crystfel: enable aarch64-* and external filter plugins on Darwin

diff --git a/meson.build b/meson.build

new file mode 100644

index 0000000..8fc0631

--- /dev/null

+++ b/meson.build

@@ -0,0 +1,110 @@

+# Meson file for libccp4c (CCP4 core libraries, C part only)

+project('libccp4c', 'c', version: '8.0.0', meson_version: '>=0.49.0', license: 'LGPL-3.0-or-later')

+

+cc = meson.get_compiler('c')

+mdep = cc.find_library('m', required: false)

+

+# Note that the source code assumes that datadir='share'.

+# If it is not, programs using the library will not be able

+# to find 'environ.def'.

+datadir = get_option('datadir') / 'ccp4'

+

+add_project_arguments('-DPACKAGE_ROOT="@0@"'.format(get_option('prefix')), language: 'c')

+add_project_arguments(

+  cc.get_supported_arguments(

+    '-Wno-uninitialized',

+    '-Wno-unused-function',

+    '-Wno-stringop-truncation',

+    '-Wno-stringop-overflow',

+    '-Wno-format-overflow',

+    '-Wno-misleading-indentation',

+    '-Wno-pointer-compare',

+  ),

+  language: 'c',

+)

+

+# C library

+libccp4c = library(

+  'ccp4c',

+  'ccp4/ccp4_array.c',

+  'ccp4/cmap_accessor.c',

+  'ccp4/cmap_open.c',

+  'ccp4/csymlib.c',

+  'ccp4/pack_c.c',

+  'ccp4/ccp4_general.c',

+  'ccp4/cmap_close.c',

+  'ccp4/cmap_skew.c',

+  'ccp4/cvecmat.c',

+  'ccp4/ccp4_parser.c',

+  'ccp4/cmap_data.c',

+  'ccp4/cmap_stats.c',

+  'ccp4/library_err.c',

+  'ccp4/ccp4_program.c',

+  'ccp4/cmap_header.c',

+  'ccp4/cmap_symop.c',

+  'ccp4/library_file.c',

+  'ccp4/ccp4_unitcell.c',

+  'ccp4/cmap_labels.c',

+  'ccp4/cmtzlib.c',

+  'ccp4/library_utils.c',

+  dependencies: mdep,

+  install: true,

+)

+

+# CCP4 headers are included with prefix: <ccp4/header.h>

+incdir = include_directories('.')

+

+install_headers(

+  'ccp4/ccp4_file_err.h',

+  'ccp4/ccp4_program.h',

+  'ccp4/ccp4_unitcell.h',

+  'ccp4/cmap_errno.h',

+  'ccp4/cmap_stats.h',

+  'ccp4/csymlib.h',

+  'ccp4/library_file.h',

+  'ccp4/ccp4_fortran.h',

+  'ccp4/ccp4_spg.h',

+  'ccp4/ccp4_utils.h',

+  'ccp4/cmap_header.h',

+  'ccp4/cmaplib.h',

+  'ccp4/cvecmat.h',

+  'ccp4/mtzdata.h',

+  'ccp4/ccp4_array.h',

+  'ccp4/ccp4_general.h',

+  'ccp4/ccp4_sysdep.h',

+  'ccp4/ccp4_vars.h',

+  'ccp4/cmap_labels.h',

+  'ccp4/cmaplib_f.h',

+  'ccp4/overview.h',

+  'ccp4/ccp4_errno.h',

+  'ccp4/ccp4_parser.h',

+  'ccp4/ccp4_types.h',

+  'ccp4/cmap_data.h',

+  'ccp4/cmap_skew.h',

+  'ccp4/cmtzlib.h',

+  'ccp4/pack_c.h',

+  subdir: 'ccp4',

+)

+

+# Data files

+install_data(

+  'data/atomsf_electron.lib',

+  'data/atomsf.lib',

+  'data/atomsf_neutron.lib',

+  'data/syminfo.lib',

+  'data/symop.lib',

+  install_dir: datadir,

+)

+

+# pkg-config file

+pkg = import('pkgconfig')

+pkg.generate(

+  libccp4c,

+  filebase: 'libccp4c',

+  description: 'CCP4 core C libraries',

+)

+

+libccp4c_dep = declare_dependency(

+  include_directories: incdir,

+  link_with: libccp4c,

+)

, 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 = "http://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 = [

      # This circumvents the original autoconf/CMake based build and uses meson instead

      ./add-meson-build.patch

      ./libccp4-use-hardcoded-syminfo-lib.patch

      ./0002-fix-ftbfs-with-gcc-10.patch

    ];

  };

  # This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult

    pname = "HDF5-External-Filter-Plugins";

    version = "0.1.0";

    src = fetchFromGitHub {

      owner = "nexusformat";

      owner = "spanezz";

      repo = pname;

      rev = "d469f175e5273c1d488e71a6134f84088f57d39c";

      sha256 = "1jrzzh75i68ad1yrim7s1nx9wy0s49ghkziahs71mm5azprm6gh9";

      rev = "master";

      hash = "sha256-Lkhhfhs0dIEplTAod1VBeO4vWH5/MIdfRvhAI3bCgD4=";

    };

    nativeBuildInputs = [ cmake ];

  ] ++ 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 = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" "aarch64-darwin" ];

  };

}

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;