From d65f93924d187ebcfa65aa61fa3701e0eb0f12ff Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Thu, 23 Jan 2025 23:07:53 -0500
Subject: [PATCH 1/2] mirtk: remove itk_5_2 dependency

---
 .../science/biology/mirtk/default.nix         | 22 ++++++++-----------
 pkgs/top-level/all-packages.nix               |  2 +-
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/pkgs/development/libraries/science/biology/mirtk/default.nix b/pkgs/development/libraries/science/biology/mirtk/default.nix
index 6726fe3002bf..e1fbd437fef0 100644
--- a/pkgs/development/libraries/science/biology/mirtk/default.nix
+++ b/pkgs/development/libraries/science/biology/mirtk/default.nix
@@ -8,7 +8,6 @@
   eigen,
   libGLU,
   fltk,
-  itk,
   vtk,
   zlib,
   tbb,
@@ -28,18 +27,16 @@ stdenv.mkDerivation {
 
   cmakeFlags = [
     "-DWITH_VTK=ON"
-    "-DBUILD_ALL_MODULES=ON"
+    "-DMODULE_Deformable=ON"
+    "-DMODULE_Mapping=ON"
+    "-DMODULE_Scripting=ON"
+    "-DMODULE_Viewer=ON"
+    "-DMODULE_DrawEM=OFF"
     "-DWITH_TBB=ON"
-    "-DWITH_ITK=ON"
     "-DWITH_GIFTICLIB=ON"
     "-DWITH_NIFTILIB=ON"
   ];
 
-  # tries to download data during configuration
-  postPatch = ''
-    substituteInPlace Packages/DrawEM/CMakeLists.txt --replace "include(Atlases.cmake)" ""
-  '';
-
   # tests don't seem to be maintained and gtest fails to link with BUILD_TESTING=ON;
   # unclear if specific to Nixpkgs
   doCheck = false;
@@ -55,7 +52,6 @@ stdenv.mkDerivation {
     boost186
     eigen
     fltk
-    itk
     libGLU
     python3
     tbb
@@ -63,12 +59,12 @@ stdenv.mkDerivation {
     zlib
   ];
 
-  meta = with lib; {
+  meta = {
     homepage = "https://github.com/BioMedIA/MIRTK";
     description = "Medical image registration library and tools";
     mainProgram = "mirtk";
-    maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.linux;
-    license = licenses.asl20;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    platforms = lib.platforms.linux;
+    license = lib.licenses.asl20;
   };
 }
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 5062eb74a5fb..7c0e8e814fa9 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15201,7 +15201,7 @@ with pkgs;
     inherit (llvmPackages) openmp;
   };
 
-  mirtk = callPackage ../development/libraries/science/biology/mirtk { itk = itk_5_2; };
+  mirtk = callPackage ../development/libraries/science/biology/mirtk { };
 
   nest = callPackage ../applications/science/biology/nest { };
 

From 677c2617d3aa287320f14cd220988d846a956c27 Mon Sep 17 00:00:00 2001
From: Ben Darwin <bcdarwin@gmail.com>
Date: Thu, 31 Jul 2025 14:19:11 -0400
Subject: [PATCH 2/2] mirtk: move to pkgs/by-name

---
 .../biology/mirtk/default.nix => by-name/mi/mirtk/package.nix}  | 0
 pkgs/top-level/all-packages.nix                                 | 2 --
 2 files changed, 2 deletions(-)
 rename pkgs/{development/libraries/science/biology/mirtk/default.nix => by-name/mi/mirtk/package.nix} (100%)

diff --git a/pkgs/development/libraries/science/biology/mirtk/default.nix b/pkgs/by-name/mi/mirtk/package.nix
similarity index 100%
rename from pkgs/development/libraries/science/biology/mirtk/default.nix
rename to pkgs/by-name/mi/mirtk/package.nix
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 7c0e8e814fa9..845dd4b14a36 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -15201,8 +15201,6 @@ with pkgs;
     inherit (llvmPackages) openmp;
   };
 
-  mirtk = callPackage ../development/libraries/science/biology/mirtk { };
-
   nest = callPackage ../applications/science/biology/nest { };
 
   nest-mpi = callPackage ../applications/science/biology/nest { withMpi = true; };