From c79b61877b9e4082423b35856f59bad644609a41 Mon Sep 17 00:00:00 2001 From: Yousuf Ali Date: Thu, 5 Jan 2023 15:00:59 -0500 Subject: [PATCH] vscode setting and other file added --- .devcontainer/Dockerfile | 86 ++++ .devcontainer/devcontainer.json | 49 ++ .../library-scripts/common-debian.sh | 454 ++++++++++++++++++ .lintr | 10 + .vscode/cspell.json | 14 + .vscode/settings.json | 26 + 6 files changed, 639 insertions(+) create mode 100644 .devcontainer/Dockerfile create mode 100644 .devcontainer/devcontainer.json create mode 100644 .devcontainer/library-scripts/common-debian.sh create mode 100644 .lintr create mode 100644 .vscode/cspell.json create mode 100644 .vscode/settings.json diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile new file mode 100644 index 0000000..c795327 --- /dev/null +++ b/.devcontainer/Dockerfile @@ -0,0 +1,86 @@ +# [Choice] R version: 4, 4.2, 4.1, 4.0 +ARG VARIANT=4 +# [Choice] Base image. Minimal (r-ver), tidyverse installed (tidyverse), or full image (binder): rocker/r-ver, rocker/tidyverse, rocker/binder +ARG BASE_IMAGE=rocker/r-ver +FROM ${BASE_IMAGE}:${VARIANT} + +# [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=rstudio +ARG USER_UID=1000 +ARG USER_GID=$USER_UID +USER root +COPY library-scripts/*.sh /tmp/library-scripts/ +RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ + && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \ + && usermod -a -G staff ${USERNAME} \ + && apt-get -y install \ + python3-pip \ + libgit2-dev \ + libcurl4-openssl-dev \ + libssl-dev \ + libxml2-dev \ + libxt-dev \ + libfontconfig1-dev \ + libcairo2-dev \ + && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/* /tmp/library-scripts \ + && python3 -m pip --no-cache-dir install radian \ + && install2.r --error --skipinstalled --ncpus -1 \ + devtools \ + languageserver \ + httpgd \ + shiny \ + ggplot2 \ + data.table \ + dplyr \ + shinycssloaders \ + DT \ + officer \ + flextable \ + ggiraph \ + patchwork \ + RSQLite \ + htmltools \ + shinyjs \ + RColorBrewer \ + stringr \ + shinytest2 \ + shinyvalidate \ + + && rm -rf /tmp/downloaded_packages + +# VSCode R Debugger dependency. Install the latest release version from GitHub without using GitHub API. +# See https://github.com/microsoft/vscode-dev-containers/issues/1032 +RUN export TAG=$(git ls-remote --tags --refs --sort='version:refname' https://github.com/ManuelHentschel/vscDebugger v\* | tail -n 1 | cut --delimiter='/' --fields=3) \ + && Rscript -e "remotes::install_git('https://github.com/ManuelHentschel/vscDebugger.git', ref = '"${TAG}"', dependencies = FALSE)" + +# R Session watcher settings. +# See more details: https://github.com/REditorSupport/vscode-R/wiki/R-Session-watcher +RUN echo 'if (interactive() && Sys.getenv("TERM_PROGRAM") == "vscode") source(file.path(Sys.getenv("HOME"), ".vscode-R", "init.R"))' >>"${R_HOME}/etc/Rprofile.site" + +# [Option] Enable vscode-jupyter support +ARG ENABLE_JUPYTER="false" +RUN if [ "${ENABLE_JUPYTER}" = "true" ]; then \ + if [ -z "$(dpkg --get-selections | grep libzmq3-dev)" ]; then \ + apt-get update \ + && export DEBIAN_FRONTEND=noninteractive \ + && apt-get -y install --no-install-recommends libzmq3-dev \ + && apt-get autoremove -y && apt-get clean -y && rm -rf /var/lib/apt/lists/*; \ + fi \ + && install2.r --error --skipinstalled --ncpus -1 IRkernel \ + && rm -rf /tmp/downloaded_packages \ + && python3 -m pip --no-cache-dir install jupyter \ + && R --vanilla -s -e 'IRkernel::installspec(user = FALSE)'; \ + fi + +# [Optional] Uncomment this section to install additional OS packages. +# RUN apt-get update \ +# && export DEBIAN_FRONTEND=noninteractive \ +# && apt-get -y install --no-install-recommends + +# [Optional] Uncomment this section to install additional R packages. +# RUN install2.r --error --skipinstalled --ncpus -1 diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 0000000..d219aab --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,49 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: +// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.0/containers/r +{ + "name": "R (Community)", + "build": { + "dockerfile": "Dockerfile", + "args": { + // Update VARIANT to pick a R version: 4, 4.2, 4.1, 4.0 + "VARIANT": "4.1", + // Start with a minimal image (rocker/r-ver) or a expanded image. + // See more details about rocker/r-ver's derived images: https://github.com/rocker-org/rocker-versioned2 + "BASE_IMAGE": "rocker/r-ver", + // Options + "ENABLE_JUPYTER": "false", + "UPGRADE_PACKAGES": "true" + } + }, + + // Configure tool-specific properties. + "customizations": { + // Configure properties specific to VS Code. + "vscode": { + // Set *default* container specific settings.json values on container create. + "settings": { + "r.rterm.linux": "/usr/local/bin/radian", + "r.bracketedPaste": true, + "r.plot.useHttpgd": true, + "[r]": { + "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?" + } + }, + + // Add the IDs of extensions you want installed when the container is created. + "extensions": [ + "reditorsupport.r", + "rdebugger.r-debugger" + ] + } + }, + + // Use 'forwardPorts' to make a list of ports inside the container available locally. + // "forwardPorts": [], + + // Use 'postCreateCommand' to run commands after the container is created. + // "postCreateCommand": "R --version", + + // Comment out to connect as root instead. More info: https://aka.ms/vscode-remote/containers/non-root. + "remoteUser": "rstudio" +} diff --git a/.devcontainer/library-scripts/common-debian.sh b/.devcontainer/library-scripts/common-debian.sh new file mode 100644 index 0000000..2f36814 --- /dev/null +++ b/.devcontainer/library-scripts/common-debian.sh @@ -0,0 +1,454 @@ +#!/usr/bin/env bash +#------------------------------------------------------------------------------------------------------------- +# Copyright (c) Microsoft Corporation. All rights reserved. +# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information. +#------------------------------------------------------------------------------------------------------------- +# +# Docs: https://github.com/microsoft/vscode-dev-containers/blob/main/script-library/docs/common.md +# Maintainer: The VS Code and Codespaces Teams +# +# Syntax: ./common-debian.sh [install zsh flag] [username] [user UID] [user GID] [upgrade packages flag] [install Oh My Zsh! flag] [Add non-free packages] + +set -e + +INSTALL_ZSH=${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 [ "${PACKAGES_ALREADY_INSTALLED}" != "true" ]; then + + package_list="apt-utils \ + openssh-client \ + gnupg2 \ + dirmngr \ + iproute2 \ + procps \ + lsof \ + htop \ + net-tools \ + psmisc \ + curl \ + wget \ + rsync \ + ca-certificates \ + unzip \ + zip \ + nano \ + vim-tiny \ + less \ + jq \ + lsb-release \ + apt-transport-https \ + dialog \ + libc6 \ + libgcc1 \ + libkrb5-3 \ + libgssapi-krb5-2 \ + libicu[0-9][0-9] \ + liblttng-ust[0-9] \ + libstdc++6 \ + zlib1g \ + locales \ + sudo \ + ncdu \ + man-db \ + strace \ + manpages \ + manpages-dev \ + init-system-helpers" + + # Needed for adding manpages-posix and manpages-posix-dev which are non-free packages in Debian + if [ "${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 $USERNAME + fi +fi + +# Add add sudo support for non-root user +if [ "${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!" diff --git a/.lintr b/.lintr new file mode 100644 index 0000000..fa16b65 --- /dev/null +++ b/.lintr @@ -0,0 +1,10 @@ + + +linters: linters_with_defaults( + line_length_linter(120), + commented_code_linter = NULL, + cyclocomp_linter = NULL, + object_name_linter = NULL, + object_usage_linter = NULL + + ) \ No newline at end of file diff --git a/.vscode/cspell.json b/.vscode/cspell.json new file mode 100644 index 0000000..1960d46 --- /dev/null +++ b/.vscode/cspell.json @@ -0,0 +1,14 @@ +{ + "version": "0.2", + "ignorePaths": ["R", "app.R"], + "dictionaryDefinitions": [], + "dictionaries": [], + "words": [ + "dontrun", + "fread", + "MRHD", + "studyid" + ], + "ignoreWords": [], + "import": [] +} diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000..b0ebae3 --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,26 @@ +{ + "workbench.colorCustomizations": { + "activityBar.activeBackground": "#1f6fd0", + "activityBar.background": "#1f6fd0", + "activityBar.foreground": "#e7e7e7", + "activityBar.inactiveForeground": "#e7e7e799", + "activityBarBadge.background": "#ee90bb", + "activityBarBadge.foreground": "#15202b", + "commandCenter.border": "#e7e7e799", + "sash.hoverBorder": "#1f6fd0", + "statusBar.background": "#1857a4", + "statusBar.foreground": "#e7e7e7", + "statusBarItem.hoverBackground": "#1f6fd0", + "statusBarItem.remoteBackground": "#1857a4", + "statusBarItem.remoteForeground": "#e7e7e7", + "titleBar.activeBackground": "#1857a4", + "titleBar.activeForeground": "#e7e7e7", + "titleBar.inactiveBackground": "#1857a499", + "titleBar.inactiveForeground": "#e7e7e799" + }, + "peacock.color": "#1857a4", + "cSpell.words": [ + "NOAEL", + "pkgload" + ] +} \ No newline at end of file