public inbox for gentoo-commits@lists.gentoo.org
 help / color / mirror / Atom feed
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2015-04-13  6:25 Justin Lecher
  0 siblings, 0 replies; 14+ messages in thread
From: Justin Lecher @ 2015-04-13  6:25 UTC (permalink / raw
  To: gentoo-commits

commit:     e1b5c57763609c4498f50be71829d7e3c0f58b8c
Author:     layman <layman <AT> localhost>
AuthorDate: Sun Apr 12 16:06:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 12 16:06:39 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1b5c577

sci-biology/bx-python: add bx-python

Package-Manager: portage-2.2.14-prefix

 sci-biology/bx-python/ChangeLog              | 10 ++++++++++
 sci-biology/bx-python/bx-python-0.7.2.ebuild | 21 +++++++++++++++++++++
 sci-biology/bx-python/bx-python-9999.ebuild  | 21 +++++++++++++++++++++
 sci-biology/bx-python/metadata.xml           |  9 +++++++++
 4 files changed, 61 insertions(+)

diff --git a/sci-biology/bx-python/ChangeLog b/sci-biology/bx-python/ChangeLog
new file mode 100644
index 0000000..f2d5809
--- /dev/null
+++ b/sci-biology/bx-python/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/bx-python
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*bx-python-0.7.2 (12 Apr 2015)
+*bx-python-9999 (12 Apr 2015)
+
+  12 Apr 2015; Michael Schubert <mschu.dev@gmail.com> +bx-python-0.7.2.ebuild,
+  +bx-python-9999.ebuild, +metadata.xml:
+  sci-biology/bx-python: add bx-python

diff --git a/sci-biology/bx-python/bx-python-0.7.2.ebuild b/sci-biology/bx-python/bx-python-0.7.2.ebuild
new file mode 100644
index 0000000..102c4d3
--- /dev/null
+++ b/sci-biology/bx-python/bx-python-0.7.2.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="Library for rapid implementation of genome scale analyses. "
+HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
+SRC_URI="mirror://pypi/b/bx-python/bx-python-${PV}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+
+DEPEND="dev-python/cython[${PYTHON_USEDEP}]
+	    dev-python/numpy[${PYTHON_USEDEP}]"
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
new file mode 100644
index 0000000..8bd0553
--- /dev/null
+++ b/sci-biology/bx-python/bx-python-9999.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 mercurial
+
+DESCRIPTION="Library for rapid implementation of genome scale analyses. "
+HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
+EHG_REPO_URI="https://bitbucket.org/james_taylor/bx-python"
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""
+
+DEPEND="dev-python/cython[${PYTHON_USEDEP}]
+        dev-python/numpy[${PYTHON_USEDEP}]"
+RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"

diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml
new file mode 100644
index 0000000..b7551a6
--- /dev/null
+++ b/sci-biology/bx-python/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>


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2015-04-13  6:25 Justin Lecher
  0 siblings, 0 replies; 14+ messages in thread
From: Justin Lecher @ 2015-04-13  6:25 UTC (permalink / raw
  To: gentoo-commits

commit:     8e28a734e4f096e8b7611f18fe230d26099c5eb9
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 13 06:10:46 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr 13 06:12:29 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e28a734

sci-biology/bx-python: Streamline ebuild

Package-Manager: portage-2.2.18
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/bx-python/ChangeLog              | 4 ++++
 sci-biology/bx-python/bx-python-0.7.2.ebuild | 9 +++++----
 sci-biology/bx-python/bx-python-9999.ebuild  | 8 +++++---
 3 files changed, 14 insertions(+), 7 deletions(-)

diff --git a/sci-biology/bx-python/ChangeLog b/sci-biology/bx-python/ChangeLog
index f2d5809..87a3239 100644
--- a/sci-biology/bx-python/ChangeLog
+++ b/sci-biology/bx-python/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  13 Apr 2015; Justin Lecher <jlec@gentoo.org> bx-python-0.7.2.ebuild,
+  bx-python-9999.ebuild:
+  sci-biology/bx-python: Streamline ebuild
+
 *bx-python-0.7.2 (12 Apr 2015)
 *bx-python-9999 (12 Apr 2015)
 

diff --git a/sci-biology/bx-python/bx-python-0.7.2.ebuild b/sci-biology/bx-python/bx-python-0.7.2.ebuild
index 102c4d3..4167df9 100644
--- a/sci-biology/bx-python/bx-python-0.7.2.ebuild
+++ b/sci-biology/bx-python/bx-python-0.7.2.ebuild
@@ -8,14 +8,15 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit distutils-r1
 
-DESCRIPTION="Library for rapid implementation of genome scale analyses. "
+DESCRIPTION="Library for rapid implementation of genome scale analyses"
 HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
-SRC_URI="mirror://pypi/b/bx-python/bx-python-${PV}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-DEPEND="dev-python/cython[${PYTHON_USEDEP}]
-	    dev-python/numpy[${PYTHON_USEDEP}]"
 RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]"

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 8bd0553..3cb8abe 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -8,14 +8,16 @@ PYTHON_COMPAT=( python2_7 )
 
 inherit distutils-r1 mercurial
 
-DESCRIPTION="Library for rapid implementation of genome scale analyses. "
+DESCRIPTION="Library for rapid implementation of genome scale analyses"
 HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
+SRC_URI=""
 EHG_REPO_URI="https://bitbucket.org/james_taylor/bx-python"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS=""
 IUSE=""
 
-DEPEND="dev-python/cython[${PYTHON_USEDEP}]
-        dev-python/numpy[${PYTHON_USEDEP}]"
 RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+	dev-python/cython[${PYTHON_USEDEP}]"


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2015-06-07 18:33 Justin Lecher
  0 siblings, 0 replies; 14+ messages in thread
From: Justin Lecher @ 2015-06-07 18:33 UTC (permalink / raw
  To: gentoo-commits

commit:     cf7e830a2958c50ad65f6ac99155e6a8ff79379f
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jun  7 18:33:15 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jun  7 18:33:15 2015 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf7e830a

sci-biology/bx-python: Add bitbucket to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-biology/bx-python/ChangeLog    | 3 +++
 sci-biology/bx-python/metadata.xml | 1 +
 2 files changed, 4 insertions(+)

diff --git a/sci-biology/bx-python/ChangeLog b/sci-biology/bx-python/ChangeLog
index 87a3239..6c33466 100644
--- a/sci-biology/bx-python/ChangeLog
+++ b/sci-biology/bx-python/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  07 Jun 2015; Justin Lecher <jlec@gentoo.org> metadata.xml:
+  sci-biology/bx-python: Add bitbucket to remote-id in metadata.xml
+
   13 Apr 2015; Justin Lecher <jlec@gentoo.org> bx-python-0.7.2.ebuild,
   bx-python-9999.ebuild:
   sci-biology/bx-python: Streamline ebuild

diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml
index 8c2353e..1e685c9 100644
--- a/sci-biology/bx-python/metadata.xml
+++ b/sci-biology/bx-python/metadata.xml
@@ -8,5 +8,6 @@
   </maintainer>
   <upstream>
     <remote-id type="pypi">bx-python</remote-id>
+    <remote-id type="bitbucket">james_taylor/bx-python</remote-id>
   </upstream>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2016-07-01 10:49 Martin Mokrejs
  0 siblings, 0 replies; 14+ messages in thread
From: Martin Mokrejs @ 2016-07-01 10:49 UTC (permalink / raw
  To: gentoo-commits

commit:     10579e2234915ea0ec505f3f49896d00baf2c782
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul  1 10:49:09 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul  1 10:49:09 2016 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=10579e22

sci-biology/bx-python: record file collision issue with sci-biology/RSeQC

Package-Manager: portage-2.2.28

 sci-biology/bx-python/bx-python-0.7.2.ebuild | 2 ++
 sci-biology/bx-python/bx-python-9999.ebuild  | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/sci-biology/bx-python/bx-python-0.7.2.ebuild b/sci-biology/bx-python/bx-python-0.7.2.ebuild
index 5008ea9..17fe93e 100644
--- a/sci-biology/bx-python/bx-python-0.7.2.ebuild
+++ b/sci-biology/bx-python/bx-python-0.7.2.ebuild
@@ -20,3 +20,5 @@ IUSE=""
 RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]"
+
+# has file collision with sci-biology/RSeQC

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 66353c4..24f86e8 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -21,3 +21,5 @@ IUSE=""
 RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
 DEPEND="${RDEPEND}
 	dev-python/cython[${PYTHON_USEDEP}]"
+
+# has file collision with sci-biology/RSeQC


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2020-09-26 12:10 Horea Christian
  0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2020-09-26 12:10 UTC (permalink / raw
  To: gentoo-commits

commit:     0c8e98814fa800e7960d92fc5c73fd4cdc30a5f3
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Sep 26 12:10:52 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Sep 26 12:10:52 2020 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0c8e9881

sci-biology/bx-python: version bump 0.8.9

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

 .../{bx-python-0.7.2.ebuild => bx-python-0.8.9.ebuild}         |  8 ++++----
 sci-biology/bx-python/bx-python-9999.ebuild                    | 10 +++++-----
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.7.2.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
similarity index 74%
rename from sci-biology/bx-python/bx-python-0.7.2.ebuild
rename to sci-biology/bx-python/bx-python-0.8.9.ebuild
index 1fa0ebbf6..c4d4b6060 100644
--- a/sci-biology/bx-python/bx-python-0.7.2.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -1,15 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
 DESCRIPTION="Library for rapid implementation of genome scale analyses"
 HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 10cbc8f5d..778cdd06e 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -1,16 +1,16 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6..9} )
 
-inherit distutils-r1 mercurial
+inherit distutils-r1 git-r3
 
 DESCRIPTION="Library for rapid implementation of genome scale analyses"
 HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
 SRC_URI=""
-EHG_REPO_URI="https://bitbucket.org/james_taylor/bx-python"
+EGIT_REPO_URI="https://github.com/bxlab/bx-python"
 
 LICENSE="MIT"
 SLOT="0"


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2021-01-04  5:38 Horea Christian
  0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2021-01-04  5:38 UTC (permalink / raw
  To: gentoo-commits

commit:     3916dc47dbb884e2a8b8f5b541f992d2e93ff98f
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Dec 30 17:47:02 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan  4 05:36:39 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=3916dc47

sci-biology/bx-python: drop py3.6, add dep on cython and six

add blocker with RSeQC

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
Closes https://github.com/gentoo/sci/pull/1007

 sci-biology/bx-python/bx-python-0.8.9.ebuild | 18 ++++++++++++------
 sci-biology/bx-python/bx-python-9999.ebuild  | 16 +++++++++++-----
 2 files changed, 23 insertions(+), 11 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
index c4d4b6060..15647034a 100644
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6..9} )
+PYTHON_COMPAT=( python3_{7..9} )
 
 inherit distutils-r1
 
@@ -13,11 +13,17 @@ SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
+KEYWORDS="~amd64 ~x86"
 
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]"
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	!sci-biology/RSeQC
+"
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
 
 # has file collision with sci-biology/RSeQC
+
+# ToDo: fix doc building:
+# Reason: TemplateNotFound('i')
+#distutils_enable_sphinx doc/source

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 778cdd06e..8d92b0a18 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6..9} )
+PYTHON_COMPAT=( python3_{7..9} )
 
 inherit distutils-r1 git-r3
 
@@ -15,10 +15,16 @@ EGIT_REPO_URI="https://github.com/bxlab/bx-python"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
-IUSE=""
 
-RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}
-	dev-python/cython[${PYTHON_USEDEP}]"
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+	!sci-biology/RSeQC
+"
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
 
 # has file collision with sci-biology/RSeQC
+
+# ToDo: fix doc building:
+# Reason: TemplateNotFound('i')
+#distutils_enable_sphinx doc/source


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2021-01-10 19:05 Andrew Ammerlaan
  0 siblings, 0 replies; 14+ messages in thread
From: Andrew Ammerlaan @ 2021-01-10 19:05 UTC (permalink / raw
  To: gentoo-commits

commit:     850d51ef8122e1fba897370534503313e4cda323
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sun Jan 10 19:04:32 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sun Jan 10 19:04:32 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=850d51ef

sci-biology/bx-python: remove blocker with RSeQC

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/bx-python/bx-python-0.8.9.ebuild | 3 +--
 sci-biology/bx-python/bx-python-9999.ebuild  | 3 +--
 2 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
index 15647034a..90d0e1fd4 100644
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.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
@@ -18,7 +18,6 @@ KEYWORDS="~amd64 ~x86"
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/six[${PYTHON_USEDEP}]
-	!sci-biology/RSeQC
 "
 BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
 

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 8d92b0a18..40d4866e1 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.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
@@ -19,7 +19,6 @@ KEYWORDS=""
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/six[${PYTHON_USEDEP}]
-	!sci-biology/RSeQC
 "
 BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
 


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2021-02-05 11:51 Andrew Ammerlaan
  0 siblings, 0 replies; 14+ messages in thread
From: Andrew Ammerlaan @ 2021-02-05 11:51 UTC (permalink / raw
  To: gentoo-commits

commit:     6ab0a2a03037b813e057c38240e648e2e157ff8e
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Fri Feb  5 11:47:33 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Fri Feb  5 11:47:33 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ab0a2a0

sci-biology/bx-python: update homepage

Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-biology/bx-python/bx-python-0.8.9.ebuild | 2 +-
 sci-biology/bx-python/bx-python-9999.ebuild  | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
index 90d0e1fd4..a0d3ae3df 100644
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python3_{7..9} )
 inherit distutils-r1
 
 DESCRIPTION="Library for rapid implementation of genome scale analyses"
-HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
+HOMEPAGE="https://github.com/bxlab/bx-python"
 SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 40d4866e1..6f0b1c9ca 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -8,8 +8,7 @@ PYTHON_COMPAT=( python3_{7..9} )
 inherit distutils-r1 git-r3
 
 DESCRIPTION="Library for rapid implementation of genome scale analyses"
-HOMEPAGE="https://bitbucket.org/james_taylor/bx-python/wiki/Home"
-SRC_URI=""
+HOMEPAGE="https://github.com/bxlab/bx-python"
 EGIT_REPO_URI="https://github.com/bxlab/bx-python"
 
 LICENSE="MIT"


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2023-01-13  9:18 Horea Christian
  0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2023-01-13  9:18 UTC (permalink / raw
  To: gentoo-commits

commit:     0f1eeb5f8d889cc546f592e867cd64cf1c8d70e5
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 09:07:51 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 09:07:51 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=0f1eeb5f

sci-biology/bx-python: updated PYTHON_COMPAT

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

 sci-biology/bx-python/bx-python-0.8.9.ebuild | 6 +++---
 sci-biology/bx-python/bx-python-9999.ebuild  | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
index a0d3ae3df..86ef4f79a 100644
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 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_{10..10} )
 
 inherit distutils-r1
 

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 6f0b1c9ca..115fda468 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2023 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_{10..10} )
 
 inherit distutils-r1 git-r3
 


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2023-01-13  9:18 Horea Christian
  0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2023-01-13  9:18 UTC (permalink / raw
  To: gentoo-commits

commit:     8411b6dbba5a94a2e74255cf96c3bfa208f4b81a
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 09:10:28 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 09:10:28 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=8411b6db

sci-biology/bx-python: add 0.9.0

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

 sci-biology/bx-python/bx-python-0.9.0.ebuild | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild
new file mode 100644
index 000000000..86ef4f79a
--- /dev/null
+++ b/sci-biology/bx-python/bx-python-0.9.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Library for rapid implementation of genome scale analyses"
+HOMEPAGE="https://github.com/bxlab/bx-python"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/six[${PYTHON_USEDEP}]
+"
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+
+# has file collision with sci-biology/RSeQC
+
+# ToDo: fix doc building:
+# Reason: TemplateNotFound('i')
+#distutils_enable_sphinx doc/source


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2023-01-13  9:18 Horea Christian
  0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2023-01-13  9:18 UTC (permalink / raw
  To: gentoo-commits

commit:     be1b86867b05d343a1303c1a7a0f2acf205824f5
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 09:11:36 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 09:11:36 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=be1b8686

sci-biology/bx-python: GH SRC_URI suffix

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

 sci-biology/bx-python/bx-python-0.8.9.ebuild | 2 +-
 sci-biology/bx-python/bx-python-0.9.0.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
index 86ef4f79a..f0f211f4e 100644
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
 
 DESCRIPTION="Library for rapid implementation of genome scale analyses"
 HOMEPAGE="https://github.com/bxlab/bx-python"
-SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"

diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild
index 86ef4f79a..f0f211f4e 100644
--- a/sci-biology/bx-python/bx-python-0.9.0.ebuild
+++ b/sci-biology/bx-python/bx-python-0.9.0.ebuild
@@ -9,7 +9,7 @@ inherit distutils-r1
 
 DESCRIPTION="Library for rapid implementation of genome scale analyses"
 HOMEPAGE="https://github.com/bxlab/bx-python"
-SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2023-01-13  9:30 Horea Christian
  0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2023-01-13  9:30 UTC (permalink / raw
  To: gentoo-commits

commit:     eadc057d986704101528304a2e9bb331b050e78c
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Jan 13 09:30:29 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Jan 13 09:30:29 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=eadc057d

sci-biology/bx-python: attempting to enable tests

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

 sci-biology/bx-python/bx-python-0.8.9.ebuild | 9 ++++++++-
 sci-biology/bx-python/bx-python-0.9.0.ebuild | 9 ++++++++-
 sci-biology/bx-python/bx-python-9999.ebuild  | 9 ++++++++-
 3 files changed, 24 insertions(+), 3 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild
index f0f211f4e..6cffba1be 100644
--- a/sci-biology/bx-python/bx-python-0.8.9.ebuild
+++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild
@@ -14,15 +14,22 @@ SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
 
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/six[${PYTHON_USEDEP}]
 "
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+"
 
 # has file collision with sci-biology/RSeQC
 
 # ToDo: fix doc building:
 # Reason: TemplateNotFound('i')
 #distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest

diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild
index f0f211f4e..6cffba1be 100644
--- a/sci-biology/bx-python/bx-python-0.9.0.ebuild
+++ b/sci-biology/bx-python/bx-python-0.9.0.ebuild
@@ -14,15 +14,22 @@ SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
 
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/six[${PYTHON_USEDEP}]
 "
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+"
 
 # has file collision with sci-biology/RSeQC
 
 # ToDo: fix doc building:
 # Reason: TemplateNotFound('i')
 #distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest

diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild
index 115fda468..b29975b58 100644
--- a/sci-biology/bx-python/bx-python-9999.ebuild
+++ b/sci-biology/bx-python/bx-python-9999.ebuild
@@ -14,15 +14,22 @@ EGIT_REPO_URI="https://github.com/bxlab/bx-python"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
+# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science)
+# (and might need some more work beyond that)
+RESTRICT=test
 
 RDEPEND="
 	dev-python/numpy[${PYTHON_USEDEP}]
 	dev-python/six[${PYTHON_USEDEP}]
 "
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+BDEPEND="
+	dev-python/cython[${PYTHON_USEDEP}]
+"
 
 # has file collision with sci-biology/RSeQC
 
 # ToDo: fix doc building:
 # Reason: TemplateNotFound('i')
 #distutils_enable_sphinx doc/source
+
+distutils_enable_tests pytest


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2023-02-17 21:10 Horea Christian
  0 siblings, 0 replies; 14+ messages in thread
From: Horea Christian @ 2023-02-17 21:10 UTC (permalink / raw
  To: gentoo-commits

commit:     62d83379b39a9745ed94de5296f3739dc9ead8c4
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Fri Feb 17 21:10:37 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Feb 17 21:10:37 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=62d83379

sci-biology/bx-python: remove bitbucket upstream metadata

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

 sci-biology/bx-python/metadata.xml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml
index 80a22b44a..f1fc4360e 100644
--- a/sci-biology/bx-python/metadata.xml
+++ b/sci-biology/bx-python/metadata.xml
@@ -10,8 +10,7 @@
 		<name>Gentoo Biology Project</name>
 	</maintainer>
 	<upstream>
-		<remote-id type="bitbucket">james_taylor/bx-python</remote-id>
-		<remote-id type="pypi">bx-python</remote-id>
 		<remote-id type="github">bxlab/bx-python</remote-id>
+		<remote-id type="pypi">bx-python</remote-id>
 	</upstream>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 14+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/
@ 2024-11-13 13:37 Nowa Ammerlaan
  0 siblings, 0 replies; 14+ messages in thread
From: Nowa Ammerlaan @ 2024-11-13 13:37 UTC (permalink / raw
  To: gentoo-commits

commit:     ce12d41df7b9ff0999b2998d407edb57abe7b9ea
Author:     Michael Schubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Mon Nov 11 13:59:05 2024 +0000
Commit:     Nowa Ammerlaan <nowa <AT> gentoo <DOT> org>
CommitDate: Wed Nov 13 13:33:24 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ce12d41d

sci-biology/bx-python: version bump 0.13.0

Signed-off-by: Michael Schubert <mschu.dev <AT> gmail.com>
Closes: https://github.com/gentoo/sci/pull/1297
Signed-off-by: Nowa Ammerlaan <nowa <AT> gentoo.org>

 .../bx-python/{bx-python-0.12.0.ebuild => bx-python-0.13.0.ebuild}  | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/sci-biology/bx-python/bx-python-0.12.0.ebuild b/sci-biology/bx-python/bx-python-0.13.0.ebuild
similarity index 82%
rename from sci-biology/bx-python/bx-python-0.12.0.ebuild
rename to sci-biology/bx-python/bx-python-0.13.0.ebuild
index 1a00b0395..0062da958 100644
--- a/sci-biology/bx-python/bx-python-0.12.0.ebuild
+++ b/sci-biology/bx-python/bx-python-0.13.0.ebuild
@@ -17,6 +17,7 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 
+BDEPEND="test? ( dev-python/python-lzo[${PYTHON_USEDEP}] )"
 RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]"
 DEPEND="dev-python/cython[${PYTHON_USEDEP}]"
 
@@ -28,11 +29,6 @@ PATCHES=(
 distutils_enable_tests pytest
 
 # https://github.com/bxlab/bx-python/issues/101
-EPYTEST_DESELECT=(
-	lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_file_lzo
-	lib.linux-x86_64-cpython-312/bx/binned_array_tests.py::test_binned_array_writer
-)
-
 python_test() {
 	cd "${BUILD_DIR}/build" || die
 	ln -s "${S}/pytest.ini" . || die


^ permalink raw reply related	[flat|nested] 14+ messages in thread
end of thread, other threads:[~2024-11-13 13:37 UTC | newest]

Thread overview: 14+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2021-01-04  5:38 [gentoo-commits] proj/sci:master commit in: sci-biology/bx-python/ Horea Christian
  -- strict thread matches above, loose matches on Subject: below --
2024-11-13 13:37 Nowa Ammerlaan
2023-02-17 21:10 Horea Christian
2023-01-13  9:30 Horea Christian
2023-01-13  9:18 Horea Christian
2023-01-13  9:18 Horea Christian
2023-01-13  9:18 Horea Christian
2021-02-05 11:51 Andrew Ammerlaan
2021-01-10 19:05 Andrew Ammerlaan
2020-09-26 12:10 Horea Christian
2016-07-01 10:49 Martin Mokrejs
2015-06-07 18:33 Justin Lecher
2015-04-13  6:25 Justin Lecher
2015-04-13  6:25 Justin Lecher

This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox