text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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from six import PY3
import sys
import unittest
from six.moves import StringIO
from io import BytesIO
from robot.result import ExecutionResult
from robot.reporting.outputwriter import OutputWriter
from robot.utils import XmlWriter
from robot.utils.asserts import assert_equals
from robot.utils import ET, ETSource
fro... | userzimmermann/robotframework-python3 | utest/result/test_resultserializer.py | Python | apache-2.0 | 1,897 | [
"VisIt"
] | 72e1a60b35edf898399503688177f55270404ef7bea678da7001ca2e68599fe2 |
"""
Implements megnet models.
"""
from typing import Callable, Dict, List
import numpy as np
from tensorflow.keras.layers import (Add, Concatenate, Dense, Dropout,
Embedding, Input)
from tensorflow.keras.models import Model
from tensorflow.keras.optimizers import Adam
from tensorf... | materialsvirtuallab/megnet | megnet/models/megnet.py | Python | bsd-3-clause | 14,892 | [
"CRYSTAL",
"Gaussian"
] | 5fd42b6b6a7c4eae6d047fc10c8b93a43b2d8582109932372cfed783daf8d876 |
"""
Accessibility tests for Studio Library pages.
Run just this test with:
SELENIUM_BROWSER=phantomjs paver test_bokchoy -d accessibility -t test_studio_library_axs.py
"""
from ..tests.studio.base_studio_test import StudioLibraryTest
from ..pages.studio.library import LibraryEditPage
class StudioLibraryAxsTest(Studi... | tiagochiavericosta/edx-platform | common/test/acceptance/accessibility/test_studio_library_axs.py | Python | agpl-3.0 | 1,338 | [
"VisIt"
] | eda02e91aae7b8458724cdd93dcc83a7089cfbf6f4d4942ccc500e932b7bdf89 |
# -*- coding=utf-8 -*-
from __future__ import absolute_import, print_function, unicode_literals
import sys
from ctypes import create_string_buffer, c_uint64
from .clib import _get_c_library
from .misc import ChemfilesError, _last_error
if sys.version_info >= (3, 0):
string_type = str
else:
string_type = base... | Luthaf/Chemharp-python | chemfiles/utils.py | Python | mpl-2.0 | 3,962 | [
"Chemfiles"
] | 1904d2ff308851a8610aec8db99a179ba5c6e5969521b2293b2925c4d66990d7 |
#!/usr/bin/env python
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 6.0
calc = GPAW(gpts=(32, 36, 32), nbands=4)
O = Atoms([Atom('O', (a/2, a/2 + 0.5, a/2), magmom=2)],
pbc=False, cell=(a, a + 1, a), calculator=calc)
e0 = O.get_potential_energy()
niter0 = calc.get_number_o... | qsnake/gpaw | gpaw/test/IP_oxygen.py | Python | gpl-3.0 | 798 | [
"ASE",
"GPAW"
] | 2efb991a4254f6dc4d65662342882c12253ffda27085fd4473d8beac159b42a6 |
# encoding: utf-8
# Released under The MIT License (MIT)
# http://opensource.org/licenses/MIT
# Copyright (c) 2013-2016 SCoT Development Team
"""Vector autoregressive (VAR) model."""
from __future__ import division
import numpy as np
import scipy as sp
from . import config
from . import xvschema as xv
from scot.dat... | scot-dev/scot | scot/varbase.py | Python | mit | 15,679 | [
"Gaussian"
] | 08ed9e62f2c3363324722d671d686d4c232eb9017dc6b970a46cc56e8189393a |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-documentai | scripts/fixup_documentai_v1_keywords.py | Python | apache-2.0 | 6,232 | [
"VisIt"
] | 6baf79475d34be7834e56ea437c0bb6ac1856df5c192573eb5b92176cf61233e |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap(src_... | dcherian/pyroms | examples/Yellow_Sea/Inputs/Initial/remap.py | Python | bsd-3-clause | 4,970 | [
"NetCDF"
] | 94a5b32d865c20cb9187ae78aa9fb01fce450ce750539c90490c3f34dbe6a6c4 |
#!/usr/bin/env python
#
# Copyright 2008 Jose Fonseca
#
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU Lesser General Public License as published
# by the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This ... | jonnyhtw/cylc | lib/xdot.py | Python | gpl-3.0 | 97,799 | [
"FLEUR"
] | 7b0fd7340bc711201c7263d9477d942bee900aa77bd6d088cf65e9ba9050ee55 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Provides classes for generating high-symmetry k-paths using different conventions.
"""
import abc
import itertools
import operator
from math import ceil, cos, e, pi, sin, tan
from warnings import warn
imp... | gmatteo/pymatgen | pymatgen/symmetry/kpath.py | Python | mit | 94,761 | [
"CRYSTAL",
"pymatgen"
] | ef466eaacb0dd841ba34ab8ae0c9187909cd93d1179b7844ea397e738094d24e |
# Copyright (c) 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | dims/nova | nova/tests/unit/compute/test_resource_tracker.py | Python | apache-2.0 | 57,495 | [
"exciting"
] | 1280bbc3fe17b4577c2c8db1062867707bffbe53afc91c2d1e8d42170971d963 |
from __future__ import print_function
from distutils.ccompiler import new_compiler
import os
import sys
import tempfile
"""
Check for OpenMP based on
https://github.com/MDAnalysis/mdanalysis/tree/develop/package/setup.py
retrieved 06/15/15
"""
__all__ = ['detect']
def detect():
"""Does this compiler support OpenMP ... | mindriot101/batman | batman/openmp.py | Python | gpl-3.0 | 1,777 | [
"MDAnalysis"
] | b5db66587d0762dbd9c235e65bd0822ed7553df0aeebb92acbe0746014e5a8be |
"""
Quadratic Discriminant Analysis
"""
# Author: Matthieu Perrot <matthieu.perrot@gmail.com>
#
# License: BSD 3 clause
import warnings
import numpy as np
from .base import BaseEstimator, ClassifierMixin
from .externals.six.moves import xrange
from .utils import check_array, check_X_y
from .utils.validation import ... | ashhher3/scikit-learn | sklearn/qda.py | Python | bsd-3-clause | 7,608 | [
"Gaussian"
] | 982e22c6702cd861ec6e47d03732e72e3f7dfca16a0c92ecc26c3f32c9cd8b35 |
import matplotlib.pyplot as plt
import numpy as np
from utils.tuningcurve import plot as plot_tuningcurve
from utils.process_spikes import read_spikes, bin_data
# parameters for plotting this data
folder = "data/8_reaches/spiking_data"
num_reaches = 8
num_trials = 5
plot_raster = True
spikes = read_spikes(folder=fol... | studywolf/REACH-paper | analysis/02-tuningcurve_rasterplot.py | Python | gpl-3.0 | 1,876 | [
"NEURON"
] | 4b785544a04b150ddf8be7263653bf3f65254af737433e95aa765548e1075094 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@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) an... | dcrosta/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 17,899 | [
"Galaxy"
] | ccd6edf011af865ac46d65fc89405d6a20437a185d5f9d70d7e8a31c9cafd311 |
# Ver 11-29-15
# albumCoverFinder - Brian Tran, btran29@gmail.com
# This program scans a tree of directories containing mp3 files. For
# each directory, it attempts to download the cover image from the
# Apple iTunes service. Subdirectories must be named <Artist>/<Album>
# contain .mp3 files to be considered. The cove... | btran29/yet-another-album-cover-finder | albumCoverFinder.py | Python | mit | 4,092 | [
"Brian"
] | 6a8473aeae3fcd23ed41bbdffaf5ac739d0eaeda55e2615b2cb04b603a8bbfd6 |
# -*- coding: utf-8 -*-
"""Tests for transfer of knowledge and inference functions."""
import unittest
from pybel.examples.statin_example import (
avorastatin,
ec_11134,
ec_11188,
fluvastatin,
hmgcr,
hmgcr_inhibitor,
mevinolinic_acid,
statin,
statin_graph,
synthetic_statin,
)
... | pybel/pybel | tests/test_struct/test_transformations/test_transfer.py | Python | mit | 4,017 | [
"Pybel"
] | 056f3d68d01a5c015b05cabc37d98e4e125fcb55e53e850ceb8f34bfbeba9aca |
import sys
import pymol
import os
import time
pdb1 = sys.argv[1]
pdb2 = sys.argv[2]
# load pdb files
cmd.load(pdb1,"native")
cmd.load(pdb2,"other")
# full path to first pdb file
full_path = os.path.abspath(pdb1)
dir_path = os.path.dirname(full_path)
# parse residue list
reslist = []
sitem = sys.argv[3].split(",")
r... | larsbratholm/pymol_residue_compare | pymol_residue_compare.py | Python | mit | 1,807 | [
"PyMOL"
] | 89518403040ab33445376b5baabc63baad6cfdc0cd1d6fe9fe235d7bdb14b138 |
# Copyright 2017 The TensorFlow 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
#
# Unless required by applica... | ghchinoy/tensorflow | tensorflow/python/autograph/pyct/templates.py | Python | apache-2.0 | 9,527 | [
"VisIt"
] | f38e1f4fc2f30948c58c6d329aa15087deb9537c29c3d93c8af8de612049017b |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | mrchristine/spark-examples-dbc | src/main/python/sql/datasource.py | Python | apache-2.0 | 6,038 | [
"COLUMBUS"
] | 50d1dd76f6c9946d604d3ef839dfb47cb7bdb75d4663f8aac9a07dbe879fd8a7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 29 01:48:17 2017
@author: Aretas
"""
#tranfer MD_NP data to excel sheets
import re
import argparse
import os
import xlsxwriter
import collections
import csv
parser = argparse.ArgumentParser()
parser.add_argument('-f1', '--file1',
help='choose t... | aretas2/High-throughput-molecular-docking | excel-py/xcl2_NP.py | Python | mit | 7,049 | [
"CRYSTAL"
] | 695ca6487e29aee356d3e3df5e130d18f1b7372909c727ca7433debaf85c9468 |
"""This module contains operations to manipulate the database
Warning: since it involves manipulating source code, some operations may not be
very reliable.
Additionaly, we currently do not have tests for this file.
Thus, my suggestion is to use only the :meth:`~insert` and :meth:`~set_attribute` functions.
These fun... | JoaoFelipe/snowballing | snowballing/dbmanager.py | Python | mit | 25,981 | [
"VisIt"
] | bf2097e2f0bd9825e47aaf7b0b0ea3802d6bffb4e3346686264503c71c1439e7 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | chuckchen/spark | python/pyspark/pandas/generic.py | Python | apache-2.0 | 105,853 | [
"Elk"
] | f46565474eca590bd1ff41b6088125046fac0540395c345450adee25c7b09b6f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
* Copyright (C) 2017 Music Technology Group - Universitat Pompeu Fabra
*
* This file is part of jingjuSingingPhraseMatching
*
* pypYIN is free software: you can redistribute it and/or modify it under
* the terms of the GNU Affero General Public License as publis... | ronggong/jingjuSingingPhraseMatching | phoneticSimilarity/acousticModelTraining.py | Python | agpl-3.0 | 14,072 | [
"Gaussian"
] | 4178cf8fd4968dfbb4bda03a237bdfc801b4b5cd824881e2b7ad90aca7e2ecf9 |
'''
Created on 26/01/2010
@author: jose
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of project.
# franklin 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... | JoseBlanca/franklin | test/backbone/create_project_test.py | Python | agpl-3.0 | 23,138 | [
"BLAST"
] | e3cfda81d182b6247a92a349317d7a2f9840febe3277076f6bbb7e751b1a9a46 |
#!/usr/bin/env python
#
# Copyright (c) 2012 OpenDNS, Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this... | PowerDNS/pdns | regression-tests.recursor-dnssec/clientsubnetoption.py | Python | gpl-2.0 | 12,262 | [
"Brian"
] | 199bbf22d964521ffc56c6a378beb82e364467776b45ed55017c62d0e6875cf5 |
from ase.test import NotAvailable
from ase.lattice import bulk
from ase.calculators.calculator import get_calculator
required = {'abinit': dict(ecut=200, toldfe=0.0001, chksymbreak=0),
'aims': dict(sc_accuracy_rho=5.e-3),
'elk': dict(tasks=0, rgkmax=5.0),
'gpaw': dict(mode='pw')}
... | askhl/ase | ase/test/al.py | Python | gpl-2.0 | 1,194 | [
"ABINIT",
"ASE",
"Elk",
"GPAW"
] | cfbea65ef25a239e409d9abf12e4432a11dfec8c0a6e12c728f74ac2963189a7 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import collections
import os
import gyp
import gyp.common
import gyp.msvs_emulation
import json
import sys
generator_supports_multiple_toolsets = True
generator_... | Yukarumya/Yukarum-Redfoxes | gfx/skia/dump_mozbuild.py | Python | mpl-2.0 | 3,031 | [
"VisIt"
] | 5bc33da61289ee9d4199a5e43a18a0a228e651cbf0bd1ead8f7deae7b73efa7a |
# Copyright (C) 2016 Christopher M. Biwer, Collin Capano
# 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 progr... | cmbiwer/pycbc | pycbc/distributions/gaussian.py | Python | gpl-3.0 | 9,787 | [
"Gaussian"
] | b9ff6df0286e68070d96002646884e57a09bb4ba1b45c05c7edc8695dce34ced |
r"""*Module for* ``sphobjinv`` *CLI* |Inventory| *loading*.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
17 Nov 2020
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
https://gith... | bskinn/sphobjinv | src/sphobjinv/cli/load.py | Python | mit | 5,725 | [
"Brian"
] | 2343cc5e6921e4eaa2b08c6f766c7995de6c6973b0d7c4e6e2f6e799d6ac7450 |
import Gears as gears
from .. import *
class SmallDog(Component, gears.SpatialFilter) :
def __init__(self, **args):
gears.SpatialFilter.__init__(self)
Component.__init__(self, **args)
def applyWithArgs(
self,
stimulus,
*,
sigma1 : 'Standard de... | szecsi/Gears | GearsPy/Project/Components/Spatial/SmallDog.py | Python | gpl-2.0 | 2,080 | [
"Gaussian"
] | 556f69ee3fcb50ce963377a5503ef69733b130b89b3a2544611a1391c3949f55 |
import pytest
from .utils import *
import psi4
import numpy as np
from .addons import using
pytestmark = pytest.mark.quick
__potentials = {
'pna_6w':
"""
@COORDINATES
18
AA
O 9.37100000 2.95300000 -6.07800000 1
H 8.87200000 2.13400000 -6.04900000 2
H 9.87300000 2... | jturney/psi4 | tests/pytests/test_cppe.py | Python | lgpl-3.0 | 14,524 | [
"Psi4"
] | 595c22bc5af9266ea4a416e2bbd2318aaf895b147083c56aa9dbbd0f800db299 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Team-XBMC
#
# 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 versio... | mrquim/repository.mrquim | service.xbmc.versioncheck/lib/common.py | Python | gpl-2.0 | 7,310 | [
"VisIt"
] | 48334ac1876ca723e61cad0e36297b39b35fe858345c589fed62e4b6a99cd445 |
import collections
import copy
import warnings
import numpy
import six
from chainer.backends import cuda
from chainer import link as link_module
from chainer import serializer as serializer_module
from chainer import variable
def _sum_sqnorm(arr):
sq_sum = collections.defaultdict(float)
for x in arr:
... | aonotas/chainer | chainer/optimizer.py | Python | mit | 34,897 | [
"Gaussian"
] | 7ed396f667908d0134132504a4c17dcb51459dd2499884d449da00ac15f112f6 |
from __future__ import print_function
from builtins import range
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator
def link_correct_default():
print("Reading in original prostate data.")
h2o_data = h2o.upload_file(path=... | YzPaul3/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_link_correct_default_glm_large.py | Python | apache-2.0 | 2,770 | [
"Gaussian"
] | 6fdd168d30dfa4e1a7fef4093cef76952c918e30adfc9caaa7cdd62177a3da35 |
# Copyright (C) 2015 Philipp Baumgaertel
# All rights reserved.
#
# This software may be modified and distributed under the terms
# of the BSD license. See the LICENSE.txt file for details.
import numpy as np
class GaussianProcess(object):
"""
A Gaussian Process implementation based on Girard's work.
(Girard, A... | snphbaum/scikit-gpuppy | skgpuppy/GaussianProcess.py | Python | bsd-3-clause | 4,756 | [
"Gaussian"
] | bac7c25aa801f4c76d9f12b261ad0df5519f7eb4d834c1454e3ab8b95c58b0c4 |
"""
MiniCPS Software Defined Networking (SDN) module.
It contains OpenFlow data objects.
It contains platform-specific SDN controller e.g., pox.
POX prefixed ClassNames indicate controller coded into script/pox dir
and symlinked to ~/pox/pox/forwarding dir.
Minicps assumes that pox is cloned into your $HOME dir.
For ... | remmihsorp/minicps | minicps/sdns.py | Python | mit | 5,144 | [
"VisIt"
] | 0422a34efd8d021782cbd8ddbff6ba88dc7af0a147574b4033b80cc45232217f |
#!/usr/bin/python3
# -*- Mode:Python; indent-tabs-mode:nil; tab-width:4 -*-
#
# Copyright (C) 2015, 2016 Canonical Ltd
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License version 3 as
# published by the Free Software Foundation.
#
# This progra... | dholbach/snapcraft | snapcraft/main.py | Python | gpl-3.0 | 12,582 | [
"VisIt"
] | 86a453e1d305d16179d4ef1734c46405bb694009e059169c4858fdf2bf17d05c |
#
# Copyright (c) 2010, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyrigh... | ptosco/rdkit | rdkit/Chem/UnitTestFunctionalGroups.py | Python | bsd-3-clause | 6,363 | [
"RDKit"
] | ae395bb7ec7d3f0dad6a32a13dec5d6c335b6a97c43617fca6d8359111f33b94 |
import contextlib
import socket
import urllib
import urllib2
import urlparse
import re
from django.conf import settings
from django.utils.http import urlencode
import commonware.log
from statsd import statsd
from amo.helpers import absolutify
from amo.urlresolvers import reverse
class PaypalError(Exception):
i... | jbalogh/zamboni | apps/paypal/__init__.py | Python | bsd-3-clause | 10,184 | [
"VisIt"
] | 7d6c8162a149dc135917190bd6211b875df32d1fa879a72619e6b4fd4e1c3f63 |
import sys
from math import sqrt
import numpy as np
import gpaw.mpi as mpi
MASTER = mpi.MASTER
from ase.parallel import paropen
from ase.units import Hartree
from gpaw import debug
import gpaw.mpi as mpi
from gpaw.poisson import PoissonSolver
from gpaw.output import initialize_text_stream
from gpaw.lrtddft.excitation... | robwarm/gpaw-symm | gpaw/lrtddft/omega_matrix.py | Python | gpl-3.0 | 24,387 | [
"ASE",
"GPAW"
] | 97c7b008015b140456893da4667ef31ad365e64e594d36c6c307f018274222ba |
#!env/python3
# coding: utf-8
try:
import ipdb
except ImportError:
pass
import os
import datetime
import sqlalchemy
import subprocess
import multiprocessing as mp
import reprlib
import gzip
from pysam import VariantFile
from core.managers.imports.abstract_import_manager import AbstractImpor... | REGOVAR/Regovar | regovar/core/managers/imports/ped.py | Python | agpl-3.0 | 2,784 | [
"pysam"
] | 04763eb23a9b5297ea46a1e36e4444415c9f9136612b42052906d21522e4741e |
from marshmallow import fields, validate
from common.schemas import SerializableSchema, StringEnum
from common.schemas.fields import validate_output, validate_zim_filename
# https://github.com/puppeteer/puppeteer/blob/main/src/common/DeviceDescriptors.ts
validate_devicelist = validate.OneOf(
sorted(
[
... | openzim/zimfarm | dispatcher/backend/src/common/schemas/offliners/zimit.py | Python | gpl-3.0 | 9,353 | [
"Galaxy"
] | 3f3b2b8e7037d9cae003a4eb08f61c76d9e471914a9919d76c8fcc12ec7f5bad |
#!/usr/bin/env python
import sqlite3
import unittest
from SDDetector.Entities.Alignment import Alignment
from SDDetector.Entities.Region import Region
from SDDetector.Parser.Blast.BlastXMLParserExpat import BlastXMLParserExpat
class TestBlastXMLParserExpat(unittest.TestCase):
def setUp(self):
pass
... | nlapalu/SDDetector | tests/test_BlastXMLParserExpat.py | Python | gpl-3.0 | 2,764 | [
"BLAST"
] | 708aad4ec0abb50f6c1062551d590d95a87f98870abe910422824a07f97e4471 |
import os
import time
import tempfile
from latex import latex
def preview(expr, output='png', viewer=None, euler=True):
"""View expression or LaTeX markup in PNG, DVI, PostScript or
PDF form.
If the expr argument is an expression, it will be exported to
LaTeX and then compiled using availabl... | Cuuuurzel/KiPyCalc | sympy_old/printing/preview.py | Python | mit | 7,034 | [
"VisIt"
] | be56aa8f319725056b21e7fbcefc7557781cd8a3bf8a445470b62fd762fafff6 |
import scipy.integrate
import simtk.openmm as mm
import pandas as pd
box = 4.0
cutoff = box / 2.
q = 0.1
epsilon = 0.0
system = mm.System()
system.setDefaultPeriodicBoxVectors((box, 0, 0), (0, box, 0), (0, 0, box))
system.addParticle(1.0)
system.addParticle(1.0)
f = mm.NonbondedForce()
f.setCutoffDistance(cutoff)
f.... | kyleabeauchamp/HMCNotes | code/correctness/line_integral_charged.py | Python | gpl-2.0 | 2,130 | [
"OpenMM"
] | 9c555df551f1405fc574ee5e709281b4e9fb1ae0a7aafe9da3bbaedff82bba59 |
#####
# select_fasta_based_on_BLAST.py
#
# author
# Joe Parker, RBG Kew, 2016
#
# description
# Uses a list of sequences (e.g. that meet some arbitrary
# threshold in a BLAST analysis) to filter a .fasta file
#
# usage:
# python select_fasta_based_on_BLAST.py --fasta <fasta input> --good <list of good sequences>
#
#... | lonelyjoeparker/real-time-phylogenomics | wales_analyses/phylogenome_wales/select_fasta_based_on_BLAST.py | Python | gpl-2.0 | 2,530 | [
"BLAST"
] | 9382b3891c8b06f5e3d5cace72f20ece2802834e6bf3ddd73595b154afb77705 |
# -*- coding:utf-8 -*-
#
# Copyright 2012 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 vers... | fccoelho/pypln.backend | setup.py | Python | gpl-3.0 | 2,384 | [
"NAMD"
] | 626b60552a6e976c3afe143432757164891d3d37a28f11d65e06f2159f36b8df |
"""Rewrite assertion AST to produce nice error messages"""
from __future__ import absolute_import, division, print_function
import ast
import _ast
import errno
import itertools
import imp
import marshal
import os
import re
import six
import struct
import sys
import types
import py
from _pytest.assertion import util
... | anthgur/servo | tests/wpt/web-platform-tests/tools/third_party/pytest/_pytest/assertion/rewrite.py | Python | mpl-2.0 | 36,215 | [
"VisIt"
] | 7ead2938ad6f82977b59fef7b7bf2bafac5d662605ea6484f8ee9d6ed4723756 |
# -*- coding: utf-8 -*-
# -------------------------------------------------------------------------------
# Purpose: Extract data from an ArcGIS Service, in chunks defined by
# the service Max Record Count to get around that limitation.
# Requires that JSON is supported by the service
#
# ... | gdherbert/DataPillager | Desktop/DataServicePillagerPy27.py | Python | mit | 35,346 | [
"BLAST"
] | 85d6e3e13e6910c548e55f3dbce909d41ada7ae71cc2110dcbbc0361a8f0387b |
from i3pystatus.core.util import internet, require
from i3pystatus.weather import WeatherBackend
from datetime import datetime
from urllib.request import urlopen
GEOLOOKUP_URL = 'http://api.wunderground.com/api/%s/geolookup%s/q/%s.json'
STATION_QUERY_URL = 'http://api.wunderground.com/api/%s/%s/q/%s.json'
class Wun... | ncoop/i3pystatus | i3pystatus/weather/wunderground.py | Python | mit | 11,546 | [
"VisIt"
] | fde2a9088c970498df8e244ebbf928054c9b7f3dc6c7e423908dbc102182ae7c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
dimensions= 1
size1d = 100 if dimensions==1 else 10
# must have three components, because yade is inherently 3D and uses Vector3r. Remaining components will be used for AABB
halfSize = [size1d,0.1,0.1]
## This is a simple test:
## - a freely moving particle according to Sc... | cosurgi/trunk | examples/qm/1d-free-propagation.py | Python | gpl-2.0 | 4,446 | [
"Gaussian"
] | 7916e6b872894ada4931028999e6d8426dcd84c80127f04ee33d3ae661508a19 |
"""Module containing results and parameters that can be used to store `BRIAN data`_.
Parameters handling BRIAN data are instantiated by the
:class:`~pypet.brian.parameter.BrianParameter` class for any BRIAN Quantity.
The :class:`~pypet.brian.parameter.BrianResult` can store BRIAN Quantities
and the :class:`~pypet.bri... | nigroup/pypet | pypet/brian/parameter.py | Python | bsd-3-clause | 31,450 | [
"Brian",
"NEURON"
] | daa4593edb7aaa5d10dd184fc418f76f3103bfddfbfbb97807dff2d52f566b1b |
""" XVM (c) https://modxvm.com 2013-2020 """
import compileall
import traceback
import ast
import sys
import os
import glob
from xfw.constants import PATH
from xfw_loader.python import XFWLOADER_PATH_TO_ROOT
from consts import *
from logger import *
# Compile subdirectories
for root, dirnames, filenames in os.walk(... | KnechtRootrechtCH/Mimir | content/Mods/XVM/XVM_Base/res_mods_content/mods/xfw_packages/xvm_main/python/python_macro.py | Python | mit | 5,021 | [
"VisIt"
] | b9c793ce1376820792e845028e67d4f37c83275de3776cee8ac04ae519127333 |
# -*- coding: utf-8 -*-
"""Provide the Statistic object.
Statistic provides definition of objective function and optimization method for fitting process.
"""
from abc import ABCMeta, abstractmethod
import warnings
import numpy as np
import scipy
import scipy.linalg
class Statistic():
"""Abstract class for the ... | AnnaChmielinska/fluo | fluo/statistics.py | Python | gpl-3.0 | 9,228 | [
"Gaussian"
] | e0fd2d7cec795b850f549a2c0b0e5af169e6618bccdaa5cdcbc546a7a76746d1 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | nudles/incubator-singa | python/singa/tensor.py | Python | apache-2.0 | 48,444 | [
"Gaussian"
] | 2dab2c79e70b8c8e8bc94e43a28fc3d77d99a0b9aa2d016b26728c694630af5d |
from collections import OrderedDict
# Up to four brickpi3s can be stacked
OUTPUT_A = 'spi0.1:MA'
OUTPUT_B = 'spi0.1:MB'
OUTPUT_C = 'spi0.1:MC'
OUTPUT_D = 'spi0.1:MD'
OUTPUT_E = 'spi0.1:ME'
OUTPUT_F = 'spi0.1:MF'
OUTPUT_G = 'spi0.1:MG'
OUTPUT_H = 'spi0.1:MH'
OUTPUT_I = 'spi0.1:MI'
OUTPUT_J = 'spi0.1:MJ'
OUTPUT_K = 's... | dwalton76/ev3dev-lang-python | ev3dev2/_platform/brickpi3.py | Python | mit | 1,111 | [
"Amber"
] | 98318b68b1e46dee2903be6da9c0861183a37a7e78191e2d61fa161d39bfc48d |
#the generation of a CSX file from a quantum chemistry package output file
#using cclib as a parser
from . import filewriter
class CSX(filewriter.Writer):
def __init__(self, ccdata, splitfiles=False,
firstgeom=False, lastgeom=True, allgeom=False,
*args, **kwargs):
# Call the ... | ChemSem/cclib | src/cclib/writer/csxwriter.py | Python | lgpl-2.1 | 43,452 | [
"cclib"
] | 8788939cc5aa843a258ca2afdb66a726f277f241a276f67a6bbe6952c4bceaa5 |
#!/usr/bin/env python
#
# fastq_sniffer.py: "sniff" FASTQ file to determine quality encoding
# Copyright (C) University of Manchester 2013 Peter Briggs
#
########################################################################
#
# fastq_sniffer.py
#
##############################################################... | fw1121/genomics | NGS-general/fastq_sniffer.py | Python | artistic-2.0 | 5,079 | [
"Galaxy"
] | 1588db63ba2c163cfb430d918bc90f900b78f0f8cd07eff48ff56a1510811760 |
# Copyright 2011 VMware, Inc.
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ... | mahak/neutron | neutron/agent/common/ovs_lib.py | Python | apache-2.0 | 54,211 | [
"VisIt"
] | 4be311137c360eb951c77ee2a7f8fc452f5438ae1284c5c52a6862abf9c1ece4 |
##
# TRACK 2
# RHAPSODY IN GREY
# From Data-Driven DJ (datadrivendj.com) by Brian Foo (brianfoo.com)
# This file builds the sequence file for use with ChucK from the data supplied
##
# Library dependancies
import csv
import json
import math
import os
import time
# Config
BPM = 75 # Beats per minute, e.g. 60, 75, 100,... | rblades/music-lab-scripts | 02_brain/brain.py | Python | mit | 16,373 | [
"Brian"
] | 7043059adaf4613475181f40bb4b6c5cd9fa60313eaeb5219be64f9610dbc53c |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/model/stats.py | Python | mit | 6,015 | [
"VisIt"
] | b8fe3cde6dfbc41ebad7eb579de5c3b5a53e05ab13c8ff3a33a6bf345ae92123 |
from __future__ import division
'''
consensus.py
This is the collation and aggregation code for the Radio Galaxy Zoo project. The main
intent of the code is to take in the raw classifications generated by Ouroboros
(as a MongoDB file), combine classifications by independent users, and generate
a single consensus ans... | willettk/rgz-analysis | python/consensus.py | Python | mit | 55,278 | [
"Galaxy"
] | 4fedf4aac817029a8ffc6a95e14c009dbd207ecb773fc6a9c1dcd7d19abec857 |
'''
*******************************************************************
* File: readSBML.py
* Description:
* Author: HarshaRani
* E-mail: hrani@ncbs.res.in
********************************************************************/
/**********************************************************... | BhallaLab/moose | moose-core/python/moose/SBML/readSBML.py | Python | gpl-3.0 | 70,228 | [
"Avogadro",
"MOOSE"
] | 65167ceecb9be00c6d4cfa127916083361276febed013b6b088c59f897bf329d |
"""Test iterating through a vtkCollection with the standard python syntax"""
import vtk
from vtk.test import Testing
class TestIterateCollection(Testing.vtkTest):
def setUp(self):
self.vtkObjs = [vtk.vtkObject() for _ in range(30)]
self.collection = vtk.vtkCollection()
for obj in self.vt... | keithroe/vtkoptix | Common/Core/Testing/Python/TestIterateCollection.py | Python | bsd-3-clause | 1,600 | [
"VTK"
] | 035b182b5a1bfe40270b342917a6a090cf187e1c9f0573a019d1d2a6504740af |
"""
Models used to implement SAML SSO support in third_party_auth
(inlcuding Shibboleth support)
"""
import json
import logging
import re
from config_models.models import ConfigurationModel, cache
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.exceptions import Validat... | edx/edx-platform | common/djangoapps/third_party_auth/models.py | Python | agpl-3.0 | 38,967 | [
"VisIt"
] | e852095c27b0ba7bcc81f0da16c9483334fac2b24052acf894dda20a6fd35005 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/plugins/kgapplications/tests/test_all_pages.py | Python | gpl-3.0 | 1,720 | [
"Brian"
] | 9b2d27e0c618750ea0df9dd95881dc41ed1eebd1b57764171e08e5f3ad69f619 |
from lettuce import before, step, world
from lettuce.django import django_url
from nose.tools import assert_equal
from splinter.exceptions import ElementDoesNotExist
from storybase_user.models import create_organization, Organization, Project
@before.each_scenario
def setup_organization(scenario):
matching_scenari... | denverfoundation/storybase | apps/storybase_user/features/project-steps.py | Python | mit | 3,940 | [
"VisIt"
] | 7ca77921f93c377283014ab5e5428f1ec305cc811183ee6e51763ef7517758a1 |
### ############################################################################################################
### #
### # Project: # teh_tools - by The Highway 2013.
### # Author: # The Highway
### # Version: # (ever changing)
### # Description: # My collection of common tools.
### #
### #############... | azumimuo/family-xbmc-addon | plugin.image.kissmanga/teh_tools.py | Python | gpl-2.0 | 104,180 | [
"VisIt"
] | 44ab1ca3fe318ca71e04560b1a3c5b2c5849e7e9f44f742791447d193b164f48 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | capoe/espressopp.soap | src/analysis/LBOutput.py | Python | gpl-3.0 | 2,783 | [
"ESPResSo"
] | c2b9a9279e8b4a809fd72a598dc8fd64df96e5f82c6d0a2c2e5818b000843f61 |
import numpy as np
import os
import shutil as sh
import subprocess as sub
def read_input(espinp):
record = {}
inpstr = ''
for line in espinp:
inpstr += line
inplines = inpstr.split('\n')
for lidx,line in enumerate(inplines):
if '=' in line:
spl = line.split()
if len(spl) < 3:
... | bbusemeyer/busempyer | busempyer/qefiles_io.py | Python | gpl-2.0 | 3,396 | [
"ESPResSo"
] | c1571987805e7755d8419624e1e0d1e26bfc4d9e4036bf99b5bbbf97a24699ee |
#
# QAPI parser test harness
#
# Copyright (c) 2013 Red Hat Inc.
#
# Authors:
# Markus Armbruster <armbru@redhat.com>
#
# This work is licensed under the terms of the GNU GPL, version 2 or later.
# See the COPYING file in the top-level directory.
#
from qapi import *
from pprint import pprint
import os
import sys
c... | J-Liu/qemu | tests/qapi-schema/test-qapi.py | Python | gpl-2.0 | 2,149 | [
"VisIt"
] | 849410aa2bec28935edb47d2492295a8ae298f0cee67e130e83da679c685e939 |
# Copyright 2013-2015 James S Blachly, MD and The Ohio State University
#
# This file is part of Mucor.
#
# Mucor 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,... | blachlylab/mucor | detect_union_bin_errors.py | Python | gpl-3.0 | 3,925 | [
"HTSeq"
] | 4fa0b69afc7e33fc1c57ebcdcde1fac6475c966feb471d95e529513cdeeccb5c |
from allensdk.model.biophys_sim.config import Config
from allensdk.model.biophys_sim.neuron.hoc_utils import HocUtils
class Utils(HocUtils):
def __init__(self, description=None):
description = Config().load('manifest.json')
super(Utils, self).__init__(description)
self.generate_cell()
de... | thekerrlab/netpyne | examples/saveLoadV1/IL/cell_utils.py | Python | mit | 2,400 | [
"NEURON"
] | 434a9fd3daec6f18e555d74e17ee315da81014fae37bec70e5379f2cd274e4b7 |
'''
Created on Aug 5, 2014
@author: David Zwicker <dzwicker@seas.harvard.edu>
'''
from __future__ import division
import numpy as np
from .base import VideoBase
from utils.math import safe_typecast
class VideoGaussianNoise(VideoBase):
""" class that creates Gaussian noise for each frame """
def __ini... | david-zwicker/video-analysis | video/io/computed.py | Python | bsd-3-clause | 1,125 | [
"Gaussian"
] | 079bd74f75c60414318ef309ec5ceb3e8dd541a8c36174fde058f54f2ffaf9d2 |
"""
stringjumble.py
Author: Brian
Credit: None
Assignment:
The purpose of this challenge is to gain proficiency with
manipulating lists.
Write and submit a Python program that accepts a string from
the user and prints it back in three different ways:
* With all letters in reverse.
* With words in reverse order... | brianseltzer1738/String-Jumble | stringjumble.py | Python | mit | 1,187 | [
"Brian"
] | 8ebceddf28295fe04d96387ac3c922880645c44e603e65f264d41f68c676fc0f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
chose m, c (parameters) for a straight line
from the line pick N points (N=3, 5, 50, 100, 1000)
pick sigma (size of the noise)
randomly deviate(offset) points in y direction by using
sigma*random number from normal distribution
sigma the same for all points
then defin... | lefthandedroo/Cosmo-models | History/Stats/emcee_ex_0.py | Python | mit | 4,991 | [
"Gaussian"
] | 199f83b35714cbd5fb3eed8d24f047e890e96c0b9e852f8ffc6e1d8200e2c85c |
""" Base class for DIRAC Client """
__RCSID__ = "$Id$"
from DIRAC.Core.DISET.RPCClient import RPCClient
class Client( object ):
""" Simple class to redirect unknown actions directly to the server. Arguments
to the constructor are passed to the RPCClient constructor as they are.
Some... | Andrew-McNab-UK/DIRAC | Core/Base/Client.py | Python | gpl-3.0 | 3,300 | [
"DIRAC"
] | a7e405472d3f9191e5777096ddb864fa1f6370f0c4c35a8ec55b5e8a258fc297 |
# -*- 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-compute | tests/unit/gapic/compute_v1/test_networks.py | Python | apache-2.0 | 161,347 | [
"Octopus"
] | 681eb5d769b006e48e066b1b21d04efaf23b58d08272d20c48f2f3d89494b813 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | kain88-de/mdanalysis | package/MDAnalysis/analysis/encore/__init__.py | Python | gpl-2.0 | 1,605 | [
"MDAnalysis"
] | 97e6a960810f8d821345011f158e6cd42b7c149a359fa8c4c8ce17408c652e2a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# createfreeze - front end to create frozen archives
# Copyright (C) 2003-2014 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General ... | heromod/migrid | mig/cgi-bin/createfreeze.py | Python | gpl-2.0 | 1,092 | [
"Brian"
] | ef11607ee53ef9ac814fb320064fe435d7200751d2cf796f34d2a3d8a945fc3c |
"""Next generation sequencing genome alignment.
Classes:
ReferenceGenome
HTSeqCountOutput
Methods:
create_reference_genome
standardize_reference_genome
find_bai_file
get_samtools_version
get_bcfutils_version
get_vcfutils_version
get_radia_version
call_samtools_idxstats
get_bowtie1_version
make_bowtie1_command
par... | jefftc/changlab | genomicode/alignlib.py | Python | mit | 56,427 | [
"BWA",
"Bowtie",
"HTSeq"
] | 2a8f2fcf856e7616bc12e4dfc25296b22f189f231712186bb2eb89de13d1f58d |
# -*- coding: utf-8 -*-
# chains.py - functions for finding chains in a graph
#
# Copyright 2004-2019 NetworkX developers.
#
# This file is part of NetworkX.
#
# NetworkX is distributed under a BSD license; see LICENSE.txt for more
# information.
"""Functions for finding chains in a graph."""
import networkx as nx
fro... | sserrot/champion_relationships | venv/Lib/site-packages/networkx/algorithms/chains.py | Python | mit | 6,820 | [
"VisIt"
] | 30059023b0e60f2a3e477a237137e879f811ad23bf241586222a97471d6ea5b3 |
# $Id: ShowFeats.py 537 2007-08-20 14:54:35Z landrgr1 $
#
# Created by Greg Landrum Aug 2006
#
#
_version = "0.3.2"
_usage = """
ShowFeats [optional args] <filenames>
if "-" is provided as a filename, data will be read from stdin (the console)
"""
_welcomeMessage = "This is ShowFeats version %s" % (_version)
... | greglandrum/rdkit | rdkit/Chem/Features/ShowFeats.py | Python | bsd-3-clause | 12,210 | [
"PyMOL",
"RDKit"
] | d87aab705fa5fe7a8e88867973edff917f3d0db64860906185ec88a3b6ab8858 |
# coding: utf8
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as... | blond-admin/BLonD | __BENCHMARKS/BM1_OTFB_Vind_beam_1.py | Python | gpl-3.0 | 16,881 | [
"Gaussian"
] | 709fab04d44c8186b408fe3d886efbaa206ec2003fe8d4bd032e158c6a744efa |
"""Universal feed parser
Handles RSS 0.9x, RSS 1.0, RSS 2.0, CDF, Atom 0.3, and Atom 1.0 feeds
Visit https://code.google.com/p/feedparser/ for the latest version
Visit http://packages.python.org/feedparser/ for the latest documentation
Required: Python 2.4 or later
Recommended: iconv_codec <http://cjkpython.i18n.org... | gylian/sickrage | lib/feedparser/feedparser.py | Python | gpl-3.0 | 156,146 | [
"NetCDF",
"VisIt"
] | 237b23c0a9af0a0cfcdd5a6f8f6c5a8c576163b4ba146b792256245bf2be7080 |
#!/usr/bin/env python
import sys
import os
import math
# ensure that the kicad-footprint-generator directory is available
#sys.path.append(os.environ.get('KIFOOTPRINTGENERATOR')) # enable package import from parent directory
#sys.path.append("D:\hardware\KiCAD\kicad-footprint-generator") # enable package im... | pointhi/kicad-footprint-generator | scripts/Oscillators_SMD/make_oscillators.py | Python | gpl-3.0 | 14,145 | [
"ASE",
"CRYSTAL"
] | 434e2219f07c093dde0ef941c16eb72a6ad7c9f1bf85b8449328d49e259e468d |
#!/usr/bin/env python2
import datetime as dt
import glob as glob
import os as os
import re
import shutil as shutil
import signal as signal
import subprocess as sp
import sys as sys
def write_min_in():
"""
Write an Amber input file for minimization
"""
if os.path.isfile('min.in'):
sp.call('rm m... | Janeyin600/WaterBot | waterbot_eq.py | Python | gpl-3.0 | 2,805 | [
"Amber"
] | 2779f3c0b2c5c7abdec85a4c22196c2be9e4957377ccd0461893776f9b9ac914 |
"""
test_validate.py
Testing code for Validation class
Contributors: mitra.sidddhartha@gmail.com
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_alias... | thekerrlab/netpyne | netpyne/tests/validate_tests.py | Python | mit | 147,008 | [
"NEURON"
] | 2ef2df228709d0b833e8a33e6e735a4386612bb2c677bf2f83f797172971aa87 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk, gobject, os, pango
from zeroinstall import _
from zeroinstall.injector import model, writer
from zeroinstall import support
import utils
def _build_stability_menu(policy, impl):
menu = gtk.Menu()
upstr... | timdiels/zeroinstall | zeroinstall/0launch-gui/impl_list.py | Python | lgpl-2.1 | 6,064 | [
"VisIt"
] | ef32a746b8134e4aaf9810418bc8f25c19f160578a5d8165a8e3eb44ce618a6c |
#
# 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/dpd.py | Python | gpl-3.0 | 16,249 | [
"ESPResSo"
] | c8ac3848e6962283676c3d3585aab056097b3c450aa30c0028b9bb87cbd6a9a0 |
""" Class that contains client access to the job monitoring handler. """
########################################################################
# $Id$
# $HeadURL$
########################################################################
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client import Cli... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/Client/JobMonitoringClient.py | Python | gpl-3.0 | 951 | [
"DIRAC"
] | dda1150acd28ca6bacf602227df3fb474bde3a2b4589aed2ffb5df88cdd1472e |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2015 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | LunarLanding/Pythics | pythics/start.py | Python | gpl-3.0 | 24,632 | [
"Brian"
] | 02dfea1896c4c88596f494298e68289daa706fc32033eda3803186a9711b1652 |
from aces.materials import Material
from aces.modify import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt
from ase.dft.kpoints import ibz_points
class structure(Material):
def set_parameters(self):
self.bond=6.059141
def setup(self):
self.elements=["In","As"]
self.bandpoints=ibz_points['... | vanceeasleaf/aces | aces/materials/InAs.py | Python | gpl-2.0 | 949 | [
"ASE"
] | d377f0fe2abb5878308fa85d3eac4bf2fb9d2c82252a7ad89a7b124ed8a2932c |
#!/usr/bin/env python3
#
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, e... | espressopp/espressopp | testsuite/lattice_boltzmann/test_LatticeBoltzmann.py | Python | gpl-3.0 | 3,667 | [
"ESPResSo"
] | d1d655600eec84c619a72901e7ce9c57cfc60be78997df6da90f546e4a912eb6 |
#!/usr/bin/python
#
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
#
# 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/LICE... | nouiz/fredericbastien-ipaddr-py-speed-up | tags/2.0.0/ipaddr_test.py | Python | apache-2.0 | 41,156 | [
"FEFF"
] | 8f058f9bfcf682cf0f5468ad1fa1d5ac2f8d739e05073e110d862df511e05754 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2011 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU Lesser General Public License as published by
## the Free Software F... | tiagocardosos/stoq | stoqlib/reporting/paymentsreceipt.py | Python | gpl-2.0 | 3,072 | [
"VisIt"
] | 0054ea85343d53375173f058b346a5182f01c256e3f2da7960d007cf790a2134 |
#!/usr/bin/env python
import OCC
from OCC import VERSION
from OCC.gp import gp_Ax1, gp_Pnt, gp_Dir, gp_Trsf, gp_Quaternion,gp_Vec, gp_XYZ
from OCC.TopLoc import TopLoc_Location
#from OCC.Display.SimpleGui import get_backend
from OCC.STEPControl import STEPControl_Reader, STEPControl_Writer, STEPControl_AsIs
from O... | siconos/siconos-deb | io/swig/io/pprocess.py | Python | apache-2.0 | 10,145 | [
"VTK"
] | 0624c72d7fd3e770000bf4d6b45f4e66243878acb6afc84cd30b597fb170e36a |
# -*- coding: utf-8 -*-
"""
Created on Wed Jun 1 11:19:04 2016
@author: eilers
"""
import numpy as np
import pickle
from astropy.io import fits
from astropy.table import Table
from astropy.table import Column
from scipy import ndimage
from astropy.io import ascii
import errno
# -------------------------------------... | aceilers/cygnet | functions_cannon.py | Python | mit | 30,844 | [
"Gaussian"
] | aa439679954148cac792d5926b43706ee93830a133bd6e5fcef828383ed32204 |
#!/usr/bin/env python3
# Version 1.1
# Author Alexis Blanchet-Cohen
# Date: 09/06/2014
import argparse
import glob
import os
import os.path
import pandas
import subprocess
import util
# Read the command line arguments.
parser = argparse.ArgumentParser(description='Generate mergeBAMFiles scripts.')
parser.add_argumen... | blancha/abcngspipelines | utils/mergebamfiles.py | Python | gpl-3.0 | 2,752 | [
"BWA"
] | 92563be6394f25c6a4c973e0aa2b5952095b7bc6f7f29873a81946a9cd163d80 |
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