DOC - adding a guide on how to write examples (#1578)

Author: rcap107

CONTRIBUTING.rst

@@ -1,3 +1,5 @@
+.. _contributing:
+
 Contributing to skrub
 =====================
 
@@ -59,6 +61,15 @@ To help us resolve the issue quickly, please include:
 - A **code snippet** that reproduces the issue, if applicable.
 - **Version information** for Python, skrub, and relevant dependencies (e.g., scikit-learn, numpy, pandas).
 
+How to write an example?
+^^^^^^^^^^^^^^^^^^^^^^^^^
+We highly encourage contributors to add examples to the documentation
+when they add new features, or if they have a use case that is not yet covered
+in the documentation.
+
+You can find a guide on how to write examples in the :ref:`example guide <tutorial_write_example>`.
+
+
 Suggesting enhancements
 ~~~~~~~~~~~~~~~~~~~~~~~
 

doc/development.rst

@@ -14,4 +14,5 @@ facilitate learning on databases.
     vision
     about
     CONTRIBUTING
+    tutorial_example
     RELEASE_PROCESS

doc/tutorial_example.rst

@@ -0,0 +1,239 @@
+.. _tutorial_write_example:
+
+.. |TableVectorizer| replace:: :class:`~skrub.TableVectorizer`
+
+How to write an example for the gallery
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+This tutorial explains to new contributors how to format their examples so that
+they are properly rendered in the skrub documentation gallery.
+
+While examples are written in plain Python code, there are some quirks to be aware of
+when writing them, due to the way Sphinx and the sphinx-gallery extension work.
+This tutorial explains these quirks and how to work around them.
+
+Location of the examples
+-----------------------
+
+Once you decide on the subject of your example, start writing the code as a Python
+script. Place the script in the ``examples/`` folder of the repository. The example
+should be self-contained and runnable as a standalone script. The documentation is
+built by executing the code and generating additional content from it.
+
+The name of the file should start with a number, followed by an underscore,
+and then a short description of the example. The number is used to order the examples
+in the documentation. For instance, if your example is about using the
+|TableVectorizer| class, you might want to name the file ``01_table_vectorizer.py``.
+
+Note that the ``examples/`` folder is covered by ``pre-commit`` hooks, which run
+various checks on your code when you try to commit. These checks may block you from
+pushing.
+
+Dealing with typos in the example
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+If your code includes any kind of intentional typo, for example if you are trying
+to correct names by replacing a string with a typo with the new one, the
+``codespell`` hook will block your commit. To bypass this, update ``pyproject.toml``
+by adding the typo to the ``ignore-word-list`` entry in the ``tool.codespell``
+section. After this, commit the updated ``pyproject.toml`` file using
+``git commit --no-verify`` to bypass local checks so that following commits will
+ignore the typos.
+Note that without updating ``pyproject.toml``, the CI will still reject commits
+with typos, as it runs the same hooks that are run locally.
+
+Writing the example
+-----------------------
+Your python script should start with a docstring that briefly explains what the example
+is about. This docstring can contain multiple paragraphs and will be rendered
+as a RST file in the documentation, so you can use RST syntax
+in it.
+
+Importantly, the first line of the docstring should be the title of the example,
+not an RST directive (such as ``.. replace::`` or ``.. note::``). Sphinx
+adds a reference to the example at the top of the page using the file name as the
+title. Adding a directive at the top of the docstring would prevent proper HTML
+rendering.
+
+This is an example of what the beginning of your example may look like:
+
+.. code-block:: python
+
+    """
+    Title of the example
+    ====================
+
+    This is a brief description of the example. It can contain multiple paragraphs,
+    and it can use RST syntax.
+
+    .. note::
+
+        You can use RST directives in the docstring, such as ``.. note::``,
+        ``.. warning::``, ``.. seealso::``, etc.
+
+    After the definition of the title, you may also add directives such as
+    ``.. replace::``, and they will be rendered properly. For example, you can add:
+
+    .. |TableVectorizer| replace:: :class:`~skrub.TableVectorizer`
+
+
+    """
+
+Then, you can start writing the code for the example. The content of your Python script
+should be a sequence of code cells, each delimited by a line starting with ``# %%``.
+These code cells may contain comments, which will be rendered as rst in the final
+documentation.
+
+After the docstring, write the code for your example as a sequence of code cells,
+each delimited by a line starting with ``# %%``. Comments in these cells will be
+rendered as RST in the final documentation.
+
+.. code-block:: python
+
+    # %%
+    # This is a comment that will be rendered as markdown in the final documentation.
+    # You can use multiple lines for comments, and you can use RST syntax in them.
+
+    import pandas as pd
+    from skrub import TableVectorizer
+
+    # %%
+    # This is another code cell. You can write any python code here.
+    df = pd.DataFrame({
+        "A": [1, 2, 3],
+        "B": ["a", "b", "c"]
+    })
+    tv = TableVectorizer()
+    X = tv.fit_transform(df)
+    print(X)
+
+Running the example
+-------------------
+
+Once you have written the code for the example (or while writing it), you can run
+it to see how it looks in the final documentation. Depending on your setup, you
+may need to install some dependencies. Refer to your IDE's documentation for more
+information on running interactive Python scripts. For example, VSCode documentation
+is available `here <https://code.visualstudio.com/docs/python/jupyter-support-py>`_.
+
+Once you are happy with your example, you can submit a pull request to the repository,
+following the instructions in the :ref:`contributing guide <contributing>`.
+
+Adding cross-references
+-----------------------
+
+Adding cross-references to the documentation helps users find more information
+about the concepts and functions used in your example. This step is optional, and
+you may ask the maintainers for help on which cross-references to add. Good
+cross-references include relevant user guide sections, the documentation of the
+objects used in the example (like the |TableVectorizer|), or other examples.
+
+You can add cross-references in the docstring and comments of your example in several ways:
+
+- You can add references to the objects in the skrub API using the ``:class:`~skrub.ClassName```
+  or ``:func:`~skrub.function_name``` directives.
+- If your example uses the same objects multiple times, you can define a replacement at the top
+  of the docstring using the ``.. replace::`` directive, and then use the replacement
+  instead of the full directive.
+- You can also add references to other sections of the documentation using the
+  ``:ref:`label``` directive, where ``label`` is the label of the section you want to reference.
+
+
+For example, if your example uses the |TableVectorizer| class multiple times, define
+a replacement at the top of the docstring. You may also want to add a reference
+to the user guide section about the |TableVectorizer| class. This can be done as follows:
+
+.. code-block:: python
+
+    """
+    Title of the example
+    ====================
+
+    .. |TableVectorizer| replace:: :class:`~skrub.TableVectorizer`
+
+    This example demonstrates how to use the |TableVectorizer| class to vectorize a dataframe.
+
+    See the :ref:`user_guide_building_pipeline_index` guide for more information about the |TableVectorizer| class.
+    """
+
+    # %%
+    import pandas as pd
+    from skrub import TableVectorizer
+
+    df = pd.DataFrame({
+        "A": [1, 2, 3],
+        "B": ["a", "b", "c"]
+    })
+    tv = TableVectorizer()
+    X = tv.fit_transform(df)
+    print(X)
+
+You may find more information on the cross-references in the
+`official Sphinx documentation <https://www.sphinx-doc.org/en/master/usage/referencing.html>`_.
+
+
+Generating the new documentation
+-------------------------------
+Once you have written your example and added any necessary cross-references, you can
+generate the new documentation to see how it looks. This can be done in two ways:
+
+- You can run the commands ``make html`` or ``make html-noplot`` in the ``doc/``
+  folder of the repository to generate the HTML documentation for the entire project.
+- Alternatively, you can use ``pixi run -e doc build-doc`` or ``pixi run -e doc build-doc-quick``
+  from the root folder to generate the documentation. The advantage of using ``pixi`` is that
+  it automatically sets up a virtual environment with the necessary dependencies, so you
+  don't need to worry about installing them manually.
+
+The ``make html`` and ``pixi run -e doc build-doc`` commands generate complete
+documentation by executing all example code. The ``-noplot`` (or ``-quick``)
+versions skip code execution, making documentation generation much faster. Use
+these faster versions to check formatting when you've already tested your example
+code locally.
+
+The CI pipeline will always run the full documentation build, so you can safely
+use ``make html-noplot`` or ``pixi run -e doc build-doc-quick`` for local testing.
+
+
+After generating the documentation, open the ``index.html`` file in the ``doc/_build/html/``
+folder with a web browser to review the results. Check that:
+
+- Section titles are properly formatted.
+- Any formatting in docstrings or comments is rendered as intended. For example,
+  Sphinx uses spaces to delimit lists and code blocks, so if you have them in the
+  example, make sure that they render correctly.
+- Cross-references are working. You can check the logs of the Sphinx
+  generation to see if there are any broken references.
+
+
+Linking your work to examples already in the documentation
+----------------------------------------------------------
+After generating the documentation, you may want to add references to your example
+in other relevant parts of the documentation. This helps users find your example
+when reading about related topics.
+
+
+This step is done after generating the documentation because you need the final
+reference name, which is created dynamically from your file name. For example,
+if your file is named ``99_my_example.py``:
+
+1. The generated files will be in ``doc/auto_examples``
+2. A reference file will be created at ``doc/auto_examples/99_my_example.rst``
+3. The reference label will be ``.. _sphx_glr_auto_examples_99_my_example.py``
+
+To link to your example from other documentation pages, use:
+
+.. code-block:: rst
+
+    :ref:`sphx_glr_auto_examples_99_my_example.py`
+
+
+
+Merging your example
+-----------------------
+Finally, if everything looks good, commit your changes and submit a pull request
+to the repository. For more information, see the :ref:`contributing guide <contributing>`.
+
+
+Your PR will be reviewed by the maintainers, who may suggest changes or improvements.
+Once approved, it will be merged into the main branch, and your example will
+become part of the official documentation. Thank you!