bashrc

shopt -s globstar

alias R='R --no-restore '

alias bc='bc -l'
alias cp='cp -iv'
( command -v duckdb >/dev/null 2>&1 ) && alias ddb='duckdb '
alias e='vim --ttyfail'
[[ "$(uname -s)" = 'Linux' ]] && alias ls='ls --quoting-style=shell-always --time-style="long-iso" '
alias l='ls '
alias la='ls -a'
if [[ "$(uname -s)" = "Darwin" ]]; then
  alias ll='ls -l -D "%Y-%m-%d %H:%M:%S" '
  alias lla='ls -la -D "%Y-%m-%d %H:%M:%S" '
  alias llh='ls -lh -D "%Y-%m-%d %H:%M:%S" '
else
  alias ll='ls -l'
  alias lla='ls -la'
  alias llh='ls -lh'
fi
alias mv='mv -iv'
alias rm='rm -iv'
[[ -f "${HOME}/.sqliterc" ]] && alias sqlite3='sqlite3 -init ${HOME}/.sqliterc '
alias tree="tree --gitignore -I '*.pyc' -I '__init__.py*' -I '__pycache__' "
## alias sudo='sudo -v; sudo '
alias v="view -c 'map <SPACE> <C-F>zz' -c 'map b <C-B>zz' -c 'map q :q<CR>' "
alias view="view -c 'map <SPACE> <C-F>zz' -c 'map b <C-B>zz' -c 'map q :q<CR>' "

# fix some typos
alias sl='ls'
alias c='cd'
alias vo='vim --ttyfail'
alias ci='vim --ttyfail'
alias iv='vim --ttyfail'
alias grpe='grep'
alias Grep='grep'
alias les='less'
alias Les='less'
alias Less='less'
alias cd.='cd .'
alias cd..='cd ..'
[[ "$(uname -s)" == "Linux" && $(command -v xsel) ]] && alias pbcopy='xsel --clipboard --input' pbpaste='xsel --clipboard --output'

## ## This only works in zsh!
## # Make piping easier...
## # $ ls -la LL
## # $ ls -la VV
## alias VV=' |& view -'
## alias LL=' |& less'

git-branch-info() {
  local branch sha res
  branch="$(git symbolic-ref --short HEAD 2>/dev/null)"
  sha="$(git rev-parse --short=10 HEAD 2>/dev/null)"
  if [[ -n "${branch}" ]]; then
    res="$(printf "(%s - %s)" "${branch}" "${sha}")"
  else
    res=""
  fi
  echo "${res}"
}

upgradeoutdated() {
  local sys=$(grep "^ID=" /etc/os-release | tr -d $'"') cmd=""
  case "${sys##*=}" in
    ("ubuntu" | "debian") cmd="sudo DEBIAN_FRONTEND=noninteractive apt-get update --yes && sudo DEBIAN_FRONTEND=noninteractive apt-get upgrade --yes && sudo DEBIAN_FRONTEND=noninteractive apt-get autoclean --yes && sudo DEBIAN_FRONTEND=noninteractive apt-get autoremove --yes" ;;
    ("amzn") cmd="sudo yum update --assumeyes && sudo yum clean all --assumeyes && sudo yum autoremove --assumeyes" ;;
    ("alpine") cmd="sudo apk update && sudo apk upgrade" ;;
    ("freebsd") cmd="sudo pkg update && sudo pkg upgrade --yes && sudo freebsd-update fetch install" ;;
    (*) cmd="echo 'Do not know how to upgrade this system.'";;
  esac
  echo -e "Will run: ${cmd//&& /&& \\ '\n'}\n"
  eval "${cmd}"
}

updatecondaenvs() {
  local env="" envs=() red=$(tput setaf 1) green=$(tput setaf 2) bold=$(tput bold) reset=$(tput sgr0)
  micromamba self-update
  ## for env in $(conda env list | awk '!/^#/{print $1}'); do
  envs=( $(micromamba env list --quiet | awk 'NR>2{print $1}') )
  for env in "${envs[@]}"; do
    micromamba update --all --yes --quiet --name "${env}"
    printf "%b\n" "Updated micromamba environment:   ${bold}${green}${env}${reset}"
  done
}

# replace alias date=date -u -Iseconds
date() {
  if [[ ${#@} == 0 ]]; then
    command date -u -Iseconds
  else
    command date "${@}"
  fi
}

removeduplicates() {
    ## Use this to remove duplicates from PATH and MANPATH
    ## Call it like:
    ##
    ##
    ## $ removeduplicates ${PATH} : | tr ':' '\n'
    ## $ # compare the above with echo ${PATH} | tr ':' '\n'
    ##
    ## $ export PATH=$(removeduplicates ${PATH} :)
    echo -n "$1" | awk -v RS="$2" -v ORS="$2" '{if (!arr[$0]++) {print $0}}' | sed -e "s@$2\$@@"
}

export PROMPT_DIRTRIM=7
export PS1='\u@\h [SHLVL: ${SHLVL}]: \w\n[jobs: \j] $(git-branch-info) \$ '
export EDITOR="vim"
export VISUAL="${EDITOR}"

## Neat idea from https://github.com/jessfraz/dotfiles/blob/master/.bashrc
for file in ~/.{aliases,functions,path,dockerfunc,extra,exports}; do
    if [[ -r ${file} ]] && [[ -f ${file} ]]; then
        source "${file}"
    fi
done
unset file

## #### ## Some very useful functions
## ## following from https://www.datafix.com.au/cookbook/functions.html
## fields() { head -n 1 "$1" | tr "\t" "\n" | nl -w1 | pr -t -2; }
## broken() { awk -F"\t" '{print NF}' "$1" | sort | uniq -c | sed 's/^[ ]*//;s/ /\t/' | sort -nr; }
## recbyfld() { paste <(head -n1 "$1" | tr '\t' '\n') <(sed -n "$2p" "$1" | tr '\t' '\n') | nl ; }
## tally() { tail -n +2 "$1" | cut -f"$2" | sort | uniq -c | sed 's/^[ ]*//;s/ /\t/'; }
## csv2tsv() {
##   sed 's/""/@@@/g' "$1" | awk -v FPAT='[^,]*|"[^"]*"' -v OFS="\t" '{$1=$1; gsub(/"/,""); print}' | sed 's/\t@@@\t/\t\t/g;s/@@@/"/g' > tsv_"$1"
## }
## tsv2csv() {
##   sed 's/\t/","/g;s/^/"/;s/$/"/' "$1" > "$2"
## }
vf() {
  if which fzf 2>/dev/null 1>&2 ; then
    export FZF_DEFAULT_OPTS='--height 40% --border'
    vim -o "$(fzf --reverse --preview='head -n 10 {}' --preview-window=up:10)"
  else
    vim
  fi
}

if [[ ! -x $(command -v pandoc) ]]; then
  pandoc() {
    docker run -ti --rm --volume "$(pwd):/data" --user "$(id -u):$(id -g)" pandoc/latex:3.1 "$@"
  }
fi

[[ -z "${TIME_STYLE}" ]] && export TIME_STYLE="long-iso"
[[ -z "${QUOTING_STYLE}" ]] && export QUOTING_STYLE="shell-always"

## Some Python related stuff
## export PYTHONOPTIMIZE=2  ## causes lots of scripts to break (especially in ubuntu and miniconda)
## export PYTHONWARNINGS=error ## Should be set, at least, during developing...
## export PYTHONPROFILEIMPORTTIME=true ## ditto
## export PYTHONUTF8=1 ## aspire to uncomment this!
export PYTHONSAFEPATH=1 ## don't add pwd to sys.path. To avoid custom code execution/injection!

## gdal related ... see https://gdal.org/gdal.pdf
export GDAL_CACHE_MAX=512
case "$(uname)" in
  "Linux")  export GDAL_NUM_THREADS=$(( $(nproc) - 2 )) ;;
  "Darwin") export GDAL_NUM_THREADS=$(( $(sysctl -n hw.physicalcpu) - 2 )) ;;
  "*")      export GDAL_NUM_THREADS=2 ;;
esac
export NUM_THREADS=${GDAL_NUM_THREADS}
## export OPJ_NUM_THREADS=${GDAL_NUM_THREADS} # typo? 2023.04.21
export COMPRESS=LERC_ZSTD
export PREDICTOR=3
export ZLEVEL=5
export ZSTD_LEVEL=7
export PG_USE_COPY=YES
# https://trac.osgeo.org/gdal/wiki/ConfigOptions#GDAL_DISABLE_READDIR_ON_OPEN
# export GDAL_DISABLE_READDIR_ON_OPEN=YES
export GDAL_DISABLE_READDIR_ON_OPEN=EMPTY_DIR
export GDAL_MAX_RAW_BLOCK_CACHE_SIZE=200000000
export GDAL_SWATH_SIZE=200000000
export VSI_CURL_CACHE_SIZE=200000000
## Dask related
# Dask searches for all environment variables that start with DASK_, then transforms keys by converting to lower case and changing double-underscores to nested structures.
export DASK_ARRAY__CHUNK_SIZE="128 MiB"
export DASK_DISTRIBUTED__WORKERS__MEMORY__SPILL=0.85
export DASK_DISTRIBUTED__WORKERS__MEMORY__TARGET=0.75
export DASK_DISTRIBUTED__WORKERS__MEMORY__TERMINATE=0.98
export PGTZ='utc'
export PGDATESTYLE='ISO,MDY'
export RUSTFLAGS="-C link-arg=-fuse-ld=lld"

postpath() {
  for d in $@; do
    case "${PATH}" in
      *${d}*) ;;
      *) [[ -d "$d" ]] && export PATH=${PATH:+${PATH}:}$d ;;
    esac
  done
}

prepath() {
  for d in $@; do
    case "${PATH}" in
      *${d}*) ;;
      *) [[ -d "$d" ]] && export PATH=${d}${PATH:+:${PATH}} ;;
    esac
  done
}

[[ -d "${HOME}/VROOT" ]] && export VROOT="${HOME}/VROOT" VIRTUALROOT="${HOME}/VROOT"
postpath "${VROOT}/bin" "${HOME}/.local/bin" "${HOME}/go/bin"

[[ -f "${HOME}/.ripgreprc" ]] && export RIPGREP_CONFIG_PATH="${HOME}/.ripgreprc"

hadolint() { docker run --rm -i --mount type=bind,src="$(pwd)",dst=/app --workdir /app hadolint/hadolint "$@" ; }
ocaml() { docker run --rm -it --mount type=bind,src="$(pwd)",dst=/app --workdir /app ocaml/opam ocaml "$@" ; }
node() { docker run --rm -it --mount type=bind,src="$(pwd)",dst=/app --workdir /app node "$@" ; }
julia() { docker run --rm -it --mount type=bind,src="$(pwd)",dst=/app,ro --workdir /app julia "$@" ; }