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"""
Ensure that we can use pathlib.Path objects in all relevant IO functions.
"""
import sys
from pathlib import Path
import numpy as np
import scipy.io
import scipy.io.wavfile
from scipy._lib._tmpdirs import tempdir
import scipy.sparse
class TestPaths:
data = np.arange(5).astype(np.int64)
def test_savemat... | WarrenWeckesser/scipy | scipy/io/tests/test_paths.py | Python | bsd-3-clause | 3,241 | [
"NetCDF"
] | 36562d8c6b94cc51a3453a9f274bddaf84533de701c6326ee756228d357aa1d1 |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Bio.SearchIO objects to model high scoring regions between query and hit."""
from __fu... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SearchIO/_model/hsp.py | Python | apache-2.0 | 45,567 | [
"BLAST",
"Biopython"
] | 170f76293175820a654e649eb055eccb5ba8b2605f3acf1c95363989c84236a0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import itertools
from pymatgen.core.lattice import Lattice
import numpy as np
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.operations impo... | matk86/pymatgen | pymatgen/core/tests/test_lattice.py | Python | mit | 20,062 | [
"pymatgen"
] | 1ed6cad6bdb6407af4877c3f61f7103dcef5be00dce319177245cb4386ab8e94 |
#!/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/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/pluginlistread.py | Python | gpl-2.0 | 5,260 | [
"VisIt"
] | ea595760d2ae3d1323bb4f34d7281796d5147c70a56f619d17bfbd6724a55617 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | dustpedia/core/dataprocessing.py | Python | agpl-3.0 | 6,518 | [
"Galaxy"
] | 3ef308abe14d172ade5ae6d5a52306ddc8247c33e71ab3d7777d8c99a40a9926 |
# Copyright 2019 The Magenta Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | adarob/magenta | magenta/models/latent_transfer/common_joint.py | Python | apache-2.0 | 27,043 | [
"Gaussian"
] | a9e20a604ad127cdb29b338e759a1ae72ea7b04d85778c72dddcf904a2bc15de |
#
# Brian C. Lane <bcl@redhat.com>
#
# Copyright 2012 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use, modify,
# copy, or redistribute it subject to the terms and conditions of the GNU
# General Public License v.2. This program is distributed in the hope that it
# will be useful,... | dashea/pykickstart | tests/commands/reboot.py | Python | gpl-2.0 | 2,617 | [
"Brian"
] | bebc01211eb34f61faa1da79dd8a0fce2b4fd9f65c76da7cd81ac5e6b78ee430 |
# $HeadURL$
"""
DIRAC Wrapper to execute python and system commands with a wrapper, that might
set a timeout.
3 FUNCTIONS are provided:
- shellCall( iTimeOut, cmdSeq, callbackFunction = None, env = None ):
it uses subprocess.Popen class with "shell = True".
If cmdSeq is a string, it specifies the... | sposs/DIRAC | Core/Utilities/Subprocess.py | Python | gpl-3.0 | 20,842 | [
"DIRAC"
] | 93219575fd02d4092739cc3785c3025f46f12d23109f76fc9b53beab4e8f2975 |
IMEI_TACS = [
"01124500", # Apple iPhone
"01161200", # Apple iPhone 3G
"01194800", # Apple iPhone 3GS
"01233600", # Apple iPhone 4
"01300600", # Apple iPhone 4S
"01332700", # Apple iPhone 5
"35875505", # Apple iPhone 5S
"35881505", # Apple iPhone 5C
"35925406", # Apple iPhon... | wikkiewikkie/elizabeth | elizabeth/intd/code.py | Python | mit | 1,415 | [
"Galaxy"
] | 00b38b839936892b7aed7ada57e7fa76736ee9f82c48355e16cade1dfa189ba6 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
from RPi import GPIO
from functools import partial
import time
class fsEncoder():
data = {
"com": { "outer": { "pinA": 11, "pinB": 12, "stateA": 0, "stateB": 0, "click": 0, "dt": 1 }, "inner": { "pinA": 15, "pinB": 16, "stateA": 0, "stateB": 0, "click": 0, "d... | neksysinfo/fspanel | fsEncoder.py | Python | gpl-3.0 | 4,673 | [
"ADF"
] | 7820f26855538af045cd57749a81a6e66247ac753e25af78ffed6dfec7058683 |
# Copyright (c) 2015, Frappe Technologies Pvt. Ltd. and Contributors
# License: GNU General Public License v3. See license.txt
from __future__ import unicode_literals
import frappe
import json
import frappe.utils
from frappe.utils import cstr, flt, getdate, comma_and, cint
from frappe import _
from frappe.model.mapper... | utkarsh-goswami/erpnext | erpnext/selling/doctype/sales_order/sales_order.py | Python | gpl-3.0 | 25,468 | [
"VisIt"
] | 804eee7f1471c12c6839f4a64ee550702492fd76f952526fc3f7db233e603a05 |
from math import sqrt, pi
import numpy as np
from ase.data import atomic_numbers
from gpaw.utilities import pack2, divrl
from gpaw.setup import BaseSetup
from gpaw.spline import Spline
from gpaw.grid_descriptor import AERadialGridDescriptor
from gpaw.grid_descriptor import EquidistantRadialGridDescriptor
from gpaw.at... | qsnake/gpaw | gpaw/hgh.py | Python | gpl-3.0 | 21,735 | [
"ASE",
"GPAW",
"Gaussian"
] | 60ae2d9dcc3da4384c23b72376faa96f60f31b82732366abe1c78a963f0e1180 |
# -*- coding: utf-8 -*-
""" Chemical Signalling model loaded into moose can be save into Genesis-Kkit format """
__author__ = "Harsha Rani"
__copyright__ = "Copyright 2017, Harsha Rani and NCBS Bangalore"
__credits__ = ["NCBS Bangalore"]
__license__ = "GNU GPL"
__version__ =... | BhallaLab/moose | moose-core/python/moose/genesis/writeKkit.py | Python | gpl-3.0 | 39,029 | [
"MOOSE"
] | 76d858f38441b53b4d61776e5a289b6e13b6d46d107fc48c5293249ef03b50d3 |
##
# Copyright 2009-2021 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | hpcuantwerpen/easybuild-easyblocks | easybuild/easyblocks/b/bioconductor.py | Python | gpl-2.0 | 2,256 | [
"Bioconductor"
] | a9efb89f739da51ab46bff92b1bdc9508ac279462fdb3ab1787c74f403496d39 |
# coding: utf-8
"""
Test for the BED12 module.
"""
import unittest
from Bio import Seq, SeqRecord
from ..parsers import bed12, GTF, GFF
from ..loci import Transcript
from re import sub
from ..utilities.log_utils import create_default_logger
import pysam
import pkg_resources
class OrfTester(unittest.TestCase):
"... | lucventurini/mikado | Mikado/tests/orf_test.py | Python | lgpl-3.0 | 35,968 | [
"pysam"
] | 92f3554ba133d249ae29b38ab6713d6fb8f89c075aeb5f76d7813a48279e1a78 |
import glob
import pandas as pd
import numpy as np
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27mcell*")
print(len(mcell))
trito = glob.glob("binary_position_RRBS_trito_pool*")
print(len(trito))
totalfiles = mcell... | evanbiederstedt/RRBSfun | epiphen/tests/normalCll5.py | Python | mit | 9,222 | [
"MCell"
] | 6b87865be8ceb0a2785d97351ab4cdb1283f873d44c030acfe20da669a40c81e |
# -*- coding: utf-8 -*-
"""
Dummy implementation for process control.
Qudi is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
Qudi is distribu... | childresslab/MicrocavityExp1 | hardware/process_dummy.py | Python | gpl-3.0 | 3,746 | [
"Avogadro"
] | 6659ec03ab1c610e049392ecac08c344a5a4be378db441d61e07dc8b71a102be |
# -*- coding: utf-8 -*-
import threading
from math import sqrt
import numpy as np
import ase.parallel as mpi
from ase.calculators.calculator import Calculator
from ase.calculators.singlepoint import SinglePointCalculator
from ase.io import read
from ase.optimize import BFGS
from ase.utils.geometry import find_mic
c... | suttond/MODOI | ase/neb.py | Python | lgpl-3.0 | 15,925 | [
"ASE"
] | df95271afe253b688efe7814c5ccfddc545e928b0464835564ab64564cd44639 |
import vtk
import h5py
file_path1 = "/home/ksansom/caseFiles/mri/VWI_proj/case1/vmtk/dsa2mra_trans.vtp"
file_path2 = "/home/ksansom/caseFiles/mri/VWI_proj/case1/vmtk/smooth_case1_vmtk_decimate.vtp"
out_path = "/home/ksansom/caseFiles/mri/VWI_proj/case1/vmtk/dsa2mra_icp.vtp"
reader1 = vtk.vtkXMLPolyDataReader()
reade... | kayarre/Tools | vtk/surface_matching.py | Python | bsd-2-clause | 1,664 | [
"VTK"
] | ee5cdc25ca58fd5783b6848021533b05de41a6083b67408798ba295594a6ba19 |
# -*- coding: utf-8 -*-
"""
Cosmic Rays
===========
This scripts derives simple cosmic ray statististics from Gaia RVS data.
:requires: pyfits (tested with 3.3)
:requires: numpy (tested with 1.9.2)
:requires: scipy (tested with 0.15.1)
:requires: matplotlib (tested with 1.4.3)
:requires: astropy (tested with 1.01)
:r... | sniemi/EuclidVisibleInstrument | analysis/analyseGaiaRVSCosmicRayData.py | Python | bsd-2-clause | 13,377 | [
"Gaussian"
] | 58e762ebe35ddd0027763ac1cc49ce8a38838d52ceb2d6700da3090d7538ac5d |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/shciscf/test/test_shci.py | Python | apache-2.0 | 8,814 | [
"PySCF"
] | d0de5c28bba36d9e162c07cd038005d241e45f811ccb938b7c24ccf051f46b78 |
#!/bin/false
# This file is part of Espruino, a JavaScript interpreter for Microcontrollers
#
# Copyright (C) 2013 Gordon Williams <gw@pur3.co.uk>
#
# 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 h... | nkolban/Espruino | boards/PICO_R1_3.py | Python | mpl-2.0 | 4,166 | [
"CRYSTAL"
] | 00f1ddf1b1f8aed2ef552d5c573678e6b5012622b9cc551d56b56ae58377fc5a |
"""Test vtkVariant support in VTK-Python
The following vtkVariant features have to be tested:
- Construction from various types
- Automatic arg conversion for methods with vtkVariant args
- Access of various types
- Operators < <= == > >=
- Use of vtkVariant as a dict key
The following features are not suppo... | hlzz/dotfiles | graphics/VTK-7.0.0/Common/Core/Testing/Python/TestVariant.py | Python | bsd-3-clause | 7,698 | [
"VTK"
] | 9c112dafb80ccef79555716d26a895dd7f2a722f1817e89927ec9eca9e7b3311 |
#!/usr/bin/env python
from __future__ import print_function
from __future__ import division
from builtins import range
from builtins import object
from past.utils import old_div
import numpy
import os
import sys
import tableio
from scipy import interpolate
#import scipy
import math
from cosmopy import cosmopy
class ... | boada/planckClusters | scripts/HMF/pyTinker/tinker.py | Python | mit | 6,856 | [
"TINKER"
] | 6f3378892abdf728832d0a2db4e79f9552e3368326d3687bc9e92e431f6434db |
"""This file provides a class used for incrementally updating a single gaussian inference problem.
The functionality 'setting apart' this class, is that includes a method that flattens the parameter distributions, while retaining the
predictive distribution. This allows simple moving average calculation without... | azane/for-learnings-sake | bayes/clustering/parametric/analytic/singlegauss.py | Python | mit | 4,658 | [
"Gaussian"
] | 64e991390b554f249c1f977e9a2d4da6897ed6b8ca133906b39c3970203a1970 |
import logging
import os
import numpy as np
from cis.data_io.Coord import CoordList
from cis.exceptions import InvalidVariableError, FileFormatError
from cis.data_io.products import AProduct
from cis.data_io.ungridded_data import UngriddedCoordinates, UngriddedData, Metadata
from cis.utils import add_to_list_if_not_n... | cedadev/cis | cis/data_io/products/NCAR_NetCDF_RAF.py | Python | lgpl-3.0 | 29,035 | [
"NetCDF"
] | 5567c06479fa5fc45f8bd39f5cf81a297c1601382cbe563e9948b993e3abc14d |
# Copyright 2019 The PlaNet 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 applicable... | google-research/planet | planet/models/ssm.py | Python | apache-2.0 | 3,921 | [
"Gaussian"
] | 9a0ddeaeb8119e1479481f46560a13d9820f4d0d227b125a814a0140e3ad1439 |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2013-2019 ITB - CNR
This file is part of isoSegmenter.
isoSegmenter 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... | bunop/isochoreFinder | setup.py | Python | gpl-3.0 | 6,362 | [
"Biopython"
] | fab60a2682045bdfe94a64c00935336fbb42a0a1206be71792cf84b0f601abb3 |
unit_labels = {
'abampere': 'Abampere',
'abampere per square centimeter': 'AbamperePerSquareCentimeter',
'abcoulomb': 'Abcoulomb',
'abcoulomb per square centimeter': 'AbcoulombPerSquareCentimeter',
'abfarad': 'Abfarad',
'abfarad per centimeter': 'AbfaradPerCentimeter',
'abhenry': 'Abhenry',
... | DURAARK/pyIfcExtract | util/qudt.py | Python | gpl-3.0 | 33,276 | [
"Dalton"
] | 794c3a9c7681bd58436f5bbe42a56637c4272f3504e8451b21c26919e2a041f1 |
# See http://ipython.org/ipython-doc/1/interactive/public_server.html for more information.
# Configuration file for ipython-notebook.
c = get_config()
c.NotebookApp.ip = '0.0.0.0'
c.NotebookApp.port = 6789
c.NotebookApp.open_browser = False
c.NotebookApp.profile = u'default'
c.IPKernelApp.matplotlib = 'inline'
import... | bgruening/docker-recipes | ipython-notebook-plus/ipython_notebook_config.py | Python | mit | 1,284 | [
"Galaxy"
] | c23a6070df26f00c99c335b846689f9e5d5d188c1fff3c0ad4a2da221c734bb0 |
##############################################################################
# Copyright (c) 2017 Mark Olesen, OpenCFD Ltd.
#
# This file was authored by Mark Olesen <mark.olesen@esi-group.com>
# and is released as part of spack under the LGPL license.
# LLNL-CODE-647188
#
# For details, see https://github.com/llnl/s... | TheTimmy/spack | var/spack/repos/builtin/packages/openfoam-com/package.py | Python | lgpl-2.1 | 29,435 | [
"ParaView"
] | 39f62e0d41a32cc0a0cd6ed8d76a6e746b29f20838410f75138ad6e47f21851e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from pymatgen.core.tensors import SquareTensor
from collections import namedtuple
from pymatgen.core.units import FloatWithUnit
from pymatgen.core.periodic_table import Specie
from pymatgen.core.structure imp... | montoyjh/pymatgen | pymatgen/analysis/nmr.py | Python | mit | 8,227 | [
"pymatgen"
] | be7ed19c304003dfa269f2fedfd3bab363568e194bd4494684bb892c38f6d7d9 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/diversity/_driver.py | Python | bsd-3-clause | 14,954 | [
"scikit-bio"
] | 382bc831a925121d15b22f2ed6beca2221e754e2e12dd902b2809a4225972e0d |
"""
Collection of passes for the declaration, allocation, movement and deallocation
of symbols and data.
"""
from collections import OrderedDict, namedtuple
from functools import singledispatch
from operator import itemgetter
import cgen as c
from devito.ir import (EntryFunction, List, LocalExpression, FindSymbols,
... | opesci/devito | devito/passes/iet/definitions.py | Python | mit | 13,865 | [
"VisIt"
] | e70364755279bc83bcfdc01fdb800fe85e567f9adb68f1f3010210c0a5a3f020 |
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
import copy
import io
import os
import pickle
import re
import shutil
import tempfile
import threading
import time
import unittest
from unittest import mock
from django.conf import settings
from django.core import manageme... | fenginx/django | tests/cache/tests.py | Python | bsd-3-clause | 93,229 | [
"Brian"
] | bfd3672d38ea4dff723a87c933d5b65c664d9c5c987327d90141516008ae51bf |
'''
ZMGaussDistr.py
Zero-mean, full-covariance Gaussian
Attributes
--------
Choose either covariance or precision representation.
Covariance: DxD matrix Sigma
Precision: DxD matrix L
Matrices must *always* be symmetric, and positive definite.
'''
import numpy as np
import scipy.linalg
from bnpy.util import dotAT... | daeilkim/refinery | refinery/bnpy/bnpy-dev/bnpy/distr/ZMGaussDistr.py | Python | mit | 3,879 | [
"Gaussian"
] | 8df1ab32d33c292dcaacdce99aa1ff2d97faa8666a1410498bbaba1a431124b6 |
""" Datatypes for Galaxy-M.
"""
from galaxy.datatypes.binary import (
Binary,
SQlite,
)
class SQliteSPS(SQlite):
file_ext = "sps.sqlite"
Binary.register_sniffable_binary_format("sps.sqlite", "sps.sqlite", SQliteSPS)
class SQliteTM(SQlite):
file_ext = "tm.sqlite"
Binary.register_sniffable_binary_f... | Viant-Metabolomics/Galaxy-M | lib/galaxy/datatypes/galaxym.py | Python | gpl-2.0 | 782 | [
"Galaxy"
] | 139a2e78aebed32fec38d64754841b8dd452583f1bef99cdca8a9510ab170056 |
#
# Copyright (C) 2016 greg Landrum
#
# @@ 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 for IPython/Jupyter integration
"""
im... | rvianello/rdkit | rdkit/Chem/Draw/UnitTestIPython.py | Python | bsd-3-clause | 1,418 | [
"RDKit"
] | c3fe99f7c780f8c1600821e178fc1f4d4259bb3aaaa7331568088fbc5848e4dd |
# coding=utf-8
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | google-research/ott | tests/core/discrete_barycenter_test.py | Python | apache-2.0 | 4,009 | [
"Gaussian"
] | 1574da8c06a228fba1d44f146c5883def26faf3d0bad99f06e5b2ba0d72b4bf4 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/quips/admin.py | Python | gpl-3.0 | 1,106 | [
"Brian"
] | 2263c2bc3e229253c8930924d26c11b6480a18b6c2998ffd7848190445390c82 |
""" Simple multi-layer perception neural network using Minpy """
# import minpy
# import minpy.numpy as np
from minpy.core import Function
from minpy.nn import layers
from minpy.nn.model import ModelBase
from minpy.nn.solver import Solver
from minpy.nn.io import NDArrayIter
from examples.utils.data_utils import get_CIF... | shadowleaves/deep_learning | twolayer/minpy_mxnet.py | Python | mit | 3,606 | [
"Gaussian"
] | 7ea4e7616f68e1d3e5599ae7b0f600bcc0638d51eff917aad139d32f26659ecb |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | liuwenf/moose | python/MooseDocs/tests/listings/test_listings.py | Python | lgpl-2.1 | 7,387 | [
"MOOSE"
] | c15c9ececbac7ae9840270d2dd5fafa22c33bf90f7790302929b0a29de3c2d09 |
#!/usr/bin/python2.6
##############################################################################
#
# Copyright (c) 2009-2013 by University of Queensland
# http://www.uq.edu.au
#
# Primary Business: Queensland, Australia
# Licensed under the Open Software License version 3.0
# http://www.opensource.org/lice... | AuScope/vgml | src/main/resources/org/auscope/portal/server/scriptbuilder/templates/escript-gravity-point.py | Python | gpl-3.0 | 6,914 | [
"NetCDF",
"VisIt"
] | 83ecca207ecb3130f2a8693344b06ceafee575740b87bdaf5009dfc75924516c |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2011'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
'''
Contains class for common routines for loading all CANON data
Mike McCann
MBARI 22 April 2012
@undocumented: __doc__ parser
@status: production
@license: GPL
'''
import os
i... | duane-edgington/stoqs | stoqs/loaders/CANON/__init__.py | Python | gpl-3.0 | 84,795 | [
"NetCDF"
] | c0d8685d3f2ea9910c3a90f823674dad17d8fba4714ca67e6cee82ad83e06fc8 |
"""A collection of tools to handle genomic tests, in particular Tajima's D.
Part of the biostructmap package.
"""
from __future__ import absolute_import, division, print_function
from io import StringIO
import warnings
from math import log
from Bio import AlignIO
from Bio.Data import IUPACData
from numpy import mean
... | andrewguy/biostructmap | biostructmap/gentests.py | Python | mit | 12,715 | [
"Biopython"
] | 4a2ff10d3a19e41458d0222a202fe7c3f4f1444dff916fda0640a961f38c904e |
import numpy
from copy import deepcopy
from orbkit.qcinfo import QCinfo
from orbkit.orbitals import AOClass, MOClass
from orbkit.display import display
from orbkit.tools import orbit, lquant
from .tools import descriptor_from_file
def read_gaussian_fchk(fname, all_mo=False, spin=None, **kwargs):
'''Reads all infor... | orbkit/orbkit | orbkit/read/gaussian_fchk.py | Python | lgpl-3.0 | 10,246 | [
"Gaussian"
] | 0a02949031cf7ade0b09e46921f96e0a60e2d4724982b0b6d928a2d723c48bff |
# -*- coding: mbcs -*-
typelib_path = 'd:\\bogo\\bogo-win32\\interfaces\\bogo.tlb'
_lcid = 0 # change this if required
from ctypes import *
import comtypes.gen._00020430_0000_0000_C000_000000000046_0_2_0
from comtypes import GUID
from ctypes import HRESULT
from comtypes import helpstring
from comtypes import COMMETHOD
... | BoGoEngine/bogo-win | interfaces/gen/_C4E07FAB_27D8_45C1_A647_DB6D4F590C31_0_0_0.py | Python | gpl-3.0 | 77,889 | [
"ASE"
] | 0ac2684b2748b941ce47e7ae63fa3fbc9eec769a60f7ed3a260fa2a44d5eadd6 |
from ase.test import cli
from ase.db import connect
cmd = """
ase-build H | ase-run emt -d y.json &&
ase-build H2O | ase-run emt -d y.json &&
ase-build O2 | ase-run emt -d y.json &&
ase-build H2 | ase-run emt -f 0.02 -d y.json &&
ase-build O2 | ase-run emt -f 0.02 -d y.json &&
ase-build -x fcc Cu | ase-run emt -E 5 -d... | suttond/MODOI | ase/test/db.py | Python | lgpl-3.0 | 1,149 | [
"ASE"
] | 1bb85e5e1a524f209557601c6b1c3c18df36d0f6a922db19c7cfc458fd9215af |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
#======================================================================
#
# tcjump.py -
#
# Created by skywind on 2020/10/29
# Last Modified: 2020/10/29 17:33:02
#
#======================================================================
from __future__ import uni... | skywind3000/collection | script/tcjump.py | Python | mit | 4,869 | [
"VisIt"
] | 280d3b327cdbb238d1e4abea0adf2152ad48784c873ac42d43f2520c4d200fb4 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/executor/module_common.py | Python | bsd-3-clause | 40,201 | [
"VisIt"
] | 827c0fd51225e5e04a159fd9d6ba65a1a8cc674a75e070f8db3d80afc0ef12c1 |
#!/usr/bin/env python
"""
Logout
Example:
$ dirac-logout
"""
import os
import sys
import DIRAC
from DIRAC import gLogger, S_OK, S_ERROR, gConfig
from DIRAC.Core.Security import Locations
from DIRAC.Core.Base.Script import Script
from DIRAC.Resources.IdProvider.IdProviderFactory import IdProviderFactory
from DIRAC.F... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_logout.py | Python | gpl-3.0 | 3,670 | [
"DIRAC"
] | c21755628b9f7793e27f4bae8ad002d16810dcae33f6236858ee2137e346f16b |
import numpy as np
import h5py
import matplotlib.pyplot as plt
%matplotlib inline
plt.rcParams['figure.figsize'] = (5.0, 4.0) # set default size of plots
plt.rcParams['image.interpolation'] = 'nearest'
plt.rcParams['image.cmap'] = 'gray'
%load_ext autoreload
%autoreload 2
np.random.seed(1)
# GRADED FUNCTION: zer... | jw2100/beginning.github.io | DeepLearning/wuenda/04_ConvolutionalNeuralNetworks/week1-01.py | Python | gpl-3.0 | 13,574 | [
"NEURON"
] | 6a206e4565212f070158d3757a7a2628efb3781ce213138ae2321aa539cdc748 |
"""
SALTS XBMC Addon
Copyright (C) 2014 tknorris
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
T... | AMOboxTV/AMOBox.LegoBuild | plugin.video.salts/scrapers/2ddl_scraper.py | Python | gpl-2.0 | 8,868 | [
"ADF"
] | 294806d8552ce05a5ae3b0de5dfe406ad5ccfde8cff8cb3b4276fc273cd3e16a |
# Generated with tools/generate-isocodes.py
LANGUAGES = set((
"aa",
"aaa",
"aab",
"aac",
"aad",
"aae",
"aaf",
"aag",
"aah",
"aai",
"aak",
"aal",
"aam",
"aan",
"aao",
"aap",
"aaq",
"aas",
"aat",
"aau",
"aaw",
"aax",
"aaz",
"... | pombreda/git-git.code.sf.net-p-rpmlint-code | __isocodes__.py | Python | gpl-2.0 | 89,758 | [
"ADF",
"ASE",
"BWA",
"Elk",
"MOE",
"VMD",
"xTB"
] | 3885dc77f273174c869c88ec0f795bf580ddbc243c5d8fd262d67c87138d091d |
#!/usr/bin/env python
"""
Copyright 2014 Novartis Institutes for Biomedical Research
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 ... | Novartis/yap | bin/yap_summary.py | Python | apache-2.0 | 33,933 | [
"HTSeq"
] | bd74992b9ae5d9a433490379360ea55c1141b2a4216312611428a4909037953d |
#-*- coding: utf-8 -*-
import re
import os
from markdown.extensions import Extension
from markdown.preprocessors import Preprocessor
from django.conf import settings
emojis_set = {
"+1", "-1", "100", "1234", "8ball", "a", "ab", "abc", "abcd", "accept", "aerial_tramway", "airplane",
"alarm_clock", "alien", ... | SPARLab/BikeMaps | spirit/utils/markdown/emoji.py | Python | mit | 12,896 | [
"Bowtie",
"Octopus"
] | 7cd7b819cefa74cb6ea89bdb6a6dcd3a25092ea66100c8e6ce037e1252c4bb14 |
import argparse
import configparser
from io import StringIO
import os
from pathlib import Path
import shutil
import sys
from pysisyphus import logger
CONFIG_DIR = Path(os.path.abspath(os.path.dirname(__file__)))
LIB_DIR = CONFIG_DIR / "geom_library"
T_DEFAULT = 298.15 # Kelvin
p_DEFAULT = 101325 # Pascal
OUT_DIR_... | eljost/pysisyphus | pysisyphus/config.py | Python | gpl-3.0 | 3,251 | [
"GAMESS",
"Jmol",
"MOPAC",
"ORCA",
"OpenMolcas",
"xTB"
] | 694129ebaa3c4ed6d61d4b1d0b39079c49a08c79f9b8ac056dac62464e2eebf9 |
import optimizer_plots as plots
import cPickle as pickle
import copy
import json
import math
import os
import shutil
import time
import warnings
import sys
import numpy as np
import skopt
from scipy.optimize import fmin_l_bfgs_b
from six.moves import configparser
from sklearn import clone
from sklearn.externals.joblib... | JeroenZegers/Nabu-MSSS | nabu/hyperparameteroptimization/hyper_param_optimizer.py | Python | mit | 29,847 | [
"Gaussian"
] | ed5660bac5e1f953512ad221e854716cd2aa8c0d9a24aa7911c46479669e6eeb |
# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the NiBabel package for the
# copyright and license terms.
#
### ### ### #... | ME-ICA/me-ica | meica.libs/nibabel/nifti1.py | Python | lgpl-2.1 | 66,275 | [
"Gaussian"
] | 513715ef5203b49ff6d052c030a5e11c08328d009cd104d5fba7afe9f39e68ef |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0132_h2o_uhf_nonin_pb.py | Python | apache-2.0 | 1,561 | [
"PySCF"
] | 65554799e6e9a796afc88e0bd03da02ae0d53293d1821a412254c9a188deccd1 |
#!/usr/bin/env python
"""
Ben Payne
ben.is.located@gmail.com
Yoga graph
Use:
This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International License.
To view a copy of this license, visit http://creativecommons.org/licenses/by-sa/4.0/.
"""
import os
import glob
import networkx as nx # for... | bhpayne/yoga_graph | src/generate_static_webpages.py | Python | gpl-2.0 | 7,967 | [
"VisIt"
] | 4124acab312c7ba0656b685a1794a4079da699d66d918796bf7533bfc06a4146 |
# 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/Version.py | Python | gpl-3.0 | 2,337 | [
"ESPResSo"
] | de3b0db9c2cafb39c1d2b0d3facf6dd6c40b51ab1e2551493efbd8df236a8576 |
"""
linear_two.py: Estimation for general linear constraints with Gaussian noise.
"""
from __future__ import division
import numpy as np
import scipy.sparse.linalg
# Import other subpackages in vampyre
import vampyre.common as common
# Import individual classes and methods from the current sub-package
from vampyre.... | GAMPTeam/vampyre | vampyre/estim/linear_two.py | Python | mit | 26,348 | [
"Gaussian"
] | 3e75f6e40ab58c746be294a02204b94b3265e42581d51d799a7bc479798affe3 |
"""
note on np.unique
this module expands on a the functionality one would currently bootstrap from np.unique
to facilitate the functionality implemented in this module, a generalization of unique is proposed
that is, the version of unique implemented here also takes a lex-sortable tuple,
or multidimensional array vie... | yuginboy/from_GULP_to_FEFF | feff/libs/numpy_group_by_ep_second_draft.py | Python | gpl-3.0 | 32,262 | [
"Gaussian"
] | b993504ad8cd934b7fd9cc7215a91d6177ae749a48f68b75b271e077f614c0d8 |
##
# Copyright 2009-2018 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | bartoldeman/easybuild-easyblocks | easybuild/easyblocks/r/rserve.py | Python | gpl-2.0 | 1,694 | [
"Bioconductor"
] | 78992bf9e96814c9e105263ac6c773dd7be8c46781cafc3ebf8bd9489c9b7c77 |
import gzip
import struct
import numpy as np
from netCDF4 import Dataset
#SHOULD BE UNIVERSAL FOR ALL OUR ENSIGHT FILES
ENSIGHT_GRID_OFFSET=644 # put 56 for normal grid file
ENSIGHT_DATA_OFFSET=244 # put 52 for normal 3d binary
#GENERATE THE DATASET (new)
ncf=Dataset('2048_004.nc','w',format='NETCDF4')
#PU... | zrick/tlab | scripts/python/ensight2nc.py | Python | gpl-3.0 | 4,790 | [
"NetCDF"
] | 4366cb460b2d2d74612f825b351454ca78ff8a5c3f82a8b2fac49d88b85e3e9b |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Ghost atom has nuclear charge 0
The global basis set assignment such as ``basis = "sto3g"`` cannot be used on
ghost atom. One needs explicitly assign basis for ghost atom using eg
:func:`gto.basis.load`.
'''
from pyscf import gto
mol = gto.M... | gkc1000/pyscf | examples/gto/03-ghost_atom.py | Python | apache-2.0 | 2,521 | [
"PySCF"
] | 01e33d695f97816c8e0b77f3f183d70c4b228835ccbe2f1ace2e8d56f1c9b7bf |
#!/usr/bin/python
#
# 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... | nya3jp/hyou | tools/upload_sheet.py | Python | apache-2.0 | 3,237 | [
"VisIt"
] | 6e24f8c7c7e0ae1ab6b8888ca29a772ac77d165c882e13f71a007b719bf21837 |
# Copyright (C) 2015 Henrique Pereira Coutada Miranda, Alejandro Molina-Sanchez
# All rights reserved.
#
# This file is part of yambopy
#
from subprocess import Popen, PIPE
import os
import json
from time import sleep
import re
class YamboIn():
"""
Class to read, write, create and manipulate yambo input files ... | henriquemiranda/yambopy | yambopy/io/inputfile.py | Python | bsd-3-clause | 12,841 | [
"Yambo"
] | b7edfa6c784508fdfc617bb42a0f25ed5945c43ab95a2ae08d435ad95ca7840b |
""" This is the Job Repository which stores and manipulates DIRAC job metadata in CFG format """
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.CFG import CFG
import os, time, tempfile, shutil
class JobRepository( object ):
def __init__( self, repository = None ):
self.... | Sbalbp/DIRAC | Interfaces/API/JobRepository.py | Python | gpl-3.0 | 4,597 | [
"DIRAC"
] | 6e2a813c067812239bff806da85e1f7b55366bc2f5db52dd646bdec992b39c8c |
import datetime
import asyncio
import strawpy
import pytz
import re
import requests
import aiohttp
import json
import discord
import os
import glob
import git
import io
from PIL import Image
from discord.ext import commands
from cogs.utils.checks import *
from bs4 import BeautifulSoup
from urllib import parse
from urll... | chenzw95/Discord-Selfbot | cogs/utility.py | Python | gpl-3.0 | 39,226 | [
"MOE"
] | 4d3b050eb2e266ad217d65491a5760198df426f2a527ba7871e28dcfd2595332 |
class DummyMPICom(object):
rank = 0
size = 1
def barrier(self):
pass
try:
from mpi4py import MPI # @UnusedImport @IgnorePep8 This is imported before NEURON to avoid a bug in NEURON
except ImportError:
mpi_comm = DummyMPICom()
else:
mpi_comm = MPI.COMM_WORLD
MPI_ROOT = 0
def is_mpi... | tclose/PyPe9 | pype9/utils/mpi.py | Python | mit | 370 | [
"NEURON"
] | 95cf74e23b15dee317251fc831c22fb9a60d00b0a8b9fea1a8972495db7692cb |
"""
.. class:: LineLuminosityFunction
.. class:: ModelLuminosityFunction
.. moduleauthor:: Johan Comparat <johan.comparat__at__gmail.com>
The class LineLuminosityFunction is dedicated to measuring the line luminosity functions. The class ModelLuminosityFunction is dedicated to fitting models to the LFs.
"""
import o... | JohanComparat/pySU | galaxy/python/LineLuminosityFunction.py | Python | cc0-1.0 | 15,556 | [
"Galaxy"
] | de5331029d4f3759699f3b879e8362ce83c43fd198c3a8f5a1de82733fa2f097 |
from django.db import transaction
class VisitSequenceError(Exception):
pass
class VisitSequence:
"""A class that calculates the previous_visit and can enforce
that the sequence of visits are completed in order.
"""
def __init__(self, appointment=None):
self.appointment = appointment
... | botswana-harvard/edc-visit-tracking | edc_visit_tracking/visit_sequence.py | Python | gpl-2.0 | 2,671 | [
"VisIt"
] | 224019f9cd398ace1b3b5f0ee0ea4f314fc6cd7ddf7231adf111d0ba32bd79cc |
'''
Created on 2009 uzt 28
@author: peio
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of franklin.
# franklin is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Softwar... | JoseBlanca/franklin | test/utils/seqio_utils_test.py | Python | agpl-3.0 | 3,293 | [
"Biopython"
] | bc8316cefa34de321e5cc15f4afb96fc9d54d34ccfa90d5500e2c9b97c05bfde |
from __future__ import division
import sys
import datetime
import itertools
import ntpath
import multiprocessing as mp
try:
import simplejson as json
except ImportError:
import json
import numpy as np
from pymongo.errors import PyMongoError
from pymongo import MongoClient, GEOSPHERE
from netCDF4 import Dataset
... | RDCEP/atlas-viewer | atlas/nc4_to_mongodb.py | Python | apache-2.0 | 8,364 | [
"NetCDF"
] | 4718f38e14ca1239dd0e5c36d9d76ab2797bb5ee2fe3400ee86ce2a328d4b510 |
#!/usr/bin/env python
__author__ = "Antonio Gonzalez Pena"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Antonio Gonzalez Pena"]
__license__ = "GPL"
__version__ = "1.9.1-dev"
__maintainer__ = "Antonio Gonzalez Pena"
__email__ = "antgonza@gmail.com"
from qiime.plot_semivariogram import hist_bins... | ssorgatem/qiime | tests/test_plot_semivariogram.py | Python | gpl-2.0 | 12,517 | [
"Gaussian"
] | 4bf4955c58a30ac13bb5ee1f7c4ad2db0e6040331bd881185efe96d5bef024a7 |
from bitstring import BitArray
__number_to_word = [
"A", "ABE", "ACE", "ACT", "AD", "ADA", "ADD",
"AGO", "AID", "AIM", "AIR", "ALL", "ALP", "AM", "AMY",
"AN", "ANA", "AND", "ANN", "ANT", "ANY", "APE", "APS",
"APT", "ARC", "ARE", "ARK", "ARM", "ART", "AS", "ASH",
"ASK", "AT", "ATE", "AUG", "AUK", "A... | montaggroup/montag-token-redeemer | redeemer/tokenwords/tokenconverter.py | Python | gpl-3.0 | 19,719 | [
"Elk",
"MOE"
] | 42ed5201964eddb7b3326ad67982b7d5b33110b5fb7b840a0e3fe33659b92b37 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010 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 Software F... | andrebellafronte/stoq | stoqlib/gui/dialogs/clientcategorydialog.py | Python | gpl-2.0 | 2,236 | [
"VisIt"
] | 39ed37be5b54fbf6625502e8f1aa7c2d967119c9be795bf776715e08a6d9af5d |
#!/usr/bin/env python
#
# tcl2py.py - try to Pythonize a vtk tcl script
#
# This code is based on tcl2py.py from VTK 3.2 which was written by
# Randy Heiland.
#
# Changes:
#
# (21/12/2002) -- Prabhu Ramachandran
# Made to work with re instead of regex. Superficial cleanup of the
# code, fixed a few issues, using ne... | SimVascular/VTK | Utilities/tcl2py.py | Python | bsd-3-clause | 8,336 | [
"VTK"
] | 4034df1ac36547f45620b1cc9b8dd4b213c62653db2511d42387b1e55ca29e4b |
"""Univariate and multivariate polynomials with coefficients in the integer ring. """
from sympy.polys.galoispolys import (
gf_from_int_poly, gf_to_int_poly, gf_degree, gf_from_dict,
gf_lshift, gf_add_mul, gf_mul, gf_div, gf_quo, gf_rem,
gf_gcd, gf_gcdex, gf_sqf_p, gf_factor_sqf)
from sympy.ntheory import... | gnulinooks/sympy | sympy/polys/integerpolys.py | Python | bsd-3-clause | 61,670 | [
"Gaussian"
] | 5bd1fcfff2ec9f2341cdc6afde6088fe2b97013eebe52b8dfa86e8ed73bf462a |
#! /usr/bin/env python3
#
# update_po - a gramps tool to update translations
#
# Copyright (C) 2006-2006 Kees Bakker
# Copyright (C) 2006 Brian Matherly
# Copyright (C) 2008 Stephen George
# Copyright (C) 2012
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | beernarrd/gramps | po/update_po.py | Python | gpl-2.0 | 23,609 | [
"Brian"
] | 01148c9b9435fe79e6ff07740b52fec0c8f8e1e68ac85008a85d5407be0b3220 |
__author__ = 'nielso'
import os
import numpy
# This module requires the package: python-scientific
# To query netcdf files with ncdump also install netcdf-bin
# The package libnetcdf-dev is also required but is automatically
# installed as a dependency on python-scientific
from Scientific.IO.NetCDF import NetCDFFile
... | maning/inasafe | realtime/netcdf_utilities.py | Python | gpl-3.0 | 4,706 | [
"NetCDF"
] | a680974e8678b5f5efa3499f1a0f559117967862268e2bf4c8a5ece2cd2c1149 |
"""Support for control of ElkM1 sensors."""
from __future__ import annotations
from elkm1_lib.const import (
SettingFormat,
ZoneLogicalStatus,
ZonePhysicalStatus,
ZoneType,
)
from elkm1_lib.util import pretty_const, username
import voluptuous as vol
from homeassistant.components.sensor import SensorEn... | rohitranjan1991/home-assistant | homeassistant/components/elkm1/sensor.py | Python | mit | 9,777 | [
"Elk"
] | ce08e47ed5f5a2af265e57b8deb9e0cf3dd70a8e6dff534221e7957cc52618bb |
import logging
import multiprocessing
import time
import PIL.Image
from . import _clib
logger = logging.getLogger(__name__)
def ace(img_in, slope=10, limit=1000, samples=100, seed=None, nb_threads=None):
"""
Automatic Color Equalization
"""
if seed is None:
seed = int(time.time())
if i... | jflesch/libpillowfight | src/pillowfight/__init__.py | Python | gpl-2.0 | 7,475 | [
"Gaussian"
] | 96eb4ff339ba17d0e2d760b219c923578e3d996c345073846a7e47a52c41972e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# <sure - utility belt for automated testing in python>
# Copyright (C) <2010-2013> Gabriel Falcão <gabriel@nacaolivre.org>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the... | thedrow/sure | setup.py | Python | gpl-3.0 | 2,209 | [
"VisIt"
] | eddb25db47c494d6c312c63a19f1e60809c1d66c4e49656c331e753988ed304c |
"""
VolumeVisualizationCT
:Authors:
Berend Klein Haneveld
"""
import math
from VolumeVisualization import VolumeVisualization
from VolumeVisualization import VisualizationTypeCT
from vtk import vtkVolumeProperty
from vtk import vtkColorTransferFunction
from vtk import vtkPiecewiseFunction
from PySide.QtGui import QWi... | berendkleinhaneveld/Registrationshop | ui/visualizations/VolumeVisualizationCT.py | Python | mit | 4,455 | [
"VTK"
] | f75b693bf8842cfb8618876e4e4d2bd9e797abea2105a5dec1351b747b82aa70 |
"""
=============================
Neurons
1.each neuron will have synapses['connections'] with other neurons
(it could be presented as directed graph, where vectors connections go
from input data to last neuron layer and finally to activation function)
2.each neuron will have its importance||strength of the impul... | LowerSilesians/geo-squizzy | geosquizzy/optimum/neurons.py | Python | mit | 2,187 | [
"NEURON"
] | 462ad13c2702b9a1d2c385221279ec6c5c296d4e2652c504229226470c1bb4e7 |
"""Functions for downloading/building/finding SWIG"""
from typing import Tuple
import ast
import os
import subprocess
import re
def find_swig() -> str:
"""Get name and version of SWIG executable
We need version >=3.0. Probably we should try some default paths and names,
but this should do the trick for ... | FFroehlich/AMICI | python/amici/swig.py | Python | bsd-2-clause | 4,975 | [
"VisIt"
] | 6caa546618c3865d05a8398cf38702ea2a37c0f4fb1571699f45018bf8616b75 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Miscellaneous utility functions.
"""
from abc import ABCMeta, abstractmethod
from collections.abc import Hashable, Iterab... | rcomer/iris | lib/iris/util.py | Python | lgpl-3.0 | 64,124 | [
"NetCDF"
] | 0c2bc4b667a200d0fb44875d631c45f45664d1a57a6b49ec2bc9fc3c031d615c |
from lettuce.django import django_url
from lettuce import step,world
# Steps first appearing in feature "Sign in"
@step(u'I go to (.*)')
def go_to_page(step, page):
if page in world.page_map.keys():
url = world.page_map[page]
world.response = world.browser.visit(django_url(url))
@step(u'"([^"]*)" ... | DummyDivision/Tsune | cardbox/features/steps.py | Python | mit | 6,111 | [
"VisIt"
] | a38482b13edfc198ac987e52eb82f540333bc65cc0dbd53181f9a730e98d5012 |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | Stumble Upon Evergreen Classification Challenge/stumble-baseline.py | Python | mit | 3,011 | [
"Gaussian"
] | bd69b5751f9ca4e33daed5160036e10f6b716a16bcc5426a4e1ea0139293c19a |
import cv2
import numpy as np
'''
Notes:
1- In image processing, a kernel, convolution matrix, or mask is a small matrix.
a. Kernels are used for blurring, sharpening, embossing, edge detection, and more.
b. This is accomplished by doing a convolution between a kernel and an image.
Reference:
http://docs.ope... | RyanChinSang/ECNG3020-ORSS4SCVI | BETA/TestCode/OpenCV/TUT-BlurrSmooth.py | Python | gpl-3.0 | 2,571 | [
"Gaussian"
] | 0ef216ca8e74e33ad4352b1031f6901f05bcdb69d7ba0853337917c5975639c8 |
#
# Copyright John Reid 2006
#
from _biopsy import *
def _aligned_sequences_str( self ):
"""Returns the aligned sequences as a string"""
return "\n".join( str(s) for s in self.get_sequence_ids() )
Remome.AlignedSequenceSet.__str__ = _aligned_sequences_str
class RemomeAnalysis:
def __init__( self, remo... | JohnReid/biopsy | Python/biopsy/remo.py | Python | mit | 7,110 | [
"BLAST"
] | 7e07da97a7d51fe83052ba79842b8981050fa4838f7a7e399f16e448f9b725ce |
"""
Tests the forum notification views.
"""
import itertools
import json
import logging
from datetime import datetime
from unittest.mock import ANY, Mock, call, patch
import ddt
import pytest
from django.http import Http404
from django.test.client import Client, RequestFactory
from django.test.utils import override_se... | arbrandes/edx-platform | lms/djangoapps/discussion/tests/test_views.py | Python | agpl-3.0 | 94,266 | [
"VisIt"
] | e14741e7c8e2d86b8780757f6610c64f07e3e453bd4a699d8f318374d56949cf |
# ---
# jupyter:
# jupytext:
# text_representation:
# extension: .py
# format_name: light
# format_version: '1.5'
# jupytext_version: 1.9.1
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# + [markdown] id="eYrSpUncKGSk"
# # Faster predictions... | GPflow/GPflow | doc/source/notebooks/advanced/fast_predictions.pct.py | Python | apache-2.0 | 5,083 | [
"Gaussian"
] | 833af3975882c9bd7d7fba7a6f43aa461a8b481d4249cf22a540c5ac555f3684 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2013 Async Open Source
##
## 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 version 2
## of the License, or... | tiagocardosos/stoq | stoqlib/lib/colorutils.py | Python | gpl-2.0 | 1,919 | [
"VisIt"
] | 4255b104abcf570b153316bddd318282f798a4008c4182051d688e561a147a77 |
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import support
import os
import shutil
def align_bwa_pe... | INNUENDOWEB/INNUca | src/SPAdes-3.9.0-Linux/share/spades/spades_pipeline/common/alignment.py | Python | gpl-3.0 | 2,765 | [
"BWA"
] | 4093957632653c487a852a9ddc883ef626119834f12d525d3edaff07c4c78544 |
#
# @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
#... | dgasmith/psi4 | psi4/driver/qcdb/libmintsbasissetparser.py | Python | lgpl-3.0 | 18,326 | [
"Gaussian",
"Psi4"
] | 3ec5c9d3c11b378769f52c64013a4483ec9a6377a7d725525939515a4a9e983f |
#!/bin/env python
#
# Copyright (C) 2012 by Adam Ewing (adam.ewing@gmail.com)
#
# Released under the MIT license, see LICENSE.txt
#
import re, os, subprocess, tempfile, pysam, sys, argparse, peakparser
from string import maketrans
def checkfile(fname):
try:
open(fname)
except IOError as e:
pr... | adamewing/discord-retro | lib/pinpoint.py | Python | mit | 24,611 | [
"BWA",
"pysam"
] | 83f9e739df113e2896f9eb325b5dfca9d0be702ac1eff426a8454cc1f85eca6d |
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