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"""
Author: Jon Ander Gomez Adrian (jon@dsic.upv.es, http://personales.upv.es/jon)
Version: 1.0
Date: June 2014
Universitat Politecnica de Valencia
Technical University of Valencia TU.VLC
"""
import sys
import numpy
from . import MyKernel
class MyKernelClassifier:
"""
This class implemen... | jonandergomez/machine_learning_for_students | machine_learning/MyKernelClassifier.py | Python | mit | 2,519 | [
"Gaussian"
] | 9763e1af459817a0fc1a87ff4075b6e3c38d5c2d6a2c17ff3e2313c565cacb6c |
"""
This pipeline is intended to extract pixel information from T2W images.
"""
import os
import numpy as np
from protoclass.data_management import T2WModality
from protoclass.data_management import GTModality
from protoclass.preprocessing import RicianNormalization
from protoclass.preprocessing import GaussianNorm... | I2Cvb/mp-mri-prostate | pipeline/feature-extraction/t2w/pipeline_extraction_intensity_t2w.py | Python | mit | 3,763 | [
"Gaussian"
] | 2bf9b94e3e021e003155712c6d824c3eee26cd8ad337cd61f976900e319c49c8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@gmail.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 So... | sysadmind/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 15,209 | [
"Firefly"
] | 8126854225c3226e3798482431323f5743057191bec0e25ca7969173327701ce |
#!/usr/bin/env python
#
'''
Calculating densities with DF-MP2, demonstrated for the dipole moment of CH3Cl.
'''
from numpy.linalg import norm
from pyscf.gto import Mole
from pyscf.scf import RHF
from pyscf.mp.dfmp2_native import DFMP2
mol = Mole()
mol.atom = '''
C 0.000000 0.000000 0.000000
Cl 0.000000 0.00... | sunqm/pyscf | examples/mp/11-dfmp2-density.py | Python | apache-2.0 | 1,383 | [
"PySCF"
] | 54c06c52f72bbac4982f7b141c13f22d4d062836dc10f6e484af9900be9836ed |
from mpi4py import MPI
simulator = 'neuron'
import nineml
if simulator == 'neuron':
from pype9.cells.neuron import CellMetaClass # @UnusedImport
from neuron import h
else:
from pype9.cells.nest import CellMetaClass # @Reimport
import os.path
import sys
import matplotlib.pyplot as plt
h.load_file("multisp... | DaisukeMiyamoto/nineml_test | nineml/dcn_test.py | Python | mit | 5,923 | [
"NEURON"
] | 74335441eed39f1b66fee47e9e3a08d8af026fab7a0842305c5d2325c085744b |
#
# AUTHORS:
# Hakan Ozadam
# Rachel Brown
#
# Moore Laboratory
# UMASS Medical School / HHMI
# RNA Therapeutics Institute
# Albert Sherman Center, ASC4-1009
# 368 Plantation Street
# Worcester, MA 01605
# USA
#
#############################################... | hakanozadam/bal | bal/core/make_bp_reference.py | Python | gpl-2.0 | 5,956 | [
"pysam"
] | 0a0512b9b14bce269238c742808f9c3f6902b027cc6fad8a0d49264df4e554b7 |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 Foundation, either version 3 ... | pwillworth/galaxyharvester | html/nameAvailable.py | Python | gpl-3.0 | 1,522 | [
"Galaxy"
] | cf8134643c3eda881cc0a580d741a3110b63b6165300980300d100094bde228e |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import os
import xml.sax
import numpy as np
from gpaw import setup_paths
from gpaw.setup_data import search_for_file
from gpaw.atom.radialgd import EquidistantRadialGridDescriptor
try:
import gzip
except ImportError:
... | ajylee/gpaw-rtxs | gpaw/basis_data.py | Python | gpl-3.0 | 10,519 | [
"GPAW"
] | 73206b717cac6d0c36c9692613bd3c59d61f8f73283d52fe94f5294ac96b072d |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import math
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_etree_fromstring,
compat_getpass,
compat_http_client,
... | maleficarium/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 81,417 | [
"VisIt"
] | 9815230fc33d9eda6d4d350119261e0336f96e315abf2d78ccffdfff74128b9a |
from __future__ import division, print_function
import numpy as np
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
from mpl_toolkits.axes_grid1 import make_axes_locatable
from mpl_toolkits.mplot3d import Axes3D
import streakline
#import streakline2
import ... | abonaca/stream_information | scripts/stream_info/stream_info.py | Python | mit | 191,260 | [
"Galaxy"
] | 702d493c395eea7adafb124655d8a038a68a71a90980eafd6187546120e5d151 |
# Copyright 2014 Roberto Brian Sarrionandia
#
# 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 t... | sarrionandia/tournatrack | deletestatus.py | Python | apache-2.0 | 1,320 | [
"Brian"
] | a608e1c13e88ba7e2ea3fd411e3324998eb64b0cfdcd45828f2b1526897f2a33 |
# -*- coding: utf-8 -*-
# Copyright (C) 2016 Google Inc. All Rights Reserved.
#
# Authors:
# Arkadiusz Socała <as277575@mimuw.edu.pl>
# Michael Cohen <scudette@google.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 obt... | dsweet04/rekall | tools/layout_expert/layout_expert/visitors/layout_computing_visitor.py | Python | gpl-2.0 | 8,271 | [
"VisIt"
] | 46b74e47901c35993fef849f5088fc379adb49fd63aaa4c3b81adc606a04637f |
# -*- coding: utf-8 -*-
"""
=================
Plot multiple EMD
=================
Shows how to compute multiple EMD and Sinkhorn with two differnt
ground metrics and plot their values for diffeent distributions.
"""
# Author: Remi Flamary <remi.flamary@unice.fr>
#
# License: MIT License
import numpy as np
import m... | aje/POT | examples/plot_compute_emd.py | Python | mit | 2,404 | [
"Gaussian"
] | 72cac7c12226c0433abdcf1e901fb98efc611f2111315245deef31fd45fc0e77 |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
""" Various bits and pieces for calculating Molecular descriptors
"""
from rdkit import RDConfig
from rdkit.ML.Descriptors import Descriptors
from rdkit.Chem import Descriptors as DescriptorsMod
from rdkit.RDLogger import logger
logger = l... | rdkit/rdkit-orig | rdkit/ML/Descriptors/MoleculeDescriptors.py | Python | bsd-3-clause | 3,247 | [
"RDKit"
] | 15f6b3913d1ca15cc24341923906b0f54b880bd03110c3c278a5b487bf178b09 |
# 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google/burst-denoising | tf_image.py | Python | apache-2.0 | 20,387 | [
"Gaussian"
] | 00e312a76547fbfe49ef0a25c94bccbdd80862330484947c46155be8a3811c47 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
'''
Nonlinear noise reduction
This is how the three of us got into this business. Since spectral
filters are problematic with chaotic, broad band signals, new
techniques were necessary. All the implementations here use phase
space projections for noise reduction. The... | sdia/tisane | nonlinear_noise_reduction.py | Python | gpl-3.0 | 9,629 | [
"Gaussian"
] | caac8c0d62815421ec444022b2d7840f2c9825eeed8b6478be51cbc3c468f471 |
from distutils.core import setup
import os
def version():
setupDir = os.path.dirname(os.path.realpath(__file__))
versionFile = open(os.path.join(setupDir, 'checkm', 'VERSION'))
return versionFile.read().strip()
setup(
name='checkm-genome',
version=version(),
author='Donovan Parks, Michael Im... | fw1121/CheckM | setup.py | Python | gpl-3.0 | 939 | [
"pysam"
] | 08f386df14647908a457b501570a34fc7d96376f39377d57d419cb94f96eba0a |
#!/usr/bin/python
# -*- coding: utf-8
'''
This file is part of VetApp.
VetApp 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 ver... | mape90/VetApp | models/visit.py | Python | gpl-3.0 | 6,757 | [
"VisIt"
] | 2ee4876f2a44bbb0a2598e1148b05f39a87c7311db8268cf3c0003d6046700c7 |
#!/usr/bin/python
# _*_ coding:utf-8 _*_
import flickrapi
import json
import time
#Flickrapi documentation: https://stuvel.eu/flickrapi-doc/2-calling.html
#FIRST: get your own API-keys!
api_key = u"YOUR_API_KEY_HERE" #Request your own key and place the key inside the quotes.
api_secret = u"YO... | Frederic-P/flickr-API-Scraper | City Scraper.py | Python | mit | 5,867 | [
"VisIt"
] | 38db483b70a6a04779954272ff3ca7e31b24d9227728f845bc9dfc95a25e330f |
# Copyright (c) 2016 Robert Bosch LLC, USA.
# All rights reserved.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.
#
# This source code is based on Neon
# https://github.com/NervanaSystems/neon/
# Copyright 2015 Nervana Systems Inc., lice... | DL-Benchmarks/DL-Benchmarks | neon/stackedAE/sda.py | Python | mit | 8,171 | [
"Gaussian"
] | 3f21ef9753fd60d0bd2356293fc7653a75b6275cdbbd00370cee147637563499 |
# ----------------------------------------------------------------------
# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
# https://www.lammps.org/ Sandia National Laboratories
# Steve Plimpton, sjplimp@sandia.gov
#
# Copyright (2003) Sandia Corporation. Under the terms of Contract
# DE-A... | akohlmey/lammps | python/lammps/mliap/pytorch.py | Python | gpl-2.0 | 2,354 | [
"LAMMPS"
] | aa5c4ee8edbd754f03968f1c50e166baf0d5cc13ba209031550476d5061d453f |
# -*- coding: utf-8 -*-
# Copyright (C) 2011-2015 Martin Sandve Alnæs
#
# This file is part of UFLACS.
#
# UFLACS 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 3 of the License, or
# (a... | FEniCS/uflacs | uflacs/analysis/graph_symbols.py | Python | gpl-3.0 | 3,926 | [
"VisIt"
] | 55eb7b3afa9d714bfbb69feffe533678a8f300cde0848025d89f49f1c4af035a |
import os
import unittest
import pysal
import numpy as np
class TestDistanceWeights(unittest.TestCase):
def setUp(self):
np.random.seed(1234)
self.polyShp = pysal.examples.get_path('columbus.shp')
self.arcShp = pysal.examples.get_path('stl_hom.shp')
self.points = [(
10,... | spreg-git/pysal | pysal/weights/tests/test_Distance.py | Python | bsd-3-clause | 7,005 | [
"COLUMBUS",
"Gaussian"
] | 2bf07b3422049e024fa2d2d1dd64882f9de4a81bb29520277bd1d7eb2ceb7683 |
'''
PathwayGenie (c) GeneGenie Bioinformatics Ltd. 2018
PathwayGenie is licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=too-many-arguments
# pylint: disable=too-many-branches
# pylint: disable=too-many-locals
#... | neilswainston/PathwayGenie | parts_genie/rbs_calculator.py | Python | mit | 23,199 | [
"VisIt"
] | e9018af414eb86fe66e501f5f7e408a232ad75fd0b461309d36704d3e546177b |
import os
import pathlib
import platform
import tempfile
import meshio
import meshzoo
import numpy as np
import pytest
import meshplex
from ..helpers import assert_norms, is_near_equal, run
this_dir = pathlib.Path(__file__).resolve().parent
def _compute_polygon_area(pts):
# shoelace formula
return (
... | nschloe/voropy | tests/mesh_tri/test_mesh_tri.py | Python | mit | 22,491 | [
"VTK"
] | 6bedeacb91a675c0badf254121c93d4243be81d634baa7af1f82a4220c15eef7 |
from pyscf.pbc.gto import Cell
from pyscf.pbc.scf import KRHF
from pyscf.pbc.tdscf.krhf_slow import TDRHF
from pyscf.pbc.gw import KRGW
cell = Cell()
cell.atom = '''
C 0.000000000000 0.000000000000 0.000000000000
C 1.67 1.68 1.69
'''
cell.basis = {'C': [[0, (0.8, 1.0)],
[1, (1.0, 1.0)]]}
ce... | sunqm/pyscf | examples/gw/31-pbc_slow.py | Python | apache-2.0 | 696 | [
"PySCF"
] | fbed8b12376572eb985d3ed44af8ec81135186ed6be13baaf22e5049b0c6dcc1 |
# -*- coding: utf-8 -*-
#
# This file is part of Sequana software
#
# Copyright (c) 2016-2020 - Sequana Development Team
#
# File author(s):
# Thomas Cokelaer <thomas.cokelaer@pasteur.fr>
#
# Distributed under the terms of the 3-clause BSD license.
# The full license is in the LICENSE file, distributed with t... | sequana/sequana | sequana/fastq.py | Python | bsd-3-clause | 39,267 | [
"pysam"
] | d715a9f9745a07828d45c4e39949906d5834569a2911bbf4aa95865f67c878ac |
# $Id$
#
# Copyright (C) 2000-2008 greg Landrum and Rational Discovery LLC
# All Rights Reserved
#
""" code for dealing with composite models
For a model to be useable here, it should support the following API:
- _ClassifyExample(example)_, returns a classification
Other compatibility notes:
1) To use _Compo... | rvianello/rdkit | rdkit/ML/Composite/Composite.py | Python | bsd-3-clause | 20,637 | [
"RDKit"
] | fea1a71d2013021e4a63ca5a94e5addf9822a0ce716d713d016a318d2cef74bb |
"""Tests for the thumbs module"""
from workbench import scenarios
from workbench.test.selenium_test import SeleniumTest
class ThreeThumbsTest(SeleniumTest):
"""Test the functionalities of the three thumbs test XBlock."""
def setUp(self):
super(ThreeThumbsTest, self).setUp()
scenarios.add_xm... | dcadams/xblock-sdk | workbench/test/test_thumbs.py | Python | agpl-3.0 | 4,791 | [
"VisIt"
] | 9e23d284649ce88bc349f7be16253e3ea40da5f7e834b9f8e1d97fc4b55a0f67 |
#!/usr/bin/env python
# generate figures in Getting Started section of User's Manual
# usage:
# $ python basemapfigs.py FILEROOT [FIELD] [DPI]
# where
# FILEROOT root of NetCDF filename and output .png figures
# FIELD optional: one of {velbase_mag, [velsurf_mag], mask, usurf} (edit script to add more)
#... | citibeth/twoway | pism/std-greenland/basemapfigs.py | Python | gpl-3.0 | 6,416 | [
"NetCDF"
] | 925e57b55ca2a21d51be2bc10aecf262fe043f17159fc46d2304140b5e0d1a7f |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------------------------
# Copyright (c) 2015 Eric Pascual
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software w... | dwalton76/ev3dev-lang-python | ev3dev2/_platform/ev3.py | Python | mit | 2,283 | [
"Amber"
] | 848a1a917ae2e475c76645d73c230a8a85031fa94e6f0acdea6a6cd6037ba587 |
# lintory - keep track of computers and licenses
# Copyright (C) 2008-2009 Brian May
#
# 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 ... | VPAC/lintory | lintory/views.py | Python | gpl-3.0 | 26,596 | [
"Brian"
] | a8096736c4772f72fbe4452359a7c7473af799a50cf9d88222e5ce857e20357c |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2011, 2012, 2015 CERN.
#
# Invenio 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 optio... | Panos512/invenio | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 147,640 | [
"VisIt"
] | ce377e10344d0009493513fe551b478b376168e9634041b98148bbafae3527d4 |
#!/usr/bin/python
# File created on 27 Jan 2012.
from __future__ import division
__author__ = "Kishori M Konwar"
__copyright__ = "Copyright 2013, MetaPathways"
__credits__ = ["r"]
__version__ = "1.0"
__maintainer__ = "Kishori M Konwar"
__status__ = "Release"
try:
from multiprocessing import Process, cpu_count, P... | wholebiome/MetaPathways_Python_Koonkie.3.0 | libs/python_scripts/MetaPathways_parse_blast_threaded.py | Python | mit | 25,140 | [
"BLAST"
] | b0649ac3c16640d643cc166f8d601e2c1d0c524af2f11b8698488b47a72c0918 |
"""Initializer of parameters."""
import numpy as np
class Initializer(object):
"""The base class of an initializer."""
def __init__(self, **kwargs):
self._kwargs = kwargs
def __call__(self, desc, arr):
"""Initialize an array
Parameters
----------
desc : str
... | ZihengJiang/nnvm | python/nnvm/testing/init.py | Python | apache-2.0 | 3,494 | [
"Gaussian"
] | 8f1ba1e3dc78ad7bc8512f6264003a8d9f88b74446af5506fa59aa1e7a353877 |
import os
import sys
import logging
import datetime
import zlib
import base64
import copy
import socket
import struct
import random
from functools import partial
from time import time
import ujson as json
import tornado.ioloop
import tornado.web
from tornado.httpclient import AsyncHTTPClient, HTTPRequest
from querypa... | mcholste/galaxy | lib/handlers.py | Python | mit | 26,452 | [
"Galaxy"
] | cf8a198a3ef7fb8f561781a79c3f328e2fedeae390fa16b45a969c31c2aabf2e |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | d3pm/images/main_test_config.py | Python | apache-2.0 | 2,693 | [
"Gaussian"
] | 9e83548be97a0c04cc4627463b14274b502ba5da6728bd230172e85ff4cbc906 |
# This file creates 1D visualizations for our model
# Can create channel or neuron visualizwtions
import numpy as np
import lucid.optvis.objectives as objectives
import lucid.optvis.render as render
import dla_lucid
from dla_lucid import DLA
def vis_channel(model, layer, channel_n):
"""
This function crea... | davidparks21/qso_lya_detection_pipeline | lucid_work/vis_1d.py | Python | mit | 4,602 | [
"NEURON"
] | b9af82313338f551766bb63892ee60c50444363a99c6098689120d60e98a054c |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2013 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/remindor-qt | remindor_qt/ReminderDialog.py | Python | gpl-3.0 | 14,927 | [
"Brian"
] | 98c12b28354998da5a90c992bbd7b7ef99ea6e5bdd81d8f6759fb1f17dd26bcb |
import sys
import numpy as np
from ase.units import Bohr, Hartree
from ase.parallel import paropen
from ase.data import vdw_radii
import _gpaw
from gpaw.io.fmf import FMF
class ExteriorElectronDensity:
"""Exterior electron density to describe MIES spectra.
Simple approach to describe MIES spectra after
... | robwarm/gpaw-symm | gpaw/analyse/eed.py | Python | gpl-3.0 | 3,089 | [
"ASE",
"GPAW"
] | 4ce7fde8a4cec3638a1adce8da26848eb3e887d6cdc6ec08e80a619ca6924655 |
"""
This software is an implementation of
Deep MRI brain extraction: A 3D convolutional neural network for skull stripping
You can download the paper at http://dx.doi.org/10.1016/j.neuroimage.2016.01.024
If you use this software for your projects please cite:
Kleesiek and Urban et al, Deep MRI brain extraction: A 3... | GUR9000/Deep_MRI_brain_extraction | utils/helper_seg.py | Python | mit | 18,821 | [
"NEURON"
] | 3773a15a162b24957840cf3104c5ac64ab17417faee524f090f2ef189a1f27ea |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010-2011 The Orca Team
# Copyright 2012 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... | pvagner/orca | src/orca/orca.py | Python | lgpl-2.1 | 27,027 | [
"ORCA"
] | 32a17f5e93f755e4522b640ff28c199a54fc90bf2da66a3adddda1d347e9fea9 |
"""
picasso/imageprocess
~~~~~~~~~~~~~~~~~~~~
Image processing functions
:author: Joerg Schnitzbauer, 2016
:copyright: Copyright (c) 2016 Jungmann Lab, MPI of Biochemistry
"""
import matplotlib.pyplot as _plt
import numpy as _np
from numpy import fft as _fft
import lmfit as _lmfit
from tqdm import... | jungmannlab/picasso | picasso/imageprocess.py | Python | mit | 3,919 | [
"Gaussian"
] | 09a4eb1c1490a750b47f9a5161b90f34c668534fe56cf6998838bf1022bcdbc0 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | ctk3b/mdtraj | mdtraj/tests/test_mdconvert.py | Python | lgpl-2.1 | 9,785 | [
"MDTraj",
"NetCDF"
] | 283a8a9661ce59621406ee50454eaeef4133dd3b31f50fff1e8b35053ff37874 |
#!/usr/bin/env python3
#* 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/lgp... | harterj/moose | python/moosesqa/test/test_SQAReport.py | Python | lgpl-2.1 | 4,138 | [
"MOOSE"
] | 00113b7dd02139ac9dec3776f26c359aecae168c292bc55f9f620c23cd7d4df8 |
"""
This script compares Amber energies from GMIN binding and two different ways via OpenMM.
GMIN Input files are coords.inpcrd, coords.prmtop and min.in. From Fortran code the energy is -21.7345926639 kcal/mol
One of the OpenMM calculation uses coords.inpcrd for coordinates and coords.prmtop for ff params.
T... | js850/PyGMIN | examples/amber/gmin_vs_openmm.py | Python | gpl-3.0 | 2,319 | [
"Amber",
"OpenMM"
] | 6b4518588797e6cc7014ab4ba53bfdd42d88ee88d987eaba6aaeba0daf92cdf8 |
# 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.
#
"""Example of connecting with exPASy and parsing SwissProt records."""
# biopython
from __future__ import print_function
from Bio import ExPASy, Sw... | updownlife/multipleK | dependencies/biopython-1.65/Doc/examples/swissprot.py | Python | gpl-2.0 | 766 | [
"Biopython"
] | 9b4c0b42c196e79467a7c11f368947c05559040ab25adbc86d89dffff747362f |
"""
This module adapted ANUGA
https://anuga.anu.edu.au/
"""
#FIXME: Ensure that all attributes of a georef are treated everywhere
#and unit test
import types, sys
import copy
import numpy as num
DEFAULT_ZONE = -1
TITLE = '#geo reference' + "\n" # this title is referred to in the test format
DEFAULT_PROJECTION = ... | bugobliterator/MAVProxy | MAVProxy/modules/lib/ANUGA/geo_reference.py | Python | gpl-3.0 | 16,841 | [
"NetCDF"
] | 7496fc55ce60765e7fb3a4f90fed04147852772eaca4ad923a13fa7e30e264af |
# Copyright 2017 Max Planck Society
# Distributed under the BSD-3 Software license,
# (See accompanying file ./LICENSE.txt or copy at
# https://opensource.org/licenses/BSD-3-Clause)
"""Training AdaGAN on various datasets.
Refer to the arXiv paper 'AdaGAN: Boosting Generative Models'
Coded by Ilya Tolstikhin, Carl-Joha... | tolstikhin/adagan | adagan_cifar.py | Python | bsd-3-clause | 7,802 | [
"Gaussian"
] | 2b9d42dfad5041956a5803f0ade684e40a47103e21bb135d18666ae8dd35d504 |
# 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_0161_bse_h2b_spin1_uhf_cis.py | Python | apache-2.0 | 2,081 | [
"PySCF"
] | 79be5b7cf75f24c63c6bac8a6cb4d2916f536ece45a25fae77bfed5c02a5cc31 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 2000
n = 1000
display = True
worldRank = ... | birm/Elemental | examples/interface/CPDense.py | Python | bsd-3-clause | 1,815 | [
"Gaussian"
] | ea39d4f2be566c4d51d02b20d88f8026081f5f5f223fa59a1225b63096d7ab17 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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
#... | amjames/psi4 | psi4/driver/qcdb/molparse/from_arrays.py | Python | lgpl-3.0 | 25,534 | [
"Psi4"
] | d6c1feb1232b0c275d06502e7e8e3634a8623408caecb0c69280e33aed81c05f |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Utilities for manipulating coordinates or list of coordinates, under periodic
boundary conditions or otherwise. Many of these are heavily vectorized in
numpy for performance.
"""
import itertools
import math
import nump... | vorwerkc/pymatgen | pymatgen/util/coord.py | Python | mit | 15,668 | [
"pymatgen"
] | a07eca6e9eb7fead688161827926e64de3d10f264906ecd4f500a50d2b13ee27 |
from math import sqrt, pi
import numpy as np
from gpaw.xc.gga import GGA
from gpaw.utilities.blas import axpy
from gpaw.fd_operators import Gradient
from gpaw.lfc import LFC
from gpaw.sphere.lebedev import weight_n
class MGGA(GGA):
orbital_dependent = True
def __init__(self, kernel, nn=1):
"""Meta ... | ajylee/gpaw-rtxs | gpaw/xc/mgga.py | Python | gpl-3.0 | 7,381 | [
"GPAW"
] | d0f7b99524cac289d1cd8451817afc27c515974f5d41d49cae3d4818e3b09025 |
import os
import sys
import subprocess
import shutil
import contextlib
import json
current_dir = os.path.dirname(__file__)
_base_dir = None
def which(cmd):
try:
return shutil.which(cmd)
except AttributeError:
import distutils.spawn
return distutils.spawn.find_executable(cmd)
def ... | vivsh/django-ginger | ginger/scripts/bootstrap.py | Python | mit | 6,698 | [
"GULP"
] | 79ea0f5b20ff96edc5db179d41916d787ab34d10a243415fccce57177b9fb7eb |
import os
import shutil
import argparse
import subprocess
def pg_ctl(database_path, database_version, mod='start'):
"""
Start/Stop PostgreSQL with variable data_directory.
mod = [start, end, restart, reload]
"""
pg_conf = '/etc/postgresql/%s/main/postgresql.conf' % database_version
new... | chambm/docker-galaxy-stable | galaxy/setup_postgresql.py | Python | mit | 3,592 | [
"Galaxy"
] | 250a538391f388d2bbb9f50f65ba9ff2fc54b8bc15b5e64ccacc599a38475fb6 |
# Copyright 2003-2009 by Bartek Wilczynski. All rights reserved.
# Copyright 2012-2013 by Michiel JL de Hoon. 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.
"""Tools for sequen... | zjuchenyuan/BioWeb | Lib/Bio/motifs/__init__.py | Python | mit | 18,757 | [
"Biopython"
] | 720df290cd36eabd90ac97ab99481506812c27bbbeaeffd4644a46b7e4f55e67 |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015 Nervana Systems Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# ... | chetan51/neon | examples/mnist_mlp.py | Python | apache-2.0 | 4,752 | [
"Gaussian"
] | 1cb77972b1dfc9ae54376d4be6469300c5660a2c4e5fd14f8f938759800eebb2 |
# 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... | capoe/espressopp.soap | src/interaction/HarmonicUnique.py | Python | gpl-3.0 | 3,896 | [
"ESPResSo"
] | f4258b413d94ff2ee692ea9566fcee7142bd65df2a3fc6fb29af89ea397743ea |
#!/usr/bin/env python
from traits.api import HasTraits, Instance, Array, Bool, Dict, \
on_trait_change, Delegate, List, Color, Any, Instance, Int, File, \
Button, Enum, Str, DelegatesTo, Property, CFloat,Range
from traitsui.api import View, Item, HGroup, VGroup, \
Group, Handler, HSplit, VSplit, RangeEd... | mattcieslak/DSI2 | dsi2/ui/ltpa_result.py | Python | gpl-3.0 | 9,331 | [
"Mayavi"
] | bccae8742838fc56d2cd570ef65dca4048cee2f9a433304c4c1c966ed4f81f4f |
#!/usr/bin/env python
#
# Appcelerator Titanium Module Packager
#
#
import os, subprocess, sys, glob, string
import zipfile
from datetime import date
cwd = os.path.abspath(os.path.dirname(sys._getframe(0).f_code.co_filename))
os.chdir(cwd)
required_module_keys = ['architectures', 'name','version','moduleid','descripti... | crissmoldovan/tisip | iphone/build.py | Python | mit | 8,643 | [
"VisIt"
] | 5cb5f150c9c6b45f36f2d8e9a53f5fffaed9205bee62384b8fb57b717ab30c54 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-bigquery-datatransfer | scripts/fixup_bigquery_datatransfer_v1_keywords.py | Python | apache-2.0 | 7,039 | [
"VisIt"
] | a37695b36847a28d959252322a12359b9d79620b7614b19fce5fad68e43bebca |
#!/usr/bin/env python
import sys
extras = {}
try:
from setuptools import setup
extras['zip_safe'] = False
if sys.version_info < (2, 6):
extras['install_requires'] = ['multiprocessing']
except ImportError:
from distutils.core import setup
setup(name='futures',
version='2.1.2',
descr... | santegoeds/pythonfutures | setup.py | Python | bsd-2-clause | 1,249 | [
"Brian"
] | 9dea5a6189ee511751c86af387d95cca7be69eb09dead531ed1cc79fe21e0596 |
import setuptools
with open("README.md") as fp:
long_description = fp.read()
setuptools.setup(
name="cdk",
version="0.0.1",
description="BGTools CDK App",
long_description=long_description,
long_description_content_type="text/markdown",
author="Peter Gorniak",
package_dir={"": "cdk"}... | sumpfork/bgtools_web | setup.py | Python | mit | 1,141 | [
"CDK"
] | 1da50106753ae8a7421e0e2f358362dbedafce55f75ee3f944814d02d7e329d5 |
from assembler import Assembler
from assembler import Form
from assembler import Kernel
from diagnostics import Verbose
from fem import QuadFE
from fem import DofHandler
from fem import Basis
from function import Constant
from function import Explicit
from function import Map
from function import Nodal
from gmrf im... | hvanwyk/quadmesh | experiments/optimal_control/ex03_pw_deterministic_1d.py | Python | mit | 6,517 | [
"Gaussian"
] | 146c25a37d378a15894b731140cb3f88e37a7f5d20f99ff34147ab3ab992e755 |
#!/usr/bin/env python3
""" Computer-based immigration office for Kanadia """
__author__ = 'Susan Sim'
__email__ = "ses@drsusansim.org"
__copyright__ = "2014 Susan Sim"
__license__ = "MIT License"
__status__ = "Prototype"
"""
The program is designed by Zhong Yan and Tao Ran,Liu. The basic function for this program ... | hebe889900/info1340_assignment2 | papers.py | Python | mit | 7,875 | [
"VisIt"
] | 2845a6aaff5591dc271874e9cf35a32a63da568687c9e628cbf7b174cf721849 |
#! /usr/bin/python
####################################################################
# MaterialsStudio Cell File To Abinit Config file Converter
# zhoubo
# 2006.9.26
####################################################################
import sys
import re
if __name... | qsnake/abinit | util/users/Cell2Abinit.py | Python | gpl-3.0 | 3,431 | [
"ABINIT"
] | 2fd7e3482f86c8ee587c365963d7b5e9cc9f720f60cb08f75d5be407d791d3a0 |
#! /usr/bin/env python
# coding:utf-8
# Author: bingwang
# Email: toaya.kase@gmail.com
# Copylight 2012-2012 Bing Wang
# LICENCES: GPL v3.0
__docformat__ = "epytext en"
"""
This program will take two fasta file as input,
use balst compare them and return
exact same pairs back as table.
>>> import compare2fsa
>>> c... | BingW/yeast_anno_pipe | src/compare2fsa.py | Python | gpl-3.0 | 1,914 | [
"BLAST"
] | bcd6c014ee8cab4e209f732765fb2a84be4e94f90fff8d427b8c9fd3d535dd9f |
"""
this file does variant calling for DNAseq
"""
#============= import required packages =================
import os
import sys,subprocess
sys.path.append('/home/shangzhong/Codes/Projects')
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from Modules.f00_Message import Message
from Modules.f01_l... | shl198/Projects | VariantCall/01_GATK_DNA_vari_call.py | Python | mit | 11,232 | [
"BWA"
] | abf14bad5be6bd7b8986d30d70a4e94407b6af721a6c008e44c23045dc4a9a27 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/gromacs/package.py | Python | lgpl-2.1 | 4,055 | [
"Gromacs"
] | 74b619122a3ae9fe6a328c64eecc7e5b7b90fbd83da2844a39e6c735197543c4 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Demonstrate how to extract polygonal cells with an implicit function
# get the interactor ui
# create a sphere source and actor
#
sphere = vtk.vtkSphereSource()
sphere.Se... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/Extraction/Testing/Python/extractPolyData.py | Python | bsd-3-clause | 2,894 | [
"VTK"
] | 327b036540f2bf38000799f5b9276fd412b09774fe986180471d5fe49e3219d0 |
#!/usr/bin/python
# This example shows how to implement deep linking (https://core.telegram.org/bots#deep-linking)
# with the pyTelegramBotAPI.
# Note: This is not a working, production-ready sample.
#
# In this example we are connecting a user account on a website with a Telegram bot.
# Implementing this will enable ... | sgomez/pyTelegramBotAPI | examples/deep_linking.py | Python | gpl-2.0 | 2,971 | [
"VisIt"
] | 41af199a480bfa3ced90c3f543cd873e8822bc1f114e3de09fe6c59f37d9cedc |
#!/usr/bin/env python
###########################################################################
## ##
## Language Technologies Institute ##
## Carnegie Mellon University ... | leahrnh/ticktock_text_api | galbackend_AHC.py | Python | gpl-2.0 | 20,555 | [
"Galaxy"
] | 0be422fecdce3d6a0a4cc8fb517a406f3bea0572e3e371d91aad439b4387343d |
# Copyright (C) 2012,2013,2016
# 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 ... | espressopp/espressopp | src/tools/replicate.py | Python | gpl-3.0 | 3,037 | [
"ESPResSo"
] | f759b0f98c1098e4ae3247dbae180f7296c8bccc98f10e340bfb2032476f6827 |
"""@camvtk docstring
This module provides helper classes for testing and debugging OCL
This module is part of OpenCAMLib (ocl), a toolpath-generation library.
Copyright 2010-2011 Anders Wallin (anders.e.e.wallin "at" gmail.com)
Published under the GNU General Public License, see http://www.gnu.org/licenses/
"""
#impo... | play113/swer | opencamlib-read-only/lib/pyocl.py | Python | mit | 2,483 | [
"VTK"
] | 402f9621398d2999f87d49576f2c18a7af35eb7f8e35c47376e039d7c5876344 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/core/AtomGroup.py | Python | gpl-2.0 | 2,443 | [
"MDAnalysis"
] | 90600d2b17b3cdef8b3088ea2b6e2b5c9d8864a0a185b077a251fbe7d5978a43 |
"""
.. versionadded:: v6r20
FTS3Agent implementation.
It is in charge of submitting and monitoring all the transfers. It can be duplicated.
::
FTS3Agent
{
PollingTime = 120
MaxThreads = 10
# How many Operation we will treat in one loop
OperationBulkSize = 20
# How many Job we will monit... | arrabito/DIRAC | DataManagementSystem/Agent/FTS3Agent.py | Python | gpl-3.0 | 16,959 | [
"DIRAC"
] | 3cf9e856c1996b41b0a283a175b71c9f4ad716c5c0869b066e7be9aa6a925d99 |
import sqlite3
from owade.constants import *
class GetChromeHistory:
def getChromeHistoryData(self, myPath):
"""
From https://github.com/OsandaMalith/ChromeFreak/blob/master/ChromeFreak.py CC license
"""
historyValues = {}
try:
sqlitePath = myPath + "/chro... | CarlosLannister/OwadeReborn | owade/fileAnalyze/historyChrome.py | Python | gpl-3.0 | 5,028 | [
"VisIt"
] | 5ba708168184ed06abdfe9379bbf6128364ab6963cb2ebdbfc49f9363f85ef4e |
from __future__ import print_function
from typing import cast, Any, Iterable, Mapping, Optional, Sequence, Tuple, Text
import mandrill
from confirmation.models import Confirmation
from django.conf import settings
from django.core.mail import EmailMultiAlternatives
from django.template import loader
from django.utils ... | isht3/zulip | zerver/lib/notifications.py | Python | apache-2.0 | 22,548 | [
"VisIt"
] | a3f1c82ce685e7dca8a1e342f96efcbe5e727a8d99dd51d7ff25e84b222b1f5b |
"""
Convenience routines for performing common operations.
@since: 0.28
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
import os
from zeroinstall import SafeException
DontUseGUI = object()
def should_use_gui(use_gui):
... | linuxmidhun/0install | zeroinstall/helpers.py | Python | lgpl-2.1 | 684 | [
"VisIt"
] | 8efb9674afbc24f91470b681fe47f9e69e188cd5451ecf6782998d5bcdaebf58 |
""" Frontend to MySQL DB AccountingDB
"""
__RCSID__ = "$Id$"
import datetime
import time
import threading
import random
from DIRAC.Core.Base.DB import DB
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.FrameworkSystem.Client.MonitoringClient import gMonitor
from DIRAC.Core.Utilities import List, ThreadSafe, Time... | arrabito/DIRAC | AccountingSystem/DB/AccountingDB.py | Python | gpl-3.0 | 66,426 | [
"DIRAC"
] | 1fc92955bdd050ab14ee6b97c21ed86cf9fcdda925c6ec77d3369760c4bc4e27 |
# -*- coding: utf-8 -*-
#This is generated code - do not edit
encoding = 'utf-8'
dict = {
' of ': ' van ',
'&About...': '&Info...',
'&Close Document': 'Document &sluiten',
'&Comment Region': '&Commentaar toevoegen',
'&Delete Window': '&Venster verwijderen',
'&Describe Action': 'Actie beschrijven',
'&Describe Key': 'Toe... | robmcmullen/peppy | peppy/i18n/nl.py | Python | gpl-2.0 | 10,493 | [
"Elk"
] | 6a1254bd41c493609545a7c1d3783c7ac5fce474a84eb2565c4525d06874e969 |
# BOLD monitoring example to demonstrate the two-input model
#
# please note: This example is just intented to demonstrate the coupling between the source and input variables.
# The coupling used in this script are not based on biological constraints.
#
# More details can be found in the recent art... | ANNarchy/ANNarchy | examples/bold_monitor/BOLD_two_inputs.py | Python | gpl-2.0 | 3,003 | [
"NEURON"
] | c02037a89b851eae13bde93ce1def93d7b16751c43e1709934b79cf40f7733e2 |
################################################################################
# Copyright (C) 2011-2013 Jaakko Luttinen
#
# This file is licensed under the MIT License.
################################################################################
"""
Functions for plotting nodes.
Functions
=========
.. curren... | SalemAmeen/bayespy | bayespy/plot.py | Python | mit | 35,411 | [
"Gaussian"
] | 9a927c2ed137b318bbe293d4a1a36c52a1f4e8b23bc514b59e18f6332fc8e841 |
# Copyright 2005-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# Author(s): Brian Harring (ferringb@gentoo.org)
import os as _os
import sys
from portage.cache import template
from portage import os
from portage.proxy.lazyimport import lazyimport
lazyimport(globals(),
'port... | ptisserand/portage | pym/portage/cache/fs_template.py | Python | gpl-2.0 | 2,810 | [
"Brian"
] | 69e384bd650b475d75dee78eed9a4e1612967b7b8b2bfd7b033393ad6a520484 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
JahnTeller distortion analysis.
"""
import os
import sys
import warnings
from typing import Any, Dict, Optional, Tuple, Union, cast
import numpy as np
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen... | vorwerkc/pymatgen | pymatgen/analysis/magnetism/jahnteller.py | Python | mit | 20,898 | [
"CRYSTAL",
"pymatgen"
] | 9a8bf630645b1b12a6671b8b15061d030e37dcedd7586d7a02721a299d160ad4 |
"""Alignment with SNAP: http://snap.cs.berkeley.edu/
"""
import os
from bcbio import bam, utils
from bcbio.distributed.transaction import file_transaction
from bcbio.pipeline import config_utils
from bcbio.ngsalign import novoalign, postalign
from bcbio.provenance import do
def align(fastq_file, pair_file, index_dir,... | gifford-lab/bcbio-nextgen | bcbio/ngsalign/snap.py | Python | mit | 2,111 | [
"Galaxy"
] | 58edf1719a611e4e1e257f1ca03f371a05c30453e5e2abd76d7b572e8678d2a9 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2015 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your option) any later... | chokribr/invenio | invenio/modules/search/walkers/elasticsearch.py | Python | gpl-2.0 | 5,833 | [
"VisIt"
] | 88e9bb668e4f8e882cd73756964a62ff218f69b321a4ad7bf7723f395637c923 |
import io
import pickle
import tempfile
import typing as t
from contextlib import contextmanager
from copy import copy
from copy import deepcopy
import pytest
from werkzeug import datastructures as ds
from werkzeug import http
from werkzeug.exceptions import BadRequestKeyError
class TestNativeItermethods:
def t... | pallets/werkzeug | tests/test_datastructures.py | Python | bsd-3-clause | 39,436 | [
"TINKER"
] | d96f4fe973f781eb660c69695e4808bf4729d762dd5323af3b29c43372af54c7 |
from eventlet import hubs
from eventlet.support import greenlets as greenlet
__all__ = ['Event']
class NOT_USED:
def __repr__(self):
return 'NOT_USED'
NOT_USED = NOT_USED()
class Event(object):
"""An abstraction where an arbitrary number of coroutines
can wait for one event from another.
Ev... | JeremyGrosser/python-eventlet | eventlet/event.py | Python | mit | 5,664 | [
"VisIt"
] | b3b91a2fd1f9abf1487e866bc9f1854d5b499f688125ced2064128cf564bb468 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# .. _salt-fingering-example:
#
# .. py:currentmodule:: dolfin_adjoint
#
# Generalised stability analysis of double-diffusive salt fingering
# =================================================================
#
# .. sectionauthor:: Patrick E. Farrell <patrick.farrell@maths... | pf4d/dolfin-adjoint | examples/salt-fingering/salt-fingering.py | Python | lgpl-3.0 | 13,660 | [
"ParaView"
] | b1e62a39f40b2d175a60fb96270ae57fd107c5a9f0b4b1ba3ecfe70bba44e51f |
#!/usr/bin/env python3
#* 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/lgp... | nuclear-wizard/moose | python/peacock/tests/input_tab/ParamsTable/test_ParamsTable.py | Python | lgpl-2.1 | 8,324 | [
"MOOSE"
] | 589435f89ac4d73afc483c504da112e0cd96a311711936214a33f7a256edf403 |
from nose.plugins.attrib import attr
from unittest import skipIf
import tempfile
import os
from openmoltools import utils
import numpy as np
import mdtraj as md
from distutils.spawn import find_executable
import tarfile
import pickle
import os
import numpy as np
@skipIf(find_executable('obabel') is None, 'You need o... | jchodera/openmoltools | openmoltools/tests/test_freesolv.py | Python | gpl-2.0 | 1,799 | [
"MDTraj"
] | f5254b102356136a998b4fb0f47e1bec31f2f27615540dec05c7ac411128550a |
# -*- coding: utf-8 -*-
import numpy as np
import abel
import matplotlib.pyplot as plt
IM = np.loadtxt("data/VMI_art1.txt.bz2")
legendre_orders = [0, 2, 4] # Legendre polynomial orders
proj_angles = np.arange(0, np.pi/2, np.pi/10) # projection angles in 10 degree steps
radial_step = 1 # pixel grid
smoothing = 1 #... | stggh/PyAbel | examples/example_linbasex_hansenlaw.py | Python | mit | 3,185 | [
"Gaussian"
] | 0b43f3529a01f6d1399211c027f61c1170806f8ac23ee0df368c673b25ad69fe |
"""
Quantum ESPRESSO basic parser
Author: Evgeny Blokhin
TODO: check ibrav settings, parsing might be wrong
"""
from __future__ import division
import os
import datetime, time
from numpy import dot, array, transpose, linalg
from tilde.parsers import Output
from tilde.core.electron_structure import Ebands
from ase i... | tilde-lab/tilde | tilde/parsers/QuantumESPRESSO/QuantumESPRESSO.py | Python | mit | 15,615 | [
"ASE",
"CRYSTAL",
"Quantum ESPRESSO"
] | 5d2b1508e1e41edf8506220b376c341897b00261c8319e478cc231c2cfdc0bc5 |
import unittest
import netCDF4
import os
test_ncdump="""netcdf ubyte {
dimensions:
d = 2 ;
variables:
byte ub(d) ;
ub:_Unsigned = "true" ;
byte sb(d) ;
// global attributes:
:_Format = "classic" ;
}
"""
test_ncdump2="""netcdf ubyte {
dimensions:
d = 2 ;
variables:
byte ub(d) ;
ub:_Unsigned = "true" ;
byte... | Unidata/netcdf4-python | test/tst_cdl.py | Python | mit | 1,517 | [
"NetCDF"
] | 32eb8336df4fe1b75a87ab1a10bc6df8442c40fda168ec68409f9dc30ce38544 |
# $Id$
#
# Copyright (C) 2015 Novartis Institute of BioMedical Research
# All Rights Reserved
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above co... | rvianello/rdkit | Code/GraphMol/FilterCatalog/Wrap/rough_test.py | Python | bsd-3-clause | 20,042 | [
"RDKit"
] | 558b6081df2d543882da25bbca550e20d1c880a51ed41b1f5ec0f7fe52d72ef9 |
"""
Single Bubble Model: Droplet simulations
=========================================
Use the ``TAMOC`` `single_bubble_model` to simulate the trajectory of a light
oil droplet rising through the water column. This script demonstrates the
typical steps involved in running the single bubble model.
It uses the ambient... | socolofs/tamoc | bin/sbm/drop.py | Python | mit | 2,035 | [
"NetCDF"
] | f516a16c8fb5bc50c270754b2d2925c72757a63258f90f6484e47f59b8445435 |
#! /usr/bin/env python
import sys
import os
import glob
import re
import yaml
from collections import namedtuple
def expandOsPath(path):
"""
To expand the path with shell variables.
Arguments:
- `path`: path string
"""
return os.path.expanduser(os.path.expandvars(path))
def genFilesWithPatter... | shenlab-sinai/chip-seq_preprocess | project/script/results_parser.py | Python | gpl-2.0 | 8,835 | [
"Bowtie"
] | da79b03f4af65a920445547b17ea2f8ad591ce1adeb4b9c837e5f1a276411569 |
"""
Acceptance tests for Studio related to the container page.
The container page is used both for display units, and for
displaying containers within units.
"""
from nose.plugins.attrib import attr
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.component_editor import ComponentEditorView
from .... | UQ-UQx/edx-platform_lti | common/test/acceptance/tests/studio/test_studio_container.py | Python | agpl-3.0 | 35,463 | [
"VisIt"
] | 195983e10d230d5018bf524140823d8a224ef304d41d6938375e8043f6b3a140 |
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