HideyoshiNakazone/DicePlayer
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Adds Formatter to Project

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This commit is contained in:
Vitor Hideyoshi
2023-06-11 16:04:25 -03:00
parent 82f3092f3e
commit c4dae5e8d1
29 changed files with 1151 additions and 721 deletions
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317
tests/shared/interface/test_dice_interface.py
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@@ -1,18 +1,17 @@
from diceplayer.shared.interface.dice_interface import DiceInterface
from diceplayer import logger
from diceplayer.shared.config.player_config import PlayerConfig
from diceplayer.shared.environment.atom import Atom
from diceplayer.shared.environment.molecule import Molecule
from diceplayer.shared.environment.system import System
from diceplayer.shared.environment.atom import Atom
from diceplayer import logger
import yaml
import io
from diceplayer.shared.interface.dice_interface import DiceInterface
from tests.mocks.mock_inputs import get_config_example
from tests.mocks.mock_proc import MockConnection, MockProc
from unittest import mock
import yaml
import io
import unittest
from unittest import mock
class TestDiceInterface(unittest.TestCase):
@@ -20,7 +19,7 @@ class TestDiceInterface(unittest.TestCase):
logger.set_logger(stream=io.StringIO())
config = yaml.load(get_config_example(), Loader=yaml.Loader)
self.config = PlayerConfig.from_dict(config['diceplayer'])
self.config = PlayerConfig.from_dict(config["diceplayer"])
def test_class_instantiation(self):
dice = DiceInterface()
@@ -44,24 +43,26 @@ class TestDiceInterface(unittest.TestCase):
dice.configure(self.config, System())
self.assertTrue(hasattr(dice, 'step'))
self.assertTrue(hasattr(dice, 'system'))
self.assertTrue(hasattr(dice, "step"))
self.assertTrue(hasattr(dice, "system"))
dice.reset()
self.assertFalse(hasattr(dice, 'step'))
self.assertFalse(hasattr(dice, 'system'))
self.assertFalse(hasattr(dice, "step"))
self.assertFalse(hasattr(dice, "system"))
@mock.patch('diceplayer.shared.interface.dice_interface.Process', MockProc())
@mock.patch('diceplayer.shared.interface.dice_interface.connection', MockConnection)
@mock.patch("diceplayer.shared.interface.dice_interface.Process", MockProc())
@mock.patch("diceplayer.shared.interface.dice_interface.connection", MockConnection)
def test_start(self):
dice = DiceInterface()
dice.configure(self.config, System())
dice.start(1)
@mock.patch('diceplayer.shared.interface.dice_interface.connection', MockConnection)
@mock.patch('diceplayer.shared.interface.dice_interface.Process', MockProc(exitcode=1))
@mock.patch("diceplayer.shared.interface.dice_interface.connection", MockConnection)
@mock.patch(
"diceplayer.shared.interface.dice_interface.Process", MockProc(exitcode=1)
)
def test_start_with_process_error(self):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -75,10 +76,16 @@ class TestDiceInterface(unittest.TestCase):
with self.assertRaises(SystemExit):
dice._simulation_process(1, 1)
@mock.patch('diceplayer.shared.interface.dice_interface.DiceInterface._make_proc_dir')
@mock.patch('diceplayer.shared.interface.dice_interface.DiceInterface._make_dice_inputs')
@mock.patch('diceplayer.shared.interface.dice_interface.DiceInterface._run_dice')
def test_simulation_process(self, mock_run_dice, mock_make_dice_inputs, mock_make_proc_dir):
@mock.patch(
"diceplayer.shared.interface.dice_interface.DiceInterface._make_proc_dir"
)
@mock.patch(
"diceplayer.shared.interface.dice_interface.DiceInterface._make_dice_inputs"
)
@mock.patch("diceplayer.shared.interface.dice_interface.DiceInterface._run_dice")
def test_simulation_process(
self, mock_run_dice, mock_make_dice_inputs, mock_make_proc_dir
):
dice = DiceInterface()
dice._simulation_process(1, 1)
@@ -87,8 +94,8 @@ class TestDiceInterface(unittest.TestCase):
self.assertTrue(dice._make_dice_inputs.called)
self.assertTrue(dice._run_dice.called)
@mock.patch('diceplayer.shared.interface.dice_interface.Path.mkdir')
@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists')
@mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
@mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
def test_make_proc_dir_if_simdir_exists(self, mock_path_exists, mock_path_mkdir):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -99,9 +106,11 @@ class TestDiceInterface(unittest.TestCase):
self.assertEqual(mock_path_mkdir.call_count, 2)
@mock.patch('diceplayer.shared.interface.dice_interface.Path.mkdir')
@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists')
def test_make_proc_dir_if_simdir_doesnt_exists(self, mock_path_exists, mock_path_mkdir):
@mock.patch("diceplayer.shared.interface.dice_interface.Path.mkdir")
@mock.patch("diceplayer.shared.interface.dice_interface.Path.exists")
def test_make_proc_dir_if_simdir_doesnt_exists(
self, mock_path_exists, mock_path_mkdir
):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -145,9 +154,13 @@ class TestDiceInterface(unittest.TestCase):
self.assertFalse(dice._make_npt_ter.called)
self.assertFalse(dice._make_npt_eq.called)
@mock.patch('builtins.open', new_callable=mock.mock_open, read_data='test')
@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=True)
def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_two(self, mock_path_exists, mock_open):
@mock.patch("builtins.open", new_callable=mock.mock_open, read_data="test")
@mock.patch(
"diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
)
def test_make_dice_inputs_nstep_len_two_with_randoninit_first_cycle_two(
self, mock_path_exists, mock_open
):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -176,8 +189,12 @@ class TestDiceInterface(unittest.TestCase):
self.assertFalse(dice._make_npt_ter.called)
self.assertFalse(dice._make_npt_eq.called)
@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=False)
def test_make_dice_inputs_raises_exception_on_last_not_found(self, mock_path_exists):
@mock.patch(
"diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
)
def test_make_dice_inputs_raises_exception_on_last_not_found(
self, mock_path_exists
):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -223,10 +240,14 @@ class TestDiceInterface(unittest.TestCase):
self.assertTrue(dice._make_npt_ter.called)
self.assertTrue(dice._make_npt_eq.called)
@mock.patch('diceplayer.shared.interface.dice_interface.os')
@mock.patch('diceplayer.shared.interface.dice_interface.shutil')
@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=True)
def test_run_dice_on_first_cycle_run_successful(self, mock_path_exists, mock_shutils, mock_os):
@mock.patch("diceplayer.shared.interface.dice_interface.os")
@mock.patch("diceplayer.shared.interface.dice_interface.shutil")
@mock.patch(
"diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
)
def test_run_dice_on_first_cycle_run_successful(
self, mock_path_exists, mock_shutils, mock_os
):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -257,10 +278,14 @@ class TestDiceInterface(unittest.TestCase):
self.assertEqual(dice.run_dice_file.call_count, 2)
self.assertTrue(mock_shutils.copy.called)
@mock.patch('diceplayer.shared.interface.dice_interface.os')
@mock.patch('diceplayer.shared.interface.dice_interface.shutil')
@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=True)
def test_run_dice_on_second_cycle_run_successful(self, mock_path_exists, mock_shutils, mock_os):
@mock.patch("diceplayer.shared.interface.dice_interface.os")
@mock.patch("diceplayer.shared.interface.dice_interface.shutil")
@mock.patch(
"diceplayer.shared.interface.dice_interface.Path.exists", return_value=True
)
def test_run_dice_on_second_cycle_run_successful(
self, mock_path_exists, mock_shutils, mock_os
):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -287,10 +312,14 @@ class TestDiceInterface(unittest.TestCase):
self.assertEqual(dice.run_dice_file.call_count, 1)
self.assertTrue(mock_shutils.copy.called)
@mock.patch('diceplayer.shared.interface.dice_interface.os')
@mock.patch('diceplayer.shared.interface.dice_interface.shutil')
@mock.patch('diceplayer.shared.interface.dice_interface.Path.exists', return_value=False)
def test_run_dice_on_second_cycle_run_successful(self, mock_path_exists, mock_shutils, mock_os):
@mock.patch("diceplayer.shared.interface.dice_interface.os")
@mock.patch("diceplayer.shared.interface.dice_interface.shutil")
@mock.patch(
"diceplayer.shared.interface.dice_interface.Path.exists", return_value=False
)
def test_run_dice_on_second_cycle_run_successful(
self, mock_path_exists, mock_shutils, mock_os
):
dice = DiceInterface()
dice.configure(self.config, System())
@@ -299,7 +328,7 @@ class TestDiceInterface(unittest.TestCase):
with self.assertRaises(FileNotFoundError):
dice._run_dice(1, 1)
@mock.patch('builtins.open', new_callable=mock.mock_open)
@mock.patch("builtins.open", new_callable=mock.mock_open)
def test_make_init_file(self, mock_open):
example_atom = Atom(
lbl=1,
@@ -312,10 +341,10 @@ class TestDiceInterface(unittest.TestCase):
sig=1.0,
)
main_molecule = Molecule('main_molecule')
main_molecule = Molecule("main_molecule")
main_molecule.add_atom(example_atom)
secondary_molecule = Molecule('secondary_molecule')
secondary_molecule = Molecule("secondary_molecule")
secondary_molecule.add_atom(example_atom)
system = System()
@@ -328,15 +357,17 @@ class TestDiceInterface(unittest.TestCase):
dice.step.dice.nmol = [1, 1]
last_xyz_file = io.StringIO()
last_xyz_file.writelines([
' TEST\n',
' Configuration number : TEST = TEST TEST TEST\n',
' H 1.00000 1.00000 1.00000\n',
' H 1.00000 1.00000 1.00000\n',
])
last_xyz_file.writelines(
[
" TEST\n",
" Configuration number : TEST = TEST TEST TEST\n",
" H 1.00000 1.00000 1.00000\n",
" H 1.00000 1.00000 1.00000\n",
]
)
last_xyz_file.seek(0)
dice._make_init_file('test', last_xyz_file)
dice._make_init_file("test", last_xyz_file)
mock_handler = mock_open()
calls = mock_handler.write.call_args_list
@@ -344,14 +375,14 @@ class TestDiceInterface(unittest.TestCase):
lines = list(map(lambda x: x[0][0], calls))
expected_lines = [
' 1.000000 1.000000 1.000000\n',
' 1.000000 1.000000 1.000000\n',
'$end'
" 1.000000 1.000000 1.000000\n",
" 1.000000 1.000000 1.000000\n",
"$end",
]
self.assertEqual(lines, expected_lines)
@mock.patch('builtins.open', new_callable=mock.mock_open)
@mock.patch("builtins.open", new_callable=mock.mock_open)
def test_new_density(self, mock_open):
example_atom = Atom(
lbl=1,
@@ -364,10 +395,10 @@ class TestDiceInterface(unittest.TestCase):
sig=1.0,
)
main_molecule = Molecule('main_molecule')
main_molecule = Molecule("main_molecule")
main_molecule.add_atom(example_atom)
secondary_molecule = Molecule('secondary_molecule')
secondary_molecule = Molecule("secondary_molecule")
secondary_molecule.add_atom(example_atom)
system = System()
@@ -378,95 +409,166 @@ class TestDiceInterface(unittest.TestCase):
dice.configure(self.config, system)
last_xyz_file = io.StringIO()
last_xyz_file.writelines([
' TEST\n',
' Configuration number : TEST = 1 1 1\n',
' H 1.00000 1.00000 1.00000\n',
' H 1.00000 1.00000 1.00000\n',
])
last_xyz_file.writelines(
[
" TEST\n",
" Configuration number : TEST = 1 1 1\n",
" H 1.00000 1.00000 1.00000\n",
" H 1.00000 1.00000 1.00000\n",
]
)
last_xyz_file.seek(0)
density = dice._new_density(last_xyz_file)
self.assertEqual(density, 85.35451545000001)
@mock.patch('builtins.open', new_callable=mock.mock_open)
@mock.patch('diceplayer.shared.interface.dice_interface.random')
@mock.patch("builtins.open", new_callable=mock.mock_open)
@mock.patch("diceplayer.shared.interface.dice_interface.random")
def test_make_nvt_ter(self, mock_random, mock_open):
mock_random.random.return_value = 1
dice = DiceInterface()
dice.configure(self.config, System())
dice._make_nvt_ter(1, 'test')
dice._make_nvt_ter(1, "test")
mock_handler = mock_open()
calls = mock_handler.write.call_args_list
lines = list(map(lambda x: x[0][0], calls))
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']
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",
]
self.assertEqual(lines, expected_lines)
@mock.patch('builtins.open', new_callable=mock.mock_open)
@mock.patch('diceplayer.shared.interface.dice_interface.random')
@mock.patch("builtins.open", new_callable=mock.mock_open)
@mock.patch("diceplayer.shared.interface.dice_interface.random")
def test_make_nvt_eq(self, mock_random, mock_open):
mock_random.random.return_value = 1
dice = DiceInterface()
dice.configure(self.config, System())
dice._make_nvt_eq(1, 'test')
dice._make_nvt_eq(1, "test")
mock_handler = mock_open()
calls = mock_handler.write.call_args_list
lines = list(map(lambda x: x[0][0], calls))
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']
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",
]
self.assertEqual(lines, expected_lines)
@mock.patch('builtins.open', new_callable=mock.mock_open)
@mock.patch('diceplayer.shared.interface.dice_interface.random')
@mock.patch("builtins.open", new_callable=mock.mock_open)
@mock.patch("diceplayer.shared.interface.dice_interface.random")
def test_make_npt_ter(self, mock_random, mock_open):
mock_random.random.return_value = 1
dice = DiceInterface()
dice.configure(self.config, System())
dice._make_npt_ter(1, 'test')
dice._make_npt_ter(1, "test")
mock_handler = mock_open()
calls = mock_handler.write.call_args_list
lines = list(map(lambda x: x[0][0], calls))
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']
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",
]
self.assertEqual(lines, expected_lines)
@mock.patch('builtins.open', new_callable=mock.mock_open)
@mock.patch('diceplayer.shared.interface.dice_interface.random')
@mock.patch("builtins.open", new_callable=mock.mock_open)
@mock.patch("diceplayer.shared.interface.dice_interface.random")
def test_make_npt_eq(self, mock_random, mock_open):
mock_random.random.return_value = 1
dice = DiceInterface()
dice.configure(self.config, System())
dice._make_npt_eq('test')
dice._make_npt_eq("test")
mock_handler = mock_open()
calls = mock_handler.write.call_args_list
lines = list(map(lambda x: x[0][0], calls))
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']
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)
@mock.patch("builtins.open", new_callable=mock.mock_open)
def test_make_potentials(self, mock_open):
example_atom = Atom(
lbl=1,
@@ -479,10 +581,10 @@ class TestDiceInterface(unittest.TestCase):
sig=1.0,
)
main_molecule = Molecule('main_molecule')
main_molecule = Molecule("main_molecule")
main_molecule.add_atom(example_atom)
secondary_molecule = Molecule('secondary_molecule')
secondary_molecule = Molecule("secondary_molecule")
secondary_molecule.add_atom(example_atom)
system = System()
@@ -492,49 +594,68 @@ class TestDiceInterface(unittest.TestCase):
dice = DiceInterface()
dice.configure(self.config, system)
dice._make_potentials('test')
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']
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')
@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')
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.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')
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.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')
dice.run_dice_file(1, 1, "test")
if __name__ == '__main__':
if __name__ == "__main__":
unittest.main()