Fix concat bug when concatenating unlabeled dimensions.

doc/whats-new.rst

@@ -27,6 +27,8 @@ Bug fixes
 - Line plots with the ``x`` or ``y`` argument set to a 1D non-dimensional coord
   now plot the correct data for 2D DataArrays.
   (:issue:`3334`). By `Tom Nicholas <http://github.com/TomNicholas>`_.
+- Fix error in concatenating unlabeled dimensions (:pull:`3362`).
+  By `Deepak Cherian <https://github.com/dcherian/>`_.
 
 Documentation
 ~~~~~~~~~~~~~

xarray/core/concat.py

@@ -177,8 +177,6 @@ def _calc_concat_over(datasets, dim, dim_names, data_vars, coords, compat):
             if dim not in ds.dims:
                 if dim in ds:
                     ds = ds.set_coords(dim)
-                else:
-                    raise ValueError("%r is not present in all datasets" % dim)
         concat_over.update(k for k, v in ds.variables.items() if dim in v.dims)
         concat_dim_lengths.append(ds.dims.get(dim, 1))
 
@@ -362,12 +360,21 @@ def ensure_common_dims(vars):
     # n.b. this loop preserves variable order, needed for groupby.
     for k in datasets[0].variables:
         if k in concat_over:
-            vars = ensure_common_dims([ds.variables[k] for ds in datasets])
+            try:
+                vars = ensure_common_dims([ds.variables[k] for ds in datasets])
+            except KeyError:
+                raise ValueError("%r is not present in all datasets." % k)
             combined = concat_vars(vars, dim, positions)
             assert isinstance(combined, Variable)
             result_vars[k] = combined
 
     result = Dataset(result_vars, attrs=result_attrs)
+    absent_coord_names = coord_names - set(result.variables)
+    if absent_coord_names:
+        raise ValueError(
+            "Variables %r are coordinates in some datasets but not others."
+            % absent_coord_names
+        )
     result = result.set_coords(coord_names)
     result.encoding = result_encoding
 

xarray/tests/test_concat.py

@@ -41,8 +41,10 @@ def test_concat_compat():
     for var in ["has_x", "no_x_y"]:
         assert "y" not in result[var]
 
+    with raises_regex(ValueError, "coordinates in some datasets but not others"):
+        concat([ds1, ds2], dim="q")
     with raises_regex(ValueError, "'q' is not present in all datasets"):
-        concat([ds1, ds2], dim="q", data_vars="all", compat="broadcast_equals")
+        concat([ds2, ds1], dim="q")
 
 
 class TestConcatDataset:
@@ -89,7 +91,11 @@ def test_concat_coords_kwarg(self, data, dim, coords):
             assert_equal(data["extra"], actual["extra"])
 
     def test_concat(self, data):
-        split_data = [data.isel(dim1=slice(3)), data.isel(dim1=slice(3, None))]
+        split_data = [
+            data.isel(dim1=slice(3)),
+            data.isel(dim1=3),
+            data.isel(dim1=slice(4, None)),
+        ]
         assert_identical(data, concat(split_data, "dim1"))
 
     def test_concat_dim_precedence(self, data):