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docs: Jupyterlab template packages #1755

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9bd1e7f
Add JupyterLab section
christopher-hakkaart Aug 19, 2026
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Deslop
christopher-hakkaart Aug 19, 2026
c681cb8
Merge branch 'master' into docs/edu-1367-jupyterlab-template-packages
christopher-hakkaart Aug 19, 2026
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55 changes: 30 additions & 25 deletions platform-cloud/docs/studios/container-images.md
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Expand Up @@ -2,7 +2,7 @@
title: "Container image templates"
description: "Use container images with Studios."
date created: "2025-10-16"
last updated: "2026-06-03"
last updated: "2026-08-17"
tags: [containers, container images, sessions, studios]
---

Expand All @@ -16,7 +16,7 @@ The image template tag has the format:
<tool_version>-[u<update_version>]-<connect_version>
```

- `<tool_version>`: Third-party analysis application that follows its own semantic versioning `<major>.<minor>.<patch>`, such as `4.2.5` for JupyterLab.
- `<tool_version>`: Third-party analysis application that follows its own semantic versioning `<major>.<minor>.<patch>`, such as `4.6.0` for JupyterLab.
- `<update_version>`: Optional analysis application update version, such as `u1`, for instances where a backwards incompatible change is introduced.
- `<connect_version>`: Seqera Connect client version, such as `0.12` or `0.12.0`.

Expand All @@ -37,29 +37,34 @@ When pushed to the container registry, an image template is tagged with the foll

To view the latest versions of the images, see [public.cr.seqera.io](https://public.cr.seqera.io/). You can also augment the Seqera-provided image templates or use your own custom container image templates. This is the recommended approach for managing reproducible analysis environments. For more information, see [Custom environments][custom-envs].

## JupyterLab 4.2.5

The default user is the `root` account. The following [conda-forge](https://conda-forge.org/) packages are available by default:

- `python=3.13.0`
- `pip=24.2`
- `jedi-language-server=0.41.4`
- `jupyterlab=4.2.5`
- `jupyter-collaboration=1.2.0`
- `jupyterlab-git=0.50.1`
- `jupytext=1.16.4`
- `jupyter-dash=0.4.2`
- `ipywidgets=7.8.4`
- `pandas[all]=2.2.3`
- `scikit-learn=1.5.2`
- `statsmodels=0.14.4`
- `itables=2.2.2`
- `seaborn[stats]=0.13.2`
- `altair=5.4.1`
- `plotly=5.24.1`
- `r-ggplot2=3.5.1`
- `nb_black=1.0.7`
- `qgrid=1.3.1`
## JupyterLab

The latest JupyterLab image template version is `4.6.0`. The default user is the `root` account. The following [conda-forge](https://conda-forge.org/) packages are available by default:

- `python=3.13`
- `pip=25.3`
- `jedi-language-server=0.46.0`
- `jupyterlab=4.6.0`
- `jupyter-collaboration=4.1.2`
- `jupyterlab-git=0.51.2`
- `jupyterlab_code_formatter=3.0.3`
- `black=25.1.0`
- `isort=6.1.0`
- `jupytext=1.18.1`
- `ipywidgets=8.1.8`
- `pandas=2.3.3`
- `scikit-learn=1.7.2`
- `statsmodels=0.14.5`
- `itables=2.5.2`
- `seaborn=0.13.2`
- `altair=6.0.0`
- `plotly=6.5.0`
- `r-ggplot2=4.0.1`
- `polars=1.35.2`

:::note
Current templates specify `pandas` and `seaborn` without extras because libmamba 2.x rejects the extras syntax used in earlier templates (`pandas[all]`, `seaborn[stats]`). Remove the extras from any package list you copy from an older template into a custom environment.
:::

To install additional Python packages during a running Studio session, execute `!pip install <packagename>` commands in your notebook environment. Install additional system-level packages in a terminal window with `apt install <packagename>`.

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59 changes: 32 additions & 27 deletions platform-enterprise_docs/studios/container-images.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
title: "Container image templates"
description: "Use container images with Studios."
date created: "2025-10-16"
last updated: "2026-05-29"
last updated: "2026-08-17"
tags: [containers, container images, sessions, studios]
---

Expand All @@ -16,7 +16,7 @@ The image template tag has the format:
<tool_version>-[u<update_version>]-<connect_version>
```

- `<tool_version>`: Third-party analysis application that follows its own semantic versioning `<major>.<minor>.<patch>`, such as `4.2.5` for JupyterLab.
- `<tool_version>`: Third-party analysis application that follows its own semantic versioning `<major>.<minor>.<patch>`, such as `4.6.0` for JupyterLab.
- `<update_version>`: Optional analysis application update version, such as `u1`, for instances where a backwards incompatible change is introduced.
- `<connect_version>`: Seqera Connect client version, such as `0.12` or `0.12.0`.

Expand All @@ -37,31 +37,36 @@ When pushed to the container registry, an image template is tagged with the foll

To view the latest versions of the images, see [public.cr.seqera.io](https://public.cr.seqera.io/). You can also augment the Seqera-provided image templates or use your own custom container image templates. This is the recommended approach for managing reproducible analysis environments. For more information, see [Custom environments][custom-envs].

### JupyterLab 4.2.5

The default user is the `root` account. The following [conda-forge](https://conda-forge.org/) packages are available by default:

- `python=3.13.0`
- `pip=24.2`
- `jedi-language-server=0.41.4`
- `jupyterlab=4.2.5`
- `jupyter-collaboration=1.2.0`
- `jupyterlab-git=0.50.1`
- `jupytext=1.16.4`
- `jupyter-dash=0.4.2`
- `ipywidgets=7.8.4`
- `pandas[all]=2.2.3`
- `scikit-learn=1.5.2`
- `statsmodels=0.14.4`
- `itables=2.2.2`
- `seaborn[stats]=0.13.2`
- `altair=5.4.1`
- `plotly=5.24.1`
- `r-ggplot2=3.5.1`
- `nb_black=1.0.7`
- `qgrid=1.3.1`

To install additional Python packages during a running Studio session, execute `!pip install <packagename>` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install <packagename>`.
### JupyterLab

The latest JupyterLab image template version is `4.6.0`. The default user is the `root` account. The following [conda-forge](https://conda-forge.org/) packages are available by default:

- `python=3.13`
- `pip=25.3`
- `jedi-language-server=0.46.0`
- `jupyterlab=4.6.0`
- `jupyter-collaboration=4.1.2`
- `jupyterlab-git=0.51.2`
- `jupyterlab_code_formatter=3.0.3`
- `black=25.1.0`
- `isort=6.1.0`
- `jupytext=1.18.1`
- `ipywidgets=8.1.8`
- `pandas=2.3.3`
- `scikit-learn=1.7.2`
- `statsmodels=0.14.5`
- `itables=2.5.2`
- `seaborn=0.13.2`
- `altair=6.0.0`
- `plotly=6.5.0`
- `r-ggplot2=4.0.1`
- `polars=1.35.2`

:::note
Current templates specify `pandas` and `seaborn` without extras because libmamba 2.x rejects the extras syntax used in earlier templates (`pandas[all]`, `seaborn[stats]`). Remove the extras from any package list you copy from an older template into a custom environment.

@georgi-seqera georgi-seqera Aug 19, 2026

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Above versions themselves look correct, but I can't speak to this note here - @robnewman since you made the jupyter lab update change, does the above sounds right?

@christopher-hakkaart christopher-hakkaart Aug 19, 2026

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Thanks @georgi-seqera

:::

To install additional Python packages during a running Studio session, execute `!pip install <packagename>` commands in your notebook environment. Install additional system-level packages in a terminal window with `apt install <packagename>`.

To see all JupyterLab image templates, including security scan results, or to inspect the container specification, see [public.cr.seqera.io/repo/platform/data-studio-jupyter][ds-jupyter].

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1 change: 1 addition & 0 deletions project-words.txt
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Expand Up @@ -88,6 +88,7 @@ inlines
javax
Kallisto
keypair
libmamba
logback
lymphoblastoid
Mailpit
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