Merge pull request #218968 from pmiddend/crystfel-aarch64

CrystFEL: support aarch64-linux and HDF5 on Darwin

pkgs/applications/science/physics/crystfel/0002-fix-ftbfs-with-gcc-10.patch

···
-Description: Fixing argument mismatches in Fortran code, addressing #957430.
-Author: Andrius Merkys <[e-mail]>
-Forwarded: [e-mail]
---- a/fortran/pack_f.f
-+++ b/fortran/pack_f.f
-@@ -106,7 +106,7 @@
-          endif
-  10   continue
-       filnarray(len(filn) + 1) = 0
--      call pack_wordimage_f(data, x, y, filnarray)
-+      call pack_longimage_f(data, x, y, filnarray)
-       return
-       end
- 
-@@ -138,7 +138,7 @@
-          endif
-  10   continue
-       filnarray(len(filn) + 1) = 0
--      call v2pack_wordimage_f(data, x, y, filnarray)
-+      call v2pack_longimage_f(data, x, y, filnarray)
-       return
-       end
- 
---- a/fortran/lgglib.f
-+++ b/fortran/lgglib.f
-@@ -1236,7 +1236,7 @@
-       B3(2) = XYZ(2) * CELL(2)
-       B3(3) = XYZ(3) * CELL(3)
- C
--      CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
-+      CALL matmult(3,3,3,1,ORTH,B3,XYZ)
-       END
- c
- c
-@@ -1274,7 +1274,7 @@
-       B3(1) = XYZ(1)
-       B3(2) = XYZ(2)
-       B3(3) = XYZ(3)
--      CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
-+      CALL matmult(3,3,3,1,ORTH,B3,XYZ)
-       END
-       character*80 function getnam(filnam)
-       character*(*) filnam

pkgs/applications/science/physics/crystfel/default.nix

···
 , fetchurl
 , fetchFromGitHub
 , fetchpatch
+, fetchzip
 , cmake
 , lz4
 , bzip2
-, gfortran
 , m4
 , hdf5
 , gsl
···
 let
   libccp4 = stdenv.mkDerivation rec {
     pname = "libccp4";
-    version = "6.5.1";
+    version = "8.0.0";
     src = fetchurl {
-      # Original mirror, now times out
-      # url = "ftp://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
-      url = "https://deb.debian.org/debian/pool/main/libc/${pname}/${pname}_${version}.orig.tar.gz";
-      sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";
+      url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
+      hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";
     };
-    nativeBuildInputs = [ gfortran m4 ];
+    nativeBuildInputs = [ meson ninja ];
     buildInputs = [ hdf5 gsl ];
 
     configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
···
     # libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility.
     # We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a
     # preprocessor flag.
-    preBuild = ''
-      makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"')
-      export NIX_LDFLAGS="-L${gfortran.cc}/lib64 -L${gfortran.cc}/lib $NIX_LDFLAGS";
-    '';
-    makeFlags = [ "CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/syminfo.lib\"" ];
+    env.NIX_CFLAGS_COMPILE = "-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/ccp4/syminfo.lib\"";
 
     patches = [
       ./libccp4-use-hardcoded-syminfo-lib.patch
-      ./0002-fix-ftbfs-with-gcc-10.patch
     ];
+
+    postPatch =
+      let
+        mesonPatch = fetchzip {
+          url = "https://wrapdb.mesonbuild.com/v2/libccp4c_8.0.0-1/get_patch#somefile.zip";
+          hash = "sha256-ohskfKh+972Pl56KtwAeWwHtAaAFNpCzz5vZBAI/vdU=";
+        };
+      in
+      ''
+        cp ${mesonPatch}/meson.build .
+      '';
   };
   # This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
   # since the build process is very hard-coded for a specific machine, architecture, and libraries.
···
     src = fetchFromGitHub {
       owner = "nexusformat";
       repo = pname;
-      rev = "d469f175e5273c1d488e71a6134f84088f57d39c";
-      sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";
+      rev = "49e3b65eca772bca77af13ba047d8b577673afba";
+      hash = "sha256-bEzfWdZuHmb0PDzCqy8Dey4tLtq+4coO0sT0GzqrTYI=";
     };
 
+    patches = [
+      (fetchpatch {
+        url = "https://github.com/spanezz/HDF5-External-Filter-Plugins/commit/6b337fe36da97a3ef72354393687ce3386c0709d.patch";
+        hash = "sha256-wnBEdL/MjEyRHPwaVtuhzY+DW1AFeaUQUmIXh+JaRHo=";
+      })
+    ];
+
     nativeBuildInputs = [ cmake ];
     buildInputs = [ hdf5 lz4 bzip2 ];
 
···
   ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
   ++ lib.optionals stdenv.isDarwin [
     argp-standalone
+  ] ++ lib.optionals (stdenv.isDarwin && !stdenv.isAarch64) [
     memorymappingHook
   ]
-  # hdf5-external-filter-plugins doesn't link on Darwin
-  ++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];
+  ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];
 
   patches = [
     ./link-to-argp-standalone-if-needed.patch
+    ./disable-fmemopen-on-aarch64-darwin.patch
     (fetchpatch {
       url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";
       hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";
···
     sed -i -e 's#execlp("mosflm"#execl("${mosflm}/bin/mosflm"#' libcrystfel/src/indexers/mosflm.c;
   '';
 
-  postInstall = lib.optionalString (withBitshuffle && !stdenv.isDarwin) ''
+  postInstall = lib.optionalString withBitshuffle ''
     for file in $out/bin/*; do
       wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
     done
···
     downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
     license = licenses.gpl3Plus;
     maintainers = with maintainers; [ pmiddend ];
-    platforms = [ "x86_64-linux" "x86_64-darwin" ];
+    platforms = platforms.unix;
   };
 
 }

pkgs/applications/science/physics/crystfel/disable-fmemopen-on-aarch64-darwin.patch

···
+diff --git a/libcrystfel/src/image-cbf.c b/libcrystfel/src/image-cbf.c
+index b8f09a1f..f8a15c1b 100644
+--- a/libcrystfel/src/image-cbf.c
++++ b/libcrystfel/src/image-cbf.c
+@@ -287,7 +287,7 @@ static float *read_cbf_data(const char *filename, int gz, int *w, int *h)
+ 
+ 	} else {
+ 
+-		#ifdef HAVE_ZLIB
++		#if defined(HAVE_ZLIB) && !(defined(__aarch64__) && defined(__APPLE__))
+ 		gzFile gzfh;
+ 		int len_read;
+ 		size_t len;