text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
#!/usr/bin/env python
# ***** BEGIN LICENSE BLOCK *****
# 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/.
# ***** END LICENSE BLOCK *****
import copy
import os
import pla... | walac/build-mozharness | mozharness/mozilla/testing/testbase.py | Python | mpl-2.0 | 28,711 | [
"VisIt"
] | 50ead9908b2021d568bf778026ffff603d96d456147ebcfe5e00410df849dbce |
#!/usr/bin/python2.6
# This file is a part of Metagam project.
#
# Metagam is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# any later version.
#
# Metagam is distributed ... | JoyTeam/metagam | mg/core/auth.py | Python | gpl-3.0 | 73,211 | [
"VisIt"
] | 55063824a9ad810322c17ce8850720f9a8d9b094a9e9d5b6688ff6ee7d2b3f58 |
""" DIRAC FileCatalog component representing a flat directory tree
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access
__RCSID__ = "$Id$"
import six
import os
import stat
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.U... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/DB/FileCatalogComponents/DirectoryManager/DirectoryFlatTree.py | Python | gpl-3.0 | 7,780 | [
"DIRAC"
] | c9c6ef8643b38c45374f60875ffc28d880d813f1ddac16a36fffc63b4a6c7ba3 |
from __future__ import division
import collections
import re
import sector
import vector3
# "Imagine the galaxy is a giant slice of Battenberg
# which for reasons beyond our ken has had small chunks
# of carrot cake pushed into it all over the place..."
# - CMDR Jackie Silver
# This does not validate sector name... | KayJohnston/jackies-map | pgdata.py | Python | bsd-3-clause | 62,783 | [
"Galaxy"
] | 0458542664aee1256fd9e675071105f3f5c2df0dab17a3c3011167b4c5196706 |
# Original code: Copyright 2014 The University of Melbourne
# Copyright 2015 VPAC
#
# This file is part of Karaage.
#
# Karaage 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, ... | Karaage-Cluster/karaage-debian | karaage/tests/client.py | Python | gpl-3.0 | 6,504 | [
"VisIt"
] | bc8b8ed27f47ccdec0a00bd3a118ed7329f7bd330296e8e4eb8cf1313a1a6561 |
# -*- coding: utf-8 -*-
import itertools
import functools
import os
import re
import urllib
import logging
import pymongo
import datetime
import urlparse
from collections import OrderedDict
import warnings
import pytz
from flask import request
from django.core.urlresolvers import reverse
from modularodm import Q
from... | petermalcolm/osf.io | website/project/model.py | Python | apache-2.0 | 129,819 | [
"VisIt"
] | 5be1ad62358a4e35f2ccf1ab35dce0682f8d0b939752f94ad099b5a73b0bce6b |
#!/usr/bin/env python
import os
from setuptools import setup
PROJECT = u'gnucash-util'
VERSION = '0.1'
URL = 'https://github.com/bstpierre/gnucash-util'
AUTHOR = u'Brian St. Pierre'
AUTHOR_EMAIL = u'brian@bstpierre.org'
DESC = "A collection of utilities for automating GnuCash 2.4+."
def read_file(file_name):
fi... | bstpierre/gnucash-util | setup.py | Python | mit | 1,242 | [
"Brian"
] | 1b2f86b61178e82b01053defef230467007ac9563d52653c44b7c9ba1a35d6e4 |
#!/usr/bin/env python2.4
"""
Script that imports locally stored data as a new dataset for the user
Usage: import id outputfile
"""
import sys, os
from shutil import copyfile
#tempfile, shutil
BUFFER = 1048576
uids = sys.argv[1].split(",")
out_file1 = sys.argv[2]
#remove NONE from uids
have_none = True
while have_non... | jmchilton/galaxy-central | tools/data_source/microbial_import.py | Python | mit | 2,528 | [
"Galaxy"
] | 211f1958a2722a9142f6df7ddca6916f38955a3ad021b661614271ce20227fdb |
import os, sys, re
import optparse
import shutil
import pandas
import numpy
import gc
import subprocess
import uniprot as uni
from natsort import natsorted, ns
import warnings
##### TAKEN FROM STACK OVERFLOW ##### (to redirect Pandas warnings to STDOUT instead of STDERR for Galaxy...)
def customwarn(message, category,... | wohllab/milkyway_proteomics | galaxy_milkyway_files/tools/wohl-proteomics/SAINTq/saintq_wrapper.py | Python | mit | 17,364 | [
"Galaxy"
] | 8502b6ad5e415d1764e84bbbbd47b05a0aaaf4d6ff1c1787ffc35ebce90cdb6b |
"""
Distributions
-------------
A widget for plotting attribute distributions.
"""
from math import sqrt
import sys
import collections
from xml.sax.saxutils import escape
from PyQt4 import QtGui, QtCore
from PyQt4.QtCore import Qt
from PyQt4.QtGui import QToolTip
import numpy
import pyqtgraph as pg
import Orange.da... | kwikadi/orange3 | Orange/widgets/visualize/owdistributions.py | Python | bsd-2-clause | 27,981 | [
"Gaussian"
] | 7fba339241c0ae183fe44ac44aeb86ae6115aedab25ac7d238bf157b33ec7667 |
"""0MQ Constants."""
#-----------------------------------------------------------------------------
# Copyright (c) 2013 Brian E. 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 of ... | IsCoolEntertainment/debpkg_python-pyzmq | zmq/sugar/constants.py | Python | lgpl-3.0 | 4,371 | [
"Brian"
] | 1dbd396fb1baad7a794b5facf17120124c8191d70ccdc09e8fcc71f057161d9b |
# Autodetecting setup.py script for building the Python extensions
#
import sys, os, importlib.machinery, re, optparse
from glob import glob
import importlib._bootstrap
import importlib.util
import sysconfig
from distutils import log
from distutils import text_file
from distutils.errors import *
from dist... | Orav/kbengine | kbe/src/lib/python/setup.py | Python | lgpl-3.0 | 100,060 | [
"VisIt"
] | 3cfc575ad69c7418e4cea6dbca4e79aaa8c9e290a5dafab3a222f471fe8a6afb |
# This new verion (6/11/10) hasn't been tested yet.
# Can't run unit tests on my MacPro w/o Nio.
#---------------------------------------------------
# S.D. Peckham
# Sept 2014 (new version to use netCDF4)
# May, June 2010
import os
import sys
import time
import numpy as np
import file_utils
import netCDF4 as nc
... | peckhams/topoflow | topoflow/utils/ncts_files.py | Python | mit | 27,069 | [
"NetCDF"
] | 22e06176749ed8fa18ac89e25499af145799e93d3e5785c4f39c3315a94800a8 |
"""
"""
import os
import imp
import unittest
utility = imp.load_source( 'utility', os.path.join( os.path.dirname( __file__ ), '../../util/utility.py' ) )
log = utility.set_up_filelogger( __name__ + '.log' )
utility.add_galaxy_lib_to_path( 'test/unit/web/base' )
from galaxy.web.base.pluginframework import PageServingP... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/web/base/test_PageServingPluginManager.py | Python | gpl-3.0 | 5,382 | [
"Galaxy"
] | 3019f54ad2320a538666a46b0e93e9b713e2cfa87e88303d5f60706d211ce2c2 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-gke-hub | scripts/fixup_gkehub_v1_keywords.py | Python | apache-2.0 | 6,730 | [
"VisIt"
] | 51ff8bee2c87eea5124de48945ba80cb6ed0e94a0866d79bf2d6bba614f3261c |
# Copyright 2018 The Cirq Developers
#
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | quantumlib/Cirq | cirq-core/cirq/sim/state_vector.py | Python | apache-2.0 | 14,082 | [
"DIRAC"
] | 90748fe1953eb15f0f9c309a1241acd1a9a937ac363c76712f1bfe30ac96d5cc |
""" WebApp handler for Downtimes WebApp
"""
import json
from datetime import datetime
from DIRAC import gLogger
from DIRAC.ResourceStatusSystem.Client.PublisherClient import PublisherClient
from WebAppDIRAC.Lib.WebHandler import _WebHandler as WebHandler, WErr
class DowntimesHandler(WebHandler):
DEFAULT_AUTHOR... | DIRACGrid/WebAppDIRAC | src/WebAppDIRAC/WebApp/handler/DowntimesHandler.py | Python | gpl-3.0 | 3,845 | [
"DIRAC"
] | 2ab763f3a70ce369ddebb45974a803f6044b8bf2f908c6fe962c0c92d79bf90b |
# encoding: utf-8
# py3k support
from __future__ import print_function
#import setuptools # for bdist_egg and console_scripts entry point
from setuptools import setup,Extension
#import distutils.command.install_scripts
#import distutils.command.sdist
#import distutils.command.build_ext
import os.path, os, shutil, re, ... | gladk/woodem | setup.py | Python | gpl-2.0 | 18,140 | [
"VTK"
] | 089d20606c79f78219b748151e0c21c67ea9f72c7efbc7404ff6fbdbda0cffdc |
#!/usr/bin/env python
"""Script for checking the ABINIT automatic tests."""
from __future__ import print_function, division, absolute_import #, unicode_literals
import sys
import os
from pprint import pprint
from optparse import OptionParser
try:
from cStringIO import StringIO
except ImportError:
from io imp... | abinit/abinit | tests/check_testsuite.py | Python | gpl-3.0 | 6,283 | [
"ABINIT"
] | 090964362c5a882a79798c31c5bc30b9fffc8922e53f162665cee810532c07ad |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# Proxy Agent - Agent enabling secured ingoing traffic via a MiG proxy
# without opening services to anything other than localhost.
#
# Can be used as either a library or a command-line client.
#
# @author Simon Andreas Frimann Lund
... | heromod/migrid | mig/vm-proxy/deprecated/proxyagentPreDaemon.py | Python | gpl-2.0 | 6,939 | [
"Brian"
] | 1d5ca3aba2e4815902416abb2a9f245f80e2058f029bed25dd50cc35d6210bb0 |
#!/usr/bin/python
# Copyright (C) 2016 Bitergia
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option) any later version.
#
# This program is di... | dicortazar/ceres | cereslib/events/events.py | Python | lgpl-3.0 | 35,417 | [
"Elk"
] | fd46d4d55e59b267c4e1d55d70ed6b593bec9629e5ddfc5ba9b35dd980494def |
#!/usr/bin/env python3
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | espressopp/espressopp | examples/thd_integration_solvation/methanol-TI.py | Python | gpl-3.0 | 21,683 | [
"ESPResSo",
"Gromacs"
] | c4436babc7318132c8767e1b9d4281e81a81b304a72ab7615c1eea329f80b8d6 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
#-----------------------------------------------------------------------------
# Name: setup.py
# Purpose:
# Author: Fabien Marteau <fabien.marteau@armadeus.com>
# Created: 16/02/2009
#-----------------------------------------------------------------------------
# Co... | xcthulhu/periphondemand | setup.py | Python | lgpl-2.1 | 3,550 | [
"VisIt"
] | 2dbd561d7bcbe08e762b78fd9ed447fe9010d97944dee8760038642229bbca69 |
"""
Functions for visualizing results of quantum dynamics simulations,
visualizations of quantum states and processes.
"""
__all__ = ['hinton', 'sphereplot', 'energy_level_diagram',
'plot_energy_levels', 'fock_distribution',
'plot_fock_distribution', 'wigner_fock_distribution',
'plot_w... | qutip/qutip | qutip/visualization.py | Python | bsd-3-clause | 57,042 | [
"Mayavi"
] | 3d467647404334702806693d1d7c53b3a55de071c268004f1b58b81206ef6c1d |
"""Definitions for the review request detail view."""
from __future__ import unicode_literals
import hashlib
import logging
from collections import Counter, defaultdict
from datetime import datetime
from itertools import chain
from django.db.models import Q
from django.utils import six
from django.utils.timezone imp... | chipx86/reviewboard | reviewboard/reviews/detail.py | Python | mit | 73,785 | [
"VisIt"
] | 33ddde9311250a7facc98ce85a376fe573df6f857bbe8fc855bff349fc837f16 |
import os
import shutil
import subprocess
first_revision = 1625
last_revision = 1630
make_inc="""
MAKE = make
F90 = mpif90
CXX = mpicxx
CC = mpicc
CPP_OPTS = -D_MPI_ -D_LIBAPW_
F90_OPTS = -O3 -Wall -cpp $(CPP_OPTS) -fopenmp -I/Users/anton/local/include
F90_LINK_OPTS=-fopenmp -lstdc++
#LAPACK_LIB = -llapack -lbla... | shedsaw/exciting-plus-rgvw-mod | utilities/elk-svn-test.py | Python | gpl-3.0 | 5,922 | [
"Elk",
"exciting"
] | ad4974103c79e93e12d01d4c6194f2ae355a49e5417249d683b7f01e877d4053 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes for predicting new structures from existing ones.
"""
import functools
import itertools
import logging
from operator import mul
from monty.json import MSONable
from pymatgen.alchemy.filters ... | vorwerkc/pymatgen | pymatgen/analysis/structure_prediction/substitutor.py | Python | mit | 10,471 | [
"pymatgen"
] | 0e54085c0a9a910ccbde93183074083bc3d8da860cde2bdf514578f967c2704a |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2009-2013 Zuza Software Foundation
# Copyright 2013 Evernote Corporation
#
# This file is part of Pootle.
#
# Pootle 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 Softwar... | arky/pootle-dev | pootle/apps/pootle_language/models.py | Python | gpl-2.0 | 7,236 | [
"VisIt"
] | cad3d33e3ac6a946d461ac61b98e15c088a64d2b9efc1c745d060e9610be5ed4 |
"""
This is a sample implementation for working DGL with DeepChem!
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from deepchem.models.losses import Loss, L2Loss, SparseSoftmaxCrossEntropy
from deepchem.models.torch_models.torch_model import TorchModel
class CGCNNLayer(nn.Module):
"""The co... | lilleswing/deepchem | deepchem/models/torch_models/cgcnn.py | Python | mit | 13,202 | [
"CRYSTAL",
"pymatgen"
] | 13d2de6ffd904b79d323d73f59c4ed5bd6c859b512994678eb63d9ac68340176 |
"""
===============================================
Compute all-to-all connectivity in sensor space
===============================================
Computes the Phase Lag Index (PLI) between all gradiometers and shows the
connectivity in 3D using the helmet geometry. The left visual stimulation data
are used which pro... | rajegannathan/grasp-lift-eeg-cat-dog-solution-updated | python-packages/mne-python-0.10/examples/connectivity/plot_sensor_connectivity.py | Python | bsd-3-clause | 3,926 | [
"Mayavi"
] | d9ba2b15a2a94b5b68c333bcb378b1dacb119f81e10422feb85ed56deef6547c |
data = """
type: opls_111
! O TIP3P Water
template: [O (H)(H)]
type: opls_112
! H TIP3P Water
template: [H [O(H)]]
type: opls_135
! alkane CH3
template: [C (C)(H)(H)(H)]
type: opls_136
! alkane CH2
template: [C (C)(C)(H)(H)]
type: opls_137
! alkane CH
template: [C (C)(C)(C)(H)]
type: opls_138
! a... | csmm/multiase | multiasecalc/lammps/oplsaatypes.py | Python | gpl-2.0 | 33,538 | [
"Gromacs"
] | ba3256bac192b83228d7706361b248acba86f327606bf43d3e0b34e356268fa2 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 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 General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_sellableunitsearch.py | Python | gpl-2.0 | 1,373 | [
"VisIt"
] | f305812815a00ac393e1bb97c829bb11e69253e992fc2f7e55f6b0a626f3c213 |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.com>
#
# 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 ... | simobasso/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 20,751 | [
"Galaxy"
] | fd045f7025f5b00deee66d4c61ff6eef51b30ff1362415823cd501309faad673 |
"""
.. module: FSRStools.refind
:platform: Windows
.. moduleauthor:: Daniel Dietze <daniel.dietze@berkeley.edu>
A collection of functions related to the optical refractive index.
Apart from providing tabulated indices for commonly used optical materials including dielectrics, common solvents and metals,
this... | ddietze/FSRStools | refind/__init__.py | Python | gpl-3.0 | 21,337 | [
"Gaussian"
] | c69430270301b3afd002164f27ee8ab34e0a23e6f3f9f2b8b0fe19bac34c1830 |
"""
sewpy: Source Extractor Wrapper for Python
Recent improvements (latest on top):
- better verbosity about masked output of ASSOC procedure
- ASSOC helper implemented
- run() now returns a dict containing several objects, such as the output astropy table, catfilepath, workdir, and logfilepath.
- now also works with... | dr-guangtou/hs_galphot | mask/hsRunSewpy.py | Python | bsd-3-clause | 51,622 | [
"Gaussian"
] | 3d18228bfdd88f0ca2537dcc47bc7265c75237170756c874dfeac5412e076bb5 |
# Copyright 2015 Emille Ishida
# This program is distributed under the terms of the GNU General Purpose License (GPL).
# Refer to http://www.gnu.org/licenses/gpl.txt
#
# 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 Fre... | emilleishida/snclass | snclass/bin/fit_plot_lc.py | Python | gpl-3.0 | 6,196 | [
"Gaussian"
] | dc3cde17d1383cac8b7f3cf2c5a131417cefe1ecdc5a8e0a6974e912f2ecf17f |
# -*- coding: utf-8 -*-
#GSASIImath - major mathematics routines
########### SVN repository information ###################
# $Date: 2018-06-14 01:48:33 +0300 (Thu, 14 Jun 2018) $
# $Author: vondreele $
# $Revision: 3434 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIImath.py $
# $Id: GSASIImath... | AntonGagin/GSAS_USE | patchSystErrors/originalOld/GSASIImath.py | Python | gpl-3.0 | 199,608 | [
"CRYSTAL"
] | c20343d3cd265a0d88c6af6eff6004ef8310c604235c65359c7af0de38bd8a29 |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
"""
test_cpinterface
~~~~~~~~~~~~~~
Test chemical program interface code that is not tied to any one specific
back-end.
"""
import sys
import unittest
import cpinterface
import geoprep
fr... | mattbernst/polyhartree | tests/test_cpinterface.py | Python | gpl-3.0 | 3,415 | [
"GAMESS"
] | 19f53815e9162dfcb489cd2449daf161e4d00cdef0e74150b7fbdbaa7d575419 |
"""
A Python interface for Discount, the C Markdown parser
This module contains ``libmarkdown``, a ctypes binding for Discount,
as well as ``Markdown``, a helper class built on top of this library.
Visit the Discount homepage:
http://www.pell.portland.or.us/~orc/Code/discount/
Basic usage examples:
>>> md = Mar... | trapeze/python-discount | discount/__init__.py | Python | bsd-3-clause | 11,262 | [
"VisIt"
] | f2c7fe24470fa1fb4df816d995e8d02065fbcac5afa61a8f3964781ce8a08917 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
import itk
import module_kits.itk_kit as itk_kit
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
class gaussianConvolve(ScriptedConfigModuleMixin, ModuleBase):
_orders = ['Zero', 'F... | nagyistoce/devide | modules/insight/gaussianConvolve.py | Python | bsd-3-clause | 3,720 | [
"Gaussian"
] | 42f04cabf3c278281fb629e6475954dba41152f0dd48be6f63baf58acf05c42a |
#!/usr/bin/python
# coding=utf-8
import logging as log
import argparse
import os
import datetime
import time
import urllib
import mimetypes
import BaseHTTPServer
import socket
from operator import attrgetter
VERBOSITY = (
log.ERROR,
log.WARNING,
log.INFO,
log.DEBUG,
)
class Config:
__version__ =... | tbienko/catfeed | catfeed.py | Python | mit | 10,641 | [
"VisIt"
] | 5653a1e08ca647d617f9aa2c9c19f55351d557097d42631f2b4a76c466da5a95 |
#
# 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/src/bigdl/orca/learn/pytorch/pytorch_pyspark_estimator.py | Python | apache-2.0 | 21,919 | [
"ORCA"
] | b7bff9988fb58aa0ca64a4e38fc3b0d789514994046b249369712dcd93331f73 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
#######################################################################
#
# MetrixWeather for Enigma2
# Coded by Sinthex IT-Solutions (c) 2017
# www.sinthex.de
#
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.... | openmips/stbgui | lib/python/Components/Converter/OMMetrixWeather.py | Python | gpl-2.0 | 5,193 | [
"VisIt"
] | f15b4df04f10b53d68147047e1109187d5bccbd299e732bdc8b4d8798e20fb0d |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
# This software is licensed as described in the README.rst and LICENSE files,
# which you should have received as part of this distribution.
import argparse
from raspi_sensor.main import setup_default_mqtt_args
from raspi_relay.relay import Relay
def setup_args():
ap ... | ricco386/broadcaster | RPi.Relay/raspi_relay/main.py | Python | bsd-3-clause | 1,053 | [
"VisIt"
] | 52b36d3518d5676a7632764702e293c165a93d489ea1958e92b67f4452432742 |
'''Multiple Testing and P-Value Correction
Author: Josef Perktold
License: BSD-3
'''
import numpy as np
from statsmodels.stats._knockoff import RegressionFDR
__all__ = ['fdrcorrection', 'fdrcorrection_twostage', 'local_fdr',
'multipletests', 'NullDistribution', 'RegressionFDR']
# ====================... | jseabold/statsmodels | statsmodels/stats/multitest.py | Python | bsd-3-clause | 24,374 | [
"Gaussian"
] | 50ae762692d3b20708a34beeb81d87a3dc99417d24223bbfd76cb6757b3d0cb6 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-install-mysql
# Author : Ricardo Graciani
########################################################################
"""
Do the initial installation and configuration of the DIRAC MySQL server
"""... | Andrew-McNab-UK/DIRAC | Core/scripts/dirac-install-mysql.py | Python | gpl-3.0 | 720 | [
"DIRAC"
] | f7e766af2097423f7145a981d9d33566dfe0cb105b45d8176162c13aca859f00 |
# Copyright 2010 Google Inc.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, modify, merge, publish, dis-
# trib... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/boto-2.27.0-py2.7.egg/boto/gs/key.py | Python | gpl-3.0 | 42,479 | [
"VisIt"
] | 6e035313eeef9af3346381fdc732ba9174967db01837712d5bcc577b908545a4 |
"""
Methods for dealing with the Group hierarchy.
"""
import ncobj
from ncobj import Group, Variable, Dimension, Attribute
from collections import namedtuple
def walk_group_objects(group, of_types=None):
"""
Iterate over all contained components, recursively.
Args:
* of_types (type or iterable of t... | pp-mo/ncobj | lib/ncobj/grouping.py | Python | gpl-3.0 | 14,331 | [
"NetCDF"
] | e878fad4f912c51fbbe5da4d79c8ad759e5f37e0239aace09a1219da01ef0941 |
#! /usr/bin/env python3
import sys
import os
import numpy as np
d = os.path.dirname(os.path.realpath(__file__))
sys.path.append(d+"/..")
from Functions import *
from trexi.TREXI import *
from cirexi.CIREXI import *
from brexi.BREXI import *
from elrexi.ELREXI import *
sys.path.pop()
for rexi_method in [
#"... | schreiberx/sweet | mule_local/python/mule_local/rexi/tests/test_rexi_approximations.py | Python | mit | 7,999 | [
"Gaussian"
] | b3b655288868c7b8e644f46e304e02047d79ffe98a2692c84424df8b3a6907e8 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2007, 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.community.CelerraFileSystem | ZenPacks/community/CelerraFileSystem/modeler/plugins/CelerraDf.py | Python | gpl-2.0 | 2,254 | [
"VisIt"
] | 22c63ed1fa7e507c495b3a98a986a27b340561571304fd1c25750a41b6648e79 |
# -*- coding: utf-8 -*-
"""
Created on Wed May 17 09:51:50 2017
@author: banggui
"""
import numpy as np # linear algebra
import pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)
from glob import glob
import SimpleITK as sitk
import os
import scipy.ndimage
import matplotlib.pyplot as plt
from skimage im... | shihuai/TCAI-2017 | preprocess/step1.py | Python | mit | 10,440 | [
"Gaussian"
] | b601315c8fe7c8cdf943978b9ecbb6a1ca2829d0588b3c3a56e8311f03785bf6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# 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... | richardcs/ansible-modules-core | system/systemd.py | Python | gpl-3.0 | 13,996 | [
"Brian"
] | 1349e007fa13f81e78b83c036f09a0b605e0ed8efa872da377174a05caf1b314 |
#!/usr/bin/env python
#
# $File: popInfo.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute it... | BoPeng/simuPOP | docs/popInfo.py | Python | gpl-2.0 | 1,411 | [
"VisIt"
] | 0877c2a790202924a1e61865ee2631b45749d3002fb8e96f001786117fec4f89 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/io/DumpXYZ.py | Python | gpl-3.0 | 3,334 | [
"ESPResSo"
] | a6f0431d01a0c519566a86fae030cf1667ebaaae5d5737bcff291b6d12f41653 |
"""
Implementation of ADAptive LInear NEuron (Adaline) algorithm from Chapter 2 of
"Python Machine Learning"
"""
import numpy as np
def train_adeline(observations, labels, learning_rate=0.0001, max_training_iterations=100):
"""
Trains a (binary) perceptron, returning a function that can predict / classify
... | krosaen/ml-study | python-ml-book/ch02/adeline.py | Python | mit | 1,919 | [
"NEURON"
] | 31eac43c2c6f03cd4e833bc5c818f39e7ef4b0e961e51ee4e01d597d26a4e4ee |
#!/usr/bin/python
"""
fisher.py
"""
from __future__ import print_function
import sys
import os
import re
import pysam
import scipy.special
from scipy.stats import fisher_exact as fisher
import argparse
import logging
import math
import subprocess
from . import print_vcf
from . import print_anno
from . import util
f... | Genomon-Project/GenomonFisher | genomon_fisher/fisher.py | Python | gpl-3.0 | 22,179 | [
"pysam"
] | 8ef6f886b4fb51e7d9737e8ab4599c3680cf3b89d8a7d5e98491e124d535e485 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/procrouting/dft_funcs/gga_superfuncs.py | Python | lgpl-3.0 | 8,817 | [
"Psi4"
] | 9172bf573b6621f96b340f6dc1a619bd044e9bd00c2f18ce5a90f45bafe5f250 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from .MeshV... | harterj/moose | python/peacock/Input/plugins/__init__.py | Python | lgpl-2.1 | 403 | [
"MOOSE"
] | 864abbc479c278f1542230b39a1c5a56eba768e6e71d0a35c1a53145a556153b |
'''
PartsGenie (c) University of Manchester 2017
PartsGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-arguments
# pylint: disable=too-many-branches
# pylint: disable=too-many-locals
# pylint: ... | synbiochem/PathwayGenie | parts_genie/rbs_calculator.py | Python | mit | 22,917 | [
"VisIt"
] | a3c17f1c909e8849809dbee6efa2350690a6dd736bca1c627b38f63fc62a6d7b |
# ANNarchy - AEIF_cond_exp
#
# Adaptive exponential integrate-and-fire model.
#
# http://www.scholarpedia.org/article/Adaptive_exponential_integrate-and-fire_model
#
# Introduced in
#
# Brette R. and Gerstner W. (2005), Adaptive Exponential Integrate-and-Fire Model as an Effective Description of Neuronal Activi... | vitay/ANNarchy | examples/pyNN/AEIF_cond_exp.py | Python | gpl-2.0 | 1,644 | [
"Brian",
"NEURON"
] | c162b92d51a7dc372c76d6ad2e5e340848882b8873c4d6f695935bd4c7c27752 |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
"""
Objects Maker module:
This module contains functions for creating the (singleton) objects
used by the genetic algorithm during the search.
"""
from ga... | henniggroup/GASP-python | gasp/objects_maker.py | Python | mit | 34,327 | [
"GULP",
"LAMMPS",
"VASP",
"pymatgen"
] | 71ae0ed1199bcf2cdf3a3bebc4fe1a252602d935f915f09775c95549aec7c0d2 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2009-2013 Red Hat, Inc.
# This file is part of python-fedora
#
# python-fedora 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 Lice... | nirik/python-fedora | fedora/client/proxyclient.py | Python | gpl-2.0 | 23,068 | [
"VisIt"
] | d0d50345217207aa971196386863cdfd55d138569b9ddd602cd8b0d8845132c7 |
##
# Copyright 2009-2020 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/s/sas.py | Python | gpl-2.0 | 4,717 | [
"ASE"
] | e91e5040f043fe6798c7c42dd3fc1a83a5d030a6e2ab78ab69efaa7e8c1622b2 |
"""Ops and optimizations for using BLAS calls
BLAS = Basic Linear Algebra Subroutines
Learn more about BLAS here:
http://www.netlib.org/blas/blast-forum/
The standard BLAS libraries implement what is called "legacy BLAS" in that
document.
This documentation describes Theano's BLAS optimization pipeline.
Where th... | Weihonghao/ECM | Vpy34/lib/python3.5/site-packages/theano/tensor/blas.py | Python | agpl-3.0 | 92,128 | [
"BLAST"
] | 52edf62ed62c78561bf06be2dc27bb8e2ef6e9a4f4f20ece0ba6c3bd1aac545c |
# 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... | alshedivat/tensorflow | tensorflow/python/autograph/converters/call_trees.py | Python | apache-2.0 | 12,664 | [
"VisIt"
] | d508d098e8fbd650a4af0c50ca56cfbcc28e3f717b8c1dd3662d06ceb18da9c1 |
''' Convienence methods on VTK routines only '''
import ddapp.vtkAll as vtk
import ddapp.vtkNumpy as vnp
from ddapp.shallowCopy import shallowCopy
import numpy as np
def thresholdPoints(polyData, arrayName, thresholdRange):
assert(polyData.GetPointData().GetArray(arrayName))
f = vtk.vtkThresholdPoints()
... | gizatt/director | src/python/ddapp/filterUtils.py | Python | bsd-3-clause | 2,663 | [
"VTK"
] | af3f72c340253b8a2d0136b3a12b2f40f14dd030d8a5b44140b6c91a1dd9235c |
# Copyright (C) 2014 Sereina Riniker
#
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" Torsion Fingerprints (Deviation) (TFD)
According to a paper from Schulz-Gasch et a... | AlexanderSavelyev/rdkit | rdkit/Chem/TorsionFingerprints.py | Python | bsd-3-clause | 19,695 | [
"RDKit"
] | 10c10c8ca90ddf7d28555ca209f49ab32dd5c4dcb985f2722d28ef6fcd20e401 |
import FFPopSim as h
import numpy as np
from matplotlib import pyplot as plt
import random as rd
from Bio import Phylo
print "This script is meant to illustrate and explore the effect of\n\
positive selection on genealogies in asexual and sexual populations. \n\n\
Simulations are performed using an infinite sites mode... | wrshoemaker/ffpopsim | examples/genealogies_with_selection.py | Python | gpl-3.0 | 2,468 | [
"Biopython"
] | d875232d65972c6a23545a1ab7b77a316c736e518e85a3869cb5cd21e3f553ac |
# -*- mode: python; coding: utf-8 -*-
#
# Copyright (C) 2017 <contact@redhat.com>
#
# Author: Loic Dachary <loic@dachary.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 3 o... | SpandanKumarSahu/python-crush | crush/ceph/__init__.py | Python | gpl-3.0 | 29,537 | [
"Firefly"
] | 4bcb175add4419ddb18ef99c77635ab7c85423024e222d6b5da7375b7f0c5996 |
class IOSystem(object):
def __init__(self):
pass
@classmethod
def from_file(cls,geofile,basisfile):
if geofile.endswith('.xyz'):
from moha.io.iogeometry import load_xyz
molecule = load_xyz(geofile)
else:
raise ValueError('Unknown file format')
... | fhqgfss/MoHa | moha/io/iosystem.py | Python | mit | 764 | [
"NWChem"
] | 3f487411dddc33ea5077ded5356c9b1b7e6070616857b40bc0124c75f73988e9 |
__all__ = ['weingarten_image_curvature']
import numpy as np
from .. import core
from ..core import ants_image as iio
from .. import utils
def weingarten_image_curvature(image, sigma=1.0, opt='mean'):
"""
Uses the weingarten map to estimate image mean or gaussian curvature
ANTsR function: `weingartenIm... | ANTsX/ANTsPy | ants/utils/weingarten_image_curvature.py | Python | apache-2.0 | 1,875 | [
"Gaussian"
] | 994c8a89f16e3f6ebea67e15b8b940daf8dfc3d744badff0bef0291ffac28d79 |
''' Provide a base class for all objects (called Bokeh Models) that can go in
a Bokeh |Document|.
'''
from __future__ import absolute_import, print_function
import logging
logger = logging.getLogger(__file__)
from json import loads
from operator import itemgetter
from six import iteritems
from .core.json_encoder i... | DuCorey/bokeh | bokeh/model.py | Python | bsd-3-clause | 25,355 | [
"VisIt"
] | 244c855f4d74fcf1ba8dcd98218b3adea16e6f33bc3499f75996c038ca2a9e25 |
import sys
sys.path.insert(1, "../../../")
import h2o, tests
def link_correct_default(ip,port):
print("Reading in original prostate data.")
h2o_data = h2o.upload_file(path=h2o.locate("smalldata/prostate/prostate.csv.zip"))
print("Compare models with link unspecified and canonical link specified.")
print("GAU... | bospetersen/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_link_correct_default_largeGLM.py | Python | apache-2.0 | 1,995 | [
"Gaussian"
] | 864668a50556700f0467935b9a7db1f541942a5ede07357e8ee633d28e413b71 |
from pyv8 import PyV8
import datetime
class Console(PyV8.JSClass):
def log(self, text):
print "[JAVASCRIPT LOG] %s" % text
class Unknown(PyV8.JSClass):
def __init__(self):
self.isUnknown = True
def __getattr__(self, nm):
return Unknown()
def __call__(self, v):
return... | wayetender/whip | whip/src/adapter/util/js.py | Python | gpl-2.0 | 9,411 | [
"VisIt"
] | de5ef1b613349914478901ef7600205110dcfd4db1b30e1c8e6148480fd32843 |
# This file is part of ts_wep.
#
# Developed for the LSST Telescope and Site Systems.
# This product includes software developed by the LSST Project
# (https://www.lsst.org).
# See the COPYRIGHT file at the top-level directory of this distribution
# for details of code ownership.
#
# This program is free software: you ... | lsst-ts/ts_wep | tests/task/test_generateDonutCatalogWcsTask.py | Python | gpl-3.0 | 12,707 | [
"VisIt"
] | bf6148f98e9e3c457be3c0d5b5ba006fade9ea84b05eb7e983304cce40d5a2d2 |
"""Utility routines to handle degeneracy."""
# Copyright (C) 2014 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source c... | atztogo/phonopy | phonopy/phonon/degeneracy.py | Python | bsd-3-clause | 5,261 | [
"phonopy"
] | 4e9f519e2651abc50157fd2c09a1983ae095166d953c5db63498851b923f9b98 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
class Node(object):
"""Node class collects helper functions for BinarySearchTree."""
def __init__(self, val, left=None, right=None, parent=None):
self.val = val
self.left = left
... | bowen0701/algorithms_data_structures | ds_binary_search_tree.py | Python | bsd-2-clause | 13,181 | [
"VisIt"
] | 9a795b971cde79d805db0bb127bc7f2e4b707d1c3f660cbf7c5f0f7d2e893c8c |
#!/usr/bin/python
#-*- coding: UTF-8 -*-
# File: blocks.py
# Solely for identifying Unicode blocks for unicode characters.
# Based on code from:
# http://stackoverflow.com/questions/243831/unicode-block-of-a-character-in-python
# But updated for 2013.
# Copyright (C) 2013-2020 Peter Murphy <peterkmurphy@gmail.com>
#
# ... | peterkmurphy/glyphviewer | glyphviewer/blocks.py | Python | gpl-3.0 | 13,058 | [
"FEFF"
] | bc2e8e1559fce0fb42cb1a9c8c57627d4416f8d5364b84af512dd50ec4f1ee96 |
import vtk, qt, slicer
import os, sys, shutil
import uuid
from scipy import io
import numpy as np
from . import WarpDriveUtil, GridNodeHelper
import ImportSubject
try:
import h5py
except:
slicer.util.pip_install('h5py')
import h5py
try:
import hdf5storage
except:
slicer.util.pip_install('hdf5storage')
im... | andreashorn/lead_dbs | ext_libs/SlicerNetstim/WarpDrive/WarpDriveLib/Helpers/LeadDBSCall.py | Python | gpl-3.0 | 8,726 | [
"VTK"
] | 920650df2fc02c1f34cfb4e53b6e10599596642f7197258c05e8fff70ff4560f |
import gpflow
import gpflowopt
import numpy as np
from ..utility import GPflowOptTestCase
class TestRecompile(GPflowOptTestCase):
"""
Regression test for #37
"""
def test_vgp(self):
with self.test_session():
domain = gpflowopt.domain.UnitCube(2)
X = gpflowopt.design.Ran... | GPflow/GPflowOpt | testing/unit/test_regression.py | Python | apache-2.0 | 1,146 | [
"Gaussian"
] | a4db539da586cb0c1523a5f82bfdcb46e2e6facff7c7e5dc4f5e8d9519988230 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rabipanda/tensorflow | tensorflow/contrib/py2tf/converters/break_canonicalization.py | Python | apache-2.0 | 3,729 | [
"VisIt"
] | f84307d99c0736f34a9646f354ac1bae3c29be80c415f8cdc916b3158877c3a9 |
class BladeMap(object):
'''
A Map Relating Blades in two different algebras
Examples
-----------
>>> from clifford import Cl
>>> # Dirac Algebra `D`
>>> D, D_blades = Cl(1, 3, firstIdx=0, names='d')
>>> locals().update(D_blades)
>>> # Pauli Algebra `P`
>>> P, P_blades = Cl(3,... | arsenovic/clifford | clifford/_blademap.py | Python | bsd-3-clause | 1,846 | [
"DIRAC"
] | edbb42f19d3848f822bf51315156c3473d8771326eb80e9ec8446b7cf3c1ca96 |
#!/usr/bin/python
import Scientific.IO.NetCDF as nc
import numpy as np
import sys
import math
import pylab as pl
import matplotlib.colors as colors
from numpy import floor, sqrt, sin, cos, arccos, arctan2, pi
fName = sys.argv[1]
try:
dFile = nc.NetCDFFile(fName, "r")
except IOError:
print "Error reading file, e... | dronir/EM | python/xrSingleDirPlot.py | Python | gpl-3.0 | 2,663 | [
"NetCDF"
] | 12bdcd0683e26293ef5c29f43a3ee4a64dfb61f10b09b4b6b4ae0d7bb53c74b4 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""Utilities for handling, displaying and exporting Phylo trees.
Third-party libraries ... | asherkhb/coge | bin/last_wrapper/Bio/Phylo/_utils.py | Python | bsd-2-clause | 14,391 | [
"Biopython"
] | 158e109db405b0201ecc220502349af4cc465f177c5edbfbff1a92d4474e6bf4 |
from ...common import RTOL, ATOL, pandas
from ...cg.kdtree import KDTree, RADIUS_EARTH_KM
from ..util import get_points_array
from ... import cg
from ... import weights
from .. import distance as d, contiguity as c
from ...io import geotable as pdio
from ...io.fileio import FileIO as psopen
import numpy as np
from ...... | lixun910/pysal | pysal/lib/weights/tests/test_distance.py | Python | bsd-3-clause | 12,184 | [
"COLUMBUS",
"Gaussian"
] | 7f4875fa4d7ae128e4efb63077eb89195c82ccc31f3e211a9a315891ec7a000f |
# pylint: disable=arguments-differ
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import json
import analytics
from io import BytesIO
from django.db.models import Q, F
import py... | louyihua/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 91,614 | [
"VisIt"
] | b6e96c1a57c3b7548dc5c9d40ddd185de0139f802dda84156bb9b82cf968c6c1 |
#-------------------------------------------------------------------------------
# . File : QMCallerGaussian.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#--------------------------------------------... | mfx9/MolarisTools | MolarisTools/QMMM/QMCallerGaussian.py | Python | gpl-3.0 | 7,677 | [
"Gaussian"
] | 8eb4f29bdecabad18e6679cc2b6bb4961f8e1b9e0d4814e4e24f4e9995804b96 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
from __future__ import division
from __future__ import unicode_literals
from deepchem.feat import Featurizer
class RawFeaturizer(Featurizer):
def __init__(self, smiles=False):
self.smiles = smiles
def _featurize(self, mol):
from rdkit import Chem
if se... | ktaneishi/deepchem | deepchem/feat/raw_featurizer.py | Python | mit | 393 | [
"RDKit"
] | 3ca9cf586fec67f996d3b5c71bca609f0ad383574ca3bb8c63c4cdac44094c3b |
# -*- coding: utf-8 -*-
# Copyright 2020 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... | sasha-gitg/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_featurestore_online_serving_service.py | Python | apache-2.0 | 62,346 | [
"Octopus"
] | e57972c747389e180e63b207e970e1dd18aecf79c34f187771d58293499ac24b |
"""
Classes of taxonomy data
"""
import os
import sys
class NoNameFoundError(Exception):
"""No name was found for this entry"""
def __init__(self, message):
self.message = message
class TaxonNode:
def __init__(self, t=None, p=None, r=None, e=None, d=None, i=None, gc=None, igc=False, mgc=None, i... | linsalrob/EdwardsLab | taxon/taxonomy/taxonomy.py | Python | mit | 4,030 | [
"BLAST"
] | 696ab896f17c31a8e99d946449be4c2bb25442bbc3fd080a768186bd5cc55b88 |
# gaussfitter.py
# created by Adam Ginsburg (adam.ginsburg@colorado.edu or keflavich@gmail.com) 3/17/08)
# latest version available at http://code.google.com/p/agpy/source/browse/trunk/agpy/gaussfitter.py
import numpy
from numpy.ma import median
from numpy import pi
#from scipy import optimize,stats,pi
from mpfit impor... | chrox/RealTimeElectrophy | Experimenter/DataProcessing/Fitting/gaussfitter.py | Python | bsd-2-clause | 26,671 | [
"Gaussian"
] | 4cf256a467c1edc543d0699f301197c9977b399a311e10715ec437c64f9b1ef9 |
from rdkit import DataStructs
from rdkit import RDConfig
import unittest, os
def feq(a, b, tol=1e-4):
return abs(a - b) < tol
class TestCase(unittest.TestCase):
def setUp(self):
self.dirname = os.path.join(RDConfig.RDBaseDir, 'Code', 'DataStructs', 'testData')
self.filename = os.path.join(self.dirname,... | rvianello/rdkit | Code/DataStructs/Wrap/testFPB.py | Python | bsd-3-clause | 11,861 | [
"RDKit"
] | 8df5a368dcd2d58950e85020b8c815a2ae75687741e9d14345f1593563ea646a |
"""
It is used to test client->db-> service.
It requires the Monitoring service to be running and installed (so discoverable in the .cfg),
and this monitoring service should be connecting to an ElasticSeach instance
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import pr... | ic-hep/DIRAC | tests/Integration/Monitoring/Test_MonitoringSystem.py | Python | gpl-3.0 | 8,716 | [
"DIRAC"
] | 6edffc73eea2bce63eae2cebc65a406da4edcc8063265e42746241d5af985daa |
from sqlalchemy import *
from migrate import *
import datetime
now = datetime.datetime.utcnow
# Need our custom types, but don't import anything else from model
from galaxy.model.custom_types import *
import logging
log = logging.getLogger( __name__ )
metadata = MetaData( migrate_engine )
# New table in changeset ... | volpino/Yeps-EURAC | lib/galaxy/model/migrate/versions/0002_metadata_file_table.py | Python | mit | 971 | [
"Galaxy"
] | 1e0170502414d39a278295a4272bb5654f9c127f603f5b166ec0daed5f616a39 |
import tensorflow as tf
import numpy as np
import autoencoder
import datasets
# #################### #
# Flags definition #
# #################### #
flags = tf.app.flags
FLAGS = flags.FLAGS
# Global configuration
flags.DEFINE_string('model_name', '', 'Model name.')
flags.DEFINE_string('dataset', 'mnist', 'Which ... | HoliestCow/ece692_deeplearning | project3/run_autoencoder.py | Python | mit | 5,200 | [
"Gaussian"
] | 250f9b03e53f646831481a4b98ab46282cb063208e0b4a9585d54b4c0ed32ca7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright © 2016 Matthew Stone <mstone5@mgh.harvard.edu>
# Distributed under terms of the MIT license.
"""
"""
import sys
import argparse
import re
from collections import Counter
import numpy as np
import pysam
from rpc import ReadPair
META = """##fileformat=VCFv4.... | talkowski-lab/Holmes | readpaircluster/rpc2vcf.py | Python | mit | 11,914 | [
"pysam"
] | 5ccf3415da47945156f88045cea4db8e6836b828550f4a9fc2f77ac4b67657d2 |
#!/usr/bin/env python3
#
# Argument Clinic
# Copyright 2012-2013 by Larry Hastings.
# Licensed to the PSF under a contributor agreement.
#
import abc
import ast
import collections
import contextlib
import copy
import cpp
import functools
import hashlib
import inspect
import io
import itertools
import os
import pprint
... | FFMG/myoddweb.piger | monitor/api/python/Python-3.7.2/Tools/clinic/clinic.py | Python | gpl-2.0 | 154,883 | [
"VisIt"
] | 737cba91663d9d65df55fd85462596d154d061a953c1d437a5f79e5a6a50ce0e |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
import sys
class TextProgress:
def __init__(self):
self.nstep = 0
self.text = None
self.ol... | cclib/cclib | cclib/progress/textprogress.py | Python | bsd-3-clause | 1,307 | [
"cclib"
] | 100f44bfddc25546a54c49f4c3ff6b04b0bc0e3d1621ec5846bd535f04489c91 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
#from enthought.tvtk.api import tvtk
#from enthought.tvtk.tools import ivtk
#from mayavi import ivtk
#from gui.plotutils import AsyncCall
#from enthought.traits.api import Instance
#from ray_trace.system import System
#from wx import CallAfter
#class _PlotFrame(ivtk.IVT... | coupdair/pyoptools | pyoptools/gui/plot_frame.py | Python | bsd-3-clause | 3,213 | [
"Mayavi"
] | 146465a3b164499a520b447771e05a7b7044b5bee5534175b10109281869e864 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | keras-team/keras | keras/layers/regularization/gaussian_dropout.py | Python | apache-2.0 | 2,819 | [
"Gaussian"
] | 236ad0f8b44fc0ac2926592e3e067295ec4d78f159934e089003d2712ab6a129 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.