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import unittest
from flask import json
from api import db
from api.BucketListAPI import app
from instance.config import application_config
class ItemTestCase(unittest.TestCase):
def setUp(self):
app.config.from_object(application_config['TestingEnv'])
self.client = app.test_client()
# Bin... | patlub/BucketListAPI | tests/test_item.py | Python | mit | 7,121 | [
"VisIt"
] | f25f3e2bf2d388a7025aec79e56c500c04b9148c99b98b16854d3bf7c346b6a5 |
import pandas
import random
import pycuda.driver as cuda
#import pycuda.autoinit
import atexit
from pycuda.compiler import SourceModule
import numpy as np
import numpy.random
import math
from mpi4py import MPI
import itertools
import time
import pycuda.gpuarray as ga
class Kern:
srt = """
__global__ v... | JohnCEarls/tcDirac | tcdirac/gpu.py | Python | gpl-2.0 | 19,808 | [
"DIRAC"
] | e6263f65479ee2176da24646f82a0c9df6e3b86d5fbbbf0bf2867ad1077974bd |
from django.contrib.auth.models import User
from django.db import models
from django.core.exceptions import ObjectDoesNotExist
from epl.custommodels import IntegerRangeField
from hyquest.constants import QUESTSET_TITLE_LEN, QUESTSET_DESC_LEN, QUEST_TITLE_LEN, \
TASK_TITLE_LEN, TASK_CODE_LE... | Edmonton-Public-Library/centennial | hyquest/models.py | Python | mit | 8,918 | [
"VisIt"
] | 6fa0c6fa0a5dcb4d0c88ed034b9a8ea5ddbd7d9466168f39fc41113577ef7ef3 |
###########################################################
# File: CloudEndpoint.py
# Original author: Victor Mendez
# Modified: A.T.
###########################################################
"""
CloudEndpoint is a base class for the clients used to connect to different
cloud providers
"""
from __future__ im... | DIRACGrid/VMDIRAC | VMDIRAC/Resources/Cloud/CloudEndpoint.py | Python | gpl-3.0 | 16,777 | [
"DIRAC"
] | e25868c9139b35615aa654638a061e2a9c6310aea7be2a3df8d70b191547ec5f |
from classdict import ClassDictionary
from ..image import load_faces
import numpy as np
# XXX: this may become PlainFacesDictionary later
class FacesDictionary(ClassDictionary):
@staticmethod
def frame_and_samples(
dbname, training, testing, resize=(), **class_kws
):
training,... | miketrumpis/machine_learning_project | recog/dict/facedicts.py | Python | bsd-2-clause | 1,974 | [
"Gaussian"
] | 1830eaf15933a6b2ee8f9578f2792e6ecff1922d30ea0610d1d8db8cd23b1195 |
#! /usr/bin/python
#
# This simple script scans a simple c soure file generates a set of stubs.
#
# (c) 2018 by Sebastian Bauer
#
from __future__ import print_function
from pycparser import parse_file, c_ast, c_parser, c_generator
from pycparser.c_ast import FuncDecl, TypeDecl
import argparse
import re
import subproc... | sba1/simplemail | devtools/gen-stubs.py | Python | gpl-2.0 | 2,117 | [
"VisIt"
] | 423f3407a459a34b15553ad42f5a9804e70b3c050d7606646e3f22f9d221b602 |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/r-bumphunter/package.py | Python | lgpl-2.1 | 2,363 | [
"Bioconductor"
] | ca7b45a5dfbf11ed3bc3dd782c962a10c8f74512cb2c67f0dfc3c51bb5fddfa5 |
# -*- coding: utf-8 -*-
"""
=========================================================
Logistic function
=========================================================
Shown in the plot is how the logistic regression would, in this
synthetic dataset, classify values as either 0 or 1,
i.e. class one or two, using the logisti... | manhhomienbienthuy/scikit-learn | examples/linear_model/plot_logistic.py | Python | bsd-3-clause | 1,553 | [
"Gaussian"
] | df3a765dd9966bc74578303ae422c24339323954c501385d6d5e264a92a11456 |
# -*- 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.
"""Contains all writers for standard chemical representations"""
from .cjsonwriter import CJSON as CJSONWriter
from .cmlw... | gaursagar/cclib | src/cclib/io/__init__.py | Python | bsd-3-clause | 713 | [
"cclib"
] | 0ba733d57f50c3163ca06bc028ac103aa2b1e13c0595aa0b77c4b3f40900479b |
#
# This file is part of Healpy.
#
# Healpy is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# Healpy is distributed in the h... | pchanial/healpy | healpy/sphtfunc.py | Python | gpl-2.0 | 32,762 | [
"Gaussian"
] | 92be694dd5fb2725eb6853aa7af9fa4f3850a8a798d7307096fbdcf833043ed5 |
# 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... | fedepad/espressopp | src/check/System.py | Python | gpl-3.0 | 1,318 | [
"ESPResSo"
] | 74e09f10f07b1759d751002e3c7e355d55b9de7b198a22e5efbaebcf803aafd8 |
"""
Simple GLM with two neurons connected by a complete network with Gaussian weights.
"""
SimpleSparseModel = \
{
# Number of neurons (parametric model!)
'N' : 2,
# Parameters of the nonlinearity
'nonlinearity' :
{
'type' : 'exp'
},
# Parameters of the bias ... | slinderman/theano_pyglm | pyglm/models/simple_sparse_model.py | Python | mit | 1,863 | [
"Gaussian"
] | 6422cea3789da45084c1eeedf21c475adbdaf6af109cb69866b659248f4cca5f |
# proxy module
from __future__ import absolute_import
from mayavi.action.help import *
| enthought/etsproxy | enthought/mayavi/action/help.py | Python | bsd-3-clause | 87 | [
"Mayavi"
] | d6a8552d2c1d11c9072401722a9b5566d59b7f21aa90932f9b1125ab9aa53b1e |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
import sys
sys.path.append("..")
import pycsp.greenlets as pycsp
@pycsp.process
def readP(cin):
cin()
A = pycsp.... | runefriborg/pycsp | examples/1MillionProcesses.py | Python | mit | 549 | [
"Brian"
] | 3e66b6224aa4f6b45f4e46ba4cae59d93fe564e5ba6cfb9325c4781c9dd408e8 |
# converter.py ---
#
# Filename: mtoneuroml.py
# Description:
# Author:
# Maintainer:
# Created: Mon Apr 22 12:15:23 2013 (+0530)
# Version:
# Last-Updated: Wed Jul 10 16:36:14 2013 (+0530)
# By: subha
# Update #: 819
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
# Utility for conv... | subhacom/moose-core | python/moose/neuroml2/converter.py | Python | gpl-3.0 | 7,358 | [
"MOOSE",
"NEURON"
] | 25a1a4ef753ed1b3b82f3fa79002744674cc179bfb59eb5c96d2d21fbbc42277 |
""" Tools for compiling C/C++ code to extension modules
The main function, build_extension(), takes the C/C++ file
along with some other options and builds a Python extension.
It uses distutils for most of the heavy lifting.
choose_compiler() is also useful (mainly on windows anyway)
for trying to... | sargas/scipy | scipy/weave/build_tools.py | Python | bsd-3-clause | 26,114 | [
"Jaguar"
] | 471e538f9c9484b2b503b620e89af42c7c5c224ca6621c8334eec975cdc6ff65 |
# -*- coding: utf-8 -*-
import ast
import base64
import csv
import glob
import itertools
import logging
import operator
import datetime
import hashlib
import os
import re
import simplejson
import time
import urllib
import urllib2
import urlparse
import xmlrpclib
import zlib
from xml.etree import ElementTree
from cStri... | henrytao-me/openerp.positionq | openerp/addons/web/controllers/main.py | Python | agpl-3.0 | 68,395 | [
"VisIt"
] | 531d7f751e519a4ca31aaae9c144c52d01e6ec2b5e081997c4d38ec8c78c383d |
#!/bin/env python2
from alife.worlds.world import World, Point
from alife.agents.UtilityAgent import SimpleAgent
from alife.utils.utils import dumpToArray
import math
import sys
import numpy
from nupic.encoders.extras.utility import SimpleUtilityEncoder
# common settings:
items=None
target=Point(4,9)
agent=None
food... | breznak/ALife | alife/experiments/behavior/utility_map.py | Python | gpl-2.0 | 3,974 | [
"Mayavi"
] | 6ce12ccc4e3e31ba936fb88985fd2317a40bdbfd0527577ccb976e4f5bbfe8d4 |
from func import *
# ATTTENTION! Maybe there are some mistakes in neuron parameters!
# Write to alexey.panzer@gmail.com.
logger = logging.getLogger('neuromodulation')
startbuild = datetime.datetime.now()
nest.ResetKernel()
nest.SetKernelStatus({'overwrite_files': True,
'local_num_threads': 4,
... | vitaliykomarov/NEUCOGAR | nest/IntegrationCUBE/neuromodulation.py | Python | gpl-2.0 | 21,846 | [
"NEURON"
] | d036d67907af5dba11b75889ea83582a399c77838a4f0fc7dba92984eedecc95 |
#
# Copyright 2001 - 2011 Ludek Smid [http://www.ospace.net/]
#
# This file is part of IGE - Outer Space.
#
# IGE - Outer Space is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Lice... | Lukc/ospace-lukc | server/lib/ige/ospace/IPlayer.py | Python | gpl-2.0 | 47,542 | [
"Galaxy"
] | 70282461217eabb735ebc096b0e15fee3d17e482826c939fd3e10f5e68f4556c |
# Copyright 2020 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/experimental/mcmc/sample_sequential_monte_carlo_test.py | Python | apache-2.0 | 10,739 | [
"Gaussian"
] | 63322e17953404e087a1e63d0aa43eb7638b654137bcab4ba907a44767076e5b |
"""
Test dashboard search
"""
from __future__ import absolute_import
import json
import os
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from co... | jolyonb/edx-platform | common/test/acceptance/tests/lms/test_lms_dashboard_search.py | Python | agpl-3.0 | 7,435 | [
"VisIt"
] | ee5181980c29650cb1413206f4d2259d89e2a0788ca6a3f3d3c754d6a79e8ae5 |
#!/usr/bin/python
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016-2018 Francois Beaune, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any... | Biart95/appleseed | sandbox/share/mitsuba2appleseed.py | Python | mit | 36,267 | [
"VisIt"
] | e1c67ddef95dd851d34acb5b4b2d37335082fc0d3718573a0f48c6ae4501e701 |
# -*- encoding: utf-8 -*-
"""
Gaussian optics.
The module implements:
- Ray transfer matrices for geometrical and gaussian optics.
See RayTransferMatrix, GeometricRay and BeamParameter
- Conjugation relations for geometrical and gaussian optics.
See geometric_conj*, gauss_conj and conjugate_gauss_beams
The co... | lidavidm/mathics-heroku | venv/lib/python2.7/site-packages/sympy/physics/gaussopt.py | Python | gpl-3.0 | 19,626 | [
"Gaussian"
] | 393eec095614bc9bea4c11a7fb736c1ec8b7b3fdcf6d53affafeb8327c83f154 |
""" JobMonitoringHandler is the implementation of the JobMonitoring service
in the DISET framework
The following methods are available in the Service interface
"""
__RCSID__ = "$Id$"
from types import IntType, LongType, ListType, DictType, StringTypes, StringType, NoneType, BooleanType
from DIRAC.Core.DISET.... | coberger/DIRAC | WorkloadManagementSystem/Service/JobMonitoringHandler.py | Python | gpl-3.0 | 18,881 | [
"DIRAC"
] | 8c9256dc0217aa0975c1fbd55a63c975dd844f68e44e624e366c31de0de71db4 |
'''This example illustrates how pypmc can be used to integrate a
non-negative function. The presented algorithm needs very little
analytical knowledge about the function.
'''
import numpy as np
import pypmc
# The idea is to find a good proposal function for importance sampling
# with as little information about the ... | fredRos/pypmc | examples/uniting_markov_chains_and_variational_bayes.py | Python | gpl-2.0 | 10,216 | [
"Gaussian"
] | 76bd06494dfcfc1c148c5263ae0d5d6cf4cff6196587d7059988bdd16b74ebb3 |
import os
def lrc_mk_paraljob(**kwargs):
"""
Writes a submission script for lawrencium clusters
--------------------------------------------------
Optional arguments:
jobname : str, default "job"
dirname : str, default './'
cluster : str, default 'nokomis'
nproc : int, default 16
... | trangel/OPTpy | OPTpy/utils/jobs_lrc.py | Python | gpl-3.0 | 3,345 | [
"ABINIT"
] | ccf0cde52d09664d8bd5b72e7a0b7b62fe2fa5c50bdb74c4f5f8d3b3cdee870c |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, 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.
"""Parser for NWChem output files"""
import itertools
import re
import numpy
from cclib.parser import l... | cclib/cclib | cclib/parser/nwchemparser.py | Python | bsd-3-clause | 64,148 | [
"Gaussian",
"NWChem",
"cclib"
] | 3f1b6a98957383402e0d035349584850f9517772b5c820c154bdd269a7374af2 |
# ==================================================================================================
# Copyright 2012 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | imsut/commons | src/python/twitter/pants/tasks/python/setup.py | Python | apache-2.0 | 6,511 | [
"Brian"
] | ebe83a38c96e14a6cdd57a60d485b2c2af0611ed13f3fd0b125cac39b644c7c9 |
import PythonQt
from PythonQt import QtCore, QtGui, QtUiTools
import director
from director import lcmUtils
from director import applogic as app
from director.utime import getUtime
from director.timercallback import TimerCallback
from director.lcmframe import positionMessageFromFrame
import numpy as np
import math
fro... | patmarion/director | src/python/director/navigationpanel.py | Python | bsd-3-clause | 19,138 | [
"VTK"
] | 0ae27832526f3699cba2cea577cacca04b9d46fa155f0f032c44681f78029d38 |
from pycket.interpreter import (
App,
Begin,
Begin0,
BeginForSyntax,
CaseLambda,
Cell,
CellRef,
DefineValues,
If,
Lambda,
Let,
Letrec,
LexicalVar,
Module,
ModuleVar,
LinkletVar,
Quote,
QuoteSyntax,
Require,
SetBang,
ToplevelVar,
Va... | cderici/pycket | pycket/ast_visitor.py | Python | mit | 7,596 | [
"VisIt"
] | 58a965b7f33f06a60826854e3fdacfb5d5668a6cab84cd46f06c462687185b02 |
'''
Created on Feb 9, 2017
The definition of BiasCorrection classes, which actually implement the bias-correction methods. We have to keep the class
definition in a separate module, so it can be pickled and imported in other modules.
@author: Andre R. Erler, GPL v3
'''
# external imports
import os, gzip, p... | aerler/GeoPy | src/processing/bc_methods.py | Python | gpl-3.0 | 33,921 | [
"NetCDF"
] | 99e364e100820d46ce3752e4a6fff730015e94ed34c72516a038d27d71300c5a |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/r-multtest/package.py | Python | lgpl-2.1 | 1,703 | [
"Bioconductor"
] | 3ecec82aa958896b81f54eb55f58289f95bbd72a3d634a7818bb2b6610647ca1 |
from pysamimport import pysam
import re, os, hashlib
class SplitBAM(object):
def __init__(self,bamfile,readgroups,batchsize=10,directory='.',index=False,region=None,limit=None):
self.bamfile = os.path.realpath(bamfile)
self.bambase,self.bamextn = self.bamfile.rsplit('.',1)
self.bambase = o... | HorvathLab/NGS | common/src/split.py | Python | mit | 2,471 | [
"pysam"
] | 2cf76abf796a8610facd2296107d1471a509a73b8963b752dda30ba359d8689b |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/driver/qcdb/libmintsbasisset.py | Python | lgpl-3.0 | 64,454 | [
"CFOUR",
"Gaussian",
"Psi4"
] | d1d408f9cf1ad063bc251c5cc424fb2e4d07e032d5b3391352dd5fed2b7231bd |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import unittest
class TestCblast(unittest.TestCase):
"""Test formats.cblast - BLAST parsing"""
def setUp(self):
from jcvi.formats.cblast import BlastLine
# Test parser
self.b = BlastLine(
"Os09g11510 Os08g13650 92.31 39 3 0 2... | tanghaibao/jcvi | tests/formats/test_cblast.py | Python | bsd-2-clause | 859 | [
"BLAST"
] | eddfbb77a0a2052e895abf47bf0d5b0ae3f70390d960aebe8870a476a3898a19 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# Copyright (c) 2009-2010 Arista Networks, Inc.
#
# 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
... | si618/pi-time | node_modules/grunt-pylint/tasks/lib/pylint/checkers/base.py | Python | gpl-3.0 | 86,457 | [
"VisIt"
] | a024e9be6653f7b480662902e9cc029a04ecec9c51e268f561a4ab1169c43445 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import S_OK, gLogger
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.StorageManagementSystem.Client.StorageManagerClient import StorageManagerClient
from DIRAC.Core... | yujikato/DIRAC | src/DIRAC/StorageManagementSystem/Agent/RequestFinalizationAgent.py | Python | gpl-3.0 | 7,277 | [
"DIRAC"
] | 9da5d9c6eeb46ad76d2414a42dffa7ee1c859009b9613cc5fae8cb9a1bf39d81 |
import numpy as np
class FullyConnectedLayer(object):
"""A layer with weights connecting every input to every output node.
The weights are a matrix W and forward propagation is just matrix
multiplication with W from the right.
"""
def __init__(self, input_shape, output_shape):
"""Create ... | Knuppknou/academia_ai | academia_ai/neural_network/layers/fully_connected.py | Python | mit | 2,511 | [
"Gaussian"
] | 655c82f20a3f20f3df24ddb7bf80d16fc4423526cf2ef8f3bf36dd634b805283 |
import warnings
from functools import partial
from itertools import chain
from abc import ABCMeta, abstractmethod
from . import templates
from .ast import Constructor
from .parser import Includes, TypeInfo
from .defaultconfig import Config
from .template_specialization import (ClassSpecializer, FunctionSpecializer,
... | AlexanderFabisch/cythonwrapper | pywrap/exporter.py | Python | bsd-3-clause | 20,580 | [
"VisIt"
] | 95bb34b6f6cd36e7302298320ca2dba03af2300a6fe2ffb28ca5808ac2091592 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, 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.
"""Functions used across multiple data tests."""
import itertools
import numpy
def get_minimum_carbon_separation(data)... | Schamnad/cclib | test/data/common.py | Python | bsd-3-clause | 827 | [
"cclib"
] | 4a61164a8af1c1fd84a6e0944d8e9e8b0cf8ac77bb3d61368c1fa793a36d7a7a |
"""Enables the plotting of 3-dimensional visualizations.
Use `conda install -c clinicalgraphics vtk` to install the required Visualization Toolkit (VTK) with anaconda.
Examples:
The first example computes the surface-to-surface distance of a unit sphere and unit cube.
>>> # create sphere and cube
>>... | istb-mia/miapy | miapy/plotting/surfacedistance.py | Python | apache-2.0 | 4,436 | [
"VTK"
] | d7751e541f1f514c53a4a0f28537250f18e2f8d08afd96e91fb60110febedb56 |
# Copyright 2008, 2009
# CAMd (see accompanying license files for details).
import os
import sys
from optparse import OptionParser, SUPPRESS_HELP
import ase.gui.i18n
from gettext import gettext as _
# Grrr, older versions (pre-python2.7) of optparse have a bug
# which prevents non-ascii descriptions. How do we circ... | grhawk/ASE | tools/ase/gui/ag.py | Python | gpl-2.0 | 5,515 | [
"ASE"
] | e0c1dbd14973b7c24bda399fd3b1c1fad9279e435f6bef793f42730439f6bd0c |
import pysam
from numpy.random import RandomState
def assign_random_gt(input_vcf, output, sample_name="HG", default_af=0.01, seed=None):
vcf_pointer = pysam.VariantFile(filename=input_vcf)
new_header = vcf_pointer.header.copy()
if "GT" not in new_header.formats:
new_header.formats.add("GT", "1", "... | sbg/Mitty | mitty/simulation/genome/sampledgenome.py | Python | apache-2.0 | 1,276 | [
"pysam"
] | b24e7d923d6961103d3a411b498007e423e4dffee23e1e3952d6bfad108dd2dd |
import sys
sys.path.append("./../bin/")
import matplotlib.pyplot as plt
import numpy as np
from glob import glob
import filter
import math
import pandas as pd
from plothelp import fit_line
# Read csv
#datf = pd.read_csv("./../logs/dual_hes_long1000.csv")
datf = pd.read_csv("./../logs/sensor_calibration... | cbosoft/pi_rheo_proj | etc/archive/plot_dual_hes_cal.py | Python | gpl-3.0 | 3,083 | [
"Gaussian"
] | acf2db5beccda5b0685f0d9b3b770d13f5bcf4a84bc69ab80ee43893d5927283 |
from __future__ import absolute_import, division, print_function
import _ast
from jaspyx.context.block import BlockContext
from jaspyx.visitor import BaseVisitor
class IfElse(BaseVisitor):
def visit_If(self, node, skip_indent=False):
if not skip_indent:
self.indent()
self.output('if(')... | ztane/jaspyx | jaspyx/visitor/if_else.py | Python | mit | 809 | [
"VisIt"
] | 8b52c7f29f78dd49726413decbbf677dd7899f0f878fbf3476f491deff6406d6 |
# Copyright 2007-2010 by Peter Cock. All rights reserved.
# Revisions copyright 2010 by Uri Laserson. 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.
"""Internal code for parsin... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/GenBank/Scanner.py | Python | apache-2.0 | 87,903 | [
"Biopython"
] | 91c125d4b2acf6669c117a6109e99eef6e3f28632d8e3d08573f13e8ac2091aa |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits, load_iris
from sklearn.cross_validation import cross_val_score, train_test_split
from sklearn.externals.six.moves import zip
from sklearn.utils.testing import assert_almost_equal
from sklearn.utils.te... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/tests/test_naive_bayes.py | Python | gpl-2.0 | 17,860 | [
"Gaussian"
] | 4ba05548a039f07f14514c2bbc3301fb7c350e91ad215d50c0e6b6899ba7ed36 |
# -*- coding: utf-8 -*-
# Generated by Django 1.11.3 on 2017-10-24 21:16
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('cases', '0002_nodule_lung_orientation'),
]
operati... | vessemer/concept-to-clinic | interface/backend/cases/migrations/0003_radiology_reporting_template.py | Python | mit | 8,324 | [
"VisIt"
] | ee0d9ce332c97d6cd82e08647eae27608c21005cf8be069e38bb55e1297de81e |
"""Ansible specific plyint plugin for checking deprecations."""
# (c) 2018, Matt Martz <matt@sivel.net>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# -*- coding: utf-8 -*-
from __future__ import annotations
import datetime
import re
import astroid
from pylint.interfac... | mattclay/ansible | test/lib/ansible_test/_util/controller/sanity/pylint/plugins/deprecated.py | Python | gpl-3.0 | 12,001 | [
"VisIt"
] | 926eb22304459b47206f7cf918adb87a84b20d8c64bba13aa10ae81880ec2c8f |
#! test c. v1.1 Schema for gradient
import numpy as np
import psi4
psi4.set_output_file("output.dat", False)
# Generate JSON data
json_data = {}
json_data["molecule"] = """He 0 0 0\n--\nHe 0 0 1"""
json_data["driver"] = "gradient"
json_data["method"] = 'SCF'
json_data["kwargs"] = {}
json_data["options"] = {"BASIS": ... | amjames/psi4 | tests/json/v11-gradient/input.py | Python | lgpl-3.0 | 1,360 | [
"Psi4"
] | 6bf97bd294a01f7b559e6f1c51b3aa1a4786aee5aae5278e2a630983888052b2 |
#THIS TOOL SEARCHES A LOCAL CVE VULNERABILITY DATABASE FOR VULNERABILITIES PRESENT IN SERVICES FOUND IN A BANNER.
#IT CONSISTS OF TWO SEARCH ENGINES - ONE THAT ATTEMPTS TO PULL OUT SERVICE NAMES AND NUMBERS AND FIND DIRECT MATCHES
#AND A SECOND THAT PERFORMS A WEIGHTED SEARCH ON TERM RELEVANT WORDS FOUND IN THE BANNER... | deontp/misc | zenoic_api/vulnhoo/vulnHoo.py | Python | gpl-3.0 | 17,689 | [
"VisIt"
] | 9a57f752beb3f030be10a0b39bce8935b42bde7bf3483e238061c446c6def5d2 |
from __future__ import division
from mmtbx.command_line import nonbonded_overlaps
from libtbx.utils import null_out
from libtbx.utils import Sorry
from libtbx import easy_run
import iotbx.pdb
import getpass
import sys
import os
class NBO_results(object):
""" Container for the test results """
def __init__(self):
... | youdar/work | work/Clashes/nonbonded_pdb_data_collect.py | Python | mit | 8,999 | [
"CRYSTAL"
] | d7eb2b28fdd87867f822c0470b951745d84767cfb25ab74c1c91656e6e1c7f78 |
# Copyright 2008-2015 Nokia Solutions and Networks
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable l... | kyle1986/robortframe | src/robot/model/keyword.py | Python | apache-2.0 | 4,346 | [
"VisIt"
] | 95f17db0c20010b02c61d6ff3f7cdd205d314f342b9a26b1f59fa2a64eaa45d5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
from setuptools import setup
import re
import os
import sys
# load version form _version.py
VERSIONFILE = "Henbun/_version.py"
verstrline = open(VERSIONFILE, "rt").read()
VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(VSRE... | fujii-team/Henbun | setup.py | Python | apache-2.0 | 1,651 | [
"Gaussian"
] | 9071e346a72c86516f6dd5ae13c5bed23d38bbb56835c7596e5d3dabfb620df3 |
#!/usr/bin/env python
import glob
import os
import defopt
import numpy as np
import pandas as pd
import seawater
import xarray as xr
import data.observational
from data.observational import DataType, Platform, Sample, Station
VARIABLES = ["TEMP", "PSAL"]
META_FIELDS = {
"PLATFORM_NUMBER": None,
"PROJECT_NA... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | scripts/data_importers/seal.py | Python | gpl-3.0 | 4,473 | [
"NetCDF"
] | a6839960121dec3f73889b7c015ca5d1cba78a90104901aa4e7a6965a0008f1c |
# Copyright 2018-2019 The Kubeflow 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 ... | kubeflow/pipelines | sdk/python/kfp/deprecated/compiler/compiler.py | Python | apache-2.0 | 58,394 | [
"VisIt"
] | 4bf695bc7e653f80037e7ade81f6d55f1f515fb8db8228966fc6f7245c1ea375 |
#!/usr/bin/env python
"""
Functions for specifiying convolutional neural network architectures.
"""
from __future__ import print_function
import argparse
import sys
import os
import time
import numpy as np
from scipy.io import netcdf
import theano
import theano.tensor as T
import lasagne
theano.config.floatX='floa... | vanessajurtz/lasagne4bio | peptide_MHCII/scripts/NN_func.py | Python | gpl-3.0 | 5,648 | [
"NetCDF"
] | 14ed2f3490fa8bef72333a6c9dfa683dd7d9c1848c30bd6de974b166bc9645dd |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/util/tests/test_testing.py | Python | bsd-3-clause | 10,301 | [
"scikit-bio"
] | 88f36a9f4a3dd623990cd1d621085289a766fef253673f0dcef62885a63d42c4 |
# 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 writing, software
# distributed under t... | dhermes/bezier | docs/custom_html_writer.py | Python | apache-2.0 | 2,184 | [
"VisIt"
] | 151cabc99a202e43616e1c1baee3ee9d7a6e73e7c70623831dfea5aaaac3f62c |
#!/usr/bin/env python
##
## @file print_sedml.py
## @brief Prints an overview of the elments in the given SED-ML document
## @author Frank T. Bergmann
##
## <!--------------------------------------------------------------------------
## This file is part of libSEDML. Please visit http://sed-ml.org for more
## ... | 0u812/libSEDML | examples/python/print_sedml.py | Python | bsd-2-clause | 4,503 | [
"VisIt"
] | a2fa267f575a682e74f46f12c5bc23513c22ddb1ff18f0466a4b48a809ef10ae |
import unittest
import cerebro.neuron as neu
class TestNeuron(unittest.TestCase):
def setUp(self):
neu.cfg.add_neurons_location(neu.STR_DEFAULT_NEURONS_PATH)
self.finder = neu.find
self.manager = neu.NeuronsManager()
self.command_args = ("arg1", "arg2")
def test_neuron_cre... | Le-Bot/cerebro | cerebro/tests/neuron/test_neuron.py | Python | mit | 1,482 | [
"NEURON"
] | 06b4ac00b76deac96146fc8f90ee927e69bb4e1728dc8a8a5d84c7e4231ea8a0 |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@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.
import unittest
import os
import os.path
from Bio.Phylo.PAML import baseml
from Bio.Phylo.... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_PAML_baseml.py | Python | gpl-2.0 | 12,879 | [
"Biopython"
] | 9ef8ac368f9cc1a9efd5dad27c5a93f1278aed9f991310f975a5c60e6a222a63 |
# -*- coding: iso-8859-1 -*-
"""
Create files (from Rugheimer metadata) that give the atmospheric profile, i.e. mixing ratio, temperature and pressure as a function of altitude.
Since the Rugheimer T/P and mixing ratio files are generated from different codes, they have different abscissa, and so different files are ge... | sukritranjan/ranjansasselov2016b | form_atmospheric_profiles.py | Python | mit | 34,641 | [
"Avogadro"
] | d291a5a9c033fd3d8fc7f84154ad2fa9eb53bb436511cf8ffbd45cce86c1ddc3 |
'''
Rules of play
Each casino may set which bets are offered and different payouts for them,
though a core set of bets and payouts is typical. Players take turns rolling two
dice and whoever is throwing the dice is called the "shooter". Players can bet
on the various options by placing chips directly on the appropria... | StoneyJackson/craps | craps.py | Python | gpl-2.0 | 3,372 | [
"CASINO"
] | bbb8bfa958df1f4a7613d6a9a280b9d092c21948922506844da9764586f48264 |
"""
Converting the 'parse-tree' output of pyparsing to a SPARQL Algebra expression
http://www.w3.org/TR/sparql11-query/#sparqlQuery
"""
import functools
import operator
import collections
from functools import reduce
from rdflib import Literal, Variable, URIRef, BNode
from rdflib.plugins.sparql.sparql import Prol... | RDFLib/rdflib | rdflib/plugins/sparql/algebra.py | Python | bsd-3-clause | 50,348 | [
"VisIt"
] | 323e11e3ed57728c795a9e3e335297ffb88b488aa728f43353ebf715595e91f5 |
Class = "Blank"
choice = "Blank"
class Warrior:
def __init__(self):
self.str = 8
self.dex = 4
self.wis = 2
def greet(self):
print "Grand, fan of hitting and kicking huh? Your stats are below."
print ""
print "Strength = %d" % self.str
print "Dexterity = ... | chrisortman/CIS-121 | k0808273/gagerim.py | Python | mit | 3,708 | [
"VisIt"
] | ac793fc6a225425ec3db03460ad6e4b2f1db58386a20081c659d0083f611ee04 |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/r-interactivedisplaybase/package.py | Python | lgpl-2.1 | 1,946 | [
"Bioconductor"
] | 8e333db7c5d9afa9e55ecc7181f480c7671ab3fdbc0ae2c13e7f0876bcf61dc9 |
#!/usr/bin/env python
#The MIT License (MIT)
#Copyright (c) 2016 Massimiliano Patacchiola
#
#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
#MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE ... | mpatacchiola/deepgaze | deepgaze/motion_detection.py | Python | mit | 7,320 | [
"Gaussian"
] | acecea80a2bb23b8b318354c3c94a2a1265746fdef6a92085bcb1b3d24f58b45 |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | badock/nova | nova/tests/network/test_manager.py | Python | apache-2.0 | 153,051 | [
"FEFF"
] | ff08af3ced963d2295b7718f5d93ab5e6de93c1aaa3bd9c8e0615623c6814659 |
import simtk.openmm as mm
import matplotlib.pyplot as pp
import numpy as np
from numpy import Inf, exp
class MullerForce(mm.CustomExternalForce):
"""OpenMM custom force for propagation on the Muller Potential. Also
includes pure python evaluation of the potential energy surface so that
you can do some plotting""... | rbharath/switch | Switch/MullerForce.py | Python | bsd-2-clause | 1,909 | [
"OpenMM"
] | 33eb8951dc8c49d30aafb11f2316db7ad57cb17c8278e72f5153121d7adbbde2 |
import os, glob
import nesoni
from nesoni import config, clip, samshrimp, bowtie, samconsensus, working_directory, reference_directory, \
workspace, io, reporting
class Context(object): pass
@config.help('Analyse reads from a single sample.')
@config.Positional('reference', 'Reference directory ... | Victorian-Bioinformatics-Consortium/nesoni | nesoni/workflows.py | Python | gpl-2.0 | 21,209 | [
"Bowtie"
] | 35f627acc29cf00da71784785fa6b1ab83a1a5c7b6832447793838578dc050a3 |
# -*- coding: utf-8 -*-
#
# mbuild documentation build configuration file, created by
# sphinx-quickstart on Wed Oct 1 08:59:12 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | summeraz/mbuild | docs/conf.py | Python | mit | 11,630 | [
"MDTraj"
] | a49a5e219d7ea15cbd54d6a02318b89b5a4bf9372d1fc642a4c13c880e56503f |
#########
# ps_drone.py
# (w)+(c) J. Philipp de Graaff, www.playsheep.de, drone@playsheep.de, 2012-2014
# Project homepage: www.playsheep.de/drone and https://sourceforge.net/projects/ps-drone/
# Dependencies: a POSIX OS, openCV2 for video-support.
# Base-program of the PS-Drone API: "An open and enhanced API for unive... | CCoffie/secret-robot | ps_drone.py | Python | gpl-3.0 | 119,935 | [
"VisIt"
] | 94ef7dfd954263380814a4d0fcf409e12aebd844b2f2fad43935fc1ab2af8e9f |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0023_auto_20150518_1901'),
]
operations = [
migrations.AddField(
model_name='student',
name... | koebbe/homeworks | visit/migrations/0024_auto_20150521_0211.py | Python | mit | 665 | [
"VisIt"
] | 72180bb7f3673b7b9ec7920e453b996ef4a0d6b12a87b5e2996fd3d8a91d838f |
__all__ = ['ChunksNAMD']
import shutil
from typing import Optional
from miles import (BaseChunks, Configuration, get_random_name, delete_files) # noqa: E501
class ChunksNAMD(BaseChunks):
"""Sequence of NAMD trajectory chunks.
"""
suffixes = {'coor', 'vel', 'xsc'}
extra_suffixes = {'colvars.traj'... | clsb/miles | miles/chunks_namd.py | Python | mit | 1,521 | [
"NAMD"
] | 7c2dbdbdc57ac7ddc26af3c9b2a4b9d70c89ba518f067a73d97501799e5dbc36 |
from yambopy import *
import numpy as np
import shutil
import os
from netCDF4 import Dataset
def abs2(x):
return x.real**2 + x.imag**2
class YamboWFDB():
def __init__(self,savedb,path=None,save='SAVE',filename='ns.wf'):
"""
load wavefunction from yambo
"""
if path is None:
... | alexandremorlet/yambopy | yambopy/dbs/wfdb.py | Python | bsd-3-clause | 3,051 | [
"Yambo"
] | 47bee8c447f1f97d9f4960a920fb78092b173e73b2f1e01b84e79808dedbb3c5 |
#!/usr/bin/env python
"""Unit tests for sitemap_gen.py, a script for generating sitemaps
for a web server.
"""
# Please be careful that all syntax used in this file can be parsed on
# Python 1.5 -- this version check is not evaluated until after the
# entire file has been parsed.
import sys
if sys.hexversion < 0x0202... | pagefreezer/SitemapGenerator | test_sitemap_gen.py | Python | bsd-3-clause | 28,682 | [
"COLUMBUS"
] | 71bf4c932ea4c04431738024540f877e0920907854a21e77058a1830610c9912 |
import os
def getName(filename):
return os.path.splitext(os.path.basename(filename))[0]
def getFiles(filename, batch, config, code):
name = getName(filename)
id = '{0}_{1}'.format(config, code)
names = {
'json': filename,
'id': id,
'log' : os.path.join(batch, '{0}.log.gz'.format(id)),
'data'... | nicmcd/ratesim | batch/common.py | Python | bsd-3-clause | 2,276 | [
"BWA"
] | f7e24f16a1b64ec2253f152539ac5dddb0910f89cfe2ccf6130a1a5c1833f795 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# adminfreeze - back end to request freeze files in write-once fashion
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms o... | heromod/migrid | mig/shared/functionality/adminfreeze.py | Python | gpl-2.0 | 20,119 | [
"Brian"
] | 6598c7502b61fdd8e9abce4aa9fe67e4e255602d3147babce721f9ffb51fc149 |
../../../../../../../share/pyshared/orca/scripts/apps/gnome_segv2/__init__.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gnome_segv2/__init__.py | Python | gpl-3.0 | 77 | [
"ORCA"
] | 369c91e1d7cc2238b67cb8c2095b34fe156e3327110eb6349065cb778545ee20 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2017, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | neuroidss/nupic.research | projects/union_path_integration/infer_hand_crafted_objects.py | Python | agpl-3.0 | 7,264 | [
"Gaussian"
] | f4adb81a6c623843b9942d68ddd449ee734214d5b167a9941249c2740f420696 |
import unittest
import pysal
import numpy as np
from pysal.spreg import probit as PB
class TestBaseProbit(unittest.TestCase):
def setUp(self):
db=pysal.open(pysal.examples.get_path("columbus.dbf"),"r")
y = np.array(db.by_col("CRIME"))
y = np.reshape(y, (49,1))
self.y = (y>40).astype... | spreg-git/pysal | pysal/spreg/tests/test_probit.py | Python | bsd-3-clause | 5,106 | [
"COLUMBUS"
] | fc39efc0ab42cc74a232ee64845688fbd132ca671598f1764b18cf0b34819148 |
# coding: utf8
{
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"是一个可选表达式, " field1=\'newvalue\'",你不能更新或删除结果的连接',
'# of International Staff': '#的国际工作人员',
'# of National Staff': '#的国家工作人员',
'# of Vehicles': '#的车辆',
'%(msg)s\nIf the request type is "%(... | flavour/porto | languages/zh-cn.py | Python | mit | 242,813 | [
"VisIt"
] | 4790946b3b5c2289b7ab4b0862f64ca30c48fe1936940e4a94355e0e8e6fc457 |
"""
Bok choy acceptance and a11y tests for problem types in the LMS
See also lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
import random
import textwrap
from abc import ABCMeta, abstractmethod
from nose import SkipTest
from nose.plugins.attrib import attr
from selenium.webdriver import Acti... | prarthitm/edxplatform | common/test/acceptance/tests/lms/test_problem_types.py | Python | agpl-3.0 | 36,865 | [
"VisIt"
] | e7418349785fef2d516aabb81e04dcdf95e7054398512c3dffe502884260d010 |
import datetime
import sqlalchemy.orm.exc
from inbox.log import get_logger
log = get_logger()
from inbox.auth.oauth import OAuthAuthHandler
from inbox.basicauth import OAuthError
from inbox.models import Namespace
from inbox.config import config
from inbox.models.backends.outlook import OutlookAccount
from inbox.mod... | PriviPK/privipk-sync-engine | inbox/auth/outlook.py | Python | agpl-3.0 | 4,059 | [
"VisIt"
] | 17fe6e990e6cc267b9bf0c58ebf8cfe93242b96fb7478f28d6f5c42d9f36bbcf |
# Python test set -- part 1, grammar.
# This just tests whether the parser accepts them all.
# NOTE: When you run this test as a script from the command line, you
# get warnings about certain hex/oct constants. Since those are
# issued by the parser, you can't suppress them by adding a
# filterwarnings() call to this... | bruderstein/PythonScript | PythonLib/full/lib2to3/tests/data/py2_test_grammar.py | Python | gpl-2.0 | 30,910 | [
"GULP"
] | 253e51525c7e1ef847ab32b2556bc4213371e636fb498e0040980036bdd3f8ed |
from __future__ import (absolute_import, division, print_function)
import AbinsModules
import io
import six
import numpy as np
from math import sqrt
from mantid.kernel import Atom
class LoadDMOL3(AbinsModules.GeneralAbInitioProgram):
"""
Class for loading DMOL3 ab initio vibrational data.
"""
def __in... | ScreamingUdder/mantid | scripts/AbinsModules/LoadDMOL3.py | Python | gpl-3.0 | 11,305 | [
"DMol3"
] | cce68fd790b182f4723a6f9415e0ca6c2447762514f3efaa7463f69b4b315b4a |
"""Support for naming expressions
In order to use elastic search named query, we need to be able to assign names to expressions
and retrieve their positions in the query text.
This module adds support for that.
"""
from .utils import LuceneTreeVisitorV2
#: Names are added to tree items via an attribute named `_luq... | adsabs/object_service | object_service/luqum/naming.py | Python | mit | 4,345 | [
"VisIt"
] | 2891089e6fb57ee378410ede1d3460eb790d5ee681088f782edd7b264ab53407 |
def agts(queue):
queue.add('nanoparticle.agts.py',
walltime=2 * 60 + 15,
ncpus=8,
creates=['nanoparticle.csv'])
if __name__ == "__main__":
from ase.optimize.test.nanoparticle import *
| qsnake/gpaw | doc/devel/ase_optimize/nanoparticle.agts.py | Python | gpl-3.0 | 235 | [
"ASE"
] | 6ef9948e8d5ae5856c635daf561786888b934473501fa3ff7bdb5dbc5a6fbba3 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# 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.
#
"""unit testing code f... | soerendip42/rdkit | rdkit/Chem/UnitTestArom.py | Python | bsd-3-clause | 3,129 | [
"RDKit"
] | eb3dc480db2fb564d4b780df21c0b6690995ffd1520186480a8bd340873889c2 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2001-2006 Donald N. Allingham
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | arunkgupta/gramps | gramps/gui/plug/report/_fileentry.py | Python | gpl-2.0 | 3,893 | [
"Brian"
] | 48d0a5bc680d1830440452a1f353bc1e5dd0234b3ab6c84f030eab4f0cd1836d |
"""
Contains the UCSC proxy
"""
from galaxy import web
import common
import re, urllib, logging
log = logging.getLogger( __name__ )
class UCSCProxy(common.Root):
def create_display(self, store):
"""Creates a more meaningulf display name"""
track = store.get('hgta_track','no track')
tab... | jmchilton/galaxy-central | galaxy/interfaces/proxy.py | Python | mit | 8,284 | [
"Galaxy"
] | cf5a40bbc6da80ca0fe9c5e5b581be3de5d69c22f2741071ea50db543bbc5695 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkWin32VideoSource(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
v... | nagyistoce/devide | modules/vtk_basic/vtkWin32VideoSource.py | Python | bsd-3-clause | 480 | [
"VTK"
] | 48d2953ffea22661297b24251196c9dd8b2bddadcae036df521a575725ae991a |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-wms-job-status
# Author : Stuart Paterson
########################################################################
"""
Retrieve status of the given DIRAC job
"""
__RCSID__ = "$Id$"
import os
... | Sbalbp/DIRAC | Interfaces/scripts/dirac-wms-job-status.py | Python | gpl-3.0 | 2,207 | [
"DIRAC"
] | d82a67aec5e6d80f3319146656d5e48b72e1592542c43cfbadca795b0582e736 |
#!/usr/bin/env python
from __future__ import print_function
import sys, getopt
from Bio import SeqIO
import random
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
import os.path
from scipy.stats import norm
plot=1
totall=0
readall=[]
subreads=[]
meantot=0
mea... | fg6/random_subreads | subrand.py | Python | gpl-3.0 | 9,171 | [
"Gaussian"
] | 4c25410a8fcd73bdfa6136c083725a40dd4363eae649024690fcc8642d0ece22 |
"""
.. _tut_compute_covariance:
Computing a covariance matrix
=============================
Many methods in MNE, including source estimation and some classification
algorithms, require covariance estimations from the recordings.
In this tutorial we cover the basics of sensor covariance computations and
construct a no... | Teekuningas/mne-python | tutorials/source-modeling/plot_compute_covariance.py | Python | bsd-3-clause | 8,933 | [
"Gaussian"
] | be8117a8bf4182058a3bd9621da7bf047dd9a6a2adc8937bc3f650cf6a5270e8 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | lib/python/aliases.py | Python | gpl-2.0 | 10,431 | [
"Psi4"
] | 8894693c079004f0b1f4e84a341a26506244b1cec8d49ad39143f784f32916f8 |
#! /usr/bin/env python
"circAnno.py -- "
import sys, os, ConfigParser, argparse
parser = argparse.ArgumentParser(description='circAnno is a pipeline to annotate circular RNA')
parser.add_argument('config_file', help='')
parser.add_argument('-s', '--step', choices=range(5), type=int, help='0:all steps, 1:combine libra... | bioxfu/circRNAFinder | src/circRNAAnno.py | Python | gpl-3.0 | 7,984 | [
"Bowtie"
] | cc0741c056c77efe627c20dbe4a71e69e569c2a9d3dc2a10728d2562defa6a4d |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | lidakanari/NeuroM | neurom/view/view.py | Python | bsd-3-clause | 14,676 | [
"NEURON"
] | cde125c7363941e05a14ff3459babc29fc8ac36df8c408fe480620811ed39fec |
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