[MRG+1] Change named_steps to Bunch object #8586

herilalaina · 2017-03-14T21:54:15Z

Reference Issue

What does this implement/fix? Explain your changes.

This PR changes pipeline.named_steps into bunch object instead of dictionary.

Any other comments?

Usage example

> clf = svm.SVC(kernel='linear')
> anova_svm = Pipeline([('anova', anova_filter), ('svc', clf)])
> anova_svm.named_steps.anova
SelectKBest(k=5, score_func=<function f_regression at 0x7f1d984d8620>)

To do

Update source code
Test
Documentation

codecov · 2017-03-14T22:29:12Z

Codecov Report

Merging #8586 into master will increase coverage by <.01%.
The diff coverage is 99.56%.

@@            Coverage Diff             @@
##           master    #8586      +/-   ##
==========================================
+ Coverage   95.49%   95.49%   +<.01%     
==========================================
  Files         342      342              
  Lines       61072    61088      +16     
==========================================
+ Hits        58318    58334      +16     
  Misses       2754     2754

Impacted Files	Coverage Δ
sklearn/feature_selection/univariate_selection.py	`99.46% <ø> (ø)`	⬆️
sklearn/linear_model/coordinate_descent.py	`96.94% <ø> (ø)`	⬆️
sklearn/ensemble/forest.py	`98.16% <ø> (ø)`	⬆️
sklearn/metrics/classification.py	`97.77% <ø> (ø)`	⬆️
sklearn/mixture/tests/test_gaussian_mixture.py	`99.63% <ø> (ø)`	⬆️
sklearn/model_selection/_validation.py	`98.71% <ø> (ø)`	⬆️
sklearn/tree/tree.py	`98.41% <ø> (ø)`	⬆️
sklearn/calibration.py	`98.87% <ø> (ø)`	⬆️
sklearn/neighbors/approximate.py	`98.95% <ø> (ø)`	⬆️
sklearn/mixture/gaussian_mixture.py	`100% <ø> (ø)`	⬆️
... and 62 more

Continue to review full report at Codecov.

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jnothman · 2017-03-14T22:32:31Z

Thanks. please add tests and documentation, and prefix the issue title with [WIP] until those are done

…

On 15 Mar 2017 9:29 am, "codecov[bot]" ***@***.***> wrote: Codecov <https://codecov.io/gh/scikit-learn/scikit-learn/pull/8586?src=pr&el=h1> Report Merging #8586 <https://codecov.io/gh/scikit-learn/scikit-learn/pull/8586?src=pr&el=desc> into master <https://codecov.io/gh/scikit-learn/scikit-learn/commit/4ab99c75b4486f5e1a67be730b7afa6d9551ed7e?src=pr&el=desc> will *increase* coverage by <.01%. The diff coverage is 100%. @@ Coverage Diff @@## master #8586 +/- ## ==========================================+ Coverage 95.48% 95.48% +<.01% ========================================== Files 342 342 Lines 61034 61035 +1 ==========================================+ Hits 58280 58281 +1 Misses 2754 2754 Impacted Files <https://codecov.io/gh/scikit-learn/scikit-learn/pull/8586?src=pr&el=tree> Coverage Δ sklearn/pipeline.py <https://codecov.io/gh/scikit-learn/scikit-learn/compare/4ab99c75b4486f5e1a67be730b7afa6d9551ed7e...60a87763ec1ac8c61edb03516ebc16113c073895?src=pr&el=tree#diff-c2tsZWFybi9waXBlbGluZS5weQ==> 99.26% <100%> (ø) ✅ ------------------------------ Continue to review full report at Codecov <https://codecov.io/gh/scikit-learn/scikit-learn/pull/8586?src=pr&el=continue> . *Legend* - Click here to learn more <https://docs.codecov.io/docs/codecov-delta> Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov <https://codecov.io/gh/scikit-learn/scikit-learn/pull/8586?src=pr&el=footer>. Last update 4ab99c7...60a8776 <https://codecov.io/gh/scikit-learn/scikit-learn/compare/4ab99c75b4486f5e1a67be730b7afa6d9551ed7e...60a87763ec1ac8c61edb03516ebc16113c073895?src=pr&el=footer&el=lastupdated>. Read the comment docs <https://docs.codecov.io/docs/pull-request-comments> . — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#8586 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEz698gCKrmpJUVUrb6q4cdyjAPRt68ks5rlxS6gaJpZM4MdNFz> .

jnothman

You should also test what happens when step names conflict with attributes of dict such as values.

jnothman · 2017-03-20T13:17:57Z

sklearn/pipeline.py

@@ -20,6 +20,7 @@
 from .externals import six
 from .utils import tosequence
 from .utils.metaestimators import if_delegate_has_method
+from .datasets.base import Bunch


I don't think we want a dependency on datasets. Move Bunch to utils.

jnothman · 2017-03-20T13:17:57Z

sklearn/pipeline.py

@@ -122,7 +123,7 @@ class Pipeline(_BasePipeline):

    Attributes
    ----------
-    named_steps : dict
+    named_steps : bunch object
        Read-only attribute to access any step parameter by user given name.
        Keys are step names and values are steps parameters.


Comment on what a bunch is: a dict with attribute access.

lesteve · 2017-03-22T10:45:33Z

Travis is failing because you have some PEP8 violations, please invest some time to configure on-the-fly flake8 checks inside your editor of choice. This allows you to spot these kind of problems while editing.

herilalaina · 2017-03-22T20:20:17Z

Hi @jnothman @lesteve , thank you for your comment.
Actually, the Bunch object didn't work when step names conflict with attribute of dict like values, items ..
So I decide to override __getattribute__ on Bunch class.

jnothman · 2017-03-22T20:49:33Z

To be sure, correct behaviour would be to provide dict's keys method, even if a step is named 'keys'. We can't just break the existing dict behaviour. Nor can we accept an error if a user chooses keys for a step name; they just don't get the new functionality.

…

On 23 Mar 2017 7:20 am, "RAKOTOARISON Herilalaina" ***@***.***> wrote: Hi @jnothman <https://github.com/jnothman> @lesteve <https://github.com/lesteve> , thank you for your comment. Actually, the Bunch object didn't work when step names conflict with attribute of dict like values, items .. So I decide to override __getattribute__ on Bunch class. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#8586 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAEz6xqn2JCmA-Mv9RYXAp9dKM8wxrCRks5roYKCgaJpZM4MdNFz> .

herilalaina · 2017-03-22T22:30:14Z

To confirm what you said. I will remove the __getattribute__ in the Bunch class then change test_pipeline.py (line 524) with

pipeline = Pipeline([('values', transf), ("items", mult2)])
assert_true(pipeline.named_steps.values is not transf)
assert_true(pipeline.named_steps.items is not mult2)

jnothman

I still think this deserves a brief mention in doc/modules/pipeline.rst, where it says "and as a dict in named_steps", with something like:

Attributes of named_steps map to keys, enabling tab completion in interactive environments:
    >>> pipe.named_steps.reduce_dim is pipe.named_steps['reduce_dim']
    True

Otherwise LGTM. Please add an entry to what's new.

jnothman · 2017-03-23T02:18:35Z

sklearn/tests/test_pipeline.py

+    assert_true(pipeline.named_steps.mult is mult2)
+
+    # Test bunch with conflict attribute of dict
+    pipeline = Pipeline([('values', transf), ("items", mult2)])


Seeing as I could imagine a bad implementation where a Bunch was only used if the step names did not conflict, I would rather a test that included conflicting and non-conflicting names together. That is, include these steps all in the above pipeline.

jnothman · 2017-03-24T01:03:00Z

doc/whats_new.rst

@@ -247,6 +247,12 @@ API changes summary
     needed for the perplexity calculation. :issue:`7954` by
     :user:`Gary Foreman <garyForeman>`.



I think this should mention pipeline

Hi, I tried to organize into section each entry in API change summary. This resulted the conflict. I resolved it but appveyor test still failed (without merge). Should I remove my last commit ?

Don't worry about sections. We'll do that at release

Ok, thank you. I cleaned it.

amueller · 2017-03-30T14:55:11Z

Awesome, thanks!

amueller · 2017-03-30T14:56:00Z

doc/whats_new.rst

@@ -270,6 +270,12 @@ API changes summary
     needed for the perplexity calculation. :issue:`7954` by
     :user:`Gary Foreman <garyForeman>`.

+   - Replace attribute ``named_steps`` ``dict`` to :class:`sklearn.utils.Bunch`
+     in :class:`sklearn.pipeline.Pipeline` to enable tab completion in interactive
+     environment. In the case conflict value on ``named_steps`` and ``dict``


I'm not sure I understand this sentence.

* Change named_steps to Bunch object * Update named_steps attribute documentation * Add test for named steps bunch object * Delete whitespace in test_pipeline * Update test_pipeline.py * Add comment for named_steps usage * Move dataset/Bunch to utils * Fix to PEP8 format * Add __getattribute method to Bunch class, Fix pep8 bug * Remove __getattribute__, update test_pipeline * Update test with conflict and non-conflict named_steps * Add reference to class Pipeline

Change named_steps to Bunch object

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herilalaina changed the title ~~Change named_steps to Bunch object~~ [WIP] Change named_steps to Bunch object Mar 15, 2017

herilalaina added 4 commits Mar 15, 2017

Update named_steps attribute documentation

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Add test for named steps bunch object

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Delete whitespace in test_pipeline

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Update test_pipeline.py

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herilalaina changed the title ~~[WIP] Change named_steps to Bunch object~~ [MRG] Change named_steps to Bunch object Mar 17, 2017

Add comment for named_steps usage

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jnothman reviewed Mar 20, 2017

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Move dataset/Bunch to utils

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herilalaina added 2 commits Mar 22, 2017

Fix to PEP8 format

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Add __getattribute method to Bunch class, Fix pep8 bug

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Remove __getattribute__, update test_pipeline

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jnothman reviewed Mar 23, 2017

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Update test with conflict and non-conflict named_steps

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jnothman reviewed Mar 24, 2017

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jnothman changed the title ~~[MRG] Change named_steps to Bunch object~~ [MRG+1] Change named_steps to Bunch object Mar 24, 2017

herilalaina force-pushed the herilalaina:autocomplete-ipython branch 3 times, most recently from 4fb4dad to 7b25de2 Mar 26, 2017

herilalaina added 2 commits Mar 26, 2017

Add reference to class Pipeline

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Merge branch 'master' into autocomplete-ipython

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TomDLT approved these changes Mar 30, 2017

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scikit-learn / scikit-learn

[MRG+1] Change named_steps to Bunch object #8586

[MRG+1] Change named_steps to Bunch object #8586

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		@@ -247,6 +247,12 @@ API changes summary
		needed for the perplexity calculation. :issue:`7954` by
		:user:`Gary Foreman <garyForeman>`.

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[MRG+1] Change named_steps to Bunch object #8586

[MRG+1] Change named_steps to Bunch object #8586

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herilalaina commented Mar 14, 2017 • edited

Reference Issue

What does this implement/fix? Explain your changes.

Any other comments?

To do

codecov bot commented Mar 14, 2017 • edited

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