Merge branch 'master' into cmor_3.4.0

Test/CMOR_input_example.json

@@ -1,4 +1,5 @@
 {
+    "#note":           "explanation of what source_type is goes here",
     "source_type":            "AOGCM ISM AER",
 
     "#note":                  "CMIP6 valid experiment_ids are found in CMIP6_CV.json",
@@ -67,7 +68,7 @@
     "tracking_prefix":        "hdl:21.14100",
     "_history_template":       "%s ;rewrote data to be consistent with <activity_id> for variable <variable_id> found in table <table_id>.",
 
-    "#output_path_template":   "Template for output path directory using tables keys or global attributes",
+    "#output_path_template":   "Template for output path directory using tables keys or global attributes, these should follow the relevant data reference syntax",
     "output_path_template":    "<mip_era><activity_id><institution_id><source_id><experiment_id><_member_id><table><variable_id><grid_label><version>",
     "output_file_template":    "<variable_id><table><source_id><experiment_id><_member_id><grid_label>",
  }

Test/test_doc.py

@@ -1,29 +1,43 @@
 import cmor
 
-cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE_4)
+cmor.setup(
+	# inpath has to point to the CMOR 
+	# tables path (CMIP6, input4MIPs or otherwise)
+	inpath='Tables',  
+	netcdf_file_action=cmor.CMOR_REPLACE_4
+)
 
-cmor.dataset_json("Test/CMOR_input_example.json")
-
-table = 'CMIP6_Amon.json'
+cmor.dataset_json("Test/CMOR_input_example.json")    
+
+# Loading this test table overwrites the normal CF checks on valid variable values.
+# This is perfect for testing but shouldn't be done when writing real data.
+table='CMIP6_Amon.json'
 cmor.load_table(table)
 
-itime = cmor.axis(table_entry='time',
-                  units='days since 2000-01-01 00:00:00',
-                  coord_vals=[15, ],
-                  cell_bounds=[0, 30])
-ilat = cmor.axis(table_entry='latitude',
-                 units='degrees_north',
-                 coord_vals=[0],
-                 cell_bounds=[-1, 1])
-ilon = cmor.axis(table_entry='longitude',
-                 units='degrees_east',
-                 coord_vals=[90],
-                 cell_bounds=[89, 91])
 
-axis_ids = [itime, ilat, ilon]
+# here is where you add your axes
+itime = cmor.axis(table_entry= 'time',
+                  units= 'days since 2000-01-01 00:00:00',
+                  coord_vals= [15,],
+                  cell_bounds= [0, 30])
+ilat = cmor.axis(table_entry= 'latitude',
+                 units= 'degrees_north',
+                 coord_vals= [0],
+                 cell_bounds= [-1, 1])
+ilon = cmor.axis(table_entry= 'longitude',
+                 units= 'degrees_east',
+                 coord_vals= [90],
+                 cell_bounds= [89, 91])
 
+axis_ids = [itime,ilat,ilon]
+
+# here we create a variable with appropriate name, units and axes
 varid = cmor.variable('ts', 'K', axis_ids)
+
+# then we can write the variable along with the data
 cmor.write(varid, [273])
+
+# finally we close the file and print where it was saved
 outfile = cmor.close(varid, file_name=True)
-print "File written: ", outfile
+print("File written to: {}".format(outfile))
 cmor.close()

Test/test_python_CMIP6_CV_load_tables.py

@@ -0,0 +1,25 @@
+from __future__ import print_function
+import cmor
+import glob
+import unittest
+
+
+
+def run():
+    unittest.main()
+
+class TestLoadTables(unittest.TestCase):
+    def testLoadTables(self):
+        tables = glob.glob("Tables/CMIP6*json")
+        for table in tables:
+            if "formula_terms" in table:
+                continue
+            cmor.setup(inpath='Tables', netcdf_file_action=cmor.CMOR_REPLACE)
+            cmor.dataset_json("Test/CMOR_input_example.json")
+            print("Loading table:", table)
+            ierr = cmor.load_table(table)
+            self.assertEqual(ierr, 0)
+            cmor.close()
+
+if __name__ == '__main__':
+    run()