minor adjustment to docs, conf files and code after tests

ACDD_conf.yaml

@@ -174,4 +174,4 @@ attrs:
     parent: !!bool false 
     # CMOR will add a tracking_id if you want to define a prefix add here
     tracking_id_prefix: 
-    comment: "post-processed using ACCESS-MOPPeR v0.6.0 https://doi.org/10.5281/zenodo.10346216"
+    comment: "post-processed using ACCESS-MOPPeR v1.0.0 https://doi.org/10.5281/zenodo.10346216"

CMIP6_conf.yaml

@@ -91,6 +91,8 @@ cmor:
     # walltime in "hh:mm:ss"
     walltime: '8:00:00'
     mode: cmip6
+    # conda_env: <custom-env-path>/bin/activate
+    conda_env: default
 
 # Global attributes: these will be added to each files comment unwanted ones
 # the labels CMIP6/ACDD indicates which ones are necessary to comply with respective standards
@@ -161,4 +163,4 @@ attrs:
     #CMOR will add a tracking_id if you want to define a prefix add here
     tracking_id_prefix:
     Conventions: "CF-1.7 CMIP-6.2" 
-    comment: "post-processed using ACCESS-MOPPeR v0.6.0 https://doi.org/10.5281/zenodo.10346216"
+    comment: "post-processed using ACCESS-MOPPeR v1.0.0 https://doi.org/10.5281/zenodo.10346216"

docs/mopdb_command.rst

@@ -57,16 +57,19 @@ A user that wants to create a mapping table for another AUS2200 simulation can u
 
 Create a mapping file
 ---------------------
-.. code-block::
 
 This can be done by providing the model output path and a pattern to match or directly a varlist file
 
 From output path:
 
+.. code-block::
+
     mopdb template  -f <output-path> -m <string-to-match> -v <access-version>
 
 From varlist file:
 
+.. code-block::
+
     mopdb template  -f <varlist-out> -v <access-version>
 
 This will create a map_<exp>.csv file using, if available, information from the mapping table.
@@ -110,20 +113,25 @@ The other groups of records require checking, as either the version or the frequ
 
 Create an intake catalogue
 --------------------------
-.. code-block::
 
 This represents an extra step on top of the mapping, so it can be start directly from an existing mapping or from scratch by providing the model ouptut path and a match. 
 
 From output path:
 
+.. code-block::
+
     mopdb intake  -f <output-path> -m <string-to-match> -v <access-version> { -a <alias> }
 
 From varlist file:
 
+.. code-block::
+
     mopdb intake  -f <output-path> -fl <varlist-out> -v <access-version> { -a <alias> }
 
 From mapping file:
 
+.. code-block::
+
     mopdb intake  -f <output-path> -fl <mapping-out> -v <access-version> { -a <alias> }
 
 NB the model output path is still needed even when passing an existing mapping or variable list.

src/mopdata/update_db.py.txt

@@ -37,7 +37,8 @@ def update_map(conn, varid, ctable):
     """Read mappings for variable from map file and
     update them in filelist
     """
-    keys = ['frequency','realm','timeshot','calculation', 'positive', 'resample']
+    keys = ['frequency','realm','timeshot','calculation',
+            'positive', 'resample']
     keys2 = {'vin': 'input_vars', 'in_units': 'units'}
     fname = f"maps/{ctable}.json"
     with open(fname, 'r') as f:
@@ -48,6 +49,12 @@ def update_map(conn, varid, ctable):
     args = {k: row[k] for k in keys}
     for k,v in keys2.items():
         args[k] = row[v]
+    if 'datadir' in row.keys():
+        paths = row['file_structure'].split()
+        infile = ''
+        for x in paths:
+            infile += f"{row['datadir']}/{x} "
+        args['infile'] = infile
     cur = conn.cursor()
     sql = f"UPDATE filelist SET"
     for k,v in args.items(): 

src/mopper/mop_utils.py

@@ -564,9 +564,13 @@ def get_coords(ctx, ovar, coords):
     var_log = logging.getLogger(ctx.obj['var_log'])
     # open ancil grid file to read vertices
     #PP be careful this is currently hardcoded which is not ok!
-    ancil_file = ctx.obj[f"grid_{ctx.obj['realm']}"]
+    ancil_dir = ctx.obj.get('ancils_path', '')
+    ancil_file = ancil_dir + "/" + ctx.obj.get(f"grid_{ctx.obj['realm']}", '')
+    if ancil_file == '' or not Path(ancil_file).exists():
+        var_log.error(f"Ancil file {ancil_file} not set or inexistent")
+        sys.exit()
     var_log.debug(f"getting lat/lon and bnds from ancil file: {ancil_file}")
-    ds = xr.open_dataset(f"{ctx.obj['ancils_path']}/{ancil_file}")
+    ds = xr.open_dataset(ancil_file)
     var_log.debug(f"ancil ds: {ds}")
     # read lat/lon and vertices mapping
     cfile = import_files('mopdata').joinpath('latlon_vertices.yaml')
@@ -793,8 +797,9 @@ def get_bounds_values(ctx, ds, bname):
     calc = False
     var_log = logging.getLogger(ctx.obj['var_log'])
     var_log.debug(f"Getting bounds values for {bname}")
-    ancil_file =  ctx.obj[f"grid_{ctx.obj['realm']}"]
+    ancil_file =  ctx.obj.get(f"grid_{ctx.obj['realm']}", '')
     if bname in ds.variables:
+        var_log.debug(f"Bounds for {bname} in file")
         bnds_val = ds[bname].values
     elif ancil_file != "":     
         fname = f"{ctx.obj['ancils_path']}/{ancil_file}"