Mise à jour des dépendances R et amélioration du processus de build

Cette mise à jour apporte plusieurs améliorations : 
- Ajout d'un script R dédié pour l'installation des packages (install_R_packages.R)
- Refactorisation du Dockerfile pour une meilleure gestion des dépendances R et système
- Amélioration du script start-jupyterhub.sh avec gestion dynamique de docker-compose et vérification des timestamps
- Mise à jour de la documentation dans Readme.md pour refléter les nouvelles images Docker et les changements de structure
- Ajout de 'reserve' dans .gitignore

.gitignore

@@ -18,3 +18,4 @@ ncbitaxo_*
 Readme_files
 Readme.html
 tmp.*
+reserve

Readme.md

@@ -75,10 +75,13 @@ OBIJupyterHub
 ├── start-jupyterhub.sh                  - single entry point (build + render + start)
 ├── obijupyterhub                        - Docker images and stack definitions
 │   ├── docker-compose.yml
-│   ├── Dockerfile
+│   ├── install_R_packages.R             - An R script used to install all need R packages
-│   ├── Dockerfile.hub
+│   ├── Dockerfile                       - Image used by the students
+│   ├── Dockerfile.hub                   - Image for the jupyter hub
+│   ├── Dockerfile.builder               - Image for the builder
 │   └── jupyterhub_config.py
 ├── jupyterhub_volumes                   - data persisted on the host
+│   ├── builder                          - R packages cache for building lectures
 │   ├── course                           - read-only for students (notebooks, data, bin, R packages)
 │   ├── shared                           - shared read/write space for everyone
 │   ├── users                            - per-user persistent data
@@ -86,7 +89,7 @@ OBIJupyterHub
 └── web_src                              - Quarto sources for the course website
 ```
 
-Note: The `obijupyterhub/` directory also contains `Dockerfile.builder` which provides the build environment, the `tools/` directory contains utility scripts including `install_quarto_deps.R` for automatic R dependency detection, and `jupyterhub_volumes/builder/` stores cached R packages for faster builds.
+Note: The `tools/` directory contains utility scripts including `install_quarto_deps.R` for automatic R dependency detection.
 
 3) Prepare course materials (optional before first run):
 - Put notebooks, datasets, scripts, binaries, or PDFs for students under `jupyterhub_volumes/course/`. They will appear read-only at `/home/jovyan/work/course/`.

obijupyterhub/Dockerfile

@@ -19,37 +19,63 @@ RUN TEMP=. curl -L https://raw.githubusercontent.com/metabarcoding/obitools4/mas
     && cp $HOME/obitools-build/bin/* /usr/local/bin
 RUN ls -l /usr/local/bin
 
-
 # ---------- Stage 2 : image finale ----------
 FROM jupyter/base-notebook:latest
 
 USER root
 
 # Installer seulement les dépendances d'exécution (sans build-essential)
-RUN apt-get update && apt-get install -y \
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    # R et dépendances de base
     r-base \
-    libcurl4-openssl-dev libssl-dev libxml2-dev \
+    r-base-dev \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    libicu-dev \
+    zlib1g-dev \
+    # Polices et rendu graphique (indispensable pour ggplot2, ragg, etc.)
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libfontconfig1-dev \
+    libfreetype6-dev \
+    libpng-dev \
+    libtiff5-dev \
+    libjpeg-dev \
+    pandoc \
+    # Outils de compilation et gestion de versions
+    libgit2-dev \
+    cmake \
+    # Utilitaires systèmes déjà présents dans votre Dockerfile
     curl \
+    wget \
     git \
-    texlive-xetex texlive-fonts-recommended texlive-plain-generic \
+    vim \
-    ruby ruby-dev \
+    nano \
-    vim nano \
+    less \
+    gdebi-core \
+    ripgrep \
+    # Pour générer des PDF/rapports depuis R Markdown / Jupyter
+    texlive-xetex \
+    texlive-luatex \
+    texlive-fonts-recommended \
+    texlive-fonts-extra \
+    texlive-latex-extra \
+    texlive-plain-generic \
+    lmodern \
+    fonts-lmodern \
+    librsvg2-bin \
+    cm-super \
+    # Ruby (si vous en avez besoin pour autre chose)
+    ruby \
+    ruby-dev \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
 # Installer R et packages
-RUN R -e "install.packages(c('IRkernel','tidyverse','vegan','ade4','BiocManager','remotes','igraph'), \
+COPY install_R_packages.R /tmp/install_R_packages.R
-                             dependencies=TRUE, \
+RUN Rscript /tmp/install_R_packages.R --no-save --no-restore && \
-                             repos='http://cran.rstudio.com/')" && \
+    rm -rf /tmp/Rtmp* /tmp/install_R_packages.R
-    R -e "BiocManager::install('biomformat')" && \
-    R -e "remotes::install_github('metabaRfactory/metabaR')" && \
-    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBIUtils.git')" && \
-    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBITaxonomy.git')" && \
-    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBITools.git')" && \
-    R -e "remotes::install_git('https://forge.metabarcoding.org/obitools/ROBITaxonomy.git')" && \
-    R -e "remotes::install_git('https://forge.metabarcoding.org/MetabarcodingSchool/biodiversity-metrics.git')" && \
-    R -e "IRkernel::installspec(user = FALSE)" && \
-    rm -rf /tmp/Rtmp*
 
 # Installer les autres outils
 RUN pip install --no-cache-dir bash_kernel csvkit && \
@@ -57,9 +83,17 @@ RUN pip install --no-cache-dir bash_kernel csvkit && \
 
 RUN gem install youplot
 
+# Installation de Quarto (multi-arch)
+RUN ARCH=$(dpkg --print-architecture) && \
+    QUARTO_VERSION="1.8.27" && \
+    wget https://github.com/quarto-dev/quarto-cli/releases/download/v${QUARTO_VERSION}/quarto-${QUARTO_VERSION}-linux-${ARCH}.deb && \
+    gdebi --non-interactive quarto-${QUARTO_VERSION}-linux-${ARCH}.deb && \
+    rm quarto-${QUARTO_VERSION}-linux-${ARCH}.deb
+
 # 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}
+
 
 
 # Copier uniquement le binaire csvlens du builder

obijupyterhub/install_R_packages.R

@@ -0,0 +1,43 @@
+#!/usr/bin/env Rscript
+
+# Installer pak (lui-même en binaire si possible)
+install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
+pak::pkg_install("cli")
+
+# Détection automatique du système et installation de tous les paquets en binaire
+pak::pkg_install(c(
+  "IRkernel",
+  "tidyverse",
+  "vegan",
+  "ade4",
+  "BiocManager",
+  "remotes",
+  "igraph",
+  "Rdpack"
+))
+
+# ------------------------------------------------------------
+# Paquets Bioconductor (toujours via BiocManager)
+# ------------------------------------------------------------
+pak::pkg_install("bioc::biomformat")
+
+# ------------------------------------------------------------
+# Paquets depuis GitHub / dépôts git
+# ------------------------------------------------------------
+pak::pkg_install("metabaRfactory/metabaR")
+pak::pkg_install("git::https://forge.metabarcoding.org/obitools/ROBIUtils.git")
+pak::pkg_install("git::https://forge.metabarcoding.org/obitools/ROBITaxonomy.git")
+pak::pkg_install("git::https://forge.metabarcoding.org/obitools/ROBITools.git")
+pak::pkg_install("git::https://forge.metabarcoding.org/MetabarcodingSchool/biodiversity-metrics.git")
+
+# ------------------------------------------------------------
+# Installation du noyau Jupyter pour IRkernel
+# ------------------------------------------------------------
+# Si on est root -> installation système, sinon -> user
+if (Sys.info()["user"] == "root") {
+  IRkernel::installspec(user = FALSE)
+} else {
+  IRkernel::installspec(user = TRUE)
+}
+
+cat("\n✅ Tous les paquets R ont été installés avec succès.\n")

start-jupyterhub.sh

@@ -35,6 +35,10 @@ Options:
 EOF
 }
 
+
+dockercompose=$(which docker-compose || echo 'docker compose')
+
+
 while [[ $# -gt 0 ]]; do
     case "$1" in
         --no-build|--offline) NO_BUILD=true ;;
@@ -78,31 +82,57 @@ if [ ! -f "Dockerfile" ] || [ ! -f "docker-compose.yml" ]; then
     exit 1
 fi
 
+get_file_timestamp() {
+    local file="$1"
+    case "$(uname -s)" in
+        Linux)
+            stat -c %Y "$file"
+            ;;
+        Darwin)
+            # BSD stat : -f pour format, %m = timestamp modification
+            stat -f %m "$file"
+            ;;
+        *)
+            echo "Système non supporté" >&2
+            return 1
+            ;;
+    esac
+}
+
 check_if_image_needs_rebuild() {
     local image_name="$1"
     local dockerfile="$2"
-    
+
+    echo -e "${BLUE}Checking image ${image_name}...${NC}"
+
     # Check if image exists
     if ! docker image inspect "$image_name" >/dev/null 2>&1; then
+        echo -e "${YELLOW}Docker image ${image_name} doesn't exist.${NC}"
         return 0  # Need to build (image doesn't exist)
     fi
-    
+
     # If force rebuild, always rebuild
     if $FORCE_REBUILD; then
+        echo -e "${YELLOW}Docker image build is forced.${NC}"
         return 0  # Need to rebuild
     fi
-    
+
     # Compare Dockerfile modification time with image creation time
     if [ -f "$dockerfile" ]; then
-        local dockerfile_mtime=$(stat -c %Y "$dockerfile" 2>/dev/null || echo 0)
+        local dockerfile_mtime=$(get_file_timestamp "$dockerfile" 2>/dev/null || echo 0)
-        local image_created=$(docker image inspect "$image_name" --format='{{.Created}}' 2>/dev/null | sed 's/\.000000000//' | xargs -I {} date -d "{}" +%s 2>/dev/null || echo 0)
+        local image_created=$(docker image inspect "$image_name" --format='{{.Created}}' 2>/dev/null \
-        
+              | sed -E 's/\.[0-9]+//' \
+              | (read d; if [[ "$(uname -s)" == "Darwin" ]]; then date -ju -f "%Y-%m-%dT%H:%M:%S" "${d%Z}" +%s; else date -d "$d" +%s; fi) 2>/dev/null || echo 0)
+
+        echo -e "${BLUE}Docker image ${image_name} created at: ${image_created}.${NC}"
+        echo -e "${BLUE}Docker file ${dockerfile} modified at: ${dockerfile_mtime}.${NC}"
+
         if [ "$dockerfile_mtime" -gt "$image_created" ]; then
             echo -e "${YELLOW}Dockerfile is newer than image, rebuild needed${NC}"
             return 0  # Need to rebuild
         fi
     fi
-    
+
     return 1  # No need to rebuild
 }
 
@@ -112,7 +142,7 @@ build_builder_image() {
         if $FORCE_REBUILD; then
             build_flag+=(--no-cache)
         fi
-        
+
         echo ""
         echo -e "${BLUE}Building builder image...${NC}"
         docker build "${build_flag[@]}" -t "$BUILDER_IMAGE" -f Dockerfile.builder .
@@ -136,7 +166,7 @@ run_in_builder() {
 
 stop_stack() {
     echo -e "${BLUE}Stopping existing containers...${NC}"
-    docker-compose down 2>/dev/null || true
+    ${dockercompose} down 2>/dev/null || true
 
     echo -e "${BLUE}Cleaning up student containers...${NC}"
     docker ps -aq --filter name=jupyter- | xargs -r docker rm -f 2>/dev/null || true
@@ -237,7 +267,7 @@ build_website() {
 start_stack() {
     echo ""
     echo -e "${BLUE}Starting JupyterHub...${NC}"
-    docker-compose up -d --remove-orphans
+    ${dockercompose} up -d --remove-orphans
 
     echo ""
     echo -e "${YELLOW}Waiting for JupyterHub to start...${NC}"
@@ -268,13 +298,13 @@ print_success() {
         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 view logs:    ${dockercompose} logs -f jupyterhub"
-        echo "To stop:         docker-compose down"
+        echo "To stop:         ${dockercompose} down"
         echo ""
     else
         echo ""
         echo -e "${YELLOW}JupyterHub container doesn't seem to be starting${NC}"
-        echo "Check logs with: docker-compose logs jupyterhub"
+        echo "Check logs with: ${dockercompose} logs jupyterhub"
         exit 1
     fi
 }