biology/wfa2-lib2.3.6

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future.  I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required.  I am therefore releasing most of my scientific ports, along
with a few others, to ports@.  I will continue to maintain ports I am
actively using and those for which I am upstream.

biology/wfa2-lib: Update to 2.3.6

Bug fix release
Changes: https://github.com/smarco/WFA2-lib/commits/main/

Reported by:    portscout

biology/wfa2-lib: fix build without libomp

/wrkdirs/usr/ports/biology/wfa2-lib/work/WFA2-lib-2.3.5/tools/align_benchmark/align_benchmark.c:32:10: fatal error: 'omp.h' file not found
   32 | #include <omp.h>
      |          ^~~~~~~
1 error generated.

biology/wfa2-lib: Update to 2.3.5

A few bug fixes.
Changes: https://github.com/smarco/WFA2-lib/releases

Reported by:    portscout

biology/wfa2-lib: Update to 2.3.4

A few bug fixes
Changes: https://github.com/smarco/WFA2-lib/releases

Reported by:    portscout

*/*: Sunset 12.3-RELEASE from ports tree

- Mk/bsd.port.mk: mark FreeBSD 12.3 as unsupported.
- Mk/Uses/cabal.mk: Remove the text-2 workaround for 12.3-RELEASE
- biology/wfa2-lib: remove obsolete patch
- databases/mongodb60: remove IGNORE for EOL FreeBSD 12.3
- devel/concurrencpp: remove workaround for EOL FreeBSD 12.3
- devel/electron22: remove IGNORE for EOL FreeBSD 12.3
- devel/malloy: this should build fine on 12.4-RELEASE
- devel/qcoro: remove BROKEN for EOL FreeBSD 12.3
- devel/root: remove workaround for EOL FreeBSD 12.3
- editors/imhex: remove IGNORE for EOL FreeBSD 12.3
- emulators/ppsspp: remove workaround for EOL FreeBSD 12.3
- emulators/rpcs3: remove workaround for EOL FreeBSD 12.3
- emulators/yuzu: remove workaround for EOL 12.3-RELEASE
- games/aquaria: remove support for EOL FreeBSD 12.3
- games/punchy: remove workaround for EOL FreeBSD 12.3
- graphics/cxxplot: remove support for EOL FreeBSD 12.3
- lang/gcc11*: bump a __FreeBSD_version in libphobos to 1204000
- lang/rust: untangle OSVERSION logic a bit
- misc/mbuffer: remove workaround for EOL FreeBSD 12.3 for aarch64
- sysutils/libdisplay-info: remove workaround for EOL FreeBSD 12.3
- www/*chromium: remove IGNORE for EOL FreeBSD 12.3
- x11/hyprpaper: remove workaround for expired FreeBSD 12.3
- x11-wm/labwc: remove workaround for EOL FreeBSD 12.3
- x11-wm/kwinft: remove workaround for EOL FreeBSD 12.3
- www/iridium: remove IGNORE for EOL FreeBSD 12.3

Differential Revision: https://reviews.freebsd.org/D38664

biology/wfa2-lib: Unbreak build on aarch64, probably others

Patch out hard-coded -march=native, not supported by clang aarch64

Reported by:    pkg-fallout

biology/wfa2-lib: Exact gap-affine algorithm using homology

The wavefront alignment (WFA) algorithm is an exact gap-affine
algorithm that takes advantage of homologous regions between the
sequences to accelerate the alignment process.  Unlike traditional
dynamic programming algorithms that run in quadratic time, the WFA runs
in time O(ns+s^2), proportional to the sequence length n and the
alignment score s, using O(s^2) memory (or O(s) using the
ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple
computational patterns that the modern compilers can automatically
vectorize for different architectures without adapting the code.