diff --git a/pkgs/applications/science/physics/crystfel/0002-fix-ftbfs-with-gcc-10.patch b/pkgs/applications/science/physics/crystfel/0002-fix-ftbfs-with-gcc-10.patch deleted file mode 100644 index ddd91aec9a6e..000000000000 --- a/pkgs/applications/science/physics/crystfel/0002-fix-ftbfs-with-gcc-10.patch +++ /dev/null @@ -1,43 +0,0 @@ -Description: Fixing argument mismatches in Fortran code, addressing #957430. -Author: Andrius Merkys -Forwarded: ccp4-dev@dl.ac.uk ---- 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 diff --git a/pkgs/applications/science/physics/crystfel/default.nix b/pkgs/applications/science/physics/crystfel/default.nix index 0a981f0adf4e..1428ef826525 100644 --- a/pkgs/applications/science/physics/crystfel/default.nix +++ b/pkgs/applications/science/physics/crystfel/default.nix @@ -3,10 +3,10 @@ , fetchurl , fetchFromGitHub , fetchpatch +, fetchzip , cmake , lz4 , bzip2 -, gfortran , m4 , hdf5 , gsl @@ -38,14 +38,12 @@ 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}-${version}.tar.gz"; + hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0="; }; - nativeBuildInputs = [ gfortran m4 ]; + nativeBuildInputs = [ meson ninja ]; buildInputs = [ hdf5 gsl ]; configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ]; @@ -53,16 +51,22 @@ let # libccp4 tries to read syminfo.lib by looking at an environment variable, which hinders reproducibility. # We hard-code this by providing a little patch and then passing the absolute path to syminfo.lib as a # preprocessor flag. - preBuild = '' - makeFlagsArray+=(CFLAGS='-DNIX_PROVIDED_SYMOP_FILE=\"${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 ${mesonPatch}/meson.build . + ''; }; # This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult # since the build process is very hard-coded for a specific machine, architecture, and libraries. @@ -145,10 +149,17 @@ let src = fetchFromGitHub { owner = "nexusformat"; repo = pname; - rev = "d469f175e5273c1d488e71a6134f84088f57d39c"; - sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9"; + rev = "49e3b65eca772bca77af13ba047d8b577673afba"; + hash = "sha256-bEzfWdZuHmb0PDzCqy8Dey4tLtq+4coO0sT0GzqrTYI="; }; + patches = [ + (fetchpatch { + url = "https://github.com/spanezz/HDF5-External-Filter-Plugins/commit/6b337fe36da97a3ef72354393687ce3386c0709d.patch"; + hash = "sha256-wnBEdL/MjEyRHPwaVtuhzY+DW1AFeaUQUmIXh+JaRHo="; + }) + ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ hdf5 lz4 bzip2 ]; @@ -184,13 +195,14 @@ stdenv.mkDerivation rec { ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ] ++ lib.optionals stdenv.isDarwin [ argp-standalone + ] ++ lib.optionals (stdenv.isDarwin && !stdenv.isAarch64) [ memorymappingHook ] - # hdf5-external-filter-plugins doesn't link on Darwin - ++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ]; + ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ]; patches = [ ./link-to-argp-standalone-if-needed.patch + ./disable-fmemopen-on-aarch64-darwin.patch (fetchpatch { url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff"; hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc="; @@ -204,7 +216,7 @@ stdenv.mkDerivation rec { sed -i -e 's#execlp("mosflm"#execl("${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 @@ -224,7 +236,7 @@ stdenv.mkDerivation rec { 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; }; } diff --git a/pkgs/applications/science/physics/crystfel/disable-fmemopen-on-aarch64-darwin.patch b/pkgs/applications/science/physics/crystfel/disable-fmemopen-on-aarch64-darwin.patch new file mode 100644 index 000000000000..c35350d0008f --- /dev/null +++ b/pkgs/applications/science/physics/crystfel/disable-fmemopen-on-aarch64-darwin.patch @@ -0,0 +1,13 @@ +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;