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from __future__ import absolute_import
import pytest
import re
import responses
import six
from symbolic import SourceMapTokenMatch
from mock import patch
from requests.exceptions import RequestException
from sentry import http
from sentry.lang.javascript.processor import (
JavaScriptStacktraceProcessor,
dis... | looker/sentry | tests/sentry/lang/javascript/test_processor.py | Python | bsd-3-clause | 28,824 | [
"VisIt"
] | ee1519e6f1eaa028261cf2a2ef2ddc5502b88d0e56c78dcf5e1f75129203ddc6 |
########################################################################
# File : GlobusComputingElement.py
# Author : A.S.
########################################################################
""" Globus Computing Element
Allows direct submission to Globus Computing Elements with a SiteDirector Agent
Nee... | Andrew-McNab-UK/DIRAC | Resources/Computing/GlobusComputingElement.py | Python | gpl-3.0 | 9,326 | [
"DIRAC"
] | c27414e720c035b812c202751c8888388cc18622e0bff9df65f85c22d0dddb93 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
import pytest
import numpy as np
from inspect import signature
from sklearn.gaussian_process.kernels import _approx_fprime
from sklearn.metrics.pairwise \
import PAIRWISE_KERNEL_... | chrsrds/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 12,489 | [
"Gaussian"
] | 02c5639df7641906cda12a77bbc27cd8abb8023a2dba183b4f416df26c8cdace |
#!/usr/bin/env python
import argparse
import binascii
import copy
import datetime
import hashlib
import json
import logging
import os
import shutil
import struct
import subprocess
import tempfile
import xml.etree.ElementTree as ET
from collections import defaultdict
from Bio.Data import CodonTable
logging.basicConfig(... | dpryan79/tools-iuc | tools/jbrowse/jbrowse.py | Python | mit | 37,817 | [
"BLAST",
"Galaxy"
] | da55fdc77a325975ac459348a0addd527ff86ef11e10ac766bdede0909a44cb5 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | vortex-ape/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 36,009 | [
"Gaussian"
] | da720a272c64043902eb9a36d575f94fc89d9e7ca72a026053e847f5de17e8bb |
# Copyright 2013 Gokcen Eraslan. 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.
"""Unit test for Bio.PDB.NACCESS which needs NACCESS tool.
See also test_PDB.py for dependency ... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_NACCESS_tool.py | Python | gpl-2.0 | 1,259 | [
"Biopython"
] | f1dc1dec6e0777b54fe823646f2056957bc48f09c84cbfb5dba121d24ee02966 |
# -*- coding: utf-8 -*-
# This file is part of beets.
# Copyright 2016, Adrian Sampson.
#
# 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 limitation t... | lengtche/beets | beetsplug/discogs.py | Python | mit | 21,763 | [
"VisIt"
] | ef4190f001bdc2a7ca338993f920156b78826fda16acf588bc4c0e9ba7a11e8d |
# coding: utf-8
#
# Copyright 2014 NAMD-EMAP-FGV
#
# This file is part of PyPLN. You can get more information at: http://pypln.org/.
#
# PyPLN 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 o... | NAMD/pypln.backend | tests/test_worker_wordcloud.py | Python | gpl-3.0 | 1,543 | [
"NAMD"
] | b2fa2546921500a1b81d9a45a9708acc7cb5267146fd31effd38c9514f5f9bca |
# -*- coding: utf-8 -*-
def check_unresolved(locstr):
for key in fix_unresolved:
if locstr in key: return fix_unresolved[key]
def tests():
assert(check_unresolved('nyc') == 'United States')
assert(check_unresolved('perú') == 'Peru')
assert(check_unresolved('###############') == None)
prin... | yaph/gh-commit-locations | loclists.py | Python | mit | 35,900 | [
"Galaxy",
"MOOSE"
] | 4eb46a03154f4927ee1070b7698e75b8b0ec04bbaf55fbfe27e51781d162fa80 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | HuaweiSwitch/ansible | lib/ansible/modules/network/avi/avi_ipaddrgroup.py | Python | gpl-3.0 | 4,785 | [
"VisIt"
] | a727d03911e1e51a54d8c68aee40b54d12e1b90222aff874a814eb76d6ab9c42 |
# -*- coding: utf-8 -*-
r"""A collection of commonly used one- and two-dimensional functions in neutron scattering,
=============== ==========================================================
gaussian Vector or matrix norm
gaussian2d Inverse of a square matrix
lorentzian Solve a linear system of equati... | granrothge/neutronpy | neutronpy/functions.py | Python | mit | 16,146 | [
"Gaussian"
] | caf0f55501b4690e597003e21e2478a194cd55db83552dfc19c785275a15c898 |
""" Affine image registration module consisting of the following classes:
AffineMap: encapsulates the necessary information to perform affine
transforms between two domains, defined by a `static` and a `moving`
image. The `domain` of the transform is the set of points in the
`static` image'... | jyeatman/dipy | dipy/align/imaffine.py | Python | bsd-3-clause | 51,745 | [
"Gaussian"
] | 2715603cff1caf09edffa330cde53cada230f0d38d01715a5a78424ec3c82a79 |
# Version: 0.21
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/python-versioneer/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible with: Python 3.6, 3.7, 3.8, 3.9 and pypy3
* [![Latest Version][pypi... | geopandas/geopandas | versioneer.py | Python | bsd-3-clause | 80,049 | [
"Brian"
] | af355ac4100f79018973351a91141dbf00931ef07e29e633404ec033d8f5c89b |
#@+leo-ver=5-thin
#@+node:lee.20141224110313.46: * @file wsgi.py
#@@language python
#@@tabwidth -4
#@+<<decorations>>
#@+node:lee.20141215164031.47: ** <<decorations>>
import cherrypy
import os
from symbol import *
import random
from mako.lookup import TemplateLookup
#@-<<decorations>>
#@+others
#@+node:lee.20141... | dora40323106/2014cpa_final_project | wsgi.py | Python | gpl-3.0 | 4,218 | [
"VisIt"
] | 5f7e6d45be461ce5b564f8eb50329b8392e8a5dd6bf7e1ea9dcf1ad8920fec43 |
'''
This code is used only for calibration and testing to ensure the neuron models implemented using BRIAN simulator
have the same dynamics as those implemented by Yamazaki and Nagao (2012), which we base our model off of
'''
from pylab import *
class YamazakiNeuron(object):
def __init__(self, Vth, Cm, El, E... | blennon/MLI_PKJ_net | MLI_PKJ_net/yamazaki_neuron.py | Python | mit | 3,270 | [
"Brian",
"NEURON"
] | a0a6434a581f21fa000d71e848475b2cabe42dec05b14247845787efd8792ba0 |
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr, Callable, Iterable
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.models.query import QuerySet
from django.db... | amanharitsh123/zulip | zerver/models.py | Python | apache-2.0 | 82,673 | [
"VisIt"
] | 1716dacd42c413e566a22c0073c4dccf94ecd8128c541b58392a8deed88c0fa6 |
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... | ajylee/gpaw-rtxs | gpaw/analyse/vdwradii.py | Python | gpl-3.0 | 2,195 | [
"ASE",
"GPAW"
] | 523ac887dbe8e3d6994e49473abba287d406923757ca5174d2f035c5f7553f4e |
""" Python test discovery, setup and run of test functions. """
import re
import fnmatch
import functools
import py
import inspect
import sys
import pytest
from _pytest.mark import MarkDecorator, MarkerError
from py._code.code import TerminalRepr
try:
import enum
except ImportError: # pragma: no cover
# Only ... | chillbear/pytest | _pytest/python.py | Python | mit | 85,253 | [
"VisIt"
] | 926e39ba36126bd1528d2e95d88f7d11a16126c95c91016c117e960cf5587a1e |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-job-pilots
# Author : Stuart Paterson
########################################################################
"""
Retrieve info about pilots that have matched a given Job
Example:
$ dirac-admi... | ic-hep/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_get_job_pilots.py | Python | gpl-3.0 | 3,067 | [
"DIRAC"
] | c14687db947ece3a203fa78b958b2eaba477da1fd3cb23242be8e720a793eb0c |
# Copyright (C) 2010-2011 Ben Breslauer
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distribu... | bbreslauer/PySciPlot | src/modules/CurveFitting.py | Python | gpl-3.0 | 30,735 | [
"Gaussian"
] | d3a988ec52c637eaecebc788c1d07a646c1c3fa90d108ae256123d872566a887 |
from __future__ import absolute_import
from __future__ import print_function
import logging
import sys
import os
import os.path
import multiprocessing as mp
import warnings
# os.environ['R_LIBS_USER'] = '/project/projectdirs/metatlas/r_pkgs/'
# curr_ld_lib_path = ''
from metatlas.datastructures import metatlas_object... | metabolite-atlas/metatlas | metatlas/plots/dill2plots.py | Python | bsd-3-clause | 147,019 | [
"RDKit"
] | 30f5268aa3d1a2050e32072fa835b9ac226a2416c23bcee2f171da22f4bac4fd |
#!/usr/bin/env python3
########################################################################
# Solves problem 129 from projectEuler.net.
# Finds the n so that the first R(k) divisible by n is > R(10 ** 6).
# Copyright (C) 2011 Santiago Alessandri
#
# This program is free software: you can redistribute it a... | sanSS/programming-contests | project-euler/problem129.py | Python | gpl-3.0 | 1,490 | [
"VisIt"
] | 8ae9a33d8f280dacb2cee1f9a06ed369e2137189fa45fb759dc8eaea1ed1784f |
# coding: utf-8
"""Test mdn.compatibility"""
from __future__ import unicode_literals
from django.utils.six import text_type
from mdn.compatibility import (
CellVersion, CompatFeatureVisitor, CompatFootnoteVisitor,
CompatSectionExtractor, CompatSupportVisitor, Footnote,
compat_feature_grammar, compat_suppo... | renoirb/browsercompat | mdn/tests/test_compatibility.py | Python | mpl-2.0 | 41,045 | [
"VisIt"
] | 3b401840437aa1e1e826d6596ca702e108e9f17909574a535deb91223eef03d4 |
"""
========================================
Special functions (:mod:`scipy.special`)
========================================
.. module:: scipy.special
Nearly all of the functions below are universal functions and follow
broadcasting and automatic array-looping rules. Exceptions are noted.
Error handling
==========... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/special/__init__.py | Python | apache-2.0 | 21,520 | [
"Gaussian"
] | 525ce0eee1fe5b46d0b6e1081f99972402fde38720717ca5ee32402aad8a9257 |
def gather_exposures(filter, cluster):
search_params = {'path':path, 'cluster':cluster, 'filter':filter, 'PHOTCONF':PHOTCONF, 'DATACONF':os.environ['DATACONF'], 'TEMPDIR':TEMPDIR,'fwhm':1.00}
searchstr = "/%(path)s/%(filter)s*/SCIENCE/*fits" % search_params
print searchstr
files = glob(searchstr)
... | deapplegate/wtgpipeline | non_essentials/calc_test/calc_tmp.savefeb10.py | Python | mit | 31,312 | [
"Galaxy"
] | 76cf72dc03e0b29cd3e14db8567108f7cb93b7d46103338859584cc04e04297a |
"""Joint variant calling with multiple samples: aka squaring off, or backfilling.
Handles the N+1 problem of variant calling by combining and recalling samples
previously calling individually (or in smaller batches). Recalls at all positions found
variable in any of the input samples within each batch. Takes a general... | biocyberman/bcbio-nextgen | bcbio/variation/joint.py | Python | mit | 12,850 | [
"pysam"
] | d4e9c02b2bf50e85c9dda9fe80bf91a2fe1ce508d605b76b5959a4d01991c185 |
#!/usr/bin/env python
# This tests vtkAMRExtractLevel
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
class TestAMRExtractLevel(Testing.vtkTest):
def testAMR(self):
filename= VTK_DATA_ROOT +"/Data/AMR/Enzo/DD0010/moving7_0010.hierar... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/AMR/Testing/Python/TestAMRExtractLevel.py | Python | bsd-3-clause | 882 | [
"VTK"
] | 88c0326b4354fd78562f698bf5caf859c259e7f9421ffa9a86c8733675a5caa2 |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
import pytest
from sklearn.datasets import load_digits, load_iris
from sklearn.model_selection import train_test_split
from sklearn.model_selection import cross_val_score
from sklearn.utils._testing import assert_almost_equal
from sklearn.u... | ndingwall/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 33,293 | [
"Gaussian"
] | 97ee8b5d5f69a6c687330a3c476ebb33341fc7aa305e2507d5b5a06c43e0ee1d |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Dominic Lowe <d.lowe@rl.ac.uk>
#
# Contact email: d.lowe@rl.ac.uk
# ========================... | b-cube/pipeline-demo | demo/bcube_owslib/coverage/wcs100.py | Python | mit | 20,709 | [
"NetCDF"
] | b11173853304700b151070d54aef45a5bd3814ecd73a585db4e5d89e8e03ea8a |
# -*- coding: utf-8 -*-
""" Tests for student account views. """
import logging
import re
from unittest import skipUnless
from urllib import urlencode
import mock
import ddt
from django.conf import settings
from django.core import mail
from django.core.files.uploadedfile import SimpleUploadedFile
from django.core.url... | itsjeyd/edx-platform | lms/djangoapps/student_account/test/test_views.py | Python | agpl-3.0 | 28,886 | [
"VisIt"
] | dfc36a0dfde30050a0e5a32c149ffa55504ba7df23263be9841f924e5fadba05 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for CMS Video Module.
"""
import os
from mock import patch
from nose.plugins.attrib import attr
from unittest import skipIf
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.studio.video.video import Vid... | cecep-edu/edx-platform | common/test/acceptance/tests/video/test_studio_video_module.py | Python | agpl-3.0 | 12,152 | [
"VisIt"
] | f1a3b4a1056337b19ba04b4c588a893a6367b6bdaa41e506280db0405eab359b |
import ovito
import math
from ovito.io import import_file
from ovito.modifiers import *
import subprocess
import sys
if len(sys.argv)!=2:
print("%s [file]" % (sys.argv[0]))
sys.exit()
pfile=open(sys.argv[1],"r")
line=pfile.readline()
box_x=float(line.split()[2])
box_y=float(line.split()[3])
box_z=float(line.split... | russojohn/watermodeling | scripts/display_water_cell.py | Python | gpl-3.0 | 1,367 | [
"OVITO"
] | d8ecaf614ca8b462aded9a9973a782dffe993f110491ca156183c58e114afffc |
""" This tests only need the PilotAgentsDB, and connects directly to it
Suggestion: for local testing, run this with::
python -m pytest -c ../pytest.ini -vv tests/Integration/WorkloadManagementSystem/Test_PilotAgentsDB.py
"""
# pylint: disable=wrong-import-position
from DIRAC.Core.Base.Script import par... | chaen/DIRAC | tests/Integration/WorkloadManagementSystem/Test_PilotAgentsDB.py | Python | gpl-3.0 | 725 | [
"DIRAC"
] | 7a1be064339899b052094f7813d73bc1856e714495131b441f9bbaaa8d10e4b1 |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Oliver Clements <olcl@pml.ac.uk>
#
# Contact email: olcl@pml.ac.uk
# =======================... | tomkralidis/OWSLib | owslib/coverage/wcs201.py | Python | bsd-3-clause | 19,738 | [
"NetCDF"
] | a4fd5682e9d895d5d7fc4eb926099041b078af419bfd9016136705ebba1bec8f |
import os
import re
import time
import json
from collections import OrderedDict
import pkg_resources
import pandas as pd
from Bio import SeqIO
from Bio import Entrez
Entrez.email = "testing@ucsd.edu"
def untag(rule):
return re.sub('\?P<.*?>', '', rule)
def parse_antiSMASH(content):
""" Parse antiSMASH out... | NP-Omix/BioCompass | BioCompass/BioCompass.py | Python | bsd-3-clause | 11,128 | [
"BLAST"
] | e2e34400b106d8770142edd3a7d7ec944cb441e5bb433d8c63067d8952e4b79e |
# -*- coding: utf-8 -*-
"""
Deal with DER encoding and decoding.
Adapted from python-ecdsa at https://github.com/warner/python-ecdsa
Copyright (c) 2010 Brian Warner
Portions written in 2005 by Peter Pearson and placed in the public domain.
The MIT License (MIT)
Copyright (c) 2013 by Richard Kiss
Permission is here... | cvegaj/ElectriCERT | venv3/lib/python3.6/site-packages/pycoin/tx/script/der.py | Python | gpl-3.0 | 4,353 | [
"Brian"
] | 655236ebe79b4c35efeb0ea38490a70da1174725b71d357b63a25184241035e3 |
"""
gaussian.py: Classes for Gaussian estimation
"""
from __future__ import division
from __future__ import print_function
import numpy as np
from vampyre.common.utils import get_var_shape, repeat_axes, repeat_sum
from vampyre.common.utils import VpException
from vampyre.estim.base import BaseEst
class GaussEst(Base... | GAMPTeam/vampyre | vampyre/estim/gaussian.py | Python | mit | 6,954 | [
"Gaussian"
] | 724e842eec679b804f3f3ec627a59b2af81c9910f076910e4c4b78192bbf1170 |
#!/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 | lib/shrinkypic/process/__init__.py | Python | mit | 984 | [
"VisIt"
] | dc68de208dbca3bb04ec595e73890843c2c42f34bdc440cf6d71edaeac882a83 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/analysis/test_align.py | Python | gpl-2.0 | 24,653 | [
"MDAnalysis",
"VMD"
] | 30e2d34d6fdf9b9f9c137fb4bfa9e9f7b32991b7a4c71869f09009dd26d4640d |
#! /usr/bin/env python
#
# PyWeather
# (c) 2010 Patrick C. McGinty <pyweather@tuxcoder.com>
# (c) 2005 Christopher Blunck <chris@wxnet.org>
#
# You're welcome to redistribute this software under the
# terms of the GNU General Public Licence version 2.0
# or, at your option, any higher version.
#
# You can read the comp... | cmcginty/PyWeather | setup.py | Python | gpl-3.0 | 1,388 | [
"VisIt"
] | e415eddedf510a1cf097d97e5ac6aa5addfbea847191efaeaa53ea838f6d1f3b |
from pkg_resources import get_distribution
__version__ = get_distribution('BioUtil').version
__all__ = ['xzFile', 'xzopen',
'tsv', 'tsvFile', 'tsvRecord',
'vcf', 'vcfFile', 'vcfReader', 'vcfWriter',
'samFile',
'fastaFile', 'fastqFile', 'fastaRecord', 'fastqRecord',
'cachedFasta'... | sein-tao/pyBioUtil | BioUtil/__init__.py | Python | gpl-2.0 | 808 | [
"pysam"
] | fa38e71646bade2aac18066ff5b49573946b40b41206b1daaffaa3dc0f1c6c17 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
'''
Created on Jan 24, 2012
'''
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "S... | sonium0/pymatgen | pymatgen/io/tests/test_cssr.py | Python | mit | 1,887 | [
"VASP",
"pymatgen"
] | d9b5032f944bb7a8ae8ea20115b09b9fac5b232626dbfea3245fd4293d58a1fb |
"""
cclib (http://cclib.sf.net) is (c) 2006, the cclib development team
and licensed under the LGPL (http://www.gnu.org/copyleft/lgpl.html).
"""
__revision__ = "$Revision: 631 $"
from density import Density
from cspa import CSPA
from mpa import MPA
from lpa import LPA
from opa import OPA
from mbo import MBO
from frag... | keceli/RMG-Java | source/cclib/method/__init__.py | Python | mit | 370 | [
"cclib"
] | 440e2ca517cc7f2e4612a35e9958a6623b00cb32a005b243e58d13d66e635dec |
#!/usr/bin/env python
"cluster across samples using vsearch or from bam files and bedtools"
# py2/3 compatible
from __future__ import print_function
try:
from builtins import range
from itertools import izip, chain
except ImportError:
from itertools import chain
izip = zip
import os
import pty
import... | dereneaton/ipyrad | ipyrad/assemble/clustmap_across.py | Python | gpl-3.0 | 50,414 | [
"pysam"
] | f94795073341355a49cf3b6d31a296c8ecd09b5f361fe6bce30b90018a80236d |
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 25 15:50:57 2016
@author: Gaspar Pandy
"""
from build.management.commands.base_build import Command as BaseBuild
from django.db.models import Q
from protein.models import Protein, ProteinConformation, ProteinSequenceType, ProteinSource, ProteinState
from residue.models i... | protwis/protwis | structure/management/commands/new_xtals.py | Python | apache-2.0 | 35,404 | [
"CRYSTAL"
] | e74925c2321649324cbff6f0734626fd953b13726c9cc17c591fa69f813846a4 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | xguse/scikit-bio | skbio/io/_fileobject.py | Python | bsd-3-clause | 4,967 | [
"scikit-bio"
] | dd4a8b99b6b8557f3f7853c2b20171dc6ebfb9fcc6711f834c2dfc7f9e4cae83 |
# node.py
#
# Base class and non-recursive visitor implementation.
# Used by various example files.
import types
class Node:
pass
import types
class NodeVisitor:
def visit(self, node):
stack = [ node ]
last_result = None
while stack:
try:
last = stack[-1]
... | tuanavu/python-cookbook-3rd | src/8/implementing_the_visitor_pattern_without_recursion/node.py | Python | mit | 1,070 | [
"VisIt"
] | bce05a3689bc25f322081e0af4ccc746f831bd789f879f775b0f78ab6274dd9f |
"""
Spatial Error Models with regimes module
"""
__author__ = "Luc Anselin luc.anselin@asu.edu, Pedro V. Amaral pedro.amaral@asu.edu"
import numpy as np
import multiprocessing as mp
import regimes as REGI
import user_output as USER
import summary_output as SUMMARY
from pysal import lag_spatial
from ols import BaseOLS... | dfolch/pysal | pysal/spreg/error_sp_regimes.py | Python | bsd-3-clause | 64,261 | [
"COLUMBUS"
] | 83826780b2e7ffe82e746565e82194d9a778e1804e592eba7af35aec39ec4edb |
from wheezy.http import WSGIApplication
from wheezy.web.middleware import bootstrap_defaults
from wheezy.web.middleware import path_routing_middleware_factory
from config import options
from urls import all_urls
main = WSGIApplication([
bootstrap_defaults(url_mapping=all_urls),
path_routing_middleware_factor... | saggit/memerybox | app.py | Python | mit | 670 | [
"VisIt"
] | 1c80f95dcc2f4d13239ae804f74d9a0f67c408b0e39cb5c15bd912068509c5c8 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, Zhijiang Yao, Jie Dong and Dongsheng Cao
# All rights reserved.
# This file is part of the PyBioMed.
# 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 PyBioMed source tree.
"""
#####... | gadsbyfly/PyBioMed | PyBioMed/PyMolecule/molproperty.py | Python | bsd-3-clause | 7,505 | [
"RDKit"
] | 5ff2dbf6ddb1d03f98a5e5520d17c264c05da7d1dc8503292efa3de77cce6fc7 |
"""
The B{0install} command-line interface.
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _, logger
import os, sys
from optparse import OptionParser
import logging
from zeroinstall import SafeEx... | afb/0install | zeroinstall/cmd/__init__.py | Python | lgpl-2.1 | 4,351 | [
"VisIt"
] | cc57ec418443f95f28b5262ed013e20f4f9d5fcfe8034e1b19bea1da0fd2371f |
from string import capwords
from django.db import models
CAPWORDS_ATTRS = ('name', 'firstname')
class PatientManager(models.Manager):
"""
custum patient manger to modifie create and update
"""
attrs = CAPWORDS_ATTRS
# paremeter to capwords
# def create_patient(self, name=Non... | jgirardet/unolog | unolog/patients/models.py | Python | gpl-3.0 | 2,704 | [
"ASE"
] | 684c5673d32b49f7625e678e938197ef2eb501a982a3c00573ec199503b2ba18 |
import numpy as np
import pytest
from sklearn.utils._testing import assert_allclose, assert_raises
from sklearn.neighbors import KernelDensity, KDTree, NearestNeighbors
from sklearn.neighbors._ball_tree import kernel_norm
from sklearn.pipeline import make_pipeline
from sklearn.datasets import make_blobs
from sklearn.... | xuewei4d/scikit-learn | sklearn/neighbors/tests/test_kde.py | Python | bsd-3-clause | 9,814 | [
"Gaussian"
] | 99017f14d73075160081728296849c533c0878a3ebec071cf6af972976caf4db |
#
# 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... | psci2195/espresso-ffans | testsuite/python/writevtf.py | Python | gpl-3.0 | 5,876 | [
"ESPResSo"
] | 13f7e0dbfedbe3acee119dd83e9132cd8d28671c777640d76cabed02603c8fac |
#!/usr/bin/python
"""
This module contains an OpenSoundControl implementation (in Pure Python), based
(somewhat) on the good old 'SimpleOSC' implementation by Daniel Holth & Clinton
McChesney.
This implementation is intended to still be 'simple' to the user, but much more
complete (with OSCServer & OSCClient classes) ... | jsudano/WaveFront | python/OSC.py | Python | gpl-3.0 | 89,922 | [
"VisIt"
] | db7d6f2052a13ccfa55664ca499e2f2427d61a12a8f3e07b72d380c085062d41 |
## INFO ########################################################################
## ##
## COUBLET ##
## ======= ... | petervaro/coublet | widgets/media.py | Python | mit | 7,680 | [
"VisIt"
] | b9e6388ce663bae00149f8a9812286ca17f097ddf556b1989d365d8cfc254735 |
# Copyright 2016 Uri Laserson
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,... | lasersonlab/phip-stat | phip/cli.py | Python | apache-2.0 | 33,134 | [
"Bowtie"
] | 13b03c00bd01d5fb586e79e6b6948994c514fef421abb4f3c6647c91558f6761 |
import argparse
from collections import defaultdict
import numpy
import pysam
def Parser():
the_parser = argparse.ArgumentParser()
the_parser.add_argument(
'--input', action="store", type=str, help="bam alignment file")
the_parser.add_argument(
'--minquery', type=int,
help="Minim... | drosofff/tools-artbio | tools/small_rna_signatures/signature.py | Python | mit | 10,056 | [
"pysam"
] | 808be14d90dc010dd12b045f12fa644fe12a918f47bc75445dc2410563d52993 |
# Boil.py
# Aaron Taylor
# Moose Abumeeiz
#
# This is the class for the red boil that appears as an enemy
# and shoots in random directions
#
from pygame import *
from func import *
from const import *
from Enemy import *
from Animation import *
from time import time as cTime
from random import choice
from Tear impo... | ExPHAT/binding-of-isaac | Boil.py | Python | mit | 2,158 | [
"MOOSE"
] | 394db5b3a57649a4daf4aad0d011a4bdf128d3de906a96fe0f02e70fd9ccbb45 |
"""Module defining ``Eigensolver`` classes."""
import numpy as np
from gpaw.utilities.blas import axpy, gemm, rk, r2k
from gpaw.utilities.lapack import general_diagonalize
from gpaw.utilities import unpack
from gpaw.eigensolvers.eigensolver import Eigensolver
class RMM_DIIS(Eigensolver):
"""RMM-DIIS eigensolve... | robwarm/gpaw-symm | gpaw/eigensolvers/rmm_diis.py | Python | gpl-3.0 | 15,823 | [
"GPAW"
] | 69066fc0a321b5a802b63aebb92cbda126d05064da1708ae0c5eb7ce1ebf1d88 |
# suppyrFRB.py ---
#
# Filename: suppyrFRB.py
# Description:
# Author: subhasis ray
# Maintainer:
# Created: Mon Sep 21 01:45:00 2009 (+0530)
# Version:
# Last-Updated: Fri Oct 21 17:10:23 2011 (+0530)
# By: Subhasis Ray
# Update #: 129
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
... | BhallaLab/moose-thalamocortical | DEMOS/pymoose/traub2005/py/suppyrFRB.py | Python | lgpl-2.1 | 6,656 | [
"MOOSE",
"NEURON"
] | ddc7ca8d6bde6c8d1dfa8e5ef9841142784ece83e5767361b0c4065f523047ff |
'''Module containing a DensityFunc abstract class, with common probability densities
@since: Jan 10, 2013
@author: kroon
'''
from __future__ import division
import numpy as np
class Gaussian(object):
'''
Class for representing a multi-dimensional Gaussian distribution of dimension d,
given mean and c... | scjrobertson/xRange | kalman/gaussian.py | Python | gpl-3.0 | 4,271 | [
"Gaussian"
] | 628de464465455801ed54f015bba294970140620be98a11325418d3fc923aeee |
# we should be able to load in a plugin multiple times without issues,
# as long as it's the same plugin.
import sys
import paraview.simple
paraview.simple.LoadDistributedPlugin("EyeDomeLightingView", True, globals())
print 'loaded the first time successfully'
paraview.simple.LoadDistributedPlugin("EyeDomeLightingVie... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/Plugins/EyeDomeLighting/ParaViewPlugin/Testing/ReloadPlugin.py | Python | gpl-3.0 | 385 | [
"ParaView"
] | afbd33b1115f51f1dd386c5d667708b38d719ab65d4033010ba24edf88e0f8df |
# coding=utf-8
import os, datetime
from decimal import Decimal
from django.test import TestCase
from tao import workflow, time
from tao.forms import FormsGraph
from tao.output_format_form import OutputFormatForm
from tao.record_filter_form import RecordFilterForm
from tao.xml_util import xml_print, xml_parse
from t... | IntersectAustralia/asvo-tao | web/tao/tests/workflow_tests.py | Python | gpl-3.0 | 40,664 | [
"Galaxy"
] | 277fc7ff3efb7437b336558bc65747e127e8b10ea367dda9ea43ace71af0a56b |
import numpy as np
from numpy.testing import (
assert_array_equal,
)
from MDAnalysis.topology.base import squash_by, change_squash
class TestSquash(object):
atom_resids = np.array([2, 2, 1, 1, 5, 5, 4, 4])
atom_resnames = np.array(['A', 'A', 'B', 'B', 'C', 'C', 'D', 'D'],
dtyp... | alejob/mdanalysis | testsuite/MDAnalysisTests/topology/test_topology_base.py | Python | gpl-2.0 | 1,744 | [
"MDAnalysis"
] | abff8ad4474d7a9b6af9bf143b6234fe047cf506e6f6280159ec938066215e64 |
#!/usr/bin/python
# -*- coding:UTF-8 -*-
################################################################################
#
# Copyright 2010-2014 Carlos Ramisch, Vitor De Araujo, Silvio Ricardo Cordeiro,
# Sandra Castellanos
#
# XMLFormatter.py is part of mwetoolkit
#
# mwetoolkit is free software: you can redistribut... | KWARC/mwetoolkit | gui/libs/XMLFormatter.py | Python | gpl-3.0 | 2,617 | [
"VisIt"
] | 16ba3549b5e1162d4558a4597510ddf06a893209c76f6be347b5a24d860caa7a |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## 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 v... | graik/biskit | biskit/md/amberLeap.py | Python | gpl-3.0 | 8,351 | [
"Amber"
] | eacada5d9dabc6d70322dd723d312146f5f343d2172beacc3582a0034065f359 |
'''
Created on Nov 11, 2014
@author: alucard
'''
import vtk
from SceneObject import SceneObject
from Text import Text
class MenuItem(SceneObject):
def __init__(self, renderManager, width, height, parent, name, vtkTextureSelected, vtkTextureUnselected, callbackFunction = None, callbackObject = None):
... | GearsAD/semisorted_arnerve | arnerve/scene/MenuItem.py | Python | mit | 8,376 | [
"VTK"
] | 0c045cc127bf2ff8fbfb9a070c110ef05013704ab5eb96cfe3539ecc8ad4eff3 |
#
# This file is a part of Siesta Help Scripts
#
# (c) Andrey Sobolev, 2013
#
import per_atom
import per_evol
import per_type
import per_step
class Data(object):
_types = ['Function', 'Histogram', 'Time evolution']
def __init__(self):
import inspect
# dirty hack; I don't know how to populate ... | ansobolev/shs | shs/data/__init__.py | Python | mit | 1,696 | [
"SIESTA"
] | ee0c18106dbb93e53a65e211f3f329e05d7248bf5fb9a6721e01a96ba3f1c532 |
#
# 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... | KaiSzuttor/espresso | testsuite/python/interactions_dihedral.py | Python | gpl-3.0 | 7,742 | [
"ESPResSo"
] | 9e17e8de37915aabc9afa123cd7ba318e0066672e1b0a2a0d727bb5dcd549829 |
# $HeadURL: $
""" ResourceManagementClient
Client to interact with the ResourceManagementDB.
"""
from DIRAC import gLogger, S_ERROR
from DIRAC.Core.DISET.RPCClient import RPCClient
__RCSID__ = '$Id: $'
class ResourceManagementClient( object ):
"""
The :class:`ResourceManagementClient`... | Sbalbp/DIRAC | ResourceStatusSystem/Client/ResourceManagementClient.py | Python | gpl-3.0 | 41,110 | [
"DIRAC"
] | 827d5c9546966c6b0d9c7e70576d54aa40385c399e5b0feedd4c7231fc1958f4 |
# modified mexican hat wavelet test.py
# spectral analysis for RADAR and WRF patterns
import os, shutil
import time
import pickle
import numpy as np
from scipy import signal, ndimage
import matplotlib.pyplot as plt
from armor import defaultParameters as dp
from armor import pattern
from armor import objects4 as ob
... | yaukwankiu/armor | tests/modifiedMexicanHatTest8.py | Python | cc0-1.0 | 5,809 | [
"Gaussian"
] | cb8cdff0f9023c1bfcc787b1402653229d386042600f62ff53850d01ab71940f |
# -*- coding: utf-8 -*-
## Sid Meier's Civilization 4
## Copyright Firaxis Games 2005
#import string
#from time import time
#from copy import deepcopy
from threading import Timer
import re
from CvPythonExtensions import *
import CvUtil
from CvWBDesc import CvPlayerDesc
import Popup as PyPopup
import ScreenInput
impor... | YggdrasiI/PBStats | tests/Updater/Mods/Updater/Assets/Python/Screens/CvModUpdaterScreen.py | Python | gpl-2.0 | 22,672 | [
"VisIt"
] | 1e48d5a09b9010a6a5b702abf066788e815abfcf7f53c8304c7f88c79e37d0ae |
#####################################################################
# $HeadURL $
# File: ReqManagerHandler.py
########################################################################
"""
:mod: ReqManagerHandler
.. module: ReqManagerHandler
:synopsis: Implementation of the RequestDB service in the DISET framework
... | calancha/DIRAC | RequestManagementSystem/Service/ReqManagerHandler.py | Python | gpl-3.0 | 10,989 | [
"DIRAC"
] | cb906bc2500176393afc6350a76ab637798023014e34201ab555326c1cfbf6be |
#!/usr/bin/env python
from math import pi, cos, sin, sqrt
import vtk
LEVEL = 6
def as_polyline(points, level):
"""
Koch Snowflake as a vtkPolyLine
"""
# Use the points from the previous iteration to create the points of the next
# level. There is an assumption on my part that the curve is traver... | lorensen/VTKExamples | src/Python/Visualization/KochSnowflake.py | Python | apache-2.0 | 6,018 | [
"VTK"
] | e2c2a70b0ad287161e144bb719849b09adc320904bbdf78d1cde2fc26077790c |
#!/usr/bin/env python
# encoding: utf-8
import MySQLdb
import os
import re
import scrapy
from scrapy.loader import ItemLoader
from ForumSpider.items import BbsComment,BbsAsk,Person,ForumItem,ForumVisit,TopicPage
from scrapy.spiders import Spider
from scrapy.http import Request, FormRequest
from scrapy.selector import S... | zhouqilin1993/IntelliDE | crawler/ForumSpider/ForumSpider/spiders/forum_list_spider.py | Python | gpl-3.0 | 3,160 | [
"VisIt"
] | c96bc8f569cb1b506952c2411e8200c873d5179fefb92afd0cf4da9bf839c5eb |
"""
Tests the classification functions
"""
import unittest
import os
from mollib.core import Molecule, load_settings
import mollib.core.settings
from mollib.hbonds import classify_residues, find_hbond_partners, settings
def convert_dssp(string):
"""Convert a DSSP classification (like) string into a classificati... | jlorieau/mollib | tests/hbonds/test_classify.py | Python | gpl-3.0 | 4,408 | [
"CRYSTAL"
] | 4db9a3736c2e9ad72abb642eb866fb9c4c08acc5f6ac255faaa66263954d4b93 |
# 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 the G... | espressopp/espressopp | src/analysis/Pressure.py | Python | gpl-3.0 | 1,656 | [
"ESPResSo"
] | 3991c597c09fe0bbcc7a8d17616875c6e3ff68ac9592634cc907489ac5ecdca4 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import coll... | harterj/moose | python/peacock/base/PluginManager.py | Python | lgpl-2.1 | 6,979 | [
"MOOSE",
"VTK"
] | d96b71b20f8a962db2f6ee53e480baa411349f2d9f0b38a273f498de981cbc64 |
import threading
try:
from Queue import Queue
except ImportError:
from queue import Queue
from os import getenv
from .client import JobClient
from .client import InputCachingJobClient
from .client import MessageJobClient
from .client import MessageCLIJobClient
from .interface import HttpPulsarInterface
from .i... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/pulsar/client/manager.py | Python | gpl-3.0 | 8,432 | [
"Galaxy"
] | 17465becd73a8eef7d8714e48f999a0eb5a72228fb27060aec03cba77770829d |
""" Some general standard classifier routines for astronomical data. """
import pickle
import gc
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn import metrics
from pandas import DataFrame, MultiIndex
from IPython.display import display
from sklearn.preprocessing import PolynomialFe... | yen223/mclass-sky | mclearn/classifier.py | Python | bsd-3-clause | 30,619 | [
"Galaxy"
] | ee35471fb53c0e1df8e1d58000387da8e8288b223e1cbf697e36d8bbb78da80e |
from frontpage.models import Article, Profile, Media, ArticleMedia, MediaUpload, Post, Settings
from django.contrib.auth.models import User
# This function assumes that the create superuser command has already been run.
def make_testing_db():
m = Media()
m.headline = "Most ugly image"
m.lowResFile = "htt... | Technikradio/C3FOCSite | c3shop/test/tools.py | Python | bsd-3-clause | 1,768 | [
"VisIt"
] | 978d2e7c81dc142227b314c95f0085cf12ddf0cf463c80ea134ad94bfa05ea7d |
# Copyright 2016 Mycroft AI, Inc.
#
# This file is part of Mycroft Core.
#
# Mycroft Core 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 versio... | seymour-bootay/my-mycroft-skills | presence-detection/__init__.py | Python | gpl-3.0 | 4,111 | [
"VisIt"
] | bc422e19c789ff5860cb436c100c9ea7a365e0f5f5f5e4e622c73d784f652099 |
# (c) 2015, Brian Coca <briancoca+dev@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | jnerin/ansible | lib/ansible/plugins/action/patch.py | Python | gpl-3.0 | 2,558 | [
"Brian"
] | 3f66e4e87d9578f458e36bf73f61f284ea30d78e962fc7d6af5ad85be6f3ef51 |
# -*- coding: utf-8 -*-
"""Entry points for PyKEEN.
PyKEEN is a machine learning library for knowledge graph embeddings that supports node clustering,
link prediction, entity disambiguation, question/answering, and other tasks with knowledge graphs.
It provides an interface for registering plugins using Python's entr... | pybel/pybel | src/pybel/io/pykeen.py | Python | mit | 4,191 | [
"Pybel"
] | 3e271917e185b580bb4046b869947bb1141722d00191448b133f36c1987d16ab |
# Copyright (c) 2012, 2013 by California Institute of Technology
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice... | pombredanne/nTLP | tulip/gridworld.py | Python | bsd-3-clause | 65,320 | [
"VisIt"
] | aef20d08bca1a7c738ea87461649160d63e3140b358dad9f301348ee878a453d |
""" Runs through the whole range of PWM Duty Cycles
For the complete modbus map, visit the Modbus support page:
http://labjack.com/support/Modbus
Note: Low-level commands that are commented out work only for U6/U3. UE9 is a
little more complicated.
"""
import u3, u6, ue9
from time import sleep
# Open the ... | bmazin/SDR | DataReadout/ReadoutControls/lib/LabJackPython-8-26-2011/Examples/PWM-looping.py | Python | gpl-2.0 | 1,507 | [
"VisIt"
] | 29ab1d33cd6d416b7c7ba4350bf690373eee3eebf96291b9fada3bf4d3ecc1ec |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Tools for the submission of Tasks."""
from __future__ import unicode_literals, division, print_function
import os
import time
import ruamel.yaml as yaml
import pickle
from collections import deque
from date... | czhengsci/pymatgen | pymatgen/io/abinit/launcher.py | Python | mit | 48,636 | [
"ABINIT",
"pymatgen"
] | f7fb8880c68bbaabf45c2eb5136ee292f6db6ceb908d306ea2840eb608cf9755 |
#----------Import-Modules-START-----------------------------
import os
import posixpath
import pyexiv2
import urllib.parse
import threading
from bs4 import BeautifulSoup
#----------Import-Modules-END-------------------------------
#----------Global-Variables-START---------------------------
__std_links_to_visit = ["... | lennoxho/scrapper2 | lib2/scrapper2_templates.py | Python | bsd-3-clause | 6,279 | [
"VisIt"
] | 13015d19e8194b028c307a6d19be3b4a6a742c595fe147c7080a06c2b19d1605 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
from collections import OrderedDict
from io import StringIO
import itertools
import re
import warnings
import numpy as ... | czhengsci/pymatgen | pymatgen/io/lammps/data.py | Python | mit | 45,838 | [
"LAMMPS",
"pymatgen"
] | a8b74c45d89b1351e813cb4976af9122d26a44d09dfacb7aa728a0d2491133fb |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/tree/_tree.py | Python | bsd-3-clause | 88,326 | [
"VisIt",
"scikit-bio"
] | 8068bacedc1e96be2db0fbb96f6adfd12be1f692ffbe536f485e96d0b951ec49 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes used to enumerate surface sites
and to find adsorption sites on slabs
"""
import numpy as np
from pymatgen import Structure, Lattice, vis
import itertools
import os
from monty... | blondegeek/pymatgen | pymatgen/analysis/adsorption.py | Python | mit | 31,445 | [
"Jmol",
"pymatgen"
] | 7383d31e1be0b62fc8ca19ac3f72917885d3b61c2e5161322084a3156adb2d6d |
# $HeadURL$
""" ErrorMessageMonitor gets new errors that have been injected into the
SystemLoggingDB and reports them by mail to the person(s) in charge
of checking that they conform with DIRAC style. Reviewer option
contains the list of users to be notified.
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Base... | Sbalbp/DIRAC | FrameworkSystem/Agent/ErrorMessageMonitor.py | Python | gpl-3.0 | 3,908 | [
"DIRAC"
] | f7ab8298266b282ee8cea883fd092486621dd22e7b79cb404725f9f42e9ff047 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes Authors All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unle... | Kaffa-MY/kubernetes | hack/boilerplate/boilerplate.py | Python | apache-2.0 | 5,204 | [
"VisIt"
] | 6e5f00b7268f417d916b8fb331cf462098fcfe8c583a716264900a69becf7586 |
# 10.07.2007, c
# last revision: 25.03.2008
from __future__ import absolute_import
from sfepy import data_dir
from sfepy.mechanics.matcoefs import stiffness_from_lame
filename_meshes = ['/meshes/3d/cube_medium_tetra.mesh',
'/meshes/3d/cube_medium_tetra.mesh',
'/meshes/3d/cube_medi... | rc/sfepy | tests/test_elasticity_small_strain.py | Python | bsd-3-clause | 5,744 | [
"VTK"
] | bb76c97630d6079426556f72ee3d3761d77ef1345fef20f7d15ff0da2b9b56ec |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''Copyright (C) 2012 Computational Neuroscience Group, NMBU.
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at you... | LFPy/LFPy | LFPy/run_simulation.py | Python | gpl-3.0 | 7,588 | [
"NEURON"
] | 7cb534882dd06f03d13dc106bd5bdfc5026276b44f12fe89a37a7742481c9833 |
# Local Polynomial Approximation Smoother using Numba JIT Acceleration - single thread version
#
# Smooths the data by fitting a 2nd order polynomial to a small window around
# each data sample using gaussian weighted least squares. This implementation uses the Numba JIT to
# accelerate the convolution.
#
import sys,o... | waynegm/OpendTect-Plugins | bin/python/wmpy/Experimental/LocalPolynomialApproximation/ex_lpa_smooth_single.py | Python | gpl-3.0 | 1,916 | [
"Gaussian"
] | 6dcfc1b09cfbe45f9b94f43cccb815a86b938e37e0dde40ca2bf786cc419f421 |
#
# -*- coding: utf-8 -*-
#
# Copyright (C) 2008-2011 Red Hat, Inc.
# This file is part of python-fedora
#
# python-fedora is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the Li... | fedora-infra/python-fedora | fedora/wsgi/csrf.py | Python | lgpl-2.1 | 12,944 | [
"VisIt"
] | a40fe88feabb5daa38f48e6a0bd11669b42be86cf23bb629e234cb2112805e0d |
#!/usr/bin/env python
from __future__ import division
import os
import argparse
import console
import fileinput
"""
When running BLAST with GenBank (INSDC) data using seperate partitions, this script
helps to merge different BLAST results together by sorting best hits using BLAST
score. Input is taken from STDIN,... | ut-planteco/ssu-pipeline | pipeline_merge_blasts.py | Python | gpl-3.0 | 941 | [
"BLAST"
] | ac66b51ec22dc20bb4ffcac986928522890cfcb1c48753cae6e3a1a146505a65 |
"""
Global configurations
"""
import os
'''
Dirs
'''
# Directory for pickled data
DATA_DIR = './data'
# Directory for temporary data
TMP_DIR = './tmp'
# Directory for figures
FIG_DIR = './fig'
# Directory for human-readable data
HR_DIR = './hr'
# Directory for news and tweets data by Dr. Meng Jiang
# DEPRECATED
M... | adamwang0705/cross_media_affect_analysis | develop/config.py | Python | mit | 8,394 | [
"Brian"
] | fcb8e7e82c7166129d5dbba01f2b33103e538c3b8ac8fce07b89312f10902fe2 |
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