From cc45a8ccbeb146fdfc4461519e33e7b797604615 Mon Sep 17 00:00:00 2001
From: Diego Jahn <jahndiego@mailbox.org>
Date: Mon, 15 Apr 2024 19:44:18 +0200
Subject: [PATCH] morpheus-develop: Refactor `install` method according to
 Homebrew-Core

See https://github.com/Homebrew/homebrew-core/blob/master/Formula/m/morpheus.rb.
---
 Formula/morpheus-develop.rb | 51 +++++++++++++++++--------------------
 1 file changed, 23 insertions(+), 28 deletions(-)

diff --git a/Formula/morpheus-develop.rb b/Formula/morpheus-develop.rb
index c8d090a..63d703e 100644
--- a/Formula/morpheus-develop.rb
+++ b/Formula/morpheus-develop.rb
@@ -1,58 +1,53 @@
 class MorpheusDevelop < Formula
-  desc "Modelling environment for multi-cellular systems biology"
+  desc "Modeling environment for multi-cellular systems biology"
   homepage "https://morpheus.gitlab.io/"
   license "BSD-3-Clause"
   head "https://gitlab.com/morpheus.lab/morpheus.git", branch: "develop"
 
+  option "with-sbml", "Enable SBML import via the internal libSBML build"
+
   depends_on "boost" => :build
   depends_on "cmake" => :build
   depends_on "doxygen" => :build
-  depends_on "ffmpeg" # Runtime dependencies
+  depends_on "ninja" => :build
   depends_on "gnuplot"
   depends_on "graphviz"
   depends_on "libomp"
   depends_on "libtiff"
   depends_on "qt@5"
+  depends_on "ffmpeg" => :recommended # Runtime dependencies
 
   uses_from_macos "bzip2"
   uses_from_macos "libxml2"
   uses_from_macos "zlib"
 
   def install
-    args = std_cmake_args
-    args << "-DMORPHEUS_RELEASE_BUNDLE=ON" if OS.mac?
-
-    system "cmake", ".", *args
-    system "make", "install"
+    # has to build with Ninja until: https://gitlab.kitware.com/cmake/cmake/-/issues/25142
+    args = ["-G Ninja"]
 
     if OS.mac?
-      bin.write_exec_script "#{prefix}/Morpheus.app/Contents/MacOS/morpheus"
+      args << "-DMORPHEUS_RELEASE_BUNDLE=ON"
+      args << "-DBREW_FORMULA_DEPLOYMENT=ON"
 
-      (bin/"morpheus-gui").write <<~EOS
-        #!/bin/bash
-        open #{prefix}/Morpheus.app
-      EOS
-      (bin/"morpheus-gui").chmod 0555
+      # SBML import currently disabled by default due to libSBML build errors with some macOS SDKs
+      args << "-DMORPHEUS_SBML=OFF" if build.without? "sbml"
     end
-  end
 
-  def post_install
-    if OS.mac?
-      # Set PATH environment variable including Homebrew prefix in macOS app bundle
-      inreplace "#{prefix}/Morpheus.app/Contents/Info.plist", "<key>CFBundleExecutable</key>",
-        <<~EOS.chomp
-          <key>LSEnvironment</key>
-          <dict>
-              <key>PATH</key>
-              <string>#{ENV["PATH"]}</string>
-          </dict>
-          <key>CFBundleExecutable</key>
-        EOS
-    end
+    system "cmake", "-S", ".", "-B", "build", *args, *std_cmake_args
+    system "cmake", "--build", "build"
+    system "cmake", "--install", "build"
+
+    return unless OS.mac?
+
+    bin.write_exec_script "#{prefix}/Morpheus.app/Contents/MacOS/morpheus"
+    bin.write_exec_script "#{prefix}/Morpheus.app/Contents/MacOS/morpheus-gui"
+
+    # Set PATH environment variable including Homebrew prefix in macOS app bundle
+    inreplace "#{prefix}/Morpheus.app/Contents/Info.plist", "HOMEBREW_BIN_PATH", "#{HOMEBREW_PREFIX}/bin"
   end
 
   def caveats
-    if OS.mac?
+    on_macos do
       <<~EOS
         To start the Morpheus GUI, type the following command: