From d6e49da338f6a6ce88c7bab2a4bbb643d603d95b Mon Sep 17 00:00:00 2001
From: Martin Mokrejs <mmokrejs@gmail.com>
Date: Fri, 7 Feb 2020 10:42:34 +0100
Subject: sci-biology/bcftools: fix PYTHON_COMPAT, add missing matplotlib dep

From NEWS one can infer bcftools was at least from about 1.7 version
python3 compatible. Moreover, at the moment the shenbang lines specifically
call python3.6. So, adjust the PYTHON_COMPAT accordingly. matplotlib is
used by the python scripts, unconditionally.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Closes: https://github.com/gentoo/gentoo/pull/14421
Signed-off-by: Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
Signed-off-by: David Seifert <soap@gentoo.org>
---
 sci-biology/bcftools/bcftools-1.9-r1.ebuild        | 47 ++++++++++++++++++++++
 sci-biology/bcftools/bcftools-1.9.ebuild           | 47 ----------------------
 .../bcftools/files/bcftools-1.9-buildsystem.patch  | 10 +++++
 3 files changed, 57 insertions(+), 47 deletions(-)
 create mode 100644 sci-biology/bcftools/bcftools-1.9-r1.ebuild
 delete mode 100644 sci-biology/bcftools/bcftools-1.9.ebuild
 create mode 100644 sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch

(limited to 'sci-biology/bcftools')

diff --git a/sci-biology/bcftools/bcftools-1.9-r1.ebuild b/sci-biology/bcftools/bcftools-1.9-r1.ebuild
new file mode 100644
index 000000000000..8141e6d22924
--- /dev/null
+++ b/sci-biology/bcftools/bcftools-1.9-r1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_6 )
+
+inherit python-single-r1
+
+DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
+HOMEPAGE="http://www.htslib.org"
+SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+RDEPEND="
+	dev-lang/perl
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	=sci-libs/htslib-${PV}*:=
+	sys-libs/zlib:=
+	${PYTHON_DEPS}"
+DEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.9-buildsystem.patch
+	"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
+)
+
+src_prepare() {
+	default
+
+	python_fix_shebang misc/{guess-ploidy,plot-roh}.py
+
+	# remove bundled htslib
+	rm -r htslib-* || die
+}
+
+src_configure() {
+	econf \
+		--disable-bcftools-plugins \
+		--disable-libgsl \
+		--disable-configure-htslib \
+		--with-htslib=system
+}
diff --git a/sci-biology/bcftools/bcftools-1.9.ebuild b/sci-biology/bcftools/bcftools-1.9.ebuild
deleted file mode 100644
index 53e47bc01a81..000000000000
--- a/sci-biology/bcftools/bcftools-1.9.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2018 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-single-r1
-
-DESCRIPTION="Utilities for variant calling and manipulating VCF and BCF files"
-HOMEPAGE="http://www.htslib.org"
-SRC_URI="https://github.com/samtools/${PN}/releases/download/${PV}/${P}.tar.bz2"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="
-	dev-lang/perl
-	=sci-libs/htslib-${PV}*:=
-	sys-libs/zlib:=
-	${PYTHON_DEPS}"
-DEPEND="${RDEPEND}"
-
-PATCHES=(
-	"${FILESDIR}"/${PN}-1.5-buildsystem.patch
-	"${FILESDIR}"/${PN}-1.9-fix-shebangs.patch
-)
-
-src_prepare() {
-	default
-
-	python_fix_shebang misc/{guess-ploidy,plot-roh}.py
-
-	# remove bundled htslib
-	rm -r htslib-* || die
-}
-
-src_configure() {
-	econf \
-		--disable-bcftools-plugins \
-		--disable-libgsl \
-		--disable-configure-htslib \
-		--with-htslib=system
-}
diff --git a/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
new file mode 100644
index 000000000000..a0df4b917bcb
--- /dev/null
+++ b/sci-biology/bcftools/files/bcftools-1.9-buildsystem.patch
@@ -0,0 +1,10 @@
+--- a/Makefile
++++ b/Makefile
+@@ -282,7 +282,6 @@
+ 	$(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
+ 	$(INSTALL_SCRIPT) $(MISC_SCRIPTS) $(DESTDIR)$(misc_bindir)
+ 	$(INSTALL_MAN) doc/bcftools.1 $(DESTDIR)$(man1dir)
+-	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
+ 
+ clean: testclean clean-plugins
+ 	-rm -f gmon.out *.o *~ $(PROGRAMS) version.h plugins/*.so plugins/*.P
-- 
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