Merge pull request #61 from rcaneill/issue11

add standard names and units when possible in domcfg

README.md

@@ -75,9 +75,10 @@ the latest version of the code, and publish them to `example` when commiting to
 
 ## What's new
 
-### not released yet
+### v0.4.2 (2023-08-07)
 * Allow additional dimension names occurring when variables on inner grid are diagnosed, e.g. `x_grid_U_inner` or `x_grid_U`.
 * Add coordinates into the DataArrays
+* Add some standard names and units in domcfg
 
 ### v0.4.1 (2023-03-29)
 * Allow to open files if time bounds are missing

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "xnemogcm"
-version = "0.4.1"
+version = "0.4.2"
 description = "Interface to open NEMO global circulation model output dataset and create a xgcm grid."
 license = "MIT"
 homepage = "https://github.com/rcaneill/xnemogcm"

xnemogcm/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.4.1"
+__version__ = "0.4.2"
 
 from .domcfg import open_domain_cfg
 from .nemo import open_nemo, process_nemo

xnemogcm/domcfg.py

@@ -6,6 +6,34 @@
 from .tools import get_domcfg_points, _dir_or_files_to_files
 
 
+def _add_cf(domcfg):
+    """
+    Add cf standard_name and units when possible
+    """
+    for i in domcfg.variables:
+        if "glam" in i:
+            domcfg[i].attrs.update(
+                {"standard_name": "longitude", "units": "degrees_east"}
+            )
+        if "gphi" in i:
+            domcfg[i].attrs.update(
+                {"standard_name": "latitude", "units": "degrees_north"}
+            )
+        if "gdep" in i:
+            domcfg[i].attrs.update(
+                {"standard_name": "depth", "units": "m", "positive": "down"}
+            )
+        if "e1" in i or "e2" in i:
+            domcfg[i].attrs.update({"units": "m"})
+        if "e3" in i:
+            domcfg[i].attrs.update({"standard_name": "cell_thickness", "units": "m"})
+        if i in ["ff", "ff_f", "ff_t"]:
+            domcfg[i].attrs.update(
+                {"standard_name": "coriolis_parameter", "units": "s-1"}
+            )
+    return domcfg
+
+
 def domcfg_preprocess(ds):
     """
     Preprocess domcfg / meshmask files when needed to be recombined (= 1 file per processor)
@@ -197,4 +225,8 @@ def open_domain_cfg(datadir=None, files=None, add_coordinates=True):
     # adding variables as coordinates
     if add_coordinates:
         domcfg = _add_coordinates(domcfg)
+    # Remove nav_lon and nav_lat
+    domcfg = domcfg.drop_vars(["nav_lon", "nav_lat"], errors="ignore")
+    # Add cf
+    domcfg = _add_cf(domcfg)
     return domcfg

xnemogcm/test/test_domcfg.py

@@ -100,3 +100,24 @@ def test_compare_domcfg_mesh_mask(data_path):
     domcfg_1 = open_domain_cfg(datadir=(data_path / "mesh_mask_1_file"))
     domcfg_multi = open_domain_cfg(datadir=(data_path / "mesh_mask_multi_files"))
     assert (domcfg_1 == domcfg_multi).all()
+
+
+def test_coordinates_horizontal(data_path):
+    """Test that coordinates are added to nemo files"""
+    domcfg = open_domain_cfg(
+        datadir=data_path / "mesh_mask_1_file",
+    )
+    assert "glamt" in domcfg.e1t.coords
+    if "ff_f" in domcfg:
+        assert "glamf" in domcfg.ff_f.coords
+    else:
+        # NEMO 3.6
+        assert "glamf" in domcfg.ff.coords
+
+
+def test_attributes(data_path):
+    """Test that coordinates are added to nemo files"""
+    domcfg = open_domain_cfg(
+        datadir=data_path / "mesh_mask_1_file",
+    )
+    assert domcfg.glamt.attrs.get("standard_name") == "longitude"

xnemogcm/test/test_nemo.py

@@ -149,7 +149,7 @@ def test_use_preprocess(data_path):
 
 
 def test_coordinates_horizontal(data_path):
-    """Test opening of nemo files"""
+    """Test that coordinates are added to nemo files"""
     domcfg = open_domain_cfg(
         datadir=data_path / "mesh_mask_1_file",
     )
@@ -162,7 +162,7 @@ def test_coordinates_horizontal(data_path):
 
 
 def test_coordinates_vertical(data_path, request):
-    """Test opening of nemo files"""
+    """Test that coordinates are added to nemo files"""
     if request.node.callspec.id == "3.6":
         pytest.xfail(
             "Failing for nemo <= 3.6 as gdept_0 and gdepw_0 are not in mesh mask"