From 5b400a988a1312623837cc1003541ffd0148121c Mon Sep 17 00:00:00 2001
From: Diego Jahn <jahndiego@mailbox.org>
Date: Fri, 25 Oct 2024 13:17:56 +0200
Subject: [PATCH] morpheus-qt6 (new formula)

---
 Formula/morpheus-qt6.rb | 107 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 107 insertions(+)
 create mode 100644 Formula/morpheus-qt6.rb

diff --git a/Formula/morpheus-qt6.rb b/Formula/morpheus-qt6.rb
new file mode 100644
index 0000000..c324fb5
--- /dev/null
+++ b/Formula/morpheus-qt6.rb
@@ -0,0 +1,107 @@
+class MorpheusQt6 < Formula
+  desc "Modeling environment for multi-cellular systems biology"
+  homepage "https://morpheus.gitlab.io/"
+  license "BSD-3-Clause"
+  head "https://gitlab.com/morpheus.lab/dev/morpheus.git", branch: "qt6-port"
+
+  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 "ninja" => :build
+  depends_on "gnuplot"
+  depends_on "graphviz"
+  depends_on "libomp"
+  depends_on "libtiff"
+  depends_on "qt@6"
+  depends_on "ffmpeg" => :recommended # Runtime dependencies
+  uses_from_macos "bzip2"
+  uses_from_macos "libxml2"
+  uses_from_macos "zlib"
+
+  # conflicts_with "qt@5", because: "this formula is designed to work with qt@6 only"
+
+  def install
+    # has to build with Ninja until: https://gitlab.kitware.com/cmake/cmake/-/issues/25142
+    args = ["-G Ninja"]
+
+    if OS.mac?
+      args << "-DMORPHEUS_RELEASE_BUNDLE=ON"
+      args << "-DBREW_FORMULA_DEPLOYMENT=ON"
+
+      # Append branch name and Git commit hash to binary suffix
+      args << "-DMORPHEUS_BINARY_SUFFIX=#{self.class.head.specs[:branch]}-#{`git rev-parse HEAD`.strip[0, 7]}"
+
+      # SBML import currently disabled by default due to libSBML build errors with some macOS SDKs
+      args << "-DMORPHEUS_SBML=OFF" if build.without? "sbml"
+
+      # Qt6 paths
+      # args << "-DCMAKE_PREFIX_PATH=#{Formula["qt@6"].opt_prefix}"
+      # args << "-DQt6_DIR=#{Formula["qt@6"].opt_lib}/cmake/Qt6"
+
+      # Set the Qt WebEngine resources directory explicitly
+      # qt_webengine_resources_dir = "#{Formula["qt@6"].opt_lib}/QtWebEngineCore.framework/Versions/A/Resources"
+      # args << "-DQT_WEBENGINE_RESOURCES_DIR=#{qt_webengine_resources_dir}"
+    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
+    on_macos do
+      <<~EOS
+        To start the Morpheus GUI, type the following command:
+
+          morpheus-gui
+
+        Or add Morpheus to your Applications folder with:
+
+          ln -sf #{opt_prefix}/Morpheus.app /Applications/Morpheus-#{self.class.head.specs[:branch]}.app
+
+        For more information about this branch, visit: https://gitlab.com/morpheus.lab/morpheus/-/tree/#{self.class.head.specs[:branch]}
+      EOS
+    end
+  end
+
+  test do
+    (testpath/"test.xml").write <<~EOF
+      <?xml version='1.0' encoding='UTF-8'?>
+      <MorpheusModel version="4">
+          <Description>
+              <Details></Details>
+              <Title></Title>
+          </Description>
+          <Space>
+              <Lattice class="linear">
+                  <Neighborhood>
+                      <Order>1</Order>
+                  </Neighborhood>
+                  <Size value="100,  0.0,  0.0" symbol="size"/>
+              </Lattice>
+              <SpaceSymbol symbol="space"/>
+          </Space>
+          <Time>
+              <StartTime value="0"/>
+              <StopTime value="0"/>
+              <TimeSymbol symbol="time"/>
+          </Time>
+          <Analysis>
+              <ModelGraph include-tags="#untagged" format="dot" reduced="false"/>
+          </Analysis>
+      </MorpheusModel>
+    EOF
+
+    assert_match "Simulation finished", shell_output("#{bin}/morpheus --file test.xml")
+  end
+end