From d6eb7d4826527d2ef9379631ce1c858e53355c0b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sun, 9 Mar 2025 16:33:58 +0100
Subject: [PATCH] docs: use uv to set up Python environment

---
 README.md   |  4 ++--
 init-env.sh | 21 +++++++++++++++++----
 2 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 6027e79..4b3f477 100644
--- a/README.md
+++ b/README.md
@@ -68,12 +68,12 @@ It supports initialising all environments or specific ones based on the provided
 ### Script Details
 
 - **Options**:
-  - `--what/-w`: Specify which environment(s) to initialise (`all`, `r`, `python`, `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.
   - For R, it sets up `renv` and installs required packages.
-  - For Python, it sets up a virtual environment and installs required libraries.
+  - For Python, it sets up uv and installs required libraries.
   - For Julia, it sets up an environment and installs required packages.
 
 ## Contributing
diff --git a/init-env.sh b/init-env.sh
index 4bb7249..bd80e38 100644
--- a/init-env.sh
+++ b/init-env.sh
@@ -5,7 +5,7 @@ show_help() {
   echo "  --what/-w: Specify what to initialise (default: all)."
   echo "    all: Initialise R (renv), Python (virtualenv), and Julia (project)."
   echo "    r: Initialise R (renv)."
-  echo "    python: Initialise Python (virtualenv)."
+  echo "    python: Initialise Python (uv)."
   echo "    julia: Initialise Julia (project)."
   echo "  --force/-f: Force initialisation regardless of existing files."
   echo "  --help/-h: Show this help message."
@@ -13,8 +13,11 @@ show_help() {
 
 initialise_r() {
   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
     Rscript -e 'renv::init(bare = FALSE)'
-    Rscript -e 'renv::install("rmarkdown")'
+    Rscript -e 'renv::install(c("rmarkdown", "prompt", "languageserver", "lintr", "styler", "cli"))'
     Rscript -e 'renv::snapshot(type = "all")'
   fi
 }
@@ -28,6 +31,16 @@ initialise_python() {
   fi
 }
 
+initialise_uv() {
+  if [ "$FORCE" = true ] || [ ! -f "uv.lock" ]; then
+    uv init --no-package --vcs none --bare --no-readme --author-from none
+    uv venv
+    source .venv/bin/activate
+    uv add jupyter papermill
+    uv sync
+  fi
+}
+
 initialise_julia() {
   if [ "$FORCE" = true ] || [ ! -f "Project.toml" ]; then
     julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate()'
@@ -63,14 +76,14 @@ done
 case $WHAT in
   all)
     initialise_r
-    initialise_python
+    initialise_uv
     initialise_julia
     ;;
   r)
     initialise_r
     ;;
   python)
-    initialise_python
+    initialise_uv
     ;;
   julia)
     initialise_julia