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Fix some minor issues in docs

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Ayaz Salikhov
2025-02-24 16:59:47 +00:00
parent 955ee9f987
commit fc542dae88
11 changed files with 24 additions and 24 deletions
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2
docs/contributing/issues.md
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@@ -1,6 +1,6 @@
# Project Issues # Project Issues
We appreciate your taking the time to report an issue you encountered using the Jupyter Docker Stacks. We appreciate you taking the time to report an issue you encountered while using the Jupyter Docker Stacks.
Please review the following guidelines when reporting your problem. Please review the following guidelines when reporting your problem.
- If you believe you've found a security vulnerability in any of the Jupyter projects included in Jupyter Docker Stacks images, - If you believe you've found a security vulnerability in any of the Jupyter projects included in Jupyter Docker Stacks images,

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docs/contributing/lint.md
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@@ -27,10 +27,10 @@ pre-commit install
### Run ### Run
Now, _pre-commit_ (and so configured hooks) will run automatically on `git commit` on each changed file. Now, _pre-commit_ (and so configured hooks) will run automatically on `git commit` on each changed file.
However, it is also possible to trigger it against all files. However, you can also run it against all files manually.
```{note} ```{note}
Hadolint pre-commit uses Docker to run, so `docker` should be running while running this command. Hadolint pre-commit uses Docker to run, so `docker` should be running while executing this command.
``` ```
```sh ```sh
@@ -58,7 +58,7 @@ The following rules are ignored by default for all images in the `.hadolint.yaml
- [`DL3008`][dl3008]: System packages are always updated (`apt-get`) to the latest version. - [`DL3008`][dl3008]: System packages are always updated (`apt-get`) to the latest version.
- [`DL3013`][dl3013]: We always install the latest packages using `pip` - [`DL3013`][dl3013]: We always install the latest packages using `pip`
The preferred way to do it for other rules is to flag ignored ones in the `Dockerfile`. The preferred way to ignore other rules is to flag them in the `Dockerfile`.
> It is also possible to ignore rules by using a special comment directly above the Dockerfile instruction you want to make an exception for. > It is also possible to ignore rules by using a special comment directly above the Dockerfile instruction you want to make an exception for.
> Ignore rule comments look like `# hadolint ignore=DL3001,SC1081`. > Ignore rule comments look like `# hadolint ignore=DL3001,SC1081`.

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docs/contributing/packages.md
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@@ -12,8 +12,8 @@ We pin major.minor version of Python, so this will stay the same even after invo
## Outdated packages ## Outdated packages
To help identify packages that can be updated, you can use the following helper tool. To help identify packages that can be updated, you can use the following helper tool.
It will list all the outdated packages installed in the `Dockerfile` -- It will list all the outdated packages installed in the `Dockerfile`.
dependencies are filtered to focus only on requested packages. Dependencies are filtered to display only the requested packages.
```bash ```bash
make check-outdated/base-notebook make check-outdated/base-notebook

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docs/contributing/recipes.md
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@@ -1,6 +1,6 @@
# New Recipes # New Recipes
We welcome contributions of [recipes](../using/recipes.md), and short examples of using, configuring, or extending the Docker Stacks for inclusion in the documentation site. We welcome contributions of [recipes](../using/recipes.md), which are short examples of using, configuring, or extending the Docker Stacks for inclusion in the documentation site.
Follow the process below to add a new recipe: Follow the process below to add a new recipe:
1. Open the `docs/using/recipes.md` source file. 1. Open the `docs/using/recipes.md` source file.

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docs/contributing/stacks.md
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@@ -35,8 +35,8 @@ This will serve as both the git repository name and the part of the Docker image
stack_name [my-jupyter-stack]: stack_name [my-jupyter-stack]:
``` ```
Enter the user or organization name under which this stack will reside on Quay.io. Enter the user or organization name under which this stack will reside on Docker Hub.
You must have access to manage this Quay.io organization to push images here. You must have access to manage this Docker Hub organization to push images here.
```text ```text
stack_org [my-project]: stack_org [my-project]:

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docs/using/common.md
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@@ -35,7 +35,7 @@ You do so by passing arguments to the `docker run` command.
- `-e NB_USER=<username>` - The desired username and associated home folder. - `-e NB_USER=<username>` - The desired username and associated home folder.
The default value is `jovyan`. The default value is `jovyan`.
Setting `NB_USER` refits the `jovyan` default user and ensures that the desired user has the correct file permissions Setting `NB_USER` redefines the `jovyan` default user and ensures that the desired user has the correct file permissions
for the new home directory created at `/home/<username>`. for the new home directory created at `/home/<username>`.
For this option to take effect, you **must** run the container with `--user root`, set the working directory `-w "/home/<username>"` For this option to take effect, you **must** run the container with `--user root`, set the working directory `-w "/home/<username>"`
and set the environment variable `-e CHOWN_HOME=yes`. and set the environment variable `-e CHOWN_HOME=yes`.
@@ -90,7 +90,7 @@ You do so by passing arguments to the `docker run` command.
While the default `umask` value should be sufficient for most use cases, you can set the `NB_UMASK` value to fit your requirements. While the default `umask` value should be sufficient for most use cases, you can set the `NB_UMASK` value to fit your requirements.
```{note} ```{note}
`NB_UMASK` when set only applies to the Jupyter process itself - When `NB_UMASK` is set, it only applies to the Jupyter process itself -
you cannot use it to set a `umask` for additional files created during `run-hooks.sh`. you cannot use it to set a `umask` for additional files created during `run-hooks.sh`.
For example, via `pip` or `conda`. For example, via `pip` or `conda`.
If you need to set a `umask` for these, you **must** set the `umask` value for each command. If you need to set a `umask` for these, you **must** set the `umask` value for each command.
@@ -122,7 +122,7 @@ You do so by passing arguments to the `docker run` command.
- `-e RESTARTABLE=yes` - Runs Jupyter in a loop so that quitting Jupyter does not cause the container to exit. - `-e RESTARTABLE=yes` - Runs Jupyter in a loop so that quitting Jupyter does not cause the container to exit.
This may be useful when installing extensions that require restarting Jupyter. This may be useful when installing extensions that require restarting Jupyter.
- `-v /some/host/folder/for/work:/home/jovyan/work` - Mounts a host machine directory as a folder in the container. - `-v /some/host/folder/for/work:/home/jovyan/work` - Mounts a host machine directory as a folder in the container.
This configuration is useful for preserving notebooks and other work even after the container is destroyed. This configuration is useful for preserving notebooks and other work even after the container has been destroyed.
**You must grant the within-container notebook user or group (`NB_UID` or `NB_GID`) write access to the host directory (e.g., `sudo chown 1000 /some/host/folder/for/work`).** **You must grant the within-container notebook user or group (`NB_UID` or `NB_GID`) write access to the host directory (e.g., `sudo chown 1000 /some/host/folder/for/work`).**
- `-e JUPYTER_ENV_VARS_TO_UNSET=ADMIN_SECRET_1,ADMIN_SECRET_2` - Unsets specified environment variables in the default startup script. - `-e JUPYTER_ENV_VARS_TO_UNSET=ADMIN_SECRET_1,ADMIN_SECRET_2` - Unsets specified environment variables in the default startup script.
The variables are unset after the hooks have been executed but before the command provided to the startup script runs. The variables are unset after the hooks have been executed but before the command provided to the startup script runs.
@@ -136,7 +136,7 @@ You do so by passing arguments to the `docker run` command.
You can further customize the container environment by adding shell scripts (`*.sh`) to be sourced You can further customize the container environment by adding shell scripts (`*.sh`) to be sourced
or executables (`chmod +x`) to be run to the paths below: or executables (`chmod +x`) to be run to the paths below:
- `/usr/local/bin/start-notebook.d/` - handled **before** any of the standard options noted above are applied - `/usr/local/bin/start-notebook.d/` - handled **before** any of the standard options noted above is applied
- `/usr/local/bin/before-notebook.d/` - handled **after** all the standard options noted above are applied - `/usr/local/bin/before-notebook.d/` - handled **after** all the standard options noted above are applied
and ran right before the Server launches and ran right before the Server launches
@@ -246,7 +246,7 @@ This script is handy when you derive a new Dockerfile from this image and instal
The default Python 3.x [Conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) resides in `/opt/conda`. The default Python 3.x [Conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) resides in `/opt/conda`.
The `/opt/conda/bin` directory is part of the default `jovyan` user's `${PATH}`. The `/opt/conda/bin` directory is part of the default `jovyan` user's `${PATH}`.
That directory is also searched for binaries when run using `sudo` (`sudo my_binary` will search for `my_binary` in `/opt/conda/bin/` That directory is also searched for binaries when run using `sudo` (`sudo my_binary` will search for `my_binary` in `/opt/conda/bin/`).
The `jovyan` user has full read/write access to the `/opt/conda` directory. The `jovyan` user has full read/write access to the `/opt/conda` directory.
You can use either `mamba`, `pip`, or `conda` (`mamba` is recommended) to install new packages without any additional permissions. You can use either `mamba`, `pip`, or `conda` (`mamba` is recommended) to install new packages without any additional permissions.

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docs/using/faq.md
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@@ -2,7 +2,7 @@
## How to persist user data ## How to persist user data
There are 2 types of data, which you might want to persist. There are two types of data, which you might want to persist.
1. If you want to persist your environment (i.e. packages installed by `mamba`, `conda`, `pip`, `apt-get`, and so on), 1. If you want to persist your environment (i.e. packages installed by `mamba`, `conda`, `pip`, `apt-get`, and so on),
then you should create an inherited image and install packages only once while building your Dockerfile. then you should create an inherited image and install packages only once while building your Dockerfile.
@@ -22,7 +22,7 @@ There are 2 types of data, which you might want to persist.
You can find [an example of using a bind mount here](./running.md#example-2). You can find [an example of using a bind mount here](./running.md#example-2).
There is also [a mount troubleshooting section](./troubleshooting.md#permission-denied-when-mounting-volumes) if you experience any issues. There is also [a mount troubleshooting section](./troubleshooting.md#permission-denied-when-mounting-volumes) if you experience any issues.
## Why we do not add your favorite package ## Why we don't add your favorite package
We have lots of users with different packages they want to use. We have lots of users with different packages they want to use.
Adding them all is impossible, so we have several images to choose from. Adding them all is impossible, so we have several images to choose from.

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docs/using/recipes.md
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@@ -60,7 +60,7 @@ docker run -it --rm \
The default version of `Python` that ships with the image may not be the version you want. The default version of `Python` that ships with the image may not be the version you want.
The instructions below permit adding a conda environment with a different `Python` version and making it accessible to Jupyter. The instructions below permit adding a conda environment with a different `Python` version and making it accessible to Jupyter.
You may also use older images like `jupyter/base-notebook:python-3.10`. You may also use older images like `jupyter/base-notebook:python-3.10`.
A list of all tags can be found [here](https://github.com/jupyter/docker-stacks/wiki) A list of all tags can be found [here](https://github.com/jupyter/docker-stacks/wiki).
```{literalinclude} recipe_code/custom_environment.dockerfile ```{literalinclude} recipe_code/custom_environment.dockerfile
:language: docker :language: docker
@@ -400,7 +400,7 @@ docker run -it --rm \
## Enable nbclassic-extension spellchecker for markdown (or any other nbclassic-extension) ## Enable nbclassic-extension spellchecker for markdown (or any other nbclassic-extension)
```{note} ```{note}
This recipe only works for NBCassic with Jupyter Notebook < 7. This recipe only works for NBClassic with Jupyter Notebook < 7.
It is recommended to use [jupyterlab-spellchecker](https://github.com/jupyterlab-contrib/spellchecker) in modern environments. It is recommended to use [jupyterlab-spellchecker](https://github.com/jupyterlab-contrib/spellchecker) in modern environments.
``` ```

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docs/using/selecting.md
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@@ -244,7 +244,7 @@ It contains:
We provide CUDA accelerated versions of the `pytorch-notebook` and `tensorflow-notebook` images. We provide CUDA accelerated versions of the `pytorch-notebook` and `tensorflow-notebook` images.
Prepend a CUDA prefix (versioned prefix like `cuda12-` for `pytorch-notebook` or just `cuda-` for `tensorflow-notebook`) to the image tag Prepend a CUDA prefix (versioned prefix like `cuda12-` for `pytorch-notebook` or just `cuda-` for `tensorflow-notebook`) to the image tag
to allow PyTorch or TensorFlow operations to use compatible NVIDIA GPUs for accelerated computation. to allow PyTorch or TensorFlow operations to use compatible NVIDIA GPUs for accelerated computation.
We only build `pytorch-notebook` for last two major versions of CUDA. We only build `pytorch-notebook` for the last two major versions of CUDA.
The `tensorflow-notebook` image only supports the latest CUDA version listed in the [officially tested build configurations](https://www.tensorflow.org/install/source#gpu). The `tensorflow-notebook` image only supports the latest CUDA version listed in the [officially tested build configurations](https://www.tensorflow.org/install/source#gpu).
For example, you could use the image `quay.io/jupyter/pytorch-notebook:cuda12-python-3.11.8` or `quay.io/jupyter/tensorflow-notebook:cuda-latest`. For example, you could use the image `quay.io/jupyter/pytorch-notebook:cuda12-python-3.11.8` or `quay.io/jupyter/tensorflow-notebook:cuda-latest`.

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docs/using/troubleshooting.md
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@@ -108,7 +108,7 @@ The following sections cover a few of these scenarios and how to fix them.
where: where:
- `NB_IUD` and `NB_GID` should match the local user's UID and GID. - `NB_UID` and `NB_GID` should match the local user's UID and GID.
- You **must** use `--user root` to ensure that the `UID` and `GID` are updated at runtime. - You **must** use `--user root` to ensure that the `UID` and `GID` are updated at runtime.
````{admonition} Additional notes ````{admonition} Additional notes
@@ -273,7 +273,7 @@ conda config --show default_channels
You can install packages from other conda channels (e.g. `bioconda`) by disabling the `channel_priority` setting: You can install packages from other conda channels (e.g. `bioconda`) by disabling the `channel_priority` setting:
```bash ```bash
# install by disabling channel priority at еру command level # install by disabling channel priority at the command level
conda install --no-channel-priority -c bioconda bioconductor-geoquery conda install --no-channel-priority -c bioconda bioconductor-geoquery
``` ```