standalone-installer-unix

#!/bin/bash
#
# Bash program to download the latest Nextstrain CLI standalone installation
# archive for Linux or macOS, extract it into the current user's app data
# directory, and check if PATH includes the installation destination.
#
# It maintains rough parity with the PowerShell program for Windows,
# standalone-installer-windows.
#
# Set DESTINATION to change the installation location.
#
# Set VERSION to change the version downloaded and installed, or pass the
# desired version as the first argument to this program.
#
set -euo pipefail
shopt -s failglob

: "${NEXTSTRAIN_DOT_ORG:=https://nextstrain.org}"

# Globals declared here to make them more obvious, but set by main() to avoid
# source ordering requirements and delay execution until the full file is
# parsed.
declare VERSION KERNEL TARGET DESTINATION

# Wrap everything in a function which we call at the end to avoid execution of
# a partially-downloaded program.
main() {
    VERSION="${1:-${VERSION:-latest}}"

    KERNEL="${KERNEL:-$(uname -s)}"
    TARGET="${TARGET:-$(target-triple)}"
    DESTINATION="${DESTINATION:-${NEXTSTRAIN_HOME:-$HOME/.nextstrain}/cli-standalone}"

    local archive archive_url tmp

    archive="standalone-${TARGET}.tar.gz"
    archive_url="${NEXTSTRAIN_DOT_ORG}/cli/download/${VERSION}/${archive}"

    # Move into a temporary working dir
    tmp="$(mktemp -d)"
    if ! debug; then
        # shellcheck disable=SC2064
        trap "rm -rf $tmp" EXIT
    fi
    pushd "$tmp" >/dev/null
    log "Temporary working directory: $tmp"

    log "Downloading $archive_url"
    curl "$archive_url" \
        --fail --show-error --location --proto "=https" \
        > "$archive"

    log "Extracting $archive"
    mkdir standalone
    tar xz"$(if-debug v)"f "$archive" -C standalone

    if [[ -d "$DESTINATION" ]]; then
        log "Removing existing $DESTINATION"
        rm -rf "$DESTINATION"
    fi

    log "Installing to $DESTINATION"
    mkdir -p "$(dirname "$DESTINATION")"
    mv standalone "$DESTINATION"

    popd >/dev/null

    if ! debug; then
        log "Cleaning up"
        rm -rf "$tmp"
    fi

    log "Checking installation"
    local installed_version
    if ! installed_version="$("$DESTINATION"/nextstrain --version)"; then
        die "installation check failed: unable to run \`\"$DESTINATION\"/nextstrain --version\`; look for error message above."
    fi

    cat <<~~
______________________________________________________________________________

Nextstrain CLI ($installed_version) installed to $DESTINATION.

~~

    if [[ "$(type -p nextstrain 2>/dev/null)" != "$DESTINATION/nextstrain" ]]; then
        local shell rc
        shell="$(default-shell)"
        rc="$(shell-rc "$shell")"

        cat <<~~
To make the "nextstrain" command available in your default shell ($shell)
without using the full path, please run these two commands now:

    printf '\n%s\n' 'eval "\$("$DESTINATION/nextstrain" init-shell $shell)"' >> $rc
    eval "\$("$DESTINATION/nextstrain" init-shell $shell)"

The first adds a line to your shell initialization file ($rc) for future
sessions.  The second sets up your current shell session.  You only need to run
these once.
~~
    fi
}

target-triple() {
    local machine vendor os

    machine="$(uname -m)"

    case "$KERNEL" in
        Linux)
            [[ "$machine" == x86_64 ]] || die "unsupported architecture: $machine"
            vendor=unknown
            os=linux-gnu
            ;;

        Darwin)
            # Rosetta 2 will not be needed for the standalone version of
            # Nextstrain CLI itself as of 8.2.0.  The Conda runtime still
            # requires it and the Docker runtime can benefit from it, but we
            # now check for it in their setup instead.
            #  -trs, 1 Feb 2024
               version-gte 8.2.0 \
            || [[ "$machine" != arm64 ]] \
            || pgrep -qU _oahd 2>/dev/null \
            || die "Rosetta 2 not enabled.  Please run:"$'\n\n'"    softwareupdate --install-rosetta"$'\n\n'"and then retry this installation of Nextstrain CLI."

            # aarch64 builds will only be available starting with 8.2.0.  Older
            # versions only provide x86_64, which will run under Rosetta.
            case "$machine" in
                x86_64) ;;
                arm64) version-gte 8.2.0 && machine=aarch64 || machine=x86_64;;
                *) die "unsupported architecture: $machine";;
            esac
            vendor=apple
            os=darwin
            ;;

        *)
            die "unknown kernel: $KERNEL"
    esac

    echo "$machine-$vendor-$os"
}

version-gte() {
    local minimum="$1"

    # If $minimum sorts before $VERSION, then $VERSION is at least ≥$minimum.
    # Note that non-numeric values sort by byte order, so "latest" and
    # "pr-build/123" and so on end up after (greater than) a numeric value like
    # 8.1.0.  Both macOS/BSD sort and GNU sort support -V.
    [[ $(printf '%s\n%s\n' "$minimum" "$VERSION" | sort -V | head -n1) == "$minimum" ]]
}

default-shell() {
    local shell

    case "$KERNEL" in
        Linux)
            shell=$(getent passwd "$(id -u)" | awk -F: '{print $NF}');;

        Darwin)
            shell=$(dscl . -read ~/ UserShell | sed 's/UserShell: //');;

        *)
            die "unknown kernel: $KERNEL"
    esac

    shell="$(basename "$shell")"

    # Remove any -x.y version from the name
    echo "${shell%%-*}"
}

shell-rc() {
    local shell="$1"

    # Paths below are presumed to be meta-char safe and returned with
    # unexpanded ~/… prefixes for a nicer appearance in suggested commands,
    # i.e. expansion of ~ is expected to happen after the user pastes and runs
    # the commands, rather than here and now.
    case "$shell" in
        bash)
            case "$KERNEL" in
                Darwin)
                    # macOS Terminal.app (and iTerm2.app) always launches login
                    # shells, i.e. for all windows and tabs, so use the login
                    # initialization file instead of the interactive one
                    # because Bash (unlike zsh) only reads one or the other.
                    # Although it's common practice for users to source their
                    # bashrc from their bash_profile, we can't rely on this.
                    #
                    # The order and conditions on files here follows bash(1) §
                    # INVOCATION:
                    #
                    #   After reading [/etc/profile], [bash] looks for
                    #   ~/.bash_profile, ~/.bash_login, and ~/.profile, in that
                    #   order, and reads and executes commands from the first one
                    #   that exists and is readable.
                    #
                    if [[ -r ~/.bash_profile ]]; then
                        # shellcheck disable=SC2088
                        echo "~/.bash_profile"

                    elif [[ -r ~/.bash_login ]]; then
                        # shellcheck disable=SC2088
                        echo "~/.bash_login"

                    elif [[ -r ~/.profile ]]; then
                        # shellcheck disable=SC2088
                        echo "~/.profile"

                    else
                        # If none exist, then we fallback to ~/.bash_profile
                        # and expect it to be created by our suggested shell
                        # init commands.
                        #
                        # shellcheck disable=SC2088
                        echo "~/.bash_profile"
                    fi;;
                *)
                    # shellcheck disable=SC2088
                    echo "~/.bashrc";;
            esac;;
        zsh)
            echo "${ZDOTDIR:-~}/.zshrc";;
        sh)
            # sh, whether a historic version or bash in sh-compat mode, doesn't
            # use any default startup file for interactive shells.  It only
            # uses a default startup file for login shells.  We'll have to
            # assume here that anyone using sh as their default shell will also
            # be using login shells appropriately.  On macOS, at least, common
            # terminal emulators spawn login shells (see commentary above).
            #   -trs, 26 September 2023

            # shellcheck disable=SC2088
            echo "~/.profile";;
        *)
            # A decent guess?
            #
            # shellcheck disable=SC2088
            echo "~/.${shell}rc";;
    esac
}

debug() {
    [[ -n "${DEBUG:-}" ]]
}

if-debug() {
    if debug; then
        echo "$@"
    fi
}

log() {
    echo "--> $*"
}

die() {
    echo "ERROR:" "$@" >&2
    exit 1
}

main "$@"