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 |
|---|---|---|---|---|---|---|---|
# Copyright (C) 2021 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU Affero General Public License version 3, or any later version
# See top-level LICENSE file for more information
from typing import Set
from django.core.management.base import Ba... | SoftwareHeritage/swh-web-ui | swh/web/common/management/commands/refresh_savecodenow_statuses.py | Python | agpl-3.0 | 2,391 | [
"VisIt"
] | 242990c6aef528c3f70edb8981610a708f33f570f56bc823582d44fceb14f17d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import os
from datetime import datetime
from django.test import SimpleTestCase
from django.utils import html, safestring, six
from django.utils._os import upath
from django.utils.encoding import force_text
from django.utils.functional import la... | yephper/django | tests/utils_tests/test_html.py | Python | bsd-3-clause | 10,232 | [
"ADF"
] | 633c72a06aacbf17691c10d86d29377e9e3e7f61e1372b81ac8071d91ddf49f9 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/cc/gccsd_t_lambda.py | Python | apache-2.0 | 5,817 | [
"PySCF"
] | c381ceeddfa81098bc94a72478375629cef62d2586f79c1662a6b0d8b6a3d037 |
#!/usr/bin/env python
""" Get a proxy from the proxy manager
"""
from __future__ import print_function
import os
from DIRAC.Core.Base import Script
Script.setUsageMessage( '\n'.join( [ __doc__.split( '\n' )[1],
'Usage:',
' %s [option|cfgFile] U... | petricm/DIRAC | tests/Jenkins/dirac-proxy-download.py | Python | gpl-3.0 | 1,283 | [
"DIRAC"
] | 2722986168876a1285c3862eb7cc62798e3d141f4ea63bdc8b87d5b17417c9a1 |
""" Client for the SandboxStore.
Will connect to the WorkloadManagement/SandboxStore service.
"""
__RCSID__ = "$Id$"
import os
import tarfile
import hashlib
import tempfile
import re
import StringIO
from DIRAC import gLogger, S_OK, S_ERROR, gConfig
from DIRAC.Core.DISET.TransferClient import TransferClient
from... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Client/SandboxStoreClient.py | Python | gpl-3.0 | 12,273 | [
"DIRAC"
] | 2ea9fe923ca1ec0b692a7dbb11acff4c770e0ddf29c6aa66773d27c52846fcf6 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* Copyright (c) Schrodinger, LLC.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove this copyright notice.
#F* -------... | gratefulfrog/lib | python/pymol/xray.py | Python | gpl-2.0 | 173,446 | [
"PyMOL"
] | c69b98a457062b05168e1c2646f13f046339531434537ef5dc716bb2079665ee |
"""
Provide data from text files while transparently caching for efficiency.
This module handles the loading of external data used to initialise the
core smact.Element and smact.Species classes. It implements a
transparent data-caching system to avoid a large amount of I/O when
naively constructing several of t... | WMD-group/SMACT | smact/data_loader.py | Python | mit | 22,600 | [
"pymatgen"
] | 2ae9962598357647e709fd91481c4988df3bd2c33f6187c4464fd2ff7a4f67ef |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin1 = vtk.vtkRenderWindow()
renWin1.AddRenderer(ren1)
importer = vtk.vtk3DSImporter()
importer.SetRenderWindow(renWin1)
importer.ComputeNormalsOn()
impor... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/Hybrid/Testing/Python/largeImageOffset.py | Python | gpl-3.0 | 1,600 | [
"VTK"
] | 1d3952cac44027085461fee455837b40d34ec95d5b0b21e1ea3c845638458038 |
from __future__ import print_function
import os
import re
import sqlite3
import sys
import numpy as np
from Bio import SeqIO
from cachetools import LRUCache, cachedmethod
from collections import defaultdict
from functools import partial
from json import load
from operator import attrgetter, itemgetter
from os.path imp... | acorg/dark-matter | dark/civ/proteins.py | Python | mit | 94,022 | [
"Biopython"
] | 74f295bc567706443e12c12d7288c6d82febdffd7a97ad0832fa8343e4769d3d |
#!/usr/bin/env python
from Bio import Entrez, SwissProt
Entrez.email="name@domain.com"
# get info about NCBI databases
handle = Entrez.einfo()
record = Entrez.read(handle)
print record
# define database
db="protein"
# look for `opsin 1` from human p53_human
query = '"opsin 1" AND "homo sapiens"[organism]'
handle = E... | lpryszcz/bin | teaching/idt10.py | Python | gpl-3.0 | 2,730 | [
"BLAST"
] | c289c8394f491a8dcfe6415e2868c835ffa67568c6aef29ba0f84d9a3f90b933 |
import random
from hashlib import md5
from DIRAC.Core.Utilities.ThreadSafe import Synchronizer
from DIRAC.Core.DISET.private.BaseClient import BaseClient
from DIRAC.Core.DISET.private.MessageBroker import getGlobalMessageBroker
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR, isReturnStructure
from DIRAC.C... | DIRACGrid/DIRAC | src/DIRAC/Core/DISET/MessageClient.py | Python | gpl-3.0 | 5,645 | [
"DIRAC"
] | af6849e21bdc3f86579b18ba1a1b95623f9e9ab273c8e75f3a190835206d736b |
"""Main script.
Command line args:
config file that starts with "sim".
Usage:
python flexce.py ../config/sim0.cfg
"""
from __future__ import print_function, division, absolute_import
import os
from os.path import join
import sys
import numpy as np
from fileio.cfg_io import read_sim_cfg
from fileio.pickle_... | bretthandrews/flexCE | flexCE/flexce.py | Python | mit | 4,481 | [
"Galaxy"
] | e470b27fe3098ca209f0a9e155644ae228fe5b319af758d6c180b70624e21aa6 |
# -*- coding: utf-8 -*-
"""Tests for :mod:`pybel.struct`."""
| pybel/pybel | tests/test_struct/__init__.py | Python | mit | 62 | [
"Pybel"
] | f0eb4aa787ff724ed86f14a763db40a3b03338071f69279a00f21c872c188d86 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | JWDebelius/scikit-bio | skbio/io/tests/test_registry.py | Python | bsd-3-clause | 40,044 | [
"scikit-bio"
] | ad4b19e113d8c19fd8fb48929a1d44cb23db1b127a369d1fd4a6253752c1e6e8 |
# This file is part of PyEMMA.
#
# Copyright (c) 2015, 2014 Computational Molecular Biology Group, Freie Universitaet Berlin (GER)
#
# PyEMMA 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 versi... | markovmodel/PyEMMA | pyemma/coordinates/data/featurization/util.py | Python | lgpl-3.0 | 10,552 | [
"MDTraj"
] | 3cde45bdbcfd64354d57238dfc6bb89e94b21a7daf3d5b8c0c71fa590d1e65cb |
#parsing the xml output
import os
import re
import subprocess
from Bio.Blast import NCBIXML
from Bio import Entrez
from Bio import SeqIO
genotypes = ["Cvi", "Ler"]
roi = {1:[[174952, 3112850], [23698501, 24905939]]}
Entrez.email = ""
print "starting with:"
os.getcwd()
for g in genotypes: # g = geno type
geno = ... | tgbio/function | arabidopsis_call_semphy.py | Python | apache-2.0 | 1,789 | [
"BLAST"
] | a983c6a3977d326a33e0f1fca27babed16811cbd641b41f3503c7ba4a4b1a767 |
from __future__ import division
from __future__ import print_function
from past.utils import old_div
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import pandas as pd
import zipfile
import statsmodels.api as sm
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
def link... | YzPaul3/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_link_functions_gaussian_glm.py | Python | apache-2.0 | 1,710 | [
"Gaussian"
] | b88f95fcedc22e9a8d89b9dc570bc87f11e53d188260b4e545890ec5002041b5 |
from PySide import QtGui, QtCore, QtSql
import Util
class TabAdmin(QtGui.QTabWidget):
def __init__(self, parent):
super(TabAdmin, self).__init__(parent)
# Inherit stuff
self.parent = parent
self.statBar = parent.statBar
self.db = parent.db
self.viewShitList = QtGu... | galbrads/Gear_Manager | TabAdmin.py | Python | mit | 15,983 | [
"COLUMBUS"
] | 77509dd3f0b9b8800bf32a79b96e24eb8441d74f141dcc32e8b48cd99b5bcba8 |
"""Compatibility fixes for older versions of libraries
If you add content to this file, please give the version of the package
at which the fix is no longer needed.
# originally copied from scikit-learn
"""
# Authors: Emmanuelle Gouillart <emmanuelle.gouillart@normalesup.org>
# Gael Varoquaux <gael.varoquau... | drammock/mne-python | mne/fixes.py | Python | bsd-3-clause | 36,671 | [
"Gaussian"
] | 87f73618cda93a6a2e3ae44478b720f94143d56ba2ec1a2e3ce6079fba2552c9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Zappa CLI
Deploy arbitrary Python programs as serverless Zappa applications.
"""
from __future__ import unicode_literals
from __future__ import division
from past.builtins import basestring
from builtins import input, bytes
import argcomplete
import argparse
import... | longzhi/Zappa | zappa/cli.py | Python | mit | 98,542 | [
"VisIt"
] | ca41f2b0cbdc203340515ee48acf18b7a4cf03b49e2450e22357709d4b5218f8 |
#!/usr/bin/python
#
# pir.py
# Detect movement using a PIR module
#
# Author : Joe Lones
# Date : 21/01/2013
# Import required Python libraries
import RPi.GPIO as GPIO
import time
import signal
import sys
import subprocess
import os
import logging
import ConfigParser
import datetime
import threading
import glob
impo... | zach714/PiHQ | bin/pir/pir.py | Python | mit | 10,758 | [
"VisIt"
] | 05141779818b89fdaadf551ff681282f51504371ffa3ce456392457bda8220a7 |
import json
class lattice_node:
'''used int fca_lattice'''
def __init__(self,i,u,d,a,o,oi):
self.intent = a
self.object = o
self.object_index = oi
self.up = u
self.down = d
self.index = i
self.weight = 1
def __str__(self):
return str([self.ind... | kis3lori/fca-tools-bundle | bin/fca/gistfile1.py | Python | gpl-3.0 | 13,154 | [
"VisIt"
] | b9543a8e960cca7697822a2427488f47bc054db3240b097e5dc45df3bd5084b8 |
#! /usr/bin/env python
# FIXME: if it requires a dirac.cfg it is not a unit test and should be moved to tests directory
from __future__ import print_function
import unittest
import time
import os
import shutil
import sys
import types
from DIRAC.Core.Base.Script import parseCommandLine, getPos... | fstagni/DIRAC | Resources/Storage/test/FIXME_Test_StorageElement.py | Python | gpl-3.0 | 38,940 | [
"DIRAC"
] | 7e3590f8fbf2c02d1b615762844fe51e33858940c3d954c36b62da636c75b894 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-yapsa/package.py | Python | lgpl-2.1 | 2,814 | [
"Bioconductor"
] | b4f7e2a2564e813c473714df6a037e10d411fbb798a8f5c8f3e5ff0a42f33164 |
import copy
import csv
import datetime
import json
import mock
import re
import urllib
import pyquery
from cStringIO import StringIO
from nose.tools import eq_, ok_, assert_raises
from nose.plugins.skip import SkipTest
from django.test.client import RequestFactory
from django.test.utils import override_settings
from ... | Tchanders/socorro | webapp-django/crashstats/crashstats/tests/test_views.py | Python | mpl-2.0 | 199,378 | [
"VisIt"
] | f61af671b0e2dc4a6cafaa9100d38941dda64b8918fd86448431edd9b0ec0cdc |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013-2015 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/domain/workorder.py | Python | gpl-2.0 | 61,958 | [
"VisIt"
] | 1ad39b16beb571789134f2202001189d8c2bf5aaab35b43dd829281bdca07ad8 |
"""Tests for utilities module"""
import json
import pytest
from onix import scrapers
from onix import utilities
from onix.model import PokeStats, Forme, Moveset
class TestSanitizeString(object):
def test_sanitize_string_1(self):
input_string = 'Rayquaza-Mega-X'
expected = 'rayquazamegax'
... | Antar1011/Onix | tests/test_utilities.py | Python | gpl-3.0 | 15,055 | [
"BLAST"
] | bbaaa47b584088e8a5d03a632e1fda76f893421ead80ead7f027467f497c01da |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | psci2195/espresso-ffans | samples/slice_input.py | Python | gpl-3.0 | 2,787 | [
"ESPResSo"
] | 8c11c163b9d5f33d8c0a17061a10bc46507daa05f3ce8ad739c0219c49b6b80d |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-reset-job
# Author : Stuart Paterson
########################################################################
"""
Reset a job or list of jobs in the WMS
Example:
$ dirac-admin-reset-job 1848
Rese... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_reset_job.py | Python | gpl-3.0 | 1,309 | [
"DIRAC"
] | ecce8d92b41e028254823efe7a9775c366295ed7a9f56743cf5f118b9f89423b |
"""
Role: takes a job as an argument and updates various parameters
"""
import Tkinter
import Pmw
import tkFileDialog
import viewer.initialisetk
import os,getpass
from viewer.paths import paths
from viewer.defaults import defaults
class EntryPair( Tkinter.Frame ):
""" A widget with two Pmw entry frames that has... | alexei-matveev/ccp1gui | interfaces/jobed.py | Python | gpl-2.0 | 51,732 | [
"GAMESS"
] | f405e7d55736699b08d27d5c50628881d8ced3c2d37944c0d17d8ffc468dca89 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Copyright (C) 2020 Computational Neuroscience Group, NMBU.
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 you... | LFPy/LFPy | LFPy/eegmegcalc.py | Python | gpl-3.0 | 23,731 | [
"NEURON"
] | fd66094e6594037007ca9ad146ccb6c72b9d2867975f430f514783b0278ced6e |
# Copyright 2000 by Jeffrey Chang. 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.
"""Collection of modules for dealing with biological data in Python.
The Biopython Project is ... | zjuchenyuan/BioWeb | Lib/Bio/__init__.py | Python | mit | 3,699 | [
"Biopython"
] | c6e3332ebb75338ba0f22071641f1ac036b6964e1501ba3d5c18e0a1eb9f3ead |
""" Abstracts the Gradient editors provided for Qt and wxPython so these
can be used from TraitsUI.
Author: Prabhu Ramachandran
Copyright (c) 2012-2013 Enthought Inc., Mumbai, India.
"""
from traits.etsconfig.api import ETSConfig
from traitsui.api import CustomEditor
from tvtk.api import tvtk
#####################... | dmsurti/mayavi | tvtk/util/traitsui_gradient_editor.py | Python | bsd-3-clause | 3,430 | [
"VTK"
] | 5a38cdcccc00ecdae53717e2af78d5f22f7bec6966ed10b450efbe748bba4734 |
###############################################################################
##
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary forms, with or without
## modification, ... | Nikea/VisTrails | vistrails/packages/vtk/identifiers.py | Python | bsd-3-clause | 1,966 | [
"VTK"
] | 7356ab4aad0a7ef765c18d1a03cd80648a5c8a21387938bbf17d8ff4406d4e1f |
"""Importers for bookmarks"""
import json
import os
import random
import string
import time
import transaction
from datetime import datetime
from dateutil import parser as dateparser
from BeautifulSoup import BeautifulSoup
from lxml import etree
from lxml.etree import XMLSyntaxError
from bookie.lib.urlhash import gene... | ojengwa/Bookie | bookie/lib/importer.py | Python | agpl-3.0 | 20,421 | [
"VisIt"
] | e9f83231e830749da8ead454d9115ffb1dbc0f96b7bb7d6459f3b5979e381e66 |
"""
Classes encapsulating Galaxy tool parameters.
"""
from basic import *
from grouping import *
from galaxy.util.json import *
def visit_input_values( inputs, input_values, callback, name_prefix="", label_prefix="" ):
"""
Given a tools parameter definition (`inputs`) and a specific set of
parameter `val... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/parameters/__init__.py | Python | gpl-3.0 | 5,818 | [
"Galaxy",
"VisIt"
] | 986f694130c4663de4a687399a3ed9d32aeb570a38308539b4717cac2a2da442 |
import director.applogic as app
from director import lcmUtils
from director import transformUtils
from director import visualization as vis
from director import filterUtils
from director import drcargs
from director.shallowCopy import shallowCopy
from director.timercallback import TimerCallback
from director import vtk... | manuelli/director | src/python/director/cameraview.py | Python | bsd-3-clause | 32,679 | [
"VTK"
] | 88fe90dc4d20a5c27b3d016a6698d7934515129f368cdc08e6a8e8e637834464 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-acde/package.py | Python | lgpl-2.1 | 2,247 | [
"Bioconductor"
] | 30cd10b60ebad415f1b5279ebb90f6bc22296545d0d5973d8bb70291318bdf90 |
########################################################################
# $HeadURL$
# File : InputDataAgent.py
########################################################################
"""
The Input Data Agent queries the file catalog for specified job input data and adds the
relevant information to the job opti... | fibbo/DIRAC | WorkloadManagementSystem/Executor/InputData.py | Python | gpl-3.0 | 13,531 | [
"DIRAC"
] | 2f56e4e860ef33f9ea890343d02bee0157e625a52b4e4956900b3a525f6f3bd8 |
from django.forms import ModelForm, Textarea
from django.core.exceptions import ValidationError
from django import forms
from django.utils.translation import ugettext_lazy as _
from .models import Voorval, Club, Maatregel, AantalStarts, Bestand, Club_mail
class VoorvalForm(ModelForm):
boolean_set = ( 'mens', 'uitr... | jefke-glider/gliding | ato/report_ia/forms.py | Python | mit | 10,170 | [
"Elk"
] | a273c070597d9210dc9d820a4a70914d2949db9c2908cb5b7560ae2ad26b8453 |
# Filename: cider.py
#
# Description: Describes the class to compute the CIDEr (Consensus-Based Image Description Evaluation) Metric
# by Vedantam, Zitnick, and Parikh (http://arxiv.org/abs/1411.5726)
#
# Creation Date: Sun Feb 8 14:16:54 2015
#
# Authors: Ramakrishna Vedantam <vrama91@vt.edu> and Tsung-... | danieljl/keras-image-captioning | pycocoevalcap/cider/cider.py | Python | mit | 1,678 | [
"Gaussian"
] | 2a9f2e5a65b187da1f713a6451402a7e6f80edad3d499d62dd1b4e38f00e265f |
import click
import subprocess
import os
import re
import yaml
import csv
from dgl import library_constants
@click.group()
def cli():
pass
@cli.command()
@click.argument('fasta_in')
@click.argument('index_prefix')
@click.argument('mm')
@click.argument('chromosome_constant')
@click.argument('five_prime_trim', de... | DeskGen/dgcli | library_design/dgl/bowtie_testing.py | Python | gpl-2.0 | 8,666 | [
"Bowtie"
] | f6d4535217e1e0ea2f17cbf02810ece0c80a8fa21c989b92eecbac579ed09bf1 |
# sql/compiler.py
# Copyright (C) 2005-2014 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.com... | FRC-Team-3140/north-american-happiness | lib/python2.7/site-packages/sqlalchemy/sql/compiler.py | Python | mit | 111,213 | [
"VisIt"
] | 2c45b1fa97be71b5f0bbde9d9b1fe079d282a8f645c3b543363ff567b3ca3fbb |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | yipenggao/moose | python/chigger/tests/contours/levels.py | Python | lgpl-2.1 | 1,454 | [
"MOOSE",
"VTK"
] | 9422106638de89f2ce979b229e8f12df6c8c977a060e0aa8ab6b80c2849acb59 |
#assume price and category are given:
from PIL import Image
import sys
import math
import numpy
import json
import sys
import os
import web
import sqlite3 as sqlite
# set boundaries in query_padmapper
# from query_padmapper import MAX_LAT, MAX_LON, MIN_LAT, MIN_LON
APP_PATH = os.getcwd()
MIN_LAT = 37.3
MAX_LAT = 37... | selinerguncu/Yelp-Spatial-Analysis | maps/pilMap.py | Python | mit | 8,141 | [
"Gaussian"
] | 4ae970246a28bf577b796f29e6ec3dca1860eeaafd45452b3f5ef9b82cec73f2 |
"""
Copyright 2019 Google Inc. All Rights Reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in... | google-pay/passes-rest-samples | python/resourceDefinitions.py | Python | apache-2.0 | 26,466 | [
"VisIt"
] | 7a330c473175becc197f36cadd778cfe9615e78b43e8d55d9b585bc65a2513e4 |
"""
Extract Topography
~~~~~~~~~~~~~~~~~~
This example will demonstrate how to add a cell data field to an input data
set that defines whether that cell should be active. The activity of the cell
is determined by whether it is beneath and input topography surface.
This filter adds a new cell data field to an input d... | banesullivan/ParaViewGeophysics | examples/grids/extract-topography.py | Python | bsd-3-clause | 4,058 | [
"ParaView",
"VTK"
] | bb5c43b4d553ed6dc54a804a5bd8d96119f0f75188532ee7085dd6ec9749e13f |
from __future__ import absolute_import
import numpy as np
from sklearn.base import BaseEstimator, clone
from sklearn.utils import check_array, as_float_array
from joblib import Parallel, delayed
from functools import partial
from .inverse_covariance import _init_coefs
from . import QuicGraphicalLasso
def _check_psd... | skggm/skggm | inverse_covariance/model_average.py | Python | mit | 14,919 | [
"Gaussian"
] | 5c43c85a7bff89e0135bc344b3afc427c3ef8e01d7079e7b5c1f6e124f925698 |
import unittest
import utils
import os
import sys
import subprocess
import shutil
TOPDIR = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))
utils.set_search_paths(TOPDIR)
import cryptosite.setup
# Simply copy pre-built outputs at each step, rather than running BLAST,
# fpocket, etc. (these are tested e... | salilab/cryptosite | test/test_setup.py | Python | lgpl-2.1 | 3,847 | [
"BLAST"
] | c0d8282f1ecc18e58d30a16f692ef3f7bcc7c7ced724b4b339c21bfab14977e1 |
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.o... | SalemAmeen/neon | tests/test_recurrent.py | Python | apache-2.0 | 10,610 | [
"Gaussian"
] | ec7a5b5f6b09ef8fcc02226f1276fb71b1bc34dd1f240771daad68e3250eac03 |
# -*- coding: utf8
"""Random Projection transformers.
Random Projections are a simple and computationally efficient way to
reduce the dimensionality of the data by trading a controlled amount
of accuracy (as additional variance) for faster processing times and
smaller model sizes.
The dimensions and distribution of R... | scikit-learn/scikit-learn | sklearn/random_projection.py | Python | bsd-3-clause | 24,411 | [
"Gaussian"
] | 428988159a821db3a8cbd1f0c8e54241bf0a5ab9523d3490e2c5dc9026f82641 |
"""
Copyright 2013 Google Inc. All Rights Reserved.
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in... | android-pay/s2ap-quickstart-python | offer.py | Python | apache-2.0 | 3,689 | [
"VisIt"
] | f143a3150d54ba4ffd3bdc5bfa2c030a7a419942581284d5a849aa295d0be9b6 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on 17/03/17 at 10:47 AM
@author: neil
Program description here
Version 0.0.0
"""
import numpy as np
from astropy.table import Table
from astropy.stats import LombScargle
from photutils import find_peaks
import MySQLdb
import pandas
# =====================... | njcuk9999/neil_superwasp_periodogram | periodogram_functions.py | Python | mit | 26,378 | [
"Gaussian"
] | fb1fc783e3f2d65408e7a135dbb219e9a15e448c0818bdc1c4dd620cddf288b7 |
#########################################################################################
# $HeadURL$
# Torque.py
# 10.11.2014
# Author: A.T.
#########################################################################################
""" Torque.py is a DIRAC independent class representing Torque batch system.
Torque... | Andrew-McNab-UK/DIRAC | Resources/Computing/BatchSystems/Torque.py | Python | gpl-3.0 | 6,275 | [
"DIRAC"
] | 34a6d968d1b96f6b947e7adb59cba56b016336cb2288108b002e2e403874116a |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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
#
# Unle... | dmirubtsov/k8s-executor | vendor/k8s.io/kubernetes/hack/boilerplate/boilerplate.py | Python | apache-2.0 | 5,238 | [
"VisIt"
] | 56162fcbd9952d0bae784adb1d038c2276a5e0f38afc1ba8823f5a996b27a0cc |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#
# Python motu client
#
# Motu, a high efficient, robust and Standard compliant Web Server for Geographic
# Data Dissemination.
#
# http://cls-motu.sourceforge.net/
#
# (C) Copyright 2009-2010, by CLS (Collecte Localisation Satellites) -
# http://www.cls.fr - and Cont... | clstoulouse/motu-client-python | src/motuclient/motuclient.py | Python | lgpl-3.0 | 16,828 | [
"NetCDF"
] | 898a22bd5a0fa9e8f1dee4aa2c5bb994348fd76bb9ed6bcb7f86f293ab8a6a10 |
"""
Class Coverage
==============
.. autosummary::
:toctree: generated/
Coverage.creategrid
Coverage.cover
Coverage.sinr
Coverage.best
Coverage.show
"""
from pylayers.util.project import *
#from pylayers.measures.mesuwb import *
from pylayers.simul.radionode import *
import pylayers.util.pyu... | buguen/pylayers | pylayers/antprop/coverage.py | Python | lgpl-3.0 | 35,697 | [
"Mayavi"
] | 8385fdd54722158f945a5cc7fc08d6ef8fb09e792b0ae404f94181c98f1a6b14 |
import copy
from hearthbreaker.cards.base import SecretCard, SpellCard
from hearthbreaker.cards.minions.mage import SpellbenderMinion, MirrorImageMinion
from hearthbreaker.constants import CHARACTER_CLASS, CARD_RARITY
from hearthbreaker.tags.base import BuffUntil, Buff, CardQuery
from hearthbreaker.tags.condition impor... | kingoflolz/hearthbreaker | hearthbreaker/cards/spells/mage.py | Python | mit | 12,894 | [
"BLAST"
] | b43b160dd73eaed70d4c3d560dfca1a3aeff8c11a2249c952c73a1b933d7cbbb |
#!/usr/bin/env python
from __future__ import division
import os
import argparse
import console
import sys
"""
Parsing XML BLAST output for tab delimited file for easier parsing with samples,
hit descripttions, hit identities and hit aligment length values. Input is taken
from STDIN, use it in pipe command.
"""
pa... | ut-planteco/ssu-pipeline | pipeline_parse_blast.py | Python | gpl-3.0 | 3,045 | [
"BLAST"
] | a96c7a955de535af24ba50bdeaebe85bec5866c762aaa080dccbf38f9a2ab6a3 |
# Encoding: utf-8
# Copyright (C) 2012-2016 Olivier Castany
# This program is free software (see LICENCE file)
"""Berreman4x4: module implementing Berreman's 4x4 matrix method.
See file "documentation.pdf"
"""
import numpy
import scipy.linalg
from numpy import pi, newaxis
import matplotlib, matplotlib.pyplot
#####... | ocastany/Berreman4x4 | Berreman4x4.py | Python | gpl-3.0 | 58,361 | [
"CRYSTAL",
"Gaussian"
] | 5f245f2641f0d10ffcc5d91f05bd4d254b9b103285990aa955a6ce1256f6d95e |
""" A Gaussian estimator for use with minimum message length. """
__all__ = ["GaussianEstimator"]
import logging
import numpy as np
import scipy.optimize as op
logger = logging.getLogger(__name__)
from . import estimator
def _log_prior(sigma, bounds, quantum):
r"""
Return the log likelihood of the prior.... | andycasey/snob | snob/gaussian.py | Python | mit | 10,156 | [
"Gaussian"
] | ea15bc283387f3574a1747fc50587d9e8999601ff6e12b96603d041d5047e59c |
# #
# Copyright 2009-2021 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 (... | akesandgren/easybuild-framework | easybuild/tools/filetools.py | Python | gpl-2.0 | 113,516 | [
"NetCDF"
] | 44cc3cfec84ddd1e2775cdd85e8bb65b6d3ccd0afef8a642cab4ba7949b7b745 |
# 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.
"""Classes corresponding to Newick trees, also used for Nexus trees.
See classes in `Bi... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Phylo/Newick.py | Python | gpl-2.0 | 1,167 | [
"Biopython"
] | 7361ad57adde5d243bee1ee0a961ddc4fa3fb4ad0cf053b1b474f50087c29297 |
"""
Various bayesian regression
"""
# Authors: V. Michel, F. Pedregosa, A. Gramfort
# License: BSD 3 clause
from math import log
import numpy as np
from scipy import linalg
from .base import LinearModel
from ..utils import as_float_array
from ..utils.extmath import fast_logdet
#####################################... | joshbohde/scikit-learn | sklearn/linear_model/bayes.py | Python | bsd-3-clause | 15,648 | [
"Gaussian"
] | 51b13f608f622135bb5fa40be1209539286a269113dc8b4281ff500839c81293 |
#!/usr/bin/env python
#encoding=utf8
'''
Module describing layers of neurons for multi-layered neural network.
Neurons have complex weights.
Layers are closely tied with networks that use them. Networks create them
and manage them. Although it is sort of design antipattern - here it's used
more for lighter code of n... | MiraHead/mlmvn | src/network/layer.py | Python | gpl-2.0 | 10,791 | [
"NEURON"
] | 3b3687cea76e564f5d75a1d5b2b1246ed6c04171c2e65ea899e688b77ce33989 |
"""
Test the about xblock
"""
import datetime
import pytz
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.core.urlresolvers import reverse
from django.test.utils import override_settings
from mock import patch
from nose.plugins.attrib import attr
from opaque_keys.edx.locations impo... | alu042/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 25,126 | [
"VisIt"
] | e782b1eeb067d43674c0310842b093e29684263a5cc43f0ad600805f407e84e7 |
#!/usr/bin/env python
#
# DNSChef is a highly configurable DNS Proxy for Penetration Testers
# and Malware Analysts. Please visit http://thesprawl.org/projects/dnschef/
# for the latest version and documentation. Please forward all issues and
# concerns to iphelix [at] thesprawl.org.
DNSCHEF_VERSION = "0.3"
# Copyri... | xujun10110/dnschef | dnschef.py | Python | bsd-3-clause | 31,580 | [
"VisIt"
] | 23fa0ac14adfd7a934bfabbcb05f205aa36ad9dbb5f3f4872458070ffa3a9b28 |
import mixtape.featurizer, mixtape.tica, mixtape.cluster, mixtape.markovstatemodel, mixtape.ghmm
import numpy as np
import mdtraj as md
from parameters import load_trajectories, build_full_featurizer
import sklearn.pipeline, sklearn.externals.joblib
import mixtape.utils
stride = 1
lag_time = 1
trj0, trajectories, fil... | kyleabeauchamp/PMTStuff | code/test_cv_cluster_kcenters.py | Python | gpl-2.0 | 1,272 | [
"MDTraj"
] | ac0383463915061cbb0d2b0f8e8cceced33ea882520634086e27ed01aba3b5fb |
"""Image class which is a DisplayElement which shows images on the display."""
# image.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 pygame
import... | spierepf/mpf | mpf/media_controller/elements/image.py | Python | mit | 6,747 | [
"Brian"
] | f916466087a7bca8e39f6c6bebf11beafe6ec0e835baa7407a9749793bf4f94f |
"""
Created on Apr 21, 2016
@author: Chris Smith -- csmith55@utk.edu
"""
import numpy as np
from ioFuncs import readData
import pyqtgraph as pg
from pyqtgraph import QtGui
class BEPSwindow(QtGui.QMainWindow):
'''
Window object that will handle all the plotting
'''
def __init__(self, **kwargs):
... | anugrah-saxena/pycroscopy | pycroscopy/visualizers/BEPSvisSHO/plotFunctions.py | Python | mit | 43,255 | [
"VisIt"
] | 416c7111f0ebbace2b5ba71c956d0c2461e039c15ef4e25f0559b28a2879a1eb |
../../../../../../../share/pyshared/orca/scripts/toolkits/CALLY/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/toolkits/CALLY/__init__.py | Python | gpl-3.0 | 75 | [
"ORCA"
] | af383244b4d729d8c959fb5e73775d6b6ba48eb4a4a35659de141130c5fe1838 |
"""
SALTS XBMC Addon
Copyright (C) 2014 tknorris
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.
T... | mrquim/mrquimrepo | repo/plugin.video.salts/scrapers/2ddl_scraper.py | Python | gpl-2.0 | 10,261 | [
"ADF"
] | ff5615e4ed3b0b81c53b6a9f76072d125350c136b9f4808a4664170aedf16902 |
#pylint: disable=missing-docstring
#* 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/... | nuclear-wizard/moose | python/chigger/misc/__init__.py | Python | lgpl-2.1 | 459 | [
"MOOSE"
] | 7286f776537e9d7debb0c936440ce468213aaadb8374d07465c5f9f08a656718 |
# ***************************************************************************
# This file is part of the GAMer software.
# Copyright (C) 2016-2018
# by Christopher Lee, Tom Bartol, John Moody, Rommie Amaro, J. Andrew McCammon,
# and Michael Holst
# This library is free software; you can redistribute it and/or
# mod... | mcellteam/gamer | tools/blendgamer/src/tetrahedralization.py | Python | gpl-2.0 | 13,067 | [
"MCell",
"ParaView",
"VTK"
] | acb79ce17e263974febfbe01edfcba56493c8aab227e7f7022502f21242600e7 |
r"""
Ordination results format (:mod:`skbio.io.format.ordination`)
=============================================================
.. currentmodule:: skbio.io.format.ordination
The ordination results file format (``ordination``) stores the results of an
ordination method in a human-readable, text-based format. The form... | kdmurray91/scikit-bio | skbio/io/format/ordination.py | Python | bsd-3-clause | 14,424 | [
"scikit-bio"
] | 29bfb24f8cdce43598cbcf6fa8c5ff290ca62dcff602f9ca5d40ea8ec3d62c4a |
'''Path
os.path really pisses me off. It's full of suprising behavior:
- normpath('') == '.'
- normpath('fu/') == 'fu' vs normpath('/') == '/'
- join('/foo/bar', '/wtf') = '/wtf'
- join('file.txt', '') = 'file.txt/'
'''
from __future__ import with_statement
import os
import pwd
import grp
import glob
import s... | njharman/cuprum | cu/path.py | Python | mit | 30,087 | [
"VisIt"
] | c9e8d0593ca2d39f7a7111a9c89ab97a34f3426fa3c06ee9200c3af4f044bfdd |
#
# @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 ... | andysim/psi4 | psi4/driver/p4util/__init__.py | Python | gpl-2.0 | 1,167 | [
"Psi4"
] | c96fcc4b3b0aebd861e15abb989595d33ea84439d60a7cad9225906ccdd400a4 |
# parsetree.py
# Copyright (C) 2006, 2007, 2008, 2009, 2010 Michael Bayer mike_mp@zzzcomputing.com
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""defines the parse tree components for Mako templates."""
from mako import exceptions, ast, u... | bdoms/mako | parsetree.py | Python | mit | 15,124 | [
"VisIt"
] | 05a648295d496f6545f1b1bbd88ebe887603d6a362890b18121910ee67637bfe |
""" This module contains functions for calculating single-ifo ranking
statistic values
"""
import numpy
def effsnr(snr, reduced_x2, fac=250.):
"""Calculate the effective SNR statistic. See (S5y1 paper) for definition.
"""
snr = numpy.array(snr, ndmin=1, dtype=numpy.float64)
rchisq = numpy.array(reduce... | cmbiwer/pycbc | pycbc/events/ranking.py | Python | gpl-3.0 | 4,328 | [
"Gaussian"
] | 8ffd731a761aaf828707f07cac3868afcf0561dbc55520c1e14d659b90d75fb3 |
"""
Support for integration with the Biostar application
"""
import logging
import hmac
import urlparse
import re
from unicodedata import normalize
from galaxy.web.base.controller import url_for
from galaxy.tools.errors import ErrorReporter
from . import smart_str
log = logging.getLogger( __name__ )
_punct_re = re.c... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/util/biostar.py | Python | gpl-3.0 | 7,283 | [
"Galaxy"
] | 01e17408ddbc5b1732e41d74bbdffe8030644f94e365c187dfa09a42f4900af3 |
import os
def write_mol_file(material, simulation_path):
"""Writes .mol file for structural information."""
s = material.structure
file_name = os.path.join(simulation_path, "{}.mol".format(material.uuid))
with open(file_name, "w") as mol_file:
mol_file.write(
" Molecule_name: ... | WilmerLab/HTSOHM-dev | htsohm/simulation/raspa.py | Python | mit | 5,788 | [
"TINKER"
] | 829527b5d6a6dfa52f17580c1f73e5ee2b63762f80caf78880c309949f05abfe |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/system/systemd.py | Python | bsd-3-clause | 18,120 | [
"Brian"
] | 8e9ee944db15159fc7fbec4f5abd7986cf626549a8a0b025f7afa486c0661402 |
HOUSING_AD_00 = """
<p class="row" data-pid="5505576050">
<a href="/apa/5505576050.html" class="i" data-ids="0:00J0J_gss8d0U8fWG,0:01010_8j2pRi4cNpY,0:00n0n_4h2qcAaFCtf,0:00f0f_leV0VnfLl9S,0:00v0v_5BJA1ywTXma,0:01515_t6OFaDAsdo,0:00505_7o1HwCAANX6,0:00d0d_jI5DU2npq38,0:00606_7wxacKGKQ68"></a>
<span class="txt">... | rgreinho/craigomatic | craigomatic/apps/craigmine/tests/ad_samples.py | Python | mit | 62,856 | [
"MOPAC"
] | 6df8aa9b295739f66d052845409e7ffc8eacaa51e224788de12d70e2d2f07d25 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""shadowoui_spectro1: an utility toolbox to raytrace a
wavelength-dispersive spectrometer with SHADOW3_ from Python, via
ShadowOui_ layer
.. note:: requires python3.4
.. note:: this is only an idea (e.g. example) on how to automatize
some repetitive steps in S... | maurov/xraysloth | sloth/raytracing/shadowoui_spectro1.py | Python | bsd-3-clause | 15,079 | [
"CRYSTAL"
] | 67bb3c5b4678f82b24ce4f8c46d33d4721d2aa961e4d575aaed464ec8bbf58f7 |
# Copyright (c) 2012, Siu Kwan Lam
# All rights reserved.
import logging
import ast
from contextlib import contextmanager
from pymothoa.util.descriptor import Descriptor, instanceof
from pymothoa import dialect
from pymothoa.compiler_errors import *
from pymothoa.backend import CodeGenerationBase
from types import *... | sklam/pymothoa | pymothoa/llvm_backend/backend.py | Python | bsd-2-clause | 12,051 | [
"VisIt"
] | 24b9423a52537e58cfa1f9129fdb8365222f18981e8269e0e94b1c0b0fb2c0c6 |
#!/usr/bin/env python
# generate Python Manifest for the OpenEmbedded build system
# (C) 2002-2007 Michael 'Mickey' Lauer <mickey@Vanille.de>
# MIT license
import os
import sys
import time
VERSION = "2.4.4"
# increase when touching python-core
BASEREV = 2
__author__ = "Michael 'Mickey' Lauer <mickey@Vanille.de>"
__... | mrchapp/arago-oe-dev | contrib/python/generate-manifest-2.4.py | Python | mit | 13,550 | [
"VisIt"
] | abe08828ae1aa4715b7c40d58c7e50ebba8ee6a1f1261ce48e111a134ddfb599 |
#!/usr/bin/env python
#JSON {"lot": "RKS/6-31G(d)",
#JSON "scf": "CDIISSCFSolver",
#JSON "er": "cholesky",
#JSON "difficulty": 6,
#JSON "description": "Basic RKS DFT example with MGGA exhange-correlation functional (TPSS)"}
import numpy as np
from horton import * # pylint: disable=wildcard-import,unused-wildcard-... | theochem/horton | data/examples/hf_dft/rks_water_mgga.py | Python | gpl-3.0 | 3,570 | [
"Gaussian"
] | e49b9d9e633d2fe5bd631066ef8688e2d35f1ab3034e3d85d0e5a713ce59d543 |
# ============================================================================
#
# 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/model_thread/no_thread_model_thread.py | Python | gpl-2.0 | 2,793 | [
"VisIt"
] | b5059b3fc7d068d5858c8d772ab6e2060ad730badb5176282ef42c5a247ee4d3 |
# -*- coding: utf-8 -*-
#
##############################################################################
#
# Authors: Adrien Peiffer
# Copyright (c) 2014 Acsone SA/NV (http://www.acsone.eu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero Genera... | Noviat/l10n-belgium | account_companyweb/__manifest__.py | Python | agpl-3.0 | 2,963 | [
"VisIt"
] | a968d5c55a5dd1506c6e0c0a2fc3799ac7f244a12dbef504349ecac35cdcb3b8 |
from scipy import reshape, dot, outer
import numpy
from pybrain.structure.connections.connection import Connection
from pybrain.structure.parametercontainer import ParameterContainer
from pybrain.structure import FeedForwardNetwork
from pybrain.structure import FullConnection
from pybrain.structure import LinearLayer,... | ioam/svn-history | contrib/pybrainstuff.py | Python | bsd-3-clause | 8,281 | [
"Gaussian"
] | 721d167a35538bb3ee1854876d26d2262142cc137cf64e655633a40cc5aa1f53 |
import os, sys, time
from shutil import copyfile
class AssemblyComp:
def __init__(self, sequencefile, assemblyreport, adaptright, adaptleft, sequence, report):
workingdir = os.getcwd() + '/'
copyfile('/home/jonas/galaxy/tools/straintracer/AssemblyComp.class', workingdir + "/AssemblyComp.class")
reportDir = "/ho... | jeezes/Straintracer | AssemblyComp.py | Python | bsd-3-clause | 970 | [
"Galaxy"
] | 7565a2a28e7948db07d3970bc371ec77427ee0a79220eff64cf977f137c313e1 |
from mdtraj.formats.arc import ArcTrajectoryFile
from mdtraj.formats.dcd import DCDTrajectoryFile
from mdtraj.formats.binpos import BINPOSTrajectoryFile
from mdtraj.formats.xtc import XTCTrajectoryFile
from mdtraj.formats.trr import TRRTrajectoryFile
from mdtraj.formats.hdf5 import HDF5TrajectoryFile
from mdtraj.format... | ctk3b/mdtraj | mdtraj/formats/__init__.py | Python | lgpl-2.1 | 843 | [
"MDTraj",
"NetCDF"
] | eb001fa2b34cb20c13897144b3dd83251a3e93d7c6bf736b3b2fad29daa507fe |
"""Axis binary sensor platform tests."""
from unittest.mock import Mock
from homeassistant import config_entries
from homeassistant.components import axis
from homeassistant.setup import async_setup_component
import homeassistant.components.binary_sensor as binary_sensor
EVENTS = [
{
'operation': 'Initi... | MartinHjelmare/home-assistant | tests/components/axis/test_binary_sensor.py | Python | apache-2.0 | 2,992 | [
"VMD"
] | f1f18252919368b913c116ebd55be15e38bd66068945ab04f228c8f17a53fc3b |
import numpy as np
from datetime import datetime
import netCDF4 as netCDF
import pyroms
import pyroms_toolbox
## load 2-dimentional interannual discharge data
## from 1948-2007. See Dai and Trenberth (2002) and Dai et al. (2009)
print 'Load interannual discharge data'
nc_data = netCDF.Dataset('/archive/u1/uaf/kat... | dcherian/pyroms | examples/rivers/compute_daitren_remap_weights.py | Python | bsd-3-clause | 4,063 | [
"NetCDF"
] | 2b9050b034bd985a2bcf886bd9d4044a1802854e518434151be613e735f90326 |
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
import ast
import unidiff
import sys
def read_file(filename):
with open(filename, 'r') as fin:
return fin.read()
def line_num_for_phrase_in_file(phrase, filename):
with open(filename,'r') as f:
for (i, line) in enumerate(f):
if phrase... | anokata/pythonPetProjects | checkpydoc.py | Python | mit | 5,345 | [
"VisIt"
] | d6e064df269bb2832eca8986a40fe53f1fc1935a9d9b391863875cd0e403d3f3 |
# -*- coding: utf-8 -*-
#
# GromacsWrapper documentation build configuration file, created by
# sphinx-quickstart on Tue Jun 23 19:38:56 2009.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# The contents of this file are pickled, so don't put values in the namespace
# that aren't ... | CTCNano/GromacsWrapper | doc/sphinx/source/conf.py | Python | gpl-3.0 | 6,605 | [
"Gromacs"
] | 686ae25e79bec166ea027dd474a8df218c40db9502ddd1693ae491c3a5e569df |
#!/usr/bin/python
# (C) 2011-2013, Markus Wildi, markus.wildi@one-arcsec.org
#
# rts2saf_imgp.py is the script called by IMGP after expusre has been
# completed.
# It serves as a wrapper for several tasks to be performed, currently
# 1) define the FWHM and write it to the log file (rts2-debug)
# 2) do astrome... | xyficu/rts2 | scripts/rts2saf/rts2saf_imgp.py | Python | gpl-2.0 | 9,214 | [
"VisIt"
] | 7c6944323299f3be067c69b686472c5e31c8c1bbb4f58f89c29cf09769b7a415 |
from setuptools import setup
setup(
name='moltemplate',
packages=['moltemplate',
'moltemplate.nbody_alt_symmetry'],
package_dir={'moltemplate': 'moltemplate'}, #.py files are in "moltemplate/"
package_data={'moltemplate': ['force_fields/*.lt']}, #.lt files are in "moltemplate/force_f... | ibethune/lammps | tools/moltemplate/setup.py | Python | gpl-2.0 | 3,316 | [
"ESPResSo",
"LAMMPS"
] | 4633cbb0c0a2afbd905b7be6045c6d7cced391e3db7b1f159149a58cd60fb5bc |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/diversity/alpha/tests/test_ace.py | Python | bsd-3-clause | 1,497 | [
"scikit-bio"
] | 44f15b01156b0970f9abfe5f0ecc7cd6ac0a0de42420e1591d1ebe5e38446d3c |
""" Test_RSS_Policy_JobRunningMatchedRatioPolicy
"""
import unittest
import DIRAC.ResourceStatusSystem.Policy.JobRunningMatchedRatioPolicy as moduleTested
################################################################################
class JobRunningMatchedRatioPolicy_TestCase(unittest.TestCase):
def setUp(se... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/test/Test_RSS_Policy_JobRunningMatchedRatioPolicy.py | Python | gpl-3.0 | 3,991 | [
"DIRAC"
] | f8f670183612f7a81a3a168888f8c94bab942e6b08ca2f081eba7c6914ef5d86 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.