Some robustness changes picked up to pass testing

The tests required some changes to the configuration and stage config paths. Some minor changes to the tests to account for slightly changed behaviours.

Author: Whyborn

payu/models/staged_cable.py

@@ -46,7 +46,8 @@ def setup(self):
         # Initialise the configuration log
         self.configuration_log = {}
 
-        if not os.path.isfile('configuration_log.yaml'):
+        conf_log_p = os.path.join(self.control_path, 'configuration_log.yaml')
+        if not os.path.isfile(conf_log_p):
             # Build a new configuration log
             self._build_new_configuration_log()
         else:
@@ -60,18 +61,14 @@ def setup(self):
         # Make the logging directory
         mkdir_p(os.path.join(self.work_path, "logs"))
 
-        # Get the additional restarts from older restart dirs
-        # self._get_further_restarts()
-
-        # Make necessary adjustments to the configuration log
-        # self._handle_configuration_log_setup()
-
         self._set_current_stage()
+
     def _build_new_configuration_log(self):
         """Build a new configuration log for the first stage of the run."""
 
+        stage_conf_p = os.path.join(self.control_path, 'stage_config.yaml')
         # Read the stage_config.yaml file
-        with open('stage_config.yaml', 'r') as stage_conf_f:
+        with open(stage_conf_p, 'r') as stage_conf_f:
             self.stage_config = yaml.safe_load(stage_conf_f)
 
         # On the first run, we need to read the 'stage_config.yaml' file.
@@ -86,9 +83,12 @@ def _build_new_configuration_log(self):
 
     def _read_configuration_log(self):
         """Read the existing configuration log."""
-        with open('configuration_log.yaml') as conf_log_file:
+        conf_log_p = os.path.join(self.control_path, 'configuration_log.yaml')
+        with open(conf_log_p, 'r') as conf_log_file:
             self.configuration_log = yaml.safe_load(conf_log_file)
 
+        print(f"After reading configuration_log: {self.configuration_log}")
+
     def _prepare_configuration(self):
         """Prepare the stages in the CABLE configuration."""
 
@@ -231,7 +231,8 @@ def _set_current_stage(self):
                 self.configuration_log['queued_stages'].pop(0)
 
         self._save_configuration_log()
-        shutil.copy('configuration_log.yaml', self.work_path)
+        conf_log_p = os.path.join(self.control_path, 'configuration_log.yaml')
+        shutil.copy(conf_log_p, self.work_path)
 
     def archive(self):
         """Store model output to laboratory archive and update the
@@ -250,9 +251,10 @@ def archive(self):
               "number of queued stages in the configuration log.")
         self.expt.n_runs = remaining_stages
 
-        if len(self.configuration_log["queued_stages"]) == 0:
+        conf_log_p = os.path.join(self.control_path, 'configuration_log.yaml')
+        if self.expt.n_runs == 0:
             # Configuration successfully completed
-            os.remove('configuration_log.yaml')
+            os.remove(conf_log_p)
 
         super(StagedCable, self).archive()
 
@@ -261,26 +263,28 @@ def _collect_restarts(self):
         merge of the files in work_path/restart and in prior_restart_path, with
         the files in work_path/restart taking precedence."""
 
-        # Move the files in work_path/restart first
-        for f in os.listdir(self.work_restart_path):
-            shutil.move(os.path.join(self.work_restart_path, f),
-                        self.restart_path)
-        os.rmdir(self.work_restart_path)
-
-        # Now collect any restarts from prior_restart_path only if said restart
-        # doesn't already exist (except on first run)
+        # First, collect restarts which do not have a newer version (when the
+        # counter is greater than 0)
         if self.expt.counter > 0:
-            # self.prior_restart_path nor expt.prior_restart_path are defined here
-            # build it as in experiment.py
             prior_restart_dir = 'restart{0:03}'.format(self.expt.counter - 1)
             prior_restart_path = os.path.join(self.expt.archive_path,
                                               prior_restart_dir)
 
-            current_restarts = os.listdir(self.restart_path)
+            # For each restart, check if newer version was created. If not,
+            # copy into the work restart path.
+            generated_restarts = os.listdir(self.work_restart_path)
+
             for f in os.listdir(prior_restart_path):
-                if f not in current_restarts:
+                if f not in generated_restarts:
                     shutil.copy(os.path.join(prior_restart_path, f),
-                            self.restart_path)
+                            self.work_restart_path)
+
+
+        # Move the files in work_path/restart first
+        for f in os.listdir(self.work_restart_path):
+            shutil.move(os.path.join(self.work_restart_path, f),
+                        self.restart_path)
+        os.rmdir(self.work_restart_path)
 
     def _archive_current_stage(self):
         """Move the current stage to the list of completed stages."""
@@ -291,12 +295,14 @@ def _archive_current_stage(self):
         self._save_configuration_log()
 
         # Copy the configuration log to the restart directory for shareability
-        shutil.copy('configuration_log.yaml', self.restart_path)
+        conf_log_p = os.path.join(self.control_path, 'configuration_log.yaml')
+        shutil.copy(conf_log_p, self.restart_path)
 
     def collate(self):
         pass
 
     def _save_configuration_log(self):
         """Write the updated configuration log back to the staging area."""
-        with open('configuration_log.yaml', 'w+') as config_log_f:
+        conf_log_p = os.path.join(self.control_path, 'configuration_log.yaml')
+        with open(conf_log_p, 'w+') as config_log_f:
             yaml.dump(self.configuration_log, config_log_f)

test/models/test_staged_cable.py

@@ -33,6 +33,8 @@ def setup_module(module):
         ctrldir.mkdir()
         expt_workdir.mkdir(parents=True)
         archive_dir.mkdir()
+        restart_dir = archive_dir / 'ctrl' / 'restart000'
+        restart_dir.mkdir(parents=True)
     except Exception as e:
         print(e)
 
@@ -107,10 +109,10 @@ def teardown_module(module):
     if verbose:
         print("teardown_module   module:%s" % module.__name__)
 
-    try:
-        shutil.rmtree(tmpdir)
-    except Exception as e:
-        print(e)
+    # try:
+        # shutil.rmtree(tmpdir)
+    # except Exception as e:
+        # print(e)
 
 
 def test_staged_cable():
@@ -123,50 +125,47 @@ def test_staged_cable():
         expt = payu.experiment.Experiment(lab, reproduce=False)
         model = expt.models[0]
 
-    # Since we've called the initialiser, we should be able to inspect the
-    # stages immediately (through the configuration log)
-    expected_queued_stages = [
-        'stage_1',
-        'stage_2',
-        'stage_3',
-        'stage_4',
-        'stage_3',
-        'stage_3',
-        'stage_5',
-        'stage_6',
-        'stage_6',
-        'stage_7']
-    assert model.configuration_log['queued_stages'] == expected_queued_stages
-
-    # Now prepare for a stage- should see changes in the configuration log
-    # and the patched namelist in the workdir
-    model.setup()
-    expected_current_stage = expected_queued_stages.pop(0)
-    assert model.configuration_log['current_stage'] == expected_current_stage
-    assert model.configuration_log['queued_stages'] == expected_queued_stages
-
-    # Now check the namelist
-    expected_namelist = {
-        'cablenml': {
-            'option1': 10,
-            'struct1': {
-                'option2': 20,
-                'option3': 3,
-                'option5': 50
-            },
-            'option4': 4,
-            'option6': 60
+        # Now prepare for a stage- should see changes in the configuration log
+        # and the patched namelist in the workdir
+        model.setup()
+
+        # Since we've called the initialiser, we should be able to inspect the
+        # stages immediately (through the configuration log)
+        expected_queued_stages = [
+            'stage_2',
+            'stage_3',
+            'stage_4',
+            'stage_3',
+            'stage_3',
+            'stage_5',
+            'stage_6',
+            'stage_6',
+            'stage_7']
+        assert model.configuration_log['queued_stages'] == expected_queued_stages
+        assert model.configuration_log['current_stage'] == 'stage_1'
+
+        # Now check the namelist
+        expected_namelist = {
+            'cablenml': {
+                'option1': 10,
+                'struct1': {
+                    'option2': 20,
+                    'option3': 3,
+                    'option5': 50
+                },
+                'option4': 4,
+                'option6': 60
+            }
         }
-    }
 
-    with open(expt_workdir / 'cable.nml') as stage_nml_f:
-        stage_nml = f90nml.read(stage_nml_f)
+        with open(expt_workdir / 'cable.nml') as stage_nml_f:
+            stage_nml = f90nml.read(stage_nml_f)
 
-    assert stage_nml == expected_namelist
+        assert stage_nml == expected_namelist
 
-    # Archive the stage and make sure the configuration log is correct
-    model.archive()
-    expected_comp_stages = [expected_current_stage]
-    expected_current_stage = ''
-    assert model.configuration_log['completed_stages'] == expected_comp_stages
-    assert model.configuration_log['current_stage'] == expected_current_stage
+        # Archive the stage and make sure the configuration log is correct
+        model.archive()
+        expected_comp_stages = ['stage_1']
+        expected_current_stage = ''
+        assert model.configuration_log['completed_stages'] == expected_comp_stages
+        assert model.configuration_log['current_stage'] == expected_current_stage