diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 7c4038e2..0628cc51 100644 --- a/.devcontainer/Dockerfile +++ b/.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 diff --git a/.devcontainer/bcftools/devcontainer-feature.json b/.devcontainer/bcftools/devcontainer-feature.json new file mode 100644 index 00000000..b78959a4 --- /dev/null +++ b/.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" + ] +} diff --git a/.devcontainer/bcftools/install.sh b/.devcontainer/bcftools/install.sh new file mode 100644 index 00000000..0694f4f0 --- /dev/null +++ b/.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!" diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index c824f107..dffd45e5 100644 --- a/.devcontainer/devcontainer.json +++ b/.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" + ] + } } } } diff --git a/inst/setup/lock.R b/.devcontainer/eggla/R/lock.R similarity index 92% rename from inst/setup/lock.R rename to .devcontainer/eggla/R/lock.R index 6e9c844b..bd3d94ec 100644 --- a/inst/setup/lock.R +++ b/.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, diff --git a/inst/setup/pkg.lock b/.devcontainer/eggla/R/pkg.lock similarity index 100% rename from inst/setup/pkg.lock rename to .devcontainer/eggla/R/pkg.lock diff --git a/.devcontainer/eggla/bin/plink2 b/.devcontainer/eggla/bin/plink2 new file mode 100755 index 00000000..514bc4ae Binary files /dev/null and b/.devcontainer/eggla/bin/plink2 differ diff --git a/.devcontainer/eggla/devcontainer-feature.json b/.devcontainer/eggla/devcontainer-feature.json new file mode 100644 index 00000000..c02ecc89 --- /dev/null +++ b/.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" + ] +} diff --git a/.devcontainer/eggla/install.sh b/.devcontainer/eggla/install.sh new file mode 100644 index 00000000..0a8ef8df --- /dev/null +++ b/.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!" diff --git a/inst/setup/eggla-example.R b/.devcontainer/eggla/tests/eggla-example.R similarity index 100% rename from inst/setup/eggla-example.R rename to .devcontainer/eggla/tests/eggla-example.R diff --git a/.github/workflows/devcontainer.yml b/.github/workflows/devcontainer.yml new file mode 100644 index 00000000..aa0f46bb --- /dev/null +++ b/.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/ci@v0.3 + if: github.ref_name == 'main' + with: + subFolder: .github + imageName: ghcr.io/mcanouil/eggla + cacheFrom: ghcr.io/mcanouil/eggla + imageTag: ${{github.ref_name}} + platform: linux/amd64 + push: always + runCmd: Rscript eggla-example.R + + - name: Build and run Dev Container + uses: devcontainers/ci@v0.3 + if: github.ref_name != 'main' + with: + subFolder: .github + imageName: ghcr.io/mcanouil/eggla + cacheFrom: ghcr.io/mcanouil/eggla + imageTag: "devel" + platform: linux/amd64 + push: always + runCmd: Rscript eggla-example.R diff --git a/inst/setup/Dockerfile b/inst/setup/Dockerfile deleted file mode 100644 index fc2cdd2a..00000000 --- a/inst/setup/Dockerfile +++ /dev/null @@ -1,79 +0,0 @@ -ARG VARIANT="bullseye" -FROM --platform=linux/amd64 buildpack-deps:${VARIANT}-curl - -LABEL org.opencontainers.image.title="eggla" -LABEL org.opencontainers.image.description="Docker image for the 'eggla' R package." -LABEL org.opencontainers.image.source="https://github.com/mcanouil/eggla" -LABEL org.opencontainers.image.base.name="mcr.microsoft.com/vscode/devcontainers/base:${VARIANT}" - -ARG INSTALL_ZSH="true" -ARG UPGRADE_PACKAGES="true" -ARG USERNAME=eggla -ARG USER_UID=1000 -ARG USER_GID=$USER_UID -COPY inst/setup/common-debian.sh /tmp/library-scripts/ -RUN bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \ - && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts - -# ** [Optional] Uncomment this section to install additional packages. ** -# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ -# && apt-get -y install --no-install-recommends - -RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ - && apt-get -y install --no-install-recommends \ - curl \ - build-essential \ - libcurl4-openssl-dev \ - ca-certificates \ - bash-completion \ - gzip \ - libxt6 \ - bzip2 \ - wget \ - autoconf \ - automake \ - make \ - cmake \ - libbz2-dev \ - liblzma-dev \ - libjpeg-dev \ - libxml2-dev \ - zlib1g-dev \ - libgdal-dev \ - libfontconfig1-dev \ - libharfbuzz-dev \ - libfribidi-dev \ - libv8-dev \ - libudunits2-dev \ - libfftw3-dev - -ARG BCFTOOLS_VERSION=1.16 -RUN wget -q -P /tmp/ https://github.com/samtools/bcftools/releases/download/${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} - -COPY inst/bin/plink2 /usr/bin/plink2 -RUN chmod +x /usr/bin/plink2 - -ARG RIG_VERSION="latest" -ARG R_VERSION="4.2.0" -COPY inst/setup/pkg.lock pkg.lock -RUN wget -q -P /tmp/ "https://github.com/r-lib/rig/releases/download/${RIG_VERSION}/rig-linux-${RIG_VERSION#v}.tar.gz" \ - && tar -C /usr/local -zxvf /tmp/rig-linux-${RIG_VERSION#v}.tar.gz \ - && rig add ${R_VERSION} \ - && Rscript -e "pak::lockfile_install(update = TRUE)" \ - && Rscript -e "pak::pkg_install('mcanouil/eggla', upgrade = FALSE, dependencies = TRUE)" \ - && Rscript -e "pak::cache_clean()" - -COPY inst/setup/eggla-example.R eggla-example.R -RUN chmod +x eggla-example.R - -RUN apt-get autoremove -y \ - && apt-get autoclean -y \ - && rm -rf /var/lib/apt/lists/* \ - && rm -rf /tmp/* diff --git a/inst/setup/common-debian.sh b/inst/setup/common-debian.sh deleted file mode 100644 index 35f06f5b..00000000 --- a/inst/setup/common-debian.sh +++ /dev/null @@ -1,454 +0,0 @@ -#!/usr/bin/env bash -#------------------------------------------------------------------------------------------------------------- -# Copyright (c) Microsoft Corporation. All rights reserved. -# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information. -#------------------------------------------------------------------------------------------------------------- -# -# Docs: https://github.com/microsoft/vscode-dev-containers/blob/main/script-library/docs/common.md -# Maintainer: The VS Code and Codespaces Teams -# -# Syntax: ./common-debian.sh [install zsh flag] [username] [user UID] [user GID] [upgrade packages flag] [install Oh My Zsh! flag] [Add non-free packages] - -set -e - -INSTALL_ZSH=${1:-"true"} -USERNAME=${2:-"automatic"} -USER_UID=${3:-"automatic"} -USER_GID=${4:-"automatic"} -UPGRADE_PACKAGES=${5:-"true"} -INSTALL_OH_MYS=${6:-"true"} -ADD_NON_FREE_PACKAGES=${7:-"false"} -SCRIPT_DIR="$(cd $(dirname "${BASH_SOURCE[0]}") && pwd)" -MARKER_FILE="/usr/local/etc/vscode-dev-containers/common" - -if [ "$(id -u)" -ne 0 ]; then - echo -e 'Script must be run as root. Use sudo, su, or add "USER root" to your Dockerfile before running this script.' - exit 1 -fi - -# Ensure that login shells get the correct path if the user updated the PATH using ENV. -rm -f /etc/profile.d/00-restore-env.sh -echo "export PATH=${PATH//$(sh -lc 'echo $PATH')/\$PATH}" > /etc/profile.d/00-restore-env.sh -chmod +x /etc/profile.d/00-restore-env.sh - -# If in automatic mode, determine if a user already exists, if not use vscode -if [ "${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 [ "${USERNAME}" = "" ]; then - USERNAME=vscode - fi -elif [ "${USERNAME}" = "none" ]; then - USERNAME=root - USER_UID=0 - USER_GID=0 -fi - -# Load markers to see which steps have already run -if [ -f "${MARKER_FILE}" ]; then - echo "Marker file found:" - cat "${MARKER_FILE}" - source "${MARKER_FILE}" -fi - -# Ensure apt is in non-interactive to avoid prompts -export DEBIAN_FRONTEND=noninteractive - -# Function to call apt-get if needed -apt_get_update_if_needed() -{ - if [ ! -d "/var/lib/apt/lists" ] || [ "$(ls /var/lib/apt/lists/ | wc -l)" = "0" ]; then - echo "Running apt-get update..." - apt-get update - else - echo "Skipping apt-get update." - fi -} - -# Run install apt-utils to avoid debconf warning then verify presence of other common developer tools and dependencies -if [ "${PACKAGES_ALREADY_INSTALLED}" != "true" ]; then - - package_list="apt-utils \ - openssh-client \ - gnupg2 \ - dirmngr \ - iproute2 \ - procps \ - lsof \ - htop \ - net-tools \ - psmisc \ - curl \ - wget \ - rsync \ - ca-certificates \ - unzip \ - zip \ - nano \ - vim-tiny \ - less \ - jq \ - lsb-release \ - apt-transport-https \ - dialog \ - libc6 \ - libgcc1 \ - libkrb5-3 \ - libgssapi-krb5-2 \ - libicu[0-9][0-9] \ - liblttng-ust0 \ - libstdc++6 \ - zlib1g \ - locales \ - sudo \ - ncdu \ - man-db \ - strace \ - manpages \ - manpages-dev \ - init-system-helpers" - - # Needed for adding manpages-posix and manpages-posix-dev which are non-free packages in Debian - if [ "${ADD_NON_FREE_PACKAGES}" = "true" ]; then - # Bring in variables from /etc/os-release like VERSION_CODENAME - . /etc/os-release - sed -i -E "s/deb http:\/\/(deb|httpredir)\.debian\.org\/debian ${VERSION_CODENAME} main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME} main contrib non-free/" /etc/apt/sources.list - sed -i -E "s/deb-src http:\/\/(deb|httredir)\.debian\.org\/debian ${VERSION_CODENAME} main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME} main contrib non-free/" /etc/apt/sources.list - sed -i -E "s/deb http:\/\/(deb|httpredir)\.debian\.org\/debian ${VERSION_CODENAME}-updates main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME}-updates main contrib non-free/" /etc/apt/sources.list - sed -i -E "s/deb-src http:\/\/(deb|httpredir)\.debian\.org\/debian ${VERSION_CODENAME}-updates main/deb http:\/\/\1\.debian\.org\/debian ${VERSION_CODENAME}-updates main contrib non-free/" /etc/apt/sources.list - sed -i "s/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main contrib non-free/" /etc/apt/sources.list - sed -i "s/deb-src http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}\/updates main contrib non-free/" /etc/apt/sources.list - sed -i "s/deb http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main/deb http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main contrib non-free/" /etc/apt/sources.list - sed -i "s/deb-src http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main/deb http:\/\/deb\.debian\.org\/debian ${VERSION_CODENAME}-backports main contrib non-free/" /etc/apt/sources.list - # Handle bullseye location for security https://www.debian.org/releases/bullseye/amd64/release-notes/ch-information.en.html - sed -i "s/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main contrib non-free/" /etc/apt/sources.list - sed -i "s/deb-src http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main/deb http:\/\/security\.debian\.org\/debian-security ${VERSION_CODENAME}-security main contrib non-free/" /etc/apt/sources.list - echo "Running apt-get update..." - apt-get update - package_list="${package_list} manpages-posix manpages-posix-dev" - else - apt_get_update_if_needed - fi - - # Install libssl1.1 if available - if [[ ! -z $(apt-cache --names-only search ^libssl1.1$) ]]; then - package_list="${package_list} libssl1.1" - fi - - # Install appropriate version of libssl1.0.x if available - libssl_package=$(dpkg-query -f '${db:Status-Abbrev}\t${binary:Package}\n' -W 'libssl1\.0\.?' 2>&1 || echo '') - if [ "$(echo "$LIlibssl_packageBSSL" | grep -o 'libssl1\.0\.[0-9]:' | uniq | sort | wc -l)" -eq 0 ]; then - if [[ ! -z $(apt-cache --names-only search ^libssl1.0.2$) ]]; then - # Debian 9 - package_list="${package_list} libssl1.0.2" - elif [[ ! -z $(apt-cache --names-only search ^libssl1.0.0$) ]]; then - # Ubuntu 18.04, 16.04, earlier - package_list="${package_list} libssl1.0.0" - fi - fi - - echo "Packages to verify are installed: ${package_list}" - apt-get -y install --no-install-recommends ${package_list} 2> >( grep -v 'debconf: delaying package configuration, since apt-utils is not installed' >&2 ) - - # Install git if not already installed (may be more recent than distro version) - if ! type git > /dev/null 2>&1; then - apt-get -y install --no-install-recommends git - fi - - PACKAGES_ALREADY_INSTALLED="true" -fi - -# Get to latest versions of all packages -if [ "${UPGRADE_PACKAGES}" = "true" ]; then - apt_get_update_if_needed - apt-get -y upgrade --no-install-recommends - apt-get autoremove -y -fi - -# Ensure at least the en_US.UTF-8 UTF-8 locale is available. -# Common need for both applications and things like the agnoster ZSH theme. -if [ "${LOCALE_ALREADY_SET}" != "true" ] && ! grep -o -E '^\s*en_US.UTF-8\s+UTF-8' /etc/locale.gen > /dev/null; then - echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen - locale-gen - LOCALE_ALREADY_SET="true" -fi - -# Create or update a non-root user to match UID/GID. -group_name="${USERNAME}" -if id -u ${USERNAME} > /dev/null 2>&1; then - # User exists, update if needed - if [ "${USER_GID}" != "automatic" ] && [ "$USER_GID" != "$(id -g $USERNAME)" ]; then - group_name="$(id -gn $USERNAME)" - groupmod --gid $USER_GID ${group_name} - usermod --gid $USER_GID $USERNAME - fi - if [ "${USER_UID}" != "automatic" ] && [ "$USER_UID" != "$(id -u $USERNAME)" ]; then - usermod --uid $USER_UID $USERNAME - fi -else - # Create user - if [ "${USER_GID}" = "automatic" ]; then - groupadd $USERNAME - else - groupadd --gid $USER_GID $USERNAME - fi - if [ "${USER_UID}" = "automatic" ]; then - useradd -s /bin/bash --gid $USERNAME -m $USERNAME - else - useradd -s /bin/bash --uid $USER_UID --gid $USERNAME -m $USERNAME - fi -fi - -# Add sudo support for non-root user -if [ "${USERNAME}" != "root" ] && [ "${EXISTING_NON_ROOT_USER}" != "${USERNAME}" ]; then - echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME - chmod 0440 /etc/sudoers.d/$USERNAME - EXISTING_NON_ROOT_USER="${USERNAME}" -fi - -# ** Shell customization section ** -if [ "${USERNAME}" = "root" ]; then - user_rc_path="/root" -else - user_rc_path="/home/${USERNAME}" -fi - -# Restore user .bashrc defaults from skeleton file if it doesn't exist or is empty -if [ ! -f "${user_rc_path}/.bashrc" ] || [ ! -s "${user_rc_path}/.bashrc" ] ; then - cp /etc/skel/.bashrc "${user_rc_path}/.bashrc" -fi - -# Restore user .profile defaults from skeleton file if it doesn't exist or is empty -if [ ! -f "${user_rc_path}/.profile" ] || [ ! -s "${user_rc_path}/.profile" ] ; then - cp /etc/skel/.profile "${user_rc_path}/.profile" -fi - -# .bashrc/.zshrc snippet -rc_snippet="$(cat << 'EOF' - -if [ -z "${USER}" ]; then export USER=$(whoami); fi -if [[ "${PATH}" != *"$HOME/.local/bin"* ]]; then export PATH="${PATH}:$HOME/.local/bin"; fi - -# Display optional first run image specific notice if configured and terminal is interactive -if [ -t 1 ] && [[ "${TERM_PROGRAM}" = "vscode" || "${TERM_PROGRAM}" = "codespaces" ]] && [ ! -f "$HOME/.config/vscode-dev-containers/first-run-notice-already-displayed" ]; then - if [ -f "/usr/local/etc/vscode-dev-containers/first-run-notice.txt" ]; then - cat "/usr/local/etc/vscode-dev-containers/first-run-notice.txt" - elif [ -f "/workspaces/.codespaces/shared/first-run-notice.txt" ]; then - cat "/workspaces/.codespaces/shared/first-run-notice.txt" - fi - mkdir -p "$HOME/.config/vscode-dev-containers" - # Mark first run notice as displayed after 10s to avoid problems with fast terminal refreshes hiding it - ((sleep 10s; touch "$HOME/.config/vscode-dev-containers/first-run-notice-already-displayed") &) -fi - -# Set the default git editor if not already set -if [ -z "$(git config --get core.editor)" ] && [ -z "${GIT_EDITOR}" ]; then - if [ "${TERM_PROGRAM}" = "vscode" ]; then - if [[ -n $(command -v code-insiders) && -z $(command -v code) ]]; then - export GIT_EDITOR="code-insiders --wait" - else - export GIT_EDITOR="code --wait" - fi - fi -fi - -EOF -)" - -# code shim, it fallbacks to code-insiders if code is not available -cat << 'EOF' > /usr/local/bin/code -#!/bin/sh - -get_in_path_except_current() { - which -a "$1" | grep -A1 "$0" | grep -v "$0" -} - -code="$(get_in_path_except_current code)" - -if [ -n "$code" ]; then - exec "$code" "$@" -elif [ "$(command -v code-insiders)" ]; then - exec code-insiders "$@" -else - echo "code or code-insiders is not installed" >&2 - exit 127 -fi -EOF -chmod +x /usr/local/bin/code - -# systemctl shim - tells people to use 'service' if systemd is not running -cat << 'EOF' > /usr/local/bin/systemctl -#!/bin/sh -set -e -if [ -d "/run/systemd/system" ]; then - exec /bin/systemctl "$@" -else - echo '\n"systemd" is not running in this container due to its overhead.\nUse the "service" command to start services instead. e.g.: \n\nservice --status-all' -fi -EOF -chmod +x /usr/local/bin/systemctl - -# Codespaces bash and OMZ themes - partly inspired by https://github.com/ohmyzsh/ohmyzsh/blob/master/themes/robbyrussell.zsh-theme -codespaces_bash="$(cat \ -<<'EOF' - -# Codespaces bash prompt theme -__bash_prompt() { - local userpart='`export XIT=$? \ - && [ ! -z "${GITHUB_USER}" ] && echo -n "\[\033[0;32m\]@${GITHUB_USER} " || echo -n "\[\033[0;32m\]\u " \ - && [ "$XIT" -ne "0" ] && echo -n "\[\033[1;31m\]➜" || echo -n "\[\033[0m\]➜"`' - local gitbranch='`\ - if [ "$(git config --get codespaces-theme.hide-status 2>/dev/null)" != 1 ]; then \ - export BRANCH=$(git symbolic-ref --short HEAD 2>/dev/null || git rev-parse --short HEAD 2>/dev/null); \ - if [ "${BRANCH}" != "" ]; then \ - echo -n "\[\033[0;36m\](\[\033[1;31m\]${BRANCH}" \ - && if git ls-files --error-unmatch -m --directory --no-empty-directory -o --exclude-standard ":/*" > /dev/null 2>&1; then \ - echo -n " \[\033[1;33m\]✗"; \ - fi \ - && echo -n "\[\033[0;36m\]) "; \ - fi; \ - fi`' - local lightblue='\[\033[1;34m\]' - local removecolor='\[\033[0m\]' - PS1="${userpart} ${lightblue}\w ${gitbranch}${removecolor}\$ " - unset -f __bash_prompt -} -__bash_prompt - -EOF -)" - -codespaces_zsh="$(cat \ -<<'EOF' -# Codespaces zsh prompt theme -__zsh_prompt() { - local prompt_username - if [ ! -z "${GITHUB_USER}" ]; then - prompt_username="@${GITHUB_USER}" - else - prompt_username="%n" - fi - PROMPT="%{$fg[green]%}${prompt_username} %(?:%{$reset_color%}➜ :%{$fg_bold[red]%}➜ )" # User/exit code arrow - PROMPT+='%{$fg_bold[blue]%}%(5~|%-1~/…/%3~|%4~)%{$reset_color%} ' # cwd - PROMPT+='$([ "$(git config --get codespaces-theme.hide-status 2>/dev/null)" != 1 ] && git_prompt_info)' # Git status - PROMPT+='%{$fg[white]%}$ %{$reset_color%}' - unset -f __zsh_prompt -} -ZSH_THEME_GIT_PROMPT_PREFIX="%{$fg_bold[cyan]%}(%{$fg_bold[red]%}" -ZSH_THEME_GIT_PROMPT_SUFFIX="%{$reset_color%} " -ZSH_THEME_GIT_PROMPT_DIRTY=" %{$fg_bold[yellow]%}✗%{$fg_bold[cyan]%})" -ZSH_THEME_GIT_PROMPT_CLEAN="%{$fg_bold[cyan]%})" -__zsh_prompt - -EOF -)" - -# Add RC snippet and custom bash prompt -if [ "${RC_SNIPPET_ALREADY_ADDED}" != "true" ]; then - echo "${rc_snippet}" >> /etc/bash.bashrc - echo "${codespaces_bash}" >> "${user_rc_path}/.bashrc" - echo 'export PROMPT_DIRTRIM=4' >> "${user_rc_path}/.bashrc" - if [ "${USERNAME}" != "root" ]; then - echo "${codespaces_bash}" >> "/root/.bashrc" - echo 'export PROMPT_DIRTRIM=4' >> "/root/.bashrc" - fi - chown ${USERNAME}:${group_name} "${user_rc_path}/.bashrc" - RC_SNIPPET_ALREADY_ADDED="true" -fi - -# Optionally install and configure zsh and Oh My Zsh! -if [ "${INSTALL_ZSH}" = "true" ]; then - if ! type zsh > /dev/null 2>&1; then - apt_get_update_if_needed - apt-get install -y zsh - fi - if [ "${ZSH_ALREADY_INSTALLED}" != "true" ]; then - echo "${rc_snippet}" >> /etc/zsh/zshrc - ZSH_ALREADY_INSTALLED="true" - fi - - # Adapted, simplified inline Oh My Zsh! install steps that adds, defaults to a codespaces theme. - # See https://github.com/ohmyzsh/ohmyzsh/blob/master/tools/install.sh for official script. - oh_my_install_dir="${user_rc_path}/.oh-my-zsh" - if [ ! -d "${oh_my_install_dir}" ] && [ "${INSTALL_OH_MYS}" = "true" ]; then - template_path="${oh_my_install_dir}/templates/zshrc.zsh-template" - user_rc_file="${user_rc_path}/.zshrc" - umask g-w,o-w - mkdir -p ${oh_my_install_dir} - git clone --depth=1 \ - -c core.eol=lf \ - -c core.autocrlf=false \ - -c fsck.zeroPaddedFilemode=ignore \ - -c fetch.fsck.zeroPaddedFilemode=ignore \ - -c receive.fsck.zeroPaddedFilemode=ignore \ - "https://github.com/ohmyzsh/ohmyzsh" "${oh_my_install_dir}" 2>&1 - echo -e "$(cat "${template_path}")\nDISABLE_AUTO_UPDATE=true\nDISABLE_UPDATE_PROMPT=true" > ${user_rc_file} - sed -i -e 's/ZSH_THEME=.*/ZSH_THEME="codespaces"/g' ${user_rc_file} - - mkdir -p ${oh_my_install_dir}/custom/themes - echo "${codespaces_zsh}" > "${oh_my_install_dir}/custom/themes/codespaces.zsh-theme" - # Shrink git while still enabling updates - cd "${oh_my_install_dir}" - git repack -a -d -f --depth=1 --window=1 - # Copy to non-root user if one is specified - if [ "${USERNAME}" != "root" ]; then - cp -rf "${user_rc_file}" "${oh_my_install_dir}" /root - chown -R ${USERNAME}:${group_name} "${user_rc_path}" - fi - fi -fi - -# Persist image metadata info, script if meta.env found in same directory -meta_info_script="$(cat << 'EOF' -#!/bin/sh -. /usr/local/etc/vscode-dev-containers/meta.env - -# Minimal output -if [ "$1" = "version" ] || [ "$1" = "image-version" ]; then - echo "${VERSION}" - exit 0 -elif [ "$1" = "release" ]; then - echo "${GIT_REPOSITORY_RELEASE}" - exit 0 -elif [ "$1" = "content" ] || [ "$1" = "content-url" ] || [ "$1" = "contents" ] || [ "$1" = "contents-url" ]; then - echo "${CONTENTS_URL}" - exit 0 -fi - -#Full output -echo -echo "Development container image information" -echo -if [ ! -z "${VERSION}" ]; then echo "- Image version: ${VERSION}"; fi -if [ ! -z "${DEFINITION_ID}" ]; then echo "- Definition ID: ${DEFINITION_ID}"; fi -if [ ! -z "${VARIANT}" ]; then echo "- Variant: ${VARIANT}"; fi -if [ ! -z "${GIT_REPOSITORY}" ]; then echo "- Source code repository: ${GIT_REPOSITORY}"; fi -if [ ! -z "${GIT_REPOSITORY_RELEASE}" ]; then echo "- Source code release/branch: ${GIT_REPOSITORY_RELEASE}"; fi -if [ ! -z "${BUILD_TIMESTAMP}" ]; then echo "- Timestamp: ${BUILD_TIMESTAMP}"; fi -if [ ! -z "${CONTENTS_URL}" ]; then echo && echo "More info: ${CONTENTS_URL}"; fi -echo -EOF -)" -if [ -f "${SCRIPT_DIR}/meta.env" ]; then - mkdir -p /usr/local/etc/vscode-dev-containers/ - cp -f "${SCRIPT_DIR}/meta.env" /usr/local/etc/vscode-dev-containers/meta.env - echo "${meta_info_script}" > /usr/local/bin/devcontainer-info - chmod +x /usr/local/bin/devcontainer-info -fi - -# Write marker file -mkdir -p "$(dirname "${MARKER_FILE}")" -echo -e "\ - PACKAGES_ALREADY_INSTALLED=${PACKAGES_ALREADY_INSTALLED}\n\ - LOCALE_ALREADY_SET=${LOCALE_ALREADY_SET}\n\ - EXISTING_NON_ROOT_USER=${EXISTING_NON_ROOT_USER}\n\ - RC_SNIPPET_ALREADY_ADDED=${RC_SNIPPET_ALREADY_ADDED}\n\ - ZSH_ALREADY_INSTALLED=${ZSH_ALREADY_INSTALLED}" > "${MARKER_FILE}" - -echo "Done!"