Merge pull request #31781 from robertodr/hdf5-fortran-2003

Update HDF5 and add option to compile Fortran2003 interface

pkgs/tools/misc/hdf5/1_8.nix

@@ -0,0 +1,76 @@
+{ stdenv
+, fetchurl
+, gcc
+, 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";
+  name = "hdf5-${version}";
+  src = fetchurl {
+    url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${name}/src/${name}.tar.bz2";
+    sha256 = "0f3jfbqpaaq21ighi40qzs52nb52kc2d2yjk541rjmsx20b3ih2r" ;
+ };
+
+  passthru = {
+    mpiSupport = (mpi != null);
+    inherit mpi;
+  };
+
+  nativeBuildInputs = [ removeReferencesTo ];
+
+  buildInputs = []
+    ++ optional (gfortran != null) gfortran
+    ++ optional (szip != null) szip;
+
+  propagatedBuildInputs = []
+    ++ optional (zlib != null) zlib
+    ++ optional (mpi != null) mpi;
+
+  configureFlags = []
+    ++ optional cpp "--enable-cxx"
+    ++ optional (gfortran != null) "--enable-fortran"
+    ++ optional fortran2003 "--enable-fortran2003"
+    ++ optional (szip != null) "--with-szlib=${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;
+  };
+}

pkgs/tools/misc/hdf5/default.nix

@@ -14,17 +14,14 @@
 # (--enable-unsupported could be used to force the build)
 assert !cpp || mpi == 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 = "1.8.18";
+  version = "1.10.1";
   name = "hdf5-${version}";
   src = fetchurl {
-    url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/${name}/src/${name}.tar.bz2";
-    sha256 = "13542vrnl1p35n8vbq0wzk40vddmm33q5nh04j98c7r1yjnxxih1";
+    url = "https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/${name}/src/${name}.tar.bz2";
+    sha256 = "1wpbi15za7kbsvih88kfcxblw412pjndl16x88dgnqr47piy2p4w";
  };
 
   passthru = {
@@ -59,8 +56,8 @@ stdenv.mkDerivation rec {
     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 
+      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

pkgs/top-level/all-packages.nix

@@ -2590,6 +2590,12 @@ with pkgs;
     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;