Should Dataset constructor align DataArrays based on coords?

We have a DataArray unaligned to coords here:

In [12]:

coords={'a': range(4), 'b': range(3)}
da = xray.DataArray(np.random.rand(4,3), coords=coords)
da
Out[12]:
<xray.DataArray (a: 4, b: 3)>
array([[ 0.05126985,  0.95460352,  0.12853847],
       [ 0.20577943,  0.80265117,  0.46370886],
       [ 0.0226791 ,  0.33068145,  0.55748573],
       [ 0.15943175,  0.20183347,  0.46907727]])
Coordinates:
  * a        (a) int64 0 1 2 3
  * b        (b) int64 0 1 2
In [13]:

da_reindex = da.reindex(b=[1,2,0])
da_reindex
Out[13]:
<xray.DataArray (a: 4, b: 3)>
array([[ 0.95460352,  0.12853847,  0.05126985],
       [ 0.80265117,  0.46370886,  0.20577943],
       [ 0.33068145,  0.55748573,  0.0226791 ],
       [ 0.20183347,  0.46907727,  0.15943175]])
Coordinates:
  * a        (a) int64 0 1 2 3
  * b        (b) int64 1 2 0

If we add this to Dataset and supply coords=coords, it raises, since there are conflicting coords:

In [16]:

:
ds = xray.Dataset(variables={'da':da_reindex}, coords=coords)
ds
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-16-8e4afa10f781> in <module>()
----> 1 ds = xray.Dataset(variables={'da':da_reindex}, coords=coords)
      2 ds

/usr/local/lib/python2.7/dist-packages/xray/core/dataset.pyc in __init__(self, variables, coords, attrs, compat)
    317             coords = set()
    318         if variables or coords:
--> 319             self._set_init_vars_and_dims(variables, coords, compat)
    320         if attrs is not None:
    321             self.attrs = attrs

/usr/local/lib/python2.7/dist-packages/xray/core/dataset.pyc in _set_init_vars_and_dims(self, vars, coords, compat)
    371         aligned = _align_variables(variables)
    372         new_variables, new_coord_names = _expand_variables(aligned,
--> 373                                                            compat=compat)
    374 
    375         new_coord_names.update(coords)

/usr/local/lib/python2.7/dist-packages/xray/core/dataset.pyc in _expand_variables(raw_variables, old_variables, compat)
    142                     add_variable(dim, coord.variable)
    143             var = var.variable
--> 144         add_variable(name, var)
    145 
    146     return new_variables, new_coord_names

/usr/local/lib/python2.7/dist-packages/xray/core/dataset.pyc in add_variable(name, var)
    130                 raise ValueError('conflicting value for variable %s:\n'
    131                                  'first value: %r\nsecond value: %r'
--> 132                                  % (name, variables[name], var))
    133             if compat == 'broadcast_equals':
    134                 maybe_promote_or_replace(name, var)

ValueError: conflicting value for variable b:
first value: <xray.Coordinate 'b' (b: 3)>
array([1, 2, 0])
second value: <xray.Coordinate 'b' (b: 3)>
array([0, 1, 2])

But adding with __setitem__ aligns as expected:

In [17]:

ds
ds = xray.Dataset(coords=coords)
ds['da']=da_reindex
ds
Out[17]:
<xray.Dataset>
Dimensions:  (a: 4, b: 3)
Coordinates:
  * a        (a) int64 0 1 2 3
  * b        (b) int64 0 1 2
Data variables:
    da       (a, b) float64 0.05127 0.9546 0.1285 0.2058 0.8027 0.4637 ...

Is this desired behavior? I could imagine aligning to coords if they are explicitly supplied, but I don’t know the nuances here.

[max-sixty]

I’d be up for implementing this, if people agree. Let me know…

[shoyer]

Yes. I think we have some existing internal machinery for this in align (see indexes). Indexes that are explicitly provided in coords (e.g., coords={'time': time_values}) should take precedence. Indexes that are incidentally included on another coordinate should not (e.g., coords={'day_of_week': DataArray(values, coords=[('time', time_values)])}).