crystfel: review fixes

3 files changed, 23 insertions, 165 deletions

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 ddd91aec9a6e7..0000000000000
--- 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 <merkys@debian.org>
-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/add-meson-build.patch b/pkgs/applications/science/physics/crystfel/add-meson-build.patch
deleted file mode 100644
index 7d77ba47a37e5..0000000000000
--- a/pkgs/applications/science/physics/crystfel/add-meson-build.patch
+++ /dev/null
@@ -1,116 +0,0 @@
-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 116c3f5d84569..e916e9c44654b 100644
--- a/pkgs/applications/science/physics/crystfel/default.nix
+++ b/pkgs/applications/science/physics/crystfel/default.nix
@@ -3,6 +3,7 @@
 , fetchurl
 , fetchFromGitHub
 , fetchpatch
+, fetchzip
 , cmake
 , lz4
 , bzip2
@@ -39,7 +40,7 @@ let
     pname = "libccp4";
     version = "8.0.0";
     src = fetchurl {
-      url = "http://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
+      url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
       hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";
     };
     nativeBuildInputs = [ meson ninja ];
@@ -53,10 +54,19 @@ let
     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
     ];
+
+    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.
@@ -137,12 +147,19 @@ let
     pname = "HDF5-External-Filter-Plugins";
     version = "0.1.0";
     src = fetchFromGitHub {
-      owner = "spanezz";
+      owner = "nexusformat";
       repo = pname;
       rev = "master";
-      hash = "sha256-Lkhhfhs0dIEplTAod1VBeO4vWH5/MIdfRvhAI3bCgD4=";
+      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 ];
 
@@ -219,7 +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" "aarch64-linux" "aarch64-darwin" ];
+    platforms = platforms.unix;
   };
 
 }