DEPR: Deprecate NDFrame.as_matrix #18458

topper-123 · 2017-11-23T22:21:30Z

[x ] xref DEPR: let's deprecate #18262
[x ] passes git diff upstream/master -u -- "*.py" | flake8 --diff
[ x] whatsnew entry

Deprecating NDFrame.as_matrix as per discussion in #18262.

codecov · 2017-11-24T04:23:36Z

Codecov Report

Merging #18458 into master will increase coverage by 0.02%.
The diff coverage is 85.71%.

@@            Coverage Diff             @@
##           master   #18458      +/-   ##
==========================================
+ Coverage    91.3%   91.32%   +0.02%     
==========================================
  Files         163      163              
  Lines       49781    49783       +2     
==========================================
+ Hits        45451    45464      +13     
+ Misses       4330     4319      -11

Flag	Coverage Δ
#multiple	`89.12% <85.71%> (+0.02%)`	⬆️
#single	`40.72% <64.28%> (-0.01%)`	⬇️

Impacted Files	Coverage Δ
pandas/core/panel.py	`96.85% <0%> (-0.29%)`	⬇️
pandas/core/internals.py	`94.47% <100%> (ø)`	⬆️
pandas/core/generic.py	`95.78% <83.33%> (+0.05%)`	⬆️
pandas/plotting/_converter.py	`65.25% <0%> (+1.81%)`	⬆️

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jorisvandenbossche

Thanks for the PR! Left some comments

jorisvandenbossche · 2017-11-24T08:55:56Z

doc/source/whatsnew/v0.22.0.txt


 - ``Series.from_array`` and ``SparseSeries.from_array`` are deprecated. Use the normal constructor ``Series(..)`` and ``SparseSeries(..)`` instead (:issue:`18213`).
-
+- ``NDFrame.as_matrix`` is deprecated. Use ``NDFrame.values`` instead (:issue:`18458`).


Can you use DataFrame instead of NDFrame (basically NDFrame should never show up in the docs, it is an internal implementation detail, although there are some places where it leaks through ..)

jorisvandenbossche · 2017-11-24T08:58:08Z

pandas/core/generic.py

    def as_matrix(self, columns=None):
        """
+        DEPRECATED: This method will be removed in a future version.
+        Use :meth:`NDFrame.values` instead.


same comment here

jorisvandenbossche · 2017-11-24T09:00:13Z

pandas/core/generic.py

        pandas.DataFrame.values
        """
+        warnings.warn("This method will be removed in a future version. "
+                      "Use ``.values`` instead.")


This needs to be a FutureWarning, and you also need to set a stacklevel (this is a top-level method, stacklevel=2 should be the correct one)

Can you also mention as_matrix explicitly in the message (that is clearer as you don't always directly see what line or what method on a certain line is causing the warning).
And also follow a bit the typical message like "'as_matrix' is deprecated and will be removed in a future version. Use .."

jorisvandenbossche · 2017-11-24T09:07:11Z

pandas/tests/frame/test_api.py

        assert len(self.frame) == len(self.frame.index)

-    def test_as_matrix(self):
+    def test_values(self):


Can you leave one test (or now add a test_as_matrix_deprecated that copies eg the first case of this test) that uses as_matrix and that asserts it raises a warning and is the same as .values

Ok. I've added in below test_repr_with_mi_nat

jorisvandenbossche · 2017-11-24T12:37:28Z

General question: I am wondering if we shouldn't rather recommend to do np.asarray(df) instead of df.values ?

topper-123 · 2017-11-24T13:05:17Z

Interesting, does it conform to .values in all cases?.

Anyway, I suggest that that will be a separate issue from this one.

topper-123 · 2017-11-24T13:52:30Z

I've changed the PR according to the comments. Is this ok?

jreback · 2017-11-24T19:52:30Z

pandas/core/generic.py

        int32. By numpy.find_common_type convention, mixing int64 and uint64
        will result in a flot64 dtype.
        """
-        return self.as_matrix()


just return .values

This is the def of .values

oh, then we should push this entirely down to the BlockManager, so pass the axis as well. The BM can then do the transpose, we don't like to do things in user code like this.

We should actually deprecate .values as well, in favor of .to_numpy() which is the future spelling anyhow.

This is already almost entirely pushed down, since it is calling directly BlockManager.as_matrix (but OK, the transpose could be done inside BlockManager.as_matrix). The consolidate_inplace needs to happens in NDFrame I think.

Deprecating .values is a no-go IMO, but let's deprecate that in another issue if you want

oh, then we should push this entirely down to the BlockManager, so pass the axis as well. The BM can then do the transpose, we don't like to do things in user code like this.

I'm not too familiar with the BlockManager, except accessing it with ._data. How do I pass the axis to it, and how do I transpose in a BlockManager? E.g. it doesn't have a .transpose method.

look at _take in pandas/core/generic.py, you just pass the get_block_manager_axis to it.

then add axis= to def as_matrix in pandas/core/internals and do the transpose there.

The reason for pushing this to internals is to avoid all of the wrapping layers (e.g. frame/series, etc.) to know about internal details like this.

as_matrix doesn't have a axis parameter. Do you mean adding a new axis parameter there and transposing inside, if axis=0 (where I assume from my limited knowledge that BlockManager.axes[0] is always the same as dataFrame.axes[1], correct?)

Hi @jreback, I've tried quite a bit today and I can't push this down while getting the tests to pass.

Could you look at my latest commit (not passing ATM) and give some advice?

jreback · 2017-11-24T19:52:48Z

pandas/tests/frame/test_api.py

        assert (self.frame.values[:, 0] == 5).all()

+    def test_as_matrix_deprecated(self):
+        with tm.assert_produces_warning(FutureWarning):


add the issue number

jreback · 2017-11-25T23:06:32Z

pandas/core/internals.py

        if len(self.blocks) == 0:
            return np.empty(self.shape, dtype=float)

+        other_axis = abs(axis-1)


don't do this

jreback · 2017-11-25T23:06:38Z

pandas/core/internals.py

+        other_axis = abs(axis-1)
        if items is not None:
-            mgr = self.reindex_axis(items, axis=0)
+            mgr = self.reindex_axis(items, axis=other_axis)


leave this alone

jreback · 2017-11-25T23:09:09Z

pandas/core/generic.py

-        return self.as_matrix()
+        self._consolidate_inplace()
+        bm_axis = self._get_block_manager_axis(axis=1)
+        return self._data.as_matrix(axis=bm_axis)


instead of this, just pass transpose = self._AXIS_REVERSED in.

But _data.as_matrix has no transpose parameter, do you mean axis=self._AXIS_REVERSED?

no I mean add the argument transpose=False rather than axis prob simpler for now.

jreback · 2017-11-25T23:09:28Z

pandas/core/internals.py

        if self._is_single_block or not self.is_mixed_type:
-            return mgr.blocks[0].get_values()
+            arr = mgr.blocks[0].get_values()
        else:


change this to transpose instead. should be straightforward from here.

Thanks a lot, transpose is of course much better than axis.

The issue was actually in the if len(self.blocks) == 0: block, as the empty array also must be transposed.

Everything is green now locally and I've pushed that upstream.

topper-123 · 2017-11-26T00:11:25Z

A thought: BlockManager.as_matrix is a strange name as it implies a np.matrix is returned.

Should I not just change it to BlockManager.as_array? Or, do any external libraries rely on calling BlockManager directly, e.g. statsmodel?

jreback · 2017-11-26T00:12:24Z

@topper-123 ok this lgtm. ping on green.

jreback · 2017-11-26T00:13:20Z

Should I not just change it to BlockManager.as_array? Or, do any external libraries rely on calling BlockManager directly, e.g. statsmodel?

this is completely private and internal. as_array would be fine. while you are at it, can you add a doc-string.

ping when ready.

jreback · 2017-11-26T00:28:17Z

pandas/core/generic.py

+                      "Use ``values`` instead.", FutureWarning, stacklevel=2)
        self._consolidate_inplace()
        if self._AXIS_REVERSED:
-            return self._data.as_matrix(columns).T


this should just return self.values

Returning self.values implies that columns=None which isn't necessary true for user code.

jreback · 2017-11-26T00:28:42Z

pandas/core/generic.py


        NOTE: the dtypes of the blocks WILL BE PRESERVED HERE (unlike in
-              as_matrix)
+              as_array)


leave this spelling, this is a top-level method name

jreback · 2017-11-26T00:28:56Z

pandas/core/internals.py


-    def as_matrix(self, items=None):
+    def as_array(self, transpose=False, items=None):
        if len(self.blocks) == 0:


can you add a doc-string

jreback · 2017-11-26T00:41:46Z

pandas/core/generic.py

+        warnings.warn("method ``as_matrix`` will be removed in a future version. "
+                      "Use ``values`` instead.", FutureWarning, stacklevel=2)
        self._consolidate_inplace()
        if self._AXIS_REVERSED:


ok so this should be the same as below (e.g. passing transpose=). make sure we still have a test on this (e.g. that passes columns).

Ok, and test_as_matrix_deprecated has been modified to a take columns param.

jreback · 2017-11-26T01:02:53Z

pandas/core/generic.py

        --------
        pandas.DataFrame.values
        """
+        warnings.warn("method ``as_matrix`` will be removed in a future version. "


"method method .as_matrix()...."
"Use .values instead"

I not sure I understand, assume you want the backticks gone. Change uploaded.

topper-123 · 2017-11-26T14:39:47Z

All green, @jreback

jreback · 2017-11-26T15:04:08Z

thanks @topper-123

as_matrix() got removed with Pandas 1.0.0 (pandas-dev/pandas#18458), replaced with values

See GH18458（pandas-dev/pandas#18458). Since as_matrix is deprecated for pd.DataFrame and pd.Series, use data.values instead.

Pandas.DataFrame.as_matrix is deprecated since version 0.23.0 (see docs and PR 18458). According to the documentation for Pandas 0.25.1, the recommended function is DataFrame.to_numpy() in place of DataFrame.values or DataFrame.as_matrix(). pandas-dev/pandas#18458 https://pandas.pydata.org/pandas-docs/version/0.23/generated/pandas.DataFrame.as_matrix.html https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.values.html

topper-123 force-pushed the deprecate_as_matrix branch 2 times, most recently from d981cb8 to 7fd4b71 Compare November 24, 2017 00:34

jorisvandenbossche added the Deprecate Functionality to remove in pandas label Nov 24, 2017

jorisvandenbossche added this to the 0.22.0 milestone Nov 24, 2017

jsexauer mentioned this pull request Nov 24, 2017

DEPR: Clean up list of deprecations from prior versions #6581

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DEPR: let's deprecate #18262

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Deprecate NDFrame.as_matrix

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updating according to comments

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rename BlockManager.as_matrix to .as_array

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jreback merged commit f26bed6 into pandas-dev:master Nov 26, 2017

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jeremiahpslewis mentioned this pull request May 16, 2018

Fix pandas 0.23.0 deprecation of as_matrix shap/shap#87

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jreback mentioned this pull request Nov 20, 2019

DEPR: deprecations log for removed issues #13777

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giantZorg added a commit to giantZorg/multivariate_time_series_forecasting that referenced this pull request Feb 4, 2020

as_matrix replaced

8e8bdd9

as_matrix() got removed with Pandas 1.0.0 (pandas-dev/pandas#18458), replaced with values

giantZorg mentioned this pull request Feb 4, 2020

as_matrix replaced opringle/multivariate_time_series_forecasting#2

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atangfan added a commit to atangfan/Deep-Portfolio-Management that referenced this pull request May 11, 2020

Replace pd.as_matrix by pd.values

36ac2c0

See GH18458（pandas-dev/pandas#18458). Since as_matrix is deprecated for pd.DataFrame and pd.Series, use data.values instead.

mcrowson mentioned this pull request Jul 1, 2020

pandas deprecated to_matrix Kismuz/btgym#139

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jnirschl mentioned this pull request Aug 10, 2020

Update Deprecated Pandas Function Call ustunb/risk-slim#9

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xaf-cv mentioned this pull request Jan 26, 2022

.as_matrix() -> .to_numpy() hpatches/hpatches-benchmark#44

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DEPR: Deprecate NDFrame.as_matrix #18458

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