Adding metadata

5 files changed, 34 insertions, 100 deletions

diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index 4e828eff1360..afb22bd8917b 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,2 +1,2 @@
+DIST paml-4.10.10.tar.gz 3835148 BLAKE2B 170915e094bd7f4c95895b4cb56e31d4e11f7b70c0f4b8c5c9104a88c68af62c635e18b36a7f56c96170e7eb490966d9ece0ab0e73aa42142def867a1bdce0bc SHA512 e3a3a0f2300213823f4126914073f538fc9859a2378a8494303c3b5fedf935e42c44311e9a89dac4eebc97fdd5653aa95c4d20e1b3ec62866f3bffffcbc9689c
 DIST paml-4.10.7.tar.gz 5250841 BLAKE2B 4d2a7fdc8eb93abe200165f7805520a02f4251dc651f26c4e1bf6fb11eee3d0721fd9d6f3c96979bae0f51b77f168e8d8a12f3dd3cbbfec7e8210a70b7c4bb9e SHA512 e450c0a28ecef946279fd92834eb5ddfb50805167655364cc959ef21839a75280a37d79209918373e80dacb0fc35decaccdb1477e53a81fd99fb140a0ce839fe
-DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758
diff --git a/sci-biology/paml/files/paml-4.9j-fno-common.patch b/sci-biology/paml/files/paml-4.9j-fno-common.patch
deleted file mode 100644
index 66eeb8a56b86..000000000000
--- a/sci-biology/paml/files/paml-4.9j-fno-common.patch
+++ /dev/null
@@ -1,14 +0,0 @@
---- a/src/paml.h
-+++ b/src/paml.h
-@@ -372,9 +372,9 @@
- void printSptree(void);
- 
- 
--enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
-+typedef enum {BASEseq=0, CODONseq, AAseq, CODON2AAseq, BINARYseq, BASE5seq} SeqTypes;
- 
--enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
-+typedef enum {PrBranch=1, PrNodeNum=2, PrLabel=4, PrNodeStr=8, PrAge=16, PrOmega=32} OutTreeOptions;
- 
- 
- /* use mean (0; default) for discrete gamma instead of median (1) */
diff --git a/sci-biology/paml/files/paml-4.9j-makefile.patch b/sci-biology/paml/files/paml-4.9j-makefile.patch
deleted file mode 100644
index 611b80444c89..000000000000
--- a/sci-biology/paml/files/paml-4.9j-makefile.patch
+++ /dev/null
@@ -1,42 +0,0 @@
---- a/src/Makefile
-+++ b/src/Makefile
-@@ -1,27 +1,18 @@
--PRGS =  baseml codeml basemlg mcmctree pamp evolver yn00 chi2 

--CC = cc # cc, gcc, cl

-+PRGS =  baseml basemlg codeml evolver pamp mcmctree infinitesites yn00 chi2

- 

--CFLAGS = -O3

-+CFLAGS += -Wno-unused-result

- #CFLAGS = -fast

- 

--LIBS = -lm # -lM

-+LDLIBS = -lm

- 

- all : $(PRGS)

- 

--baseml : baseml.c tools.c treesub.c treespace.c paml.h 

--	$(CC) $(CFLAGS) -o $@ baseml.c tools.c $(LIBS)

--basemlg : basemlg.c  tools.c treesub.c treespace.c paml.h 

--	$(CC) $(CFLAGS) -o $@ basemlg.c tools.c $(LIBS)

--codeml : codeml.c  tools.c treesub.c treespace.c paml.h 

--	$(CC) $(CFLAGS) -o $@ codeml.c tools.c $(LIBS)

--evolver : evolver.c  tools.c treesub.c treespace.c paml.h 

--	$(CC) $(CFLAGS) -o $@ evolver.c tools.c $(LIBS)

--pamp : pamp.c  tools.c treesub.c treespace.c paml.h 

--	$(CC) $(CFLAGS) -o $@ pamp.c tools.c $(LIBS)

--mcmctree : mcmctree.c  tools.c treesub.c treespace.c paml.h 

--	$(CC) $(CFLAGS) -o $@ mcmctree.c tools.c $(LIBS)

--	$(CC) $(CFLAGS) -o infinitesites -D INFINITESITES mcmctree.c tools.c $(LIBS)

--yn00: yn00.c tools.c paml.h

--	$(CC) $(CFLAGS) -o $@ yn00.c tools.c $(LIBS)

--chi2 : chi2.c

--	$(CC) $(CFLAGS) -o $@ chi2.c $(LIBS)

-+baseml: tools.o paml.h 

-+basemlg: tools.o paml.h 

-+codeml: tools.o paml.h 

-+evolver: tools.o paml.h 

-+pamp: tools.o paml.h 

-+mcmctree: tools.o paml.h 

-+infinitesites: tools.o paml.h 

-+	$(CC) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -DINFINITESITES mcmctree.c -o infinitesites tools.o $(LDLIBS)

-+yn00: tools.o paml.h

diff --git a/sci-biology/paml/paml-4.10.10.ebuild b/sci-biology/paml/paml-4.10.10.ebuild
new file mode 100644
index 000000000000..068e46ee72dd
--- /dev/null
+++ b/sci-biology/paml/paml-4.10.10.ebuild
@@ -0,0 +1,33 @@
+# Copyright 1999-2026 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
+HOMEPAGE="https://github.com/abacus-gene/paml/wiki"
+SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+src_compile() {
+	emake -C src CC="$(tc-getCC)" CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
+
+	dodoc -r README.md doc/.
+
+	insinto /usr/share/${PN}/control
+	doins examples/*.ctl
+
+	insinto /usr/share/${PN}/dat
+	doins -r examples/stewart* examples/*.dat dat/.
+
+	insinto /usr/share/${PN}
+	doins -r examples
+}
diff --git a/sci-biology/paml/paml-4.9j.ebuild b/sci-biology/paml/paml-4.9j.ebuild
deleted file mode 100644
index e8a5d07ee40c..000000000000
--- a/sci-biology/paml/paml-4.9j.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit toolchain-funcs
-
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="http://abacus.gene.ucl.ac.uk/software/${P/-/}.tgz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-S="${WORKDIR}/${P/-/}"
-PATCHES=(
-	"${FILESDIR}"/${PN}-4.9j-makefile.patch
-	"${FILESDIR}"/${PN}-4.9j-fno-common.patch
-)
-
-src_configure() {
-	tc-export CC
-}
-
-src_compile() {
-	emake -C src
-}
-
-src_install() {
-	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
-
-	dodoc -r README.txt doc/.
-
-	insinto /usr/share/${PN}/control
-	doins *.ctl
-
-	insinto /usr/share/${PN}/dat
-	doins -r stewart* *.dat dat/.
-
-	insinto /usr/share/${PN}
-	doins -r examples
-}