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

3 files changed, 144 insertions, 20 deletions

diff --git a/pkgs/applications/science/physics/crystfel/add-meson-build.patch b/pkgs/applications/science/physics/crystfel/add-meson-build.patch
new file mode 100644
index 000000000000..7d77ba47a37e
--- /dev/null
+++ b/pkgs/applications/science/physics/crystfel/add-meson-build.patch
@@ -0,0 +1,116 @@
+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,
++)
diff --git a/pkgs/applications/science/physics/crystfel/default.nix b/pkgs/applications/science/physics/crystfel/default.nix
index 0a981f0adf4e..116c3f5d8456 100644
--- a/pkgs/applications/science/physics/crystfel/default.nix
+++ b/pkgs/applications/science/physics/crystfel/default.nix
@@ -6,7 +6,6 @@
 , cmake
 , lz4
 , bzip2
-, gfortran
 , m4
 , hdf5
 , gsl
@@ -38,14 +37,12 @@
 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}_${version}.orig.tar.gz";
-      sha256 = "1rfvjliny29vy5bdi6rrjaw9hhhhh72pw536xwvqipqcjlylf2r8";
+      url = "http://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
+      hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";
     };
-    nativeBuildInputs = [ gfortran m4 ];
+    nativeBuildInputs = [ meson ninja ];
     buildInputs = [ hdf5 gsl ];
 
     configureFlags = [ "FFLAGS=-fallow-argument-mismatch" ];
@@ -53,15 +50,12 @@ 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 = [
+      # 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
@@ -143,10 +137,10 @@ let
     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 ];
@@ -184,13 +178,14 @@ 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 +199,7 @@ 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 +219,7 @@ 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 = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" "aarch64-darwin" ];
   };
 
 }
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;