From 126830081a9665acb6520736cf4687c0c2550aeb Mon Sep 17 00:00:00 2001
From: Carsten Behring <carsten.behring@gmail.com>
Date: Thu, 23 May 2024 22:14:30 +0200
Subject: [PATCH 1/2] fixes #107

---
 .devcontainer/Dockerfile        | 28 ++++++++++++++---
 .devcontainer/devcontainer.json | 53 ++++++++++++++++++++++-----------
 CHANGELOG.md                    |  5 ++++
 3 files changed, 64 insertions(+), 22 deletions(-)

diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile
index b4b07f7..e5089c0 100644
--- a/.devcontainer/Dockerfile
+++ b/.devcontainer/Dockerfile
@@ -1,5 +1,25 @@
-FROM mcr.microsoft.com/devcontainers/java:11-bullseye
+FROM clojure:temurin-21-tools-deps-1.11.3.1456-jammy
+
+ARG USERNAME=vscode
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+
+# Create the user
+RUN groupadd --gid $USER_GID $USERNAME \
+    && useradd --uid $USER_UID --gid $USER_GID -m $USERNAME \
+    #
+    # [Optional] Add sudo support. Omit if you don't need to install software after connecting.
+    && apt-get update \
+    && apt-get install -y sudo \
+    && echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME \
+    && chmod 0440 /etc/sudoers.d/$USERNAME
+
+# ********************************************************
+# * Anything else you want to do like clean up goes here *
+# ********************************************************
+
+# [Optional] Set the default user. Omit if you want to keep the default as root.
+USER $USERNAME
+SHELL ["/bin/bash", "-ec"]
+ENTRYPOINT ["bash"]
 
-RUN bash -c "bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install)"
-RUN bash -c "bash < <(curl -s https://raw.githubusercontent.com/clojure-lsp/clojure-lsp/master/install)"
-RUN apt-get update && apt-get install -y rlwrap gfortran libblas-dev liblapack-dev  libpng-dev libfontconfig1-dev libfreetype-dev gfortran  libicu-dev cmake
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 774c7f5..9d81927 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -1,31 +1,48 @@
 {
-	"name": "my Clojure app",
 	"build": {
 		"dockerfile": "Dockerfile"
+	},
 
-		},
-
-
-    "features": {
-	    	"ghcr.io/devcontainers-contrib/features/clojure-asdf:2": {},
-		"ghcr.io/rocker-org/devcontainer-features/r-apt:0": {}
-
+	"features": {
 
-},
-    "forwardPorts": ["12345","7777"],
+		"ghcr.io/devcontainers-contrib/features/apt-get-packages:1": {
+			"packages": "rlwrap,r-base-dev"
+		},
+		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {},
+		"ghcr.io/rocker-org/devcontainer-features/r-apt:0": {},
+		"ghcr.io/rocker-org/devcontainer-features/rstudio-server": {},
+		"ghcr.io/devcontainers/features/docker-in-docker:2": {},
+		"ghcr.io/rocker-org/devcontainer-features/r-packages:1": {
+			"packages": "nloptr,Rserve,ranger,randomForest,ggthemes,ggplot2,mice,dplyr",
+			"additionalRepositories": "rforge= 'https://rforge.net'",
+			"installSystemRequirements": true
+		},
+		"ghcr.io/wxw-matt/devcontainer-features/command_runner:latest": {
+            "command1": "bash < <(curl -s https://raw.githubusercontent.com/clojure-lsp/clojure-lsp/master/install)",
+            "command2": "bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install)",
+			"command3": "bash -c 'wget https://raw.githubusercontent.com/technomancy/leiningen/stable/bin/lein -O /usr/local/bin/lein && chmod +x /usr/local/bin/lein'"
+        }
+	},
+	"overrideFeatureInstallOrder": [
+     "ghcr.io/rocker-org/devcontainer-features/r-apt",
+	 "ghcr.io/devcontainers-contrib/features/apt-get-packages",
+ 	 "ghcr.io/rocker-org/devcontainer-features/r-packages"
+    ],
+	"forwardPorts": [12345],
+	"portsAttributes": {
+		"12345": {
+			"label": "nrepl"
+		}
+	},
 	"customizations": {
 		"vscode": {
-			"settings": { 
-			},
-			"extensions": 
-			[
-				"vscjava.vscode-java-pack",
-				"borkdude.clj-kondo",
+			"extensions": [
 				"betterthantomorrow.calva"
 			]
 		}
 	},
 
-	"remoteUser": "vscode",
-	"onCreateCommand": "Rscript -e 'pak::pkg_install(c(\"ranger\",\"randomForest\",\"ggthemes\",\"ggplot2\",\"mice\",\"dplyr\",\"url::https://rforge.net/Rserve/snapshot/Rserve_1.8-12.tar.gz\"))'"
+	"postAttachCommand":
+	{ "prepare": ["bash","-c", "-i", "source ./.devcontainer/setup.sh"]
+	}
 }
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f7f3dd4..f36d16e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,6 +1,11 @@
 # Change Log
 All notable changes to this project will be documented in this file. This change log follows the conventions of [keepachangelog.com](http://keepachangelog.com/).
 
+## unreleased
+
+- use devcontainer setup following template
+
+
 ## [1.0.0]
 - `require-r` creates namespace as `r.namespace`, also `namespace` as an alias
 - dependencies update, TMD 7.029

From 08ebc4c8a92bd1a76fcd0cb96afb0dfd23af338c Mon Sep 17 00:00:00 2001
From: Carsten Behring <carsten.behring@gmail.com>
Date: Mon, 27 May 2024 21:16:10 +0200
Subject: [PATCH 2/2] added forgoten setup file

---
 .devcontainer/setup.sh | 3 +++
 1 file changed, 3 insertions(+)
 create mode 100755 .devcontainer/setup.sh

diff --git a/.devcontainer/setup.sh b/.devcontainer/setup.sh
new file mode 100755
index 0000000..b187cd0
--- /dev/null
+++ b/.devcontainer/setup.sh
@@ -0,0 +1,3 @@
+#!/bin/bash -xe
+
+clj -Sthreads 1 -P