Skip to content

Conversation

@drammock
Copy link
Member

@drammock drammock commented Feb 14, 2020

This PR adds a proper deprecation cycle to the API changes in #7206

It also restores parameter order to more closely match what it used to be, to minimize downstream code breakage with positional argument passing.

@drammock drammock changed the title properly deprecate changes in to_data_frame API: properly deprecate changes in to_data_frame Feb 14, 2020
Copy link
Member

@larsoner larsoner left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM +1 for merge

@codecov
Copy link

codecov bot commented Feb 15, 2020

Codecov Report

❗ No coverage uploaded for pull request base (master@9f3b76f). Click here to learn what that means.
The diff coverage is 100%.

@@            Coverage Diff            @@
##             master    #7326   +/-   ##
=========================================
  Coverage          ?   89.88%           
=========================================
  Files             ?      450           
  Lines             ?    81251           
  Branches          ?    12915           
=========================================
  Hits              ?    73033           
  Misses            ?     5396           
  Partials          ?     2822

@drammock
Copy link
Member Author

Travis failures are unrelated:

Xdawn:

       3 failed
         - mne/inverse_sparse/tests/test_mxne_inverse.py:34 test_mxne_inverse_standard
         - mne/preprocessing/tests/test_xdawn.py:63 test_xdawn_fit
         - mne/utils/tests/test_numerics.py:239 test_reg_pinv
mne/preprocessing/xdawn.py:189: in _fit_xdawn

    evals, evecs = linalg.eigh(evo_cov, signal_cov)

../../../virtualenv/python3.7.1/lib/python3.7/site-packages/scipy/linalg/decomp.py:491: in eigh

    " computed." % (info-b1.shape[0]))

E   numpy.linalg.LinAlgError: the leading minor of order 8 of 'b' is not positive definite. The factorization of 'b' could not be completed and no eigenvalues or eigenvectors were computed.

Numerics:

mne/utils/tests/test_numerics.py:270: in test_reg_pinv

    assert_array_equal(a_inv_np, a_inv_mne)

E   AssertionError: 

E   Arrays are not equal

E   

E   Mismatched elements: 1 / 9 (11.1%)

E   Max absolute difference: 2.77555756e-17

E   Max relative difference: 2.22044605e-16

E    x: array([[ 0.375   ,  0.      , -0.125   ],

E          [ 0.      ,  0.333333,  0.      ],

E          [-0.125   ,  0.      ,  0.375   ]])

E    y: array([[ 0.375   ,  0.      , -0.125   ],

E          [ 0.      ,  0.333333,  0.      ],

E          [-0.125   ,  0.      ,  0.375   ]])

MXNE:

mne/inverse_sparse/tests/test_mxne_inverse.py:154: in test_mxne_inverse_standard

    pick_ori='vector')

</home/travis/build/mne-tools/mne-python/mne/externals/decorator.py:decorator-gen-436>:2: in tf_mixed_norm

    ???

mne/utils/_logging.py:90: in wrapper

    return function(*args, **kwargs)

mne/inverse_sparse/mxne_inverse.py:630: in tf_mixed_norm

    weights, weights_min)

mne/inverse_sparse/mxne_inverse.py:69: in _prepare_gain

    use_cps=True, **depth)

mne/minimum_norm/inverse.py:1387: in _prepare_forward

    gain = np.dot(whitener, forward['sol']['data'])

<__array_function__ internals>:6: in dot

    ???

E   Failed: Timeout >120.0s

@agramfort agramfort merged commit 1a3b639 into mne-tools:master Feb 15, 2020
@agramfort
Copy link
Member

error is unrelated. Maybe due to some update of numpy/scipy on conda a few days ago

https://anaconda.org/anaconda/scipy/files
https://anaconda.org/anaconda/numpy/files

@larsoner
Copy link
Member

error is unrelated. Maybe due to some update of numpy/scipy on conda a few days ago

FYI I have some of these fixed in #7325, I'll try to squash the last failure or two there

@drammock drammock deleted the param-deprecation branch February 19, 2020 18:09
AdoNunes pushed a commit to AdoNunes/mne-python that referenced this pull request Apr 6, 2020
* properly deprecate changes in to_data_frame

* fix test
AdoNunes pushed a commit to AdoNunes/mne-python that referenced this pull request Apr 6, 2020
* properly deprecate changes in to_data_frame

* fix test
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

3 participants