fix: type error in cli argument handling

src/Taggers.jl

@@ -227,7 +227,7 @@ function parsekwargs!(args, kwargs)
 end
 
 function run(tagger, switch, kwargs, extra...)
-    args = ["--model-instance", tagger.model_instance]
+    args = Any["--model-instance", tagger.model_instance]
     for (p, v) in pairs(extra)
         if !isnothing(v)
             push!(args, p)

test/deploy_and_test.sh

@@ -10,22 +10,21 @@
 # * LOCAL_SCENARII: can be set to 1 to overwrite LarvaTagger.jl's test/scenarii.sh file
 #   with the scenarii.sh file that comes along the present script (same directory)
 # * LAUNCHER: default is "srun" if Slurm is available, otherwise nothing
-# * JULIA_PROJECT: where to find PyCall (do not modify)
 
 # Example on Maestro (GPU-accelerated):
 #   SLURM_OPTS='-p dbc_pmo -q dbc -c 4' JULIA_THREADS=4 ./deploy_and_test.sh
 # or (CPU-only):
 #   SLURM_OPTS='-p dedicated -q fast -c 16' JULIA_THREADS=16 ./deploy_and_test.sh
 
-if [ -n "$1" ] && [ "$1" = "-f" ] || [ "$1" = "--force" ]; then
-  rm -rf LarvaTagger
-elif [ -d LarvaTagger ]; then
-  echo "\`$0\` needs to make a local LarvaTagger directory"
-  echo "but this directory already exists."
-  echo "Run \`$0 --force\` or pick another location."
+if ! [ -f scripts/install.sh ]; then
+  echo "Call `basename $0` from the project's root directory:"
+  echo "    test/deploy_and_test.sh"
   exit 1
 fi
 
+scripts/install.sh --uninstall
+scripts/install.sh --with-backend --experimental
+
 #############
 ## Maestro ##
 #############
@@ -33,13 +32,6 @@ fi
 # SSL verification can be disabled for git clone to work:
 #   export GIT_SSL_NO_VERIFY=true
 
-if ! julia -v &> /dev/null; then
-  # do NOT use juliaup to install Julia
-  module load Python &> /dev/null # Maestro
-  python3 -m pip install jill
-  python3 -m jill install -v 1.10.0 -c
-fi
-
 # h5diff (for tests) on Maestro
 if ! h5diff -V &> /dev/null; then
   module load hdf5 &> /dev/null
@@ -60,68 +52,39 @@ fi
 #############
 
 CURDIR=$(pwd)
-
-mkdir -p LarvaTagger && cd $_
+LTROOT=$HOME/.local/share/larvatagger/LarvaTagger.jl
 
 # shunit2 is for tests specifically
 if [ -z "$(which shunit2)" ]; then
-  git clone -c advice.detachedHead=false -b v2.1.8 https://github.com/kward/shunit2
+  (cd "$LTROOT/test" && \
+    git clone -c advice.detachedHead=false -b v2.1.8 https://github.com/kward/shunit2)
 fi
 
-## comment out the below line to build a development environment
-#CLONE_OPTS=" --depth 1 --no-tags --single-branch -b dev"
-#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/planarlarvae.jl PlanarLarvae
-#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/LarvaTagger.jl
-BRANCH=dev
-wget -O- https://gitlab.pasteur.fr/nyx/planarlarvae.jl/-/archive/${BRANCH}/planarlarvae.jl-${BRANCH}.tar.gz | tar zxv && mv planarlarvae.jl-${BRANCH} PlanarLarvae
-wget -O- https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/archive/${BRANCH}/larvatagger.jl-${BRANCH}.tar.gz | tar zxv && mv larvatagger.jl-${BRANCH} LarvaTagger.jl
-ln -s $(realpath LarvaTagger.jl) LarvaTagger
-#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/TaggingBackends
-#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter
-wget -O- https://gitlab.pasteur.fr/nyx/TaggingBackends/-/archive/${BRANCH}/TaggingBackends-${BRANCH}.tar.gz | tar zxv && mv TaggingBackends-${BRANCH} TaggingBackends
-wget -O- https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter/-/archive/${BRANCH}/MaggotUBA-adapter-${BRANCH}.tar.gz | tar zxv && mv MaggotUBA-adapter-${BRANCH} MaggotUBA-adapter
-ln -s $(realpath MaggotUBA-adapter) MaggotUBA
-
-# the poetry install step may not be necessary
-(cd TaggingBackends && julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.develop(path="../PlanarLarvae")' && poetry env use python3.8 && poetry install)
-# the step below may not be necessary
-(cd TaggingBackends && JULIA_PROJECT=$(pwd) poetry run python -c 'import julia; julia.install()')
-
-(cd MaggotUBA && poetry env use python3.8 && (cat requirements.txt | xargs -I % sh -c 'poetry add "%"') && poetry install -v && poetry remove taggingbackends && poetry add ../TaggingBackends && scripts/make_models.jl default)
-
-cd LarvaTagger || exit 1
-julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.develop(path="../PlanarLarvae")'
-
-# the remainder of this script is test-specific
-
-if [ -f ../../LarvaTagger_test_data.tgz ]; then
+if [ -f LarvaTagger_test_data.tgz ]; then
   # To generate the test data, first run the tests with environment variable KEEP_MODEL_FILES=1
   # copy the LarvaTagger/MaggotUBA/models/test_train_* directories into LarvaTagger/LarvaTagger.jl/test/data
   # and build the archive from the LarvaTagger/LarvaTagger.jl directory.
   # For example:
   #   KEEP_MODEL_FILES=1 ./deploy_and_test.sh
-  #   cd LarvaTagger/LarvaTagger.jl
+  #   cd ~/.local/share/larvatagger/LarvaTagger/LarvaTagger.jl
   #   rm -rf test/data/test_train_*
   #   cp -Rp ../MaggotUBA/models/test_train_* test/data/
   #   tar zcvf LarvaTagger_test_data.tgz test/data/*
-  #   mv LarvaTagger_test_data.tgz ../../
-  tar zxvf ../../LarvaTagger_test_data.tgz
+  (cd "$LTROOT" && tar zxvf LarvaTagger_test_data.tgz)
 else
   # Not recommended; reproducibility is not guarantee across hosts or architectures yet
   #wget -O- https://dl.pasteur.fr/fop/8MvgygD4/LarvaTagger_test_data.tgz | tar zxv
-  wget -O- https://dl.pasteur.fr/fop/WdnyHdKR/240208_LarvaTagger_test_data.tgz | tar zxv
+  (cd "$LTROOT" && \
+    wget -O- https://dl.pasteur.fr/fop/t8CtkCpY/240208_LarvaTagger_test_data.tgz | tar zxv)
 fi
 
 if [ "$LOCAL_SCENARII" = "1" ]; then
-  if [ -f "$CURDIR/scenarii.sh" ]; then cp "$CURDIR/scenarii.sh" test/
-  elif [ -f "$CURDIR/test/scenarii.sh" ]; then cp "$CURDIR/test/scenarii.sh" test/
-  else echo "Cannot find a local scenarii.sh file"
+  if [ -f "test/scenarii.sh" ]; then
+    cp "test/scenarii.sh" "$LTROOT/test/"
+  else
+    echo "Cannot find a local scenarii.sh file"
   fi
 fi
 
-if [ -z "$(which shunit2)" ]; then
-  ln -s "$CURDIR/LarvaTagger/shunit2/shunit2" test/
-fi
-
 echo "${launcher}test/scenarii.sh"
-${launcher}test/scenarii.sh
+(cd "$LTROOT" && ${launcher}test/scenarii.sh)