From c147fdb2367d79fa2839f6d413addcd9eb8f81b0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Fran=C3=A7ois=20Laurent?= <francois.laurent@posteo.net>
Date: Sat, 4 Jun 2022 18:25:20 +0200
Subject: [PATCH] hotfix in larvatagger.jl
---
README.md | 5 +++--
scripts/larvatagger.jl | 4 ++--
scripts/make_demonstrator.sh | 12 ++++++------
3 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/README.md b/README.md
index 6d58c65..bffde07 100644
--- a/README.md
+++ b/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
diff --git a/scripts/larvatagger.jl b/scripts/larvatagger.jl
index 4506d0c..ec83991 100755
--- a/scripts/larvatagger.jl
+++ b/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" $infile
+ @error "File not found" infile
return
end
if parsed_args["--viewer"]
diff --git a/scripts/make_demonstrator.sh b/scripts/make_demonstrator.sh
index bdc43a7..1b2bc86 100755
--- a/scripts/make_demonstrator.sh
+++ b/scripts/make_demonstrator.sh
@@ -8,18 +8,18 @@
# Nyx tagging UI, with specific options for our beloved alpha-testers.
if ! [ -x ~/.local/bin/julia ]; then
-# install Jill with pip
+# install JILL with pip
python3 -m pip install jill
-# install Julia with Jill
+# install Julia with JILL
python3 -m jill install --confirm
fi
# make the `julia` command available on the commandline
export PATH=~/.local/bin:$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
--
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