Prerelease for v1.1.1

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 
@@ -186,4 +189,4 @@ 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 v1.1.0 https://doi.org/10.5281/zenodo.13841181"
+    comment: "post-processed using ACCESS-MOPPeR v1.1.1 https://doi.org/10.5281/zenodo.14010850"

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     # use this only if current package version is obsolete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 :-)
@@ -175,4 +180,4 @@ 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 v1.1.0 https://doi.org/10.5281/zenodo.13841181"
+    comment: "post-processed using ACCESS-MOPPeR v1.1.1 https://doi.org/10.5281/zenodo.14010850"

README.md

@@ -1,6 +1,6 @@
 # [ACCESS Model Output Post-Processor (MOPPeR)](https://access-mopper.readthedocs.io/en/latest)
 [![Read the docs](https://readthedocs.org/projects/access-mopper/badge/?version=latest)](https://access-mopper.readthedocs.io/en/latest/)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13841181.svg)](https://doi.org/10.5281/zenodo.13841181)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14010850.svg)](https://doi.org/10.5281/zenodo.14010850)
 
 This code is derived from the [APP4](https://doi.org/10.5281/zenodo.7703469), initially created by Peter Uhe for CMIP5, and further developed for CMIP6-era by Chloe Mackallah from CSIRO, O&A Aspendale.
 
@@ -11,8 +11,6 @@ It used [CMOR3](https://cmor.llnl.gov/) and files created with the [CMIP6 data r
 
 CMOR uses Controlled Vocabularies as metadata constraints, with [CMIP6_CV.json](https://cmor.llnl.gov/mydoc_cmor3_CV/) being the main one. This has an effect on how the data is written in the files, variables' names, directory structure, filenames, and global attributes. The APP4 also relied on mapping files to match the raw model output to CMOR defined variables. To make this approach more flexible we introduced a new tool `mopdb` that helps the users create their own mapping and handling CMOR tables definitions.
 
-Designed for use on ACCESS model output that has been archived using the [ACCESS Archiver tool](https://github.com/ACCESS-Hive/ACCESS-Archiver).
-
 Although we retained a differentiation between `custom` and `cmip` mode the main workflow is the same and `mode` is now only another field in the main  configuration file.
 
 See [MOPPeR ReadtheDocs](https://access-mopper.readthedocs.io/en/stable/) for the full documentation.

conda/meta.yaml

@@ -1,14 +1,14 @@
 package:
     name: mopper 
-    #version: "{{ environ.get('GIT_DESCRIBE_TAG', '1.1.0') }}"
-    version: '1.1.0'
+    #version: "{{ environ.get('GIT_DESCRIBE_TAG', '1.0') }}"
+    version: '1.1.1'
 #source:
 # path: ../.
 
 source:
   #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: "1.1.0"
+  git_tag: "1.1.1"
   #git_rev: "1.1.0"
   #git_depth: 1 # (Defaults to -1/not shallow)
 

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"