This PR adds support for nemo 5.0 (#127)

* add data, rm e3t_0 as not always present * no real need to test for this metric * better test for depth * update new vertical dimensions * no need to use keys, removes a xarray future warning --------- Co-authored-by: Romain <romain.caneill@zaclys.net>
rcaneill · Jan 15, 2025 · 3de4680 · 3de4680
1 parent 993f627
commit 3de4680
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Showing 52 changed files with 65 additions and 9 deletions.
diff --git a/xnemogcm/nemo.py b/xnemogcm/nemo.py
@@ -42,6 +42,14 @@ def _get_point_type(filename, description):
     return point_type
 
 
+def _is_depth_dim(i, attrs):
+    if "depth" == i[:5]:
+        return True
+    if "long_name" not in attrs.keys():
+        return False
+    return attrs["long_name"][:8] == "Vertical" and attrs["long_name"][-6:] == "levels"
+
+
 def nemo_preprocess(ds, domcfg, point_type=None):
     """
     Preprocess function for the nemo files.
@@ -73,17 +81,23 @@ def nemo_preprocess(ds, domcfg, point_type=None):
         )
 
     point = akp.Point(point_type)
-    # get the name of the depth variable e.g. deptht, depthu, etc
-    try:
-        z_nme = [i for i in ds.dims if "depth" in i][0]
-    except IndexError:
+
+    # the depth variable name can be either deptht, depthu, etc
+    # or grid_T_3D_inner, etc
+    all_z_nme = [i for i in ds.dims if _is_depth_dim(i, ds[i].attrs)]
+    if len(all_z_nme) >= 1:
+        z_nme = all_z_nme[0]
+        ds = ds.swap_dims({i: "depth_tmp_xnemogcm" for i in all_z_nme}).swap_dims(
+            {"depth_tmp_xnemogcm": z_nme}
+        )
+    else:
         # This means that there is no depth dependence of the data (surface data)
         z_nme = None
 
     # get the name of the dimension along i e.g. x, x_grid_U, x_grid_U_inner etc
-    x_nme = [i for i in ds.dims.keys() if "x_grid" in i or i == "x"]
+    x_nme = [i for i in ds.dims if "x_grid" in i or i == "x"]
     # get the name of the dimension along j e.g. y, y_grid_U, y_grid_U_inner etc
-    y_nme = [i for i in ds.dims.keys() if "y_grid" in i or i == "y"]
+    y_nme = [i for i in ds.dims if "y_grid" in i or i == "y"]
 
     for x in x_nme:
         to_rename.update({x: point.x})

diff --git a/xnemogcm/test/conftest.py b/xnemogcm/test/conftest.py
@@ -5,7 +5,7 @@
 TEST_PATH = Path(os.path.dirname(os.path.abspath(__file__)))
 DATA_PATH = TEST_PATH / "data"
 
-nemo_versions = ["3.6", "4.0", "4.2.0"]
+nemo_versions = ["3.6", "4.0", "4.2.0", "5.0"]
 
 
 def pytest_generate_tests(metafunc):

diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0000.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0000.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/domain_cfg_out_0000.nc
diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0001.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0001.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/domain_cfg_out_0001.nc
diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0002.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0002.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/domain_cfg_out_0002.nc
diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0003.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/domain_cfg_out_0003.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/domain_cfg_out_0003.nc
diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0000.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0000.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0000.nc
diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0001.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0001.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0001.nc
diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0002.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0002.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0002.nc
diff --git a/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0003.nc b/xnemogcm/test/data/5.0/domcfg_mesh_mask/mesh_mask_0003.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0003.nc
diff --git a/xnemogcm/test/data/5.0/mesh_mask_1_file/mesh_mask.nc b/xnemogcm/test/data/5.0/mesh_mask_1_file/mesh_mask.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/mesh_mask.nc
diff --git a/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0000.nc b/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0000.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0000.nc
diff --git a/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0001.nc b/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0001.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0001.nc
diff --git a/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0002.nc b/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0002.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0002.nc
diff --git a/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0003.nc b/xnemogcm/test/data/5.0/mesh_mask_multi_files/mesh_mask_0003.nc
@@ -0,0 +1 @@
+../runs/EXP_4_proc/mesh_mask_0003.nc
diff --git a/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_T.nc b/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_T.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_U.nc b/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_U.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_U.nc
diff --git a/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_V.nc b/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_V.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_V.nc
diff --git a/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_W.nc b/xnemogcm/test/data/5.0/nemo/GYRE_1y_00010101_00011230_grid_W.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_W.nc
diff --git a/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/T.nc b/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/T.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/U.nc b/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/U.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_U.nc
diff --git a/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/V.nc b/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/V.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_V.nc
diff --git a/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/W.nc b/xnemogcm/test/data/5.0/nemo_no_grid_in_filename/W.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_W.nc
diff --git a/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_T.nc b/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_T.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_U.nc b/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_U.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_U.nc
diff --git a/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_V.nc b/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_V.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_V.nc
diff --git a/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_W.nc b/xnemogcm/test/data/5.0/open_and_merge/GYRE_1y_00010101_00011230_grid_W.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_W.nc
diff --git a/xnemogcm/test/data/5.0/open_and_merge/mesh_mask.nc b/xnemogcm/test/data/5.0/open_and_merge/mesh_mask.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/mesh_mask.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_T.nc b/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_U.nc b/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_U.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_V.nc b/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_V.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_W.nc b/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_W.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_surface_grid_T.nc b/xnemogcm/test/data/5.0/runs/EXP_1_proc/GYRE_1y_00010101_00011230_surface_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_1_proc/domain_cfg_out.nc b/xnemogcm/test/data/5.0/runs/EXP_1_proc/domain_cfg_out.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_1_proc/mesh_mask.nc b/xnemogcm/test/data/5.0/runs/EXP_1_proc/mesh_mask.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_T.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_U.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_U.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_V.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_V.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_W.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_grid_W.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_surface_grid_T.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/GYRE_1y_00010101_00011230_surface_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0000.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0000.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0001.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0001.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0002.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0002.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0003.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/domain_cfg_out_0003.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0000.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0000.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0001.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0001.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0002.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0002.nc
diff --git a/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0003.nc b/xnemogcm/test/data/5.0/runs/EXP_4_proc/mesh_mask_0003.nc
diff --git a/xnemogcm/test/data/5.0/surface_fields/GYRE_1y_00010101_00011230_grid_T.nc b/xnemogcm/test/data/5.0/surface_fields/GYRE_1y_00010101_00011230_grid_T.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_T.nc
diff --git a/xnemogcm/test/data/5.0/surface_fields/GYRE_1y_00010101_00011230_surface_grid_T.nc b/xnemogcm/test/data/5.0/surface_fields/GYRE_1y_00010101_00011230_surface_grid_T.nc
@@ -0,0 +1 @@
+../runs/EXP_1_proc/GYRE_1y_00010101_00011230_surface_grid_T.nc
diff --git a/xnemogcm/test/test_merge.py b/xnemogcm/test/test_merge.py
@@ -19,8 +19,6 @@ def test_merge_non_linear_free_surface(data_path, request):
     nemo_ds = open_nemo(**nemo_kwargs)
     ds = _merge_nemo_and_domain_cfg(nemo_ds, domcfg, linear_free_surface=False)
     assert "e3t" in ds
-    if request.node.callspec.id != "3.6":
-        assert "e3t_0" in ds
     assert "t" in ds.e3t.coords
     assert "e3f" not in ds
     ds2 = open_nemo_and_domain_cfg(

diff --git a/xnemogcm/test/test_nemo.py b/xnemogcm/test/test_nemo.py
@@ -181,6 +181,10 @@ def test_coordinates_vertical(data_path, request):
         pytest.xfail(
             "Failing for nemo <= 3.6 as gdept_0 and gdepw_0 are not in mesh mask"
         )
+    if request.node.callspec.id == "5.0":
+        pytest.xfail(
+            "Failing for nemo <= 5.0 as gdept_0 and gdepw_0 are not in mesh mask"
+        )
     domcfg = open_domain_cfg(
         datadir=data_path / "mesh_mask_1_file",
     )
@@ -189,3 +193,15 @@ def test_coordinates_vertical(data_path, request):
         domcfg=domcfg,
     )
     assert "gdept_0" in nemo_ds.toce.coords
+
+
+def test_coordinates_vertical_1d(data_path, request):
+    """Test that coordinates are added to nemo files"""
+    domcfg = open_domain_cfg(
+        datadir=data_path / "mesh_mask_1_file",
+    )
+    nemo_ds = open_nemo(
+        datadir=data_path / "nemo",
+        domcfg=domcfg,
+    )
+    assert "gdept_1d" in nemo_ds.toce.coords
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		../runs/EXP_1_proc/GYRE_1y_00010101_00011230_grid_T.nc