JAL-3830 JAL-3421 Conda launch script for 2.11.3 and new CLI with OS compatibility...

diff --git a/utils/conda/jalview.sh b/utils/conda/jalview.sh
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+#!/usr/bin/env bash
+
+###############################
+# Wrapper for Jalview
+#
+# 2023-08-16 Jalview 2.11.3.0 has new command line arguments
+# Old command line arguments are currently detected and actioned
+# but are no longer supported and will be removed at a later date.
+#
+# See
+#   Jalview -> Help -> Documentation -> Command Line -> introduction and reference
+# or
+#   https://www.jalview.org/help/html/features/clarguments.html
+# for details of the new command line arguments.
+#
+# Note, in order to run commandline-only calls use
+#   --headless
+#
+# By default, this wrapper executes java -version to determine the JRE version
+# Set JALVIEW_JRE=j1.8 or JALVIEW_JRE=j11 to skip the version check.
+#
+# By default, this wrapper does NOT restrict the memory consumption of Jalview.
+# Set eg. JALVIEW_MAXMEM=1g to set the maximal memory of Jalview's VM
+#
+# This script is maintained in the Jalview repository in utils/conda/jalview.sh
+###############################
+
+declare -a ARGS=("${@}")
+ARG1=$1
+
+# this function is because there's no readlink -f in Darwin/macOS
+function readlinkf() {
+  FINDFILE="$1"
+  FILE="${FINDFILE}"
+  PREVFILE=""
+  C=0
+  MAX=100 # just in case we end up in a loop
+  FOUND=0
+  while [ "${C}" -lt "${MAX}" -a "${FILE}" != "${PREVFILE}" -a "${FOUND}" -ne 1 ]; do
+    PREVFILE="${FILE}"
+    FILE="$(readlink "${FILE}")"
+    if [ -z "${FILE}" ]; then
+      # the readlink is empty means we've arrived at the script, let's canonicalize with pwd
+      FILE="$(cd "$(dirname "${PREVFILE}")" &> /dev/null && pwd -P)"/"$(basename "${PREVFILE}")"
+      FOUND=1
+    elif [ "${FILE#/}" = "${FILE}" ]; then
+      # FILE is not an absolute path link, we need to add the relative path to the previous dir
+      FILE="$(dirname "${PREVFILE}")/${FILE}"
+    fi
+    C=$((C+1))
+  done
+  if [ "${FOUND}" -ne 1 ]; then
+    echo "Could not determine path to actual file '$(basename "${FINDFILE}")'" >&2
+    exit 1
+  fi
+  echo "${FILE}"
+}
+
+ISMACOS=0
+if [ "$( uname -s )" = "Darwin" ]; then
+  ISMACOS=1
+fi
+
+# check for headless mode
+HEADLESS=0
+GUI=0
+HELP=0
+DEBUG=0
+for ARG in "${@}"; do
+  case "${ARG}" in
+    "--headless")
+      HEADLESS=1
+      ;;
+    "--help")
+      HELP=1
+      ;;
+    --help-*)
+      HELP=1
+      ;;
+    "--gui")
+      GUI=1
+      ;;
+    "--debug")
+      DEBUG=1
+      ;;
+  esac
+  
+  if [ "${HELP}" = 1 ]; then
+    # --help takes precedence
+    HEADLESS=1
+    GUI=0
+  elif [ "${GUI}" = 1 ]; then
+    # --gui takes precedence over --headless
+    HEADLESS=0
+  fi
+done
+
+declare -a JVMARGS=()
+
+# set vars for being inside the macos App Bundle
+if [ "${ISMACOS}" = 1 ]; then
+# MACOS ONLY
+  DIR="$(dirname "$(readlinkf "$0")")"
+  JVMARGS=( "${JVMARGS[@]}" "-Xdock:icon=${DIR}/jalview_logo.png" )
+else
+# NOT MACOS
+  DIR="$(dirname "$(readlink -f "$0")")"
+fi
+
+if [ "${HEADLESS}" = 1 ]; then
+  # this suppresses the Java icon appearing in the macOS Dock and maybe other things in other OSes
+  JVMARGS=( "${JVMARGS[@]}" "-Djava.awt.headless=true" )
+fi
+
+JAVA=java
+
+# decide which jalview jar to launch - either 'j11' or 'j1.8'
+if [[ "$JALVIEW_JRE" != "j11" && "$JALVIEW_JRE" != "j1.8" ]]; then
+  JALVIEW_JRE="j11"
+  # if java 8 is installed we pick the j1.8 build
+  if [[ $( "${JAVA}" -version 2>&1 | grep '"1.8' ) != "" ]]; then
+    JALVIEW_JRE="j1.8"
+  fi
+fi
+
+JARPATH="${DIR}/jalview-all-${JALVIEW_JRE}.jar"
+
+# check if memory maximum is set and if so forward to java-based jalview call
+if [ \! -z "$JALVIEW_MAXMEM" ]; then
+  JVMARGS=( "${JVMARGS[@]}" "-Xmx${JALVIEW_MAXMEM}" )
+fi
+
+# WINDOWS ONLY (Cygwin or WSL)
+# change paths for Cygwin or Windows Subsystem for Linux (WSL)
+if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
+  if [ "$(uname -o)" = "Cygwin" ]; then
+  # CYGWIN
+    JARPATH="$(cygpath -pw "${JARPATH}")"
+    # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
+    ARGS=()
+    for ARG in "${@}"; do
+      if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+        ARGS=( "${ARGS[@]}" "$(cygpath -aw "${ARG}")" )
+      else
+        ARGS=( "${ARGS[@]}" "${ARG}" )
+      fi
+    done
+  elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
+  # WSL
+    JARPATH="$(wslpath -aw "${JARPATH}")"
+    ARGS=()
+    for ARG in "${@}"; do
+      if [ "${ARG}" != "${ARG#@(/|./|../|~)}" ]; then
+        # annoyingly wslpath does not work if the file doesn't exist!
+        ARGBASENAME="$(basename "${ARG}")"
+        ARGDIRNAME="$(dirname "${ARG}")"
+        ARGS=( "${ARGS[@]}" "$(wslpath -aw "${ARGDIRNAME}")\\${ARGBASENAME}" )
+      else
+        ARGS=( "${ARGS[@]}" "${ARG}" )
+      fi
+    done
+    JAVA="${JAVA}.exe"
+  fi
+fi
+
+# get console width -- three ways to try, just in case
+if command -v tput 2>&1 >/dev/null; then
+  COLUMNS=$(tput cols) 2>/dev/null
+elif command -v stty 2>&1 >/dev/null; then
+  COLUMNS=$(stty size | cut -d" " -f2) 2>/dev/null
+elif command -v resize 2>&1 >/dev/null; then
+  COLUMNS=$(resize -u | grep COLUMNS= | sed -e 's/.*=//;s/;//') 2>/dev/null
+fi
+JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" )
+
+if [ "${DEBUG}" = 1 ]; then
+ echo Shell running: "${JAVA}" "${JVMARGS[@]}" -jar \""${JARPATH}"\" jalview.bin.Launcher "${ARGS[@]}"
+fi
+
+"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" jalview.bin.Launcher "${ARGS[@]}"