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