541 lines
18 KiB
Python
541 lines
18 KiB
Python
from diceplayer.shared.interface.dice_interface import DiceInterface
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from diceplayer.shared.config.player_config import PlayerConfig
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from diceplayer.shared.environment.molecule import Molecule
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from diceplayer.shared.environment.system import System
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from diceplayer.shared.environment.atom import Atom
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from diceplayer import logger
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import yaml
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import io
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from tests.mocks.mock_inputs import get_config_example
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from tests.mocks.mock_proc import MockConnection, MockProc
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from unittest import mock
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import unittest
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class TestDiceInterface(unittest.TestCase):
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def setUp(self):
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logger.set_logger(stream=io.StringIO())
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config = yaml.load(get_config_example(), Loader=yaml.Loader)
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self.config = PlayerConfig.from_dict(config['diceplayer'])
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def test_class_instantiation(self):
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dice = DiceInterface()
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self.assertIsInstance(dice, DiceInterface)
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def test_configure(self):
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dice = DiceInterface()
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self.assertIsNone(dice.step)
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self.assertIsNone(dice.system)
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# Ignoring the types for testing purposes
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dice.configure(self.config, System())
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self.assertIsNotNone(dice.step)
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self.assertIsNotNone(dice.system)
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def test_reset(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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self.assertTrue(hasattr(dice, 'step'))
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self.assertTrue(hasattr(dice, 'system'))
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dice.reset()
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self.assertFalse(hasattr(dice, 'step'))
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self.assertFalse(hasattr(dice, 'system'))
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@mock.patch('diceplayer.shared.interface.dice_interface.Process', MockProc())
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@mock.patch('diceplayer.shared.interface.dice_interface.connection', MockConnection)
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def test_start(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.start(1)
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@mock.patch('diceplayer.shared.interface.dice_interface.connection', MockConnection)
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@mock.patch('diceplayer.shared.interface.dice_interface.Process', MockProc(exitcode=1))
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def test_start_with_process_error(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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with self.assertRaises(SystemExit):
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dice.start(1)
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def test_simulation_process_raises_exception(self):
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dice = DiceInterface()
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with self.assertRaises(SystemExit):
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dice._simulation_process(1, 1)
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@mock.patch('diceplayer.shared.interface.dice_interface.DiceInterface._make_proc_dir')
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@mock.patch('diceplayer.shared.interface.dice_interface.DiceInterface._make_dice_inputs')
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@mock.patch('diceplayer.shared.interface.dice_interface.DiceInterface._run_dice')
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def test_simulation_process(self, mock_run_dice, mock_make_dice_inputs, mock_make_proc_dir):
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dice = DiceInterface()
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dice._simulation_process(1, 1)
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self.assertTrue(dice._make_proc_dir.called)
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self.assertTrue(dice._make_dice_inputs.called)
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self.assertTrue(dice._run_dice.called)
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.mkdir')
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists')
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def test_make_proc_dir_if_simdir_exists(self, mock_path_exists, mock_path_mkdir):
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dice = DiceInterface()
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dice.configure(self.config, System())
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mock_path_exists.return_value = False
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dice._make_proc_dir(1, 1)
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self.assertEqual(mock_path_mkdir.call_count, 2)
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.mkdir')
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists')
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def test_make_proc_dir_if_simdir_doesnt_exists(self, mock_path_exists, mock_path_mkdir):
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dice = DiceInterface()
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dice.configure(self.config, System())
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mock_path_exists.return_value = False
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dice._make_proc_dir(1, 1)
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self.assertEqual(mock_path_mkdir.call_count, 2)
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def test_make_dice_seed(self):
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seed = DiceInterface._make_dice_seed()
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self.assertIsInstance(seed, int)
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def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_one(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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dice._make_dice_inputs(1, 1)
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self.assertTrue(dice._make_potentials.called)
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self.assertFalse(dice._make_init_file.called)
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self.assertFalse(dice._new_density.called)
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self.assertTrue(dice._make_nvt_ter.called)
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self.assertTrue(dice._make_nvt_eq.called)
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self.assertFalse(dice._make_npt_ter.called)
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self.assertFalse(dice._make_npt_eq.called)
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@mock.patch('builtins.open', new_callable=mock.mock_open, read_data='test')
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=True)
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def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_two(self, mock_path_exists, mock_open):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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dice._make_dice_inputs(2, 1)
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self.assertTrue(dice._make_potentials.called)
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self.assertTrue(dice._make_init_file.called)
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self.assertTrue(dice._new_density.called)
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self.assertFalse(dice._make_nvt_ter.called)
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self.assertTrue(dice._make_nvt_eq.called)
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self.assertFalse(dice._make_npt_ter.called)
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self.assertFalse(dice._make_npt_eq.called)
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=False)
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def test_make_dice_inputs_raises_exception_on_last_not_found(self, mock_path_exists):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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with self.assertRaises(FileNotFoundError):
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dice._make_dice_inputs(2, 1)
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def test_make_dice_inputs_nstep_len_three_with_randoninit_first_cycle_one(self):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_potentials = mock.Mock()
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dice._make_init_file = mock.Mock()
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dice._new_density = mock.Mock()
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dice._make_nvt_ter = mock.Mock()
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dice._make_nvt_eq = mock.Mock()
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dice._make_npt_ter = mock.Mock()
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dice._make_npt_eq = mock.Mock()
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dice._make_dice_inputs(1, 1)
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self.assertTrue(dice._make_potentials.called)
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self.assertFalse(dice._make_init_file.called)
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self.assertFalse(dice._new_density.called)
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self.assertTrue(dice._make_nvt_ter.called)
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self.assertFalse(dice._make_nvt_eq.called)
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self.assertTrue(dice._make_npt_ter.called)
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self.assertTrue(dice._make_npt_eq.called)
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@mock.patch('diceplayer.shared.interface.dice_interface.os')
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@mock.patch('diceplayer.shared.interface.dice_interface.shutil')
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=True)
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def test_run_dice_on_first_cycle_run_successful(self, mock_path_exists, mock_shutils, mock_os):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1, 1]
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dice.run_dice_file = mock.Mock()
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dice._run_dice(1, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 3)
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self.assertTrue(mock_shutils.copy.called)
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.step.dice.nstep = [1, 1]
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dice.run_dice_file = mock.Mock()
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dice._run_dice(1, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 2)
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self.assertTrue(mock_shutils.copy.called)
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@mock.patch('diceplayer.shared.interface.dice_interface.os')
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@mock.patch('diceplayer.shared.interface.dice_interface.shutil')
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=True)
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def test_run_dice_on_second_cycle_run_successful(self, mock_path_exists, mock_shutils, mock_os):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.run_dice_file = mock.Mock()
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dice._run_dice(2, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 2)
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self.assertTrue(mock_shutils.copy.called)
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.run_dice_file = mock.Mock()
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dice._run_dice(2, 1)
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self.assertTrue(mock_os.getcwd.called)
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self.assertTrue(mock_os.chdir.called)
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self.assertEqual(dice.run_dice_file.call_count, 1)
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self.assertTrue(mock_shutils.copy.called)
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@mock.patch('diceplayer.shared.interface.dice_interface.os')
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@mock.patch('diceplayer.shared.interface.dice_interface.shutil')
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@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=False)
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def test_run_dice_on_second_cycle_run_successful(self, mock_path_exists, mock_shutils, mock_os):
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice.run_dice_file = mock.Mock()
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with self.assertRaises(FileNotFoundError):
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dice._run_dice(1, 1)
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@mock.patch('builtins.open', new_callable=mock.mock_open)
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def test_make_init_file(self, mock_open):
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example_atom = Atom(
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lbl=1,
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na=1,
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rx=1.0,
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ry=1.0,
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rz=1.0,
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chg=1.0,
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eps=1.0,
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sig=1.0,
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)
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main_molecule = Molecule('main_molecule')
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main_molecule.add_atom(example_atom)
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secondary_molecule = Molecule('secondary_molecule')
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secondary_molecule.add_atom(example_atom)
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system = System()
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system.add_type(main_molecule)
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system.add_type(secondary_molecule)
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dice = DiceInterface()
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dice.configure(self.config, system)
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dice.step.dice.nmol = [1, 1]
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last_xyz_file = io.StringIO()
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last_xyz_file.writelines([
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' TEST\n',
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' Configuration number : TEST = TEST TEST TEST\n',
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' H 1.00000 1.00000 1.00000\n',
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' H 1.00000 1.00000 1.00000\n',
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])
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last_xyz_file.seek(0)
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dice._make_init_file('test', last_xyz_file)
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = [
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' 1.000000 1.000000 1.000000\n',
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' 1.000000 1.000000 1.000000\n',
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'$end'
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]
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self.assertEqual(lines, expected_lines)
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@mock.patch('builtins.open', new_callable=mock.mock_open)
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def test_new_density(self, mock_open):
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example_atom = Atom(
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lbl=1,
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na=1,
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rx=1.0,
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ry=1.0,
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rz=1.0,
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chg=1.0,
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eps=1.0,
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sig=1.0,
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)
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main_molecule = Molecule('main_molecule')
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main_molecule.add_atom(example_atom)
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secondary_molecule = Molecule('secondary_molecule')
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secondary_molecule.add_atom(example_atom)
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system = System()
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system.add_type(main_molecule)
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system.add_type(secondary_molecule)
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dice = DiceInterface()
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dice.configure(self.config, system)
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last_xyz_file = io.StringIO()
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last_xyz_file.writelines([
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' TEST\n',
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' Configuration number : TEST = 1 1 1\n',
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' H 1.00000 1.00000 1.00000\n',
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' H 1.00000 1.00000 1.00000\n',
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])
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last_xyz_file.seek(0)
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density = dice._new_density(last_xyz_file)
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self.assertEqual(density, 85.35451545000001)
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@mock.patch('builtins.open', new_callable=mock.mock_open)
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@mock.patch('diceplayer.shared.interface.dice_interface.random')
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def test_make_nvt_ter(self, mock_random, mock_open):
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mock_random.random.return_value = 1
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_nvt_ter(1, 'test')
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = ['title = Diceplayer run - NVT Thermalization\n', 'ncores = 4\n', 'ljname = phb.ljc\n', 'outname = phb\n', 'nmol = 1 50\n', 'dens = 0.75\n', 'temp = 300.0\n', 'init = yes\n', 'nstep = 2000\n', 'vstep = 0\n', 'mstop = 1\n', 'accum = no\n', 'iprint = 1\n', 'isave = 0\n', 'irdf = 0\n', 'seed = 1000000\n', 'upbuf = 360']
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self.assertEqual(lines, expected_lines)
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@mock.patch('builtins.open', new_callable=mock.mock_open)
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@mock.patch('diceplayer.shared.interface.dice_interface.random')
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def test_make_nvt_eq(self, mock_random, mock_open):
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mock_random.random.return_value = 1
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_nvt_eq('test')
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = ['title = Diceplayer run - NVT Production\n', 'ncores = 4\n', 'ljname = phb.ljc\n', 'outname = phb\n', 'nmol = 1 50\n', 'dens = 0.75\n', 'temp = 300.0\n', 'init = no\n', 'nstep = 3000\n', 'vstep = 0\n', 'mstop = 1\n', 'accum = no\n', 'iprint = 1\n', 'isave = 1000\n', 'irdf = 40\n', 'seed = 1000000\n']
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self.assertEqual(lines, expected_lines)
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@mock.patch('builtins.open', new_callable=mock.mock_open)
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@mock.patch('diceplayer.shared.interface.dice_interface.random')
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def test_make_npt_ter(self, mock_random, mock_open):
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mock_random.random.return_value = 1
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_npt_ter(1, 'test')
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = ['title = Diceplayer run - NPT Thermalization\n', 'ncores = 4\n', 'ljname = phb.ljc\n', 'outname = phb\n', 'nmol = 1 50\n', 'press = 1.0\n', 'temp = 300.0\n', 'init = no\n', 'vstep = 600\n', 'nstep = 5\n', 'mstop = 1\n', 'accum = no\n', 'iprint = 1\n', 'isave = 0\n', 'irdf = 0\n', 'seed = 1000000\n']
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self.assertEqual(lines, expected_lines)
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@mock.patch('builtins.open', new_callable=mock.mock_open)
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@mock.patch('diceplayer.shared.interface.dice_interface.random')
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def test_make_npt_eq(self, mock_random, mock_open):
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mock_random.random.return_value = 1
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dice = DiceInterface()
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dice.configure(self.config, System())
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dice._make_npt_eq('test')
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mock_handler = mock_open()
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calls = mock_handler.write.call_args_list
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lines = list(map(lambda x: x[0][0], calls))
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expected_lines = ['title = Diceplayer run - NPT Production\n', 'ncores = 4\n', 'ljname = phb.ljc\n', 'outname = phb\n', 'nmol = 1 50\n', 'press = 1.0\n', 'temp = 300.0\n', 'nstep = 5\n', 'vstep = 800\n', 'init = no\n', 'mstop = 1\n', 'accum = no\n', 'iprint = 1\n', 'isave = 1000\n', 'irdf = 40\n', 'seed = 1000000\n']
|
|
|
|
self.assertEqual(lines, expected_lines)
|
|
|
|
@mock.patch('builtins.open', new_callable=mock.mock_open)
|
|
def test_make_potentials(self, mock_open):
|
|
example_atom = Atom(
|
|
lbl=1,
|
|
na=1,
|
|
rx=1.0,
|
|
ry=1.0,
|
|
rz=1.0,
|
|
chg=1.0,
|
|
eps=1.0,
|
|
sig=1.0,
|
|
)
|
|
|
|
main_molecule = Molecule('main_molecule')
|
|
main_molecule.add_atom(example_atom)
|
|
|
|
secondary_molecule = Molecule('secondary_molecule')
|
|
secondary_molecule.add_atom(example_atom)
|
|
|
|
system = System()
|
|
system.add_type(main_molecule)
|
|
system.add_type(secondary_molecule)
|
|
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, system)
|
|
|
|
dice._make_potentials('test')
|
|
|
|
mock_handler = mock_open()
|
|
calls = mock_handler.write.call_args_list
|
|
|
|
lines = list(map(lambda x: x[0][0], calls))
|
|
|
|
expected_lines = ['*\n', '2\n', '1 main_molecule\n', '1 1 1.00000 1.00000 1.00000 1.000000 1.00000 1.0000\n', '1 secondary_molecule\n', '1 1 1.00000 1.00000 1.00000 1.000000 1.00000 1.0000\n']
|
|
|
|
self.assertEqual(lines, expected_lines)
|
|
|
|
@mock.patch('diceplayer.shared.interface.dice_interface.subprocess')
|
|
@mock.patch('builtins.open', new_callable=mock.mock_open, read_data='End of simulation\nBLABLA')
|
|
def test_run_dice_file(self, mock_open, mock_subprocess):
|
|
mock_subprocess.call.return_value = 0
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, System())
|
|
|
|
dice.run_dice_file(1, 1, 'test')
|
|
|
|
self.assertTrue(mock_subprocess.call.called)
|
|
self.assertTrue(mock_open.called)
|
|
|
|
@mock.patch('diceplayer.shared.interface.dice_interface.subprocess')
|
|
@mock.patch('builtins.open', new_callable=mock.mock_open, read_data='Error\nBLABLA')
|
|
def test_run_dice_file_raises_runtime_error_on_dice_file(self, mock_open, mock_subprocess):
|
|
mock_subprocess.call.return_value = 0
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, System())
|
|
|
|
with self.assertRaises(RuntimeError):
|
|
dice.run_dice_file(1, 1, 'test')
|
|
|
|
@mock.patch('diceplayer.shared.interface.dice_interface.subprocess')
|
|
@mock.patch('builtins.open', new_callable=mock.mock_open, read_data='End of simulation\nBLABLA')
|
|
def test_run_dice_file_raises_runtime_error_of_dice_exit_code(self, mock_open, mock_subprocess):
|
|
mock_subprocess.call.return_value = 1
|
|
dice = DiceInterface()
|
|
dice.configure(self.config, System())
|
|
|
|
with self.assertRaises(RuntimeError):
|
|
dice.run_dice_file(1, 1, 'test')
|
|
|
|
|
|
if __name__ == '__main__':
|
|
unittest.main()
|