From 29e0f46a46e0762b61237a6c46a0791f27b39fef Mon Sep 17 00:00:00 2001 From: Sebastian Funk Date: Thu, 12 Dec 2024 12:01:33 +0000 Subject: [PATCH 1/3] remove docker action --- .github/workflows/build-and-push-image.yaml | 49 --------------------- 1 file changed, 49 deletions(-) delete mode 100644 .github/workflows/build-and-push-image.yaml diff --git a/.github/workflows/build-and-push-image.yaml b/.github/workflows/build-and-push-image.yaml deleted file mode 100644 index 576c65a82..000000000 --- a/.github/workflows/build-and-push-image.yaml +++ /dev/null @@ -1,49 +0,0 @@ -name: Create and publish a Docker image - -on: - push: - branches: ['release', 'main'] - workflow_dispatch: - -env: - REGISTRY: ghcr.io - IMAGE_NAME: ${{ github.repository }} - -jobs: - build-and-push-image: - runs-on: ubuntu-latest - permissions: - contents: read - packages: write - - steps: - - - name: Cancel previous builds if present - uses: n1hility/cancel-previous-runs@v3 - with: - token: ${{ secrets.GITHUB_TOKEN }} - - - name: Checkout repository - uses: actions/checkout@v4 - - - name: Log in to the Container registry - uses: docker/login-action@v3 - with: - registry: ${{ env.REGISTRY }} - username: ${{ github.actor }} - password: ${{ secrets.GITHUB_TOKEN }} - - - name: Extract metadata (tags, labels) for Docker - id: meta - uses: docker/metadata-action@v5 - with: - images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} - - - name: Build and push Docker image - uses: docker/build-push-action@v6 - with: - context: . - file: ./.devcontainer/Dockerfile - push: true - tags: ${{ steps.meta.outputs.tags }} - labels: ${{ steps.meta.outputs.labels }} From c22ad24fdb89e85e4e1982ed2168b617edaabe3d Mon Sep 17 00:00:00 2001 From: Sebastian Funk Date: Thu, 12 Dec 2024 14:20:37 +0000 Subject: [PATCH 2/3] remove devcontainer dir --- .devcontainer/Dockerfile | 53 --- .devcontainer/devcontainer.json | 44 -- .../library-scripts/common-debian.sh | 450 ------------------ 3 files changed, 547 deletions(-) delete mode 100644 .devcontainer/Dockerfile delete mode 100644 .devcontainer/devcontainer.json delete mode 100644 .devcontainer/library-scripts/common-debian.sh diff --git a/.devcontainer/Dockerfile b/.devcontainer/Dockerfile deleted file mode 100644 index 9318a7091..000000000 --- a/.devcontainer/Dockerfile +++ /dev/null @@ -1,53 +0,0 @@ -# R version: latest, ... ,4.0.1 , 4.0.0 -ARG VARIANT="latest" -FROM rocker/r-ver:${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=$USER_UID -COPY .devcontainer/library-scripts/*.sh /tmp/library-scripts/ -RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \ - && /bin/bash /tmp/library-scripts/common-debian.sh "${INSTALL_ZSH}" "${USERNAME}" "${USER_UID}" "${USER_GID}" "${UPGRADE_PACKAGES}" "true" "true" \ - && usermod -a -G staff ${USERNAME} \ - && apt-get -y install \ - python3-pip \ - libgit2-dev \ - libcurl4-openssl-dev \ - libssl-dev \ - libxml2-dev \ - libxt-dev \ - libmagick++-6.q16-9t64 \ - pandoc \ - libglpk-dev \ - libv8-dev \ - libpng-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 pre-commit \ - && install2.r --error --skipinstalled --repos ${CRAN} --ncpus -1 \ - devtools \ - languageserver \ - git2r \ - precommit \ - tinytex \ - && rm -rf /tmp/downloaded_packages - -# install vscode dev deps -RUN Rscript -e 'devtools::install_github("mdlincoln/docthis")' -RUN Rscript -e 'devtools::install_github("lorenzwalthert/precommit")' -RUN Rscript -e 'devtools::install_github("milesmcbain/fnmate")' -RUN Rscript -e 'devtools::install_github("milesmcbain/datapasta")' - -# install dependencies -COPY . /tmp/package/ -RUN Rscript -e "devtools::install_dev_deps('/tmp/package')" - -## Install the local version of EpiNow2 -Run R CMD INSTALL --no-multiarch --with-keep.source /tmp/package/ diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json deleted file mode 100644 index a3ed4cf45..000000000 --- a/.devcontainer/devcontainer.json +++ /dev/null @@ -1,44 +0,0 @@ -// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at: -// https://github.com/microsoft/vscode-dev-containers/tree/v0.183.0/containers/r -{ - "name": "epinow2", - "image": "ghcr.io/epiforecasts/epinow2/epinow2:latest", - // Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename. - - // Set *default* container specific settings.json values on container create. - "settings": { - "r.rterm.linux": "/usr/local/bin/radian", - "r.bracketedPaste": true, - "r.sessionWatcher": true, - "[r]": { - "editor.wordSeparators": "`~!@#%$^&*()-=+[{]}\\|;:'\",<>/?" - } - }, - - // Add the IDs of extensions you want installed when the container is created. - "extensions": [ - "ikuyadeu.r", - "tomoki1207.pdf", - "ivan-bocharov.stan-vscode", - "github.vscode-pull-request-github", - "formulahendry.code-runner", - "mutantdino.resourcemonitor", - "searking.preview-vscode" - ], - - // 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": "Rscript -e 'precommit::use_precommit()'", - - // 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", - "shutdownAction": "none" -} diff --git a/.devcontainer/library-scripts/common-debian.sh b/.devcontainer/library-scripts/common-debian.sh deleted file mode 100644 index 6d4269eb4..000000000 --- a/.devcontainer/library-scripts/common-debian.sh +++ /dev/null @@ -1,450 +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] - -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 [ "${PACKAGES_ALREADY_INSTALLED}" != "true" ]; then - - PACKAGE_LIST="apt-utils \ - git \ - openssh-client \ - gnupg2 \ - iproute2 \ - procps \ - lsof \ - htop \ - net-tools \ - psmisc \ - curl \ - wget \ - rsync \ - ca-certificates \ - unzip \ - zip \ - nano \ - vim-tiny \ - less \ - jq \ - lsb-release \ - apt-transport-https \ - dialog \ - libc6 \ - libgcc1 \ - libkrb5-3 \ - libgssapi-krb5-2 \ - libicu[0-9][0-9] \ - libstdc++6 \ - zlib1g \ - locales \ - sudo \ - ncdu \ - man-db \ - strace \ - manpages \ - manpages-dev \ - init-system-helpers" - - # Needed for adding manpages-posix and manpages-posix-dev which are non-free packages in Debian - if [ "${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!" From 606e6f3f801f9dfe0365673ca9cb076596088cbc Mon Sep 17 00:00:00 2001 From: Sebastian Funk Date: Thu, 12 Dec 2024 14:20:47 +0000 Subject: [PATCH 3/3] remove reference in the README --- README.Rmd | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.Rmd b/README.Rmd index 60a489d77..404dc479f 100644 --- a/README.Rmd +++ b/README.Rmd @@ -104,8 +104,7 @@ remotes::install_github("epiforecasts/EpiNow2") To build `{EpiNow2}` from source, users will need to configure their C toolchain. This is because `{EpiNow2}` implements the underlying models in Stan (a statistical modelling programming language), which is built on C++. -Each operating system has a different set up procedure. Windows users need to install an appropriate version of [RTools](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows). Mac users can [follow these steps](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Mac), and Linux users can use [this guide](https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux). For -simple deployment/development a prebuilt docker image is also available (see documentation [here](https://github.com/epiforecasts/EpiNow2/wiki/Docker)). +Each operating system has a different set up procedure. Windows users need to install an appropriate version of [RTools](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Windows). Mac users can [follow these steps](https://github.com/stan-dev/rstan/wiki/Configuring-C---Toolchain-for-Mac), and Linux users can use [this guide](https://github.com/stan-dev/rstan/wiki/Configuring-C-Toolchain-for-Linux). ## Resources