Adds Functionality to Logger

diceplayer/__init__.py

@@ -0,0 +1,4 @@
+from diceplayer.shared.utils.logger import Logger
+
+
+logger = Logger(__name__)

diceplayer/__main__.py

@@ -1,5 +1,6 @@
 from diceplayer.shared.interface.dice_interface import DiceInterface
 from diceplayer.player import Player
+from diceplayer import logger
 
 from pathlib import Path
 import argparse
@@ -40,6 +41,7 @@ def main():
     args = parser.parse_args()
 
     # Open OUTFILE for writing and print keywords and initial info
+    logger.set_logger(args.outfile, logging.INFO)
 
     try:
 
@@ -55,12 +57,6 @@ def main():
     except Exception as err:
         sys.exit(err)
 
-    logging.basicConfig(
-        filename=args.outfile,
-        format='%(message)s',
-        level=logging.INFO
-    )
-
     player = Player(args.infile)
 
     player.start()

diceplayer/shared/environment/system.py

@@ -42,6 +42,29 @@ class System:
             raise TypeError("Error: nmols is not an integer")
         self.nmols.append(nmols)
 
+    def update_molecule(self, position: np.ndarray, fh: TextIO) -> None:
+        """Updates the position of the molecule in the Output file
+
+                Args:
+                    position (np.ndarray): numpy position vector
+                    fh (TextIO): Output file
+                """
+
+        position_in_ang = (position * BOHR2ANG).tolist()
+        self.add_type(self.nmols[0], deepcopy(self.molecule[0]))
+
+        for atom in self.molecule[-1].atom:
+
+            atom.rx = position_in_ang.pop(0)
+            atom.ry = position_in_ang.pop(0)
+            atom.rz = position_in_ang.pop(0)
+
+        rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
+        self.molecule.pop(-1)
+
+        fh.write("\nProjected new conformation of reference molecule with RMSD fit\n")
+        fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd))
+
     def rmsd_fit(self, p_index: int, r_index: int) -> Tuple[float, Molecule]:
 
         projecting_mol = self.molecule[p_index]
@@ -176,65 +199,43 @@ class System:
     #     self.molecule.pop(-1)
     #
     #     return min_dist, nearestmol
-    def update_molecule(self, position: np.ndarray, fh: TextIO) -> None:
-        """Updates the position of the molecule in the Output file
-
-                Args:
-                    position (np.ndarray): numpy position vector
-                    fh (TextIO): Output file
-                """
-
-        position_in_ang = (position * BOHR2ANG).tolist()
-        self.add_type(self.nmols[0], deepcopy(self.molecule[0]))
-
-        for atom in self.molecule[-1].atom:
-
-            atom.rx = position_in_ang.pop(0)
-            atom.ry = position_in_ang.pop(0)
-            atom.rz = position_in_ang.pop(0)
-
-        rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
-        self.molecule.pop(-1)
-
-        fh.write("\nProjected new conformation of reference molecule with RMSD fit\n")
-        fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd))
 
 
-    def print_geom(self, cycle: int, fh: TextIO) -> None:
+    # def print_geom(self, cycle: int, fh: TextIO) -> None:
-        """
+    #     """
-                Print the geometry of the molecule in the Output file
+    #             Print the geometry of the molecule in the Output file
-
+    #
-                Args:
+    #             Args:
-                    cycle (int): Number of the cycle
+    #                 cycle (int): Number of the cycle
-                    fh (TextIO): Output file
+    #                 fh (TextIO): Output file
-                """
+    #             """
-
+    #
-        fh.write("Cycle # {}\n".format(cycle))
+    #     fh.write("Cycle # {}\n".format(cycle))
-        fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
+    #     fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
-        for atom in self.molecule[0].atom:
+    #     for atom in self.molecule[0].atom:
-            symbol = atomsymb[atom.na]
+    #         symbol = atomsymb[atom.na]
-            fh.write(
+    #         fh.write(
-                "{:<2s}    {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
+    #             "{:<2s}    {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
-                    symbol, atom.rx, atom.ry, atom.rz
+    #                 symbol, atom.rx, atom.ry, atom.rz
-                )
+    #             )
-            )
+    #         )
-
+    #
-    def printChargesAndDipole(self, cycle: int, fh: TextIO) -> None:
+    # def printChargesAndDipole(self, cycle: int, fh: TextIO) -> None:
-        """
+    #     """
-                Print the charges and dipole of the molecule in the Output file
+    #             Print the charges and dipole of the molecule in the Output file
-
+    #
-                Args:
+    #             Args:
-                    cycle (int): Number of the cycle
+    #                 cycle (int): Number of the cycle
-                    fh (TextIO): Output file
+    #                 fh (TextIO): Output file
-                """
+    #             """
-
+    #
-        fh.write("Cycle # {}\n".format(cycle))
+    #     fh.write("Cycle # {}\n".format(cycle))
-        fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
+    #     fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
-
+    #
-        chargesAndDipole = self.molecule[0].charges_and_dipole()
+    #     chargesAndDipole = self.molecule[0].charges_and_dipole()
-
+    #
-        fh.write(
+    #     fh.write(
-            "{:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
+    #         "{:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}  {:>10.6f}\n".format(
-                chargesAndDipole[0], chargesAndDipole[1], chargesAndDipole[2], chargesAndDipole[3], chargesAndDipole[4]
+    #             chargesAndDipole[0], chargesAndDipole[1], chargesAndDipole[2], chargesAndDipole[3], chargesAndDipole[4]
-            )
+    #         )
-        )
+    #     )

diceplayer/shared/utils/logger.py

@@ -1,27 +1,54 @@
 import logging
 
 
+def valid_logger(func):
+    def wrapper(*args, **kwargs):
+        logger = args[0]
+        assert logger._was_set, \
+            "Logger is not set. Please call set_logger() first."
+
+        return func(*args, **kwargs)
+
+    return wrapper
+
+
 class Logger:
     outfile = None
 
     _logger = None
-    _instance = None
 
-    def __new__(cls, *args, **kwargs):
+    _was_set = False
-        if not getattr(cls, '_instance'):
-            cls._instance = super(Logger, cls).__new__(cls)
-        return cls._instance
 
-    def set_logger(self, logger_name, outfile='run.log', level=logging.INFO):
+    def __init__(self, logger_name):
+        if self._logger is None:
+            self._logger = logging.getLogger(logger_name)
+
+    def set_logger(self, outfile='run.log', level=logging.INFO):
         self.outfile = outfile
 
-        self._logger = logging.getLogger(logger_name)
-
         if level is not None:
             self._logger.setLevel(level)
 
         self._create_handlers()
 
+        self._was_set = True
+
+    @valid_logger
+    def info(self, message):
+        self._logger.info(message)
+
+    @valid_logger
+    def debug(self, message):
+        self._logger.debug(message)
+
+    @valid_logger
+    def warning(self, message):
+        self._logger.warning(message)
+
+    @valid_logger
+    def error(self, message):
+        self._logger.error(message)
+
     def _create_handlers(self):
         handlers = []
         if self.outfile is not None:

tests/shared/utils/test_logger.py

@@ -1,34 +1,96 @@
-from diceplayer.shared.utils.logger import Logger
+from diceplayer.shared.utils.logger import Logger, valid_logger
 
+import logging
+
+from unittest import mock
 import unittest
 
 
+class TestValidateLogger(unittest.TestCase):
+    def test_validate_logger(self):
+        class MockLogger:
+            _was_set = True
+
+            @valid_logger
+            def test_func(self):
+                pass
+
+        MockLogger().test_func()
+
+    def test_validate_logger_exception(self):
+        class MockLogger:
+            _was_set = False
+
+            @valid_logger
+            def test_func(self):
+                pass
+
+        with self.assertRaises(AssertionError):
+            MockLogger().test_func()
+
+
 class TestLogger(unittest.TestCase):
     def test_class_instantiation(self):
-        logger = Logger()
+        logger = Logger('test')
 
         self.assertIsInstance(logger, Logger)
 
-    def test_singleton(self):
+    @mock.patch('builtins.open', mock.mock_open())
-        logger1 = Logger()
-        logger2 = Logger()
-
-        self.assertIs(logger1, logger2)
-
     def test_set_logger(self):
-        logger = Logger()
+        logger = Logger('test')
-        logger.set_logger('test_logger')
+        logger.set_logger()
 
         self.assertIsNotNone(logger._logger)
-        self.assertEqual(logger._logger.name, 'test_logger')
+        self.assertEqual(logger._logger.name, 'test')
 
+    @mock.patch('builtins.open', mock.mock_open())
     def test_close(self):
-        logger = Logger()
+        logger = Logger('test')
-        logger.set_logger('test_logger')
+        logger.set_logger()
         logger.close()
 
         self.assertEqual(len(logger._logger.handlers), 0)
 
+    @mock.patch('builtins.open', mock.mock_open())
+    def test_info(self):
+        logger = Logger('test')
+        logger.set_logger()
+
+        with self.assertLogs(level='INFO') as cm:
+            logger.info('test')
+
+        self.assertEqual(cm.output, ['INFO:test:test'])
+
+    @mock.patch('builtins.open', mock.mock_open())
+    def test_debug(self):
+        logger = Logger('test')
+        logger.set_logger(level=logging.DEBUG)
+
+        with self.assertLogs(level='DEBUG') as cm:
+            logger.debug('test')
+
+        self.assertEqual(cm.output, ['DEBUG:test:test'])
+
+    @mock.patch('builtins.open', mock.mock_open())
+    def test_warning(self):
+        logger = Logger('test')
+        logger.set_logger()
+
+        with self.assertLogs(level='WARNING') as cm:
+            logger.warning('test')
+
+        self.assertEqual(cm.output, ['WARNING:test:test'])
+
+    @mock.patch('builtins.open', mock.mock_open())
+    def test_error(self):
+        logger = Logger('test')
+        logger.set_logger()
+
+        with self.assertLogs(level='ERROR') as cm:
+            logger.error('test')
+
+        self.assertEqual(cm.output, ['ERROR:test:test'])
+
 
 if __name__ == '__main__':
     unittest.main()