Merge pull request #305305 from pmiddend/update-crystfel-to-0.11.0
crystfel: 0.10.2 -> 0.11.0
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3eabaa6c36
@ -6,15 +6,16 @@
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, fetchzip
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, cmake
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, lz4
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, gfortran
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, bzip2
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, m4
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, hdf5
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, gsl
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, unzip
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, makeWrapper
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, zlib
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, meson
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, git
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, ninja
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, pandoc
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, eigen
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, pkg-config
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, wrapGAppsHook
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@ -40,7 +41,7 @@ let
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pname = "libccp4";
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version = "8.0.0";
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src = fetchurl {
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url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
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url = "https://ftp.ccp4.ac.uk/opensource/libccp4-${version}.tar.gz";
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hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";
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};
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nativeBuildInputs = [ meson ninja ];
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@ -87,7 +88,7 @@ let
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};
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mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";
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in
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stdenv.mkDerivation rec {
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stdenv.mkDerivation {
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pname = "mosflm";
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inherit version src;
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@ -111,7 +112,7 @@ let
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pname = "xgandalf";
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version = "c6c5003ff1086e8c0fb5313660b4f02f3a3aab7b";
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src = fetchurl {
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url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
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url = "https://gitlab.desy.de/thomas.white/xgandalf/-/archive/${version}/xgandalf-${version}.tar.gz";
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hash = "sha256-/uZlBwAINSoYqgLQFTMz8rS1Rpadu79JkO6Bu/+Nx9E=";
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};
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@ -121,10 +122,10 @@ let
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pinkIndexer = stdenv.mkDerivation rec {
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pname = "pinkindexer";
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version = "5d4e016941eb2a9e50a10df96ded7ff1e2464503";
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version = "15caa21191e27e989b750b29566e4379bc5cd21a";
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src = fetchurl {
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url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";
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hash = "sha256-VnJOJJ247dNoBlos4Fu3GQBlAnTk9el+yZDRiicJtu0=";
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hash = "sha256-v/SCJiHAV05Lc905y/dE8uBXlW+lLX9wau4XORYdbQg=";
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};
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nativeBuildInputs = [ meson pkg-config ninja ];
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@ -169,13 +170,27 @@ let
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"-DENABLE_BZIP2_PLUGIN=yes"
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];
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};
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millepede-ii = stdenv.mkDerivation rec {
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pname = "millepede-ii";
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version = "04-13-06";
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src = fetchurl {
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url = "https://gitlab.desy.de/claus.kleinwort/millepede-ii/-/archive/V${version}/millepede-ii-V${version}.tar.gz";
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hash = "sha256-aFoo8AGBsUEN2u3AmnSpTqJ6JeNV6j9vkAFTZ34I+sI=";
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};
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nativeBuildInputs = [ gfortran ];
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buildInputs = [ zlib ];
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makeFlags = [ "PREFIX=$(out)" ];
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};
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in
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stdenv.mkDerivation rec {
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pname = "crystfel";
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version = "0.10.2";
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version = "0.11.0";
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src = fetchurl {
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url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";
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sha256 = "sha256-nCO9ndDKS54bVN9IhFBiCVNzqk7BsCljXFrOmlx+sP4=";
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url = "https://www.desy.de/~twhite/crystfel/crystfel-${version}.tar.gz";
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sha256 = "sha256-ogNHWYfbxRmB5TdK8K0JpcCnYOOyXapQGSPh8mfp+Tc=";
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};
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nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ]
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++ lib.optionals withGui [ wrapGAppsHook ];
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@ -192,6 +207,7 @@ stdenv.mkDerivation rec {
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mosflm
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pinkIndexer
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xgandalf
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pandoc
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] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]
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++ lib.optionals stdenv.isDarwin [
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argp-standalone
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@ -201,12 +217,12 @@ stdenv.mkDerivation rec {
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++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];
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patches = [
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# on darwin at least, we need to link to a separate argp library;
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# this patch adds a test for this and the necessary linker options
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./link-to-argp-standalone-if-needed.patch
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./disable-fmemopen-on-aarch64-darwin.patch
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(fetchpatch {
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url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";
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hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";
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})
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# hotfix for an issue that occurs (at least) on NixOS:
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# if the temporary path is too long, we get a segfault
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./gui-path-issue.patch
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];
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# CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but
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@ -218,7 +234,9 @@ stdenv.mkDerivation rec {
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postInstall = lib.optionalString withBitshuffle ''
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for file in $out/bin/*; do
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wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins
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wrapProgram $file \
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--set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins \
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--prefix PATH ":" ${lib.makeBinPath [ millepede-ii ]}
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done
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'';
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@ -0,0 +1,27 @@
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diff --git a/src/gui_index.c b/src/gui_index.c
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index 2cc8e8db..13be77d5 100644
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--- a/src/gui_index.c
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+++ b/src/gui_index.c
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@@ -540,6 +540,7 @@ static void delete_gui_tempdir(char *tmpdir)
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{
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char *path;
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int i;
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+ size_t pathlen;
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/* List of files which it's safe to delete */
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char *files[] = {"gmon.out", "mosflm.lp", "SUMMARY", "XDS.INP",
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@@ -552,11 +553,12 @@ static void delete_gui_tempdir(char *tmpdir)
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if ( tmpdir == NULL ) return;
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- path = calloc(strlen(tmpdir)+64, 1);
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+ pathlen = strlen(tmpdir)+64;
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+ path = calloc(pathlen, 1);
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if ( path == NULL ) return;
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for ( i=0; i<n_files; i++ ) {
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- snprintf(path, 127, "%s/%s", tmpdir, files[i]);
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+ snprintf(path, pathlen, "%s/%s", tmpdir, files[i]);
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unlink(path);
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}
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@ -1,8 +1,8 @@
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diff --git a/meson.build b/meson.build
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index 59bbcfb7..dd75d4e2 100644
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index 4717bb2a..38d8693f 100644
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--- a/meson.build
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+++ b/meson.build
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@@ -80,6 +80,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>')
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@@ -70,6 +70,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>')
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conf_data.set10('HAVE_CLOCK_GETTIME', true)
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endif
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@ -12,15 +12,15 @@ index 59bbcfb7..dd75d4e2 100644
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+ argpdep = dependency('', required : false)
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+endif
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+
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# ************************ libcrystfel (subdir) ************************
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subdir('libcrystfel')
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@@ -180,7 +186,7 @@ endif
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if cc.has_function('sched_setaffinity',
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prefix: '#include <sched.h>',
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args: '-D_GNU_SOURCE')
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@@ -186,7 +192,7 @@ endif
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indexamajig = executable('indexamajig', indexamajig_sources,
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dependencies: [mdep, libcrystfeldep, gsldep,
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- pthreaddep, zmqdep, asapodep],
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+ pthreaddep, zmqdep, asapodep, argpdep],
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- pthreaddep, zmqdep, asapodep, asapoproddep],
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+ pthreaddep, zmqdep, asapodep, asapoproddep, argpdep],
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install: true,
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install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')
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install_rpath: crystfel_rpath)
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