subject:"\[gentoo\-commits\] repo\/gentoo\:master commit in\: sci\-biology\/pysam\/"

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

2024-05-24 Thread David Seifert

commit: a300fad43f75217ec5ca16d5262e578e0af853a9
Author: David Seifert  gentoo  org>
AuthorDate: Fri May 24 09:54:01 2024 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri May 24 09:54:01 2024 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a300fad4

sci-biology/pysam: drop 0.21.0

Closes: https://bugs.gentoo.org/923243
Closes: https://bugs.gentoo.org/927872
Closes: https://bugs.gentoo.org/929754
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/pysam/Manifest |  1 -
 .../pysam/files/pysam-0.21.0-cython-3.patch| 24 
 sci-biology/pysam/pysam-0.21.0.ebuild  | 72 --
 3 files changed, 97 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index fae7b9793388..2859d25293fc 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-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/files/pysam-0.21.0-cython-3.patch 
b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch
deleted file mode 100644
index 303a4fb0dcdc..
--- a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001
-From: John Marshall 
-Date: Sat, 8 Apr 2023 11:00:46 +1200
-Subject: [PATCH] Remove incorrect type annotation
-
-The annotation already in pysam/libcbcf.pyi is correct.
-Fixes #1179 as reopened on April 6th.

- pysam/libcbcf.pyx | 2 +-
- 1 file changed, 1 insertion(+), 1 deletion(-)
-
-diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx
-index 8c088af2..8ecfe5f3 100644
 a/pysam/libcbcf.pyx
-+++ b/pysam/libcbcf.pyx
-@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object):
- return bcf_format_get_alleles(self)
- 
- @alleles.setter
--def alleles(self, value: tuple):
-+def alleles(self, value):
- # Sets the genotype, supply a tuple of alleles to set.
- # The supplied alleles need to be defined in the correspoding 
pysam.libcbcf.VariantRecord
- # The genotype is reset when an empty tuple, None or (None,) is 
supplied

diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild 
b/sci-biology/pysam/pysam-0.21.0.ebuild
deleted file mode 100644
index 77292ed29613..
--- a/sci-biology/pysam/pysam-0.21.0.ebuild
+++ /dev/null
@@ -1,72 +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 -> 
${P}.gh.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.17*:="
-DEPEND="${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
-
-PATCHES=(
-   # backport
-   # 
https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9
-   "${FILESDIR}"/${P}-cython-3.patch
-)
-
-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

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2024-05-24 Thread David Seifert

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

sci-biology/pysam: add 0.22.1

Signed-off-by: David Seifert  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 ..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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

2023-04-08 Thread David Seifert

commit: e88f627a3bada9db443b5234ac3fa71c6102c63d
Author: David Seifert  gentoo  org>
AuthorDate: Sat Apr  8 17:53:38 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Apr  8 17:53:38 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e88f627a

sci-biology/pysam: fix build with cython 3

Closes: https://bugs.gentoo.org/898730
Signed-off-by: David Seifert  gentoo.org>

 .../pysam/files/pysam-0.21.0-cython-3.patch| 24 ++
 sci-biology/pysam/pysam-0.21.0.ebuild  |  6 ++
 2 files changed, 30 insertions(+)

diff --git a/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch 
b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch
new file mode 100644
index ..303a4fb0dcdc
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.21.0-cython-3.patch
@@ -0,0 +1,24 @@
+From 17bb13dcfdb56ac238458dcef23fe01893a892e9 Mon Sep 17 00:00:00 2001
+From: John Marshall 
+Date: Sat, 8 Apr 2023 11:00:46 +1200
+Subject: [PATCH] Remove incorrect type annotation
+
+The annotation already in pysam/libcbcf.pyi is correct.
+Fixes #1179 as reopened on April 6th.
+---
+ pysam/libcbcf.pyx | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/pysam/libcbcf.pyx b/pysam/libcbcf.pyx
+index 8c088af2..8ecfe5f3 100644
+--- a/pysam/libcbcf.pyx
 b/pysam/libcbcf.pyx
+@@ -3479,7 +3479,7 @@ cdef class VariantRecordSample(object):
+ return bcf_format_get_alleles(self)
+ 
+ @alleles.setter
+-def alleles(self, value: tuple):
++def alleles(self, value):
+ # Sets the genotype, supply a tuple of alleles to set.
+ # The supplied alleles need to be defined in the correspoding 
pysam.libcbcf.VariantRecord
+ # The genotype is reset when an empty tuple, None or (None,) is 
supplied

diff --git a/sci-biology/pysam/pysam-0.21.0.ebuild 
b/sci-biology/pysam/pysam-0.21.0.ebuild
index 588cd1bc4f1b..77292ed29613 100644
--- a/sci-biology/pysam/pysam-0.21.0.ebuild
+++ b/sci-biology/pysam/pysam-0.21.0.ebuild
@@ -31,6 +31,12 @@ distutils_enable_tests pytest
 
 DISTUTILS_IN_SOURCE_BUILD=1
 
+PATCHES=(
+   # backport
+   # 
https://github.com/pysam-developers/pysam/commit/17bb13dcfdb56ac238458dcef23fe01893a892e9
+   "${FILESDIR}"/${P}-cython-3.patch
+)
+
 EPYTEST_DESELECT=(
# only work with bundled htslib
'tests/tabix_test.py::TestRemoteFileHTTP'

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2023-04-06 Thread David Seifert

commit: 1cea5dc52d7f3cb7f2451d8e58bef8908b8df687
Author: David Seifert  gentoo  org>
AuthorDate: Thu Apr  6 19:29:06 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Apr  6 19:29:06 2023 +
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  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..
--- 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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2023-04-06 Thread David Seifert

commit: a46d8d048179a0c699775baa9eb4157949e4671c
Author: David Seifert  gentoo  org>
AuthorDate: Thu Apr  6 18:10:36 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Apr  6 18:10:36 2023 +
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  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 ..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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2023-03-30 Thread David Seifert

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

sci-biology/pysam: add 

Signed-off-by: David Seifert  gentoo.org>

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

diff --git a/sci-biology/pysam/pysam-.ebuild 
b/sci-biology/pysam/pysam-.ebuild
new file mode 100644
index ..a162ddf2158b
--- /dev/null
+++ b/sci-biology/pysam/pysam-.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 [[ ${PV} == * ]]; then
+   inherit git-r3
+   EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git;
+else
+   
SRC_URI="https://github.com/pysam-developers/pysam/archive/v${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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2023-02-19 Thread David Seifert

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

sci-biology/pysam: drop 0.19.1

Signed-off-by: David Seifert  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..
--- 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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2023-02-19 Thread David Seifert

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

sci-biology/pysam: add 0.20.0

Signed-off-by: David Seifert  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 ..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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2022-06-19 Thread David Seifert

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

sci-biology/pysam: enable py3.11

Signed-off-by: David Seifert  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

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2022-06-19 Thread David Seifert

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

sci-biology/pysam: drop 0.17.0

Signed-off-by: David Seifert  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..
--- 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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2022-06-10 Thread David Seifert

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

sci-biology/pysam: add 0.19.1

Signed-off-by: David Seifert  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 ..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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

2021-10-11 Thread David Seifert

commit: 3b93bba18c14598747eda127476f093040e6b3b6
Author: David Seifert  gentoo  org>
AuthorDate: Mon Oct 11 14:55:08 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Oct 11 14:55:08 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3b93bba1

sci-biology/pysam: drop 0.16.0.1-r1

Closes: https://bugs.gentoo.org/812242
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/pysam/Manifest |  1 -
 .../pysam/files/pysam-0.16.0.1-fix-tests.patch | 37 -
 sci-biology/pysam/pysam-0.16.0.1-r1.ebuild | 60 --
 3 files changed, 98 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 1e305c998da..91ca2cac79c 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-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/files/pysam-0.16.0.1-fix-tests.patch 
b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
deleted file mode 100644
index 9d269878e65..000
--- a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
+++ /dev/null
@@ -1,37 +0,0 @@
 a/tests/pysam_data/Makefile
-+++ b/tests/pysam_data/Makefile
-@@ -3,7 +3,7 @@
- BAI=$(BAM:%.bam=%.bam.bai)
- CRAM=ex1.cram ex2.cram ex3.cram
- CRAI=$(CRAM:%.cram=%.cram.crai)
--NO_PG:=$(findstring --no-PG,$(shell samtools view))
-+NO_PG:=--no-PG
- 
- # ex2.bam - bam file without index
- 
 a/tests/tabix_test.py
-+++ b/tests/tabix_test.py
-@@ -14,6 +14,7 @@
- import subprocess
- import glob
- import re
-+import pytest
- from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
- load_and_convert, TABIX_DATADIR, get_temp_filename
- 
-@@ -1014,6 +1015,7 @@
- globals()[n] = type(n, (TestVCFFromVariantFile,), 
dict(filename=vcf_file,))
- 
- 
-+@pytest.mark.skip(reason="requires internet connectivity")
- class TestRemoteFileHTTP(unittest.TestCase):
- 
- url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz;
-@@ -1053,6 +1055,7 @@
- self.assertEqual(list(self.local_file.header), [])
- 
- 
-+@pytest.mark.skip(reason="requires internet connectivity")
- class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
- 
- url = 
"http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz;

diff --git a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild 
b/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
deleted file mode 100644
index e27c998bb91..000
--- a/sci-biology/pysam/pysam-0.16.0.1-r1.ebuild
+++ /dev/null
@@ -1,60 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-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 -> 
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="=sci-libs/htslib-1.10*:="
-DEPEND="${RDEPEND}"
-BDEPEND="
-   dev-python/cython[${PYTHON_USEDEP}]
-

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2021-10-09 Thread Arthur Zamarin

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

sci-biology/pysam: block https://bugs.gentoo.org/812242
Signed-off-by: Arthur Zamarin  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}]
+

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2021-10-03 Thread David Seifert

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

sci-biology/pysam: add 0.17.0

Signed-off-by: David Seifert  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 000..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
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

2020-08-03 Thread David Seifert

commit: ebcdc8895b15d89af6600d8241e5cda417a4f7e3
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 21:11:13 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 21:11:13 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ebcdc889

sci-biology/pysam: Remove old

Closes: https://bugs.gentoo.org/645060
Closes: https://bugs.gentoo.org/646986
Closes: https://bugs.gentoo.org/718472
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/pysam/Manifest |  1 -
 .../pysam/files/pysam-0.12-fix-buildsystem.patch   | 63 --
 sci-biology/pysam/pysam-0.12.0.1.ebuild| 47 
 3 files changed, 111 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 661592294a2..f349d8ddc8a 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
-DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 
4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28
 SHA512 
31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d
 DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 
8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece
 SHA512 
5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28

diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch 
b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
deleted file mode 100644
index 8b323a63fba..000
--- a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
+++ /dev/null
@@ -1,63 +0,0 @@
-The build system is not designed with partial out-of-source
-builds in mind. This is evident by using relative includes
-such as '-Isamtools' instead of proper relative or absolute
-paths.
-
-Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
-
 a/setup.py
-+++ b/setup.py
-@@ -359,6 +359,8 @@
- 
- define_macros = []
- 
-+samtools_include_dirs = [os.path.abspath("samtools")]
-+
- chtslib = Extension(
- "pysam.libchtslib",
- [source_pattern % "htslib",
-@@ -385,7 +387,7 @@
- htslib_sources +
- os_c_files,
- library_dirs=htslib_library_dirs,
--include_dirs=["pysam", "samtools", "."] + include_os + 
htslib_include_dirs,
-+include_dirs=["pysam", "."] + samtools_include_dirs + include_os + 
htslib_include_dirs,
- libraries=external_htslib_libraries + internal_htslib_libraries,
- language="c",
- extra_compile_args=extra_compile_args,
-@@ -404,7 +406,7 @@
- htslib_sources +
- os_c_files,
- library_dirs=htslib_library_dirs,
--include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs,
-+include_dirs=["pysam"] + samtools_include_dirs + include_os + 
htslib_include_dirs,
- libraries=external_htslib_libraries + internal_htslib_libraries,
- language="c",
- extra_compile_args=extra_compile_args,
-@@ -423,7 +425,7 @@
- htslib_sources +
- os_c_files,
- library_dirs=htslib_library_dirs,
--include_dirs=["pysam", "samtools", "."] + include_os + 
htslib_include_dirs,
-+include_dirs=["pysam", "."] + samtools_include_dirs + include_os + 
htslib_include_dirs,
- libraries=external_htslib_libraries + internal_htslib_libraries,
- language="c",
- extra_compile_args=extra_compile_args,
-@@ -467,7 +469,7 @@
- htslib_sources +
- os_c_files,
- library_dirs=["pysam"] + htslib_library_dirs,
--include_dirs=["samtools", "pysam", "."] +
-+include_dirs=["pysam", "."] + samtools_include_dirs +
- include_os + htslib_include_dirs,
- libraries=external_htslib_libraries + internal_htslib_libraries,
- language="c",
-@@ -482,7 +484,7 @@
- htslib_sources +
- os_c_files,
- library_dirs=["pysam"] + htslib_library_dirs,
--include_dirs=["bcftools", "pysam", "."] +
-+include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs +
- include_os + htslib_include_dirs,
- libraries=external_htslib_libraries + internal_htslib_libraries,
- language="c",

diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild 
b/sci-biology/pysam/pysam-0.12.0.1.ebuild
deleted file mode 100644
index e7567f3501b..000
--- a/sci-biology/pysam/pysam-0.12.0.1.ebuild
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( 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="~amd64 ~x86"
-

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

2020-08-03 Thread David Seifert

commit: 98949b9dddb793b4f2834beb4888df6204322699
Author: David Seifert  gentoo  org>
AuthorDate: Mon Aug  3 16:54:29 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Aug  3 16:54:29 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=98949b9d

sci-biology/pysam: Bump to 0.16.0.1

Bug: https://bugs.gentoo.org/645060
Bug: https://bugs.gentoo.org/646986
Bug: https://bugs.gentoo.org/718472
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/pysam/Manifest |  1 +
 .../pysam/files/pysam-0.16.0.1-fix-tests.patch | 37 +
 sci-biology/pysam/pysam-0.16.0.1.ebuild| 60 ++
 3 files changed, 98 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 76bd71ffeb5..661592294a2 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
 DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 
4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28
 SHA512 
31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d
+DIST pysam-0.16.0.1.tar.gz 3294073 BLAKE2B 
8df1c9b061b0d4b3962ff4b0e30f1589e02d7df41ce362bff861596d3599bf800bb16b2fa4de326fc07102dc7801b48c6b821e5d47e694a3536bec2c5b1cfece
 SHA512 
5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28

diff --git a/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch 
b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
new file mode 100644
index 000..9d269878e65
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.16.0.1-fix-tests.patch
@@ -0,0 +1,37 @@
+--- a/tests/pysam_data/Makefile
 b/tests/pysam_data/Makefile
+@@ -3,7 +3,7 @@
+ BAI=$(BAM:%.bam=%.bam.bai)
+ CRAM=ex1.cram ex2.cram ex3.cram
+ CRAI=$(CRAM:%.cram=%.cram.crai)
+-NO_PG:=$(findstring --no-PG,$(shell samtools view))
++NO_PG:=--no-PG
+ 
+ # ex2.bam - bam file without index
+ 
+--- a/tests/tabix_test.py
 b/tests/tabix_test.py
+@@ -14,6 +14,7 @@
+ import subprocess
+ import glob
+ import re
++import pytest
+ from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check_url, \
+ load_and_convert, TABIX_DATADIR, get_temp_filename
+ 
+@@ -1014,6 +1015,7 @@
+ globals()[n] = type(n, (TestVCFFromVariantFile,), 
dict(filename=vcf_file,))
+ 
+ 
++@pytest.mark.skip(reason="requires internet connectivity")
+ class TestRemoteFileHTTP(unittest.TestCase):
+ 
+ url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz;
+@@ -1053,6 +1055,7 @@
+ self.assertEqual(list(self.local_file.header), [])
+ 
+ 
++@pytest.mark.skip(reason="requires internet connectivity")
+ class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
+ 
+ url = 
"http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz;

diff --git a/sci-biology/pysam/pysam-0.16.0.1.ebuild 
b/sci-biology/pysam/pysam-0.16.0.1.ebuild
new file mode 100644
index 000..acc0cb99892
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.16.0.1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+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 -> 
${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="=sci-libs/htslib-1.10*:="
+DEPEND="${RDEPEND}
+   dev-python/cython[${PYTHON_USEDEP}]
+   dev-python/setuptools[${PYTHON_USEDEP}]"
+BDEPEND="
+   test? (
+   =sci-biology/bcftools-1.10*
+   =sci-biology/samtools-1.10*
+   )"
+
+distutils_enable_tests pytest
+
+DISTUTILS_IN_SOURCE_BUILD=1
+
+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 $ORIGIN)
+   sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
+   -i setup.py || die
+
+   eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch
+
+   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
+   local MAKEOPTS=-j1
+   distutils-r1_python_compile
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2020-02-11 Thread Michał Górny

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

sci-biology/pysam: Remove py2

Signed-off-by: Michał Górny  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

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2017-09-17 Thread David Seifert

commit: d18c0d93f7ff2d46209b941999530a0eda735cd9
Author: David Seifert  gentoo  org>
AuthorDate: Sun Sep 17 10:55:14 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Sep 17 10:55:14 2017 +
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..000
--- 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
-   :
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2017-09-17 Thread David Seifert

commit: 25236fc56b39f744e9c57b3b6fc6255a50c6207f
Author: David Seifert  gentoo  org>
AuthorDate: Sun Sep 17 10:53:46 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Sep 17 10:53:46 2017 +
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 000..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
+   :
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

2017-09-02 Thread David Seifert

commit: e4dbb5c139e2c3dfe8a7d6eaa7f19a08da9b88b0
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 18:34:46 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 18:35:42 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e4dbb5c1

sci-biology/pysam: Fix broken relative -I

Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
Package-Manager: Portage-2.3.8, Repoman-2.3.3

 .../pysam/files/pysam-0.12-fix-buildsystem.patch   | 63 ++
 sci-biology/pysam/pysam-0.12.ebuild|  6 ++-
 2 files changed, 68 insertions(+), 1 deletion(-)

diff --git a/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch 
b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
new file mode 100644
index 000..8b323a63fba
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.12-fix-buildsystem.patch
@@ -0,0 +1,63 @@
+The build system is not designed with partial out-of-source
+builds in mind. This is evident by using relative includes
+such as '-Isamtools' instead of proper relative or absolute
+paths.
+
+Bug: https://bugs.gentoo.org/show_bug.cgi?id=629670
+
+--- a/setup.py
 b/setup.py
+@@ -359,6 +359,8 @@
+ 
+ define_macros = []
+ 
++samtools_include_dirs = [os.path.abspath("samtools")]
++
+ chtslib = Extension(
+ "pysam.libchtslib",
+ [source_pattern % "htslib",
+@@ -385,7 +387,7 @@
+ htslib_sources +
+ os_c_files,
+ library_dirs=htslib_library_dirs,
+-include_dirs=["pysam", "samtools", "."] + include_os + 
htslib_include_dirs,
++include_dirs=["pysam", "."] + samtools_include_dirs + include_os + 
htslib_include_dirs,
+ libraries=external_htslib_libraries + internal_htslib_libraries,
+ language="c",
+ extra_compile_args=extra_compile_args,
+@@ -404,7 +406,7 @@
+ htslib_sources +
+ os_c_files,
+ library_dirs=htslib_library_dirs,
+-include_dirs=["pysam", "samtools"] + include_os + htslib_include_dirs,
++include_dirs=["pysam"] + samtools_include_dirs + include_os + 
htslib_include_dirs,
+ libraries=external_htslib_libraries + internal_htslib_libraries,
+ language="c",
+ extra_compile_args=extra_compile_args,
+@@ -423,7 +425,7 @@
+ htslib_sources +
+ os_c_files,
+ library_dirs=htslib_library_dirs,
+-include_dirs=["pysam", "samtools", "."] + include_os + 
htslib_include_dirs,
++include_dirs=["pysam", "."] + samtools_include_dirs + include_os + 
htslib_include_dirs,
+ libraries=external_htslib_libraries + internal_htslib_libraries,
+ language="c",
+ extra_compile_args=extra_compile_args,
+@@ -467,7 +469,7 @@
+ htslib_sources +
+ os_c_files,
+ library_dirs=["pysam"] + htslib_library_dirs,
+-include_dirs=["samtools", "pysam", "."] +
++include_dirs=["pysam", "."] + samtools_include_dirs +
+ include_os + htslib_include_dirs,
+ libraries=external_htslib_libraries + internal_htslib_libraries,
+ language="c",
+@@ -482,7 +484,7 @@
+ htslib_sources +
+ os_c_files,
+ library_dirs=["pysam"] + htslib_library_dirs,
+-include_dirs=["bcftools", "pysam", "."] +
++include_dirs=["bcftools", "pysam", "."] + samtools_include_dirs +
+ include_os + htslib_include_dirs,
+ libraries=external_htslib_libraries + internal_htslib_libraries,
+ language="c",

diff --git a/sci-biology/pysam/pysam-0.12.ebuild 
b/sci-biology/pysam/pysam-0.12.ebuild
index e181e06ac9b..1f4f58fdfe2 100644
--- a/sci-biology/pysam/pysam-0.12.ebuild
+++ b/sci-biology/pysam/pysam-0.12.ebuild
@@ -22,10 +22,14 @@ 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)
-   export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+   rm -r htslib || die
 
# prevent setup.py from adding RPATHs
sed -e "/ext\.extra_link_args += \['-Wl,-rpath,\$ORIGIN'\]/d" \

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

2017-09-02 Thread David Seifert

commit: de55574a2c871cd8baaf5fdc33960f90401d3e44
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 11:07:41 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 12:36:59 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de55574a

sci-biology/pysam: Remove old

Package-Manager: Portage-2.3.8, Repoman-2.3.3
Closes: https://github.com/gentoo/gentoo/pull/5593

 sci-biology/pysam/Manifest |  1 -
 .../pysam/files/pysam-0.9.0-missing-config.h.patch | 40 ---
 sci-biology/pysam/pysam-0.9.0.ebuild   | 45 --
 3 files changed, 86 deletions(-)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index b2e7af85717..c95db9a1dcd 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,2 +1 @@
 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/files/pysam-0.9.0-missing-config.h.patch 
b/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
deleted file mode 100644
index 617786a5a58..000
--- a/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-From 55f5d8ce51ad999123a779f31fcf0fecd60de9e6 Mon Sep 17 00:00:00 2001
-From: Andreas Heger 
-Date: Mon, 21 Mar 2016 21:10:04 +
-Subject: [PATCH] {AH} create empty config.h for samtools if it does not exist,
- fixes #245
-

- setup.py | 12 +++-
- 1 file changed, 11 insertions(+), 1 deletion(-)
-
-diff --git a/setup.py b/setup.py
-index 7b59b69..2f00c37 100644
 a/setup.py
-+++ b/setup.py
-@@ -155,7 +155,7 @@ def run_configure(option):
- outf.write(
- "/* empty config.h created by pysam */\n")
- outf.write(
--"/* conservative compilation options */")
-+"/* conservative compilation options */\n")
- 
- if HTSLIB_LIBRARY_DIR:
- # linking against a shared, externally installed htslib version, no
-@@ -259,6 +259,16 @@ def run_configure(option):
-"adding shared libcurl and libcrypto")
- external_htslib_libraries.extend(["curl", "crypto"])
- 
-+# create empty config.h files if they have not been created automatically
-+# or created by the user:
-+for fn in "samtools/config.h", "htslib/config.h":
-+if not os.path.exists(fn):
-+with open(fn, "w") as outf:
-+outf.write(
-+"/* empty config.h created by pysam */\n")
-+outf.write(
-+"/* conservative compilation options */\n")
-+
- parts = ["samtools",
-  "bcftools",
-  "htslib",

diff --git a/sci-biology/pysam/pysam-0.9.0.ebuild 
b/sci-biology/pysam/pysam-0.9.0.ebuild
deleted file mode 100644
index ba886f80899..000
--- a/sci-biology/pysam/pysam-0.9.0.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_{4,5} )
-
-inherit distutils-r1 python-r1
-
-DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
-HOMEPAGE="https://github.com/pysam-developers/pysam 
http://pypi.python.org/pypi/pysam;
-SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="=sci-libs/htslib-1.3*"
-DEPEND="${RDEPEND}
-   dev-python/cython[${PYTHON_USEDEP}]
-   dev-python/setuptools[${PYTHON_USEDEP}]"
-
-PATCHES=(
-   "${FILESDIR}/${P}-missing-config.h.patch"
-)
-
-src_prepare() {
-   default
-
-   export HTSLIB_INCLUDE_DIR=${EPREFIX}/usr/include
-   export HTSLIB_LIBRARY_DIR=${EPREFIX}/usr/$(get_libdir)
-   export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
-
-   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
-}
-
-src_compile() {
-   # TODO
-   # empty compile, as the build system runs the whole build again in 
install
-   :
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2017-09-02 Thread David Seifert

commit: adb3bc8e64f8afe51ae31d8070b98f2a88a243ee
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  2 10:44:42 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  2 11:04:41 2017 +
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 000..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
+   :
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

2016-04-09 Thread David Seifert

commit: e2ab268997d872b610d931593db890f6c4dc4630
Author: David Seifert  gentoo  org>
AuthorDate: Sat Apr  9 22:05:20 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Apr  9 22:06:07 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e2ab2689

sci-biology/pysam: Version bump, add py3 support

Package-Manager: portage-2.2.28

 sci-biology/pysam/Manifest |  1 +
 .../pysam/files/pysam-0.9.0-missing-config.h.patch | 40 +++
 sci-biology/pysam/pysam-0.9.0.ebuild   | 46 ++
 3 files changed, 87 insertions(+)

diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 4aea08f..b7281db 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1 +1,2 @@
 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/files/pysam-0.9.0-missing-config.h.patch 
b/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
new file mode 100644
index 000..617786a
--- /dev/null
+++ b/sci-biology/pysam/files/pysam-0.9.0-missing-config.h.patch
@@ -0,0 +1,40 @@
+From 55f5d8ce51ad999123a779f31fcf0fecd60de9e6 Mon Sep 17 00:00:00 2001
+From: Andreas Heger 
+Date: Mon, 21 Mar 2016 21:10:04 +
+Subject: [PATCH] {AH} create empty config.h for samtools if it does not exist,
+ fixes #245
+
+---
+ setup.py | 12 +++-
+ 1 file changed, 11 insertions(+), 1 deletion(-)
+
+diff --git a/setup.py b/setup.py
+index 7b59b69..2f00c37 100644
+--- a/setup.py
 b/setup.py
+@@ -155,7 +155,7 @@ def run_configure(option):
+ outf.write(
+ "/* empty config.h created by pysam */\n")
+ outf.write(
+-"/* conservative compilation options */")
++"/* conservative compilation options */\n")
+ 
+ if HTSLIB_LIBRARY_DIR:
+ # linking against a shared, externally installed htslib version, no
+@@ -259,6 +259,16 @@ def run_configure(option):
+"adding shared libcurl and libcrypto")
+ external_htslib_libraries.extend(["curl", "crypto"])
+ 
++# create empty config.h files if they have not been created automatically
++# or created by the user:
++for fn in "samtools/config.h", "htslib/config.h":
++if not os.path.exists(fn):
++with open(fn, "w") as outf:
++outf.write(
++"/* empty config.h created by pysam */\n")
++outf.write(
++"/* conservative compilation options */\n")
++
+ parts = ["samtools",
+  "bcftools",
+  "htslib",

diff --git a/sci-biology/pysam/pysam-0.9.0.ebuild 
b/sci-biology/pysam/pysam-0.9.0.ebuild
new file mode 100644
index 000..5fcecfb
--- /dev/null
+++ b/sci-biology/pysam/pysam-0.9.0.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5} )
+
+inherit distutils-r1 python-r1
+
+DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping 
format"
+HOMEPAGE="https://github.com/pysam-developers/pysam 
http://pypi.python.org/pypi/pysam;
+SRC_URI="https://github.com/pysam-developers/${PN}/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+RDEPEND="=sci-libs/htslib-1.3*"
+DEPEND="${RDEPEND}
+   dev-python/cython[${PYTHON_USEDEP}]
+   dev-python/setuptools[${PYTHON_USEDEP}]"
+
+PATCHES=(
+   "${FILESDIR}/${P}-missing-config.h.patch"
+)
+
+src_prepare() {
+   default
+
+   export HTSLIB_INCLUDE_DIR=${EPREFIX}/usr/include
+   export HTSLIB_LIBRARY_DIR=${EPREFIX}/usr/$(get_libdir)
+   export HTSLIB_CONFIGURE_OPTIONS="--disable-libcurl"
+
+   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
+}
+
+src_compile() {
+   # TODO
+   # empty compile, as the build system runs the whole build again in 
install
+   :
+}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

2016-04-09 Thread David Seifert

commit: 76eaabc0743b8d9c067f617bbd569550941bd384
Author: David Seifert  gentoo  org>
AuthorDate: Sat Apr  9 22:12:42 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Apr  9 22:12:42 2016 +
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..000
--- 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
-}

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/files/, sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/, sci-biology/pysam/files/

[gentoo-commits] repo/gentoo:master commit in: sci-biology/pysam/

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