[gentoo-commits] proj/sci:master commit in: sci-biology/pysam/, sci-biology/pysamstats/

[Martin Mokrejs]

commit:     b1ad15e7a10105fb9f0905ea5aac0835a62b46f3
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri Jan 10 16:32:20 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jan 10 16:52:47 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b1ad15e7

sci-biology/pysamstats: version bump
sci-biology/pysam: version bump

I am not sure if the path pysam-0.12-fix-buildsystem.patch is still
needed or not. Nevertheless, the modules do not import properly into
python so the ebuild needs more work.

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/pysam/metadata.xml                     | 12 ++++++
 sci-biology/pysam/pysam-0.15.3.ebuild              | 46 ++++++++++++++++++++++
 ...stats-0.24.2.ebuild => pysamstats-1.1.2.ebuild} |  9 +++--
 3 files changed, 64 insertions(+), 3 deletions(-)

diff --git a/sci-biology/pysam/metadata.xml b/sci-biology/pysam/metadata.xml
new file mode 100644
index 000000000..6182254bd
--- /dev/null
+++ b/sci-biology/pysam/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@g.o</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <upstream>
+    <remote-id type="google-code">pysam</remote-id>
+    <remote-id type="github">pysam-developers/pysam</remote-id>
+  </upstream>
+</pkgmetadata>

diff --git a/sci-biology/pysam/pysam-0.15.3.ebuild b/sci-biology/pysam/pysam-0.15.3.ebuild
new file mode 100644
index 000000000..4224df0be
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.15.3.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_6 )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="
+	https://github.com/pysam-developers/pysam
+	https://pypi.org/project/pysam/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS=""
+
+# current code wraps 3rd-party code from htslib-1.9, samtools-1.9 and bcftools-1.9
+RDEPEND="=sci-libs/htslib-1.9*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
+	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
+	rm -r htslib || die
+
+	# prevent setup.py from adding RPATHs
+	sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \
+		-i cy_build.py || die
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	distutils-r1_python_prepare_all
+}
+
+src_compile() {
+	# TODO
+	# empty compile, as the build system runs the whole build again in install
+	:
+}

diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
similarity index 77%
rename from sci-biology/pysamstats/pysamstats-0.24.2.ebuild
rename to sci-biology/pysamstats/pysamstats-1.1.2.ebuild
index d6e1350a4..06bb7c69b 100644
--- a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
+++ b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -17,6 +17,9 @@ SLOT="0"
 KEYWORDS="" # needs working pysam, see bug #645060
 IUSE=""
 
-DEPEND="dev-python/cython
-	>=sci-biology/pysam-0.8.4"
+DEPEND="
+	dev-python/cython
+	dev-python/numpy
+	dev-python/pytables
+	>=sci-biology/pysam-0.15.1"
 RDEPEND="${DEPEND}"