fsl: new version, updated constraints and patches (#27129)

- add version 6.0.5
- add patch to allow fsl to use newer gcc versions
- add patch to allow fsl to use newer cuda versions
- remove constraints on gcc and cuda versions
- add filters to prevent using system headers and libraries
- clean up the installed tree

var/spack/repos/builtin/packages/fsl/fslpython_install_v605.patch

@@ -0,0 +1,42 @@
+diff -ru a/etc/fslconf/fslpython_install.sh b/etc/fslconf/fslpython_install.sh
+--- a/etc/fslconf/fslpython_install.sh	2021-07-15 10:05:03.000000000 +0000
++++ b/etc/fslconf/fslpython_install.sh	2021-11-01 01:01:03.088119423 +0000
+@@ -204,19 +204,19 @@
+ #  - https://github.com/conda/conda/issues/8804
+ 
+ # Try to make downloads more resilient
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs    240
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries          10
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor       5
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set safety_checks               warn
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_read_timeout_secs    240
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_connect_timeout_secs 20
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_max_retries          10
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set remote_backoff_factor       5
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set safety_checks               warn
+ 
+ # Channel priority:
+ #  - conda-forge (highest priority)
+ #  - defaults (gets automatically added on the first call)
+ #  - fsl (lowest priority)
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set    channel_priority strict
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --add    channels         conda-forge
+-"${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --append channels         https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --set    channel_priority strict
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --add    channels         conda-forge
++"${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda"  config --file "${miniconda_root_dir}"/.condarc --append channels         https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/channel
+ 
+ 
+ ##############################
+@@ -235,7 +235,7 @@
+ # different on linux. Also is likely to need
+ # updating whenever the fslpython environment
+ # specification is changed.
+-FSLDIR=$fsl_dir "${miniconda_bin_dir}/conda" env create \
++FSLDIR=$fsl_dir "${miniconda_bin_dir}/python" "${miniconda_bin_dir}/conda" env create \
+     -f "${script_dir}/fslpython_environment.yml" \
+     2>> "${miniconda_install_log}" | \
+     ${script_dir}/progress.sh 400 ${quiet} 1>> "${miniconda_install_log}"
+Only in b/etc/fslconf: fslpython_install.sh.orig
+Only in b/etc/fslconf: fslpython_install.sh.rej

var/spack/repos/builtin/packages/fsl/libxmlpp_bool.patch

@@ -0,0 +1,30 @@
+diff -ru a/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc b/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc
+--- a/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc	2019-05-20 12:50:12.000000000 +0000
++++ b/extras/src/libxmlpp/libxml++/io/istreamparserinputbuffer.cc	2021-10-31 22:29:47.465118993 +0000
+@@ -39,6 +39,6 @@
+ 
+   bool IStreamParserInputBuffer::do_close()
+   {
+-    return input_;
++    return static_cast<bool>(input_);
+   }
+ }
+diff -ru a/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc b/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc
+--- a/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc	2019-05-20 12:50:12.000000000 +0000
++++ b/extras/src/libxmlpp/libxml++/io/ostreamoutputbuffer.cc	2021-10-31 22:31:47.656434780 +0000
+@@ -29,13 +29,13 @@
+     // here we rely on the ostream implicit conversion to boolean, to know if the stream can be used and/or if the write succeded.
+     if(output_)
+       output_.write(buffer, len);
+-    return output_;
++    return static_cast<bool>(output_);
+   }
+ 
+   bool OStreamOutputBuffer::do_close()
+   {
+     if(output_)
+         output_.flush();
+-    return output_;
++    return static_cast<bool>(output_);
+   }
+ }

var/spack/repos/builtin/packages/fsl/package.py

@@ -3,6 +3,7 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import glob
 import os
 
 from spack import *
@@ -22,6 +23,7 @@ class Fsl(Package, CudaPackage):
     url      = "file://{0}/fsl-5.0.10-sources.tar.gz".format(os.getcwd())
     manual_download = True
 
+    version('6.0.5', sha256='df12b0b1161a26470ddf04e4c5d5d81580a04493890226207667ed8fd2b4b83f')
     version('6.0.4', sha256='58b88f38e080b05d70724d57342f58e1baf56e2bd3b98506a72b4446cad5033e')
     version('5.0.10', sha256='ca183e489320de0e502a7ba63230a7f55098917a519e8c738b005d526e700842')
 
@@ -33,18 +35,25 @@ class Fsl(Package, CudaPackage):
     depends_on('openblas', when='@6:')
     depends_on('vtk@:8')
 
-    conflicts('%gcc@:4.7,5.5:')
-    conflicts('^cuda@9.2:')
     conflicts('cuda_arch=none', when='+cuda',
               msg='must select a CUDA architecture')
     conflicts('platform=darwin',
               msg='currently only packaged for linux')
 
     patch('build_log.patch')
-    patch('eddy_Makefile.patch', when='@6:')
+    patch('eddy_Makefile.patch', when='@6.0.4')
     patch('iconv.patch')
     patch('fslpython_install_v5.patch', when='@:5')
-    patch('fslpython_install_v6.patch', when='@6:')
+    patch('fslpython_install_v604.patch', when='@6.0.4')
+    patch('fslpython_install_v605.patch', when='@6.0.5')
+
+    # Allow fsl to use newer versions of cuda
+    patch('https://aur.archlinux.org/cgit/aur.git/plain/005-fix_cuda_thrust_include.patch?h=fsl',
+          sha256='9471addfc2f880350eedadcb99cb8b350abf42be1c0652ccddf49e34e5e48734',
+          level=2)
+
+    # allow newer compilers
+    patch('libxmlpp_bool.patch')
 
     # These patches disable FSL's attempts to try to submit a subset of FSL
     # computations to an SGE queue system. That auto-submit mechanism only
@@ -161,10 +170,26 @@ def patch(self):
                 build_settings.filter(r'(^ptx2_MASTERBUILD)\s*=.*',
                                       r'\1 = COMPILE_GPU=0')
 
+        filter_file(r'(configure_opts=".*)"',
+                    r'\1 --x-includes={0} --x-libraries={1}"'.format(
+                        self.spec['libx11'].prefix.include,
+                        self.spec['libx11'].prefix.lib),
+                    join_path('extras', 'src', 'tk', 'unix', 'fslconfigure'))
+        filter_file(r' -L/lib64',
+                    r'',
+                    join_path('src', 'fabber_core', 'Makefile'))
+
     def install(self, spec, prefix):
-        build = Executable('./build')
+        build = Executable(join_path(self.stage.source_path, 'build'))
         build()
 
+        rm = which('rm')
+        for file in glob.glob('build*'):
+            rm('-f', file)
+        rm('-r', '-f', 'src')
+        rm('-r', '-f', join_path('extras', 'src'))
+        rm('-r', '-f', join_path('extras', 'include'))
+
         install_tree('.', prefix)
 
     @run_after('install')