding=utf-8
from ladybug.epw import EPW
from ladybug.datacollection import HourlyContinuousCollection, MonthlyCollection
from ladybug.designday import DesignDay
from ladybug.analysisperiod import AnalysisPeriod
import os
import pytest
def test_import_epw():
"""Test import standard epw."""
relative_path = ... | ladybug-analysis-tools/ladybug | tests/epw_test.py | Python | gpl-3.0 | 16,256 | [
"EPW"
] | 19ae1f28bc1efc5e525a1c6ec157347cb0b1d7e4a23c97594b96ca7961e890f1 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/StillingerWeberPairTermCapped.py | Python | gpl-3.0 | 8,215 | [
"ESPResSo"
] | 981007c352dfce3b583c201ccdd20300780fc8fbffc69eaa0809db5a476fa705 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import functools
import glob
import itertools
import jinja2
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import sys
import time
import urllib2
import zlib
from xml.etree import ElementTree
from cStringIO ... | ahu-odoo/odoo | addons/web/controllers/main.py | Python | agpl-3.0 | 67,498 | [
"VisIt"
] | c0bf53c57a48426c954751ddc3350cd813ee6f5edd4bfd21e5a3f35215c3e0b3 |
#
# 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/test/bigdl/orca/data/test_read_parquet_images.py | Python | apache-2.0 | 5,390 | [
"ORCA"
] | be9bd7a45259f7886b42974254d2c50ce7a2daa1ff679c1cbdd91ae2e85164eb |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/ui/thememanager.py | Python | gpl-2.0 | 39,562 | [
"Brian"
] | decde9864c897da8741200ddc0aad67441278c7304b8181e3549e54fae25b371 |
# coding: utf-8
#
# Copyright 2021 The Oppia 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 requi... | brianrodri/oppia | scripts/run_mypy_checks.py | Python | apache-2.0 | 19,119 | [
"VisIt"
] | 33c0b49c2556fffc0dbd4f0823ab9652d969b4887101b5712c156bc16e67265f |
# Licensed under the MIT License - see LICENSE.rst
"""
Methods for fitting transit light curves, spot occultations, or both, using
`scipy` minimizers and `emcee`.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import numpy as np
import emcee
from scipy ... | bmorris3/friedrich | friedrich/fitting.py | Python | mit | 16,547 | [
"Gaussian"
] | 8ea8482fc88f30002118c582815ef2391aa91d6d0bc3f205c5c617c73d34c1fc |
""" Test class for SiteDirector
"""
# pylint: disable=protected-access
# imports
import datetime
import pytest
from mock import MagicMock
from DIRAC import gLogger
# sut
from DIRAC.WorkloadManagementSystem.Agent.SiteDirector import SiteDirector
mockAM = MagicMock()
mockGCReply = MagicMock()
mockGCReply.return_value... | DIRACGrid/DIRAC | src/DIRAC/WorkloadManagementSystem/Agent/test/Test_Agent_SiteDirector.py | Python | gpl-3.0 | 7,215 | [
"DIRAC"
] | 8f74571b0ac8f863e2c3934a521cf2c5cb285e1ba8c41b01470488d93167f9ce |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals
from __future__ import absolute_import
"""
This module provides a base class, SQTensor, and associated methods for
creating and manipulating sq... | migueldiascosta/pymatgen | pymatgen/analysis/elasticity/tensors.py | Python | mit | 5,963 | [
"pymatgen"
] | 4c636bf608b5e304f4d608355566b2e150a5246eb05784df21c973d9807d71d1 |
"""
test_gaussian.py: Test suite for the Gaussian estimator class :class:`GaussEst`
"""
from __future__ import print_function
import unittest
import numpy as np
# Add the path to the vampyre package and import it
import env
env.add_vp_path()
import vampyre as vp
def lin_test(zshape=(500,10),Ashape=(1000,50... | GAMPTeam/vampyre | test/test_estim/test_linear.py | Python | mit | 2,552 | [
"Gaussian"
] | 586aa8b3c7624114a45df66469cb2eacfb4d8c95d3de6174148003060e8bedf1 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2017 Lenovo, Inc.
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# ... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/network/lenovo/cnos_reload.py | Python | bsd-3-clause | 4,936 | [
"VisIt"
] | ba139d4eadeeb13bd200cf8af31034e3cd49bbf7fbe53ba36898a0ffe4205114 |
import ocl
import camvtk
import time
import vtk
import datetime
import math
import random
def drawVertex(myscreen, p, vertexColor, rad=1):
myscreen.addActor( camvtk.Sphere( center=(p.x,p.y,p.z), radius=rad, color=vertexColor ) )
def drawEdge(myscreen, e, edgeColor=camvtk.yellow):
p1 = e[0]
p2 = e[1]
m... | AlanZatarain/opencamlib | scripts/voronoi/voronoi_4.py | Python | gpl-3.0 | 7,252 | [
"VTK"
] | b0cf7c1c7dab5dbebb9060fff978cf01529c20f3ecfe5c96f4a1e4bea8bb18bb |
import copy
import pymc3 as pm
import numpy as np
import seaborn as sns
import theano
import theano.tensor
import matplotlib.pyplot as plt
from Unfolder.Histogram import H1D, H2D, plotH1D, plotH2D, plotH1DWithText, plotH2DWithText, plotH1DLines
from Unfolder.ComparisonHelpers import getDataFromModel
from scipy import... | daniloefl/Unfolder | Unfolder/Unfolder.py | Python | gpl-3.0 | 51,758 | [
"Gaussian"
] | e4879a9f6f2f3350a4c479e71c83719571838e6c1cbeec3de44b8fce91d7487b |
from django.test import TestCase
from rest_framework.serializers import ValidationError
from push_notifications.api.rest_framework import APNSDeviceSerializer, GCMDeviceSerializer
GCM_DRF_INVALID_HEX_ERROR = {'device_id': [u"Device ID is not a valid hex number"]}
GCM_DRF_OUT_OF_RANGE_ERROR = {'device_id': [u"Device I... | hylje/django-push-notifications | tests/test_rest_framework.py | Python | mit | 3,845 | [
"Galaxy"
] | dc3679e19c765b1cd2e05e5a683697cc82ea856da27629a79b4758bf0f553d4a |
from __future__ import print_function, division
from sympy.core import S, sympify, Dummy, Mod
from sympy.core.function import Function, ArgumentIndexError
from sympy.core.logic import fuzzy_and
from sympy.core.numbers import Integer, pi
from sympy.core.relational import Eq
from sympy.ntheory import sieve
from math i... | ChristinaZografou/sympy | sympy/functions/combinatorial/factorials.py | Python | bsd-3-clause | 27,826 | [
"VisIt"
] | dac60b72fd765d39153d4ba10bfd94224133d27f9b5ac421061fdb7e27d0f371 |
import os
import uuid
import tempfile
import tornado.process
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Core.Security import Locations, X509Chain
BASECS = "/WebApp"
def getCSValue( opt, defValue = None ):
return gConfig.getValue( "%s/%s" % ( BASECS, opt ), defValue )
def getTitle():
defVal = gConfig.ge... | chaen/WebAppDIRAC | Lib/Conf.py | Python | gpl-3.0 | 2,817 | [
"DIRAC"
] | 7d6ae31e21c8d9602f62a11177a10385e3efe6afe7b3af48dba8ab0369446cb4 |
#!/home/OSUMC.EDU/blac96/source/venv/test_mucor_pip/bin/python
# -*- coding: utf8
# Copyright 2013-2015 James S Blachly, MD and The Ohio State University
#
# This file is part of Mucor.
#
# Mucor is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License a... | blachlylab/mucor | build/scripts-2.7/depth_gauge.py | Python | gpl-3.0 | 13,906 | [
"HTSeq",
"pysam"
] | 9e177e692979303a567f123403e89d9bb626b1f689eba9c3f433856b4deda818 |
# 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... | dhalleine/tensorflow | tensorflow/contrib/distributions/python/ops/normal.py | Python | apache-2.0 | 11,692 | [
"Gaussian"
] | 886120d94f30c90a7c08ac6775f80973034b0cbc688fa271b05a827ad7d81f98 |
"""
Gaussian Mixture Models.
This implementation corresponds to frequentist (non-Bayesian) formulation
of Gaussian Mixture Models.
"""
# Author: Ron Weiss <ronweiss@gmail.com>
# Fabian Pedregosa <fabian.pedregosa@inria.fr>
# Bertrand Thirion <bertrand.thirion@inria.fr>
import warnings
import numpy as... | loli/semisupervisedforests | sklearn/mixture/gmm.py | Python | bsd-3-clause | 27,512 | [
"Gaussian"
] | 8b9d808b1af8d8baa4a5963eb6c691e0c0c6766295ae4634d0b4965c190a75d6 |
# -*- coding: utf-8 -*-
"""test_table_streaming_support.py:
Test the streaming support in moose.Table.
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2016, Dilawar Singh"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ = "1.0.0"
__maintain... | dilawar/moose-core | tests/core/test_table_streaming_support.py | Python | gpl-3.0 | 4,468 | [
"MOOSE"
] | 28ec4482872c80cd210dd49efac528502533806d09e32a24c83db8a0f6a0b27d |
from bs_utils.utils import *
def wg_build(fasta_file, build_command, ref_path, aligner):
# ref_path is a string that contains the directory where the reference genomes are stored with
# the input Fasta filename appended
ref_path = os.path.join(ref_path,
os.path.split(fasta_fil... | BioInfoTools/BSVF | bin/BSseeker2/bs_index/wg_build.py | Python | lgpl-3.0 | 2,085 | [
"Bowtie"
] | 3329c6f5dea11365c9314ae6b08701b72a4019a5c520880bcb8a780156a7a489 |
"""
Generalized Linear Models with Exponential Dispersion Family
"""
# Author: Christian Lorentzen <lorentzen.ch@googlemail.com>
# some parts and tricks stolen from other sklearn files.
# License: BSD 3 clause
import numbers
import numpy as np
import scipy.optimize
from ...base import BaseEstimator, RegressorMixin
... | bnaul/scikit-learn | sklearn/linear_model/_glm/glm.py | Python | bsd-3-clause | 24,806 | [
"Gaussian"
] | ec13a2ec31d95b79e8281d7fd3aff31ef637285d383f2a795375a34d7b4fcc52 |
""" ResourceStatus
Module use to switch between the CS and the RSS.
"""
from datetime import datetime, timedelta
import math
from time import sleep
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.DIRACSingleton import ... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Client/ResourceStatus.py | Python | gpl-3.0 | 13,788 | [
"DIRAC"
] | e6dbe818be9f746a3f3ea6e6f5a121f0285bac94cfbd1c1529f94adab5d04160 |
# -*- coding: utf-8 -*-
#
# nistats documentation build configuration file, created by
# sphinx-quickstart on Fri Jan 8 09:13:42 2010.
#
# This file is execfile()d with the current directory set to its containing
# dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# A... | bthirion/nistats | doc/conf.py | Python | bsd-3-clause | 10,477 | [
"Mayavi"
] | 999674021c26e7d13a29db6105181c02f830041b8534bb347c7d2405d8309899 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/settings/AppSettings.py | Python | gpl-3.0 | 17,609 | [
"ORCA"
] | c35f30b76bcdbc2fa99707ecb104a3e6dcb7bf223ffe341d4ab8277fc43f147e |
#!/bin/env python
"""Script to call the DataRecoveryAgent functionality by hand."""
from DIRAC import S_OK, gLogger
from DIRAC.Core.Base import Script
__RCSID__ = '$Id$'
class Params(object):
"""Collection of Parameters set via CLI switches."""
def __init__(self):
self.enabled = False
self.transID = 0
... | andresailer/DIRAC | TransformationSystem/scripts/dirac-transformation-recover-data.py | Python | gpl-3.0 | 1,938 | [
"DIRAC"
] | bd9917537e0122ad8c1b8521989035d002345e672dbc30732bd5f54dd7f2e13f |
# -*- coding: utf-8 -*-
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2003-2005 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 lcc & Robert Jerome
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General... | sam-m888/gprime | gprime/plugins/rel/rel_pt.py | Python | gpl-2.0 | 19,304 | [
"Brian"
] | c9f2ea7e94c2af90138c80487e8df99262c0f77c30607b934817823a497a9a9f |
#!/usr/bin/env python
import pysam
import sys
inFileName = sys.argv[1]
bamFile = pysam.Samfile(sys.argv[2])
outFile = open(sys.argv[3], 'w')
if (inFileName == "stdin"):
inFile = sys.stdin
else:
inFile = open(inFileName)
for line in inFile.readlines():
region = line.split()
sup = bamFile.count(regio... | yunlongliukm/chm1_scripts | one_off/AddCoverage.py | Python | mit | 481 | [
"pysam"
] | 869cd8904f1a18b09f691e6ca27dfebc8a1f93cabe32843818ba4b0943a061bb |
#!/usr/bin/env python
import sys
import netCDF4 as nc
import numpy as np
import time
from tvtk.api import tvtk
from tvtk.tools import mlab
from tvtk.common import configure_input_data
def normalise_lons(lons):
"""
Make a copy of lons that is between -180 and 180.
"""
lons_n = np.copy(lons)
lons_... | nicjhan/mom-particles | vtk/velocity.py | Python | gpl-2.0 | 3,433 | [
"VTK"
] | 5ad7434a4a3d482c5be5eace9e897f09fac1de16def56d26e614e2357226a4be |
# -*- coding: utf-8 -*-
"""
pysteps.timeseries.autoregression
=================================
Methods related to autoregressive AR(p) models.
.. autosummary::
:toctree: ../generated/
adjust_lag2_corrcoef1
adjust_lag2_corrcoef2
ar_acf
estimate_ar_params_ols
estimate_ar_params_ols_localized
... | pySTEPS/pysteps | pysteps/timeseries/autoregression.py | Python | bsd-3-clause | 39,864 | [
"Gaussian"
] | d76817941f538da74503e5d3cb8c90cd3f659154346b4abead766631477c786f |
#
# Copyright 2014-2017 University of Southern California
# Distributed under the (new) BSD License. See LICENSE.txt for more info.
#
import re
import sys
import os
import csv
import random
import tempfile
import numpy as np
from numpy import array, float32, int32, empty, newaxis, dot, cross, zeros, ones
from numpy.l... | informatics-isi-edu/synspy | synspy/analyze/util.py | Python | bsd-3-clause | 18,746 | [
"Gaussian"
] | fb90f385a9f375df2c67e57e04b07989436d0ea4267a8a0214b52d50c3214736 |
#!/usr/bin/env python
#
# Copyright (c) 2012 OpenDNS, Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this... | hlindqvist/pdns | regression-tests.dnsdist/clientsubnetoption.py | Python | gpl-2.0 | 11,549 | [
"Brian"
] | 31b073ace28955d44c7dd59b92ed48778a9f93a8afe5c5872ef88c2235b54384 |
from sequana import sequana_data
from multiqc.utils import report
try:
# Since sept 2017 and a bioconda travis integrationupdate,
# this test fails due to an error in spectra/colormath:
# self.conversion_graph.add_edge(start_type, target_type,
# {'conversion_function': conversion_function})
... | sequana/sequana | test/multiqc/test_multiqc.py | Python | bsd-3-clause | 2,465 | [
"Bioconda"
] | f5b40d62351260ded1c24ff31ddc42358b86e97186c17e0fbc5af90d5ba89e72 |
#!/usr/bin/env python
import pysam
import numpy as np
import argparse
import sys
ap = argparse.ArgumentParser(description="Compute expected insert size")
ap.add_argument("bam", help="Input bam file.")
ap.add_argument("-n", help="Num samples", type=int, default=100000)
ap.add_argument("-M", help="Max isize", type=int... | yunlongliukm/chm1_scripts | ComputeCloneSize.py | Python | mit | 1,403 | [
"pysam"
] | d52516c49ccc782a866af97323a76e882769a7165ff4268bdc10af97e4a0a0ee |
#!/usr/bin/env python
#
# $File: PyExec.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute it ... | BoPeng/simuPOP | docs/PyExec.py | Python | gpl-2.0 | 1,527 | [
"VisIt"
] | 57680249b223d8a744ac5a9bb19bdde8be245acceb92eb0a43a78e6f032aaaaa |
import pysam
def data_points(file_path, start, stop, chrm, step, size):
start, stop, step, size = int(start), int(stop), int(step), int(size)
points = []
w_size = (stop-start)/size
print "compute(): w_size = %s" % w_size
tabixfile = pysam.Tabixfile(file_path)
i_start = start
for i in rang... | drio/bedserver | bedserver/compute.py | Python | mit | 807 | [
"pysam"
] | ec232e766ca971fee1a8c6adc4900bb25b8d342dde15664d583f84fe6c060889 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module contains an algorithm to solve the Linear Assignment Problem.
It has the same functionality as linear_assignment.pyx, but is much slower
as it is vectorized in numpy rather than cython
"""
__a... | fraricci/pymatgen | pymatgen/optimization/linear_assignment_numpy.py | Python | mit | 8,160 | [
"pymatgen"
] | 19f15a2a701339b4381348709ddeb333a2688bae209d4b46d8703ea8db37fae5 |
"""
Utilities to create replication transformations
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import six
from DIRAC.TransformationSystem.Client.Transformation import Transformation
from DIRAC import gLogger, S_OK, S_ERROR
def createDataTransforma... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Utilities/ReplicationTransformation.py | Python | gpl-3.0 | 3,787 | [
"DIRAC"
] | faeb006fc7bc2dcb6d9574dca83d9177d4df080de0e3099af68dd0255f55912f |
"""Models
This module documented some training models
+ Feedforward Neural Network (including ConvNets)
"""
from telaugesa.optimize import corrupt_input;
from telaugesa.optimize import apply_dropout;
class FeedForward(object):
"""Feedforward Neural Network model"""
def __init__(self,
l... | duguyue100/telaugesa | telaugesa/model.py | Python | mit | 6,718 | [
"Gaussian"
] | c95ebe83d749529dea8576dfb8abf5c03e43a22f2a48bf92a32736512f571a27 |
#!/usr/bin/env python
#
# spyne - Copyright (C) Spyne contributors.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later ve... | arskom/spyne | spyne/test/interface/wsdl/test_op_req_suffix.py | Python | lgpl-2.1 | 11,091 | [
"NAMD"
] | d7f4e36c8ec935e655723398269ceb03132c1038f09fcc5fd74368d12499c292 |
# Copyright 2013-2017, Brian May
#
# This file is part of python-alogger.
#
# python-alogger 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 ver... | Karaage-Cluster/python-alogger | alogger/tests/test_sge.py | Python | gpl-3.0 | 900 | [
"Brian"
] | c5f615f6f31b3cdff3f87d946fe92370e442295cd5c5ae9d3aba74e9a6ab4f53 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""A writer for chemical JSON (CJSON) files."""
import os.path
import json
import numpy as np
from cclib.io import filew... | cclib/cclib | cclib/io/cjsonwriter.py | Python | bsd-3-clause | 9,713 | [
"Open Babel",
"cclib"
] | 12d319a890860d5e9cc59eea153208518f76863f700fe1d16f794f53817a677e |
# $HeadURL$
""" Queries BDII for unknown CE.
Queries BDII for CE information and puts it to CS.
"""
__RCSID__ = "$Id$"
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.Core.Utilities ... | calancha/DIRAC | ConfigurationSystem/Agent/CE2CSAgent.py | Python | gpl-3.0 | 21,025 | [
"DIRAC"
] | 863893d778521d580e21f589cd20d62bae5ec36383a3777eba3927fbbb8be2c7 |
# -*- coding: utf-8 -*-
"""
celery.datastructures
~~~~~~~~~~~~~~~~~~~~~
Custom types and data structures.
"""
from __future__ import absolute_import
from __future__ import with_statement
import sys
import time
from collections import defaultdict
from itertools import chain
from billiard.einfo import Ex... | mozilla/firefox-flicks | vendor-local/lib/python/celery/datastructures.py | Python | bsd-3-clause | 12,131 | [
"VisIt"
] | 737af31fe4841f9f9ddaf7f76e9f75fb2490452b4c2951c5b49a695ba9b5f7fa |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/oif_volume_conservation.py | Python | gpl-3.0 | 2,842 | [
"ESPResSo",
"VTK"
] | 13c6293cae008b9aede4f67eebac2dbde356a31fef89aced2e1330a2b2864281 |
import unittest
from pymatgen.core import Structure
from veidt.monte_carlo.base import StateDict, StaticState
from veidt.monte_carlo.state import AtomNumberState, IsingState
from veidt.monte_carlo.state import SpinStructure, Chain
import os
file_path = os.path.dirname(__file__)
def unequal_site_number(list1, list2):... | materialsvirtuallab/veidt | veidt/monte_carlo/tests/test_states.py | Python | bsd-3-clause | 3,311 | [
"pymatgen"
] | a7b91100050cb09537b7f17f54de4faaceee93ef21fd69beea64b2ccf371e1c5 |
#!/usr/bin/env python
# tgraph - a python based program to plot 1D and 2D data files
# Copyright (C) 2015 Wolfgang Tichy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of th... | wofti/tgraph | tgraph.py | Python | gpl-3.0 | 39,501 | [
"VTK"
] | 52def3ca22ed93a5e2c029dfa315006a5bc2971319fec79e85e4dd39d70406bb |
'''
Neuromuscular simulator in Python.
Copyright (C) 2017 Renato Naville Watanabe
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
any late... | rnwatanabe/projectPR | PulseConductanceState.py | Python | gpl-3.0 | 7,133 | [
"NEURON"
] | 18dbcf6b26f29d38ef4ebedc082d1aa521dc6da6cbfa4a3347572ac9508a7f67 |
# Copyright 2021 Sony Group Corporation.
#
# 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 ... | sony/nnabla | python/test/utils/test_graph_converters/test_no_grad.py | Python | apache-2.0 | 1,701 | [
"VisIt"
] | 0e8ac53d6ac2112d230dc92b80b42840814f1269724cb7b283c5c1593f55a066 |
__author__ = 'jan'
import matplotlib.pyplot as plt
from prettyplotlib.utils import remove_chartjunk, maybe_get_ax
from prettyplotlib import colors as _colors
import numpy as np
import matplotlib.mlab as mlab
def _beeswarm(ax, x, notch=0, sym='b+', vert=1, whis=1.5,
positions=None, widths=None, patch_arti... | olgabot/prettyplotlib | prettyplotlib/_beeswarm.py | Python | mit | 12,196 | [
"Gaussian"
] | 862ee361544df23a32f1a8400418e201f9b358826f541a542dd0c5863fee83e3 |
# -*- coding: utf-8 -*-
# Copyright © 2012-2013 Roberto Alsina and others.
# Permission is hereby granted, free of charge, to any
# person obtaining a copy of this software and associated
# documentation files (the "Software"), to deal in the
# Software without restriction, including without limitation
# the rights t... | Proteus-tech/nikola | nikola/main.py | Python | mit | 6,777 | [
"VisIt"
] | 0f2adfc2d7934aca3468165e7380152faa4fc2876c5bfffa06048bf1cbe3b625 |
## Created 2012 by Scott Harden, AJ4VD
## Updated October 19, 2014 by Andrew Milluzzi, KK4LWR
## Edits:
## - Updated logging date
## Instructions: Update to start of Contest. See instructions on around line 130.
import sqlite3
import time
import pylab
import numpy
import datetime
def toListie(t):
for i in range... | swharden/pyHamLog | genstats.py | Python | gpl-2.0 | 5,380 | [
"Gaussian"
] | 75bbf819150b903c4f12e985d1f0b7b1cc602b06aafaabce268c2921a565391b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright: (c) 2014, Ruggero Marchei <ruggero.marchei@daemonzone.net>
# Copyright: (c) 2015, Brian Coca <bcoca@ansible.com>
# Copyright: (c) 2016-2017, Konstantin Shalygin <k0ste@k0ste.ru>
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING... | jtyr/ansible | lib/ansible/modules/find.py | Python | gpl-3.0 | 17,142 | [
"Brian"
] | dd47a61682a6074cfb10dda6586442a968f349bbcf5349f6baf984c62e667cb0 |
# -*- coding: utf-8 -*-
import numpy as np
from shapely.geometry.polygon import Polygon
import datetime
import netCDF4 as nc
import itertools
import geojson
from shapely.ops import cascaded_union
#from openclimategis.util.helpers import get_temp_path
#from openclimategis.util.toshp import OpenClimateShp
from shapely.ge... | OpenSource-/OpenClimateGIS | src/openclimategis/util/ncconv/experimental/OLD_experimental/in_memory_oo_update.py | Python | bsd-3-clause | 22,320 | [
"NetCDF"
] | ba13f904a59bdcb688ad7d0c3a6be17ec8bf5957052eff1237a36c2d1f7527fe |
# coding=utf-8
# Copyright 2020 The Google Research 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 applicab... | google-research/electra | model/modeling.py | Python | apache-2.0 | 39,858 | [
"Gaussian"
] | 8fef544eb179d8c9d89095760f76038f8d488d16edf0cc004d406d8848c2bf73 |
"""
potential.py
Experimental Data & Simulation Synthesis.
This file contains classes necessary for the integration of simulation and
experimental data. Specifically, it serves a Potential class used (by md.py
or mc.py) to run simulations. Further,
"""
import abc
import numpy as np
from mdtraj import Trajectory
... | tjlane/odin | src/python/potential.py | Python | gpl-2.0 | 6,842 | [
"MDTraj"
] | c7c6b97fe4e8ea5b3d62b9436f9c3387404c4d45f05ff784322d05acdae60710 |
from simulate import *
import matplotlib.pyplot as plt
class possum(simulate):
"""
Class for creating polarization and
faraday rotation spectra.
Frequency Coverages:
_createWSRT()
Frequency range for the Westerbork
Synthesis Radio Telescope
310 - 380 MHz
_createASKAP12()
ASKAP12 frequency cov... | sheabrown/faraday_complexity | final/possum.py | Python | mit | 4,428 | [
"Gaussian"
] | 346f0cef857aa26869ecc1dd12410ddb1f34abcda4913bf5e061b178ba2f2fee |
"""This script includes things common to the other included Python scripts
"""
import math
import os
import sys
#Constants as defined in ForceManII
ang2au=1.889725989
j2cal=4.184
kcalmol2au=1/627.5096
deg2rad=math.pi/180
k2au=kcalmol2au/(ang2au**2)
anglek2au=kcalmol2au
#Recognized param types
params={"k":"FManII::Par... | ryanmrichard/ForceManII | bin/FManII.py | Python | lgpl-3.0 | 3,164 | [
"TINKER"
] | 7f8ca7ecd51791c6925b585b314c45fdffba4a79cffdb2d4ba30d1dc13e90df4 |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | d7415/merlin | dumper.py | Python | gpl-2.0 | 12,137 | [
"Galaxy"
] | 7873c66c8acd851dacabbed16b9dd5bb4f912b10b183287690398b504f6db813 |
"""
Tests for generalized linear models. Majority of code either directly borrowed
or closely adapted from statsmodels package. Model results verfiied using glm
function in R and GLM function in statsmodels.
"""
__author__ = 'Taylor Oshan tayoshan@gmail.com'
from pysal.contrib.glm.glm import GLM
from pysal.contrib.gl... | TaylorOshan/pysal | pysal/contrib/glm/tests/test_glm.py | Python | bsd-3-clause | 67,888 | [
"COLUMBUS",
"Gaussian"
] | bce2a91db44c26edecd69400768880cf3c52be778861b27f2c9c8b3a5dc94503 |
"""testCount3.py.
Written by: Brian O'Dell, October 2017
A program to run each program a 500 times per thread count.
Then uses the data collected to make graphs and tables that
are useful to evaluate the programs running time.
"""
from subprocess import *
from numba import jit
import numpy as np
import csv as csv
im... | brian-o/CS-CourseWork | CS491/count3openMP/testCount3.py | Python | gpl-3.0 | 2,463 | [
"Brian"
] | 80536cb4fc47bfe07980ed7c1b14744c97268a9a83c893f37452f98b8d88c980 |
"""High level summaries of samples and programs with MultiQC.
https://github.com/ewels/MultiQC
"""
import collections
import glob
import mimetypes
import os
import pandas as pd
import shutil
import pybedtools
import toolz as tz
import yaml
from bcbio import utils
from bcbio.distributed.transaction import file_transa... | brainstorm/bcbio-nextgen | bcbio/qc/multiqc.py | Python | mit | 16,977 | [
"HTSeq"
] | e498f7ac31504ac5479fcd5ed3ad871225cf415ab98730226df09f66056faed6 |
import os
import csv
from paraview.simple import *
import xml.etree.ElementTree as ET
def ShowThresholdData(Data, ColourMapRange = None, NegativeThresholdValues = None, PositiveThresholdValues = None, ColourMapLegend = 'Sigma', BackgroundOpacityValue = 0.1, ScalarBarPos = None):
# create positive and negative th... | EIT-team/Reconstruction | src/python/ParaviewLoad/ShowData.py | Python | gpl-3.0 | 21,754 | [
"ParaView",
"VTK"
] | 7d4f0affc3bfbf2e0cbd908492c90b43741b5c9d7e790931686b5473fd005f9d |
import subprocess
import sys
import os
from collections import defaultdict
from scipy.interpolate import UnivariateSpline
from scipy.signal import fftconvolve
import numpy as np
import DataStructures
import Units
import RotBroad
import MakeModel_v2 as MakeModel
import FindContinuum
import FitsUtils
class Resid:
... | kgullikson88/TS23-Scripts | Correlate.temp.py | Python | gpl-3.0 | 15,540 | [
"Gaussian"
] | b865004e06df7a1edb4197e5d590f61ece30902c71dbc0d677b36a4a9475c311 |
# Some Attributes derived from the Eigenvalues of Orientation Tensor
#
# Calculates a series os attributes based on the eigenvalues of an orientation tensor
#
# Cline = (e2-e3)/(e2+e3) (Bakker, 2001)
# Cplane = (e1-e2)/(e1+e2) (Bakker, 2001)
# Cfault = Cline * (1 - Cplane) (Bakker, 2001)
# Cchaos = 4*e1*e3*(e1+e2+e3)/(... | waynegm/OpendTect-Plugins | bin/python/wmpy/Experimental/LocalPolynomialApproximation/ex_lpa_cvals.py | Python | gpl-3.0 | 3,302 | [
"Gaussian"
] | 5398766ca658009768ed5d3c1359d74aa27cf8c736be4eda685c3598300448a5 |
import numpy as np
from PIL import Image
from appJar import gui
from simple_operations.check_if_image_grey import check_if_image_grey
image_set = False
i = 0
# create a GUI variable
img_process_gui = gui("Image Processing")
img_process_gui.setGeometry("fullscreen")
img_process_gui.setBg("#c2c6c3")
img_process_gui.se... | vvvityaaa/PyImgProcess | GUI.py | Python | mit | 11,420 | [
"Gaussian"
] | 20ed6e089a645656add4e09a36637f10c38fd7da0f814948ab91967ee4ba24ff |
"""
============================================================
Empirical evaluation of the impact of k-means initialization
============================================================
Evaluate the ability of k-means initializations strategies to make
the algorithm convergence robust as measured by the relative stan... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/cluster/plot_kmeans_stability_low_dim_dense.py | Python | bsd-3-clause | 4,334 | [
"Gaussian"
] | 266a9a404e8f369d037d63056bb1a2e4a4fdd47e48c43388efdf58adb693a90d |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# -*- coding: utf-8 -*-
"""
Created on Thu Sep 29 2016
@author: violeta castelo-szekely
"""
import argparse, pysam, sys, subprocess, re
import numpy as np
transcripts= {}
tr_list = set()
sequences= {}
def get_length(sequence):
return len(sequence)
def get_gc_conte... | gatfieldlab/cross-organ_riboprof | data_analysis/transcript_features_v2.py | Python | gpl-3.0 | 5,088 | [
"pysam"
] | abb00d47dce6d113ebaeb17dd25f8e948cd3f68d6330c7a9e3ab097dbd37dfa3 |
# 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... | keras-team/keras | keras/layers/regularization/gaussian_noise_test.py | Python | apache-2.0 | 1,859 | [
"Gaussian"
] | af24fba55e76bf98f62f1875655f90a063a006d6fb0f2e12975c1ae9b3ee6805 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose | moose-examples/snippets/scriptKineticSolver.py | Python | gpl-3.0 | 4,443 | [
"MOOSE"
] | fd54cce007ba9c1013677ca4e68db8f8768f47a3a69e5e3934fbd3885dc06487 |
#!/usr/bin/env python2
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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,... | kkreis/espressopp | testsuite/FixedLocalTuple/TestFixedLocalTupleList.py | Python | gpl-3.0 | 4,612 | [
"ESPResSo"
] | f237168a098942402c43480622055db5917d4aa8fee3e5c499728811335ba531 |
#!/usr/bin/env python
import os
import sys
from glob import glob
sys.path.insert(0, os.path.abspath('lib'))
from ansible import __version__, __author__
try:
from setuptools import setup
except ImportError:
print "Ansible now needs setuptools in order to build. " + \
"Install it using your package ma... | pilwon/ansible | setup.py | Python | gpl-3.0 | 1,984 | [
"Galaxy"
] | b9760e2bcc167254a28609ee33e711efb91d14a2a43aaeb04dea8a2ac5c4de86 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program 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 F... | andrebellafronte/stoq | stoqlib/gui/wizards/loanwizard.py | Python | gpl-2.0 | 20,757 | [
"VisIt"
] | 4276fc0b15a3abcfb97caa035dbe9e402e8b923427586b401ffc901d7538f590 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | KonradBreitsprecher/espresso | testsuite/langevin_thermostat.py | Python | gpl-3.0 | 15,754 | [
"ESPResSo"
] | aa4d77a156e64903bfaddfa39bbc490b7ce5f2f0f4ca272197ceda5ea015ea2c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Licensed to Cloudera, Inc. under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. Cloudera, Inc. licenses this file
# to you under the Apache License, Version 2.0 (... | sanjeevtripurari/hue | apps/useradmin/src/useradmin/test_ldap_deprecated.py | Python | apache-2.0 | 33,296 | [
"MOE"
] | a24121088ffd23a9a32ea7d99edc60067856a19a6bfa4e17d352bc835c9aa9ee |
from hellosign_sdk.utils import HSRequest, HSException, NoAuthMethod, HSAccessTokenAuth, HSFormat, api_resource, api_resource_list
from hellosign_sdk.resource import Account, ApiApp, SignatureRequest, Template, Team, Embedded, UnclaimedDraft
from requests.auth import HTTPBasicAuth
import json
#
# The MIT License (MIT)... | HelloFax/hellosign-python-sdk | hellosign_sdk/hsclient.py | Python | mit | 106,053 | [
"VisIt"
] | 605075d73e0d94ebec2cb36aaaadd667da62b386a1ffc6fbdf12e5683b863136 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-affy/package.py | Python | lgpl-2.1 | 2,130 | [
"Bioconductor"
] | d27429d004ee61f27683cc5b9fbda9d1f135eefa7fae05180e4616ec68e01d6f |
# Copyright 2017 Max Planck Society
# Distributed under the BSD-3 Software license,
# (See accompanying file ./LICENSE.txt or copy at
# https://opensource.org/licenses/BSD-3-Clause)
"""Training AdaGAN on various datasets.
Refer to the arXiv paper 'AdaGAN: Boosting Generative Models'
Coded by Ilya Tolstikhin, Carl-Joha... | tolstikhin/adagan | iclr_celeba_began.py | Python | bsd-3-clause | 8,105 | [
"Gaussian"
] | d21b4c696e31ff48bcfc46aea6e75298aff5122cbeb9b10c12bda051dd67d46a |
#!/usr/bin/env python
## Program: VMTK
## Module: $RCSfile: vmtkadd.py,v $
## Language: Python
## Date: $Date: 2016/07/19 09:49:59 $
## Version: $Revision: 1.6 $
## Copyright (c) Jingfeng Jiang, Yu Wang. All rights reserved.
## See LICENCE file for details.
## This software is distributed... | jjiang-mtu/virtual-breast-project | quasi-static_UE/add_displacement/vmtkadd.py | Python | gpl-2.0 | 1,636 | [
"VTK"
] | 1a91e18cb5a5ec7063dc3c48c55bbb3c79690e2f0d35d4e77d3ac511e760fa1b |
"""Repository checks
These checks verify consistency with the repository (blacklisting,
other channels, existing versions).
"""
from .. import utils
from . import LintCheck, ERROR, WARNING, INFO
class in_other_channels(LintCheck):
"""A package of the same name already exists in another channel
Bioconda and ... | bioconda/bioconda-utils | bioconda_utils/lint/check_repo.py | Python | mit | 3,257 | [
"Bioconda"
] | f5e97d53d2ad8716c36b191e3125458a39695f52e9756a47b484cdc094c83e79 |
# Copyright 2001 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Parser for SAF (Simple Alignment Format).
http://www.embl-heidelberg.de/predictpr... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Saf/__init__.py | Python | apache-2.0 | 6,366 | [
"Biopython"
] | 0359936d8b5e9ff5b1ac971d4e0fc6e655b367b78b3e5da54d0b885e27af5891 |
from six import with_metaclass
import abc
import datetime
import tempfile
import os
from contextlib import contextmanager
from .tides import Tides
import numpy
ALL_FES2014_TIDAL_CONSTITUENTS = ["2N2", "EPS2", "J1", "K1", "K2", "L2", "M2", "M3", "M4", "M6", "M8",
"MF", "MKS2", "MM", "... | stephankramer/uptide | uptide/fes_interpolator.py | Python | lgpl-3.0 | 6,046 | [
"NetCDF"
] | b94fa3087228c08d34490375cf0c62c4d4acce5e9d1fa90798131c8b0fb8fa53 |
"""function y = ctemh_cryoFrank(k,params)
% from Kirkland, adapted for cryo (EMAN1) by P. Schwander
% Version V 1.1
% Copyright (c) UWM, Peter Schwander 2010 MATLAB version
% '''
% Copyright (c) Columbia University Hstau Liao 2018 (python version)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
... | hstau/covar-cryo | covariance/ctemh_cryoFrank.py | Python | gpl-2.0 | 1,344 | [
"Gaussian"
] | c599fd237c6a7edb13758383b325815284fb73bb935df6c97fc689216fbbb898 |
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