fix(mfnwtmodel.py; mf6model.py): listing file paths in name file refl…

…ect the paths entered in the configuration file, relative to the model_ws or sim_ws; resolves #2

docs/source/config-file.rst

@@ -15,7 +15,6 @@ Modflow-setup uses the `pyyaml`_ package to parse the configuration file into th
 
    Configuration file structure <config-file-structure>
    Configuration defaults <config-file-defaults>
-   Description of source datatypes <source-data>
 
 
 Some additional notes on YAML

mfsetup/mf6_defaults.yml

@@ -8,6 +8,7 @@ simulation:
 model:
   modelname: 'model'
   version: 'mf6'
+  # list file format is relative to the model workspace
   list_filename_fmt: '{}.list'
   options:
     print_input: True

mfsetup/mf6model.py

@@ -962,8 +962,7 @@ def _parse_model_kwargs(cfg):
             raise TypeError('unrecognized configuration input for simulation.')
 
         # listing file
-        cfg['model']['list'] = os.path.join(sim_ws,
-                                            cfg['model']['list_filename_fmt']
+        cfg['model']['list'] = os.path.join(cfg['model']['list_filename_fmt']
                                             .format(cfg['model']['modelname']))
 
         # newton options

mfsetup/mfnwt_defaults.yml

@@ -8,6 +8,8 @@ model:
   exe_name: 'mfnwt'
   version: 'mfnwt'
   external_path: 'external/'
+  # list file format is relative to the model workspace
+  list_filename_fmt: '{}.list'
   relative_external_filepaths: True
   hiKlakes_value: 1.e4
   default_lake_depth: 2 # m; default depth to assume when setting up lak package or high-k lakes (layer 1 bottom is adjusted to achieve this thickness)

mfsetup/mfnwtmodel.py

@@ -46,6 +46,9 @@ def __init__(self, parent=None, cfg=None,
         self._set_cfg(cfg)  # set up the model configuration dictionary
         self.relative_external_paths = self.cfg.get('model', {}).get('relative_external_paths', True)
         self.model_ws = self._get_model_ws()
+
+        # set the list file path
+        self.lst.file_name = [self.cfg['model']['list_filename_fmt'].format(self.name)]
 
         # property arrays
         self._ibound = None

mfsetup/tests/data/pfl_nwt_test.yml

@@ -4,6 +4,8 @@ model:
   exe_name: 'mfnwt'
   external_path: 'external/'
   perimeter_boundary_type: 'specified head'
+  # list file path is relative to model_ws
+  list_filename_fmt: 'external/{}.list'
   packages: ['dis',
              'bas6',
              'oc',

mfsetup/tests/test_lgr.py

@@ -181,7 +181,7 @@ def test_lgr_model_setup(pleasant_lgr_setup_from_yaml):
         specified_options = {'list', 'print_input', 'save_flows', 'newton'}
         assert not any(specified_options.difference(name_options.keys()))
         path, fname = os.path.split(name_options['list'][0])
-        assert os.path.abspath(m.model_ws).lower() == path.lower()
+        assert os.path.abspath(m.model_ws).lower() == os.path.abspath(path).lower()
         assert name_options['newton'][0] == 'under_relaxation'
 
     # check that the model names were included in the external files

mfsetup/tests/test_mf6_shellmound.py

@@ -162,6 +162,18 @@ def test_model(shellmound_model):
            os.path.normpath(os.path.join(os.path.abspath(model.model_ws), model.external_path))
 
 
+def test_namefile(shellmound_model_with_dis):
+    model = shellmound_model_with_dis
+    model.write_input()
+
+    # check that listing file was written correctly
+    expected_listfile_name = model.cfg['model']['list_filename_fmt'].format(model.name)
+    with open(model.namefile) as src:
+        for line in src:
+            if 'LIST' in line:
+                assert line.strip().split()[-1] == expected_listfile_name
+
+
 def test_snap_to_NHG(shellmound_cfg, shellmound_simulation):
     cfg = deepcopy(shellmound_cfg)
     #simulation = deepcopy(simulation)

mfsetup/tests/test_pfl_mfnwt_inset.py

@@ -72,6 +72,18 @@ def test_pfl_nwt_with_grid(pfl_nwt_with_grid):
     assert pfl_nwt_with_grid.modelgrid is not None
 
 
+def test_namefile(pfl_nwt_with_dis):
+    model = pfl_nwt_with_dis
+    model.write_input()
+
+    # check that listing file was written correctly
+    expected_listfile_name = model.cfg['model']['list_filename_fmt'].format(model.name)
+    with open(model.namefile) as src:
+        for line in src:
+            if 'LIST' in line:
+                assert line.strip().split()[-1] == expected_listfile_name
+
+
 def test_perioddata(pfl_nwt):
     model = pfl_nwt
     assert np.array_equal(model.perioddata.steady, [True, False])