flying-sheep · Nov 12, 2026 · Nov 12, 2026 · Nov 12, 2026
diff --git a/.panache.toml b/.panache.toml
@@ -0,0 +1,15 @@
+#:schema https://panache.bz/panache.schema.json
+flavor = "myst"
+extend-exclude = [".claude/"]
+
+[format]
+wrap = "preserve"
+smart-punctuation = "unicode"
+tab-stops = "preserve"
+
+# MyST syntax extensions from `scverse_doc.config.MYST_ENABLE_EXTENSIONS`
+[extensions]
+myst-colon-fence = true  # colon_fence
+definition-lists = true  # deflist
+tex-math-dollars = true  # dollarmath, amsmath
+raw-html = true          # html_image, html_admonition
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -13,6 +13,11 @@ repos:
             exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
             groups: [format]
             # further file exclusions and other options are configured in biome.jsonc
+    - repo: https://github.com/jolars/panache-pre-commit
+      rev: v3.18.0
+      hooks:
+          - id: panache-format
+            groups: [format]
     - repo: https://github.com/tox-dev/pyproject-fmt
       rev: v2.30.3
       hooks:

diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -14,5 +14,6 @@
         "editorconfig.editorconfig",
         "charliermarsh.ruff",
         "biomejs.biome",
+        "jolars.panache",
     ],
 }
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,5 +1,5 @@
 {
-    "[python][json][jsonc]": {
+    "[python][json][jsonc][yaml][markdown]": {
         "editor.formatOnSave": true,
     },
     "[python]": {
@@ -9,9 +9,12 @@
             "source.organizeImports": "always",
         },
     },
-    "[json][jsonc]": {
+    "[json][jsonc][yaml]": {
         "editor.defaultFormatter": "biomejs.biome",
     },
+    "[markdown]": {
+        "editor.defaultFormatter": "jolars.panache",
+    },
     "python.analysis.typeCheckingMode": "basic",
     "python.testing.pytestEnabled": true,
     "python.testing.pytestArgs": ["-vv", "--color=yes"],

diff --git a/AGENTS.md b/AGENTS.md
@@ -26,7 +26,7 @@ assert not isinstance(transformation, dict)
 assert_type(transformation, BaseTransformation)
 ```
 
-When all branches of a union have been handled, use `typing.assert_never` instead of a generic "should not reach here"
+When all branches of a union have been handled, use `typing.assert_never` instead of a generic “should not reach here”
 error, so the type checker tells us if a new type is added to the union and not handled:
 
 ```python
@@ -42,7 +42,7 @@ else:
 
 #### Why
 
-Because of Python's (multiple-)inheritance model, a positive `isinstance` assertion can never be rejected by a type
+Because of Python’s (multiple-)inheritance model, a positive `isinstance` assertion can never be rejected by a type
 checker, even when it contradicts the declared type:
 
 ```python
@@ -60,7 +60,7 @@ assert not isinstance(transformations, BaseTransformation)
 assert_type(transformations, dict[str, BaseTransformation])
 ```
 
-Optional values are already narrowed "negatively", so keep using `is not None`:
+Optional values are already narrowed “negatively”, so keep using `is not None`:
 
 ```python
 assert target_depth is not None

diff --git a/README.md b/README.md
@@ -64,7 +64,7 @@ Another useful resource to get started is the source code of the [`spatialdata-i
 
 ## Installation
 
-Check out the docs for more complete [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html). To get started with the "batteries included" installation, you can install via pip:
+Check out the docs for more complete [installation instructions](https://spatialdata.scverse.org/en/stable/installation.html). To get started with the “batteries included” installation, you can install via pip:
 
 ```bash
 pip install "spatialdata[extra]"

diff --git a/benchmarks/README.md b/benchmarks/README.md
@@ -14,7 +14,7 @@ pip install -e . --group dev --group test --group doc --group benchmark
 
 ## Usage
 
-Running all the benchmarks is usually not needed. You run the benchmark using `asv run`. See the [asv documentation](https://asv.readthedocs.io/en/stable/commands.html#asv-run) for interesting arguments, like selecting the benchmarks you're interested in by providing a regex pattern `-b` or `--bench` that links to a function or class method. You can run the benchmark in your current environment with `--python=same`. Some example benchmarks:
+Running all the benchmarks is usually not needed. You run the benchmark using `asv run`. See the [asv documentation](https://asv.readthedocs.io/en/stable/commands.html#asv-run) for interesting arguments, like selecting the benchmarks you’re interested in by providing a regex pattern `-b` or `--bench` that links to a function or class method. You can run the benchmark in your current environment with `--python=same`. Some example benchmarks:
 
 ### Import time benchmarks
 

diff --git a/biome.jsonc b/biome.jsonc
@@ -2,6 +2,7 @@
     "$schema": "https://biomejs.dev/schemas/2.6.4/schema.json",
     "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
+    "markdown": { "formatter": { "enabled": false } }, // handled by panache
     "overrides": [
         {
             "includes": ["./.vscode/*.json", "**/*.jsonc"],

diff --git a/docs/api/io.md b/docs/api/io.md
@@ -1,6 +1,6 @@
 # Input/Output
 
-To read the data from a specific technology (e.g., Xenium, MERSCOPE, ...), you can
+To read the data from a specific technology (e.g., Xenium, MERSCOPE, …), you can
 use any of the [spatialdata-io readers](https://spatialdata.scverse.org/projects/io/en/stable/api.html).
 
 ```{eval-rst}

diff --git a/docs/citation.md b/docs/citation.md
@@ -2,4 +2,4 @@
 
 If you use SpatialData in your work, please cite {cite:t}`marconatoSpatialDataOpenUniversal2024`:
 
-> Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. _Nature Methods_ (2024). doi: [10.1038/s41592-024-02212-x](https://doi.org/10.1038/s41592-024-02212-x).
+> Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. *Nature Methods* (2024). doi: [10.1038/s41592-024-02212-x](https://doi.org/10.1038/s41592-024-02212-x).
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -10,7 +10,6 @@ For more extensive tutorials, that also cover the absolute basics, please refer
 [scanpy developer guide]: https://scanpy.scverse.org/page/dev/
 
 :::{tip} The _hatch_ project manager
-
 We highly recommend to familiarize yourself with [`hatch`][hatch].
 Hatch is a Python project manager that
 
@@ -20,14 +19,13 @@ Hatch is a Python project manager that
 - allows to run tasks defined in `pyproject.toml`, e.g. to build documentation.
 
 While the project is setup with `hatch` in mind, it is still possible to use different tools to manage dependencies, such as `uv` or `pip`.
-
 :::
 
 [hatch]: https://hatch.pypa.io/latest/
 
 ## Installing dev dependencies
 
-In addition to the packages needed to _use_ this package, you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
+In addition to the packages needed to *use* this package, you need additional python packages to [run tests](#writing-tests) and [build the documentation](#docs-building).
 
 :::::{tab-set}
 ::::{tab-item} Hatch
@@ -46,9 +44,9 @@ hatch run docs:build  # defined in the table [tool.hatch.envs.docs]
 If you are using VS code, install the [hatch-code][] extension.
 Additionally, make sure that the `vscode-python-environments` extension is installed (should be by default) and `"python.useEnvironmentsExtension": true` is activated in your `settings.json`.
 
-Next, open the "Python Environment Managers" sidebar.
+Next, open the “Python Environment Managers” sidebar.
 You can do so by opening the command palette (Ctrl+Shift+P) and searching for `Python: Focus on Environment Managers View`.
-It will show a collapsible list where you can expand "Hatch" and activate an environment by clicking on the checkmark next to it.
+It will show a collapsible list where you can expand “Hatch” and activate an environment by clicking on the checkmark next to it.
 As the main development environment, we recommend to use `hatch-test` with the latest supported Python version.
 
 ### Other IDEs
@@ -93,8 +91,6 @@ hatch env find hatch-test.py3.14-stable
 ```
 
 and manually point it to the python binary.
-
-
 ::::
 
 ::::{tab-item} uv
@@ -111,7 +107,6 @@ uv sync --group=test --group=doc --extra=torch
 ```
 
 The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
-
 ::::
 
 ::::{tab-item} Pip
@@ -127,7 +122,6 @@ pip install -e . --group dev --group test --group doc
 ```
 
 The `.venv` directory is typically automatically discovered by IDEs such as VS Code.
-
 ::::
 :::::
 
@@ -155,7 +149,7 @@ prek will automatically download all dependencies when it is run for the first t
 If you didn’t run the checks locally, the `Pre-commit checks` job of the GitHub Actions CI runs them on your pull request and reports any failures.
 We strongly encourage installing and running the checks locally first to understand their usage.
 
-Finally, most editors have an _autoformat on save_ feature.
+Finally, most editors have an *autoformat on save* feature.
 Consider enabling this option for [ruff][ruff-editors] and [biome][biome-editors].
 
 [pre-commit]: https://pre-commit.com/
@@ -184,7 +178,6 @@ hatch test  # test with the highest supported Python version
 # or
 hatch test --all  # test with all supported Python versions
 ```
-
 ::::
 
 ::::{tab-item} uv
@@ -193,7 +186,6 @@ hatch test --all  # test with all supported Python versions
 ```bash
 uv run pytest
 ```
-
 ::::
 
 ::::{tab-item} Pip
@@ -203,7 +195,6 @@ uv run pytest
 source .venv/bin/activate
 pytest
 ```
-
 ::::
 :::::
 
@@ -349,7 +340,6 @@ If you are interested in automatically running notebooks as part of the continuo
 hatch run docs:build
 hatch run docs:open
 ```
-
 ::::
 
 ::::{tab-item} uv
@@ -360,7 +350,6 @@ cd docs
 uv run sphinx-build -M html . _build -W
 (xdg-)open _build/html/index.html
 ```
-
 ::::
 
 ::::{tab-item} Pip
@@ -372,7 +361,6 @@ cd docs
 sphinx-build -M html . _build -W
 (xdg-)open _build/html/index.html
 ```
-
 ::::
 :::::
Original file line number	Diff line number	Diff line change
Expand Up		@@ -2,4 +2,4 @@

		If you use SpatialData in your work, please cite {cite:t}`marconatoSpatialDataOpenUniversal2024`:

		> Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. _Nature Methods_ (2024). doi: [10.1038/s41592-024-02212-x](https://doi.org/10.1038/s41592-024-02212-x).
		> Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nature Methods (2024). doi: [10.1038/s41592-024-02212-x](https://doi.org/10.1038/s41592-024-02212-x).