Merge branch 'dev' into 'main'

Set of commits to be tagged v0.18.4

See merge request !19

Project.toml

 name = "LarvaTagger"
 uuid = "8b3b36f1-dfed-446e-8561-ea19fe966a4d"
 authors = ["François Laurent", "Institut Pasteur"]
-version = "0.18.3"
+version = "0.18.4"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"

recipes/Dockerfile

@@ -15,11 +15,12 @@ RUN apt-get update \
  && 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"
 
-RUN $JULIA_PROJECT/test/precompile.sh --shallow \
- && mv larvatagger.so /lib/ \
- && rm -rf $JULIA_PROJECT/test/data
+# RUN $JULIA_PROJECT/test/precompile.sh --shallow \
+#  && mv larvatagger.so /lib/ \
+#  && rm -rf $JULIA_PROJECT/test/data
 
-ENTRYPOINT ["/app/scripts/larvatagger", "-J/lib/larvatagger.so"]
+ENTRYPOINT ["/app/scripts/larvatagger"]
+#, "-J/lib/larvatagger.so"]
 
 
 FROM base AS prebuild

scripts/larvatagger

@@ -9,24 +9,26 @@
 currentdir=$(dirname "$(realpath "${BASH_SOURCE[0]}")")
 
 if [ "${1:0:2}" = "-J" ]; then
-cmd=$2
+jlargs="$1 "
+shift
 else
-cmd=$1
+jlargs=
 fi
+cmd=$1
 
 case $cmd in
 open)
   shift
   datapath=$1
   shift
-  args=
+  ltargs=
   if [ -n "$BACKENDS_PATH" ]; then
-    args="--backends=\"$BACKENDS_PATH\" $args"
+    ltargs="--backends=\"$BACKENDS_PATH\" $args"
   fi
   if [ -n "$OPEN_BROWSER" ]; then
-    args="--browser $args"
+    ltargs="--browser $args"
   fi
-  eval "\"$currentdir/larvatagger-gui.jl\" \"$datapath\" $args$@"
+  eval "\"$currentdir/larvatagger-gui.jl\" $jlargs\"$datapath\" $ltargs$@"
   ;;
 
 train|predict)
@@ -35,14 +37,14 @@ train|predict)
     shift
     backend=$1
     shift
-    "$currentdir/larvatagger-toolkit.jl" $cmd "$BACKENDS_PATH/$backend" $@
+    "$currentdir/larvatagger-toolkit.jl" $jlargs$cmd "$BACKENDS_PATH/$backend" $@
   else
-    "$currentdir/larvatagger-toolkit.jl" $@
+    "$currentdir/larvatagger-toolkit.jl" $jlargs$@
   fi
   ;;
 
 import|merge|--version|-V)
-  "$currentdir/larvatagger-toolkit.jl" $@
+  "$currentdir/larvatagger-toolkit.jl" $jlargs$@
   ;;
 
 *)

scripts/larvatagger.sh

@@ -158,7 +158,9 @@ fi
 RUN_ARGS="$RUN_ARGS --mount type=bind,src=\"$(realpath $instance)\",dst=/app/$backend/models/$(basename $instance)"
 done
 
-eval "exec $docker run $RUN_ARGS -i ${DOCKER_ARGS}\"$LARVATAGGER_IMAGE\" open \"/data/$file\" $TAGGER_ARGS $@"
+DOCKER_RUN="exec $docker run $RUN_ARGS -i ${DOCKER_ARGS}\"$LARVATAGGER_IMAGE\" open \"/data/$file\" $TAGGER_ARGS $@"
+echo $DOCKER_RUN
+eval $DOCKER_RUN
 ;;
 
 	import | merge)

src/LarvaTagger.jl

@@ -4,16 +4,18 @@ using PlanarLarvae, PlanarLarvae.Datasets, PlanarLarvae.Formats
 using ObservationPolicies
 using TidyObservables
 
+using Logging
+Logging.disable_logging(Logging.Warn) # prior to loading old libraries
 using JSServe, WGLMakie
 using JSServe: evaljs, onjs
 using Makie
+Logging.disable_logging(Logging.Debug) # restore default
 using Format
 using Colors
 using StaticArrays
 using Statistics
 using Observables
 using Meshes
-using Logging
 import Dates
 using OrderedCollections
 using Random