[gentoo-commits] repo/gentoo:master commit in: sci-biology/paml/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/paml/

[David Seifert]

commit:     5e71680b7a85431b46e92a2bb86e9f0507fcee3e
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Nov  1 18:35:56 2020 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Nov  1 18:35:56 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5e71680b

sci-biology/paml: Remove old 4.4c-r1

Closes: https://bugs.gentoo.org/706708
Package-Manager: Portage-3.0.8, Repoman-3.0.2
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/paml/Manifest            |  1 -
 sci-biology/paml/paml-4.4c-r1.ebuild | 47 ------------------------------------
 2 files changed, 48 deletions(-)

diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index e0bf2de6171..87d673016fb 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1,2 +1 @@
-DIST paml4.4c.tar.gz 2891715 BLAKE2B 04449b80e4fec080eabb69108d399a32278fcc79221e3c0d087ad1d978517ae2655bce8c300260dfb99d4d60700369ec338fa71c1d48f41a82017dbd3cae2397 SHA512 6a5f6d5baa91afa924ea392b76e59db6691fa9d6ee13a248dfe6e46d3fc83178ce41c2991de1c4cdb21952ee53771298aa0c62060f47d0dd84eaa76eb533498a
 DIST paml4.9j.tgz 6380272 BLAKE2B 58fc40904aff6ae539613e772fc0525b557c1e72c1a7a1d95176987bafed8771624ae6c53803bc71c5821a52de8212a49ad99c02c408870ec929c15b6bf217e0 SHA512 c5f3c42409bbaf5ac67c816a245f1d3175ee449dcf10232d9de539130341f80f85ae53518cbca549b1f42ddf64a6e8140a22b9da091d458b425512f11f8c1758

diff --git a/sci-biology/paml/paml-4.4c-r1.ebuild b/sci-biology/paml/paml-4.4c-r1.ebuild
deleted file mode 100644
index 27fe5ed4c76..00000000000
--- a/sci-biology/paml/paml-4.4c-r1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit toolchain-funcs versionator
-
-MY_P=$(version_format_string '${PN}$1$2')
-
-DESCRIPTION="Phylogenetic Analysis by Maximum Likelihood"
-HOMEPAGE="http://abacus.gene.ucl.ac.uk/software/paml.html"
-SRC_URI="http://abacus.gene.ucl.ac.uk/software/${PN}${PV}.tar.gz"
-
-LICENSE="free-noncomm"
-SLOT="0"
-KEYWORDS="amd64 x86"
-IUSE=""
-
-S=${WORKDIR}/${MY_P}
-
-src_prepare() {
-	# Notice send by mail to prof. Ziheng Yang
-	sed -i "s/\$(CC)/& \$(LDFLAGS)/" src/Makefile || die #335608
-}
-
-src_compile() {
-	emake -C src \
-		CC="$(tc-getCC)" \
-		CFLAGS="${CFLAGS} -Wno-unused-result" \
-		LDFLAGS="${LDFLAGS}"
-}
-
-src_install() {
-	dodoc README.txt doc/*
-
-	insinto /usr/share/${PN}/control
-	doins *.ctl
-
-	insinto /usr/share/${PN}/dat
-	doins stewart* *.dat dat/*
-
-	insinto /usr/share/${PN}
-	doins -r examples/
-
-	cd src || die
-	dobin baseml codeml basemlg mcmctree pamp evolver yn00 chi2
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/paml/

[Sam James]

commit:     8a73a8d755084a19bb9071502667bf7783f86baa
Author:     NHOrus <jy6x2b32pie9 <AT> yahoo <DOT> com>
AuthorDate: Mon Apr  1 18:08:48 2024 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Wed May  8 16:56:04 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8a73a8d7

sci-biology/paml: add 4.10.7

Project source is now hosted on github.

Closes: https://bugs.gentoo.org/831488
Closes: https://bugs.gentoo.org/919885
Signed-off-by: NHOrus <jy6x2b32pie9 <AT> yahoo.com>
Closes: https://github.com/gentoo/gentoo/pull/36048
Signed-off-by: Sam James <sam <AT> gentoo.org>

 sci-biology/paml/Manifest           |  1 +
 sci-biology/paml/metadata.xml       |  3 +++
 sci-biology/paml/paml-4.10.7.ebuild | 37 +++++++++++++++++++++++++++++++++++++
 3 files changed, 41 insertions(+)

diff --git a/sci-biology/paml/Manifest b/sci-biology/paml/Manifest
index 87d673016fbe..4e828eff1360 100644
--- a/sci-biology/paml/Manifest
+++ b/sci-biology/paml/Manifest
@@ -1 +1,2 @@
+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/metadata.xml b/sci-biology/paml/metadata.xml
index ccdff086e20b..1407729820e0 100644
--- a/sci-biology/paml/metadata.xml
+++ b/sci-biology/paml/metadata.xml
@@ -5,4 +5,7 @@
     <email>sci-biology@gentoo.org</email>
     <name>Gentoo Biology Project</name>
   </maintainer>
+  <upstream>
+    <remote-id type="github">abacus-gene/paml</remote-id>
+  </upstream>
 </pkgmetadata>

diff --git a/sci-biology/paml/paml-4.10.7.ebuild b/sci-biology/paml/paml-4.10.7.ebuild
new file mode 100644
index 000000000000..53a41c38fd11
--- /dev/null
+++ b/sci-biology/paml/paml-4.10.7.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2024 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://abacus.gene.ucl.ac.uk/software/paml.html"
+SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="free-noncomm"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_configure() {
+	tc-export CC
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_install() {
+	dobin src/{baseml,basemlg,codeml,evolver,pamp,mcmctree,infinitesites,yn00,chi2}
+
+	dodoc -r README.md doc/.
+
+	insinto /usr/share/${PN}/control
+	doins examples/*.ctl
+
+	insinto /usr/share/${PN}/dat
+	doins -r examples/stewart* examples/*.dat dat/.
+
+	insinto /usr/share/${PN}
+	doins -r examples
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/paml/

[Sam James]

commit:     c80ef338dca21186181598572dd02a4cb8daf68e
Author:     Sam James <sam <AT> gentoo <DOT> org>
AuthorDate: Wed May  8 16:55:53 2024 +0000
Commit:     Sam James <sam <AT> gentoo <DOT> org>
CommitDate: Wed May  8 16:56:06 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c80ef338

sci-biology/paml: restore ~x86

Unclear why it was dropped.

Signed-off-by: Sam James <sam <AT> gentoo.org>

 sci-biology/paml/paml-4.10.7.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/paml/paml-4.10.7.ebuild b/sci-biology/paml/paml-4.10.7.ebuild
index 598c844c5ce1..3291f74efcad 100644
--- a/sci-biology/paml/paml-4.10.7.ebuild
+++ b/sci-biology/paml/paml-4.10.7.ebuild
@@ -11,7 +11,7 @@ SRC_URI="https://github.com/abacus-gene/${PN}/archive/refs/tags/${PV}.tar.gz ->
 
 LICENSE="free-noncomm"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
 
 PATCHES=(
 	"${FILESDIR}"/${PN}-4.10.7-LDFLAGS.patch