* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2017-11-16 13:17 David Seifert
0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2017-11-16 13:17 UTC (permalink / raw
To: gentoo-commits
commit: cd2d3189dadad62ef240af7f543861f2f621bf4d
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 16 11:39:24 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Thu Nov 16 13:16:37 2017 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=cd2d3189
sci-biology/HTSeq: Initial addition
Closes: https://github.com/gentoo/sci/pull/814
Package-Manager: Portage-2.3.14, Repoman-2.3.6
sci-biology/HTSeq/HTSeq-0.9.1.ebuild | 31 +++++++++++++++++++++++++++++++
sci-biology/HTSeq/HTSeq-9999.ebuild | 31 +++++++++++++++++++++++++++++++
sci-biology/HTSeq/Manifest | 1 +
sci-biology/HTSeq/metadata.xml | 19 +++++++++++++++++++
4 files changed, 82 insertions(+)
diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
new file mode 100644
index 00000000000..446bbef36ef
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
@@ -0,0 +1,31 @@
+# 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 support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="
+ ${RDEPEND}
+ >=dev-lang/swig-3.0.8
+ dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
new file mode 100644
index 00000000000..446bbef36ef
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -0,0 +1,31 @@
+# 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 support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+else
+ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="
+ ${RDEPEND}
+ >=dev-lang/swig-3.0.8
+ dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
new file mode 100644
index 00000000000..6d90d56d352
--- /dev/null
+++ b/sci-biology/HTSeq/Manifest
@@ -0,0 +1 @@
+DIST HTSeq-0.9.1.tar.gz 596941 SHA256 af5bba775e3fb45ed4cde64c691ebef36b0bf7a86efd35c884ad0734c27ad485 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344 WHIRLPOOL da3f1d867f9cfa05e34321f75fb34ef79e943476ee650d4689e320078821703721168bfdd9e46f10f1319cc1006771cd205a80569549d21719d38aea6b0be3a8
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
new file mode 100644
index 00000000000..e9ba18c35b3
--- /dev/null
+++ b/sci-biology/HTSeq/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>proxy-maint@gentoo.org</email>
+ <name>Proxy Maintainers</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+ <upstream>
+ <remote-id type="pypi">HTSeq</remote-id>
+ </upstream>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2018-01-06 10:19 Michał Górny
0 siblings, 0 replies; 10+ messages in thread
From: Michał Górny @ 2018-01-06 10:19 UTC (permalink / raw
To: gentoo-commits
commit: 54f641dc3f2f3065b54c5c29edf8f7b19533df73
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 6 10:17:28 2018 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Sat Jan 6 10:18:57 2018 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=54f641dc
sci-biology/HTSeq: Update contact for mmokrejs
sci-biology/HTSeq/metadata.xml | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
index e9ba18c35b3..8d3c9ccebe2 100644
--- a/sci-biology/HTSeq/metadata.xml
+++ b/sci-biology/HTSeq/metadata.xml
@@ -2,7 +2,7 @@
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
+ <email>mmokrejs@gmail.com</email>
<name>Martin Mokrejs</name>
</maintainer>
<maintainer type="project">
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2020-01-16 6:39 Michał Górny
0 siblings, 0 replies; 10+ messages in thread
From: Michał Górny @ 2020-01-16 6:39 UTC (permalink / raw
To: gentoo-commits
commit: 506d03fd7b11f6257955611053672bce3874da1d
Author: Michał Górny <mgorny <AT> gentoo <DOT> org>
AuthorDate: Thu Jan 16 06:24:31 2020 +0000
Commit: Michał Górny <mgorny <AT> gentoo <DOT> org>
CommitDate: Thu Jan 16 06:37:51 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=506d03fd
sci-biology/HTSeq: Remove Python 2
Signed-off-by: Michał Górny <mgorny <AT> gentoo.org>
sci-biology/HTSeq/HTSeq-0.9.1.ebuild | 2 +-
sci-biology/HTSeq/HTSeq-9999.ebuild | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
index 8e051640e6d..18a07a7b9f9 100644
--- a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
+++ b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-PYTHON_COMPAT=( python2_7 python3_6 )
+PYTHON_COMPAT=( python3_6 )
inherit distutils-r1
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 8e051640e6d..18a07a7b9f9 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-PYTHON_COMPAT=( python2_7 python3_6 )
+PYTHON_COMPAT=( python3_6 )
inherit distutils-r1
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2020-04-14 8:35 Joonas Niilola
0 siblings, 0 replies; 10+ messages in thread
From: Joonas Niilola @ 2020-04-14 8:35 UTC (permalink / raw
To: gentoo-commits
commit: b7a4cdbb9c56d901fab2e1f7fea9d10c622e377e
Author: Joonas Niilola <juippis <AT> gentoo <DOT> org>
AuthorDate: Tue Apr 14 07:57:09 2020 +0000
Commit: Joonas Niilola <juippis <AT> gentoo <DOT> org>
CommitDate: Tue Apr 14 08:34:31 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b7a4cdbb
sci-biology/HTSeq: remove inactive maintainer
Signed-off-by: Joonas Niilola <juippis <AT> gentoo.org>
sci-biology/HTSeq/metadata.xml | 8 --------
1 file changed, 8 deletions(-)
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
index 8d3c9ccebe2..1b5a1245ecb 100644
--- a/sci-biology/HTSeq/metadata.xml
+++ b/sci-biology/HTSeq/metadata.xml
@@ -1,14 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@gmail.com</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>proxy-maint@gentoo.org</email>
- <name>Proxy Maintainers</name>
- </maintainer>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2020-08-03 16:56 David Seifert
0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2020-08-03 16:56 UTC (permalink / raw
To: gentoo-commits
commit: 90152a8f4a9c81520a37f329793c6ed8d1dc963e
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 3 16:54:32 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug 3 16:54:32 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=90152a8f
sci-biology/HTSeq: Bump to 0.12.4
Bug: https://bugs.gentoo.org/696484
Bug: https://bugs.gentoo.org/718466
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/HTSeq/HTSeq-0.12.4.ebuild | 33 +++++++++++++++++++++++++++++++++
sci-biology/HTSeq/Manifest | 1 +
2 files changed, 34 insertions(+)
diff --git a/sci-biology/HTSeq/HTSeq-0.12.4.ebuild b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild
new file mode 100644
index 00000000000..1f5693d9a13
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild
@@ -0,0 +1,33 @@
+# 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 support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/htseq/htseq.git"
+else
+ SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz"
+
+ S="${WORKDIR}"/htseq-release_${PV}
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ >=dev-lang/swig-3.0.8
+ dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
index d521aef0c0b..bc4ffd5f360 100644
--- a/sci-biology/HTSeq/Manifest
+++ b/sci-biology/HTSeq/Manifest
@@ -1 +1,2 @@
+DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64
DIST HTSeq-0.9.1.tar.gz 596941 BLAKE2B 6865c36056bff2008ae8bf18d0ac81dbf721fb97cdcc8bbd9150356fc80ae99e0cb872033fac274b40df3d1c95e9bcfd83c4f7d033184725596ffc96081e26d1 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2020-08-03 16:56 David Seifert
0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2020-08-03 16:56 UTC (permalink / raw
To: gentoo-commits
commit: 774908698f411d554226b066ec933a64afca0c4f
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Mon Aug 3 16:54:35 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Mon Aug 3 16:54:35 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=77490869
sci-biology/HTSeq: Sync live ebuild
Package-Manager: Portage-3.0.1, Repoman-2.3.23
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/HTSeq/HTSeq-9999.ebuild | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 18a07a7b9f9..1f5693d9a13 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-PYTHON_COMPAT=( python3_6 )
+PYTHON_COMPAT=( python3_{6..9} )
inherit distutils-r1
@@ -12,9 +12,11 @@ HOMEPAGE="https://htseq.readthedocs.io/"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
- EGIT_REPO_URI="https://github.com/simon-anders/htseq.git"
+ EGIT_REPO_URI="https://github.com/htseq/htseq.git"
else
- SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+ SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz"
+
+ S="${WORKDIR}"/htseq-release_${PV}
KEYWORDS="~amd64"
fi
@@ -25,7 +27,7 @@ RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/matplotlib[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="
- ${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
>=dev-lang/swig-3.0.8
dev-python/cython[${PYTHON_USEDEP}]"
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2022-07-02 13:16 David Seifert
0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2022-07-02 13:16 UTC (permalink / raw
To: gentoo-commits
commit: ad5bb34dc60813f76a4e36f79fa95293b8be5442
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 2 13:16:02 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jul 2 13:16:02 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=ad5bb34d
sci-biology/HTSeq: drop 0.12.4
Closes: https://bugs.gentoo.org/809662
Closes: https://bugs.gentoo.org/846221
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/HTSeq/HTSeq-0.12.4.ebuild | 33 ---------------------------------
sci-biology/HTSeq/Manifest | 1 -
2 files changed, 34 deletions(-)
diff --git a/sci-biology/HTSeq/HTSeq-0.12.4.ebuild b/sci-biology/HTSeq/HTSeq-0.12.4.ebuild
deleted file mode 100644
index 548684fd531b..000000000000
--- a/sci-biology/HTSeq/HTSeq-0.12.4.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2020 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 support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
-HOMEPAGE="https://htseq.readthedocs.io/"
-
-if [[ ${PV} == *9999 ]]; then
- inherit git-r3
- EGIT_REPO_URI="https://github.com/htseq/htseq.git"
-else
- SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz"
-
- S="${WORKDIR}"/htseq-release_${PV}
- KEYWORDS="~amd64"
-fi
-
-LICENSE="GPL-3+"
-SLOT="0"
-
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
-BDEPEND="
- >=dev-lang/swig-3.0.8
- dev-python/cython[${PYTHON_USEDEP}]"
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
index fbb304f1410e..89b37aa1c25b 100644
--- a/sci-biology/HTSeq/Manifest
+++ b/sci-biology/HTSeq/Manifest
@@ -1,2 +1 @@
-DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64
DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2022-07-02 13:16 David Seifert
0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2022-07-02 13:16 UTC (permalink / raw
To: gentoo-commits
commit: 52fc6e9547d84e09c0e13658617c46ceab10d3a1
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 2 13:16:01 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jul 2 13:16:01 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=52fc6e95
sci-biology/HTSeq: sync live ebuild
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/HTSeq/HTSeq-9999.ebuild | 49 +++++++++++++++++++++++++++++++------
1 file changed, 42 insertions(+), 7 deletions(-)
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 548684fd531b..678968788ff7 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -1,11 +1,12 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=7
+EAPI=8
-PYTHON_COMPAT=( python3_{7..9} )
+DISTUTILS_IN_SOURCE_BUILD=1
+PYTHON_COMPAT=( python3_{8..10} )
-inherit distutils-r1
+inherit distutils-r1 flag-o-matic
DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
HOMEPAGE="https://htseq.readthedocs.io/"
@@ -14,7 +15,7 @@ if [[ ${PV} == *9999 ]]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/htseq/htseq.git"
else
- SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.tar.gz"
+ SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz"
S="${WORKDIR}"/htseq-release_${PV}
KEYWORDS="~amd64"
@@ -22,12 +23,46 @@ fi
LICENSE="GPL-3+"
SLOT="0"
+IUSE="test"
+RESTRICT="!test? ( test )"
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"
+DEPEND="${RDEPEND}
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )"
BDEPEND="
>=dev-lang/swig-3.0.8
dev-python/cython[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+
+src_configure() {
+ # mask broken asserts in src/step_vector.h:72
+ append-cppflags -DNDEBUG
+
+ distutils-r1_src_configure
+}
+
+python_test() {
+ distutils_install_for_testing
+
+ # Due to the build directories creating a competing
+ # hierarchy, we move to the test/ dir to avoid implicitly
+ # injecting the root HTSeq/ dir into the PYTHONPATH,
+ # which leads the python module lookup astray:
+ # ${PWD}
+ # ├── build
+ # │ ├── lib
+ # │ │ └── HTSeq
+ # │ [...]
+ # ├── HTSeq
+ # └── test
+ cd test/ || die
+ ln -s ../example_data || die
+ epytest
+}
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2022-07-02 13:16 David Seifert
0 siblings, 0 replies; 10+ messages in thread
From: David Seifert @ 2022-07-02 13:16 UTC (permalink / raw
To: gentoo-commits
commit: 45b11a00d7dd6f99521af35a08cc4c7214656751
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Jul 2 13:16:00 2022 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Jul 2 13:16:00 2022 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=45b11a00
sci-biology/HTSeq: add 2.0.2
Bug: https://bugs.gentoo.org/809662
Bug: https://bugs.gentoo.org/846221
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/HTSeq/HTSeq-2.0.2.ebuild | 68 ++++++++++++++++++++++++++++++++++++
sci-biology/HTSeq/Manifest | 1 +
2 files changed, 69 insertions(+)
diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
new file mode 100644
index 000000000000..678968788ff7
--- /dev/null
+++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
@@ -0,0 +1,68 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_IN_SOURCE_BUILD=1
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1 flag-o-matic
+
+DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
+HOMEPAGE="https://htseq.readthedocs.io/"
+
+if [[ ${PV} == *9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/htseq/htseq.git"
+else
+ SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+ S="${WORKDIR}"/htseq-release_${PV}
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="GPL-3+"
+SLOT="0"
+IUSE="test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-biology/pysam[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+ test? (
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ )"
+BDEPEND="
+ >=dev-lang/swig-3.0.8
+ dev-python/cython[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+
+src_configure() {
+ # mask broken asserts in src/step_vector.h:72
+ append-cppflags -DNDEBUG
+
+ distutils-r1_src_configure
+}
+
+python_test() {
+ distutils_install_for_testing
+
+ # Due to the build directories creating a competing
+ # hierarchy, we move to the test/ dir to avoid implicitly
+ # injecting the root HTSeq/ dir into the PYTHONPATH,
+ # which leads the python module lookup astray:
+ # ${PWD}
+ # ├── build
+ # │ ├── lib
+ # │ │ └── HTSeq
+ # │ [...]
+ # ├── HTSeq
+ # └── test
+ cd test/ || die
+ ln -s ../example_data || die
+ epytest
+}
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
index 92258c60174f..fbb304f1410e 100644
--- a/sci-biology/HTSeq/Manifest
+++ b/sci-biology/HTSeq/Manifest
@@ -1 +1,2 @@
DIST HTSeq-0.12.4.tar.gz 36187218 BLAKE2B 27be4e8783f9e32c10e23ae812069b489eb11dfa4058db43b5db4b8089792351901255103e4d4de1bcf866da3acd13e742adf8d35a9b70305aa156c70dde0837 SHA512 ec4a1a7e9177f103465840ffa9f936a5e887ffd17760b99d4cbdfd5a88e2ab44275fadfcbee153aadc6e828de7be205ed7a07f3a0548457b7c66826341c3ca64
+DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] repo/gentoo:master commit in: sci-biology/HTSeq/
@ 2023-02-24 7:00 Andrew Ammerlaan
0 siblings, 0 replies; 10+ messages in thread
From: Andrew Ammerlaan @ 2023-02-24 7:00 UTC (permalink / raw
To: gentoo-commits
commit: 4575b438f9f067c711b52441caa3e5509e9d0240
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Fri Feb 24 06:48:49 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Feb 24 07:00:09 2023 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4575b438
sci-biology/HTSeq: enable py3.11
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/HTSeq/HTSeq-2.0.2.ebuild | 4 +---
sci-biology/HTSeq/HTSeq-9999.ebuild | 4 +---
sci-biology/HTSeq/metadata.xml | 1 +
3 files changed, 3 insertions(+), 6 deletions(-)
diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
index 25620147ddb8..b4b7974e60d0 100644
--- a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
+++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_{9..11} )
inherit distutils-r1 flag-o-matic
@@ -23,8 +23,6 @@ fi
LICENSE="GPL-3+"
SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 25620147ddb8..b4b7974e60d0 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -4,7 +4,7 @@
EAPI=8
DISTUTILS_IN_SOURCE_BUILD=1
-PYTHON_COMPAT=( python3_{9..10} )
+PYTHON_COMPAT=( python3_{9..11} )
inherit distutils-r1 flag-o-matic
@@ -23,8 +23,6 @@ fi
LICENSE="GPL-3+"
SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml
index 649077f8337e..6ada1a530737 100644
--- a/sci-biology/HTSeq/metadata.xml
+++ b/sci-biology/HTSeq/metadata.xml
@@ -7,5 +7,6 @@
</maintainer>
<upstream>
<remote-id type="pypi">HTSeq</remote-id>
+ <remote-id type="github">htseq/htseq</remote-id>
</upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
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