DOC: Fix pydantic_autosummary for sphinx-rtd >= 3

Also fixes an indentation issue.

docs/ext/pydantic_autosummary/__init__.py

@@ -152,6 +152,8 @@ def autosummary_table_visit_html(
 
 
 class FakeApplication:
+    verbosity = 0
+
     def __init__(self) -> None:
         self.doctreedir = None
         self.events = None

docs/ext/pydantic_autosummary/generate.py

@@ -24,6 +24,7 @@
 import re
 import sys
 from os import path
+from pathlib import Path
 from typing import TYPE_CHECKING, Any, NamedTuple
 
 import sphinx.locale
@@ -151,7 +152,7 @@ def __init__(self, app: Sphinx) -> None:
             # ``jinja2.ext.i18n`` extension
             self.env.install_gettext_translations(app.translator)  # type: ignore[attr-defined]
 
-    def render(self, template_name: str, context: dict) -> str:
+    def render(self, template_name: str, context: dict[str, Any]) -> str:
         """Render a template file."""
         try:
             template = self.env.get_template(template_name)
@@ -286,7 +287,7 @@ def generate_autosummary_content(
     imported_members: bool,
     app: Any,
     recursive: bool,
-    context: dict,
+    context: dict[str, Any],
     modname: str | None = None,
     qualname: str | None = None,
 ) -> str:
@@ -505,10 +506,11 @@ def _get_modules(
         fullname = name + "." + modname
         try:
             module = import_module(fullname)
-            if module and hasattr(module, "__sphinx_mock__"):
-                continue
         except ImportError:
             pass
+        else:
+            if module and hasattr(module, "__sphinx_mock__"):
+                continue
 
         items.append(fullname)
         if public_members is not None:
@@ -529,16 +531,18 @@ def generate_autosummary_docs(
     app: Any = None,
     overwrite: bool = True,
     encoding: str = "utf-8",
-) -> None:
+) -> list[Path]:
+    """Generate autosummary documentation for the given sources.
+
+    :returns: list of generated files (both new and existing ones)
+    """
+    assert app is not None, "app is required"
+
     showed_sources = sorted(sources)
     if len(showed_sources) > 20:
         showed_sources = showed_sources[:10] + ["..."] + showed_sources[-10:]
 
     # ----------- pydantic_autosummary change
-    logger.info(
-        __("[pydantic_autosummary] generating autosummary for: %s")
-        % ", ".join(showed_sources)
-    )
     if output_dir:
         logger.info(__("[pydantic_autosummary] writing to %s") % output_dir)
     # ----------/ pydantic_autosummary change
@@ -552,7 +556,8 @@ def generate_autosummary_docs(
     items = find_autosummary_in_files(sources)
 
     # keep track of new files
-    new_files = []
+    new_files: list[Path] = []
+    all_files: list[Path] = []
 
     filename_map = app.config.autosummary_filename_map if app else {}
 
@@ -593,9 +598,7 @@ def generate_autosummary_docs(
                 # ----------/ pydantic_autosummary change
                 continue
 
-        context: dict[str, Any] = {}
-        if app:
-            context.update(app.config.autosummary_context)
+        context: dict[str, Any] = {**app.config.autosummary_context}
 
         content = generate_autosummary_content(
             name,
@@ -611,34 +614,39 @@ def generate_autosummary_docs(
             qualname,
         )
 
-        filename = os.path.join(path, filename_map.get(name, name) + suffix)
-        if os.path.isfile(filename):
-            with open(filename, encoding=encoding) as f:
+        file_path = Path(path, filename_map.get(name, name) + suffix)
+        all_files.append(file_path)
+        if file_path.is_file():
+            with file_path.open(encoding=encoding) as f:
                 old_content = f.read()
 
             if content == old_content:
                 continue
             if overwrite:  # content has changed
-                with open(filename, "w", encoding=encoding) as f:
+                with file_path.open("w", encoding=encoding) as f:
                     f.write(content)
-                new_files.append(filename)
+                new_files.append(file_path)
         else:
-            with open(filename, "w", encoding=encoding) as f:
+            with open(file_path, "w", encoding=encoding) as f:
                 f.write(content)
-            new_files.append(filename)
+            new_files.append(file_path)
 
     # descend recursively to new files
     if new_files:
-        generate_autosummary_docs(
-            new_files,
-            output_dir=output_dir,
-            suffix=suffix,
-            base_path=base_path,
-            imported_members=imported_members,
-            app=app,
-            overwrite=overwrite,
+        all_files.extend(
+            generate_autosummary_docs(
+                [str(f) for f in new_files],
+                output_dir=output_dir,
+                suffix=suffix,
+                base_path=base_path,
+                imported_members=imported_members,
+                app=app,
+                overwrite=overwrite,
+            )
         )
 
+    return all_files
+
 
 # -- Finding documented entries in files ---------------------------------------
 
@@ -848,6 +856,15 @@ def get_parser() -> argparse.ArgumentParser:
             "(default: %(default)s)"
         ),
     )
+    parser.add_argument(
+        "--remove-old",
+        action="store_true",
+        dest="remove_old",
+        default=False,
+        help=__(
+            "Remove existing files in the output directory that were not generated"
+        ),
+    )
 
     return parser
 
@@ -863,18 +880,29 @@ def main(argv: Sequence[str] = (), /) -> None:
 
     if args.templates:
         app.config.templates_path.append(path.abspath(args.templates))
-    app.config.autosummary_ignore_module_all = (  # type: ignore[attr-defined]
-        not args.respect_module_all
-    )
+    app.config.autosummary_ignore_module_all = not args.respect_module_all
 
-    generate_autosummary_docs(
+    written_files = generate_autosummary_docs(
         args.source_file,
         args.output_dir,
         "." + args.suffix,
         imported_members=args.imported_members,
         app=app,
     )
 
+    if args.remove_old:
+        for existing in Path(args.output_dir).glob(f"**/*.{args.suffix}"):
+            if existing not in written_files:
+                try:
+                    existing.unlink()
+                except OSError as exc:
+                    logger.warning(
+                        __("Failed to remove %s: %s"),
+                        existing,
+                        exc.strerror,
+                        type="autosummary",
+                    )
+
 
 if __name__ == "__main__":
     main(sys.argv[1:])

pyproject.toml

@@ -69,7 +69,7 @@ docs = [
     "myst-parser",
     "pydocstyle",
     "sphinx-autodoc-typehints<1.23",
-    "sphinx-rtd-theme<3.0.0",
+    "sphinx-rtd-theme",
     "sphinx-togglebutton",
     "Sphinx",
     "sphinxcontrib-apidoc",

src/fmu/dataio/dataio.py

@@ -309,9 +309,9 @@ class ExportData:
             to metadata will from version 0.9 be different (API change)
 
         vertical_domain: Optional. String with vertical domain either "time" or "depth"
-           (default). It is also possible to provide a reference for the vertical scale,
-            see the domain_reference key. Note that if the ``content`` is "depth" or
-            "time" the vertical_domain will be set accordingly.
+            (default). It is also possible to provide a reference for the vertical
+            scale, see the domain_reference key. Note that if the ``content`` is "depth"
+            or "time" the vertical_domain will be set accordingly.
 
         workflow: Short tag desciption of workflow (as description)