Providing a fill value in merge() leads to a MergeError

[Ockenfuss]

Dear xarray community,

I tried to set the fill_value argument in xarray.merge(), see the minimal example below. The first merge() call works as I would expect it, the second call throws a MergeError for me (xarray Version 0.18.2): "conflicting values for variable 'var1' on objects to be combined. ...".

Is this intended behaviour? I expected fill_value to be a value which is inserted in case the merge creates missing values in the new DataArray/Dataset. Providing it, especially in a case where no voids are created, should not affect the result. Please correct me if I understand something wrong!

import xarray as xr
da=xr.DataArray([1,2],dims=("x"), coords={"x":[1,2]})
da.name="var1"
db=xr.DataArray([3],dims=("x"), coords={"x":[3]})
db.name="var1"
test1=xr.merge([da, db])#Succeeds as expected
test2=xr.merge([da, db], fill_value=0.0)#Throws a MergeError

Thank you!

[keewis]

Internally, merge will first align both objects and then "join" variables with the same name together using the method specified by compat. For the first call, that will be:

a: <xarray.Variable (x: 3)>
array([ 1.,  2., nan])
b: <xarray.Variable (x: 3)>
array([nan, nan,  3.])

while interpreting nan as missing. However, with the fill value, this becomes:

a: <xarray.Variable (x: 3)>
array([1., 2., 0.])
b: <xarray.Variable (x: 3)>
array([0., 0., 3.])

with this, the default compat method ("no_conflicts") will detect conflicting values for both arrays and thus raise.

You can get the second call to work by specifying a different compat method, e.g. "override", or by using a different function to combine, e.g. combine_by_coords or concat.

[TomNicholas]

I think perhaps the docstring should be clarified then - all it says on this is Value to use for newly missing values., which doesn't really explain that it will fill values before checking for compatibility.

[Ockenfuss]

Thank you @keewis , this clarifies what is happening! But I agree with @TomNicholas that this behavious is hard to explain from the docstring, at least for me as an enduser of xarray.