Merge pull request #282666 from wegank/ebtks-refactor

ebtks: fix build on darwin, refactor

pkgs/applications/science/biology/N3/default.nix

@@ -1,6 +1,6 @@
 { lib, stdenv, fetchFromGitHub, cmake, makeWrapper,
   perlPackages,
-  libminc, EBTKS }:
+  libminc, ebtks }:
 
 stdenv.mkDerivation rec {
   pname = "N3";
@@ -13,11 +13,16 @@ stdenv.mkDerivation rec {
     sha256 = "06hci7gzhy8p34ggvx7gah2k9yxpwhgmq1cgw8pcd1r82g4rg6kd";
   };
 
+  postPatch = ''
+    substituteInPlace src/VolumeHist/DHistogram.cc \
+      --replace "register " ""
+  '';
+
   nativeBuildInputs = [ cmake makeWrapper ];
-  buildInputs = [ libminc EBTKS ];
+  buildInputs = [ libminc ebtks ];
   propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${ebtks}/lib/" ];
 
   postFixup = ''
     for p in $out/bin/*; do

pkgs/applications/science/biology/inormalize/default.nix

@@ -1,6 +1,6 @@
 { lib, stdenv, fetchFromGitHub, cmake, makeWrapper,
   perlPackages,
-  libminc, EBTKS }:
+  libminc, ebtks }:
 
 stdenv.mkDerivation rec {
   pname = "inormalize";
@@ -15,11 +15,16 @@ stdenv.mkDerivation rec {
 
   patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ];
 
+  postPatch = ''
+    substituteInPlace inormalize.cc \
+      --replace "clamp" "::clamp"
+  '';
+
   nativeBuildInputs = [ cmake makeWrapper ];
-  buildInputs = [ libminc EBTKS ];
+  buildInputs = [ libminc ebtks ];
   propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${ebtks}/lib/" ];
 
   postFixup = ''
     for p in $out/bin/*; do

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

@@ -1,12 +1,12 @@
 { lib, stdenv, fetchFromGitHub, cmake, libminc }:
 
-stdenv.mkDerivation rec {
-  pname = "EBTKS";
+stdenv.mkDerivation {
+  pname = "ebtks";
   version  = "unstable-2017-09-23";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
-    repo   = pname;
+    repo   = "EBTKS";
     rev    = "67e4e197d8a32d6462c9bdc7af44d64ebde4fb5c";
     sha256 = "1a1qw6i47fs1izx60l1ysabpmyx9j5sjnbdv8b47wi2xcc9i3hpq";
   };
@@ -15,6 +15,10 @@ stdenv.mkDerivation rec {
   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 ];
@@ -23,7 +27,7 @@ stdenv.mkDerivation rec {
   cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
 
   meta = with lib; {
-    homepage = "https://github.com/BIC-MNI/${pname}";
+    homepage = "https://github.com/BIC-MNI/EBTKS";
     description = "Library for working with MINC files";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;

pkgs/top-level/aliases.nix

@@ -229,6 +229,7 @@ mapAliases ({
 
   ### E ###
 
+  EBTKS = ebtks; # Added 2024-01-21
   ec2_ami_tools = ec2-ami-tools; # Added 2021-10-08
   ec2_api_tools = ec2-api-tools; # Added 2021-10-08
   ec2-utils = amazon-ec2-utils; # Added 2022-02-01

pkgs/top-level/all-packages.nix

@@ -5207,8 +5207,6 @@ with pkgs;
 
   easyocr = with python3.pkgs; toPythonApplication easyocr;
 
-  EBTKS = callPackage ../development/libraries/science/biology/EBTKS { };
-
   ecasound = callPackage ../applications/audio/ecasound { };
 
   edac-utils = callPackage ../os-specific/linux/edac-utils { };