Improve help messages and interface for single job

bgcval2/UKESMpython.py

@@ -72,7 +72,7 @@ def folder(name):
 	    It also accepts lists of strings.
 	"""
     if type(name) == type(['a', 'b', 'c']):
-        name = join(name, '/')
+        name = os.path.join(name)
     if name[-1] != '/':
         name = name + '/'
     if exists(name) is False:

bgcval2/analysis_compare.py

@@ -4245,7 +4245,7 @@ def load_yml_and_run(compare_yml, config_user):
         print(jobID, 'suite:', suites[jobID])
 
     for jobID in jobs:
-        # even if you don't want to download, we run this 
+        # even if you don't want to download, we run this
         # as it clears up the path and ensures recently downloed data is
         # correctly symlinked.
         download_from_mass(jobID, doMoo=do_mass_download)
@@ -4338,15 +4338,15 @@ def main():
     compare_ymls = args.compare_yml
 
     for compare_yml in compare_ymls:
-        print(f"analysis_timeseries: Comparison config file {compare_yml}")
+        print(f"analysis_compare: Comparison config file {compare_yml}")
 
         if not os.path.isfile(compare_yml):
-            print(f"analysis_timeseries: Could not find comparison config file {compare_yml}")
+            print(f"analysis_compare: Could not find comparison config file {compare_yml}")
             sys.exit(1)
 
         load_yml_and_run(compare_yml, config_user)
 
-    print("Finished... ")
+    print("Finished analysis_compare... ")
 
 
 if __name__ == "__main__":

bgcval2/analysis_p2p.py

@@ -32,15 +32,16 @@
 
 #####
 #Standard Python modules:
-from sys import argv, exit
-from os.path import exists
 from calendar import month_name
 from socket import gethostname
 from getpass import getuser
 from glob import glob
 from netCDF4 import Dataset
 import numpy as np
 import sys
+import os
+import argparse
+import itertools
 
 #####
 #Specific local code:
@@ -50,6 +51,7 @@
 from .p2p.patternAnalyses import InterAnnualPatterns, BGCvsPhysics
 from .bgcvaltools.pftnames import months
 from .p2p.shelveToDictionary import shelveToDictionary
+from .download_from_mass import findLastFinishedYear
 
 #####
 # User defined set of paths pointing towards the datasets.
@@ -85,7 +87,7 @@
 
 p2pKeys_annual = [
     'T',
-    'S',  #'MLD', 
+    'S',  #'MLD',
     'Chl_CCI',
     'N',
     'Si',
@@ -113,7 +115,7 @@
 
 p2pKeys_physics = [
     'T',
-    'S',  #'MLD', 
+    'S',  #'MLD',
     'ZonalCurrent',
     'MeridionalCurrent',
     'VerticalCurrent'
@@ -139,7 +141,7 @@ def analysis_p2p(
     noTargets=True,
 ):
     """
-	
+
 	"""
     #####
     # Switches:
@@ -1499,44 +1501,99 @@ def single_p2p(jobID, key, year):
         print("Error: %s" % sys.exc_info()[0])
 
 
-def run():
+def get_args():
+    """Parse command line arguments."""
+    parser = argparse.ArgumentParser(
+        description=__doc__,
+        formatter_class=argparse.RawDescriptionHelpFormatter)
+    accepted_keys = ['debug', 'physics', 'leve2', 'annual']
+
+    parser.add_argument('-j',
+                        '--jobID',
+                        nargs='+',
+                        type=str,
+                        default=None,
+                        help='One or more UKESM Job IDs (automatically generated by cycl/rose suite).',
+                        required=True,
+                        )
+    parser.add_argument('-k',
+                        '--keys',
+                        default=['level2', ],
+                        nargs='+',
+                        type=str,
+                        help=''.join(['Runtime keys - each key links to a pre-determined list of variables to analyse. ',
+                                      'Keys are: ', ', '.join( accepted_keys)]),
+                        required=False,
+                        )
+    parser.add_argument('-y',
+                        '--years',
+                        default=['best',],
+                        nargs='+',
+                        type=str,
+                        help=''.join(['Years to analysis. Default is "best". ']),
+                        required=False,
+                        )
+
+    parser.add_argument('-c',
+                        '--config-file',
+                        default=os.path.join(os.path.dirname(os.path.realpath(__file__)),
+                                             'default-bgcval2-config.yml'),
+                        help='User configuration file (for paths).',
+                        required=False)
+
+    args = parser.parse_args()
+
+    return args
+
+
+
+def main():
     from ._version import __version__
     print(f'BGCVal2: {__version__}')
-    if "--help" in argv or len(argv) == 1:
-        print("Running with no arguments. Exiting.")
-        if "--help" in argv:
-            print("Read the documentation.")
-        sys.exit(0)
-    try:
-        jobID = argv[1]
-    except:
-        jobID = 'u-ab749'
+    args = get_args()
+
+    jobIDs = args.jobID
+    keys = args.keys
+    years = args.years
+
+    accepted_keys = ['debug', 'physics', 'leve2', 'annual']
+    for jobID, year, suite in itertools.product(jobIDs, years, keys):
+        print('p2p:', jobID, year, suite)
+        if year == 'best':
+            best_year = False
+            for divby in [100, 50, 25, 10, 5, 1]:
+                if best_year:
+                    continue
+                print("analysis_p2p:\t find best year", divby, year,best_year )
+                best_year = findLastFinishedYear(jobID,
+                                            dividby=divby, debug= False) #  numberfiles=numberfiles)
+            if best_year == False:
+                continue
+            else:
+                year = best_year
 
-    try:
-        year = argv[2]
-    except:
-        year = '2007'
-
-    if 'debug' in argv[1:]:
-        analysisSuite = 'debug'
-    elif 'level2' in argv[1:]:
-        analysisSuite = 'level2'
-    elif 'physics' in argv[1:]:
-        analysisSuite = 'physics'
-    else:
-        analysisSuite = 'annual'
-
-    analysis_p2p(
-        models=[
-            'NEMO',
-            'MEDUSA',
-        ],
-        jobID=jobID,
-        years=[
-            year,
-        ],  #'2075','2076',
-        modelGrid='eORCA1',
-        annual=True,
-        noPlots=False,
-        analysisSuite=analysisSuite,
-    )
+        analysis_p2p(
+            models=[
+                'NEMO',
+                'MEDUSA',
+            ],
+            jobID=jobID,
+            years=[
+                year,
+            ],  #'2075','2076',
+            modelGrid='eORCA1',
+            annual=True,
+            noPlots=False,
+            analysisSuite=[suite,
+            ],
+        )
+
+
+        print('analysis_p2p:', jobID, year, suite)
+        single_p2p(jobID, suite, year)
+
+    print("Finished p2p... ")
+
+
+if __name__ == "__main__":
+    main()

bgcval2/analysis_timeseries.py

@@ -4991,7 +4991,7 @@ def main():
               "Will proceed with defaults.")
         config_user = None
 
-    for jobID, suite in itertools.product(keys, jobIDs):
+    for jobID, suite in itertools.product(jobIDs, keys):
         analysis_timeseries(
             jobID=jobID,
             analysisSuite=suite,