mrtrix: 3.0.4 -> 3.0.4-unstable-2025-04-09 (#397641)

  libXext,

  less,

  withGui ? true,

  fetchFromGitLab,

  fetchpatch,

}:

let

  # reverts 'eigen: 3.4.0 -> 3.4.0-unstable-2022-05-19'

  # https://github.com/NixOS/nixpkgs/commit/d298f046edabc84b56bd788e11eaf7ed72f8171c

  eigen' = (

    eigen.overrideAttrs (old: rec {

      version = "3.4.0";

      src = fetchFromGitLab {

        owner = "libeigen";

        repo = "eigen";

        tag = version;

        hash = "sha256-1/4xMetKMDOgZgzz3WMxfHUEpmdAm52RqZvz6i0mLEw=";

      };

      patches = (old.patches or [ ]) ++ [

        # Fixes e.g. onnxruntime on aarch64-darwin:

        # https://hydra.nixos.org/build/248915128/nixlog/1,

        # originally suggested in https://github.com/NixOS/nixpkgs/pull/258392.

        #

        # The patch is from

        # ["Fix vectorized reductions for Eigen::half"](https://gitlab.com/libeigen/eigen/-/merge_requests/699)

        # which is two years old,

        # but Eigen hasn't had a release in two years either:

        # https://gitlab.com/libeigen/eigen/-/issues/2699.

        (fetchpatch {

          url = "https://gitlab.com/libeigen/eigen/-/commit/d0e3791b1a0e2db9edd5f1d1befdb2ac5a40efe0.patch";

          hash = "sha256-8qiNpuYehnoiGiqy0c3Mcb45pwrmc6W4rzCxoLDSvj0=";

        })

      ];

    })

  );

in

stdenv.mkDerivation rec {

  pname = "mrtrix";

  version = "3.0.4";

  version = "3.0.4-unstable-2025-04-09";

  src = fetchFromGitHub {

    owner = "MRtrix3";

    repo = "mrtrix3";

    tag = version;

    hash = "sha256-87zBAoBLWQPccGS37XyQ8H0GhL01k8GQFgcLL6IwbcM=";

    rev = "7843bfc53a75f465901804ccf3fd6797d77531dd";

    hash = "sha256-C4Io3VkX10eWia4djrYvN12fWmwm0j1G60I8lmFH49w=";

    fetchSubmodules = true;

  };

  nativeBuildInputs = [

    eigen

    makeWrapper

    less

    python

  ] ++ lib.optional withGui qt5.wrapQtAppsHook;

  buildInputs =

    [

      ants

      eigen'

      python

      fftw

      libtiff

  nativeInstallCheckInputs = [ bc ];

  postPatch = ''

    patchShebangs ./build ./configure ./run_tests ./bin/*

    patchShebangs --build ./build ./configure ./run_tests

    patchShebangs --host ./bin/*

    # patching interpreters before fixup is needed for tests:

    patchShebangs ./bin/*

    patchShebangs testing/binaries/data/vectorstats/*py

    substituteInPlace ./run_tests  \

      --replace 'git submodule update --init $datadir >> $LOGFILE 2>&1' ""

      --replace-fail 'git submodule update --init $datadir >> $LOGFILE 2>&1' ""

    # reduce build noise

    substituteInPlace ./configure \

      --replace-fail "[ '-Wall' ]" "[]"

    # fix error output (cuts off after a few lines otherwise)

    substituteInPlace ./build  \

      --replace '"less -RX "' '"${less}/bin/less -RX "'

      --replace-fail 'stderr=subprocess.PIPE' 'stderr=None'

  '';

  configurePhase = ''

    export EIGEN_CFLAGS="-isystem ${eigen}/include/eigen3"

    runHook preConfigure

    export EIGEN_CFLAGS="-isystem ${eigen'}/include/eigen3"

    unset LD  # similar to https://github.com/MRtrix3/mrtrix3/issues/1519

    ./configure ${lib.optionalString (!withGui) "-nogui"};

    runHook postConfigure

  '';

  buildPhase = ''

    runHook preBuild

    ./build

    (cd testing && ../build)

    runHook postBuild

  '';

  installCheckPhase = ''

    runHook preInstallCheck

    ./run_tests units

    ./run_tests binaries

    # can also `./run_tests scripts`, but this fails due to lack of FSL package

    # (and there's no convenient way to disable individual tests)

    runHook postInstallCheck

  '';

  doInstallCheck = true;

    runHook postInstall

  '';

  postInstall = ''

  preFixup =

    if withGui then

      ''

        qtWrapperArgs+=(--prefix PATH : ${lib.makeBinPath [ ants ]})

      ''

    else

      ''

        for prog in $out/bin/*; do

          if [[ -x "$prog" ]]; then

            wrapProgram $prog --prefix PATH : ${lib.makeBinPath [ ants ]}