add tests to read logger output files, longer test made faster, clean

pyDeltaRCM/init_tools.py

@@ -444,7 +444,7 @@ def init_output_grids(self):
                                                              ('total_time', 'length', 'width'))
                 velocity.units = 'meters per second'
 
-            _msg = 'Output netCDF file created.'
+            _msg = 'Output netCDF file created'
             self.logger.info(_msg)
             if self.verbose >= 2:
                 print(_msg)

run_pyDeltaRCM.py

@@ -3,7 +3,7 @@
 
 if __name__ == '__main__':
 
-    delta = DeltaModel(input_file = os.path.join(os.getcwd(), 'tests', 'test.yaml'))
+    delta = DeltaModel()
 
     for time in range(0, 1):
         delta.update()

tests/test_consistent.py

@@ -59,11 +59,11 @@ def test_long_multi_validation(tmp_path):
     _exp1 = np.array([-4.971009,  -3.722004,  -4.973,     -3.7240038, -3.7250037])
     assert np.all(delta.eta[:5, 62] == pytest.approx(_exp1))
 
-    for _ in range(0, 30):
+    for _ in range(0, 10):
         delta.update()
 
     # slice is: test_DeltaModel.eta[:5, 4]
     print(delta.eta[:5, 62])
 
-    _exp2 = np.array([-4.962428,  -1.3612521, -2.2904062, -1.4572337, -0.864957])
+    _exp2 = np.array([-4.971052,  -2.0813923, -2.0824013, -4.6614914, -1.5570664])
     assert np.all(delta.eta[:5, 62] == pytest.approx(_exp2))

tests/test_deltaRCM_tools.py

@@ -6,16 +6,205 @@
 import os
 import numpy as np
 
+import glob
+
+from pyDeltaRCM.model import DeltaModel
+
 from utilities import test_DeltaModel
+import utilities
 
 
 def test_run_one_timestep(test_DeltaModel):
     test_DeltaModel.run_one_timestep()
     # basically assume sediment has been added at inlet
+    assert test_DeltaModel.H_SL == 0.0
     assert test_DeltaModel.qs[0, 4] != 0.
 
 
 def test_finalize_timestep(test_DeltaModel):
     test_DeltaModel.finalize_timestep()
     # check that sea level rose as expected
     assert test_DeltaModel.H_SL == 0.3
+
+
+def test_verbose_printing_0(tmp_path, capsys):
+    """
+    This test should create the log, and then print nothing at all.
+    """
+    file_name = 'user_parameters.yaml'
+    p, f = utilities.create_temporary_file(tmp_path, file_name)
+    utilities.write_parameter_to_file(f, 'out_dir', tmp_path / 'out_dir')
+    utilities.write_parameter_to_file(f, 'verbose', 0)
+    utilities.write_parameter_to_file(f, 'Length', 10.0)
+    utilities.write_parameter_to_file(f, 'Width', 10.0)
+    utilities.write_parameter_to_file(f, 'dx', 1.0)
+    utilities.write_parameter_to_file(f, 'L0_meters', 1.0)
+    utilities.write_parameter_to_file(f, 'itermax', 1)
+    utilities.write_parameter_to_file(f, 'Np_water', 10)
+    utilities.write_parameter_to_file(f, 'N0_meters', 2.0)
+    utilities.write_parameter_to_file(f, 'h0', 1.0)
+    utilities.write_parameter_to_file(f, 'Np_sed', 10)
+    utilities.write_parameter_to_file(f, 'f_bedload', 0.5)
+    utilities.write_parameter_to_file(f, 'C0_percent', 0.1)
+    f.close()
+    delta = DeltaModel(input_file=p)
+    assert os.path.isfile(os.path.join(delta.prefix, 'pyDeltaRCM_output.nc'))
+    assert len(glob.glob(os.path.join(delta.prefix, '*.log'))
+               ) == 1  # log file exists
+    delta.update()
+    captd = capsys.readouterr()
+    assert not 'Timestep: 0.0' in captd.out
+
+
+def test_verbose_printing_1(tmp_path, capsys):
+    file_name = 'user_parameters.yaml'
+    p, f = utilities.create_temporary_file(tmp_path, file_name)
+    utilities.write_parameter_to_file(f, 'out_dir', tmp_path / 'out_dir')
+    utilities.write_parameter_to_file(f, 'verbose', 1)
+    utilities.write_parameter_to_file(f, 'Length', 10.0)
+    utilities.write_parameter_to_file(f, 'Width', 10.0)
+    utilities.write_parameter_to_file(f, 'dx', 1.0)
+    utilities.write_parameter_to_file(f, 'L0_meters', 1.0)
+    utilities.write_parameter_to_file(f, 'itermax', 1)
+    utilities.write_parameter_to_file(f, 'Np_water', 10)
+    utilities.write_parameter_to_file(f, 'N0_meters', 2.0)
+    utilities.write_parameter_to_file(f, 'h0', 1.0)
+    utilities.write_parameter_to_file(f, 'Np_sed', 10)
+    utilities.write_parameter_to_file(f, 'f_bedload', 0.5)
+    utilities.write_parameter_to_file(f, 'C0_percent', 0.1)
+    f.close()
+    delta = DeltaModel(input_file=p)
+    captd1 = capsys.readouterr()
+    delta.update()
+    captd2 = capsys.readouterr()
+    assert captd1.out == ''
+    assert len(glob.glob(os.path.join(delta.prefix, '*.log'))
+               ) == 1  # log file exists
+    assert 'Timestep: 0.0' in captd2.out  # if verbose >= 1
+    assert not 'Creating output directory' in captd2.out  # goes to logger
+
+
+def test_verbose_printing_2(tmp_path, capsys):
+    file_name = 'user_parameters.yaml'
+    p, f = utilities.create_temporary_file(tmp_path, file_name)
+    utilities.write_parameter_to_file(f, 'out_dir', tmp_path / 'out_dir')
+    utilities.write_parameter_to_file(f, 'verbose', 2)
+    utilities.write_parameter_to_file(f, 'seed', 10)
+    utilities.write_parameter_to_file(f, 'Length', 10.0)
+    utilities.write_parameter_to_file(f, 'Width', 10.0)
+    utilities.write_parameter_to_file(f, 'dx', 1.0)
+    utilities.write_parameter_to_file(f, 'L0_meters', 1.0)
+    utilities.write_parameter_to_file(f, 'itermax', 1)
+    utilities.write_parameter_to_file(f, 'Np_water', 10)
+    utilities.write_parameter_to_file(f, 'N0_meters', 2.0)
+    utilities.write_parameter_to_file(f, 'h0', 1.0)
+    utilities.write_parameter_to_file(f, 'Np_sed', 10)
+    utilities.write_parameter_to_file(f, 'f_bedload', 0.5)
+    utilities.write_parameter_to_file(f, 'C0_percent', 0.1)
+    f.close()
+    delta = DeltaModel(input_file=p)
+    captd1 = capsys.readouterr()
+    delta.update()
+    captd2 = capsys.readouterr()
+    assert len(glob.glob(os.path.join(delta.prefix, '*.log'))
+               ) == 1  # log file exists
+    assert 'Setting random seed to' in captd1.out   # if verbose >= 2
+    assert 'Timestep: 0.0' in captd2.out  # if verbose >= 1
+    assert delta.seed == 10
+
+
+def test_logger_has_initialization_lines(tmp_path):
+    file_name = 'user_parameters.yaml'
+    p, f = utilities.create_temporary_file(tmp_path, file_name)
+    utilities.write_parameter_to_file(f, 'out_dir', tmp_path / 'out_dir')
+    utilities.write_parameter_to_file(f, 'verbose', 1)
+    utilities.write_parameter_to_file(f, 'seed', 10)
+    utilities.write_parameter_to_file(f, 'Length', 10.0)
+    utilities.write_parameter_to_file(f, 'Width', 10.0)
+    utilities.write_parameter_to_file(f, 'dx', 1.0)
+    utilities.write_parameter_to_file(f, 'L0_meters', 1.0)
+    utilities.write_parameter_to_file(f, 'itermax', 1)
+    utilities.write_parameter_to_file(f, 'Np_water', 10)
+    utilities.write_parameter_to_file(f, 'N0_meters', 2.0)
+    utilities.write_parameter_to_file(f, 'h0', 1.0)
+    utilities.write_parameter_to_file(f, 'Np_sed', 10)
+    utilities.write_parameter_to_file(f, 'f_bedload', 0.5)
+    utilities.write_parameter_to_file(f, 'C0_percent', 0.1)
+    f.close()
+    delta = DeltaModel(input_file=p)
+    _logs = glob.glob(os.path.join(delta.prefix, '*.log'))
+    assert len(_logs) == 1  # log file exists
+    with open(_logs[0], 'r') as _logfile:
+        _lines = _logfile.readlines()
+        _lines = ' '.join(_lines)  # collapse to a single string
+        assert 'Setting model constant' in _lines
+        assert 'Setting random seed to: 10' in _lines
+        assert 'Random seed is: 10' in _lines
+        assert 'Creating model domain' in _lines
+        assert 'Generating netCDF file for output grids' in _lines
+        assert 'Output netCDF file created' in _lines
+        assert 'Model initialization complete' in _lines
+
+
+def test_logger_has_timestep_lines(tmp_path):
+    file_name = 'user_parameters.yaml'
+    p, f = utilities.create_temporary_file(tmp_path, file_name)
+    utilities.write_parameter_to_file(f, 'out_dir', tmp_path / 'out_dir')
+    utilities.write_parameter_to_file(f, 'verbose', 1)
+    utilities.write_parameter_to_file(f, 'seed', 10)
+    utilities.write_parameter_to_file(f, 'Length', 10.0)
+    utilities.write_parameter_to_file(f, 'Width', 10.0)
+    utilities.write_parameter_to_file(f, 'dx', 1.0)
+    utilities.write_parameter_to_file(f, 'L0_meters', 1.0)
+    utilities.write_parameter_to_file(f, 'itermax', 1)
+    utilities.write_parameter_to_file(f, 'Np_water', 10)
+    utilities.write_parameter_to_file(f, 'N0_meters', 2.0)
+    utilities.write_parameter_to_file(f, 'h0', 1.0)
+    utilities.write_parameter_to_file(f, 'Np_sed', 10)
+    utilities.write_parameter_to_file(f, 'f_bedload', 0.5)
+    utilities.write_parameter_to_file(f, 'C0_percent', 0.1)
+    f.close()
+    delta = DeltaModel(input_file=p)
+    _logs = glob.glob(os.path.join(delta.prefix, '*.log'))
+    assert len(_logs) == 1  # log file exists
+    for _ in range(0, 2):
+        delta.update()
+    assert len(_logs) == 1  # log file exists, still only one
+    with open(_logs[0], 'r') as _logfile:
+        _lines = _logfile.readlines()
+        _lines = ' '.join(_lines)  # collapse to a single string
+        assert '---- Timestep 0.0 ----' in _lines
+        assert '---- Timestep 1.0 ----' in _lines
+        assert not '---- Timestep 2.0 ----' in _lines
+
+
+@pytest.mark.xfail(raises=ValueError, strict=True)
+def test_logger_random_seed_always_recorded(tmp_path):
+    file_name = 'user_parameters.yaml'
+    p, f = utilities.create_temporary_file(tmp_path, file_name)
+    utilities.write_parameter_to_file(f, 'out_dir', tmp_path / 'out_dir')
+    utilities.write_parameter_to_file(f, 'verbose', 0)
+    # do not set the seed explicitly, let it be set by the model
+    # utilities.write_parameter_to_file(f, 'seed', None)
+    f.close()
+    delta = DeltaModel(input_file=p)
+    _logs = glob.glob(os.path.join(delta.prefix, '*.log'))
+    assert len(_logs) == 1  # log file exists
+    with open(_logs[0], 'r') as _logfile:
+        _lines = _logfile.readlines()
+        _joinedlines = ' '.join(_lines)  # collapse to a single string
+        assert 'Random seed is: ' in _joinedlines
+
+        # determine the index of the line
+        _idx = ['Random seed is: ' in _l for _l in _lines]
+        assert sum(_idx) == 1  # one and only one True in list
+        _idx = _idx.index(True)
+
+        # try to covert to int, otherwise fail
+        _seed = _lines[_idx].split(':')[-1]  # pull the seed value
+        try:
+            _intseed = int(_seed)
+        except ValueError:
+            raise ValueError('Could not convert the seed to int')
+
+        assert _intseed >= 0