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## numpy-oldnumeric calls replaced by custom script; 09/06/2016
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public L... | graik/biskit | biskit/dock/complex.py | Python | gpl-3.0 | 47,693 | [
"FoldX"
] | 5823da46248baf7ec08fcb1699923fdd81aea89a7319c064f181b3997e07df36 |
import functools
import numpy as np
import math
import types
import warnings
# trapz is a public function for scipy.integrate,
# even though it's actually a NumPy function.
from numpy import trapz
from scipy.special import roots_legendre
from scipy.special import gammaln
__all__ = ['fixed_quad', 'quadrature', 'romber... | aeklant/scipy | scipy/integrate/quadrature.py | Python | bsd-3-clause | 31,375 | [
"Gaussian"
] | 1b487724bb6718a6fbf99288c39f47cfdb9cccc02e480c850e4816aed9625052 |
import chainer
from chainer import Variable
import chainer.functions as F
import mlp
import time
class VAEGaussian(chainer.Chain):
def __init__(self, x_dim, z_dim, h_dim, n_layers,
activate, use_dropout, use_bn, wmean, wlogvar):
self.loss_fun = loss_fun
super(VAEGaussian, self).__i... | hillbig/dgen | dgen/vae.py | Python | mit | 2,521 | [
"Gaussian"
] | 4a94f3e3ca1f6b890d6b7c30b50ddc45c53acef664f9e92fd1bbe5340232bd16 |
# -*- coding: utf-8 -*-
# Copyright 2015 Spotify AB. All rights reserved.
#
# The contents of this file are 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... | napalm-automation/napalm-junos | test/unit/TestJunOSDriver.py | Python | apache-2.0 | 5,191 | [
"Firefly"
] | cc2db8868a913e13608bc02a6650bdc248d5728682fb9bcc4436797bf5f52cd5 |
# Script initially by Tom Kazimiers 2013-01-12
# Adapted by Albert Cardona 2013-01-25
#
# The purpose of this script is to connect to a django session
# in a remote computer, and to retrieve information from the database
# such as the skeleton of a neuronal arbor and its synapses
# in the form of a NetworX graph.
impo... | htem/CATMAID | scripts/remote/access.py | Python | agpl-3.0 | 6,235 | [
"NEURON"
] | 0169abc01f8ddc2d8a0c9319c153acfe5ad28554e605c418bf0542aadd570843 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/py-cdat-lite/package.py | Python | lgpl-2.1 | 2,380 | [
"NetCDF"
] | 106aa436eec03ba24f9463a8b650f602332ff7a9ba30b7c6e4094cae8faa5ccd |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import json
import warnings
import numpy as np
from pymatgen import Lattice, Structure, Specie, Molecule
from pymatgen.transformations.standard_transformations import (
OxidationS... | mbkumar/pymatgen | pymatgen/transformations/tests/test_advanced_transformations.py | Python | mit | 32,390 | [
"VASP",
"pymatgen"
] | 192eeee4d8170cc99fb54987ed68803c4873df5bd2589d5382012fd8785dfece |
###############################################################################
# lazyflow: data flow based lazy parallel computation framework
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/o... | stuarteberg/lazyflow | lazyflow/operators/ioOperators/opInputDataReader.py | Python | lgpl-3.0 | 23,207 | [
"VisIt"
] | fef5bf6a742f0251740adbe7ef933cea7fa1f4a730f944ae696628c40375c7c4 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/component/galaxy.py | Python | agpl-3.0 | 62,236 | [
"Galaxy"
] | ecb966c1a117b9908ec0df68748d6d719fe877463dc0180edb7cbd5a1448a571 |
# -*- coding: utf-8 -*-
"""QGIS Unit tests for edit widgets.
.. 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.
"""
__au... | stevenmizuno/QGIS | tests/src/python/test_qgsrelationeditwidget.py | Python | gpl-2.0 | 12,055 | [
"Galaxy"
] | d392c4837b4436ab210e72e1c5ba6cdca9850a5285f8041694d4b39f4a88a685 |
# Copyright 2018 The trfl 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 applicable law... | deepmind/trfl | trfl/distribution_ops.py | Python | apache-2.0 | 7,309 | [
"Gaussian"
] | 1fc8e041d79c284ef2ed5c0e95e6a4e7ebc76ce5fb8aba1b6fd54a102fc4d2e8 |
from neuron import h
import neuron.gui
soma = h.Section(name='soma')
soma.insert('hh')
ampa = h.AMPA(0.5, sec=soma)
ampa.gbar = 1 # Just increasing, for testing purpose
#expSyn = h.ExpSyn(0.5, soma)
#expSyn.e = 10
#expSyn.i = 3
#expSyn.tau = 3
netStim = h.NetStim()
netStim.start = 1
netStim.interval= 1
netStim.numb... | mattions/TimeScales | mod/test_input.py | Python | bsd-3-clause | 420 | [
"NEURON"
] | f34e5d9dc72ffdb8e5e2567b91e43a205b0045086f9d4f0f7b07397363f7bb08 |
__author__ = 'mnowotka'
from django.conf import settings
from rdkit.Chem import InchiToInchiKey
from rdkit.Chem import MolFromInchi
from rdkit.Chem import Kekulize
from rdkit.Chem import MolToMolBlock
from rdkit.Chem import MolFromMolBlock
from rdkit.Chem.rdmolfiles import MolToSmiles
from rdkit.Chem.rdMolDescriptors ... | thesgc/chembiohub_ws | chembl_business_model/models/compounds.py | Python | gpl-3.0 | 9,709 | [
"RDKit"
] | e8ffecb64c1ee5740dca20729d162bdabb1fb31a89b56cadcca0050f3f5e5ebc |
from DIRAC.WorkloadManagementSystem.Client.SandboxStoreClient import SandboxStoreClient
from WebAppDIRAC.Lib.WebHandler import WebHandler, WErr, WOK, asyncGen
from DIRAC.Core.DISET.RPCClient import RPCClient
from DIRAC import gConfig, S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities import Time
from WebAppDIRAC.WebApp... | chaen/WebAppDIRAC | WebApp/handler/JobMonitorHandler.py | Python | gpl-3.0 | 22,194 | [
"DIRAC"
] | c3987fd119998475be4bb943d75e706dcfb90487db716d285e1199c77fc32167 |
# The parse script expects on stdin:
# filepath variable_name line_number
# And is expected to output on stdout:
# {scope:{start:<num>,end:<num>},decl:{line:<num>}}
# If there is a syntax error in running the given file, it should return the error as:
# {error:[error_string]}
# Any error thrown while running thi... | OmarShehata/atom-tracer | lib/langs/python/parse.py | Python | mit | 6,309 | [
"VisIt"
] | f5bb784b7a0d9202b496a83cc9da47a86f128cda345061bfab7a78feea8001c3 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | jhunufernandes/ArduWatchRaspSerial | virtualenv/lib/python3.4/site-packages/setuptools/command/easy_install.py | Python | mit | 86,546 | [
"VisIt"
] | c7b82b4a18e638e49636e24ff17a13ab28a1c4779d8f4381a4b5893248a4ac8f |
import vtk
#renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName("C:/Users/Rinske/Documents/GitHub/scientific-visualization/ass3/SMRX.vtk")
reader.UpdateW... | stablum/scientific-visualization | ass3/glyph_visualization.py | Python | gpl-3.0 | 2,085 | [
"VTK"
] | 847355be2cff408d03ec2dfb99fca34019c3ab547eb652d0b4898d3d17d9169f |
# Nexus.py - a NEXUS parser
#
# Copyright 2005 by Frank Kauff & Cymon J. Cox. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Bug reports welcome: fkauff@duke.edu
#
"""Parse ... | JohnReid/bioinf-utilities | python/corebio/seq_io/_nexus/__init__.py | Python | mit | 69,365 | [
"Biopython"
] | 9a235f89d6c739ffe3dbcd9317badd1f09a411ef9684d4ad0bf6b390cc9b4115 |
########################################################################
# This example illustrates how a function can be used to control a reaction
# rate. This kind of calculation is appropriate when we need to link
# different kinds of physical processses with chemical reactions, for
# example, membrane curvature... | dilawar/moose-core | tests/rdesigneur/test_76_func_func_control_reac_rates.py | Python | gpl-3.0 | 4,535 | [
"MOOSE"
] | e4be5859502ee7da41ce57b7cbab4a264fbc3f19fc03765fcfd2ce6ed6901add |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import warnings
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.periodic_table import Element, Specie
from pymatgen.core.comp... | johnson1228/pymatgen | pymatgen/core/tests/test_structure.py | Python | mit | 54,084 | [
"pymatgen"
] | 5b69c63e01aad4b4e231ee9f14ed3e2f02a7eed7096a61c212fb310c917359e9 |
import sys, os, re, types, html.parser, urllib, datetime, signal, json, pdb, pathlib, csv, logging, io, fnmatch, traceback
import dbc.db, dbc.data, dbc.constants, dbc.parser, dbc.file
# Special hotfix flags for spells to mark that the spell has hotfixed effects or powers
SPELL_EFFECT_HOTFIX_PRESENT = 0x80000000000000... | johnroot/simc | dbc_extract3/dbc/generator.py | Python | gpl-3.0 | 181,539 | [
"BLAST",
"CRYSTAL"
] | 33353eaa22340f3890f01f48f42e2ac2f7213b6a57b47e4d700959184946afce |
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 28 14:26:44 2011
@author: Shreejoy
"""
from SPARQLWrapper import SPARQLWrapper, JSON, XML, N3, RDF
import re
dir('C:\Python27\Scripts\biophys\pubdb\pubdir')
from pubapp.models import Neuron, Synonym, Species
neurons = Neuron.objects.all()
for neuron in neur... | neuroelectro/neuroelectro_org | neurolex_integration/get_neuron_props.py | Python | gpl-2.0 | 1,869 | [
"NEURON"
] | a6d12ddeb238a69d780e230b5e13a015d94c6d7986c74738f770bee7544639a8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ =... | Bismarrck/pymatgen | pymatgen/io/zeoio.py | Python | mit | 596 | [
"pymatgen"
] | 8e780ed0b438674b1ebbb68dd0fa5b8511338781f47eef371efc4ed0c75a0286 |
# This file is part of BurnMan - a thermoelastic and thermodynamic toolkit
# for the Earth and Planetary Sciences
# Copyright (C) 2012 - 2021 by the BurnMan team, released under the GNU
# GPL v2 or later.
import numpy as np
from scipy.linalg import expm
from numpy.linalg import cond
from .mineral import Mineral
from .m... | geodynamics/burnman | burnman/classes/anisotropicmineral.py | Python | gpl-2.0 | 21,521 | [
"Avogadro"
] | 910b09a88d7bb93f914aed7c566f6f5e2249f33d5993309df2909e8e86afee04 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'ui_meshnetcdf.ui'
#
# Created: Mon Dec 10 16:39:54 2012
# by: PyQt4 UI code generator 4.9.1
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except A... | janhui/test_engine | dev/plugins/mesh_netcdf/ui_meshnetcdf.py | Python | lgpl-2.1 | 16,801 | [
"NetCDF"
] | 310af067284c153e9e3286adc30835e8ea8beed6ea50dfdf487f709d389a920f |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/timeeditor.py | Python | gpl-2.0 | 2,934 | [
"VisIt"
] | 3f83c800c7bf205d7e7590dea7a033347a7d75d3d1002667dd01319ca020a3ec |
"""
# Notes:
- This simulation seeks to emulate the COBAHH benchmark simulations of (Brette
et al. 2007) using the Brian2 simulator for speed benchmark comparison to
DynaSim. However, this simulation includes CLOCK-DRIVEN synapses, for direct
comparison to DynaSim's clock-driven architecture. The synaptic connec... | asoplata/dynasim-benchmark-brette-2007 | Brian2/brian2_benchmark_COBAHH_clocksyn_lodens_compiled_250.py | Python | gpl-3.0 | 3,912 | [
"Brian"
] | 98cf61c3d08910973b108820cf0c6724270e73bd39db51c4c70d1340dd7ab933 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
'''Pychemqt, Chemical Engineering Process simulator
Copyright (C) 2009-2017, Juan José Gómez Romera <jjgomera@gmail.com>
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 Softwar... | jjgomera/pychemqt | lib/mEoS/O2.py | Python | gpl-3.0 | 30,074 | [
"Jmol"
] | 1b25c0c24df86e73d4e3c7aceba6c69d93fc92828083b50dd1f7d1fe2e179d32 |
#############################################################################
# Code for a variational Walkout model (kind of like a GSN). #
#############################################################################
# basic python
import cPickle
import numpy as np
import numpy.random as npr
from coll... | Philip-Bachman/Sequential-Generation | WalkoutModel.py | Python | mit | 29,871 | [
"Gaussian"
] | b41a2a28cc37885c163a2488387dd0eef689c934b453bc0269de4ae1ab783ab6 |
'''
filtering the target genome to reduce the search space to those scaffolds
over 400 or 500bp in length.
'''
# Requires numpy, matplotlib and biopython libraries for execution
# Syntax:
# python createfasta.py --query [queryfile] --output [outputfile]
from Bio import SeqIO
import argparse
parser = argparse.Argume... | jasdumas/DouglasFir | createfasta.py | Python | gpl-2.0 | 1,254 | [
"Biopython"
] | 41b29cb9af25c1d9eb34aa98e19985c9dac3b2ebe712a70e5bcf8abad79d072b |
from Module import AbstractModule
class Module(AbstractModule):
def __init__(self):
AbstractModule.__init__(self)
def run(
self, network, in_data, out_attributes, user_options, num_cores,
out_filename):
import os
from genomicode import jmath
from genomicode impo... | jefftc/changlab | Betsy/Betsy/modules/extract_rsem_signal.py | Python | mit | 8,335 | [
"Bowtie"
] | 30f01a70c14102e351d5e071d9a84e8c75e90008f323182ad21a7d952583bf24 |
from PyQt5 import QtCore, QtWidgets
import peacock
class MeshBlockSelectorWidget(peacock.base.MooseWidget, QtWidgets.QWidget):
"""
A generic widget for controlling visible blocks, nodesets, and sidesets of the current mesh.
Args:
type[int]: The block type from vtk (see BlockControls.py).
"""
... | yipenggao/moose | python/peacock/Input/MeshBlockSelectorWidget.py | Python | lgpl-2.1 | 2,247 | [
"VTK"
] | dc5e0e5420943401b77d34b274f2c9c9ae5d202d0ffe305185de52ea0526b97d |
import ast
from copy import deepcopy
from artiq.transforms.tools import eval_ast, value_to_ast
def _count_stmts(node):
if isinstance(node, list):
return sum(map(_count_stmts, node))
elif isinstance(node, ast.With):
return 1 + _count_stmts(node.body)
elif isinstance(node, (ast.For, ast.Whi... | kgilmo/penning_artiq | artiq/transforms/unroll_loops.py | Python | gpl-3.0 | 2,584 | [
"VisIt"
] | 13dde783d771429d796bd3ec6a2d192d85b2e53f8890f6e6a76afc2c72c582f8 |
#!/usr/bin/env python
########################################################################
#
# (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 ... | wkeeling/ansible | lib/ansible/galaxy/api.py | Python | gpl-3.0 | 10,574 | [
"Galaxy"
] | 8450a20f19d3c80a64a9e367fce66f5cc6c42ff2536e08146517c42435f321e8 |
from __future__ import absolute_import, division, print_function, unicode_literals
import functools
import logging
import math
import operator
import socket
from datetime import datetime
from io import open
import numpy as np
log = logging.getLogger(__name__)
from .ssp_dicts import Dicts
from .ssp_aux import SspAux... | hydroffice/hyo_ssp | hydroffice/ssp/ssp.py | Python | lgpl-3.0 | 70,193 | [
"NetCDF"
] | 2b6073748f520589f63ebb96c15d6ee1efe08dd539eaf63662d1ef6d0873601a |
#!/usr/local/bin/Python3
from vector import Vector
from plane import Plane
from hyperplane import Hyperplane
from linsys import LinearSystem
from linsysHyper import LinearSystemHyper
def main():
test_row_ops = False
test_triangular_form = False
test_rref = False
test_ge_solution = False
test_para... | HKuz/Test_Code | LinearAlgebra/linSysTest.py | Python | mit | 11,447 | [
"Gaussian"
] | d983edbe17b4cad176b828aef0972208bcc7cb5e9bb84e7529103ebd0db820dd |
# Copyright (C) 2017 Martin Nilsson
# This file is part of the Memtran compiler.
#
# The Memtran compiler 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
# ... | LJMNilsson/memtran | src/end_expansion.py | Python | gpl-3.0 | 5,090 | [
"VisIt"
] | c14888c06f0fd5146899374f1e9ab3da2975f79b4f5edb4df5aa194df4a243a9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# PyNAM -- Python Neural Associative Memory Simulator and Evaluator
# Copyright (C) 2015 Andreas Stöckel
#
# 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 Sof... | hbp-sanncs/pynam | misc/measure_epsp.py | Python | gpl-3.0 | 2,939 | [
"NEURON"
] | 28ce68660f486c8bd7690b904f4e00ceddfb0b09adc0c5bed9c8a848d8a22a08 |
# -*- coding: utf-8 -*-
#
# brunel_alpha_nest.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... | lekshmideepu/nest-simulator | pynest/examples/brunel_alpha_nest.py | Python | gpl-2.0 | 13,308 | [
"NEURON"
] | a601819c7f5723f8ecd6526aae6a7a934136a0ce69c6b1f2dc3166c66087cfea |
import decimal
import gc
import itertools
import multiprocessing
import weakref
import sqlalchemy as sa
from sqlalchemy import ForeignKey
from sqlalchemy import inspect
from sqlalchemy import Integer
from sqlalchemy import MetaData
from sqlalchemy import select
from sqlalchemy import String
from sqlalchemy import test... | monetate/sqlalchemy | test/aaa_profiling/test_memusage.py | Python | mit | 46,748 | [
"VisIt"
] | 85f7f7f2dc98b8163e4ca6cbad79fffa72a456c54427169dc8bfbe1ef8f68e22 |
# Copyright 2016 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... | jjas0nn/solvem | tensorflow/lib/python2.7/site-packages/tensorflow/contrib/bayesflow/python/ops/special_math.py | Python | mit | 7,930 | [
"Gaussian"
] | 76e9ff0209612e89f6e00bf9a8b4bf275424f41df49940a0642c5722d318bf3f |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/test/http_proxy.py | Python | gpl-2.0 | 8,188 | [
"VisIt"
] | 3620cf2e018f1cd5687bbee8abd6e99e2b35e7a73c1a66ff7b3bfa5a6319b5df |
""" Plugin for osu! commands
This plugin will notify any registered user's pp difference and if they
set a new best also post that. It also includes many osu! features, such
as a signature generator, pp calculation and user map updates.
TUTORIAL:
A member with Manage Server permission must first assign one... | PcBoy111/PC-BOT-V2 | plugins/osu.py | Python | mit | 50,673 | [
"MOE"
] | 95019df0ce1d7e196266355c90bc7ac4cb281ac5c308f392e9633af43176f964 |
#!/usr/bin/env python
from __future__ import print_function
from builtins import input
from builtins import str
from builtins import range
import sys
import matplotlib
if matplotlib.get_backend() != "TKAgg":
matplotlib.use("TKAgg")
import pmagpy.pmagplotlib as pmagplotlib
import pmagpy.pmag as pmag
def main():
"... | Caoimhinmg/PmagPy | programs/chi_magic.py | Python | bsd-3-clause | 9,840 | [
"xTB"
] | d13cca51c6a6bd427ccf6ef91bc37d6e89ab9e956bb61f073ea539cc431303f7 |
"""An agent to ensure consistency for transformation jobs, tasks and files.
Depending on what is the status of a job and its input and output files different actions are performed.
.. warning:: Before fully enabling this agent make sure that your transformation jobs fulfill the assumptions of the
agent. Otherwise ... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Agent/DataRecoveryAgent.py | Python | gpl-3.0 | 26,327 | [
"DIRAC"
] | 6045340b2561dd43528233dbe7817cfac4c0dac7518e486f65d9fa3782a38e9a |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | testsuite/python/mass-and-rinertia_per_particle.py | Python | gpl-3.0 | 22,975 | [
"ESPResSo"
] | dc00031b3f42306434d0c362214b4c8289a3d8d0156f75bb2af2c1ed3e5b789d |
"""
Test support for the HANDLE_OWNERS_NOT_AVAILABLE group flag, and calling
GetHandleOwners on MUC members.
By default, MUC channels should have the flag set. The flag should be unset
when presence is received that includes the MUC JID's owner JID.
"""
import dbus
from gabbletest import make_result_iq, exec_test, ... | community-ssu/telepathy-gabble | tests/twisted/muc/test-muc-ownership.py | Python | lgpl-2.1 | 4,178 | [
"Brian"
] | 85059f98512527ebdb7905b800aa21f839ab29dc54d26921cfb6fef59ff907bb |
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import ChemicalForceFields, rdtrajectory
from rdkit.Chem.rdtrajectory import Snapshot, \
Trajectory, ReadAmberTrajectory, ReadGromosTrajectory
import os, sys
import unittest
from rdkit import RDConfig
def feq(v1, v2, tol=1.0e-4):
return... | rvianello/rdkit | Code/GraphMol/Wrap/testTrajectory.py | Python | bsd-3-clause | 19,507 | [
"Amber",
"RDKit"
] | 51648ed099267742aa18e8631dd3facc2902a26ff22d3b04c12e13ef3496add9 |
"""
View for Courseware Index
"""
# pylint: disable=attribute-defined-outside-init
from datetime import datetime
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.core.context_processors import csrf
from django.core.urlreso... | chrisndodge/edx-platform | lms/djangoapps/courseware/views/index.py | Python | agpl-3.0 | 22,651 | [
"VisIt"
] | 79a815739637545e79589960b4423b9370a89ac204cf4dff72848031a01e6c5c |
from __future__ import absolute_import, division, print_function
import functools
import inspect
import sys
import warnings
from collections import OrderedDict, deque, defaultdict
import six
from more_itertools import flatten
import attr
import py
from py._code.code import FormattedExcinfo
import _pytest
from _pyte... | davidszotten/pytest | src/_pytest/fixtures.py | Python | mit | 52,729 | [
"VisIt"
] | 54fffc56b6c4acee7f4f5ebdfde659a9fecb4c378f13e4fd41bf4d2667cb8271 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-install-service
# Author : Ricardo Graciani
########################################################################
"""
Do the initial installation and configuration of a DIRAC service
"""
__RC... | avedaee/DIRAC | Core/scripts/dirac-install-service.py | Python | gpl-3.0 | 3,147 | [
"DIRAC"
] | de535fa3ef6a214782b680c19626cd042769b46f9c8444dcde4dd60665d01d05 |
'''
python module for ASE2-free and Numeric-free dacapo
U{John Kitchin<mailto:jkitchin@andrew.cmu.edu>} December 25, 2008
This module supports numpy directly.
* ScientificPython2.8 is required
- this is the first version to use numpy by default.
see https://wiki.fysik.dtu.dk/stuff/nc/ for dacapo netcdf variable
d... | askhl/ase | ase/calculators/jacapo/jacapo.py | Python | gpl-2.0 | 150,670 | [
"ASE",
"Gaussian",
"NetCDF"
] | 4856f96f6bb13c4414768930649af4744af780662dad42148ab8149946b5caa9 |
#! /usr/bin/env python3.4
# -*- coding:utf-8 -*-
#
# Krypton - A little tool for GAMESS (US) users
#
# Copyright (C) 2012-20.. Mathias M.
#
# 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... | mathiasmch/Krypton | krypton.py | Python | gpl-3.0 | 2,464 | [
"GAMESS"
] | d1ac942f2dba1e663be15d4079986a817ecf5312b55114d9a8391d2243cb3867 |
__author__ = 'jrc'
import os
#Application Detail - Put Your App Info Here
APP_SCOPES = 'SPEECH,STTC,TTS'
APP_KEY = 'xiprzvi7s0kg5lhb0kqybkm92cqy805q'
APP_SECRET = 'migubmxi0gk9ebgiodkuo46a6xvsquis'
#APP_KEY = 'your app key here'
#APP_SECRET = 'your app secret here'
APP_GRANT_TYPE = 'client_credentials'
#API URLs
URL_... | jcallegari/raspberry_pi | config.py | Python | unlicense | 1,965 | [
"CRYSTAL"
] | d25d04ef0efac8717d2f151be44ab3759caf78fdd5f9c0d51b49ecc1bae559c5 |
import sis
import numpy as np
import math # for exp()
import matplotlib.pyplot as plt
import scipy.integrate as sp
## measurement noise
sigma_y = 0.01
## initial value of state
X0 = np.array([1.0,0.0])
## uncertainty in the initial state
SIGMA_X0 = np.array([0.1,0.1])
def eqom(x,t):
dx = np.zeros(2)
dx[0] = x... | fatadama/estimation | filters/python/sis_particle/sis_test.py | Python | gpl-2.0 | 4,919 | [
"Gaussian"
] | 13638d53a91f949443e8401ed091e64ba37b2e27a708c04a9e8c117da792a620 |
from visitor import Visitor
class PlainFormatVisitor(Visitor):
def __init__(self):
self.indent = 0
def visit_dict(self, node):
if not node:
return ''
buf = '\n'
self.indent += 2
parts = []
for k, v in sorted(node.items()):
parts.append('... | AmadeusITGroup/python-jiffybox | jiffybox/format.py | Python | gpl-3.0 | 1,010 | [
"VisIt"
] | a6ba4f2e4ab315b3673a1269eb5d1bb37b51f196cb0b45f00f4afc5c02e17829 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Youtube-dl PyGtk Gui
#
# Copyright 2014 Chiheb Nexus
#
# 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.
#
# This... | Chiheb-Nexus/Youtube-dl_PyGtk_Gui | langue_gui.py | Python | gpl-3.0 | 3,535 | [
"VisIt"
] | 7900f8f84da5f75bda166fffdfe8d54997dba90377f40c5c4012480a10747bc9 |
from gpiozero import LED, Buzzer, Button
from signal import pause
button = Button(2)
buzzer = Buzzer(3)
red = LED(4)
amber = LED(5)
green = LED(6)
things = [red, amber, green, buzzer]
def things_on():
for thing in things:
thing.on()
def things_off():
for thing in things:
thing.off()
button.... | MrHarcombe/python-gpiozero | docs/examples/all_on_3.py | Python | bsd-3-clause | 388 | [
"Amber"
] | 70af2ab4b9a83673ca8fae4d39acd7a7c5e358309c29a76757d233e478f0d4e0 |
import tensorflow as tf
import sys
import time
import os
# Set train_nn to True for training the neural network or False for performing classification.
train_nn = True
if train_nn == False :
# If the following is set to True, training will start if no checkpoint is found in the
# current directry.
continue_trai... | kchng/Quantum_machine_learning | conv_kelvin.py | Python | apache-2.0 | 18,524 | [
"NEURON"
] | 864e37970df8c65b433eb38a1be4e7ccb1f20250d061e785c528c451a0ae001a |
#
# ENVISIoN
#
# Copyright (c) 2018 Elvis Jakobsson
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list... | rartino/ENVISIoN | envisionpy/hdf5parser/vasp/parchg.py | Python | bsd-2-clause | 8,441 | [
"VASP"
] | e33b31c21a33f27111f5c7dde3758f7c599209bc844a12222aedf9196c864e7e |
# Import required modules
import pysam
import collections
import gzip
import multiprocessing
from ngs_python.system import iohandle
from general_python import writeFile
def concordant(reads, maxSize):
''' Function to find concordant pairs. Input is a list/tuple
that sequentially contains the chromosome, start,... | adam-rabinowitz/ngs_analysis | structure/alignedPair.py | Python | gpl-2.0 | 7,249 | [
"pysam"
] | 184f4066f82da0bb60a76ffa41815a95eac2bfe7a189f9a2363883f9b3244fd4 |
"""
batch/batch.py
Class to setup and run batch simulations
Contributors: salvadordura@gmail.com
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from builtins import zip
from builtins import range
from builtins... | thekerrlab/netpyne | netpyne/batch/batch.py | Python | mit | 39,127 | [
"NEURON"
] | 56a65fb5b13c24a0fbe72a687000c8624e705e48b6f8f87f207d61e31a2842de |
import aiohttp
import discord
import urllib.parse
from utils.checks import check_if_user_can_sr
from discord.ext import commands
from inspect import cleandoc
class Assistance(commands.Cog, command_attrs=dict(cooldown=commands.Cooldown(1, 30.0, commands.BucketType.channel))):
"""
Commands that will mostly be ... | thedax/Kurisu | cogs/assistance.py | Python | apache-2.0 | 97,762 | [
"VisIt"
] | bad1108a9ac2e0672a6f2433fbcea1586991f7b41d592bb72facb6ac5ed3589c |
# -*- coding: utf-8 -*-
"""Defines fixtures available to all tests."""
import os
import pytest
from webtest import TestApp
from octopus.settings import TestConfig
from octopus.app import create_app
from octopus.database import db as _db
from .factories import UserFactory
@pytest.yield_fixture(scope='function')
def... | quaintm/octopus | tests/conftest.py | Python | bsd-3-clause | 795 | [
"Octopus"
] | 4e7bb72505a2bd6cfe34133479b5607598209a03bf35193c63b36618f14a2a02 |
import bs
import random
import bsUtils
import bsPowerup
def bsGetAPIVersion():
# see bombsquadgame.com/apichanges
return 4
def bsGetGames():
return [SurviveCurseGame]
class Icon(bs.Actor):
def __init__(self,player,position,scale,showLives=True,showDeath=True,
nameScale=1.0,... | Mrmaxmeier/BombSquad-Community-Mod-Manager | mods/surviveCurse.py | Python | unlicense | 38,535 | [
"BLAST"
] | 988b3938e12dd2a3031a98528c985340df22173b47d9861ab15abf384111386c |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Project'
__version__ = '0.1'
__maintainer__ = 'Shyue Ping Ong'
__email__ = 'ongsp@... | xhqu1981/pymatgen | pymatgen/util/tests/test_num_utils.py | Python | mit | 1,058 | [
"pymatgen"
] | 942961a2689770e4a96636e568aaa80598ae867699689d7970517cf76e1af97f |
# sql/util.py
# Copyright (C) 2005-2013 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
from .. import exc, schema, util, sql
from ..util import topological
from . import express... | Drvanon/Game | venv/lib/python3.3/site-packages/sqlalchemy/sql/util.py | Python | apache-2.0 | 31,001 | [
"VisIt"
] | 2cfdc4a1460ef595636bd89f5976127f63ecd88a1d82b81b5bf319d29c350f34 |
"""Classes for fitting red sequence and related parameters.
This file contains the classes used to fit the red sequence model, including
the median relations, mean relations, scatter, covariance, etc.
"""
import numpy as np
from scipy import special
import scipy.optimize
import esutil
import warnings
from .utilities ... | erykoff/redmapper | redmapper/fitters.py | Python | apache-2.0 | 45,548 | [
"Gaussian"
] | 10cfc4136b22d80b51cc2b53c2e1af4f75dbbe249dad4c68cd3cadd6b7fd49cf |
import pytest
from interpreter.ast import Num
from interpreter.interpreter import Interpreter, NodeVisitor
from interpreter.lexer import Lexer
from interpreter.parser import Parser
from interpreter.tokens import Token, INTEGER
class TestNodeVisitor(object):
num_token = Num(Token(INTEGER, 1))
def test_generi... | LucasMagnum/simple-interpreter | tests/unit/test_interpreter.py | Python | mit | 1,152 | [
"VisIt"
] | b4bc09b06d40cf469f6b63bae0c7d0bc4b8cb2941f885dbdd630e5e51ea38997 |
# -*- 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-orchestration-airflow | tests/unit/gapic/service_v1beta1/test_environments.py | Python | apache-2.0 | 107,421 | [
"Octopus"
] | 6e97d416545455e654aec9e89d9d87dc6eb6de458479286046da0979a57a376d |
# $Id$
#
# Copyright (C) 2002-2008 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
"""unit testing code ... | soerendip42/rdkit | rdkit/Chem/UnitTestCrippen.py | Python | bsd-3-clause | 5,800 | [
"RDKit"
] | e90697789790d3c46e4a5f4b3fc8622ac7aa10e491bab92b499c05c713fc83cf |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | dgasmith/psi4 | psi4/driver/procrouting/dft/hyb_functionals.py | Python | lgpl-3.0 | 16,605 | [
"Psi4"
] | a9fafe318667ffc6b409c4348abff1e62f02ccc765bed05bebda8c9268dbb4a4 |
#!/usr/bin/env python
#
# $File: newOperator.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribut... | BoPeng/simuPOP | docs/newOperator.py | Python | gpl-2.0 | 2,477 | [
"VisIt"
] | ae470ede62548d33f327ae06022beae8d49c198860ff4c23d59a60c93737b4a2 |
# Copyright (C) 2015 Google Inc., authors, and contributors <see AUTHORS file>
# Licensed under http://www.apache.org/licenses/LICENSE-2.0 <see LICENSE file>
# Created By: miha@reciprocitylabs.com
# Maintained By: miha@reciprocitylabs.com
import textwrap
from integration.ggrc import TestCase
from freezegun import free... | prasannav7/ggrc-core | test/integration/ggrc_workflows/notifications/test_middle_level_one_time_wf.py | Python | apache-2.0 | 5,820 | [
"NAMD"
] | e57b2d725711b5eec66e749fcf10a11aecea3a6293b6a7f1343b2ce65709d91f |
"""
Integration tests for singletask vector feature models.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = "MIT"
import os
import unittest
import temp... | joegomes/deepchem | deepchem/models/tests/test_api.py | Python | mit | 6,343 | [
"RDKit"
] | cd0e8963163958ccfe8a95467ad2f180ab16266228f094a141fb020c16ccfc9d |
# Copyright (c) 2004 Canonical Limited
# Author: Robert Collins <robert.collins@canonical.com>
#
# 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 y... | facebook/mysql-5.6 | xtrabackup/test/python/subunit/tests/TestUtil.py | Python | gpl-2.0 | 2,790 | [
"VisIt"
] | 8d8712c0976ebab77043c761315902ef4865503182b101d4fecdeaa539f804cb |
import sys
import os
import json
import re
from biokbase.workspace.client import Workspace
"""
This provides some useful functions for genome_util
By Fei He
"""
#get gene sequences from workspace by gene_id
def get_seq(gene_id):
seq='proteinsequencesssssssssss'
return seq
def get_genome(genome_id=None,worksp... | plane83/genome_util | lib/biokbase/genome_util/script_util.py | Python | mit | 1,972 | [
"BLAST"
] | 7eb30fdbc8b162ee0afb4a8e8531c4a3fa9023fbb10f7aa244611ad92d45c608 |
from flask import Flask, render_template, request, redirect, session
import random
from time import gmtime, strftime
app = Flask(__name__)
app.secret_key = "JQ;hcF1AZ59>mO^S7xhrXXK?c|Z3N&Siu(BT'[tp;DFw]YA%g't;|Oa>hv"
@app.route('/')
def index():
# session['gold'] = 0
# session.pop('response')
if not sessi... | JosiahRooney/Python | ninja_gold/server.py | Python | mit | 1,714 | [
"CASINO"
] | cbe3e9ce1642081981518605cb878eddce16907a656dd1b8b77b94fc4c2b8050 |
"""
Splits bam by whether they are positive or negative strand
Usage:
python cutsite_matrix.py something.bam annotation.bed
"""
import pysam
import numpy as np
def get_cutsite():
pass
def main():
import optparse
p = optparse.OptionParser(__doc__)
p.add_option("-D", "--debug", action="store_tr... | jeffhsu3/genda | scripts/PWM/bam_cuts.py | Python | bsd-3-clause | 1,970 | [
"pysam"
] | 28c10ecf59a2991deeae863e160f3214fe2c7954a96d8f3c57195e446a2ad7d6 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | sam-m888/gramps | gramps/plugins/tool/mergecitations.py | Python | gpl-2.0 | 10,159 | [
"Brian"
] | 322615211c606544ea3e3255222b3acea613c9a2ef5a33ee9d418852dc3dea46 |
"""Merge the PNG IFC files into the daily netcdf file"""
import datetime
import sys
import os
import pytz
from osgeo import gdal
import numpy as np
from pyiem import iemre
from pyiem.util import ncopen, logger
LOG = logger()
def run(ts):
"""Process this date's worth of data"""
now = ts.replace(hour=0, minut... | akrherz/iem | scripts/iemre/merge_ifc.py | Python | mit | 1,925 | [
"NetCDF"
] | 539bad7e4b317ed90eb9112489dc513abd064625da0e983ea33d110d100ef35d |
"""
Unit tests for instructor.api methods.
"""
import datetime
import functools
import io
import json
import random
import shutil
import tempfile
from unittest.mock import Mock, NonCallableMock, patch
import ddt
import pytest
from boto.exception import BotoServerError
from django.conf import settings
from django.contr... | eduNEXT/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 193,341 | [
"VisIt"
] | f5301597e2dd268044c27934a6efc501dd140767791aa2dc87a3b7d4df12ef77 |
import numpy as np
from gpaw import GPAW, PW
from ase.calculators.dftd3 import DFTD3
from ase.build import bulk
from ase.constraints import UnitCellFilter
from ase.optimize import LBFGS
np.random.seed(0)
diamond = bulk('C')
diamond.rattle(stdev=0.1, seed=0)
diamond.cell += np.random.normal(scale=0.1, size=(3,3))
df... | miroi/open-collection | theoretical_chemistry/software_runs/ase/runs/dftd3-ase/diamond_dftd3.py | Python | mit | 542 | [
"ASE",
"GPAW"
] | d32eb9bde6313565f3b4031f1cc6a095ca9c1e106fae7737e2be6216057bdc96 |
from sqlalchemy import extract
from sqlalchemy import select
from sqlalchemy import sql
from sqlalchemy.databases import sybase
from sqlalchemy.testing import assert_raises_message
from sqlalchemy.testing import AssertsCompiledSQL
from sqlalchemy.testing import fixtures
class CompileTest(fixtures.TestBase, AssertsCom... | wujuguang/sqlalchemy | test/dialect/test_sybase.py | Python | mit | 1,839 | [
"ASE"
] | c074f363d177eaae3d7336c401617cb04167776840080e2d79f82a2770d27a12 |
""" ConstantFolding performs some kind of partial evaluation. """
from pythran.analyses import ConstantExpressions, ASTMatcher
from pythran.passmanager import Transformation
from pythran.tables import MODULES
from pythran.conversion import to_ast, ConversionError, ToNotEval, mangle
from pythran.analyses.ast_matcher i... | pombredanne/pythran | pythran/optimizations/constant_folding.py | Python | bsd-3-clause | 8,826 | [
"VisIt"
] | da4eb1cc114ed099c477426ff531a6621b75459a2be647a8019a956cdd69ea3b |
from rdkit import Chem
from rdkit.Chem import ChemicalForceFields, rdDistGeom
from rdkit import RDConfig
import unittest
import os
import numpy
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
class TestCase(unittest.TestCase):
def setUp(self):
self.dirName = os.path.join(RDConfig.RDBaseDir, 'Code',... | ptosco/rdkit | Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py | Python | bsd-3-clause | 14,751 | [
"RDKit"
] | ae027efe706ef968e51eb20e0fbcceb6712050f9f0835288dded2d253079847c |
# Orca
#
# Copyright 2018-2019 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at y... | GNOME/orca | src/orca/scripts/toolkits/Chromium/script.py | Python | lgpl-2.1 | 16,071 | [
"ORCA"
] | fe7a2a04c06a3765c5c1ca7945ab4aaa0e44b4acbe98b6461577ab6badc5d669 |
# Copyright 2002 by Katharine Lindner. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
Module to represent the NDB Atlas structure (a minimal subset of PDB format).
Hetero,... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Crystal/__init__.py | Python | gpl-2.0 | 8,361 | [
"Biopython",
"CRYSTAL"
] | 71d9f296cc8cbe9d85c44b41061c77e3ccca7804b73ae54bcd41a13f0a2f55a7 |
from __future__ import absolute_import
input_name = '../examples/linear_elasticity/linear_elastic_up.py'
output_name = 'test_linear_elastic_up.vtk'
from tests_basic import TestInput
class Test( TestInput ):
pass
| rc/sfepy | tests/test_input_linear_elastic_up.py | Python | bsd-3-clause | 217 | [
"VTK"
] | 2bdec9d43a4940f452cf1acc9c499f7b376b473379648d71a7bcbed67f0e39a1 |
# -*- coding: utf-8 -*-
import logging
from openerp import api, fields, models, _
_logger = logging.getLogger(__name__)
class AppThemeConfigSettings(models.TransientModel):
_inherit = 'res.config.settings'
_name = 'app.theme.config.settings'
_description = u"App Odoo Customize settings"
app_system... | luoguizhou/gooderp_addons | app_odoo_customize/models/app_theme_config_settings.py | Python | agpl-3.0 | 6,066 | [
"VisIt"
] | f370fc50220684a3af0b88916d54e1f5af4f92f6c0e2957741f5148bc858dfea |
#!/usr/bin/env python3
"""
Copyright 2020 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 ... | pwillworth/galaxyharvester | html/getFeedback.py | Python | gpl-3.0 | 7,434 | [
"Galaxy"
] | f7b1bee80e067cb2ffb367c3932e3beb05da66baae6b9b954e045ca39c8c03f3 |
from collections import defaultdict
import shutil
from defaults import *
from vcf_utils import *
from sv_interval import SVInterval, get_gaps_file, interval_overlaps_interval_list, merge_intervals, merge_intervals_recursively
from pindel_reader import PindelReader
from breakdancer_reader import BreakDancerReader
from ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/MetaSV-0.5-py2.7.egg/metasv.bak/main.py | Python | apache-2.0 | 17,324 | [
"pysam"
] | c1c14d79c79b76e8014bc8bbf789c9502c379d01ff5b89dae82cd92e5bb300ac |
#!/usr/bin/env python3
from __future__ import print_function
import argparse
import io
import os
import subprocess
import sys
import tempfile
import time
from collections import namedtuple
from contextlib import ExitStack
from functools import partial
from threading import Thread
import pysam
AlleleStats = namedtup... | loraine-gueguen/tools-iuc | tools/varscan/varscan.py | Python | mit | 66,886 | [
"ADF",
"pysam"
] | 2ef4be076dc9debdc42efb18f1200cea84260e155496641c4dbaa8706239e6b3 |
## This file is part of Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 CERN.
##
## Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either version 2 of the
## License, ... | pombredanne/invenio | modules/miscutil/lib/dbquery.py | Python | gpl-2.0 | 13,787 | [
"BLAST"
] | dfcfda44b65d26550417e31c46c3af946cf2fabec274809a0be68c3a70275978 |
#!/usr/bin/env python
#
# !!! This is NOT the original extractFormants.py file !!! ##
#
# - all comments beginning with a double pound sign ("##") ##
# - docstrings for all classes and functions ##
# - alphabetic ordering outside of main program: ... | sgraetzer/FAVE | FAVE-extract/bin/extractFormants.py | Python | gpl-3.0 | 105,089 | [
"Gaussian"
] | 60dff4034162d8a3b739975769eb81ae55b246409aee3aa5efbd26533aea770a |
# -*- coding: utf-8 -*-
# -*- coding: utf-8 -*-
import numpy as np
import os.path as op
import pyhrf
#from pottsfield import pottsfield_c
from random import randrange
from pyhrf.tools import buildPolyMat
from field import genPotts
from pyhrf.graph import graph_from_lattice, kerMask2D_4n , kerMask3D_6n
from numpy.ra... | philouc/pyhrf | python/pyhrf/boldsynth/scenarios.py | Python | gpl-3.0 | 43,735 | [
"Gaussian"
] | 2f910d7e8c16881e5372f1591d556ea3605496d9853ee375b911b20a6c36ef55 |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements an XRD pattern calculator.
"""
from six.moves import filter
from six.moves import map
from six.moves import zip
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__mai... | Dioptas/pymatgen | pymatgen/analysis/diffraction/xrd.py | Python | mit | 14,721 | [
"CRYSTAL",
"pymatgen"
] | 480886cc162f0f011f9738ae1a03cb18f6cfb978eae3f15386c94d4333588516 |
""" Cache
This module provides a generic Cache extended to be used on RSS, RSSCache.
This cache features a lazy update method. It will only be updated if it is
empty and there is a new query. If not, it will remain in its previous state.
However, Cache class internal cache: DictCache sets a validity to its entries.
Af... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Utilities/RSSCacheNoThread.py | Python | gpl-3.0 | 12,416 | [
"DIRAC"
] | 8177cca322b71204c638c6facc48bd9629eb7882ecd2f5bfa1a8c6f1fbb6e582 |
# Copyright 2018 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 to in writing, s... | googlearchive/rgc-models | response_model/python/metric_learning/end_to_end/response_embedding.py | Python | apache-2.0 | 17,502 | [
"Gaussian"
] | 1521d4e731d5c23403f546cc0e4bf37b9d60dda22bd926517a9995955a77ad58 |
import glob
import hashlib
import os
from subprocess import check_call
import h5py
import openmc
import pytest
from tests.testing_harness import TestHarness
from tests.regression_tests import config
vtk = pytest.importorskip('vtk')
class PlotVoxelTestHarness(TestHarness):
"""Specialized TestHarness for running ... | walshjon/openmc | tests/regression_tests/plot_voxel/test.py | Python | mit | 1,856 | [
"VTK"
] | c54bd30a93f7cd579de1a15c9d6f82594df465813ebe226eb5cc0f96d1a9c6a7 |
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