biology/paml: Update to 4.10.5

https://github.com/abacus-gene/paml/releases/tag/v4.10.0
https://github.com/abacus-gene/paml/releases/tag/untagged-a5659203e8ec0ddb58b8
https://github.com/abacus-gene/paml/releases/tag/v4.10.5

Sponsored by:	The FreeBSD Foundation

4 files changed, 39 insertions, 41 deletions

diff --git a/biology/paml/Makefile b/biology/paml/Makefile
index a8c84d9fb60c..d0f49022b3f7 100644
--- a/biology/paml/Makefile
+++ b/biology/paml/Makefile
@@ -1,21 +1,22 @@
 PORTNAME=	paml
-PORTVERSION=	4.9j
+DISTVERSIONPREFIX=	v
+DISTVERSION=	4.10.5
 CATEGORIES=	biology
-MASTER_SITES=	http://abacus.gene.ucl.ac.uk/software/
-DISTNAME=	${PORTNAME}${DISTVERSION}
 
 MAINTAINER=	jrm@FreeBSD.org
 COMMENT=	Phylogenetic Analysis by Maximum Likelihood (PAML)
 
 LICENSE=	GPLv3
 
-USES=		dos2unix gmake tar:tgz
-
-DOS2UNIX_GLOB=	*.HKYG5 *.aa *.c *.ctl *.dat *.nexus *.nuc *.phy *.result *.tre \
+USES=		dos2unix gmake
+DOS2UNIX_GLOB=	*.aa *.c *.ctl *.dat *.HKYG5 *.nexus *.nuc *.phy *.result *.tre \
 		*.trees *.txt *.xml paupblock paupend
+USE_GITHUB=	yes
+GH_ACCOUNT=	abacus-gene
 
 BINARIES=	baseml basemlg chi2 codeml evolver evolverNSbranches \
-		evolverNSbranchsites evolverNSsites pamp yn00
+		evolverNSbranchsites evolverNSsites infinitesites mcmctree pamp \
+		yn00
 
 OPTIONS_DEFINE=	DOCS EXAMPLES
 
@@ -37,15 +38,12 @@ do-install:
 do-install-DOCS-on:
 	@${MKDIR} ${STAGEDIR}${DOCSDIR}
 	${INSTALL_DATA} ${WRKSRC}/doc/* ${STAGEDIR}${DOCSDIR}
-	${INSTALL_DATA} ${WRKSRC}/README.txt ${STAGEDIR}${DOCSDIR}
+	${INSTALL_DATA} ${WRKSRC}/README.md ${STAGEDIR}${DOCSDIR}
 
 do-install-EXAMPLES-on:
 	@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
 	(cd ${WRKSRC} && ${COPYTREE_SHARE} "dat Technical" \
 		${STAGEDIR}${EXAMPLESDIR})
 	(cd ${WRKSRC}/examples && ${COPYTREE_SHARE} . ${STAGEDIR}${EXAMPLESDIR})
-.for f in *.aa *.ctl *.dat *.nuc *.trees *.txt paup*
-	${INSTALL_DATA} ${WRKSRC}/${f} ${STAGEDIR}${EXAMPLESDIR}
-.endfor
 
 .include <bsd.port.mk>
diff --git a/biology/paml/distinfo b/biology/paml/distinfo
index c6e205ca7ab2..f52a021a50de 100644
--- a/biology/paml/distinfo
+++ b/biology/paml/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1574435935
-SHA256 (paml4.9j.tgz) = 97aac6cb8f23844202545e9ba4e42020231c2a30051b36f4e4d2f423e270d461
-SIZE (paml4.9j.tgz) = 6562281
+TIMESTAMP = 1661485713
+SHA256 (abacus-gene-paml-v4.10.5_GH0.tar.gz) = 1bb40ea7c976d961a4f46b76e950423f6f252d7060bc621cbf29c9743b88a063
+SIZE (abacus-gene-paml-v4.10.5_GH0.tar.gz) = 3393889
diff --git a/biology/paml/files/patch-src_paml.h b/biology/paml/files/patch-src_paml.h
deleted file mode 100644
index c7e35c89038f..000000000000
--- a/biology/paml/files/patch-src_paml.h
+++ /dev/null
@@ -1,14 +0,0 @@
---- src/paml.h.orig	2020-08-20 16:14:50 UTC
-+++ src/paml.h
-@@ -372,9 +372,9 @@ void copySptree(void);
- void printSptree(void);
- 
- 
--enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
-+enum SeqTypes {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq};
- 
--enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
-+enum OutTreeOptions {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32};
- 
- 
- /* use mean (0; default) for discrete gamma instead of median (1) */
diff --git a/biology/paml/pkg-plist b/biology/paml/pkg-plist
index 9c0041d7c15f..8ba55f7dfe03 100644
--- a/biology/paml/pkg-plist
+++ b/biology/paml/pkg-plist
@@ -1,5 +1,17 @@
+bin/baseml
+bin/basemlg
+bin/chi2
+bin/codeml
+bin/evolver
+bin/evolverNSbranches
+bin/evolverNSbranchsites
+bin/evolverNSsites
+bin/infinitesites
+bin/mcmctree
+bin/pamp
+bin/yn00
 %%PORTDOCS%%%%DOCSDIR%%/MCMCtree.Tutorials.pdf
-%%PORTDOCS%%%%DOCSDIR%%/README.txt
+%%PORTDOCS%%%%DOCSDIR%%/README.md
 %%PORTDOCS%%%%DOCSDIR%%/pamlDOC.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlFAQs.pdf
 %%PORTDOCS%%%%DOCSDIR%%/pamlHistory.txt
@@ -77,7 +89,6 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock1.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock2.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.FluH1/mcmctreeClock3.ctl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/FigTree.tre
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.tre
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/HIV2ge.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/README.txt
@@ -85,7 +96,7 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/in.BV.HKYG5
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ExactlnL.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/TipDate.HIV2/mcmctree.ctl
-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/YN00abglobin.result.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/aaml.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.aa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/abglobin.nuc
@@ -154,6 +165,19 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtCDNAape/mtCDNAape.txt
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/mtprim9.nuc
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/codeml-M0.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.aln
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/myxo/myxovirus.tree
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata-maintree.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.trees
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/4s-ndata.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/README.txt
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree-ml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata-maintree.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/baseml-ndata.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree-ml.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata-maintree.ctl
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ndata/codeml-ndata.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/pamp.ctl
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupblock
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/paupend
@@ -161,13 +185,3 @@
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.aa
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/stewart.trees
 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/yn00.ctl
-bin/baseml
-bin/basemlg
-bin/chi2
-bin/codeml
-bin/evolver
-bin/evolverNSbranches
-bin/evolverNSbranchsites
-bin/evolverNSsites
-bin/pamp
-bin/yn00