.bash_aliases

# export EDITOR='/home/hielke/.linuxbrew/bin/nvim'
# export EDITOR='/bin/nvim'
export EDITOR='/bin/nvim'
export EDITOR="$HOME/.linuxbrew/bin/nvim"
alias vim="$EDITOR"
# alias vi="$EDITOR"
alias vimrc="$EDITOR ~/.vimrc"

vi() {
  local -a args
  local arg file line col input loc from_stdin=0

  # 1. Pull in piped text (traceback, grep output, linter output, ...)
  if [[ ! -t 0 ]]; then
    input=$(cat)
    from_stdin=1
  fi

  # 2. A pasted traceback frame as arguments counts as input too
  if [[ $# -gt 0 && "$*" == *'File "'*'", line '* ]]; then
    input="$input"$'\n'"$*"
    set --
  fi

  # 3. Turn that text into one path:line argument
  if [[ -n $input ]]; then
    input=$(printf '%s\n' "$input" | sed $'s/\033\\[[0-9;]*m//g')   # strip color

    loc=$(printf '%s\n' "$input" | grep -oE 'File "[^"]+", line [0-9]+' | tail -1)
    if [[ -n $loc ]]; then                      # Python frame: innermost wins
      file=${loc#File \"}; file=${file%%\"*}
      line=${loc##*line }
      set -- "$file:$line" "$@"
    else                                        # grep/ruff/pytest: first hit wins
      loc=$(printf '%s\n' "$input" | grep -oE '[^[:space:]:]+:[0-9]+(:[0-9]+)?' | head -1)
      [[ -n $loc ]] && set -- "$loc" "$@"
    fi
  fi

  # 4. Argument munging: path:line[:col] -> +cursor
  for arg in "$@"; do
    if [[ $arg == -* || -e $arg ]]; then
      args+=("$arg"); continue
    fi
    file=${arg%:}
    line= col=
    while [[ $file == *:* && ! -e $file ]]; do
      local num=${file##*:}
      [[ $num =~ ^[0-9]+$ ]] || break
      col=$line; line=$num
      file=${file%:*}
      [[ -n $col ]] && break
    done
    if [[ -n $line ]]; then
      args+=(+"call cursor(${line},${col:-1})|normal! zv" "$file")
    else
      args+=("$arg")
    fi
  done

  # 5. Launch — reattach the terminal if stdin was a pipe
  if (( from_stdin )); then
    command $EDITOR "${args[@]}" < /dev/tty
  else
    command $EDITOR "${args[@]}"
  fi
}

alias pytest="python3 -m pytest"
alias pw="npx playwright test --no-deps"
alias lst="ls -trlh"
alias python2="$HOME/.pyenv/versions/2.7.18/bin/python"

alias bulk="cd $BULK"
alias software="cd $SOURCE_SOFTWARE"
export SACCT_FORMAT="jobid,jobname%70,state,alloccpus,start,elapsed,timelimit,MaxRSS,CPUTime"
alias sacct="sacct --units=M"
export RANDOM_SEED="1234"
alias curlpost='curl --header "Content-Type: application/json" --request POST --data'

export NINJA_STATUS="[%p: %f/%t (%es)] "

# tmux panes
alias ipython3='echo $(tmux display -pt ${TMUX_PANE} "#{pane_index}") > $HOME/.tmux-panes/ipython3; ipython3'
alias matlab='echo $(tmux display -pt ${TMUX_PANE} "#{pane_index}") > $HOME/.tmux-panes/matlab; matlab'

alias awk=bioawk
alias tawk="awk -F '\t' -v OFS='\t'"
alias mtawk="mawk -F '\t' -v OFS='\t'"
alias les="less -S -N -#2"
alias lower="tr '[:upper:]' '[:lower:]'"
alias upper="tr '[:lower:]' '[:upper:]'"
alias blockdistr="sed -i 's/# 0.0.0.0/0.0.0.0/' /etc/hosts"
alias pytest-pudb="pytest --pdbcls=pudb.debugger:Debugger --pdb --capture=no"

alias neofetch="neofetch; sleep infinity;"
# alias crypt="openssl aes-128-cbc -a -A -md md5 -kfile key"
alias noti="yes FINISHED | head | xargs figlet"
alias which="type -a"
alias rot13="tr 'A-Za-z' 'N-ZA-Mn-za-m'"
alias open="xdg-open"

alias parallize="xargs -P `nproc` -0 -n1 -I {} bash -c"
alias freeproc="ps -eo pcpu --no-headers | awk -v P=`nproc` '{S+=\$1}END{print P-S/100}'"
alias freemem="free --giga | sed -n 2p | awk '{print \$NF}'"

alias rs="./src/manage.py runserver"
alias dm="./src/manage.py "
alias dt="DEMAP_TESTING=1 "

alias mountbulk="sshfs -oauto_cache,reconnect,workaround=all hwalinga@sftp.tudelft.nl:/staff-bulk/tnw/BN/SB/Shared/ /data1/bulk/hwalinga/shared"
alias unmountbulk="fusermount -u /data1/bulk/hwalinga/shared"
alias autobulk="unmountbulk;mountbulk"
alias forceautomountbulk="pkill sshfs;autobulk"

alias localmountbulkhome="sshfs -oauto_cache,reconnect,workaround=all hwalinga@sftp.tudelft.nl:/student-homes/w/hwalinga /home/hielke/bulkhome"
alias localunmountbulkhome="fusermount -u /home/hielke/bulkhome"
alias localautobulkhome="localunmountbulkhome;localmountbulkhome"
alias localforceautomountbulkhome="pkill sshfs;localautobulkhome"
alias tudmount="localautobulkhome"

alias apt-install="apt-get --yes -t stretch-backports install"
alias sudo='sudo '
alias ssh='xdotool key F10; ssh'

alias please='sudo $(fc -ln -1)'
alias f='TF_CMD=$(TF_ALIAS=f PYTHONIOENCODING=utf-8 TF_SHELL_ALIASES=$(alias) thefuck $(fc -ln -1 | tail -n 1)) && eval $TF_CMD && print -s $TF_CMD'
# eval $(thefuck --alias f)
# alias f='thefuck $(fc -ln -1)'
alias py=python
alias cleanlatex='rm -f main.{bcf,d,fls,out.make,run.xml,aux.make,auxtarget.make,0-1.log,0-2.log,1-2.log,ps,pdf,log,aux,out,dvi,bbl,blg}'

alias r="/usr/bin/r"
# unalias fd

alias lg='lazygit'

alias fclaude="$HOME/repos/fence/fence -- claude --permission-mode auto"
alias hnterm="~/repos/hnterm/build/bin/hnterm"

export PGDATABASE=cdatest
export RANDOM_SEED="937162211"
export BAT_THEME="GitHub"
export PATH="$HOME/bin:$PATH"
export PATH="$HOME/programs:$PATH"
export PYTHONBREAKPOINT="pudb.set_trace"

export PATH="$HOME/npm/bin:$PATH"
export NODE_PATH="$HOME/home/npm/lib/node_modules"
export GEM_HOME=$HOME/.gem
export PATH="$GEM_HOME/bin:$PATH"

export GREP_COLORS=${GREP_COLOR}
unset GREP_COLOR

# export NO_COLOR=1


# export PATH="/home/hielke/repos/imgur-screenshot:$PATH"

# LESSOPEN="|lesspipe.sh %s"; export LESSOPEN

loadenv() {
    set -a
    source "$1"
    set +a
}

cantrans() {
    curl -H 'accept: application/json' 'http://rest.ensembl.org/lookup/symbol/homo_sapiens/'$1'?expand=1&mane=1' | jq -r '.Transcript[] | select(.is_canonical==1) | .MANE[0].refseq_match'
}
cantrans37() {
    curl -H 'accept: application/json' 'http://grch37.rest.ensembl.org/lookup/symbol/homo_sapiens/'$1'?expand=1&mane=1' | jq -r '.Transcript[] | select(.is_canonical==1) | .MANE[0].refseq_match'
}
cantransen37() {
    curl -H 'accept: application/json' 'http://grch37.rest.ensembl.org/lookup/symbol/homo_sapiens/'$1'?expand=1&mane=1' | jq -r '.Transcript[] | select(.is_canonical==1) | .id'
}

pdfcat() {
    pdftotext $1 -
}

m() {
    man $1 || help2man $1 | man -l -
}
alias man=m

ee () {
    "$@" &! exit;
}

glout() {
    if [[ -t 1 ]]; then
        # output goes to a terminal
        out=xclip
    else
        # output is redirected
        out=cat
    fi
    tmux capture-pane -p -J -S - | sed 's:\s*$::g' | tac |
        awk '/»/{f++} f; f>1 {exit}' |
        tail +4 |
        tac | tail +2 | perl -pe 'chomp if eof'| $out
}
gout() {
    if [[ -t 1 ]]; then
        # output goes to a terminal
        out=xclip
    else
        # output is redirected
        out=cat
    fi
    tmux capture-pane -p -J -S - > /tmp/command-output
    command=$(grep » /tmp/command-output | sed 's/»//; /^\s*$/d' | fzf | sed 's:/:\\/:g' )
    sed -n '/^»'$command'\s*$/,/^»/p' /tmp/command-output |
        head -n -3 | tail -n +2 | perl -pe 'chomp if eof' | $out
}

xcl() {
    /usr/bin/column -t -s $'\t' $1 | less -S -N -#2
}

vimpipe() {
    # http://javascript-ninja.fr/using-vimpipe-to-have-the-power-of-vim-to-manipulate-stdin/
  vim -u NONE -c "exec \"%norm $1\"" -es '+%print|q!' "${2:-/dev/stdin}"
}

how_in() { where="$1"; shift; IFS=+ curl "https://cht.sh/$where/$*"; }

dgrep() {
    awk -v target=$1 '
    BEGIN{spacer=0; ORS="";}
    /^>/{
    if (spacer) { print "\n"; }
    if ($0 ~ target) { spacer=1; next; }
    spacer=0; next;
    }
    spacer
    END{if (spacer) { print "\n"; } }
    ' $2;
}

slugify() {
  echo "$@" | \
  tr '[:upper:]' '[:lower:]' | \
  sed 's/[^a-z0-9]/-/g' | \
  sed 's/--*/-/g' | \
  sed 's/^-//' | \
  sed 's/-$//'
}

revs() {
    [[ -n $1 ]] && { revs <<< $1; return; }
    revseq /dev/stdin /dev/stdout 2>/dev/null | tail -n+2 |
        awk 1 ORS="" && echo
}

translate() { wget -U "Mozilla/5.0" -qO - "http://translate.googleapis.com/translate_a/single?client=gtx&sl=auto&tl=$2&dt=t&q=$(echo $1 | sed "s/[\"'<>]//g")" | sed "s/,,,0]],,.*//g" | awk -F'"' '{print $2, $6}'; }