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# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
import os
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
# To set up environmenta... | TwilioDevEd/api-snippets | notifications/rest/credentials/create-apn-credential/create-apn-credential.7.x.py | Python | mit | 700 | [
"VisIt"
] | 748efcd5b7a2f1ef17b0779d0f538e52f0123352cc0a9bf7494b60e7ce88cd30 |
#!/usr/bin/env python
# Copyright (C) 2012 Tianyang Li
# tmy1018@gmail.com
#
# 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 lat... | tianyang-li/bi-misc | bam_paired_frag_len_distr_0.py | Python | gpl-3.0 | 1,181 | [
"pysam"
] | 363eb383dfe337a40e1d390b788e9df75d91994f116a8f3f2e754b69eabe1b96 |
# Copyright 2016 Uri Laserson
#
# 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 writing,... | lasersonlab/pepsyn | pepsyn/codons.py | Python | apache-2.0 | 6,926 | [
"Amber"
] | 59bf5bf62c903fe5b73ffd168469e9d98b57a9c6ae81a499ad738aa304625147 |
""" This is a test of the chain
ProductionClient -> ProductionManagerHandler -> ProductionDB
It supposes that the ProductionDB, TransformationDB and the FileCatalogDB to be present
It supposes the ProductionManager, TransformationManager and that DataManagement/FileCatalog services running
"""
from __futur... | ic-hep/DIRAC | tests/Integration/ProductionSystem/Test_Client_TS_Prod.py | Python | gpl-3.0 | 10,874 | [
"DIRAC"
] | 5c55cece7b366b8a9285d9899b4a6c3fdb8310fb12609e21e0be347e8936408f |
#!@Python_EXECUTABLE@
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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 redistri... | psi-rking/psi4 | psi4/run_psi4.py | Python | lgpl-3.0 | 14,651 | [
"Psi4"
] | eaf8c632b22f04ef89d094919e1b81a353de06036a40e6aad20b688fb48bfb38 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import with_statement
import errno
import filecmp
import os.path
import re
import tempfile
import sys
# A minimal memoizing decorator. It'll blo... | Samsung/skia | third_party/externals/gyp/pylib/gyp/common.py | Python | bsd-3-clause | 17,016 | [
"VisIt"
] | 0f18aa86caaa937305549485a019f242e51cd6908285052cb601f6509bb51457 |
from __future__ import print_function
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
import os
import random
from h2o.estimators.gbm import H2OGradientBoostingEstimator
def milsong_checkpoint():
milsong_train = h2o.upload_file(pyunit_utils.locate("bigd... | h2oai/h2o-dev | h2o-py/tests/testdir_algos/gbm/pyunit_milsongs_large_gbm.py | Python | apache-2.0 | 2,791 | [
"Gaussian"
] | 19463368ffcd43ef7281f066d6a7578134ec5c81133a64320080e09ff59b3616 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | tests/crystal/test_neighbors.py | Python | gpl-3.0 | 4,312 | [
"CRYSTAL",
"VASP"
] | 40ca518dd2596f5d45fcd99d0598c1e885d45a677c4408be37ad76d57b994e26 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
"""
Copyright 2017 Ronnasayd Machado <ronnasayd@hotmail.com>
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.... | Ronnasayd/Ifuzzy2py | Mfunction.py | Python | apache-2.0 | 4,030 | [
"Gaussian"
] | 220e420fdc11558b818c5fab5f69d13211f305f1394aa5f220b9cd01af15f2e1 |
"""
Configuration module
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
# Constants
SOCKETS_CONNECT_TIMEOUT = 0
SOCKETS_CONNECT_RETRY_DELAY = 1
SOCKETS_BIND_TIMEOUT = ... | runefriborg/pycsp | pycsp/parallel/configuration.py | Python | mit | 1,841 | [
"Brian"
] | 4b17474949f2a7714b812c86c51f1926666493e6f94746f9dfc1cb258906b084 |
# -*- coding: utf-8 -*-
#
# hpc_benchmark.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, ... | espenhgn/nest-simulator | pynest/examples/hpc_benchmark.py | Python | gpl-2.0 | 16,027 | [
"NEURON"
] | 7de2b5cf37d6c75dcb107ab84a501a2f2c3dab62920002aca51739699613dda0 |
# Natural Language Toolkit: Expectation Maximization Clusterer
#
# Copyright (C) 2004-2006 University of Melbourne
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# Porting: Steven Bird <sb@csse.unimelb.edu.au>
# URL: <http://nltk.sf.net>
# For license information, see LICENSE.TXT
from nodebox_linguistics_extended.parser.n... | RensaProject/nodebox_linguistics_extended | nodebox_linguistics_extended/parser/nltk_lite/cluster/em.py | Python | gpl-2.0 | 10,001 | [
"Gaussian"
] | b8d097a6d99d3a4456fd9cedee26a643854a660420523b3c2fb0b75ba52d1097 |
# -*- coding: utf-8 -*-
'''
Module for retrieving random information from Random.org
.. versionadded:: 2015.5.0
:configuration: This module can be used by either passing an api key and version
directly or by specifying both in a configuration profile in the salt
master/minion config.
For example:
..... | stephane-martin/salt-debian-packaging | salt-2016.3.3/salt/modules/random_org.py | Python | apache-2.0 | 25,262 | [
"Gaussian"
] | f77ce7ba2766edfa06f76cc828ef1d5b8102cff4040f4fedf9381d2fffb754d2 |
#######################################################################################
# Python-code: Bubblebeam wrapper
# Author: Adam L Borne
# Contributers: Paul A Stewart, Brent Kuenzi
#######################################################################################
# This program runs the R script that gene... | bornea/APOSTL | APOSTL_Static_Bubblegraph_Generator/toolshed_version/APOSTL_Static_Bubblegraph_Generator.py | Python | gpl-2.0 | 3,626 | [
"Galaxy"
] | 3512a9c4521c854b16e007edc588783adfc8c13f9e9d2fb2140d143499d9e18e |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | drpngx/tensorflow | tensorflow/contrib/autograph/converters/decorators.py | Python | apache-2.0 | 4,247 | [
"VisIt"
] | afaf1c0a3cfaccaf0dab6db1125bca148bad2c563559863e22d1a1ceb84910f9 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import subp... | harterj/moose | python/TestHarness/tests/test_CSVDiffs.py | Python | lgpl-2.1 | 1,987 | [
"MOOSE"
] | 616d2ce802dcc21050784998383c8d04dece4be03a0d8046a2ffd3fa0f97d523 |
# -*- coding: utf-8 -*-
"""Functions for inducing graphs based on edge annotations."""
import logging
from typing import Iterable, Optional, Union
from .utils import get_subgraph_by_edge_filter
from ...filters.edge_predicate_builders import (
build_annotation_dict_all_filter,
build_annotation_dict_any_filter... | pybel/pybel | src/pybel/struct/mutation/induction/annotations.py | Python | mit | 1,870 | [
"Pybel"
] | f40b51c79578972e6784b93c595b37d8ef37137931b61d7b51c6fd0bb4c4fef8 |
'''Hidden module to abstract the cclib interface and convert it to chemlab
'''
from .base import FormatNotSupported, IOHandler
from ...core import Molecule
from ...db import ChemlabDB
import numpy as np
import logging
from cclib.parser import (ADF,
GAMESS,
GAMESSU... | chemlab/chemlab | chemlab/io/handlers/_cclib.py | Python | gpl-3.0 | 1,941 | [
"ADF",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | 8c9834f9b61772a7a486ab31ea96d76faa1ae3f5b2b29f47f7f7b69ebe23142d |
#!/usr/bin/env python
try:
from magpy.stream import *
from magpy.absolutes import *
from magpy.transfer import *
from magpy.database import *
except:
from magpy.stream import *
from magpy.absolutes import *
from magpy.transfer import *
from magpy.database import *
import wx
from matpl... | leonro/magpy-git | magpy/gui/analysispage.py | Python | gpl-3.0 | 5,850 | [
"Gaussian"
] | c721cfac5be66e41701a88724b621f6eb54cec073f2eb0779d9d59630c2b5104 |
# /* megatest texts, C-ified */
# // Copyright 2010 Kurt Hackenberg & William S. Yerazunis, each individually
# // with full rights to relicense.
# //
# // This collection contains texts in the public domain; the copyright
# // is not on the texts themselves but on their use as test texts for
# // the LGPLed CRM... | alisaifee/pycrm114 | tests/data/texts.py | Python | mit | 107,540 | [
"BLAST",
"exciting"
] | 06cc5c35ffc7064e9076a4cb449b52003425d974369eba292b5bac4e235b1703 |
import os
import unittest
from bcbio.rnaseq import count
from bcbio.utils import safe_makedir, file_exists
import tempfile
import stat
import shutil
from nose.plugins.attrib import attr
DATA_DIR = os.path.join(os.path.dirname(__file__), "bcbio-nextgen-test-data", "data")
class TestHtseqCount(unittest.TestCase):
... | hjanime/bcbio-nextgen | tests/unit/test_count.py | Python | mit | 2,392 | [
"HTSeq"
] | 1664b3720c1c9dc6c360c093a1e04713fd98f254bc2f602bf5d0bfba5164492c |
# $Id$
#
# @@ 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.
#
from rdkit import RDConfig
import unittest,os
from rdkit.six.moves import cPickle
from rdki... | AlexanderSavelyev/rdkit | rdkit/Chem/Fraggle/UnitTestFraggle.py | Python | bsd-3-clause | 1,570 | [
"RDKit"
] | 821bc8f3771496138eae731c64011318d500c0a8338a243e8560de049281a485 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/settings/setttingtypes/SettingPicture.py | Python | gpl-3.0 | 3,072 | [
"ORCA"
] | dfafa0bc57b1e7500f711f1f7e60bef13a200fc93348afd0532bcdda98623093 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
#pylint: disable=no-init,invalid-name,too-man... | mganeva/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SimulatedDensityOfStates.py | Python | gpl-3.0 | 34,813 | [
"CASTEP",
"Gaussian"
] | ba6a711b6a00bd5baa998c179f9bd092967323178a5a6f86a556074580b1b26e |
import numpy as np
from scipy.optimize import newton, brentq
from scipy.special import logsumexp, airy
from dppy.utils import check_random_state
def shift_pol(P, x0):
""" Return polynomial P(x-x0) as poly1d object
"""
X_x0 = np.poly1d([1, -x0])
return sum(X_x0**n * c_n for n, c_n in enumerate(P.co... | guilgautier/DPPy | dppy/beta_ensemble_polynomial_potential_core.py | Python | mit | 23,809 | [
"Gaussian"
] | 3f7993f453e33ce2a2c4acd9b63a345f920e88ddaa8202e26a707e69a4fc698e |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" generation of 2D ph... | AlexanderSavelyev/rdkit | rdkit/Chem/Pharm2D/Generate.py | Python | bsd-3-clause | 4,765 | [
"RDKit"
] | 5bf26fa4677112f01abb1a6873a3378e107dd37110c3c3b17a7f8cb3a861eff6 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/etsf-io/package.py | Python | lgpl-2.1 | 2,709 | [
"NetCDF"
] | c2a3c17d8bc78d13cb0a6057065e15d60e36e558caafa9a75cccab281d47231f |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC.Core.Base.Client import Client, createClient
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.JEncode import encode, decode
@createClient('DataManagement/FTS3Manager')
class FTS3Client(Clie... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Client/FTS3Client.py | Python | gpl-3.0 | 3,406 | [
"DIRAC"
] | 0fe35f003009744e2eef6bf6163de5fcc5e06646b63cb999dd68e439b69ad2c5 |
#
# ast_neuron.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any l... | kperun/nestml | pynestml/meta_model/ast_neuron.py | Python | gpl-2.0 | 3,323 | [
"NEURON"
] | c70152ee2ee0d0a994074593268a5744e80d375a8579596456f45d575d9f2286 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | testsuite/python/particle_slice.py | Python | gpl-3.0 | 15,965 | [
"ESPResSo"
] | 7deef8785a9a3988c9aae3a34aa1fb8b4c0ec682e0963ee49c836d29fa615ff3 |
'''
description: Download KNMI radar hdf5 files (inside a tar archive) from ftp
license: APACHE 2.0
author: Ronald van Haren, NLeSC (r.vanharen@esciencecenter.nl)
Natalie Theeuwes
'''
from wradlib import georef
import datetime
import numpy
import datetime
from netCDF4 import Dataset
fr... | ERA-URBAN/fm128_radar_knmi | fm128_radar_knmi/convert_to_netcdf.py | Python | apache-2.0 | 9,177 | [
"NetCDF"
] | 7cf20e78a7359f6e71abfe7ebe098291bc20d469abf902c0169c0b8e4e8e4e8a |
#!/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... | pli3/e2-openwbif | plugin/controllers/views/mobile/about.py | Python | gpl-2.0 | 8,266 | [
"VisIt"
] | e314f2580b56163f9ced43824fdf8bb22a26521ebe292bb7173d32489876e807 |
import numpy as np
from PIL import Image
from plat.interpolate import get_interpfn
from scipy.special import ndtri
def grid2img(arr, rows, cols, with_space):
"""Convert an image grid to a single image"""
N = len(arr)
channels, height, width = arr[0].shape
total_height = rows * height
total_width ... | dribnet/plat | plat/grid_layout.py | Python | mit | 8,121 | [
"Gaussian"
] | 2506cb23a1d0c34d6a42203e1654227679e24fdb01d9a6f6cd6a8e57457285c8 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | testsuite/python/swimmer_reaction.py | Python | gpl-3.0 | 2,266 | [
"ESPResSo"
] | b11646c1d906a52aa2734edcea344d65aebd948cc4d72cd5c7bc5883333579d7 |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. currentmodule:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules.
.. seealso::
`scipy.special.cython_s... | e-q/scipy | scipy/special/__init__.py | Python | bsd-3-clause | 27,790 | [
"Gaussian"
] | 73bcba7aead82c1337480dda1b79f660c21fe8998030547f2e77f4ac5ecfc9dd |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTableAlgorithm(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | nagyistoce/devide | modules/vtk_basic/vtkTableAlgorithm.py | Python | bsd-3-clause | 483 | [
"VTK"
] | e79fa607c7de2cf3751b531ff4502fbef4ca201786fa3082e687aa4e3dbc256a |
r"""
Linear elasticity solved in a single patch NURBS domain using the isogeometric
analysis (IGA) approach.
Find :math:`\ul{u}` such that:
.. math::
\int_{\Omega} D_{ijkl}\ e_{ij}(\ul{v}) e_{kl}(\ul{u})
= 0
\;, \quad \forall \ul{v} \;,
where
.. math::
D_{ijkl} = \mu (\delta_{ik} \delta_{jl}+\delta_... | rc/sfepy | examples/linear_elasticity/linear_elastic_iga.py | Python | bsd-3-clause | 1,941 | [
"VTK"
] | a397d3fdbf3ed27b61ae8463fa119ab9a8efd016f1a6074a5cde1ec2746b720f |
#!/usr/bin/python
description = """
NuoDB AWS cluster quickstart\n
============================\n
This script creates a multiregion sandbox cluster of a given number of nodes in AWS EC2.
It is intended for creating a testing platform.
"""
import argparse
import nuodbTools.aws
import nuodbTools.cluster
import json
imp... | nuodb/nuodbTools | nuodb_aws_quickstart.py | Python | bsd-3-clause | 28,870 | [
"VisIt"
] | e5b3b6ef16c4f1e80330494deae90af591c89acd05d2dee05ac7f3014e7f7a98 |
#
# Copyright (C) 2003 greg Landrum and Rational Discovery LLC
#
""" """
import os
import unittest
from rdkit.ML.DecTree import ID3, PruneTree, CrossValidate
from rdkit.TestRunner import redirect_stdout
from rdkit.six import StringIO
def feq(a, b, tol=1e-4):
return abs(a - b) <= tol
class TreeTestCase(unittest... | rvianello/rdkit | rdkit/ML/DecTree/UnitTestPrune.py | Python | bsd-3-clause | 2,016 | [
"RDKit"
] | 8dcfe41cb06aeb868db53ecc306bfa22a3e4292a0653d5ec9f3425ad6a017efd |
# -*- coding: UTF-8 -*-
"""
``TransDecoder``
-----------------------------------------------------------------
:Authors: Menachem Sklarz
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
A module for running ``TransDecoder`` on a transc... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/RNA_seq/Trinotate_modules/TransDecoder.py | Python | gpl-3.0 | 8,110 | [
"BLAST"
] | 1eca3c6a8b665849a5558d284a41b8078fb11d704c40688132df01e49e8ec5ff |
from orbkit.qcinfo import QCinfo
from orbkit.orbitals import AOClass, MOClass
from orbkit.tools import *
import numpy
from .tools import descriptor_from_file
def read_wfn(fname, all_mo=False, spin=None, **kwargs):
'''Reads all information desired from a wfn file.
**Parameters:**
fname: str, file descrip... | orbkit/orbkit | orbkit/read/wfn.py | Python | lgpl-3.0 | 4,347 | [
"Gaussian"
] | a1a8c9c35d0a5d2d3aa8fb907262c454338d5909830defb2d0f22b22887a7cf5 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
def GetRGBColor(colorName):
'''
Return the red, green and blue components for a
color as doubles.
'''
rgb = [0.0, 0.0, 0.0] # black
vtk.vt... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Hybrid/Testing/Python/3DMorph.py | Python | bsd-3-clause | 2,892 | [
"VTK"
] | 132422c870d549fa143cb79e4b47ed62ca4dd55fb03ba8543f189eecc1813285 |
# -*- coding: utf-8 -*-
"""
Output Plugin for MP3 Encoder
Copyright (c) 2006-2007 by Nyaochi
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your opt... | rinrinne/cueproc-alternative | src/ce_lame_eyed3.py | Python | gpl-2.0 | 6,557 | [
"VisIt"
] | 38df756d651e7b86450d3ee467bf5b548e89e89def708f1117a7fb75077d3172 |
import testutils
import json
import string
import psycopg2
# Test for collection.distinct operation
class TestCollectionDiscinct(testutils.BedquiltTestCase):
def test_distinct_on_empty_collection(self):
_ = self._query("select bq_create_collection('people');")
result = self._query("""
sel... | BedquiltDB/bedquilt-core | test/test_distinct.py | Python | mit | 2,704 | [
"Brian"
] | 10b4b6ee44be314c942fb1152bbea3b2524fd6e82341ab266613ccaa07d442ef |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Module for the NaiveKDE.
"""
import numbers
import itertools
import numpy as np
from KDEpy.BaseKDE import BaseKDE
class NaiveKDE(BaseKDE):
"""
This class implements a naive computation of a kernel density estimate. The
advantages are that choices of bandw... | tommyod/KDEpy | KDEpy/NaiveKDE.py | Python | gpl-3.0 | 5,034 | [
"Gaussian"
] | 348f2553af728ddb4e21dce723a5e47cf1bf0e42ed90bb12ab02d55c2d9fdede |
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import io
import os
import unittest
from rdki... | rvianello/rdkit | rdkit/Chem/UnitTestCatalog.py | Python | bsd-3-clause | 9,253 | [
"RDKit"
] | 76f0ce0dd4d053774b7744b02f49afc58396001ae2aa11249baf144f8b253073 |
import contextlib
import functools
import logging
from typing import (
TYPE_CHECKING,
Dict,
FrozenSet,
Iterable,
Iterator,
List,
Mapping,
NamedTuple,
Optional,
Sequence,
Set,
Tuple,
TypeVar,
cast,
)
from pip._vendor.packaging.requirements import InvalidRequiremen... | sbidoul/pip | src/pip/_internal/resolution/resolvelib/factory.py | Python | mit | 28,298 | [
"VisIt"
] | d1b6f19d44928da7939ad20481e78ab44aa11057cd86fdf1a6aee3f4868cab67 |
class OWLNamedObjectVisitor(object):
"""Marker class"""
def visit(self, visitee):
"""
:param visitee: an object of one of the following classes:
- owlapy.model.OWLClass
- owlapy.model.OWLObjectProperty
- owlapy.model.OWLDataProperty
- owlapy.model... | patrickwestphal/owlapy | owlapy/model/owlnamedobjectvisitor.py | Python | gpl-3.0 | 1,056 | [
"VisIt"
] | ac18264dcffb4d3a17b5e280f0e9477778da951a5739f6d332de98eae01df2d6 |
"""
FASTA/QUAL format (:mod:`skbio.io.fasta`)
=========================================
.. currentmodule:: skbio.io.fasta
The FASTA file format (``fasta``) stores biological (i.e., nucleotide or
protein) sequences in a simple plain text format that is both human-readable
and easy to parse. The file format was first i... | Achuth17/scikit-bio | skbio/io/fasta.py | Python | bsd-3-clause | 37,914 | [
"BLAST",
"scikit-bio"
] | 6af74cf68365a06a8800f664251bb029cd16124dcd0645ed88201c1ab35b824d |
from setuptools import setup
setup(
name='GaussOpt',
version='1.1.3',
author='John Garrett',
author_email='garrettj403@gmail.com',
description='Gaussian beam analysis',
license='MIT',
keywords='gaussian optics millimeter terahertz thz',
url='https://github.com/garrettj403/GaussOpt/',
... | garrettj403/GaussOpt | setup.py | Python | mit | 899 | [
"Gaussian"
] | 192cb48c5150c105a5c1bc78da72a51556ca741bf06f06f527664af6c2b4e4ae |
#!/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/timerchange.py | Python | gpl-2.0 | 5,203 | [
"VisIt"
] | 3db9ec1b8a8b7aa1321c11761c7001d498116e266c4b41f48f308eddf973bef6 |
# This file is part of OpenHatch.
# Copyright (C) 2010 Parker Phinney
# Copyright (C) 2009, 2010 OpenHatch, Inc.
# Copyright (C) 2010 Mark Freeman
#
# This program 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 Software Fo... | mzdaniel/oh-mainline | mysite/profile/models.py | Python | agpl-3.0 | 37,117 | [
"VisIt"
] | c721cd9ca72e6f76ac2c0e29360bee9b35852dc8609e07daf14150536c4a13ef |
"""Quandl.com is a collection of thousands of finance and economic databases. Please visit Quandl.com for a detailed list of available data.
This module provides an API to quandl.com. You can get an api key for free by signing up with quandl.com. You can find the api key
in the account settings.
"""
from urllib.re... | kscheltat/quandl | docs/quandl.py | Python | gpl-3.0 | 3,584 | [
"VisIt"
] | 96c564ab41eb942c8c55795384afccd89ac12a198d010c2d474139ee7486377e |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright (c) 2012 OpenStack, LLC.
# 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... | tylertian/Openstack | openstack F/nova/nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 23,820 | [
"exciting"
] | 03efdc3f39bb18769e2c3e3f1ad3ddba8daaf80bc11ba8e8c47621c0c6a4b453 |
# ===========================================================================
# eXe
# Copyright 2004-2005, University of Auckland
# Copyright 2006-2009 eXe Project, http://eXeLearning.org/
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as ... | luisgg/iteexe | exe/xului/mainpage.py | Python | gpl-2.0 | 53,305 | [
"VisIt"
] | 9f8b26d29861fcd9f66c8c840e66e9d3da4e084134569810f01dc4cbe70d1d86 |
# -*- coding: iso-8859-1 -*-
# Copyright (C) 2007-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any la... | FedoraScientific/salome-paravis | src/Plugins/MEDReader/Test/testMEDReader5.py | Python | lgpl-2.1 | 4,333 | [
"ParaView"
] | 10e23d7b8665a44f0b48dfe22e89ebee0f3985b6f61675faed869daad4f74686 |
#!/usr/bin/python
# Copyright (c) 2006-2013 Regents of the University of Minnesota.
# For licensing terms, see the file LICENSE.
# This script sends email reminders for the landmarks experiment.
# SYNC_ME: Search: Scripts: Load pyserver.
import os
import sys
sys.path.insert(0, os.path.abspath('%s/../util'
... | lbouma/Cyclopath | scripts/daily/lmrk_send_emails.py | Python | apache-2.0 | 1,728 | [
"VisIt"
] | 5107dc5d2ce1bf5d097d8abe6bef5ede08bd671150e4174f0afcc42e602e6338 |
# -*- coding: utf-8 -*-
# Node and graph implementation
# Developer
# Ismail AKBUDAK
# ismailakbudak.com
from matplotlib import pyplot as plt
import networkx as nx
import random
from collections import OrderedDict
import pprint
pp = pprint.PrettyPrinter(indent=4)
# Node objects for graph structure
class Node(object)... | ismailakbudak/election-algorithm-on-graph | graph.py | Python | mit | 24,608 | [
"VisIt"
] | e7c3bc902916853d98e6e3c577de64ff156486453fae99c8f9a2365165afb6a6 |
"""
Copyright (c) 2013-2014 Benedicte Ofstad
Distributed under the GNU Lesser General Public License v3.0.
For full terms see the file LICENSE.md.
"""
import read_input as ri
import Molecule as mol
import Propertyclasses as pr
import pydoc
"""
The module working as the interface of the command line based program.
I... | Benedicte/vibrational_motion | abavib.py | Python | lgpl-3.0 | 3,355 | [
"Dalton"
] | aeee315a26be3572b717439d463a6747ccd4ba671735f6e3d5af8eb7e5d758bc |
#!/usr/bin/env python
# Copyright 2014-2019 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/grad/roks.py | Python | apache-2.0 | 2,981 | [
"PySCF"
] | ecd829176641316c1ab241926544d21848b88122ad84e69b430ec06835ae0043 |
# DIALS_ENABLE_COMMAND_LINE_COMPLETION
from __future__ import annotations
import concurrent.futures
import copy
import logging
import sys
import iotbx.phil
from dxtbx.model.experiment_list import ExperimentList
from dials.algorithms.indexing import DialsIndexError, indexer
from dials.array_family import flex
from ... | dials/dials | command_line/index.py | Python | bsd-3-clause | 8,692 | [
"CRYSTAL"
] | 82af41ce8b4b0b21ff9512050ef4c3af3bf9aa651c97f50f404d679c7d1014f6 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010 Orca Team.
# Copyright 2014-2015 Igalia, S.L.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 ... | chrys87/orca-beep | src/orca/scripts/web/script.py | Python | lgpl-2.1 | 72,605 | [
"ORCA"
] | 83e074fbdbda409cc4aff56b397a36558a8dace5974b4c82ae70625d14926363 |
"""
VOMS2CSAgent performs the following operations:
- Adds new users for the given VO taking into account the VO VOMS information
- Updates the data in the CS for existing users including DIRAC group membership
-
"""
from DIRAC import S_OK, gConfig, S_ERROR
from DIRAC.Core.Base.AgentModule import AgentM... | arrabito/DIRAC | ConfigurationSystem/Agent/VOMS2CSAgent.py | Python | gpl-3.0 | 7,683 | [
"DIRAC"
] | 13622d7eece2b6d41eae02b3b9c51d9e34a8503e31a1601d5ba9d4c21010169f |
"""
Created on 27/04/2013
@author: thom
"""
import unittest
import string
import copy
from rdkit.Chem import AllChem as Chem
from rdkit.rdBase import DisableLog, EnableLog
from molecule import Molecule
from chemistry_model.chemistry_factory import ChemistryFactory
class Test(unittest.TestCase):
def setUp(self... | th0mmeke/toyworld | tests/test_molecule.py | Python | gpl-3.0 | 5,894 | [
"RDKit"
] | 5fc646feaaf0c77e06dd3ac67e25878d826d527561dadd058f04ac6cc17b9803 |
#!/usr/bin/env python
"""
Name: mean_distance_from_alignments.py
Author: Michael G. Harvey
Date: 21 July 2014
Description: Calculate mean pairwise distances between samples in a dataset from multiple
alignments (as well as standard deviations of those distances). Not all samples have to be
in each alignment (each ... | mgharvey/misc_python | bin/mean_distances_from_alignments.py | Python | bsd-3-clause | 7,127 | [
"Biopython"
] | b085590f5414d452dab33a04c210ef7e719c45798efaa167b2f1e59ad3293b73 |
import ast
symbols = {
ast.Eq: "==",
ast.NotEq: '!=',
ast.Pass: '/*pass*/',
ast.Mult: '*',
ast.Add: '+',
ast.Sub: '-',
ast.Div: '/',
ast.FloorDiv: '/',
ast.Mod: '%',
ast.Lt: '<',
ast.Gt: '>',
ast.GtE: '>=',
ast.LtE: '<=',
ast.LShift: '<<',
ast.RShift: '>>',
... | lukasmartinelli/py14 | py14/clike.py | Python | mit | 2,928 | [
"VisIt"
] | 769cf1e66388969333ac87da19644d75875be40ebfb67c82b7fc09c7936992c9 |
#!/usr/bin/env python
# -*- coding: latin-1; py-indent-offset:4 -*-
################################################################################
#
# This file is part of Bfplusplus
#
# Bfplusplus is a graphical interface to the Betfair Betting Exchange
# Copyright (C) 2010 Daniel Rodriguez (aka Daniel Rodriksson)
... | mementum/bfplusplus | bfplusplus/gui/UpdateChecker.py | Python | gpl-3.0 | 6,217 | [
"VisIt"
] | 2c6a16601957692cb359c660af364f43d39df6131b4cab37de971b9f9813bbff |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# 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.
# Python stuff
import numpy
# My stuff
from Entity import DisorderedEntityWrap... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/Atom.py | Python | mit | 8,832 | [
"Biopython"
] | 861d18ff17c89dc2388edd738c1341f553c8c2d1c1c9e3d792d8a4e3269072e6 |
import numpy as np
from .._shared.utils import warn
from ._nl_means_denoising import (
_nl_means_denoising_2d,
_nl_means_denoising_3d,
_fast_nl_means_denoising_2d,
_fast_nl_means_denoising_3d)
def denoise_nl_means(image, patch_size=7, patch_distance=11, h=0.1,
multichannel=None, f... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/skimage/restoration/non_local_means.py | Python | gpl-3.0 | 6,699 | [
"Gaussian"
] | d3cfddd411f79e6fabd8f16327789664e7878af7ffbdd7b15bf10212f84ca058 |
#
# Post-processing script QE --> EPW
# 14/07/2015 - Samuel Ponce
#
import numpy as np
import os
# Enter the number of irr. q-points
user_input = raw_input('Enter the prefix used for PH calculations (e.g. diam)\n')
prefix = str(user_input)
# Enter the number of irr. q-points
user_input = raw_input('Enter the numb... | mmdg-oxford/papers | Verdi-NCOMMS-2017/code/EPW/tests/Inputs/t04/pp.py | Python | gpl-3.0 | 954 | [
"EPW"
] | 8ae722d906e42e0fd9d31838ca920693255f0a910fb1af7c42e24b748440c5c0 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
#################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment #
# #... | Chuban/moose | python/chigger/tests/chigger/test_chigger.py | Python | lgpl-2.1 | 2,346 | [
"MOOSE"
] | 4bd3901b5f4ccc2962fb4db2d7d35e3a3862c4eca966347f501efb386f629d5a |
"""
Implementation of a language model class.
TODO: write more documentation
"""
__docformat__ = 'restructedtext en'
__authors__ = ("Razvan Pascanu "
"KyungHyun Cho "
"Caglar Gulcehre ")
__contact__ = "Razvan Pascanu <r.pascanu@gmail>"
import numpy
import itertools
import logging
impo... | tuzhaopeng/NMT-Coverage | build/lib/groundhog/models/LM_model.py | Python | bsd-3-clause | 10,541 | [
"Gaussian"
] | 85047402585b5ebf35e3fe2a7824b3458c39f2cc7e2371521175c2a4a46b9b6b |
"""
Django settings for bongo project.
For more information on this file, see
https://docs.djangoproject.com/en/dev/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/dev/ref/settings/
"""
import os
import yaml
# Build paths inside the project like this: os.path.j... | BowdoinOrient/bongo | bongo/settings/common.py | Python | mit | 6,016 | [
"Brian"
] | f946173e3d0b8522069be7ed5d797d1c9def833ac6e9485e623b717fffcc70a0 |
# $HeadURL$
__RCSID__ = "$Id$"
import types
import os
import DIRAC
from DIRAC.Core.Utilities import List
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSystem.private.Refresher import gRefresher
from DIRAC.Core.Utilities.ReturnValues import S_OK, S_ERROR
from ... | avedaee/DIRAC | ConfigurationSystem/private/ConfigurationClient.py | Python | gpl-3.0 | 5,983 | [
"DIRAC"
] | d13c3d314b59cf8503bdc2887bffe1e9b623c4635a9e8cfa158a3597fb5bdbae |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import warnings
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.periodic_table import Element, Specie
from pymatgen.core.comp... | nisse3000/pymatgen | pymatgen/core/tests/test_structure.py | Python | mit | 56,184 | [
"pymatgen"
] | fcffe2c17ab5bcc23fb337117281d405f0098d2b67097cdb942c34fa29cbbd67 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC.FrameworkSystem.private.standardLogging.LoggingRoot import LoggingRoot
gLogger = LoggingRoot()
def getLogger():
return gLogger
| yujikato/DIRAC | src/DIRAC/FrameworkSystem/Client/Logger.py | Python | gpl-3.0 | 272 | [
"DIRAC"
] | e5d88d150138b274d4b4ca8fc7539f4f2d1d2d34c126a3c6103460fa509692cd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Provides classes for generating high-symmetry k-paths using different conventions.
"""
import abc
from math import cos, sin, tan, e, pi, ceil
import itertools
from warnings import warn
import operator
impo... | mbkumar/pymatgen | pymatgen/symmetry/kpath.py | Python | mit | 94,123 | [
"CRYSTAL",
"pymatgen"
] | 60f5cb229be89579e3129b3c88ce953fa7ffd62460a892d7aa6ddd30e4c508c9 |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
import os
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
# To set up environmenta... | TwilioDevEd/api-snippets | notifications/rest/services/create-service/create-service.7.x.py | Python | mit | 789 | [
"VisIt"
] | bce574d337e9f41b30cb59be715cd4ebc83a26db93ca0e7928edb86e48025cbe |
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ve... | to266/hyperspy | hyperspy/tests/component/test_component_active_array.py | Python | gpl-3.0 | 2,448 | [
"Gaussian"
] | 1fada664d9375d59d5e9888da146a174cfdbb48f5aa998221c5ffaf5647fabf9 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/lb_poiseuille_cylinder.py | Python | gpl-3.0 | 7,161 | [
"ESPResSo"
] | c52f0c9ead2cd19ae02892a35ac2d21be7d99379bc553d13254992fa109e4bbd |
from galaxy.util import bunch
from galaxy.model import mapping
class MockTrans( object ):
def __init__( self ):
self.app = TestApp()
class TestApp( object ):
def __init__( self ):
self.config = bunch.Bunch(
tool_secret="awesome_secret",
)
self.model = mapping.in... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/workflows/workflow_support.py | Python | gpl-3.0 | 886 | [
"Galaxy"
] | 8666b8f533f92f495ae7ded3da961ed464d3b62f0086f4af4d6e2c7a0c144c76 |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/aetemplate/aeaslayeredshadertemplate.py | Python | mit | 9,894 | [
"VisIt"
] | 7682636ee72c935c8a2ee81a04c610479f9dd5f05c8346ddcc33d0580520037e |
import logging
from PyQt5.QtCore import (QCoreApplication, QLineF, QPoint, QRectF, QMimeData)
from PyQt5.QtGui import (QDrag, QPen, QTransform)
from PyQt5.QtWidgets import (QDialogButtonBox, QToolBar, QToolButton, QSizePolicy, QSplitter,
QTreeWidget, QTreeWidgetItem, QGraphicsScene, QGraphi... | CNR-Engineering/PyTelTools | pyteltools/workflow/mono_gui.py | Python | gpl-3.0 | 25,281 | [
"VTK"
] | a8a010a4dd6a5a99a74d7a6f5bd2926614673caa681613256483d8f5e0c0cdb9 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
########################################################################
# Solves problem 39 from projectEuler.net.
# Finds the perimeter below than 1000 that can be formed by the most
# number of rectangular triangles of integral lengths.
# Copyright (C) 2010 Sa... | sanSS/programming-contests | project-euler/problem039.py | Python | gpl-3.0 | 1,674 | [
"VisIt"
] | e01dad611472d5cab11021693dec639ce3b43fd2a0259e961f967fb41269292c |
#!/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/hessian/test/test_rhf.py | Python | apache-2.0 | 4,931 | [
"PySCF"
] | 7f06fd7b2c32f9cd6a72c557c55a7836a30184720d2399344ec951d953e615d3 |
# coding=utf8
#
# Copyright 2013 Dreamlab Onet.pl
#
# This library 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;
# version 3.0.
# This library is distributed in the hope that it will be useful,
# bu... | tikan/rmock | src/rmock/runners/http/proxy/handler.py | Python | lgpl-3.0 | 2,108 | [
"VisIt"
] | cba7698481fb4c6dd03f4f75cf8e8bec5bc2071f0905b1e7f52cc40a36b9c863 |
#!/usr/bin/env python
"""
Base neuron class used by LPU.
"""
from abc import ABCMeta, abstractmethod, abstractproperty
import os.path
import neurokernel.LPU.neurons as neurons
import numpy as np
import pycuda.gpuarray as garray
from pycuda.tools import dtype_to_ctype
import pycuda.driver as cuda
from pycuda.compiler... | cerrno/neurokernel | neurokernel/LPU/neurons/baseneuron.py | Python | bsd-3-clause | 13,603 | [
"NEURON"
] | 1b21763fdb7c06356ae412c8441633ea51d4e420aa867b7ca0bfa6640d0dc782 |
# build_assistant/autogen/content_items/ContentItemCodeGenerator.py
#
# (C) Copyright 2014-present Cristian Dinu <goc9000@gmail.com>
#
# This file is part of Uniarchive II.
#
# Licensed under the GPL-3
from build_assistant.autogen.AutoGenConfig import ContentItemConfig
from build_assistant.autogen.GenericPolymorphicC... | goc9000/uniarchive2 | build_assistant/autogen/content_items/ContentItemCodeGenerator.py | Python | gpl-3.0 | 5,544 | [
"VisIt"
] | b643fa161ec11fa60f8ea2fd8ca863805a300173294264d9b25110a6d568c75e |
import os
import pysam
import string
import shlex
import subprocess
import argparse
import math
def get_genome_stats(genome_fasta):
reference_fasta_index = genome_fasta + '.fai'
if not os.path.exists(reference_fasta_index):
print("\nIndexing %s\n" % os.path.abspath(genome_fasta))
pysam.faidx(g... | BennerLab/atg | atg/util/index.py | Python | gpl-3.0 | 5,346 | [
"pysam"
] | 5e8e9fcc2a6af31ea6a6c3c5773c027ac29bd70b7b84b044f9cc68102090228f |
#
# Copyright (c) SAS Institute Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in w... | sassoftware/catalog-service | catalogService/rest/drivers/xenent/xenentclient.py | Python | apache-2.0 | 29,080 | [
"VMD"
] | 6cb7e228752c3d013b56314ebfbf3732cb16a3399591c179b4d3cd1a1c61a855 |
# Copyright 2018 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 to in writing, s... | quartzmo/gcloud-ruby | google-cloud-speech/synth.py | Python | apache-2.0 | 5,786 | [
"VisIt"
] | bf3289ae0a385b2c9dd2c07aa58a75d1cbedb49305853a23f43d6a7a3b23c751 |
# -*- coding: utf-8 -*-
r"""
ALBA CLÆSS beamline
-------------------
Files in ``\examples\withRaycing\08_CLAESS_BL``
See the optical scheme of the beamline
`here <http://www.cells.es/Beamlines/CLAESS/optics_layout.html>`_.
This script produces images at various positions along the beamline.
The following 13 images ... | kklmn/xrt | examples/withRaycing/08_CLAESS_BL/__init__.py | Python | mit | 1,853 | [
"CRYSTAL"
] | 2bcf4eb56005b96e1dd028c69b5a1994f66730d9598c42a23816e37702852c31 |
__author__ = 'jiataogu, memray'
import theano
import logging
import copy
import emolga.basic.objectives as objectives
import emolga.basic.optimizers as optimizers
from theano.compile.nanguardmode import NanGuardMode
from emolga.utils.generic_utils import visualize_
from emolga.layers.core import Dropout, Dense, Dense2... | memray/seq2seq-keyphrase | emolga/models/covc_encdec.py | Python | mit | 108,092 | [
"Gaussian"
] | ed46e75df08373a5718092f6d012e0f21068cb736509ea1a4d020d315c5c8784 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkSubPixelPositionEdgels(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkSubPixelPositionEdgels.py | Python | bsd-3-clause | 527 | [
"VTK"
] | b44050eb0dcd1ec7ae9944b4f2218fc39086cc0c24c9ed4a3e43c2024a2618b2 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2007-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | test/testMP.py | Python | lgpl-2.1 | 2,581 | [
"cclib"
] | a108b0bd18e44fabd5fbb0782849dc31f5be2aeebf64024d7052060936ff169b |
#!/usr/bin/env python
"""
--------------------------------------------------------------------------------
(c) 2017 Julian Rees
License: GNU GPLv3
Description: Plot the SCF cycle trajectory of a geometry optimization in ORCA.
Run: python scfenergymap.py filename
Arguments: filename - file name with extension
Depen... | julianrees/scripts | python/scfenergymap.py | Python | gpl-3.0 | 1,150 | [
"ORCA"
] | 2e16595b5283fc298d6e841bcdc5ba378ac21921825f47eaaa111ae9c3e2f305 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Charge Decomposition Analysis (CDA)"""
from __future__ import print_function
import random
import numpy
from .fragm... | gaursagar/cclib | src/cclib/method/cda.py | Python | bsd-3-clause | 4,449 | [
"cclib"
] | d35f04c8d65a8a49fb30c82659ecc883cf58b9bad5fdda2fa3900f2dc0f1b957 |
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy.dual import eig
from scipy.special import comb
from scipy import linspace, pi, exp
from scipy.signal import convolve
__all__ = ['daub', 'qmf', 'cascade', 'morlet', 'ricker', 'cwt']
def daub(p):
"""
The coefficient... | jlcarmic/producthunt_simulator | venv/lib/python2.7/site-packages/scipy/signal/wavelets.py | Python | mit | 10,458 | [
"Gaussian"
] | 6db4750887d36273d13f047283f30359db3d90c52ad74970eac6274cd469bfbb |
import numpy as np
from dipy.sims.voxel import add_noise
from dipy.segment.mrf import (ConstantObservationModel,
IteratedConditionalModes)
class TissueClassifierHMRF(object):
r"""
This class contains the methods for tissue classification using the Markov
Random Fields modelin... | nilgoyyou/dipy | dipy/segment/tissue.py | Python | bsd-3-clause | 6,207 | [
"Gaussian"
] | ceb6edb2dc3e1af38bbd1d5dc59381d70f6402472af44e392fd2c6f0f808b999 |
# 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 RShortread(RPackage):
"""FASTQ input and manipulation.
This package implements sam... | iulian787/spack | var/spack/repos/builtin/packages/r-shortread/package.py | Python | lgpl-2.1 | 2,726 | [
"Bioconductor"
] | da3e4b073ad874542461c4ea69e63fbc001f7264887b998bf1b393422894eb09 |
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