Merge branch 'develop' into flynt

Author: PGijsbers

.all-contributorsrc

@@ -1,3 +1,15 @@
+<!--
+It is recommended to check that your issue complies with the
+following rules before submitting:
+
+-  Verify that your issue is not being currently addressed by other
+   issues (https://github.com/openml/openml-python/issues)
+   or pull requests (https://github.com/openml/openml-python/pulls).
+
+-  Please ensure all code snippets and error messages are formatted in
+   appropriate code blocks. See https://help.github.com/articles/creating-and-highlighting-code-blocks
+-->
+
 #### Description
 <!-- Example: Joblib Error thrown when calling fit on LatentDirichletAllocation with evaluate_every > 0-->
 
@@ -20,7 +32,10 @@ it in the issue: https://gist.github.com
 
 #### Versions
 <!--
-Please run the following snippet and paste the output below.
+Please include your operating system type and version number, as well
+as your Python, openml, scikit-learn, numpy, and scipy versions. This information
+can be found by running the following code snippet:
+
 import platform; print(platform.platform())
 import sys; print("Python", sys.version)
 import numpy; print("NumPy", numpy.__version__)
@@ -30,4 +45,5 @@ import openml; print("OpenML", openml.__version__)
 -->
 
 
-<!-- Thanks for contributing! -->
+<!-- Thanks for contributing! -->
+

CONTRIBUTING.md

@@ -4,8 +4,8 @@ the contribution guidelines: https://github.com/openml/openml-python/blob/main/C
 
 Please make sure that:
 
+* the title of the pull request is descriptive
 * this pull requests is against the `develop` branch
-* you updated all docs, this includes the changelog (doc/progress.rst)
 * for any new function or class added, please add it to doc/api.rst
     * the list of classes and functions should be alphabetical 
 * for any new functionality, consider adding a relevant example
@@ -14,15 +14,20 @@ Please make sure that:
 * add the BSD 3-Clause license to any new file created
 -->
 
-#### Reference Issue
-<!-- Example: Fixes #1234 -->
+#### Metadata
+* Reference Issue: <!-- Example: Fixes #1234 or NA-->
+* New Tests Added: <!-- Yes/No/NA -->
+* Documentation Updated: <!-- Yes/No/NA -->
+* Change Log Entry: <!-- Short String, example: "Add new function `foo()` to module `bar`"; or "Fixes a bug with `bar`" -->
 
 
-#### What does this PR implement/fix? Explain your changes.
-
-
-#### How should this PR be tested?
-
+#### Details 
+<!--
+if necessary, please share the following:
 
-#### Any other comments?
+* What does this PR implement/fix? Explain your changes.
+* Why is this change necessary? What is the problem it solves?
+* How can I reproduce the issue this PR is solving and its solution?
+* Any other comments?
+-->
 

ISSUE_TEMPLATE.md

@@ -5,7 +5,7 @@
 <div id="user-content-toc">
   <ul align="center" style="list-style: none;">
     <summary>
-      <img src="https://github.com/openml/openml.org/blob/master/app/public/static/svg/logo.svg" width="50" alt="OpenML Logo"/> 
+      <img src="https://github.com/openml/openml.org/blob/master/app/public/static/svg/logo.svg" width="50" alt="OpenML Logo"/>
       <h1>OpenML-Python</h1>
       <img src="https://github.com/openml/docs/blob/master/docs/img/python.png" width="50" alt="Python Logo"/>
     </summary>

PULL_REQUEST_TEMPLATE.md

@@ -16,10 +16,7 @@ In particular, a few ways to contribute to openml-python are:
  * A contribution to an openml-python extension. An extension package allows OpenML to interface
    with a machine learning package (such as scikit-learn or keras). These extensions
    are hosted in separate repositories and may have their own guidelines.
-   For more information, see the :ref:`extensions` below.
-
- * Bug reports. If something doesn't work for you or is cumbersome, please open a new issue to let
-   us know about the problem. See `this section <https://github.com/openml/openml-python/blob/main/CONTRIBUTING.md>`_.
+   For more information, see the :ref:`extensions`.
 
  * `Cite OpenML <https://www.openml.org/cite>`_ if you use it in a scientific publication.
 

README.md

@@ -19,7 +19,7 @@
 # List datasets
 # =============
 
-datasets_df = openml.datasets.list_datasets(output_format="dataframe")
+datasets_df = openml.datasets.list_datasets()
 print(datasets_df.head(n=10))
 
 ############################################################################
@@ -48,7 +48,7 @@
 # attribute_names - the names of the features for the examples (X) and
 # target feature (y)
 X, y, categorical_indicator, attribute_names = dataset.get_data(
-    dataset_format="dataframe", target=dataset.default_target_attribute
+    target=dataset.default_target_attribute
 )
 
 ############################################################################
@@ -63,9 +63,9 @@
 # Visualize the dataset
 # =====================
 
+import matplotlib.pyplot as plt
 import pandas as pd
 import seaborn as sns
-import matplotlib.pyplot as plt
 
 sns.set_style("darkgrid")
 

doc/contributing.rst

@@ -7,9 +7,9 @@
 
 # License: BSD 3-Clause
 
-import openml
 from sklearn import ensemble, neighbors
 
+import openml
 
 ############################################################################
 # .. warning::

examples/20_basic/simple_datasets_tutorial.py

@@ -8,29 +8,24 @@
 
 # License: BSD 3-Clauses
 
-import openml
 import pandas as pd
+
+import openml
 from openml.datasets import edit_dataset, fork_dataset, get_dataset
 
 ############################################################################
 # Exercise 0
 # **********
 #
-# * List datasets
-#
-#   * Use the output_format parameter to select output type
-#   * Default gives 'dict' (other option: 'dataframe', see below)
-#
-# Note: list_datasets will return a pandas dataframe by default from 0.15. When using
-# openml-python 0.14, `list_datasets` will warn you to use output_format='dataframe'.
-datalist = openml.datasets.list_datasets(output_format="dataframe")
+# * List datasets and return a dataframe
+datalist = openml.datasets.list_datasets()
 datalist = datalist[["did", "name", "NumberOfInstances", "NumberOfFeatures", "NumberOfClasses"]]
 
 print(f"First 10 of {len(datalist)} datasets...")
 datalist.head(n=10)
 
 # The same can be done with lesser lines of code
-openml_df = openml.datasets.list_datasets(output_format="dataframe")
+openml_df = openml.datasets.list_datasets()
 openml_df.head(n=10)
 
 ############################################################################

examples/20_basic/simple_flows_and_runs_tutorial.py

@@ -32,9 +32,7 @@
 # Required filters can be applied to retrieve results from runs as required.
 
 # We shall retrieve a small set (only 10 entries) to test the listing function for evaluations
-openml.evaluations.list_evaluations(
-    function="predictive_accuracy", size=10, output_format="dataframe"
-)
+openml.evaluations.list_evaluations(function="predictive_accuracy", size=10)
 
 # Using other evaluation metrics, 'precision' in this case
 evals = openml.evaluations.list_evaluations(
@@ -162,7 +160,10 @@ def plot_flow_compare(evaluations, top_n=10, metric="predictive_accuracy"):
 # List evaluations in descending order based on predictive_accuracy with
 # hyperparameters
 evals_setups = openml.evaluations.list_evaluations_setups(
-    function="predictive_accuracy", tasks=[31], size=100, sort_order="desc"
+    function="predictive_accuracy",
+    tasks=[31],
+    size=100,
+    sort_order="desc",
 )
 
 ""