git: 8d0b7976cd07 - main - biology/hyphy: Update to 2.5.52

The branch main has been updated by jrm:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8d0b7976cd078892b48202aa8acc0810135bf02a

commit 8d0b7976cd078892b48202aa8acc0810135bf02a
Author:     Joseph Mingrone <jrm@FreeBSD.org>
AuthorDate: 2023-08-09 15:23:50 +0000
Commit:     Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2023-08-09 17:39:17 +0000

    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/Makefile                                |  6 ++----
 biology/hyphy/distinfo                                |  6 +++---
 biology/hyphy/files/patch-src_core_include_likefunc.h | 12 ------------
 biology/hyphy/pkg-plist                               |  1 +
 4 files changed, 6 insertions(+), 19 deletions(-)

diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index 68438851d8b7..2ac2c78ea0c5 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,5 +1,5 @@
 PORTNAME=	hyphy
-DISTVERSION=	2.5.51hf
+DISTVERSION=	2.5.52
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
@@ -9,7 +9,7 @@ WWW=		https://www.hyphy.org/
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
-ONLY_FOR_ARCHS=	aarch64 amd64 armv7 i386 powerpc powerpc64 powerpc64le
+ONLY_FOR_ARCHS=	aarch64 amd64 i386 powerpc powerpc64 powerpc64le
 
 LIB_DEPENDS=	libcurl.so:ftp/curl
 TEST_DEPENDS=	bash:shells/bash
@@ -24,6 +24,4 @@ AVX_DESC=	Advanced vector extensions support
 
 AVX_CMAKE_OFF=	-DNOAVX:BOOL=ON
 
-# FEL test is failing. See https://github.com/veg/hyphy/issues/1585
-
 .include <bsd.port.mk>
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index 8a097550734b..d0aac6efd8a0 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1685303680
-SHA256 (veg-hyphy-2.5.51hf_GH0.tar.gz) = 403a5d07a4e7e67d3d8136fa83649713ad28223a2519e5fba3aa82697a03375f
-SIZE (veg-hyphy-2.5.51hf_GH0.tar.gz) = 5620954
+TIMESTAMP = 1691588992
+SHA256 (veg-hyphy-2.5.52_GH0.tar.gz) = 9e57d7af4a2bb765c48e4eccd025f22a64b692e8951f258e7b9134f7bd8bffed
+SIZE (veg-hyphy-2.5.52_GH0.tar.gz) = 5633837
diff --git a/biology/hyphy/files/patch-src_core_include_likefunc.h b/biology/hyphy/files/patch-src_core_include_likefunc.h
deleted file mode 100644
index bd2ab76cc7cb..000000000000
--- a/biology/hyphy/files/patch-src_core_include_likefunc.h
+++ /dev/null
@@ -1,12 +0,0 @@
---- src/core/include/likefunc.h.orig	2023-06-27 12:50:39 UTC
-+++ src/core/include/likefunc.h
-@@ -282,9 +282,6 @@ class   _LikelihoodFunction: public BaseObj { (public)
-     long        GetThreadCount            (void) {
-         return 1L;
-     }
--    void        SetThreadCount            (long) {
--        
--    }
- #endif
- #endif
- 
diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist
index 6636b69c97e8..9f46ee3e53d6 100644
--- a/biology/hyphy/pkg-plist
+++ b/biology/hyphy/pkg-plist
@@ -190,6 +190,7 @@ bin/hyphy
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/SingleOmega.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/aBSREL.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-fel.bf
+%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/contrast-meme.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/grid_compute.ibf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/io_functions.ibf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/modules/selection_lib.ibf