crystfel: 0.10.1 → 0.10.2

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

@@ -2,6 +2,7 @@
 , stdenv
 , fetchurl
 , fetchFromGitHub
+, fetchpatch
 , cmake
 , lz4
 , bzip2
@@ -9,7 +10,6 @@
 , m4
 , hdf5
 , gsl
-, slurm
 , unzip
 , makeWrapper
 , meson
@@ -161,10 +161,10 @@ let
 in
 stdenv.mkDerivation rec {
   pname = "crystfel";
-  version = "0.10.1";
+  version = "0.10.2";
   src = fetchurl {
     url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";
-    sha256 = "0i9d5ggalic7alj97dxjdys7010kxhm2cb4lwakvigl023j8ms79";
+    sha256 = "sha256-nCO9ndDKS54bVN9IhFBiCVNzqk7BsCljXFrOmlx+sP4=";
   };
   nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ]
     ++ lib.optionals withGui [ wrapGAppsHook ];
@@ -186,12 +186,16 @@ stdenv.mkDerivation rec {
     argp-standalone
     memorymappingHook
   ]
-  # slurm is not available for Darwin; when it is, remove the condition
-  ++ lib.optionals (!stdenv.isDarwin) [ slurm ]
   # hdf5-external-filter-plugins doesn't link on Darwin
   ++ lib.optionals (withBitshuffle && !stdenv.isDarwin) [ hdf5-external-filter-plugins ];
 
-  patches = [ ./link-to-argp-standalone-if-needed.patch ];
+  patches = [
+    ./link-to-argp-standalone-if-needed.patch
+    (fetchpatch {
+      url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";
+      hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";
+    })
+  ];
 
   # CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but
   # we'd have to do that for every CrystFEL executable (indexamajig, crystfel, partialator). Better to just

pkgs/applications/science/physics/crystfel/link-to-argp-standalone-if-needed.patch

@@ -1,9 +1,9 @@
 diff --git a/meson.build b/meson.build
-index efc9002b..070f37e4 100644
+index 59bbcfb7..dd75d4e2 100644
 --- a/meson.build
 +++ b/meson.build
-@@ -34,6 +34,12 @@ if slurmdep.found()
-   conf_data.set10('HAVE_SLURM', 1)
+@@ -80,6 +80,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>')
+   conf_data.set10('HAVE_CLOCK_GETTIME', true)
  endif
  
 +if build_machine.system() == 'darwin' or build_machine.system() == 'freebsd' or not cc.links('#include <argp.h>\nstatic error_t parse_opt (int key, char *arg, struct argp_state *state) { argp_usage(state); return 0; }; void main() {}')
@@ -12,15 +12,15 @@ index efc9002b..070f37e4 100644
 +    argpdep = dependency('', required : false)
 +endif
 +
- # Find HDF5 using inbuilt Meson methods.  Requires Meson >= 0.50.0
- hdf5dep = dependency('hdf5', language: 'c', required: true)
+ # ************************ libcrystfel (subdir) ************************
  
-@@ -180,7 +186,7 @@ if zmqdep.found()
- endif
+ subdir('libcrystfel')
+@@ -180,7 +186,7 @@ endif
  
- executable('indexamajig', indexamajig_sources,
--           dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep],
-+           dependencies: [mdep, libcrystfeldep, gsldep, pthreaddep, zmqdep, argpdep],
-            install: true,
-            install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')
+ indexamajig = executable('indexamajig', indexamajig_sources,
+                          dependencies: [mdep, libcrystfeldep, gsldep,
+-                                        pthreaddep, zmqdep, asapodep],
++                                        pthreaddep, zmqdep, asapodep, argpdep],
+                          install: true,
+                          install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')