Image multistage

2025-10-15 14:08:52 +02:00
parent 60130d6b42
commit 64cb75e40a
5 changed files with 86 additions and 90 deletions
--- a/58
+++ b/58
@@ -1,47 +1,49 @@
-FROM jupyter/base-notebook:latest
+# ---------- Stage 1 : builder ----------
+FROM jupyter/base-notebook:latest AS builder

 USER root

-# Install R and system dependencies
+# 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 \
-    git \
-    build-essential \
-    curl \
+    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/*

-# Install R kernel for Jupyter (as 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/')"

-# Install some useful R packages for labs
-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

-# Install bash kernel (as root also)
-RUN pip install bash_kernel && \
-    python -m bash_kernel.install --sys-prefix
-
-# Install obitools4 (written in Go)
+# Install obitools4
 RUN curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/master/install_obitools.sh | bash

 # Install csvkit
 RUN pip install csvkit

-# Install csvlens
-RUN curl https://sh.rustup.rs -sSf | bash -s -- -y \
-    && . $HOME/.cargo/env \
-    && cargo install csvlens \
-    && mv $HOME/.cargo/bin/csvlens /usr/local/bin/ \
-    && rm -rf $HOME/.cargo $HOME/.rustup
+# Install csvlens via Rust
+RUN curl https://sh.rustup.rs -sSf | bash -s -- -y && \
+    . $HOME/.cargo/env && \
+    cargo install csvlens

-# Create necessary directories with proper permissions
+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} 

-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/Readme.md
+++ b/Readme.md
@@ -47,7 +47,7 @@ chmod +x start-jupyterhub.sh

 ### 5. Access JupyterHub

-Open your browser and go to: **http://localhost:8000**
+Open your browser and go to: **http://localhost:8888**

 You can log in with any username and password: `metabar2025`

@@ -109,11 +109,24 @@ docker volume prune -f

 ### Directory Structure for Each Student

-Each student will see these directories in their JupyterLab:
- **`work/`** : Personal workspace (persistent, private)
- **`shared/`** : Shared workspace between all students (read/write)
- **`course/`** : Course files (read-only, you deposit files)
-  - **`course/R_packages/`** : Shared R packages (read-only for students, only admin can install)
+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
+```
+
+**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
+
+**Important:** Everything is under `work/`, so all student files are automatically saved in their persistent volume.

 ### User Accounts

@@ -148,8 +161,8 @@ This script:
 Login as `admin` and create an R notebook:

 ```r
-# Install packages in course directory (admin only)
-course_lib <- "/home/jovyan/course/R_packages"
+# 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'), 
@@ -159,24 +172,39 @@ install.packages(c('reshape2', 'plotly', 'knitr'),

 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)  # Loads from course/R_packages/ automatically
+library(reshape2)  # R checks: 1) work/R_packages/ 2) work/course/R_packages/ 3) system
 library(plotly)
 ```

-R automatically finds packages in `/home/jovyan/course/R_packages/` thanks to the `R_LIBS_USER` environment variable.
+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
+# List all available packages (personal + course + system)
 installed.packages()[,"Package"]

-# Or check course packages specifically
-list.files("/home/jovyan/course/R_packages")
+# 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
@@ -205,10 +233,10 @@ Students can collaborate via the `shared/` directory:
 ```python
 # In a notebook, to read a shared file
 import pandas as pd
-df = pd.read_csv('/home/jovyan/shared/group_data.csv')
+df = pd.read_csv('/home/jovyan/work/shared/group_data.csv')

 # To write a shared file
-df.to_csv('/home/jovyan/shared/alice_results.csv')
+df.to_csv('/home/jovyan/work/shared/alice_results.csv')
 ```

 ### Retrieve Student Work
--- a/install_packages.sh
+++ b/install_packages.sh
@@ -50,9 +50,9 @@ docker run --rm \
    exit 1
 }

-# Copy to course volume
+# Copy to course R packages directory
 echo ""
-echo -e "${BLUE}💾 Copying to course volume...${NC}"
+echo -e "${BLUE}💾 Copying to course/R_packages...${NC}"
 docker run --rm \
    -v jupyterhub-course:/target \
    -v "${TEMP_DIR}:/source" \
@@ -65,7 +65,7 @@ rm -rf "${TEMP_DIR}"
 echo ""
 echo -e "${GREEN}✅ Installation complete!${NC}"
 echo ""
-echo -e "${BLUE}📦 Installed packages in course/R_packages:${NC}"
+echo -e "${BLUE}📦 Installed packages in work/course/R_packages:${NC}"
 docker run --rm \
    -v jupyterhub-course:/course \
    alpine ls -1 /course/R_packages/
--- a/jupyterhub_config.py
+++ b/jupyterhub_config.py
@@ -54,23 +54,6 @@ c.DockerSpawner.volumes = {
 c.DockerSpawner.mem_limit = '2G'
 c.DockerSpawner.cpu_limit = 1.0

-# Environment variables for student containers
-c.DockerSpawner.environment = {
-    # R package library in read-only course directory under work/
-    'R_LIBS_USER': '/home/jovyan/work/R_packages',
-    'R_LIBS_SITE': '/home/jovyan/work/course/R_packages',
-     # Path to R packages in read-only
-    'PATH': '/home/jovyan/work/course/bin:${PATH}'
-}
-
-# Create user R lib directory 
-#async def create_user_hierarchy(spawner):
-#    cmd = "mkdir -p /home/jovyan/work/R_packages && chown jovyan:jovyan /home/jovyan/work/R_packages"
-#    spawner.extra_create_kwargs.update({'command': f"/bin/bash -c '{cmd} && start-notebook.sh'"})
-
-#c.Spawner.pre_spawn_hook = create_user_r_libs
-
-
 # User configuration - Simple password authentication for lab
 from jupyterhub.auth import DummyAuthenticator

@@ -166,26 +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
@@ -72,9 +72,12 @@ if docker ps | grep -q jupyterhub; then
    echo "   Password: admin2025"
    echo ""
    echo "📂 Each student will have access to:"
-    echo "   - work/        : personal workspace (everything here is saved)"
-    echo "   - work/shared/ : shared workspace"
-    echo "   - work/course/ : course files (read-only)"
+    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"