crystfel: review fixes
This commit is contained in:
Philipp Middendorf
parent
da46337f0e
commit
d980b91866
@ -1,43 +0,0 @@
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Description: Fixing argument mismatches in Fortran code, addressing #957430.
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Author: Andrius Merkys <merkys@debian.org>
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Forwarded: ccp4-dev@dl.ac.uk
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--- a/fortran/pack_f.f
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+++ b/fortran/pack_f.f
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@@ -106,7 +106,7 @@
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endif
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10 continue
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filnarray(len(filn) + 1) = 0
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- call pack_wordimage_f(data, x, y, filnarray)
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+ call pack_longimage_f(data, x, y, filnarray)
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return
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end
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@@ -138,7 +138,7 @@
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endif
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10 continue
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filnarray(len(filn) + 1) = 0
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- call v2pack_wordimage_f(data, x, y, filnarray)
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+ call v2pack_longimage_f(data, x, y, filnarray)
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return
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end
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--- a/fortran/lgglib.f
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+++ b/fortran/lgglib.f
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@@ -1236,7 +1236,7 @@
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B3(2) = XYZ(2) * CELL(2)
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B3(3) = XYZ(3) * CELL(3)
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C
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- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
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+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
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END
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c
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c
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@@ -1274,7 +1274,7 @@
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B3(1) = XYZ(1)
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B3(2) = XYZ(2)
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B3(3) = XYZ(3)
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- CALL matmult(3,3,3,1,ORTH,B3,XYZ,B1)
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+ CALL matmult(3,3,3,1,ORTH,B3,XYZ)
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END
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character*80 function getnam(filnam)
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character*(*) filnam
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@ -1,116 +0,0 @@
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diff --git a/meson.build b/meson.build
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new file mode 100644
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index 0000000..8fc0631
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--- /dev/null
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+++ b/meson.build
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@@ -0,0 +1,110 @@
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+# Meson file for libccp4c (CCP4 core libraries, C part only)
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+project('libccp4c', 'c', version: '8.0.0', meson_version: '>=0.49.0', license: 'LGPL-3.0-or-later')
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+
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+cc = meson.get_compiler('c')
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+mdep = cc.find_library('m', required: false)
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+
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+# Note that the source code assumes that datadir='share'.
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+# If it is not, programs using the library will not be able
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+# to find 'environ.def'.
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+datadir = get_option('datadir') / 'ccp4'
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+
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+add_project_arguments('-DPACKAGE_ROOT="@0@"'.format(get_option('prefix')), language: 'c')
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+add_project_arguments(
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+ cc.get_supported_arguments(
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+ '-Wno-uninitialized',
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+ '-Wno-unused-function',
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+ '-Wno-stringop-truncation',
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+ '-Wno-stringop-overflow',
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+ '-Wno-format-overflow',
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+ '-Wno-misleading-indentation',
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+ '-Wno-pointer-compare',
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+ ),
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+ language: 'c',
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+)
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+
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+# C library
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+libccp4c = library(
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+ 'ccp4c',
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+ 'ccp4/ccp4_array.c',
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+ 'ccp4/cmap_accessor.c',
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+ 'ccp4/cmap_open.c',
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+ 'ccp4/csymlib.c',
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+ 'ccp4/pack_c.c',
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+ 'ccp4/ccp4_general.c',
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+ 'ccp4/cmap_close.c',
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+ 'ccp4/cmap_skew.c',
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+ 'ccp4/cvecmat.c',
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+ 'ccp4/ccp4_parser.c',
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+ 'ccp4/cmap_data.c',
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+ 'ccp4/cmap_stats.c',
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+ 'ccp4/library_err.c',
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+ 'ccp4/ccp4_program.c',
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+ 'ccp4/cmap_header.c',
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+ 'ccp4/cmap_symop.c',
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+ 'ccp4/library_file.c',
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+ 'ccp4/ccp4_unitcell.c',
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+ 'ccp4/cmap_labels.c',
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+ 'ccp4/cmtzlib.c',
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+ 'ccp4/library_utils.c',
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+ dependencies: mdep,
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+ install: true,
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+)
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+
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+# CCP4 headers are included with prefix: <ccp4/header.h>
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+incdir = include_directories('.')
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+
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+install_headers(
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+ 'ccp4/ccp4_file_err.h',
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+ 'ccp4/ccp4_program.h',
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+ 'ccp4/ccp4_unitcell.h',
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+ 'ccp4/cmap_errno.h',
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+ 'ccp4/cmap_stats.h',
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+ 'ccp4/csymlib.h',
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+ 'ccp4/library_file.h',
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+ 'ccp4/ccp4_fortran.h',
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+ 'ccp4/ccp4_spg.h',
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+ 'ccp4/ccp4_utils.h',
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+ 'ccp4/cmap_header.h',
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+ 'ccp4/cmaplib.h',
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+ 'ccp4/cvecmat.h',
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+ 'ccp4/mtzdata.h',
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+ 'ccp4/ccp4_array.h',
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+ 'ccp4/ccp4_general.h',
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+ 'ccp4/ccp4_sysdep.h',
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+ 'ccp4/ccp4_vars.h',
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+ 'ccp4/cmap_labels.h',
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+ 'ccp4/cmaplib_f.h',
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+ 'ccp4/overview.h',
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+ 'ccp4/ccp4_errno.h',
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+ 'ccp4/ccp4_parser.h',
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+ 'ccp4/ccp4_types.h',
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+ 'ccp4/cmap_data.h',
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+ 'ccp4/cmap_skew.h',
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+ 'ccp4/cmtzlib.h',
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+ 'ccp4/pack_c.h',
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+ subdir: 'ccp4',
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+)
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+
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+# Data files
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+install_data(
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+ 'data/atomsf_electron.lib',
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+ 'data/atomsf.lib',
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+ 'data/atomsf_neutron.lib',
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+ 'data/syminfo.lib',
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+ 'data/symop.lib',
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+ install_dir: datadir,
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+)
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+
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+# pkg-config file
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+pkg = import('pkgconfig')
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+pkg.generate(
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+ libccp4c,
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+ filebase: 'libccp4c',
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+ description: 'CCP4 core C libraries',
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+)
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+
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+libccp4c_dep = declare_dependency(
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+ include_directories: incdir,
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+ link_with: libccp4c,
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+)
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@ -3,6 +3,7 @@
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, fetchurl
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, fetchFromGitHub
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, fetchpatch
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, fetchzip
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, cmake
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, lz4
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, bzip2
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@ -39,7 +40,7 @@ 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 = "http://ftp.ccp4.ac.uk/opensource/${pname}-${version}.tar.gz";
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url = "https://ftp.ccp4.ac.uk/opensource/${pname}-${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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@ -53,10 +54,19 @@ let
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env.NIX_CFLAGS_COMPILE = "-DNIX_PROVIDED_SYMOP_FILE=\"${placeholder "out"}/share/ccp4/syminfo.lib\"";
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patches = [
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# This circumvents the original autoconf/CMake based build and uses meson instead
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./add-meson-build.patch
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./libccp4-use-hardcoded-syminfo-lib.patch
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];
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postPatch =
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let
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mesonPatch = fetchzip {
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url = "https://wrapdb.mesonbuild.com/v2/libccp4c_8.0.0-1/get_patch#somefile.zip";
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hash = "sha256-ohskfKh+972Pl56KtwAeWwHtAaAFNpCzz5vZBAI/vdU=";
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};
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in
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''
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cp ${mesonPatch}/meson.build .
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'';
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};
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# This is the statically-linked, pre-built binary of mosflm. Compiling it ourselves turns out to be very difficult
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# since the build process is very hard-coded for a specific machine, architecture, and libraries.
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@ -137,12 +147,19 @@ let
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pname = "HDF5-External-Filter-Plugins";
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version = "0.1.0";
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src = fetchFromGitHub {
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owner = "spanezz";
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owner = "nexusformat";
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repo = pname;
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rev = "master";
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hash = "sha256-Lkhhfhs0dIEplTAod1VBeO4vWH5/MIdfRvhAI3bCgD4=";
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hash = "sha256-bEzfWdZuHmb0PDzCqy8Dey4tLtq+4coO0sT0GzqrTYI=";
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};
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patches = [
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(fetchpatch {
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url = "https://github.com/spanezz/HDF5-External-Filter-Plugins/commit/6b337fe36da97a3ef72354393687ce3386c0709d.patch";
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hash = "sha256-wnBEdL/MjEyRHPwaVtuhzY+DW1AFeaUQUmIXh+JaRHo=";
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})
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];
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nativeBuildInputs = [ cmake ];
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buildInputs = [ hdf5 lz4 bzip2 ];
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@ -219,7 +236,7 @@ stdenv.mkDerivation rec {
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downloadPage = "https://www.desy.de/~twhite/crystfel/download.html";
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license = licenses.gpl3Plus;
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maintainers = with maintainers; [ pmiddend ];
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platforms = [ "x86_64-linux" "x86_64-darwin" "aarch64-linux" "aarch64-darwin" ];
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platforms = platforms.unix;
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};
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}
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