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'''
This script (generate_reaction_templates) uses a MongoDB collection
with atom-mapped reaction SMILES strings and parses them into a new
collection containing the transforms.
'''
from __future__ import print_function
from global_config import USE_STEREOCHEMISTRY
import argparse
from numpy.random import shuffle # ... | connorcoley/ochem_predict_nn | data/generate_reaction_templates.py | Python | mit | 28,770 | [
"RDKit"
] | f8372a092aeec04463281677d4294b1a1356c598c8db6256342c4a080e19bb63 |
"""
The ``fatiando`` package contains all the subpackages and modules required for
most tasks.
Modules for each geophysical method are group in subpackages:
* :mod:`gravmag <fatiando.gravmag>`:
Gravity and magnetics (i.e., potential fields)
* :mod:`seismic <fatiando.seismic>`:
Seismics and seismology
* :mod:`geot... | eusoubrasileiro/fatiando | fatiando/__init__.py | Python | bsd-3-clause | 2,118 | [
"Mayavi"
] | 3dae121462f1ae2dfc1f72b4fbcfa35b7478b679bfadcd6ab1a748af2dd7e85e |
"""
Weak Lensing Performance Calculator
===================================
SMN
systematic ellipticities e_s(x,y)
- CTI: richard already worked on this
- bias: needs a model
- flat fielding: probably not systematic
- non-linerarity:
-
SMN
2d power spectra C(l)
unit test: gaussian random field + known power spec... | sniemi/EuclidVisibleInstrument | sandbox/CosmologyCalculator.py | Python | bsd-2-clause | 506 | [
"Gaussian"
] | ee7eda1dd06719f9513043fd1f85e70e43ba0252f7dfd24d95c92bdc9276cd51 |
"""
Class for management of MQ communication
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.ObjectLoader import ObjectLoader
from DIRAC.Core.Utilities.DErrno import EMQUKN
__RCSID__ = "... | yujikato/DIRAC | src/DIRAC/Resources/MessageQueue/MQConnector.py | Python | gpl-3.0 | 3,799 | [
"DIRAC"
] | 9c8a7b15e2cb352c740826f785908750347efa356c45781c690e5e385a74ee80 |
#!/usr/bin/env python
""" Visualization functions for connectivity analysis. """
import sys
import os.path as op
import numpy as np
import scipy as sci
import matplotlib.pyplot as pl
import mne
import yaml
import pickle
def sensor_connectivity_3d(raw, picks, con, idx, n_con=20, min_dist=0.05,
... | fboers/jumegX | connectivity/con_viz.py | Python | bsd-3-clause | 10,426 | [
"Mayavi"
] | c961b055a0a48a5e6b3e93a6f1ac75cb24002d91d2ab174f35748bd2f45312b7 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.core.units import Ha_to_eV, bohr_to_ang
from pymatgen.io.abinit.abiobjects import (
Electrons,
ElectronsAlgorithm,
KSamplin... | materialsproject/pymatgen | pymatgen/io/abinit/tests/test_abiobjects.py | Python | mit | 7,646 | [
"ABINIT",
"pymatgen"
] | 0a81eb19b5517720a3d4402e8e4da64a12dceddeea356d789589a64773438888 |
from Firefly import logging
from Firefly.const import SERVICE_CONFIG_FILE
from Firefly.helpers.service import Service
import configparser
from forecastiopy import ForecastIO, FIOCurrently, FIOAlerts, FIODaily
from Firefly import scheduler
TITLE = 'Dark Sky Service for Firefly'
AUTHOR = 'Zachary Priddy me@zpriddy.com'... | Firefly-Automation/Firefly | Firefly/services/darksky.py | Python | apache-2.0 | 3,196 | [
"Firefly"
] | d883885b193df90a1fe36d77cc9dc4078e685b81bb814703fd665108b93ab438 |
# -*- coding: utf-8 -*-
# xbmctr MEDIA CENTER, is an XBMC add on that sorts and displays
# video content from several websites to the XBMC user.
#
# Copyright (C) 2011, Dr Ayhan Colak
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publis... | noba3/KoTos | addons/script.module.xbmctr/lib/cozucu.py | Python | gpl-2.0 | 33,035 | [
"VisIt"
] | 58f1182163adfd5c551da935f19641394e0878b9af202dc4d7b8112ae84a6b64 |
# -*- coding: utf-8 -*-
"""
chemreac.core
=============
In ``chemreac.core`` you will find :py:class:`ReactionDiffusion` which
is the class describing the system of ODEs.
"""
from __future__ import (absolute_import, division, print_function)
from collections import defaultdict, OrderedDict
from functools import reduc... | chemreac/chemreac | chemreac/core.py | Python | bsd-2-clause | 21,344 | [
"ChemPy"
] | 44fcbd6c0a937457f7d3b1cfe7940426ef5de11992cc99faa168d0c991be8f46 |
#!/usr/bin/env python
__author__ = 'Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>'
import os.path
import re
import clang.cindex as ci
import app
import violations
RULE_NAMING_CONSTANT = 'naming.constant'
RULE_NAMING_STRUCT = 'naming.struct'
RULE_NAMING_UNION = 'naming.union'
RULE_NAMING_CLASS = 'naming.class'
R... | catkira/seqan | util/py_lib/seqan/pyclangcheck/rules.py | Python | bsd-3-clause | 8,182 | [
"VisIt"
] | af83a1cbe6025639a56cc3b05fb19117d242a3d883a469ee18514d30a9be2bb4 |
# -*- coding: utf-8 -*-
'''
*A simple problem solver written in pure Python*
Module provides an easy way to solve various problems that require some
calculations. Lets imagine a problem formulated in
a text file using a some template language. Some places
within the problem formulation text correspond to variables
tha... | scidam/solver | solver/base.py | Python | mit | 10,955 | [
"VisIt"
] | b29665db56657fb20f12b840a56f22f77285289544eabcb0ab02d5f81f8bbd62 |
"""
This module contains an interface to the Adas Data File type 15 (ADF 15),
that contain Photon Emissivity Coefficients (PEC). See [1] for an example
file.
[1] http://www.adas.ac.uk/man/appxa-15.pdf
"""
import os
import _xxdata_15
# Some hard coded parameters to run src/xxdata_15/xxdata_15.for routine. The
# value... | ezekial4/atomic_neu | atomic/adf15.py | Python | mit | 3,145 | [
"ADF"
] | f4f02f8b4220c71337a3f2ee53abbc8b8128736f952b47799fbb826f9ea96861 |
#!/usr/bin/env python
#
# $File: HaplodiploidMating.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redi... | BoPeng/simuPOP | docs/HaplodiploidMating.py | Python | gpl-2.0 | 1,668 | [
"VisIt"
] | 916e3e2b262abe17ba736766efb1adaf8f194519a89235acd0b6caa5fa560b11 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import absolute_import
from __future__ import division
from __future__ import unicode_literals
from future import standard_library
standard_library.install_aliases()
from builtins import *
from builtins import object
... | genestack/python-client | docs/source/sample_scripts/run_vc_pipeline.py | Python | mit | 5,537 | [
"Bowtie"
] | f454c9e00fe0f0282ac45793b99ce8e2a14bdb70616e169c029553e7f91877ea |
# -*- test-case-name: twisted.web.test.test_domhelpers -*-
# Copyright (c) 2001-2009 Twisted Matrix Laboratories.
# See LICENSE for details.
"""
A library for performing interesting tasks with DOM objects.
"""
import StringIO
from twisted.web import microdom
from twisted.web.microdom import getElementsByTagName, esc... | sorenh/cc | vendor/Twisted-10.0.0/twisted/web/domhelpers.py | Python | apache-2.0 | 8,572 | [
"VisIt"
] | ee56b05cbab3bdcaebbf7b350f52433519123bfbe6e10916aa168bc0e10a5b36 |
"""
Artificial Intelligence for Humans
Volume 1: Fundamental Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2013 by Jeff Heaton
Licensed under the Apache License, Version 2.0 (the "License");
... | PeterLauris/aifh | vol1/python-examples/lib/aifh/equilateral.py | Python | apache-2.0 | 2,876 | [
"VisIt"
] | df2f09dc9d67b4b2866918f7e2b93dff74973beca528c69d334a8db3b2e9e82a |
"""
Development tool and utility functions for testing and test data generation.
"""
# Copyright (C) 2009-2021 Thomas Aglassinger
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either ... | roskakori/cutplace | tests/dev_test.py | Python | lgpl-3.0 | 19,440 | [
"Amber",
"Brian",
"CRYSTAL"
] | 0064b4e79ab930695a23807eb12d9015070843493e5af1c9b285c856c447337d |
import numpy as np
from pyiid.adp import has_adp
from pyiid.experiments.elasticscatter.kernels.cpu_nxn import *
from pyiid.experiments.elasticscatter.kernels.cpu_flat import (
get_normalization_array as flat_norm)
__author__ = 'christopher'
def wrap_fq(atoms, qbin=.1, sum_type='fq'):
"""
Generate the red... | CJ-Wright/pyIID | pyiid/experiments/elasticscatter/cpu_wrappers/nxn_cpu_wrap.py | Python | bsd-3-clause | 6,631 | [
"ASE"
] | 1445dbcc4a6e47a3ee592f883078ffda94448acb77ec3a0194f3a03674ff5ba6 |
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
# Standard imports
from future import standard_library
standard_library.install_aliases()
from builtins import *
import logging
# Our imports
import emission.analysis.int... | shankari/e-mission-server | emission/analysis/intake/segmentation/section_segmentation_methods/smoothed_high_confidence_with_visit_transitions.py | Python | bsd-3-clause | 6,940 | [
"VisIt"
] | 8c07c26d4e3ea6ff54ff38a9ce44b72ae4aceca919681cf4cbe6a5d6cb35914d |
# $Id$
__author__ = 'Martin Felder'
import numpy as np
from pybrain.supervised.trainers import RPropMinusTrainer, BackpropTrainer
from pybrain.structure.modules.mixturedensity import MixtureDensityLayer
def gaussian(x, mean, stddev):
""" return value of homogenous Gaussian at given vector point
x: vector, me... | arabenjamin/pybrain | pybrain/supervised/trainers/mixturedensity.py | Python | bsd-3-clause | 3,420 | [
"Gaussian"
] | f99c16e39b77480a05a6e3febbe31dbb14695535622584ca50173c0c99b84c13 |
from __future__ import absolute_import
from typing import Any, List, Set, Tuple, TypeVar, \
Union, Optional, Sequence, AbstractSet
from typing.re import Match
from django.db import models
from django.db.models.query import QuerySet
from django.conf import settings
from django.contrib.auth.models import AbstractBas... | Vallher/zulip | zerver/models.py | Python | apache-2.0 | 58,960 | [
"VisIt"
] | d58e85669c7932cd77d0d57fe897211e8d69a065851738c66765a211f93f7686 |
# -*- coding: utf-8 -*-
import click
import pytumblr
from exceptions import DumblrException
from httplib2 import ServerNotFoundError
from requests.exceptions import RequestException
from requests_oauthlib import OAuth1Session
class Tumblr(object):
def __init__(self, ckey, skey, oauth, oauth_s):
self.tumblr... | devty1023/dumblr | dumblr/tumblr.py | Python | mit | 5,213 | [
"VisIt"
] | 9606a643dc54fb7d4608e8a3a2614e015dfdb0f272a3b9aeca77116603455372 |
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | neeasthana/CS498MachineLearning | HW8/part4/cifar10part4.py | Python | unlicense | 13,908 | [
"Gaussian"
] | 9749a13434b9f04e1b767434c615457b5782a926fc3f698de7a558b797f8c54f |
# Copyright 1999 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.
"""
This module provides code to work with the enzyme.dat file from
Enzyme.
http://www.expasy.... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Enzyme/__init__.py | Python | apache-2.0 | 8,109 | [
"Biopython"
] | 2ace4df3b39d2a4ad4fdf39b58ca36919a5dbdb8a702b8f51f5cb71810ea3fc5 |
"""
Extracts minimal phrases from symmetrized word alignments
"""
from collections import defaultdict, deque
def as_words(phrase, id2word):
return tuple(id2word[i] for i in phrase)
def try_expand(f, f2e, f_min, f_max, e_min, e_max):
"""
Try to expand the boundaries of a phrase pair based on the alignm... | wilkeraziz/smtutils | atools/minphrases.py | Python | apache-2.0 | 5,841 | [
"VisIt"
] | 683934696a5ef10aacaa3353012c0a51be9e802d1d2b8a951f5eee2f315cc810 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | andersinno/foosball | config/urls.py | Python | mit | 1,691 | [
"VisIt"
] | d92fc6055cc096862ecb4047077f9f4f49fe06eba9e244a7282e86add446612e |
'''
Created on Aug 5, 2014
@author: gearsad
'''
import vtk
from SceneObject import SceneObject
class Sphere(SceneObject):
'''
A template for drawing a sphere.
'''
def __init__(self, renderers, scale = 1, color = [1.0, 0, 0]):
'''
Initialize the sphere.
'''
# Call the ... | GearsAD/semisorted_arnerve | arnerve/scene/Sphere.py | Python | mit | 1,136 | [
"VTK"
] | 88c4766bea77cad144d3888a0d138f04a772f3d7b7ed11d517ce623376147044 |
from __future__ import print_function
import numpy as np
from theano.compat.six.moves import cStringIO, xrange
import theano.tensor as T
from theano.tests import disturb_mem
from theano.tests.record import Record, RecordMode
from pylearn2.compat import first_key
from pylearn2.costs.cost import Cost, SumOfCosts, Defau... | CKehl/pylearn2 | pylearn2/training_algorithms/tests/test_sgd.py | Python | bsd-3-clause | 60,662 | [
"VisIt"
] | 8a3e7442390a7cb06a60fc27b73910e9c6c5a9e8178291e773145be51b155225 |
# -*- coding: utf-8 -*-
__author__ = 'ke4roh'
# Copyright © 2016 James E. Scarborough
#
# 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) an... | ke4roh/RPiNWR | tests/test_Si4707.py | Python | gpl-3.0 | 12,599 | [
"CRYSTAL"
] | a1d1be77666bbbdb8f741f85bc4b776cfcd4a292fbf4e0c0c79b4f4ae7ed70f2 |
#!/usr/bin/env python
#
# -----------------------------------------------------------------------------
# Copyright (c) 2018 The Regents of the University of California
#
# This file is part of kevlar (http://github.com/dib-lab/kevlar) and is
# licensed under the MIT license: see LICENSE.
# ----------------------------... | dib-lab/kevlar | kevlar/tests/test_reference.py | Python | mit | 3,472 | [
"BWA"
] | 120c2d4638728c6244888f4000973fa5c92bbe90dc910e528982e41e11256485 |
from libmyriad import ResultCode
import datetime
import json
import logging
import multiprocessing
import os
import psutil
import re
import requests
import shutil
import subprocess
import time
import zipfile
class Myriad:
def __init__(self):
self.config = []
self.maestroAPIGateway = None
self.myriadJobsFolder... | russellthackston/comp-chem-util | myriad/v1/myriad.py | Python | mit | 18,545 | [
"Psi4"
] | 7d50344a52e763d5f2755fbee890f328db1d40dbbde05c3a90b2bb78a98baa47 |
# -*- coding: utf-8 -*-
from distutils.core import setup
setup(name='abouttag',
version='1.3.1',
description='Normalizes about tags for Fluidinfo',
author='Nicholas J. Radcliffe',
author_email='njr@StochasticSolutions.com',
packages=['abouttag'],
url="http://github.com/njr0/abouttag... | njr0/abouttag | setup.py | Python | mit | 2,321 | [
"VisIt"
] | 9cfd29e91ae8fc306f76cfb02d7b3c84e1ef16702625faf6e0803309ce410114 |
import random
import copy
from itertools import repeat
from collections import Sequence
# Mutator with "rubber-like" behaviour. Doesn't go out of bounds, moves in a gaussian way.
# 3.3.1 Local Gaussian Mutation in report.
def mutRubber(individual, sigma, border, indpb, lower_bound=0):
size = len(individual)
i... | eastlund/evolutionary_square_packing | mutation.py | Python | mit | 1,227 | [
"Gaussian"
] | 1cff31701929e193162406917d20a4c6884d79ba337e242a4df0553034ef9673 |
import random
import time
import itertools
import numpy as np
import pandas as pd
from sklearn.model_selection import train_test_split
from sklearn import preprocessing
from keras.preprocessing import sequence
from keras.utils import np_utils
from keras.models import Sequential
from keras.layers import Dense, Activat... | AlexGidiotis/Multimodal-Gesture-Recognition-with-LSTMs-and-CTC | early_fusion/early_multimodal.py | Python | mit | 15,549 | [
"Gaussian"
] | 2f95f5e48a5094b48d384f4e97eac874fbe28e4889a7335191572b63ba1c1e11 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module implementing classes and functions to use Zeo++.
Zeo++ Installation Steps:
========================
1) Zeo++ requires Voro++. Download Voro++ from code.lbl.gov using
subversion:
"svn checkout ... | fraricci/pymatgen | pymatgen/io/zeopp.py | Python | mit | 18,471 | [
"GULP",
"pymatgen"
] | 369ad7d13ae738f016984d6238485eba71ee5408c26f98adb788dca4451bec13 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('datapoints', '0003_load_ng_regions'),
]
operations = [
migrations.RunSQL("""
INSERT INTO auth_group
(name)
SELECT '... | unicef/polio | datapoints/migrations/0004_load_indicators_campaigns_permissions.py | Python | agpl-3.0 | 180,207 | [
"VisIt"
] | 50a8951a89e09fa3b6758cabc9a70f9095a583670950d795c769d815a4b4d233 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006-2014 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... | tiagocardosos/stoq | stoqlib/reporting/product.py | Python | gpl-2.0 | 5,347 | [
"VisIt"
] | 1fbbf4604786102d669ca79000e7f3b8066355316ce620d1b8a0aa717a245cd5 |
# -*- coding: utf-8 -*-
"""
jinja2.visitor
~~~~~~~~~~~~~~
This module implements a visitor for the nodes.
:copyright: (c) 2009 by the Jinja Team.
:license: BSD.
"""
from jinja2.nodes import Node
class NodeVisitor(object):
"""Walks the abstract syntax tree and call visitor functions for every... | yesudeep/tisshrmlr | app/jinja2/jinja2/visitor.py | Python | mit | 3,316 | [
"VisIt"
] | 5f192b3b8c82ac6254af1099700f95260ba784ba17e19fcd7ba43cdee80218b2 |
# Docstrings for generated ufuncs
#
# The syntax is designed to look like the function add_newdoc is being
# called from numpy.lib, but in this file add_newdoc puts the
# docstrings in a dictionary. This dictionary is used in
# generate_ufuncs.py to generate the docstrings for the ufuncs in
# scipy.special at the C lev... | DailyActie/Surrogate-Model | 01-codes/scipy-master/scipy/special/add_newdocs.py | Python | mit | 189,015 | [
"Gaussian"
] | 174e0190e871aeeeb1fc7ecb574640f195d1cabdd7e6bac2249d2ac9fb64aa1b |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | xflin/spark | python/pyspark/ml/tests.py | Python | apache-2.0 | 89,730 | [
"Gaussian"
] | 45849ef59db2cd33b57b73a95f62d491acf9189712de7c269d70b740af1727d4 |
''' DIRAC.ResourceStatusSystem.Agent package
'''
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
| yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Agent/__init__.py | Python | gpl-3.0 | 179 | [
"DIRAC"
] | 400076fdeccf404657dac96f3b2a3831d8ae89a8596a5c8fc04b677844a7a415 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# 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... | mheap/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 111,203 | [
"VisIt"
] | 8533bcbc52b5180dfd89e4c7d843be2bd75ad2d37d79fc5d8931462ba772f809 |
#! /usr/bin/env python
########################################################################
# $HeadURL: $
########################################################################
__RCSID__ = "$Id: $"
from DIRAC.Core.Base import Script
Script.setUsageMessage( """
Monitor the status of the given FTS request
Usag... | avedaee/DIRAC | DataManagementSystem/scripts/dirac-dms-fts-monitor.py | Python | gpl-3.0 | 1,304 | [
"DIRAC"
] | 67bc468d5d7732a0b61f8714e6b549796c3a15c003c883b08b0112cac643de1f |
"""
Script entry point
"""
from src.calrissian.particle333_network import Particle333Network
from src.calrissian.layers.particle333 import Particle333
from src.calrissian.optimizers.particle333_sgd import Particle333SGD
from multiprocessing import Pool
import numpy as np
import time
import pandas as pd
import pickle
... | awlange/brainsparks | tests/particle333_test.py | Python | mit | 15,864 | [
"Gaussian"
] | 090061faa44601eb12f125b64b70f1981f32b0af485907c254a7aebb49ceb5ef |
"""
Hodgekin-Huxley Network
"""
import numpy as np
from SimulationMethods import eul, rk4
from NeuronModels import HodgekinHuxley
class HhNetwork:
"""
"""
def __init__(self, _neuronsPerLayer, _Dmax):
"""
Initialise network with given number of neurons
Inputs:
_neuronsPe... | cpsnowden/ComputationalNeurodynamics | HH_Braitenberg/HhNetwork.py | Python | gpl-3.0 | 5,100 | [
"NEURON"
] | 69cdd599100367ba5ec83cdaf441ff02e6017cdc82015ab4f50d8dde421489c3 |
import numpy as np
from .. import Variable
from ..core import indexing
from ..core.utils import Frozen, FrozenDict
from .common import AbstractDataStore, BackendArray
from .file_manager import CachingFileManager
from .locks import HDF5_LOCK, NETCDFC_LOCK, SerializableLock, combine_locks, ensure_lock
# PyNIO can invok... | jhamman/xarray | xarray/backends/pynio_.py | Python | apache-2.0 | 2,661 | [
"NetCDF"
] | bd418d97f6f608080404251763782131106b697011678e508feae8f6c4ecb349 |
#!/usr/bin/env python
"""
.. See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
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
... | Multiscale-Genomics/mg-process-fastq | process_mnaseseq.py | Python | apache-2.0 | 6,459 | [
"BWA"
] | 42cb68db2b6f42bebef4142e9155466821e9a59443b1da1c0ee0b3a102d112e0 |
#####################################################################
# $HeadURL $
# File: RequestManagerHandler.py
########################################################################
""" :mod: RequestManagerHandler
===========================
.. module: RequestManagerHandler
:synopsis: Implementatio... | avedaee/DIRAC | RequestManagementSystem/Service/RequestManagerHandler.py | Python | gpl-3.0 | 10,079 | [
"DIRAC"
] | 7aaa57cb7c1d32eda01291ad4602318114957ef3c5ea78e69c45a2456839fd18 |
# Copyright 1999-2017. Plesk International GmbH. All rights reserved.
#!@@PYTHON@@
#------------------------------------------------------------------------
# Copyright (c) 1998 by Total Control Software
# All Rights Reserved
#-------------------------------------------------------... | wlanowski/wlanowski.github.io | tkalook/backup/test/fcgi/fcgi.py | Python | mit | 15,057 | [
"TINKER"
] | 3793bf7e1ac59f29bbaf1350eff7de475dbbbc8a4ef7bc9c3acb2d2395ee38ca |
import warnings
from scipy.linalg import toeplitz
import scipy.sparse.linalg
import scipy.interpolate
from scipy.ndimage import zoom, gaussian_filter1d
import numpy as np
import numba
import cooler
from functools import partial
from ._numutils import (
iterative_correction_symmetric as _iterative_correction_symmet... | open2c/cooltools | cooltools/lib/numutils.py | Python | mit | 50,305 | [
"Gaussian"
] | 0eb38312d2d3ea18b81ed52a9011a10991d681fec3bdbceb8905fdc8a78be4be |
# Copyright 2009 by Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Command line wrapper for the multiple alignment program Clustal W.
"""
from __future__ impor... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Align/Applications/_Clustalw.py | Python | gpl-2.0 | 19,835 | [
"Biopython"
] | f3b1d28944c3fda1df252c9e6487b91dc2342d91a825365d26e92bc537896b67 |
########################################################################
# $HeadURL$
# File : CloudDirector.py
# Author : Victor Mendez
########################################################################
#DIRAC
from DIRAC import S_OK, S_ERROR, gConfig
#VMDIRAC
from VMDIRAC.Resources.Cloud.VMDirector ... | myco/VMDIRAC | Resources/Cloud/CloudDirector.py | Python | gpl-3.0 | 3,532 | [
"DIRAC"
] | b2f6c9c578a9af8a50e10b057ab9e5ba8aa9a05c294a2b74d808bd82c837a9b9 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-speech | scripts/fixup_speech_v1p1beta1_keywords.py | Python | apache-2.0 | 6,672 | [
"VisIt"
] | 24c88cec18f460da881ef40878ba9a13cb4f9b9676fcc5b653e63616cf538c8d |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Workflow.Parameter import *
from DIRAC.Core.Workflow.Module import *
from DIRAC.Core.Workflow.Step import *
from DIRAC.Core.Workflow.Workflow import *
from DIRAC.Core.Workflow.WorkflowReader impo... | yujikato/DIRAC | src/DIRAC/Core/Workflow/test/step_g.py | Python | gpl-3.0 | 22,676 | [
"DIRAC"
] | c3cb199c38b2d5580b95ade438bdb63aefd7d22c6bca7602ee0f2f377c09dddf |
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from matplotlib.externals import six
import os
import sys
from hashlib import md5
from docutils import nodes
from docutils.parsers.rst import directives
import warnings
from matplotlib import rcParams
from m... | yuanagain/seniorthesis | venv/lib/python2.7/site-packages/matplotlib/sphinxext/mathmpl.py | Python | mit | 3,754 | [
"VisIt"
] | e9a3176b71f00ef53524735cb0cc840a8241ab7b609e98c1d6f886b67b66b389 |
#! PsiAPI pubchem access
import psi4
hartree2ev = psi4.constants.hartree2ev
psi4.set_output_file("output.dat", False)
benz = psi4.geometry("""
pubchem:benzene
""")
psi4.set_options({"REFERENCE" : "RHF",
"MAX_ENERGY_G_CONVERGENCE" : 8,
"BASIS" ... | CDSherrill/psi4 | tests/python/pubchem/input.py | Python | lgpl-3.0 | 1,449 | [
"Psi4"
] | e1eb74b558253d08816cea1fe486048f2a5ce7232e77417df6081da8b622e577 |
tests = [
("python", "UnitTestDraw.py", {}),
("python", "UnitTestSimilarityMaps.py", {}),
("python", "UnitTestIPython.py", {}),
]
longTests = []
if __name__ == '__main__':
import sys
from rdkit import TestRunner
failed, tests = TestRunner.RunScript('test_list.py', 0, 1)
sys.exit(len(failed))
| ptosco/rdkit | rdkit/Chem/Draw/test_list.py | Python | bsd-3-clause | 309 | [
"RDKit"
] | 3856e423a89f8f11fe37f099c6e0ce1269b641048f85a26b01f466a278b24481 |
from datetime import datetime, timedelta
from flask import jsonify, Blueprint, request, json
from werkzeug.datastructures import MultiDict
from projectp import db, socketio
from projectp.auth import requires_auth
from projectp.locations.models import Location
from projectp.visits.forms import VisitForm, DateForm
from... | Proj-P/project-p-api | projectp/visits/views.py | Python | mit | 2,768 | [
"VisIt"
] | 7a4c171c0f8d4dd3e2cbb6c5172dcea73486db8caa51b5a0fdb8f68c7fbf7eec |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
from __future__ import division
from pandas import *
import os, os.path
import sys
import numpy as np
sys.path.append('/home/will/HIVReportGen/AnalysisCode/')
sys.path.append('/home/will/PySeqUtils/')
# <codecell>
store = HDFStore('/home/will/HIVRepor... | JudoWill/ResearchNotebooks | TimeCourseSeqs.py | Python | mit | 6,164 | [
"VisIt"
] | 78a646f58fc93bff8ea9a1b21c97b1ffa7b775e02bd8ab194d793f43179b24ef |
# 10.07.2007, c
# last revision: 25.03.2008
filename_meshes = ['database/kostka_medium_tetra.mesh',
'database/kostka_medium_tetra.mesh',
'database/kostka_medium.mesh']
all_your_bases = [{'Omega' : '3_4_P1'},
{'Omega' : '3_4_P2'},
{'Omega' : '3_8_Q1'... | certik/sfepy | tests/test_elasticity_small_strain.py | Python | bsd-3-clause | 5,322 | [
"VTK"
] | 2875cb9693afc7ae0ff05ec5b1657512709a84d86cd26b89da82e8a8b96f10f3 |
#!/usr/bin/env python
# Author: Benjamin Menkuec
# Copyright 2015 Benjamin Menkuec
# License: LGPL
import sys
import os.path
import subprocess
import argparse
import platform
import multiprocessing
# this function calls a subroutine that will call samtools to
# sort the bam file and then build an index of it
def ind... | charite/Q | scripts/preprocess.py | Python | bsd-2-clause | 8,778 | [
"Bowtie"
] | 958918259050555ae7d7c078eebdc67d77e80b4a89953b3aff1de9c3cd20c5c9 |
#!/usr/bin/env python
# vim:fileencoding=UTF-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid@kovidgoyal.net>'
__docformat__ = 'restructuredtext en'
from collections import OrderedDict
fro... | sharad/calibre | src/calibre/ebooks/metadata/sources/google_images.py | Python | gpl-3.0 | 4,869 | [
"VisIt"
] | 3f9fb34752988d3b8fc8abc056f7cb49fe605169269fdbbe81acf28248dd9080 |
import galaxy.datatypes.data as data
import galaxy.datatypes.binary
from galaxy.datatypes.binary import Binary
class Matlab(Binary):
file_ext = "mat"
def __init__( self, **kwd ):
Binary.__init__( self, **kwd )
def sniff( self, filename ):
# The header of any psysound matlab file starts w... | IntersectAustralia/hcsvlab-galaxy | tools/psysound/psysound.py | Python | gpl-3.0 | 5,884 | [
"Galaxy"
] | eb7598ded294c75d59bac43f056e862b5b7cbf0a5313224a3cfc8c6ee0163ab1 |
r"""OS routines for Mac, DOS, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, mac, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, ntpath, or macpath
- os.name is 'posix', 'nt', 'os2', 'mac', 'ce' or 'riscos'
- os.curdir is a string r... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.4/Lib/os.py | Python | mit | 23,147 | [
"VisIt"
] | e57dbe4d9fb2c030e2d7ec9d4d1a9f348d55a40419fcd186e25974333dd841f4 |
"""
test views
"""
import datetime
import json
import re
import pytz
from mock import patch
from nose.plugins.attrib import attr
from capa.tests.response_xml_factory import StringResponseXMLFactory
from courseware.field_overrides import OverrideFieldData # pylint: disable=import-error
from courseware.tests.factories ... | antonve/s4-project-mooc | lms/djangoapps/ccx/tests/test_views.py | Python | agpl-3.0 | 30,393 | [
"VisIt"
] | aa178dde99606ec5205d7ba70a2215b524a030383a8f790a3d15368286c80023 |
#!/usr/bin/env python
'''
Master loader for CANON October (Fall) Campaign 2020
'''
import os
import sys
from datetime import datetime
parentDir = os.path.join(os.path.dirname(__file__), "../")
sys.path.insert(0, parentDir)
from CANON import CANONLoader
import timing
cl = CANONLoader('stoqs_canon_october2020', 'CANO... | duane-edgington/stoqs | stoqs/loaders/CANON/loadCANON_october2020.py | Python | gpl-3.0 | 6,445 | [
"NetCDF"
] | 21c7fc23be905e1485b79b5ae6a6de5281814b9a387605f4ff7018337343f08a |
# Lint as: python2, python3
# Copyright 2020 Google LLC
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law ... | googleinterns/wss | core/preprocess_utils.py | Python | apache-2.0 | 28,986 | [
"Gaussian"
] | 962dd59d2cd442fe2118ff186f20c4781f64c2470107d30e00327c302d89dcde |
"""
==================
Test the SeqSearch
==================
"""
# Modules #
import os, inspect
from seqenv.fasta import FASTA
from seqenv.seqsearch.parallel import ParallelSeqSearch
# Constants #
current_script = inspect.getframeinfo(inspect.currentframe()).filename
current_dir = os.path.dirname(os.path.abspath(curr... | xapple/seqenv | tests/seqsearch.py | Python | mit | 582 | [
"BLAST"
] | 746d5499d8b2d82da2860c5e9c1f748e8b2be39342a0abcc979bdb98ce609e32 |
#===============================================================================
# LICENSE XOT-Framework - CC BY-NC-ND
#===============================================================================
# This work is licenced under the Creative Commons
# Attribution-Non-Commercial-No Derivative Works 3.0 Unported Li... | SMALLplayer/smallplayer-image-creator | storage/.xbmc/addons/net.rieter.xot.smallplayer/resources/libs/helpers/htmlhelper.py | Python | gpl-2.0 | 2,786 | [
"VisIt"
] | a1e911a29f10085c3080527a0516e7346fbea3ec56a768ec15df936a07168f51 |
../../../../../../../share/pyshared/orca/scripts/apps/gdmlogin/script.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/scripts/apps/gdmlogin/script.py | Python | gpl-3.0 | 72 | [
"ORCA"
] | 8643df406ba4a4cdd6013098a8a49f7f0f452e7c2cb8a6666a6b666e4a31a504 |
import nipype.interfaces.utility as util # utility
import nipype.pipeline.engine as pe # pypeline engine
import nipype.interfaces.camino as camino
import nipype.interfaces.fsl as fsl
import nipype.interfaces.camino2trackvis as cam2trk
import nipype.algorithms.misc as misc
from ...misc.utils import get_affi... | christianbrodbeck/nipype | nipype/workflows/dmri/camino/diffusion.py | Python | bsd-3-clause | 10,454 | [
"ParaView",
"VTK"
] | cb4d3b5fb054f93d8d73d490b1d3fcda5da8dd511bbae259efa653a5d379dcf0 |
"""
Linear Discriminant Analysis and Quadratic Discriminant Analysis
"""
# Authors: Clemens Brunner
# Martin Billinger
# Matthieu Perrot
# Mathieu Blondel
# License: BSD 3-Clause
import warnings
import numpy as np
from scipy import linalg
from scipy.special import expit
from .base import ... | bnaul/scikit-learn | sklearn/discriminant_analysis.py | Python | bsd-3-clause | 30,056 | [
"Gaussian"
] | 6af8faddf2957c23c2e44bbc9008dd528b3601c3806d1509834c5f7224482ffb |
from brian2 import *
import numpy as np
import matplotlib.pyplot as plt
import seaborn as sns
sns.set(font_scale=2.0)
# Neuron Parameters
g_l = 0.05 * msiemens / cm2
cm = 1.0 * ufarad / cm2 # Specific membrane capacitance
E_l = -60 * mV # Resting potential
V_t = -50 * mV # Threshold
tau_w = 600 * ms # Adaptation ... | h-mayorquin/camp_india_2016 | project3_sustained_activity/dynamical_study_jump.py | Python | mit | 2,647 | [
"NEURON"
] | c0e78e6fc5a5e9fa92e1bfeb456d048789df06715676f7d9c7271f01eeafd72b |
from Screens.Screen import Screen
from Components.Label import Label, MultiColorLabel
from Components.Pixmap import Pixmap
from Components.ServiceEventTracker import ServiceEventTracker
from Components.config import config
from enigma import eTimer, eEnv, iServiceInformation, iPlayableService, eDVBFrontendParametersSat... | kingvuplus/nn-gui | lib/python/Nemesis/nemesisExtraInfoBar.py | Python | gpl-2.0 | 22,381 | [
"Galaxy"
] | 3ac480fc7633dcefe109c757123dc55700571bc156a9723c01bd13fb4977d3a3 |
# -*- coding: utf-8 -*-
"""Tests for PyBEL induction functions."""
import string
import unittest
from pybel import BELGraph
from pybel.constants import (
CITATION_AUTHORS,
CITATION_TYPE_PUBMED,
IDENTIFIER,
NAMESPACE,
)
from pybel.dsl import BaseEntity, gene, protein, rna
from pybel.struct.mutation.ex... | pybel/pybel | tests/test_struct/test_transformations/test_induction.py | Python | mit | 15,582 | [
"Pybel"
] | 6add5bb6d45862c8f81ead281d0ec1dcb8426fb930d054db5cdaea3ce41ab091 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | brianmay/karaage | karaage/tests/projects/test_projects.py | Python | gpl-3.0 | 8,530 | [
"Brian"
] | e275d7a498203d73b53f58b1a47c68ea0484d852678e4f0385c785e4a108ce29 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 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 ... | kannon92/psi4 | psi4/src/psi4/libfunctional/matlab/mfiles/assemble.py | Python | gpl-2.0 | 2,877 | [
"Psi4"
] | 3bcd9fd867e30d24f90d307507834f52d09a7dc1a4e26f05b78dc8b17d7a3c3d |
# Main script of the game
# Reference http://renpyhandbook.tumblr.com/code-tutorials as needed
#########################################
# Defines backgrounds we'll use
image bg outside = "assets/backgrounds/outside_bg.png"
image bg outside_rain = im.MatrixColor("assets/backgrounds/outside_bg.png", im.matrix.tint(0.7... | ELHmk1/TouchFluffyTail | HellhoundVN/game/scripts/Old Script.py | Python | gpl-3.0 | 13,460 | [
"CRYSTAL"
] | b24c5c7a0452e3d4f560d1a050c93abfde4169ad3680358c85165a9e70b8ac22 |
__author__ = 'zeek'
import time
import notify2
from splinter import Browser
import html
browser = Browser()
browser.visit('http://www.douyutv.com/zeek')
last_list = 0
last_yuwan = 0
while True:
if last_list % 20 == 10:
browser.reload()
time.sleep(2)
try:
element_list_chat = browser.find_b... | zephyrzoom/douyu | test/splinter_t.py | Python | mit | 1,248 | [
"VisIt"
] | 92488c0e65943c1b92fc70676e0faf67ae730efd23f131aad6562744b3ef93d0 |
# -*- coding: utf-8 -*-
"""
This script opens data files and extracts relevant data. Then, using a sklearn
gaussian process package, fits a gaussian to the crosswind (1d) temperature
measurements and interpolates temparture values (relative, not absolute) at a
2 mm interval.
Created on Mon Dec 01 11:51:44 2014
@auth... | sazamore/GP-temperature-interpolation | gptempdata-3d.py | Python | mit | 3,540 | [
"Gaussian"
] | bd18ce3925c30140974d604a425696cf058c45a5779700dea9daed13ae833fb2 |
import numpy as np
from flatdict import FlatDict
from xml.etree import ElementTree as ET
from openpnm.io import GenericIO, Dict
from openpnm.utils import logging, Workspace
logger = logging.getLogger(__name__)
ws = Workspace()
class VTK(GenericIO):
r"""
The Visualization Toolkit (VTK) format defined by Kitwar... | PMEAL/OpenPNM | openpnm/io/_vtk.py | Python | mit | 9,179 | [
"ParaView",
"VTK"
] | f5fe0b8be2a3fae6b1d9f1adf95b4fd388eaf53608a4854705c4c2e332874c46 |
# -*- coding: utf-8 -*-
"""
Bok choy acceptance tests for problems in the LMS
See also old lettuce tests in lms/djangoapps/courseware/features/problems.feature
"""
from nose.plugins.attrib import attr
from textwrap import dedent
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.accept... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 37,760 | [
"VisIt"
] | 6347a2910aec178d96ecb3397eacade31e1900dbb125e3e882e7a2c519f57f1d |
# -*- coding: utf-8 -*-
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import copy
import json
import os
import py... | ilpianista/ansible | test/units/galaxy/test_collection_install.py | Python | gpl-3.0 | 33,974 | [
"Galaxy"
] | 7a959739b5c38b4f3d5a7d807818a881845abd210acbabf5aaa6736576752c39 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/timeseries/python/timeseries/math_utils.py | Python | apache-2.0 | 43,089 | [
"Gaussian"
] | 9f0cbbcea03a4f90b16a01827ab3fbc6a9bac0899e67fca4c7294b73837b2279 |
##############################################################################
# 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... | TheTimmy/spack | var/spack/repos/builtin/packages/r-glmnet/package.py | Python | lgpl-2.1 | 2,113 | [
"Gaussian"
] | 5ba4105dfed9d856d056478f8c405a187f0b5253c6e3e778f477821ce9dbb21c |
#! /usr/bin/env python
# PBS cluster job submission in Python
# BWA alignment to Painted Turtle Genome
# By Jean P. Elbers
# jean.elbers@gmail.com
# Last modified 22 Jan 2015
###############################################################################
Usage = """
03-bwa.py - version 1.0
Command:
1.Uses BWA Mem to... | jelber2/immunome_2014 | 03-bwa-run2.py | Python | mit | 3,867 | [
"BWA"
] | cff8848b5e8df9c2856e2c1f51bc8a39626736eba16718eab6d5405e2321f28c |
"""
___ _
/ _ \ ___| |_ ___ _ __ _ _ ___
| | | |/ __| __/ _ \| '_ \| | | / __|
| |_| | (__| || (_) | |_) | |_| \__ \
\___/ \___|\__\___/| .__/ \__,_|___/
|_|
<HSC-Herve Schauer Consultants 2015>
Licensed to the Apache Software Foundation (ASF) under one
or more contributo... | hsc-lab/octopus | src/masternode.py | Python | apache-2.0 | 25,227 | [
"Octopus"
] | f3cb4a0ad210ea5dc9e868f345b5a87c3a58210f9f4dbe2635e9690d68521ce8 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/mediaplayerplay.py | Python | gpl-2.0 | 5,233 | [
"VisIt"
] | e3bb549dd434820499c5be31916c479a7683c2446e4edc15665a7f21fc3c79eb |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-pilot-logging-info.py
# Author : Stuart Paterson
########################################################################
"""
Retrieve logging info of a Grid pilot
"""
__RCSID__ = "$Id$"
# pyl... | andresailer/DIRAC | Interfaces/scripts/dirac-admin-get-pilot-logging-info.py | Python | gpl-3.0 | 1,294 | [
"DIRAC"
] | 97ea47495746c8c1e1426304d8ce06afd2efc5a25bcebdbcb798dd2b1211fbcd |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RDose(RPackage):
"""Disease Ontology Semantic and Enrichment analysis.
This packag... | rspavel/spack | var/spack/repos/builtin/packages/r-dose/package.py | Python | lgpl-2.1 | 1,982 | [
"Bioconductor"
] | 1e7d1e2a5174eac6ed35f3c5cf8e6d625910de87055368a24088accda279c91d |
"""
Test the about xblock
"""
import datetime
import ddt
import mock
import pytz
import six
from ccx_keys.locator import CCXLocator
from django.conf import settings
from django.test.utils import override_settings
from django.urls import reverse
from milestones.tests.utils import MilestonesTestCaseMixin
from mock imp... | cpennington/edx-platform | lms/djangoapps/courseware/tests/test_about.py | Python | agpl-3.0 | 26,979 | [
"VisIt"
] | 6978c812696188c66fd91d5b9e4d8e98c9ea604895c80d3d7ac495aae70a0d77 |
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as np
import traceback
from alis import almsgs
import sys
msgs=almsgs.msgs()
class Base :
"""
Returns a 1-dimensional gaussian of form:
p[0] = amplitude
p[1] = x offset
p[2] = dispersion (sigma)
"""
... | rcooke-ast/ALIS | alis/alfunc_base.py | Python | gpl-3.0 | 37,539 | [
"Gaussian"
] | 8408b0c0c4a44b48f862ed3b8eec9ab1a52cc4ed398c859cef728d945cdd2af8 |
# -*- coding: utf-8 -*-
import pprint
from collections import defaultdict
from string import punctuation
# Get a word count for each word in a pair of wordlists that appear in a block of text.
# Exclude the appearance of a word from the count if any of the 3 words before or after the word
# in question are a member of... | jlyoung/stackoverflow_answers | negator_parser/negatorparser.py | Python | mit | 7,417 | [
"MOOSE"
] | e1bafcc9d4de1cc79a684dfefb6af9286858ef5ea278da8240adfee934296bd0 |
# Portions copyright (c) 2014 ZMAN(ZhangNing)
#
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
#
# Name: WebZ轻量级自动化框架
# Description: keyword-driven automated testing f... | lsp84ch83/PyText | WebZ轻量级自动化框架/process.py | Python | gpl-3.0 | 7,006 | [
"VisIt"
] | f77814d9e95c25af1318a8c1dbd4cee439a49ff47bd5f38e3d1446229acf6e2d |
#!/usr/bin/env python
from __future__ import print_function
import itertools
import subprocess
import os.path
import sys
import pickle
import yaml
from parser import *
CACHEFILE="runall_cache.pycache"
readCache = True
writeCache = True
debug = False
OPERDEFSFILE="operdefs.tex"
writeOperDefs = False
RESULTSTABLEFI... | kbansal/servois | test/runall.py | Python | bsd-3-clause | 10,678 | [
"Bowtie"
] | 8c8cfff86a8feecd0c5bc798dc342e9375e169b042e26c54a280d9268781aa91 |
import argparse
import torch
import pickle
import numpy as np
from torch.autograd import Variable
import torch.nn as nn
import torch.nn.functional as F
import torch.optim as optim
# Training settings
parser = argparse.ArgumentParser(description='PyTorch semi-supervised MNIST')
parser.add_argument('--batch-size', type... | fducau/AAE_pytorch | script/aae_pytorch_basic.py | Python | gpl-3.0 | 8,635 | [
"Gaussian"
] | 4f9314c4e03e70e4d44df09dd6aa1f167de1f53157313621a68a3555c8e21fba |
import paraview.simple
pxm = paraview.simple.servermanager.ProxyManager()
proxy = pxm.NewProxy('testcase', 'None')
print proxy
| HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Catalyst/Editions/Enable-Python/Testing/Base-Python/import.py | Python | gpl-3.0 | 128 | [
"ParaView"
] | e971b82bd6189224ff2fc4c75c99c95e4a382c654c95edc4341b7ac747bf22f3 |
# -*- coding:utf-8 -*-
__author__ = 'q00222219@huawei'
import time
from heat.openstack.common import log as logging
import heat.engine.resources.cloudmanager.commonutils as commonutils
import heat.engine.resources.cloudmanager.constant as constant
import heat.engine.resources.cloudmanager.exception as exception
impor... | hgqislub/hybird-orchard | code/cloudmanager/install/hws/hws_cascaded_configer.py | Python | apache-2.0 | 4,081 | [
"VisIt"
] | e7fa32df50fe543c3a06dc1966fa2a807f0e6d6ab854006839b62ad8a79b7a5b |
"""
This file contains view functions for wrapping the django-wiki.
"""
import logging
import re
import cgi
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.exceptions import ImproperlyConfigured
from django.shortcuts import redirect
from django.utils.translation import ug... | MakeHer/edx-platform | lms/djangoapps/course_wiki/views.py | Python | agpl-3.0 | 4,668 | [
"VisIt"
] | 2c6f8be8485ad00a42c735ba3c04a3342920980a34d12297248492ec08ec75f8 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2014 Nick Hall
#
# This program is ... | pmghalvorsen/gramps_branch | gramps/gen/plug/docgen/stylesheet.py | Python | gpl-2.0 | 18,041 | [
"Brian"
] | 63a13f68f876a7dc3bf2b12bb2497410bb74186f85a5e11f84cc3048119b79f6 |
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