to_numpy_matrix example fails

[spakin]

Description

The example given at https://docs.ocean.dwavesys.com/projects/dimod/en/stable/reference/bqm/generated/dimod.BinaryQuadraticModel.to_numpy_matrix.html fails to run.

Steps To Reproduce

Simply enter the code from the to_numpy_matrix example:

$ python
Python 3.8.3 (default, Jul  2 2020, 16:21:59) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import dimod
>>> import numpy as np
>>> model = dimod.BinaryQuadraticModel({'a': 1, 'b': -1, 'c': .5},
...                                    {('a', 'b'): .5, ('b', 'c'): 1.5},
...                                    1.4,
...                                    dimod.BINARY)
>>> model.to_numpy_matrix(variable_order=['d', 'c', 'b', 'a'])
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/pakin/.anaconda3/lib/python3.8/site-packages/dimod/core/bqm.py", line 1073, in to_numpy_matrix
    raise ValueError("variable_order does not include all variables")
ValueError: variable_order does not include all variables

Expected Behavior

I expected to see

array([[ 0. ,  0. ,  0. ,  0. ],
       [ 0. ,  0.5,  1.5,  0. ],
       [ 0. ,  0. , -1. ,  0.5],
       [ 0. ,  0. ,  0. ,  1. ]])

Environment

• OS: Ubuntu 20.10
• Python version: 3.8.3
• dimod version: 0.9.13

[JoelPasvolsky]

Looks to me that it needs the , 'd': 0 in the model creation line:

>>> model = dimod.BinaryQuadraticModel({'a': 1, 'b': -1, 'c': .5, 'd': 0},
                                               {('a', 'b'): .5, ('b', 'c'): 1.5},
                                               1.4,
                                               dimod.BINARY)
>>> model.to_numpy_matrix(variable_order=['d', 'c', 'b', 'a'])
array([[0, 0.0, 0.0, 0.0],
       [0, 0.5, 1.5, 0.0],
       [0, 0, -1.0, 0.5],
       [0, 0, 0, 1.0]], dtype=object)

Sorry, just noticed that the problem is that it is not adding the d by itself, once it is specified in the order, as should be expected.

[spakin]

Sorry, just noticed that the problem is that it is not adding the d by itself, once it is specified in the order, as should be expected.

Right. If you remove the d from variable_order or add it, as you did, to the model, the example works. However, the documentation claims that the d should be added automatically:

This example converts a binary quadratic model to NumPy array format while ordering variables and adding one (‘d’).