Fix coverage (#114)

Author: flying-sheep

.github/workflows/ci.yml

@@ -14,7 +14,8 @@ concurrency:
 
 env:
   PIP_ROOT_USER_ACTION: ignore
-  COLUMNS: 200
+  COLUMNS: "200"
+  FORCE_COLOR: "1"
 
 jobs:
   build:

codecov.yml

@@ -0,0 +1,6 @@
+coverage:
+  status:
+    project:
+      default:
+        target: 100%
+        if_not_found: failure

docs/_templates/autosummary/base.rst

@@ -10,8 +10,20 @@ Included extensions
 .. autosummary::
    :toctree: .
 
-   autosummary_generate_imported
    definition_list_typed_field
    elegant_typehints
    rtd_github_links
    theme
+
+.. hidden deprecated extension(s):
+
+.. toctree::
+   :hidden:
+
+   scanpydoc.autosummary_generate_imported
+
+..
+    .. autosummary::
+       :toctree: .
+
+       autosummary_generate_imported

docs/_templates/autosummary/module.rst

@@ -76,10 +76,12 @@ strict = true
 length-sort = true
 lines-after-imports = 2
 known-first-party = ['scanpydoc']
+required-imports = ["from __future__ import annotations"]
 
 [tool.mypy]
 strict = true
 explicit_package_bases = true
+disallow_untyped_defs = false  # handled by Ruff
 mypy_path = ['$MYPY_CONFIG_FILE_DIR/src']
 
 [tool.hatch.version]
@@ -103,6 +105,7 @@ features = ['test', 'typehints']
 run = 'pytest -vv {args}'
 cov = [
     'coverage run -m pytest -vv {args}',
+    'coverage xml',
     'coverage-rich report',
 ]
 
@@ -111,6 +114,10 @@ addopts = [
     '--import-mode=importlib',
     '-psphinx.testing.fixtures',
 ]
+filterwarnings = [
+    'error',
+    'ignore:The frontend.Option:DeprecationWarning',
+]
 
 [tool.coverage.run]
 source_pkgs = ["scanpydoc"]
@@ -122,8 +129,6 @@ exclude_lines = [
   "if __name__ == .__main__.:",
   "if TYPE_CHECKING:",
 ]
-[tool.coverage_rich]
-fail-under = 70
 
 [build-system]
 requires = ['hatchling', 'hatch-vcs']

docs/index.rst

@@ -37,8 +37,7 @@ def _setup_sig(fn: C) -> C:
 
 @_setup_sig
 def setup(app: Sphinx) -> dict[str, Any]:
-    """Set up all included extensions!."""
-    app.setup_extension("scanpydoc.autosummary_generate_imported")
+    """Set up all included extensions!"""  # noqa: D400
     app.setup_extension("scanpydoc.definition_list_typed_field")
     app.setup_extension("scanpydoc.elegant_typehints")
     app.setup_extension("scanpydoc.rtd_github_links")

pyproject.toml

@@ -1,69 +1,33 @@
-"""Generate autosummary docs for imported members.
+"""Generate autosummary for imported members.
 
-This extension patches the :mod:`~sphinx.ext.autosummary` extension
-to generate docs for imported members.
-It needs to be loaded and :confval:`autosummary_generate` needs to be set to ``True``.
+.. deprecated:: 0.11.0
 
-This will hopefully be superseded by the ability to add ``:imported-members:``
-to `autosummary templates`_ in the future. See `Sphinx issue 4372`_.
-
-.. _autosummary templates: http://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html#customizing-templates
-.. _Sphinx issue 4372: https://github.com/sphinx-doc/sphinx/issues/4372
+   Use ``autosummary_imported_members = True`` instead.
 """
+
 from __future__ import annotations
 
-import logging
-from typing import TYPE_CHECKING, Any
-from pathlib import Path
+import sys
+from typing import TYPE_CHECKING
 
-from sphinx.ext import autosummary
-from sphinx.ext.autosummary.generate import generate_autosummary_docs
 
-from . import metadata, _setup_sig
+if sys.version_info >= (3, 11):
+    from typing import Never
+else:  # pragma: no cover
+    from typing import NoReturn as Never
+
+from . import _setup_sig
 
 
 if TYPE_CHECKING:
     from sphinx.application import Sphinx
 
 
-logger = logging.getLogger(__name__)
-
-
-def _generate_stubs(app: Sphinx) -> None:
-    gen_files = app.config.autosummary_generate
-
-    if gen_files and not hasattr(gen_files, "__len__"):
-        env = app.builder.env
-        gen_files = [
-            env.doc2path(x, base=False)
-            for x in env.found_docs
-            if Path(env.doc2path(x)).is_file()
-        ]
-    if not gen_files:
-        return
-
-    ext = app.config.source_suffix
-    gen_files = [
-        genfile + ("" if genfile.endswith(tuple(ext)) else ext[0])
-        for genfile in gen_files
-    ]
-
-    suffix = autosummary.get_rst_suffix(app)
-    if suffix is None:
-        return
-
-    generate_autosummary_docs(
-        gen_files,
-        suffix=suffix,
-        base_path=app.srcdir,
-        imported_members=True,
-        app=app,
-    )
-
-
 @_setup_sig
-def setup(_app: Sphinx) -> dict[str, Any]:
-    """Patch autosummary to generate docs for imported members as well."""
-    autosummary.process_generate_options = _generate_stubs
-
-    return metadata
+def setup(_app: Sphinx) -> Never:  # pragma: no cover
+    """Throws an :exc:`ImportError`."""
+    msg = (
+        "Please use `autosummary_imported_members = True` "
+        f"instead of the {__name__} Sphinx extension."
+    )
+    raise ImportError(msg)

src/scanpydoc/__init__.py

@@ -7,7 +7,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, cast
+from typing import TYPE_CHECKING
 
 from sphinx import addnodes
 from docutils import nodes
@@ -60,11 +60,11 @@ def handle_item(
 
             field_type = types.pop(fieldarg, None)
             if field_type is not None:
+                # convert `param : SomeClass` into reference
                 if len(field_type) == 1 and isinstance(field_type[0], nodes.Text):
-                    [text_node] = cast(tuple[nodes.Text], field_type)
                     classifier_content = make_refs(
                         self.typerolename,
-                        text_node.astext(),
+                        field_type[0].astext(),
                         addnodes.literal_emphasis,
                     )
                 else:

src/scanpydoc/autosummary_generate_imported.py

@@ -49,12 +49,10 @@ def x() -> Tuple[int, float]:
 
 from typing import TYPE_CHECKING, Any
 from pathlib import Path
-from functools import partial
 from collections import ChainMap
 from dataclasses import dataclass
 
 from sphinx.ext.autodoc import ClassDocumenter
-from docutils.parsers.rst import roles
 
 from scanpydoc import metadata, _setup_sig
 
@@ -113,14 +111,9 @@ def setup(app: Sphinx) -> dict[str, Any]:
     app.add_config_value("annotate_defaults", default=True, rebuild="html")
     app.connect("config-inited", _init_vars)
 
-    from ._formatting import _role_annot, typehints_formatter
+    from ._formatting import typehints_formatter
 
     app.config["typehints_formatter"] = PickleableCallable(typehints_formatter)
-    for name in ["annotation-terse", "annotation-full"]:
-        roles.register_canonical_role(
-            name,
-            partial(_role_annot, additional_classes=name.split("-")),
-        )
 
     from ._autodoc_patch import dir_head_adder