small updates

_episodes/09-cmorization.md

@@ -147,38 +147,44 @@ name that was created to store the raw observation data files, i.e.
 If everything is okay, the output should look something like this:
 
 ~~~
-...
-... Starting the CMORization Tool at time: 2022-07-26 14:02:16 UTC
+... Writing program log files to:
+/scratch/b/b309059/esmvaltool_output/data_formatting_20240527_132448/run/main_log.txt
+/scratch/b/b309059/esmvaltool_output/data_formatting_20240527_132448/run/main_log_debug.txt
+... Starting the CMORization Tool at time: 2024-05-27 13:24:48 UTC
 ... ----------------------------------------------------------------------
-... input_dir  = /home/peter/data/RAWOBS
-... output_dir = /home/peter/esmvaltool_output/data_formatting_20220726_140216
+... input_dir  = /work/bd0854/DATA/ESMValTool2/RAWOBS
+... output_dir = /scratch/b/b309059/esmvaltool_output/data_formatting_20240527_132448
 ... ----------------------------------------------------------------------
 ... Running the CMORization scripts.
 ... Processing datasets ['FLUXCOM']
-... Input data from: /home/peter/data/RAWOBS/Tier3/FLUXCOM
-... Output will be written to: /home/peter/esmvaltool_output/
-      data_formatting_20220726_140216/Tier3/FLUXCOM
-... Reformat script: /home/peter/mambaforge/envs/esmvaltool/lib/python3.9/
-      site-packages/esmvaltool/cmorizers/data/formatters/datasets/fluxcom
-... CMORizing dataset FLUXCOM using Python script /home/peter/mambaforge/envs/
-      esmvaltool/lib/python3.9/site-packages/esmvaltool/cmorizers/data/formatters/
-      datasets/fluxcom.py
-... Found input file '/home/peter/data/RAWOBS/Tier3/FLUXCOM/GPP.ANN.CRUNCEPv6.monthly.*.nc'
+... Input data from: /work/bd0854/DATA/ESMValTool2/RAWOBS/Tier3/FLUXCOM
+... Output will be written to: /scratch/b/b309059/esmvaltool_output/data_formatting_20240527_132448/Tier3/FLUXCOM
+... Reformat script: /home/b/b309059/ESMValTool/ESMValTool/esmvaltool/cmorizers/data/formatters/datasets/fluxcom
+... CMORizing dataset FLUXCOM using Python script /home/b/b309059/ESMValTool/ESMValTool/esmvaltool/cmorizers/data/formatters/datasets/fluxcom.py
+... Found input file '/work/bd0854/DATA/ESMValTool2/RAWOBS/Tier3/FLUXCOM/GPP.ANN.CRUNCEPv6.monthly.*.nc'
 ... CMORizing variable 'gpp'
 ... Lmon
 ... Var is gpp
-... ... UserWarning: Ignoring netCDF variable 'GPP' invalid units 'gC m-2 day-1'
+...  WARNING /work/bd0854/b309059/utils/mambaforge/envs/esmvaltool/lib/python3.11/site-packages/iris/fileformats/_nc_load_rules/helpers.py:913: _WarnComboIgnoringCfLoad: Ignoring invalid u
+nits 'gC m-2 day-1' on netCDF variable 'GPP'.
+  warnings.warn(
 
 ... Fixing time...
 ... Fixing latitude...
 ... Fixing longitude...
 ... Flipping dimensional coordinate latitude...
 ... Saving file
-... Saving: /home/peter/esmvaltool_output/data_formatting_20220726_140216/Tier3/
-      FLUXCOM/OBS_FLUXCOM_reanaly_ANN-v1_Lmon_gpp_200001-200012.nc
+... Saving: /scratch/b/b309059/esmvaltool_output/data_formatting_20240527_132448/Tier3/FLUXCOM/OBS_FLUXCOM_reanaly_ANN-v1_Lmon_gpp_198001-198012.nc
 ... Cube has lazy data [lazy is preferred]
+... WARNING /work/bd0854/b309059/utils/mambaforge/envs/esmvaltool/lib/python3.11/site-packages/iris/fileformats/netcdf/saver.py:2670: IrisDeprecation: Saving to netcdf with legacy-style a
+ttribute handling for backwards compatibility.
+This mode is deprecated since Iris 3.8, and will eventually be removed.
+Please consider enabling the new split-attributes handling mode, by setting 'iris.FUTURE.save_split_attrs = True'.
+  warn_deprecated(message)
+
 ... CMORization of dataset FLUXCOM finished!
 ... Formatting successful for dataset FLUXCOM
+
 ~~~
 {: .output}
 
@@ -629,17 +635,23 @@ If we now run the test recipe on our newly 'CMORized' data,
 esmvaltool run recipe_check_fluxcom.yml --config_file <path to config-user.yml> --log_level debug
 ```
 
-it should be able to find the correct file, but it does not succeed yet. The first
-thing that the ESMValTool CMOR checker brings up is:
+it should be able to find the correct file, but it does not succeed yet. The ESMValTool CMOR checker
+brings up is:
 
 ~~~
-iris.exceptions.UnitConversionError: Cannot convert from unknown units. The
-"units" attribute may be set directly.
+esmvalcore.cmor.check.CMORCheckError: There were errors in variable GPP:
+ GPP: units should be kg m-2 s-1, not unknown
+ lon: standard_name should be longitude, not None
+ lat: standard_name should be latitude, not None
+ lon: units should be degrees_east, not unknown
+ lon: has values < valid_min = 0.0
+ lat: units should be degrees_north, not unknown
+ GPP: does not match coordinate rank
 ~~~
 {: .error}
 
-If you look closely at the error messages, you can see that this error concerns
-the units of the coordinates. ESMValTool tries to fix them automatically,
+If you look closely at the error messages, you can see that these error concern
+e.g. the units of the coordinates. ESMValTool tries to fix them automatically,
 but since no units are defined on the coordinates, this fails.
 
 The cmorizer utilities also include a function called `fix_coords`, but before
@@ -696,7 +708,7 @@ The next error is:
 
 ~~~
 esmvalcore.cmor.check.CMORCheckError: There were errors in variable GPP:
-Variable GPP units unknown can not be converted to kg m-2 s-1 in cube:
+ GPP: units should be kg m-2 s-1, not unknown
 ~~~
 {: .error}