[MRG+1] Deprecate `Imputer.axis` argument #9672

petrushev · 2017-09-01T14:11:46Z

Reference Issue

Fixes: #9463

What does this implement/fix? Explain your changes.

Deprecated the argument axis on the Imputer class.

glemaitre

This changes should make the CI happy.

Also edit the title with [WIP] when working on the PR and change it to [MRG] when this is ready for revision.

glemaitre · 2017-09-02T13:38:31Z

doc/whats_new.rst

@@ -47,6 +47,11 @@ Model evaluation and meta-estimators

 - A scorer based on :func:`metrics.brier_score_loss` is also available.
  :issue:`9521` by :user:`Hanmin Qin <qinhanmin2014>`.
+- The ``axis`` parameter in


Add a blank line

glemaitre · 2017-09-02T13:41:23Z

sklearn/preprocessing/imputation.py

        self.verbose = verbose
        self.copy = copy

+        self.axis = axis
+        if axis is not None:


The warning should be raised in fit method. The validation is postponed for the SearhCV: object: http://scikit-learn.org/stable/developers/contributing.html#instantiation

glemaitre · 2017-09-02T13:45:07Z

sklearn/preprocessing/imputation.py

@@ -169,8 +178,12 @@ def fit(self, X, y=None):

    def _sparse_fit(self, X, strategy, missing_values, axis):
        """Fit the transformer on sparse data."""
+        if axis is None:


no need if using since self.axis_ will be 0 or 1 already

glemaitre · 2017-09-02T13:45:50Z

sklearn/preprocessing/imputation.py

        # Imputation is done "by column", so if we want to do it
        # by row we only need to convert the matrix to csr format.
+


remove the blank line. we try to minimize the diff which bring nothing

glemaitre · 2017-09-02T13:45:55Z

sklearn/preprocessing/imputation.py

@@ -249,6 +262,9 @@ def _sparse_fit(self, X, strategy, missing_values, axis):

    def _dense_fit(self, X, strategy, missing_values, axis):
        """Fit the transformer on dense data."""
+        if axis is None:


no need if using since self.axis_ will be 0 or 1 already

glemaitre · 2017-09-02T13:46:05Z

sklearn/preprocessing/imputation.py

@@ -306,7 +322,7 @@ def transform(self, X):
        X : {array-like, sparse matrix}, shape = [n_samples, n_features]
            The input data to complete.
        """
-        if self.axis == 0:
+        if self.axis is None or self.axis == 0:


no need if using since self.axis_ will be 0 or 1 already

glemaitre · 2017-09-02T13:46:10Z

sklearn/preprocessing/imputation.py

@@ -341,7 +357,7 @@ def transform(self, X):
        valid_statistics_indexes = np.where(valid_mask)[0]
        missing = np.arange(X.shape[not self.axis])[invalid_mask]

-        if self.axis == 0 and invalid_mask.any():
+        if (self.axis is None or self.axis == 0) and invalid_mask.any():


no need if using since self.axis_ will be 0 or 1 already

glemaitre · 2017-09-02T13:46:16Z

sklearn/preprocessing/imputation.py

@@ -366,7 +382,7 @@ def transform(self, X):
            n_missing = np.sum(mask, axis=self.axis)
            values = np.repeat(valid_statistics, n_missing)

-            if self.axis == 0:
+            if self.axis is None or self.axis == 0:


no need if using since self.axis_ will be 0 or 1 already

glemaitre · 2017-09-02T13:46:23Z

sklearn/preprocessing/imputation.py

            raise ValueError("Can only impute missing values on axis 0 and 1, "
                             " got axis={0}".format(self.axis))

        # Since two different arrays can be provided in fit(X) and
        # transform(X), the imputation data will be computed in transform()
        # when the imputation is done per sample (i.e., when axis=1).
-        if self.axis == 0:
+        if self.axis == 0 or self.axis is None:


no need if using since self.axis_ will be 0 or 1 already

glemaitre · 2017-09-02T13:47:27Z

sklearn/preprocessing/imputation.py

        The axis along which to impute.

        - If `axis=0`, then impute along columns.
        - If `axis=1`, then impute along rows.

+        .. deprecated:: 0.20
+           ``axis`` will be removed from ``Imputer``, and it will only impute
+           along columns (axis=0) in 0.22.


(axis=0) -> (i.e., ``axis=0``)

…and equals to 0 when axis is None.

glemaitre · 2017-09-03T20:48:22Z

LGTM @jnothman could yo have a look.

jnothman · 2017-09-03T23:06:53Z

sklearn/preprocessing/imputation.py

@@ -143,27 +147,35 @@ def fit(self, X, y=None):
                             " got strategy={1}".format(allowed_strategies,
                                                        self.strategy))

-        if self.axis not in [0, 1]:
+        if self.axis is None:
+            self.axis_ = 0


This attribute implicitly becomes part of the public API. Either use a private attribute (beginning _) or use a local variable

Ups my bad ... I should have advise to make it private

jnothman · 2017-09-05T21:45:02Z

LGTM

glemaitre · 2017-09-06T21:21:24Z

@ogrisel @lesteve Would you like to have a look if it can be merged?

lesteve

Small comment in the deprecation message.

It would be great to add a test to make sure we get the DeprecationWarning when axis is set explicitly (test either to axis=0 or axis=1 or both)

lesteve · 2017-09-07T08:24:37Z

sklearn/preprocessing/imputation.py

+        if self.axis is None:
+            self._axis = 0
+        else:
+            warnings.warn("'axis' will be removed from Imputer, and it will "


The convention is to add the version the deprecation happened as well as the on it will be removed.

From http://scikit-learn.org/stable/developers/contributing.html#deprecation:

As in these examples, the warning message should always give both the version in which the deprecation happened and the version in which the old behavior will be removed.

qinhanmin2014

ping @petrushev This looks good overall. Could you please (please also refer to the comments above)
(1) Solve the conflict
(2) Improve the deprecation message
(3) Add a test to ensure the warning is raised
(4) Move what's new entry to API changes summary
Thanks :)

rth · 2018-01-25T22:19:03Z

@petrushev Would you be able to address minor comments above, this is almost good to merge )

(3) Add a test to ensure the warning is raised

@qinhanmin2014 Do we really want to add a test at each deprecation warning?

qinhanmin2014 · 2018-01-26T14:11:23Z

@qinhanmin2014 Do we really want to add a test at each deprecation warning?

@rth I don't know too much about the history but we have tests for most API changes in 0.20. I think at least it's not harmful to test the deprecation warning. WDYT?

Also see lesteve's comment above (#9672 (review)):
It would be great to add a test to make sure we get the DeprecationWarning when axis is set explicitly (test either to axis=0 or axis=1 or both)

rth · 2018-01-26T18:24:58Z

we have tests for most API changes in 0.20. I think at least it's not harmful to test the deprecation warning. WDYT?
Also see lesteve's comment above..

Good to know, thanks, I missed that.

qinhanmin2014 · 2018-01-31T08:32:45Z

@petrushev I've continued the work in #10558 since we've not heard from you for several months, hope you won't mind.

Deprecate Imputer.axis argument

c900dd5

petrushev force-pushed the deprecate-imputer-axis-1 branch from dee866d to c900dd5 Compare September 1, 2017 14:15

glemaitre reviewed Sep 2, 2017

View reviewed changes

Add proxy property Imputer.axis_ that is used in the fit/transform …

7d40c5f

…and equals to 0 when axis is None.

petrushev changed the title ~~Deprecate Imputer.axis argument~~ [MRG] Deprecate Imputer.axis argument Sep 3, 2017

jnothman reviewed Sep 3, 2017

View reviewed changes

Switch to private proxy property Imputer._axis

7f88b5f

jnothman changed the title ~~[MRG] Deprecate Imputer.axis argument~~ [MRG+1] Deprecate Imputer.axis argument Sep 5, 2017

lesteve reviewed Sep 7, 2017

View reviewed changes

qinhanmin2014 reviewed Dec 2, 2017

View reviewed changes

qinhanmin2014 mentioned this pull request Jan 31, 2018

[MRG+1] Deprecate axis parameter in imputer #10558

Merged

jnothman closed this in #10558 Feb 8, 2018

		# Imputation is done "by column", so if we want to do it
		# by row we only need to convert the matrix to csr format.

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[MRG+1] Deprecate Imputer.axis argument #9672

[MRG+1] Deprecate Imputer.axis argument #9672

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petrushev commented Sep 1, 2017

Reference Issue

What does this implement/fix? Explain your changes.

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glemaitre commented Sep 3, 2017

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jnothman commented Sep 5, 2017

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glemaitre commented Sep 6, 2017

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rth commented Jan 25, 2018

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qinhanmin2014 commented Jan 26, 2018

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rth commented Jan 26, 2018

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qinhanmin2014 commented Jan 31, 2018

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[MRG+1] Deprecate `Imputer.axis` argument #9672

[MRG+1] Deprecate `Imputer.axis` argument #9672