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* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2016-04-09 22:14 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2016-04-09 22:14 UTC (permalink / raw
  To: gentoo-commits

commit:     76eaabc0743b8d9c067f617bbd569550941bd384
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Apr  9 22:12:42 2016 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Apr  9 22:12:42 2016 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=76eaabc0

sci-biology/pysam: Remove old

Package-Manager: portage-2.2.28

 sci-biology/pysam/Manifest            |  1 -
 sci-biology/pysam/pysam-0.6-r1.ebuild | 25 -------------------------
 2 files changed, 26 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index b7281db..24afdea 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.6.tar.gz 841790 SHA256 081c980481f31a81acb06f6fa5638b899321eddfd9eeb5075393e4dad84a1fc8 SHA512 b60df4551600f04e8ae67aec0f2745846d2411e2a1cc4c874ef296ee80ab075256190ebb0ec64eb78231d4d7b59670c5259818cd315f52c923774cc4c0b8b391 WHIRLPOOL eddeb19f3ebf0c6326f7c1b6b7224b2b8cb708e0bf7ceb66b1cac18909abafd1704b264452b70ee6721af4b3b360b51285dcffd7f137c6128920f91dc0dec7b2
 DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463

diff --git a/sci-biology/pysam/pysam-0.6-r1.ebuild b/sci-biology/pysam/pysam-0.6-r1.ebuild
deleted file mode 100644
index 6faa5a9..0000000
--- a/sci-biology/pysam/pysam-0.6-r1.ebuild
+++ /dev/null
@@ -1,25 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI="5"
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="https://code.google.com/p/pysam https://pypi.python.org/pypi/pysam"
-SRC_URI="https://${PN}.googlecode.com/files/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND="dev-python/setuptools[${PYTHON_USEDEP}]"
-
-python_compile() {
-	python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing"
-	distutils-r1_python_compile
-}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2017-09-02 11:04 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2017-09-02 11:04 UTC (permalink / raw
  To: gentoo-commits

commit:     adb3bc8e64f8afe51ae31d8070b98f2a88a243ee
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep  2 10:44:42 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep  2 11:04:41 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=adb3bc8e

sci-biology/pysam: Bump to 0.12

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/pysam/Manifest          |  1 +
 sci-biology/pysam/pysam-0.12.ebuild | 43 +++++++++++++++++++++++++++++++++++++
 2 files changed, 44 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 24afdea8b62..b2e7af85717 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
+DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3
 DIST pysam-0.9.0.tar.gz 2701721 SHA256 dd4946c8efa6786a754e2b50c6027dd03aa82c8ee6c2be3b4e51384da80b4c7c SHA512 9189ef2b56df0f5e2c84586c0c2b2cd46a77dbedd3aa6fd25ddcc4a93320038bead073206fff528ae9775f153c875838726dd0af8e4c7bf4e0c6063145e2bc06 WHIRLPOOL 6c7d459057fed3961e983b3e8563e10a47cb87f5da2fb99ca893eff9e19a8b9e4c27b5d82a978a611d615eba8052fbe3e36498ea461e03521a075d9aee8da463

diff --git a/sci-biology/pysam/pysam-0.12.ebuild b/sci-biology/pysam/pysam-0.12.ebuild
new file mode 100644
index 00000000000..e181e06ac9b
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.12.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="
+	https://github.com/pysam-developers/pysam
+	https://pypi.python.org/pypi/pysam"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.5*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+python_prepare_all() {
+	export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
+	export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+	# 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
+	:
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2017-09-17 10:55 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2017-09-17 10:55 UTC (permalink / raw
  To: gentoo-commits

commit:     d18c0d93f7ff2d46209b941999530a0eda735cd9
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 17 10:55:14 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Sep 17 10:55:14 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d18c0d93

sci-biology/pysam: Remove old

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/pysam/Manifest          |  1 -
 sci-biology/pysam/pysam-0.12.ebuild | 47 -------------------------------------
 2 files changed, 48 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index b01df416d50..700b3a8a08e 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
 DIST pysam-0.12.0.1.tar.gz 2672020 SHA256 04837bf0b1313e57d50076f228463262b9982c410b973eb184c033528f83d523 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d WHIRLPOOL 5bd9f29e7458cac3839aaa9703d4c5740b1268644947f31ce7d3ddd12e0ec1948611ca5228323ce9b3b8fa5a5e0623c6fa0a0e2ce7f197fdb81aa5465915af36
-DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3

diff --git a/sci-biology/pysam/pysam-0.12.ebuild b/sci-biology/pysam/pysam-0.12.ebuild
deleted file mode 100644
index 1f4f58fdfe2..00000000000
--- a/sci-biology/pysam/pysam-0.12.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
-
-inherit distutils-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
-HOMEPAGE="
-	https://github.com/pysam-developers/pysam
-	https://pypi.python.org/pypi/pysam"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.5*:="
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-
-PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
-
-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
-	:
-}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2017-09-17 10:55 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2017-09-17 10:55 UTC (permalink / raw
  To: gentoo-commits

commit:     25236fc56b39f744e9c57b3b6fc6255a50c6207f
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 17 10:53:46 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Sep 17 10:53:46 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=25236fc5

sci-biology/pysam: Version bump to 0.12.0.1

Package-Manager: Portage-2.3.8, Repoman-2.3.3

 sci-biology/pysam/Manifest              |  1 +
 sci-biology/pysam/pysam-0.12.0.1.ebuild | 47 +++++++++++++++++++++++++++++++++
 2 files changed, 48 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index c95db9a1dcd..b01df416d50 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
+DIST pysam-0.12.0.1.tar.gz 2672020 SHA256 04837bf0b1313e57d50076f228463262b9982c410b973eb184c033528f83d523 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d WHIRLPOOL 5bd9f29e7458cac3839aaa9703d4c5740b1268644947f31ce7d3ddd12e0ec1948611ca5228323ce9b3b8fa5a5e0623c6fa0a0e2ce7f197fdb81aa5465915af36
 DIST pysam-0.12.tar.gz 2537142 SHA256 33922cb3277ed9a63457c1b6a9dcad2774a217ababcc97a854435be87ba80488 SHA512 095a47cd7258ef093a172445c425f382996da886e44e1beb81ecdec2325024e099d14bee6fcd928c4449099f51ad92b6d7ceb464815c463ab4478f162a40f21e WHIRLPOOL 2331e24d817cd3e7372df8e115498456e685ac426796b29c6d5a28edbaab2321f7efc9db0f14a000750fcd9e30391c02b81e439a07596813bdf7fc6c6e1a3ae3

diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild
new file mode 100644
index 00000000000..1f4f58fdfe2
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.12.0.1.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="
+	https://github.com/pysam-developers/pysam
+	https://pypi.python.org/pypi/pysam"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.5*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+
+PATCHES=( "${FILESDIR}"/${PN}-0.12-fix-buildsystem.patch )
+
+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
+	:
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2020-02-11 12:25 Michał Górny
  0 siblings, 0 replies; 16+ messages in thread
From: Michał Górny @ 2020-02-11 12:25 UTC (permalink / raw
  To: gentoo-commits

commit:     c08cc93ef718f0cd2d9b1ef4b74086fb580192f1
Author:     Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Tue Feb 11 12:17:22 2020 +0000
Commit:     Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Tue Feb 11 12:17:22 2020 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c08cc93e

sci-biology/pysam: Remove py2

Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>

 sci-biology/pysam/pysam-0.12.0.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild
index e6500903f84..e7567f3501b 100644
--- a/sci-biology/pysam/pysam-0.12.0.1.ebuild
+++ b/sci-biology/pysam/pysam-0.12.0.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_6 )
+PYTHON_COMPAT=( python3_6 )
 
 inherit distutils-r1
 


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2021-10-03 17:41 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2021-10-03 17:41 UTC (permalink / raw
  To: gentoo-commits

commit:     938a340079ee1b725936dad3e441faf8cc3420cd
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Oct  3 17:41:39 2021 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Oct  3 17:41:39 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=938a3400

sci-biology/pysam: add 0.17.0

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 +
 sci-biology/pysam/pysam-0.17.0.ebuild | 66 +++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index f349d8ddc8a..1e305c998da 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
 DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece SHA512 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28
+DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552

diff --git a/sci-biology/pysam/pysam-0.17.0.ebuild b/sci-biology/pysam/pysam-0.17.0.ebuild
new file mode 100644
index 00000000000..afdc4777e20
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.17.0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.13*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		=sci-biology/bcftools-1.13*
+		=sci-biology/samtools-1.13*
+	)"
+
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+EPYTEST_DESELECT=(
+	# only work with bundled htslib
+	'tests/tabix_test.py::TestRemoteFileHTTP'
+	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
+)
+
+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 (except $ORIGIN)
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	# breaks with parallel build
+	# need to avoid dropping .so plugins into
+	# build-lib, which breaks tests
+	esetup.py build_ext --inplace -j1
+	distutils-r1_python_compile -j1
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2021-10-09  9:32 Arthur Zamarin
  0 siblings, 0 replies; 16+ messages in thread
From: Arthur Zamarin @ 2021-10-09  9:32 UTC (permalink / raw
  To: gentoo-commits

commit:     1c82ccd2949ea6d046c696906c83464ea9f43ec9
Author:     Arthur Zamarin <arthurzam <AT> gentoo <DOT> org>
AuthorDate: Sat Oct  9 08:52:39 2021 +0000
Commit:     Arthur Zamarin <arthurzam <AT> gentoo <DOT> org>
CommitDate: Sat Oct  9 09:31:29 2021 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1c82ccd2

sci-biology/pysam: block <setuptools-58 for 0.16.0.1

Was fixed for 0.17.0

Bug: https://bugs.gentoo.org/812242
Signed-off-by: Arthur Zamarin <arthurzam <AT> gentoo.org>

 .../pysam/{pysam-0.16.0.1.ebuild => pysam-0.16.0.1-r1.ebuild}     | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/pysam/pysam-0.16.0.1.ebuild b/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
similarity index 92%
rename from sci-biology/pysam/pysam-0.16.0.1.ebuild
rename to sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
index ec09bbe1f8c..e27c998bb91 100644
--- a/sci-biology/pysam/pysam-0.16.0.1.ebuild
+++ b/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -18,10 +18,10 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
 RDEPEND="=sci-libs/htslib-1.10*:="
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
 BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	<dev-python/setuptools-58[${PYTHON_USEDEP}]
 	test? (
 		=sci-biology/bcftools-1.10*
 		=sci-biology/samtools-1.10*


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2022-06-10 12:42 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2022-06-10 12:42 UTC (permalink / raw
  To: gentoo-commits

commit:     524b1d19c53df3a7f3ba688a0fd08f92a1539fa3
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Jun 10 12:41:49 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Jun 10 12:41:49 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=524b1d19

sci-biology/pysam: add 0.19.1

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 +
 sci-biology/pysam/pysam-0.19.1.ebuild | 66 +++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 91ca2cac79c1..1e0c911e03c6 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
 DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552
+DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479

diff --git a/sci-biology/pysam/pysam-0.19.1.ebuild b/sci-biology/pysam/pysam-0.19.1.ebuild
new file mode 100644
index 000000000000..70bfcb09dfe8
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.19.1.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.15.1*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		=sci-biology/bcftools-1.15.1*
+		=sci-biology/samtools-1.15.1*
+	)"
+
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+EPYTEST_DESELECT=(
+	# only work with bundled htslib
+	'tests/tabix_test.py::TestRemoteFileHTTP'
+	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
+)
+
+python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
+	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
+	rm -r htslib || die
+
+	# prevent setup.py from adding RPATHs (except $ORIGIN)
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	# breaks with parallel build
+	# need to avoid dropping .so plugins into
+	# build-lib, which breaks tests
+	esetup.py build_ext --inplace -j1
+	distutils-r1_python_compile -j1
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2022-06-19  8:09 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2022-06-19  8:09 UTC (permalink / raw
  To: gentoo-commits

commit:     d3866d06942c293186a4fca7108a74c6a54ec10b
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 19 08:08:42 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 19 08:08:42 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d3866d06

sci-biology/pysam: drop 0.17.0

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 -
 sci-biology/pysam/pysam-0.17.0.ebuild | 66 -----------------------------------
 2 files changed, 67 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 1e0c911e03c6..f1a1fe7298b7 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.17.0.tar.gz 3579324 BLAKE2B 6b88fe771350f20fa7c90a4c02c60fefd6a34d979c687fce1e34a17e1ff203c7d2d07e36b64f7a73f99676b805334df7f049932ce15e26362a5214da03435d64 SHA512 16740f08fb68a1f24656454b834dd9ac52ad9f864f307564566fc244bbd2efb7cb17107b2e85ca5c56af817918a138d1c071533de1b80e5bba42b01bbad7f552
 DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479

diff --git a/sci-biology/pysam/pysam-0.17.0.ebuild b/sci-biology/pysam/pysam-0.17.0.ebuild
deleted file mode 100644
index afdc4777e20e..000000000000
--- a/sci-biology/pysam/pysam-0.17.0.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{8..10} )
-
-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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.13*:="
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-BDEPEND="
-	test? (
-		=sci-biology/bcftools-1.13*
-		=sci-biology/samtools-1.13*
-	)"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-EPYTEST_DESELECT=(
-	# only work with bundled htslib
-	'tests/tabix_test.py::TestRemoteFileHTTP'
-	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-)
-
-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 (except $ORIGIN)
-	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-		-i setup.py || die
-
-	if use test; then
-		einfo "Building test data"
-		emake -C tests/pysam_data
-		emake -C tests/cbcf_data
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	# breaks with parallel build
-	# need to avoid dropping .so plugins into
-	# build-lib, which breaks tests
-	esetup.py build_ext --inplace -j1
-	distutils-r1_python_compile -j1
-}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2022-06-19  8:09 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2022-06-19  8:09 UTC (permalink / raw
  To: gentoo-commits

commit:     19342ac5cfa9a2337ddd970ce36b589f0516f1f4
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Jun 19 08:08:43 2022 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Jun 19 08:08:43 2022 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=19342ac5

sci-biology/pysam: enable py3.11

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/pysam-0.19.1.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/pysam/pysam-0.19.1.ebuild b/sci-biology/pysam/pysam-0.19.1.ebuild
index 70bfcb09dfe8..41afb5307775 100644
--- a/sci-biology/pysam/pysam-0.19.1.ebuild
+++ b/sci-biology/pysam/pysam-0.19.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{8..10} )
+PYTHON_COMPAT=( python3_{8..11} )
 
 inherit distutils-r1
 


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2023-02-19 15:23 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-02-19 15:23 UTC (permalink / raw
  To: gentoo-commits

commit:     cd493f9e3374c2cf9f36ebd06d8dac3f2732faf1
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 19 15:22:52 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 19 15:22:52 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cd493f9e

sci-biology/pysam: add 0.20.0

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 +
 sci-biology/pysam/pysam-0.20.0.ebuild | 69 +++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index f1a1fe7298b7..fc762c874c2d 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
 DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479
+DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49

diff --git a/sci-biology/pysam/pysam-0.20.0.ebuild b/sci-biology/pysam/pysam-0.20.0.ebuild
new file mode 100644
index 000000000000..6372f1602f70
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.20.0.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.16*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		=sci-biology/bcftools-1.16*
+		=sci-biology/samtools-1.16*
+	)"
+
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+EPYTEST_DESELECT=(
+	# only work with bundled htslib
+	'tests/tabix_test.py::TestRemoteFileHTTP'
+	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
+	# broken test
+	# https://github.com/pysam-developers/pysam/issues/1151#issuecomment-1365662253
+	'tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope'
+)
+
+python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
+	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
+	rm -r htslib || die
+
+	# prevent setup.py from adding RPATHs (except $ORIGIN)
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	# breaks with parallel build
+	# need to avoid dropping .so plugins into
+	# build-lib, which breaks tests
+	esetup.py build_ext --inplace -j1
+	distutils-r1_python_compile -j1
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2023-02-19 15:44 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-02-19 15:44 UTC (permalink / raw
  To: gentoo-commits

commit:     3fa05869a3f147c226aa4dcfcc87c2d7919cf1b5
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 19 15:44:18 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sun Feb 19 15:44:18 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3fa05869

sci-biology/pysam: drop 0.19.1

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 -
 sci-biology/pysam/pysam-0.19.1.ebuild | 66 -----------------------------------
 2 files changed, 67 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index fc762c874c2d..fc19ef776276 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479
 DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49

diff --git a/sci-biology/pysam/pysam-0.19.1.ebuild b/sci-biology/pysam/pysam-0.19.1.ebuild
deleted file mode 100644
index 1164fd6bc091..000000000000
--- a/sci-biology/pysam/pysam-0.19.1.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-
-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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.15.1*:="
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-BDEPEND="
-	test? (
-		=sci-biology/bcftools-1.15.1*
-		=sci-biology/samtools-1.15.1*
-	)"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-EPYTEST_DESELECT=(
-	# only work with bundled htslib
-	'tests/tabix_test.py::TestRemoteFileHTTP'
-	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-)
-
-python_prepare_all() {
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
-	rm -r htslib || die
-
-	# prevent setup.py from adding RPATHs (except $ORIGIN)
-	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-		-i setup.py || die
-
-	if use test; then
-		einfo "Building test data"
-		emake -C tests/pysam_data
-		emake -C tests/cbcf_data
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	# breaks with parallel build
-	# need to avoid dropping .so plugins into
-	# build-lib, which breaks tests
-	esetup.py build_ext --inplace -j1
-	distutils-r1_python_compile -j1
-}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2023-03-30 11:11 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-03-30 11:11 UTC (permalink / raw
  To: gentoo-commits

commit:     b29c8f32c0c043d2fcb82195fb58d00fcd771449
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Mar 30 11:11:01 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Mar 30 11:11:01 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b29c8f32

sci-biology/pysam: add 9999

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/pysam-9999.ebuild | 72 +++++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)

diff --git a/sci-biology/pysam/pysam-9999.ebuild b/sci-biology/pysam/pysam-9999.ebuild
new file mode 100644
index 000000000000..a162ddf2158b
--- /dev/null
+++ b/sci-biology/pysam/pysam-9999.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit distutils-r1
+
+if [[ ${PV} == *9999 ]]; then
+	inherit git-r3
+	EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git"
+else
+	SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+	KEYWORDS="~amd64 ~x86"
+fi
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format"
+HOMEPAGE="
+	https://github.com/pysam-developers/pysam
+	https://pypi.org/project/pysam/"
+
+LICENSE="MIT"
+SLOT="0"
+
+RDEPEND=">=sci-libs/htslib-1.17"
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		>=sci-biology/bcftools-1.17
+		>=sci-biology/samtools-1.17
+	)"
+
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+EPYTEST_DESELECT=(
+	# only work with bundled htslib
+	'tests/tabix_test.py::TestRemoteFileHTTP'
+	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
+)
+
+python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
+	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
+	rm -r htslib || die
+
+	# prevent setup.py from adding RPATHs (except $ORIGIN)
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	# breaks with parallel build
+	# need to avoid dropping .so plugins into
+	# build-lib, which breaks tests
+	esetup.py build_ext --inplace -j1
+	distutils-r1_python_compile -j1
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2023-04-06 18:10 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-04-06 18:10 UTC (permalink / raw
  To: gentoo-commits

commit:     a46d8d048179a0c699775baa9eb4157949e4671c
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Apr  6 18:10:36 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Apr  6 18:10:36 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a46d8d04

sci-biology/pysam: add 0.21.0

Bug: https://bugs.gentoo.org/836857
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 +
 sci-biology/pysam/pysam-0.21.0.ebuild | 66 +++++++++++++++++++++++++++++++++++
 2 files changed, 67 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index fc19ef776276..0e0b82641fc1 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
 DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49
+DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7

diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild b/sci-biology/pysam/pysam-0.21.0.ebuild
new file mode 100644
index 000000000000..588cd1bc4f1b
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.21.0.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.17*:="
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	test? (
+		=sci-biology/bcftools-1.17*
+		=sci-biology/samtools-1.17*
+	)"
+
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+EPYTEST_DESELECT=(
+	# only work with bundled htslib
+	'tests/tabix_test.py::TestRemoteFileHTTP'
+	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
+)
+
+python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
+	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
+	rm -r htslib || die
+
+	# prevent setup.py from adding RPATHs (except $ORIGIN)
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	# breaks with parallel build
+	# need to avoid dropping .so plugins into
+	# build-lib, which breaks tests
+	esetup.py build_ext --inplace -j1
+	distutils-r1_python_compile -j1
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2023-04-06 19:29 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2023-04-06 19:29 UTC (permalink / raw
  To: gentoo-commits

commit:     1cea5dc52d7f3cb7f2451d8e58bef8908b8df687
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Apr  6 19:29:06 2023 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Apr  6 19:29:06 2023 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1cea5dc5

sci-biology/pysam: drop 0.20.0

Closes: https://bugs.gentoo.org/836857
Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 -
 sci-biology/pysam/pysam-0.20.0.ebuild | 69 -----------------------------------
 2 files changed, 70 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 0e0b82641fc1..2bc79f89f441 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49
 DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7

diff --git a/sci-biology/pysam/pysam-0.20.0.ebuild b/sci-biology/pysam/pysam-0.20.0.ebuild
deleted file mode 100644
index 6372f1602f70..000000000000
--- a/sci-biology/pysam/pysam-0.20.0.ebuild
+++ /dev/null
@@ -1,69 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..11} )
-
-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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.16*:="
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]
-	dev-python/setuptools[${PYTHON_USEDEP}]"
-BDEPEND="
-	test? (
-		=sci-biology/bcftools-1.16*
-		=sci-biology/samtools-1.16*
-	)"
-
-distutils_enable_tests pytest
-
-DISTUTILS_IN_SOURCE_BUILD=1
-
-EPYTEST_DESELECT=(
-	# only work with bundled htslib
-	'tests/tabix_test.py::TestRemoteFileHTTP'
-	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
-	# broken test
-	# https://github.com/pysam-developers/pysam/issues/1151#issuecomment-1365662253
-	'tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope'
-)
-
-python_prepare_all() {
-	# unbundle htslib
-	export HTSLIB_MODE="external"
-	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
-	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
-	rm -r htslib || die
-
-	# prevent setup.py from adding RPATHs (except $ORIGIN)
-	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-		-i setup.py || die
-
-	if use test; then
-		einfo "Building test data"
-		emake -C tests/pysam_data
-		emake -C tests/cbcf_data
-	fi
-
-	distutils-r1_python_prepare_all
-}
-
-python_compile() {
-	# breaks with parallel build
-	# need to avoid dropping .so plugins into
-	# build-lib, which breaks tests
-	esetup.py build_ext --inplace -j1
-	distutils-r1_python_compile -j1
-}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/
@ 2024-05-24  9:54 David Seifert
  0 siblings, 0 replies; 16+ messages in thread
From: David Seifert @ 2024-05-24  9:54 UTC (permalink / raw
  To: gentoo-commits

commit:     baa67260b08ba489b0790e989e04dd1eb7f54c55
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri May 24 09:53:59 2024 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri May 24 09:53:59 2024 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=baa67260

sci-biology/pysam: add 0.22.1

Signed-off-by: David Seifert <soap <AT> gentoo.org>

 sci-biology/pysam/Manifest            |  1 +
 sci-biology/pysam/pysam-0.22.1.ebuild | 68 +++++++++++++++++++++++++++++++++++
 2 files changed, 69 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 2bc79f89f441..fae7b9793388 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
 DIST pysam-0.21.0.gh.tar.gz 3842829 BLAKE2B 83db290ec0bae71106276ed4f1721292c0d2fa55053c7451f0a8a79619b1c4d8444b99293ac5d8051bfb0b59e984e32a89798bab091e3a019b7c2a3fb7414d1c SHA512 b2ac986b6a352df1d2066a224d710648a88d8ad44273623a89ae0f4bb2645b00f0d0e1685c8ccedfd379259255957e653f3c3199621ac1d4c26098f538b6bfa7
+DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350

diff --git a/sci-biology/pysam/pysam-0.22.1.ebuild b/sci-biology/pysam/pysam-0.22.1.ebuild
new file mode 100644
index 000000000000..9070476873e1
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.22.1.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+
+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="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.20*:="
+DEPEND="${RDEPEND}
+	dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+	test? (
+		=sci-biology/bcftools-1.20*
+		=sci-biology/samtools-1.20*
+	)"
+
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+EPYTEST_DESELECT=(
+	# only work with bundled htslib
+	'tests/tabix_test.py::TestRemoteFileHTTP'
+	'tests/tabix_test.py::TestRemoteFileHTTPWithHeader'
+
+	'tests/AlignedSegment_test.py::TestBaseModifications'
+)
+
+python_prepare_all() {
+	# unbundle htslib
+	export HTSLIB_MODE="external"
+	export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include
+	export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir)
+	rm -r htslib || die
+
+	# prevent setup.py from adding RPATHs (except $ORIGIN)
+	sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+		-i setup.py || die
+
+	if use test; then
+		einfo "Building test data"
+		emake -C tests/pysam_data
+		emake -C tests/cbcf_data
+	fi
+
+	distutils-r1_python_prepare_all
+}
+
+python_compile() {
+	# breaks with parallel build
+	# need to avoid dropping .so plugins into
+	# build-lib, which breaks tests
+	esetup.py build_ext --inplace -j1
+	distutils-r1_python_compile -j1
+}


^ permalink raw reply related	[flat|nested] 16+ messages in thread
end of thread, other threads:[~2024-05-24  9:54 UTC | newest]

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