MetabarcodingSchool/OBIJupyterHub
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🔧 Add selective image rebuild flags and enhance R dependency scanning

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- Added --rebuild-builder, -student, hub flags to start-jupyterhub.sh for granular Docker rebuilds
- Updated check_if_image_needs_rebuild to accept per-image force flag and propagate no-cache option
- Added libuv1-dev dependency in Dockerfile.builder (likely for quarto or R runtime)
- Rewrote install_quarto_deps.R to:
a) Manually parse library()/require() and remotes::install_git/github calls
b) Distinguish between quarto-required packages (must reside in persistent target_lib)
c), CRAN and git/github dependencies
d) Install with robust error handling, skipping unavailable packages
- Removed dependency on attachment package for scanning
This commit is contained in:
Eric Coissac
2026-04-30 18:24:35 +02:00
parent 7075b3f52b
commit 9484857d9a
3 changed files with 137 additions and 40 deletions
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start-jupyterhub.sh
+27 -14
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@@ -20,6 +20,9 @@ FORCE_REBUILD=false
STOP_SERVER=false
UPDATE_LECTURES=false
BUILD_OBIDOC=false
REBUILD_BUILDER=false
REBUILD_STUDENT=false
REBUILD_HUB=false
usage() {
cat <<EOF
@@ -27,7 +30,10 @@ Usage: ./start-jupyterhub.sh [options]
Options:
--no-build | --offline Skip Docker image builds (use existing images)
--force-rebuild Rebuild images without cache
--force-rebuild Rebuild all images without cache
--rebuild-builder Force rebuild the builder image only
--rebuild-student Force rebuild the student image only
--rebuild-hub Force rebuild the JupyterHub image only
--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 rebuild of obidoc documentation
@@ -43,6 +49,9 @@ while [[ $# -gt 0 ]]; do
case "$1" in
--no-build|--offline) NO_BUILD=true ;;
--force-rebuild) FORCE_REBUILD=true ;;
--rebuild-builder) REBUILD_BUILDER=true ;;
--rebuild-student) REBUILD_STUDENT=true ;;
--rebuild-hub) REBUILD_HUB=true ;;
--stop-server) STOP_SERVER=true ;;
--update-lectures) UPDATE_LECTURES=true ;;
--build-obidoc) BUILD_OBIDOC=true ;;
@@ -102,6 +111,7 @@ get_file_timestamp() {
check_if_image_needs_rebuild() {
local image_name="$1"
local dockerfile="$2"
local force="${3:-false}"
echo -e "${BLUE}Checking image ${image_name}...${NC}"
@@ -111,8 +121,8 @@ check_if_image_needs_rebuild() {
return 0 # Need to build (image doesn't exist)
fi
# If force rebuild, always rebuild
if $FORCE_REBUILD; then
# If force rebuild (global or per-image), always rebuild
if $FORCE_REBUILD || $force; then
echo -e "${YELLOW}Docker image build is forced.${NC}"
return 0 # Need to rebuild
fi
@@ -137,9 +147,9 @@ check_if_image_needs_rebuild() {
}
build_builder_image() {
if check_if_image_needs_rebuild "$BUILDER_IMAGE" "Dockerfile.builder"; then
if check_if_image_needs_rebuild "$BUILDER_IMAGE" "Dockerfile.builder" "$REBUILD_BUILDER"; then
local build_flag=()
if $FORCE_REBUILD; then
if $FORCE_REBUILD || $REBUILD_BUILDER; then
build_flag+=(--no-cache)
fi
@@ -178,25 +188,28 @@ build_images() {
return
fi
local build_flag=()
if $FORCE_REBUILD; then
build_flag+=(--no-cache)
fi
# Check and build student image
if check_if_image_needs_rebuild "jupyterhub-student:latest" "Dockerfile"; then
if check_if_image_needs_rebuild "jupyterhub-student:latest" "Dockerfile" "$REBUILD_STUDENT"; then
local student_flag=()
if $FORCE_REBUILD || $REBUILD_STUDENT; then
student_flag+=(--no-cache)
fi
echo ""
echo -e "${BLUE}Building student image...${NC}"
docker build "${build_flag[@]}" -t jupyterhub-student:latest -f Dockerfile .
docker build "${student_flag[@]}" -t jupyterhub-student:latest -f Dockerfile .
else
echo -e "${BLUE}Student image is up to date, skipping build.${NC}"
fi
# Check and build JupyterHub image
if check_if_image_needs_rebuild "jupyterhub-hub:latest" "Dockerfile.hub"; then
if check_if_image_needs_rebuild "jupyterhub-hub:latest" "Dockerfile.hub" "$REBUILD_HUB"; then
local hub_flag=()
if $FORCE_REBUILD || $REBUILD_HUB; then
hub_flag+=(--no-cache)
fi
echo ""
echo -e "${BLUE}Building JupyterHub image...${NC}"
docker build "${build_flag[@]}" -t jupyterhub-hub:latest -f Dockerfile.hub .
docker build "${hub_flag[@]}" -t jupyterhub-hub:latest -f Dockerfile.hub .
else
echo -e "${BLUE}JupyterHub image is up to date, skipping build.${NC}"
fi