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""" FTS3Job module containing only the FTS3Job class """
__RCSID__ = "$Id $"
import datetime
import errno
# Requires at least version 3.3.3
import fts3.rest.client.easy as fts3
from fts3.rest.client.exceptions import FTS3ClientException
from fts3.rest.client.request import Request as ftsSSLRequest
from DIRAC.Resou... | petricm/DIRAC | DataManagementSystem/Client/FTS3Job.py | Python | gpl-3.0 | 20,898 | [
"DIRAC"
] | 58903d51da6676d4b7453203be226bd74e8c9f4ea7003b59600983b42f734c5c |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2008, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.SCC.ShowGraphPortlet | setup.py | Python | gpl-2.0 | 3,273 | [
"VisIt"
] | 678a25d67c4892bb90bb313633cfc542957aad047a99bb7a6a88eef09aee6ab5 |
# 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... | nburn42/tensorflow | tensorflow/contrib/autograph/converters/list_comprehension.py | Python | apache-2.0 | 2,628 | [
"VisIt"
] | 881d9b063e2901bd888aa913464260a4f0f25a72c6876e50bd0aff33ee9639d2 |
#
# @file TestCompartment.py
# @brief Compartment unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file locate... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestCompartment.py | Python | bsd-3-clause | 8,125 | [
"VisIt"
] | 5415390e11f898212753e0698a6b1f00481784e1dfee75a2194ecdb035f03e71 |
# (C) British Crown Copyright 2010 - 2017, Met Office
#
# This file is part of Iris.
#
# Iris 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
# (at your option) any l... | QuLogic/iris | lib/iris/tests/test_netcdf.py | Python | gpl-3.0 | 42,843 | [
"NetCDF"
] | 35047f225951b0780771542c0b2820921cb9d450b3c3cb355490b95c97a0f2fb |
#import brian_no_units
from brian import *
from scipy.optimize import fsolve
import time
from brian.library.IF import *
from brian.library.synapses import *
import matplotlib.pyplot as plt
from sys import argv
import Graphics as artist
from matplotlib import rcParams
rcParams['text.usetex'] = True
N=1000
Vr = -70 * ... | mac389/csd-sansa | astrocytes-explore-separatrix.py | Python | gpl-2.0 | 11,239 | [
"Brian",
"Gaussian",
"NEURON"
] | d77a6de761abfd18b4ca7d71483757773b90c7b1466d779e13d7becf5dff8f0f |
import json
import logging
import os
import tempfile
from galaxy import util
from galaxy.datatypes import checkers
from galaxy.model.orm import and_
from galaxy.tools.data_manager.manager import DataManager
from galaxy.tools.test import TestCollectionDef
from galaxy.web import url_for
from tool_shed.repository_types ... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/metadata/metadata_generator.py | Python | gpl-3.0 | 71,290 | [
"Galaxy"
] | 7abfb8aa220001f07969b9bb57b9da0079571e6855c05407f552e188eeed874d |
# Copyright 2016 Uri Laserson
#
# 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,... | lasersonlab/pepsyn | setup.py | Python | apache-2.0 | 1,298 | [
"Biopython"
] | 08c118aac98d365f85bdf3ff2208f1b019c2e3daf8405155de149590b8daf068 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
This implements the method described in Tang et al. 2010 PNAS paper,
<http://www.pnas.org/content/107/1/472>
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage
The main pipeline assumes starting with defined synteny blocks in .anchors
format... | sgordon007/jcvi_062915 | compara/pad.py | Python | bsd-2-clause | 9,261 | [
"BLAST"
] | 002ade770f1508a7cf016ef562a5e0083fe6477e496dcf054d10c85038d23059 |
# coding=utf-8
"""
Contains an abstract base class that supports data transformations.
"""
import os
import logging
import numpy as np
import scipy
import scipy.ndimage
import time
import deepchem as dc
import tensorflow as tf
import warnings
from deepchem.data import NumpyDataset
logger = logging.getLogger(__name__)
... | miaecle/deepchem | deepchem/trans/transformers.py | Python | mit | 61,364 | [
"Gaussian",
"RDKit"
] | 273822809957ffe776c9a8da0050ed4dd5f0c005c6eb999fda381aff88b3541a |
#!/Users/github/bldmconda3/bin/python
#!/home/psilocaluser/bldmconda3/bin/python
#!/Users/github/bldmconda3/bin/python
#/usr/bin/env python3
# [LAB 4 Apr 2017]
# Adapt for Mac and Linux
# Separate psi4-core dest_channel from other defaults
# [LAB 24 Mar 2017]
# Confirmed a nightly build set
# Outputs stdout in real... | psi4/psi4meta | conda-recipes/pre-cb3-recipes-mac/kitandkapoodle.py | Python | gpl-2.0 | 18,440 | [
"Psi4"
] | fbf4e76a151d7a598f509e5250a35ee065a6eeb374a3fb4af7bee4be72e8732e |
import json
from . import Transport
from smarthouse.models import Arduino,Log,Sensors
from django.utils import timezone
import hashlib
from . import dbwork
import time
import RPi.GPIO as GPIO
# isInitGPIO = False
transporter = Transport.TransportProtocol()
class LightControl:
pin = None
@staticmethod
de... | dev-sirius/smart-home-controller | mysite/jsonparse.py | Python | apache-2.0 | 3,272 | [
"NEURON"
] | 5f67f541e05fe4c46c883ac0cb377d679aa91ec5257098ae292b4f7357ace717 |
# -*- coding: utf-8 -*-
"""Tests for :mod:`pybel.struct.summary.errors`."""
import unittest
from pybel import BELGraph
from pybel.exceptions import NakedNameWarning, UndefinedAnnotationWarning
from pybel.struct.summary import count_error_types, count_naked_names, get_naked_names
from pybel.testing.utils import n
c... | pybel/pybel | tests/test_struct/test_summary/test_errors.py | Python | mit | 2,021 | [
"Pybel"
] | c3c123e7384cb28e9b8b4c4ef35e6da6fb0a3e001fd2914775068584018d16f4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
########################################################################
# $HeadURL$
# File : dirac-distribution-create-tarball
# Author : Adria Casajus
########################################################################
"""
Create tarballs for a given DIRAC rele... | sposs/DIRAC | Core/scripts/dirac-create-distribution-tarball.py | Python | gpl-3.0 | 20,544 | [
"DIRAC"
] | 43e0a49c39c1c3fba7b4e612879f67ce049339d9a455a4264877a3d5a1e62b7b |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | kain88-de/mdanalysis | package/MDAnalysis/coordinates/XYZ.py | Python | gpl-2.0 | 15,349 | [
"MDAnalysis",
"VMD"
] | 19e55b9765bee605146c5e6706b6861f53c67032a7a9eff365eac94b979ee129 |
# Copyright 2002 by Andrew Dalke. All rights reserved.
# Revisions 2007-2010 copyright by Peter Cock. All rights reserved.
# Revisions 2009 copyright by Brad Chapman. All rights reserved.
# Revisions 2013 copyright by Tiago Antao. All rights reserved.
# This code is part of the Biopython distribution and governed b... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/BioSQL/DBUtils.py | Python | gpl-2.0 | 3,602 | [
"Biopython"
] | 79a730b4bd8dfcec321f49503ce9386f766b05a684f962053e5cbaa687d8f90e |
from enum import Enum
from typing import Any, Collection, Dict, List, NamedTuple, Union, cast
from ..language import print_ast, visit, ObjectValueNode, Visitor
from ..pyutils import inspect, natural_comparison_key, Undefined
from ..type import (
GraphQLEnumType,
GraphQLField,
GraphQLList,
GraphQLNamedT... | graphql-python/graphql-core | src/graphql/utilities/find_breaking_changes.py | Python | mit | 21,183 | [
"VisIt"
] | bedd52c8e0dc0e66dd17a60940c5a1066a39e73db8111a67797de1d5dc9e1c78 |
import numpy as np
import os
import pandas as pd
import time
import math
from itertools import chain
from itertools import product
import bifacial_radiance
from dask.distributed import Client
import math
# Generate spectra for DNI, DHI and albedo using smarts
# Run simulation using the given timestamp and wavelength
... | NREL/bifacial_radiance | bifacial_radiance/HPCScripts/BasicSimulations/simulate_fixedtilt_gencumsky.py | Python | bsd-3-clause | 3,126 | [
"EPW"
] | 247720e95e791cc197537d62a87ca82fe93d2c58846af9f9edb7432ae81f1187 |
"""GFSA: Generalized Fine-Structure Analysis
"""
__license__ = "Apache License, Version 2.0"
__author__ = "Roland Kwitt, University of Salzburg; Stefan Huber, IST Austria, 2013"
__email__ = "E-Mail: roland.kwitt@kitware.com"
__status__ = "Development"
from collections import defaultdict
import matplotlib.pyplot... | rkwitt/pyfsa | beta/gpart.py | Python | apache-2.0 | 12,479 | [
"VisIt"
] | 191d378b9cd7eb773ad3b9bb42eb06ff44823d65f6bd3c32bc8fe6f793a2fd1a |
from asap3 import *
import cPickle as pickle
from numpy import *
import sys, os, time
from asap3.testtools import *
from asap3.mpi import world
from ase.lattice.cubic import *
debug = 0
if debug == 1:
DebugOutput("moveatoms%d.log", nomaster=True)
elif debug == 2:
time.sleep(world.rank)
print "PID:", os.get... | auag92/n2dm | Asap-3.8.4/Test/parallel/moveatoms.py | Python | mit | 1,914 | [
"ASE"
] | f24d90581902566df92d6afbc1618140418a052a3d87671601e815f46ba503b2 |
from __future__ import absolute_import
import logging
import mimetypes
import os
import shutil
import tempfile
import zipfile
from cgi import escape
from inspect import isclass
from six import string_types
from . import metadata
from galaxy import util
from galaxy.datatypes.metadata import MetadataElement # import di... | icaoberg/cellorganizer-galaxy-tools | datatypes/data.py | Python | gpl-3.0 | 44,361 | [
"Galaxy"
] | 47b99b82a04335556ca903a18868ee65e16f98e7eb67fedd9aa78a951205256b |
from setuptools import setup
from setuptools.command.install import install as DistutilsInstall
import subprocess
import os
from mykatlas.version import __version__
__version__ = __version__[1:].split("-")[0]
class MyInstall(DistutilsInstall):
def run(self):
mccortex_dir = os.path.dirname(os.path.realpat... | Phelimb/atlas | setup.py | Python | mit | 1,508 | [
"Biopython"
] | c23bbc036b5aadbf73d09d1b99c86b06bbd88096c654aa77e5115bf65887993f |
#!/usr/bin/env python3
# Copyright 2016-2018 Brian Warner
#
# 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... | OSSHealth/ghdata | workers/facade_worker/facade_worker/facade02utilitymethods.py | Python | mit | 3,842 | [
"Brian"
] | 5cca010e879c79d604fe45b716f2adaba98c77d007f02fa63356327854867e11 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed May 10 15:23:19 2017
@author: DangoMelon0701
"""
from scipy.io import netcdf
import os
import matplotlib.pyplot as plt
import numpy as np
import matplotlib as mpl
#%%
def plot_data(data,cbar=0,save_img=0,name='image'):
norm = mpl.colors.Normalize(v... | DangoMelon0701/PyRemote-Sensing | NETCDF scripts/QuikSCAT/wndstrss_read_nc.py | Python | mit | 3,641 | [
"Gaussian",
"NetCDF"
] | d763667f27897475c11b5664252e8409c888368702b98a861ecea1991a5b4c90 |
"""
Creates a dependency graph that stores the commands for the ancient DNA pipeline.
"""
import os
import logging
from ngadnap.dependency_graph.graph import CommandGraph, CommandNode
from ngadnap.command_templates.adapter_removal import adapter_removal
from ngadnap.command_templates.bwa import *
from ngadnap.c... | smilefreak/NGaDNAP | ngadnap/create_ngadnap_graph.py | Python | mit | 6,579 | [
"BWA"
] | 9b28d863b498452e7ec7a0b1d4ff75784d1adebfb52fd7a73d0248647f8c9ace |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# (c) 2012-2014 Michal Kalewski <mkalewski at cs.put.poznan.pl>
#
# This file is a part of the Simple Network Simulator (sim2net) project.
# USE, MODIFICATION, COPYING AND DISTRIBUTION OF THIS SOFTWARE IS SUBJECT TO
# THE TERMS AND CONDITIONS OF THE MIT LICENSE. YOU SHO... | mkalewski/sim2net | sim2net/simulator.py | Python | mit | 6,698 | [
"VisIt"
] | 89180bf30e4e53356b5660739b31c9b39ba902f7ed7158c8fd8fe5e0caae44f5 |
# savemodel.py ---
#
# Filename: savemodel.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Wed Oct 29 00:08:50 2014 (+0530)
# Version:
# Last-Updated:Thr Dec 23 16:31:00 2015 (+0530)
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#... | BhallaLab/moose | moose-examples/snippets/savemodel.py | Python | gpl-3.0 | 1,471 | [
"MOOSE"
] | d00becadfe514750cc8a6b9086748721f266f012ed0d0484ade150b513ca10ed |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/editors/abstractmanytooneeditor.py | Python | gpl-2.0 | 2,783 | [
"VisIt"
] | 36f119f7bed92f42d66b8ceb6b3639739f09d6b0a5c7f2049d7db6d8017ce6ed |
#!/usr/bin/env python
import roslib
import rospkg
import rospy
import actionlib
import sys, os
from tf2_msgs.msg import *
from map_store.msg import *
from map_store.srv import *
from nav_msgs.msg import *
from nav_msgs.srv import *
from geometry_msgs.msg import *
from visualization_msgs.msg import *
import yaml
from ... | MohitShridhar/multi_map_navigation | src/scripts/navigation/multi_map_navigation_manager.py | Python | mit | 37,119 | [
"BLAST"
] | a7635d36175c2fc195684b3dd1e569188d43eafbc8b526af96e0795d8813ebb6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# 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 Licens... | ravibhure/ansible | lib/ansible/modules/network/cnos/cnos_backup.py | Python | gpl-3.0 | 11,398 | [
"VisIt"
] | 01caaf962a3e89db9eb2e3edef0cb63dfc8326f9e1d140dea60ccd8381eb07da |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-monitoring | tests/unit/gapic/monitoring_v3/test_notification_channel_service.py | Python | apache-2.0 | 164,318 | [
"Octopus"
] | 5bda392d8519e96ca86eb3acb271639a81cb61f455d628612bb12e76a7ea4364 |
"""
SkCode links tag definitions code.
"""
from gettext import gettext as _
from html import escape as escape_html
from html import unescape as unescape_html_entities
from ..etree import TreeNode
from ..tools import sanitize_url, slugify
from ..utility.relative_urls import get_relative_url_base
class UrlLinkTreeNo... | TamiaLab/PySkCode | skcode/tags/links.py | Python | agpl-3.0 | 11,571 | [
"VisIt"
] | f634ab53905ba7b5e72b29347d04b4cc5efbb006b154eb1c5ca7fe199a1e736c |
"""
=============================================
Whitening evoked data with a noise covariance
=============================================
Evoked data are loaded and then whitened using a given noise covariance
matrix. It's an excellent quality check to see if baseline signals match
the assumption of Gaussian white... | olafhauk/mne-python | examples/visualization/plot_evoked_whitening.py | Python | bsd-3-clause | 3,103 | [
"Gaussian"
] | 9dac0a0244c84ecc03d11c9f2fe81f15f5fc357e85708fae3dc99d4c2dc70674 |
"""Soundex algorithm
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: 1.2 $"
__date__ = "$Date: 2004/05/06 21:36:36 $"
__copyright__ ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/soundex/stage1/soundex1d.py | Python | mit | 2,390 | [
"VisIt"
] | ecfc8b4e3523af9e4419dd5e80a31931da8e76f991aa8e2ac95e4ee40c7b052f |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | zhreshold/mxnet | python/mxnet/ndarray/numpy/random.py | Python | apache-2.0 | 37,862 | [
"Gaussian"
] | 09dfed799616a3b884ef06c397fb61dfae64f8084220996459321c01e37c8044 |
"""
CLASS INFO
-------------------------------------------------------------------------------------------
Dataset_transformations contains every method that has to do with processing or altering a
dataset's structure. Regularyl used in netCDF data for easy transformation of N-dim arrays
to 2D and ... | iaklampanos/bde-pilot-2 | backend/Dataset_transformations.py | Python | apache-2.0 | 2,715 | [
"NetCDF"
] | 5629260363cd7c4674e56bf008743d4cd90b1f3dd32ee18f52b544c3583318dc |
"""
DIRAC - Distributed Infrastructure with Remote Agent Control
The distributed data production and analysis system of LHCb and other VOs.
DIRAC is a software framework for distributed computing which
allows to integrate various computing resources in a single
system. At the same time it integrates al... | ic-hep/DIRAC | src/DIRAC/__init__.py | Python | gpl-3.0 | 6,208 | [
"DIRAC"
] | 91c6bdc84859ad5b7e4ebd66bd79d7d5968d2227cc33dcda7fca56613baeb994 |
"""
Created on Apr 7, 2015
@author: ayan
"""
from __future__ import (absolute_import, division, print_function)
import pytest
import numpy as np
from ..sgrid import SGrid, load_grid
from .write_nc_test_files import (deltares_sgrid,
deltares_sgrid_no_optional_attr)
"""
Test SGri... | NOAA-ORR-ERD/pysgrid | pysgrid/tests/test_sgrid_deltares.py | Python | bsd-3-clause | 7,973 | [
"NetCDF"
] | 2d4f522c74c751a55d145a249a7f8b21effd1c3848b389ce163dececeaca86a4 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2011 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 Softw... | andrebellafronte/stoq | stoqlib/database/admin.py | Python | gpl-2.0 | 14,763 | [
"VisIt"
] | c0cca0f2dfd0de8becffce0bf6d954ecc9849a25646c52f3dbe9bfaac06217bb |
# Copyright (c) 2003-2014 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, o... | si618/pi-time | node_modules/grunt-pylint/tasks/lib/pylint/checkers/classes.py | Python | gpl-3.0 | 47,800 | [
"VisIt"
] | d4f812dd1e5a460d49f89447d5f07bdf17595f90f0b9d07eff0a3580727428f1 |
import ast
from typing import TYPE_CHECKING, List, Tuple, Union
from breakfast.position import Position
from breakfast.scope import Scope
if TYPE_CHECKING:
from breakfast.source import Source
def find_occurrences(
sources: List["Source"], old_name: str, position: Position
) -> List[Position]:
visitor ... | thisfred/breakfast | breakfast/occurrences.py | Python | bsd-2-clause | 8,075 | [
"VisIt"
] | 9fec996d49a4ecafa7ea5052add3607c7d799c86574de5b6dd8551962f0a6f79 |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import datetime
import math
import random
import os
def writeFrame(w2if, lwr, n):
w2if.Modified()
current_dir = os.getcwd()
filename = current_dir + "/frames/vd500_zoomout" + ('%05d' % n) + ".png"
lwr.SetFileName(filename)
# lwr.Write(... | aewallin/openvoronoi | python_examples/line-segment/lineseg_separator_case.py | Python | lgpl-2.1 | 3,953 | [
"VTK"
] | df1bf75a76b0f3277a53ee6f72fc19385391b3207a3481c6bd0aea9a42e55e13 |
"""
Cell 1 Features
====================================
Compute features for 1-cells
"""
# sphinx_gallery_thumbnail_number = 1
from __future__ import print_function, division
import nifty.cgp as ncgp
import nifty.segmentation as nseg
import skimage.data as sdata
import skimage.filters as sfilt
# plotting
impor... | DerThorsten/nifty | src/python/examples/cgp/plot_cgp_features.py | Python | mit | 1,230 | [
"Gaussian"
] | 22492be7e6f1e6977b6dbe0e3f325898e57f4231e725f9b1202c260714c2acfd |
# encoding: utf-8
import os
import numpy as np
import glob
import re
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import pyroms
import pyroms_toolbox
import _remapping
import matplotlib.pyplot as plt
import datetime
def remapping(varname, srcfile, wts_files, srcgrd, dstgrd, \
ro... | kshedstrom/pyroms | pyroms_toolbox/pyroms_toolbox/remapping.py | Python | bsd-3-clause | 21,813 | [
"NetCDF"
] | 1591bf89a3f118220710fa5ed634c5db561d6fd1dc64f38b6df0f4246ae2974d |
#!/usr/bin/env python
'''
@author Brian McKenna <bmckenna@asascience.com>
@file ion/processes/data/upload/upload_calibration_processing.py
'''
from pyon.public import OT, RT, PRED
from pyon.core.exception import BadRequest
from pyon.ion.process import ImmediateProcess
from pyon.event.event import EventPublisher
from p... | ooici/coi-services | ion/processes/data/upload/upload_calibration_processing.py | Python | bsd-2-clause | 9,902 | [
"Brian"
] | e562ccd9b50786a8f17b45afe377becc11efc69c83c28d0582ef867797ef5c3b |
# -*- coding: utf-8 -*-
"""
This models contains the Kernels for Kernel smoothing.
Hopefully in the future they may be reused/extended for other kernel based
method
References:
----------
Pointwise Kernel Confidence Bounds
(smoothconf)
http://fedc.wiwi.hu-berlin.de/xplore/ebooks/html/anr/anrhtmlframe62.html
"""
# ... | statsmodels/statsmodels | statsmodels/sandbox/nonparametric/kernels.py | Python | bsd-3-clause | 19,792 | [
"Gaussian"
] | b5613c720e728f7abb7fa3fddd80f330e3ee04489677f158640500531f5438cf |
"""
Linter classes containing logic for checking various filetypes.
"""
import ast
import os
import re
import textwrap
from xsslint.reporting import ExpressionRuleViolation, FileResults, RuleViolation
from xsslint.rules import Rules
from xsslint.utils import Expression, ParseString, StringLines, is_skip_dir
from xssli... | procangroup/edx-platform | scripts/xsslint/xsslint/linters.py | Python | agpl-3.0 | 59,263 | [
"VisIt"
] | 59a834b3a4a32cfa12985c64638d117544e83d825c794779419068f4467d847b |
#uses modified cclib 1.00
import sys
sys.path.append(sys.argv[2])#add $RMG/source to the PYTHONPATH so that import statements below work properly
import logging
from cclib.parser import ccopen
myfile=ccopen(sys.argv[1])
myfile.logger.setLevel(logging.ERROR) #cf. http://cclib.sourceforge.net/wiki/index.php/Using_... | faribas/RMG-Java | scripts/GaussianPM3ParsingScript.py | Python | mit | 1,733 | [
"cclib"
] | 0614b3ac905b1bb0fe28a979bea3c2f0f01cf4f7cfb5a3c8c6aedcd9c494378e |
from .gamess import GAMESSEnergyJob
from .orca import OrcaEnergyJob
from .dalton import DALTONEnergyJob
program_matrix = {
'energy': {'gamess': GAMESSEnergyJob, 'orca': OrcaEnergyJob, 'dalton': DALTONEnergyJob}
}
def EnergyJob(basename, program=None, **kwargs):
""" Convenience wrapper for energy calculati... | cstein/calcit | calcit/jobs.py | Python | mit | 921 | [
"Dalton",
"GAMESS",
"ORCA"
] | 6c5c97563c0a9f7212b9f7fdd0193cea6817c2b56bd6bc9eaec61c139d0ee44e |
#!/bin/python
import math
import bdn
"""
Single Layer Rosenblatt (1957) Perceptron implementation
The Ronseblatt perceptron always converges to a correct solution, if the
problem can be learned by a single-layer net, no matter how the initial
weights are chosen.
Here such weights are chosen as random positive values... | qwattash/AI | perceptron/perceptron.py | Python | mit | 4,489 | [
"NEURON"
] | e127ba11b1f73d50277bcdc5b83aa966f4ca6fb9070e9a1a10f66d54f5606d2d |
"""
Created on Tue Feb 24 16:08:39 2015
@author: mukherjee
"""
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn import preprocessing, metrics
from sklearn.learning_curve import learning_curve
# read Form data
DATA_FORM_FILE = 'all-merged-cat.csv'
#rawdata = pd.read_cs... | sankar-mukherjee/CoFee | scikit_algo/All.py | Python | apache-2.0 | 8,995 | [
"Gaussian"
] | 9962f8e4d7618d1880ce7a2a65ebdb8791a0da81a049512ec68b0cd4d3f65862 |
# python3
# Copyright 2019 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in... | google/pyctr | transformers/virtualization/scoping_test.py | Python | apache-2.0 | 6,243 | [
"VisIt"
] | cbca373f8f19edbd3d6c08caf0c533fa84cb83633e09899ccf5a70c014770bfa |
from ovito.io import import_file
from ovito.modifiers import SelectParticleTypeModifier, CommonNeighborAnalysisModifier
node = import_file("simulation.dump")
cnamod = CommonNeighborAnalysisModifier()
node.modifiers.append(cnamod)
modifier = SelectParticleTypeModifier(property = "Structure Type")
modifier.types = { Co... | srinath-chakravarthy/ovito | doc/python/example_snippets/select_particle_type_modifier.py | Python | gpl-3.0 | 563 | [
"OVITO"
] | a75583130522e466fb2af246fce25a62d8ca12253277cc99f1620fb0b80e1541 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/dependency_check.py | Python | gpl-2.0 | 1,591 | [
"Psi4"
] | faaed85d74b6f25ef1d92ddfeb20db54808cf96c0ca65a0a0f62efb6103877da |
import sys
from PySide2.QtCore import Qt
import numpy as np
import do.sara as sara
import do.shakti as shakti
import cv2
def user_main():
video_file = sys.argv[1]
video_stream = sara.VideoStream()
video_stream.open(video_file)
h, w, _ = video_stream.sizes()
video_frame = np.empty(video_strea... | DO-CV/sara | python/do/sara/benchmark/image_processing.py | Python | mpl-2.0 | 7,557 | [
"Gaussian"
] | 5e09b26540a4e6a9bc57ca7786aadce47eaa44968e1e82c1a95c0affbf96e1d4 |
# Copyright 2008-2010 by Peter Cock. 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.
"""Multiple sequence alignment input/output as alignment objects.
The Bio.AlignIO interface... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/AlignIO/__init__.py | Python | gpl-2.0 | 19,930 | [
"BioPerl",
"Biopython"
] | 28747385428b12978782116a817c8128c676081f4511d586c5894dd1fe5899fa |
'''The script counts reads mapped across each splice junction
from in gene models. It requires gene models in BED format
and read alignments in BAM format. Note that reads must be
mapped to transcripts derived from the same gene models.
Transcripts can be obtained using get_transcript_seq.py provided
in this package.
... | likit/gimme | src/utils/count_spliced_reads2.py | Python | gpl-3.0 | 3,919 | [
"pysam"
] | bdf1ace294b60fd10e897b4312bdf6e582f2b0f9dfdb1f9a1e9862a39d6aefdb |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | mlperf/training_results_v0.7 | Fujitsu/benchmarks/resnet/implementations/implementation_closed/train_imagenet.py | Python | apache-2.0 | 7,895 | [
"Gaussian"
] | 4c72551284c7034989839d90686f94c071bffea5607b8a3be13e16c4825b46c9 |
from __future__ import division
import logging
import re
import os.path
import warnings
from math import ceil
import numpy as np
import tables as tb
import matplotlib as mpl
import matplotlib.gridspec as gridspec
from matplotlib import ticker
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.backen... | YannickDieter/testbeam_analysis | testbeam_analysis/tools/plot_utils.py | Python | mit | 72,510 | [
"Gaussian"
] | d14889d5adacf5d49dc5133dac3e5e01aea883b0fdabd5a0570578a59d685639 |
#!/usr/bin/env python3
# coding: utf-8
from __future__ import unicode_literals, print_function
import itertools
import csv
from collections import OrderedDict, defaultdict
from molbiox.frame import streaming, containers, interactive
@interactive.castable
def read(infile, fieldlist=None, sep=None):
"""
Read a... | frozflame/molbiox | molbiox/io/tabular.py | Python | gpl-2.0 | 5,226 | [
"BLAST"
] | abc36006788f6447503a53c825521b5087cbe9f41e3c78c11738c6551603ad85 |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
from plotting_functions import *
import sys
import os
import MDAnalysis
start = int(sys.argv[1])
end = int(sys.argv[2])
step = int(sys.argv[3])
pd... | rbdavid/RMSF_calc | comparison_plotting.py | Python | gpl-3.0 | 7,080 | [
"MDAnalysis"
] | 4cc80e1dddc1a31e2f359a57b50ea929dcaf9c9348c2e44c48724e88503c6212 |
"""Animation class which is a DisplayElement which plays animations."""
# animation.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 time
from mpf.m... | spierepf/mpf | mpf/media_controller/elements/animation.py | Python | mit | 13,596 | [
"Brian"
] | 3153de70f4f1bb389d8036d908d1c5989d126f6ed0e6becb0ab36c2fcd82b7b2 |
import numpy as np
import matplotlib.pyplot as plt
def init_two_layer_model(input_size, hidden_size, output_size):
"""
Initialize the weights and biases for a two-layer fully connected neural
network. The net has an input dimension of D, a hidden layer dimension of H,
and performs classification over C classes... | Alexoner/mooc | cs231n/assignment2/cs231n/classifiers/neural_net.py | Python | apache-2.0 | 6,815 | [
"NEURON"
] | 04c35fa91bac4a37323d8b3ead872b531c2df61dd5aa84adc1a5828003b7331d |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module provides classes for predicting new structures from existing ones.
"""
from six.moves import zip
__author__ = "Will Richards, Geoffroy Hautier"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "1.2"
__maintainer__... | rousseab/pymatgen | pymatgen/structure_prediction/substitutor.py | Python | mit | 10,509 | [
"pymatgen"
] | 41653070814bd2b7ecf8b5ed19fabc52544be147029c5d12a4df718a8048a1f5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# care_get_structures_gdt_ranges.py
#
# Copyright 2016 Carlos Eduardo Sequeiros Borja <casebor@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free So... | casebor/labioscripts | python/care_get_structures_gdt_ranges.py | Python | gpl-3.0 | 2,119 | [
"Amber"
] | 4a739002f38474e91566a577dddc82d0f9b6b56730defe50751bfdbed7f2bc6f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import pytest
from numpy import array, zeros, ones
from numpy.testing import assert_array_equal
from gnpy.core.info import create_arbitrary_spectral_information
from gnpy.core.exceptions import SpectrumError
def test_create_arbitrary_spectral_information():
si = cr... | Telecominfraproject/gnpy | tests/test_info.py | Python | bsd-3-clause | 2,934 | [
"ASE"
] | 086941e84f6fd882a444c6da7ad79fd2ca5b829884d038b1648bc13f79db16b4 |
#! /usr/bin/env python
# if_curve.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at... | gewaltig/cython-neuron | pynest/examples/if_curve.py | Python | gpl-2.0 | 4,260 | [
"NEURON"
] | b908932894c63168b3477a376f1cf3ad0636762e749fd7dfa201f8ae231b6d6b |
# Copyright 2009-2010 by Peter Cock. 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.
#
# This module is for reading and writing FASTQ and QUAL format files as
# SeqRecord objects... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/SeqIO/QualityIO.py | Python | gpl-2.0 | 74,832 | [
"BioJava",
"BioPerl",
"Biopython"
] | 157f89558309423a3781aa1193807f21f8d7eac8ae65d4552733a63807449823 |
import SimpleITK as sitk
import sys
if len ( sys.argv ) < 4:
print "Usage: SimpleGaussian <input> <sigma> <output>";
sys.exit ( 1 )
reader = sitk.ImageFileReader()
reader.SetFileName ( sys.argv[1] )
image = reader.Execute()
pixelID = image.GetPixelIDValue()
gaussian = sitk.SmoothingRecursiveGaussianImageF... | SimpleITK/Staging | Examples/SimpleGaussian.py | Python | apache-2.0 | 603 | [
"Gaussian"
] | b2ff7a0a453b270daa942baf40a70582be1ff14287e7ab8f4ba6c3a1e4473caf |
"""
Module for managing the installation of DIRAC components:
MySQL, DB's, NoSQL DBs, Services, Agents, Executors
It only makes use of defaults in LocalInstallation Section in dirac.cfg
The Following Options are used::
/DIRAC/Setup: Setup to be used for any operation
/LocalInstallation/InstanceName: ... | chaen/DIRAC | FrameworkSystem/Client/ComponentInstaller.py | Python | gpl-3.0 | 93,531 | [
"DIRAC"
] | f50fb6fdc5bb31147a35572ce2325487c3518bf65909dd2d12c9f70b43335361 |
#! /usr/bin/python3
# -*- coding:Utf-8 -*-
"""
MyNotes - Sticky notes/post-it
Copyright 2016-2019 Juliette Monsel <j_4321@protonmail.com>
MyNotes 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 o... | j4321/MyNotes | mynoteslib/sticky.py | Python | gpl-3.0 | 52,023 | [
"FLEUR"
] | 7da718457be842672ff541b0e678efab72052d952b43929046596a09f71311ab |
""" Base class for all the executor modules for Jobs Optimization
"""
import threading
import datetime # Because eval(valenc) might require it
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DEncode, List
from DIRAC.Core.Base.ExecutorModule import ExecutorModule
from DIRAC.WorkloadManagementSystem.Cli... | ic-hep/DIRAC | src/DIRAC/WorkloadManagementSystem/Executor/Base/OptimizerExecutor.py | Python | gpl-3.0 | 7,143 | [
"DIRAC"
] | 4c34ff36aabf0bfbf8fef3b1d11d8fcfcafc83a246c184526c0d629eafc39798 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import socorro.lib.prioritize as prioritize
class TestNode:
def testConstructor(self):
n = prioritize.Node()
... | Serg09/socorro | socorro/unittest/lib/testPrioritize.py | Python | mpl-2.0 | 7,490 | [
"VisIt"
] | 65ecaff6d4588901659fe6250f5375232e0765cd1d8ad15b5682ff703b77f119 |
#!/usr/bin/env python
from __future__ import division
from __future__ import print_function
from builtins import zip
from builtins import range
from itertools import groupby
from operator import itemgetter
import itertools
import numpy
import quantities as pq
import neo
from nineml.user import (
Projection, Network... | tclose/PyPe9 | test/unittests/test_simulations/test_network.py | Python | mit | 52,184 | [
"NEURON"
] | cc5ac3e293898ddcfa3e6da731c4da00a46e7183737ac0f18d1a5311f05516f9 |
"""
===========
gaussfitter
===========
.. codeauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com> 3/17/08
Latest version available at <https://github.com/keflavich/gaussfitter>, where
it was moved from google code on January 30, 2014
"""
from __future__ import print_function, division, absolute_import
import numpy a... | keflavich/gaussfitter | gaussfitter/gaussfitter.py | Python | bsd-3-clause | 25,433 | [
"Gaussian"
] | 5baf66626f5339c48f966c2d9023ac58b20f60de3703621e48948ce7ea76f904 |
"""Support for the Amazon Polly text to speech service."""
import logging
import boto3
import botocore
import voluptuous as vol
from homeassistant.components.tts import PLATFORM_SCHEMA, Provider
import homeassistant.helpers.config_validation as cv
_LOGGER = logging.getLogger(__name__)
CONF_REGION = "region_name"
CO... | tboyce021/home-assistant | homeassistant/components/amazon_polly/tts.py | Python | apache-2.0 | 7,471 | [
"Brian"
] | 0f9a4970077f19bdadd790889fcb061a49c1e15b648e5b4d29ef0c9fe3af4df7 |
# -*- coding: utf-8 -*-
#
"""Checker for triangle coefficients.
"""
import numpy as np
# import pynosh.numerical_methods as nm
# import pynosh.ginla_modelevaluator as gm
def _main():
args = _parse_input_arguments()
# # define triangle
# x0 = np.array([0.0, 0.0])
# v1 = np.array([1.0, 1.0])
# v1 ... | nschloe/pynosh | tools/triangle_test.py | Python | mit | 7,656 | [
"VTK"
] | 0ca404a6478ff1f5dc4da3966f911dd8d405f0be8bf5a8ce4fe9e0081de6bb80 |
""" Test class for AccountingDB
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access
# imports
import unittest
from mock import MagicMock
import DIRAC.AccountingSystem.DB.AccountingDB as moduleTested
class TestCase(unitt... | yujikato/DIRAC | src/DIRAC/AccountingSystem/DB/test/Test_AccountingDB.py | Python | gpl-3.0 | 16,243 | [
"DIRAC"
] | 81b8679f192037cbe8d1537b594d41080ba92a6540021ec9d7e785b699a65d8e |
# -*- coding: utf-8 -*-
# Copyright 2012 by Christian Brueffer. 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.
"""Command line wrapper for the motif finding program XXmotif.""... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/motifs/applications/_xxmotif.py | Python | apache-2.0 | 9,460 | [
"Biopython"
] | c9a07d53b273bd10ec85289bf95ea2f0724db03372d942a425206a8d7ef46c23 |
# -*- coding: utf-8 -*-
#
# brunel_exp_multisynapse_nest.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 o... | Silmathoron/nest-simulator | pynest/examples/brunel_exp_multisynapse_nest.py | Python | gpl-2.0 | 13,495 | [
"NEURON"
] | a6e937be812ae070b9946f84cd98eb4b73b07cf46556dd9ad42f9e2af01ed59e |
from textwrap import dedent
import _pytest._code
import py
import pytest
from _pytest.config import PytestPluginManager
from _pytest.main import EXIT_NOTESTSCOLLECTED, EXIT_USAGEERROR
@pytest.fixture(scope="module", params=["global", "inpackage"])
def basedir(request, tmpdir_factory):
from _pytest.tmpdir import ... | malinoff/pytest | testing/test_conftest.py | Python | mit | 15,351 | [
"VisIt"
] | 280cd19de1c2ad34273307b46d3620250397f262b85ab56a65346dd2e2d70582 |
""" codecs -- Python Codec Registry, API and helpers.
Written by Marc-Andre Lemburg (mal@lemburg.com).
(c) Copyright CNRI, All Rights Reserved. NO WARRANTY.
"""#"
import builtins, sys
### Registry and builtin stateless codec functions
try:
from _codecs import *
except ImportError as why:
raise SystemErro... | lfcnassif/MultiContentViewer | release/modules/ext/libreoffice/program/python-core-3.3.0/lib/codecs.py | Python | lgpl-3.0 | 35,371 | [
"FEFF"
] | 242899f7c8b7cda0a5897943bbaf15776dfbff8d849878a74be02db43bcb5000 |
import h5py
import numpy
from rdkit import Chem
from steps.interpretation.extractsaliencymapsubstructures2d import substructure_set
from steps.preprocessing.shared.tensor2d import tensor_2d_array
from util import data_validation, file_structure, file_util, progressbar, logger, misc, hdf5_util, buffered_queue,\
con... | patrick-winter-knime/mol-struct-nets | molstructnets/steps/interpretation/extractsaliencymapsubstructures2d/extract_saliency_map_substructures_2d.py | Python | gpl-3.0 | 12,118 | [
"RDKit"
] | e885314262ff2c3a1b5f82470eba2b95cf9a470c85ccdc8f251eb8ccc4d5bc09 |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-today OpenERP SA (<http://www.openerp.com>)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms o... | ATSTI/administra | open_colegio/ea_import/project.py | Python | gpl-2.0 | 73,351 | [
"VisIt"
] | 22eb444da0ef36f39f480abd71d460d5ad0194894edd23e5e800fd2d21e0f269 |
"""\
DFunctionals.py Exchange and Correlation Density Functionals
This program is part of the PyQuante quantum chemistry program suite.
Copyright (c) 2004, Richard P. Muller. All Rights Reserved.
PyQuante version 1.2 and later is covered by the modified BSD
license. Please see the file LICENSE that is part of ... | gabrielelanaro/pyquante | PyQuante/DFunctionals.py | Python | bsd-3-clause | 28,753 | [
"DIRAC"
] | 6d757fd0c946ac64b06f80f81f5aa3f578b106f8adfca53698ba186e49814013 |
# Copyright (c), Michael DeHaan <michael.dehaan@gmail.com>, 2012-2013
# Copyright (c), Toshio Kuratomi <tkuratomi@ansible.com> 2016
# Simplified BSD License (see licenses/simplified_bsd.txt or https://opensource.org/licenses/BSD-2-Clause)
from __future__ import absolute_import, division, print_function
SIZE_RANGES = ... | mheap/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 116,232 | [
"VisIt"
] | 520540786fd27d0543ff8acb323f69425660a74b0f2ec15d76cab219ec3b6025 |
########################################################################
# Author : Andrei Tsaregorodtsev
########################################################################
"""
Utilities for managing DIRAC configuration:
getCEsFromCS
getUnusedGridCEs
getUnusedGridSEs
getSiteUpdates
getSEUpdates
"""
... | arrabito/DIRAC | ConfigurationSystem/Client/Utilities.py | Python | gpl-3.0 | 22,521 | [
"DIRAC"
] | 532205d1bf6677970b9f58f9280d5562c52b57eadce207379c55a3d36d2cbf01 |
from __future__ import print_function
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
from tests import pyunit_utils
# This method test to make sure when a user set lambda_search=True and choose a lambda value, a warning me... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_PUBDEV_7645_lambda_search_warning.py | Python | apache-2.0 | 1,108 | [
"Gaussian"
] | 7bcc89e08de925030a3abc596a4465ea3e43330bf5c0c9f336f1bcf0c9215790 |
from nesoni import grace
import numpy
from numpy import random, linalg
import gtk
from matplotlib.figure import Figure
# uncomment to select /GTK/GTKAgg/GTKCairo
#from matplotlib.backends.backend_gtk import FigureCanvasGTK as FigureCanvas
from matplotlib.backends.backend_gtkagg import FigureCanvasGTKAgg as FigureC... | Victorian-Bioinformatics-Consortium/nesoni | nesoni/graph_layout.py | Python | gpl-2.0 | 26,014 | [
"VisIt"
] | 08678643ff84eed66f19663af2f961386036907fcd12599fb715c3de94358d1d |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-binary-authorization | tests/unit/gapic/binaryauthorization_v1/test_validation_helper_v1.py | Python | apache-2.0 | 53,865 | [
"Octopus"
] | ae78a1d17b08a00852b029c06c5cd7d9e873835957a0142e9f046bc889e46756 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Peter Eastman, Robert McGibbon
# Contributors: Kyle A. Beaucha... | msultan/mdtraj | mdtraj/core/topology.py | Python | lgpl-2.1 | 49,995 | [
"MDTraj",
"OpenMM",
"VMD"
] | 8b507b2bdfa592150f3772ab30ab9aba22aedafdae7415f155f2e87a562d35cb |
import numpy
from _surface import SurfaceModel
from sys import stderr
from Segger import timing
from time import clock
class Segmentation ( SurfaceModel ):
def __init__(self, name, volume = None, open = True):
SurfaceModel.__init__(self)
self.name = name
if volume is None:
s... | gregdp/segger | Segger/regions.py | Python | mit | 70,270 | [
"Gaussian"
] | 4b08309d1e64f8baca308f0833283ac0f13b2c3aab04c4938a60ea296c0c66f0 |
#! /usr/bin/env python
import macrodensity as md
import math
import numpy as np
import matplotlib.pyplot as plt
import csv
from itertools import izip
#------------------------------------------------------------------
# Get the potential
# This section should not be altered
#----------------------------------------... | WMD-group/MacroDensity | examples/InputControl.py | Python | mit | 6,745 | [
"ASE",
"VASP"
] | 848e04b01eefc570cdaab43af42aeb0285185112362bd36ddec121449e5b8ca3 |
#! /usr/bin/env python
from MDAnalysis import *
from MDAnalysis.analysis.align import rotation_matrix
import numpy
import math
u = Universe("init.pdb", "sampled.pos.pdb")
v = Universe("init.pdb")
mob1 = u.selectAtoms("segid A and resid 4:77 or segid B and resid 1:90")
ref1 = v.selectAtoms("segid A and resid 4:77 or ... | demharters/git_scripts | rmsd_1sjh.py | Python | apache-2.0 | 518 | [
"MDAnalysis"
] | 3544f898b8e5964f9d499a0a9ae9d05c355003471b905543e1c17e3250d4b57d |
from nanopore.analyses.abstractAnalysis import AbstractAnalysis
from nanopore.analyses.utils import AlignedPair, getFastaDictionary, getFastqDictionary, samIterator
import os
import pysam
import numpy
import xml.etree.cElementTree as ET
from jobTree.src.bioio import reverseComplement, prettyXml, system
class IndelCou... | mitenjain/nanopore | nanopore/analyses/indels.py | Python | mit | 6,347 | [
"pysam"
] | 6f66a8a9459c63ef8dda50248de0a999f898a8f41064a13b5a214e5936a783b2 |
__author__ = 'Christoph Heindl'
__copyright__ = 'Copyright 2017, Profactor GmbH'
__license__ = 'BSD'
import numpy as np
import tensorflow as tf
from tensorflow.contrib.staging import StagingArea
from tensorflow.python.ops import data_flow_ops
import time
import math
from sensor_correction.gp_cpu import GPRegressor
f... | cheind/rgbd-correction | sensor_correction/apps/compare_cpu_gpu.py | Python | bsd-3-clause | 2,914 | [
"Gaussian"
] | c382b49a41f8ca19605b7f91ab97d75b217023f3807ad03dee3a026fcac11a22 |
"""
Robust location and covariance estimators.
Here are implemented estimators that are resistant to outliers.
"""
# Author: Virgile Fritsch <virgile.fritsch@inria.fr>
#
# License: BSD 3 clause
import warnings
import numbers
import numpy as np
from scipy import linalg
from scipy.stats import chi2
from . import empi... | xuewei4d/scikit-learn | sklearn/covariance/_robust_covariance.py | Python | bsd-3-clause | 32,345 | [
"Gaussian"
] | e23a165239158d4971a87e0db11cc03da0923d3e76b009114394880f7097f877 |
# -*- coding: utf-8 -*-
"""Tests for txStatHat"""
from __future__ import division, print_function, unicode_literals
from decimal import Decimal
import os
from twisted.internet import defer
from twisted.trial import unittest
from twisted.web.client import getPage
import txstathat
EZ_KEY = os.environ.get('TEST_EZ... | hynek/txStatHat | test/test_txstathat.py | Python | mit | 3,242 | [
"TINKER"
] | 60abd6475536baed3d557999cb94aeaecc0c91ca9275075d737ad07d3de6299d |
# -*- coding:utf-8 -*-
from django import forms
from django.contrib.auth.models import User
import bootstrap_toolkit
from bootstrap_toolkit.widgets import *
from django.forms import ModelForm
from atap.models import Tool, Input, Param, Output
def validate_name(value):
if value[0].isdigit():
raise forms.Val... | hewie7/tool-wrapper-web | atap/forms.py | Python | unlicense | 11,976 | [
"BWA"
] | e6ea10e55f4079302cd3e1a38a0d392263712c9a80712d94c2b2fb674cd69748 |
'''
module to integrate git with jasp using the commands module and command line git commands. The only reason for this (as opposed to the git-python interface) is simplicity and transparency.
if the status of "git status" is 32768 it means not a git repository.
this returns true if you are in a repository
git rev-pa... | jboes/jasp | jasp/vc/git_commands.py | Python | gpl-2.0 | 1,944 | [
"VASP"
] | 5b6b3f42589bfb758f4ae5117beb2e986764db0ebb8acfa54f083869c26b9383 |
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