refactor: docker setup using devcontainer

.devcontainer/Dockerfile

@@ -1,2 +1,2 @@
-ARG TAG=latest
-FROM --platform=linux/amd64 ghcr.io/mcanouil/eggla:${TAG}
+ARG VARIANT="bullseye"
+FROM --platform=linux/amd64 buildpack-deps:${VARIANT}-curl

.devcontainer/bcftools/devcontainer-feature.json

@@ -0,0 +1,20 @@
+{
+	"name": "BCFtools",
+	"id": "bcftools",
+	"version": "1.0.0",
+	"description": "Installs the BCFtools software.",
+	"documentationURL": "https://github.com/mcanouil/eggla/tree/main/.devcontainer/bcftools",
+	"options": {
+		"version": {
+			"type": "string",
+			"proposals": [
+				"latest"
+			],
+			"default": "latest",
+			"description": "Select version of the BCFtools software, if not 'latest'."
+		}
+	},
+	"installsAfter": [
+		"ghcr.io/devcontainers/features/common-utils"
+	]
+}

.devcontainer/bcftools/install.sh

@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+
+BCFTOOLS_VERSION=${VERSION:-"1.16"}
+
+set -e
+
+apt_get_update() {
+    if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
+        echo "Running apt-get update..."
+        apt-get update -y
+    fi
+}
+
+# Checks if packages are installed and installs them if not
+check_packages() {
+    if ! dpkg -s "$@" >/dev/null 2>&1; then
+        apt_get_update
+        apt-get -y install --no-install-recommends "$@"
+    fi
+}
+
+check_packages curl \
+    build-essential \
+    libcurl4-openssl-dev \
+    ca-certificates \
+    bash-completion \
+    gzip \
+    libxt6 \
+    bzip2 \
+    wget \
+    autoconf \
+    automake \
+    make \
+    cmake \
+    libbz2-dev \
+    liblzma-dev \
+    libjpeg-dev \
+    libxml2-dev \
+    zlib1g-dev
+
+wget -q -P /tmp/ https://github.com/samtools/bcftools/releases/download/${BCFTOOLS_VERSION}/bcftools-${BCFTOOLS_VERSION}.tar.bz2
+tar -C /tmp/ -xjf /tmp/bcftools-${BCFTOOLS_VERSION}.tar.bz2
+cd /tmp/bcftools-${BCFTOOLS_VERSION}
+autoreconf -i
+./configure --prefix=/usr
+make
+make install
+rm -rf /tmp/bcftools-${BCFTOOLS_VERSION}
+
+# Clean up
+rm -rf /var/lib/apt/lists/*
+
+echo "Done!"

.devcontainer/devcontainer.json

@@ -3,7 +3,7 @@
 	"build": {
 		"dockerfile": "Dockerfile", 
 		"args": {
-			"TAG": "devel"
+			"VARIANT": "bullseye"
 		}
 	},
 	"remoteUser": "vscode",
@@ -15,20 +15,41 @@
 			"userGid": "1001",
 			"upgradePackages": "true"
 		},
-		"ghcr.io/devcontainers/features/docker-from-docker:1": {
-			"version": "latest"
+		"ghcr.io/devcontainers/features/git:1": {
+			"version": "latest",
+			"ppa": "false"
+		},
+		"ghcr.io/rocker-org/devcontainer-features/r-rig:1": {
+			"version": "4.2.0",
+			"vscodeRSupport": "full",
+			"installDevTools": "false",
+			"installREnv": "true",
+			"installRMarkdown": "false"
 		},
 		"ghcr.io/rocker-org/devcontainer-features/quarto-cli:1": {
 			"version": "prerelease",
 			"installTinyTex": "false",
 			"installChromium": "false"
+		},
+		"./bcftools": {
+			"version": "1.16"
+		},
+		"./eggla": {
+			"version": "main"
 		}
 	},
 	"customizations": {
 		"vscode": {
 			"extensions": [
 				"REditorSupport.r"
-			]
+			],
+			"settings": {
+				"r.rterm.option": [
+					"--no-save",
+					"--no-restore-data",
+					"--quiet"
+				]
+			}
 		}
 	}
 }

inst/setup/lock.R → .devcontainer/eggla/R/lock.R

@@ -1,7 +1,7 @@
 pkgs <- setdiff(rownames(old.packages(repos = "https://cloud.r-project.org/")), "pak")
 if (length(pkgs) > 0) pak::pkg_install(pkgs)
 
-lock_file <- "inst/setup/pkg.lock"
+lock_file <- ".github/.devcontainer/eggla/R/pkg.lock"
 pak::lockfile_create(
   pkg = c(".", "data.table", "devtools", "languageserver", "httpgd", "svglite", "ragg"),
   lockfile = lock_file,

.devcontainer/eggla/devcontainer-feature.json

@@ -0,0 +1,21 @@
+{
+	"name": "eggla",
+	"id": "eggla",
+	"version": "1.0.0",
+	"description": "Installs the eggla R package.",
+	"documentationURL": "https://github.com/mcanouil/eggla/tree/main/.devcontainer/eggla",
+	"options": {
+		"version": {
+			"type": "string",
+			"proposals": [
+				"latest"
+			],
+			"default": "latest",
+			"description": "Select version of the eggla R package, if not 'latest'."
+		}
+	},
+	"installsAfter": [
+		"ghcr.io/devcontainers/features/common-utils",
+		"ghcr.io/rocker-org/devcontainer-features/r-rig"
+	]
+}

.devcontainer/eggla/install.sh

@@ -0,0 +1,127 @@
+#!/usr/bin/env bash
+
+
+USERNAME=${USERNAME:-${_REMOTE_USER:-"automatic"}}
+EGGLA_VERSION=${VERSION:-"main"}
+
+FEATURE_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+set -e
+
+# 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 "${USERNAME}" >/dev/null 2>&1; then
+    USERNAME=root
+fi
+
+if [ "${USERNAME}" = "root" ]; then
+    user_home="/root"
+# Check if user already has a home directory other than /home/${USERNAME}
+elif [ "/home/${USERNAME}" != $( getent passwd $USERNAME | cut -d: -f6 ) ]; then
+    user_home=$( getent passwd $USERNAME | cut -d: -f6 )
+else
+    user_home="/home/${USERNAME}"
+    if [ ! -d "${user_home}" ]; then
+        mkdir -p "${user_home}"
+        chown ${USERNAME}:${group_name} "${user_home}"
+    fi
+fi
+
+apt_get_update() {
+    if [ "$(find /var/lib/apt/lists/* | wc -l)" = "0" ]; then
+        echo "Running apt-get update..."
+        apt-get update -y
+    fi
+}
+
+# Checks if packages are installed and installs them if not
+check_packages() {
+    if ! dpkg -s "$@" >/dev/null 2>&1; then
+        apt_get_update
+        apt-get -y install --no-install-recommends "$@"
+    fi
+}
+
+check_packages curl \
+    build-essential \
+    libcurl4-openssl-dev \
+    ca-certificates \
+    bash-completion \
+    gzip \
+    libxt6 \
+    bzip2 \
+    wget \
+    autoconf \
+    automake \
+    make \
+    cmake \
+    libbz2-dev \
+    liblzma-dev \
+    libjpeg-dev \
+    libxml2-dev \
+    zlib1g-dev \
+    libgdal-dev \
+    libfontconfig1-dev \
+    libharfbuzz-dev \
+    libfribidi-dev \
+    libv8-dev \
+    libudunits2-dev \
+    libfftw3-dev
+
+install_pak() {
+    local version=$1
+
+    if [ "${version}" = "auto" ]; then
+        if su "${USERNAME}" -c "R -s -e 'packageVersion(\"pak\")'" >/dev/null 2>&1; then
+            echo "pak is already installed. Skip pak installation..."
+            return
+        else
+            version="devel"
+        fi
+    fi
+
+    echo "Installing pak ${version}..."
+    # shellcheck disable=SC2016
+    su "${USERNAME}" -c 'R -q -e "install.packages(\"pak\", repos = sprintf(\"https://r-lib.github.io/p/pak/'"${version}"'/%s/%s/%s\", .Platform\$pkgType, R.Version()\$os, R.Version()\$arch))"'
+}
+
+export DEBIAN_FRONTEND=noninteractive
+
+echo "Install R packages..."
+mkdir /tmp/r-packages
+pushd /tmp/r-packages
+
+install_pak "auto"
+
+su "${USERNAME}" -c "R -q -e \"pak::lockfile_install(update = TRUE)\""
+
+if [ "${EGGLA_VERSION}" = "main" ]; then
+    su "${USERNAME}" -c "R -q -e \"pak::pkg_install('mcanouil/eggla', upgrade = FALSE, dependencies = TRUE)\""
+else
+    su "${USERNAME}" -c "R -q -e \"pak::pkg_install('mcanouil/eggla@${EGGLA_VERSION}', upgrade = FALSE, dependencies = TRUE)\""
+fi
+
+su "${USERNAME}" -c "R -q -e \"pak::cache_clean()\""
+
+cp ${FEATURE_DIR}/tests/eggla-example.R ${user_home}/eggla-example.R
+chmod +x ${user_home}/eggla-example.R
+
+cp ${FEATURE_DIR}/bin/plink2 /usr/bin/plink2
+chmod +x /usr/bin/plink2
+
+popd
+rm -rf /tmp/r-packages
+rm -rf /tmp/Rtmp*
+
+echo "Done!"

.github/workflows/devcontainer.yml

@@ -0,0 +1,56 @@
+name: Build & Test Docker Image
+
+on:
+  workflow_dispatch:
+  workflow_run:
+    workflows: "R-CMD-check"
+    branches: main
+    types: completed
+  release:
+    types: [published]
+
+concurrency:
+  group: ${{ github.workflow }}
+  cancel-in-progress: true
+
+jobs:
+  build-docker:
+    runs-on: ubuntu-latest
+    if: |
+      github.event_name == 'workflow_dispatch' || 
+        github.event_name == 'release' || 
+        (github.event_name == 'workflow_run' && github.event.workflow_run.conclusion == 'success')
+    strategy:
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build and run Dev Container
+        uses: devcontainers/[email protected]
+        if: github.ref_name == 'main'
+        with:
+          subFolder: .github
+          imageName: ghcr.io/mcanouil/eggla
+          cacheFrom: ghcr.io/mcanouil/eggla
+          imageTag: ${{github.ref_name}}
+          platform: linux/amd64
+          push: always
+          runCmd: Rscript eggla-example.R
+
+      - name: Build and run Dev Container
+        uses: devcontainers/[email protected]
+        if: github.ref_name != 'main'
+        with:
+          subFolder: .github
+          imageName: ghcr.io/mcanouil/eggla
+          cacheFrom: ghcr.io/mcanouil/eggla
+          imageTag: "devel"
+          platform: linux/amd64
+          push: always
+          runCmd: Rscript eggla-example.R