Image multistage

Ajout des obitools
Traduction en anglais des fichiers
2025-10-15 14:58:46 +02:00 · 2025-10-15 09:06:58 +02:00 · 2025-10-15 07:14:53 +02:00
7 changed files with 507 additions and 188 deletions
--- a/57
+++ b/57
@@ -1,34 +1,49 @@
-FROM jupyter/base-notebook:latest
+# ---------- Stage 1 : builder ----------
+FROM jupyter/base-notebook:latest AS builder

 USER root

-# Installation de R et des dépendances système
+# Install system dependencies for R, build tools and Go/Rust
 RUN apt-get update && apt-get install -y \
-    r-base \
-    r-base-dev \
-    libcurl4-openssl-dev \
-    libssl-dev \
-    libxml2-dev \
-    texlive-xetex \
-    texlive-fonts-recommended \
-    texlive-plain-generic \
+    r-base r-base-dev \
+    libcurl4-openssl-dev libssl-dev libxml2-dev \
+    build-essential git curl \
    && apt-get clean && rm -rf /var/lib/apt/lists/*

-# Installation du kernel R pour Jupyter (en tant que root)
+# Install R kernel + useful packages
 RUN R -e "install.packages('IRkernel', repos='http://cran.rstudio.com/')" && \
-    R -e "IRkernel::installspec(user = FALSE)"
+    R -e "IRkernel::installspec(user = FALSE)" && \
+    R -e "install.packages(c('tidyverse','vegan','ade4'), repos='http://cran.rstudio.com/')"

-# Installation de quelques packages R utiles pour les TP
-RUN R -e "install.packages(c('tidyverse','vegan','ade4'), repos='http://cran.rstudio.com/')"
+# Install bash kernel
+RUN pip install bash_kernel && python -m bash_kernel.install --sys-prefix

-# Installation du kernel bash (en tant que root aussi)
-RUN pip install bash_kernel && \
-    python -m bash_kernel.install --sys-prefix
+# Install obitools4
+RUN curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash

-# Créer les répertoires nécessaires avec les bonnes permissions
+# Install csvkit
+RUN pip install csvkit
+
+# Install csvlens via Rust
+RUN curl https://sh.rustup.rs -sSf | bash -s -- -y && \
+    . $HOME/.cargo/env && \
+    cargo install csvlens
+
+RUN apt-get update && apt-get install -y ruby ruby-dev build-essential \
+    && gem install youplot
+
+# Copy csvlens to /usr/local/bin for final use
+RUN cp $HOME/.cargo/bin/csvlens /usr/local/bin/
+
+# Set permissions for Jupyter user
 RUN mkdir -p /home/${NB_USER}/.local/share/jupyter && \
-    chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}
+    chown -R ${NB_UID}:${NB_GID} /home/${NB_USER} 

-USER ${NB_UID}
+# Switch back to Jupyter user
+USER ${NB_UID}:${NB_GID}
+WORKDIR /home/${NB_USER}/work

-WORKDIR /home/${NB_USER}
+# Environment variables
+ENV PATH="/home/${NB_USER}/work/course/bin:${PATH}"
+ENV R_LIBS_USER="/home/${NB_USER}/work/R_packages"
+ENV R_LIBS_SITE="/home/${NB_USER}/work/course/R_packages:/usr/local/lib/R/site-library:/usr/lib/R/site-library"
--- a/Dockerfile.hub
+++ b/Dockerfile.hub
@@ -1,16 +1,16 @@
 FROM jupyterhub/jupyterhub:latest

-# Installation de DockerSpawner
+# Install DockerSpawner
 RUN pip install dockerspawner

-# Copie de la configuration
+# Copy configuration
 COPY jupyterhub_config.py /srv/jupyterhub/jupyterhub_config.py

-# Port exposé
+# Expose port
 EXPOSE 8000

-# Répertoire de travail
+# Working directory
 WORKDIR /srv/jupyterhub

-# Commande de démarrage
+# Startup command
 CMD ["jupyterhub", "-f", "/srv/jupyterhub/jupyterhub_config.py"]
--- a/Readme.md
+++ b/Readme.md
@@ -1,258 +1,350 @@
-# Configuration JupyterHub avec OrbStack sur Mac (tout en Docker)
+# JupyterHub Configuration with OrbStack on Mac (all in Docker)

-## Prérequis
- OrbStack installé et démarré
+## Prerequisites
+- OrbStack installed and running

-## Structure des fichiers
+## File Structure

-Votre dossier `~/jupyterhub-tp` doit contenir :
+Your `~/jupyterhub-tp` directory should contain:
 ```
 ~/jupyterhub-tp/
-├── Dockerfile                  # Image pour les étudiants (déjà créée)
-├── Dockerfile.hub              # Image pour JupyterHub (nouvelle)
+├── Dockerfile                  # Image for students (already created)
+├── Dockerfile.hub              # Image for JupyterHub (new)
 ├── jupyterhub_config.py        # Configuration
-└── docker-compose.yml          # Orchestration
+├── docker-compose.yml          # Orchestration
+└── start-jupyterhub.sh         # Startup script
 ```

-## Étapes d'installation
+## Installation Steps

-### 1. Créer la structure de dossiers
+### 1. Create Directory Structure

 ```bash
 mkdir -p ~/jupyterhub-tp
 cd ~/jupyterhub-tp
 ```

-### 2. Créer tous les fichiers nécessaires
+### 2. Create All Necessary Files

-Créez les fichiers suivants avec le contenu des artifacts :
- `Dockerfile` (artifact "Dockerfile pour JupyterHub avec R et Bash")
- `Dockerfile.hub` (artifact "Dockerfile pour le container JupyterHub")
- `jupyterhub_config.py` (artifact "Configuration JupyterHub")
+Create the following files with the content from artifacts:
+- `Dockerfile` (artifact "Dockerfile for JupyterHub with R and Bash")
+- `Dockerfile.hub` (artifact "Dockerfile for JupyterHub container")
+- `jupyterhub_config.py` (artifact "JupyterHub Configuration")
 - `docker-compose.yml` (artifact "docker-compose.yml")
+- `start-jupyterhub.sh` (artifact "start-jupyterhub.sh")

-### 3. Construire les images Docker
+### 3. Make Startup Script Executable

 ```bash
-# Image pour les étudiants
-docker build -t jupyterhub-student:latest -f Dockerfile .
-
-# Image pour le hub JupyterHub
-docker build -t jupyterhub-hub:latest -f Dockerfile.hub .
+chmod +x start-jupyterhub.sh
 ```

-### 4. Démarrer JupyterHub avec Docker Compose
+### 4. Start JupyterHub

 ```bash
-docker-compose up -d
+./start-jupyterhub.sh
 ```

-### 5. Accéder à JupyterHub
+### 5. Access JupyterHub

-Ouvrez votre navigateur et allez à : **http://localhost:8000**
+Open your browser and go to: **http://localhost:8888**

-Vous pouvez vous connecter avec n'importe quel nom d'utilisateur.
+You can log in with any username and password: `metabar2025`

-## Commandes utiles
+## Useful Commands

-### Voir les logs de JupyterHub
+### View JupyterHub logs
 ```bash
 docker-compose logs -f jupyterhub
 ```

-### Voir tous les containers (hub + étudiants)
+### View all containers (hub + students)
 ```bash
 docker ps
 ```

-### Arrêter JupyterHub
+### Stop JupyterHub
 ```bash
 docker-compose down
 ```

-### Redémarrer JupyterHub (après modification du config)
+### Restart JupyterHub (after config modification)
 ```bash
 docker-compose restart jupyterhub
 ```

-### Reconstruire après modification du Dockerfile
+### Rebuild after Dockerfile modification
 ```bash
-# Pour l'image étudiants
+# For student image
 docker build -t jupyterhub-student:latest -f Dockerfile .
 docker-compose restart jupyterhub

-# Pour l'image hub
+# For hub image
 docker-compose up -d --build
 ```

-### Voir les logs d'un étudiant spécifique
+### View logs for a specific student
 ```bash
-docker logs jupyter-nom_utilisateur
+docker logs jupyter-username
 ```

-### Nettoyer après le TP
+### Clean up after lab
 ```bash
-# Arrêter et supprimer tous les containers
+# Stop and remove all containers
 docker-compose down

-# Supprimer les containers étudiants
+# Remove student containers
 docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f

-# Supprimer les volumes (ATTENTION : supprime les données étudiants)
+# Remove volumes (WARNING: deletes student data)
 docker volume ls | grep jupyterhub-user | awk '{print $2}' | xargs docker volume rm

-# Tout nettoyer (containers + volumes + réseau)
+# Clean everything (containers + volumes + network)
 docker-compose down -v
 docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
 docker volume prune -f
 ```

-## Gestion des données partagées
+## Managing Shared Data

-### Structure des dossiers pour chaque étudiant
+### Directory Structure for Each Student

-Chaque étudiant verra ces dossiers dans son JupyterLab :
- **`work/`** : Son espace personnel (persistant, privé)
- **`shared/`** : Espace partagé entre tous les étudiants (lecture/écriture)
- **`course/`** : Fichiers du cours (lecture seule, vous déposez les fichiers)
+Each student will see this directory structure in their JupyterLab (everything under `work/` is persistent):
+```
+work/                              # Personal workspace root (persistent)
+├── [student files]               # Their own files and notebooks
+├── R_packages/                   # Personal R packages (writable by student)
+├── shared/                       # Shared workspace (read/write, shared with all)
+└── course/                       # Course files (read-only, managed by admin)
+    ├── R_packages/               # Shared R packages (read-only, installed by prof)
+    ├── bin/                      # Shared executables (in PATH)
+    └── [course materials]        # Your course files
+```

-### Déposer des fichiers pour le cours
+**R Package Priority:**
+1. R checks `work/R_packages/` first (personal, writable)
+2. Then `work/course/R_packages/` (shared, read-only, installed by prof)
+3. Then system libraries

-Pour mettre des fichiers dans le dossier `course/` (accessible en lecture seule) :
+**Important:** Everything is under `work/`, so all student files are automatically saved in their persistent volume.
+
+### User Accounts
+
+**Admin Account:**
+- Username: `admin`
+- Password: `admin2025` (change in docker-compose.yml: `JUPYTERHUB_ADMIN_PASSWORD`)
+- Can write to `course/` directory
+
+**Student Accounts:**
+- Username: any name
+- Password: `metabar2025` (change in docker-compose.yml: `JUPYTERHUB_PASSWORD`)
+- Read-only access to `course/` directory
+
+### Installing R Packages (Admin Only)
+
+**From your Mac (recommended):**

 ```bash
-# Créer un dossier temporaire
+chmod +x install-r-packages-admin.sh
+
+# Install packages
+./install-r-packages-admin.sh reshape2 plotly knitr
+```
+
+This script:
+- Installs packages in the `course/R_packages/` directory
+- All students can use them (read-only)
+- No need to rebuild the image
+
+**From admin notebook:**
+
+Login as `admin` and create an R notebook:
+
+```r
+# Install packages in course/R_packages (admin only, available to all students)
+course_lib <- "/home/jovyan/work/course/R_packages"
+dir.create(course_lib, recursive = TRUE, showWarnings = FALSE)
+
+install.packages(c('reshape2', 'plotly', 'knitr'), 
+                 lib = course_lib,
+                 repos = 'http://cran.rstudio.com/')
+```
+
+Note: Admin account has write access to the course directory.
+
+**Students can also install their own packages:**
+
+Students can install packages in their personal `work/R_packages/`:
+
+```r
+# Install in personal library (each student has their own)
+install.packages(c('mypackage'))  # Will install in work/R_packages/
+```
+
+### Using R Packages (Students)
+
+Students simply load packages normally:
+```r
+library(reshape2)  # R checks: 1) work/R_packages/ 2) work/course/R_packages/ 3) system
+library(plotly)
+```
+
+R automatically searches in this order:
+1. Personal packages: `/home/jovyan/work/R_packages/` (R_LIBS_USER)
+2. Prof packages: `/home/jovyan/work/course/R_packages/` (R_LIBS_SITE)
+3. System packages
+
+### List Available Packages
+
+```r
+# List all available packages (personal + course + system)
+installed.packages()[,"Package"]
+
+# Check personal packages
+list.files("/home/jovyan/work/R_packages")
+
+# Check course packages (installed by prof)
+list.files("/home/jovyan/work/course/R_packages")
+```
+
+### Deposit Files for Course
+
+To put files in the `course/` directory (accessible read-only):
+
+```bash
+# Create a temporary directory
 mkdir -p ~/jupyterhub-tp/course-files

-# Copier vos fichiers dedans
-cp mes_notebooks.ipynb ~/jupyterhub-tp/course-files/
-cp mes_donnees.csv ~/jupyterhub-tp/course-files/
+# Copy your files into it
+cp my_notebooks.ipynb ~/jupyterhub-tp/course-files/
+cp my_data.csv ~/jupyterhub-tp/course-files/

-# Copier dans le volume Docker
+# Copy into Docker volume
 docker run --rm \
  -v jupyterhub-course:/target \
  -v ~/jupyterhub-tp/course-files:/source \
  alpine sh -c "cp -r /source/* /target/"
 ```

-### Accéder aux fichiers partagés entre étudiants
+### Access Shared Files Between Students

-Les étudiants peuvent collaborer via le dossier `shared/` :
+Students can collaborate via the `shared/` directory:

 ```python
-# Dans un notebook, pour lire un fichier partagé
+# In a notebook, to read a shared file
 import pandas as pd
-df = pd.read_csv('/home/jovyan/shared/donnees_groupe.csv')
+df = pd.read_csv('/home/jovyan/work/shared/group_data.csv')

-# Pour écrire un fichier partagé
-df.to_csv('/home/jovyan/shared/resultats_alice.csv')
+# To write a shared file
+df.to_csv('/home/jovyan/work/shared/alice_results.csv')
 ```

-### Récupérer les travaux des étudiants
+### Retrieve Student Work

 ```bash
-# Lister les volumes utilisateurs
+# List user volumes
 docker volume ls | grep jupyterhub-user

-# Copier les fichiers d'un étudiant spécifique
+# Copy files from a specific student
 docker run --rm \
  -v jupyterhub-user-alice:/source \
-  -v ~/rendus:/target \
+  -v ~/submissions:/target \
  alpine sh -c "cp -r /source/* /target/alice/"

-# Copier tous les travaux partagés
+# Copy all shared work
 docker run --rm \
  -v jupyterhub-shared:/source \
-  -v ~/rendus/shared:/target \
+  -v ~/submissions/shared:/target \
  alpine sh -c "cp -r /source/* /target/"
 ```

-## Gestion des utilisateurs
+## User Management

-### Option 1 : Liste d'utilisateurs prédéfinis
-Dans `jupyterhub_config.py`, décommentez et modifiez :
+### Option 1: Predefined User List
+In `jupyterhub_config.py`, uncomment and modify:
 ```python
-c.Authenticator.allowed_users = {'etudiant1', 'etudiant2', 'etudiant3'}
+c.Authenticator.allowed_users = {'student1', 'student2', 'student3'}
 ```

-### Option 2 : Autoriser tout le monde (pour tests)
-Par défaut, la configuration autorise n'importe quel utilisateur :
+### Option 2: Allow Everyone (for testing)
+By default, the configuration allows any user:
 ```python
 c.Authenticator.allow_all = True
 ```

-⚠️ **Attention** : DummyAuthenticator est UNIQUEMENT pour les tests locaux !
+⚠️ **Warning**: DummyAuthenticator is ONLY for local testing!

-## Vérification des kernels
+## Kernel Verification

-Une fois connecté, créez un nouveau notebook et vérifiez que vous avez accès à :
- **Python 3** (kernel par défaut)
- **R** (kernel R)
- **Bash** (kernel bash)
+Once logged in, create a new notebook and verify you have access to:
+- **Python 3** (default kernel)
+- **R** (R kernel)
+- **Bash** (bash kernel)

-## Personnalisation pour vos TP
+## Customization for Your Labs

-### Ajouter des packages R supplémentaires
-Modifiez le `Dockerfile` (avant `USER ${NB_UID}`) :
+### Add Additional R Packages
+Modify the `Dockerfile` (before `USER ${NB_UID}`):
 ```dockerfile
-RUN R -e "install.packages(c('votre_package'), repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages(c('your_package'), repos='http://cran.rstudio.com/')"
 ```

-Puis reconstruisez :
+Then rebuild:
 ```bash
 docker build -t jupyterhub-student:latest -f Dockerfile .
 docker-compose restart jupyterhub
 ```

-### Ajouter des packages Python
-Ajoutez dans le `Dockerfile` (avant `USER ${NB_UID}`) :
+### Add Python Packages
+Add to the `Dockerfile` (before `USER ${NB_UID}`):
 ```dockerfile
 RUN pip install numpy pandas matplotlib seaborn
 ```

-### Distribuer des fichiers aux étudiants
-Créez un dossier `files_tp/` et ajoutez dans le `Dockerfile` :
+### Distribute Files to Students
+Create a `files_lab/` directory and add to the `Dockerfile`:
 ```dockerfile
-COPY files_tp/ /home/${NB_USER}/tp/
-RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/tp
+COPY files_lab/ /home/${NB_USER}/lab/
+RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/lab
 ```

-### Changer le port (si 8000 est occupé)
-Modifiez dans `docker-compose.yml` :
+### Change Port (if 8000 is occupied)
+Modify in `docker-compose.yml`:
 ```yaml
 ports:
-  - "8001:8000"  # Accessible sur localhost:8001
+  - "8001:8000"  # Accessible on localhost:8001
 ```

-## Avantages de cette approche
+## Advantages of This Approach

-✅ **Tout en Docker** : Plus besoin d'installer Python/JupyterHub sur votre Mac  
-✅ **Portable** : Facile à déployer sur un autre Mac ou serveur  
-✅ **Isolé** : Pas de pollution de votre environnement système  
-✅ **Facile à nettoyer** : Un simple `docker-compose down` suffit  
-✅ **Reproductible** : Les étudiants auront exactement le même environnement
+✅ **Everything in Docker**: No need to install Python/JupyterHub on your Mac  
+✅ **Portable**: Easy to deploy on another Mac or server  
+✅ **Isolated**: No pollution of your system environment  
+✅ **Easy to Clean**: A simple `docker-compose down` is enough  
+✅ **Reproducible**: Students will have exactly the same environment

-## Dépannage
+## Troubleshooting

-**Erreur "Cannot connect to Docker daemon"** :
- Vérifiez qu'OrbStack est démarré
- Vérifiez que le socket existe : `ls -la /var/run/docker.sock`
+**Error "Cannot connect to Docker daemon"**:
+- Check that OrbStack is running
+- Verify the socket exists: `ls -la /var/run/docker.sock`

-**Les containers étudiants ne démarrent pas** :
- Vérifiez les logs : `docker-compose logs jupyterhub`
- Vérifiez que l'image étudiants existe : `docker images | grep jupyterhub-student`
+**Student containers don't start**:
+- Check logs: `docker-compose logs jupyterhub`
+- Verify student image exists: `docker images | grep jupyterhub-student`

-**Port 8000 déjà utilisé** :
- Changez le port dans `docker-compose.yml`
+**Port 8000 already in use**:
+- Change port in `docker-compose.yml`

-**Après modification du config, les changements ne sont pas pris en compte** :
+**After config modification, changes are not applied**:
 ```bash
 docker-compose restart jupyterhub
 ```

-**Je veux repartir de zéro** :
+**I want to start from scratch**:
 ```bash
 docker-compose down -v
 docker rmi jupyterhub-hub jupyterhub-student
-# Puis reconstruire tout
-```
+# Then rebuild everything
+./start-jupyterhub.sh
+```
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -8,19 +8,21 @@ services:
    ports:
      - "8888:8000"
    volumes:
-      # Accès au socket Docker pour spawner les containers étudiants
+      # Access to Docker socket to spawn student containers
      - /var/run/docker.sock:/var/run/docker.sock
-      # Persistance de la base de données JupyterHub
+      # JupyterHub database persistence
      - jupyterhub-data:/srv/jupyterhub
-      # Montage du fichier de config en direct (pour modifications faciles)
+      # Mount config file directly (for easy modifications)
      - ./jupyterhub_config.py:/srv/jupyterhub/jupyterhub_config.py:ro
    networks:
      - jupyterhub-network
    restart: unless-stopped
    environment:
-      # Mot de passe partagé pour tous les étudiants
+      # Shared password for all students
      JUPYTERHUB_PASSWORD: metabar2025
-      # Variables d'environnement optionnelles
+      # Admin password (for installing R packages)
+      JUPYTERHUB_ADMIN_PASSWORD: admin2025
+      # Optional environment variables
      DOCKER_NOTEBOOK_DIR: /home/jovyan/work

 networks:
@@ -31,4 +33,5 @@ networks:
 volumes:
  jupyterhub-data:
  jupyterhub-shared:
-  jupyterhub-course:
+  jupyterhub-course:
+  
--- a/install_packages.sh
+++ b/install_packages.sh
@@ -0,0 +1,74 @@
+#!/bin/bash
+
+# Script to install R packages in the course directory (admin only)
+# Usage: ./install-r-packages.sh package1 package2 package3
+
+set -e
+
+GREEN='\033[0;32m'
+BLUE='\033[0;34m'
+YELLOW='\033[1;33m'
+RED='\033[0;31m'
+NC='\033[0m'
+
+echo -e "${BLUE}📦 R Package Installer (Admin)${NC}"
+echo "================================"
+echo ""
+
+# Check if packages are provided
+if [ $# -eq 0 ]; then
+    echo -e "${RED}❌ Error: No packages specified${NC}"
+    echo ""
+    echo "Usage:"
+    echo "  ./install-r-packages.sh package1 package2 package3"
+    echo ""
+    echo "Example:"
+    echo "  ./install-r-packages.sh reshape2 plotly knitr"
+    exit 1
+fi
+
+# Build package list
+PACKAGES=$(IFS=,; echo "$*")
+R_PACKAGES=$(echo "$PACKAGES" | sed "s/,/', '/g")
+
+echo -e "${YELLOW}📋 Packages to install: ${R_PACKAGES}${NC}"
+echo ""
+
+# Create a temporary directory for installation
+TEMP_DIR=$(mktemp -d)
+echo -e "${BLUE}📁 Creating temporary directory: ${TEMP_DIR}${NC}"
+
+# Install packages in temporary directory
+echo -e "${BLUE}🔨 Installing R packages...${NC}"
+docker run --rm \
+    --user root \
+    -v "${TEMP_DIR}:/temp_packages" \
+    jupyterhub-student:latest \
+    R -e "install.packages(c('${R_PACKAGES}'), lib='/temp_packages', repos='http://cran.rstudio.com/')" || {
+    echo -e "${RED}❌ Failed to install packages${NC}"
+    rm -rf "${TEMP_DIR}"
+    exit 1
+}
+
+# Copy to course R packages directory
+echo ""
+echo -e "${BLUE}💾 Copying to course/R_packages...${NC}"
+docker run --rm \
+    -v jupyterhub-course:/target \
+    -v "${TEMP_DIR}:/source" \
+    alpine sh -c "mkdir -p /target/R_packages && cp -r /source/* /target/R_packages/"
+
+# Clean up
+rm -rf "${TEMP_DIR}"
+
+# List installed packages
+echo ""
+echo -e "${GREEN}✅ Installation complete!${NC}"
+echo ""
+echo -e "${BLUE}📦 Installed packages in work/course/R_packages:${NC}"
+docker run --rm \
+    -v jupyterhub-course:/course \
+    alpine ls -1 /course/R_packages/
+
+echo ""
+echo -e "${YELLOW}ℹ️  Students need to restart their R kernels to use new packages.${NC}"
--- a/jupyterhub_config.py
+++ b/jupyterhub_config.py
@@ -1,5 +1,100 @@
 import os

+# Base configuration
+c.JupyterHub.spawner_class = 'dockerspawner.DockerSpawner'
+
+# Enable debug logs
+c.JupyterHub.log_level = 'DEBUG'
+c.Spawner.debug = True
+
+# Docker image to use for student containers
+c.DockerSpawner.image = 'jupyterhub-student:latest'
+
+# Docker network (create with: docker network create jupyterhub-network)
+c.DockerSpawner.network_name = 'jupyterhub-network'
+
+# Connection to OrbStack Docker socket from the hub container
+c.DockerSpawner.client_kwargs = {'base_url': 'unix:///var/run/docker.sock'}
+
+# IMPORTANT: Internal URL for communication between containers
+# The hub container communicates with user containers via Docker network
+c.JupyterHub.hub_ip = '0.0.0.0'
+c.JupyterHub.hub_connect_ip = 'jupyterhub'
+
+# Network configuration for student containers
+c.DockerSpawner.use_internal_ip = True
+c.DockerSpawner.network_name = 'jupyterhub-network'
+c.DockerSpawner.extra_host_config = {'network_mode': 'jupyterhub-network'}
+
+# Remove containers after disconnection (optional, set to False to keep containers)
+c.DockerSpawner.remove = True
+
+# Container naming
+c.DockerSpawner.name_template = "jupyter-{username}"
+
+# Volume mounting to persist student data
+# Set root to work/ - everything is persistent
+notebook_dir = '/home/jovyan/work'
+c.DockerSpawner.notebook_dir = notebook_dir
+
+# Personal volume for each student + shared volumes under work/
+c.DockerSpawner.volumes = {
+    # Personal volume (persistent) - root directory
+    'jupyterhub-user-{username}': '/home/jovyan/work',
+    # Shared volume between all students - under work/
+    'jupyterhub-shared': '/home/jovyan/work/shared',
+    # Shared read-only volume for course files - under work/
+    'jupyterhub-course': {
+        'bind': '/home/jovyan/work/course',
+        'mode': 'ro'  # read-only
+    }
+}
+
+# Memory and CPU configuration (adjust according to your needs)
+c.DockerSpawner.mem_limit = '2G'
+c.DockerSpawner.cpu_limit = 1.0
+
+# User configuration - Simple password authentication for lab
+from jupyterhub.auth import DummyAuthenticator
+
+class SimplePasswordAuthenticator(DummyAuthenticator):
+    """Simple authenticator with a shared password for everyone"""
+    
+    def check_allowed(self, username, authentication=None):
+        """Check if user is allowed"""
+        if authentication is None:
+            return False
+        
+        provided_password = authentication.get('password', '')
+        
+        # Admin user with special password
+        if username == 'admin':
+            admin_password = os.environ.get('JUPYTERHUB_ADMIN_PASSWORD', 'admin2025')
+            return provided_password == admin_password
+        
+        # Regular students with shared password
+        student_password = os.environ.get('JUPYTERHUB_PASSWORD', 'metabar2025')
+        return provided_password == student_password
+
+c.JupyterHub.authenticator_class = SimplePasswordAuthenticator
+
+# To create a list of allowed users, uncomment and modify:
+# c.Authenticator.allowed_users = {'student1', 'student2', 'student3'}
+
+# Or allow any user with the correct password:
+c.Authenticator.allow_all = True
+
+# Admin configuration
+c.Authenticator.admin_users = {'admin'}
+
+# Listening port
+c.JupyterHub.bind_url = 'http://0.0.0.0:8000'
+
+# Timeout
+c.Spawner.start_timeout = 300
+c.Spawner.http_timeout = 120
+import os
+
 # Configuration de base
 c.JupyterHub.spawner_class = 'dockerspawner.DockerSpawner'

@@ -34,7 +129,7 @@ c.DockerSpawner.name_template = "jupyter-{username}"

 # Montage de volumes pour persister les données des étudiants
 # Définir la racine à /home/jovyan pour voir tous les dossiers
-notebook_dir = '/home/jovyan'
+notebook_dir = '/home/jovyan/work'
 c.DockerSpawner.notebook_dir = notebook_dir

 # Volume personnel pour chaque étudiant + volume partagé
@@ -42,10 +137,10 @@ c.DockerSpawner.volumes = {
    # Volume personnel (persistant) - monté dans work/
    'jupyterhub-user-{username}': '/home/jovyan/work',
    # Volume partagé entre tous les étudiants
-    'jupyterhub-shared': '/home/jovyan/shared',
+    'jupyterhub-shared': '/home/jovyan/work/shared',
    # Volume partagé en lecture seule pour les fichiers du cours (optionnel)
    'jupyterhub-course': {
-        'bind': '/home/jovyan/course',
+        'bind': '/home/jovyan/work/course',
        'mode': 'ro'  # read-only
    }
 }
@@ -54,26 +149,6 @@ c.DockerSpawner.volumes = {
 c.DockerSpawner.mem_limit = '2G'
 c.DockerSpawner.cpu_limit = 1.0

-# Configuration des utilisateurs - Mot de passe simple pour TP
-from jupyterhub.auth import DummyAuthenticator
-
-class SimplePasswordAuthenticator(DummyAuthenticator):
-    """Authentificateur simple avec un mot de passe partagé pour tous"""
-    
-    def check_allowed(self, username, authentication=None):
-        """Vérifie si l'utilisateur est autorisé"""
-        if authentication is None:
-            return False
-        
-        # Récupérer le mot de passe depuis la variable d'environnement
-        expected_password = os.environ.get('JUPYTERHUB_PASSWORD', 'metabar2025')
-        provided_password = authentication.get('password', '')
-        
-        # Vérifier le mot de passe
-        return provided_password == expected_password
-
-c.JupyterHub.authenticator_class = SimplePasswordAuthenticator
-
 # Pour créer une liste d'utilisateurs autorisés, décommentez et modifiez:
 # c.Authenticator.allowed_users = {'etudiant1', 'etudiant2', 'etudiant3'}

--- a/setup.sh
+++ b/setup.sh
@@ -1,30 +1,90 @@
-#!/usr/bin/env bash
-set -e
+#!/bin/bash

-# === Variables ===
-WORKDIR="$PWD"
-NETWORK="jupyterhub-net"
-HUB_IMAGE="jupyterhub-hub"
-USER_IMAGE="jupyter-tp-singleuser"
+# JupyterHub startup script for labs
+# Usage: ./start-jupyterhub.sh

-# === Préparation ===
-mkdir -p "$WORKDIR"
-cd "$WORKDIR"
+set -e  # Stop on error

-echo "[1/5] Création du réseau Docker..."
-docker network inspect $NETWORK >/dev/null 2>&1 || docker network create $NETWORK
+echo "🚀 Starting JupyterHub for Lab"
+echo "=============================="
+echo ""

-echo "[2/5] Construction des images..."
-docker build -t $USER_IMAGE -f Dockerfile .
-docker build -t $HUB_IMAGE -f Dockerfile.hub .
+# Colors for display
+GREEN='\033[0;32m'
+BLUE='\033[0;34m'
+YELLOW='\033[1;33m'
+NC='\033[0m' # No Color

-echo "[3/5] Lancement de JupyterHub..."
-docker compose up -d
+# Check we're in the right directory
+if [ ! -f "Dockerfile" ] || [ ! -f "docker-compose.yml" ]; then
+    echo "❌ Error: Run this script from the jupyterhub-tp/ directory"
+    exit 1
+fi

-echo "[4/5] Hub accessible sur http://localhost:8888"
-echo "      Login avec n'importe quel nom et mot de passe : metabar2025"
+# Stop existing containers
+echo -e "${BLUE}📦 Stopping existing containers...${NC}"
+docker-compose down 2>/dev/null || true

-echo "[5/5] Pour voir les utilisateurs actifs :"
-echo "      docker ps | grep jupyterhub-user"
+# Remove old student containers
+echo -e "${BLUE}🧹 Cleaning up student containers...${NC}"
+docker ps -aq --filter name=jupyter- | xargs -r docker rm -f 2>/dev/null || true

-echo "Terminé."
+# Build student image
+echo ""
+echo -e "${BLUE}🔨 Building student image...${NC}"
+docker build -t jupyterhub-student:latest -f Dockerfile .
+
+# Build hub image
+echo ""
+echo -e "${BLUE}🔨 Building JupyterHub image...${NC}"
+docker build -t jupyterhub-hub:latest -f Dockerfile.hub .
+
+# Create volumes if they don't exist
+echo ""
+echo -e "${BLUE}💾 Creating shared volumes...${NC}"
+docker volume create jupyterhub-shared 2>/dev/null || echo "  Volume jupyterhub-shared already exists"
+docker volume create jupyterhub-course 2>/dev/null || echo "  Volume jupyterhub-course already exists"
+
+# Start the stack
+echo ""
+echo -e "${BLUE}🚀 Starting JupyterHub...${NC}"
+docker-compose up -d
+
+# Wait for service to be ready
+echo ""
+echo -e "${YELLOW}⏳ Waiting for JupyterHub to start...${NC}"
+sleep 3
+
+# Check that container is running
+if docker ps | grep -q jupyterhub; then
+    echo ""
+    echo -e "${GREEN}✅ JupyterHub is running!${NC}"
+    echo ""
+    echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+    echo -e "${GREEN}🌐 JupyterHub available at: http://localhost:8888${NC}"
+    echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━"
+    echo ""
+    echo "📝 Password: metabar2025"
+    echo "👥 Students can connect with any username"
+    echo ""
+    echo "🔑 Admin account:"
+    echo "   Username: admin"
+    echo "   Password: admin2025"
+    echo ""
+    echo "📂 Each student will have access to:"
+    echo "   - work/                     : personal workspace (everything saved)"
+    echo "   - work/R_packages/          : personal R packages (writable)"
+    echo "   - work/shared/              : shared workspace"
+    echo "   - work/course/              : course files (read-only)"
+    echo "   - work/course/R_packages/   : shared R packages by prof (read-only)"
+    echo "   - work/course/bin/          : shared executables (in PATH)"
+    echo ""
+    echo "🔍 To view logs:    docker-compose logs -f jupyterhub"
+    echo "🛑 To stop:         docker-compose down"
+    echo ""
+else
+    echo ""
+    echo -e "${YELLOW}⚠️  JupyterHub container doesn't seem to be starting${NC}"
+    echo "Check logs with: docker-compose logs jupyterhub"
+    exit 1
+fi
Author	SHA1	Message	Date
Eric Coissac	64cb75e40a	Image multistage	2025-10-15 14:58:46 +02:00
Eric Coissac	60130d6b42	Ajout des obitools	2025-10-15 09:06:58 +02:00
Eric Coissac	21fc3a2c1f	Traduction en anglais des fichiers	2025-10-15 07:14:53 +02:00