Merge pull request #93675 from bcdarwin/update-libminc

libminc: 2.4.03 -> unstable-2020-07-17

14 files changed, 41 insertions, 138 deletions

diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix
index 7502a4ffd2abf..a9661ee2db787 100644
--- a/pkgs/applications/science/biology/EZminc/default.nix
+++ b/pkgs/applications/science/biology/EZminc/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "EZminc";
-  name  = "${pname}-unstable-2019-03-12";
+  version = "unstable-2019-03-12";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake pkgconfig ];
   buildInputs = [ itk4 libminc bicpl fftwFloat gsl ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
                  "-DEZMINC_BUILD_TOOLS=TRUE"
                  "-DEZMINC_BUILD_MRFSEG=TRUE"
                  "-DEZMINC_BUILD_DD=TRUE" ];
diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix
index d2dbcf1853307..13ffc305d3926 100644
--- a/pkgs/applications/science/biology/N3/default.nix
+++ b/pkgs/applications/science/biology/N3/default.nix
@@ -4,20 +4,20 @@
 
 stdenv.mkDerivation rec {
   pname = "N3";
-  name  = "${pname}-2017-09-18";
+  version = "unstable-2018-08-09";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "2fdd939f0f2b24a4039bc6a8ade4a190a1d8e75d";
-    sha256 = "13z21c4r09hna3q1csvcn4i7ws5ixbdaja6ch421xv6nydjh2w5g";
+    rev    = "010fc2ac58ce1d67b8e6a863fac0809d3203cb9b";
+    sha256 = "06hci7gzhy8p34ggvx7gah2k9yxpwhgmq1cgw8pcd1r82g4rg6kd";
   };
 
   nativeBuildInputs = [ cmake makeWrapper ];
   buildInputs = [ libminc EBTKS ];
   propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ];
 
   postFixup = ''
     for p in $out/bin/*; do
@@ -26,7 +26,7 @@ stdenv.mkDerivation rec {
   '';
 
   meta = with stdenv.lib; {
-    homepage = "https://github.com/BIC-MNI/${pname}";
+    homepage = "https://github.com/BIC-MNI/N3";
     description = "MRI non-uniformity correction for MINC files";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix
index 971e2f23055b2..8fb8e17eef860 100644
--- a/pkgs/applications/science/biology/conglomerate/default.nix
+++ b/pkgs/applications/science/biology/conglomerate/default.nix
@@ -3,7 +3,7 @@
 
 stdenv.mkDerivation rec {
   pname = "conglomerate";
-  name  = "${pname}-2017-09-10";
+  version = "unstable-2017-09-10";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
@@ -16,7 +16,10 @@ stdenv.mkDerivation rec {
   buildInputs = [ libminc zlib bicpl ];
   propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]);
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBICPL_DIR=${bicpl}/lib/" ];
+  cmakeFlags = [
+    "-DLIBMINC_DIR=${libminc}/lib/cmake"
+    "-DBICPL_DIR=${bicpl}/lib"
+  ];
 
   postFixup = ''
     for p in $out/bin/*; do
diff --git a/pkgs/applications/science/biology/inormalize/default.nix b/pkgs/applications/science/biology/inormalize/default.nix
index 9e63b92b24ed5..e6293bb90ef38 100644
--- a/pkgs/applications/science/biology/inormalize/default.nix
+++ b/pkgs/applications/science/biology/inormalize/default.nix
@@ -19,7 +19,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ libminc EBTKS ];
   propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ];
 
   postFixup = ''
     for p in $out/bin/*; do
diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix
index b2029842bbba3..c594897f4b6fd 100644
--- a/pkgs/applications/science/biology/minc-tools/default.nix
+++ b/pkgs/applications/science/biology/minc-tools/default.nix
@@ -3,28 +3,20 @@
 
 stdenv.mkDerivation rec {
   pname   = "minc-tools";
-  version = "unstable-2019-12-04";
+  version = "unstable-2020-07-25";
 
   src = fetchFromGitHub {
     owner  = "BIC-MNI";
     repo   = pname;
-    rev    = "d4dddfdb4e4fa0cea389b8fdce51cfc076565d94";
-    sha256 = "1wwdss59qq4hz1jp35qylfswzzv0d37if23al0srnxkkgc5f8zng";
+    rev    = "fb0a68a07d281e4e099c5d54df29925240de14c1";
+    sha256 = "0zcv2sdj3k6k0xjqdq8j5bxq8smm48dzai90vwsmz8znmbbm6kvw";
   };
 
-  patches = [ ./fix-netcdf-header.patch ];
-
-  # add missing CMake module to build NIFTI support
-  # (the maintainers normally build libminc and minc-tools in a meta-project)
-  postPatch = ''
-    cp ${libminc.src}/cmake-modules/FindNIFTI.cmake cmake-modules
-  '';
-
   nativeBuildInputs = [ cmake flex bison makeWrapper ];
   buildInputs = [ libminc libjpeg nifticlib zlib ];
   propagatedBuildInputs = [ perl TextFormat ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/"
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
                  "-DZNZ_INCLUDE_DIR=${nifticlib}/include/nifti"
                  "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti" ];
 
diff --git a/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch b/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch
deleted file mode 100644
index 89c7564f8b626..0000000000000
--- a/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff --git a/progs/mincdump/mincdump.h b/progs/mincdump/mincdump.h
-index 14c95cd..117ab26 100644
---- a/progs/mincdump/mincdump.h
-+++ b/progs/mincdump/mincdump.h
-@@ -3,6 +3,7 @@
-  *   See netcdf/COPYRIGHT file for copying and redistribution conditions.
-  *   $Header: /private-cvsroot/minc/progs/mincdump/mincdump.h,v 1.1 2004-04-27 15:35:15 bert Exp $
-  *********************************************************************/
-+#include <netcdf_meta.h>
- 
- 
- /* error checking macro */
diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix
index 254d874f9d912..40ec9e0de6d21 100644
--- a/pkgs/applications/science/biology/mni_autoreg/default.nix
+++ b/pkgs/applications/science/biology/mni_autoreg/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "mni_autoreg";
-  name  = "${pname}-2017-09-22";
+  version = "unstable-2017-09-22";
 
   src = fetchFromGitHub {
     owner = "BIC-MNI";
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ libminc ];
   propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
   # testing broken: './minc_wrapper: Permission denied' from Testing/ellipse0.mnc
 
   postFixup = ''
diff --git a/pkgs/development/libraries/libminc/default.nix b/pkgs/development/libraries/libminc/default.nix
index 53b6af40b512b..ce39285e0d239 100644
--- a/pkgs/development/libraries/libminc/default.nix
+++ b/pkgs/development/libraries/libminc/default.nix
@@ -2,15 +2,15 @@
 
 stdenv.mkDerivation rec {
   pname   = "libminc";
-  version = "2.4.03";
+  version = "unstable-2020-07-17";
 
   owner = "BIC-MNI";
 
   src = fetchFromGitHub {
     inherit owner;
     repo   = pname;
-    rev    = "release-${version}";
-    sha256 = "0kpmqs9df836ywsqj749qbsfavf5bnldblxrmnmxqq9pywc8yfrm";
+    rev    = "ffb5fb234a852ea7e8da8bb2b3b49f67acbe56ca";
+    sha256 = "0yr4ksghpvxh9zg0a4p7hvln3qirsi08plvjp5kxx2qiyj96zsdm";
   };
 
   postPatch = ''
@@ -18,7 +18,8 @@ stdenv.mkDerivation rec {
   '';
 
   nativeBuildInputs = [ cmake ];
-  buildInputs = [ zlib netcdf nifticlib hdf5 ];
+  buildInputs = [ zlib nifticlib ];
+  propagatedBuildInputs = [ netcdf hdf5 ];
 
   cmakeFlags = [
     "-DLIBMINC_MINC1_SUPPORT=ON"
@@ -29,17 +30,16 @@ stdenv.mkDerivation rec {
   doCheck = !stdenv.isDarwin;
   checkPhase = ''
     export LD_LIBRARY_PATH="$(pwd)"  # see #22060
-    ctest -E 'ezminc_rw_test|minc_conversion' --output-on-failure
-    # ezminc_rw_test can't find libminc_io.so.5.2.0; minc_conversion hits netcdf compilation issue
+    ctest -j1 -E 'ezminc_rw_test' --output-on-failure
+    # -j1: see https://github.com/BIC-MNI/libminc/issues/110
+    # ezminc_rw_test: can't find libminc_io.so.5.2.0
   '';
 
-  enableParallelBuilding = true;
-
   meta = with stdenv.lib; {
-    homepage = "https://github.com/${owner}/${pname}";
+    homepage = "https://github.com/BIC-MNI/libminc";
     description = "Medical imaging library based on HDF5";
     maintainers = with maintainers; [ bcdarwin ];
     platforms = platforms.unix;
-    license   = licenses.free;
+    license = licenses.free;
   };
 }
diff --git a/pkgs/development/libraries/science/biology/EBTKS/default.nix b/pkgs/development/libraries/science/biology/EBTKS/default.nix
index f4353f51d66cb..c60fe31aaaff4 100644
--- a/pkgs/development/libraries/science/biology/EBTKS/default.nix
+++ b/pkgs/development/libraries/science/biology/EBTKS/default.nix
@@ -14,7 +14,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
 
   meta = with stdenv.lib; {
     homepage = "https://github.com/BIC-MNI/${pname}";
diff --git a/pkgs/development/libraries/science/biology/bicgl/default.nix b/pkgs/development/libraries/science/biology/bicgl/default.nix
index 3c9b8f8257cef..4cc7dcada5220 100644
--- a/pkgs/development/libraries/science/biology/bicgl/default.nix
+++ b/pkgs/development/libraries/science/biology/bicgl/default.nix
@@ -2,21 +2,24 @@
 
 stdenv.mkDerivation rec {
   pname = "bicgl";
-  name  = "${pname}-2017-09-10";
+  version = "unstable-2018-04-06";
 
   owner = "BIC-MNI";
 
   src = fetchFromGitHub {
     inherit owner;
     repo   = pname;
-    rev    = "b7f7e52d1039d6202a93d9055f516186033656cc";
+    rev    = "61a035751c9244fcca1edf94d6566fa2a709ce90";
     sha256 = "0lzirdi1mf4yl8srq7vjn746sbydz7h0wjh7wy8gycy6hq04qrg4";
   };
 
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc bicpl freeglut mesa_glu ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" "-DBICPL_DIR=${bicpl}/lib" ];
+  cmakeFlags = [
+    "-DLIBMINC_DIR=${libminc}/lib/cmake"
+    "-DBICPL_DIR=${bicpl}/lib"
+  ];
 
   meta = with stdenv.lib; {
     homepage = "https://github.com/${owner}/${pname}";
diff --git a/pkgs/development/libraries/science/biology/bicpl/default.nix b/pkgs/development/libraries/science/biology/bicpl/default.nix
index 0c634c0f265c1..96199f0478ea9 100644
--- a/pkgs/development/libraries/science/biology/bicpl/default.nix
+++ b/pkgs/development/libraries/science/biology/bicpl/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "bicpl";
-  name  = "${pname}-2017-09-10";
+  version = "unstable-2017-09-10";
 
   owner = "BIC-MNI";
 
@@ -17,7 +17,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc netpbm ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ];
 
   doCheck = false;
   # internal_volume_io.h: No such file or directory
diff --git a/pkgs/development/libraries/science/biology/oobicpl/default.nix b/pkgs/development/libraries/science/biology/oobicpl/default.nix
index 8755b7fd2eba5..e5ecda0390bdd 100644
--- a/pkgs/development/libraries/science/biology/oobicpl/default.nix
+++ b/pkgs/development/libraries/science/biology/oobicpl/default.nix
@@ -2,7 +2,7 @@
 
 stdenv.mkDerivation rec {
   pname = "oobicpl";
-  name  = "${pname}-2016-03-02";
+  version = "unstable-2016-03-02";
 
   owner = "BIC-MNI";
 
@@ -16,7 +16,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake ];
   buildInputs = [ libminc bicpl arguments pcre-cpp ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib"
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake"
                  "-DBICPL_DIR=${bicpl}/lib"
                  "-DARGUMENTS_DIR=${arguments}/lib"
                  "-DOOBICPL_BUILD_SHARED_LIBS=TRUE" ];
diff --git a/pkgs/tools/misc/hdf5/1_8.nix b/pkgs/tools/misc/hdf5/1_8.nix
deleted file mode 100644
index 849fa6b9ac3b9..0000000000000
--- a/pkgs/tools/misc/hdf5/1_8.nix
+++ /dev/null
@@ -1,75 +0,0 @@
-{ stdenv
-, fetchurl
-, removeReferencesTo
-, cpp ? false
-, gfortran ? null
-, fortran2003 ? false
-, zlib ? null
-, szip ? null
-, mpi ? null
-, enableShared ? true
-}:
-
-# cpp and mpi options are mutually exclusive
-# (--enable-unsupported could be used to force the build)
-assert !cpp || mpi == null;
-
-# Need a Fortran compiler for Fortran2003 bindings
-assert fortran2003 -> gfortran != null;
-
-# No point splitting version 1.8.18 into multiple outputs.
-# The library /lib/libhdf5.so has a reference to gcc-wrapper
-
-let inherit (stdenv.lib) optional optionals; in
-
-stdenv.mkDerivation rec {
-  version = "1.8.19";
-  pname = "hdf5";
-  src = fetchurl {
-    url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${pname}-${version}/src/${pname}-${version}.tar.bz2";
-    sha256 = "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r" ;
- };
-
-  passthru = {
-    mpiSupport = (mpi != null);
-    inherit mpi;
-  };
-
-  nativeBuildInputs = [ removeReferencesTo ];
-
-  buildInputs = []
-    ++ optional (gfortran != null) gfortran
-    ++ optional (szip != null) szip;
-
-  propagatedBuildInputs = []
-    ++ optional (zlib != null) zlib
-    ++ optional (mpi != null) mpi;
-
-  configureFlags = []
-    ++ optional cpp "--enable-cxx"
-    ++ optional (gfortran != null) "--enable-fortran"
-    ++ optional fortran2003 "--enable-fortran2003"
-    ++ optional (szip != null) "--with-szlib=${szip}"
-    ++ optionals (mpi != null) ["--enable-parallel" "CC=${mpi}/bin/mpicc"]
-    ++ optional enableShared "--enable-shared";
-
-  patches = [./bin-mv.patch];
-
-  postInstall = ''
-    find "$out" -type f -exec remove-references-to -t ${stdenv.cc} '{}' +
-  '';
-
-  meta = {
-    description = "Data model, library, and file format for storing and managing data";
-    longDescription = ''
-      HDF5 supports an unlimited variety of datatypes, and is designed for flexible and efficient
-      I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing
-      applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and
-      applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
-    '';
-    license = stdenv.lib.licenses.free; # BSD-like
-    homepage = "https://www.hdfgroup.org/HDF5/";
-    platforms = stdenv.lib.platforms.unix;
-    broken = (gfortran != null) && stdenv.isDarwin;
-  };
-}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index b08c9fbfe0b3e..82429dcff87fb 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -4370,12 +4370,6 @@ in
     mpi = null;
   };
 
-  hdf5_1_8 = callPackage ../tools/misc/hdf5/1_8.nix {
-    gfortran = null;
-    szip = null;
-    mpi = null;
-  };
-
   hdf5-mpi = appendToName "mpi" (hdf5.override {
     szip = null;
     mpi = pkgs.openmpi;
@@ -13927,9 +13921,7 @@ in
 
   libmilter = callPackage ../development/libraries/libmilter { };
 
-  libminc = callPackage ../development/libraries/libminc {
-    hdf5 = hdf5_1_8;
-  };
+  libminc = callPackage ../development/libraries/libminc { };
 
   libmirage = callPackage ../misc/emulators/cdemu/libmirage.nix { };