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"""Core visualization operations."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Eric Larson <larson.eric.d@gmail.com>
# Joan Massich <mailsik@gmail.com>
# Guillaume Favelier <guillaume.favelier@gmail.com>
#
# License: Simplified BSD
from contextlib import contextmanager
i... | Teekuningas/mne-python | mne/viz/backends/renderer.py | Python | bsd-3-clause | 8,989 | [
"Mayavi"
] | aa6fbb27a9bc76c5b728b7b7a4d6f60ff1904c2a4f40b205ab49ac7c09b3c48b |
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2020, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/or modify
# it unde... | mrcslws/nupic.research | projects/visual_recognition_grid_cells/python2_htm_docker/docker_dir/GridCellNet_base.py | Python | agpl-3.0 | 27,631 | [
"Gaussian",
"NEURON"
] | 1b51ba422ee7358c49cb3c37a52812c09aafe37bd37e2e11f6becf8300690acf |
#!/usr/bin/env python
"""
Name: ref_diff.py
Purpose: Use tophat and deseq to compare RNA-seq results from two reference
genome versions and create ready to use read count lists for
downstream analysis. The tool is mainly designed to compare data
from GRCh37/hg19 and GRCh38/hg38 but can ... | dfjenkins3/ref_diff | ref_diff.py | Python | mit | 5,689 | [
"HTSeq"
] | 55e1960a6c68766c29b19b8775a80d0571364782317d070e530dd21fcadd023a |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Apr 19 17:28:37 2017
@author: wolfensb
"""
import numpy as np
import matplotlib.pyplot as plt
from cosmo_query import config, SSH, Query
from cosmo_query import save_netcdf, load_netcdf
from cosmo_query import extract, coords_profile
###
## We initia... | wolfidan/cosmo_query | cosmo_query/examples/example1.py | Python | gpl-3.0 | 3,509 | [
"NetCDF"
] | fc173c543c71fe0446cd9c280c916f8cd42177448168b6ce36748fca50b6714e |
from rest_framework import serializers
from moto.moe import models
from django.contrib.auth import get_user_model
from django.core.urlresolvers import reverse
from django.conf import settings
from six.moves.urllib.parse import urlparse
import os
from django_comments_threaded.api.serializers import CommentSerializer as... | bung87/moto-moe | moto/moe/api/serializers.py | Python | mit | 6,799 | [
"MOE"
] | 857f1a8f066c81b5b4cd2a3030cdfaf35c4eaafc34ddf57dc52cc96ff856e474 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: maybelinot
# @Email: edik.trott@yandex.ru
# @Date: 2015-09-12 16:06:18
# @Last Modified by: maybelinot
# @Last Modified time: 2015-09-12 20:14:58
from __future__ import unicode_literals, absolute_import
import logging
import os
import subprocess
import sys
... | maybelinot/findltr | findltr/utils.py | Python | gpl-3.0 | 4,673 | [
"BLAST"
] | 60935c5f13e7e27cab6040961b1b63bb654c9d5d0a00a2d120e60b9402932853 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# 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 version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gcalctool/__init__.py | Python | gpl-3.0 | 844 | [
"ORCA"
] | 3c239fc6cc2bd48b244ac6831a9323e50bb89584a411c75531ee4de97f347dab |
"""
This module contains code for running a reciprocal HMMer-BLAST search in Goat,
including forward HMMer search, parsing of results and generation of
intermediate queries, reverse BLAST search, and parsing of results, together
with summarizing of forward and reverse searches.
"""
| chris-klinger/Goat | analyses/reciprocal_hmmer_blast.py | Python | gpl-3.0 | 285 | [
"BLAST"
] | aae7782d53b2e79f021d14e9d6cff72a292050979d9d324ac7c8a975ffbab19e |
#! /usr/bin/env python
###############################################################################
# Copyright 2017 Adam Jackson
###############################################################################
# This program is free software: you can redistribute it and/or modify
# it under the terms of the G... | ajjackson/mctools | mctools/get_energy.py | Python | gpl-3.0 | 1,657 | [
"ASE"
] | 7d297e84f648d8937325e03a0a52f544df3d4089e69d79c7f328e305811a45a5 |
# Copyright 2012 Nebula, 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 agree... | coreycb/horizon | horizon/base.py | Python | apache-2.0 | 38,783 | [
"VisIt"
] | 4d327d30a00fd61adc193c6cbd5e164bef61c063fa3d90aea1b584caabf51f4a |
import logging
import datetime
import pytest
import mongomock
import mock
from bripipetools import model as docs
from bripipetools import annotation
logging.basicConfig(level=logging.DEBUG)
logger = logging.getLogger(__name__)
@pytest.fixture(scope='function')
def mock_db():
# GIVEN a mock_ed version of the TG... | BenaroyaResearch/bripipetools | tests/test_annotation.py | Python | mit | 39,006 | [
"Galaxy"
] | f880043989e66986004c8ba34c8730fd6d4777c94221b3b92f8e1c2ab98ab26c |
# -*- coding: utf-8 -*-
"""views.py - View code for the repository application.
Author: Paul Brian
(C) 2012 Rice University
This software is subject to the provisions of the GNU Lesser General
Public License Version 2.1 (LGPL). See LICENSE.txt for details.
"""
import os
import sys
import datetime
import md5
import ... | philschatz/rhaptos2.repo | rhaptos2/repo/views.py | Python | lgpl-2.1 | 13,438 | [
"Brian"
] | dc84ed42f747d4b935de2820f01d83821f11bfdc067e5492e64651e264f4f6e4 |
import raptureAPI
import multipart
import json
import time
import base64
import random
# TODO These need to be parameters
repo = '//NightlyPython'
blobRepoUri = 'blob:'+repo
docRepoUri = 'document:'+repo
seriesRepoUri = 'series:'+repo
rapture = 'localhost:8665/rapture'
username = 'rapture'
password = 'rapture'
rapt... | amkimian/Rapture | Apps/RaptureIntTests/src/test/python/searchTests.py | Python | mit | 9,625 | [
"CRYSTAL"
] | 96311c713d46738484809bf1a7202281cef930e2a2c881be8d3730aeccc8dd99 |
import sys
import os
from subprocess import PIPE, Popen, call
import re
import pysam
import tempfile
import gzip
import shutil
import logging
import multiprocessing as mp
from itertools import repeat
from collections import defaultdict
from .cigar_scorer import CigarScorer
from .reverse_complement import reverse_comple... | gantzgraf/bacta | bacta/find_contaminants.py | Python | gpl-3.0 | 62,456 | [
"BWA",
"pysam"
] | efd6c79fad172504451bfeb843b9cd9e3039ee4c026a6260b1e7d534caf61592 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | detiber/ansible-modules-core | cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 39,099 | [
"Dalton"
] | a9ecd58f3c8d77740032569666dbf332b283f830305e23390187e45ea8f94d54 |
##############################################################################
# Copyright (c) 2013-2018, 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-biomart/package.py | Python | lgpl-2.1 | 2,963 | [
"Bioconductor"
] | 7f50d0b1ec8423e9dc390cd490aa16ddf976b93f93960ac15eeb1ca92f9af005 |
"""
Example1
This example is used to demo the brute force silhouette detection for a 3D mesh
1) Loads an example airway mesh
2) Identifies the silhouette points (This is slow for a large mesh)
3) Projects the silhouette points onto a 2D plane
Benjamin Irving
2013 / 08 / 25
"""
print __doc__
#Python modules
import n... | benjaminirving/Mesh-Silhouette-Projection | Example1_mesh_silhouette_and_projection.py | Python | bsd-3-clause | 2,329 | [
"Mayavi"
] | c7f529d5574f2b8041a950917498466f288003c0b5288e1420256b1ef73061ff |
########################################################################
# File : PoolComputingElement.py
# Author : A.T.
########################################################################
""" The Pool Computing Element is an "inner" CE (meaning it's used by a jobAgent inside a pilot)
It's used running se... | fstagni/DIRAC | Resources/Computing/PoolComputingElement.py | Python | gpl-3.0 | 9,636 | [
"DIRAC"
] | 7de705111a7128759f509f3f9a884c98ddaf819be645618e0895aee0af9ecebc |
# 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 writing, software
# distributed under t... | sjsucohort6/openstack | python/venv/lib/python2.7/site-packages/openstack/tests/unit/test_resource.py | Python | mit | 45,853 | [
"Brian",
"MOE"
] | e30d38c85b18578e717da8bac5da29e0c545e736d63a987c24f7176a854614da |
#!/usr/bin/python
# -*- coding: ISO-8859-1 -*-
"""
Mara.ANN.Learn (v. 0.1):
Learning algorithms for neural networks.
Author: Martti Louhivuori (martti.louhivuori@helsinki.fi)
Date: 14.2.2006
"""
class Teacher:
def __init__(self, net, method='bp', targets=None, rate=1,
gradient_delta=... | navjeet0211/Mara | ANN/Learn.py | Python | gpl-2.0 | 2,320 | [
"NEURON"
] | 5867f3e897ea70b2152b11afb4550e7819cef1b61cd8e4cd38e2279197b2563f |
##############################################################################
# Copyright (c) 2013-2018, 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-bsgenome/package.py | Python | lgpl-2.1 | 2,660 | [
"Bioconductor"
] | 2f8535007fe6505cfc4ffddd6af8d76eb03af1842d7cf0c3282369745d227581 |
#!/usr/bin/python
#
# Take a BAM file and calculate the coverage of each base
# Output some general statistics for each column
from optparse import OptionParser
import sys
import pysam
import csv
import os
if __name__ == '__main__':
#parse user options
parser = OptionParser()
parser.add_option("-a", "-... | JoshDaly/scriptShed | calculateBAMCoverage.py | Python | gpl-2.0 | 1,821 | [
"pysam"
] | 11174c1af6a117cc566e9d6bc71221235e6c20d1d2ed5462c6ab2e88a0fdce1b |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | properties/nodes/normal.py | Python | mit | 3,397 | [
"VisIt"
] | 19ff2625c9a2f4707041c5f3a44e090f5edde991667c3cfcfc1b5da157f9bfe5 |
# -*- coding: utf-8 -*-
"""
Generators for random graphs.
"""
# Copyright (C) 2004-2011 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
__author__ = "\n".join(['Aric Hagberg (hagberg@lanl.gov)',
... | koorukuroo/networkx_for_unicode | networkx/generators/random_graphs.py | Python | bsd-3-clause | 27,626 | [
"VisIt"
] | a26f2bde688f1c35ffc06ebc7a99dcb94ceb0ddc748eb8f58b8f3d2a4cf776b6 |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2017-2018 Esteban Tovagliari, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaini... | luisbarrancos/appleseed | src/appleseed.studio/python/studio/plugins.py | Python | mit | 2,935 | [
"VisIt"
] | 227319934622157e966a3e9e97b7982bcadb7ce067216da93b2f781ce16b3c43 |
#
# Copyright 2008, 2009 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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 t... | LunarLanding/Pythics | pythics/instruments/Mikrotron_Inspecta4C.py | Python | gpl-3.0 | 7,314 | [
"Brian"
] | fc7b1fed32e334e24dfe7b61958f9c29f7f56ee05575eac0c05781380234abf9 |
"""
Courseware views functions
"""
import logging
import urllib
import urllib2
import json
from util.json_request import JsonResponse
from pytz import timezone
import cgi
from datetime import datetime
from django.utils import translation
from django.utils.translation import ugettext as _
from django.utils.translation... | jbassen/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 72,500 | [
"VisIt"
] | bb9f2402efaf7145e95cef13fdb8bfd920464fdaabe47e5a03d1316ef6705f80 |
import unittest
from floodfill import FloodFill
class Node(int):
def __init__(self, *args):
self.linked = []
self.block_label = None
super(Node, self).__init__(*args)
def accept(self, visitor):
notseen = visitor.visit(self)
if notseen:
for elem in self.linke... | semkiv/heppy_fcc | fastsim/pfalgo/test_floodfill.py | Python | gpl-3.0 | 2,390 | [
"VisIt"
] | 35c98cbc57a4f386dd9b250fd3ff655509f90c8f38cf48b7d1ebbe476da2e68e |
#! /usr/bin/env python
""" cryptopy.cipher.icedoll_test
Tests for icedoll encryption algorithm
Copyright (c) 2002 by Paul A. Lambert
Read LICENSE.txt for license information.
"""
from cryptopy.cipher.icedoll import Icedoll
from cryptopy.cipher.base import noPadding
from binascii import ... | repotvsupertuga/tvsupertuga.repository | script.module.cryptolib/lib/cryptopy/cipher/icedoll_test.py | Python | gpl-2.0 | 3,898 | [
"Brian"
] | c000f78e72b8ff8265a9aee5ecb1d148a37a6328e14fc266d0b889d488927353 |
# Copyright 2015 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... | lucius-feng/yapf | yapf/yapflib/split_penalty.py | Python | apache-2.0 | 14,922 | [
"VisIt"
] | 2c277e9f99c1c03a1c2542e1480b7166dab833032ae61b3ccd2035c1772d883a |
#------------------------------------------------------------------------------
# setlx2py: setlxc
#
# CLI for setlx2py
#
# Copyright (C) 2014, Jan-Christoph Klie
# License: Apache v2
#------------------------------------------------------------------------------
from argparse import ArgumentParser
import os.path
fr... | Rentier/setlx2py | setlxc.py | Python | apache-2.0 | 2,778 | [
"VisIt"
] | b6724555a6df9b9ca49c983beee5247ac5c36d6b8cc6695642c017f4b3628e37 |
#Contains objects for accessing external services applications
import logging
from parameters import ExternalServiceParameter
from actions import ExternalServiceAction
from galaxy.util.bunch import Bunch
log = logging.getLogger( __name__ )
class ExternalServiceActionsGroup( object ):
def __init__( self, parent, ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/external_services/service.py | Python | gpl-3.0 | 10,536 | [
"Galaxy"
] | 818533f8035c133c4acb15b6091c723ea84701033ce496ade1d476b96b988113 |
# Copyright 2014 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 required by applicable ... | sunu/oh-missions-oppia-beta | core/controllers/galleries_test.py | Python | apache-2.0 | 24,061 | [
"VisIt"
] | 41ee6ca79d02df94b02dc424dcbd5a36fc8a4b2dc81efe923b4d33f123293639 |
"""
Scriptable Packages Installer - Parcks
Copyright (C) 2017 JValck - Setarit
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.... | Parcks/core | src/cli/argument_parser.py | Python | gpl-2.0 | 1,902 | [
"VisIt"
] | 9b853bc46e72afd618cfe39502716d80c7f4b22e8593af1dfce4d7c40e65e898 |
__RCSID__ = "$Id$"
import types
import threading
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from DIRAC.Core.Utilities.ThreadSafe import Synchronizer
from DIRAC.FrameworkSystem.Client.Logger import gLogger
gEventSync = Synchronizer()
class EventDispatcher(object):
def __init__(self):
self.__e... | arrabito/DIRAC | Core/Utilities/EventDispatcher.py | Python | gpl-3.0 | 2,822 | [
"DIRAC"
] | f29c1e8081cc8a7f93c5646121a51459dff5d0898555693b03e972816a501702 |
import unittest
import sys
from io import StringIO
from rdkit import Chem
from rdkit.Chem import rdFMCS
class BondMatchOrderMatrix:
def __init__(self, ignoreAromatization):
self.MatchMatrix = [[False]*(Chem.BondType.ZERO + 1)
for i in range(Chem.BondType.ZERO + 1)]
for ... | rdkit/rdkit | Code/GraphMol/FMCS/Wrap/testFMCS.py | Python | bsd-3-clause | 46,398 | [
"RDKit"
] | 4d183ebad559fb6d186abfbb717a7aa5e4a322e554c9a966f06d50b9ad962796 |
# -*- coding: utf-8 -*-
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
#
# Authors: Aric Hagberg <hagberg@lanl.gov>
# Loïc Séguin-C. <loicseguin@gmail.com>
# Da... | andnovar/networkx | networkx/algorithms/shortest_paths/weighted.py | Python | bsd-3-clause | 42,700 | [
"VisIt"
] | 54e6847c3e828a5606ac780d13f282f4a570a4748f3e0a9c210729ba686f1655 |
import os
import time
import random
import string
from rdkit.Chem import Draw
from rdkit import DataStructs
from rdkit.Chem.Fingerprints import FingerprintMols
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors
from rdkit.ML.Descriptors import MoleculeDescriptors
from molvs impor... | JonnaStalring/AZOrange | tests/standardizationTestSuite/testStandardization.py | Python | lgpl-3.0 | 5,985 | [
"RDKit"
] | 0ba5be34ee88aaf6637f373c8e0e021e5e0d664c052d1b47491658eae2bba9a0 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
test_geotext
----------------------------------
Tests for `geotext` module.
"""
import unittest
import geotext
class TestGeotext(unittest.TestCase):
def setUp(self):
pass
def test_cities(self):
text = """São Paulo é a capital do estado de S... | elyase/geotext | tests/test_geotext.py | Python | mit | 5,521 | [
"VisIt"
] | cab14d5729817d1e12a922f84373511f961a9ea12224e5eee7034beae5e6a645 |
# -*- coding:utf-8 -*-
# Copyright (C) 2013-2014 Germán Poo-Caamaño <gpoo@gnome.org>
#
# 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 ... | gpoo/MailingListStats | pymlstats/tests/test_analyzer.py | Python | gpl-2.0 | 8,556 | [
"Brian"
] | f019f7e98a3839774450e8df35bd9eb71b17a46ff5eb988c881a6590fdd833ab |
#!/usr/bin/env python
#! -*- coding: utf-8 -*-
###
# Copyright (c) Rice University 2012
# This software is subject to
# the provisions of the GNU Lesser General
# Public License Version 2.1 (LGPL).
# See LICENCE.txt for details.
###
Staff = [("Paul Brian", "paul@mikadosoftware.com"),
("Ed Woodward", "ecw... | philschatz/rhaptos2.repo | docs/blog/gravatartest.py | Python | lgpl-2.1 | 1,232 | [
"Brian"
] | d5cf71d64c1a84032e47749ac84f076e65ae9ffa93fb23594812219ccf7b3856 |
"""
Pyramids (Szeliski 3.5.3)
"""
import numpy as np
import scipy.signal as sig
from compvis.imgproc.filters import kernels
def interpolate(img):
"""
Interpolates an image with upsampling rate r=2.
"""
img_up = np.zeros((2*img.shape[0], 2*img.shape[1]))
# Upsample
img_up[::2, ::2] = img
#... | pauljxtan/pystuff | pycompvis/compvis/imgproc/pyramids.py | Python | mit | 1,437 | [
"Gaussian"
] | 1ca0df474c1781139638ad258a8485ae0c6a158f3689acd90839d7e214c5ba01 |
# Copyright 2012, 2013 The GalSim developers:
# https://github.com/GalSim-developers
#
# This file is part of GalSim: The modular galaxy image simulation toolkit.
#
# GalSim 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... | mardom/GalSim | tests/test_config_gsobject.py | Python | gpl-3.0 | 51,689 | [
"Galaxy",
"Gaussian"
] | 551b6b16823670467a9d64bbf19b1e8ff3241a41d598cddf824cd2b829e9b760 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
from .externals.six import string_types
import os
from os import path as op
import sys
from struct import pac... | effigies/mne-python | mne/surface.py | Python | bsd-3-clause | 47,438 | [
"Mayavi"
] | a57d4886732526eb1e7b3010c991f09b8e69c7958fa47fac8762808e41c06544 |
#
# 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/learn/ray/pytorch/test_estimator_pytorch_backend.py | Python | apache-2.0 | 22,835 | [
"ORCA"
] | 863196ffd4d2b2134d76256580ea06724e4857d43cc0028782573744b6090f67 |
'''
@author: Victor Barrera
Description: This scripts makes use of the siq module to obtain the methylation value for the two positions of
a restriction site.
'''
import sys
import pysam
import re
from siq import *
# Obtain the Restriction Enzime positions file,
# the sam-file and the minimum read filter
resEnzPos_p... | vbarrera/thesis | Genomic_Evaluation_of_individual_CpG_Methylation/Python/REMethStatus.py | Python | gpl-2.0 | 1,255 | [
"pysam"
] | 343f1d477b6c04e26be32b304cadb3a05756b305342c01750d8b89145f9cb510 |
# 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.
# Python stuff
from Numeric import array, sum, sqrt, matrixmultiply
# My stuff... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PDB/Atom.py | Python | apache-2.0 | 8,231 | [
"Biopython"
] | b194126373ca845269aba8316b5086893f33c8c5052a4238a615d5ee23119201 |
"""
This module implements the functionality to take any Python expression as a
string and fix all numbers and other things before evaluating it,
thus
1/2
returns
Integer(1)/Integer(2)
We use the Python ast module for that, which is in python2.6 and later. It is
well documented at docs.python.org.
Some tips to und... | kaushik94/sympy | sympy/parsing/ast_parser.py | Python | bsd-3-clause | 2,843 | [
"VisIt"
] | 6a915ad0a7860d030c7fa0f8e64ccde128df204b6ee73c5267810e97339f5bd7 |
#!/usr/bin/env python
# generate Python Manifest for the OpenEmbedded build system
# (C) 2002-2009 Michael 'Mickey' Lauer <mlauer@vanille-media.de>
# (C) 2007 Jeremy Laine
# licensed under MIT, see COPYING.MIT
import os
import sys
import time
VERSION = "2.6.2"
__author__ = "Michael 'Mickey' Lauer <mlauer@vanille-me... | JrCs/opendreambox | contrib/python/generate-manifest-2.6.py | Python | mit | 14,875 | [
"VisIt"
] | f6b4973f88d174263c2c7d22b750b57952c5805f127797aca5ee82adb4101818 |
##############################################################################
# Copyright (c) 2013-2018, 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... | krafczyk/spack | var/spack/repos/builtin/packages/r-alpine/package.py | Python | lgpl-2.1 | 2,342 | [
"Bioconductor"
] | 4120c3986dd9dc2974270c2debac62fb6b69141101182dc6baeffff4898f0806 |
###############################################################################
#
# Copyright (c) 2011 Ruslan Spivak
#
# 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, inc... | moses-palmer/slimit | src/slimit/visitors/nodevisitor.py | Python | mit | 2,830 | [
"VisIt"
] | 8224a2a0ecb2bc25540114413b67b750a41e4631d88049e634db1e2277f672f9 |
"""
Basic Selenium_ :class:`Webdriver` steps for Aloe_.
"""
from aloe import step, world
from aloe_webdriver.util import (
ElementSelector,
find_any_field,
find_button,
find_field,
find_option,
option_in_select,
wait_for,
string_literal,
)
from selenium.webdriver.support.ui import Sel... | aloetesting/aloe_webdriver | aloe_webdriver/__init__.py | Python | mit | 25,686 | [
"VisIt"
] | 4caec55d46be266c1aeaba2910960be2bc66ed9c14279c62ac3baad3ef5c26df |
#!/usr/bin/env python
"""
Takes an MD-trajectory and a topology file of a molecule, analyzes the hydrogen
bond network and generates in input-JSON file for use in FlarePlot
(http://GPCRviz.github.io/FlarePlot). Each vertex will be a residue-number from
the structure and each edge will represent a hydrogen bond betw... | GPCRviz/FlarePlot | input/flare-scripts/legacy/hbonds2flare.py | Python | apache-2.0 | 5,016 | [
"MDTraj"
] | 627ef437c215fefbad90fa91c1d94b627f3a2bdb99552650aba6d0013770e2d9 |
from logging import getLogger
import xcffib
from cffi import FFI
ffi = FFI()
ffi.include(xcffib.ffi)
ffi.cdef("""
typedef uint32_t xcb_cursor_t;
typedef struct xcb_cursor_context_t xcb_cursor_context_t;
int xcb_cursor_context_new(
xcb_connection_t *conn,
xcb_screen_t *screen,
xcb_... | aniruddhkanojia/qtile | libqtile/xcursors.py | Python | mit | 5,111 | [
"FLEUR"
] | 94b208e28d71c225d44e4f098a6ea3b079d52f2e04ce018ced0627e63ddeacfd |
# ----------------------------------------------------------------------------
# Copyright 2014 Nervana Systems 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.o... | coufon/neon-distributed | neon/layers/layer.py | Python | apache-2.0 | 63,592 | [
"Gaussian"
] | 5190e61e8c9d1836a6b303d70d7b295df6563f26f1dc5ec60259d270725d550e |
# LIBTBX_SET_DISPATCHER_NAME dev.dials.ssx_integrate
#!/usr/bin/env python
#
# dials.ssx_integrate.py
#
# Copyright (C) 2022 Diamond Light Source
#
# Author: James Beilsten-Edmands
#
# This code is distributed under the BSD license, a copy of which is
# included in the root directory of this package.
"""
This progr... | dials/dials | command_line/ssx_integrate.py | Python | bsd-3-clause | 14,564 | [
"CRYSTAL"
] | 28139f605808033fc9e0e4ecfba7acc3db6a51926ddbca2c64f81e59851e1995 |
__author__ = 'ddeconti'
import FileHandler
import pandas
import random
import sys
from bokeh.palettes import Blues9
from bokeh.charts import HeatMap, output_file, show
from rdkit.Chem.Fingerprints import FingerprintMols
from rdkit.Chem import AllChem, DataStructs, SDMolSupplier, Fingerprints
def randomly_pick_from... | dkdeconti/PAINS-train | training_methods/classifier/heatmap.py | Python | mit | 2,166 | [
"RDKit"
] | e8573c56a6fcb817e848bad068458df02871b7b8d403f2d0dd078ac2e98c0e53 |
#-----------------------------------------------------------------
# pycparser: func_defs.py
#
# Using pycparser for printing out all the calls of some function
# in a C file.
#
# Copyright (C) 2008-2011, Eli Bendersky
# License: BSD
#-----------------------------------------------------------------
from __fut... | kk1987/pycparser | examples/func_calls.py | Python | bsd-3-clause | 1,305 | [
"VisIt"
] | 8f66724a12492c40f99ca6fd50dd478c6150c9691e6785a227e4c7e7d8c1eb67 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
from pycsp_import import *
from pycsp.common.plugNplay import *
# We are using plugNplay processes
# Prefix
# Pair... | runefriborg/pycsp | examples/Fibonacci.py | Python | mit | 683 | [
"Brian"
] | 0b20f554c2afaa725d313b8aa24a460a182665d1e622021c71aededd70804a24 |
#!/usr/bin/python
import os
import datetime
import numpy as np
import pylab as pl
def count(dir, pattern):
if not os.path.isdir(dir):
return 0
p = os.popen('wc -l `find %s -name %s` | tail -1' % (dir, pattern), 'r')
return int(p.read().split()[0])
def polygon(x, y1, y2, *args, **kwargs):
x ... | robwarm/gpaw-symm | tools/code-count.py | Python | gpl-3.0 | 3,551 | [
"GPAW"
] | 0aa8fb61794eaca5644f4e47761753f136a21a75ce30d625f7c0caee655982cb |
# -*- coding: utf-8 -*-
"""Single-dipole functions and classes."""
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Eric Larson <larson.eric.d@gmail.com>
#
# License: Simplified BSD
from copy import deepcopy
from functools import partial
import re
import numpy as np
from scipy impor... | teonlamont/mne-python | mne/dipole.py | Python | bsd-3-clause | 54,155 | [
"Mayavi"
] | a05b5c2f8c0f7c0da42dad11397432ce8b3d00d9aa9abfa71cf0273e029bc85f |
from __future__ import print_function, division
from sympy.core.compatibility import range
"""
Algorithms and classes to support enumerative combinatorics.
Currently just multiset partitions, but more could be added.
Terminology (following Knuth, algorithm 7.1.2.5M TAOCP)
*multiset* aaabbcccc has a *partition* aaabc... | kaichogami/sympy | sympy/utilities/enumerative.py | Python | bsd-3-clause | 43,446 | [
"VisIt"
] | 0ea2350f9b885ca75e0d743d227ecc1314087d8ec232f9681343bc5f26350c49 |
import matplotlib
matplotlib.use('agg')
import sys, itertools, time, os
print(os.uname())
import emcee
from emcee.utils import MPIPool
#from helper_funcs import *
from eb_fitting import *
kic = int(sys.argv[1])
try:
prefix = sys.argv[2]
except:
prefix = '/astro/store/gradscratch/tmp/windemut/eb_fitting_mini/'
... | savvytruffle/cauldron | apogee_lcs.py | Python | mit | 27,819 | [
"Gaussian",
"VisIt"
] | 265c5a4b6bfa99c4c3e5b1f419cf56b6e866ebe75d4efe31b41702d5d7ca7ccd |
""" Module containing a front-end to the ElasticSearch-based ElasticJobParametersDB.
This module interacts with one ES index: "ElasticJobParametersDB",
which is a drop-in replacement for MySQL-based table JobDB.JobParameters.
While JobDB.JobParameters in MySQL is defined as::
CREATE TABLE `JobParamet... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/DB/ElasticJobParametersDB.py | Python | gpl-3.0 | 7,148 | [
"DIRAC"
] | 2d9b4848d8921730f369a6c87e60299c58dd1491e426be6701b87f9f0bba308c |
# Copyright (c) 2015-2018, 2020 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015-2016 Ceridwen <ceridwenv@gmail.com>
# Copyright (c) 2016 Jakub Wilk <jwilk@jwilk.net>
# Copyright (c) 2018 Bryce Guinta <bryce.paul.guinta@gmail.com>
# Copyright (c) 2019 Ashley Whetter <ashley@awhetter.co.uk>
# Copyright (c) 2020... | PyCQA/astroid | tests/unittest_transforms.py | Python | lgpl-2.1 | 8,809 | [
"VisIt"
] | 126da3b296cf02fe02c61d068e31e372509ecbc150ee8fb0da9ed36047ef6f1e |
#!/usr/bin/env python3
"""Cheap and simple API helper
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.3 $"
__date__ = "$Date: 2004... | jtraver/dev | python3/str/apihelper.py | Python | mit | 1,807 | [
"VisIt"
] | 4adaa6c5d379f053759d98a7020f3a715972690de8bbcf900507e970426989d8 |
#!/usr/bin/env python
import skimage
import cv2
import numpy as np
from skimage.feature import blob_dog, blob_log, blob_doh, daisy
from selam import colorconstancy as cc
from lib.moments.zernike import Zernikemoment
from lib.moments import pseudozernike, pyefd
from lib.IDSC import describe
from selam.utils import img
... | jinified/selam | examples/detect.py | Python | mit | 10,553 | [
"Gaussian"
] | 0649ab7004ad53344069b3269ff0a566964897c6ffb20f5d099939503c17dd59 |
import os
import threading
import time
import pytest
import splinter
import waitress
from .demo import app
APP_HTTP_PORT = 65431
APP_URL = f'http://0.0.0.0:{APP_HTTP_PORT}/'
WAIT_DELAY = 0.5
# See .travis.yml to know why we use Chrome by default. You are
# encouraged to also test with `DRIVER_NAME="firefox" pytest... | dbaty/deform_ext_autocomplete | tests/test_browser.py | Python | bsd-3-clause | 4,511 | [
"VisIt"
] | 4bea5b7625902d706d80064f221abfceff58b1ab32f79a6e363788ffa925a9f9 |
"""
Generalized linear models currently supports estimation using the one-parameter
exponential families
References
----------
Gill, Jeff. 2000. Generalized Linear Models: A Unified Approach.
SAGE QASS Series.
Green, PJ. 1984. "Iteratively reweighted least squares for maximum
likelihood estimation, and some ... | matthew-brett/draft-statsmodels | scikits/statsmodels/glm.py | Python | bsd-3-clause | 23,069 | [
"Gaussian"
] | d6aadf4b79577ba6ba043ec46f4e56d3e5cf76ca435484060df0cbd618f43c87 |
"""Deal with representations of Markov Models.
"""
# standard modules
import copy
import math
import random
# biopython
from Bio.Seq import MutableSeq
class MarkovModelBuilder:
"""Interface to build up a Markov Model.
This class is designed to try to separate the task of specifying the
Markov Model from ... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/HMM/MarkovModel.py | Python | gpl-2.0 | 19,282 | [
"Biopython"
] | ac6e02c1cea03b7989538c140ac38269934a28f1f2ad19bebe86367f91059031 |
HEROES_LIST = {
1: {
"name": "antimage",
"localized_name": "Anti-Mage"
},
2: {
"name": "axe",
"localized_name": "Axe"
},
3: {
"name": "bane",
"localized_name": "Bane"
},
4: {
"name": "bloodseeker",
"localized_name": "Bloodseeker... | lucashanke/houseofdota | app/util/dota_util.py | Python | mit | 10,397 | [
"CRYSTAL",
"TINKER"
] | d5f8903cd2904aae0d0d12c86eb31a1dc14f527085500cb2916cab270dd7f806 |
import numpy as np
import pytest
from pysisyphus.calculators.AnaPot import AnaPot
from pysisyphus.calculators.PySCF import PySCF
from pysisyphus.helpers import geom_loader
from pysisyphus.irc.initial_displ import cubic_displ_for_geom
from pysisyphus.irc import EulerPC
from pysisyphus.testing import using
@pytest.fix... | eljost/pysisyphus | tests/test_irc/test_initial_displ.py | Python | gpl-3.0 | 2,187 | [
"PySCF"
] | b7892c3323887e05b3a892ddffd5bc5339ac2e56ee9bf57d80822f29525d6eae |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/theme/__init__.py | Python | gpl-2.0 | 2,305 | [
"Brian"
] | 834e1813920170c42b9ef85f35f57e10437276307205e9adb4205e39cd7d0bda |
# coding=utf-8
# 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 app... | S-YOU/grumpy | compiler/stmt_test.py | Python | apache-2.0 | 18,304 | [
"VisIt"
] | 88f47228c7a5ba756e21d9c57b2e6823a22fa97af5a76b5f51d726aed39108a5 |
import time
from org.gumtree.gumnix.sics.control.events import DynamicControllerListenerAdapter
from org.gumtree.gumnix.sics.control import IStateMonitorListener
from org.gumtree.gumnix.sics.io import SicsProxyListenerAdapter
from org.eclipse.swt.events import DisposeListener
from org.eclipse.swt.widgets import Ty... | Gumtree/Kookaburra_scripts | Internal/Initialise_analysis.py | Python | epl-1.0 | 6,945 | [
"Gaussian"
] | 5d57e169fdeeeb1af6a4c45930cf41e491e96c13c4bc1ce849236f7c6f44370b |
# coding: utf-8
# Copyright 2014-2017 Álvaro Justen <https://github.com/turicas/rows/>
# 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 Foundation, either version 3 of the License, or
# ... | berinhard/rows | tests/tests_fields.py | Python | lgpl-3.0 | 23,313 | [
"MOE"
] | ac22b6b6b9f66db8315e76641eb2414f760a0890b00a7d9653b83b134760cc5c |
import numpy as np
import Oscillators as osc
from OpticalModel import OpticalModel
# Creating Optical model
om = OpticalModel('Two Oscillator Example')
# Creating a Lorentz oscillator
l = osc.Lorentz(1, 0.3, 2)
print(l)
# Adding Lorentz to the model
om.add(l)
om.show()
# Creating and adding a Gaussian
g = osc.Gaus... | francescorandi/optics | example_1.py | Python | gpl-3.0 | 748 | [
"Gaussian"
] | b50698b633537d399d093fb12626cc93e578ab9854d32b9fac4ac1a0938d0226 |
import batoid
import numpy as np
from test_helpers import timer, init_gpu, rays_allclose, checkAngle, do_pickle
@timer
def test_properties():
rng = np.random.default_rng(5)
size = 10
for i in range(100):
x = rng.normal(size=size)
y = rng.normal(size=size)
z = rng.normal(size=size)
... | jmeyers314/jtrace | tests/test_RayVector.py | Python | bsd-2-clause | 36,752 | [
"Gaussian"
] | f647019f7ce78ce6cfe4b4f1f92256ee6fbf35b198419cbb88c4247e528bfcc2 |
#!/usr/bin/env python
########################################################################
# $HeadURL: svn+ssh://svn.cern.ch/reps/dirac/DIRAC/trunk/DIRAC/FrameworkSystem/scripts/dirac-proxy-upload.py $
# File : dirac-proxy-init.py
# Author : Adrian Casajus
#######################################################... | vmendez/DIRAC | FrameworkSystem/scripts/dirac-proxy-get-uploaded-info.py | Python | gpl-3.0 | 2,578 | [
"DIRAC"
] | c550b2a769e7d1d5fdc3e5a6f2013cea8747ce9a9c4a444bcf20b2b27630595a |
import sys
import textwrap
import pytest
from _pytest import fixtures
from _pytest.fixtures import FixtureLookupError
from _pytest.fixtures import FixtureRequest
from _pytest.pathlib import Path
from _pytest.pytester import get_public_names
def test_getfuncargnames_functions():
"""Test getfuncargnames for normal... | alfredodeza/pytest | testing/python/fixtures.py | Python | mit | 129,834 | [
"VisIt"
] | 8a6f5be69017558108e95b269db3d65fac97744e345b3f324cc708775adf9231 |
from django.test import TestCase
from django.core.urlresolvers import reverse
from django.contrib.auth.models import Group
from django.contrib.auth.models import User
import json
class StoriesListTestCase(TestCase):
fixtures = ['test_fixtures']
def setUp(self):
user = User.objects.create_user(userna... | iCHAIT/whats-fresh-api | whats_fresh/whats_fresh_api/tests/views/test_stories_list.py | Python | apache-2.0 | 3,267 | [
"Galaxy"
] | b14fdb9d9065176bc1418d356b7b604498973a2a1f2325cc9568ac3be6f63960 |
"""
base catalog building pipeline 2.0
"""
import logging
from collections import Counter
from itertools import chain, count
import astropy.constants
import astropy.units
import numexpr as ne
import numpy as np
from astropy.coordinates import SkyCoord, search_around_sky
from astropy.table import join, vstack, unique
f... | sagasurvey/saga | SAGA/objects/build2.py | Python | mit | 42,434 | [
"Galaxy"
] | b7579f156f575103baf412e6b52104739c2e39a0ec1f953c1c54e9dd27f79623 |
import requests
import h2o
import h2o_test_utils
from h2o_test_utils import ModelSpec
def build_and_test(a_node, pp, datasets, algos, algo_additional_default_params):
####################################################################################################
# Build and do basic validation checks on... | pchmieli/h2o-3 | py/rest_tests/test_models.py | Python | apache-2.0 | 9,930 | [
"Gaussian"
] | 852156db67b1eced3db2239c84cf624141b760a39cf52b3e3133fae082a3e4d5 |
from rdkit import RDConfig
from rdkit.Dbase import DbModule
from rdkit.Dbase.DbConnection import DbConnect
import cPickle
from rdkit import Chem
if RDConfig.usePgSQL:
dbName="::RDTests"
else:
dbName="data.sqlt"
molTblName = 'simple_mols1'
fpTblName = 'simple_mols1_fp'
conn = DbConnect(dbName,molTblName)
conn.Add... | rdkit/rdkit-orig | rdkit/SimDivFilters/test_data/genfps.py | Python | bsd-3-clause | 625 | [
"RDKit"
] | a35faa1c45d31709faa7b43206f61f1d07bd0bae8e8d9288d9d4600fac5d9452 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RSomaticsignatures(RPackage):
"""Somatic Signatures.
The SomaticSignatures package... | rspavel/spack | var/spack/repos/builtin/packages/r-somaticsignatures/package.py | Python | lgpl-2.1 | 1,816 | [
"Bioconductor"
] | 7bd3415ff670e382dd08169c8df2198039ea359517023a6c555b1a8abe9aea30 |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@vub.ac.be)
# 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.
"""
SVDSuperimposer finds the best rotation and translation to put
two point sets on top of ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SVDSuperimposer/__init__.py | Python | apache-2.0 | 5,270 | [
"Biopython",
"CRYSTAL"
] | cb4abcd3dbfa152e101def322894e89c75c0775ca22eb324c780246904737dc7 |
#
# GMSK modulation and demodulation.
#
#
# Copyright 2005-2007,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from __future__ import un... | jdemel/gnuradio | gr-digital/python/digital/gmsk.py | Python | gpl-3.0 | 10,563 | [
"Gaussian"
] | bf05b3579c27764807d5ffc42381a13b78aa0b44154c399a5626911517f4d2f5 |
##############################################################################
##############################################################################
# Estimating the volatility of synthetic data
# using a stochastic volatility (SV) model with Gaussian log-returns.
#
# The SV model is inferred using the SP... | compops/gpo-abc2015 | scripts-paper/example1-spsa.py | Python | mit | 3,787 | [
"Gaussian"
] | 7d00d7977699e1e503b75b263c0059ee83e741d383d667e11c0ffbc5fd1d3462 |
import os
import time
import random
import string
from rdkit.Chem import Draw
from rdkit import DataStructs
from rdkit.Chem.Fingerprints import FingerprintMols
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Descriptors
from rdkit.ML.Descriptors import MoleculeDescriptors
from molvs impor... | JonnaStalring/AZOrange | tests/standardizationTestSuite/testStandardizationSave.py | Python | lgpl-3.0 | 5,500 | [
"RDKit"
] | e4a564595cbecc532b4074e5b632334cef91bc5a6fb866ea01bfd550b87aeb57 |
#!/usr/bin/env python
#
# $File: forwardTrajectory.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 redis... | BoPeng/simuPOP | docs/forwardTrajectory.py | Python | gpl-2.0 | 2,287 | [
"VisIt"
] | 33044391633720a7958a6fed8fb140f64c942b53e5b3df576b6e2f14c8def838 |
# Author: Travis Oliphant
# 1999 -- 2002
from __future__ import division, print_function, absolute_import
import warnings
import threading
import sys
if sys.version_info.major >= 3 and sys.version_info.minor >= 5:
from math import gcd
else:
from fractions import gcd
from . import sigtools
from ._upfirdn impo... | larsmans/scipy | scipy/signal/signaltools.py | Python | bsd-3-clause | 94,290 | [
"Gaussian"
] | 5da2ebeac3747d9a7414552900d6ce58b76ca4fc64e497840202674c61173969 |
# Copyright (C) 2010,2011,2012,2013,2014,2015,2016 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
# (a... | KonradBreitsprecher/espresso | testsuite/dipolar_mdlc_p3m_scafacos_p2nfft.py | Python | gpl-3.0 | 7,705 | [
"ESPResSo"
] | 906e21d07189a93e51e9a4fb1a1aa35811c4fd880612323513a41b282370bc00 |
"""
This module defines export functions for decision trees.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Dawe <noel@dawe.me>
# Satrajit Gosh <satrajit.ghosh@gmail.com>
# Trevor... | aabadie/scikit-learn | sklearn/tree/export.py | Python | bsd-3-clause | 16,020 | [
"Brian"
] | 93cb393e5e440d6fab7f25231bc589a36fa9f89d440db9ef1786030a2bbf09f9 |
# -*- coding: utf-8 -*-
"""
Created on Thu Nov 26 14:15:32 2015
@author: Hanna
"""
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as io
from sklearn import svm
def plotData(data):
plt.figure()
pos = data[data[:,2] == 1]
neg = data[data[:,2] == 0]
plt.scatter(pos[:,0], pos[:,1... | gpiatkovska/Machine-Learning-in-Python | Ex6_SVM/Ex6.py | Python | mit | 5,494 | [
"Gaussian"
] | 482f4fd9d70c3faab83d102108c3ed1ed6619ea2ca0a35fe67bb5e1118caad6d |
"""This module implements a Neighbourhood and a StateAccessor for beta-asynchronous
step function execution.
The idea behind beta asynchronous execution is, that in a physical realisation of
a cellular automaton, there may be delays in communication between the cells
whenever the value of a neighbour is read.
This is... | timo/zasim | zasim/cagen/beta_async.py | Python | bsd-3-clause | 7,274 | [
"VisIt"
] | 71bc0d64acca798d6f3a7991aeeaece959c179b6d9cfdd6e1659b548900d7bf8 |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['name','version','moduleid','description','copyright','... | jhester/pdfreader-titanium | src/build.py | Python | mit | 6,804 | [
"VisIt"
] | f5383da407928eba76ad7cba410c88c9742ba48ff13f361f4e7e89ced8425027 |
#!/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 | hummaptexture.py | Python | mit | 2,639 | [
"Gaussian"
] | 8d94bb82a037c0f62ec4a026dc3eec72fcdc267a69e420cb0c64d390b47945ca |
# coding=utf-8
# Copyright 2020 The SimCLR 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... | tensorflow/similarity | tensorflow_similarity/augmenters/simclr.py | Python | apache-2.0 | 22,178 | [
"Gaussian"
] | 6a27b6c7406a96603e4017213edce9a2992fffa8fbae36fbc5ee7e2d04de5623 |
#!/usr/bin/env python
from DIRAC.Core.Base.Script import parseCommandLine
parseCommandLine()
import sys
if len( sys.argv ) < 2:
print 'Usage: dirac-transformation-clean transID [transID] [transID]'
sys.exit()
else:
transIDs = [int( arg ) for arg in sys.argv[1:]]
from DIRAC.TransformationSystem.Agent.Transforma... | Sbalbp/DIRAC | TransformationSystem/scripts/dirac-transformation-clean.py | Python | gpl-3.0 | 922 | [
"DIRAC"
] | b49899c3f0f1c404e78b63e318753fa336c982856b13a78cb5e94ae5c63db20b |
# -*- coding: utf8 -*-
#-----------------------------------------------------------------------------
# Copyright (c) 2010-2012 Brian Granger, Min Ragan-Kelley
#
# This file is part of pyzmq
#
# Distributed under the terms of the New BSD License. The full license is in
# the file COPYING.BSD, distributed as part o... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/tests/test_socket.py | Python | lgpl-3.0 | 14,667 | [
"Brian"
] | e76a92c11ec21d66c984ec02a61c9b8a6491b4386c4058d7a4e813c48416502c |
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