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# python retrieve_test.py $subdir/MACS2243-09/W-C-RC/SCIENCE/coadd_MACS2243-09/coadd.fits $subdir/MACS2243-09/PHOTOMETRY/panstarrs.cat
# python retrieve_test.py $subdir/MACS0911+17/W-C-RC/SCIENCE/coadd_MACS0911+17/coadd.fits $subdir/MACS0911+17/PHOTOMETRY/panstarrsstar.cat
from math import *
import os, sys, anydbm, ti... | deapplegate/wtgpipeline | retrieve_test_PANSTARRS.py | Python | mit | 14,889 | [
"Galaxy"
] | 7cb11dd5af04f940fec590ae6c54d756d1b0e046009b6352e87ade6a739bc481 |
# -*- coding: utf-8 -*-
import os
# MouseClick.py - To demonstrate Tkinter key clicks
import Tkinter
from kdtree import *
class KDTreeApp:
def __init__(self):
"""App for creating KD tree dynamically"""
self.tree = KDTree()
self.master = Tkinter.Tk()
self.w = Tkinter.Frame(sel... | NicovincX2/Python-3.5 | Algorithmique/Structure de données/Arbre (structure de données)/Arbre kd/app.py | Python | gpl-3.0 | 2,428 | [
"VisIt"
] | 18bf3eec6bc03614e4d23887a11cd696f2b072b7997aef8a042d3370effa4b5e |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | wscullin/spack | var/spack/repos/builtin/packages/r-a4/package.py | Python | lgpl-2.1 | 1,842 | [
"Bioconductor"
] | 8a0fff2e1cb70d9972f374e90cb9186bf4d7872a3e98593af864850847e1346d |
# mako/codegen.py
# Copyright (C) 2006-2013 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""provides functionality for rendering a parsetree constructing into module
source code."""
impo... | akuchling/book-diary-tools | books.d/mako/codegen.py | Python | bsd-3-clause | 49,252 | [
"VisIt"
] | 8993bb8dff66669a69e8f643599e7b3cb22b113bd1de0052b28a33b565f185fb |
# sql/compiler.py
# Copyright (C) 2005-2015 the SQLAlchemy authors and contributors
# <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Base SQL and DDL compiler implementations.
Classes provided include:
:class:`.c... | ppmt/Crust | flask/lib/python2.7/site-packages/sqlalchemy/sql/compiler.py | Python | gpl-2.0 | 99,638 | [
"VisIt"
] | 27486f76c83eac46e518b3d99ebd9a57e8441a6855f34e06715583a988e86be3 |
import os
import os.path
import random
import re
import stat
import subprocess
import sys
import time
from html.parser import HTMLParser
def out(message, *args, **kwargs):
print(message.format(*args, **kwargs))
def log(message, *args, **kwargs):
print(message.format(*args, **kwargs), file=sys.stderr)
def err(*args... | nightjuggler/peaks | sps_create.py | Python | mit | 99,988 | [
"VisIt"
] | 127146907db4ede29e74ca66fd59ef530d09c5e5cdadddfdd0fcd4cd28f1497e |
#
# @file TestXMLToken.py
# @brief XMLToken unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Michael Hucka <mhucka@caltech.edu>
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting ... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/xml/TestXMLToken.py | Python | bsd-3-clause | 24,842 | [
"VisIt"
] | 08411f7e6e6258021970021b2c59e5ca3fcd45f40e2c3de0e8a3dd1311eb3817 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Provides a class for interacting with KPath classes to
generate high-symmetry k-paths using different conventions.
"""
import itertools
from warnings import warn
import networkx as nx
import numpy as np
from pymatgen.sy... | vorwerkc/pymatgen | pymatgen/symmetry/bandstructure.py | Python | mit | 14,766 | [
"pymatgen"
] | 2642c4c78615ea329383d198d779d50f4b1a87797b957e80b760c8e5aac180f1 |
#!/usr/bin/env python
import numpy
import scipy.linalg
from pyscf import lib
from mpi4pyscf.lib import logger
from mpi4pyscf.tools import mpi
class DistributedDIIS(lib.diis.DIIS):
def _store(self, key, value):
if self._diisfile is None:
if isinstance(self.filename, str):
fil... | sunqm/mpi4pyscf | mpi4pyscf/lib/diis.py | Python | gpl-3.0 | 2,393 | [
"PySCF"
] | d0099d740a5997ca7443ec9521e7aca8baadbad9f6d9942a46e6bac83787ae1e |
from enum import IntEnum
from itertools import chain
from collections import namedtuple, defaultdict
from rdkit import Chem
from ._base import Descriptor
from ._util import parse_enum
from ._atomic_property import AtomicProperty
__all__ = ("Chi",)
class ChiType(IntEnum):
__slots__ = ()
path = 1
cluste... | mordred-descriptor/mordred | mordred/Chi.py | Python | bsd-3-clause | 6,216 | [
"RDKit"
] | 4e9392df7d937b0297956e894b8c9252a6516df1e0b4baf6a1c3607cb14cd04f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides class to generate and analyze interfacial reactions.
"""
import warnings
import matplotlib.pylab as plt
import numpy as np
from pymatgen.core.composition import Composition
from pyma... | gmatteo/pymatgen | pymatgen/analysis/interface_reactions.py | Python | mit | 22,139 | [
"pymatgen"
] | bcdaf63101d02a11f8894c2ffa9675513eda93b7f345d28a4e63186a2a44773a |
# This file is part of Androguard.
#
# Copyright (C) 2012, Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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:/... | andymg/androguard | androguard/decompiler/dad/instruction.py | Python | apache-2.0 | 33,388 | [
"VisIt"
] | 90e70b544b90f4c83cc6cfe3e2f2661821a68ebb2dc0ac4f4243472972dcb78c |
"""
Model grism spectra in individual FLTs
"""
import os
from collections import OrderedDict
import copy
import numpy as np
import scipy.ndimage as nd
import matplotlib.pyplot as plt
import astropy.io.fits as pyfits
from astropy.table import Table
import astropy.wcs as pywcs
import astropy.units as u
#import stwcs
... | gbrammer/grizli | grizli/model.py | Python | mit | 195,537 | [
"Galaxy",
"Gaussian",
"VisIt"
] | a48c4132840b1ff2b3ee6999e2cb8fe98605b646fc3f0492448806c7602edb22 |
import numpy as np
from ase import Atoms, Atom
from ase.parallel import barrier, rank, size
from gpaw.cluster import Cluster
from gpaw.test import equal
from ase.structure import molecule
from math import pi, sqrt
R = 2.0
CO = Atoms([Atom('C', (1, 0, 0)), Atom('O', (1, 0, R))])
CO.rotate('y', pi/2)
equal(CO.position... | robwarm/gpaw-symm | gpaw/test/cluster.py | Python | gpl-3.0 | 2,383 | [
"ASE",
"GPAW"
] | 6b168ea51f043e9e71917983e5ec3bd82707e7d073ce346e0afbce8031b6a4ad |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/analytics-zoo | pyzoo/zoo/chronos/examples/distributed/distributed_training_network_traffic.py | Python | apache-2.0 | 4,292 | [
"ORCA"
] | 65e84ae939ffb21338fc068755cca460dcbcad1d69cd193202523d65130b823f |
# -*- coding: utf-8 -*-
##
## This file is part of Invenio.
## Copyright (C) 2011, 2012 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 opt... | kaplun/ops | modules/bibauthorid/lib/bibauthorid_webinterface.py | Python | gpl-2.0 | 148,959 | [
"VisIt"
] | 9bf077dfd1c2053898f17672848239df0a8eac223718bd79df28374f8b2d8efa |
# 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.
#
"""Provide classes for dealing with Training Neural Networks."""
# standard modules
import random
class TrainingExample(object):
"""Hold input... | zjuchenyuan/BioWeb | Lib/Bio/NeuralNetwork/Training.py | Python | mit | 3,110 | [
"Biopython"
] | f88ef7dab2a1566c4bcc3cee1f4d688e91f4102171fe19bb027d3ad4d77c5831 |
from galaxy.util import topsort
def test_topsort_level_stability():
data = [
(0, 2),
(1, 2),
(2, 3),
(2, 4),
(3, 4),
(3, 5),
(6, 2),
]
assert topsort.topsort_levels( data )[ 0 ] == [ 0, 1, 6 ]
assert topsort.topsort( data ) == [ 0, 1, 6, 2, 3, 4,... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/test/unit/test_topsort.py | Python | gpl-3.0 | 1,064 | [
"Galaxy"
] | 6d3292da64e22356caa152ad9612ef9e758ea5e01f3a9426b73dfb938b2dc9b6 |
#!/usr/bin/env python
from vtk import *
csv_source = vtkDelimitedTextReader()
csv_source.SetFieldDelimiterCharacters(",")
csv_source.SetHaveHeaders(True)
csv_source.SetDetectNumericColumns(True)
csv_source.SetFileName("authors.csv")
csv_source.Update()
T = csv_source.GetOutput()
print "Table loaded from ... | timkrentz/SunTracker | IMU/VTK-6.2.0/Examples/Infovis/Python/delimited_text_reader1.py | Python | mit | 344 | [
"VTK"
] | f53e7fe8a161dcdb89c000285b116c1dda420324aafca85daacd20836e1dfd04 |
"""
exodus.py v 1.03 (beta) is a python wrapper of some of the exodus II library
Copyright (c) 2013, 2014, 2015, 2016 Sandia Corporation.
Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation,
the U.S. Government retains certain rights in this software.
Redistribution and use in source and binary for... | SalvusHub/salvus | src/py/pysalvus/model_handling/exodus.py | Python | mit | 170,412 | [
"NetCDF"
] | 33ea530cc6442313b89a981b22744166676a9e8663ad35cb944592364800a7a4 |
#!/usr/bin/env python
import os
from ase.io import read
from ase.neb import NEB
from ase.calculators.turbomole import Turbomole
from ase.optimize import BFGS
initial = read('initial.coord')
final = read('final.coord')
os.system('rm -f coord; cp initial.coord coord')
#restart
configs = read('neb.traj@-5:')
band = N... | alexei-matveev/ase-local | doc/ase/calculators/turbomole_ex3_restart_diffuse_usingNEB.py | Python | gpl-2.0 | 501 | [
"ASE",
"TURBOMOLE"
] | 69110b7b4e9206392a2a6fe92871c228441702505267e8318b477d2fbdf17f8c |
import psi4
import numpy as np
import memory_profiler as mp
import time
import gc
"""
This is a simple script that verifies several ways of accessing numpy arrays
and ensures that their memory is properly cleaned.
"""
# If its too small, something odd happens with the memory manager
mat_size = 10000
def snapshot_mem... | jH0ward/psi4 | tests/pytest/test_np_views.py | Python | lgpl-3.0 | 1,834 | [
"Psi4"
] | 8705be81f68a9ac75438bca31d80f0326979cab97b8b66a069cca83d5e349aee |
from __future__ import (absolute_import, division, print_function)
from mantid.api import (DataProcessorAlgorithm, mtd, AlgorithmFactory,
FileProperty, FileAction,
MultipleFileProperty, WorkspaceProperty,
PropertyMode, Progress)
from mantid.simple... | ScreamingUdder/mantid | Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SingleCrystalDiffuseReduction.py | Python | gpl-3.0 | 20,442 | [
"CRYSTAL"
] | cdd1c0b57eae1f12f77c0e3ee9076df7149eb419ae3a1d812edfe0a3f12dfe68 |
# coding=utf-8
# (The line above is necessary so that I can use 世界 in the
# *comment* below without Python getting all bent out of shape.)
# Copyright 2007-2009 Google 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 o... | anlhord/gofrontend | support/codereview/codereview.py | Python | bsd-3-clause | 111,287 | [
"VisIt"
] | 7d02c127dfffdf428c0c722fae1bb1fa1448940f705850377997897d7253e2c0 |
#
# Copyright (c) 2017 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... | yashdsaraf/scancode-toolkit | src/scancode/cli.py | Python | apache-2.0 | 32,883 | [
"VisIt"
] | 39af1efa5c3deedb5ff2430aaba7daaecec822614e6d0c0432e35dfd933149a6 |
# # # # #
# Tool to downscale the CMIP5 data from the PCMDI group.
# # # # #
def shiftgrid(lon0,datain,lonsin,start=True,cyclic=360.0):
import numpy as np
"""
Shift global lat/lon grid east or west.
.. tabularcolumns:: |l|L|
============== ====================================================
Arguments D... | ua-snap/downscale | old/old_bin/ar5_model_data_downscaling_fix.py | Python | mit | 22,871 | [
"NetCDF"
] | 53b2d64aedd7e2224eb06696896df98889e05f92c45b8b0f72c5203d0435c585 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-affxparser/package.py | Python | lgpl-2.1 | 2,176 | [
"Bioconductor"
] | 792ff34e63cfe6c775372d29bb3897a4fbf078f44b95973e93c7c5ef06b4ac56 |
""" Compute the centerlines according to Kienholz et al (2014) - with
modifications.
The output is a list of Centerline objects, stored as a list in a pickle.
The order of the list is important since the lines are
sorted per order (hydrological flow level), from the lower orders (upstream)
to the higher orders (downst... | jlandmann/oggm | oggm/core/preprocessing/centerlines.py | Python | gpl-3.0 | 37,648 | [
"NetCDF"
] | 6cb13cf0a77baf42456b1cc278c61c49cd7493e81bbba2cb5941fd88d95b37f0 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/stats/ordination/_canonical_correspondence_analysis.py | Python | bsd-3-clause | 8,409 | [
"scikit-bio"
] | 4227d3dba4058aeb94c175032d71ee41c53c9b8a39ab19c74c19b9a0a06658a0 |
""" POOL XML Catalog Class
This class handles simple XML-based File Catalog following the
POOL project schema. It presents a DIRAC generic File Catalog interface
although not complete and with several extensions
"""
from __future__ import print_function
from __future__ import absolute_import
from __future__... | ic-hep/DIRAC | src/DIRAC/Resources/Catalog/PoolXMLCatalog.py | Python | gpl-3.0 | 11,925 | [
"DIRAC"
] | 65b874fd56940c88dcec10bb5ceba7ea861b92c9763ed940657d319976b7eedd |
""" Tests minimise module.
Tests the :meth:`GridSearch.fin_minimum`, method - an alternative to
calling :meth:`numpy.argmin` and :meth:`numpy.nanmin`, which are used
by default.
The main part of this test is verifying the :class:`GridSearch` class,
particularly the `meth:`GridSearch.minimise` method.
"""
import numpy... | ashleyrback/echidna | echidna/test/test_minimise.py | Python | mit | 7,878 | [
"Gaussian"
] | 765b34d3f60ffc674b30409f972e2b38159217c041c603c61ad74be620b9c27d |
# 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... | BackupTheBerlios/espressopp | src/integrator/ExtForce.py | Python | gpl-3.0 | 1,927 | [
"ESPResSo"
] | 170e591f357e3b0ceaf934f644e07d8249aefbc27b8d6ce1df6e2ee91b69d44e |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements Compatibility corrections for mixing runs of different
functionals.
"""
# flake8: ignore=E712
import os
import warnings
from itertools import groupby
from typing import List, Optional, Union
import n... | materialsproject/pymatgen | pymatgen/entries/mixing_scheme.py | Python | mit | 37,977 | [
"VASP",
"pymatgen"
] | c972b88d4a4bddea09f828af4b60259bf52229e3fe75593fc800f7e86e27348b |
#File: gini_plot.py
#Created: Mon 12 Mar 2012 03:00:01 PM CDT
#Last Change: Wed 03 Oct 2012 04:08:38 PM CDT
#Author: Steven Boada
import pylab as pyl
import cPickle as pickle
galaxies = pickle.load(open('galaxies.pickle','rb'))
galaxies = filter(lambda galaxy: galaxy.Gini is not None, galaxies)
f1 = pyl.figure(1,fig... | boada/ICD | sandbox/legacy_plot_code/plot_G_vs_M20.py | Python | mit | 1,313 | [
"Galaxy"
] | 957c87313ea3ac429bc6ef5f1015d485e8574c733afce440eb8bc4cfc10e7a57 |
# -*- coding: utf-8 -*-
#
# Minecraft-Mods documentation build configuration file, created by
# sphinx-quickstart on Sun Feb 14 15:21:55 2016.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file... | Heroes-Academy/Minecraft_Spring_2016 | docs/source/conf.py | Python | mit | 9,223 | [
"Brian"
] | 9d97539b9666aba4f986c01caeaf503ab1eef4ad71a14e1221b54b3a6dbb42d0 |
""" Simple multi-layer perception neural network using Minpy """
# import minpy
import minpy.numpy as np
from minpy.nn import layers
from minpy.nn.model import ModelBase
from minpy.nn.solver import Solver
from minpy.nn.io import NDArrayIter
from examples.utils.data_utils import get_CIFAR10_data
from minpy.context impor... | shadowleaves/deep_learning | twolayer/minpy_batchnorm.py | Python | mit | 3,754 | [
"Gaussian"
] | 55dbbabffba38d6f3980a5848c741ff9b190868771c6e4223f25266a6c977859 |
# Copyright 2006, 2007 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Bio.SeqIO support for the "phylip" (PHYLIP) file format.
You are expected to use this... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SeqIO/PhylipIO.py | Python | apache-2.0 | 14,785 | [
"Biopython"
] | 7cd21cb22cb6ca6861e263dce13d9250860e7e8a0eb74c8485a69964bcbd347a |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/core/dbprofiles.py | Python | gpl-2.0 | 9,414 | [
"VisIt"
] | d14d9062b8d39308b4d2afbf661a27e0cd15836df33ac49878810869baff7785 |
"""
.. _sfm-track:
==================================================
Tracking with the Sparse Fascicle Model
==================================================
Tracking requires a per-voxel model. Here, the model is the Sparse Fascicle
Model, described in [Rokem2014]_. This model reconstructs the diffusion signal
as... | JohnGriffiths/dipy | doc/examples/sfm_tracking.py | Python | bsd-3-clause | 4,924 | [
"Brian"
] | 74363ae87c45b8a76f040a4c2627bf93090e8e7f5a3363e8ceaa18a446a67886 |
#!/usr/bin/env python
import vtk
def get_program_parameters():
import argparse
description = 'Read and display ExodusII data.'
epilogue = '''
'''
parser = argparse.ArgumentParser(description=description, epilog=epilogue)
parser.add_argument('filename', help='A required filename e.g mug.e.')
... | lorensen/VTKExamples | src/Python/IO/ReadExodusData.py | Python | apache-2.0 | 2,101 | [
"VTK"
] | 7acc88e4f0b5cdbc2b51436e0f926f651c63042ed3cb1f927408fc0283219ef3 |
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class emp_test(SimpleVTKClassModuleBase):
"""This is the minimum you need to wrap a single VTK object. This
__doc__ string will be replaced by the __doc__ string of the encapsulated
VTK object, i.e. vtkStripper in this case.
... | chrisidefix/devide | testing/emp_test/emp_test.py | Python | bsd-3-clause | 889 | [
"VTK"
] | ddd335883a4cd0e3b91b7560113b5c48439ebcb0d5059b95da3413065ffad3ec |
"""
Copyright (C) 2011 N.D. Price Lab
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in th... | JohnCEarls/AUREA | src/AUREA/packager/DataPackager.py | Python | agpl-3.0 | 19,414 | [
"DIRAC"
] | fc8181e4b9dd9dd2a3aa817fb0ca4cf3190cbf41d5b2776ebce7f13993984b45 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import math
from collections import namedtuple, defaultdict
import six
import ruamel.yaml as yaml
import os
import json
from copy import deepcopy
from pymatg... | nisse3000/pymatgen | pymatgen/analysis/local_env.py | Python | mit | 125,931 | [
"Gaussian",
"Jmol",
"VASP",
"pymatgen"
] | 693060442095191cdf7925b16ec4ad0bff07e0d73491df4ff707ea696ed2072a |
from setuptools import setup
setup(
name='trefoil',
version='0.3.2',
packages=['trefoil',
'trefoil.analysis', 'trefoil.cli',
'trefoil.geometry', 'trefoil.geometry.tests',
'trefoil.netcdf', 'trefoil.render',
'trefoil.render.renderers', 'trefoi... | consbio/clover | setup.py | Python | bsd-3-clause | 1,246 | [
"NetCDF"
] | 71bbd49b891680eb87c631d21b5a90e5aa89d80f1d161434d9b008748e8b6215 |
#!/usr/local/bin/python-2.5/bin/python
Info="""
Module name: cfg2lammps.py
Author: (c) Andres Jaramillo-Botero
California Institute of Technology
ajaramil@wag.caltech.edu
Project: pEFF
Version: August 2009
Reads in an eff .cfg file and produces the corresponding lammps data and input files
NOTE: Unsupported functio... | quang-ha/lammps | tools/eff/cfg2lammps.py | Python | gpl-2.0 | 11,564 | [
"LAMMPS"
] | 1754ffc6bc523a1c0656d77384dc1f46bfcc315ad04bd52f6f7d9d851cb63306 |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | thempel/adaptivemd | adaptivemd/analysis/pyemma/msmanalyze.py | Python | lgpl-2.1 | 4,318 | [
"MDTraj"
] | 490ac1235c4032014626189bf910e7887f8788ea19776bbd90863ba5a2878b11 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import sys
import os
import socket
import glob
import shutil
import llnl.util.tty as tty
from os imp... | iulian787/spack | var/spack/repos/builtin/packages/ascent/package.py | Python | lgpl-2.1 | 21,094 | [
"VTK"
] | 1c029d7e06c08ae2723115cbb5765ecea3c6a164805f665bb174dc4512f71d2d |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
import json
from datetime import datetime, timedelta
import ddt
from flaky import flaky
from nose.plugins.attrib import attr
from ...fixtures.course import CourseFixture, XBlockFixtureDesc
from ...pages.common.auto_auth import AutoAuthPage
from ...pages.c... | fintech-circle/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware.py | Python | agpl-3.0 | 40,066 | [
"VisIt"
] | 15d7a8557a3f1387c20696a440e975c8dcbe74345bf9fc466e5b59a2ac084b3c |
"""
Demonstration application for range search using kd tree.
Left mouse adds point.
Right mouse click begins drag of rectangle.
"""
import tkinter
from adk.kd import KDTree, X, Y, VERTICAL
from adk.region import Region, minValue, maxValue
RectangleSize = 4
class KDTreeApp:
... | heineman/algorithms-nutshell-2ed | PythonCode/demo/app_kd_range.py | Python | mit | 5,297 | [
"VisIt"
] | b313ebe01dd8a84cfc1090ce0976414859b8ac00bff566bb693fcde61a83cb24 |
from numpy import array_split, concatenate
from pandas import DataFrame
from ._match_randomly_sampled_target_and_data_to_compute_margin_of_errors import (
_match_randomly_sampled_target_and_data_to_compute_margin_of_errors,
)
from ._match_target_and_data import _match_target_and_data
from ._permute_target_and_matc... | UCSD-CCAL/ccal | ccal/_match.py | Python | mit | 3,073 | [
"MOE"
] | 2117e9089d34a63cd5bf80305b60ed030486f83c13cc2227e8a33bf195647dde |
# Copyright 2010 United States Government as represented by the
# Administrator of the National Aeronautics and Space Administration.
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the L... | HybridF5/nova | nova/tests/unit/matchers.py | Python | apache-2.0 | 19,775 | [
"VisIt"
] | 005aa1f93d3777c7ee47476571af2276bf5aedb54611f299c3ea0de719bc7b7b |
#!/bin/python2
if __name__ == "__main__": #if run in standalone
from sys import exit
import argparse
from libs.InAndOut import importer, saveKey
parser = argparse.ArgumentParser(description='Offline analysis for\
spiking neural networks')
#Files to open
parser.add_argument('--store-dir',
... | nico202/pyNeMo | Analyze.py | Python | gpl-2.0 | 4,060 | [
"NEURON"
] | da4690941be05e906557a8cb554b9724687d368f5eeb905be6fe410c8f9d5462 |
# petclaw to vtk
import os
import numpy as np
from petsc4py import PETSc
import pickle
import glob
import shutil
def post_calculation():
pass
class IO(object):
def read_petsc(self):
if hasattr(self, 'frame'): frame = self.frame
if hasattr(self,'file_prefix'): file_prefix = self.file_pre... | nthakkar/emclaw | utils/inout.py | Python | gpl-2.0 | 7,567 | [
"VTK"
] | a3ab295e6bba4cfb2df785c2a03958ac9aa2984edc04466532455a9f6b747d60 |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
###########################################################################
# ESPResSo++ #
# Test script for Converting GROMACS tabulated file #
# ... | junghans/espressopp | examples/convert_gromacs_tables/convert_gromacs_table.py | Python | gpl-3.0 | 6,166 | [
"ESPResSo",
"Gromacs"
] | dcd8f15e6d2e174ddc7f03a4b8144258fe7138c76d29c89dbd0b38a784163af1 |
from __future__ import absolute_import, division, print_function
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed ... | JWDebelius/scikit-bio | skbio/util/_exception.py | Python | bsd-3-clause | 419 | [
"scikit-bio"
] | 995eabacd5eb14d720e370bd6d2608b3f47d6daeb9f2daafbe06b65ccd909406 |
#pylint: disable=missing-docstring
#* 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/... | nuclear-wizard/moose | python/chigger/annotations/ImageAnnotation.py | Python | lgpl-2.1 | 4,106 | [
"MOOSE",
"VTK"
] | 59adcce62770a55349f021e5e6dbce2d55c27b9ff0fae72c82bd127197a9bf0a |
def extractLolitiveMoe(item):
'''
DISABLED
Parser for 'lolitive.moe'
'''
return None | fake-name/ReadableWebProxy | WebMirror/management/rss_parser_funcs/feed_parse_extractLolitiveMoe.py | Python | bsd-3-clause | 92 | [
"MOE"
] | e2590105d7dbfaf0a2eb4ee0e8f4f531fb0da85e7b2491f818fe50300b8b7fef |
# -*- coding: utf-8 -*-
"""
Created on 20/10/2016
@author: Charlie Bourigault
@contact: bourigault.charlie@gmail.com
Please report issues and request on the GitHub project from ChrisEberl (Python_DIC)
More details regarding the project on the GitHub Wiki : https://github.com/ChrisEberl/Python_DIC/wiki
Current File: ... | ChrisEberl/Python_DIC | functions/filterFunctions.py | Python | apache-2.0 | 3,537 | [
"Gaussian"
] | f244e5f0650dab88528f1226bb9739ca54575806cdaa94e5bf44e1e769be04df |
import numpy as np
from ase.data import atomic_numbers, chemical_symbols
from ase.units import Bohr
from gpaw.setup import Setups
from gpaw.xc import XC
from gpaw.mpi import world
Bondi64jpc_vdWradii = { # units Anstrom
'He' : 1.40,
'Ne' : 1.54,
'Ar' : 1.88,
'Kr' : 2.02,
'Xe' : 2.16
}
def vdWradi... | qsnake/gpaw | gpaw/analyse/vdwradii.py | Python | gpl-3.0 | 2,296 | [
"ASE",
"GPAW"
] | 8c856dfb4c3110c7f6fa62affab538ad42b472837c3b1984b693490711c45935 |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path
here = path.absp... | mackst/glm | setup.py | Python | mit | 8,032 | [
"VisIt"
] | 1def791d2c18b9341595bb73cf0c87e79fa20ac6c801311c94fee301e834bcf3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Copyright 2014, Dennis Drescher
# All rights reserved.
#
# This library is free software; you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation; either version 2.1 of ... | thresherdj/shrinkypic | setup.py | Python | mit | 1,604 | [
"VisIt"
] | ceaffe1c6d6852f9a70e2c405fb23df0c8f9fd0dc227fe1b4afcc9b19ef9f97e |
"""Use PyMOl to create templates for bomeba"""
import numpy as np
np.set_printoptions(precision=2)
import __main__
__main__.pymol_argv = ['pymol','-qck']
import pymol
from pymol import cmd, stored
pymol.finish_launching()
import openbabel as ob
# set hydrogen names to PDB compliant
cmd.set('pdb_reformat_names_mode', ... | BIOS-IMASL/bomeba0 | bomeba0/scaffold/gen_templates_gl.py | Python | apache-2.0 | 2,639 | [
"PyMOL"
] | 8873fc30150e1f1e3b4ccceb4fe93c903aaabf9e96526359efa2afff55994730 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/simulation/neuron/simulationdatacontainers/__init__.py | Python | bsd-2-clause | 1,813 | [
"NEURON"
] | 174d40a14762037a6756411164dc5483e87058a1bd31fe6a385f62551ee409f0 |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
import sys
from pyscf import gto, scf
from pyscf import lo
from pyscf.tools import molden
'''
Write orbitals in molden format
'''
mol = gto.M(
atom = '''
C 3.2883 3.3891 0.2345
C 1.9047 3.5333 0.2237
C 3.8560 2.1213 ... | gkc1000/pyscf | examples/tools/02-molden.py | Python | apache-2.0 | 1,649 | [
"PySCF"
] | 2d41297b5a7bf973e7e7bb771aaf152941d956796fd4ca06abdafb79930efcaa |
#!/usr/bin/env python3
"""Use this if the antenna timeing callibration changes"""
import numpy as np
from scipy.signal import resample
import h5py
from LoLIM.IO.raw_tbb_IO import MultiFile_Dal1, filePaths_by_stationName, read_antenna_pol_flips, read_bad_antennas
from LoLIM.utilities import processed_data_dir, even_a... | Bhare8972/LOFAR-LIM | LIM_scripts/stationTimings/reCallibrate_pulses.py | Python | mit | 3,845 | [
"Brian"
] | f763c6ce8621472c7fcc8553f1ab170c51e2b515f6c0432707299fc313e4dfe7 |
from __future__ import print_function, division, unicode_literals
import math
import os
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.io.vasp.inputs import Incar
from mpinterfaces import VASP_STD_BIN, VDW_KERNEL, QUEUE_SYSTEM
import mpinterfaces.utils as utl
__author__ = "Michael As... | henniggroup/MPInterfaces | mpinterfaces/mat2d/friction/startup.py | Python | mit | 7,609 | [
"VASP",
"pymatgen"
] | 16298399584c51367d6f7f3c27d6a4811a1f99dcef2b254d75d4ebfb5b68a59f |
"""
DIRAC API Class
All DIRAC functionality is exposed through the DIRAC API and this
serves as a source of documentation for the project via EpyDoc.
The DIRAC API provides the following functionality:
- A transparent and secure way for users
to submit jobs to the Grid, monitor them and
re... | avedaee/DIRAC | Interfaces/API/Dirac.py | Python | gpl-3.0 | 108,354 | [
"DIRAC"
] | a05aa6ba8fbb0f4147654669e445462e5ebe59acebb84f50e71162ac1d2fd531 |
#!/usr/bin/env python
## @package linesearch
## \author Ed Bueler, University of Alaska Fairbanks, USA
## \brief A script for doing a line search over stddev parameter of PDD.
## Copyright (C) 2010, 2012 Ed Bueler
##
## see README for role of this script
## This script uses NCO (http://nco.sourceforge.net/).
import c... | matthiasmengel/pism_pik | examples/old/pddtune/linesearch.py | Python | gpl-2.0 | 11,882 | [
"NetCDF"
] | dde71a96c74413d1a784dba9a5f66b87f63b0bea554728b77eaae3120bd84020 |
from __future__ import print_function, absolute_import, unicode_literals
__all__ = ["corner", "hist2d"]
__version__ = "1.0.2"
__author__ = "Dan Foreman-Mackey (danfm@nyu.edu)"
__copyright__ = "Copyright 2013-2015 Daniel Foreman-Mackey"
__contributors__ = [
# Alphabetical by first name.
"Adrian Price-Whelan @a... | earlbellinger/asteroseismology | regression/corner.py | Python | gpl-2.0 | 21,180 | [
"Gaussian"
] | 7304e8c6d32b8a7b1d41849659b56955cb21902b2780c9f884320be3ba68eb80 |
import numpy as np
import csv
import matplotlib.pyplot as plt
plt.ion()
print '\nEnter 1 to train and test on a subsample of the training data.'
print 'Enter 0 to train on full training sample, and test on the Kaggle test data.\n'
test_on_train = raw_input('ENTER 1 or 0: ')
#read in training data
csv_file_object = cs... | jesford/bike_sharing | bikerides.py | Python | mit | 12,669 | [
"Gaussian"
] | d1491a042bfb8f659b3d0a445046db90348bed86b1437460067519d04890aea4 |
import numpy as np
import mygis
from bunch import Bunch
def write_file(date,info,cesm):
"""writes cesm input data to a netcdf file"""
filename=info.output_file+str(date).replace(" ","_")
dims=("time","level","lat","lon")
dims_3d=("time","lat","lon")
dims_2d=("lat","lon")
extra_vars=[]... | gutmann/icar | helpers/cesm/output.py | Python | mit | 3,666 | [
"NetCDF"
] | 56a5ccfe64dc75f689929fb2401f0902349060307de0a5570bdaeed02bd05aca |
##########################################################################
# this script was generated by openmm-builder. to customize it further,
# you can save the file to disk and edit it with your favorite editor.
##########################################################################
from __future__ import pri... | LCLS/Protein-Folding-Sims | hp24stab/amber03/OPENCL/amber03_implicit_noconstraints.py | Python | mit | 1,661 | [
"OpenMM"
] | a68db23e739c59435a34f5420ac464a9d4998835b77e36cb364e77eb2d35e67f |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | pkreissl/espresso | src/python/espressomd/accumulators.py | Python | gpl-3.0 | 11,637 | [
"ESPResSo",
"exciting"
] | 74ce95b1fe3aace694ce3f1ea046329a0390f3e3c2ad42ea63f6051a0fb0429e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2011 Tim G L Lyons
#
# 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... | pmghalvorsen/gramps_branch | gramps/gen/proxy/proxybase.py | Python | gpl-2.0 | 33,787 | [
"Brian"
] | 4d15991218bcac6894e4cfc65b4818c4c8cced1093e3d11510ade2304a8c9653 |
from django.utils.translation import ugettext_lazy as _
from django.forms import ValidationError # noqa
from django.core.urlresolvers import reverse
from horizon import exceptions
from horizon import forms
from horizon import messages
from crystal_dashboard.dashboards.crystal import exceptions as sdsexception
from cr... | Crystal-SDS/dashboard | crystal_dashboard/dashboards/crystal/rings/storage_policies/forms.py | Python | gpl-3.0 | 7,588 | [
"CRYSTAL"
] | 62b3eee6d327c5c153b1f402ae46b7d16740f3b8e82db0eb6547487760a205c2 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/r-nlme/package.py | Python | lgpl-2.1 | 1,745 | [
"Gaussian"
] | 3391935589c122f89b0b598df35f2a974a97a60e96a4ba7f403f225f8868f63b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#-----------------------------------------------------------------------------
# update_backscatter.py, Angeline G. Burrell (AGB), UoL
#
# Comments: Update the beam's groundscatter flag, calculate the virtual height
# and propagation path, determine the origin fie... | aburrell/davitpy | davitpy/pydarn/proc/fov/update_backscatter.py | Python | gpl-3.0 | 115,585 | [
"Gaussian"
] | 5dfff6a6505b9e42242bde9edffed3c1d82225b55db571cd5cb60cf1cceb3016 |
from pymbar import timeseries
from pymbar import testsystems
import numpy as np
from scipy import stats
from pymbar.utils_for_testing import eq, skipif
from six.moves import xrange
try:
import statsmodels.api as sm
HAVE_STATSMODELS = True
except ImportError as err:
HAVE_STATSMODELS = False
def generate_d... | kyleabeauchamp/pymbar | pymbar/tests/test_timeseries.py | Python | lgpl-2.1 | 5,513 | [
"Gaussian"
] | 58b25ce355b2148cc85876628935f9c10766d49cd7c5732e8fe53f4d7075e90a |
from flask import session, url_for
from flask_nav import Nav
from flask_nav.elements import Navbar, View, Subgroup, Link, Text, Separator, RawTag
from flask_bootstrap.nav import BootstrapRenderer
from hashlib import sha1
from dominate import tags
nav = Nav()
class SidedViewImage(View):
def __init__(self, image_u... | baliga-lab/pf1010-web | aqxWeb/nav.py | Python | lgpl-3.0 | 4,675 | [
"VisIt"
] | cfb5d2c8c3156794808e8ec0948474f997261fdddd35d89b90b1e9b4e9a2a15a |
# -*- coding: utf-8 -*-
from django.contrib import admin
from django.utils.translation import ugettext as _
from koalixcrm.crm.contact.phone_address import PhoneAddress
from koalixcrm.crm.contact.email_address import EmailAddress
from koalixcrm.crm.contact.postal_address import PostalAddress
from koalixcrm.crm.contact... | scaphilo/koalixcrm | koalixcrm/crm/contact/contact.py | Python | bsd-3-clause | 9,499 | [
"VisIt"
] | 5770b153a8bf8a2610cb0b1bfc7512fefc4aa6d017da55351af0ffa896d27e3b |
"""
Utilities for downloading or generating datasets, splitting data, and computing accuracy metrics.
"""
import os
import numpy as np
import scipy.stats as st
import requests
from io import BytesIO
from equadratures.scalers import scaler_minmax
def gen_linear(n_observations=100, n_dim=5, n_relevent=5,bias=0.0, nois... | Effective-Quadratures/Effective-Quadratures | equadratures/datasets.py | Python | lgpl-2.1 | 10,747 | [
"Gaussian",
"VisIt"
] | 425e35ba940240977fb1d6e865c5e1d74e8e3c316465b1e2d824f62a2b81088a |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2014 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | dilawar/moose-full | moose-examples/snippets/MULTI/TuringInNeuron.py | Python | gpl-2.0 | 7,210 | [
"MOOSE"
] | 80ed190b4a5932c6a6abf301f4a44a688f7c86cef2c786e9cbae01e06fe00e5d |
"""
This sample demonstrates a simple skill built with the Amazon Alexa Skills Kit.
The Intent Schema, Custom Slots, and Sample Utterances for this skill, as well
as testing instructions are located at http://amzn.to/1LzFrj6
For additional samples, visit the Alexa Skills Kit Getting Started guide at
http://amzn.to/1LG... | greginvm/groceries-bot | alexa/alexa.py | Python | mit | 8,284 | [
"VisIt"
] | f51cd51042aedafa913af8927f67a5824ee13fa01b4ede87c8d61b9c158875a0 |
import os
import glob
import mdtraj as md
class Everything(object):
def __contains__(self, other):
return True
run_whitelist = [0, 102, 104, 107, 122, 134, 139, 143, 144, 151, 155, 184, 1, 23, 2, 33, 35, 37, 38, 39, 43, 58, 60, 62, 65, 70, 71, 73, 74, 77, 79, 83, 87, 99]
#run_whitelist = Everything()
sou... | hainm/MSMs | attic/src/code/fahprocessing/concat.py | Python | gpl-2.0 | 1,157 | [
"MDTraj"
] | c4b3445ad0053ec45018f50990aa3eb20e5096fcafbc62f91e2294ed13dc8bf3 |
#!/usr/bin/env python
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl... | nuclear-wizard/moose | framework/doc/doxygen/create_dox.py | Python | lgpl-2.1 | 1,459 | [
"MOOSE"
] | 6d7493fee84650c1d1f98f876b8d5dc5cca56ad0c48c99afa34416a8514da1f4 |
# FreeCAD init script of the Fem module
# (c) 2001 Juergen Riegel
#***************************************************************************
#* (c) Juergen Riegel (juergen.riegel@web.de) 2002 *
#* *
#* This file i... | timthelion/FreeCAD | src/Mod/Fem/Init.py | Python | lgpl-2.1 | 2,560 | [
"VTK"
] | dbcad54e820ef5ccde90d744fd6aec0137734f9cc315f40433024b618411682d |
from numpy import *;
import kNN
import numpy as np
import matplotlib.pyplot as plt
from mayavi import mlab
'''
@author: Michael Wan
@since: 2014-11-01
'''
def etsIntro():
x, y = np.ogrid[-2:2:20j, -2:2:20j]
z = x * np.exp( - x**2 - y**2)
pl = mlab.surf(x, y, z, warp_scale="auto")
... | onehao/opensource | pyml/inaction/ch02/knn/mydebug.py | Python | apache-2.0 | 2,717 | [
"Mayavi"
] | 8101b6d383e19294dc42a796fca8413082fbaf503eb2cac941ca5209758d7007 |
"""
Signal
======
The signal module constains all kinds of signal processing related functions.
.. inheritance-diagram:: acoustics.signal
Filtering
*********
.. autoclass:: Filterbank
.. autofunction:: bandpass_filter
.. autofunction:: octave_filter
.. autofunction:: bandpass
.. autofunction:: lowpass
.. autofunct... | giumas/python-acoustics | acoustics/signal.py | Python | bsd-3-clause | 40,055 | [
"Gaussian"
] | dcf9dcb82dcbeb747a4e022a02782c3888b38ab6122db68f87b72563ef259b85 |
p00022 = r"""
<H1>Maximum Sum Sequence</H1>
<p>
Given a sequence of numbers <var>a<sub>1</sub></var>, <var>a<sub>2</sub></var>, <var>a<sub>3</sub></var>, ..., <var>a<sub>n</sub></var>, find the maximum sum of a contiguous subsequence of those numbers. Note that, a subsequence of one element is also a <i>contiquous</... | google-research/runtime-error-prediction | core/data/example_problem_descriptions.py | Python | apache-2.0 | 17,198 | [
"VisIt"
] | 0d0f384a56504399892821bc2f2ad579e252c99abe6fb7ca74154ff382124354 |
#
# Copyright (C) 2013-2019 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/constant_pH_stats.py | Python | gpl-3.0 | 4,194 | [
"ESPResSo"
] | d62228cb5b3bea2ea38d080f5ecd3929a9d670de99536ccdd4d5b92313ab41e1 |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns, assert_array_equal, assert_array_almost_equal)
from numpy import random
from numpy.compat import asbytes
import... | chiffa/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 59,785 | [
"Gaussian"
] | b2af98a4986b64ae1160f55d27a19ee045054143dad8019692aaee30b7297cb4 |
import unittest, random, sys, time, re, math
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_hosts, h2o_browse as h2b, h2o_import as h2i, h2o_glm
import h2o_util, h2o_browse as h2b, h2o_gbm
# use randChars for the random chars to use
def random_enum(randChars, maxEnumSize):
choiceStr = randChars
r = ... | woobe/h2o | py/testdir_single_jvm/test_GLM2_ints_unbalanced.py | Python | apache-2.0 | 6,252 | [
"Gaussian"
] | ffa735500c841b7284f66fd34374b6921f07c218aa9f885ddbb308a78de8b625 |
""" DIRAC Basic MySQL Class
It provides access to the basic MySQL methods in a multithread-safe mode
keeping used connections in a python Queue for further reuse.
These are the coded methods:
__init__( host, user, passwd, name, [maxConnsInQueue=10] )
Initializes the Queue and tries to connect to... | arrabito/DIRAC | Core/Utilities/MySQL.py | Python | gpl-3.0 | 54,673 | [
"DIRAC"
] | a59c32457fe342805a39ee905ebb537e19d327e1d9949fac85d2d61557688d6e |
# Placeholder because KDTree moved
# Remove this in version 1.0
__all__ = ['NeighborSearch']
import warnings
with warnings.catch_warnings():
warnings.simplefilter('always', DeprecationWarning)
warnings.warn(('KDTree has been removed in 0.11. Instead you can use the '
'BioPython or scikit-le... | alejob/mdanalysis | package/MDAnalysis/KDTree.py | Python | gpl-2.0 | 671 | [
"Biopython",
"MDAnalysis"
] | d8e1d4bc5b289a53d5e185f6e5fd747ad28a788d6b6418c97ad09c18fe597d0e |
from pyibex import *
from pyibex.thickset import *
from pyibex.geometry import CtcPolar
from vibes import vibes
import math
import numpy as np
vibes.beginDrawing()
class ThickRotation(ThickTest):
def __init__(self, th1, th2, y):
ThickTest.__init__(self, 2)
self.th = Interval(th1, th2)
self.y = IntervalV... | benEnsta/pyIbex | pyibex/thickset/examples/thickTransform/ex2_rotbox.py | Python | lgpl-3.0 | 4,039 | [
"VisIt"
] | b86acd690e7d9727e2865f66ddfaa851247eefc25fdaaf97405e1f7047e9182f |
import datetime
import time
import zlib
import hashlib
import redis
import re
import mongoengine as mongo
import random
import requests
import HTMLParser
from collections import defaultdict
from pprint import pprint
from BeautifulSoup import BeautifulSoup
from mongoengine.queryset import Q
from django.conf import setti... | eric-stanley/NewsBlur | apps/social/models.py | Python | mit | 137,635 | [
"BLAST"
] | 33248716eb7a1ddb22b017a8bbfc11e48163d0eae9df14b3441d1696d1d056bb |
__author__ = 'saeedamen' # Saeed Amen
#
# Copyright 2016 Cuemacro
#
# 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 ... | cuemacro/chartpy | chartpy/engine.py | Python | apache-2.0 | 96,504 | [
"ORCA"
] | 931c840cc2070103faf649834d1a110a87b5f2dc7f70f56f2472a2eb67b4dc25 |
# -*- coding: utf-8 -*-
# Documentation {{{1 #
########################
# Copyright (C) 2009-2013 Roman Zimbelmann <hut@lavabit.com>
# This configuration file is licensed under the same terms as ranger.
# ===================================================================
# This file contains ranger's commands.
# ... | alejandrogallo/dotfiles | link_config/ranger/commands.py | Python | unlicense | 38,023 | [
"VASP"
] | 55834f4b7e1307e5e1683845dc8ae1b9ee110a2a690f1696488ab4c00721af90 |
#!/usr/bin/env python
from multiprocessing import Pool
import time
import os
import sys
import argparse
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
from Bio.SeqUtils import GC
from Bio.SeqRecord import SeqRecord
#from Bio.Seq import Seq
#from Bio.Alphabet import generic_dna
# Copyrigh... | nguyenngochuy91/Ancestral-Blocks-Reconstruction | format_db.py | Python | gpl-3.0 | 12,985 | [
"BLAST"
] | 19efdfe1e37a7599eb5501b7439d4e443302118bf5d14279dc979cd7f2e79035 |
"""
Functions to calculate the downstream water surface elevation by minimizing the
difference between flows calculated via the Manning Formula for discharge and
the historical peak flood values.
(https://en.wikipedia.org/wiki/Manning_formula)
(https://en.wikipedia.org/wiki/Volumetric_flow_rate)
Author:
Matthew ... | VirtualWatershed/CoRD | cord/modelrun.py | Python | bsd-3-clause | 22,297 | [
"NetCDF"
] | 6359f02afcdb3fba36ac282f2707865a2a09d397249303992535b81f27b7ec34 |
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