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#Copyright ReportLab Europe Ltd. 2000-2004
#see license.txt for license details
#history http://www.reportlab.co.uk/cgi-bin/viewcvs.cgi/public/reportlab/trunk/reportlab/platypus/paraparser.py
__version__=''' $Id: paraparser.py 3774 2010-09-08 15:11:10Z rgbecker $ '''
__doc__='''The parser used to process markup within ... | mattjmorrison/ReportLab | src/reportlab/platypus/paraparser.py | Python | bsd-3-clause | 42,578 | [
"VisIt"
] | 448a32c9790eb42b62214c72b519017a7597e92f128ffbae821dff5ff4d48b38 |
# 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 ... | fweik/espresso | testsuite/python/lb_pressure_tensor.py | Python | gpl-3.0 | 6,864 | [
"ESPResSo"
] | 753b2b2955b0532924eccaa7d2f4562f69ad1edfa8c80377dcb5c957b9f2dc83 |
#! RHF Hessian code
# -*- coding: utf-8 -*-
"""
This script calculates nuclear Hessians of RHF Wavefunction using
derivatives of one and two electron integrals obtained from PSI4
Reference: "Derivative studies in hartree-fock and moller-plesset theories",
J. A. Pople, R. Krishnan, H. B. Schlegel and J. S. Binkley
DO... | psi4/psi4 | samples/psi4numpy/rhf-hessian/input.py | Python | lgpl-3.0 | 10,290 | [
"Psi4"
] | 4c3ccc491bb87620398a4bccd9455bb9483fb3ff9c52513363ab39df25aee456 |
#!/usr/bin/env python
""" Token Pass
TokenPasser agents will send a token to each other. This will happen in a
random way. If the Spyse platform is distributed one can see the token
being sent from one system to another.
If the application is started with 'token' as argument then a t... | davidko/evolspyse | demo/token_pass.py | Python | lgpl-2.1 | 5,733 | [
"VisIt"
] | 7ee1dcee905e75c2d4a207991d274d043e441743c1d95b552f16144fd8838ad0 |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
For each block in a maf file (read from stdin) write a sequence of ints
corresponding to the columns of the block after applying the provided sequence
mapping.
The 'correct' number of species is determined by the mapping file, blocks not having
this number of species will... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_to_int_seqs.py | Python | bsd-3-clause | 1,049 | [
"Galaxy"
] | c9bef611aee0a90a917b7dcaae96c380f11f48580dcfdded267e4c49b3e42934 |
from mayavi.tools.mlab_scene_model import MlabSceneModel
from mayavi.core.ui.mayavi_scene import MayaviScene, \
DecoratedScene
from tvtk.pyface.scene_editor import SceneEditor
from mayavi.core.ui.engine_view import EngineView
from mayavi.core.ui.engine_rich_view import EngineRichView
| dmsurti/mayavi | mayavi/core/ui/api.py | Python | bsd-3-clause | 306 | [
"Mayavi"
] | 1511eb3a634f745f3316b4463383282f1c1974582d7f5c2694d124a881de9077 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# read data
#
reader ... | hlzz/dotfiles | graphics/VTK-7.0.0/IO/EnSight/Testing/Python/EnSightOfficeBin.py | Python | bsd-3-clause | 2,148 | [
"VTK"
] | 7e732d99a75791116354109a99a46a6e5a79d54ba16ac9fef679ffbae7752c8a |
""" generate a single-file self-contained version of py.test """
import py
import sys
def find_toplevel(name):
for syspath in py.std.sys.path:
base = py.path.local(syspath)
lib = base/name
if lib.check(dir=1):
return lib
mod = base.join("%s.py" % name)
if mod.che... | geraldoandradee/pytest | _pytest/genscript.py | Python | mit | 2,666 | [
"VisIt"
] | 2d15212bd6a41d9dacf27ec699d25ebe18c5eec3a249025d3c23308481ff762d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Fou... | andrebellafronte/stoq | stoqlib/domain/test/test_account.py | Python | gpl-2.0 | 16,556 | [
"VisIt"
] | 42db1be542876e7040d775e4d9d9ee9de1c6482273162ac781610feb898dd95e |
"""
Multivariate Conditional and Unconditional Kernel Density Estimation
with Mixed Data Types.
References
----------
[1] Racine, J., Li, Q. Nonparametric econometrics: theory and practice.
Princeton University Press. (2007)
[2] Racine, Jeff. "Nonparametric Econometrics: A Primer," Foundation
and Trends in Eco... | hlin117/statsmodels | statsmodels/nonparametric/kernel_density.py | Python | bsd-3-clause | 25,847 | [
"Gaussian"
] | 303ea6136d5594556daacd87a701fc55cca711f8b7e8e03c3929a1351f6689b6 |
#!/usr/bin/env python3
# Copyright 2021 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 la... | GoogleCloudPlatform/rad-lab | radlab-launcher/radlab.py | Python | apache-2.0 | 44,933 | [
"Elk"
] | de01b0ade0d196d5d8bc8e9e18a3f5a217eb238fbeadbf562d935d1e82c9ecda |
"""
Featurizer implementations used in ChemCeption and Smiles2Vec models.
SmilesToSeq featurizer for Smiles2Vec models taken from https://arxiv.org/abs/1712.02734
SmilesToImage featurizer for ChemCeption models taken from https://arxiv.org/abs/1710.02238
"""
__author__ = "Vignesh Ram Somnath"
__license__ = "MIT"
impo... | miaecle/deepchem | deepchem/feat/smiles_featurizers.py | Python | mit | 9,948 | [
"RDKit"
] | 818c615b857f30ccca875c8fcc0b31c24c992ffba349a2634441271844600162 |
#!/usr/bin/env python
#
# Copyright (c) 2016 Matt Davis, <mdavis@ansible.com>
# Chris Houseknecht, <house@redhat.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 ... | tsdmgz/ansible | contrib/inventory/azure_rm.py | Python | gpl-3.0 | 35,171 | [
"Galaxy"
] | 6ab964c12a4886b64e599e65b8c89fbc8cb1ad39e28af42243ec6c1b3c5f7903 |
# coding: utf-8
# # Diffusion computation
# https://github.com/alvason/diffusion-computation
#
# ### Lecture001 --- Diffusion equation with analytic solution
# In a physical intuitive vision, an analytic solution is a crystal clear way for viewing the core.
#
# During numerical computation development, an analy... | alvason/diffusion-computation | code/diffusion_analytic.py | Python | gpl-2.0 | 6,497 | [
"CRYSTAL"
] | 53b112950921f355be5c3f9f70fe3691b862d6dee038745d73d30d0b39cf3551 |
import os
import pathlib
from .. import ansys, flac3d, gmsh, mdpa, ply, stl, vtk, vtu, xdmf
from .._helpers import _filetypes_from_path, read, reader_map
def add_args(parser):
parser.add_argument("infile", type=str, help="mesh file to convert")
parser.add_argument(
"--input-format",
"-i",
... | nschloe/meshio | src/meshio/_cli/_binary.py | Python | mit | 1,821 | [
"VTK"
] | 7bff21636b79018ebeff101d26d8ae02dfc4d66205a4c5eff4c0e72aaf11098e |
#!/usr/bin/env python
"""rallpack3_moose_vs_neuron.py:
This file compares moose and neuron for rallpack3.
Last modified: Sun May 25, 2014 07:05AM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NCBS Bangalore", "Bhalla Lab"]
__li... | BhallaLab/benchmarks | Rallpacks/moose_vs_neuron/rallpack1/neuron_sim.py | Python | gpl-2.0 | 4,286 | [
"MOOSE",
"NEURON"
] | decc970cf1edc4235174f59a030d60d58c1860d4a2aa975413a5ec314a3e8f37 |
from aiida import load_dbenv
load_dbenv()
from aiida.orm import Code, DataFactory, load_node
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
import numpy as np
import os
codename = 'phonopy@stern'
code = Code.get_from_string(codename)
cell = [[ 3.1900000572, 0, 0],
... | abelcarreras/aiida_extensions | plugins/launcher/launch_phonopy_gan.py | Python | mit | 2,193 | [
"phonopy"
] | 0516ae0da5f7d89d110153d7f152d38e8f0ecb2de618dffcabe2ba27e0e95de1 |
#!/usr/bin/env python
"""
dirac-my-great-script
This script prints out how great is it, shows raw queries and sets the
number of pings.
Usage:
dirac-my-great-script [option|cfgfile] <Arguments>
Arguments:
<service1> [<service2> ...]
"""
__RCSID__ = '$Id$'
from DIRAC import S_OK, S_ERRO... | arrabito/DIRAC | docs/source/DeveloperGuide/AddingNewComponents/DevelopingCommands/dirac-my-great-script.py | Python | gpl-3.0 | 2,626 | [
"DIRAC"
] | d4823219790aa5fc44ef265999f2565c18863004fd45a0cfbacc9f32ea3900f3 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
from copy import deepcopy
from distutils.version import LooseVersion
import itertools as itt
from math import... | adykstra/mne-python | mne/cov.py | Python | bsd-3-clause | 74,094 | [
"Gaussian"
] | 210da8e29dc111a8b4c832a9fb3703c6955af2fb934a2b9a3fef09496d142759 |
import numpy as np
"""
A module which implements the continuous wavelet transform
---------------------------------------------------------
Code released under the BSD 3-clause licence.
Copyright (c) 2012, R W Fearick, University of Cape Town
All rights reserved.
Redistribution and use in source and binary forms, w... | gviejo/ThalamusPhysio | python/Wavelets.py | Python | gpl-3.0 | 16,624 | [
"Gaussian"
] | 8460a4739aa4d89153237f3eae96a1df070b9aed88add5a6b9af957320ed9a49 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
import os
from ddt import ddt, unpack, data
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf, skip
from selenium.webdriver.common.by import By
from selenium.webdriver.common.action_chains import ActionChains
from common... | TheMOOCAgency/edx-platform | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 51,462 | [
"VisIt"
] | 1d6708c61e1a441132286705d87d4924ff313ad045ee45c8820850726860da6d |
# --------------------------------------------------------
# Fast R-CNN
# Copyright (c) 2015 Microsoft
# Licensed under The MIT License [see LICENSE for details]
# Written by Ross Girshick
# --------------------------------------------------------
"""Transform a roidb into a trainable roidb by adding a bunch of metada... | CharlesShang/TFFRCNN | lib/roi_data_layer/roidb.py | Python | mit | 6,128 | [
"Gaussian"
] | 8f871ac4c7d9b6a27437d0a5f70a7fab63c98d89fde4189a28488f6cf8874adb |
# -*- coding: utf-8 -*-
"""Utility functions for plotting M/EEG data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Mainak Jas <mainak... | mne-tools/mne-python | mne/viz/utils.py | Python | bsd-3-clause | 92,378 | [
"Mayavi",
"VTK"
] | e47f869e0724ac0b4894dcfe4e88598f7150c89f2f7be8a822abcfe43a3fa30f |
"""
Beta diversity measures (:mod:`skbio.diversity.beta`)
=====================================================
.. currentmodule:: skbio.diversity.beta
This package contains helper functions for working with scipy's pairwise
distance (``pdist``) functions in scikit-bio, and will eventually be expanded
to contain pair... | johnchase/scikit-bio | skbio/diversity/beta/__init__.py | Python | bsd-3-clause | 6,715 | [
"scikit-bio"
] | efd695f35901e654b124ba321a877bed84b1d12991e9dee849cd151a9c652ff9 |
# this program corresponds to special.py
### Means test is not done yet
# E Means test is giving error (E)
# F Means test is failing (F)
# EF Means test is giving error and Failing
#! Means test is segfaulting
# 8 Means test runs forever
### test_besselpoly
### test_mathieu_a
### test_mathieu_even_coef
##... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/special/tests/test_basic.py | Python | apache-2.0 | 118,104 | [
"Elk"
] | 0acb0bf8b7a1e1af1a499a840de8ac904b4ca513f8c537d53cd4d93321c5ac66 |
import cv2
import numpy as np
import sys
import math
L = 256
def salt_and_pepper(src, a, b, Pa=0, Pb=255):
dst = np.copy(src)
for i in range(dst.shape[0]):
for j in range(dst.shape[1]):
if dst[i][j] == a:
dst[i][j] = Pa
elif dst[i][j] == b:
dst[i... | rerthal/mc920 | proj05/noise.py | Python | gpl-3.0 | 1,561 | [
"Gaussian"
] | 60e838949a7907a3bd96a9e0cb8da616119eb6e3dddd55ec00ac3e3226ca933a |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list ... | Microvellum/Fluid-Designer | win64-vc/2.78/python/lib/mimetypes.py | Python | gpl-3.0 | 20,781 | [
"NetCDF"
] | a3f4d0cc6e31c159cfd99d501c3a4bf0aa6fda10474257b7bcb0280f52eee1fb |
# 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 | regcontrol.py | Python | apache-2.0 | 2,633 | [
"Brian"
] | c015506398263833c395fa073c5dca8c483e91fce2a1691a1a66e91141e4ceb8 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
"""
Wannier90
=========
Wannier90 interoperability is mainly targeted at extracting
tight-binding models from Wannier90... | zerothi/sisl | sisl/io/wannier90/__init__.py | Python | mpl-2.0 | 433 | [
"Wannier90"
] | f5d8f54fa2d0a413b6e15ace774b276ee9fe344568bd4cb8d52eb544c8cc7c9f |
# -*- coding: utf-8 -*-
## Copyright 2015 Rasmus Scholer Sorensen, rasmusscholer@gmail.com
##
## This file is part of Nascent.
##
## Nascent 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 Foundati... | scholer/na_strand_model | nascent/graph_sim_nx/componentmgr.py | Python | gpl-3.0 | 97,518 | [
"Biopython"
] | 11c8bc9471279de855fde6a97bf57cb03338eb9ff1c4cc1380ac091f4859b103 |
# Copyright 2008 Brian Boyer, Ryan Mark, Angela Nitzke, Joshua Pollock,
# Stuart Tiffen, Kayla Webley and the Medill School of Journalism, Northwestern
# University.
#
# This file is part of Crunchberry Pie.
#
# Crunchberry Pie is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | brianboyer/newsmixer | social/questions/urls.py | Python | gpl-3.0 | 1,307 | [
"Brian"
] | 42dba07f49aff76badd62385e38fc09a0765d2e9316208bd1170e764df5eb992 |
# 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 | eim/models/rejection_sampling.py | Python | apache-2.0 | 6,591 | [
"Gaussian"
] | dd1d7f3dc8030081bb0bd1ebe164886e893f5dbf81cc9d94b7c1097f07f89d0c |
#!/usr/bin/env python
import numpy as np
import numpy.random as rn
import matplotlib.pyplot as plt
from Environment import Environment
from NeuronNetwork import NeuronNetwork
from IzhikevichLayer import IzhikevichLayer
motor_max = 40
wheel_velocity_min = 0.025
wheel_velocity_max = wheel_velocity_min + wheel_velocity... | lawrencejones/neuro | iz/BraitenburgVehicleDemo.py | Python | gpl-3.0 | 6,020 | [
"NEURON"
] | 9cf56bb2776261a56f9241672e6a0f057cf4e800f87166a1647e033c8c495a15 |
# Copyright 2013-2021 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 RLdheatmap(RPackage):
"""Graphical Display of Pairwise Linkage Disequilibria Between SNPs
... | LLNL/spack | var/spack/repos/builtin/packages/r-ldheatmap/package.py | Python | lgpl-2.1 | 1,552 | [
"Bioconductor"
] | 96672e8856b54ee2d765f5758914a701574b7df7b1f33644dedd431f746d9d0b |
import logging
import os
import pandas as pd
import riboutils.ribo_filenames as filenames
logger = logging.getLogger(__name__)
class _return_key_dict(dict):
def __missing__(self,key):
return key
###
# The following labels are used to group similar ORF types.
###
orf_type_labels_mapping = {
'cano... | dieterich-lab/riboseq-utils | riboutils/ribo_utils.py | Python | mit | 82,716 | [
"pysam"
] | 7837dcb5ec2503668b4c90b5a87659de31057c10892517f11da358e65886ac47 |
import numpy as np
from PyQt4.QtGui import QIntValidator, QDoubleValidator, QApplication, QSizePolicy
from orangewidget import gui
from orangewidget.settings import Setting
from oasys.widgets import widget
import orangecanvas.resources as resources
import sys
import os
from crystalpy.diffraction.DiffractionSetupSweeps ... | edocappelli/oasys-crystalpy | orangecontrib/oasyscrystalpy/widgets/elements/CrystalCalculator.py | Python | mit | 24,535 | [
"CRYSTAL"
] | 4222c0f54a4e638d651a64f7a985abf3e64c1eb87f108b5c9d961ad143e14dd8 |
from libmproxy.protocol.http import HTTPResponse
from netlib.odict import ODictCaseless
"""
This module redirects all requests to a SMB server (Redirect to SMB)
Developed by Brian Wallace @botnet_hutner
"""
def start(context, argv):
if len(argv) != 2 and len(argv) != 3:
raise ValueError('Usage: -s "redir... | CylanceSPEAR/SMBTrap | external_project_modules/mitmproxy/smbtrap-mitmproxy-inline.py | Python | mit | 1,105 | [
"Brian"
] | c33b24d52b651a108fbca4480f38cefce3a6643391f398ea502a480240e06ada |
"""
Tests the server compute capabilities.
"""
import pytest
import qcfractal.interface as ptl
from qcfractal import testing
from qcfractal.testing import fractal_compute_server, test_server, reset_server_database, using_psi4, using_rdkit
bad_id1 = "000000000000000000000000"
bad_id2 = "000000000000000000000001"
de... | psi4/DatenQM | qcfractal/tests/test_compute.py | Python | bsd-3-clause | 18,820 | [
"Psi4",
"RDKit"
] | 45722df9ff62a2e434e7246d5b58c5f844ce62f7fdab1955972d4db07fa03093 |
#!/usr/bin/python
import socket
import ssl
import os
import re
import time
import sys
import string
import hashlib
import traceback
import irc
import getpass
from threading import Thread
from threading import RLock as Lock
import Queue
import chardet
import modjson
dec = modjson.ModJSONDecoder()
enc = modjson.ModJSONE... | shersonb/pyIRC | bouncer.py | Python | mit | 61,868 | [
"Brian"
] | cfd5b8aabf1ee6085f2a4c47d35d9ff63749514fd4a69233bbc3bd381b0d188f |
#!/usr/bin/env python
''' Example Usage of ISAM2 Fixed-Lag Smoother Class '''
# Author: Nick R. Rypkema (rypkema@mit.edu)
# License: MIT
import time
import math
import numpy as np
import matplotlib.pyplot as plt
from isam_fixed_lag_smoother import Noise1D, Noise2D, Noise3D
from isam_fixed_lag_smoother import priorFa... | spillai/pygtsam | examples/test_isam_fixed_lag_smoother.py | Python | mit | 4,591 | [
"Gaussian"
] | c5ace2055345bd65683dda9de1fbcc80e58bb8db42cb25aaf54fe5e8b512026e |
"""Traits-based GUI for head-MRI coregistration"""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
from ..externals.six.moves import queue
import re
from threading import Thread
import warnings
import numpy as np
from scipy.spatial.distance import cdist
# allow import... | jaeilepp/eggie | mne/gui/_coreg_gui.py | Python | bsd-2-clause | 54,493 | [
"Mayavi"
] | 6905479bdde27327633abcd4b20844853848c8fe8b069745e016a6ff65d80115 |
# Copyright (C) 2012-2016
# Max Planck Institute for Polymer Research
# Copyright (C) 2008-2011
# 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 the GNU Gen... | kkreis/espressopp | src/integrator/LBInitConstForce.py | Python | gpl-3.0 | 2,224 | [
"ESPResSo"
] | 9c44a901c779df30b15799ff2c15a4184bcad51405c1606e910367a04e95648e |
import numpy
from proteus import *
from proteus.default_p import *
from math import *
from proteus.mprans import VOF, NCLS, VOS3P
"""
Linear advection of a guassian with periodic bcs
"""
nd = 2#number of space dimensions
#constant velocity
velocity = numpy.array([1.0,1.0])
if nd == 3:
velocity = numpy.array([1.0,... | erdc/proteus | proteus/tests/periodic/la_periodicGauss_p.py | Python | mit | 5,749 | [
"Gaussian"
] | c32ab73ee1b88b62670a50abbff403810032ffc659a9cede71c19e3b78c429f7 |
# -*- coding: utf-8 -*-
# Part of Odoo. See LICENSE file for full copyright and licensing details.
import random
import requests
import string
from lxml import html
from werkzeug import urls
from odoo import tools, models, fields, api, _
from odoo.exceptions import UserError
from odoo.osv import expression
URL_MAX_... | jeremiahyan/odoo | addons/link_tracker/models/link_tracker.py | Python | gpl-3.0 | 12,385 | [
"VisIt"
] | 65cf05d93a52faea049d523d75fe036a1f3a300e8c0304e0e8388badb53161cf |
"""A Skeleton HTML page template, that provides basic structure and utility methods.
"""
##################################################
## DEPENDENCIES
import sys
import os
import os.path
from os.path import getmtime, exists
import time
import types
import __builtin__
from Cheetah.Version import MinCompatibleVe... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Templates/SkeletonPage.py | Python | gpl-3.0 | 10,055 | [
"VisIt"
] | 51ebb810082e7030f568009af9ee256e597c0a85f986b4f24583e7854f0efcb7 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
import os
import os.path as op
import sys
sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from goatools.obo_parser import GODag, GraphEngines
if __name__ == '__main__':
import optparse
p = optparse.OptionParser("%prog [obo_file]")
p.add_option("--des... | mfiers/goatools | scripts/plot_go_term.py | Python | bsd-2-clause | 2,049 | [
"Cytoscape"
] | eb289ab56cb38fed6993310cfa773f5419e835707137c9532ddbb15d4159a57a |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
from math import sqrt, cos, sin
import numpy as np
from gpaw.spherical_harmonics import Y
s = sqrt(0.5)
t = sqrt(3) / 3
# Points on the unit sphere:
sphere_lm = [ \
np.array([(1, 0, 0)]), # s
np.array([(1, 0, 0)... | qsnake/gpaw | gpaw/rotation.py | Python | gpl-3.0 | 1,744 | [
"GPAW"
] | 6c929d0b778bf881a0b66f1244e655cb6b4cf81757c74876768e514b5cf8329a |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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 without restriction,
# including without... | digitalbitbox/electrum | plugins/trustedcoin/qt.py | Python | mit | 10,838 | [
"VisIt"
] | 8e36aa3452fbd6dc5195ccbba0c30eb65c4c70d2d07fb07061db33e341b62b41 |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | lach76/scancode-toolkit | src/extractcode/archive.py | Python | apache-2.0 | 24,679 | [
"VisIt"
] | a5ef77194466e68309e9cf8445e817f63ea2a117dd44ff017208576443089d22 |
import numpy as np
from numpy import ix_
import xarray as xr
import os
from oggm import cfg, utils
from oggm.cfg import G, SEC_IN_YEAR, SEC_IN_DAY
def filter_ice_border(ice_thick):
"""Sets the ice thickness at the border of the domain to zero."""
ice_thick[0, :] = 0
ice_thick[-1, :] = 0
ice_thick[:, ... | OGGM/oggm | oggm/core/sia2d.py | Python | bsd-3-clause | 15,221 | [
"NetCDF"
] | 3f6f76ab8ef61fcbac5b47f45799cffbb7f7cbe2ca01159964ee53b35b48f0f6 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function
import numpy as np
import tensorflow as tf
from tensorflow.contrib.layers.python.layers import regularizers
from niftynet.engine.application_initializer import GlorotUniform
from niftynet.layer.convolution import ConvolutionalLayer as Conv... | NifTK/NiftyNet | niftynet/network/interventional_dense_net.py | Python | apache-2.0 | 12,464 | [
"Gaussian"
] | 66aa5a70d6b83847a2da175e27ed4d0234db25833ad93e5ac6b858ddd69ef0c7 |
"""Notifications for Android TV notification service."""
import base64
import io
import logging
import requests
from requests.auth import HTTPBasicAuth, HTTPDigestAuth
import voluptuous as vol
from homeassistant.components.notify import (
ATTR_DATA,
ATTR_TITLE,
ATTR_TITLE_DEFAULT,
PLATFORM_SCHEMA,
... | tboyce021/home-assistant | homeassistant/components/nfandroidtv/notify.py | Python | apache-2.0 | 9,890 | [
"Amber"
] | 84e0802e2adfd04bbcc0623d137c523d1f01440a906f02c4a03d1f3722126209 |
# -*- 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 publi... | thica/ORCA-Remote | src/ORCA/widgets/FileBrowser.py | Python | gpl-3.0 | 6,800 | [
"ORCA"
] | cbb91f60d16860619bdb76274630a0b624b13bcef3d1fc93c714b4de137e8c25 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/ajax/about.py | Python | gpl-2.0 | 8,779 | [
"VisIt"
] | ce76ff1c9e7cf8adcc51f9895c4c938555e28b348cfcda805ef81bd5a6790506 |
# Modified from function.py ---
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import moose
simtime = 1.0
def test_example():
moose.Neutral('/model')
function = moose.Function('/model/function')
function.c['c0'] = 1.0
function.c['c1'] = 2.0
#function.x... | dilawar/moose-core | tests/core/test_function_example.py | Python | gpl-3.0 | 3,483 | [
"MOOSE"
] | d66c4ef9419cfe6d836dfbc167b7c19a6de7bd65b05cdbd8f832ae5ebf7ce738 |
# vclamp.py ---
#
# Filename: vclamp.py
# Description:
# Author:
# Maintainer:
# Created: Sat Feb 2 19:16:54 2013 (+0530)
# Version:
# Last-Updated: Tue Jun 11 17:35:20 2013 (+0530)
# By: subha
# Update #: 178
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#... | dilawar/moose-full | moose-examples/snippets/vclamp.py | Python | gpl-2.0 | 4,395 | [
"MOOSE"
] | 2784ac8f109589486de53382d93673e0fd3585187b869ac6b1256f04dcd13da1 |
#! /usr/bin/python
import os
SCRIPT_PATH = os.path.dirname(os.path.realpath(__file__))
import sys
sys.path.append(SCRIPT_PATH + '/../src/')
import re;
import subprocess
import multiprocessing
import getpass
from time import gmtime, strftime
from dataspec import *
ASSEMBLER_TYPE = 'nonhybrid'; # hybrid or nonhybr... | kkrizanovic/DNAssMark | wrappers/wrapper_lqs.py | Python | mit | 42,870 | [
"BWA",
"BioPerl",
"Biopython",
"pysam"
] | 5837bda516dc13bcc7706af159d51ad1db3722d13916bde9310402f335873f50 |
from random import random
from ase.io import write
from ase.optimize import BFGS
from ase.calculators.emt import EMT
from ase.ga.data import DataConnection
from ase.ga.population import Population
from ase.ga.standard_comparators import InteratomicDistanceComparator
from ase.ga.cutandsplicepairing import CutAndSpliceP... | askhl/ase | doc/tutorials/ga/basic_example_main_run.py | Python | gpl-2.0 | 3,182 | [
"ASE"
] | 25142bee3e05468428ea6a20a181036cb3ef1aea73e6af6e604a0c40778be6d2 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Part of the PsychoPy library
# Copyright (C) 2002-2018 Jonathan Peirce (C) 2019-2022 Open Science Tools Ltd.
# Distributed under the terms of the GNU General Public License (GPL).
"""Converting code parameters and components from python (PsychoPy)
to JS (ES6/PsychoJS)
"... | psychopy/psychopy | psychopy/experiment/py2js.py | Python | gpl-3.0 | 7,711 | [
"VisIt"
] | 46314f456082b42f80c7491f1233147bf81ab4fe9569a633941e432878da3b57 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
Related scripts for the HLI-STR (TREDPARSE) paper.
"""
import os.path as op
import os
import csv
import sys
import vcf
import logging
import shutil
import json
import numpy as np
import pandas as pd
from collections import defaultdict
from random import sample
from py... | tanghaibao/jcvi | jcvi/projects/str.py | Python | bsd-2-clause | 67,829 | [
"BWA",
"pysam"
] | e5c749f5808f73408ad397add5048a20793c70d2c52aae7ece6452f3b5c5a293 |
# -*- coding: utf-8 -*-
# moose.py ---
#
# Filename: moose.py
# Description: THIS IS OUTDATED CODE AND KEPT FOR HISTORICAL REFERENCE
# moose.py in this directory is the replacement for this
# script.
#
# Author: Subhasis Ray
# Maintainer:
# Copyright (C) 2010 Subhasis Ray, all rights reserved.... | upibhalla/moose-core | python/moose/alternate.py | Python | gpl-3.0 | 39,839 | [
"MOOSE"
] | a233b9a15149a6d1cc053eac90a1da9649edb48c9d92216e798d752d6a96e26d |
#!/usr/bin/env python
# pmx Copyright Notice
# ============================
#
# The pmx source code is copyrighted, but you can freely use and
# copy it as long as you don't change or remove any of the copyright
# notices.
#
# ----------------------------------------------------------------------
# pmx is Copyright (C... | dseeliger/pmx | scripts/mutate.py | Python | lgpl-3.0 | 18,272 | [
"Amber",
"CHARMM"
] | 8e2541c5329f63d64dc0e59e55149715ebafb2c3c7794e6fe51d1f15ad567f82 |
"""
Utility functions for analysis of MRS data.
"""
import warnings
import numpy as np
import scipy.linalg as la
import scipy.stats as stats
import nitime.timeseries as nts
"""
lowess: Locally linear regression
==================================
Implementation of the LOWESS algorithm in n dimensions.
[FHT] Frie... | rhancockn/MRS | MRS/utils.py | Python | mit | 16,294 | [
"Gaussian"
] | 5252eb47273bbab5ca3d6446e1d7fd57ba50054a6952a8daadfc8d0b22292743 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import os
import random
import unittest
import json
import six
from monty.os.path import which
from pymatgen import Lattice, PeriodicSite
from monty.json impor... | matk86/pymatgen | pymatgen/transformations/tests/test_standard_transformations.py | Python | mit | 19,196 | [
"VASP",
"pymatgen"
] | b72f9bd726398941a83a0123e1b0a3d4ac8a2f5427b56c58bf62a909e76ddd72 |
'''
Second numerical example for the No-Regret work
@author: Maximilian Balandat, Walid Krichene
@date: Oct 9, 2014
'''
# from ContNoRegret import Domain, GaussianLossFunction, Problem
#
# # define some parameters
# T = 0
#
# # Create a domain
# S = Domain(parameters)
#
# # Create a list of loss functions
# loss... | Balandat/cont_no_regret | old_code/CNR_example2.py | Python | mit | 2,161 | [
"Gaussian"
] | a6323be93d5893ae4ba27a03130d34caf30f9befbfe8b2f1b4b668ec4bab2701 |
#!/usr/bin/env python2.7
from bap import bil
from bap import adt
from functools import partial
from model import BapInsn
from bitvector import ConcreteBitVector
import collections
class Memory(dict):
def __init__(self, fetch_mem, initial=None):
self.fetch_mem = fetch_mem
if initial is not None:
self.u... | KernelAnalysisPlatform/KlareDbg | tracers/concrete_executor/concrete_execution.py | Python | gpl-3.0 | 9,870 | [
"VisIt"
] | f738aa697087d28b3385b64ac72e57bf31b8960df8a2a781b89fdef7f5ca9bfa |
#!/usr/bin/env python
"""
Module merges a list a bam file sharing the same read group.
"""
import argparse
import pysam
import os
def get_bam_pairs(bams):
"""
Function returns pairs of bam files because sample ID relies
on samples being encoded with a '.'
@bams A List of Bam files.
... | smilefreak/ancient_dna_pipeline | python_scripts/merge_bams.py | Python | mit | 1,926 | [
"pysam"
] | 23b1ad8bba6be654ca1a3f505a318c9b3b7cd0fa09754def806fa28d8ee80889 |
# Copyright (C) 2018 Henrique Pereira Coutada Miranda
# All rights reserved.
#
# This file is part of yambopy
#
"""
This file contains classes and methods to generate input files
The FiniteDifferencesPhononFlow
"""
from qepy.pw import PwIn
from qepy.ph import PhIn
from qepy.pwxml import PwXML
from qepy.lattice import... | alexmoratalla/yambopy | yambopy/io/factories.py | Python | bsd-3-clause | 24,388 | [
"Yambo",
"pymatgen"
] | 552ad34b441c9f0ec9a774a2f4fe9dd5cecb75a9a70b182f938b10c97237d674 |
"""
IODINE FRANCK-CONDON FACTOR CALCULATOR
AND VIBRONIC SPECTRUM PREDICTOR
Uses a Morse potential formalism to calculate
the Franck-Condon factors for the X-->B
vibronic transition for iodine.
Experimental data taken from NIST.
Requires Robert Johansson's "wavefunction"
library, found here:
https://github.com/jrjo... | nseifert/oddities | chemistry/iodine_fc_vibronic_spec.py | Python | mit | 7,198 | [
"Gaussian"
] | 0ecaf9b1f5ebfeb063e75958b4d1cc742c66de29ff2e1f7937735a08f960fae3 |
#!/usr/bin/env python
"""Classes for storing and manipulating a phylogenetic tree.
These trees can be either strictly binary, or have polytomies
(multiple children to a parent node).
Trees consist of Nodes (or branches) that connect two nodes. The Tree can
be created only from a newick formatted string read either fr... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/cogent/core/tree.py | Python | mit | 85,847 | [
"VisIt"
] | bbc6c222f469ae30c03d77b53a923169e2f437bb78aeae83eaa9988b98b33680 |
#-*- coding: utf-8 -*-
#
# test webfs_upload.py
# PV` Created on 26/09/2015.
#
# Bases:
#---------------------------------------------------
# 2006/02 Will Holcomb <wholcomb@gmail.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# Licen... | pvvx/RTL00_WEB | tools/webfs/py/webfs_upload1.py | Python | unlicense | 5,374 | [
"Brian"
] | db2d39daca3b2c3edb8738b56e7e7ddb574724fb4f60d0ccccf32741c3686b41 |
import py
import sys
@py.test.mark.parametrize('name', [x for x in dir(py) if x[0] != '_'])
def test_dir(name):
obj = getattr(py, name)
if hasattr(obj, '__map__'): # isinstance(obj, Module):
keys = dir(obj)
assert len(keys) > 0
print (obj.__map__)
for name in list(obj.__map__)... | thiagopnts/servo | tests/wpt/web-platform-tests/tools/third_party/py/testing/root/test_py_imports.py | Python | mpl-2.0 | 1,977 | [
"VisIt"
] | cefb74819852b367800f3c68066e2f795cb1ee6ceb082e5b9f07e3ea22bc14bf |
#!/usr/bin/env python
import glob
import os
import defopt
import numpy as np
import pandas as pd
import xarray as xr
import data.observational
from data.observational import DataType, Platform, Sample, Station
# These files were created by our scripts so they don't have nice attributes
# like standard_name, etc.
# ... | DFO-Ocean-Navigator/Ocean-Data-Map-Project | scripts/data_importers/concepts_drifter.py | Python | gpl-3.0 | 4,495 | [
"NetCDF"
] | c68edb8f7a1f8f84e83e1c00e327b469ee7713b5ab6452f5b05e8f2043ccf7ff |
"""
Evolutionary statistics (:mod:`skbio.stats.evolve`)
===================================================
.. currentmodule:: skbio.stats.evolve
This package contains statistics pertaining to phylogenies and evolution.
Cophylogenetic methods
----------------------
These functions test for correlation between phylo... | jdrudolph/scikit-bio | skbio/stats/evolve/__init__.py | Python | bsd-3-clause | 1,075 | [
"scikit-bio"
] | 8daac5ce5ec843e5aef70f1a40b5198cd449b244ece2aac5b8b27a54fd68ccc3 |
# -*- coding: utf-8 -*-
#
# license: AGPLv3, see LICENSE for details. In addition we strongly encourage
# you to buy us beer if we meet and you like the software.
"""Tests for session."""
from bson import ObjectId
from passlib.context import CryptContext
from passlib.hash import pbkdf2_sha256
from amivapi.au... | amiv-eth/amivapi | amivapi/tests/auth/test_sessions.py | Python | agpl-3.0 | 9,571 | [
"VisIt"
] | ae04327950acbcd6b77b3158f5eef393dfea4ad0494b0b2deb26c55bea01cc92 |
"""
This is used to test the ElasticSearchDB module. It is used to discover all possible changes of Elasticsearch api.
If you modify the test data, you have to update the test cases...
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# TODO: move to pytes... | yujikato/DIRAC | tests/Integration/Core/Test_ElasticsearchDB.py | Python | gpl-3.0 | 21,505 | [
"DIRAC"
] | 253e03c9dd89235f565641ce6426922898acaebaa38ca9134beb292c7e7303e0 |
def get_words():
return """abacus
abased
abases
abated
abates
abbess
abbeys
abbots
abduct
abhors
abided
abides
abject
abjure
ablaze
ablest
abloom
aboard
abodes
aborts
abound
abrade
abroad
abrupt
absent
absorb
absurd
abused
abuser
abuses
acacia
accede
accent
accept
access
accord
accost
accrue
accuse
acetic
achier
achin... | ianmiell/shutit | shutit_assets.py | Python | mit | 50,564 | [
"CASINO",
"Galaxy",
"Jaguar",
"NEURON",
"SIESTA",
"TINKER"
] | b9c4dbcb16fb7ccd30ef39684f30ccc098005569bd85842a8a086a4bd11f6e29 |
"""
Acceptance tests for Content Libraries in Studio
"""
from ddt import ddt, data
from nose.plugins.attrib import attr
from flaky import flaky
from .base_studio_test import StudioLibraryTest
from ...fixtures.course import XBlockFixtureDesc
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.utils ... | RPI-OPENEDX/edx-platform | common/test/acceptance/tests/studio/test_studio_library.py | Python | agpl-3.0 | 28,099 | [
"VisIt"
] | 00d78ecc983b2d92a05ad1807b7c13e2a933996fd76614cd307f8849e9533720 |
'''
Created on 2012-11-10
@author: Andre R. Erler
'''
## imports
from numpy import array, arange, zeros, diff
import os
import re
# netcdf stuff
from netcdf import Dataset, add_coord, copy_dims, copy_ncatts, copy_vars
# data root folder
from socket import gethostname
hostname = gethostname()
if hostname=='komputer':... | aerler/WRF-Tools | Python/archive/avgWRF_1979.py | Python | gpl-3.0 | 8,599 | [
"NetCDF"
] | 36dc165a54c5113cda006a96d43ea050607e213cdf74b32e058af03875f9dac0 |
# $Id$
#
# Copyright (C) 2002-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" exposes a class for... | jandom/rdkit | rdkit/Chem/FragmentMatcher.py | Python | bsd-3-clause | 2,262 | [
"RDKit"
] | ba304ddd5169f06035ad3ff7ccb3e5febdf6498b0b70b63a4aacd0ea9c91f0b7 |
'''
This job class should not be used to create jobs. It shouldn't need changes either.
Use L{UserJob} or L{ProductionJob}.
@author: Stephane Poss
'''
from DIRAC.Interfaces.API.Job import Job as DiracJob
from DIRAC.Core.Utilities.PromptUser import promptUser
from DIRAC.Core.... | sposs/DIRACInterfaceDoc | code/Interfaces/API/Job.py | Python | gpl-2.0 | 12,765 | [
"DIRAC"
] | aeac9b2be2937ff5bedd518deaea74ba3935a78ef6e4cd84f16c6de5f124d5e5 |
tests = [("python", "UnitTestChem.py", {}), ("python", "UnitTestChemv2.py", {}),
("python", "UnitTestChemAtom.py", {}), ("python", "UnitTestChemBond.py", {}),
("python", "UnitTestChemSmarts.py", {}), ("python", "UnitTestFragmentDescriptors.py", {}),
("python", "UnitTestGraphDescriptors_2.py",... | ptosco/rdkit | rdkit/Chem/test_list.py | Python | bsd-3-clause | 2,676 | [
"RDKit"
] | 820749bae5ef71966df74ebbb5cba9edcc9c9e2b1a16e56322fc0b8dd0ad5a58 |
"""SAMPLE ENTROPY
---------------------------------------------------------------------------
Last revised: 19 May 2016 (by joe@kinsa.us)
- Moved functions out of the init method and into separate modules
- Revised normalize data to more closely match the original C script;
fixing some looping and mathematical bugs... | jbergantine/sampen | sampen/__init__.py | Python | gpl-2.0 | 1,513 | [
"VisIt"
] | d42ad03934e25b4ef5bb4162102c5f0726596c7eb082e4d0914ebf129d551053 |
#
# Copyright (C) 2003, 2004 Norwegian University of Science and Technology
# Copyright (C) 2006, 2007, 2009, 2011, 2013 UNINETT AS
#
# This file is part of Network Administration Visualized (NAV).
#
# NAV is free software: you can redistribute it and/or modify it under
# the terms of the GNU General Public License ver... | alexanderfefelov/nav | python/nav/web/__init__.py | Python | gpl-2.0 | 2,406 | [
"VisIt"
] | ddcd37bfbcbe57e1954c7fc95325614095610f4697f4f1874428f9fd5e315ce3 |
from ase.parallel import paropen
from ase.units import Hartree
from gpaw.xc.rpa import RPACorrelation
rpa1 = RPACorrelation('N.gpw', txt='rpa_N.txt')
rpa2 = RPACorrelation('N2.gpw', txt='rpa_N2.txt')
E1_i = rpa1.calculate(ecut=400)
E2_i = rpa2.calculate(ecut=400)
f = paropen('rpa_N2.dat', 'w')
for ecut, E1, E2 i... | robwarm/gpaw-symm | doc/tutorials/rpa/rpa_N2.py | Python | gpl-3.0 | 406 | [
"ASE",
"GPAW"
] | 5ea158c3e8c64570e53f15486004f9378897a2cb425ba1719e10277bfbcf033f |
"""
This module contains the objective function used by Spearmint
when searching for good hyperparameters.
In short, the objective function is the Re(r) where
r is a complex number such that exp(r * t) is the
best fit to the autocorrelation
"""
import numpy as np
import pickle
import os
import tensorflow as tf
i... | rueberger/MJHMC | mjhmc/search/objective.py | Python | gpl-2.0 | 8,155 | [
"Gaussian"
] | adf2c7b1bc3c39614da21aed808f06b65200a4db070788bba5fc3c5bdefb7233 |
"""
Module for three dimensional baroclinic solver
"""
from __future__ import absolute_import
from .utility import *
from . import shallowwater_eq
from . import momentum_eq
from . import tracer_eq
from . import turbulence
from . import coupled_timeintegrator
import thetis.limiter as limiter
import time as time_mod
impo... | tkarna/cofs | thetis/solver.py | Python | mit | 64,942 | [
"VTK"
] | 23616de1e13e03a2ff480646232036fed6301da821dc1c2b6e606ca96b8f4fc0 |
# $Id$
#
# Copyright (C) 2007 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import unittest
import doctest
from rdkit.DataStruct... | bp-kelley/rdkit | rdkit/DataStructs/UnitTestDocTests.py | Python | bsd-3-clause | 2,982 | [
"RDKit"
] | 762d147a005d66147eed076e4b46c8b685fecaf87478fe867c8a3c4b2b275739 |
# Licensed under the terms of the GPL v3. See LICENCE for details
import math
from itertools import product
from galaxy import StarSystem
from milkyway import SolX, SolY
class AStar(object):
def __init__(self, graph):
self.graph = graph
def heuristic(self, node, start, end):
raise NotImplem... | RobSis/fe2router | pathfinder.py | Python | gpl-3.0 | 3,714 | [
"Galaxy"
] | 3e8d3434a93d05fe09e6ed208d951e46996a07b23c1b8ce07d2eba4b49c99193 |
# encoding: utf8
import re
from random import *
from collections import Counter
from pprint import pprint
from heapq import nlargest
from time import time
# http://blog.echen.me/2011/08/22/introduction-to-latent-dirichlet-allocation/
# https://tedunderwood.com/2012/04/07/topic-modeling-made-just-simple-enough/
# -> h... | mobarski/sandbox | topic/lda/lda4.py | Python | mit | 5,951 | [
"COLUMBUS"
] | 6c41ab4bd546993810c1f2c1cf18ee1b689c5f503ebcf3a323aec852d9c40897 |
"""
===========================
Formaldehyde cm-line fitter
===========================
This is a formaldehyde 1_11-1_10 / 2_12-2_11 fitter. It includes hyperfine
components of the formaldehyde lines and has both LTE and RADEX LVG based
models
Module API
^^^^^^^^^^
"""
from __future__ import print_function
import nu... | jpinedaf/pyspeckit | pyspeckit/spectrum/models/formaldehyde.py | Python | mit | 23,644 | [
"Gaussian"
] | 9351bb105ad774a10b08d6a6c6ec36656d9024d0e7ad9b6a357bbbc28cc8ea61 |
import numpy as np
class Neuron:
def __init__(self, inputs, f):
self.__inputs = inputs # количество входов
self.__f = f # передаточная функция
self.v = 0 # значение последнего рассчитанного локального поля
self.s0 = (-0.5 + np.random.sample()) # значение сдвига
... | allsilaevex/NeuralNetwork | NeuralNetwork/neuron.py | Python | mit | 861 | [
"NEURON"
] | 8898b6da1bca0fdbd5e7e89b452888ab9c3800ac25a091000b854f4a1b47966e |
#!/usr/bin/env python
from __future__ import print_function
from random import randrange, choice, shuffle, randint, seed, random
from math import sqrt
from collections import deque, defaultdict
import base64
from fractions import Fraction
import operator
import itertools
from game import Game
from copy import deepcop... | ido777/Skillz | starter_kit/lib/pirates.py | Python | mit | 58,857 | [
"exciting"
] | 6d86d87463644f27121134f1ea59ea113b9e3794f27b5ba59528e1bb491325c4 |
from BrowserManager import Browser
from DataAggregator import DataAggregator
from SocketInterface import clientsocket
from PostProcessing import post_processing
from Errors import CommandExecutionError
import MPLogger
from multiprocessing import Process, Queue
from Queue import Empty as EmptyQueue
from sqlite3 import ... | lightnarcissus/PlayfulMesh | OpenWPM/automation/TaskManager.py | Python | gpl-3.0 | 20,042 | [
"VisIt"
] | 13313bda7987261481fb053fb4b68c1714af10a6bcf9404dc38f051924ea4296 |
#!/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.vtkNamedColors... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Filters/General/Testing/Python/edgePoints.py | Python | gpl-3.0 | 1,711 | [
"VTK"
] | 642062abd011a5bf459925494ba488255f06ac788079a9a16917379474bfcf4d |
"""Tests for routines in force_constants.py."""
import numpy as np
import pytest
from phonopy import Phonopy
from phonopy.harmonic.force_constants import cutoff_force_constants
from phonopy.structure.cells import get_primitive
fc_1_10_ref = [
-0.037549,
0.000000,
0.000000,
0.000000,
0.002415,
... | atztogo/phonopy | test/harmonic/test_force_constants.py | Python | bsd-3-clause | 3,131 | [
"phonopy"
] | db6e01aabdd5fdbd33d5022e7c97583267c50a73d4feca152bc74a19b1c64ccb |
#!/usr/bin/python
from Pegasus.DAX3 import *
import sys
import os
from stat import *
def split_list(alist, elements_per_slice):
results = []
for start in range(0, len(alist), elements_per_slice):
results.append(alist[start:start+elements_per_slice])
return results
def concat_outputs(dax, level... | pegasus-isi/BLAST-Workflow | dax-generator.py | Python | apache-2.0 | 3,547 | [
"BLAST"
] | 4363840cab52e678cc749a0dfc7c438ba4d0cc03d79f5b7af2a629126d117498 |
from querylist import BetterDict
from tests.base import TestCase
class BetterDictActsAsDict(TestCase):
"""BetterDicts should act just like dictionaries"""
def setUp(self):
self.src_dict = {
'foo': 1,
'bar': 2,
'kitten': 3,
'update': 4,
}
... | thomasw/querylist | tests/betterdict_dict_tests.py | Python | mit | 1,174 | [
"BLAST"
] | 5b1223b8ead9c009ff7b4f706169df1873afff5df74e8126d7159a6c20870fe1 |
#!/usr/bin/env python
import inspect
from typing import List
from typing import Union
from collections import OrderedDict
import os
import copy
import re
import glob
import argparse
import logging
from importlib import import_module
import yaml
logging.basicConfig(level=logging.DEBUG)
log = logging.getLogger()
def ni... | galaxy-iuc/command-engine | autobuilder.py | Python | gpl-3.0 | 29,156 | [
"Galaxy"
] | 4b5b6f494717ab31debf8cd748f4aa0bf02879a5b7d50c94dc9de90551f5f3b2 |
#!/usr//bin/env python
# lammps.py (2011/03/28)
# An ASE calculator for the LAMMPS classical MD code available from
# http://lammps.sandia.gov/
# The environment variable LAMMPS_COMMAND must be defined to point to the LAMMPS binary.
#
# Copyright (C) 2009 - 2011 Joerg Meyer, joerg.meyer@ch.tum.de
#
# This librar... | slabanja/ase | ase/calculators/lammps.py | Python | gpl-2.0 | 27,425 | [
"ASE",
"LAMMPS"
] | 69d180b5eff45755715bb7bd02cbbba18738789b922761158b833536b72a6299 |
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