Merge branch 'dev' into 'main'

Set of commits to be tagged v0.16.1

Closes #121 and #122

See merge request !10

Project.toml

 name = "LarvaTagger"
 uuid = "8b3b36f1-dfed-446e-8561-ea19fe966a4d"
 authors = ["François Laurent", "Institut Pasteur"]
-version = "0.16"
+version = "0.16.1"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"

recipes/README.md

@@ -163,7 +163,7 @@ docker pull flaur/larvatagger
 ```
 
 Beware that images that ship with backends are relatively large files (>5GB on disk).
-If you are not interested in automatic tagging, use the `flaur/larvatagger:0.16-standalone` image instead.
+If you are not interested in automatic tagging, use the `flaur/larvatagger:0.16.1-standalone` image instead.
 
 ### Upgrading
 

scripts/larvatagger.sh

@@ -22,6 +22,10 @@ for _ in $(seq $#); do
       shift
       ;;
     *)
+      if [ "$1" = "--no-cache" ]; then
+        # --no-cache is default for build since 0.16.1
+        no_cache=1
+      fi
       # note: if DOCKER_ARGS is externally defined, it must end with an explicit space
       DOCKER_ARGS="${DOCKER_ARGS}$1 "
       shift
@@ -78,12 +82,15 @@ DOCKER_ARGS="--build-arg BACKEND=${1:15} $DOCKER_ARGS"; shift
 TARGET=backend
 elif [ "$1" = "--no-cache" ]; then
 echo "Deprecation warning: argument $1 should now be passed before build"
-DOCKER_ARGS="--no-cache $DOCKER_ARGS"; shift
+shift
 else
 echo "argument not supported: $1"; shift
 exit 1
 fi
 done
+if [ -z "$no_cache" ]; then
+  DOCKER_ARGS="--no-cache $DOCKER_ARGS"
+fi
 DOCKER_ARGS="--target $TARGET $DOCKER_ARGS"
 if [ "$BUILD" == "--dev" ]; then
 if ! [[ "$LARVATAGGER_IMAGE" == *:* ]]; then LARVATAGGER_IMAGE="${LARVATAGGER_IMAGE}:dev"; fi
@@ -204,8 +211,14 @@ eval $DOCKER_RUN
 
 	predict)
 
+if [ "$(basename "$(dirname "$1")")" = "**" ]; then
+parentdir=$(cd "$(dirname "$(dirname "$1")")"; pwd -P)
+data_file=$(basename "$(dirname "$1")")/$(basename "$1")
+else
 parentdir=$(cd "$(dirname "$1")"; pwd -P)
-data_file=$(basename "$1"); shift
+data_file=$(basename "$1")
+fi
+shift
 
 RUN_ARGS="$RUN_ARGS -v \"$parentdir\":/data"
 

src/cli_toolkit.jl

@@ -3,7 +3,7 @@ module Toolkit
 using DocOpt
 using Pkg
 using OrderedCollections
-using PlanarLarvae, PlanarLarvae.Datasets, PlanarLarvae.Formats
+using PlanarLarvae, PlanarLarvae.Datasets, PlanarLarvae.Formats, PlanarLarvae.Dataloaders
 
 include("Taggers.jl")
 using .Taggers
@@ -191,10 +191,14 @@ function main(args=ARGS; exit_on_error=true)
             if endswith(datapath, ".txt")
                 # assume that the file lists paths to data files to be processed;
                 # in this case, the path to the txt file is not relevant
+                @info "The listed data file paths are expected to be relative to current directory" cwd=pwd()
                 pwd()
             else
                 dirname(datapath)
             end
+        elseif occursin("*", datapath)
+            repository = Dataloaders.Repository(datapath)
+            repository.root
         else
             datapath
         end

src/files.jl

@@ -408,7 +408,7 @@ function explicit_editions_needed(controller, editiontag)
     file = preload(originalfile)
     if file isa Formats.JSONLabels
         Formats.load!(file)
-        return haskey(file.run, :labels)
+        return haskey(file.run.attributes, :labels)
     elseif file isa Formats.Trxmat
         return true
     else