Add docs gallery via spatialdata-plot-notebooks submodule#656

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timtreis merged 4 commits into from
May 11, 2026
Merged

Add docs gallery via spatialdata-plot-notebooks submodule #656

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2d15392
Add docs gallery as submodule from spatialdata-plot-notebooks
timtreis May 11, 2026
e24d7a2
Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)
timtreis May 11, 2026
62a9194
Document gallery submodule workflow in contributing guide
timtreis May 11, 2026
75de4cc
Auto-pull notebooks main, add card gallery, link from README
timtreis May 11, 2026
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15 changes: 15 additions & 0 deletions .github/workflows/build.yaml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
run: uv build
- name: Check package
run: uvx twine check --strict dist/*.whl

docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v5
with:
submodules: true
fetch-depth: 0
- name: Pull latest notebooks
# Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
run: git submodule update --init --remote --recursive
- name: Install uv
uses: astral-sh/setup-uv@v7
- name: Build docs
run: uvx --with="virtualenv<21" hatch run docs:build
4 changes: 4 additions & 0 deletions .gitmodules
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@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
path = docs/notebooks
url = https://github.com/scverse/spatialdata-plot-notebooks.git
branch = main
10 changes: 10 additions & 0 deletions .readthedocs.yaml
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Expand Up@@ -6,6 +6,12 @@ build:
python: "3.13"
nodejs: latest
jobs:
post_checkout:
# Always render the latest notebooks-repo main, not the SHA pinned in
# this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
# reproducible for the gallery — a re-build shows whatever the notebooks
# repo's main looked like at build time.
- git submodule update --init --remote --recursive
create_environment:
- asdf plugin add uv
- asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
# TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
- uvx "--with=virtualenv<21" hatch run docs:build
- mv docs/_build $READTHEDOCS_OUTPUT

submodules:
include: all
recursive: false
4 changes: 3 additions & 1 deletion README.md
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Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions docs/conf.py
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Expand Up@@ -56,6 +56,7 @@
"sphinx.ext.intersphinx",
"sphinx.ext.autosummary",
"sphinx.ext.napoleon",
"sphinx_design",
"sphinxcontrib.bibtex",
"sphinxcontrib.katex",
"sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
"Thumbs.db",
".DS_Store",
"**.ipynb_checkpoints",
"tutorials/notebooks/index.md",
"tutorials/notebooks/README.md",
"tutorials/notebooks/references.md",
"tutorials/notebooks/notebooks/paper_reproducibility/*",
# Submodule meta-files: these document the notebooks repo itself, not
# spatialdata-plot, and should not be rendered into our docs.
"notebooks/README.md",
"notebooks/CONTRIBUTING.md",
"notebooks/LICENSE",
"notebooks/.github/**",
"notebooks/pyproject.toml",
]


Expand Down
59 changes: 51 additions & 8 deletions docs/contributing.md
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Original file line numberDiff line numberDiff line change
Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

Expand Down
43 changes: 43 additions & 0 deletions docs/gallery.md
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@@ -0,0 +1,43 @@
# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```
3 changes: 2 additions & 1 deletion docs/index.md
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Expand Up@@ -4,8 +4,9 @@

```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
Expand Down
1 change: 1 addition & 0 deletions docs/notebooks
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Submodule notebooks added at e0ac82
1 change: 1 addition & 0 deletions pyproject.toml
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Expand Up@@ -55,6 +55,7 @@ doc = [
"sphinx-autodoc-typehints",
"sphinx-book-theme>=1",
"sphinx-copybutton",
"sphinx-design",
"sphinx-tabs",
"sphinxcontrib-bibtex>=1",
"sphinxcontrib-katex",
Expand Down
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Add docs gallery via spatialdata-plot-notebooks submodule#656

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 Merged

timtreis
merged 4 commits into

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May 11, 2026
 Merged


Add docs gallery via spatialdata-plot-notebooks submodule
#656
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2d15392

Add docs gallery as submodule from spatialdata-plot-notebooks


timtreis May 11, 2026
e24d7a2

Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)


timtreis May 11, 2026
62a9194

Document gallery submodule workflow in contributing guide


timtreis May 11, 2026
75de4cc

Auto-pull notebooks main, add card gallery, link from README


timtreis May 11, 2026

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15 changes: 15 additions & 0 deletions
.github/workflows/build.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
 run: uv build
 - name: Check package
 run: uvx twine check --strict dist/*.whl

 docs:
 runs-on: ubuntu-latest
 steps:
 - uses: actions/checkout@v5
 with:
 submodules: true
 fetch-depth: 0
 - name: Pull latest notebooks
 # Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
 run: git submodule update --init --remote --recursive
 - name: Install uv
 uses: astral-sh/setup-uv@v7
 - name: Build docs
 run: uvx --with="virtualenv<21" hatch run docs:build

4 changes: 4 additions & 0 deletions
.gitmodules

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
	path = docs/notebooks
	url = https://github.com/scverse/spatialdata-plot-notebooks.git
	branch = main

10 changes: 10 additions & 0 deletions
.readthedocs.yaml

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,12 @@ build:
 python: "3.13"
 nodejs: latest
 jobs:
 post_checkout:
 # Always render the latest notebooks-repo main, not the SHA pinned in
 # this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
 # reproducible for the gallery — a re-build shows whatever the notebooks
 # repo's main looked like at build time.
 - git submodule update --init --remote --recursive
 create_environment:
 - asdf plugin add uv
 - asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
 # TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
 - uvx "--with=virtualenv<21" hatch run docs:build
 - mv docs/_build $READTHEDOCS_OUTPUT

submodules:
 include: all
 recursive: false

4 changes: 3 additions & 1 deletion
README.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions
docs/conf.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -56,6 +56,7 @@
 "sphinx.ext.intersphinx",
 "sphinx.ext.autosummary",
 "sphinx.ext.napoleon",
 "sphinx_design",
 "sphinxcontrib.bibtex",
 "sphinxcontrib.katex",
 "sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
 "Thumbs.db",
 ".DS_Store",
 "**.ipynb_checkpoints",
 "tutorials/notebooks/index.md",
 "tutorials/notebooks/README.md",
 "tutorials/notebooks/references.md",
 "tutorials/notebooks/notebooks/paper_reproducibility/*",
 # Submodule meta-files: these document the notebooks repo itself, not
 # spatialdata-plot, and should not be rendered into our docs.
 "notebooks/README.md",
 "notebooks/CONTRIBUTING.md",
 "notebooks/LICENSE",
 "notebooks/.github/**",
 "notebooks/pyproject.toml",
]


Expand Down

59 changes: 51 additions & 8 deletions
docs/contributing.md

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

Expand Down

43 changes: 43 additions & 0 deletions
docs/gallery.md

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,43 @@
# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```

3 changes: 2 additions & 1 deletion
docs/index.md

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Expand Up@@ -4,8 +4,9 @@

```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
Expand Down

1 change: 1 addition & 0 deletions
docs/notebooks

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added at

e0ac82


1 change: 1 addition & 0 deletions
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -55,6 +55,7 @@ doc = [
 "sphinx-autodoc-typehints",
 "sphinx-book-theme>=1",
 "sphinx-copybutton",
 "sphinx-design",
 "sphinx-tabs",
 "sphinxcontrib-bibtex>=1",
 "sphinxcontrib-katex",
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
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Add docs gallery via spatialdata-plot-notebooks submodule#656

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timtreis
merged 4 commits into

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May 11, 2026
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Add docs gallery via spatialdata-plot-notebooks submodule
#656
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2d15392

Add docs gallery as submodule from spatialdata-plot-notebooks


timtreis May 11, 2026
e24d7a2

Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)


timtreis May 11, 2026
62a9194

Document gallery submodule workflow in contributing guide


timtreis May 11, 2026
75de4cc

Auto-pull notebooks main, add card gallery, link from README


timtreis May 11, 2026

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15 changes: 15 additions & 0 deletions
.github/workflows/build.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
 run: uv build
 - name: Check package
 run: uvx twine check --strict dist/*.whl

 docs:
 runs-on: ubuntu-latest
 steps:
 - uses: actions/checkout@v5
 with:
 submodules: true
 fetch-depth: 0
 - name: Pull latest notebooks
 # Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
 run: git submodule update --init --remote --recursive
 - name: Install uv
 uses: astral-sh/setup-uv@v7
 - name: Build docs
 run: uvx --with="virtualenv<21" hatch run docs:build

4 changes: 4 additions & 0 deletions
.gitmodules

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@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
	path = docs/notebooks
	url = https://github.com/scverse/spatialdata-plot-notebooks.git
	branch = main

10 changes: 10 additions & 0 deletions
.readthedocs.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,12 @@ build:
 python: "3.13"
 nodejs: latest
 jobs:
 post_checkout:
 # Always render the latest notebooks-repo main, not the SHA pinned in
 # this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
 # reproducible for the gallery — a re-build shows whatever the notebooks
 # repo's main looked like at build time.
 - git submodule update --init --remote --recursive
 create_environment:
 - asdf plugin add uv
 - asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
 # TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
 - uvx "--with=virtualenv<21" hatch run docs:build
 - mv docs/_build $READTHEDOCS_OUTPUT

submodules:
 include: all
 recursive: false

4 changes: 3 additions & 1 deletion
README.md

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Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions
docs/conf.py

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Expand Up@@ -56,6 +56,7 @@
 "sphinx.ext.intersphinx",
 "sphinx.ext.autosummary",
 "sphinx.ext.napoleon",
 "sphinx_design",
 "sphinxcontrib.bibtex",
 "sphinxcontrib.katex",
 "sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
 "Thumbs.db",
 ".DS_Store",
 "**.ipynb_checkpoints",
 "tutorials/notebooks/index.md",
 "tutorials/notebooks/README.md",
 "tutorials/notebooks/references.md",
 "tutorials/notebooks/notebooks/paper_reproducibility/*",
 # Submodule meta-files: these document the notebooks repo itself, not
 # spatialdata-plot, and should not be rendered into our docs.
 "notebooks/README.md",
 "notebooks/CONTRIBUTING.md",
 "notebooks/LICENSE",
 "notebooks/.github/**",
 "notebooks/pyproject.toml",
]


Expand Down

59 changes: 51 additions & 8 deletions
docs/contributing.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

Expand Down

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docs/gallery.md

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@@ -0,0 +1,43 @@
# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```

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docs/index.md

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Expand Up@@ -4,8 +4,9 @@

```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
Expand Down

1 change: 1 addition & 0 deletions
docs/notebooks

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added at

e0ac82


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pyproject.toml

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Expand Up@@ -55,6 +55,7 @@ doc = [
 "sphinx-autodoc-typehints",
 "sphinx-book-theme>=1",
 "sphinx-copybutton",
 "sphinx-design",
 "sphinx-tabs",
 "sphinxcontrib-bibtex>=1",
 "sphinxcontrib-katex",
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
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(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Add docs gallery via spatialdata-plot-notebooks submodule#656

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 Merged

timtreis
merged 4 commits into

from

May 11, 2026
 Merged


Add docs gallery via spatialdata-plot-notebooks submodule
#656
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2d15392

Add docs gallery as submodule from spatialdata-plot-notebooks


timtreis May 11, 2026
e24d7a2

Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)


timtreis May 11, 2026
62a9194

Document gallery submodule workflow in contributing guide


timtreis May 11, 2026
75de4cc

Auto-pull notebooks main, add card gallery, link from README


timtreis May 11, 2026

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15 changes: 15 additions & 0 deletions
.github/workflows/build.yaml

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
 run: uv build
 - name: Check package
 run: uvx twine check --strict dist/*.whl

 docs:
 runs-on: ubuntu-latest
 steps:
 - uses: actions/checkout@v5
 with:
 submodules: true
 fetch-depth: 0
 - name: Pull latest notebooks
 # Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
 run: git submodule update --init --remote --recursive
 - name: Install uv
 uses: astral-sh/setup-uv@v7
 - name: Build docs
 run: uvx --with="virtualenv<21" hatch run docs:build

4 changes: 4 additions & 0 deletions
.gitmodules

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
	path = docs/notebooks
	url = https://github.com/scverse/spatialdata-plot-notebooks.git
	branch = main

10 changes: 10 additions & 0 deletions
.readthedocs.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,12 @@ build:
 python: "3.13"
 nodejs: latest
 jobs:
 post_checkout:
 # Always render the latest notebooks-repo main, not the SHA pinned in
 # this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
 # reproducible for the gallery — a re-build shows whatever the notebooks
 # repo's main looked like at build time.
 - git submodule update --init --remote --recursive
 create_environment:
 - asdf plugin add uv
 - asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
 # TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
 - uvx "--with=virtualenv<21" hatch run docs:build
 - mv docs/_build $READTHEDOCS_OUTPUT

submodules:
 include: all
 recursive: false

4 changes: 3 additions & 1 deletion
README.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions
docs/conf.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -56,6 +56,7 @@
 "sphinx.ext.intersphinx",
 "sphinx.ext.autosummary",
 "sphinx.ext.napoleon",
 "sphinx_design",
 "sphinxcontrib.bibtex",
 "sphinxcontrib.katex",
 "sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
 "Thumbs.db",
 ".DS_Store",
 "**.ipynb_checkpoints",
 "tutorials/notebooks/index.md",
 "tutorials/notebooks/README.md",
 "tutorials/notebooks/references.md",
 "tutorials/notebooks/notebooks/paper_reproducibility/*",
 # Submodule meta-files: these document the notebooks repo itself, not
 # spatialdata-plot, and should not be rendered into our docs.
 "notebooks/README.md",
 "notebooks/CONTRIBUTING.md",
 "notebooks/LICENSE",
 "notebooks/.github/**",
 "notebooks/pyproject.toml",
]


Expand Down

59 changes: 51 additions & 8 deletions
docs/contributing.md

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

Expand Down

43 changes: 43 additions & 0 deletions
docs/gallery.md

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,43 @@
# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```

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docs/index.md

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Expand Up@@ -4,8 +4,9 @@

```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
Expand Down

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docs/notebooks

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added at

e0ac82


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pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -55,6 +55,7 @@ doc = [
 "sphinx-autodoc-typehints",
 "sphinx-book-theme>=1",
 "sphinx-copybutton",
 "sphinx-design",
 "sphinx-tabs",
 "sphinxcontrib-bibtex>=1",
 "sphinxcontrib-katex",
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Add docs gallery via spatialdata-plot-notebooks submodule#656

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timtreis
merged 4 commits into

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May 11, 2026
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Add docs gallery via spatialdata-plot-notebooks submodule
#656
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2d15392

Add docs gallery as submodule from spatialdata-plot-notebooks


timtreis May 11, 2026
e24d7a2

Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)


timtreis May 11, 2026
62a9194

Document gallery submodule workflow in contributing guide


timtreis May 11, 2026
75de4cc

Auto-pull notebooks main, add card gallery, link from README


timtreis May 11, 2026

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15 changes: 15 additions & 0 deletions
.github/workflows/build.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
 run: uv build
 - name: Check package
 run: uvx twine check --strict dist/*.whl

 docs:
 runs-on: ubuntu-latest
 steps:
 - uses: actions/checkout@v5
 with:
 submodules: true
 fetch-depth: 0
 - name: Pull latest notebooks
 # Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
 run: git submodule update --init --remote --recursive
 - name: Install uv
 uses: astral-sh/setup-uv@v7
 - name: Build docs
 run: uvx --with="virtualenv<21" hatch run docs:build

4 changes: 4 additions & 0 deletions
.gitmodules

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
	path = docs/notebooks
	url = https://github.com/scverse/spatialdata-plot-notebooks.git
	branch = main

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.readthedocs.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,12 @@ build:
 python: "3.13"
 nodejs: latest
 jobs:
 post_checkout:
 # Always render the latest notebooks-repo main, not the SHA pinned in
 # this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
 # reproducible for the gallery — a re-build shows whatever the notebooks
 # repo's main looked like at build time.
 - git submodule update --init --remote --recursive
 create_environment:
 - asdf plugin add uv
 - asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
 # TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
 - uvx "--with=virtualenv<21" hatch run docs:build
 - mv docs/_build $READTHEDOCS_OUTPUT

submodules:
 include: all
 recursive: false

4 changes: 3 additions & 1 deletion
README.md

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Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions
docs/conf.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -56,6 +56,7 @@
 "sphinx.ext.intersphinx",
 "sphinx.ext.autosummary",
 "sphinx.ext.napoleon",
 "sphinx_design",
 "sphinxcontrib.bibtex",
 "sphinxcontrib.katex",
 "sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
 "Thumbs.db",
 ".DS_Store",
 "**.ipynb_checkpoints",
 "tutorials/notebooks/index.md",
 "tutorials/notebooks/README.md",
 "tutorials/notebooks/references.md",
 "tutorials/notebooks/notebooks/paper_reproducibility/*",
 # Submodule meta-files: these document the notebooks repo itself, not
 # spatialdata-plot, and should not be rendered into our docs.
 "notebooks/README.md",
 "notebooks/CONTRIBUTING.md",
 "notebooks/LICENSE",
 "notebooks/.github/**",
 "notebooks/pyproject.toml",
]


Expand Down

59 changes: 51 additions & 8 deletions
docs/contributing.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

Expand Down

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docs/gallery.md

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,43 @@
# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```

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docs/index.md

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Expand Up@@ -4,8 +4,9 @@

```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
Expand Down

1 change: 1 addition & 0 deletions
docs/notebooks

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added at

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1 change: 1 addition & 0 deletions
pyproject.toml

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -55,6 +55,7 @@ doc = [
 "sphinx-autodoc-typehints",
 "sphinx-book-theme>=1",
 "sphinx-copybutton",
 "sphinx-design",
 "sphinx-tabs",
 "sphinxcontrib-bibtex>=1",
 "sphinxcontrib-katex",
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Add docs gallery via spatialdata-plot-notebooks submodule#656

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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 Merged

timtreis
merged 4 commits into

from

May 11, 2026
 Merged


Add docs gallery via spatialdata-plot-notebooks submodule
#656
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2d15392

Add docs gallery as submodule from spatialdata-plot-notebooks


timtreis May 11, 2026
e24d7a2

Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)


timtreis May 11, 2026
62a9194

Document gallery submodule workflow in contributing guide


timtreis May 11, 2026
75de4cc

Auto-pull notebooks main, add card gallery, link from README


timtreis May 11, 2026

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15 changes: 15 additions & 0 deletions
.github/workflows/build.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
 run: uv build
 - name: Check package
 run: uvx twine check --strict dist/*.whl

 docs:
 runs-on: ubuntu-latest
 steps:
 - uses: actions/checkout@v5
 with:
 submodules: true
 fetch-depth: 0
 - name: Pull latest notebooks
 # Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
 run: git submodule update --init --remote --recursive
 - name: Install uv
 uses: astral-sh/setup-uv@v7
 - name: Build docs
 run: uvx --with="virtualenv<21" hatch run docs:build

4 changes: 4 additions & 0 deletions
.gitmodules

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
	path = docs/notebooks
	url = https://github.com/scverse/spatialdata-plot-notebooks.git
	branch = main

10 changes: 10 additions & 0 deletions
.readthedocs.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,12 @@ build:
 python: "3.13"
 nodejs: latest
 jobs:
 post_checkout:
 # Always render the latest notebooks-repo main, not the SHA pinned in
 # this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
 # reproducible for the gallery — a re-build shows whatever the notebooks
 # repo's main looked like at build time.
 - git submodule update --init --remote --recursive
 create_environment:
 - asdf plugin add uv
 - asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
 # TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
 - uvx "--with=virtualenv<21" hatch run docs:build
 - mv docs/_build $READTHEDOCS_OUTPUT

submodules:
 include: all
 recursive: false

4 changes: 3 additions & 1 deletion
README.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions
docs/conf.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -56,6 +56,7 @@
 "sphinx.ext.intersphinx",
 "sphinx.ext.autosummary",
 "sphinx.ext.napoleon",
 "sphinx_design",
 "sphinxcontrib.bibtex",
 "sphinxcontrib.katex",
 "sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
 "Thumbs.db",
 ".DS_Store",
 "**.ipynb_checkpoints",
 "tutorials/notebooks/index.md",
 "tutorials/notebooks/README.md",
 "tutorials/notebooks/references.md",
 "tutorials/notebooks/notebooks/paper_reproducibility/*",
 # Submodule meta-files: these document the notebooks repo itself, not
 # spatialdata-plot, and should not be rendered into our docs.
 "notebooks/README.md",
 "notebooks/CONTRIBUTING.md",
 "notebooks/LICENSE",
 "notebooks/.github/**",
 "notebooks/pyproject.toml",
]


Expand Down

59 changes: 51 additions & 8 deletions
docs/contributing.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

Expand Down

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docs/gallery.md

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# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```

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docs/index.md

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Expand Up@@ -4,8 +4,9 @@

```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
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docs/notebooks

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added at

e0ac82


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pyproject.toml

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Expand Up@@ -55,6 +55,7 @@ doc = [
 "sphinx-autodoc-typehints",
 "sphinx-book-theme>=1",
 "sphinx-copybutton",
 "sphinx-design",
 "sphinx-tabs",
 "sphinxcontrib-bibtex>=1",
 "sphinxcontrib-katex",
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Add docs gallery via spatialdata-plot-notebooks submodule#656

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timtreis
merged 4 commits into

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May 11, 2026
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Add docs gallery via spatialdata-plot-notebooks submodule
#656
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2d15392

Add docs gallery as submodule from spatialdata-plot-notebooks


timtreis May 11, 2026
e24d7a2

Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)


timtreis May 11, 2026
62a9194

Document gallery submodule workflow in contributing guide


timtreis May 11, 2026
75de4cc

Auto-pull notebooks main, add card gallery, link from README


timtreis May 11, 2026

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15 changes: 15 additions & 0 deletions
.github/workflows/build.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
 run: uv build
 - name: Check package
 run: uvx twine check --strict dist/*.whl

 docs:
 runs-on: ubuntu-latest
 steps:
 - uses: actions/checkout@v5
 with:
 submodules: true
 fetch-depth: 0
 - name: Pull latest notebooks
 # Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
 run: git submodule update --init --remote --recursive
 - name: Install uv
 uses: astral-sh/setup-uv@v7
 - name: Build docs
 run: uvx --with="virtualenv<21" hatch run docs:build

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.gitmodules

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@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
	path = docs/notebooks
	url = https://github.com/scverse/spatialdata-plot-notebooks.git
	branch = main

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.readthedocs.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,12 @@ build:
 python: "3.13"
 nodejs: latest
 jobs:
 post_checkout:
 # Always render the latest notebooks-repo main, not the SHA pinned in
 # this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
 # reproducible for the gallery — a re-build shows whatever the notebooks
 # repo's main looked like at build time.
 - git submodule update --init --remote --recursive
 create_environment:
 - asdf plugin add uv
 - asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
 # TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
 - uvx "--with=virtualenv<21" hatch run docs:build
 - mv docs/_build $READTHEDOCS_OUTPUT

submodules:
 include: all
 recursive: false

4 changes: 3 additions & 1 deletion
README.md

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Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions
docs/conf.py

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Expand Up@@ -56,6 +56,7 @@
 "sphinx.ext.intersphinx",
 "sphinx.ext.autosummary",
 "sphinx.ext.napoleon",
 "sphinx_design",
 "sphinxcontrib.bibtex",
 "sphinxcontrib.katex",
 "sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
 "Thumbs.db",
 ".DS_Store",
 "**.ipynb_checkpoints",
 "tutorials/notebooks/index.md",
 "tutorials/notebooks/README.md",
 "tutorials/notebooks/references.md",
 "tutorials/notebooks/notebooks/paper_reproducibility/*",
 # Submodule meta-files: these document the notebooks repo itself, not
 # spatialdata-plot, and should not be rendered into our docs.
 "notebooks/README.md",
 "notebooks/CONTRIBUTING.md",
 "notebooks/LICENSE",
 "notebooks/.github/**",
 "notebooks/pyproject.toml",
]


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docs/contributing.md

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Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

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docs/gallery.md

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@@ -0,0 +1,43 @@
# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```

3 changes: 2 additions & 1 deletion
docs/index.md

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Expand Up@@ -4,8 +4,9 @@

```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
Expand Down

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docs/notebooks

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added at

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pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -55,6 +55,7 @@ doc = [
 "sphinx-autodoc-typehints",
 "sphinx-book-theme>=1",
 "sphinx-copybutton",
 "sphinx-design",
 "sphinx-tabs",
 "sphinxcontrib-bibtex>=1",
 "sphinxcontrib-katex",
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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Add docs gallery via spatialdata-plot-notebooks submodule#656

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 Merged

timtreis
merged 4 commits into

from

May 11, 2026
 Merged


Add docs gallery via spatialdata-plot-notebooks submodule
#656
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2d15392

Add docs gallery as submodule from spatialdata-plot-notebooks


timtreis May 11, 2026
e24d7a2

Bump notebooks submodule (lint fix in spatialdata-plot-notebooks)


timtreis May 11, 2026
62a9194

Document gallery submodule workflow in contributing guide


timtreis May 11, 2026
75de4cc

Auto-pull notebooks main, add card gallery, link from README


timtreis May 11, 2026

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15 changes: 15 additions & 0 deletions
.github/workflows/build.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -24,3 +24,18 @@ jobs:
 run: uv build
 - name: Check package
 run: uvx twine check --strict dist/*.whl

 docs:
 runs-on: ubuntu-latest
 steps:
 - uses: actions/checkout@v5
 with:
 submodules: true
 fetch-depth: 0
 - name: Pull latest notebooks
 # Match RTD: render whatever is on notebooks-repo main, not the pinned SHA.
 run: git submodule update --init --remote --recursive
 - name: Install uv
 uses: astral-sh/setup-uv@v7
 - name: Build docs
 run: uvx --with="virtualenv<21" hatch run docs:build

4 changes: 4 additions & 0 deletions
.gitmodules

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,4 @@
[submodule "docs/notebooks"]
	path = docs/notebooks
	url = https://github.com/scverse/spatialdata-plot-notebooks.git
	branch = main

10 changes: 10 additions & 0 deletions
.readthedocs.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -6,6 +6,12 @@ build:
 python: "3.13"
 nodejs: latest
 jobs:
 post_checkout:
 # Always render the latest notebooks-repo main, not the SHA pinned in
 # this repo's index. Trade-off: docs at older lib tags are not bit-for-bit
 # reproducible for the gallery — a re-build shows whatever the notebooks
 # repo's main looked like at build time.
 - git submodule update --init --remote --recursive
 create_environment:
 - asdf plugin add uv
 - asdf install uv latest
Expand All@@ -15,3 +21,7 @@ build:
 # TODO: remove "--with=virtualenv<21" once hatch is compatible with virtualenv 21+ (pypa/hatch#2193)
 - uvx "--with=virtualenv<21" hatch run docs:build
 - mv docs/_build $READTHEDOCS_OUTPUT

submodules:
 include: all
 recursive: false

4 changes: 3 additions & 1 deletion
README.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -30,8 +30,9 @@ In concordance with the general SpatialData philosophy, all modalities of the ma

For more information on the `spatialdata-plot` library, please refer to the [documentation](https://spatialdata.scverse.org/projects/plot/en/latest/index.html). In particular, the

- [Gallery][link-gallery] — executable example notebooks demonstrating the plotting capabilities.
- [API documentation][link-api].
- [Example notebooks][link-notebooks] (section "Visiualizations")
- [SpatialData example notebooks][link-notebooks] (section "Visualizations") for plotting in the context of broader analyses.

## Installation

Expand DownExpand Up@@ -65,6 +66,7 @@ Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and univers
[issue-tracker]: https://github.com/scverse/spatialdata-plot/issues
[link-docs]: https://spatialdata-plot.readthedocs.io
[link-api]: https://spatialdata.scverse.org/projects/plot/en/stable/api.html
[link-gallery]: https://spatialdata.scverse.org/projects/plot/en/stable/gallery.html
[link-design-doc]: https://spatialdata.scverse.org/en/stable/design_doc.html
[link-notebooks]: https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks.html
[//]: # "numfocus-fiscal-sponsor-attribution"
Expand Down
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12 changes: 8 additions & 4 deletions
docs/conf.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -56,6 +56,7 @@
 "sphinx.ext.intersphinx",
 "sphinx.ext.autosummary",
 "sphinx.ext.napoleon",
 "sphinx_design",
 "sphinxcontrib.bibtex",
 "sphinxcontrib.katex",
 "sphinx_autodoc_typehints",
Expand DownExpand Up@@ -114,10 +115,13 @@
 "Thumbs.db",
 ".DS_Store",
 "**.ipynb_checkpoints",
 "tutorials/notebooks/index.md",
 "tutorials/notebooks/README.md",
 "tutorials/notebooks/references.md",
 "tutorials/notebooks/notebooks/paper_reproducibility/*",
 # Submodule meta-files: these document the notebooks repo itself, not
 # spatialdata-plot, and should not be rendered into our docs.
 "notebooks/README.md",
 "notebooks/CONTRIBUTING.md",
 "notebooks/LICENSE",
 "notebooks/.github/**",
 "notebooks/pyproject.toml",
]


Expand Down

59 changes: 51 additions & 8 deletions
docs/contributing.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -251,7 +251,7 @@ This project uses [sphinx][] with the following features:

- The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
- [Numpy-style docstrings][numpydoc] (through the [napoleon][numpydoc-napoleon] extension).
- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
- Jupyter notebooks as tutorials through [myst-nb][] (See [Gallery notebooks (submodule)](#gallery-notebooks-submodule))
- [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)

Expand All@@ -264,16 +264,48 @@ See scanpy's {doc}`scanpy:dev/documentation` for more information on how to writ
[numpydoc]: https://numpydoc.readthedocs.io/en/latest/format.html
[sphinx-autodoc-typehints]: https://github.com/tox-dev/sphinx-autodoc-typehints

### Tutorials with myst-nb and jupyter notebooks
### Gallery notebooks (submodule)

The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
It is your responsibility to update and re-run the notebook whenever necessary.
The gallery rendered into the docs lives in a separate repository,
[`scverse/spatialdata-plot-notebooks`][notebooks-repo], mounted here as a git
submodule at `docs/notebooks/`. This follows the scverse convention used by
`anndata`, `spatialdata`, `scvi-tools`, and `squidpy`.

If you are interested in automatically running notebooks as part of the continuous integration,
please check out [this feature request][issue-render-notebooks] in the `cookiecutter-scverse` repository.
Notebooks are pre-executed by humans and committed with their outputs; the
docs build performs no execution and pulls no data. A scheduled CI job in the
notebooks repo re-executes every notebook against the latest
`spatialdata-plot` release and fails on output drift.

[issue-render-notebooks]: https://github.com/scverse/cookiecutter-scverse/issues/40
#### Working with the gallery locally

```bash
# First-time clone — pull this repo with submodules
git clone --recurse-submodules https://github.com/scverse/spatialdata-plot.git

# Already cloned without submodules — initialise after the fact
git submodule update --init --recursive

# Pull the latest gallery content from the notebooks repo's main branch
git submodule update --remote docs/notebooks
```

ReadTheDocs is configured (`submodules: include: all` in `.readthedocs.yaml`)
to fetch the submodule on every build, so PR previews always render the
current pinned gallery content.

#### Adding or editing a notebook

Notebook changes are made in the [notebooks repo][notebooks-repo], not here.
See its `CONTRIBUTING.md` for the workflow. After your notebook PR merges
there, open a small follow-up PR in this repo bumping the submodule pin:

```bash
git submodule update --remote docs/notebooks
git add docs/notebooks
git commit -m "Bump notebooks submodule"
```

[notebooks-repo]: https://github.com/scverse/spatialdata-plot-notebooks

#### Hints

Expand All@@ -286,6 +318,17 @@ please check out [this feature request][issue-render-notebooks] in the `cookiecu

### Building the docs locally

:::{important}
The docs include a git submodule (`docs/notebooks` → `spatialdata-plot-notebooks`).
If you cloned this repo without `--recurse-submodules`, initialise it once before building:

```bash
git submodule update --init --recursive
```

Without the submodule, the gallery pages will be missing and sphinx will warn about broken toctree entries.
:::

:::::{tabs}
::::{group-tab} Hatch

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# Gallery

Curated, runnable examples demonstrating `spatialdata-plot` on real
spatial-omics datasets and on the lightweight `blobs` dataset.

Sources live in
[`scverse/spatialdata-plot-notebooks`](https://github.com/scverse/spatialdata-plot-notebooks);
every notebook is executable end-to-end and re-executed on a weekly schedule
against the latest `spatialdata-plot` release.

## Tutorials

End-to-end workflows on real datasets.

::::{grid} 1 2 2 2
:gutter: 3

:::{grid-item-card} Getting started
:link: notebooks/tutorials/getting_started
:link-type: doc
:img-top: _static/gallery/getting_started.png

The fluent `.pl` API, layering, and styling — on the in-memory `blobs`
dataset. Ideal first read.
:::

::::

## Examples

```{note}
No focused examples yet — contributions welcome! See
[CONTRIBUTING](https://github.com/scverse/spatialdata-plot-notebooks/blob/main/CONTRIBUTING.md)
in the notebooks repo for how to add one.
```

```{toctree}
:hidden:
:maxdepth: 2

notebooks/tutorials/index
notebooks/examples/index
```

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```{toctree}
:hidden: true
:maxdepth: 1
:maxdepth: 2

gallery.md
api.md
changelog.md
contributing.md
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pyproject.toml

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Expand Up@@ -55,6 +55,7 @@ doc = [
 "sphinx-autodoc-typehints",
 "sphinx-book-theme>=1",
 "sphinx-copybutton",
 "sphinx-design",
 "sphinx-tabs",
 "sphinxcontrib-bibtex>=1",
 "sphinxcontrib-katex",
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