Implements SelectColumns Transformer. Updating unit tests and docs. #873

freddyaboulton · 2020-06-23T17:52:59Z

Pull Request Description

Addresses #837 by implementing a SelectColumns transformer. To reduce code duplication between DropColumns and SelectColumns I created a base class called ColumnSelector. Since this PR is only a minor modification of the code written for DropColumns, I did not prepare a design document.

After creating the pull request: in order to pass the changelog_updated check you will need to update the "Future Release" section of docs/source/changelog.rst to include this pull request by adding :pr:123.

codecov · 2020-06-23T17:59:54Z

Codecov Report

Merging #873 into master will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##           master     #873   +/-   ##
=======================================
  Coverage   99.75%   99.75%           
=======================================
  Files         195      195           
  Lines        8467     8503   +36     
=======================================
+ Hits         8446     8482   +36     
  Misses         21       21

Impacted Files	Coverage Δ
evalml/pipelines/components/__init__.py	`100.00% <ø> (ø)`
...alml/pipelines/components/transformers/__init__.py	`100.00% <100.00%> (ø)`
...elines/components/transformers/column_selectors.py	`100.00% <100.00%> (ø)`
...mponent_tests/test_column_selector_transformers.py	`100.00% <100.00%> (ø)`

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 56c4521...e342e23. Read the comment docs.

…nit tests were being run.

dsherry

@freddyaboulton great first PR!! 🎊 The common base class is a helpful addition.

I left some comments. Only one blocking merge was about calling fit in transform. Others were just a couple style notes.

dsherry · 2020-06-23T19:42:06Z

evalml/pipelines/components/transformers/column_selectors.py

+    hyperparameter_ranges = {}
+
+    def _modify_columns(self, cols, X, y=None):
+        return X.drop(columns=cols, axis=1)


@freddyaboulton this is great! It's nice having the base class.

dsherry · 2020-06-23T19:42:56Z

evalml/pipelines/components/transformers/column_selectors.py

+        return X.drop(columns=cols, axis=1)
+
+    def transform(self, X, y=None):
+        """Transforms data X by dropping columns.


Did you add this method just so the docstring would be different? 👍 that's great!

dsherry · 2020-06-23T19:45:25Z

evalml/pipelines/components/transformers/column_selectors.py

+        if not isinstance(X, pd.DataFrame):
+            X = pd.DataFrame(X)
+
+        self.fit(X, y)


@freddyaboulton our general pattern is to keep fit and transform separate, and to use fit_transform to combine them. Its nice to have all our components keep that convention so let's do that here too.

Good point!

evalml/pipelines/components/transformers/column_selectors.py

dsherry · 2020-06-23T19:46:59Z

docs/source/changelog.rst

@@ -17,6 +17,7 @@ Changelog
        * Added utility methods to calculate and graph permutation importances :pr:`860`
        * Added new utility functions necessary for generating dynamic preprocessing pipelines :pr:`852`
        * Added kwargs to all components :pr:`863`
+        * Added SelectColumns transformer :pr:`873`


dsherry · 2020-06-23T19:47:09Z

evalml/pipelines/components/transformers/__init__.py

@@ -4,5 +4,5 @@
 from .feature_selection import FeatureSelector, RFClassifierSelectFromModel, RFRegressorSelectFromModel
 from .imputers import PerColumnImputer, SimpleImputer
 from .scalers import StandardScaler
-from .drop_columns import DropColumns
+from .column_selectors import DropColumns, SelectColumns


dsherry · 2020-06-23T19:50:39Z

evalml/tests/component_tests/test_column_selector_transformers.py

+    with pytest.raises(ValueError, match="Parameter columns must be a list."):
+        _ = DropColumns(columns="Column1")
+    with pytest.raises(ValueError, match="Parameter columns must be a list."):
+        _ = SelectColumns(columns="Column2")


Nice.

For maintainability, may be nice to split each of these unit tests into two, i.e. test_drop_columns_init and test_select_columns_init.

In fact, lately I've been getting into using pytest.mark.parametrize for tests which have two or three configuration options but would otherwise have mostly identical code. That could be helpful here.

Agreed, these tests looks like a good candidate for parametrize :)

Thanks for pointing this out! I've reworked the tests to use parametrize .

angela97lin

Minor comments but I think once you separate fit/transform, LGTM! 👍

angela97lin · 2020-06-23T20:07:00Z

evalml/pipelines/components/transformers/column_selectors.py

+    def fit(self, X, y=None):
+        """'Fits' the transformer by checking if the column names are present in the dataset.
+
+        Args:


Minor, and honestly we probably have "Args" floating around elsewhere but we're trying to go with "Arguments" for docstrings! (Same with other places in this PR)

Thanks for pointing this out!

angela97lin · 2020-06-23T20:11:03Z

evalml/tests/component_tests/test_column_selector_transformers.py

+    with pytest.raises(ValueError, match="Parameter columns must be a list."):
+        _ = DropColumns(columns="Column1")
+    with pytest.raises(ValueError, match="Parameter columns must be a list."):
+        _ = SelectColumns(columns="Column2")


Agreed, these tests looks like a good candidate for parametrize :)

dsherry · 2020-06-23T21:04:35Z

evalml/tests/component_tests/test_column_selector_transformers.py

+
+    assert check2(class_to_test(columns=["one"]).fit_transform(X), X)
+
+    assert check3(class_to_test(columns=list(X.columns)).fit_transform(X), X)


@freddyaboulton oh cool, I hadn't considered abstracting the checks out too! It may be easier to read in the future if we did something like

@pytest.mark.parametrize("class_to_test", [DropColumns, SelectColumns]) def test_column_transformer_fit_transform(class_to_test): X = pd.DataFrame({'one': [1, 2, 3, 4], 'two': [2, 3, 4, 5], 'three': [1, 2, 3, 4]}) assert df.empty(<stuff>) assert X == class_to_test(columns=[]).fit_transform(X) if class_to_test == DropColumns: assert X == class_to_test().fit_transform(X.drop(columns=["one"])) if class_to_test == SelectColumns: assert X == X[["one"]]

I think I'm screwing up the checks but that's a pattern I've used elsewhere recently.

But your call!

Adding SelectColumns Transformer. Updating unit tests and docs.

8f478a2

freddyaboulton linked an issue Jun 23, 2020 that may be closed by this pull request

Select Column Component #837

Closed

freddyaboulton and others added 2 commits June 23, 2020 13:53

Merge branch 'master' into 837-select-columns

ce25570

Modifying changelog for SelectColumns pr.

6a13277

freddyaboulton added 2 commits June 23, 2020 14:19

Fixing bug where not all lines in test_column_selector_transformers u…

60b55cd

…nit tests were being run.

Adding docstring to _modify_columns method

96c41bf

freddyaboulton marked this pull request as ready for review June 23, 2020 19:23

auto-assign bot assigned freddyaboulton Jun 23, 2020

freddyaboulton requested review from angela97lin and dsherry June 23, 2020 19:23

dsherry approved these changes Jun 23, 2020

View reviewed changes

dsherry requested a review from jeremyliweishih June 23, 2020 19:57

angela97lin reviewed Jun 23, 2020

View reviewed changes

Keeping fit and transform separate in ColumnSelector

e342e23

freddyaboulton merged commit b69e1ed into master Jun 23, 2020

freddyaboulton deleted the 837-select-columns branch June 23, 2020 21:02

dsherry reviewed Jun 23, 2020

View reviewed changes

angela97lin mentioned this pull request Jun 30, 2020

Release v0.11.0 #901

Merged

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Implements SelectColumns Transformer. Updating unit tests and docs. #873

Implements SelectColumns Transformer. Updating unit tests and docs. #873

freddyaboulton commented Jun 23, 2020

codecov bot commented Jun 23, 2020 •

edited

Loading

dsherry left a comment

dsherry Jun 23, 2020

dsherry Jun 23, 2020

dsherry Jun 23, 2020

freddyaboulton Jun 23, 2020

dsherry Jun 23, 2020

dsherry Jun 23, 2020

dsherry Jun 23, 2020

angela97lin Jun 23, 2020

freddyaboulton Jun 23, 2020

angela97lin left a comment

angela97lin Jun 23, 2020

freddyaboulton Jun 23, 2020

angela97lin Jun 23, 2020

dsherry Jun 23, 2020


		assert check2(class_to_test(columns=["one"]).fit_transform(X), X)

		assert check3(class_to_test(columns=list(X.columns)).fit_transform(X), X)

Implements SelectColumns Transformer. Updating unit tests and docs. #873

Implements SelectColumns Transformer. Updating unit tests and docs. #873

Conversation

freddyaboulton commented Jun 23, 2020

Pull Request Description

codecov bot commented Jun 23, 2020 • edited Loading

Codecov Report

dsherry left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

angela97lin left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

codecov bot commented Jun 23, 2020 •

edited

Loading