MetabarcodingSchool/OBIJupyterHub
1
0
Fork 0
Code Issues Pull Requests 1 Actions Packages Projects Releases Wiki Activity

Add options to startup script

Browse Source
This commit is contained in:
Eric Coissac
2025-11-25 11:59:28 +01:00
parent 4e338bc1d4
commit 2417959fbd
358 changed files with 214 additions and 676065 deletions
Download Patch File Download Diff File Expand all files Collapse all files

19
Readme.md
View File

@@ -1,4 +1,4 @@
# JupyterHub Configuration with OrbStack on Mac (all in Docker)
# OBIJupyterHub - the DNA Metabarcoding Learning Server
## Intended use
@@ -32,6 +32,14 @@ python3 --version
- renders the Quarto site from `web_src/`, generates PDF galleries and `pages.json`, and copies everything into `jupyterhub_volumes/web/`
- runs `docker-compose up -d --remove-orphans`
You can tailor what it does with a few flags:
- `--no-build` (or `--offline`): skip Docker image builds and reuse existing images (useful when offline).
- `--force-rebuild`: rebuild images without cache.
- `--stop-server`: stop the stack and remove student containers, then exit.
- `--update-lectures`: rebuild the course website only (no Docker stop/start).
- `--build-obidoc`: force rebuilding the obidoc documentation (auto-built if empty; skipped in offline mode).
## Installation and first run
1) Clone the project:
@@ -78,9 +86,14 @@ OBIJupyterHub
docker-compose down
```
### Operating the stack (with one command)
### Operating the stack (one command, a few options)
- Start or rebuild at any time with `./start-jupyterhub.sh` from the project root. It rebuilds images, regenerates the website, and starts the stack.
- Start or rebuild: `./start-jupyterhub.sh` (rebuilds images, regenerates the website, starts the stack).
- Start without rebuilding images (offline): `./start-jupyterhub.sh --no-build`
- Force rebuild without cache: `./start-jupyterhub.sh --force-rebuild`
- Stop only: `./start-jupyterhub.sh --stop-server`
- Rebuild website only (no Docker stop/start): `./start-jupyterhub.sh --update-lectures`
- Rebuild obidoc docs: `./start-jupyterhub.sh --build-obidoc` (also builds automatically if `jupyterhub_volumes/web/obidoc` is empty; skipped in offline mode)
- Access at `http://localhost:8888` (students: any username / password `metabar2025`; admin: `admin` / `admin2025`).
- Check logs from `obijupyterhub/` with `docker-compose logs -f jupyterhub`.
- Stop with `docker-compose down` (from `obijupyterhub/`). Rerun `./start-jupyterhub.sh` to start again or after config changes.