Merge 5e495c9 into b78d020

payu/cli.py

@@ -30,6 +30,20 @@
 def parse():
     """Parse the command line inputs and execute the subcommand."""
 
+    parser = generate_parser()
+
+    # Display help if no arguments are provided
+    if len(sys.argv) == 1:
+        parser.print_help()
+    else:
+        args = vars(parser.parse_args())
+        run_cmd = args.pop('run_cmd')
+        run_cmd(**args)
+
+
+def generate_parser():
+    """Parse the command line inputs generate and return parser."""
+
     # Build the list of subcommand modules
     modnames = [mod for (_, mod, _)
                 in pkgutil.iter_modules(payu.subcommands.__path__,
@@ -52,14 +66,7 @@ def parse():
         for arg in cmd.arguments:
             cmd_parser.add_argument(*arg['flags'], **arg['parameters'])
 
-    # Display help if no arguments are provided
-    if len(sys.argv) == 1:
-        parser.print_help()
-    else:
-        args = vars(parser.parse_args())
-        run_cmd = args.pop('run_cmd')
-        run_cmd(**args)
-
+    return parser
 
 def get_model_type(model_type, config):
     """Determine and validate the active model type."""

payu/experiment.py

@@ -1,5 +1,4 @@
-"""payu.experiment
-   ===============
+"""payu.experiment ===============
 
    Interface to an individual experiment managed by payu
 
@@ -45,8 +44,9 @@
 
 class Experiment(object):
 
-    def __init__(self, lab, reproduce=None):
+    def __init__(self, lab, reproduce=False, force=False):
         self.lab = lab
+        self.force = force
 
         self.start_time = datetime.datetime.now()
 
@@ -87,7 +87,7 @@ def __init__(self, lab, reproduce=None):
 
         self.set_output_paths()
 
-        if reproduce is None:
+        if not reproduce:
             # check environment for reproduce flag under PBS
             reproduce = os.environ.get('PAYU_REPRODUCE', False)
 
@@ -379,9 +379,14 @@ def setup(self, force_archive=False):
 
         # Confirm that no work path already exists
         if os.path.exists(self.work_path):
-            sys.exit('payu: error: work path already exists: {path}.\n'
-                     '             payu sweep and then payu run'
-                     .format(path=self.work_path))
+            if self.force:
+                print('payu: work path already exists.\n'
+                      '      Sweeping as --force option is True.')
+                self.sweep()
+            else:
+                sys.exit('payu: error: work path already exists: {path}.\n'
+                         '             payu sweep and then payu run'
+                         .format(path=self.work_path))
 
         mkdir_p(self.work_path)
 

payu/subcommands/args.py

@@ -98,7 +98,19 @@
     'parameters': {
         'action':   'store_true',
         'dest':     'reproduce',
-        'default':  None,
+        'default':  False,
         'help':     'Only run if manifests are correct',
     }
 }
+
+
+# Force run to proceed despite existing directories
+force = {
+    'flags': ('--force', '-f'),
+    'parameters': {
+        'action':   'store_true',
+        'dest':     'force',
+        'default':  False,
+        'help':     'Force run to proceed, overwriting existing directories',
+    }
+}

payu/subcommands/collate_cmd.py

@@ -14,14 +14,14 @@
 title = 'collate'
 parameters = {'description': 'Collate tiled output into single output files'}
 
-arguments = [args.model, args.config, args.initial, args.nruns,
-             args.laboratory, args.dir_path]
+arguments = [args.model, args.config, args.initial, args.laboratory,
+             args.dir_path]
 
 
-def runcmd(model_type, config_path, init_run, n_runs, lab_path, dir_path):
+def runcmd(model_type, config_path, init_run, lab_path, dir_path):
 
     pbs_config = fsops.read_config(config_path)
-    pbs_vars = cli.set_env_vars(init_run, n_runs, lab_path, dir_path)
+    pbs_vars = cli.set_env_vars(init_run, lab_path, dir_path)
 
     collate_config = pbs_config.get('collate', {})
 
@@ -95,13 +95,15 @@ def runscript():
 
     run_args = parser.parse_args()
 
-    pbs_vars = cli.set_env_vars(run_args.init_run, run_args.n_runs,
-                                run_args.lab_path, run_args.dir_path)
+    pbs_vars = cli.set_env_vars(run_args.init_run,
+                                run_args.lab_path,
+                                run_args.dir_path)
 
     for var in pbs_vars:
         os.environ[var] = str(pbs_vars[var])
 
-    lab = Laboratory(run_args.model_type, run_args.config_path,
+    lab = Laboratory(run_args.model_type,
+                     run_args.config_path,
                      run_args.lab_path)
     expt = Experiment(lab)
     expt.collate()

payu/subcommands/run_cmd.py

@@ -12,10 +12,11 @@
 parameters = {'description': 'Run the model experiment'}
 
 arguments = [args.model, args.config, args.initial, args.nruns,
-             args.laboratory, args.reproduce]
+             args.laboratory, args.reproduce, args.force]
 
 
-def runcmd(model_type, config_path, init_run, n_runs, lab_path, reproduce):
+def runcmd(model_type, config_path, init_run, n_runs, lab_path,
+           reproduce=False, force=False):
 
     # Get job submission configuration
     pbs_config = fsops.read_config(config_path)
@@ -114,7 +115,7 @@ def runscript():
 
     lab = Laboratory(run_args.model_type, run_args.config_path,
                      run_args.lab_path)
-    expt = Experiment(lab, reproduce=run_args.reproduce)
+    expt = Experiment(lab, reproduce=run_args.reproduce, force=run_args.force)
 
     n_runs_per_submit = expt.config.get('runspersub', 1)
     subrun = 1

payu/subcommands/setup_cmd.py

@@ -12,14 +12,16 @@
     args.config,
     args.laboratory,
     args.force_archive,
-    args.reproduce
+    args.reproduce,
+    args.force
 ]
 
 
-def runcmd(model_type, config_path, lab_path, force_archive, reproduce):
+def runcmd(model_type, config_path, lab_path, force_archive,
+           reproduce=False, force=False):
 
     lab = Laboratory(model_type, config_path, lab_path)
-    expt = Experiment(lab, reproduce=reproduce)
+    expt = Experiment(lab, reproduce=reproduce, force=force)
 
     expt.setup(force_archive=force_archive)
 

test/common.py

@@ -90,21 +90,25 @@ def payu_setup(model_type=None,
                config_path=None,
                lab_path=None,
                force_archive=None,
-               reproduce=None):
+               reproduce=None,
+               sweep=True,
+               force=False):
     """
     Wrapper around original setup command to provide default arguments
     and run in ctrldir
     """
     with cd(ctrldir):
-        payu_sweep(model_type=None,
-                   config_path=None,
-                   hard_sweep=False,
-                   lab_path=str(labdir))
+        if sweep:
+            payu_sweep(model_type=None,
+                       config_path=None,
+                       hard_sweep=False,
+                       lab_path=str(labdir))
         payu_setup_orignal(model_type,
                            config_path,
                            lab_path,
                            force_archive,
-                           reproduce)
+                           reproduce,
+                           force)
 
 
 def write_config(config):