From 4a07fd16f2a4bad9926cd427302eec1dc06acd77 Mon Sep 17 00:00:00 2001 From: seabbs Date: Thu, 1 Jul 2021 09:53:32 +0000 Subject: [PATCH 1/5] switch to devcontainer --- .Rbuildignore | 1 + .devcontainer/Dockerfile | 39 ++ .devcontainer/devcontainer.json | 41 ++ .../library-scripts/common-debian.sh | 451 ++++++++++++++++++ .github/workflows/check-full.yaml | 2 +- Dockerfile | 13 - 6 files changed, 533 insertions(+), 14 deletions(-) create mode 100644 .devcontainer/Dockerfile create mode 100644 .devcontainer/devcontainer.json create mode 100644 .devcontainer/library-scripts/common-debian.sh delete mode 100644 Dockerfile diff --git a/.Rbuildignore b/.Rbuildignore index a30f3852..4833a33f 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -27,3 +27,4 @@ SMG.md ^.*.pdf$ ^inst/paper$ ^inst/examples$ +^\.devcontainer$ \ No newline at end of file diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 00000000..223a1cbe --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,39 @@ +# R version: latest, ... ,4.0.1 , 4.0.0 +ARG VARIANT="latest" +FROM rocker/verse:${VARIANT} + +# Use the [Option] comment to specify true/false arguments that should appear in VS Code UX +# +# [Option] Install zsh +ARG INSTALL_ZSH="true" +# [Option] Upgrade OS packages to their latest versions +ARG UPGRADE_PACKAGES="false" + +# Install needed packages and setup non-root user. Use a separate RUN statement to add your own dependencies. +ARG USERNAME=vscode +ARG USER_UID=1000 +ARG USER_GID=$USER_UID +COPY library-scripts/*.sh /tmp/library-scripts/ +RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ + && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \ + && usermod -a -G staff ${USERNAME} \ + && apt-get -y install \ + python3-pip \ + libgit2-dev \ + libcurl4-openssl-dev \ + libssl-dev \ + libxml2-dev \ + libxt-dev \ + && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts \ + && python3 -m pip --no-cache-dir install radian \ + && install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \ + devtools \ + languageserver \ + && rm -rf /tmp/downloaded_packages + +# [Optional] Uncomment this section to install additional OS packages. +# RUN apt-get update \ +# && export DEBIAN_FRONTEND=noninteractive \ +# && apt-get -y install --no-install-recommends + +RUN Rscript -e "devtools::install_dev_deps()" diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 00000000..06c14b14 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,41 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: +// https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/r +{ + "name": "R (Community)", + "build": { + "dockerfile": "Dockerfile", + // Update VARIANT to pick a specific R version: latest, ... ,4.0.1 , 4.0.0 + "args": { "VARIANT": "latest" } + }, + + // Set *default* container specific settings.json values on container create. + "settings": { + "r.rterm.linux": "/usr/local/bin/radian", + "r.bracketedPaste": true, + "r.sessionWatcher": true, + "[r]": { + "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?" + } + }, + + // Add the IDs of extensions you want installed when the container is created. + "extensions": [ + "ikuyadeu.r", + "reditorsupport.r-lsp" + ], + + // Use 'forwardPorts' to make a list of ports inside the container available locally. + // "forwardPorts": [], + + // Use 'postCreateCommand' to run commands after the container is created. + // "postCreateCommand": "R --version", + + // Uncomment to use Docker from inside the container. See https://aka.ms/vscode-remote/samples/docker-from-docker. + // "mounts": [ "source=/var/run/docker.sock,target=/var/run/docker.sock,type=bind" ], + + // Uncomment when using a ptrace-based debugger like C++, Go, and Rust + // "runArgs": [ "--cap-add=SYS_PTRACE", "--security-opt", "seccomp=unconfined" ], + + // Comment out connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root. + "remoteUser": "vscode" +} diff --git a/.devcontainer/library-scripts/common-debian.sh b/.devcontainer/library-scripts/common-debian.sh new file mode 100644 index 00000000..009d9e64 --- /dev/null +++ b/.devcontainer/library-scripts/common-debian.sh @@ -0,0 +1,451 @@ +#!/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] + +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=${7:-"false"} + +set -e + +if [ "$(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 + +# 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 +MARKER_FILE="/usr/local/etc/vscode-dev-containers/common" +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 [ "${PACKAGES_ALREADY_INSTALLED}" != "true" ]; then + + PACKAGE_LIST="apt-utils \ + git \ + openssh-client \ + gnupg2 \ + iproute2 \ + procps \ + lsof \ + htop \ + net-tools \ + psmisc \ + curl \ + wget \ + rsync \ + ca-certificates \ + unzip \ + zip \ + nano \ + vim-tiny \ + less \ + jq \ + lsb-release \ + apt-transport-https \ + dialog \ + libc6 \ + libgcc1 \ + libkrb5-3 \ + libgssapi-krb5-2 \ + libicu[0-9][0-9] \ + liblttng-ust0 \ + libstdc++6 \ + zlib1g \ + locales \ + sudo \ + ncdu \ + man-db \ + strace \ + manpages \ + manpages-dev \ + init-system-helpers" + + # Needed for adding manpages-posix and manpages-posix-dev which are non-free packages in Debian + if [ "${ADD_NON_FREE_PACKAGES}" = "true" ]; then + CODENAME="$(cat /etc/os-release | grep -oE '^VERSION_CODENAME=.+$' | cut -d'=' -f2)" + sed -i -E "s/deb http:\/\/(deb|httpredir)\.debian\.org\/debian ${CODENAME} main/deb http:\/\/\1\.debian\.org\/debian ${CODENAME} main contrib non-free/" /etc/apt/sources.list + sed -i -E "s/deb-src http:\/\/(deb|httredir)\.debian\.org\/debian ${CODENAME} main/deb http:\/\/\1\.debian\.org\/debian ${CODENAME} main contrib non-free/" /etc/apt/sources.list + sed -i -E "s/deb http:\/\/(deb|httpredir)\.debian\.org\/debian ${CODENAME}-updates main/deb http:\/\/\1\.debian\.org\/debian ${CODENAME}-updates main contrib non-free/" /etc/apt/sources.list + sed -i -E "s/deb-src http:\/\/(deb|httpredir)\.debian\.org\/debian ${CODENAME}-updates main/deb http:\/\/\1\.debian\.org\/debian ${CODENAME}-updates main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb http:\/\/security\.debian\.org\/debian-security ${CODENAME}\/updates main/deb http:\/\/security\.debian\.org\/debian-security ${CODENAME}\/updates main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb-src http:\/\/security\.debian\.org\/debian-security ${CODENAME}\/updates main/deb http:\/\/security\.debian\.org\/debian-security ${CODENAME}\/updates main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb http:\/\/deb\.debian\.org\/debian ${CODENAME}-backports main/deb http:\/\/deb\.debian\.org\/debian ${CODENAME}-backports main contrib non-free/" /etc/apt/sources.list + sed -i "s/deb-src http:\/\/deb\.debian\.org\/debian ${CODENAME}-backports main/deb http:\/\/deb\.debian\.org\/debian ${CODENAME}-backports main contrib non-free/" /etc/apt/sources.list + echo "Running apt-get update..." + apt-get update + PACKAGE_LIST="${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="${PACKAGE_LIST} libssl1.1" + fi + + # Install appropriate version of libssl1.0.x if available + LIBSSL=$(dpkg-query -f '${db:Status-Abbrev}\t${binary:Package}\n' -W 'libssl1\.0\.?' 2>&1 || echo '') + if [ "$(echo "$LIBSSL" | 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 ${PACKAGE_LIST} 2> >( grep -v 'debconf: delaying package configuration, since apt-utils is not installed' >&2 ) + + PACKAGES_ALREADY_INSTALLED="true" +fi + +# Get to latest versions of all packages +if [ "${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. +if id -u ${USERNAME} > /dev/null 2>&1; then + # User exists, update if needed + if [ "${USER_GID}" != "automatic" ] && [ "$USER_GID" != "$(id -G $USERNAME)" ]; then + groupmod --gid $USER_GID $USERNAME + 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 $USERNAME + fi +fi + +# Add add sudo support for non-root user +if [ "${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/${USERNAME}" +fi + +# .bashrc/.zshrc snippet +RC_SNIPPET="$(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 + +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 "$@" +else + echo "code or code-insiders is not installed" >&2 + exit 127 +fi +EOF +chmod +x /usr/local/bin/code + +# systemctl shim - tells people to use 'service' if systemd is not running +cat << 'EOF' > /usr/local/bin/systemctl +#!/bin/sh +set -e +if [ -d "/run/systemd/system" ]; then + exec /bin/systemctl/systemctl "$@" +else + echo '\n"systemd" is not running in this container due to its overhead.\nUse the "service" command to start services intead. 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='`\ + export BRANCH=$(git rev-parse --abbrev-ref HEAD 2>/dev/null); \ + if [ "${BRANCH}" = "HEAD" ]; then \ + export BRANCH=$(git describe --contains --all HEAD 2>/dev/null); \ + fi; \ + if [ "${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`' + local lightblue='\[\033[1;34m\]' + local removecolor='\[\033[0m\]' + PS1="${userpart} ${lightblue}\w ${gitbranch}${removecolor}\$ " + unset -f __bash_prompt +} +__bash_prompt + +EOF +)" +CODESPACES_ZSH="$(cat \ +<<'EOF' +__zsh_prompt() { + local prompt_username + if [ ! -z "${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_prompt_info)%{$fg[white]%}$ %{$reset_color%}' # Git status + unset -f __zsh_prompt +} +ZSH_THEME_GIT_PROMPT_PREFIX="%{$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="%{$fg_bold[cyan]%})" +__zsh_prompt +EOF +)" + +# Add notice that Oh My Bash! has been removed from images and how to provide information on how to install manually +OMB_README="$(cat \ +<<'EOF' +"Oh My Bash!" has been removed from this image in favor of a simple shell prompt. If you +still wish to use it, remove "~/.oh-my-bash" and install it from: https://github.com/ohmybash/oh-my-bash +You may also want to consider "Bash-it" as an alternative: https://github.com/bash-it/bash-it +See here for infomation on adding it to your image or dotfiles: https://aka.ms/codespaces/omb-remove +EOF +)" +OMB_STUB="$(cat \ +<<'EOF' +#!/usr/bin/env bash +if [ -t 1 ]; then + cat $HOME/.oh-my-bash/README.md +fi +EOF +)" + +# Add RC snippet and custom bash prompt +if [ "${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 ${USERNAME}:${USERNAME} "${USER_RC_PATH}/.bashrc" + RC_SNIPPET_ALREADY_ADDED="true" +fi + +# Add stub for Oh My Bash! +if [ ! -d "${USER_RC_PATH}/.oh-my-bash}" ] && [ "${INSTALL_OH_MYS}" = "true" ]; then + mkdir -p "${USER_RC_PATH}/.oh-my-bash" "/root/.oh-my-bash" + echo "${OMB_README}" >> "${USER_RC_PATH}/.oh-my-bash/README.md" + echo "${OMB_STUB}" >> "${USER_RC_PATH}/.oh-my-bash/oh-my-bash.sh" + chmod +x "${USER_RC_PATH}/.oh-my-bash/oh-my-bash.sh" + if [ "${USERNAME}" != "root" ]; then + echo "${OMB_README}" >> "/root/.oh-my-bash/README.md" + echo "${OMB_STUB}" >> "/root/.oh-my-bash/oh-my-bash.sh" + chmod +x "/root/.oh-my-bash/oh-my-bash.sh" + fi + chown -R "${USERNAME}:${USERNAME}" "${USER_RC_PATH}/.oh-my-bash" +fi + +# Optionally install and configure zsh and Oh My Zsh! +if [ "${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 ${USERNAME}:${USERNAME} "${USER_RC_PATH}" + fi + fi +fi + +# Persist image metadata info, script if meta.env found in same directory +META_INFO_SCRIPT="$(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: ${CONTENTS_URL}"; fi +echo +EOF +)" +SCRIPT_DIR="$(cd $(dirname $0) && pwd)" +if [ -f "${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!" diff --git a/.github/workflows/check-full.yaml b/.github/workflows/check-full.yaml index 1ade1938..e238e96a 100644 --- a/.github/workflows/check-full.yaml +++ b/.github/workflows/check-full.yaml @@ -291,5 +291,5 @@ jobs: uses: docker/build-push-action@v2 with: context: . - push: true + file: .devcontainer/Dockerfile push: true tags: docker.pkg.github.com/epiforecasts/covidregionaldata/covidregionaldata:latest diff --git a/Dockerfile b/Dockerfile deleted file mode 100644 index c1a1930b..00000000 --- a/Dockerfile +++ /dev/null @@ -1,13 +0,0 @@ -## Start with the latest tidyvere (verse) image - once development is complete -## needs to be version locked with tags -## verse has pdf related tools built in (i.e latex) -FROM rocker/verse:latest - -## Copy files to working directory of server -ADD . /home/rstudio/covidregionaldata - -## Set working directory to be this folder -WORKDIR /home/rstudio/covidregionaldata - -## Install missing packages. -RUN Rscript -e "devtools::install_dev_deps()" From c030f17e03cc0976f3638706a4977e031453b64c Mon Sep 17 00:00:00 2001 From: seabbs Date: Thu, 1 Jul 2021 09:58:13 +0000 Subject: [PATCH 2/5] update naming and add docthis --- .devcontainer/Dockerfile | 7 +++++++ .devcontainer/devcontainer.json | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 223a1cbe..2df7c905 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -36,4 +36,11 @@ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ # && export DEBIAN_FRONTEND=noninteractive \ # && apt-get -y install --no-install-recommends +# install dependencies RUN Rscript -e "devtools::install_dev_deps()" + +# configure precommit +RUN Rscript -e "precommit::install_precommit(); precommit::use_precommit()" + +# add docthis +RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")' \ No newline at end of file diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 06c14b14..5e518d4f 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -1,7 +1,7 @@ // For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: // https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/r { - "name": "R (Community)", + "name": "covidregionaldata", "build": { "dockerfile": "Dockerfile", // Update VARIANT to pick a specific R version: latest, ... ,4.0.1 , 4.0.0 From ae46da44e0ff6d0055ad66e620ff7162beaddd2a Mon Sep 17 00:00:00 2001 From: Sam Abbott Date: Thu, 1 Jul 2021 11:05:19 +0100 Subject: [PATCH 3/5] Update check-full.yaml --- .github/workflows/check-full.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/check-full.yaml b/.github/workflows/check-full.yaml index e238e96a..8e759ccf 100644 --- a/.github/workflows/check-full.yaml +++ b/.github/workflows/check-full.yaml @@ -291,5 +291,6 @@ jobs: uses: docker/build-push-action@v2 with: context: . - file: .devcontainer/Dockerfile push: true + file: .devcontainer/Dockerfile + push: true tags: docker.pkg.github.com/epiforecasts/covidregionaldata/covidregionaldata:latest From 49deed2e7342a6e6ba9d5e212ce78f9af975ef25 Mon Sep 17 00:00:00 2001 From: seabbs Date: Thu, 1 Jul 2021 11:56:19 +0000 Subject: [PATCH 4/5] docker build working --- .devcontainer/Dockerfile | 19 ++++++++++--------- .devcontainer/devcontainer.json | 3 ++- 2 files changed, 12 insertions(+), 10 deletions(-) diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile index 2df7c905..5060a065 100644 --- a/.devcontainer/Dockerfile +++ b/.devcontainer/Dockerfile @@ -11,9 +11,9 @@ ARG UPGRADE_PACKAGES="false" # Install needed packages and setup non-root user. Use a separate RUN statement to add your own dependencies. ARG USERNAME=vscode -ARG USER_UID=1000 +ARG USER_UID=1100 ARG USER_GID=$USER_UID -COPY library-scripts/*.sh /tmp/library-scripts/ +COPY .devcontainer/library-scripts/*.sh /tmp/library-scripts/ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \ && usermod -a -G staff ${USERNAME} \ @@ -24,11 +24,14 @@ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ libssl-dev \ libxml2-dev \ libxt-dev \ - && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts \ - && python3 -m pip --no-cache-dir install radian \ - && install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \ + && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts + +RUN python3 -m pip --no-cache-dir install radian pre-commit +RUN install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \ devtools \ languageserver \ + precommit \ + git2r \ && rm -rf /tmp/downloaded_packages # [Optional] Uncomment this section to install additional OS packages. @@ -37,10 +40,8 @@ RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ # && apt-get -y install --no-install-recommends # install dependencies -RUN Rscript -e "devtools::install_dev_deps()" - -# configure precommit -RUN Rscript -e "precommit::install_precommit(); precommit::use_precommit()" +COPY DESCRIPTION /tmp/package/DESCRIPTION +RUN Rscript -e "devtools::install_dev_deps('/tmp/package')" # add docthis RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")' \ No newline at end of file diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 5e518d4f..9c3b5319 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -5,7 +5,8 @@ "build": { "dockerfile": "Dockerfile", // Update VARIANT to pick a specific R version: latest, ... ,4.0.1 , 4.0.0 - "args": { "VARIANT": "latest" } + "args": { "VARIANT": "latest" }, + "context": ".." }, // Set *default* container specific settings.json values on container create. From 6dc82c0c60bb7f35a9043fe9b462f5b30de48013 Mon Sep 17 00:00:00 2001 From: seabbs Date: Thu, 1 Jul 2021 12:23:59 +0000 Subject: [PATCH 5/5] update prec-commit --- .pre-commit-config.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4cf6f352..1018538f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -2,7 +2,7 @@ # R specific hooks: https://github.com/lorenzwalthert/precommit repos: - repo: https://github.com/lorenzwalthert/precommit - rev: v0.1.3 + rev: v0.1.3.9014 hooks: - id: style-files args: [--style_pkg=styler, --style_fun=tidyverse_style] @@ -40,7 +40,7 @@ repos: - id: no-browser-statement - id: deps-in-desc - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v3.4.0 + rev: v4.0.1 hooks: - id: check-added-large-files args: ['--maxkb=800']