gentoo resync : 26.08.2021

4 files changed, 111 insertions, 74 deletions

diff --git a/sci-biology/wise/Manifest b/sci-biology/wise/Manifest
index 36db61e514cd..5c4fc9140392 100644
--- a/sci-biology/wise/Manifest
+++ b/sci-biology/wise/Manifest
@@ -1,4 +1,5 @@
+AUX wise-api.tex.patch 2166 BLAKE2B 94cb69ddb9b751cf1efd7d4b98520144dc067c0dae83b2431d35f40c29d2c1d915335c610711f4a7225b3838991f8abce3bb9502aa8d540157afaddb5f389d70 SHA512 e01a902b46f00d6219d549f355b3e1f4373585baf104ff9a2193d6ac981e0aa277b0162307e0c3da17587e10138ad848da5439a0d407266c38f1ab8c7bedca4c
 DIST wise-2.4.0_alpha-patchset.tar.bz2 7244 BLAKE2B 3c921b61e6a30515d790abd8168b5fbc4f8add44f1133cf7d163a98a6935a74ae7c9f79b72874a509bb743aa5b340c92a049ad091380f9cd33b0b9154cca5974 SHA512 ca73f1b03e14cef44d84484c64d06c4856d6ef33b7434de5ac58725cea1d071d875a7b073fc181da33a7490c4f086f674a9a52db4d36e78f4f5b75b28b855cfe
 DIST wise2.4.0alpha.tar.gz 3296399 BLAKE2B a7fbac022c62606ce865250f4091497e9c86331d2d2050fc4f69614aa5e95313eac3a0fcd49451c724c9b50bc6ac63700cd44828736b7a4d15eff2bc21fc29ec SHA512 a2288d7304e7768328689514a986aeff62a0ca6538ee61177a434fb08065f83ab5db39e0cb9101dd8ae9a91f7d95d05528d7ad23df0c394587717c584bf2341c
-EBUILD wise-2.4.0_alpha.ebuild 1737 BLAKE2B 29ae17532ef9a4919db09b4f6b71b92f3b89d1a03b75b1ce90a1defe49ea9d572d9e902620a6d267ad8fc77506a25fda84ede0804f4f0676ba8a0eb41df049c9 SHA512 b73b8fd3a78cdcdda2c39326bbd4dfd99c2828c38ae78537b33c8ea50291323841d0d348eb2b6965cfe1986d808f26ef83e115715fa7c14e31cb7a7e337d867c
+EBUILD wise-2.4.0_alpha-r1.ebuild 1409 BLAKE2B 317764cdd23ecd59b6eeddcfe3efdab6a358a65a33166b504a98c05f7919864c7670e4c8516b70c98f85957ca4e9aff9700e75f6559e1718663b8535b2df6d89 SHA512 1c4910efb4a82c2ae703220cfdcf4fd9e51a38d23aa29e111559cc604d51185dd584fc33d473eec0fcd80ba177ced507eac230e4c60b589ef12f968a5aefe772
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/wise/files/wise-api.tex.patch b/sci-biology/wise/files/wise-api.tex.patch
new file mode 100644
index 000000000000..d6d56888dfb3
--- /dev/null
+++ b/sci-biology/wise/files/wise-api.tex.patch
@@ -0,0 +1,38 @@
+--- a/api.tex.old
++++ b/api.tex
+@@ -204,7 +204,7 @@
+ \item Build two Sequence objects, from a file or strings (\ref{object_Sequence})
+ \item Optionally convert the Sequence objects into Protein objects (\ref{object_Protein}). This ensures you have proteins
+ \item Read in the comparison matrix using CompMat (\ref{object_CompMat})
+-\item Use one of the algorithm calls in sw_wrap module (\ref{module_sw_wrap})
++\item Use one of the algorithm calls in sw\_wrap module (\ref{module_sw_wrap})
+ \item Show the alignment using a call in the seqaligndisaply module (\ref{module_seqaligndisplay})
+ \end{itemize}
+ 
+@@ -213,7 +213,7 @@
+ \item Read in a sequence object and convert it to a protein object (\ref{object_Protein},\ref{object_Sequence})
+ \item Make a protein database from the single protein object (\ref{object_ProteinDB})
+ \item Make a protein database from a single fasta file (\ref{object_ProteinDB})
+-\item Using one of the calls to the sw_wrap module, make a Hscore object (\ref{module_sw_wrap})
++\item Using one of the calls to the sw\_wrap module, make a Hscore object (\ref{module_sw_wrap})
+ \item Show the Hscore object using a show function (\ref{object_Hscore})
+ \item Retrieve individual protein objects from the database by taking out the
+ DataEntry objects (\ref{object_DataEntry}) and passing them into the ProteinDB object (\ref{object_ProteinDB}), giving you a protein object
+@@ -232,7 +232,7 @@
+ \item Read in a codon table (\ref{object_CodonTable})
+ \item Make a random DNA model (\ref{object_RandomModelDNA})
+ \item Make an algorithm type (\ref{module_gwrap})
+-\item Build an entire parameter set for genewise using Wise2::GeneParameter21_wrap (\ref{module_gwrap})
++\item Build an entire parameter set for genewise using Wise2::GeneParameter21\_wrap (\ref{module_gwrap})
+ \item Run the actual algorithm (\ref{module_gwrap})
+ \item show the alignment using genedisplay (\ref{module_gwrap})
+ \end{itemize}
+@@ -5055,7 +5055,7 @@
+ Member functions of RandomModel
+ 
+ \section{sequence\_codon}
+-\label{module_sequence\_codon}
++\label{module_sequence_codon}
+ This module only contains factory methods
+ 
+ \subsection{sequence\_codon factory methods}
diff --git a/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild
new file mode 100644
index 000000000000..a033ffd011bb
--- /dev/null
+++ b/sci-biology/wise/wise-2.4.0_alpha-r1.ebuild
@@ -0,0 +1,71 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs
+
+MY_PV="${PV/_}"
+MY_P="${PN}${MY_PV}"
+DESCRIPTION="Intelligent algorithms for DNA searches"
+HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
+SRC_URI="
+	ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${MY_P}.tar.gz
+	https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2
+"
+S="${WORKDIR}"/${MY_P}
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc"
+
+RDEPEND="~sci-biology/hmmer-2.3.2"
+DEPEND="${RDEPEND}"
+BDEPEND="
+	app-shells/tcsh
+	dev-lang/perl
+	virtual/latex-base
+"
+
+PATCHES=(
+	"${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch
+	"${WORKDIR}"/${P}-patchset/${P}-cflags.patch
+)
+
+src_prepare() {
+	default
+	cd docs || die
+	cat ../src/models/*.tex ../src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
+	cat wise2api.tex temp.tex apiend.tex > api.tex || die
+	eapply "${FILESDIR}"/${PN}-api.tex.patch
+}
+
+src_compile() {
+	tc-export CC
+	emake -C src all
+
+	if use doc; then
+		cd docs || die
+		for i in api appendix dynamite wise2 wise3arch; do
+			latex ${i} || die
+			latex ${i} || die
+			dvips ${i}.dvi -o || die
+		done
+	fi
+}
+
+src_test() {
+	cd src || die
+	WISECONFIGDIR="${S}/wisecfg" emake test
+}
+
+src_install() {
+	dobin src/bin/* src/dynlibsrc/testgendb
+
+	insinto /usr/share/${PN}
+	doins -r wisecfg
+
+	use doc && dodoc docs/*.ps
+	newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise
+}
diff --git a/sci-biology/wise/wise-2.4.0_alpha.ebuild b/sci-biology/wise/wise-2.4.0_alpha.ebuild
deleted file mode 100644
index c37a8972e84e..000000000000
--- a/sci-biology/wise/wise-2.4.0_alpha.ebuild
+++ /dev/null
@@ -1,73 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-inherit epatch toolchain-funcs versionator
-
-DESCRIPTION="Intelligent algorithms for DNA searches"
-HOMEPAGE="http://www.ebi.ac.uk/Wise2/"
-SRC_URI="ftp://ftp.ebi.ac.uk/pub/software/${PN}2/${PN}$(delete_version_separator 3).tar.gz
-	https://dev.gentoo.org/~mgorny/dist/${P}-patchset.tar.bz2"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="doc static-libs"
-
-RDEPEND="~sci-biology/hmmer-2.3.2"
-DEPEND="
-	${RDEPEND}
-	app-shells/tcsh
-	dev-lang/perl
-	virtual/latex-base"
-
-S="${WORKDIR}"/${PN}$(delete_version_separator 3)
-
-src_prepare() {
-	epatch \
-		"${WORKDIR}"/${P}-patchset/${P}-glibc-2.10.patch \
-		"${WORKDIR}"/${P}-patchset/${P}-cflags.patch
-	cd "${S}"/docs || die
-	cat "${S}"/src/models/*.tex "${S}"/src/dynlibsrc/*.tex | perl gettex.pl > temp.tex || die
-	cat wise2api.tex temp.tex apiend.tex > api.tex || die
-	epatch "${WORKDIR}"/${P}-patchset/${PN}-api.tex.patch
-}
-
-src_compile() {
-	emake \
-		-C src \
-		CC="$(tc-getCC)" \
-		all
-	if use doc; then
-		cd "${S}"/docs || die
-		for i in api appendix dynamite wise2 wise3arch; do
-			latex ${i} || die
-			latex ${i} || die
-			dvips ${i}.dvi -o || die
-		done
-	fi
-}
-
-src_test() {
-	cd "${S}"/src || die
-	WISECONFIGDIR="${S}/wisecfg" emake test
-}
-
-src_install() {
-	dobin "${S}"/src/bin/* "${S}"/src/dynlibsrc/testgendb
-	use static-libs && \
-		dolib.a \
-			"${S}"/src/base/libwisebase.a \
-			"${S}"/src/dynlibsrc/libdyna.a \
-			"${S}"/src/models/libmodel.a
-
-	insinto /usr/share/${PN}
-	doins -r "${S}"/wisecfg
-
-	if use doc; then
-		insinto /usr/share/doc/${PF}
-		doins "${S}"/docs/*.ps
-	fi
-	newenvd "${WORKDIR}"/${P}-patchset/${PN}-env 24wise || die "Failed to install env file"
-}