Update template to v0.3.0 (#773)

Co-authored-by: scverse-bot <None>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.cruft.json

@@ -1,7 +1,7 @@
 {
     "template": "https://github.com/scverse/cookiecutter-scverse",
-    "commit": "605f95714130c960bce12eab98a4e023e8932249",
-    "checkout": "v0.2.22",
+    "commit": "8e96abb5c3e2d5078c44713958da672711cf2a48",
+    "checkout": "v0.3.0",
     "context": {
         "cookiecutter": {
             "project_name": "squidpy",
@@ -16,6 +16,11 @@
                 ".github/workflows/**.yaml",
                 "docs/_templates/autosummary/**.rst"
             ],
+            "_render_devdocs": false,
+            "_jinja2_env_vars": {
+                "lstrip_blocks": true,
+                "trim_blocks": true
+            },
             "_template": "https://github.com/scverse/cookiecutter-scverse"
         }
     },

docs/conf.py.rej

@@ -0,0 +1,36 @@
+diff a/docs/conf.py b/docs/conf.py	(rejected hunks)
+@@ -109,12 +109,15 @@ exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]
+ #
+ html_theme = "sphinx_book_theme"
+ html_static_path = ["_static"]
++html_css_files = ["css/custom.css"]
++
+ html_title = project_name
+
+ html_theme_options = {
+     "repository_url": repository_url,
+     "use_repository_button": True,
+     "path_to_docs": "docs/",
++    "navigation_with_keys": False,
+ }
+
+ pygments_style = "default"
+@@ -124,18 +127,3 @@ nitpick_ignore = [
+     # you can add an exception to this list.
+     #     ("py:class", "igraph.Graph"),
+ ]
+-
+-
+-def setup(app):
+-    """App setup hook."""
+-    app.add_config_value(
+-        "recommonmark_config",
+-        {
+-            "auto_toc_tree_section": "Contents",
+-            "enable_auto_toc_tree": True,
+-            "enable_math": True,
+-            "enable_inline_math": False,
+-            "enable_eval_rst": True,
+-        },
+-        True,
+-    )

pyproject.toml.rej

@@ -0,0 +1,22 @@
+diff a/pyproject.toml b/pyproject.toml	(rejected hunks)
+@@ -26,7 +26,6 @@ dependencies = [
+
+ [project.optional-dependencies]
+ dev = [
+-    # CLI for bumping the version number
+     "pre-commit",
+     "twine>=4.0.2"
+ ]
+@@ -42,10 +41,11 @@ doc = [
+     "ipykernel",
+     "ipython",
+     "sphinx-copybutton",
++    "pandas",
+ ]
+ test = [
+     "pytest",
+-    "pytest-cov",
++    "coverage",
+ ]
+
+ [tool.coverage.run]