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Update the jupyterhub/repo2docker image #217

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Update the jupyterhub/repo2docker image #217

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3a7278b
Update the `repo2docker` image
jtpio Nov 14, 2023
0a76972
Make the docker image configurable
jtpio Nov 14, 2023
186673a
Update documentation
jtpio Nov 15, 2023
e960cfc
Try switching to a Python entrypoint like repo2docker
jtpio Nov 16, 2023
dd677da
Explicitely opt-in as run_as_root
jtpio Nov 20, 2023
0acb9e1
Omit - in su commmand
jtpio Nov 20, 2023
020b2e2
Re-enable container removal
jtpio Nov 21, 2023
64bff01
Fix missing quotes
jtpio Nov 22, 2023
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5 changes: 3 additions & 2 deletions ansible/tljh.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -46,6 +46,7 @@
# Pull the repo2docker image to build user images
- name: Pull the repo2docker Docker image
docker_image:
name: quay.io/jupyterhub/repo2docker
tag: main
name: "{{ repo2docker_docker_name }}"
tag: "{{ repo2docker_docker_tag }}"
source: pull
force_source: yes
3 changes: 3 additions & 0 deletions ansible/vars/default.yml
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Expand Up @@ -9,4 +9,7 @@ tljh_prefix: /opt/tljh
tljh_bootstrap_pip_spec: git+https://github.com/jtpio/the-littlest-jupyterhub.git@skip-install#"egg=the_littlest_jupyterhub"
tljh_installer_url: https://raw.githubusercontent.com/jtpio/the-littlest-jupyterhub/skip-install/bootstrap/bootstrap.py

repo2docker_docker_name: quay.io/jupyterhub/repo2docker
repo2docker_docker_tag: 2023.06.0-41.g57d229e

...
15 changes: 15 additions & 0 deletions docs/install/ansible.md
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Expand Up @@ -268,6 +268,21 @@ tagged as `v0.1`:
tljh_plasma: git+https://github.com/plasmabio/[email protected]#"egg=tljh-plasma&subdirectory=tljh-plasma"
```

## Using a specific version of `repo2docker`

`repo2docker` is used to build the user environments from the Git repositories.

By default the Ansible playbooks use a pinned version of the `jupyterhub/repo2docker`, which is defined in the
`ansible/vars/default.yml` file.

Like other Ansible variables, it is possible to use a different version of `repo2docker` by overriding the variable
via the command line:

```bash
# use an older version of the repo2docker image
ansible-playbook tljh.yml -i hosts -u ubuntu -e "repo2docker_docker_tag=2022.10.0-232.g0ea6f7d"
```

## List of available playbooks

The Ansible playbooks are located in the `ansible/` directory:
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2 changes: 2 additions & 0 deletions tljh-plasma/tljh_plasma/__init__.py
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Expand Up @@ -123,6 +123,8 @@ def tljh_custom_jupyterhub_config(c, tljh_config_file=CONFIG_FILE):
c.PlasmaSpawner.cmd = ["/srv/conda/envs/notebook/bin/jupyterhub-singleuser"]
# set the default cpu and memory limits
c.PlasmaSpawner.args = ["--ResourceUseDisplay.track_cpu_percent=True"]
# explicitely opt-in to enable the custom entrypoint logic
c.PlasmaSpawner.run_as_root = True
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@jtpio jtpio Nov 20, 2023 •
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This is now opt-in in dockerspawner>=12.0: https://jupyterhub-dockerspawner.readthedocs.io/en/latest/changelog.html#id3

Not sure why we didn't have to set it explicitly before, as it was updated in #193.


# prevent PID 1 running in the Docker container to stop when child processes are killed
# see https://github.com/plasmabio/plasma/issues/191 for more info
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2 changes: 1 addition & 1 deletion tljh-plasma/tljh_plasma/entrypoint/entrypoint.sh
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Expand Up @@ -43,4 +43,4 @@ export JUPYTER_PATH=${IMAGE_DIR}/.local/share/jupyter
cd ${IMAGE_DIR}

# execute the notebook process as the given user
exec su - $NB_USER -m -c '"$0" "$@"' -- "$@"
exec su $NB_USER -m -c '"$0" "$@"' -- "$@"
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OK this seems to be doing the trick for being able able to launch the server.

If I understand correctly, specifying - would be equivalent to starting the process with --login, which conflicts with -m / --preserve-environment.

As hinted by the the error logs:

su: ignoring --preserve-environment, it's mutually exclusive with --login
--root-prefix: 1 required TEXT missing
Run with --help for more information.
/srv/conda/envs/notebook/bin/jupyterhub-singleuser: 7: /etc/profile.d/activate-conda.sh: [[: not found
/srv/conda/envs/notebook/bin/jupyterhub-singleuser: 20: /etc/profile.d/activate-conda.sh: mamba: not found
JUPYTERHUB_API_TOKEN env is required to run jupyterhub-singleuser. Did you launch it manually?

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I guess this is related to recent update of the mamba activation scripts in repo2docker. Removing the - seems to be working fine locally so we should be able to do without now:

image

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Need to do a bit more testing on a test VM, but this change might break compatibility with existing environments built with an older version of repo2docker.

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