run_once_install-packages.sh.tmpl

#!/usr/bin/env bash

set -o xtrace -o errexit

safe_expose_remove() {
    environment=$1
    executable=$2
    if [ -d ${HOME}/.pixi/envs/${environment} ]; then
        exposed_exes=$(pixi global list --environment ${environment} | tail -n 3 | head -n 1 | tr ',' '\n')
        if [[ " ${exposed_exes[*]} " =~ [[:space:]]${executable}[[:space:]] ]]; then
            pixi global expose remove ${executable}
        fi
    fi
}

export -f safe_expose_remove

install_global_packages() {
    package_list=$1
    missing_pkgs=$(comm -13 <(ls ${HOME}/.pixi/envs | sort -u) <(sort -u ${package_list}))
    if (($(echo ${missing_pkgs} | wc -w) > 0 )); then
        pixi global install $(echo ${missing_pkgs} | tr '\n' ' ')
    fi
}

export install_global_packages

clean_global_packages() {
    package_list=$1
    uneeded_pkgs=$(comm -12 <(ls ${HOME}/.pixi/envs | sort -u) <(sort -u ${package_list}))
    if (($(echo ${unneeded_pkgs} | wc -w) > 0 )); then
        pixi global uninstall $(echo ${missing_pkgs} | tr '\n' ' ')
    fi
}

export clean_global_packages

inject_packages() {
    environment=$1
    package_list=$2
    missing_pkgs=$(comm -13 <(pixi global list --environment ${environment} | cut -f 1 -d ' ' | head -n -6 | tail -n +3 | sort -u) <(sort -u ${package_list}))
    if (($(echo ${missing_pkgs} | wc -w) > 0 )); then
        pixi global install --environment ${environment} $(echo ${missing_pkgs} | tr '\n' ' ')
    fi
}

export inject_packages

if [ ! -f $HOME/.pixi/bin/pixi ]; then
    curl -fsSL https://pixi.sh/install.sh | bash
    if [ ! -f $HOME/.bashrc ]; then
        echo 'PATH="${HOME}/.pixi/bin:${PATH}"' >> ${HOME}/.bashrc
    else
        if [ ! grep -q 'PATH="${HOME}/.pixi/bin:${PATH}"' < ${HOME}/.bashrc ]; then
            echo 'PATH="${HOME}/.pixi/bin:${PATH}"' >> ${HOME}/.bashrc
        fi
        if [ ! grep -q 'unset FPATH' < ${HOME}/.bashrc ]; then
            echo 'unset FPATH' >> ${HOME}/.bashrc
        fi
    fi
fi

export PATH="$HOME/.pixi/bin:${PATH}"

install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/package_list
safe_expose_remove moreutils combine
safe_expose_remove moreutils parallel
safe_expose_remove util-linux rename
{{ if eq .chezmoi.os "linux" -}}
safe_expose_remove util-linux kill
{{ end }}
install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/conflict_packages
inject_packages perl $HOME/.local/share/chezmoi/dot_config/chezmoi/perl_packages
clean_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/ruby_packages
inject_packages ruby $HOME/.local/share/chezmoi/dot_config/chezmoi/ruby_packages
if [ -z ${SKIP_PYTHON} ]; then
    clean_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/python_packages
    pixi global install python=3.12
    inject_packages python $HOME/.local/share/chezmoi/dot_config/chezmoi/python_packages
fi
if [ -z ${SKIP_R} ]; then
    clean_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/r_packages
    pixi global install r-base=4.4
    inject_packages r-base $HOME/.local/share/chezmoi/dot_config/chezmoi/r_packages
    cp ${HOME}/.local/share/chezmoi/dot_config/chezmoi/Rprofile ${HOME}/.pixi/envs/r-base/lib/R/etc/Rprofile.site
fi
{{ if eq .chezmoi.os "linux" -}}
install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/linux_packages
safe_expose_remove coreutils kill
safe_expose_remove coreutils uptime
install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/conflict_packages_linux
{{ end }}
{{ if eq .chezmoi.os "darwin" -}}
install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/macos_packages
brew update
brew bundle install --file=$HOME/.local/share/chezmoi/dot_config/chezmoi/Brewfile_casks
export FULL_INSTALL=1
{{ end }}
if [ ! -z ${FULL_INSTALL} ]; then
    install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/huge_packages
    install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/large_packages
else
    clean_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/huge_packages
    clean_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/large_packages
fi
{{ if eq .chezmoi.arch "amd64" -}}
    install_global_packages $HOME/.local/share/chezmoi/dot_config/chezmoi/intel_packages
{{ end }}

micromamba shell init --shell=bash $HOME/micromamba
micromamba shell init --shell zsh
micromamba config prepend channels nodefaults
micromamba config prepend channels bioconda
micromamba config prepend channels conda-forge
micromamba config prepend channels dnachun

# Create config files for rstudio
mkdir -p ${HOME}/.config/rstudio
tee ${HOME}/.config/rstudio/database.conf << EOF
directory=${HOME}/.local/var/lib/rstudio-server
EOF

tee ${HOME}/.config/rstudio/rserver.conf << EOF
rsession-which-r=${HOME}/.pixi/envs/r-base/bin/R
auth-none=1
database-config-file=${HOME}/.config/rstudio/database.conf
server-daemonize=0
server-data-dir=${HOME}/.local/var/run/rstudio-server
server-user=${USER}
EOF

# To add
# citation-langserver
# languagetool-code-comments
# ltrs
# pick
# uutils-coreutils
# uutils-findutils
# skywalking-eyes

# Install
if [ ! -d $HOME/.local/share/zinit ]; then
    export NO_INPUT=1
    export NO_ANNEXES=1
    export ZSH_DISABLE_COMPFIX="true"
    bash -c "$(curl --fail --show-error --silent --location https://raw.githubusercontent.com/zdharma-continuum/zinit/HEAD/scripts/install.sh)"
    zsh -c "source $HOME/.zshrc"
fi

if [ ! -d $HOME/.config/base16-shell ]; then
    git clone https://github.com/chriskempson/base16-shell.git $HOME/.config/base16-shell
fi

if [ ! -d $HOME/.tmux/plugins/tpm ]; then
    git clone https://github.com/tmux-plugins/tpm $HOME/.tmux/plugins/tpm
    $HOME/.tmux/plugins/tpm/bin/install_plugins
fi

if [ ! -d $HOME/.config/ranger/plugins/ranger_devicons ]; then
    git clone https://github.com/alexanderjeurissen/ranger_devicons $HOME/.config/ranger/plugins/ranger_devicons
fi