install.sh

#!/usr/bin/env bash

if [ -z "$BIN_DIR" ]; then
  BIN_DIR=~/.local/bin
fi
if [ -z "$LARVATAGGER_PATH" ]; then
  LARVATAGGER_PATH=~/.local/share/larvatagger
fi

if [ "$1" = "--uninstall" ]; then
  if [ -d "$LARVATAGGER_PATH/MaggotUBA" ]; then
    env=(cd "$LARVATAGGER_PATH/MaggotUBA" && poetry env info -p)
    if [ -d "$env" ]; then
      # clear the virtual environments
      env=$(dirname "$env")
      rm -rf "$env/maggotuba*"
      rm -rf "$env/taggingbackends*"
    fi
  fi
  rm -rf "$BIN_DIR/larvatagger"
  rm -rf "$LARVATAGGER_PATH"
else

if ! command -v curl 1>/dev/null 2>&1; then
  if command -v brew 1>/dev/null 2>&1; then
    # macOS users are not given the choice as they usually do not care about freedom
    brew install curl
  fi
fi
if ! command -v curl 1>/dev/null 2>&1; then
  echo "Command curl required; aborting"
else

if [ "`uname`" = "Darwin" ]; then
  # macOS
  if ! command -v brew 1>/dev/null 2>&1; then
    echo "Installing Homebrew; admin rights will be requested"
    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
  fi
fi

if ! command -v realpath 1>/dev/null 2>&1; then
  # macOS
  if command -v brew 1>/dev/null 2>&1; then
    brew install coreutils
  fi
fi

if ! command -v julia 1>/dev/null 2>&1; then
  if [ -z "$JULIA_INSTALL_ARGS" ]; then
    JULIA_INSTALL_ARGS=-y
  fi
  curl -fsSL https://install.julialang.org | sh -s -- $JULIA_INSTALL_ARGS
  if [ -f ~/.bashrc ]; then
    source ~/.bashrc
  elif [ -f ~/.bash_profile ]; then
    source ~/.bash_profile
  fi
fi

for arg in "$@"; do
  if [ "$arg" = "--with-default-backend" ]; then
    WITH_DEFAULT_BACKEND=1
    break
  fi
done
if [ -n "$WITH_DEFAULT_BACKEND" ]; then
  if [ "`uname`" = "Darwin" ]; then
    echo "WARNING: the default tagging backend does not work on macOS"
  fi
  if ! command -v python3.8 1>/dev/null 2>&1; then
    if command -v pyenv 1>/dev/null 2>&1; then
      pyenv install 3.8
    elif command -v brew 1>/dev/null 2>&1; then
      brew install python@3.8
    else
      echo "WARNING: command python3.8 not found"
      echo "if under Ubuntu, consider running: sudo apt install python3.8 python3.8-venv"
    fi
  fi
  if ! command -v poetry 1>/dev/null 2>&1; then
    if command -v pipx 1>/dev/null 2>&1; then
      pipx install poetry
    else
      curl -fsSL https://install.python-poetry.org | python3 -
    fi
  fi
fi

mkdir -p "$LARVATAGGER_PATH" && pushd $_
##

if [ -d PlanarLarvae ]; then
  echo "PlanarLarvae.jl installation found; skipping"
else
  if [ -z "$PLANARLARVAE_BRANCH" ]; then
    PLANARLARVAE_BRANCH=main
  fi
  curl -fsSL https://gitlab.pasteur.fr/nyx/planarlarvae.jl/-/archive/${PLANARLARVAE_BRANCH}/planarlarvae.jl-${PLANARLARVAE_BRANCH}.tar.gz | tar zxv
  mv planarlarvae.jl-${PLANARLARVAE_BRANCH} PlanarLarvae
fi

if [ -d LarvaTagger.jl ]; then
  echo "LarvaTagger.jl installation found; skipping"
else
  if [ -z "$LARVATAGGER_BRANCH" ]; then
    LARVATAGGER_BRANCH=dev
  fi
  curl -fsSL https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/archive/${LARVATAGGER_BRANCH}/larvatagger.jl-${LARVATAGGER_BRANCH}.tar.gz | tar zxv
  mv larvatagger.jl-${LARVATAGGER_BRANCH} LarvaTagger.jl
fi
(cd LarvaTagger.jl && julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.develop(path="../PlanarLarvae")')

if [ -z "$WITH_DEFAULT_BACKEND" ]; then

cat <<EOF >$BIN_DIR/larvatagger
#!/usr/bin/env bash

"$LARVATAGGER_PATH/LarvaTagger.jl/scripts/larvatagger" \$@
EOF

else

activate() {
  poetry env use 3.8
}

if [ -d TaggingBackends ]; then
  echo "TaggingBackends installation found; skipping"
else
  if [ -z "$TAGGINGBACKENDS_BRANCH" ]; then
    TAGGINGBACKENDS_BRANCH=main
  fi
  curl -fsSL https://gitlab.pasteur.fr/nyx/TaggingBackends/-/archive/${TAGGINGBACKENDS_BRANCH}/TaggingBackends-${TAGGINGBACKENDS_BRANCH}.tar.gz | tar zxv
  mv TaggingBackends-${TAGGINGBACKENDS_BRANCH} TaggingBackends
fi
(cd TaggingBackends && julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.develop(path="../PlanarLarvae")')
(cd TaggingBackends && activate && poetry install)

if [ -d MaggotUBA-core ]; then
  echo "MaggotUBA-core installation found; skipping"
else
  if [ -z "$MAGGOTUBA_CORE_BRANCH" ]; then
    MAGGOTUBA_CORE_BRANCH=main
  fi
  curl -fsSL https://gitlab.pasteur.fr/nyx/maggotuba-core/-/archive/${MAGGOTUBA_CORE_BRANCH}/maggotuba-core-${MAGGOTUBA_CORE_BRANCH}.tar.gz | tar zxv
  mv maggotuba-core-${MAGGOTUBA_CORE_BRANCH} MaggotUBA-core
fi

if [ -d MaggotUBA ]; then
  echo "MaggotUBA installation found; skipping"
else
  if [ -z "$MAGGOTUBA_ADAPTER_BRANCH" ]; then
    MAGGOTUBA_ADAPTER_BRANCH=main
  fi
  curl -fsSL https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter/-/archive/${MAGGOTUBA_ADAPTER_BRANCH}/MaggotUBA-adapter-${MAGGOTUBA_ADAPTER_BRANCH}.tar.gz | tar zxv
  mv MaggotUBA-adapter-${MAGGOTUBA_ADAPTER_BRANCH} MaggotUBA #-adapter
  #ln -s $(realpath MaggotUBA-adapter) MaggotUBA
fi
(cd MaggotUBA && activate && (cat requirements.txt | xargs -I % sh -c 'poetry add "%"') && poetry install -v && poetry remove taggingbackends && poetry add ../TaggingBackends && poetry remove maggotuba-core && poetry add ../MaggotUBA-core)
(cd MaggotUBA && scripts/make_models.jl default)

cat <<EOF >$BIN_DIR/larvatagger
#!/usr/bin/env bash

JULIA_PROJECT="$(realpath "$LARVATAGGER_PATH/TaggingBackends")" BACKENDS_PATH="$LARVATAGGER_PATH" "$LARVATAGGER_PATH/LarvaTagger.jl/scripts/larvatagger" \$@
EOF

fi

chmod a+x "$BIN_DIR/larvatagger"

if ! command -v larvatagger 1>/dev/null 2>&1; then
  # ~/.local/bin not in $PATH?
  if [ "$SHELL" = "/bin/zsh" ]; then
    rcfile=~/.zshrc
  elif [ "$SHELL" = "/bin/bash" ]; then
    if [ -f ~/.bashrc ]; then
      rcfile=~/.bashrc
    elif [ -f ~/.bash_profile ]; then
      rcfile=~/.bash_profile
    fi
  fi
  cat <<"EOF" >>$rcfile

export PATH=$PATH:~/.local/bin
EOF
  export PATH=$PATH:~/.local/bin
fi

##
popd

fi
fi