From 9bd1e7fa265d8062f6810e4cd9f8323b4fba5b15 Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Wed, 19 Aug 2026 13:42:15 +1200 Subject: [PATCH 1/2] Add JupyterLab section --- .../docs/studios/container-images.md | 55 +++++++++-------- .../studios/container-images.md | 59 ++++++++++--------- project-words.txt | 1 + 3 files changed, 63 insertions(+), 52 deletions(-) diff --git a/platform-cloud/docs/studios/container-images.md b/platform-cloud/docs/studios/container-images.md index 150b4493df..c727b6ef74 100644 --- a/platform-cloud/docs/studios/container-images.md +++ b/platform-cloud/docs/studios/container-images.md @@ -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] --- @@ -16,7 +16,7 @@ The image template tag has the format: -[u]- ``` -- ``: Third-party analysis application that follows its own semantic versioning `..`, such as `4.2.5` for JupyterLab. +- ``: Third-party analysis application that follows its own semantic versioning `..`, such as `4.6.0` for JupyterLab. - ``: Optional analysis application update version, such as `u1`, for instances where a backwards incompatible change is introduced. - ``: Seqera Connect client version, such as `0.12` or `0.12.0`. @@ -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 +Earlier JupyterLab image templates listed `pandas[all]` and `seaborn[stats]`. Because libmamba 2.x rejects this extras syntax, current templates specify `pandas` and `seaborn` without extras. If you copy a package list from an older template into a custom environment, remove the extras. +::: To install additional Python packages during a running Studio session, execute `!pip install ` commands in your notebook environment. Install additional system-level packages in a terminal window with `apt install `. diff --git a/platform-enterprise_docs/studios/container-images.md b/platform-enterprise_docs/studios/container-images.md index bd8717fc73..1a91fd97e2 100644 --- a/platform-enterprise_docs/studios/container-images.md +++ b/platform-enterprise_docs/studios/container-images.md @@ -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] --- @@ -16,7 +16,7 @@ The image template tag has the format: -[u]- ``` -- ``: Third-party analysis application that follows its own semantic versioning `..`, such as `4.2.5` for JupyterLab. +- ``: Third-party analysis application that follows its own semantic versioning `..`, such as `4.6.0` for JupyterLab. - ``: Optional analysis application update version, such as `u1`, for instances where a backwards incompatible change is introduced. - ``: Seqera Connect client version, such as `0.12` or `0.12.0`. @@ -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 ` commands in your notebook environment. Additional system-level packages can be installed in a terminal window using `apt install `. +### 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 +Earlier JupyterLab image templates listed `pandas[all]` and `seaborn[stats]`. Because libmamba 2.x rejects this extras syntax, current templates specify `pandas` and `seaborn` without extras. If you copy a package list from an older template into a custom environment, remove the extras. +::: + +To install additional Python packages during a running Studio session, execute `!pip install ` commands in your notebook environment. Install additional system-level packages in a terminal window with `apt install `. 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]. diff --git a/project-words.txt b/project-words.txt index bcf1d0e920..8504b3bddb 100644 --- a/project-words.txt +++ b/project-words.txt @@ -88,6 +88,7 @@ inlines javax Kallisto keypair +libmamba logback lymphoblastoid Mailpit From 2bcb85d02c7bb923b567cbb2e51f0d942097382e Mon Sep 17 00:00:00 2001 From: Christopher Hakkaart Date: Wed, 19 Aug 2026 13:46:51 +1200 Subject: [PATCH 2/2] Deslop --- platform-cloud/docs/studios/container-images.md | 2 +- platform-enterprise_docs/studios/container-images.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/platform-cloud/docs/studios/container-images.md b/platform-cloud/docs/studios/container-images.md index c727b6ef74..09401bde76 100644 --- a/platform-cloud/docs/studios/container-images.md +++ b/platform-cloud/docs/studios/container-images.md @@ -63,7 +63,7 @@ The latest JupyterLab image template version is `4.6.0`. The default user is the - `polars=1.35.2` :::note -Earlier JupyterLab image templates listed `pandas[all]` and `seaborn[stats]`. Because libmamba 2.x rejects this extras syntax, current templates specify `pandas` and `seaborn` without extras. If you copy a package list from an older template into a custom environment, remove the extras. +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 ` commands in your notebook environment. Install additional system-level packages in a terminal window with `apt install `. diff --git a/platform-enterprise_docs/studios/container-images.md b/platform-enterprise_docs/studios/container-images.md index 1a91fd97e2..20816098b7 100644 --- a/platform-enterprise_docs/studios/container-images.md +++ b/platform-enterprise_docs/studios/container-images.md @@ -63,7 +63,7 @@ The latest JupyterLab image template version is `4.6.0`. The default user is the - `polars=1.35.2` :::note -Earlier JupyterLab image templates listed `pandas[all]` and `seaborn[stats]`. Because libmamba 2.x rejects this extras syntax, current templates specify `pandas` and `seaborn` without extras. If you copy a package list from an older template into a custom environment, remove the extras. +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 ` commands in your notebook environment. Install additional system-level packages in a terminal window with `apt install `.