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# coding: utf-8
from __future__ import division, unicode_literals
"""
Created on Mar 18, 2012
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyue@mit.edu"
__date__ = "Mar 18, 2012"
import unittest
import ... | Dioptas/pymatgen | pymatgen/apps/borg/tests/test_queen.py | Python | mit | 1,133 | [
"pymatgen"
] | d01ad9dc8a26c5857b20c668984657f6c4dd1a1e9c7a09a0104c24a463b4e824 |
# encoding: utf-8
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding model 'Protein'
db.create_table('neuroelectro_protein', (
('id', self.gf(... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0001_initial.py | Python | gpl-2.0 | 11,097 | [
"NEURON"
] | 84e149d92a89cf841ef7ddb95e8094726ab5bd983874325e17260e3a6fbf5841 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RPreprocesscore(RPackage):
"""A collection of pre-processing functions
A library o... | LLNL/spack | var/spack/repos/builtin/packages/r-preprocesscore/package.py | Python | lgpl-2.1 | 934 | [
"Bioconductor"
] | d42cfb5582a1cdc0a8f9f7236058b590465431933129c64b5df286bfd28bc020 |
###############################################################################
# #
# 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 #
... | dparks1134/mingle | mingle/blast_workflow.py | Python | gpl-3.0 | 27,972 | [
"BLAST"
] | 9ea6c1ae2165930daefd7e005e6c66e71ffbae465c21648b2c9f74b702033c20 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.intersphinx',
'sphinx.ext.viewcode',
'sphinx.ext.graphviz',
'sphinx.ext.imgmath',
'matplotlib.sphinxext.plot_directive'
]
source_suffix = '.rst'
master_doc = 'index'
project = 'J... | rosswhitfield/javelin | docs/conf.py | Python | mit | 1,331 | [
"ASE"
] | 83bd4bacb03ba6003eb6a39076035a03b4ae2988e8384ad8bd41777e127a4ae9 |
#!/usr/bin/env python
#
# Prepares Amazon network to run either vagrant-development or
# vagrant-production. Configures subnets, virtual private clouds,
# security groups, etc
#
# Currently is a one-way operation, you have to delete these
# manually. Visit https://console.aws.amazon.com/vpc and remove the
# VPC tagg... | PermeAgility/FrameworkBenchmarks | deployment/vagrant-aws/setup_aws.py | Python | bsd-3-clause | 5,828 | [
"VisIt"
] | e0eee4445962e2389d93c8e48eae82975b48304ae554ad5618c754b534bf4e5e |
#
# rml_send_gui
# graphical interface for sending jobs to the Roland Modela
#
# Brian Mayton <bmayton@media.mit.edu>
# MIT 2011-2014
#
# (c) Massachusetts Institute of Technology 2011-2014
# Permission granted for experimental and personal use;
# license for commercial sale available from MIT.
# imports
from __futu... | fibasile/pi.mill | pimill/server/rml_send.py | Python | mit | 10,028 | [
"Brian"
] | eb5549c94a3bcb082ed9f1434fd5bb41741120ae1fad3dee007c7e7600c4ac5a |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2010 Brian G. Matherly
# Copyright (C) 2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | gramps-project/gramps | gramps/gen/display/name.py | Python | gpl-2.0 | 45,879 | [
"Brian"
] | ded1903dc3a5cd5bf960a20c04e93170288878728f234e926f4bcbbd5a2936b7 |
import base64
import zlib
import json
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from DIRAC.Core.Utilities import DEncode
from DIRAC.Core.DISET.ThreadConfig import ThreadConfig
from DIRAC.FrameworkSystem.Client.UserProfileClient import UserProfileClient
class UPHandler( WebHandler ):
A... | chaen/WebAppDIRAC | WebApp/handler/UPHandler.py | Python | gpl-3.0 | 12,236 | [
"DIRAC"
] | 44f962640b154a859078e42af0841b97e3cfc0eef094f7171dcadfb703f25abb |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from builtins import range, object
import sys
sys.path.append('../')
try:
import vtk
except ImportError:
pass
from mupif import Timer
import numpy as np
from mupif import Mesh
#from mupif import VertexserverHost
from mupif import Cell
from mupif import Field
from... | mupif/mupif | obsolete/EnsightReader.py | Python | lgpl-3.0 | 9,660 | [
"VTK"
] | 897aa0d795151f82a6f48794e2af3a6a43c9df3e79f69ef93f8e49b8ce172755 |
# -*- coding: utf-8 -*-
from __future__ import (unicode_literals, division, absolute_import, print_function)
store_version = 9 # Needed for dynamic plugin loading
__license__ = 'GPL 3'
__copyright__ = '2011-2014, Tomasz Długosz <tomek3d@gmail.com>'
__docformat__ = 'restructuredtext en'
import urllib
from base64 imp... | sharad/calibre | src/calibre/gui2/store/stores/woblink_plugin.py | Python | gpl-3.0 | 3,887 | [
"VisIt"
] | 687063b1a07487dbc28e64d2f826a9664a1958e2d287aa38d8e4ae96cef4da2e |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | Achuth17/scikit-bio | skbio/sequence/_protein.py | Python | bsd-3-clause | 3,712 | [
"scikit-bio"
] | 27638293c55f06c955e59ba50f373d8fe17bb60e2942c00aafbe513342288431 |
from django.core.management.base import BaseCommand, CommandError
from django.conf import settings
from optparse import make_option
import os
import sys
import glob
import shutil
try:
set
except NameError:
from sets import Set as set # Python 2.3 fallback
# Based on the collectmedia management command by Brian... | ingenieroariel/pinax | apps/misc/management/commands/build_media.py | Python | mit | 11,666 | [
"Brian"
] | 8bf4db758ad5427a703de13c0bd358ae2194a9a0e071e962f3d24f22ca7061bf |
import nibabel as nib
import numpy as np
from sklearn.mixture import GaussianMixture
def assign_gaussian(data, n_components, covariance_type,
init_params='kmeans',
n_init=50,
):
classifier = GaussianMixture(
n_components=n_components,
covariance_type=covariance_type,
init_params=init_params,
n_init=n_init,... | IBT-FMI/SAMRI | samri/analysis/segmentation.py | Python | gpl-3.0 | 2,769 | [
"Gaussian"
] | 1649673b66a4b5153b429ceb1a83490542e68f6a11b71b57280e36b51966ff2c |
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | redhat-cip/horizon | horizon/base.py | Python | apache-2.0 | 39,033 | [
"VisIt"
] | f96c5b658cbe5fd93dc90afcaabf36983bd80b7eb60c871e0a35094126f5d5fe |
import ops_piggybacker as oink
import openpathsampling as paths
from .tools import *
from . import common_test_data as common
from openpathsampling.tests.test_helpers import make_1d_traj
import os.path
import sys
try:
import mdtraj as md
except ImportError:
HAS_MDTRAJ = False
else:
HAS_MDTRAJ = True
clas... | dwhswenson/OPSPiggybacker | ops_piggybacker/tests/test_one_way_tps_converters.py | Python | lgpl-2.1 | 14,133 | [
"Gromacs",
"MDTraj",
"OpenMM"
] | a9691d0481fbbfa4946b030a087028c469c419e8fdb68bf5a448e9a5f7e2c26e |
def main():
"""
Takes in an existing bad pixel mask, and additionally masks out inner radii of galaxy
Version history
2013.10.17 - Eric Gentry - initial draft completed
"""
from astropy.io import fits
import numpy as np
###
main_dir = '/home/egentry/Data/HST/Picto... | egentry/Galaxy_Subtraction | Create_OuterRadii_mask.py | Python | gpl-2.0 | 1,291 | [
"Galaxy"
] | d9b3abed6a7e39cc0ec0331f22641f197a0037e69b12bbd12ce92f115914037c |
tests=[
("testExecs/test1.exe","",{}),
("testExecs/testMolSupplier.exe","",{}),
("testExecs/testMolWriter.exe","",{}),
("testExecs/testTplParser.exe","",{}),
("testExecs/testMol2ToMol.exe","",{}),
]
longTests=[]
if __name__=='__main__':
import sys
from rdkit import TestRunner
failed,tests = TestR... | soerendip42/rdkit | Code/GraphMol/FileParsers/test_list.py | Python | bsd-3-clause | 380 | [
"RDKit"
] | 1205d9a3c9094f94767a09bacace7af341d62d3669c03842070ae103b4cc6578 |
#!/usr/bin/python
# from https://github.com/jameslz/benchmark
import sys
if len(sys.argv) != 4:
print "\nUsage: %s <alignment> <evalue> <bit_score>\n" % sys.argv[0]
sys.exit(1)
blast = sys.argv[1]
max_evalue = float(sys.argv[2])
min_bit_score = float(sys.argv[3])
with open(blast, 'r') as fp:
... | DawnEve/bio_scripts | blast/blast_best_hit_outfmt6.py | Python | mit | 703 | [
"BLAST"
] | 0b0ae42fc6cdae4659aee9c88174b62345c0eb946c0f44cebd50f3245f7592c4 |
'''
* Author: Lukasz Jachym
* Date: 9/14/13
* Time: 3:43 PM
*
* This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.
* To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.
'''
from collections import namedtuple
import csv
... | b1r3k/recruitment-challanges | data-hacking/src/task1/task1_crunchstats.py | Python | mit | 6,464 | [
"VisIt"
] | 4ff492d176621d93b3f76a93dabd619d27e3be7150677a6b3976c783719a5cf6 |
import numpy as np
from scipy import interpolate
from progressbar import ProgressBar, Bar, Percentage
class ImpulseResponseFunction(object):
'''Internal bemio object to contain impulse response function (IRF) data
'''
pass
class WaveElevationTimeSeries(object):
'''Internal bemio object to contain wave... | NREL/OpenWARP | source/automated_test/bemio/data_structures/wave_excitation.py | Python | apache-2.0 | 4,833 | [
"exciting"
] | 1ca4e4a98c7d2b1ede7358ab4873935ebb08cbeeb7594e7c5b93423602ab309f |
'''
NOTE: This is adapted from
http://sociograph.blogspot.com/2011/11/scalable-mean-shift-clustering-in-few.html
'''
import numpy as np
from sklearn.neighbors import BallTree, NearestNeighbors
from sklearn.utils import extmath
from sklearn.metrics.pairwise import euclidean_distances
from collections import defaultdic... | colincsl/pyKinectTools | pyKinectTools/algs/MeanShift.py | Python | bsd-2-clause | 3,990 | [
"Gaussian"
] | 5a8f764fd76794e00edb7e8b032075888c0800d6d2dd04b9e8a4b6f3e0a02a8e |
# -*- coding: utf-8 -*-
#
# synaptic_elements.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Licen... | zifeo/nest-simulator | pynest/nest/tests/test_msp/synaptic_elements.py | Python | gpl-2.0 | 3,443 | [
"Gaussian",
"NEURON"
] | 930b22ef5c45bc255e25b717484e2b449b8562a632e5028c3012a4da3271e1a9 |
import os
import pprint
import sys
import textwrap
import py
import pytest
from _pytest.config import ExitCode
from _pytest.main import _in_venv
from _pytest.main import Session
from _pytest.pytester import Testdir
class TestCollector:
def test_collect_versus_item(self):
from pytest import Collector, It... | alfredodeza/pytest | testing/test_collection.py | Python | mit | 44,974 | [
"VisIt"
] | 72dcff1ef27338a2b29bc60893f9efd83050078a273dec31f185cf42d5b3d671 |
"""
# Definition for a Node.
class Node(object):
def __init__(self, val=0, left=None, right=None, next=None):
self.val = val
self.left = left
self.right = right
self.next = next
"""
# 核心思路
# 为了连接第N+1层的结点的sibling，我们需要在第N层操作（因为需要访问左右子结点）
# 利用start来逐层向下，并且在每一层用p遍历每一个节点；这一层的sibling已经在遍历... | kingsamchen/Eureka | crack-data-structures-and-algorithms/leetcode/populating_next_right_pointers_in_each_node_q116.py | Python | mit | 1,150 | [
"VisIt"
] | 500bcefdb47ae5596c5eabe313aec4d47de54cd66039323070c7cd95551c7c66 |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
import collections
import logging
import threading
import itertools
import time
import types
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
... | nateprewitt/pipenv | pipenv/vendor/concurrent27/futures/_base.py | Python | mit | 22,424 | [
"Brian"
] | 96f12df22f52336066489cae99977c99fc5d0882afc1530a796fa5e50c9fa602 |
# $Id$
#
# Copyright (C) 2007-2008 Greg Landrum
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from rdkit import Chem
from rdkit.Chem import AllCh... | adalke/rdkit | rdkit/Chem/MolDb/Loader_orig.py | Python | bsd-3-clause | 6,608 | [
"RDKit"
] | 9ea8f9d6e082dd1715ec032b747c156e254c3ea2b90e71757d161fca940c07ca |
"""
Utilities for traversing `CWNode` trees.
"""
from collections import deque
def preorder_traversal(node, start=None, end=None) -> "iterator(CWNode)":
"""
Yields every node in the tree. Each node is yielded before its descendants.
Mutation is disallowed.
- *start*: If specified, only yield nodes f... | irskep/computerwords | computerwords/cwdom/traversal.py | Python | bsd-3-clause | 5,871 | [
"VisIt"
] | 5bf1475198f0596e6605e8bac65d1a8ff565fff31334f316f0c1d870fb6dc13b |
import numpy as np
from . import atomic_mass
class Atom:
# Static variables #
one_letter_elements = {"H","B","C","N","O","F","P","K","S","V","I","U","Y","W","I"} # one letter elements
two_letter_elements = {"He","Li","Be","Ne",
"Na","Mg","Al","Si","Cl","Ar","C... | alinar/Molar | molar/atom.py | Python | gpl-2.0 | 4,127 | [
"Gromacs",
"VTK"
] | f71ce69bb80084c711e2fd97a429832504eef61e6c54bdc5e73f6e5089da007c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2012 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2012-2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | sam-m888/gramps | gramps/plugins/textreport/ancestorreport.py | Python | gpl-2.0 | 14,703 | [
"Brian"
] | 42e9c9327ebac2a3196c342e52fbf937e5490ad49a6a077e30f8898d7f15b6af |
#!/usr/bin/python
## Adapted from code sample in
## http://stackoverflow.com/questions/11685716/how-to-extract-chains-from-a-pdb-file
##
## Change includes reading domain names from PDB40D file
from os.path import expanduser
from Bio import PDB
USER_HOME = expanduser("~")
INFILE = "%s/Downloads/pdb40d_j.fa" %USE... | xulesc/general | download_pdb40d.py | Python | gpl-3.0 | 3,243 | [
"CRYSTAL"
] | bca1b478dc480dae1f9ba2bc8eb4606039964f34cc457ec9eb4fa295fcca3051 |
# -*- test-case-name: pyflakes -*-
# (c) 2005-2010 Divmod, Inc.
# See LICENSE file for details
import __builtin__
import os.path
import _ast
from . import messages
# utility function to iterate over an AST node's children, adapted
# from Python 2.6's standard ast module
try:
import ast
iter_child_nodes = as... | pronto/dotfiles | .vim/pylibs/pyflakes/checker.py | Python | bsd-2-clause | 22,259 | [
"VisIt"
] | bdb745b9ae6a0922d67223cb6f7cfdbb47ad284d3301eeee82be8326933c0def |
import os
import pathlib
from .. import cgns, h5m, vtu, xdmf
from .._common import error
from .._helpers import _filetypes_from_path, read, reader_map
def add_args(parser):
parser.add_argument("infile", type=str, help="mesh file to decompress")
parser.add_argument(
"--input-format",
"-i",
... | nschloe/meshio | src/meshio/_cli/_decompress.py | Python | mit | 1,480 | [
"VTK"
] | 1d2d471a519d75c32e7150bf1aca44c6d3a4e8978bd58ae51959f21d5fc19509 |
"""
MUSE -- A Multi-algorithm-collaborative Universal Structure-prediction Environment
Copyright (C) 2010-2017 by Zhong-Li Liu
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
version 2 of ... | zhongliliu/muse | muse/Symmetry/Findspg.py | Python | gpl-2.0 | 1,216 | [
"VASP"
] | 6f8967530cc3c3b8c6bfa69de843dbc0482ed6e22e3288bc8226662718167d38 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Tests for the bencode parser plugin for Transmission BitTorrent files."""
from __future__ import unicode_literals
import unittest
from plaso.lib import definitions
from plaso.parsers import bencode_parser
from tests.parsers.bencode_plugins import test_lib
class Be... | rgayon/plaso | tests/parsers/bencode_plugins/transmission.py | Python | apache-2.0 | 1,970 | [
"Brian"
] | 0d24317362a161808602ce70b262ee0462bfbf23c904ce8c0aeda327643a89dd |
########################################################################
#
# (C) 2013, James Cammarata <jcammarata@ansible.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 ... | fernandezcuesta/ansible | lib/ansible/cli/galaxy.py | Python | gpl-3.0 | 31,758 | [
"Galaxy"
] | 0e7bdd2f65b312a75b59fb88f6f14ce645f72fd30baa3b5b7f3f05212dedc518 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/diversity/alpha/_chao1.py | Python | bsd-3-clause | 6,329 | [
"scikit-bio"
] | 947fa6461dd3e7cdfbdb71d7f6befd6df70fd95b97d4519101ace42131595669 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright (c) 2015, PAL Team.
# All rights reserved. See LICENSE for details.
CHAINS = set([
"A&W Restaurants",
"America's Incredible Pizza Company",
"Applebee's",
"Arby's",
"Arctic Circle Restaurants",
"Arthur Treacher's Fish & Chips",
"Atlanta Bre... | Machyne/pal | pal/name_entities/chains.py | Python | bsd-3-clause | 6,461 | [
"MOE"
] | cfafe871e374e4b7ccf544f25bbf447f3dd59b36f65bf022b39a9a066f70940e |
# Copyright 2004-2017 Tom Rothamel <pytom@bishoujo.us>
#
# 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 the rights to use, copy, modify, m... | kfcpaladin/sze-the-game | renpy/atl.py | Python | mit | 51,943 | [
"VisIt"
] | 226860d327027d13c583e799b5ae51d58304a2138384466066b6a52d95512537 |
from parametrized_set import ParametrizedSet
from sympy import integrate, Expr, Number, NumberSymbol, S
#FIXME 0-measure
#FIXME Dirac measure
#FIXME allow numeric for special set.
# computing quad points for triangles
class Measure(object):
'''Integral over domain describing points in Cartesian coordinate system.... | MiroK/vector_calculus | vector_calculus/measures/measure.py | Python | mit | 3,144 | [
"DIRAC"
] | 3d76bc94346e3b6ee1b9c4008fb0ce5ebaddf52c8d76595047e3fb625a2864c9 |
import urllib.request, urllib.parse, urllib.error
import urllib.request, urllib.error, urllib.parse
import re
try:
import json
except ImportError:
import simplejson as json
__author__ = 'Ehsan Foroughi'
__email__ = 'ehsan.foroughi@teltub.com',
__copyright__ = 'Copyright 2010, TELTUB Inc'
__credits__ = ['Ehsan... | mtmosier/gateAlarm | gateAlarmLib/pygvoicelib.py | Python | gpl-3.0 | 13,082 | [
"VisIt"
] | 865515bf2b35862be497572d1a1d7a2769d36d6f614fa1fc8a7ec406c02aaefd |
#red blue green rbg, dashes squares triangles -- s ^
from ase.io import read
from ase.io.trajectory import PickleTrajectory
from ase.calculators.neighborlist import NeighborList
import matplotlib.pyplot as plt
from ase.units import fs, kB
from matplotlib.backends.backend_pdf import PdfPages
def plot_energies(path,md_t... | csmm/multiase | plot/plot_e_bond.py | Python | gpl-2.0 | 4,293 | [
"ASE"
] | 4cdb2809a0d69982dc621f4f716314d1a9b4c1722925880a371a5a142ace9989 |
#!/usr/bin/env python
import argparse
import csv
import alnclst
import code
import copy
from os import path
from Bio import AlignIO, SeqIO
from Bio.SeqRecord import SeqRecord
from hyperfreq.cluster import load_cluster_map, parse_clusters
from hyperfreq.core import Alignment, AlignmentSet, analysis_defaults
from hyperf... | fhcrc/hyperfreq | hyperfreq/scripts/cli.py | Python | gpl-3.0 | 16,714 | [
"Biopython"
] | 6ce6b75f9fd8a428a0f7368ea21f8c35474902c1f8921d4a94f362762e8c3f5b |
"""
This is used to test the ElasticSearchDB module. It is used to discover all possible changes of Elasticsearch api.
If you modify the test data, you have to update the test cases...
"""
import unittest
import datetime
import time
from DIRAC import gLogger
from DIRAC.Core.Utilities.El... | hgiemza/DIRAC | tests/Integration/Test_ElasticsearchDB.py | Python | gpl-3.0 | 15,280 | [
"DIRAC"
] | 50d216f3ed5bc94869fe3639eda525a7c8d12e6d5880dfe8bbe863caa0384541 |
#!/usr/bin/python
class Node:
"""Klasa reprezentujaca wezel listy jednokierunkowej."""
def __init__(self, data=None, next=None):
self.data = data
self.next = next
def __str__(self):
return str(self.data) # bardzo ogolnie
def traverse(node, visit):
"""Iteracyjne przejscie p... | Damian9449/Python | lab9_strukturyDanych/9.1.py | Python | mit | 1,655 | [
"VisIt"
] | 67781897386999870d9361577c306180948ce68b531a7cc455a05e89c199d901 |
from scipy import io
import numpy as np
from evtk.hl import imageToVTK
from evtk.hl import gridToVTK
test = {}
io.loadmat('iCPC3D04a_v3d_x1_uint8.mat',mdict=test)
vox3dnp = np.array(test['vox3d'])
imageToVTK('./test', origin=(0.0,0.0,0.0), spacing = (sp,sp,sp), cellData = {'grayscale': np.ascontiguousarray(vox3dnp)})... | kayarre/dicomwrangle | mat2vtk.py | Python | bsd-2-clause | 919 | [
"VTK"
] | c1e9ffba9c8f813bcc9d886c08b27828ba8d281d542c9b0b4b1babc419f6ea08 |
# Copyright (C) 2010-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | hmenke/espresso | src/python/object_in_fluid/oif_utils.py | Python | gpl-3.0 | 22,295 | [
"ESPResSo",
"ParaView",
"VTK"
] | ce52e51cca5207de0799fec51c714ee7dd558ecd44abce30aa68ee9e089eb7e6 |
import os
import re
import glob
import shutil
from nose.tools import (assert_true, assert_equal, assert_is_not_none)
import nipype.pipeline.engine as pe
import qixnat
from qixnat.helpers import xnat_path
from qipipe.pipeline import registration
from ... import (ROOT, PROJECT, CONF_DIR)
from ...helpers.logging import lo... | ohsu-qin/qipipe | test/unit/pipeline/test_registration.py | Python | bsd-2-clause | 5,168 | [
"VisIt"
] | 38d895295aef63e14b85041be5b81409ec646de05edfa5c0f44ead97d31b0ab5 |
#
# The Python Imaging Library.
# $Id$
#
# the Image class wrapper
#
# partial release history:
# 1995-09-09 fl Created
# 1996-03-11 fl PIL release 0.0 (proof of concept)
# 1996-04-30 fl PIL release 0.1b1
# 1999-07-28 fl PIL release 1.0 final
# 2000-06-07 fl PIL release 1.1
# 2000-10-20 fl PIL release 1.1.1... | isabernardes/Heriga | Herigaenv/lib/python2.7/site-packages/PIL/Image.py | Python | mit | 95,395 | [
"Gaussian"
] | 47764c8c51bdae16d8bb45b08996be2650d4dd624e0d1ab2f3545a97be41884c |
#-------------------------------------------------------------------------------
# Name: module1
# Purpose:
#
# Author: Eli
#
# Created: 06/04/2014
# Copyright: (c) Eli 2014
# Licence: <your licence>
#-------------------------------------------------------------------------------
def m... | ejspina/Gene_expression_tools | Python/FilterByID_batch_oneID.py | Python | gpl-2.0 | 1,685 | [
"BLAST"
] | 326c24fa04f6a3cdf0b3469c9c871247509b0f321d0e46f5855f9253d27e05b1 |
"""
=======================================
Calculate number of Si in a LAMOST pixel
=======================================
*By: Jianrong Deng 20170517
-------------------
"""
##############################################################################
# LAMOST pixel size 12 um x 12 um
# pixel thickness, no... | jianrongdeng/LAMOST | ana/scripts/pixel_number-of-Si.py | Python | gpl-3.0 | 814 | [
"Avogadro"
] | 7905aece94a220740acc60d44949e03f0b2169224ba4e4cc9b09c2919ce706a0 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_dataset_service.py | Python | apache-2.0 | 154,357 | [
"Octopus"
] | 6fe2fe9d7eccc976a7ccd2f8213b26289f4a983445339f16015dfccdf572d22f |
# 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.
#
"""Model a single layer in a nueral network.
These classes deal with a layers in the neural network (ie. the input layer,
hidden layers and the outp... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/NeuralNetwork/BackPropagation/Layer.py | Python | gpl-2.0 | 11,144 | [
"Biopython"
] | 09d3b748e20726a7bfef95a0c94dd445ac7b986fdabc520450209363712e6e7c |
import tensorflow as tf
from .template import BaseLayer
class Dropout(BaseLayer):
@BaseLayer.init_name_scope
def __init__(self, dropout_below=0.5, noise_shape=None):
'''
Args:
dropout_below(float): probability of the inputs from the layer below
been masked out
... | hycis/TensorGraph | tensorgraph/layers/noise.py | Python | apache-2.0 | 1,668 | [
"NEURON"
] | b935333a76a1a3d72fde96096a56911145f8b00c286a0203f8040539404a6cb4 |
# -*- coding: utf-8 -*-
# note that internally 'yes'/'no' are converted to True/False; and so one can use 'yes'/'no'
# but definitely *do not* use 'True'/'False' since they are not the same as True/False...
# CSSSTYLESHEET presupposes './server/css' as part of its path; i.e. you
# will want to put custom CSS in the s... | e-gun/HipparchiaServer | server/sample_settings/htmlandcssstylesettings.py | Python | gpl-3.0 | 3,185 | [
"VisIt"
] | 4a148461f4335ac3e0a07ae141fbc814876bf202c798eb8041263a62d45568c4 |
#!/usr/bin/env python
""" Convert BLOSUM62 from log odds to a probability matrix
This script is used to generate ``hw2/blosum62.py`` by calling::
python convert_blosum.py > hw2/blosum62.py
BLOSUM62 uses the log odds of the probability of an amino acid substitution
to align protien sequences. The CPASS similarit... | david-joy/bmi203-hw2 | convert_blosum.py | Python | apache-2.0 | 2,448 | [
"BLAST"
] | e703f2c3fccddd5bfc8171b5018bb030f81c368b389d9e19479c4c38131aa775 |
""" Test Gaussian estimator. """
import numpy as np
import unittest
from .. import gaussian
class TestShortHash(unittest.TestCase):
def test_gaussian_init(self):
data = np.random.normal(3, 0.5, size=10)
estimator = gaussian.GaussianEstimator(data)
class TestGaussianEstimator(unit... | andycasey/snob | snob/tests/test_gaussian.py | Python | mit | 3,591 | [
"Gaussian"
] | aa05537ef4f710950efa396fa0d922138bf4e7c23e55f75645eaa5d20c2c85b4 |
"""
ioHub
.. file: ioHub/examples/ioHubAccessDelayTest/run.py
Copyright (C) 2012 Sol Simpson
Distributed under the terms of the GNU General Public License (GPL version 3 or any later version).
.. moduleauthor:: Sol Simpson <sol@isolver-software.com> + contributors, please see credits section of documentation.
.. file... | peteristhegreat/ioHub | examples/ioHubAccessDelayTest/run.py | Python | gpl-3.0 | 13,760 | [
"Gaussian"
] | ce17680dcc7e4dde790ae9db6dcfedbe6a4bf6f6580b9f1d4cba33f5b89c073c |
from __future__ import division
from . import cholesky_errors, mahalanobis, VariogramFourthRoot
from . import pivoted_cholesky
import numpy as np
from numpy.linalg import solve, cholesky
from scipy.linalg import cho_solve
import scipy.stats as stats
from statsmodels.sandbox.distributions.mv_normal import MVT
import se... | jordan-melendez/buqeyemodel | gsum/diagnostics.py | Python | mit | 26,203 | [
"Gaussian"
] | 71fe4bc969e9590d3b2cc2ebb02f99106f4e4f6d7adbb25398216a87d60b2874 |
# Author: David Goodger
# Contact: goodger@users.sourceforge.net
# Revision: $Revision: 21817 $
# Date: $Date: 2005-07-21 13:39:57 -0700 (Thu, 21 Jul 2005) $
# Copyright: This module has been placed in the public domain.
"""
Docutils document tree element class library.
Classes in CamelCase are abstract base classes ... | garinh/cs | docs/support/docutils/nodes.py | Python | lgpl-2.1 | 57,112 | [
"VisIt"
] | 9d252f3d7115099da8a25e5d01521493a7c0edf0d4a7662dcd85a2d611ef969d |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, John D. Cho... | leeping/mdtraj | mdtraj/formats/mol2.py | Python | lgpl-2.1 | 8,848 | [
"MDTraj",
"OpenMM"
] | f26024695196cce931fdf61c07edb427922cf880ae29b4732de9f94af308f89c |
# -*- coding: utf-8 -*-
"""QGIS Unit tests for QgsRasterFileWriter.
.. note:: This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
"... | pblottiere/QGIS | tests/src/python/test_qgsrasterfilewriter.py | Python | gpl-2.0 | 16,469 | [
"NetCDF"
] | 123bc24c2283588a3fc629595c2071ef9f05e6693d0ac6037dc05855a157c7f3 |
# Copyright 2015 Allen Institute for Brain Science
# This file is part of Allen SDK.
#
# Allen SDK 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, version 3 of the License.
#
# Allen SDK is distributed in the ... | wvangeit/AllenSDK | allensdk/api/queries/glif_api.py | Python | gpl-3.0 | 5,717 | [
"NEURON"
] | cde7019aff424d37c939c8c36310d8dc5c602cec6e0ee6a70e8d11ba4859a710 |
#!/usr/bin/env python2
#
# Copyright 2015 Anthony Scemama
#
# 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 appli... | scemama/qmcchem | ocaml/ninja_ocaml.py | Python | gpl-2.0 | 8,180 | [
"cclib"
] | 94576f5b52605daee284cfebd037834353add738377a9ff5c2d70e0d73333204 |
#!/usr/bin/env python3
# -*- encoding: <utf-8> -*-
# Sprax Lines 2017.04.01 Written with Python 3.5
# sum_file.py (2019.06) based on test_filters.py (2017.04.01)
# To re-import a library in Python 3.4+ (re-import), do:
# import importlib
# importlib.reload(nameOfModule)
'''selected text-filtering functions, ... | sprax/python | txt/sum_file.py | Python | lgpl-3.0 | 14,334 | [
"Octopus"
] | 6bce79a0982a4897af1ba7b0de1299627f6df03029dea62e9f738c147419195e |
# Copyright (C) 2012,2013, 2017
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of... | espressopp/espressopp | src/interaction/VSphereSelf.py | Python | gpl-3.0 | 4,263 | [
"ESPResSo"
] | 9914bd3204ab19b3b845a2112027235036b7f6f742b3f24aec67032e12ab4a94 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# Firefly documentation build configuration file, created by
# sphinx-quickstart on Wed Jun 21 11:32:55 2017.
#
# 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
# au... | rorodata/firefly | docs/conf.py | Python | apache-2.0 | 4,698 | [
"Firefly"
] | 1762dea7e4185690ae4c0431df69a1cfa4f289e3bed8201f4449896033b5a3f6 |
"""
========================================================
Gaussian process regression (GPR) on Mauna Loa CO2 data.
========================================================
This example is based on Section 5.4.3 of "Gaussian Processes for Machine
Learning" [RW2006]. It illustrates an example of complex kernel engine... | RPGOne/Skynet | scikit-learn-0.18.1/examples/gaussian_process/plot_gpr_co2.py | Python | bsd-3-clause | 5,705 | [
"Gaussian"
] | c1a1b82efa8e6142b669a3b5c40b9032ea0c76598fd3514dc70c81a3a633d0f3 |
'''
Utilities for running the external Pairwise Homogenization Algorithm (PHA) software:
Menne, M.J., and C.N. Williams, Jr., 2009: Homogenization of temperature series
via pairwise comparisons. J. Climate, 22, 1700-1717.
Copyright 2014, Jared Oyler.
This file is part of TopoWx.
TopoWx is free software: you can re... | jaredwo/topowx | twx/homog/pha.py | Python | gpl-3.0 | 25,403 | [
"NetCDF"
] | 1a6697fba6310385ce4e4021a22eba1b3843294b406fb1c124d16d85c68acb95 |
# -*- coding: utf-8 -*-
#
# pyrubberband documentation build configuration file, created by
# sphinx-quickstart on Mon Oct 19 10:40:20 2015.
#
# 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.
... | faroit/pyrubberband | docs/conf.py | Python | isc | 8,720 | [
"Brian"
] | 96b02be1dc2d5a011a7416cdb35dc62f1d3f57b37bed1ed79ef1314099137407 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/utils/Platform/android/android_GetIPAddressV6.py | Python | gpl-3.0 | 1,584 | [
"ORCA"
] | fadbf5ef63837cc579976e8f1073a864847b45ce54231637e4de020072a58229 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007-2013 Async Open Source <http://www.async.com.br>
##
## 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... | tiagocardosos/stoq | stoqlib/database/queryexecuter.py | Python | gpl-2.0 | 19,534 | [
"VisIt"
] | cc0858087bdf29203d4717663941feaaf843347df9b08d656dfb61a7924a4b4b |
# Copyright 2019, The TensorFlow 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 t... | tensorflow/privacy | tutorials/mnist_lr_tutorial.py | Python | apache-2.0 | 9,703 | [
"Gaussian"
] | 934793c2acc93c2ca4a7dc397e987f2b30483ac218cb63a7db25d9a2254217bd |
# TODO(SK): module Missing docstring
import logging
import bpy
import numpy
import mathutils
from . import pam
from . import model
from . import colormaps
from . import constants
from . import mesh
from . import connection_mapping
logger = logging.getLogger(__package__)
vis_objects = 0
def setCursor(loc):
""... | MartinPyka/Parametric-Anatomical-Modeling | pam/pam_vis.py | Python | gpl-2.0 | 28,349 | [
"NEURON"
] | f200c92101255d38cfadbdaa88053509edcd70fb8da3a776fa50eec91e49823a |
# Copyright 2020 The TensorFlow Probability 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 o... | tensorflow/probability | tensorflow_probability/python/experimental/sequential/iterated_filter.py | Python | apache-2.0 | 37,064 | [
"Gaussian"
] | bf5bc1ac138bd9588523e383e54ba625fc6f20629d2d079b083bb344bdf4ac88 |
import numpy as np
import h5py
def writeH5(pressure,u,v,w,velmag,filename):
"""
Write the h5 file that will save the information needed in proper structure.
pressure = numpy array with pressure values
u,v,w = numpy array with velocity data
filename = string with desired filename
dims = 3-tuple with the num... | stu314159/pyNFC | hdf5Helper.py | Python | mit | 3,600 | [
"ParaView"
] | 69c9c7af7a55c063afa8c90fc1ea83f46369c878640d557d78e8441f2a920730 |
from .vpfit import *
from .galaxy import * | cwfinn/igmtools | igmtools/modeling/__init__.py | Python | bsd-3-clause | 42 | [
"Galaxy"
] | f66d60f86e142446e97236b59afa439bb8389f5d27c928dad2fc2edf9b67ba8f |
# 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... | floren/go9p | lib/codereview/codereview.py | Python | bsd-3-clause | 106,676 | [
"VisIt"
] | a2e7bcc847158cedd314da6e2eafa51cdfa9a58144bd553d1c82bf5a94663a74 |
#!/usr/local/bin/python3
#
# tinker.py
# Test subroutine of the CHRUBIX project
# ...for me to tinker with things :)
import sys
import os
from chrubix import generate_distro_record_from_name, load_distro_record
from chrubix.utils import fix_broken_hyperlinks, system_or_die, call_makepkg_or_die, remaining_megabytes_fr... | ReubenAbrams/Chrubix | src/tinker.py | Python | gpl-3.0 | 14,182 | [
"TINKER"
] | 35e73051e27d78b8cb4b42ef1f1b30e089c9371ffe7ad9228379fde8c5b52168 |
from llvmlite.ir import CallInstr
class Visitor(object):
def visit(self, module):
self._module = module
for func in module.functions:
self.visit_Function(func)
def visit_Function(self, func):
self._function = func
for bb in func.blocks:
self.visit_Basic... | numba/llvmlite | llvmlite/ir/transforms.py | Python | bsd-2-clause | 1,552 | [
"VisIt"
] | a55efda41db49b837f1cb981124b30e5554ff1cc727fb01818309b4b513b7ce4 |
# TODO: handle encoding of netCDF4 specific options
from .. import Variable
from ..conventions import cf_encoder
from ..core import indexing
from ..core.utils import FrozenOrderedDict, close_on_error
from ..core.pycompat import iteritems, basestring, unicode_type, OrderedDict
from .common import AbstractWritableDataSt... | clarkfitzg/xray | xray/backends/h5netcdf_.py | Python | apache-2.0 | 3,392 | [
"NetCDF"
] | 29bc6c9dbfe93e6fc69e404740f8a2c8f6ba5c45449672386a77ab4f86ac7ab7 |
"""Tests for accounts.models."""
# pylint: disable=invalid-name, too-many-lines
from datetime import timedelta
from django.conf import settings
from django.contrib.auth import get_user_model
from django.contrib.auth.models import Permission
from django.core.cache import cache
from django.core.exceptions import Validat... | ofa/connect | open_connect/accounts/tests/test_models.py | Python | mit | 43,556 | [
"VisIt"
] | ed300d6d4dd9c13735c00d8493b80a701e394a2b9861b4800fef46940cf11cc6 |
# -*- coding: utf-8 -*-
# Copyright(C) 2012-2014 Laurent Bachelier
#
# This file is part of weboob.
#
# weboob 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 ... | laurent-george/weboob | weboob/browser/browsers.py | Python | agpl-3.0 | 26,602 | [
"VisIt"
] | f6cfb97a206f4cb841201a7473bee186016729aedff8066b190b0f3033342b5b |
# .. coding: utf8
# $Id: __init__.py 7102 2011-08-24 13:36:28Z milde $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributions from several people included, th... | chirilo/remo | vendor-local/lib/python/docutils/writers/latex2e/__init__.py | Python | bsd-3-clause | 120,566 | [
"VisIt"
] | 61ad27d7598b91abfa21bb410612c7e5733d631ef309344762f89ee3e47c8a35 |
from builtins import object
import json
import os
import os.path as op
import time
import traceback
from abc import abstractmethod
from ..splunktacollectorlib.common import log as stulog
from ..splunktalib import kv_client as kvc
from ..splunktalib.common import util
def get_state_store(meta_configs,
... | PaloAltoNetworks-BD/SplunkforPaloAltoNetworks | Splunk_TA_paloalto/bin/splunk_ta_paloalto/aob_py3/cloudconnectlib/splunktalib/state_store.py | Python | isc | 8,194 | [
"VisIt"
] | ae9abab48b992ee71efc1110743c07972f66828d0b6172928ee27b082cfcff6d |
# -*- coding:utf-8 -*-
"""
Provides different functions to analyse the neuronal network activity.
Synchronization indexes:
- Spike Train Synchrony (STS) index
- Membrane Potential Synchrony (MPS) index
- FFT peak
"""
import numpy as np
from model import PARAMETERS as ps
from scipy.misc import comb
from scipy.signa... | neuro-lyon/multiglom-model | src/analysis.py | Python | mit | 9,474 | [
"Brian",
"NEURON"
] | 8406812f64e0d7bc693361232e3b0567faa3ba0593f35e5117d4bf1b0999a339 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/vasp/extract/__init__.py | Python | gpl-3.0 | 5,629 | [
"CRYSTAL",
"VASP"
] | 80dac1f8243d2c27eba26331971004f368058ad93e421c840a7e4a2f54ad688d |
# _
# |\ | / |_ _ ._ _
# | \| \/\/ \_ | | (/_ | | |
#
import json
def extract_basis_nwchem(data, name):
"""Extract atomic orbital, charge density fitting, or exchange
correlation functional basis data from a text region passed in as
data. The charge density fitting and exchange correla... | TApplencourt/EMSL_Basis_Set_Exchange_Local | src/parser/nwchem.py | Python | mit | 7,502 | [
"GAMESS",
"NWChem"
] | 0f8058d4a11634381954620775aa2864fe5914efb96d6c00540e6d28913103bc |
from __future__ import unicode_literals
from __future__ import absolute_import
from functools import reduce
import logging
from docker.errors import APIError
from .config import get_service_name_from_net, ConfigurationError
from .const import DEFAULT_TIMEOUT, LABEL_PROJECT, LABEL_SERVICE, LABEL_ONE_OFF
from .containe... | bbirand/compose | compose/project.py | Python | apache-2.0 | 12,598 | [
"VisIt"
] | b51fa6c974e996ac1c77ad0d9762a955d05d12e8e511e9a188567343fa57d6e9 |
# Copyright (C) 2014 The ESPResSo project
# Copyright (C) 2012,2013 Olaf Lenz
#
# 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... | olenz/espresso | config/check_myconfig_complete.py | Python | gpl-3.0 | 1,676 | [
"ESPResSo"
] | 27607a105355a73c589c70ec69ed5fc695050f15ec0b859b7a36a01a940a24bc |
# -*- coding: utf-8 -*-
"""
CyNetwork class is a simple wrapper for network-related cyREST raw REST API.
It does not hold the actual network data. It's a reference to a network in current Cytoscape session.
With CyNetwork API, you can access Cytoscape data objects in more Pythonista-friendly way.
"""
import json
impo... | idekerlab/cyrest-examples | py2cytoscape_doc/py2cytoscape/data/cynetwork.py | Python | mit | 22,908 | [
"Cytoscape"
] | 6a5235f348979ab7e9a8d36647e7a7f53bffeb8977ad3c6a98ddbcda74458c23 |
# coding=utf-8
# Copyright 2021 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | google-research/leaf-audio | leaf_audio/impulse_responses.py | Python | apache-2.0 | 4,492 | [
"Gaussian"
] | 131ebb18e0a68919ce538c59b8283827210801910a45d550dbbe35fee70273f3 |
# -*- coding: utf-8 -*-
"""
.. _ex-sim-raw-sub:
=======================================
Simulate raw data using subject anatomy
=======================================
This example illustrates how to generate source estimates and simulate raw data
using subject anatomy with the :class:`mne.simulation.SourceSimulator`... | mne-tools/mne-python | examples/simulation/simulated_raw_data_using_subject_anatomy.py | Python | bsd-3-clause | 8,955 | [
"Gaussian"
] | 5a819a48d63a8fedb5fa3a83f96607b96a989e7a7daa8edb62256450bae081de |
#!/usr/bin/env python2.7
# Copyright 2014 Mark Chilenski
# This program is distributed under the terms of the GNU General Purpose License (GPL).
# Refer to http://www.gnu.org/licenses/gpl.txt
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License... | markchil/profiletools | profiletools/gui.py | Python | gpl-3.0 | 232,035 | [
"Gaussian",
"NetCDF"
] | 8b9ef9a3fb122587021c079e099e239736ab977640a1e35534b71e4ddd031352 |
#########################################################################################
# OAR.py
# 10.11.2014
# Author: Matvey Sapunov, A.T.
#########################################################################################
""" OAR.py is a DIRAC independent class representing OAR batch system.
OAR objects... | andresailer/DIRAC | Resources/Computing/BatchSystems/OAR.py | Python | gpl-3.0 | 7,033 | [
"DIRAC"
] | e4ceb388ca0d38ad4da0d40cf49e0f8e50686b9e88f70f39edc0e49e2570cadd |
"""
Extended docstrings for functions.py
"""
pi = r"""
`\pi`, roughly equal to 3.141592654, represents the area of the unit
circle, the half-period of trigonometric functions, and many other
things in mathematics.
Mpmath can evaluate `\pi` to arbitrary precision::
>>> from mpmath import *
>>> mp.dps = 50; m... | NikNitro/Python-iBeacon-Scan | mpmath/function_docs.py | Python | gpl-3.0 | 275,627 | [
"Gaussian"
] | 4c7973a9a764ba4b83df9715be93c73ad447015241d8b93a0f930643f6c805c9 |
__author__ = 'Thomas Heavey'
import re
filename = "testg.out"
def findallgeoms(filename):
"""A function that takes a file name and returns a list of
geometries. Works with Gaussian output, haven't checked with
Q-Chem."""
relevantelem = [1,3,4,5]
xyzformat = '{:>2} {: f} {: f} {: f}'
... | thompcinnamon/QM-calc-scripts | gautools/geomRegex.py | Python | apache-2.0 | 2,092 | [
"Gaussian",
"Q-Chem"
] | 60445747983305ecdae6481e59863f93aa6a78b844c1cf3fcfc3aa369ab297db |
# -*- coding: utf-8 -*-
"""
nsaba.py: (N)euro(s)ynth, (A)llen (B)rain (A)tlas
Methods to analyze genome-scale gene expression data
from the Allen Human Brain Atlas in conjunction with
fMRI activation maps from Neurosynth
Authors: Simon Haxby & Torben Noto
"""
import pickle
import os
import itertools
import collections... | voytekresearch/nsaba | nsaba/nsaba.py | Python | mit | 30,776 | [
"Gaussian"
] | 0d1794911638de37f570d9c8b1897cb938ec02053c379f8f404b63d74c5ca4a4 |
""" JobMonitoringHandler is the implementation of the JobMonitoring service
in the DISET framework
The following methods are available in the Service interface
"""
__RCSID__ = "$Id$"
from types import IntType, LongType, ListType, DictType, StringTypes, NoneType, BooleanType
from DIRAC.Core.DISET.RequestHandl... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Service/JobMonitoringHandler.py | Python | gpl-3.0 | 19,195 | [
"DIRAC"
] | a902e4dd469676701c5f049c7bb00a8c577139cfa4797691f4e4748bd2c80131 |
from datetime import datetime
from django.test import TestCase
from django.utils import timezone
from dateutil.relativedelta import relativedelta
from edc_constants.constants import POS, NEG, UNK
from hiv_status.status import Status
from hiv_status.models import HivResult, Subject, Visit, HivStatusReview
class Test... | botswana-harvard/hiv-status | hiv_status/tests/test_status.py | Python | gpl-2.0 | 14,447 | [
"VisIt"
] | 6dbda0194c3e1c4bebe2c0b456cc182746f0960b0ebfb4b8e8004939d821fb8e |
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