gentoo resync : 25.11.2020

4 files changed, 26 insertions, 57 deletions

diff --git a/sci-biology/profphd/Manifest b/sci-biology/profphd/Manifest
index 7085f0176e19..e4fd19dff774 100644
--- a/sci-biology/profphd/Manifest
+++ b/sci-biology/profphd/Manifest
@@ -1,6 +1,5 @@
 AUX profphd-1.0.39-perl.patch 376 BLAKE2B 16911d2f6952f9740f3cd16121bf6dab5e5571ce1f7e5ac671dde719146e55f2735f2951629220fe56a93c1243e792ddd820978163023b44613d8d08d037cd6a SHA512 e4004dbb835560b3a2aa140aea0ed57812ee9dc11dc18fb7b1dbdeee73bacfef3fecfd686f15fa87cde5597ddb322057d67fa61708ba3077c5449f93a0284b8e
-DIST profphd-1.0.39.tar.xz 4406776 BLAKE2B 9ac4bccd1fedf04f9556ff6953452879fc8cf9deb92853214b2c8b5c0b1c4daf3e5e0044d10ded9540e9dd3f40a6fee3a25ae808fd1e94b90e0db23f3af7b6df SHA512 0ea6a34a8dad8fcd0d8b23e7a7d476e211587bf580389e9f43ed857bab7853cbe5ce698d2a610e9344e9bc95661cf074355310ea02c1a03e6378058ba169b15b
+AUX profphd-1.0.40-symlink.patch 793 BLAKE2B 98e5f001570522bb1643d3aad1f2497bd84035c932d19b1b9c90d2933b08eb7d2b6c1871b356205494494c8225fac3d6d697aaac6229885876c439679455f092 SHA512 7985c4743ade3b73a7fdd0c697c84c3b5fdcba3c33c66d1d6aab7d4493ca4d1197c4c438ef79f44667ed2c86e6ee9c789c36928430605aac6438d9e734e8c56a
 DIST profphd-1.0.40.tar.xz 4491592 BLAKE2B 2aa1e091c0674fa5318a075148a63b15354ecb6d8d6f7ac41d1d05f8bea17c47b6f37be707cc1c738e22342c26ae9be59cabf919610e5bffd5028fc587b2995b SHA512 287f1a548030e7978119788dffdf2529e0018cd772bc820e116f79ed10cefd440645424b56415333362098a1ed32f4841d3fd4069adede2a95968f81c63956e3
-EBUILD profphd-1.0.39.ebuild 833 BLAKE2B c173db3f129f9aecf3c0d8da461ef24c07b8de59e1c7adae3e9c39f227951b889fbcb71b78deb6fe45a7850f41cfddf87004fad251fdbd0425b5a7d6f96d60e5 SHA512 a2e15d1bd08ffa70e966001cc1a9787e2ad4c736e4275dee7ea8695ff6b36869c6acc60b6ae3e1fc607f86adff8bd5ae518dac2004f6c3b9657c5a53a732a123
-EBUILD profphd-1.0.40.ebuild 841 BLAKE2B c9b34a5bd892bab4dcc868ea1c3a5404c99d6a10f82ac217ea315a2203d4f0a7c65372cf5714eb480003729931362afdeba13e21e80c4590e392cd14d0bffed4 SHA512 c08773dfc516365b2d75cd0f7869f8c1178a17921ebd65e5ea1b78c236449ea818ce3086e63fd43eeb0ed9b4919b48e7f9f9d1e5a148de5a8e63342bf45d2d9d
+EBUILD profphd-1.0.40.ebuild 787 BLAKE2B 382eef046bb2eddcbd7e8dd8a798096f4719c4df589f8022c51cf07bc7e920c161b9c9dc8dde7ee92eca9d998cc98ddc3aecdcbaa3de533a42556ff2e382931d SHA512 c583b877a4c912e473231d74ec84bb25bcc9f6d90d466fce7b73b1701e205a2c2ab57039e12ad755b7f3a296e7d8b95f752bb308337d012084ec3ea3738a69d2
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/profphd/files/profphd-1.0.40-symlink.patch b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
new file mode 100644
index 000000000000..7733d55af4a6
--- /dev/null
+++ b/sci-biology/profphd/files/profphd-1.0.40-symlink.patch
@@ -0,0 +1,11 @@
+--- a/src/prof/Makefile
++++ b/src/prof/Makefile
+@@ -40,7 +40,7 @@
+ 		./. $(DESTDIR)$(prefix)/share/profphd/prof/.
+ 	find $(DESTDIR)$(prefix)/share/profphd/prof/embl/phd.pl $(DESTDIR)$(prefix)/share/profphd/prof/scr/CONFprof.pl $(DESTDIR)$(prefix)/share/profphd/prof/prof $(DESTDIR)$(prefix)/share/profphd/prof/scr/lib/prof.pm \
+ 		-type f -exec sed -i -e 's|__PREFIX__|$(prefix)|g;s|__VERSION__|$(VERSION)|;' {} \;
+-	rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/prof
++	rm -rf $(DESTDIR)$(prefix)/bin/prof && mkdir -p $(DESTDIR)$(prefix)/bin && ln -s ../share/profphd/prof/prof $(DESTDIR)$(prefix)/bin/profphd
+ 
+ install-neuralnet:
+ 	mkdir -p $(DESTDIR)$(prefix)/share/profphd/prof/embl/para && rsync -aC \
diff --git a/sci-biology/profphd/profphd-1.0.39.ebuild b/sci-biology/profphd/profphd-1.0.39.ebuild
deleted file mode 100644
index cacbc13cbdf2..000000000000
--- a/sci-biology/profphd/profphd-1.0.39.ebuild
+++ /dev/null
@@ -1,37 +0,0 @@
-# Copyright 1999-2014 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit eutils
-
-DESCRIPTION="Secondary structure and solvent accessibility predictor"
-HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
-SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
-
-SLOT="0"
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
-	dev-perl/librg-utils-perl
-	sci-libs/profnet
-	sci-libs/profphd-utils
-"
-
-src_prepare() {
-	sed \
-		-e '/ln -s/s:prof$:profphd:g' \
-		-i src/prof/Makefile || die
-	epatch "${FILESDIR}"/${P}-perl.patch
-}
-
-src_compile() {
-	emake prefix="${EPREFIX}/usr"
-}
-
-src_install() {
-	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
-}
diff --git a/sci-biology/profphd/profphd-1.0.40.ebuild b/sci-biology/profphd/profphd-1.0.40.ebuild
index 8e24cebeb5f3..4f9a16a9fe9d 100644
--- a/sci-biology/profphd/profphd-1.0.40.ebuild
+++ b/sci-biology/profphd/profphd-1.0.40.ebuild
@@ -1,37 +1,33 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
-
-inherit eutils
+EAPI=7
 
 DESCRIPTION="Secondary structure and solvent accessibility predictor"
 HOMEPAGE="https://rostlab.org/owiki/index.php/PROFphd_-_Secondary_Structure,_Solvent_Accessibility_and_Transmembrane_Helices_Prediction"
 SRC_URI="ftp://rostlab.org/profphd/${P}.tar.xz"
 
-SLOT="0"
 LICENSE="GPL-2"
+SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
 
 DEPEND="dev-lang/perl"
-RDEPEND="${DEPEND}
+RDEPEND="
+	${DEPEND}
 	dev-perl/librg-utils-perl
 	sci-libs/profnet
-	sci-libs/profphd-utils
-"
+	sci-libs/profphd-utils"
 
-src_prepare() {
-	sed \
-		-e '/ln -s/s:prof$:profphd:g' \
-		-i src/prof/Makefile || die
-	epatch "${FILESDIR}"/${PN}-1.0.39-perl.patch
-}
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.0.39-perl.patch
+	"${FILESDIR}"/${PN}-1.0.40-symlink.patch
+)
 
 src_compile() {
-	emake prefix="${EPREFIX}/usr"
+	emake prefix="${EPREFIX}"/usr
 }
 
 src_install() {
-	emake prefix="${EPREFIX}/usr" DESTDIR="${D}" install
+	emake prefix="${EPREFIX}"/usr DESTDIR="${D}" install
+	einstalldocs
 }