Add colour and palettes tutorial#4

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Merged
timtreis merged 6 commits into from
May 12, 2026
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Add colour and palettes tutorial #4

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25cb8e1
Add colour and palettes tutorial
timtreis May 12, 2026
094804b
Add pixi config for running notebooks
timtreis May 12, 2026
f1ab577
Update Visium tutorial and refresh thumbnail
timtreis May 12, 2026
7612f4e
Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state
timtreis May 12, 2026
b4cad04
Reset visium notebook kernel to python3
timtreis May 12, 2026
ed6cb69
Harden execute workflow against local kernel names
timtreis May 12, 2026
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6 changes: 5 additions & 1 deletion .github/workflows/execute.yaml
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -79,8 +79,12 @@ jobs:
- name: Re-execute selected notebooks
if: steps.pick.outputs.files != ''
run: |
# Pin kernel_name to python3 so notebooks committed with a
# contributor-local kernel name (e.g. from a pixi `kernel-install`
# task) still execute against CI's stock python3 kernel.
while IFS= read -r nb; do
[ -z "$nb" ] && continue
echo "Executing $nb"
jupyter nbconvert --to notebook --execute --inplace "$nb"
jupyter nbconvert --to notebook --execute --inplace \
--ExecutePreprocessor.kernel_name=python3 "$nb"
done <<< "${{ steps.pick.outputs.files }}"
2 changes: 2 additions & 0 deletions .gitignore
View file
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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
Expand Down
117 changes: 58 additions & 59 deletions examples/visium_mouse_brain.ipynb
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24 changes: 23 additions & 1 deletion pyproject.toml
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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
"spatialdata-plot>=0.3",
"spatialdata-plot>=0.3.4",
"squidpy",
"jupyter",
"ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
Expand Down
769 changes: 769 additions & 0 deletions tutorials/color_and_palette.ipynb
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11 changes: 11 additions & 0 deletions tutorials/index.md
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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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})();
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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Add colour and palettes tutorial#4

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 Merged

timtreis
merged 6 commits into

from

May 12, 2026
 Merged


Add colour and palettes tutorial
#4
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25cb8e1

Add colour and palettes tutorial


timtreis May 12, 2026
094804b

Add pixi config for running notebooks


timtreis May 12, 2026
f1ab577

Update Visium tutorial and refresh thumbnail


timtreis May 12, 2026
7612f4e

Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state


timtreis May 12, 2026
b4cad04

Reset visium notebook kernel to python3


timtreis May 12, 2026
ed6cb69

Harden execute workflow against local kernel names


timtreis May 12, 2026

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6 changes: 5 additions & 1 deletion
.github/workflows/execute.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -79,8 +79,12 @@ jobs:
 - name: Re-execute selected notebooks
 if: steps.pick.outputs.files != ''
 run: |
 # Pin kernel_name to python3 so notebooks committed with a
 # contributor-local kernel name (e.g. from a pixi `kernel-install`
 # task) still execute against CI's stock python3 kernel.
 while IFS= read -r nb; do
 [ -z "$nb" ] && continue
 echo "Executing $nb"
 jupyter nbconvert --to notebook --execute --inplace "$nb"
 jupyter nbconvert --to notebook --execute --inplace \
 --ExecutePreprocessor.kernel_name=python3 "$nb"
 done <<< "${{ steps.pick.outputs.files }}"

2 changes: 2 additions & 0 deletions
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
Expand Down

117 changes: 58 additions & 59 deletions
examples/visium_mouse_brain.ipynb

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24 changes: 23 additions & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
 "spatialdata-plot>=0.3",
 "spatialdata-plot>=0.3.4",
 "squidpy",
 "jupyter",
 "ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
Expand Down

769 changes: 769 additions & 0 deletions
tutorials/color_and_palette.ipynb

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11 changes: 11 additions & 0 deletions
tutorials/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
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})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Add colour and palettes tutorial#4

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to your account

 Merged

timtreis
merged 6 commits into

from

May 12, 2026
 Merged


Add colour and palettes tutorial
#4
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25cb8e1

Add colour and palettes tutorial


timtreis May 12, 2026
094804b

Add pixi config for running notebooks


timtreis May 12, 2026
f1ab577

Update Visium tutorial and refresh thumbnail


timtreis May 12, 2026
7612f4e

Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state


timtreis May 12, 2026
b4cad04

Reset visium notebook kernel to python3


timtreis May 12, 2026
ed6cb69

Harden execute workflow against local kernel names


timtreis May 12, 2026

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6 changes: 5 additions & 1 deletion
.github/workflows/execute.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -79,8 +79,12 @@ jobs:
 - name: Re-execute selected notebooks
 if: steps.pick.outputs.files != ''
 run: |
 # Pin kernel_name to python3 so notebooks committed with a
 # contributor-local kernel name (e.g. from a pixi `kernel-install`
 # task) still execute against CI's stock python3 kernel.
 while IFS= read -r nb; do
 [ -z "$nb" ] && continue
 echo "Executing $nb"
 jupyter nbconvert --to notebook --execute --inplace "$nb"
 jupyter nbconvert --to notebook --execute --inplace \
 --ExecutePreprocessor.kernel_name=python3 "$nb"
 done <<< "${{ steps.pick.outputs.files }}"

2 changes: 2 additions & 0 deletions
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
Expand Down

117 changes: 58 additions & 59 deletions
examples/visium_mouse_brain.ipynb

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24 changes: 23 additions & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
 "spatialdata-plot>=0.3",
 "spatialdata-plot>=0.3.4",
 "squidpy",
 "jupyter",
 "ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
Expand Down

769 changes: 769 additions & 0 deletions
tutorials/color_and_palette.ipynb

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11 changes: 11 additions & 0 deletions
tutorials/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
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('^' + ".*" + '

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Add colour and palettes tutorial#4

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 Merged

timtreis
merged 6 commits into

from

May 12, 2026
 Merged


Add colour and palettes tutorial
#4
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25cb8e1

Add colour and palettes tutorial


timtreis May 12, 2026
094804b

Add pixi config for running notebooks


timtreis May 12, 2026
f1ab577

Update Visium tutorial and refresh thumbnail


timtreis May 12, 2026
7612f4e

Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state


timtreis May 12, 2026
b4cad04

Reset visium notebook kernel to python3


timtreis May 12, 2026
ed6cb69

Harden execute workflow against local kernel names


timtreis May 12, 2026

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6 changes: 5 additions & 1 deletion
.github/workflows/execute.yaml

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -79,8 +79,12 @@ jobs:
 - name: Re-execute selected notebooks
 if: steps.pick.outputs.files != ''
 run: |
 # Pin kernel_name to python3 so notebooks committed with a
 # contributor-local kernel name (e.g. from a pixi `kernel-install`
 # task) still execute against CI's stock python3 kernel.
 while IFS= read -r nb; do
 [ -z "$nb" ] && continue
 echo "Executing $nb"
 jupyter nbconvert --to notebook --execute --inplace "$nb"
 jupyter nbconvert --to notebook --execute --inplace \
 --ExecutePreprocessor.kernel_name=python3 "$nb"
 done <<< "${{ steps.pick.outputs.files }}"

2 changes: 2 additions & 0 deletions
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
Expand Down

117 changes: 58 additions & 59 deletions
examples/visium_mouse_brain.ipynb

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24 changes: 23 additions & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
 "spatialdata-plot>=0.3",
 "spatialdata-plot>=0.3.4",
 "squidpy",
 "jupyter",
 "ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
Expand Down

769 changes: 769 additions & 0 deletions
tutorials/color_and_palette.ipynb

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11 changes: 11 additions & 0 deletions
tutorials/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
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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25cb8e1

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094804b

Add pixi config for running notebooks


timtreis May 12, 2026
f1ab577

Update Visium tutorial and refresh thumbnail


timtreis May 12, 2026
7612f4e

Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state


timtreis May 12, 2026
b4cad04

Reset visium notebook kernel to python3


timtreis May 12, 2026
ed6cb69

Harden execute workflow against local kernel names


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.github/workflows/execute.yaml

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Expand Up@@ -79,8 +79,12 @@ jobs:
 - name: Re-execute selected notebooks
 if: steps.pick.outputs.files != ''
 run: |
 # Pin kernel_name to python3 so notebooks committed with a
 # contributor-local kernel name (e.g. from a pixi `kernel-install`
 # task) still execute against CI's stock python3 kernel.
 while IFS= read -r nb; do
 [ -z "$nb" ] && continue
 echo "Executing $nb"
 jupyter nbconvert --to notebook --execute --inplace "$nb"
 jupyter nbconvert --to notebook --execute --inplace \
 --ExecutePreprocessor.kernel_name=python3 "$nb"
 done <<< "${{ steps.pick.outputs.files }}"

2 changes: 2 additions & 0 deletions
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
Expand Down

117 changes: 58 additions & 59 deletions
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24 changes: 23 additions & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
 "spatialdata-plot>=0.3",
 "spatialdata-plot>=0.3.4",
 "squidpy",
 "jupyter",
 "ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
Expand Down

769 changes: 769 additions & 0 deletions
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tutorials/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
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('^' + ".*" + '

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timtreis
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25cb8e1

Add colour and palettes tutorial


timtreis May 12, 2026
094804b

Add pixi config for running notebooks


timtreis May 12, 2026
f1ab577

Update Visium tutorial and refresh thumbnail


timtreis May 12, 2026
7612f4e

Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state


timtreis May 12, 2026
b4cad04

Reset visium notebook kernel to python3


timtreis May 12, 2026
ed6cb69

Harden execute workflow against local kernel names


timtreis May 12, 2026

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.github/workflows/execute.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -79,8 +79,12 @@ jobs:
 - name: Re-execute selected notebooks
 if: steps.pick.outputs.files != ''
 run: |
 # Pin kernel_name to python3 so notebooks committed with a
 # contributor-local kernel name (e.g. from a pixi `kernel-install`
 # task) still execute against CI's stock python3 kernel.
 while IFS= read -r nb; do
 [ -z "$nb" ] && continue
 echo "Executing $nb"
 jupyter nbconvert --to notebook --execute --inplace "$nb"
 jupyter nbconvert --to notebook --execute --inplace \
 --ExecutePreprocessor.kernel_name=python3 "$nb"
 done <<< "${{ steps.pick.outputs.files }}"

2 changes: 2 additions & 0 deletions
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
Expand Down

117 changes: 58 additions & 59 deletions
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24 changes: 23 additions & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
 "spatialdata-plot>=0.3",
 "spatialdata-plot>=0.3.4",
 "squidpy",
 "jupyter",
 "ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
Expand Down

769 changes: 769 additions & 0 deletions
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tutorials/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
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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 Merged

timtreis
merged 6 commits into

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Add colour and palettes tutorial
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25cb8e1

Add colour and palettes tutorial


timtreis May 12, 2026
094804b

Add pixi config for running notebooks


timtreis May 12, 2026
f1ab577

Update Visium tutorial and refresh thumbnail


timtreis May 12, 2026
7612f4e

Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state


timtreis May 12, 2026
b4cad04

Reset visium notebook kernel to python3


timtreis May 12, 2026
ed6cb69

Harden execute workflow against local kernel names


timtreis May 12, 2026

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.github/workflows/execute.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -79,8 +79,12 @@ jobs:
 - name: Re-execute selected notebooks
 if: steps.pick.outputs.files != ''
 run: |
 # Pin kernel_name to python3 so notebooks committed with a
 # contributor-local kernel name (e.g. from a pixi `kernel-install`
 # task) still execute against CI's stock python3 kernel.
 while IFS= read -r nb; do
 [ -z "$nb" ] && continue
 echo "Executing $nb"
 jupyter nbconvert --to notebook --execute --inplace "$nb"
 jupyter nbconvert --to notebook --execute --inplace \
 --ExecutePreprocessor.kernel_name=python3 "$nb"
 done <<< "${{ steps.pick.outputs.files }}"

2 changes: 2 additions & 0 deletions
.gitignore

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Original file line numberDiff line numberDiff line change
Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
Expand Down

117 changes: 58 additions & 59 deletions
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24 changes: 23 additions & 1 deletion
pyproject.toml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
 "spatialdata-plot>=0.3",
 "spatialdata-plot>=0.3.4",
 "squidpy",
 "jupyter",
 "ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
Expand Down

769 changes: 769 additions & 0 deletions
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tutorials/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
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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 Merged

timtreis
merged 6 commits into

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May 12, 2026
 Merged


Add colour and palettes tutorial
#4
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25cb8e1

Add colour and palettes tutorial


timtreis May 12, 2026
094804b

Add pixi config for running notebooks


timtreis May 12, 2026
f1ab577

Update Visium tutorial and refresh thumbnail


timtreis May 12, 2026
7612f4e

Bump spatialdata-plot floor to 0.3.4 and ignore pixi local state


timtreis May 12, 2026
b4cad04

Reset visium notebook kernel to python3


timtreis May 12, 2026
ed6cb69

Harden execute workflow against local kernel names


timtreis May 12, 2026

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6 changes: 5 additions & 1 deletion
.github/workflows/execute.yaml

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Original file line numberDiff line numberDiff line change
Expand Up@@ -79,8 +79,12 @@ jobs:
 - name: Re-execute selected notebooks
 if: steps.pick.outputs.files != ''
 run: |
 # Pin kernel_name to python3 so notebooks committed with a
 # contributor-local kernel name (e.g. from a pixi `kernel-install`
 # task) still execute against CI's stock python3 kernel.
 while IFS= read -r nb; do
 [ -z "$nb" ] && continue
 echo "Executing $nb"
 jupyter nbconvert --to notebook --execute --inplace "$nb"
 jupyter nbconvert --to notebook --execute --inplace \
 --ExecutePreprocessor.kernel_name=python3 "$nb"
 done <<< "${{ steps.pick.outputs.files }}"

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.gitignore

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Expand Up@@ -15,6 +15,8 @@ dist/
env/
venv/
ENV/
.pixi/
pixi.lock

# Editors
.idea/
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117 changes: 58 additions & 59 deletions
examples/visium_mouse_brain.ipynb

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24 changes: 23 additions & 1 deletion
pyproject.toml

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Expand Up@@ -16,7 +16,7 @@ authors = [{ name = "scverse" }]
# the notebooks end-to-end.
[project.optional-dependencies]
exec = [
 "spatialdata-plot>=0.3",
 "spatialdata-plot>=0.3.4",
 "squidpy",
 "jupyter",
 "ipykernel",
Expand All@@ -35,6 +35,28 @@ Documentation = "https://spatialdata.scverse.org/projects/plot/en/latest/"
[tool.hatch.build.targets.wheel]
bypass-selection = true

# Pixi-managed environment for running and authoring the notebooks. After
# `pixi install`, register the Jupyter kernel once with `pixi run
# kernel-install`; the kernel will point at the pixi env's Python, so
# `pixi run lab` (or any external Jupyter) can execute the notebooks
# against the exact pinned dependencies.
[tool.pixi]
workspace.channels = ["conda-forge"]
workspace.platforms = ["linux-64", "osx-arm64"]

dependencies.python = ">=3.11"
dependencies.jupyterlab = "*"
dependencies.ipykernel = "*"
dependencies.nbconvert = "*"
dependencies.watermark = "*"

pypi-dependencies.spatialdata-plot = ">=0.3"
pypi-dependencies.squidpy = "*"

tasks.kernel-install = 'python -m ipykernel install --user --name sdata-plot-notebooks --display-name "sdata-plot-notebooks"'
tasks.lab = "jupyter lab"
tasks.execute = "jupyter nbconvert --to notebook --execute --inplace tutorials/*.ipynb examples/*.ipynb"

[tool.ruff]
line-length = 120
target-version = "py311"
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tutorials/color_and_palette.ipynb

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tutorials/index.md

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Expand Up@@ -14,11 +14,22 @@ The fluent `.pl` API, layering, and styling on the in-memory `blobs`
dataset. Ideal first read.
:::

:::{grid-item-card} Colour and palettes
:link: color_and_palette
:link-type: doc
:img-top: color_and_palette.png

How `color=` resolves, the v0.3.0 `groups` behaviour, and building
perceptually well-spaced or colourblind-safe palettes with
`make_palette` and `make_palette_from_data`.
:::

::::

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

getting_started
color_and_palette
```
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