Update instance repo (PR 154) (#42)

* Update instance repo from cookiecutter template * Update instance repo from cookiecutter template * Update instance repo from cookiecutter template * Update instance repo from cookiecutter template * Update instance repo from cookiecutter template * Update instance repo from cookiecutter template * Update instance repo from cookiecutter template --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
scverse · Mar 7, 2023 · 9ce0ca0 · 9ce0ca0
1 parent d006d41
commit 9ce0ca0
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Showing 5 changed files with 15 additions and 16 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@ repos:
       hooks:
           - id: blacken-docs
     - repo: https://github.com/pre-commit/mirrors-prettier
-      rev: v3.0.0-alpha.4
+      rev: v3.0.0-alpha.6
       hooks:
           - id: prettier
             # Newer versions of node don't work on systems that have an older version of GLIBC
@@ -25,7 +25,7 @@ repos:
             # https://github.com/jupyterlab/jupyterlab/issues/12675
             language_version: "17.9.1"
     - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.0.252
+      rev: v0.0.254
       hooks:
           - id: ruff
             args: [--fix, --exit-non-zero-on-fix]

diff --git a/docs/_templates/autosummary/class.rst b/docs/_templates/autosummary/class.rst
@@ -39,9 +39,6 @@ Attributes
 
 {% for item in attributes %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. autoattribute:: {{ [objname, item] | join(".") }}
 {%- endfor %}
 
@@ -56,9 +53,6 @@ Methods
 {% for item in methods %}
 {%- if item != '__init__' %}
 
-{{ item }}
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
 .. automethod:: {{ [objname, item] | join(".") }}
 {%- endif -%}
 {%- endfor %}

diff --git a/docs/conf.py b/docs/conf.py
@@ -87,6 +87,7 @@
 }
 
 intersphinx_mapping = {
+    "python": ("https://docs.python.org/3", None),
     "anndata": ("https://anndata.readthedocs.io/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
 }
@@ -109,6 +110,7 @@
 html_theme_options = {
     "repository_url": repository_url,
     "use_repository_button": True,
+    "path_to_docs": "docs/",
 }
 
 pygments_style = "default"

diff --git a/docs/extensions/typed_returns.py b/docs/extensions/typed_returns.py
@@ -1,24 +1,27 @@
 # code from https://github.com/theislab/scanpy/blob/master/docs/extensions/typed_returns.py
 # with some minor adjustment
+from __future__ import annotations
+
 import re
+from collections.abc import Generator, Iterable
 
 from sphinx.application import Sphinx
 from sphinx.ext.napoleon import NumpyDocstring
 
 
-def _process_return(lines):
+def _process_return(lines: Iterable[str]) -> Generator[str, None, None]:
     for line in lines:
-        m = re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line)
-        if m:
-            # Once this is in scanpydoc, we can use the fancy hover stuff
+        if m := re.fullmatch(r"(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)", line):
             yield f'-{m["param"]} (:class:`~{m["type"]}`)'
         else:
             yield line
 
 
-def _parse_returns_section(self, section):
-    lines_raw = list(_process_return(self._dedent(self._consume_to_next_section())))
-    lines = self._format_block(":returns: ", lines_raw)
+def _parse_returns_section(self: NumpyDocstring, section: str) -> list[str]:
+    lines_raw = self._dedent(self._consume_to_next_section())
+    if lines_raw[0] == ":":
+        del lines_raw[0]
+    lines = self._format_block(":returns: ", list(_process_return(lines_raw)))
     if lines and lines[-1]:
         lines.append("")
     return lines

diff --git a/pyproject.toml b/pyproject.toml
@@ -33,7 +33,7 @@ dev = [
 ]
 doc = [
     "sphinx>=4",
-    "sphinx-book-theme>=0.3.3",
+    "sphinx-book-theme>=1.0.0",
     "myst-nb",
     "sphinxcontrib-bibtex>=1.0.0",
     "sphinx-autodoc-typehints",