commit 3eabaa6c364fec9d12ccf4fd25edd8502fef814f · pyrox.dev/nixpkgs

+34 -16

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

···

       6
        
       , fetchzip

     

       7
        
       , cmake

     

       8
        
       , lz4

     

       0
        
       
     

       9
        
       , bzip2

     

       10
       -
       , m4

     

       11
        
       , hdf5

     

       12
        
       , gsl

     

       13
        
       , unzip

     

       14
        
       , makeWrapper

     

       0
        
       
     

       15
        
       , meson

     

       16
       -
       , git

     

       17
        
       , ninja

     

       0
        
       
     

       18
        
       , eigen

     

       19
        
       , pkg-config

     

       20
        
       , wrapGAppsHook

     
···

       40
        
           pname = "libccp4";

     

       41
        
           version = "8.0.0";

     

       42
        
           src = fetchurl {

     

       43
       -
             url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";

     

       44
        
             hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";

     

       45
        
           };

     

       46
        
           nativeBuildInputs = [ meson ninja ];

     
···

       87
        
                 };

     

       88
        
             mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";

     

       89
        
           in

     

       90
       -
           stdenv.mkDerivation rec {

     

       91
        
             pname = "mosflm";

     

       92
        
       

     

       93
        
             inherit version src;

     
···

       111
        
           pname = "xgandalf";

     

       112
        
           version = "c6c5003ff1086e8c0fb5313660b4f02f3a3aab7b";

     

       113
        
           src = fetchurl {

     

       114
       -
             url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";

     

       115
        
             hash = "sha256-/uZlBwAINSoYqgLQFTMz8rS1Rpadu79JkO6Bu/+Nx9E=";

     

       116
        
           };

     

       117
        
       

     
···

       121
        
       

     

       122
        
         pinkIndexer = stdenv.mkDerivation rec {

     

       123
        
           pname = "pinkindexer";

     

       124
       -
           version = "5d4e016941eb2a9e50a10df96ded7ff1e2464503";

     

       125
        
           src = fetchurl {

     

       126
        
             url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";

     

       127
       -
             hash = "sha256-VnJOJJ247dNoBlos4Fu3GQBlAnTk9el+yZDRiicJtu0=";

     

       128
        
           };

     

       129
        
       

     

       130
        
           nativeBuildInputs = [ meson pkg-config ninja ];

     
···

       169
        
             "-DENABLE_BZIP2_PLUGIN=yes"

     

       170
        
           ];

     

       171
        
         };

     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       0
        
       
     

       172
        
       in

     

       173
        
       stdenv.mkDerivation rec {

     

       174
        
         pname = "crystfel";

     

       175
       -
         version = "0.10.2";

     

       176
        
         src = fetchurl {

     

       177
       -
           url = "https://www.desy.de/~twhite/${pname}/${pname}-${version}.tar.gz";

     

       178
       -
           sha256 = "sha256-nCO9ndDKS54bVN9IhFBiCVNzqk7BsCljXFrOmlx+sP4=";

     

       179
        
         };

     

       180
        
         nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ]

     

       181
        
           ++ lib.optionals withGui [ wrapGAppsHook ];

     
···

       192
        
           mosflm

     

       193
        
           pinkIndexer

     

       194
        
           xgandalf

     

       0
        
       
     

       195
        
         ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]

     

       196
        
         ++ lib.optionals stdenv.isDarwin [

     

       197
        
           argp-standalone

     
···

       201
        
         ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];

     

       202
        
       

     

       203
        
         patches = [

     

       0
        
       
     

       0
        
       
     

       204
        
           ./link-to-argp-standalone-if-needed.patch

     

       205
       -
           ./disable-fmemopen-on-aarch64-darwin.patch

     

       206
       -
           (fetchpatch {

     

       207
       -
             url = "https://gitlab.desy.de/thomas.white/crystfel/-/commit/3c54d59e1c13aaae716845fed2585770c3ca9d14.diff";

     

       208
       -
             hash = "sha256-oaJNBQQn0c+z4p1pnW4osRJA2KdKiz4hWu7uzoKY7wc=";

     

       209
       -
           })

     

       210
        
         ];

     

       211
        
       

     

       212
        
         # CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but

     
···

       218
        
       

     

       219
        
         postInstall = lib.optionalString withBitshuffle ''

     

       220
        
           for file in $out/bin/*; do

     

       221
       -
             wrapProgram $file --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins

     

       0
        
       
     

       0
        
       
     

       222
        
           done

     

       223
        
         '';

     

       224

···

       6
        
       , fetchzip

     

       7
        
       , cmake

     

       8
        
       , lz4

     

       9
       +
       , gfortran

     

       10
        
       , bzip2

     

       0
        
       
     

       11
        
       , hdf5

     

       12
        
       , gsl

     

       13
        
       , unzip

     

       14
        
       , makeWrapper

     

       15
       +
       , zlib

     

       16
        
       , meson

     

       0
        
       
     

       17
        
       , ninja

     

       18
       +
       , pandoc

     

       19
        
       , eigen

     

       20
        
       , pkg-config

     

       21
        
       , wrapGAppsHook

     
···

       41
        
           pname = "libccp4";

     

       42
        
           version = "8.0.0";

     

       43
        
           src = fetchurl {

     

       44
       +
             url = "https://ftp.ccp4.ac.uk/opensource/libccp4-${version}.tar.gz";

     

       45
        
             hash = "sha256-y4E66GYSoIZjKd6rfO6W6sVz2BvlskA0HUD5rVMi/y0=";

     

       46
        
           };

     

       47
        
           nativeBuildInputs = [ meson ninja ];

     
···

       88
        
                 };

     

       89
        
             mosflmBinary = if stdenv.isDarwin then "bin/mosflm" else "mosflm-linux-64-noX11";

     

       90
        
           in

     

       91
       +
           stdenv.mkDerivation {

     

       92
        
             pname = "mosflm";

     

       93
        
       

     

       94
        
             inherit version src;

     
···

       112
        
           pname = "xgandalf";

     

       113
        
           version = "c6c5003ff1086e8c0fb5313660b4f02f3a3aab7b";

     

       114
        
           src = fetchurl {

     

       115
       +
             url = "https://gitlab.desy.de/thomas.white/xgandalf/-/archive/${version}/xgandalf-${version}.tar.gz";

     

       116
        
             hash = "sha256-/uZlBwAINSoYqgLQFTMz8rS1Rpadu79JkO6Bu/+Nx9E=";

     

       117
        
           };

     

       118
        
       

     
···

       122
        
       

     

       123
        
         pinkIndexer = stdenv.mkDerivation rec {

     

       124
        
           pname = "pinkindexer";

     

       125
       +
           version = "15caa21191e27e989b750b29566e4379bc5cd21a";

     

       126
        
           src = fetchurl {

     

       127
        
             url = "https://gitlab.desy.de/thomas.white/${pname}/-/archive/${version}/${pname}-${version}.tar.gz";

     

       128
       +
             hash = "sha256-v/SCJiHAV05Lc905y/dE8uBXlW+lLX9wau4XORYdbQg=";

     

       129
        
           };

     

       130
        
       

     

       131
        
           nativeBuildInputs = [ meson pkg-config ninja ];

     
···

       170
        
             "-DENABLE_BZIP2_PLUGIN=yes"

     

       171
        
           ];

     

       172
        
         };

     

       173
       +
       

     

       174
       +
         millepede-ii = stdenv.mkDerivation rec {

     

       175
       +
           pname = "millepede-ii";

     

       176
       +
           version = "04-13-06";

     

       177
       +
           src = fetchurl {

     

       178
       +
             url = "https://gitlab.desy.de/claus.kleinwort/millepede-ii/-/archive/V${version}/millepede-ii-V${version}.tar.gz";

     

       179
       +
             hash = "sha256-aFoo8AGBsUEN2u3AmnSpTqJ6JeNV6j9vkAFTZ34I+sI=";

     

       180
       +
           };

     

       181
       +
       

     

       182
       +
           nativeBuildInputs = [ gfortran ];

     

       183
       +
           buildInputs = [ zlib ];

     

       184
       +
       

     

       185
       +
           makeFlags = [ "PREFIX=$(out)" ];

     

       186
       +
         };

     

       187
        
       in

     

       188
        
       stdenv.mkDerivation rec {

     

       189
        
         pname = "crystfel";

     

       190
       +
         version = "0.11.0";

     

       191
        
         src = fetchurl {

     

       192
       +
           url = "https://www.desy.de/~twhite/crystfel/crystfel-${version}.tar.gz";

     

       193
       +
           sha256 = "sha256-ogNHWYfbxRmB5TdK8K0JpcCnYOOyXapQGSPh8mfp+Tc=";

     

       194
        
         };

     

       195
        
         nativeBuildInputs = [ meson pkg-config ninja flex bison doxygen opencl-headers makeWrapper ]

     

       196
        
           ++ lib.optionals withGui [ wrapGAppsHook ];

     
···

       207
        
           mosflm

     

       208
        
           pinkIndexer

     

       209
        
           xgandalf

     

       210
       +
           pandoc

     

       211
        
         ] ++ lib.optionals withGui [ gtk3 gdk-pixbuf ]

     

       212
        
         ++ lib.optionals stdenv.isDarwin [

     

       213
        
           argp-standalone

     
···

       217
        
         ++ lib.optionals withBitshuffle [ hdf5-external-filter-plugins ];

     

       218
        
       

     

       219
        
         patches = [

     

       220
       +
           # on darwin at least, we need to link to a separate argp library;

     

       221
       +
           # this patch adds a test for this and the necessary linker options

     

       222
        
           ./link-to-argp-standalone-if-needed.patch

     

       223
       +
           # hotfix for an issue that occurs (at least) on NixOS:

     

       224
       +
           # if the temporary path is too long, we get a segfault

     

       225
       +
           ./gui-path-issue.patch

     

       0
        
       
     

       0
        
       
     

       226
        
         ];

     

       227
        
       

     

       228
        
         # CrystFEL calls mosflm by searching PATH for it. We could've create a wrapper script that sets the PATH, but

     
···

       234
        
       

     

       235
        
         postInstall = lib.optionalString withBitshuffle ''

     

       236
        
           for file in $out/bin/*; do

     

       237
       +
             wrapProgram $file \

     

       238
       +
               --set HDF5_PLUGIN_PATH ${hdf5-external-filter-plugins}/lib/plugins \

     

       239
       +
               --prefix PATH ":" ${lib.makeBinPath [ millepede-ii ]}

     

       240
        
           done

     

       241
        
         '';

     

       242

+27

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

···

       1
       +
       diff --git a/src/gui_index.c b/src/gui_index.c

     

       2
       +
       index 2cc8e8db..13be77d5 100644

     

       3
       +
       --- a/src/gui_index.c

     

       4
       +
       +++ b/src/gui_index.c

     

       5
       +
       @@ -540,6 +540,7 @@ static void delete_gui_tempdir(char *tmpdir)

     

       6
       +
        {

     

       7
       +
        	char *path;

     

       8
       +
        	int i;

     

       9
       +
       +	size_t pathlen;

     

       10
       +
        

     

       11
       +
        	/* List of files which it's safe to delete */

     

       12
       +
        	char *files[] = {"gmon.out", "mosflm.lp", "SUMMARY", "XDS.INP",

     

       13
       +
       @@ -552,11 +553,12 @@ static void delete_gui_tempdir(char *tmpdir)

     

       14
       +
        

     

       15
       +
        	if ( tmpdir == NULL ) return;

     

       16
       +
        

     

       17
       +
       -	path = calloc(strlen(tmpdir)+64, 1);

     

       18
       +
       +	pathlen = strlen(tmpdir)+64;

     

       19
       +
       +	path = calloc(pathlen, 1);

     

       20
       +
        	if ( path == NULL ) return;

     

       21
       +
        

     

       22
       +
        	for ( i=0; i<n_files; i++ ) {

     

       23
       +
       -		snprintf(path, 127, "%s/%s", tmpdir, files[i]);

     

       24
       +
       +		snprintf(path, pathlen, "%s/%s", tmpdir, files[i]);

     

       25
       +
        		unlink(path);

     

       26
       +
        	}

     

       27
       +

+9 -9

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

···

       1
        
       diff --git a/meson.build b/meson.build

     

       2
       -
       index 59bbcfb7..dd75d4e2 100644

     

       3
        
       --- a/meson.build

     

       4
        
       +++ b/meson.build

     

       5
       -
       @@ -80,6 +80,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>')

     

       6
        
          conf_data.set10('HAVE_CLOCK_GETTIME', true)

     

       7
        
        endif

     

       8
        
        

     
···

       12
        
       +    argpdep = dependency('', required : false)

     

       13
        
       +endif

     

       14
        
       +

     

       15
       -
        # ************************ libcrystfel (subdir) ************************

     

       16
       -
        

     

       17
       -
        subdir('libcrystfel')

     

       18
       -
       @@ -180,7 +186,7 @@ endif

     

       19
        
        

     

       20
        
        indexamajig = executable('indexamajig', indexamajig_sources,

     

       21
        
                                 dependencies: [mdep, libcrystfeldep, gsldep,

     

       22
       -
       -                                        pthreaddep, zmqdep, asapodep],

     

       23
       -
       +                                        pthreaddep, zmqdep, asapodep, argpdep],

     

       24
        
                                 install: true,

     

       25
       -
                                 install_rpath: '$ORIGIN/../lib64/:$ORIGIN/../lib')

     

       26

···

       1
        
       diff --git a/meson.build b/meson.build

     

       2
       +
       index 4717bb2a..38d8693f 100644

     

       3
        
       --- a/meson.build

     

       4
        
       +++ b/meson.build

     

       5
       +
       @@ -70,6 +70,12 @@ if cc.has_function('clock_gettime', prefix: '#include <time.h>')

     

       6
        
          conf_data.set10('HAVE_CLOCK_GETTIME', true)

     

       7
        
        endif

     

       8
        
        

     
···

       12
        
       +    argpdep = dependency('', required : false)

     

       13
        
       +endif

     

       14
        
       +

     

       15
       +
        if cc.has_function('sched_setaffinity',

     

       16
       +
                           prefix: '#include <sched.h>',

     

       17
       +
                           args: '-D_GNU_SOURCE')

     

       18
       +
       @@ -186,7 +192,7 @@ endif

     

       19
        
        

     

       20
        
        indexamajig = executable('indexamajig', indexamajig_sources,

     

       21
        
                                 dependencies: [mdep, libcrystfeldep, gsldep,

     

       22
       +
       -                                        pthreaddep, zmqdep, asapodep, asapoproddep],

     

       23
       +
       +                                        pthreaddep, zmqdep, asapodep, asapoproddep, argpdep],

     

       24
        
                                 install: true,

     

       25
       +
                                 install_rpath: crystfel_rpath)

     

       26