[Backport release-25.11] {ebtks,n3,inormalize}: update and fix build with CMake >= 4 (#466531)

pkgs/by-name/ar/arguments/package.nix

@@ -5,36 +5,31 @@
   cmake,
 }:
 
-stdenv.mkDerivation rec {
+stdenv.mkDerivation {
   pname = "arguments";
-  version = "unstable-2015-11-30";
-
-  owner = "BIC-MNI";
+  version = "1.4.60-unstable-2023-01-18";
 
   src = fetchFromGitHub {
-    inherit owner;
+    owner = "BIC-MNI";
     repo = "arguments";
-    rev = "b3aad97f6b6892cb8733455d0d448649a48fa108";
-    sha256 = "1ar8lm1w1jflz3vdmjr5c4x6y7rscvrj78b8gmrv79y95qrgzv6s";
+    rev = "ed7c4c126b800d4312469e3cd3999a31e96fed0e";
+    hash = "sha256-1QxVZ17zSqx5P9nGAXHf7Fj86fuGn17PllGXFqyYJUo=";
   };
 
   nativeBuildInputs = [ cmake ];
 
-  #cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBICPL_DIR=${bicpl}/lib" ];
-
-  doCheck = false;
-  # internal_volume_io.h: No such file or directory
+  doCheck = false; # test binary not built by cmake
 
   postPatch = ''
     substituteInPlace CMakeLists.txt \
-      --replace-fail "CMAKE_MINIMUM_REQUIRED(VERSION 2.6)" "cmake_minimum_required(VERSION 3.10)"
+      --replace-fail "CMAKE_MINIMUM_REQUIRED(VERSION 3.1)" "cmake_minimum_required(VERSION 3.10)"
   '';
 
-  meta = with lib; {
-    homepage = "https://github.com/${owner}/arguments";
+  meta = {
+    homepage = "https://github.com/BIC-MNI/arguments";
     description = "Library for argument handling for MINC programs";
-    maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.unix;
-    license = licenses.gpl2Plus;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    platforms = lib.platforms.unix;
+    license = lib.licenses.gpl2Plus;
   };
 }

pkgs/by-name/eb/ebtks/package.nix

@@ -8,35 +8,25 @@
 
 stdenv.mkDerivation {
   pname = "ebtks";
-  version = "unstable-2017-09-23";
+  version = "1.6.40-unstable-2025-05-06";
 
   src = fetchFromGitHub {
     owner = "BIC-MNI";
     repo = "EBTKS";
-    rev = "67e4e197d8a32d6462c9bdc7af44d64ebde4fb5c";
-    hash = "sha256-+MIRE2NdRH7IQrstK3WRqft6l9I+UGD6j0G7Q6LhOKg=";
+    rev = "7317b54d79bd7d80b5361dc44a7966709d9a8b36";
+    hash = "sha256-kp3uPvsIker8918stsVUdMC72A6Jz0K7r5PFDLbWqNo=";
   };
 
-  # error: use of undeclared identifier 'finite'; did you mean 'isfinite'?
-  postPatch = ''
-    substituteInPlace templates/EBTKS/SimpleArray.h \
-      --replace "#define FINITE(x) finite(x)" "#define FINITE(x) isfinite(x)"
-  ''
-  # error: ISO C++17 does not allow 'register' storage class specifier
-  + ''
-    find . -type f -exec sed -i -e 's/register //g' {} +
-  '';
-
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc ];
 
   cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
 
-  meta = with lib; {
+  meta = {
     homepage = "https://github.com/BIC-MNI/EBTKS";
     description = "Library for working with MINC files";
-    maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.unix;
-    license = licenses.free;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    platforms = lib.platforms.unix;
+    license = lib.licenses.free;
   };
 }

pkgs/by-name/in/inormalize/lgmask-interp.patch

@@ -1,10 +0,0 @@
-diff --git a/lgmask.in b/lgmask.in
-index 17dbe4d..2195d91 100644
---- a/lgmask.in
-+++ b/lgmask.in
-@@ -1,4 +1,4 @@
--#! @PERL@
-+#! /usr/bin/env perl
- 
- #---------------------------------------------------------------------------
- #@COPYRIGHT :

pkgs/by-name/in/inormalize/nu_correct_norm-interp.patch

@@ -1,10 +0,0 @@
-diff --git a/nu_correct_norm.in b/nu_correct_norm.in
-index 1dc84ac..1bc6235 100644
---- a/nu_correct_norm.in
-+++ b/nu_correct_norm.in
-@@ -1,4 +1,4 @@
--#! @PERL@
-+#! /usr/bin/perl
-  
- #---------------------------------------------------------------------------
- #@COPYRIGHT :

pkgs/by-name/in/inormalize/package.nix

@@ -11,38 +11,34 @@
 
 stdenv.mkDerivation {
   pname = "inormalize";
-  version = "unstable-2014-10-21";
+  version = "1.2.00-unstable-2023-01-19";
 
   src = fetchFromGitHub {
     owner = "BIC-MNI";
     repo = "inormalize";
-    rev = "79cea9cdfe7b99abfd40afda89ab2253b596ad2f";
-    sha256 = "1ahqv5q0ljvji99a5q8azjkdf6bgp6nr8lwivkqwqs3jm0k5clq7";
+    rev = "4928e573165d76551c3d273ccf0c46f4fbab11fc";
+    hash = "sha256-ZxTsPBsaL/5BWC7ew57um8LPb96hytI30JE8saBBNw8=";
   };
 
-  patches = [
-    ./lgmask-interp.patch
-    ./nu_correct_norm-interp.patch
-  ];
-
   postPatch = ''
-    substituteInPlace inormalize.cc \
-      --replace "clamp" "::clamp"
+    substituteInPlace CMakeLists.txt \
+      --replace-fail "CMAKE_MINIMUM_REQUIRED(VERSION 3.1)" "CMAKE_MINIMUM_REQUIRED(VERSION 3.10)"
   '';
 
   nativeBuildInputs = [
     cmake
     makeWrapper
   ];
+
   buildInputs = [
     libminc
     ebtks
-  ];
-  propagatedBuildInputs = with perlPackages; [
+  ]
+  ++ (with perlPackages; [
     perl
     GetoptTabular
     MNI-Perllib
-  ];
+  ]);
 
   cmakeFlags = [
     "-DLIBMINC_DIR=${libminc}/lib/cmake"
@@ -55,11 +51,11 @@ stdenv.mkDerivation {
     done
   '';
 
-  meta = with lib; {
+  meta = {
     homepage = "https://github.com/BIC-MNI/inormalize";
     description = "Program to normalize intensity of MINC files";
-    maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.unix;
-    license = licenses.free;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    platforms = lib.platforms.unix;
+    license = lib.licenses.free;
   };
 }

pkgs/by-name/n3/n3/package.nix

@@ -11,37 +11,34 @@
 
 stdenv.mkDerivation {
   pname = "N3";
-  version = "unstable-2018-08-09";
+  version = "1.12.00-unstable-2023-01-19";
 
   src = fetchFromGitHub {
     owner = "BIC-MNI";
     repo = "N3";
-    rev = "010fc2ac58ce1d67b8e6a863fac0809d3203cb9b";
-    sha256 = "06hci7gzhy8p34ggvx7gah2k9yxpwhgmq1cgw8pcd1r82g4rg6kd";
+    rev = "96194790a577293163b6319d00539c8af45c195e";
+    hash = "sha256-iA2dMOc+dlraT44zITrvOLIaJ3iH4a/fU5aS/YzIEGQ=";
   };
 
-  postPatch = ''
-    substituteInPlace src/VolumeHist/DHistogram.cc \
-      --replace "register " ""
-  '';
-
   nativeBuildInputs = [
     cmake
     makeWrapper
   ];
+
   buildInputs = [
     libminc
     ebtks
-  ];
-  propagatedBuildInputs = with perlPackages; [
+  ]
+  ++ (with perlPackages; [
     perl
     MNI-Perllib
     GetoptTabular
-  ];
+  ]);
 
   cmakeFlags = [
     "-DLIBMINC_DIR=${libminc}/lib/cmake"
     "-DEBTKS_DIR=${ebtks}/lib/"
+    "-DCMAKE_POLICY_VERSION_MINIMUM=3.10"
   ];
 
   postFixup = ''
@@ -50,11 +47,11 @@ stdenv.mkDerivation {
     done
   '';
 
-  meta = with lib; {
+  meta = {
     homepage = "https://github.com/BIC-MNI/N3";
     description = "MRI non-uniformity correction for MINC files";
-    maintainers = with maintainers; [ bcdarwin ];
-    platforms = platforms.unix;
-    license = licenses.free;
+    maintainers = with lib.maintainers; [ bcdarwin ];
+    platforms = lib.platforms.unix;
+    license = lib.licenses.free;
   };
 }