biology/hyphy2.5.103

biology/hyphy: Update to 2.5.103

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.103
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.102

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.102
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.101

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.101
Event:		Halifax Hackathon 202606
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.98

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.98
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.97

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.97
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.96

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.96
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.94

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.94
		https://github.com/veg/hyphy/releases/tag/2.5.93
		https://github.com/veg/hyphy/releases/tag/2.5.92
		https://github.com/veg/hyphy/releases/tag/2.5.91
Sponsored by:	The FreeBSD Foundation

biology/hyphy: fix build on amd64 / i386

c++: error: unsupported option '-mno-sse3' for target 'powerpc64le-unknown-freebsd15.0'

biology/hyphy: Update to 2.5.90

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.90
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.89

Release Notes:	https://github.com/veg/hyphy/releases/tag/2.5.89
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.88

Sponsored by:	The FreeBSD Foundation

biology/hyphy: Fix build on i386

After updating to 2.5.77, the build was failing on i386 with:

/wrkdirs/usr/ports/biology/hyphy/work/hyphy-2.5.77/src/core/global_things.cpp:176:62: error: conversion from 'size_t' (aka 'unsigned int') to 'const _String' is ambiguous
  176 |     HandleApplicationError(_String("Failed to allocate '") & bytes & "' bytes'",
      |                                                              ^~~~~

Fix the build by explicitly casting size_t variables to unsigned long
when passing them to _String constructors.  _String has multiple
constructors accepting numeric types (long, unsigned long, hyFloat,
char), but not directly a size_t.

Sponsored by:	The FreeBSD Foundation

biology/hyphy: Add TARGET_NATIVE option

Add a new TARGET_NATIVE option to control -march=native and
-mtune=native.  The option is off by default so the official packages
are portable.

Reported by:	diizzy
Sponsored by:	The FreeBSD Foundation
Differential Revision:	https://reviews.freebsd.org/D51977

biology/hyphy: Update to 2.5.77

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.77
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.76

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.76
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.75

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.75
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.74

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.74
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.73

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.72
		https://github.com/veg/hyphy/releases/tag/2.5.73
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.70

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.70
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.69

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.69actual
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.68

This update fixes some broken tests.  See
https://github.com/veg/hyphy/issues/1779 for details.

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.68
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.67

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.67
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.66

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.66
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.65

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.65.actual

PR:		283452, 284161
Sponsored by:	The FreeBSD Foundation

Co-authored-by:  Älven <alster@vinterdalen.se>

biology/hyphy: Update to 2.5.64

PR:		283028

biology/hyphy: Update to 2.5.62

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.63
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.62

Commit log:	https://github.com/veg/hyphy/compare/2.5.61...2.5.62
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.61

Release notes:	https://github.com/veg/hyphy/releases/tag/2.5.61
Commit log:	https://github.com/veg/hyphy/compare/2.5.56...2.5.61
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.60

Changes:	https://github.com/veg/hyphy/compare/2.5.59...2.5.60
		https://github.com/veg/hyphy/compare/2.5.58...2.5.59
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.58

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.58
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.57

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.57
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.56

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.56
                https://github.com/veg/hyphy/releases/tag/2.5.55
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.53

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.53
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.52

- FEL test is now passing, so remove comment about it failing.
- Remove armv7 support since most tests are segfaulting.

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.52
Sponsored by:	The FreeBSD Foundation
Differential Revision: https://reviews.freebsd.org/D41393
Tested by:	fuz (armv7)

biology/hyphy: fix build on armv7

With OpenMP not present, the code had a duplicate function definition.
Get rid of one of the two to enable a build on armv7.

Approved by:	portmgr (build fix blanket)

biology/hyphy: Update to 2.5.51hf

FEL test still fails.  See https://github.com/veg/hyphy/issues/1585.

Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.50

This release fixes a bug when not using openmp.
https://github.com/veg/hyphy/compare/2.5.49...2.5.50

Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.49

Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.48

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.48
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to 2.5.47

Changes:	https://github.com/veg/hyphy/releases/tag/2.5.47
Sponsored by:	The FreeBSD Foundation

biology/hyphy: Update to upstream tag 2.5.46hf1

Sponsored by:	The FreeBSD Foundation
Differential Revision:	https://reviews.freebsd.org/D37975

biology/hyphy: Update to 2.5.43

Sponsored by:	The FreeBSD Foundation

biology/hyphy: Not broken on systems where OpenMP isn't available

PR:		265677
Reported by:	Robert Clausecker <fuz@fuz.su>

biology/hyphy: Add tests; Fix ONLY_FOR_ARCHS order

biology/hyphy: Update to 2.5.42

https://github.com/veg/hyphy/compare/2.5.41...2.5.42

Sponsored by:	The FreeBSD Foundation

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

biology/hyphy: Update 2.5.40 -> 2.5.41

PR:		265677
Approved by:	jrm@ (maintainer)

biology/hyphy: Correct BROKEN message

biology/hyphy: Broken on systems where OpenMP isn't enabled

Reported by:	fallout
Approved by:	portmgr (blanket)