switch to book theme

.github/workflows/ci.yml

@@ -28,6 +28,6 @@ jobs:
       - name: dependencies
         run: |
           pip install --upgrade pip wheel
-          pip install .[test,typehints]
+          pip install -e .[test,typehints]
       - name: tests
         run: pytest --color=yes

.pre-commit-config.yaml

@@ -17,3 +17,6 @@ repos:
     rev: v3.0.0
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@2.8.1 # plugin not yet 3.0 compatible
+          - prettier-plugin-jinja-template

.prettierrc.yaml

@@ -0,0 +1,12 @@
+plugins:
+  - prettier-plugin-jinja-template
+overrides:
+  - files: [settings.json]
+    options:
+      parser: json5
+      quoteProps: preserve
+      singleQuote: false
+      trailingComma: all
+  - files: ["*.html"]
+    options:
+      parser: jinja-template

.vscode/settings.json

@@ -7,6 +7,7 @@
         "editor.formatOnSave": true,
         "editor.codeActionsOnSave": {
             "source.fixAll": true,
+            "source.organizeImports": true,
         },
     },
 }

docs/conf.py

@@ -1,36 +1,35 @@
 import sys
 from datetime import datetime
+from importlib.metadata import metadata
 from pathlib import Path
 
 from sphinx.application import Sphinx
 
 
-# Allow importing scanpydoc itself
 HERE = Path(__file__).parent
-sys.path.insert(0, str(HERE.parent))
-import scanpydoc  # noqa
 
+# necessary for rtd_gh_links’ linkcode support
+sys.path.insert(0, HERE.parent / "src")
 
 # Clean build env
 for file in HERE.glob("scanpydoc.*.rst"):
     file.unlink()
 
-
-needs_sphinx = "1.7"  # autosummary bugfix
 extensions = [
     "sphinx.ext.intersphinx",
     "sphinx.ext.napoleon",
     "sphinx_autodoc_typehints",  # needs to be after napoleon
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
     "scanpydoc",
+    "sphinx.ext.linkcode",  # needs to be after scanpydoc
 ]
 
 intersphinx_mapping = dict(
     python=("https://docs.python.org/3", None),
     jinja=("https://jinja.palletsprojects.com/en/2.10.x/", None),
     sphinx=("https://www.sphinx-doc.org/en/master/", None),
-    sphinx_rtd_theme=("https://sphinx-rtd-theme.readthedocs.io/en/stable/", None),
+    sphinx_book_theme=("https://sphinx-book-theme.readthedocs.io/en/stable/", None),
     # examples
     numpy=("https://numpy.org/doc/stable/", None),
     anndata=("https://anndata.readthedocs.io/en/latest/", None),
@@ -39,10 +38,11 @@
 )
 
 # general information
-project = scanpydoc.__name__
-author = "Philipp Angerer"
+meta = metadata("scanpydoc")
+project = meta["name"]
+author = meta["author-email"].split(" <")[0]
 copyright = f"{datetime.now():%Y}, {author}."
-version = release = scanpydoc.__version__
+version = release = meta["version"]
 
 master_doc = "index"
 templates_path = ["_templates"]
@@ -54,11 +54,13 @@
 
 html_theme = "scanpydoc"
 html_context = dict(
-    github_user="theislab", github_repo="scanpydoc", github_version="main"
+    repository_url="https://github.com/theislab/scanpydoc",
+    repository_branch="main",
+    use_repository_button=True,
 )
 
-# proj/doc/conf.py/../.. → proj
-project_dir = Path(__file__).parent.parent
+# proj/doc/.. → proj
+project_dir = HERE.parent
 
 
 def setup(app: Sphinx):

pyproject.toml

@@ -30,12 +30,11 @@ test = [
     'pytest-cov',
 ]
 doc = [
-    'scanpydoc[typehints]',
-    'sphinx<7', # https://github.com/readthedocs/sphinx_rtd_theme/issues/1463
-    'sphinx-rtd-theme',
+    'scanpydoc[typehints,theme]',
+    'sphinx',
 ]
 typehints = ['sphinx-autodoc-typehints>=1.15.2']
-theme = ['sphinx-rtd-theme']
+theme = ['sphinx-book-theme>=1.0.1']
 
 [project.entry-points.'sphinx.html_themes']
 scanpydoc = 'scanpydoc.theme'
@@ -72,7 +71,7 @@ python = ['3.8', '3.9', '3.10', '3.11']
 [tool.hatch.envs.test]
 features = ['test', 'typehints']
 [tool.hatch.envs.test.scripts]
-test = 'pytest -vv'
+run = 'pytest -vv {args}'
 
 [tool.pytest.ini_options]
 addopts = [

src/scanpydoc/rtd_github_links.py → src/scanpydoc/rtd_github_links/__init__.py

@@ -1,14 +1,40 @@
 """GitHub URLs for class and method pages.
 
-This extension registers a :ref:`Jinja filter <jinja:filters>` called :func:`github_url`
-that you can use to convert a module path into a GitHub URL
+This extension does two things:
+
+#. It registers a :ref:`Jinja filter <jinja:filters>` called :func:`github_url`
+   that you can use to convert a module path into a GitHub URL.
+#. It configures :mod:`sphinx.ext.linkcode` for you if loaded after it in ``conf.py``:
+
+   .. code:: python
+
+      import sys
+      from pathlib import Path
+
+      HERE = Path(__file__).parent
+      # make sure modules are import from the right place
+      sys.path.insert(0, HERE.parent / "src")
+
+      extensions = [
+          "scanpydoc",
+          "sphinx.ext.linkcode",
+      ]
+
+      # no need to define `linkcode_resolve`
 
 Configuration
 -------------
 
 Uses the following config values in ``conf.py``::
 
     project_dir: Path = ...  # default: Path.cwd()
+
+    # sphinx book theme style
+    html_context = dict(
+        repository_url=...,
+        repository_branch=...,
+    )
+    # or RTD theme style:
     html_context = dict(
         github_user=...,
         github_repo=...,
@@ -18,13 +44,14 @@
 The ``project_dir`` is used to figure out the .py file path relative to the git root,
 that is to construct the path in the github URL.
 
-The ``html_context`` is e.g. also used like this in the sphinx_rtd_theme_.
+Which ``html_context`` style you want to use depends on your theme, e.g.
+:doc:`Sphinx Book Theme <sphinx_book_theme:index>`.
 
-Usage
------
+``:github_url:`` usage
+----------------------
 
 You can use the filter e.g. in `autosummary templates`_.
-To configure the sphinx_rtd_theme_,
+To configure the :doc:`Sphinx Book Theme <sphinx_book_theme:index>`,
 override the ``autosummary/base.rst`` template like this:
 
 .. code:: restructuredtext
@@ -35,7 +62,6 @@
 
 .. _autosummary templates: \
    http://www.sphinx-doc.org/en/master/usage/extensions/autosummary.html#customizing-templates
-.. _sphinx_rtd_theme: https://sphinx-rtd-theme.readthedocs.io/en/latest/
 """
 from __future__ import annotations
 
@@ -49,7 +75,7 @@
 from sphinx.application import Sphinx
 from sphinx.config import Config
 
-from . import _setup_sig, metadata
+from .. import _setup_sig, metadata
 
 
 project_dir = None  # type: Path
@@ -60,9 +86,14 @@ def _init_vars(app: Sphinx, config: Config):
     """Called when ``conf.py`` has been loaded."""
     global github_base_url, project_dir
     _check_html_context(config)
-    github_base_url = "https://github.com/{github_user}/{github_repo}/tree/{github_version}".format_map(
-        config.html_context
-    )
+    try:
+        github_base_url = "https://github.com/{github_user}/{github_repo}/tree/{github_version}".format_map(
+            config.html_context
+        )
+    except KeyError:
+        github_base_url = "{repository_url}/tree/{repository_branch}".format_map(
+            config.html_context
+        )
     project_dir = Path(config.project_dir)
 
 
@@ -120,32 +151,36 @@ def github_url(qualname: str) -> str:
     except Exception:
         print(f"Error in github_url({qualname!r}):", file=sys.stderr)
         raise
-    try:
+    try:  # only works when installed in dev mode
         path = PurePosixPath(Path(module.__file__).resolve().relative_to(project_dir))
     except ValueError:
-        # trying to document something from another package
-        path = "/".join(module.__file__.split("/")[-2:])
+        # no dev mode or something from another package
+        path = PurePosixPath(*module.__file__.split("/")[-2:])
+        if (project_dir / "src").is_dir():
+            path = "src" / path
     start, end = _get_linenos(obj)
     fragment = f"#L{start}-L{end}" if start and end else ""
     return f"{github_base_url}/{path}{fragment}"
 
 
 def _check_html_context(config: Config):
     try:
-        html_context = config.html_context
+        html_context: dict[str, Any] = config.html_context
     except AttributeError:
         raise ValueError(
             f"Extension {__name__} needs “html_context” to be defined in conf.py"
         )
-    missing_values = {
-        "github_user",
-        "github_repo",
-        "github_version",
-    } - html_context.keys()
-    if missing_values:
-        mvs = ", ".join([f"html_context[{mv!r}]" for mv in missing_values])
+    options = [
+        {"github_user", "github_repo", "github_version"},
+        {"repository_url", "repository_branch"},
+    ]
+    missing_value_sets = [opt - html_context.keys() for opt in options]
+    if all(missing_value_sets):
+        mvs = " or ".join(
+            ", ".join(repr(mv) for mv in mvs) for mvs in missing_value_sets
+        )
         raise ValueError(
-            f"Extension {__name__} needs “{mvs}” to be defined in conf.py.\n"
+            f"Extension {__name__} needs html_context {mvs} to be defined in conf.py.\n"
             f"html_context = {html_context!r}"
         )
 
@@ -163,6 +198,12 @@ def setup(app: Sphinx) -> dict[str, Any]:
     app.add_config_value("project_dir", proj_dir, "")
     app.connect("config-inited", _init_vars)
 
+    # if linkcode config not set
+    if "linkcode_resolve" not in app.config or app.config["linkcode_resolve"] is None:
+        from ._linkcode import linkcode_resolve
+
+        app.config["linkcode_resolve"] = linkcode_resolve
+
     # html_context doesn’t apply to autosummary templates ☹
     # and there’s no way to insert filters into those templates
     # so we have to modify the default filters

src/scanpydoc/rtd_github_links/_linkcode.py

@@ -0,0 +1,31 @@
+from __future__ import annotations
+
+from typing import Literal, TypedDict
+
+
+class PyInfo(TypedDict):
+    module: str
+    fullname: str
+
+
+class CInfo(TypedDict):
+    """C / C++ info."""
+
+    names: list[str]
+
+
+class JSInfo(TypedDict):
+    object: str
+    fullname: str
+
+
+def linkcode_resolve(
+    domain: Literal["py", "c", "cpp", "javascript"], info: PyInfo | CInfo | JSInfo
+) -> str | None:
+    from . import github_url
+
+    if domain != "py":
+        return None
+    if not info["module"]:
+        return None
+    return github_url(f'{info["module"]}.{info["fullname"]}')

src/scanpydoc/theme/__init__.py

@@ -1,4 +1,4 @@
-"""A widescreen extension for :doc:`sphinx_rtd_theme:index`.
+"""A widescreen extension for :doc:`sphinx_book_theme:index`.
 
 Add to ``conf.py``:
 
@@ -19,14 +19,14 @@
 
    The CSS color used for the mobile header background and the project name text.
 
-See ``sphinx_rtd_theme``’s :doc:`sphinx_rtd_theme:configuring`, e.g.:
+See ``sphinx_book_theme``’s :doc:`sphinx_book_theme:reference`, e.g.:
 
 .. code:: python
 
    html_theme_options = dict(
-       logo_only=False,
-       accent_color='rebeccapurple',
-       display_version=False,
+       repository_url="https://github.com/theislab/scanpydoc",
+       repository_branch="main",
+       use_repository_button=True,
    )
 
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