From f7677c31039f9d11fe0b723499f2e7166583eba5 Mon Sep 17 00:00:00 2001
From: Guy Chronister <guychronister@outlook.com>
Date: Wed, 22 Apr 2026 15:55:37 -0500
Subject: [PATCH] minc_tools: migrate to by-name

---
 .../mi/minc_tools/package.nix}                  | 17 +++++++++++++++--
 pkgs/top-level/all-packages.nix                 |  4 ----
 2 files changed, 15 insertions(+), 6 deletions(-)
 rename pkgs/{applications/science/biology/minc-tools/default.nix => by-name/mi/minc_tools/package.nix} (72%)

diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/by-name/mi/minc_tools/package.nix
similarity index 72%
rename from pkgs/applications/science/biology/minc-tools/default.nix
rename to pkgs/by-name/mi/minc_tools/package.nix
index a5d60ed8cae6..0baa08b201bd 100644
--- a/pkgs/applications/science/biology/minc-tools/default.nix
+++ b/pkgs/by-name/mi/minc_tools/package.nix
@@ -6,14 +6,17 @@
   makeWrapper,
   flex,
   bison,
-  perl,
-  TextFormat,
+  perlPackages,
   libminc,
   libjpeg,
   nifticlib,
   zlib,
 }:
 
+let
+  inherit (perlPackages) perl TextFormat;
+in
+
 stdenv.mkDerivation {
   pname = "minc-tools";
   version = "2.3.06-unstable-2024-11-28";
@@ -30,6 +33,16 @@ stdenv.mkDerivation {
   # Upstream issue: https://github.com/BIC-MNI/minc-tools/issues/123
   postPatch = ''
     substituteInPlace CMakeLists.txt --replace-fail "SET CMP0026 OLD" "SET CMP0026 NEW"
+
+    # FIX: Rename the colliding NAN token to MINC_NAN in the flex/bison parser files
+    sed -i 's/\bNAN\b/MINC_NAN/g' progs/minccalc/gram.y progs/minccalc/lex.l
+
+    # FIX: Rename the colliding fdiv function to avoid glibc 2.42 <math.h> conflicts
+    sed -i 's/\bfdiv\b/minc_fdiv/g' progs/mincblob/mincblob.c
+
+    # FIX: Remove legacy unprototyped C declarations that break under GCC 15 strictness
+    sed -i 's/, \*mat_create()//g' conversion/minctoecat/ecat_write.c
+    sed -i 's/\*fopen(), //g' conversion/minctoecat/ecat_write.c
   '';
 
   nativeBuildInputs = [
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 86c043c419e6..71e2e4cc76a1 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -11398,10 +11398,6 @@ with pkgs;
     useRx3d = true;
   };
 
-  minc_tools = callPackage ../applications/science/biology/minc-tools {
-    inherit (perlPackages) perl TextFormat;
-  };
-
   raxml-mpi = raxml.override { useMpi = true; };
 
   ### SCIENCE/MACHINE LEARNING