From 9f9db22fa0bcaef3170d46b39be09002efaa6bbe Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sat, 11 Jan 2025 16:41:26 +0100
Subject: [PATCH 1/6] refactor: init envs inside container

---
 .devcontainer/devcontainer.json               |   1 -
 .github/.devcontainer/Dockerfile              |   2 +-
 .github/.devcontainer/devcontainer.json       |   1 +
 .../init-env/devcontainer-feature.json        |  32 +++++
 .github/.devcontainer/init-env/install.sh     | 126 ++++++++++++++++++
 init.sh                                       |  83 ------------
 6 files changed, 160 insertions(+), 85 deletions(-)
 create mode 100644 .github/.devcontainer/init-env/devcontainer-feature.json
 create mode 100755 .github/.devcontainer/init-env/install.sh
 delete mode 100755 init.sh

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index f44b48b..09015d1 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -9,7 +9,6 @@
 		// 	"installChromium": "false"
 		// }
 	},
-	"postStartCommand": ["bash", "init.sh"],
 	"customizations": {
 		"vscode": {
 			"extensions": [
diff --git a/.github/.devcontainer/Dockerfile b/.github/.devcontainer/Dockerfile
index 197ca53..e5eae6b 100644
--- a/.github/.devcontainer/Dockerfile
+++ b/.github/.devcontainer/Dockerfile
@@ -1,2 +1,2 @@
 ARG VARIANT="jammy"
-FROM buildpack-deps:${VARIANT}-curl
+FROM --platform=linux/amd64 buildpack-deps:${VARIANT}-curl
diff --git a/.github/.devcontainer/devcontainer.json b/.github/.devcontainer/devcontainer.json
index ae5d8b2..5c4338c 100644
--- a/.github/.devcontainer/devcontainer.json
+++ b/.github/.devcontainer/devcontainer.json
@@ -35,6 +35,7 @@
 		"ghcr.io/julialang/devcontainer-features/julia:1": {
 			"channel": "release"
 		},
+		"./init-env": {},
 		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
 			"version": "prerelease",
 			"installTinyTex": "true",
diff --git a/.github/.devcontainer/init-env/devcontainer-feature.json b/.github/.devcontainer/init-env/devcontainer-feature.json
new file mode 100644
index 0000000..e8ae1ae
--- /dev/null
+++ b/.github/.devcontainer/init-env/devcontainer-feature.json
@@ -0,0 +1,32 @@
+{
+  "id": "init-env",
+  "version": "1.0.0",
+  "name": "Initialise Computing Environments",
+  "description": "Initialises R, Python, and Julia environments.",
+  "options": {
+    "what": {
+      "type": "string",
+      "enum": ["all", "r", "python", "julia"],
+      "default": "all",
+      "description": "Specify what to initialise."
+    },
+    "force": {
+      "type": "boolean",
+      "default": false,
+      "description": "Force initialisation regardless of existing files."
+    }
+  },
+  "postCreateCommand": "/usr/local/share/init-env.sh",
+  "dependsOn": {
+    "ghcr.io/devcontainers/features/common-utils": {},
+    "ghcr.io/rocker-org/devcontainer-features/r-rig": {},
+    "ghcr.io/devcontainers/features/python": {},
+    "ghcr.io/julialang/devcontainer-features/julia": {}
+  },
+  "installsAfter": [
+		"ghcr.io/devcontainers/features/common-utils",
+    "ghcr.io/rocker-org/devcontainer-features/r-rig",
+    "ghcr.io/devcontainers/features/python",
+    "ghcr.io/julialang/devcontainer-features/julia"
+	]
+}
diff --git a/.github/.devcontainer/init-env/install.sh b/.github/.devcontainer/init-env/install.sh
new file mode 100755
index 0000000..4246163
--- /dev/null
+++ b/.github/.devcontainer/init-env/install.sh
@@ -0,0 +1,126 @@
+#!/usr/bin/env bash
+
+set -e
+
+export DEBIAN_FRONTEND=noninteractive
+USERNAME=${_REMOTE_USER:-"vscode"}
+
+show_help() {
+  echo "Usage: $0 [--what/-w all|r|python|julia] [--force/-f] [--help/-h]"
+  echo "  --what/-w: Specify what to initialise (default: all)."
+  echo "    all: Initialise R (renv), Python (virtualenv), and Julia (project)."
+  echo "    r: Initialise R (renv)."
+  echo "    python: Initialise Python (virtualenv)."
+  echo "    julia: Initialise Julia (project)."
+  echo "  --force/-f: Force initialisation regardless of existing files."
+  echo "  --help/-h: Show this help message."
+}
+
+initialise_r() {
+  if [ "$FORCE" = true ] || [ ! -f "renv.lock" ]; then
+    su "${USERNAME}" -c "Rscript -e 'renv::init(bare = FALSE)'"
+    su "${USERNAME}" -c "Rscript -e 'renv::install(\"rmarkdown\")'"
+    su "${USERNAME}" -c "Rscript -e 'renv::snapshot(type = \"all\")'"
+  fi
+}
+
+initialise_python() {
+  if [ "$FORCE" = true ] || [ ! -f "requirements.txt" ]; then
+    su "${USERNAME}" -c "python3 -m venv .venv"
+    su "${USERNAME}" -c "source .venv/bin/activate"
+    su "${USERNAME}" -c "python3 -m pip install jupyter"
+    su "${USERNAME}" -c "python3 -m pip freeze > requirements.txt"
+  fi
+}
+
+initialise_julia() {
+  if [ "$FORCE" = true ] || [ ! -f "Project.toml" ]; then
+    su "${USERNAME}" -c "julia -e 'using Pkg; Pkg.activate(\".\"); Pkg.instantiate()'"
+    su "${USERNAME}" -c "julia --project=. -e 'using Pkg; Pkg.add("IJulia")'"
+  fi
+}
+
+WHAT="all"
+FORCE=false
+
+while [[ "$#" -gt 0 ]]; do
+  case $1 in
+    --what|-w)
+      WHAT="$2"
+      shift
+      ;;
+    --force|-f)
+      FORCE=true
+      ;;
+    --help|-h)
+      show_help
+      exit 0
+      ;;
+    *)
+      echo "Unknown parameter passed: $1"
+      show_help
+      exit 1
+      ;;
+  esac
+  shift
+done
+
+mkdir -p ${_REMOTE_USER_HOME}/quarto-env
+cd ${_REMOTE_USER_HOME}/quarto-env
+
+case $WHAT in
+  all)
+    initialise_r
+    initialise_python
+    initialise_julia
+    ;;
+  r)
+    initialise_r
+    ;;
+  python)
+    initialise_python
+    ;;
+  julia)
+    initialise_julia
+    ;;
+  *)
+    echo "Unknown option for --what: $WHAT"
+    show_help
+    exit 1
+    ;;
+esac
+
+INIT_ENV_PATH="/usr/local/share/init-env.sh"
+
+tee "${INIT_ENV_PATH}" > /dev/null \
+<< EOF
+#!/usr/bin/env bash
+set -e
+EOF
+
+tee -a "${INIT_ENV_PATH}" > /dev/null \
+<< 'EOF'
+while [[ "$#" -gt 0 ]]; do
+  case $1 in
+    --source|-s)
+      SOURCE_DIR="$2"
+      shift
+      ;;
+    --target|-t)
+      TARGET_DIR="$2"
+      ;;
+    *)
+      echo "Unknown parameter passed: $1"
+      show_help
+      exit 1
+      ;;
+  esac
+  shift
+done
+
+for item in "${SOURCE_DIR}"/*; do
+  ln -sf "${item}" "${TARGET_DIR}/"
+done
+EOF
+
+chmod 755 "${INIT_ENV_PATH}"
diff --git a/init.sh b/init.sh
deleted file mode 100755
index 9a74c96..0000000
--- a/init.sh
+++ /dev/null
@@ -1,83 +0,0 @@
-#!/usr/bin/env bash
-
-show_help() {
-  echo "Usage: $0 [--what/-w all|r|python|julia] [--force/-f] [--help/-h]"
-  echo "  --what/-w: Specify what to initialise (default: all)."
-  echo "    all: Initialise R (renv), Python (virtualenv), and Julia (project)."
-  echo "    r: Initialise R (renv)."
-  echo "    python: Initialise Python (virtualenv)."
-  echo "    julia: Initialise Julia (project)."
-  echo "  --force/-f: Force initialisation regardless of existing files."
-  echo "  --help/-h: Show this help message."
-}
-
-initialize_r() {
-  if [ "$FORCE" = true ] || [ ! -f "renv.lock" ]; then
-    Rscript -e 'renv::init(bare = FALSE)'
-    Rscript -e 'renv::install("rmarkdown")'
-    Rscript -e 'renv::snapshot(type = "all")'
-  fi
-}
-
-initialize_python() {
-  if [ "$FORCE" = true ] || [ ! -f "requirements.txt" ]; then
-    python3 -m venv .venv
-    source .venv/bin/activate
-    python3 -m pip install jupyter
-    python3 -m pip freeze > requirements.txt
-  fi
-}
-
-initialize_julia() {
-  if [ "$FORCE" = true ] || [ ! -f "Project.toml" ]; then
-    julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate()'
-    julia --project=. -e 'using Pkg; Pkg.add("IJulia")'
-  fi
-}
-
-WHAT="all"
-FORCE=false
-
-while [[ "$#" -gt 0 ]]; do
-  case $1 in
-    --what|-w)
-      WHAT="$2"
-      shift
-      ;;
-    --force|-f)
-      FORCE=true
-      ;;
-    --help|-h)
-      show_help
-      exit 0
-      ;;
-    *)
-      echo "Unknown parameter passed: $1"
-      show_help
-      exit 1
-      ;;
-  esac
-  shift
-done
-
-case $WHAT in
-  all)
-    initialize_r
-    initialize_python
-    initialize_julia
-    ;;
-  r)
-    initialize_r
-    ;;
-  python)
-    initialize_python
-    ;;
-  julia)
-    initialize_julia
-    ;;
-  *)
-    echo "Unknown option for --what: $WHAT"
-    show_help
-    exit 1
-    ;;
-esac

From 9044a1ec5cdf473c6da3d54c5b9ebe13d3aa4136 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sat, 11 Jan 2025 17:07:11 +0100
Subject: [PATCH 2/6] refactor: install deps as root

---
 .github/.devcontainer/devcontainer.json       |   4 +-
 .github/.devcontainer/init-env/install.sh     | 126 ------------------
 .../devcontainer-feature.json                 |  16 +--
 .../install-quarto-dependencies/install.sh    |  36 +++++
 4 files changed, 44 insertions(+), 138 deletions(-)
 delete mode 100755 .github/.devcontainer/init-env/install.sh
 rename .github/.devcontainer/{init-env => install-quarto-dependencies}/devcontainer-feature.json (60%)
 create mode 100755 .github/.devcontainer/install-quarto-dependencies/install.sh

diff --git a/.github/.devcontainer/devcontainer.json b/.github/.devcontainer/devcontainer.json
index 5c4338c..7397f99 100644
--- a/.github/.devcontainer/devcontainer.json
+++ b/.github/.devcontainer/devcontainer.json
@@ -35,7 +35,9 @@
 		"ghcr.io/julialang/devcontainer-features/julia:1": {
 			"channel": "release"
 		},
-		"./init-env": {},
+		"./install-quarto-dependencies": {
+			"dependencies": "all"
+		},
 		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
 			"version": "prerelease",
 			"installTinyTex": "true",
diff --git a/.github/.devcontainer/init-env/install.sh b/.github/.devcontainer/init-env/install.sh
deleted file mode 100755
index 4246163..0000000
--- a/.github/.devcontainer/init-env/install.sh
+++ /dev/null
@@ -1,126 +0,0 @@
-#!/usr/bin/env bash
-
-set -e
-
-export DEBIAN_FRONTEND=noninteractive
-USERNAME=${_REMOTE_USER:-"vscode"}
-
-show_help() {
-  echo "Usage: $0 [--what/-w all|r|python|julia] [--force/-f] [--help/-h]"
-  echo "  --what/-w: Specify what to initialise (default: all)."
-  echo "    all: Initialise R (renv), Python (virtualenv), and Julia (project)."
-  echo "    r: Initialise R (renv)."
-  echo "    python: Initialise Python (virtualenv)."
-  echo "    julia: Initialise Julia (project)."
-  echo "  --force/-f: Force initialisation regardless of existing files."
-  echo "  --help/-h: Show this help message."
-}
-
-initialise_r() {
-  if [ "$FORCE" = true ] || [ ! -f "renv.lock" ]; then
-    su "${USERNAME}" -c "Rscript -e 'renv::init(bare = FALSE)'"
-    su "${USERNAME}" -c "Rscript -e 'renv::install(\"rmarkdown\")'"
-    su "${USERNAME}" -c "Rscript -e 'renv::snapshot(type = \"all\")'"
-  fi
-}
-
-initialise_python() {
-  if [ "$FORCE" = true ] || [ ! -f "requirements.txt" ]; then
-    su "${USERNAME}" -c "python3 -m venv .venv"
-    su "${USERNAME}" -c "source .venv/bin/activate"
-    su "${USERNAME}" -c "python3 -m pip install jupyter"
-    su "${USERNAME}" -c "python3 -m pip freeze > requirements.txt"
-  fi
-}
-
-initialise_julia() {
-  if [ "$FORCE" = true ] || [ ! -f "Project.toml" ]; then
-    su "${USERNAME}" -c "julia -e 'using Pkg; Pkg.activate(\".\"); Pkg.instantiate()'"
-    su "${USERNAME}" -c "julia --project=. -e 'using Pkg; Pkg.add("IJulia")'"
-  fi
-}
-
-WHAT="all"
-FORCE=false
-
-while [[ "$#" -gt 0 ]]; do
-  case $1 in
-    --what|-w)
-      WHAT="$2"
-      shift
-      ;;
-    --force|-f)
-      FORCE=true
-      ;;
-    --help|-h)
-      show_help
-      exit 0
-      ;;
-    *)
-      echo "Unknown parameter passed: $1"
-      show_help
-      exit 1
-      ;;
-  esac
-  shift
-done
-
-mkdir -p ${_REMOTE_USER_HOME}/quarto-env
-cd ${_REMOTE_USER_HOME}/quarto-env
-
-case $WHAT in
-  all)
-    initialise_r
-    initialise_python
-    initialise_julia
-    ;;
-  r)
-    initialise_r
-    ;;
-  python)
-    initialise_python
-    ;;
-  julia)
-    initialise_julia
-    ;;
-  *)
-    echo "Unknown option for --what: $WHAT"
-    show_help
-    exit 1
-    ;;
-esac
-
-INIT_ENV_PATH="/usr/local/share/init-env.sh"
-
-tee "${INIT_ENV_PATH}" > /dev/null \
-<< EOF
-#!/usr/bin/env bash
-set -e
-EOF
-
-tee -a "${INIT_ENV_PATH}" > /dev/null \
-<< 'EOF'
-while [[ "$#" -gt 0 ]]; do
-  case $1 in
-    --source|-s)
-      SOURCE_DIR="$2"
-      shift
-      ;;
-    --target|-t)
-      TARGET_DIR="$2"
-      ;;
-    *)
-      echo "Unknown parameter passed: $1"
-      show_help
-      exit 1
-      ;;
-  esac
-  shift
-done
-
-for item in "${SOURCE_DIR}"/*; do
-  ln -sf "${item}" "${TARGET_DIR}/"
-done
-EOF
-
-chmod 755 "${INIT_ENV_PATH}"
diff --git a/.github/.devcontainer/init-env/devcontainer-feature.json b/.github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json
similarity index 60%
rename from .github/.devcontainer/init-env/devcontainer-feature.json
rename to .github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json
index e8ae1ae..4a7598e 100644
--- a/.github/.devcontainer/init-env/devcontainer-feature.json
+++ b/.github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json
@@ -1,22 +1,16 @@
 {
-  "id": "init-env",
+  "id": "install-quarto-dependencies",
   "version": "1.0.0",
-  "name": "Initialise Computing Environments",
-  "description": "Initialises R, Python, and Julia environments.",
+  "name": "Install Computing Dependencies for Quarto",
+  "description": "Install R, Python, and Julia dependencies for Quarto.",
   "options": {
-    "what": {
+    "dependencies": {
       "type": "string",
       "enum": ["all", "r", "python", "julia"],
       "default": "all",
-      "description": "Specify what to initialise."
-    },
-    "force": {
-      "type": "boolean",
-      "default": false,
-      "description": "Force initialisation regardless of existing files."
+      "description": "Specify what dependencies to install."
     }
   },
-  "postCreateCommand": "/usr/local/share/init-env.sh",
   "dependsOn": {
     "ghcr.io/devcontainers/features/common-utils": {},
     "ghcr.io/rocker-org/devcontainer-features/r-rig": {},
diff --git a/.github/.devcontainer/install-quarto-dependencies/install.sh b/.github/.devcontainer/install-quarto-dependencies/install.sh
new file mode 100755
index 0000000..4489299
--- /dev/null
+++ b/.github/.devcontainer/install-quarto-dependencies/install.sh
@@ -0,0 +1,36 @@
+#!/usr/bin/env bash
+
+set -e
+
+export DEBIAN_FRONTEND=noninteractive
+USERNAME=${_REMOTE_USER:-"vscode"}
+DEPENDENCIES=${DEPENDENCIES:-"all"}
+
+quarto_r_deps() {
+  su "${USERNAME}" -c "Rscript -e 'pak::pkg_install(\"rmarkdown\")'"
+}
+
+quarto_python_deps() {
+  su "${USERNAME}" -c "python3 -m pip install jupyter"
+}
+
+initialise_julia() {
+  su "${USERNAME}" -c "julia -e 'using Pkg; Pkg.add("IJulia")'"
+}
+
+case ${DEPENDENCIES} in
+  all)
+    initialise_r
+    initialise_python
+    initialise_julia
+    ;;
+  r)
+    initialise_r
+    ;;
+  python)
+    initialise_python
+    ;;
+  julia)
+    initialise_julia
+    ;;
+esac

From 1ec6b3faa4094b8be20d28a62d7a97e8afeb4676 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sat, 11 Jan 2025 17:07:24 +0100
Subject: [PATCH 3/6] fix: put back env init script

---
 init-env.sh | 83 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 init-env.sh

diff --git a/init-env.sh b/init-env.sh
new file mode 100644
index 0000000..9a74c96
--- /dev/null
+++ b/init-env.sh
@@ -0,0 +1,83 @@
+#!/usr/bin/env bash
+
+show_help() {
+  echo "Usage: $0 [--what/-w all|r|python|julia] [--force/-f] [--help/-h]"
+  echo "  --what/-w: Specify what to initialise (default: all)."
+  echo "    all: Initialise R (renv), Python (virtualenv), and Julia (project)."
+  echo "    r: Initialise R (renv)."
+  echo "    python: Initialise Python (virtualenv)."
+  echo "    julia: Initialise Julia (project)."
+  echo "  --force/-f: Force initialisation regardless of existing files."
+  echo "  --help/-h: Show this help message."
+}
+
+initialize_r() {
+  if [ "$FORCE" = true ] || [ ! -f "renv.lock" ]; then
+    Rscript -e 'renv::init(bare = FALSE)'
+    Rscript -e 'renv::install("rmarkdown")'
+    Rscript -e 'renv::snapshot(type = "all")'
+  fi
+}
+
+initialize_python() {
+  if [ "$FORCE" = true ] || [ ! -f "requirements.txt" ]; then
+    python3 -m venv .venv
+    source .venv/bin/activate
+    python3 -m pip install jupyter
+    python3 -m pip freeze > requirements.txt
+  fi
+}
+
+initialize_julia() {
+  if [ "$FORCE" = true ] || [ ! -f "Project.toml" ]; then
+    julia -e 'using Pkg; Pkg.activate("."); Pkg.instantiate()'
+    julia --project=. -e 'using Pkg; Pkg.add("IJulia")'
+  fi
+}
+
+WHAT="all"
+FORCE=false
+
+while [[ "$#" -gt 0 ]]; do
+  case $1 in
+    --what|-w)
+      WHAT="$2"
+      shift
+      ;;
+    --force|-f)
+      FORCE=true
+      ;;
+    --help|-h)
+      show_help
+      exit 0
+      ;;
+    *)
+      echo "Unknown parameter passed: $1"
+      show_help
+      exit 1
+      ;;
+  esac
+  shift
+done
+
+case $WHAT in
+  all)
+    initialize_r
+    initialize_python
+    initialize_julia
+    ;;
+  r)
+    initialize_r
+    ;;
+  python)
+    initialize_python
+    ;;
+  julia)
+    initialize_julia
+    ;;
+  *)
+    echo "Unknown option for --what: $WHAT"
+    show_help
+    exit 1
+    ;;
+esac

From ec857f14ad2e4ed3d7561ce5f0eadd448cf5b5c3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sat, 11 Jan 2025 17:26:28 +0100
Subject: [PATCH 4/6] refactor: renaming

---
 .github/.devcontainer/devcontainer.json            |  2 +-
 .../devcontainer-feature.json                      |  2 +-
 .../install-quarto-dependencies/install.sh         | 14 +++++++-------
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/.github/.devcontainer/devcontainer.json b/.github/.devcontainer/devcontainer.json
index 7397f99..08e3679 100644
--- a/.github/.devcontainer/devcontainer.json
+++ b/.github/.devcontainer/devcontainer.json
@@ -35,7 +35,7 @@
 		"ghcr.io/julialang/devcontainer-features/julia:1": {
 			"channel": "release"
 		},
-		"./install-quarto-dependencies": {
+		"./quarto-computing-dependencies": {
 			"dependencies": "all"
 		},
 		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
diff --git a/.github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json b/.github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json
index 4a7598e..e7c688c 100644
--- a/.github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json
+++ b/.github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json
@@ -1,5 +1,5 @@
 {
-  "id": "install-quarto-dependencies",
+  "id": "quarto-computing-dependencies",
   "version": "1.0.0",
   "name": "Install Computing Dependencies for Quarto",
   "description": "Install R, Python, and Julia dependencies for Quarto.",
diff --git a/.github/.devcontainer/install-quarto-dependencies/install.sh b/.github/.devcontainer/install-quarto-dependencies/install.sh
index 4489299..7e2166d 100755
--- a/.github/.devcontainer/install-quarto-dependencies/install.sh
+++ b/.github/.devcontainer/install-quarto-dependencies/install.sh
@@ -14,23 +14,23 @@ quarto_python_deps() {
   su "${USERNAME}" -c "python3 -m pip install jupyter"
 }
 
-initialise_julia() {
+quarto_julia_deps() {
   su "${USERNAME}" -c "julia -e 'using Pkg; Pkg.add("IJulia")'"
 }
 
 case ${DEPENDENCIES} in
   all)
-    initialise_r
-    initialise_python
-    initialise_julia
+    quarto_r_deps
+    quarto_python_deps
+    quarto_julia_deps
     ;;
   r)
-    initialise_r
+    quarto_r_deps
     ;;
   python)
-    initialise_python
+    quarto_python_deps
     ;;
   julia)
-    initialise_julia
+    quarto_julia_deps
     ;;
 esac

From 039597f221459f3cb0e57c85b2f2df4b9bee96f3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sat, 11 Jan 2025 17:28:17 +0100
Subject: [PATCH 5/6] refactor: rename feature

---
 .../devcontainer-feature.json                                     | 0
 .../install.sh                                                    | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename .github/.devcontainer/{install-quarto-dependencies => quarto-computing-dependencies}/devcontainer-feature.json (100%)
 rename .github/.devcontainer/{install-quarto-dependencies => quarto-computing-dependencies}/install.sh (100%)

diff --git a/.github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json b/.github/.devcontainer/quarto-computing-dependencies/devcontainer-feature.json
similarity index 100%
rename from .github/.devcontainer/install-quarto-dependencies/devcontainer-feature.json
rename to .github/.devcontainer/quarto-computing-dependencies/devcontainer-feature.json
diff --git a/.github/.devcontainer/install-quarto-dependencies/install.sh b/.github/.devcontainer/quarto-computing-dependencies/install.sh
similarity index 100%
rename from .github/.devcontainer/install-quarto-dependencies/install.sh
rename to .github/.devcontainer/quarto-computing-dependencies/install.sh

From 52b58c08ba80883b54d7aaf5df7c1652a71b8d24 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sat, 11 Jan 2025 17:42:23 +0100
Subject: [PATCH 6/6] fix: use juliaup path

---
 .../quarto-computing-dependencies/install.sh  | 30 +++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/.github/.devcontainer/quarto-computing-dependencies/install.sh b/.github/.devcontainer/quarto-computing-dependencies/install.sh
index 7e2166d..d61cf37 100755
--- a/.github/.devcontainer/quarto-computing-dependencies/install.sh
+++ b/.github/.devcontainer/quarto-computing-dependencies/install.sh
@@ -3,9 +3,35 @@
 set -e
 
 export DEBIAN_FRONTEND=noninteractive
-USERNAME=${_REMOTE_USER:-"vscode"}
+
 DEPENDENCIES=${DEPENDENCIES:-"all"}
 
+USERNAME=${USERNAME:-${_REMOTE_USER:-"automatic"}}
+
+set -e
+
+if [ "$(id -u)" -ne 0 ]; then
+  echo -e 'Script must be run as root. Use sudo, su, or add "USER root" to your Dockerfile before running this script.'
+  exit 1
+fi
+
+# Determine the appropriate non-root user
+if [ "${USERNAME}" = "auto" ] || [ "${USERNAME}" = "automatic" ]; then
+  USERNAME=""
+  POSSIBLE_USERS=("vscode" "node" "codespace" "$(awk -v val=1000 -F ":" '$3==val{print $1}' /etc/passwd)")
+  for CURRENT_USER in "${POSSIBLE_USERS[@]}"; do
+    if id -u "${CURRENT_USER}" >/dev/null 2>&1; then
+      USERNAME=${CURRENT_USER}
+      break
+    fi
+  done
+  if [ "${USERNAME}" = "" ]; then
+    USERNAME=root
+  fi
+elif [ "${USERNAME}" = "none" ] || ! id -u "${USERNAME}" >/dev/null 2>&1; then
+  USERNAME=root
+fi
+
 quarto_r_deps() {
   su "${USERNAME}" -c "Rscript -e 'pak::pkg_install(\"rmarkdown\")'"
 }
@@ -15,7 +41,7 @@ quarto_python_deps() {
 }
 
 quarto_julia_deps() {
-  su "${USERNAME}" -c "julia -e 'using Pkg; Pkg.add("IJulia")'"
+  su "${USERNAME}" -c "~/.juliaup/bin/julia -e 'using Pkg; Pkg.add(\"IJulia\")'"
 }
 
 case ${DEPENDENCIES} in