Unverified Commit 3eabaa6c authored by Sandro Jäckel's avatar Sandro Jäckel Committed by GitHub
Browse files

Merge pull request #305305 from pmiddend/update-crystfel-to-0.11.0 

crystfel: 0.10.2 -> 0.11.0
parents 789e6037 693a4f85

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

+34 −16
Original line number Diff line number Diff line
@@ -6,15 +6,16 @@ 
, fetchzip

, cmake

, lz4

, gfortran

, bzip2

, m4

, hdf5

, gsl

, unzip

, makeWrapper

, zlib

, meson

, git

, ninja

, pandoc

, eigen

, pkg-config

, wrapGAppsHook
@@ -40,7 +41,7 @@ let 
    pname = "libccp4";

    version = "8.0.0";

    src = fetchurl {

      url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";

      url = "https://ftp.ccp4.ac.uk/opensource/libccp4-${version}.tar.gz";

      hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";

    };

    nativeBuildInputs = [ meson ninja ];
@@ -87,7 +88,7 @@ let 
          };

      mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";

    in

    stdenv.mkDerivation rec {

    stdenv.mkDerivation {

      pname = "mosflm";



      inherit version src;
@@ -111,7 +112,7 @@ let 
    pname = "xgandalf";

    version = "c6c5003ff1086e8c0fb5313660b4f02f3a3aab7b";

    src = fetchurl {

      url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";

      url = "https://gitlab.desy.de/thomas.white/xgandalf/-/archive/${version}/xgandalf-${version}.tar.gz";

      hash = "sha256-/uZlBwAINSoYqgLQFTMz8rS1Rpadu79JkO6Bu/+Nx9E=";

    };
@@ -121,10 +122,10 @@ let 


  pinkIndexer = stdenv.mkDerivation rec {

    pname = "pinkindexer";

    version = "5d4e016941eb2a9e50a10df96ded7ff1e2464503";

    version = "15caa21191e27e989b750b29566e4379bc5cd21a";

    src = fetchurl {

      url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";

      hash = "sha256-VnJOJJ247dNoBlos4Fu3GQBlAnTk9el+yZDRiicJtu0=";

      hash = "sha256-v/SCJiHAV05Lc905y/dE8uBXlW+lLX9wau4XORYdbQg=";

    };



    nativeBuildInputs = [ meson pkg-config ninja ];
@@ -169,13 +170,27 @@ let 
      "-DENABLE_BZIP2_PLUGIN=yes"

    ];

  };



  millepede-ii = stdenv.mkDerivation rec {

    pname = "millepede-ii";

    version = "04-13-06";

    src = fetchurl {

      url = "https://gitlab.desy.de/claus.kleinwort/millepede-ii/-/archive/V${version}/millepede-ii-V${version}.tar.gz";

      hash = "sha256-aFoo8AGBsUEN2u3AmnSpTqJ6JeNV6j9vkAFTZ34I+sI=";

    };



    nativeBuildInputs = [ gfortran ];

    buildInputs = [ zlib ];



    makeFlags = [ "PREFIX=$(out)" ];

  };

in

stdenv.mkDerivation rec {

  pname = "crystfel";

  version = "0.10.2";

  version = "0.11.0";

  src = fetchurl {

    url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";

    sha256 = "sha256-nCO9ndDKS54bVN9IhFBiCVNzqk7BsCljXFrOmlx+sP4=";

    url = "https://www.desy.de/~twhite/crystfel/crystfel-${version}.tar.gz";

    sha256 = "sha256-ogNHWYfbxRmB5TdK8K0JpcCnYOOyXapQGSPh8mfp+Tc=";

  };

  nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ]

    ++ lib.optionals withGui [ wrapGAppsHook ];
@@ -192,6 +207,7 @@ stdenv.mkDerivation rec { 
    mosflm

    pinkIndexer

    xgandalf

    pandoc

  ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]

  ++ lib.optionals stdenv.isDarwin [

    argp-standalone
@@ -201,12 +217,12 @@ stdenv.mkDerivation rec { 
  ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];



  patches = [

    # on darwin at least, we need to link to a separate argp library;

    # this patch adds a test for this and the necessary linker options

    ./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=";

    })

    # hotfix for an issue that occurs (at least) on NixOS:

    # if the temporary path is too long, we get a segfault

    ./gui-path-issue.patch

  ];



  # CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but
@@ -218,7 +234,9 @@ stdenv.mkDerivation rec { 


  postInstall = lib.optionalString withBitshuffle ''

    for file in $out/bin/*; do

      wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins

      wrapProgram $file \

        --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins \

        --prefix PATH ":" ${lib.makeBinPath [ millepede-ii ]}

    done

  '';

pkgs/applications/science/physics/crystfel/gui-path-issue.patch

0 → 100644
+27 −0
Original line number Diff line number Diff line 
diff --git a/src/gui_index.c b/src/gui_index.c

index 2cc8e8db..13be77d5 100644

--- a/src/gui_index.c

+++ b/src/gui_index.c

@@ -540,6 +540,7 @@ static void delete_gui_tempdir(char *tmpdir)

 {

 	char *path;

 	int i;

+	size_t pathlen;

 

 	/* List of files which it's safe to delete */

 	char *files[] = {"gmon.out", "mosflm.lp", "SUMMARY", "XDS.INP",

@@ -552,11 +553,12 @@ static void delete_gui_tempdir(char *tmpdir)

 

 	if ( tmpdir == NULL ) return;

 

-	path = calloc(strlen(tmpdir)+64, 1);

+	pathlen = strlen(tmpdir)+64;

+	path = calloc(pathlen, 1);

 	if ( path == NULL ) return;

 

 	for ( i=0; i<n_files; i++ ) {

-		snprintf(path, 127, "%s/%s", tmpdir, files[i]);

+		snprintf(path, pathlen, "%s/%s", tmpdir, files[i]);

 		unlink(path);

 	}

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

+9 −9
Original line number Diff line number Diff line 
diff --git a/meson.build b/meson.build

index 59bbcfb7..dd75d4e2 100644

index 4717bb2a..38d8693f 100644

--- a/meson.build

+++ b/meson.build

@@ -80,6 +80,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>')

@@ -70,6 +70,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>')

   conf_data.set10('HAVE_CLOCK_GETTIME', true)

 endif
@@ -12,15 +12,15 @@ index 59bbcfb7..dd75d4e2 100644 
+    argpdep = dependency('', required : false)

+endif

+

 # ************************ libcrystfel (subdir) ************************

 

 subdir('libcrystfel')

@@ -180,7 +186,7 @@ endif

 if cc.has_function('sched_setaffinity',

                    prefix: '#include <sched.h>',

                    args: '-D_GNU_SOURCE')

@@ -186,7 +192,7 @@ endif

 

 indexamajig = executable('indexamajig', indexamajig_sources,

                          dependencies: [mdep, libcrystfeldep, gsldep,

-                                        pthreaddep, zmqdep, asapodep],

+                                        pthreaddep, zmqdep, asapodep, argpdep],

-                                        pthreaddep, zmqdep, asapodep, asapoproddep],

+                                        pthreaddep, zmqdep, asapodep, asapoproddep, argpdep],

                          install: true,

                          install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')

                          install_rpath: crystfel_rpath)