[refactor] Introduce multi-mode startup and registry-based images

- Replace monolithic build flow with three operating modes: pull (default), local-build, publish
- Add version.txt for image tagging and multi-platform builds via buildx (--publish)
- Switch builder to tarball-based Quarto install for better cross-platform reliability
- Update docker-compose.yml and jupyterhub_config.py to use environment variables for image names, defaulting to registry images
- Refactor start-jupyterhub.sh: modular functions for image management, clearer flag handling and error messages
- Simplify Readme.md with structured tables instead of dense paragraphs, clarify data persistence and R package workflow

obijupyterhub/Dockerfile.builder

@@ -55,12 +55,15 @@ RUN ARCH=$(dpkg --print-architecture) \
        | tar -xz -C /usr/local/bin hugo \
     && chmod +x /usr/local/bin/hugo
 
-# Install Quarto using the official .deb package (handles all dependencies properly)
+# Install Quarto from the official tarball.
+# Using tar.gz instead of .deb avoids dpkg and is more reliable in cross-arch
+# (QEMU) builds where GitHub downloads are slower and more prone to transient errors.
 ARG QUARTO_VERSION=1.6.42
 RUN ARCH=$(dpkg --print-architecture) \
-    && curl -fsSL -o /tmp/quarto.deb "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${ARCH}.deb" \
-    && dpkg -i /tmp/quarto.deb \
-    && rm /tmp/quarto.deb
+    && curl -fsSL --retry 5 --retry-delay 10 \
+       "https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${ARCH}.tar.gz" \
+       | tar -xz -C /opt \
+    && ln -s "/opt/quarto-${QUARTO_VERSION}/bin/quarto" /usr/local/bin/quarto
 
 # Create working directory
 WORKDIR /workspace

obijupyterhub/docker-compose.yml

@@ -1,11 +1,8 @@
 services:
   jupyterhub:
-    build:
-      context: .
-      dockerfile: Dockerfile.hub
     container_name: jupyterhub
     hostname: jupyterhub
-    image: jupyterhub-hub:latest
+    image: ${HUB_IMAGE:-registry.metabarcoding.org/metabarschool/obijupyterhub-hub:latest}
     expose:
       - "8000"
     volumes:
@@ -21,6 +18,8 @@ services:
       - jupyterhub-network
     restart: unless-stopped
     environment:
+      # Docker image used for student containers (read by jupyterhub_config.py)
+      STUDENT_IMAGE: ${STUDENT_IMAGE:-registry.metabarcoding.org/metabarschool/obijupyterhub-student:latest}
       # Shared password for all students
       JUPYTERHUB_PASSWORD: metabar2025
       # Admin password (for installing R packages)

obijupyterhub/jupyterhub_config.py

@@ -14,7 +14,10 @@ VOLUMES_BASE_PATH = '/volumes/users'  # Path as seen from JupyterHub container (
 HOST_VOLUMES_PATH = os.environ.get('HOST_VOLUMES_PATH', '/volumes')  # Real path on host machine (parent dir)
 
 # Docker image to use for student containers
-c.DockerSpawner.image = 'jupyterhub-student:latest'
+c.DockerSpawner.image = os.environ.get(
+    'STUDENT_IMAGE',
+    'registry.metabarcoding.org/metabarschool/obijupyterhub-student:latest'
+)
 
 # Docker network (create with: docker network create jupyterhub-network)
 c.DockerSpawner.network_name = 'jupyterhub-network'