reintroducing system image to get around with executable stack issues

recipes/Dockerfile

-FROM julia:1.9.0-bullseye AS base
+FROM julia:1.9.1-bookworm AS base
 
 ARG PROJECT_DIR=/app
 ARG BRANCH=main
@@ -12,11 +12,14 @@ RUN apt-get update \
  && git clone --depth 1 --no-tags --single-branch -b $BRANCH https://gitlab.pasteur.fr/nyx/larvatagger.jl "$JULIA_PROJECT" \
  && rm -rf "$JULIA_PROJECT/.git" \
  && julia -e 'using Pkg; try Pkg.rm("TaggingBackends"); catch end; Pkg.instantiate()' \
- && ln -s "$JULIA_PROJECT/scripts/larvatagger.jl" /bin \
+ && ln -s "$JULIA_PROJECT/scripts/larvatagger" /bin \
  && mkdir -p "$JULIA_DEPOT_PATH/logs" && rm -f "$JULIA_DEPOT_PATH/logs/manifest_usage.toml" && ln -s /dev/null "$JULIA_DEPOT_PATH/logs/manifest_usage.toml"
 
-ENTRYPOINT ["larvatagger.jl"]
-#, "-J/lib/larvatagger.so"]
+RUN $JULIA_PROJECT/test/precompile.sh --shallow \
+ && mv larvatagger.so /lib/ \
+ && rm -rf $JULIA_PROJECT/test/data
+
+ENTRYPOINT ["larvatagger", "-J/lib/larvatagger.so"]
 
 
 FROM base AS prebuild
@@ -24,7 +27,7 @@ FROM base AS prebuild
 ENV PIP_DISABLE_PIP_VERSION_CHECK=1 \
     PIP_NO_CACHE_DIR=1 \
     POETRY_VIRTUALENVS_IN_PROJECT=1 \
-    POETRY_VERSION=1.2.0
+    POETRY_VERSION=1.5.1
 
 RUN apt-get update \
  && apt-get install --no-install-recommends -y python3-dev python3-pip \

scripts/larvatagger.jl → scripts/larvatagger

@@ -8,6 +8,12 @@
 
 currentdir=$(dirname "$(realpath "${BASH_SOURCE[0]}")")
 
+if [ "${1:0:2}" = "-J" ]; then
+cmd=$2
+else
+cmd=$1
+fi
+
 case $1 in
 open)
   shift
@@ -20,16 +26,16 @@ import|merge|train|predict|--version|-V)
 
 *)
   cat << "EOT"
-LarvaTagger.jl
+LarvaTagger
 
 Usage:
-  larvatagger.jl open <file-path> [--backends=<path>] [--port=<number>] [--quiet] [--viewer] [--browser] [--manual-label=<label>]
-  larvatagger.jl import <input-path> [<output-file>] [--id=<id>] [--framerate=<fps>] [--pixelsize=<μm>] [--overrides=<comma-separated-list>] [--default-label=<label>] [--manual-label=<label>] [--decode] [--copy-labels]
-  larvatagger.jl train <backend-path> <data-path> <model-instance> [--pretrained-model=<instance>] [--labels=<comma-separated-list>] [--sample-size=<N>] [--balancing-strategy=<strategy>] [--class-weights=<csv>] [--manual-label=<label>] [--layers=<N>] [--iterations=<N>] [--seed=<seed>]
-  larvatagger.jl predict <backend-path> <model-instance> <data-path> [--output=<filename>] [--make-dataset] [--skip-make-dataset] [--data-isolation]
-  larvatagger.jl merge <input-path> <input-file> [<output-file>] [--manual-label=<label>] [--decode]
-  larvatagger.jl -V | --version
-  larvatagger.jl -h | --help
+  larvatagger open <file-path> [--backends=<path>] [--port=<number>] [--quiet] [--viewer] [--browser] [--manual-label=<label>]
+  larvatagger import <input-path> [<output-file>] [--id=<id>] [--framerate=<fps>] [--pixelsize=<μm>] [--overrides=<comma-separated-list>] [--default-label=<label>] [--manual-label=<label>] [--decode] [--copy-labels]
+  larvatagger train <backend-path> <data-path> <model-instance> [--pretrained-model=<instance>] [--labels=<comma-separated-list>] [--sample-size=<N>] [--balancing-strategy=<strategy>] [--class-weights=<csv>] [--manual-label=<label>] [--layers=<N>] [--iterations=<N>] [--seed=<seed>]
+  larvatagger predict <backend-path> <model-instance> <data-path> [--output=<filename>] [--make-dataset] [--skip-make-dataset] [--data-isolation]
+  larvatagger merge <input-path> <input-file> [<output-file>] [--manual-label=<label>] [--decode]
+  larvatagger -V | --version
+  larvatagger -h | --help
 
 Options:
   -h --help            Show this screen.