git: f7b1e0ec49b6 - main - biology/hyphy: Update to 2.5.64

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From: Joseph Mingrone <jrm_at_FreeBSD.org>
Date: Tue, 10 Dec 2024 20:33:28 UTC
The branch main has been updated by jrm:

URL: https://cgit.FreeBSD.org/ports/commit/?id=f7b1e0ec49b6360f713428b32d6aad2f514a50f8

commit f7b1e0ec49b6360f713428b32d6aad2f514a50f8
Author:     Älven <alster@vinterdalen.se>
AuthorDate: 2024-11-28 17:38:16 +0000
Commit:     Joseph Mingrone <jrm@FreeBSD.org>
CommitDate: 2024-12-10 20:31:58 +0000

    biology/hyphy: Update to 2.5.64
    
    PR:             283028
---
 biology/hyphy/Makefile  |  5 +++--
 biology/hyphy/distinfo  |  6 +++---
 biology/hyphy/pkg-plist | 10 ++++++----
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile
index f8c26082e883..b18cba727f82 100644
--- a/biology/hyphy/Makefile
+++ b/biology/hyphy/Makefile
@@ -1,10 +1,11 @@
 PORTNAME=	hyphy
-DISTVERSION=	2.5.63
+DISTVERSION=	2.5.64
 CATEGORIES=	biology
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Hypothesis testing using Phylogenies
-WWW=		https://www.hyphy.org/
+WWW=		https://www.hyphy.org/ \
+		https://github.com/veg/hyphy/
 
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
diff --git a/biology/hyphy/distinfo b/biology/hyphy/distinfo
index e765dff23918..ffa4bb48bcc2 100644
--- a/biology/hyphy/distinfo
+++ b/biology/hyphy/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1729872359
-SHA256 (veg-hyphy-2.5.63_GH0.tar.gz) = 86a94a601fa136443a8cd69f61e3a47b1dc85f10743d317715b1e433278e9ee0
-SIZE (veg-hyphy-2.5.63_GH0.tar.gz) = 5607295
+TIMESTAMP = 1732814990
+SHA256 (veg-hyphy-2.5.64_GH0.tar.gz) = 7ba1aaf82c8d876d36dc9deb63da8a5da604917fe1628cef444af0207579aea6
+SIZE (veg-hyphy-2.5.64_GH0.tar.gz) = 5613927
diff --git a/biology/hyphy/pkg-plist b/biology/hyphy/pkg-plist
index 3491aaa1b191..2f58e0cb50d2 100644
--- a/biology/hyphy/pkg-plist
+++ b/biology/hyphy/pkg-plist
@@ -129,6 +129,9 @@ bin/hyphy
 %%DATADIR%%/TemplateBatchFiles/LZ_Complexity.bf
 %%DATADIR%%/TemplateBatchFiles/LocalMolClock.bf
 %%DATADIR%%/TemplateBatchFiles/MGvsGY.bf
+%%DATADIR%%/TemplateBatchFiles/MSS-joint-fitter.bf
+%%DATADIR%%/TemplateBatchFiles/MSS-selector-2.bf
+%%DATADIR%%/TemplateBatchFiles/MSS-selector.bf
 %%DATADIR%%/TemplateBatchFiles/MergeSequences.bf
 %%DATADIR%%/TemplateBatchFiles/MergeSites.bf
 %%DATADIR%%/TemplateBatchFiles/Miscellaneous/phylohandbook/BranchAPriori.bf
@@ -147,9 +150,6 @@ bin/hyphy
 %%DATADIR%%/TemplateBatchFiles/ModelTest.bf
 %%DATADIR%%/TemplateBatchFiles/MolClockAllRoots.bf
 %%DATADIR%%/TemplateBatchFiles/MolecularClock.bf
-%%DATADIR%%/TemplateBatchFiles/MSS-joint-fitter.bf
-%%DATADIR%%/TemplateBatchFiles/MSS-selector-2.bf
-%%DATADIR%%/TemplateBatchFiles/MSS-selector.bf
 %%DATADIR%%/TemplateBatchFiles/NeighborJoining.bf
 %%DATADIR%%/TemplateBatchFiles/NielsenYang.bf
 %%DATADIR%%/TemplateBatchFiles/NucModelCompare.bf
@@ -181,8 +181,8 @@ bin/hyphy
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/BranchSiteREL.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FADE.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FEL.bf
-%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FUBAR.bf
+%%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/FitMultiModel.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/MEME.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/PRIME.bf
 %%DATADIR%%/TemplateBatchFiles/SelectionAnalyses/RELAX-Groups.bf
@@ -389,6 +389,7 @@ bin/hyphy
 %%DATADIR%%/TemplateBatchFiles/libv3/models/binary/empirical.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/models/codon.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/BS_REL.bf
+%%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_GTR.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_MH.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/models/codon/MG_REV_PROPERTIES.bf
@@ -416,6 +417,7 @@ bin/hyphy
 %%DATADIR%%/TemplateBatchFiles/libv3/tasks/distances.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/tasks/estimators.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/tasks/genetic_code.bf
+%%DATADIR%%/TemplateBatchFiles/libv3/tasks/mapping.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/tasks/mpi.bf
 %%DATADIR%%/TemplateBatchFiles/libv3/tasks/trees.bf
 %%DATADIR%%/TemplateBatchFiles/molclockBootstrap.bf