hotfix in larvatagger.jl

README.md

@@ -4,9 +4,10 @@
 
 This package features a GUI for visualizing behaving larvae and editing discrete behavior tags at each time step.
 
-To run `LarvaTagger.jl`, you will need [`julia>=1.6`](https://julialang.org/downloads/) and some input data files, *e.g.* a `trx.mat` file or a pair of `.spine`/`.outline` files, preferably at a leaf of a directory structure such as `<screen_name>/<genotype@effector>/<protocol>/<date_time>`.
+To run `LarvaTagger.jl`, you will need [`julia>=1.6`](https://julialang.org/downloads/) and some input data file, *e.g.* a `trx.mat` file or a pair of `.spine`/`.outline` files, preferably located in a repository with directory structure: `<screen_name>/<genotype@effector>/<protocol>/<date_time>`.
 
-An example install procedure can be found in `scripts/make_demontrator.sh`.
+If you are not familiar with Julia, you may appreciate installation helpers such as [JILL.py](https://github.com/johnnychen94/jill.py).
+An example install procedure can be found in [`scripts/make_demontrator.sh`](https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/blob/main/scripts/make_demonstrator.sh).
 
 ## Install
 

scripts/larvatagger.jl

@@ -38,7 +38,7 @@ function main()
     if parsed_args["import"]
         infile = parsed_args["<input-path>"]
         if !isfile(infile)
-            @error "File not found" $infile
+            @error "File not found" infile
             return
         end
         outfile = parsed_args["<output-file>"]
@@ -63,7 +63,7 @@ function main()
         verbose = !parsed_args["--quiet"]
         infile = parsed_args["<input-path>"]
         if !isfile(infile)
-            @error "File not found" $infile
+            @error "File not found" infile
             return
         end
         if parsed_args["--viewer"]

scripts/make_demonstrator.sh

@@ -8,18 +8,18 @@
 # Nyx tagging UI, with specific options for our beloved alpha-testers.
 
 if ! [ -x ~/.local/bin/julia ]; then
-# install Jill with pip
+# install JILL with pip
 python3 -m pip install jill
-# install Julia with Jill
+# install Julia with JILL
 python3 -m jill install --confirm
 fi
 # make the `julia` command available on the commandline
 export PATH=~/.local/bin:$PATH
 # get LarvaTagger.jl source
-# (the dev branch is used here for testing before release)
+# (the dev branch is used here for pre-release testing purposes)
 git clone https://gitlab.pasteur.fr/nyx/larvatagger.jl LarvaTagger -b dev
 cd LarvaTagger
-# install LarvaTagger.jl
+# install LarvaTagger.jl with Pkg
 julia --project=. -e 'using Pkg; Pkg.instantiate()'
 if ! [ -x ~/.local/bin/larvatagger.jl ]; then
 pushd ~/.local/bin
@@ -29,9 +29,9 @@ fi
 # get MaggotUBA source and trained models - open-source part
 git clone https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter MaggotUBA -b 20220418
 cd MaggotUBA
-# install Poetry
+# install Poetry with pip
 python3 -m pip install poetry
-# install MaggotUBA; this step requires access to a private repo;
+# install MaggotUBA with Poetry; this step requires access to a private repo;
 # for a new user with no ssh or gpg keys, this is done logging in with `ssh -A` instead of `su`
 python3 -m poetry install
 cd