fix: update documentation about init script and permissions (#26)

Author: mcanouil

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.

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