Align ocean CMOR output with published reference (vertices, time_bnds, lev axis)

[rhaegar325]

Overview

Four small write-time fixes in Ocean_CMORiser.update_attributes bring the CMORised ocean
output in line with the published CMIP6 reference file and clear the corresponding CF / WCRP
compliance-checker findings. Verified by re-running the WCRP cf:1.7 + wcrp_cmip6:1.0
checker on both the produced file and the published reference.

Scope: only the findings that the compliance-checker actually reports are addressed.
Differences from the reference that the checker does not flag (missing lev_bnds,
vertices_* fill values, the rest of the lev metadata) are intentionally left untouched.

Changes — src/access_moppy/ocean.py

All in Ocean_CMORiser.update_attributes.

1. vertices_latitude / vertices_longitude — drop standard_name

# before
self.ds["vertices_latitude"].attrs.update(
    {"standard_name": "latitude", "units": "degrees_north"}
)
self.ds["vertices_longitude"].attrs.update(
    {"standard_name": "longitude", "units": "degrees_east"}
)
# after — keep only units (CF §7.1; matches the published reference)
self.ds["vertices_latitude"].attrs.update({"units": "degrees_north"})
self.ds["vertices_longitude"].attrs.update({"units": "degrees_east"})

2–4. Three guarded blocks added after the existing bnds drop

# Keep `vertices` as a pure dimension (no int64 coordinate variable).
if "vertices" in self.ds.coords:
    self.ds = self.ds.drop_vars("vertices")

# Bounds variables inherit units/calendar from their parent (CF §7.1).
if "time_bnds" in self.ds:
    self.ds["time_bnds"].attrs = {}

# The vertical coordinate needs a CF axis attribute (WCRP ATTR001).
if "lev" in self.ds.coords:
    self.ds["lev"].attrs["axis"] = "Z"

Findings cleared

Change	Compliance finding cleared
drop standard_name from vertices_*	CF §7.1 (standard_name on bounds)
drop vertices coordinate	CF §2.2 (vertices int64) + CF §3.3 (no name)
empty time_bnds attrs	CF §7.1 (time_bnds units/calendar/long_name)
set lev:axis = 'Z'	WCRP [ATTR001] (lev missing axis)

Verification

End-to-end on real ESM1-5 ocean output (Oyr.no3):

vertices in coords : False   (pure dimension)
time_bnds.attrs    : {}
vertices_latitude  : {'units': 'degrees_north'}
lev.attrs['axis']  : 'Z'

Compliance-checker, produced file vs published reference:

• The four targeted findings (vertices int64, time_bnds attrs, lev:axis) are gone.
• The residual vertices_* findings (“should define standard_name…”, CF §7.1 units) are
  also present on the official published file — checker over-strictness that applies to
  the gold-standard CMIP6 file too, so it cannot be cleared without diverging from the
  reference. The produced file is in fact slightly cleaner: its vertices_* §7.1 list is
  ['units'] vs the published ['units', 'missing_value', '_FillValue'].

Tests — tests/unit/test_ocean.py

Added to TestUpdateAttributes (all 4 new lines of executable code are covered):

• test_vertices_is_pure_dimension_not_coordinate
• test_time_bnds_has_no_attributes
• test_vertices_bounds_have_no_standard_name
• test_lev_gets_cf_axis

tests/unit/test_ocean.py: 47 passed.

[codecov]

Codecov Report

❌ Patch coverage is 96.77419% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.2%. Comparing base (7142b03) to head (b8612e1).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/access_moppy/ocean.py	87.5%	0 Missing and 1 partial ⚠️
src/access_moppy/utilities.py	97.2%	0 Missing and 1 partial ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##            main    #465     +/-   ##
=======================================
+ Coverage   76.9%   77.2%   +0.3%     
=======================================
  Files         31      31             
  Lines       5974    6030     +56     
  Branches    1107    1122     +15     
=======================================
+ Hits        4594    4653     +59     
+ Misses      1131    1126      -5     
- Partials     249     251      +2     

Flag	Coverage Δ
unit	77.2% <96.8%> (+0.3%)	⬆️

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