diff --git a/Project.toml b/Project.toml index 9d6f12c1137bd1f09584dd4e1e8028942745784a..7578ac2fb8e7b080fbc9d0f1b7a426f38e8ff1a3 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ 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" diff --git a/recipes/Dockerfile b/recipes/Dockerfile index f52fe0e29a60577e1a60844e16d33dee7ccc7aad..d32d5f099714a92d387127d8cbc3d50fc81f8674 100644 --- a/recipes/Dockerfile +++ b/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 $JULIA_PROJECT/test/data -ENTRYPOINT ["/app/scripts/larvatagger", "-J/lib/larvatagger.so"] +ENTRYPOINT ["/app/scripts/larvatagger"] +#, "-J/lib/larvatagger.so"] FROM base AS prebuild diff --git a/scripts/larvatagger b/scripts/larvatagger index 91c4d7f2df592049367abc46c40ab0d0de2ebf72..db34a6ccdfeaa2001095bb07d9ec88d562b1fda7 100755 --- a/scripts/larvatagger +++ b/scripts/larvatagger @@ -9,24 +9,26 @@ currentdir=$(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" $jlargs$@ ;; *) diff --git a/scripts/larvatagger.sh b/scripts/larvatagger.sh index 3222537602cecfdee7015b6f0c38f64c21d026b6..a261c70bdf86db7854c25d1e7399a0d8c61f341c 100755 --- a/scripts/larvatagger.sh +++ b/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) diff --git a/src/LarvaTagger.jl b/src/LarvaTagger.jl index 337a0e34b730e13913282b2b9573437d5405a88c..b3484f945e8f30276e0fd401583c7cc814e09862 100644 --- a/src/LarvaTagger.jl +++ b/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