Merge pull request #192 from ACCESS-Community-Hub/issue190

Issue190

.github/workflows/mopper-conda-release.yaml

@@ -9,7 +9,7 @@ on:
 
 jobs:
   conda_deployment_with_new_tag:
-    name: Test conda deployment of package with Python ${{ matrix.python-version }}
+    name: Deploy conda package with Python ${{ matrix.python-version }}
     runs-on: ubuntu-latest
     strategy:
       matrix:

ACDD_conf.yaml

@@ -71,14 +71,17 @@ cmor:
     # use this to indicate the path used for new or modified tables
     # these will be used in preference to the package tables
     tables_path: ""
-    # ancillary files path
-    # when running model with payu ancil files are copied to work/<realm>/INPUT
-    # you can leave these empty if processing only atmos
+    # Ancil files are needed only for specific variables when
+    # grid information is not fully available from output
+    # you can usually leave these empty if processing only atmos
+    # ancillary files relative path to <appdir> or fullpath
     ancils_path: "localdata/ancils"
     grid_ocean: ""
     grid_ice: ""
     mask_ocean: ""
+    # to supply land area fraction if not available in output 
     land_frac: ""
+    # to supply tile area fraction if not available in output 
     tile_frac: ""
     # defines Controlled Vocabularies and required attributes
     # leave ACDD to follow NCI publishing requirements 

CMIP6_conf.yaml

@@ -1,6 +1,8 @@
 ################################################################
 # USER OPTIONS
 # Settings to manage cmorisation and set tables/variables to process
+# This config file is to produce files to submit to CMIP6 project
+# It's more restrictive than ACDD_conf.yaml
 cmor:
     # If test true it will just run the setup but not launch the job automatically
     test: false
@@ -62,14 +64,17 @@ cmor:
     # as you should use official CMOR cmip6 tables for CMIP6 mode
     # use this only if current package version is obsolete
     tables_path: ""
-    # ancillary files path
-    # when running model with payu ancil files are copied to work/<realm>/INPUT
-    # you can leave these empty if processing only atmos
-    ancils_path: "data/ancils"
+    # Ancil files are needed only for specific variables when
+    # grid information is not fully available from output
+    # you can usually leave these empty if processing only atmos
+    # ancillary files relative path to <appdir> or fullpath
+    ancils_path: "localdata/ancils"
     grid_ocean: ""
-    mask_ocean: ""
     grid_ice: ""
+    mask_ocean: ""
+    # to supply land area fraction if not available in output
     land_frac: ""
+    # to supply tile area fraction if not available in output
     tile_frac: ""
     history_data: ''
     # DO NOT REMOVE OR ALTER this if you don't know what you're doing :-)

conda/meta.yaml

@@ -1,17 +1,16 @@
 package:
     name: mopper 
-    #version: "{{ environ.get('GIT_DESCRIBE_TAG', '1.0') }}"
+    #version: "{{ environ.get('GIT_DESCRIBE_TAG', '1.1.0') }}"
     version: '1.1.0'
 #source:
-# path: ./
+# path: ../.
 
 source:
-  #url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR/archive/refs/tags/{{version}}.tar.gz
+  #url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR/archive/refs/tags/{{ environ.get('RELEASE_VERSION') }}.tar.gz
   git_url: https://github.com/ACCESS-Hive/ACCESS-MOPPeR.git
-  git_tag: prerelease
+  git_tag: "1.1.0"
   #git_rev: "1.1.0"
   #git_depth: 1 # (Defaults to -1/not shallow)
-  #path: ../.
 
 build:
     number: 1

src/mopper/mop_utils.py

@@ -1110,9 +1110,10 @@ def define_attrs(ctx):
     ctx : click context
         Includes obj dict with 'cmor' settings, exp attributes
     """
-    #var_log = logging.getLogger(ctx.obj['var_log'])
-    attrs = ctx.obj['attrs']
+    var_log = logging.getLogger(ctx.obj['var_log'])
+    attrs = ctx.obj['attrs'].copy()
     notes = attrs.get('notes', '')
+    var_log.debug(f"in define_attrs, notes: {notes}")
     # open file containing notes
     fname = import_files('mopdata').joinpath('notes.yaml')
     data = read_yaml(fname)['notes']
@@ -1125,7 +1126,8 @@ def define_attrs(ctx):
         fval = ctx.obj[field]
         for k,v in data[field].items():
             if k == fval or (k[0] == '~' and k[1:] in fval):
-                notes += v
+                notes += f" {v} "
     if notes != '':
-        attrs['notes'] = notes
+        attrs['notes'] = notes.strip()
+    var_log.debug(f"in define_attrs, attrs: {attrs}")
     return attrs

tests/test_mop_utils.py

@@ -22,7 +22,8 @@
 import logging
 from pathlib import Path
 
-from mopper.mop_utils import (check_timestamp, get_cmorname,)
+from mopper.mop_utils import (check_timestamp, get_cmorname,
+    define_attrs)
 
 
 ctx = click.Context(click.Command('cmd'),
@@ -121,8 +122,25 @@ def test_get_cmorname(caplog):
     assert iname == 'longitude'
     assert jname == 'latitude'
     assert zname == 'plev3'
-    # test generic axis alevel 
     ctx.obj['axes'] = 'longitude latitude alevel time'
     with ctx:
         zname = get_cmorname('theta_model_level_number')
     assert zname == 'hybrid_height'
+
+def test_define_attrs(caplog):
+    global ctx
+    caplog.set_level(logging.DEBUG, logger='varlog_1')
+    ctx.obj['attrs'] = {'notes': "some existing note"}
+    ctx.obj['variable_id'] = "ta"
+    ctx.obj['calculation'] = "... plevinterp(var[0]) "
+    with ctx:
+        out = define_attrs()
+    assert out['notes'] == "some existing note Linearly interpolated from model levels using numpy.interp() function. NaNs are assigned to pressure levels falling out of the height range covered by the model"
+    # repeating to make sure we are not using reference to ctx see issue #190
+    with ctx:
+        out = define_attrs()
+    assert out['notes'] == "some existing note Linearly interpolated from model levels using numpy.interp() function. NaNs are assigned to pressure levels falling out of the height range covered by the model"
+    ctx.obj['attrs'] = {}
+    with ctx:
+        out = define_attrs()
+    assert out['notes'] == "Linearly interpolated from model levels using numpy.interp() function. NaNs are assigned to pressure levels falling out of the height range covered by the model"