From 7009ebc9412d45bd2a75b36b08af4d92e8c71943 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Thu, 24 Apr 2025 11:03:52 +0200
Subject: [PATCH 1/3] chore: chmod +x

---
 init-env.sh | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 mode change 100644 => 100755 init-env.sh

diff --git a/init-env.sh b/init-env.sh
old mode 100644
new mode 100755

From c5e1f46eba0beea6f569db25b0e7ef70322938e8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Thu, 24 Apr 2025 11:03:58 +0200
Subject: [PATCH 2/3] refactor: use brackets

---
 init-env.sh | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/init-env.sh b/init-env.sh
index c4502e4..9505e89 100755
--- a/init-env.sh
+++ b/init-env.sh
@@ -12,7 +12,7 @@ show_help() {
 }
 
 initialise_r() {
-  if [ "$FORCE" = true ] || [ ! -f "renv.lock" ]; then
+  if [ "${FORCE}" = true ] || [ ! -f "renv.lock" ]; then
     if grep -q 'source("renv/activate.R")' .Rprofile; then
       sed -i '' '/source("renv\/activate.R")/d' .Rprofile
     fi
@@ -23,7 +23,7 @@ initialise_r() {
 }
 
 initialise_python() {
-  if [ "$FORCE" = true ] || [ ! -f "requirements.txt" ]; then
+  if [ "${FORCE}" = true ] || [ ! -f "requirements.txt" ]; then
     python3 -m venv .venv
     source .venv/bin/activate
     python3 -m pip install jupyter papermill
@@ -32,7 +32,7 @@ initialise_python() {
 }
 
 initialise_uv() {
-  if [ "$FORCE" = true ] || [ ! -f "uv.lock" ]; then
+  if [ "${FORCE}" = true ] || [ ! -f "uv.lock" ]; then
     uv init --no-package --vcs none --bare --no-readme --author-from none
     uv venv
     source .venv/bin/activate
@@ -42,7 +42,7 @@ initialise_uv() {
 }
 
 initialise_julia() {
-  if [ "$FORCE" = true ] || [ ! -f "Project.toml" ]; then
+  if [ "${FORCE}" = true ] || [ ! -f "Project.toml" ]; then
     julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate()'
     julia --project=. -e 'using Pkg; Pkg.add("IJulia")'
   fi

From d77f7510cf0e3f59b814f68c92c2177f3ea08788 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Thu, 24 Apr 2025 11:04:22 +0200
Subject: [PATCH 3/3] docs: update init script name

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 4b3f477..61b7dbc 100644
--- a/README.md
+++ b/README.md
@@ -62,13 +62,13 @@ It supports initialising all environments or specific ones based on the provided
 ### Usage
 
 ```sh
-./init.sh [--what/-w all|r|python|julia] [--force/-f] [--help/-h]
+./init-env.sh [--what/-w all|r|python|julia] [--force/-f] [--help/-h]
 ```
 
 ### Script Details
 
 - **Options**:
-  - `--what/-w`: Specify which environment(s) to initialise (`all`, `r`, `python (uv)`, `julia`).
+  - `--what/-w`: Specify which environment(s) to initialise (`all`, `r`, `python` (uv), `julia`).
   - `--force/-f`: Force reinstallation of the specified environment(s).
   - `--help/-h`: Display help message and exit.
 - **Functionality**: The script installs necessary dependencies for R, Python, and Julia, inside environments.