doc: Make Docs Work Again and Stop Progress.rst Usage (#1365)

* fix/maint: deprecate outdated examples, discounting progress.rst, and minor fixes to the tests.

* doc: update wording to reflect new state

CONTRIBUTING.md

@@ -141,7 +141,7 @@ following rules before you submit a pull request:
 
 -  If your pull request addresses an issue, please use the pull request title
    to describe the issue and mention the issue number in the pull request description. This will make sure a link back to the original issue is
-   created.
+   created. Make sure the title is descriptive enough to understand what the pull request does! 
 
 -  An incomplete contribution -- where you expect to do more work before
    receiving a full review -- should be submitted as a `draft`. These may be useful
@@ -174,8 +174,6 @@ following rules before you submit a pull request:
    For the Bug-fixes case, at the time of the PR, this tests should fail for
    the code base in develop and pass for the PR code.
 
- - Add your changes to the changelog in the file doc/progress.rst.
-
  - If any source file is being added to the repository, please add the BSD 3-Clause license to it.
 
 
@@ -201,17 +199,12 @@ Make sure your code has good unittest **coverage** (at least 80%).
 
 Pre-commit is used for various style checking and code formatting.
 Before each commit, it will automatically run:
- - [black](https://black.readthedocs.io/en/stable/) a code formatter.
+ - [ruff](https://docs.astral.sh/ruff/) a code formatter and linter.
    This will automatically format your code.
    Make sure to take a second look after any formatting takes place,
    if the resulting code is very bloated, consider a (small) refactor.
-   *note*: If Black reformats your code, the commit will automatically be aborted.
-   Make sure to add the formatted files (back) to your commit after checking them.
  - [mypy](https://mypy.readthedocs.io/en/stable/) a static type checker.
    In particular, make sure each function you work on has type hints.
- - [flake8](https://flake8.pycqa.org/en/latest/index.html) style guide enforcement.
-   Almost all of the black-formatted code should automatically pass this check,
-   but make sure to make adjustments if it does fail.
 
 If you want to run the pre-commit tests without doing a commit, run:
 ```bash
@@ -224,23 +217,6 @@ $ pre-commit run --all-files
 Make sure to do this at least once before your first commit to check your setup works.
 
 Executing a specific unit test can be done by specifying the module, test case, and test.
-To obtain a hierarchical list of all tests, run
-
-```bash
-$  pytest --collect-only
-
- <Module 'tests/test_datasets/test_dataset.py'>
-   <UnitTestCase 'OpenMLDatasetTest'>
-     <TestCaseFunction 'test_dataset_format_constructor'>
-     <TestCaseFunction 'test_get_data'>
-     <TestCaseFunction 'test_get_data_rowid_and_ignore_and_target'>
-     <TestCaseFunction 'test_get_data_with_ignore_attributes'>
-     <TestCaseFunction 'test_get_data_with_rowid'>
-     <TestCaseFunction 'test_get_data_with_target'>
-   <UnitTestCase 'OpenMLDatasetTestOnTestServer'>
-     <TestCaseFunction 'test_tagging'>
-```
-
 You may then run a specific module, test case, or unit test respectively:
 ```bash
   $ pytest tests/test_datasets/test_dataset.py
@@ -271,7 +247,7 @@ information.
 
 For building the documentation, you will need to install a few additional dependencies:
 ```bash
-$ pip install -e .[docs]
+$ pip install -e .[examples,docs]
 ```
 When dependencies are installed, run
 ```bash

doc/progress.rst

@@ -3,11 +3,11 @@
 .. _progress:
 
 =========
-Changelog
+Changelog (discontinued after version 0.15.0)
 =========
 
-next
-~~~~~~
+See GitHub releases for the latest changes.
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 0.15.0
 ~~~~~~

examples/30_extended/flows_and_runs_tutorial.py

@@ -101,7 +101,7 @@
                 [
                     (
                         "categorical",
-                        preprocessing.OneHotEncoder(sparse=False, handle_unknown="ignore"),
+                        preprocessing.OneHotEncoder(handle_unknown="ignore"),
                         cat,  # returns the categorical feature indices
                     ),
                     (
@@ -145,7 +145,7 @@
                 [
                     (
                         "categorical",
-                        preprocessing.OneHotEncoder(sparse=False, handle_unknown="ignore"),
+                        preprocessing.OneHotEncoder(handle_unknown="ignore"),
                         categorical_feature_indices,
                     ),
                     (

examples/30_extended/run_setup_tutorial.py

@@ -58,7 +58,7 @@
 
 
 cat_imp = make_pipeline(
-    OneHotEncoder(handle_unknown="ignore", sparse=False),
+    OneHotEncoder(handle_unknown="ignore"),
     TruncatedSVD(),
 )
 cont_imp = SimpleImputer(strategy="median")

examples/40_paper/2018_kdd_rijn_example.py

@@ -4,8 +4,10 @@
 
 A tutorial on how to reproduce the paper *Hyperparameter Importance Across Datasets*.
 
-This is a Unix-only tutorial, as the requirements can not be satisfied on a Windows machine (Untested on other
-systems).
+Example Deprecation Warning!
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This example is not supported anymore by the OpenML-Python developers. The example is kept for reference purposes but not tested anymore.
 
 Publication
 ~~~~~~~~~~~
@@ -14,6 +16,16 @@
 | Jan N. van Rijn and Frank Hutter
 | In *Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining*, 2018
 | Available at https://dl.acm.org/doi/10.1145/3219819.3220058
+
+Requirements
+~~~~~~~~~~~~
+
+This is a Unix-only tutorial, as the requirements can not be satisfied on a Windows machine (Untested on other
+systems).
+
+The following Python packages are required:
+
+pip install openml[examples,docs] fanova ConfigSpace<1.0
 """
 
 # License: BSD 3-Clause
@@ -26,6 +38,10 @@
     )
     exit()
 
+# DEPRECATED EXAMPLE -- Avoid running this code in our CI/CD pipeline
+print("This example is deprecated, remove this code to use it manually.")
+exit()
+
 import json
 import fanova
 import matplotlib.pyplot as plt

pyproject.toml

@@ -86,7 +86,6 @@ examples=[
     "ipykernel",
     "seaborn",
 ]
-examples_unix=["fanova"]
 docs=[
     "sphinx>=3",
     "sphinx-gallery",