Merge pull request payu-org#373 from jo-basevi/371-cesm-cmeps-read-mo…

…m6-parameter-files

Read mom6 parameter files in cesm cmeps driver

payu/models/cesm_cmeps.py

@@ -20,16 +20,19 @@
 from payu.fsops import mkdir_p, make_symlink
 from payu.models.model import Model
 from payu.models.fms import fms_collate
+from payu.models.mom6 import mom6_add_parameter_files
 
 # Add as needed
 component_info = {
     "mom": {
         "config_files": [
             "input.nml",
-            "MOM_input",
             "diag_table",
         ],
-        "optional_config_files" : ["MOM_override"]
+        "optional_config_files": [
+            "field_table",
+            "data_table",
+        ],
     },
     "cice": {
         "config_files": ["ice_in"],
@@ -114,23 +117,17 @@ def set_model_pathnames(self):
     def setup(self):
         super().setup()
 
-        # Read components from nuopc.runconfig and copy component configuration files
+        # Read components from nuopc.runconfig
         self.get_runconfig(self.work_path)
         self.get_components()
-        for f_name in self.config_files:
-            f_path = os.path.join(self.control_path, f_name)
-            shutil.copy(f_path, self.work_path)
 
-        for f_name in self.optional_config_files:
-            f_path = os.path.join(self.control_path, f_name)
-            try:
-                shutil.copy(f_path, self.work_path)
-            except IOError as exc:
-                if exc.errno == errno.ENOENT:
-                    pass
-                else:
-                    raise
-
+        if "mom" in self.components.values():
+            # Read mom6 parameter files and add to configuration files
+            mom6_add_parameter_files(self)
+
+        # Copy configuration files from control path to work path
+        self.setup_configuration_files()
+
         if self.prior_restart_path and not self.expt.repeat_run:
             start_type = 'continue'
 

payu/models/model.py

@@ -199,16 +199,9 @@ def get_prior_restart_files(self):
             print("No prior restart files found: {error}".format(error=str(e)))
             return []
 
-    def setup(self):
-
-        print("Setting up {model}".format(model=self.name))
-        # Create experiment directory structure
-        mkdir_p(self.work_init_path)
-        mkdir_p(self.work_input_path)
-        mkdir_p(self.work_restart_path)
-        mkdir_p(self.work_output_path)
-
-        # Copy configuration files from control path
+    def setup_configuration_files(self):
+        """Copy configuration and optional configuration files from control
+         path to work path"""
         for f_name in self.config_files:
             f_path = os.path.join(self.control_path, f_name)
             shutil.copy(f_path, self.work_path)
@@ -223,6 +216,18 @@ def setup(self):
                 else:
                     raise
 
+    def setup(self):
+
+        print("Setting up {model}".format(model=self.name))
+        # Create experiment directory structure
+        mkdir_p(self.work_init_path)
+        mkdir_p(self.work_input_path)
+        mkdir_p(self.work_restart_path)
+        mkdir_p(self.work_output_path)
+
+        # Copy configuration files from control path
+        self.setup_configuration_files()
+
         # Add restart files from prior run to restart manifest
         if (not self.expt.manifest.have_manifest['restart'] and
                 self.prior_restart_path):

payu/models/mom6.py

@@ -19,6 +19,29 @@
 from payu.models.fms import Fms
 
 
+def mom6_add_parameter_files(model):
+    """Add parameter files defined in input.nml to model configuration files.
+    Broken out of mom6 class so can be used in other models"""
+    input_nml = f90nml.read(os.path.join(model.control_path, 'input.nml'))
+
+    input_namelists = ['MOM_input_nml']
+    if 'SIS_input_nml' in input_nml:
+        input_namelists.append('SIS_input_nml')
+
+    for input in input_namelists:
+        input_namelist = input_nml.get(input, {})
+        filenames = input_namelist.get('parameter_filename', [])
+
+        if filenames == []:
+            print("payu: warning: MOM6: There are no parameter files "
+                  f"listed under {input} in input.nml")
+
+        if isinstance(filenames, str):
+            model.config_files.append(filenames)
+        else:
+            model.config_files.extend(filenames)
+
+
 class Mom6(Fms):
     """Interface to GFDL's MOM6 ocean model."""
 
@@ -45,7 +68,10 @@ def setup(self):
         super(Mom6, self).setup()
 
         self.init_config()
-        self.add_config_files()
+
+        # Add parameter files to config files and copy files over to work path
+        mom6_add_parameter_files(self)
+        self.setup_configuration_files()
 
     def init_config(self):
         """Patch input.nml as a new or restart run."""
@@ -65,47 +91,3 @@ def init_config(self):
             input_nml['SIS_input_nml']['input_filename'] = input_type
 
         f90nml.write(input_nml, input_fpath, force=True)
-
-    def add_config_files(self):
-        """Add to model configuration files"""
-
-        # Add parameter config files
-        config_files_to_add = self.get_parameter_files()
-
-        # Set of all configuration files
-        all_config_files = set(self.config_files).union(
-            self.optional_config_files)
-
-        for filename in config_files_to_add:
-            if filename not in all_config_files:
-                # Extend config files
-                self.config_files.append(filename)
-                all_config_files.add(filename)
-
-                # Copy file from control path to work path
-                file_path = os.path.join(self.control_path, filename)
-                shutil.copy(file_path, self.work_path)
-
-    def get_parameter_files(self):
-        """Return a list of parameter config files defined in input.nml"""
-        input_nml = f90nml.read(os.path.join(self.work_path, 'input.nml'))
-
-        input_namelists = ['MOM_input_nml']
-        if 'SIS_input_nml' in input_nml:
-            input_namelists.append('SIS_input_nml')
-
-        parameter_files = []
-        for input in input_namelists:
-            input_namelist = input_nml.get(input, {})
-            filenames = input_namelist.get('parameter_filename', [])
-
-            if filenames == []:
-                print("payu: warning: MOM6: There are no parameter files "
-                      f"listed under {input} in input.nml")
-
-            if isinstance(filenames, str):
-                parameter_files.append(filenames)
-            else:
-                parameter_files.extend(filenames)
-
-        return parameter_files

test/models/test_mom6.py

@@ -64,54 +64,42 @@ def teardown():
     # Run test
     yield
 
-    # Remove any files in expt work directory
-    for file in os.listdir(expt_workdir):
-        try:
-            os.remove(os.path.join(expt_workdir, file))
-        except Exception as e:
-            print(e)
-
 
 @pytest.mark.parametrize(
-        "input_nml, expected_files_added",
-        [
-            (
-                {
-                    "MOM_input_nml": {
-                        "parameter_filename": "MOM_Input"
-                    }
-                },
-                ["MOM_Input"]
-            ),
-            (
-                {
-                    "SIS_input_nml": {
-                        "parameter_filename": "SIS_Input"
-                    }
+    "input_nml, expected_files_added",
+    [
+        (
+            {
+                "MOM_input_nml": {
+                    "parameter_filename": "MOM_Input"
+                }
+            },
+            ["MOM_Input"]
+        ),
+        (
+            {
+                "SIS_input_nml": {
+                    "parameter_filename": "SIS_Input"
+                }
+            },
+            ["SIS_Input"]
+        ),
+        (
+            {
+                "MOM_input_nml": {
+                    "parameter_filename": ["MOM_Input", "MOM_override"]
                 },
-                ["SIS_Input"]
-            ),
-            (
-                {
-                    "MOM_input_nml": {
-                        "parameter_filename": ["MOM_Input", "MOM_override"]
-                    },
-                    "SIS_input_nml": {
-                        "output_directory": '.'
-                    }
-                },
-                ["MOM_Input", "MOM_override"]
-            )
-        ])
-def test_add_config_files(input_nml,
-                          expected_files_added):
-    # Create config files in control directory
-    for file in expected_files_added:
-        filename = os.path.join(ctrldir, file)
-        make_random_file(filename, 8)
-
+                "SIS_input_nml": {
+                    "output_directory": '.'
+                }
+            },
+            ["MOM_Input", "MOM_override"]
+        )
+    ])
+def test_mom6_add_parameter_files(input_nml,
+                                  expected_files_added):
     # Create config.nml
-    input_nml_fp = os.path.join(expt_workdir, 'input.nml')
+    input_nml_fp = os.path.join(ctrldir, 'input.nml')
     f90nml.write(input_nml, input_nml_fp)
 
     with cd(ctrldir):
@@ -122,13 +110,11 @@ def test_add_config_files(input_nml,
     prior_config_files = model.config_files[:]
 
     # Function to test
-    model.add_config_files()
+    payu.models.mom6.mom6_add_parameter_files(model)
 
     # Check files are added to config_files
     added_files = set(model.config_files).difference(prior_config_files)
     assert added_files == set(expected_files_added)
 
-    # Check the extra files are moved to model's work path
-    ctrl_path_files = os.listdir(model.work_path)
-    for file in expected_files_added:
-        assert file in ctrl_path_files
+    # Tidy up input.nml
+    os.remove(input_nml_fp)