CHANGELOG.md

FSL base project changelog

2112.4 (Tuesday 14th December 2021)

• Fixed more issues with the depend.mk rule.

2112.3 (Monday 13th December 2021)

• Fixed an issue with variable quoting in the depend.mk rule.

2112.2 (Monday 13th December 2021)

• Fixed installation permissions on the $FSLDIR/config/depend.sh script.

2112.1 (Monday 13th December 2021)

• Adjust the depend.mk rule to support automatic dependency generation for .cu CUDA source files.

2112.0 (Saturday 11th December 2021)

• Add -pthread to the standard C++ compiler flags for g++.
• Adjust the depend.mk rule to allow saving object files to a separate build directory.

2111.9 (Wednesday 8th December 2021)

• If the ${LDFLAGS} environment variable is set in the environment, any -L options are dropped from it, so that the $FSLDEVDIR can explicitly be set to take precedence over $FSLDIR.
• ${FSLDEVDIR} doesn't have to exist - if it is set before ${FSLDIR}/etc/fslconf/fsl-devel.sh is run, it will not be overridden.

2111.8 (Friday 26th November 2021)

• Work around an issue with compiling against older versions of libxml++, when using -std=c++17.
• The FSLLOCKDIR, FSLMACHINELIST, FSLREMOTECALL and FSLPARALLEL variables are not defined by default.

2111.7 (Friday 19th November 2021)

• Fixed an issue in the construction of ${NVCCFLAGS} and ${CUDACXXFLAGS}.

2111.6 (Friday 19th November 2021)

• New convention for compiling C++ files which are part of a CUDA library or executable, using ${CUDACXXFLAGS}.

2111.5 (Friday 19th November 2021)

• Set -std=c++14 for nvcc-compiled code, as CUDA 11.0 is the first version to support -std=c++17, and we are targeting older CUDA versions.

2111.4 (Wednesday 17th November 2021)

• The default C++ language standard is now -std=c++17.

2111.3 (Wednesday 17th November 2021)

• The $FSLDEVDIR/lib directory is now added to the rpath entry for shared libraries and executables, if $FSLDEVDIR is different from $FSLDIR.

2111.2 (Monday 15th November 2021)

• Added the FSL_GE_606 Makefile flag for use by projects which need to retain support for compiling against older versions of FSL.

2111.1 (Friday 12th November 2021)

• Tweak to how the -install_name option is set.

2111.0 (Thursday 11th November 2021)

• The -rpath is explicitly set on executables and shared libraries, and the -install_name set on shared libraries under macOS. This is to support local development, and execution of commands from their $FSLDIR/src/ directory.

2109.1 (Wednesday 22nd September 2021)

• Updated the supportedGencodes.sh script for CUDA 11.2, 11.3, and 11.4.

2109.0 (Monday 13th September 2021)

• Added an extra unit test.

2108.3 (Friday 13th August 2021)

• Fix to the Makefile, as $FSLDIR/doc/fsl.css was not being installed.

2108.2 (Wednesday 11th August 2021)

• Change to createFSLWrapper and removeFSLWrapper to accommodate naming conventions for FSL GUI commands (<Command>_gui on macOS, and <Command> on Linux).

2108.1 (Monday 9th August 2021)

• Reverted the python library installation directory to $FSLDIR/python - this can be changed in the future if it is ever deemed problematic.

2108.0 (Friday 6th August 2021)

• Added some files used by FEAT and MELODIC to generate HTML reports.
• The $FSLDIR/etc/fslconf/fsl.sh script now uses $FSLDIR/etc/fslversion to identify official FSL installations - if this file is present, $FSLDIR/share/fsl/bin is automatically added to the $PATH variable.
• The $FSLDIR/share/fsl/sbin/createFSLWrapper script now detects pythonw executables.

2107.3 (Monday 12th July 2021)

• Change CUDA build configuration so that now all is needed is for nvcc to be on the $PATH, or a $NVCC variable to be set.

2107.2 (Sunday 11th July 2021)

• Further tweaks to CUDA linking logic.

2107.1 (Friday 9th July 2021)

• Fix an issue with CUDA linking.

2107.0 (Thursday 8th July 2021)

• Allow CUDA projects to statically link to the CUDA runtime and toolkit components, by setting a variable CUDA_STATIC.

2106.2 (Tuesday 22nd June 2021)

• Fixed an issue with createFSLWrapper on macOS.

2106.1 (Friday 6th June 2021)

• Updated the supportedGencodes.sh script to add JIT targets for CUDA projects.
• Added a Makefile.

2101.5 (Saturday 23rd January 2021)

• Updated the supportedGencodes.sh script to support CUDA versions 10.2, 11.1 and 11.2.
• Fixed a bug in the final creation of NVCCFLAGS and NVCCLDFLAGS.

2101.4 (Friday 22nd January 2021)

• Fixed a bug in the default CFLAGS assignment under Linux.
• Cleaned up and adjusted support for NVCC-compiled CUDA projects to work better within a conda build environment. May still be in a state of flux.

2101.3 (Thursday 14th January 2021)

• The $FSLDIR/etc/fslconf/fsl.sh script now automatically adds $FSLDIR/share/fsl/bin/ to the $PATH, for official (fslinstaller-installed) FSL installations.
• The $FSLDIR/etc/fslconf/fsl-devel.sh script now activates the $FSLDIR conda environment, for official (fslinstaller-installed) FSL installations.
• The $FSLDIR/etc/fslconf/fsl-devel.sh script now assigns default values to $FSLDEVDIR and $FSLCONFDIR, if they are not set by the user.

2101.2 (Friday 8th January 2021)

• Removed the legacy bin/fsl_sub script - fsl-sub is now available on conda, so can be listed as a dependency of the fsl/base project.

2101.1 (Tuesday 5th January 2021)

• Move contents of config/common/ into config/ - there is no need for a separate directory level now that we aren't maintaining separate configurations for different architectures/compilers.
• The default C++ compilation standard is now -std=c++11 (previously it was -std=c++98/-ansi).
• Allow projects to set custom C preprocessor flags, via USRCPPFLAGS.

2101.0 (Monday 4th January 2021)

• Moved the copyright insertion machinery (script and templates) from config/common/ into share/fsl/.
• Unify fsl.sh and fsl-devel.sh so the latter simply invokes the former.
• Fix an issue with argument pass-through in the fslpython[w] wrapper scripts.
• Removed the etc/fslconf/fslmachtype.sh script, as neither it, nor the FSLMACHTYPE environment variable, are used by anything.

2012.0 (Wednesday 2nd December 2020)

• Added creeateFSLWrapper and removeFSLWrapper, utility commands, which will be used to create isolated wrapper scripts of all FSL executables in a separate sub-directory, so they can be added to the user $PATH without other executables in $PREFIX/bin/ causing conflicts (!1 (merged)).

2011.0 (Monday 2nd November 2020)

• Initial release of the FSL base project - an amalagamation of fsl/etc and fsl/config, which has been adjusted to compile shared libraries with dynamic linking, and tweaked for use as the base of a conda-managed FSL installation.