MAINT: Deprecate numpy matrix conversion functions

[rossbar]

Adds deprecation warnings + associated tests to to_numpy_matrix and from_numpy_matrix.

Originally, from_numpy_array as simply a pass-through function calling from_numpy_matrix. Re-organized so that from_numpy_matrix is now the pass-through, and the implementation is in from_numpy_array to make the removal easier down the road.

Added tests to ensure the deprecation warnings are raised, and warnings filters to suppress warnings related to to/from_numpy_matrix in the remainder of the test suite.

[jarrodmillman]

Could you a note in both:

• doc/release/release_dev.rst
• doc/developer/deprecations.rst

[jarrodmillman]

@rossbar I merged #4235. Could you rebase on master when you have a chance?

[jarrodmillman]

It looks like you will manually need to redo 0d0ebe0, since it is keeping the reformatted text and black is fine w/ it either way. I prefer the shorter lines here and the reformatting isn't relevant for this PR.

[rossbar]

It looks like you will manually need to redo 0d0ebe0, since it is keeping the reformatted text and black is fine w/ it either way. I prefer the shorter lines here and the reformatting isn't relevant for this PR.

The style from 0d0ebe0 is the one that the current version of black (20.8b1) gives me. I overrode it manually and pushed in df7e11a, but that fails CI (it fails for me locally with the pre-commit checks too).

[pep8speaks]

Hello @rossbar! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file networkx/convert_matrix.py:

Line 540:80: E501 line too long (82 > 79 characters)
Line 541:80: E501 line too long (87 > 79 characters)
Line 648:80: E501 line too long (84 > 79 characters)
Line 653:80: E501 line too long (88 > 79 characters)
Line 1273:80: E501 line too long (87 > 79 characters)
Line 1338:80: E501 line too long (85 > 79 characters)

Comment last updated at 2020-10-07 01:46:40 UTC

[jarrodmillman]

This LGTM. Two final minor suggestions:

1. In convert_matrix.py in the example for from_numpy_matrix we can change

    >>> import numpy as np
    >>> A = np.array([[1, 1], [2, 1]])
    >>> G = nx.from_numpy_array(A)
    >>> G.edges(data=True)
    EdgeDataView([(0, 0, {'weight': 1}), (0, 1, {'weight': 2}), \
(1, 1, {'weight': 1})])

to

    >>> import numpy as np
    >>> A = np.array([[1, 1], [2, 1]])
    >>> G = nx.from_numpy_array(A)
    >>> G.edges(data=True)
    EdgeDataView([(0, 0, {'weight': 1}), (0, 1, {'weight': 2}), (1, 1, {'weight': 1})])

now that we allow 88 characters per line.

2. Also in from_numpy_matrix,

    # This should never fail if you have created a numpy array with numpy...
    import numpy as np

(This was added years ago.) Should we remove those two lines, since np isn't used in the function?

[rossbar]

Yup - good suggestions! I also un-special-cased a line in the dtype-to-pytype dictionary.

[dschult]

This looks good to me. :}