phd

#!/usr/bin/env bash

PHD_VERSION="0.1"

PHD_GDOC_ID_MEETING_MINUTES=12Y79ci74ykhVJuS7kOQc5ge44owl4E4ntQK8Osy8fRE
PHD_GDOC_ID_REVIEW_FEEDBACK=1_HWrqVFU-W8_mq_OHjr4h2wzBfMor7yjy3rcX-Cs_JU
PHD_GDOC_ID_AUTHORSHIP_STMT=1LDKBHWtG_LV8v0TPnjjtPMAiorSfe4-B6njSHXIhdyY
PHD_GHUB_ID_PAPERS_TEMPLATE="https://github.com/alexcu/papers-template"
PHD_GHUB_TEMPLATE_GIT="https://github.com/alexcu/phd-template.git"
PHD_GHUB_TOOLS_GIT="https://github.com/alexcu/phd-tools.git"

OVERLEAF_URL="https://www.overleaf.com/project"

ANSI_BOLD=1
ANSI_ITALIC=3
ANSI_UNDERLINE=4
ANSI_RED=31
ANSI_YELLOW=33
ANSI_GREEN=32
ansi ()
{
  echo -e "\033[${1}m${*:2}\033[0m";
}

checkcmd ()
{
  if ! command -v "$1" &> /dev/null; then
    return 1
  else
    return 0
  fi
}

sethelp ()
{
  if [[ "$HELP_ON" -eq 0 ]]; then
    while read; do
      echo "$REPLY"
    done
    exit 0
  fi
}

chdir ()
{
  pushd "$1" > /dev/null || (ansi $ANSI_RED "Cannot work within '$1'. Please report this error." >&2 && exit 1)
}

unchdir ()
{
  popd > /dev/null || (ansi $ANSI_RED "Cannot return to previous working directory. Please report this error." >&2 && exit 1)
}

write_config ()
{
  cat > "$PHD_CONFIG" <<- EOF
PHD_GDIR_ID_AUTHSTMTS=$PHD_GDIR_ID_AUTHSTMTS
PHD_GDIR_ID_MEETINGS=$PHD_GDIR_ID_MEETINGS
PHD_GDIR_ID_REVIEWS=$PHD_GDIR_ID_REVIEWS
EOF
  chmod +x "$PHD_CONFIG"
}

get_gdir_id_retval=0
get_gdir_id ()
{
  local folder_name=$1
  local parent_folder_name=$2
  local gdrive_website="http://drive.google.com/"

  if [[ -n "$parent_folder_name" ]]; then
    local parent_folder_name_prompt=" (under '$parent_folder_name')"
  fi

  ansi $ANSI_BOLD "The '$folder_name' folder is not yet known to PhD Tools."
cat <<- EOF

PhD Tools will open Google Drive in your web browser and ask you to copy the URL
of the folder '$folder_name'$parent_folder_name_prompt. Once Google Drive is opened, please return back to
your terminal for further instructions...

EOF
  read -rp "Press enter now to open Google Drive..."

  open $gdrive_website

  ansi $ANSI_BOLD "\nWhat is URL of the Google Drive Folder named '$folder_name'$parent_folder_name_prompt?"
  cat <<- EOF

Navigate to PhD folder stored within Google Drive and then double-click to the
'$folder_name' folder$parent_folder_name_prompt. Then copy the URL from the
address bar and paste it at the prompt below.

EOF
  while [[ -z "$gdir_url" ]]; do
    read -rp "Please enter the URL to the '$folder_name' folder$parent_folder_name_prompt: " gdir_url
  done

  get_gdir_id_retval=$(basename "$gdir_url")
}

copy_gdoc_template ()
{
  local source_template_id=$1
  local destination_folder_id=$2
  local title=$3
  local gdoc_type=$4
  [[ -z $4 ]] && gdoc_type="document" || gdoc_type=$4
  local url="https://docs.google.com/$gdoc_type/d/$source_template_id/copy?id=$source_template_id&copyCollaborators=false&copyComments=false&includeResolvedCommentsOnCopy=false&title=$title&copyDestination=$destination_folder_id"

  read -rp "About to create a new document named '$title'. Press enter to continue..."
  open "$url"
}

setup ()
{
  if ! checkcmd "brew"; then
    echo "Homembrew missing. Installing Homebrew..."
    /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
    if checkcmd "brew" -ne 0; then
      ansi $ANSI_RED "ERROR: Homebrew didn't install properly. Try installing this yourself." >&2
      exit 1
    fi
  fi
  if ! checkcmd "gh"; then
    echo "GitHub CLI missing. Installing GitHub CLI via Homebrew..."
    ansi $ANSI_ORANGE "WARN: Please ensure you have a GitHub account!"
    brew install gh
    if [[ "$?" -ne 0 ]]; then
      ansi $ANSI_RED "ERROR: Could not install gh command via brew. Try installing this yourself." >&2
      exit 1
    fi
  fi
  if ! checkcmd "greadlink"; then
    echo "Coreutils missing. Installing coreutils via Homebrew..."
    brew install coreutils
    if [[ "$?" -ne 0 ]]; then
      ansi $ANSI_RED "ERROR: Could not install coreutils command via brew. Try installing this yourself." >&2
      exit 1
    fi
  fi
  if [[ ! -f "$PHD_CONFIG" || ! -x "$PHD_CONFIG" ]]; then
    echo "Config file missing or not executable. Creating new one at $PHD_CONFIG..."
    write_config
  fi
}

install ()
{
  local gdfs_mount_dir="/Volumes/GoogleDrive/My Drive"
  local gbas_mount_dir="$HOME/Google Drive"

  local gdfs_download_url="https://dl.google.com/drive-file-stream/googledrivefilestream.dmg"
  local gbas_download_url="https://dl.google.com/drive/InstallBackupAndSync.dmg"

  local gdfs_brew_formula="google-drive-file-stream"
  local gbas_brew_formula="google-backup-and-sync"

  local gdfs_exists=1
  local gbas_exists=1

  local steps=7

  ansi $ANSI_BOLD "(1/$steps) Checking if Google Drive File System (GDFS) is mounted..."
  if [[ ! -d "$gdfs_mount_dir" ]]; then
    ansi $ANSI_YELLOW "WARN: Google Drive File System (GDFS) does not seem to be mounted in the default"
    ansi $ANSI_YELLOW "      directory of '$gdfs_mount_dir'. Please ensure you have"
    ansi $ANSI_YELLOW "      installed GDFS and are logged into your GSuite account, or use GB&S."
  else
    ansi $ANSI_GREEN "OKAY: GDFS is mounted at $gdfs_mount_dir."
    local gdfs_exists=0
  fi
  ansi $ANSI_BOLD "(2/$steps) Checking for Google Backup and Sync (GB&S) directory..."
  if [[ ! -d "$gbas_mount_dir" ]]; then
    ansi $ANSI_YELLOW "WARN: Google Backup and Sync (GB&S) does not seem to be mounted in the default"
    ansi $ANSI_YELLOW "      directory of '$gbas_mount_dir'. Please ensure you have"
    ansi $ANSI_YELLOW "      installed GB&S and are logged into your Google account, or use GDFS."
  else
    ansi $ANSI_GREEN "OKAY: GB&S is mounted at ~/GoogleDrive."
    local gbas_exists=0
  fi
  if [[ "$gdfs_exists" -eq 1 && "$gbas_exists" -eq 1 ]]; then
    ansi $ANSI_RED "ERROR: You don't seem to have either GDFS or GB&S installed. You need this to" >&2
    ansi $ANSI_RED "       create relevant Google Docs." >&2
    cat >&2 <<- EOF
       Please install either one at the following first, then try again.

       Download URLs:

       - GDFS: $gdfs_download_url
       - GB&S: $gbas_download_url

       Or install via Homebrew:

       - GDFS: brew install $gdfs_brew_formula
       - GB&S: brew install $gbas_brew_formula

       Note that GDFS requires a GSuite Team, while GB&S is free up to 15GB.
EOF
    exit 1
  fi

  PHD_BASEDIR=""
  local confirm=""

  while [[ ! "$confirm" == "y" ]]; do
    ansi $ANSI_BOLD "(3/$steps) Where do you want to store your PhD base directory?"
    cat <<- EOF

PhD Tools works with Google Drive and needs to be in a GDFS or GB&S directory.
E.g., '$gdfs_mount_dir/PhD' or '$gbas_mount_dir/PhD'.

EOF
    if [[ "$gdfs_exists" -eq 0 ]]; then
      read -rp "Enter a PhD base directory now ['$gdfs_mount_dir/PhD']: " PHD_BASEDIR
      PHD_BASEDIR=${PHD_BASEDIR:-"$gdfs_mount_dir/PhD"}
    elif [[ "$gbas_exists" -eq 0 ]]; then
      read -rp "Enter a PhD base directory now ['$gbas_mount_dir/PhD']: " PHD_BASEDIR
      PHD_BASEDIR=${PHD_BASEDIR:-"$gbas_mount_dir/PhD"}
    fi

    if [[ -d "$PHD_BASEDIR" ]]; then
      ansi $ANSI_YELLOW "WARN: There is already a directory at $PHD_BASEDIR. It *will* be deleted!"
    fi

    read -rp "Your PhD base directory is '$PHD_BASEDIR'. Are you sure this is correct (y/n)? " confirm
  done

  PHD_SCRIPTDIR="$PHD_BASEDIR/Scripts"

  rm -rf "$PHD_BASEDIR"
  git clone --depth=1 --branch=master "$PHD_GHUB_TEMPLATE_GIT" "$PHD_BASEDIR"
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not clone PhD template repo $PHD_GHUB_TEMPLATE_GIT. Try cloning this yourself and report this bug." >&2
    exit 1
  fi
  rm -rf "$PHD_BASEDIR/.git"
  find "$PHD_BASEDIR" -name "*.keep" -type f -delete

  git clone --depth=1 --branch=master "$PHD_GHUB_TOOLS_GIT" "$PHD_SCRIPTDIR"
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not clone PhD tools repo $PHD_GHUB_TOOLS_GIT. Try cloning this yourself and report this bug." >&2
    exit 1
  fi

  ansi $ANSI_GREEN "OKAY: Set up your PhD base directory at '$PHD_BASEDIR'."

  ansi $ANSI_BOLD "(4/$steps) Installing necessary software..."
  PHD_CONFIG="$PHD_SCRIPTDIR/config"
  setup

  ansi $ANSI_BOLD "(5/$steps) Logging you into GitHub CLI..."
  gh auth login

  ansi $ANSI_BOLD "(6/$steps) Linking phd to /usr/local/bin..."
  ln -nsf "$PHD_SCRIPTDIR/phd" /usr/local/bin/phd

  ansi $ANSI_BOLD "(7/$steps) Ensuring all scripts executable..."
  chmod +x /usr/local/bin/phd
  find "$PHD_SCRIPTDIR" ! -name ".*" -type f -exec chmod +x {} \;

  ansi $ANSI_GREEN "Successfully installed PhD tools!"
  unset PHD_INSTALLER
  phd help

  return 0
}

find_pub_retval=""
find_pub ()
{
  local pubkey=$1
  if [[ -z "$pubkey" ]]; then
    return 1
  fi
  find_pub_retval=$(find "$PHD_PAPERSDIR" -name "$pubkey" | grep -v arxiv)
  return 0
}

unique_pubkey ()
{
  local pubkey=$1
  existing_pubkeys=$(find "$PHD_PAPERSDIR" -name "$pubkey" 2> /dev/null | wc -l)
  if [[ "$existing_pubkeys" -gt 0 ]]; then
    ansi $ANSI_RED "ERROR: A pubkey with a name '$pubkey' already exists. Please try again." >&2
    echo "Location: $(find "$PHD_PAPERSDIR" -name "$pubkey")."
    return 1
  fi
  return 0
}

pubkeywizard_retval=""
pubkeywizard ()
{
  while [[ -z "$result" ]]; do
    local venue=""
    local year=""
    local suffix=""
    local result=""
    local confirm=""

    while [[ -z "$venue" ]]; do
      ansi $ANSI_BOLD "(1/3) What is the abbreviation of the venue are you intending to publish at?"
      cat << EOF
For example, this could be 'FSE' for Foundations of Software Engineering. If the
intended venue does not have an abbreviation (e.g., 'IEEE Software') then type
in the full name of the venue. If you do not have a venue yet, use 2–3 keywords
unique to your PhD instead (e.g., 'systematic review').

EOF
      read -rp "Enter in an abbreviation: " venue
    done

    ansi $ANSI_BOLD "(2/3) Are you publishing at the same venue twice this year?"
    cat << EOF
For example, if you are publishing at two different tracks at the same venue,
such as a demonstrations track and a industry track, you can enter in 'demo' and
'industry' here. Or if you are submitting two papers to the same track, you can
add in an additional keyword here (e.g., 'slr').

EOF
    read -rp "Enter in a suffix if needed, or hit enter now to leave blank: " suffix

    while [[ -z "$year" ]]; do
      ansi $ANSI_BOLD "(3/3) What year do you intend to publish this work?"
      cat << EOF
If you aren't sure yet (e.g., you aren't sure which venue you are publishing at)
then simply enter the current year.

EOF
      read -rp "Enter in a year: " year
    done

    if [[ -z "$suffix" ]]; then
      pubkey="$venue$year"
    else
      pubkey="$venue-$suffix$year"
    fi
    pubkey=$(echo "$pubkey" | tr "[:upper:]" "[:lower:]" | tr ' ' '-')

    if ! unique_pubkey "$pubkey"; then
      exit 1
    fi

    while [[ -z "$confirm" ]]; do
      read -rp "Your publication key is '$pubkey'. Do you wish to use this pubkey (y/n)?" confirm
      if [[ "$confirm" == "y" ]]; then
        result="$pubkey"
      fi
    done
  done
  pubkeywizard_retval=$result
}

clonepub ()
{
  sethelp <<- EOF
Usage: phd clonepub pubkey [newpubkey]

Clones an existing publication repo with the existing publication key, or
pubkey, as a pubkey. If no new pubkey is provided, then a wizard will help
you select a new pubkey.
EOF

  local pubkey=$1
  if [[ -z "$pubkey" ]]; then
    ansi $ANSI_RED "ERROR: No pubkey provided! See help." >&2
    exit 1
  fi

  if ! find_pub "$pubkey"; then
    ansi $ANSI_RED "ERROR: No such publication with pubkey '$pubkey' exists." >&2
    exit 1
  fi

  local newpubkey=$2
  if [[ -z $newpubkey ]]; then
    pubkeywizard
    newpubkey=$pubkeywizard_retval
  fi
  if ! unique_pubkey "$newpubkey"; then
    exit 1
  fi

  local steps=5

  local pubdir
  local new_pubdir
  find_pub "$pubkey"
  pubdir="$find_pub_retval"
  new_pubdir="$(dirname "$find_pub_retval")/$newpubkey"

  ansi $ANSI_BOLD "(1/$steps) Creating a new repo '$newpubkey' with flag 'inprogress'..."
  chdir "$PHD_PAPERSDIR/inprogress"
  gh repo create "$newpubkey" -y --private
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not create a repo. Please report this issue." >&2
    exit 1
  fi
  unchdir

  ansi $ANSI_BOLD "(2/$steps) Copying files from '$pubkey' to '$newpubkey'..."
  rsync -avq --exclude='.git' "$pubdir/" "$new_pubdir"

  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not execute rsync command. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(3/$steps) Renaming '$pubkey.tex' to '$newpubkey.tex'..."
  mv "$new_pubdir/$pubkey.tex" "$new_pubdir/$newpubkey.tex"

  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not remame '$pubkey.tex' to '$newpubkey.tex'. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(4/$steps) Pushing copied files to GitHub under repo '$newpubkey'..."
  chdir "$new_pubdir"
  # gh repo create does not honour its own config setting!
  if [[ $(gh config get git_protocol) == "ssh" ]]; then
    echo "Updating Git remote origin URL to use ssh..."
    local gh_ssh_url=$(git config --get remote.origin.url | gsed -E "s/https:\/\/github.com\//git@github.com:/g")
    git remote set-url origin "$gh_ssh_url"
  fi
  git add .
  git commit -am "Intial commit from repo clone of '$pubkey'"
  git push origin master
  unchdir

  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not push '$newpubkey' to GitHub. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_GREEN "Pushed copied files to '$newpubkey'!"
  ansi $ANSI_BOLD "(5/$steps) Please import repo '$newpubkey' into a new Overleaf project"
  cat <<- EOF
To continue, import the repository from GitHub into Overleaf by clicking on the
'New Project' button in the top left, then 'Import from GitHub' and search for
the repository named '$newpubkey'.

EOF

  read -rp "Press enter now to open Overleaf..."
  open "$OVERLEAF_URL"

  ansi $ANSI_GREEN "Done! Your paper '$oldpubkey' was cloned to '$newpubkey'."
}

renamepub ()
{
  sethelp <<- EOF
Usage: phd renamepub oldpubkey [newpubkey]

Renames an existing publication repo with the existing publication key, or
pubkey, to a new pubkey. If no new pubkey is provided, then a wizard will help
you select a new pubkey.
EOF
  local oldpubkey=$1
  if [[ -z "$oldpubkey" ]]; then
    ansi $ANSI_RED "ERROR: No pubkey provided! See help." >&2
    exit 1
  fi

  if ! find_pub "$oldpubkey"; then
    ansi $ANSI_RED "ERROR: No such publication with pubkey '$oldpubkey' exists." >&2
    exit 1
  fi

  local steps=6

  local newpubkey=$2
  if [[ -z $newpubkey ]]; then
    pubkeywizard
    newpubkey=$pubkeywizard_retval
  fi
  if ! unique_pubkey "$newpubkey"; then
    exit 1
  fi

  local old_pubdir
  local new_pubdir
  find_pub "$oldpubkey"
  old_pubdir="$find_pub_retval"
  new_pubdir="$(dirname "$find_pub_retval")/$newpubkey"

  ansi $ANSI_BOLD "(1/$steps) Renaming '$oldpubkey' to '$newpubkey' locally..."
  mv "$old_pubdir" "$new_pubdir"
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not execute mv command. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(2/$steps) Renaming '$oldpubkey.tex' to '$newpubkey.tex'..."
  mv "$new_pubdir/$oldpubkey.tex" "$new_pubdir/$newpubkey.tex"
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not rename '$oldpubkey.tex' to '$newpubkey.tex' command. Please report this." >&2
    exit 1
  fi

  chdir "$new_pubdir"
  ansi $ANSI_BOLD "(3/$steps) Commiting change of name and pushing to GitHub..."
  git add "$newpubkey.tex"
  git commit -am "Rename '$oldpubkey.tex' to '$newpubkey.tex'"
  git push origin master

  ansi $ANSI_BOLD "(4/$steps) Updating remote GitHub 'origin' URL for '$newpubkey'"
  local old_gitremote
  local new_gitremote
  old_gitremote=$(git config --get remote.origin.url)
  new_gitremote=$(echo "$old_gitremote" | gsed -E "s/[^/]+\.git$/$newpubkey\.git/g")
  git remote set-url origin "$new_gitremote"
  unchdir

  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not push changes to GitHub. Please report this." >&2
    exit 1
  fi

  local gh_repo
  local gh_open_settings
  gh_repo=$(echo "$old_gitremote" |  gsed -E "s/^[^:]+:([^:]+)\.git$/\1/g")
  gh_open_settings="https://github.com/$gh_repo/settings"
  ansi $ANSI_BOLD "(5/$steps) Please update GitHub settings to rename the repo '$oldpubkey' to '$newpubkey'"
  cat <<- EOF
To continue, you must open up GitHub's settings page for the old repo named
'$oldpubkey' and manually change its repo name to '$newpubkey'.

If you are not sure how to rename a GitHub repo, please refer to:
https://bit.ly/2JaAKYm.

EOF
  read -rp "Press enter to open the GitHub settings page for this repo..."
  open "$gh_open_settings"

  ansi $ANSI_BOLD "(6/$steps) Please rename Overleaf project from '$oldpubkey' to '$newpubkey'"
  cat <<- EOF
To continue, you must open up the Overleaf Dashboard, click on the checkbox
next to the project listed as '$oldpubkey', then click 'More' (in the top
righthand corner), and then click 'Rename'. Please ensure you set the new name
to '$newpubkey'.

For more details on how to rename an Overleaf project, please refer to:
https://bit.ly/2HBakyi.

EOF
  read -rp "Press enter now to open Overleaf..."
  open "$OVERLEAF_URL"
  ansi $ANSI_GREEN "Done! Your paper '$oldpubkey' was renamed to '$newpubkey'."
}

newpub ()
{
  sethelp <<- EOF
Usage: phd newpub [pubkey]

Sets up a new repo and relevant subdirectories for a new paper you wish to work
on. A publication key (pubkey) is a unique identifier for a publication. Follow
the below guidelines to form a pubkey:

  1. Use the abbreviation of your venue lowercased and, if applicable
     hyphenated (e.g., 'icse' or 'ieee-software'). If you don't have an intended
     venue yet, think of the primary contribution of your paper and hyphenate it
     (e.g., 'systematic-review').
  2. Append any additional info if you plan to submit two papers at the same
     venue (e.g., a demonstrations track could have a suffix 'demo').
  3. Use the year the intended publication will be published (e.g., '2020'). Use
     the current year if you do not have an intended publication year (yet).
  4. Hyphenate (1) and (2) if applicable, and add the year at the end
     (e.g., 'ieee-software2020' or 'icse-demo2020').

If no pubkey is provided, then a small wizard will help you generate one. Once
you have an intended venue, it is advised you update it.
EOF
  local pubkey=$1
  if [[ -z $pubkey ]]; then
    pubkeywizard
    pubkey=$pubkeywizard_retval
  fi

  if ! unique_pubkey "$pubkey"; then
    exit 1
  fi

  local steps=6

  ansi $ANSI_BOLD "(1/$steps) Creating a new repo '$pubkey' on GitHub..."
  chdir "$PHD_PAPERSDIR/inprogress"
  gh repo create "$pubkey" -y --private --template $PHD_GHUB_ID_PAPERS_TEMPLATE
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not create a repo. Please report this issue." >&2
    exit 1
  fi
  unchdir

  ansi $ANSI_GREEN "Created '$pubkey' on GitHub and set up on '$PHD_PAPERSDIR/inprogress."

  ansi $ANSI_BOLD "(2/$steps) Pulling down contents of '$pubkey' from GitHub..."
  chdir "$PHD_PAPERSDIR/inprogress/$pubkey"

  # gh repo create does not honour its own config setting!
  if [[ $(gh config get git_protocol) == "ssh" ]]; then
    echo "Updating Git remote origin URL to use ssh..."
    local gh_ssh_url=$(git config --get remote.origin.url | gsed -E "s/https:\/\/github.com\//git@github.com:/g")
    git remote set-url origin "$gh_ssh_url"
  fi

  git pull origin master
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not pull contents of repo '$pubkey.tex'. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(3/$steps) Renaming template 'main.tex' to '$pubkey.tex'..."
  mv main.tex "$pubkey.tex"
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not rename 'main.tex' to '$pubkey.tex' command. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(4/$steps) Removing 'README.md'..."
  rm README.md
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not remove 'README.md'. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(5/$steps) Commiting changes and pushing to GitHub..."
  git commit -am "Remove template README.md"
  git add "$pubkey.tex"
  git commit -am "Rename 'main.tex' to '$pubkey.tex'"
  git push origin master
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not push changes to GitHub. Please report this." >&2
    exit 1
  fi
  unchdir

  ansi $ANSI_BOLD "(6/$steps) Please import repo '$pubkey' into a new Overleaf project"
  cat <<- EOF
To continue, import the repository from GitHub into Overleaf by clicking on the
'New Project' button in the top left, then 'Import from GitHub' and search for
the repository named '$pubkey'.

EOF

  read -rp "Press enter now to open Overleaf..."
  open "$OVERLEAF_URL"

  ansi $ANSI_GREEN "Done! Please refer to https://github.com/alexcu/papers-template on how to use the template."
}

flagpub ()
{
  sethelp <<- EOF
Usage: phd flagpub pubkey [abandonded|inprogress|published|rejected]

Moves the publication with the given pubkey to the new directory to indicate its
status of publication.
EOF
  local pubkey=$1
  local flag=$2

  case "$flag" in
  abandoned)  ;;
  inprogress) ;;
  published)  ;;
  rejected)   ;;
  arxiv)  ansi $ANSI_RED "ERROR: Please use the arxivpub command for this purpose." >&2 && exit 1 ;;
  *) ansi $ANSI_RED "ERROR: Unknown flag or no flag provided." >&2 && exit 1 ;;
  esac

  if ! find_pub "$pubkey"; then
    ansi $ANSI_RED "ERROR: No such publication with pubkey '$pubkey' exists." >&2
    exit 1
  fi

  local pubdir="$find_pub_retval"
  mv "$pubdir" "$PHD_PAPERSDIR/$flag"
  ansi $ANSI_GREEN "Moved '$pubkey' to '$flag' papers"
}

arxivpub ()
{
  sethelp <<- EOF
Usage: phd arxiv pubkey

Prepares the publication with the pubkey provided for submission to arXiv by
removing all comments and consolidating all .tex files (using \input) into a
single file, main.tex. Zips these files up ready to be uploaded to arXiv.
EOF
  local pubkey=$1
  if ! find_pub "$pubkey"; then
    ansi $ANSI_RED "ERROR: No such publication with pubkey '$pubkey' exists." >&2
    exit 1
  fi
  local pubdir="$find_pub_retval"
  local arxiv_dir="$PHD_PAPERSDIR/arxiv/$pubkey"
  local arxiv_zip="$PHD_PAPERSDIR/arxiv/$pubkey.zip"

  if [[ -d "$arxiv_dir" || -f "$arxiv_zip" ]]; then
    ansi $ANSI_YELLOW "WARN: There seems to be an arXiv folder for '$pubkey'."
    ansi $ANSI_YELLOW "      This *will* be deleted along with any associated ZIPs."
    read -rp "Press enter to continue, or Ctrl+C to stop..."
    rm -rf "$arxiv_dir" "$arxiv_zip"
  fi

  local steps=6

  ansi $ANSI_BOLD "(1/$steps) Making arXiv directory at $arxiv_dir..."
  mkdir "$arxiv_dir"

  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not create directory '$arxiv_dir'. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(2/$steps) Copying all non-TeX files over..."
  rsync -avq --exclude='.git' --exclude='*.tex' --exclude='*.bib' "$pubdir/" "$arxiv_dir"

  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not rsync correctly. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(3/$steps) Merging all TeX files into '$pubkey.tex' with all comments stripped..."

  chdir "$pubdir"
  local recursiveinputawk="$PHD_SCRIPTDIR/recursiveinput.awk"
  export PHD_RECUSRIVE_INPUT_AWK=\"$recursiveinputawk\"
  "$recursiveinputawk" "$pubkey.tex" 2> /dev/null | gsed '/\s*%/d' | cat -s > "$arxiv_dir/$pubkey.tex"
  unset PHD_RECUSRIVE_INPUT_AWK
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not compile merged TeX file. Please report this." >&2
    exit 1
  fi
  unchdir

  ansi $ANSI_BOLD "(4/$steps) arXiv requires all .bbl files to be added for each .bib file"
  local bib_files
  local bbl_files
  local count_bibs
  bib_files=$(ls -1 "$pubdir"/*.bib)
  count_bibs=$(echo "$bib_files" | wc -l | gsed "s/\s//g")
  bbl_files=$(echo "$bib_files" | gsed -E "s/.bib/.bbl/g")
  cat <<-EOF
You have $count_bibs .bib files. Please open up the project '$pubkey' in
Overleaf and *recompile* your project. Next, click on the 'Logs & Output Files'
button (the page icon) next to the 'Recompile' button. Scroll to the bottom of
the logs. At the bottom righthand corner, click 'Other logs & files' and
download all $count_bibs of the following .bbl file(s):

$bbl_files

Place the $count_bibs .bbl file(s) into $arxiv_dir. Note that Overleaf will name
the default bbl file as output.bbl.

EOF
  read -rp "Press enter now to open Overleaf..."
  open "$OVERLEAF_URL"

  read -rp "Press enter once you have placed all $count_bibs .bbl file(s) in $arxiv_dir..."
  while [ ! -f "$arxiv_dir/output.bbl" ]; do
    ansi $ANSI_YELLOW "WARN: There does not seem to be the default 'output.bbl' downloaded from"
    ansi $ANSI_YELLOW "      Overleaf in the directory '$arxiv_dir'. Please ensure this is placed"
    ansi $ANSI_YELLOW "      along with any other .bbl files downloaded from Overleaf (total of $count_bibs)."
    read -rp "Press enter once you have placed all $count_bibs .bbl file(s) in $arxiv_dir..."
  done

  ansi $ANSI_BOLD "(5/$steps) Renaming default 'output.bbl' to '$pubkey.bbl'..."
  mv "$arxiv_dir/output.bbl" "$arxiv_dir/$pubkey.bbl"

  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not rename 'output.bbl' to '$pubkey.bbl'. Please report this." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "(6/$steps) Preparing ZIP to be uploaded into arXiv..."
  chdir "$arxiv_dir"
  zip -r "$arxiv_zip" .
  if [[ "$?" -ne 0 ]]; then
    ansi $ANSI_RED "ERROR: Could not ZIP contents for arXiv. Please report this." >&2
    exit 1
  fi
  unchdir

  ansi $ANSI_GREEN "Prepared $arxiv_zip for submission to arXiv."
  echo "You may need to make minor modifications to your files if arXiv finds issues."
  echo "Please ensure you update your changes within $arxiv_dir."
}

reviewpub ()
{
  sethelp <<- EOF
Usage: phd review pubkey

Prepares a reviewer feedback spreadsheet for the publication with the pubkey
provided. For instructions on how to break down reviewer feedback using the
reviewer spreadsheet, please visit the following URL: https://bit.ly/33ebKGF.
Additionally asks for the .eml file containing the reviewer feedback email for
record-keeping purposes.
EOF
  local pubkey=$1
  if ! find_pub "$pubkey"; then
    ansi $ANSI_RED "ERROR: No such publication with pubkey '$pubkey' exists." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "Please drag-and-drop your reviewer email from Outlook/Mail into the 'Reviews' folder."
  cat <<- EOF
Keep a record of the email you have recieved with your reviewer feedback on the
publication '$pubkey'.

If you are using Outlook/Mail for Mac, you can drag and drop the email file out
from Outlook/Mail and into the 'Reviews' folder. If you are using a web-browser
client, please try to export an .eml file from the email recieved.

Make sure to rename the .eml file to '$pubkey.eml'.

EOF

  read -rp "Press enter now to open your Reviews folder..."
  open "$PHD_BASEDIR/Reviews"

  ansi $ANSI_BOLD "Creating copy of reviewer template."
  if [[ -z $PHD_GDIR_ID_REVIEWS ]]; then
    get_gdir_id 'Reviews'
    PHD_GDIR_ID_REVIEWS=$get_gdir_id_retval
    write_config
  fi

  copy_gdoc_template "$PHD_GDOC_ID_REVIEW_FEEDBACK" "$PHD_GDIR_ID_REVIEWS" "$pubkey" "spreadsheets"
  ansi $ANSI_GREEN "Reviewer feedback spreadsheet opened. Please press the 'Make a copy' button."
  echo "Please refer to https://bit.ly/33ebKGF for methods on how to break down reviewer feedback."
}

authorpub ()
{
  sethelp <<- EOF
Usage: phd author pubkey

Prepares an authorship statement document for the publication with the pubkey
provided. Authorship statements should be made for all publications made with
co-authors during your PhD candidature. These forms should be signed by all
authors and at the time of publication acceptance.
EOF
  local pubkey=$1
  if ! find_pub "$pubkey"; then
    ansi $ANSI_RED "ERROR: No such publication with pubkey '$pubkey' exists." >&2
    exit 1
  fi

  ansi $ANSI_BOLD "Creating copy of authorship template."
  if [[ -z $PHD_GDIR_ID_AUTHSTMTS ]]; then
    get_gdir_id 'Authorship Statements' 'Admin'
    PHD_GDIR_ID_AUTHSTMTS=$get_gdir_id_retval
    write_config
  fi

  copy_gdoc_template "$PHD_GDOC_ID_AUTHORSHIP_STMT" "$PHD_GDIR_ID_AUTHSTMTS" "$pubkey"
  ansi $ANSI_GREEN "Authorship statement document opened. Please press the 'Make a copy' button."
}

phdopen ()
{
  sethelp <<- EOF
Usage: phd open

Opens your PhD Google Drive directory.
EOF
  open "$PHD_BASEDIR"
}

meeting ()
{
  sethelp <<- EOF
Usage: phd meeting [yyyy-dd-mm]

Creates a meeting minute document set to today's date or the date provided.
EOF
  local date
  [[ -z $1 ]] && date=$(date +%F) || date=$1

  ansi $ANSI_BOLD "Creating copy of meeting minutes template."
  if [[ -z $PHD_GDIR_ID_MEETINGS ]]; then
    get_gdir_id 'Meetings'
    PHD_GDIR_ID_MEETINGS=$get_gdir_id_retval
    write_config
  fi

  copy_gdoc_template "$PHD_GDOC_ID_MEETING_MINUTES" "$PHD_GDIR_ID_MEETINGS" "$date"
  ansi $ANSI_GREEN "Meeting document opened. Please press the 'Make a copy' button."
}

lint ()
{
  sethelp <<- EOF
Usage: phd lint [type] [pubkey|/path/to/latex/file.tex]

Lints a LaTeX file, where type is one of:
  - dups     scans for two duplicate *words words* in a row;
  - tlas     scans for *TLAs* (three-letter acronyms);
  - passive  scans for phrases that *is written* in the passive tense;
  - weasel   scans for *a lot* of weasel words in your TeX file.

Unless an absolute path is provided, the path to the LaTeX file autodefaults to
a file relative to the Papers directory. Or uses the default pubkey LaTeX file.
EOF
  local script="$PHD_SCRIPTDIR/$1"
  local texfile=$2

  if [[ ! -f "$script" ]]; then
    ansi $ANSI_RED "ERROR: Unknown lint script '$1'. Run with -h or --help for linters." >&2
    exit 1
  fi

  find_pub "$texfile" # treat input as pubkey...
  local pubdir="$find_pub_retval"

  if [[ ! -f "$texfile" ]]; then
    texfile="$pubdir/$texfile.tex"
    if [[ ! -f "$texfile" ]]; then
      ansi $ANSI_RED "ERROR: Cannot find file at $texfile." >&2
      exit 1
    fi
  fi

  local recursiveinputawk="$PHD_SCRIPTDIR/recursiveinput.awk"
  export PHD_RECUSRIVE_INPUT_AWK=\"$recursiveinputawk\"
  local temp=$(mktemp)
  "$recursiveinputawk" "$texfile" 2> /dev/null > "$temp"
  unset PHD_RECUSRIVE_INPUT_AWK

  "$script" "$temp"

  rm "$temp"
}

update ()
{
  sethelp <<- EOF
Usage: phd update

Checks for the latest version.
EOF

  ansi $ANSI_BOLD "Checking for PhD Tool updates..."
  chdir "$PHD_SCRIPTDIR"
  git pull origin master
  unchdir
}

version ()
{
  sethelp <<- EOF
Usage: phd version

Prints out the current version of this tool.
EOF
  echo $PHD_VERSION
}

wordcount ()
{
  sethelp <<- EOF
Usage: phd wordcount [pubkey|/path/to/latex/file.tex]

Performs a wordcount on a LaTeX file, or a group of related LaTeX files using
the \input{another-file.tex} command. Or uses the default pubkey LaTeX file.

Unless an absolute path is provided, the path to the LaTeX file autodefaults to
a file relative to the Papers directory.
EOF
  local recursiveinputawk="$PHD_SCRIPTDIR/recursiveinput.awk"
  local texcountpl="$PHD_SCRIPTDIR/texcount.pl"
  local texfile=$1

  find_pub "$texfile" # treat input as pubkey...
  local pubdir="$find_pub_retval"

  if [[ ! -f "$texfile" ]]; then
    texfile="$pubdir/$texfile.tex"
    if [[ ! -f "$texfile" ]]; then
      ansi $ANSI_RED "ERROR: Cannot find file at $texfile." >&2
      exit 1
    fi
  fi

  ansi $ANSI_BOLD "Running word count on $texfile and its subfiles..."
  chdir "$(greadlink -f "$(dirname "$texfile")")"
  export PHD_RECUSRIVE_INPUT_AWK=\"$recursiveinputawk\"
  "$recursiveinputawk" "$texfile" 2> /dev/null | perl "$texcountpl" -col -
  unset PHD_RECUSRIVE_INPUT_AWK
  unchdir
}

help ()
{
  sethelp <<- EOF
Usage: phd help [command]

Shows a help message or help message of other commands.
EOF
  local help_command="$1"
  if [[ -n $help_command ]]; then
    HELP_ON=0
    eval "$help_command" 2> /dev/null
  fi

  ansi $ANSI_BOLD "Alex's PhD Tools (v$PHD_VERSION)"
  ansi $ANSI_ITALIC "Helping struggling PhD students organise their life since 2020"

  cat <<- EOF

Publication commands:
  phd newpub [pubkey]
  phd renamepub oldpubkey [newpubkey]
  phd clonepub pubkey [newpubkey]
  phd flagpub pubkey [abandoned|inprogress|published|rejected]
  phd arxivpub pubkey
  phd review pubkey
  phd author pubkey

Writing commands:
  phd lint [dups|tlas|passive|weasel] [pubkey|file.tex]
  phd wordcount [pubkey|file.tex]

Other commands:
  phd meeting [yyyy-mm-dd]
  phd open

Tool commands:
  phd help
  phd [command] [--help|-h]
  phd update
  phd version
EOF
}

main ()
{
  HELP_ON=1
  PHD_SCRIPTDIR=$(greadlink -f "$(dirname "$(greadlink -f "$0")")")
  PHD_BASEDIR=$(greadlink -f "$PHD_SCRIPTDIR"/..)
  PHD_CONFIG="${PHD_SCRIPTDIR}/config"
  PHD_PAPERSDIR="${PHD_BASEDIR}/Papers"
  PHD_COMMAND="$1"

  setup
  source "$PHD_CONFIG"

  for argv in "$@"; do :; done
  local lastarg="$argv"
  if [[ $lastarg == "--help" || $lastarg == "-h" ]]; then
    HELP_ON=0
  fi

  shift
  case "$PHD_COMMAND" in
  newpub)     newpub "$@";;
  touch)      newpub "$@";;
  new)        newpub "$@";;

  renamepub)  renamepub "$@";;
  mvpub)      renamepub "$@";;
  mv)         renamepub "$@";;

  clonepub)   clonepub "$@";;
  cppub)      clonepub "$@";;
  cp)         clonepub "$@";;

  arxivpub)   arxivpub "$@";;
  arxiv)      arxivpub "$@";;

  flagpub)    flagpub "$@";;
  flag)       flagpub "$@";;

  review)     reviewpub "$@";;
  author)     authorpub "$@";;

  wordcount)  wordcount "$@";;
  lint)       lint "$@";;

  meeting)    meeting "$@";;
  meet)       meeting "$@";;
  open)       phdopen "$@";;

  help)       help "$@";;
  version)    version "$@";;
  update)     update "$@";;

  *)          help "$@";;
  esac
}

if [[ -n "$PHD_INSTALLER" ]]; then
  install
else
  main "$@"
fi