[gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
commit: 8c097d1bb613ea66723b7088712299d54f3e32c0
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Wed Jan 26 16:27:00 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Wed Jan 26 16:27:00 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8c097d1b
sci-biology/chiron: bump python compat
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan gentoo.org>
sci-biology/chiron/chiron-0.6.1.1.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild
b/sci-biology/chiron/chiron-0.6.1.1.ebuild
index 645e4ed30..162a03129 100644
--- a/sci-biology/chiron/chiron-0.6.1.1.ebuild
+++ b/sci-biology/chiron/chiron-0.6.1.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2021 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_{7,8} )
+PYTHON_COMPAT=( python3_{8..9} )
DISTUTILS_USE_SETUPTOOLS=rdepend
inherit distutils-r1
[gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
commit: 5c00b7d3b2bf6c5febb225a4abf08960ca83f42d
Author: Andrew Ammerlaan riseup net>
AuthorDate: Tue Jan 5 15:53:08 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Tue Jan 5 18:05:31 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5c00b7d3
sci-biology/chiron: bump py targets, add keywords
Closes: https://github.com/gentoo/sci/pull/1037
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-biology/chiron/chiron-0.6.1.1.ebuild | 29 +
sci-biology/chiron/chiron-.ebuild| 22 --
2 files changed, 29 insertions(+), 22 deletions(-)
diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild
b/sci-biology/chiron/chiron-0.6.1.1.ebuild
new file mode 100644
index 0..645e4ed30
--- /dev/null
+++ b/sci-biology/chiron/chiron-0.6.1.1.ebuild
@@ -0,0 +1,29 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+
+inherit distutils-r1
+
+DESCRIPTION="A deep neural network basecaller for nanopore sequencing"
+HOMEPAGE="https://github.com/haotianteng/chiron
+ https://www.biorxiv.org/content/early/2017/09/12/179531;
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0"
+KEYWORDS="~amd64"
+
+RDEPEND="
+ dev-python/h5py[${PYTHON_USEDEP}]
+ sci-biology/mappy[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ sci-biology/biopython[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ sci-libs/tensorflow[${PYTHON_USEDEP}]
+"
diff --git a/sci-biology/chiron/chiron-.ebuild
b/sci-biology/chiron/chiron-.ebuild
deleted file mode 100644
index 4294326ee..0
--- a/sci-biology/chiron/chiron-.ebuild
+++ /dev/null
@@ -1,22 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python2_7 pypy )
-
-inherit distutils-r1 eutils git-r3
-
-DESCRIPTION="Basecaller for OxfordNanopore data using deep learning"
-HOMEPAGE="https://github.com/haotianteng/chiron
- https://www.biorxiv.org/content/early/2017/09/12/179531;
-EGIT_REPO_URI="https://github.com/haotianteng/chiron;
-
-LICENSE="MPL-2.0"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="~sci-libs/tensorflow-1.0.1"
-RDEPEND="${DEPEND}
- dev-python/h5py"
[gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
commit: e5ce549c694e952e624f1c4b2b751db1618294ec
Author: Martin Mokrejs fold natur cuni cz>
AuthorDate: Sat Apr 13 20:36:02 2019 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Sat Apr 13 20:36:02 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e5ce549c
sci-biology/chiron: Fix RDEPEND issue
RDEPEND uses the = operator with no revision:
'=sci-libs/tensorflow-1.0.1';
if any revision is acceptable, use '~' instead;
if only -r0 then please append '-r0' to the dep
Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: Martin Mokrejs fold.natur.cuni.cz>
sci-biology/chiron/chiron-.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/chiron/chiron-.ebuild
b/sci-biology/chiron/chiron-.ebuild
index cd99cb976..4294326ee 100644
--- a/sci-biology/chiron/chiron-.ebuild
+++ b/sci-biology/chiron/chiron-.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
PYTHON_COMPAT=( python2_7 pypy )
@@ -17,6 +17,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="=sci-libs/tensorflow-1.0.1"
+DEPEND="~sci-libs/tensorflow-1.0.1"
RDEPEND="${DEPEND}
dev-python/h5py"
[gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
commit: a12f311c601712550558fc506c30231f21c07a7d
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Jan 29 15:31:54 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Jan 29 15:31:54 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a12f311c
sci-biology/chiron: add the dependency on =sci-libs/tensorflow-1.0.1
Seems tensorflow so changing a lot and versions are really incompatible
with each other.
Package-Manager: Portage-2.3.20, Repoman-2.3.6
sci-biology/chiron/chiron-.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/chiron/chiron-.ebuild
b/sci-biology/chiron/chiron-.ebuild
index daf1c15b9..cd99cb976 100644
--- a/sci-biology/chiron/chiron-.ebuild
+++ b/sci-biology/chiron/chiron-.ebuild
@@ -17,6 +17,6 @@ SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND=""
+DEPEND="=sci-libs/tensorflow-1.0.1"
RDEPEND="${DEPEND}
dev-python/h5py"
[gentoo-commits] proj/sci:master commit in: sci-biology/chiron/
commit: 1a1e9755d0985ab7f3e9107be9125aead76d1b7c
Author: Martin Mokrejš fold natur cuni cz>
AuthorDate: Mon Jan 29 15:29:09 2018 +
Commit: Martin Mokrejs fold natur cuni cz>
CommitDate: Mon Jan 29 15:29:09 2018 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a1e9755
sci-biology/chiron: new package
Will need more work to get CPU- and GPU-based features enabled
at once, or will need two separate installs?
Package-Manager: Portage-2.3.20, Repoman-2.3.6
sci-biology/chiron/chiron-.ebuild | 22 ++
sci-biology/chiron/metadata.xml | 12
2 files changed, 34 insertions(+)
diff --git a/sci-biology/chiron/chiron-.ebuild
b/sci-biology/chiron/chiron-.ebuild
new file mode 100644
index 0..daf1c15b9
--- /dev/null
+++ b/sci-biology/chiron/chiron-.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 pypy )
+
+inherit distutils-r1 eutils git-r3
+
+DESCRIPTION="Basecaller for OxfordNanopore data using deep learning"
+HOMEPAGE="https://github.com/haotianteng/chiron
+ https://www.biorxiv.org/content/early/2017/09/12/179531;
+EGIT_REPO_URI="https://github.com/haotianteng/chiron;
+
+LICENSE="MPL-2.0"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}
+ dev-python/h5py"
diff --git a/sci-biology/chiron/metadata.xml b/sci-biology/chiron/metadata.xml
new file mode 100644
index 0..138cb7705
--- /dev/null
+++ b/sci-biology/chiron/metadata.xml
@@ -0,0 +1,12 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ mmokr...@fold.natur.cuni.cz
+ Martin Mokrejs
+
+
+ sci-biol...@gentoo.org
+ Gentoo Biology Project
+
+
