scripts/bootstrap.sh

#!/bin/bash

# This script will install git and conda (if not found on the PATH variable)
#  using micromamba (an 8mb static-linked single-file binary, conda replacement).
# For users who already have git and conda, this step will be skipped.

# This enables a user to install this project without manually installing conda and git.

source ./scripts/functions.sh

set -o pipefail

OS_NAME=$(uname -s)
case "${OS_NAME}" in
    Linux*)     OS_NAME="linux";;
    Darwin*)    OS_NAME="osx";;
    *)          echo "Unknown OS: $OS_NAME! This script runs only on Linux or Mac" && exit
esac

OS_ARCH=$(uname -m)
case "${OS_ARCH}" in
    x86_64*)    OS_ARCH="64";;
    arm64*)     OS_ARCH="arm64";;
    aarch64*)     OS_ARCH="arm64";;
    *)          echo "Unknown system architecture: $OS_ARCH! This script runs only on x86_64 or arm64" && exit
esac

if ! which curl; then fail "'curl' not found. Please install curl."; fi
if ! which tar; then fail "'tar' not found. Please install tar."; fi
if ! which bzip2; then fail "'bzip2' not found. Please install bzip2."; fi

if pwd | grep ' '; then fail "The installation directory's path contains a space character. Conda will fail to install. Please change the directory."; fi

# https://mamba.readthedocs.io/en/latest/installation.html
if [ "$OS_NAME" == "linux" ] && [ "$OS_ARCH" == "arm64" ]; then OS_ARCH="aarch64"; fi

# config
export MAMBA_ROOT_PREFIX="$(pwd)/installer_files/mamba"
INSTALL_ENV_DIR="$(pwd)/installer_files/env"
LEGACY_INSTALL_ENV_DIR="$(pwd)/installer"
MICROMAMBA_DOWNLOAD_URL="https://micro.mamba.pm/api/micromamba/${OS_NAME}-${OS_ARCH}/latest"
umamba_exists="F"

# figure out whether git and conda needs to be installed
if [ -e "$INSTALL_ENV_DIR" ]; then export PATH="$INSTALL_ENV_DIR/bin:$PATH"; fi

PACKAGES_TO_INSTALL=""

if [ ! -e "$LEGACY_INSTALL_ENV_DIR/etc/profile.d/conda.sh" ] && [ ! -e "$INSTALL_ENV_DIR/etc/profile.d/conda.sh" ]; then PACKAGES_TO_INSTALL="$PACKAGES_TO_INSTALL conda python=3.8.5"; fi
if ! hash "git" &>/dev/null; then PACKAGES_TO_INSTALL="$PACKAGES_TO_INSTALL git"; fi

if "$MAMBA_ROOT_PREFIX/micromamba" --version &>/dev/null; then umamba_exists="T"; fi

# (if necessary) install git and conda into a contained environment
if [ "$PACKAGES_TO_INSTALL" != "" ]; then
    # download micromamba
    if [ "$umamba_exists" == "F" ]; then
        echo "Downloading micromamba from $MICROMAMBA_DOWNLOAD_URL to $MAMBA_ROOT_PREFIX/micromamba"

        mkdir -p "$MAMBA_ROOT_PREFIX"
        curl -L "$MICROMAMBA_DOWNLOAD_URL" | tar -xvj -O bin/micromamba > "$MAMBA_ROOT_PREFIX/micromamba"

        if [ "$?" != "0" ]; then
            echo
            echo "EE micromamba download failed"
            echo "EE If the lines above contain 'bzip2: Cannot exec', your system doesn't have bzip2 installed"
            echo "EE If there are network errors, please check your internet setup"
            fail "micromamba download failed"
        fi

        chmod u+x "$MAMBA_ROOT_PREFIX/micromamba"

        # test the mamba binary
        echo "Micromamba version:"
        "$MAMBA_ROOT_PREFIX/micromamba" --version
    fi

    # create the installer env
    if [ ! -e "$INSTALL_ENV_DIR" ]; then
        "$MAMBA_ROOT_PREFIX/micromamba" create -y --prefix "$INSTALL_ENV_DIR" || fail "unable to create the install environment"
    fi
   
    if [ ! -e "$INSTALL_ENV_DIR" ]; then
        fail "There was a problem while installing$PACKAGES_TO_INSTALL using micromamba. Cannot continue."
    fi

    echo "Packages to install:$PACKAGES_TO_INSTALL"

    "$MAMBA_ROOT_PREFIX/micromamba" install -y --prefix "$INSTALL_ENV_DIR" -c conda-forge $PACKAGES_TO_INSTALL
    if [ "$?" != "0" ]; then
        fail "Installation of the packages '$PACKAGES_TO_INSTALL' failed."
    fi
fi