BUG: Fix serialization with Sphinx 7.3 (#1289)

Co-authored-by: Lucy Liu <[email protected]>

.circleci/config.yml

@@ -38,7 +38,7 @@ jobs:
           command: |
             pip install --upgrade --only-binary ":all:" pip setuptools
             pip install --upgrade --only-binary ":all:" \
-                numpy matplotlib seaborn statsmodels pillow joblib sphinx pytest traits pyvista memory_profiler "ipython!=8.7.0" plotly graphviz "docutils>=0.18" imageio pydata-sphinx-theme \
+                numpy matplotlib seaborn statsmodels pillow joblib "sphinx!=7.3.2,!=7.3.3,!=7.3.4,!=7.3.5,!=7.3.6" pytest traits pyvista memory_profiler "ipython!=8.7.0" plotly graphviz "docutils>=0.18" imageio pydata-sphinx-theme \
                 "jupyterlite-sphinx>=0.8.0,<0.9.0" "jupyterlite-pyodide-kernel<0.1.0" libarchive-c
             pip uninstall -yq vtk  # pyvista installs vtk above
             pip install --upgrade --only-binary ":all" --extra-index-url https://wheels.vtk.org vtk-osmesa
@@ -66,7 +66,12 @@ jobs:
       - attach_workspace:
           at: ~/
       - bash_env
-      - run: sphinx-build doc doc/_build/html -nW --keep-going -b html
+      - run: sphinx-build doc doc/_build/html -nW --keep-going -b html 2>&1 | tee sphinx_log.txt
+      - run:
+          name: Check sphinx log for warnings (which are treated as errors)
+          when: always
+          command: |
+            ! grep "^.* WARNING: .*$" sphinx_log.txt
       - store_artifacts:
           path: doc/_build/html/
           destination: html

.github/install.sh

@@ -31,6 +31,8 @@ if [ "$SPHINX_VERSION" == "dev" ]; then
     PIP_DEPENDENCIES="--upgrade --pre https://api.github.com/repos/sphinx-doc/sphinx/zipball/master --default-timeout=60 --extra-index-url 'https://pypi.anaconda.org/scientific-python-nightly-wheels/simple' $PIP_DEPENDENCIES"
 elif [ "$SPHINX_VERSION" != "default" ]; then
     PIP_DEPENDENCIES="sphinx==${SPHINX_VERSION}.* $PIP_DEPENDENCIES"
+else
+    PIP_DEPENDENCIES="sphinx!=7.3.2,!=7.3.3,!=7.3.4,!=7.3.5,!=7.3.6 $PIP_DEPENDENCIES"
 fi
 
 set -x

.pre-commit-config.yaml

@@ -5,6 +5,7 @@ repos:
       - id: ruff-format
         exclude: plot_syntaxerror
       - id: ruff
+        args: ["--fix"]
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.6

CHANGES.rst

@@ -1,6 +1,17 @@
 Changelog
 =========
 
+v0.16.0
+-------
+Sphinx 7.3.0 and above changed caching and serialization checks. Now instead of passing
+instantiated classes like ``ResetArgv()``, classes like ``FileNameSortKey``, or
+callables like ``notebook_modification_function`` in  ``sphinx_gallery_conf``,
+you should pass fully qualified name strings to classes or callables. If you change
+to using name strings, you can simply use a function as the use of classes to ensure
+a stable ``__repr__`` would be redundant.
+
+See :ref:`importing_callables` for details.
+
 v0.15.0
 -------
 

dev-requirements.txt

@@ -1,4 +1,5 @@
-sphinx >= 4, != 5.2.0
+# see https://github.com/sphinx-doc/sphinx/issues/12299
+sphinx>=4,!= 5.2.0,!=7.3.2,!=7.3.3,!=7.3.4,!=7.3.5,!=7.3.6
 pydata-sphinx-theme
 pytest
 pytest-coverage

doc/advanced.rst

@@ -216,45 +216,43 @@ It uses an approach similar to what
 :func:`sphinx_gallery.scrapers.matplotlib_scraper` does under the hood, which
 use the helper function :func:`sphinx_gallery.scrapers.figure_rst` to
 create the standardized reST. If your package will be used to write an image
-file to disk (e.g., PNG or JPEG), we recommend you use a similar approach,
-but via a class so that the ``__repr__`` can remain stable across Sphinx runs::
+file to disk (e.g., PNG or JPEG), we recommend you use a similar approach::
 
-    class MyModuleScraper():
-        def __repr__(self):
-            return 'MyModuleScraper'
+    def my_module_scraper(block, block_vars, gallery_conf):
+        import mymodule
+        # We use a list to collect references to image names
+        image_names = list()
+        # The `image_path_iterator` is created by Sphinx-Gallery, it will yield
+        # a path to a file name that adheres to Sphinx-Gallery naming convention.
+        image_path_iterator = block_vars['image_path_iterator']
 
-        def __call__(self, block, block_vars, gallery_conf):
-            import mymodule
-            # We use a list to collect references to image names
-            image_names = list()
-            # The `image_path_iterator` is created by Sphinx-Gallery, it will yield
-            # a path to a file name that adheres to Sphinx-Gallery naming convention.
-            image_path_iterator = block_vars['image_path_iterator']
+        # Define a list of our already-created figure objects.
+        list_of_my_figures = mymodule.get_figures()
 
-            # Define a list of our already-created figure objects.
-            list_of_my_figures = mymodule.get_figures()
+        # Iterate through figure objects, save to disk, and keep track of paths.
+        for fig, image_path in zip(list_of_my_figures, image_path_iterator):
+            fig.save_png(image_path)
+            image_names.append(image_path)
 
-            # Iterate through figure objects, save to disk, and keep track of paths.
-            for fig, image_path in zip(list_of_my_figures, image_path_iterator):
-                fig.save_png(image_path)
-                image_names.append(image_path)
+        # Close all references to figures so they aren't used later.
+        mymodule.close('all')
 
-            # Close all references to figures so they aren't used later.
-            mymodule.close('all')
+        # Use the `figure_rst` helper function to generate the reST for this
+        # code block's figures. Alternatively you can define your own reST.
+        return figure_rst(image_names, gallery_conf['src_dir'])
 
-            # Use the `figure_rst` helper function to generate the reST for this
-            # code block's figures. Alternatively you can define your own reST.
-            return figure_rst(image_names, gallery_conf['src_dir'])
-
-This code would be defined either in your ``conf.py`` file, or as a module that
-you import into your ``conf.py`` file. The configuration needed to use this
-scraper would look like::
+This code could be defined either in your ``conf.py`` file, or as a module that
+you import into your ``conf.py`` file (see :ref:`importing_callables`).
+The configuration needed to use this scraper would look like::
 
     sphinx_gallery_conf = {
         ...
-        'image_scrapers': ('matplotlib', MyModuleScraper()),
+        'image_scrapers': ('matplotlib', "my_module._scraper.my_module_scraper"),
     }
 
+Where Sphinx-Gallery will parse the string ``"my_module._scraper.my_module_scraper"``
+to import the callable function.
+
 Example 2: detecting image files on disk
 ----------------------------------------
 
@@ -264,67 +262,55 @@ the reST needed to embed them in the documentation. Note that the example script
 will still need to be executed to scrape the files, but the images
 don't need to be produced during the execution.
 
-We'll use a callable class in this case, and assume it is defined within your
-package in a module called ``scraper``. Here is the scraper code::
+We assume the function is defined within your
+package in a module called ``_scraper``. Here is the scraper code::
 
     from glob import glob
     import shutil
     import os
     from sphinx_gallery.scrapers import figure_rst
 
-    class PNGScraper(object):
-        def __init__(self):
-            self.seen = set()
-
-        def __repr__(self):
-            return 'PNGScraper'
-
-        def __call__(self, block, block_vars, gallery_conf):
-            # Find all PNG files in the directory of this example.
-            path_current_example = os.path.dirname(block_vars['src_file'])
-            pngs = sorted(glob(os.path.join(path_current_example, '*.png')))
-
-            # Iterate through PNGs, copy them to the sphinx-gallery output directory
-            image_names = list()
-            image_path_iterator = block_vars['image_path_iterator']
-            for png in pngs:
-                if png not in self.seen:
-                    self.seen |= set(png)
-                    this_image_path = image_path_iterator.next()
-                    image_names.append(this_image_path)
-                    shutil.move(png, this_image_path)
-            # Use the `figure_rst` helper function to generate reST for image files
-            return figure_rst(image_names, gallery_conf['src_dir'])
-
+    def png_scraper(block, block_vars, gallery_conf):
+        # Find all PNG files in the directory of this example.
+        path_current_example = os.path.dirname(block_vars['src_file'])
+        pngs = sorted(glob(os.path.join(path_current_example, '*.png')))
+
+        # Iterate through PNGs, copy them to the Sphinx-Gallery output directory
+        image_names = list()
+        image_path_iterator = block_vars['image_path_iterator']
+        seen = set()
+        for png in pngs:
+            if png not in seen:
+                seen |= set(png)
+                this_image_path = image_path_iterator.next()
+                image_names.append(this_image_path)
+                shutil.move(png, this_image_path)
+        # Use the `figure_rst` helper function to generate reST for image files
+        return figure_rst(image_names, gallery_conf['src_dir'])
 
 Then, in our ``conf.py`` file, we include the following code::
 
-   from mymodule import PNGScraper
-
    sphinx_gallery_conf = {
        ...
-       'image_scrapers': ('matplotlib', PNGScraper()),
+       'image_scrapers': ('matplotlib', 'my_module._scraper.png_scraper'),
    }
 
 Example 3: matplotlib with SVG format
 -------------------------------------
 The :func:`sphinx_gallery.scrapers.matplotlib_scraper` supports ``**kwargs``
 to pass to :meth:`matplotlib.figure.Figure.savefig`, one of which is the
 ``format`` argument. See :ref:`custom_scraper` for supported formats.
-To use SVG, you can do::
+To use SVG you can define the following function and ensure it is
+:ref:`importable <importing_callables>`::
 
-    from sphinx_gallery.scrapers import matplotlib_scraper
+    def matplotlib_svg_scraper(*args, **kwargs):
+        return matplotlib_scraper(*args, format='svg', **kwargs)
 
-    class matplotlib_svg_scraper(object):
-        def __repr__(self):
-            return self.__class__.__name__
-
-        def __call__(self, *args, **kwargs):
-            return matplotlib_scraper(*args, format='svg', **kwargs)
+Then in your ``conf.py``::
 
     sphinx_gallery_conf = {
         ...
-        'image_scrapers': (matplotlib_svg_scraper(),),
+        'image_scrapers': ("sphinxext.matplotlib_svg_scraper",),
         ...
     }
 
@@ -335,35 +321,31 @@ writing a customized scraper class or function.
 
 Example 4: Mayavi scraper
 -------------------------
-Historically, sphinx-gallery supported scraping Mayavi figures as well as
+Historically, Sphinx-Gallery supported scraping Mayavi figures as well as
 matplotlib figures. However, due to the complexity of maintaining the scraper,
 support was deprecated in version 0.12.0. To continue using a Mayavi scraping,
 consider using something like the following::
 
     from sphinx_gallery.scrapers import figure_rst
 
-    class MayaviScraper():
-        def __repr__(self):
-            return 'MyModuleScraper'
-
-        def __call__(self, block, block_vars, gallery_conf):
-            from mayavi import mlab
-            image_path_iterator = block_vars['image_path_iterator']
-            image_paths = list()
-            e = mlab.get_engine()
-            for scene, image_path in zip(e.scenes, image_path_iterator):
-                try:
-                    mlab.savefig(image_path, figure=scene)
-                except Exception:
-                    mlab.close(all=True)
-                    raise
-                # make sure the image is not too large
-                scale_image(image_path, image_path, 850, 999)
-                if 'images' in gallery_conf['compress_images']:
-                    optipng(image_path, gallery_conf['compress_images_args'])
-                image_paths.append(image_path)
-            mlab.close(all=True)
-            return figure_rst(image_paths, gallery_conf['src_dir'])
+    def mayavi_scraper(self, block, block_vars, gallery_conf):
+        from mayavi import mlab
+        image_path_iterator = block_vars['image_path_iterator']
+        image_paths = list()
+        e = mlab.get_engine()
+        for scene, image_path in zip(e.scenes, image_path_iterator):
+            try:
+                mlab.savefig(image_path, figure=scene)
+            except Exception:
+                mlab.close(all=True)
+                raise
+            # make sure the image is not too large
+            scale_image(image_path, image_path, 850, 999)
+            if 'images' in gallery_conf['compress_images']:
+                optipng(image_path, gallery_conf['compress_images_args'])
+            image_paths.append(image_path)
+        mlab.close(all=True)
+        return figure_rst(image_paths, gallery_conf['src_dir'])
 
 Integrate custom scrapers with Sphinx-Gallery
 ---------------------------------------------
@@ -421,14 +403,15 @@ For example, to reset matplotlib to always use the ``ggplot`` style, you could d
        style.use('ggplot')
 
 Any custom functions can be defined (or imported) in ``conf.py`` and given to
-the ``reset_modules`` configuration key. To add the function defined above::
+the ``reset_modules`` configuration key. To add the function defined above (assuming
+you've make it :ref:`importable <importing_callables>`)::
 
    sphinx_gallery_conf = {
        ...
-       'reset_modules': (reset_mpl, 'seaborn'),
+       'reset_modules': ("sphinxext.reset_mpl", "seaborn"),
    }
 
-In the config above ``'seaborn'`` refers to the native seaborn resetting
+In the config above ``"seaborn"`` refers to the native seaborn resetting
 function (see :ref:`reset_modules`).
 
 .. note:: Using resetters such as ``reset_mpl`` that deviate from the
@@ -441,7 +424,6 @@ after an example, a function signature with three parameters can be used, where
 the third parameter is required to be named ``when``::
 
     def reset_mpl(gallery_conf, fname, when):
-
         import matplotlib as mpl
         mpl.rcParams['lines.linewidth'] = 2
         if when == 'after' and fname=='dashed_lines':