[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Justin Lecher]

commit:     9fad98b6c4ccb13e73afb6d5b6e55854698a252d
Author:     layman <layman <AT> localhost>
AuthorDate: Sun Apr 12 16:07:42 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 12 16:07:42 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=9fad98b6

sci-biology/pybedtools: add pybedtools

Package-Manager: portage-2.2.14-prefix

 sci-biology/pybedtools/ChangeLog               |  9 +++++++++
 sci-biology/pybedtools/metadata.xml            |  9 +++++++++
 sci-biology/pybedtools/pybedtools-0.6.9.ebuild | 21 +++++++++++++++++++++
 3 files changed, 39 insertions(+)

diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog
new file mode 100644
index 0000000..8441cd2
--- /dev/null
+++ b/sci-biology/pybedtools/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/pybedtools
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*pybedtools-0.6.9 (12 Apr 2015)
+
+  12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml,
+  +pybedtools-0.6.9.ebuild:
+  sci-biology/pybedtools: add pybedtools

diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml
new file mode 100644
index 0000000..b7551a6
--- /dev/null
+++ b/sci-biology/pybedtools/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mschu.dev@gmail.com</email>
+    <name>Michael Schubert</name>
+  </maintainer>
+</pkgmetadata>

diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
new file mode 100644
index 0000000..99657ad
--- /dev/null
+++ b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION="Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working"
+HOMEPAGE="http://pythonhosted.org/pybedtools/"
+SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+
+DEPEND="sci-biology/bedtools
+		dev-python/cython[${PYTHON_USEDEP}]"
+RDEPEND="sci-biology/bedtools"

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Justin Lecher]

commit:     4d506095aa0fa6c96e45346b80f92c34d776afc7
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 13 06:20:33 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr 13 06:20:33 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d506095

sci-biology/pybedtools: Streamline ebuild

Package-Manager: portage-2.2.18

 sci-biology/pybedtools/ChangeLog               | 3 +++
 sci-biology/pybedtools/pybedtools-0.6.9.ebuild | 7 ++++---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog
index 8441cd2..d4cc478 100644
--- a/sci-biology/pybedtools/ChangeLog
+++ b/sci-biology/pybedtools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  13 Apr 2015; Justin Lecher <jlec@gentoo.org> pybedtools-0.6.9.ebuild:
+  sci-biology/pybedtools: Streamline ebuild
+
 *pybedtools-0.6.9 (12 Apr 2015)
 
   12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +metadata.xml,

diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
index 99657ad..1ab30c9 100644
--- a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
@@ -10,12 +10,13 @@ inherit distutils-r1
 
 DESCRIPTION="Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working"
 HOMEPAGE="http://pythonhosted.org/pybedtools/"
-SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz"
+SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-DEPEND="sci-biology/bedtools
-		dev-python/cython[${PYTHON_USEDEP}]"
 RDEPEND="sci-biology/bedtools"
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]"

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Justin Lecher]

commit:     302d36d9dd56ccda4ceaa0aa6b514609fe39ff6d
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  6 10:12:45 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  6 10:12:45 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=302d36d9

sci-biology/pybedtools: Add github to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-biology/pybedtools/ChangeLog    | 3 +++
 sci-biology/pybedtools/metadata.xml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/pybedtools/ChangeLog b/sci-biology/pybedtools/ChangeLog
index d4cc478..2fb878a 100644
--- a/sci-biology/pybedtools/ChangeLog
+++ b/sci-biology/pybedtools/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+  sci-biology/pybedtools: Add github to remote-id in metadata.xml
+
   13 Apr 2015; Justin Lecher <jlec@gentoo.org> pybedtools-0.6.9.ebuild:
   sci-biology/pybedtools: Streamline ebuild
 

diff --git a/sci-biology/pybedtools/metadata.xml b/sci-biology/pybedtools/metadata.xml
index b7551a6..3352804 100644
--- a/sci-biology/pybedtools/metadata.xml
+++ b/sci-biology/pybedtools/metadata.xml
@@ -6,4 +6,7 @@
     <email>mschu.dev@gmail.com</email>
     <name>Michael Schubert</name>
   </maintainer>
+  <upstream>
+    <remote-id type="github">daler/pybedtools</remote-id>
+  </upstream>
 </pkgmetadata>

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Martin Mokrejs]

commit:     f54702e57e98ae5f4bf7f867f40dd3ea29157f19
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Dec 29 11:39:28 2019 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Dec 29 11:39:28 2019 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f54702e5

sci-biology/pybedtools: upgrade from 0.6.9 to 0.8.0

0.6.9 was not fully python3 ready, due to
  https://stackoverflow.com/questions/40367569/dictionary-not-writable-generic-old-setup-py
  at least

Package-Manager: Portage-2.3.75, Repoman-2.3.17
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 .../{pybedtools-0.6.9.ebuild => pybedtools-0.8.0.ebuild}          | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
similarity index 70%
rename from sci-biology/pybedtools/pybedtools-0.6.9.ebuild
rename to sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index f0d497802..d817a594f 100644
--- a/sci-biology/pybedtools/pybedtools-0.6.9.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} )
 
 inherit distutils-r1
 
-DESCRIPTION="Wrapper for Aaron Quinlan's BEDtools, plus other useful methods for working"
+DESCRIPTION="Use BED and GFF files from python using BEDtools"
 HOMEPAGE="http://pythonhosted.org/pybedtools/"
 SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Martin Mokrejs]

commit:     ae5eb7ca6ede7e8579ade25afb8eb005c62ee35a
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed May  6 17:44:42 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May  6 17:44:49 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ae5eb7ca

sci-biology/pybedtools: update homepage, explicitly run cythonize

Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index d817a594f..cd444a09e 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} )
 inherit distutils-r1
 
 DESCRIPTION="Use BED and GFF files from python using BEDtools"
-HOMEPAGE="http://pythonhosted.org/pybedtools/"
+HOMEPAGE="https://daler.github.io/pybedtools"
 SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
@@ -16,6 +16,13 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-RDEPEND="sci-biology/bedtools"
+RDEPEND="
+	sci-biology/bedtools
+	sci-biology/pysam"
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]"
+
+src_compile(){
+	python setup.py cythonize
+	default
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Martin Mokrejs]

commit:     e29df37c8b9b02f3749a57c2075bed05f0a71260
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed May  6 18:22:00 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May  6 18:22:20 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e29df37c

sci-biology/pybedtools: respect minimal and doc USE flags

Installation of the to be generated doc pages is not tested
as I am blocked by bug #721306. Probably some dir needs to be
recursively installed.

Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index cd444a09e..9d4dc23c0 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -14,15 +14,18 @@ SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
+IUSE="doc minimal"
 
 RDEPEND="
 	sci-biology/bedtools
-	sci-biology/pysam"
+	sci-biology/pysam
+	!minimal? ( sci-libs/htslib )
+	doc? ( dev-python/sphinx )"
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]"
 
 src_compile(){
 	python setup.py cythonize
 	default
+	use doc && cd docs && emake html
 }

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Martin Mokrejs]

commit:     3a0d3cb989aa14f980ad867cb8b7d7db5284789f
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Wed May  6 18:27:40 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed May  6 18:28:05 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3a0d3cb9

sci-biology/pybedtools: hopefully install generated HTML files

Package-Manager: Portage-2.3.95, Repoman-2.3.22
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index 9d4dc23c0..440e644b7 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -29,3 +29,9 @@ src_compile(){
 	default
 	use doc && cd docs && emake html
 }
+
+src_install(){
+	default
+	insinto /usr/share/doc/"${PN}"
+	doins -r docs/build/html
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Horea Christian]

commit:     08cb203ae14acd64b0d0c5a7489d9fca813154de
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 06:50:26 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 06:50:26 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=08cb203a

sci-biology/pybedtools: PYTHON_COMPAT update and actually install files

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index 440e644b7..9edb8f366 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{5,6,7,8} )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
@@ -15,6 +15,9 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE="doc minimal"
+RESTRICT="test"
+# Tests reported to fail on Gentoo:
+# https://github.com/daler/pybedtools/issues/329
 
 RDEPEND="
 	sci-biology/bedtools
@@ -26,12 +29,16 @@ DEPEND="${RDEPEND}
 
 src_compile(){
 	python setup.py cythonize
-	default
+	distutils-r1_src_compile
 	use doc && cd docs && emake html
 }
 
 src_install(){
-	default
-	insinto /usr/share/doc/"${PN}"
-	doins -r docs/build/html
+	distutils-r1_src_install
+	if use doc; then
+		insinto /usr/share/doc/"${PN}"
+		doins -r docs/build/html
+	fi
 }
+
+distutils_enable_tests pytest

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Martin Mokrejs]

commit:     f1b4f4489e2e9181bca1dde19fffb24a9155bef7
Author:     Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Sat Dec 12 15:23:20 2020 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Dec 12 15:23:38 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f1b4f448

sci-biology/pybedtools: document more dependencies

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index 9edb8f366..a91de8cca 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -19,11 +19,18 @@ RESTRICT="test"
 # Tests reported to fail on Gentoo:
 # https://github.com/daler/pybedtools/issues/329
 
+# see requirements.txt
 RDEPEND="
 	sci-biology/bedtools
 	sci-biology/pysam
+	dev-python/numpy
+	dev-python/pandas
 	!minimal? ( sci-libs/htslib )
 	doc? ( dev-python/sphinx )"
+# optional-requirements.txt also lists:
+# ucsc-bigwigtobedgraph
+# ucsc-bedgraphtobigwig
+# ucsc-wigtobigwig
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]"
 

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Aisha Tammy]

commit:     45f4ecf6f9d5e9c4e699ea84a7b4b8bb6c9740d6
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Dec 31 10:34:09 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Thu Dec 31 12:04:10 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=45f4ecf6

sci-biology/pybedtools: drop py3.6

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Closes: https://github.com/gentoo/sci/pull/1012
Signed-off-by: Aisha Tammy <gentoo <AT> aisha.cc>

 sci-biology/pybedtools/pybedtools-0.8.0.ebuild | 32 +++++++++++---------------
 1 file changed, 13 insertions(+), 19 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
index a91de8cca..6d391b0a8 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6..9} )
+PYTHON_COMPAT=( python3_{7..9} )
 
 inherit distutils-r1
 
@@ -13,8 +13,8 @@ SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="doc minimal"
+KEYWORDS="~amd64 ~x86"
+IUSE="minimal"
 RESTRICT="test"
 # Tests reported to fail on Gentoo:
 # https://github.com/daler/pybedtools/issues/329
@@ -23,29 +23,23 @@ RESTRICT="test"
 RDEPEND="
 	sci-biology/bedtools
 	sci-biology/pysam
-	dev-python/numpy
-	dev-python/pandas
-	!minimal? ( sci-libs/htslib )
-	doc? ( dev-python/sphinx )"
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	!minimal? ( sci-libs/htslib )"
 # optional-requirements.txt also lists:
 # ucsc-bigwigtobedgraph
 # ucsc-bedgraphtobigwig
 # ucsc-wigtobigwig
-DEPEND="${RDEPEND}
+BDEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]"
 
+# ToDo: fix docs building
+# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
+# even if pybedtools is installed
+#distutils_enable_sphinx docs/source
+distutils_enable_tests pytest
+
 src_compile(){
 	python setup.py cythonize
 	distutils-r1_src_compile
-	use doc && cd docs && emake html
-}
-
-src_install(){
-	distutils-r1_src_install
-	if use doc; then
-		insinto /usr/share/doc/"${PN}"
-		doins -r docs/build/html
-	fi
 }
-
-distutils_enable_tests pytest

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Andrew Ammerlaan]

commit:     b8f4b9f92217f53077630ec58e4fe794669768a3
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Sat Jan 15 11:22:53 2022 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Sat Jan 15 11:22:53 2022 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=b8f4b9f9

sci-biology/pybedtools: bump to version 0.8.2

Closes: https://github.com/gentoo/sci/issues/983
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 ...dtools-0.8.0.ebuild => pybedtools-0.8.2.ebuild} | 35 ++++++++--------------
 1 file changed, 13 insertions(+), 22 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
similarity index 54%
rename from sci-biology/pybedtools/pybedtools-0.8.0.ebuild
rename to sci-biology/pybedtools/pybedtools-0.8.2.ebuild
index 6d391b0a8..95bee9be2 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
@@ -1,9 +1,9 @@
-# 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} )
+PYTHON_COMPAT=( python3_{8..10} )
 
 inherit distutils-r1
 
@@ -14,32 +14,23 @@ SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.g
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
-IUSE="minimal"
+
+# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
 RESTRICT="test"
-# Tests reported to fail on Gentoo:
-# https://github.com/daler/pybedtools/issues/329
 
-# see requirements.txt
 RDEPEND="
 	sci-biology/bedtools
-	sci-biology/pysam
+	sci-biology/pysam[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/pandas[${PYTHON_USEDEP}]
-	!minimal? ( sci-libs/htslib )"
-# optional-requirements.txt also lists:
-# ucsc-bigwigtobedgraph
-# ucsc-bedgraphtobigwig
-# ucsc-wigtobigwig
-BDEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]"
-
-# ToDo: fix docs building
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+"
+
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# TODO: fix docs building
 # ModuleNotFoundError: No module named 'pybedtools.cbedtools'
 # even if pybedtools is installed
 #distutils_enable_sphinx docs/source
 distutils_enable_tests pytest
-
-src_compile(){
-	python setup.py cythonize
-	distutils-r1_src_compile
-}

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Horea Christian]

commit:     50d38d2e487a86cdb5348a6ac81f227ab4b4af12
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 04:16:54 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 04:17:13 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=50d38d2e

sci-biology/pybedtools: enable py3.11, py3.9, fixed tests

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/pybedtools/pybedtools-0.8.2.ebuild | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
index 8f4ae591f..aca7eb9ed 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2022 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{9..11} )
 
 inherit distutils-r1
 
@@ -15,9 +15,6 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
-# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
-RESTRICT="test"
-
 RDEPEND="
 	sci-biology/bedtools
 	sci-biology/pysam[${PYTHON_USEDEP}]
@@ -34,3 +31,12 @@ BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
 # even if pybedtools is installed
 #distutils_enable_sphinx docs/source
 distutils_enable_tests pytest
+
+python_test() {
+	# Requires network
+	local EPYTEST_DESELECT=(
+		test/test_helpers.py::test_chromsizes
+	)
+	cd "${T}" || die
+	epytest --pyargs pybedtools
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Horea Christian]

commit:     811db2634692304728d8e765f4a7b5ad5b54f89a
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 04:19:10 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 04:19:10 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=811db263

sci-biology/pybedtools: distutils PEP 517

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/pybedtools/pybedtools-0.8.2.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
index aca7eb9ed..422d74a31 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
@@ -4,6 +4,7 @@
 EAPI=8
 
 PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517=setuptools
 
 inherit distutils-r1
 

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Horea Christian]

commit:     987fad3d4b257f83e58e20183e324b21e82f1584
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 04:23:37 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 04:23:37 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=987fad3d

sci-biology/pybedtools: add 0.9.0

Signed-off-by: Horea Christian <chr <AT> chymera.eu>

 sci-biology/pybedtools/pybedtools-0.9.0.ebuild | 43 ++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
new file mode 100644
index 000000000..422d74a31
--- /dev/null
+++ b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1
+
+DESCRIPTION="Use BED and GFF files from python using BEDtools"
+HOMEPAGE="https://daler.github.io/pybedtools"
+SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	sci-biology/bedtools
+	sci-biology/pysam[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/pandas[${PYTHON_USEDEP}]
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+"
+
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# TODO: fix docs building
+# ModuleNotFoundError: No module named 'pybedtools.cbedtools'
+# even if pybedtools is installed
+#distutils_enable_sphinx docs/source
+distutils_enable_tests pytest
+
+python_test() {
+	# Requires network
+	local EPYTEST_DESELECT=(
+		test/test_helpers.py::test_chromsizes
+	)
+	cd "${T}" || die
+	epytest --pyargs pybedtools
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/pybedtools/

[Andrew Ammerlaan]

commit:     7a7acdb52f5a587412f7f4f51529d6986e47fb9f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:23:53 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:23:53 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7a7acdb5

sci-biology/pybedtools: disable py3.9

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/pybedtools/pybedtools-0.8.2.ebuild | 2 +-
 sci-biology/pybedtools/pybedtools-0.9.0.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
index 422d74a31..bc02bda6f 100644
--- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
 DISTUTILS_USE_PEP517=setuptools
 
 inherit distutils-r1

diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
index 422d74a31..bc02bda6f 100644
--- a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
+++ b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
 DISTUTILS_USE_PEP517=setuptools
 
 inherit distutils-r1