[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: 86470a713355810e48fc85922f5f40b3f9b2b489
Author: Horea Christian chymera eu>
AuthorDate: Thu Feb 29 01:16:57 2024 +
Commit: Horea Christian gmail com>
CommitDate: Thu Feb 29 01:16:57 2024 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=86470a71
sci-libs/spyking-circus: unkeyword 1.1.0 for ~x86
Signed-off-by: Horea Christian chymera.eu>
sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
index 976a8535b..9b9233020 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
@@ -13,7 +13,7 @@
SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz -
LICENSE="CeCILL-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# Wants to run mpirun (and fails)
RESTRICT="test"
@@ -27,7 +27,7 @@ RDEPEND="
>=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1.17.4[${PYTHON_USEDEP}]
>=dev-python/psutil-5.6.7[${PYTHON_USEDEP}]
- >=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${PYTHON_USEDEP}]
>=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}]
>=dev-python/scipy-1.3.1[${PYTHON_USEDEP}]
"
[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: 9fcb881685c5b2c5997ec08032b6c56d3c7173b5
Author: Andrew Ammerlaan gentoo org>
AuthorDate: Mon Jan 31 12:38:06 2022 +
Commit: Andrew Ammerlaan gentoo org>
CommitDate: Mon Jan 31 12:39:17 2022 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9fcb8816
sci-libs/spyking-circus: bump to 1.1.0
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan gentoo.org>
...pyking-circus-1.0.6.ebuild => spyking-circus-1.1.0.ebuild} | 11 ---
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
similarity index 81%
rename from sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
rename to sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
index f453c6986..3d7feaaf0 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.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..9} )
+PYTHON_COMPAT=( python3_{8..10} )
inherit distutils-r1
@@ -15,7 +15,7 @@ LICENSE="CeCILL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-# TODO: Fix this
+# Wants to run mpirun (and fails)
RESTRICT="test"
RDEPEND="
@@ -26,13 +26,10 @@ RDEPEND="
>=dev-python/matplotlib-2.2.4[${PYTHON_USEDEP}]
>=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1.17.4[${PYTHON_USEDEP}]
- >=dev-python/pandas-0.21[${PYTHON_USEDEP}]
>=dev-python/psutil-5.6.7[${PYTHON_USEDEP}]
>=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}]
>=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}]
>=dev-python/scipy-1.3.1[${PYTHON_USEDEP}]
- >=sci-libs/scikit-learn-0.21.3
- || ( <=sys-cluster/openmpi-3.0.0 >=sys-cluster/mpich-2.0 )
"
DEPEND="${RDEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: 38a24b1f082d0f2393c25ce2c8cf0b84d11fc213
Author: Andrew Ammerlaan riseup net>
AuthorDate: Sun Jan 10 18:44:22 2021 +
Commit: Andrew Ammerlaan riseup net>
CommitDate: Sun Jan 10 18:44:22 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=38a24b1f
sci-libs/spyking-circus: correct name in SRC_URI
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
b/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
index b0881a38a..f453c6986 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -9,7 +9,7 @@ inherit distutils-r1
DESCRIPTION="Fast spike sorting by template matching"
HOMEPAGE="https://github.com/spyking-circus/spyking-circus/;
-SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz;
+SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz
-> ${P}.tar.gz"
LICENSE="CeCILL-2"
SLOT="0"
[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: b6aeb6766d4080589509466509a2450e7dcf81d6
Author: Andrew Ammerlaan riseup net>
AuthorDate: Thu Dec 31 13:41:51 2020 +
Commit: Aisha Tammy aisha cc>
CommitDate: Thu Dec 31 13:54:20 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=b6aeb676
sci-libs/spyking-circus: version bump, bump py targets
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan riseup.net>
Closes: https://github.com/gentoo/sci/pull/1019
Signed-off-by: Aisha Tammy aisha.cc>
.../spyking-circus/spyking-circus-0.9.6.ebuild | 39 --
...us-0.9.9.ebuild => spyking-circus-1.0.6.ebuild} | 12 +--
2 files changed, 9 insertions(+), 42 deletions(-)
diff --git a/sci-libs/spyking-circus/spyking-circus-0.9.6.ebuild
b/sci-libs/spyking-circus/spyking-circus-0.9.6.ebuild
deleted file mode 100644
index 8c610c478..0
--- a/sci-libs/spyking-circus/spyking-circus-0.9.6.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-PYTHON_COMPAT=( python3_{6,7} )
-
-inherit distutils-r1
-
-DESCRIPTION="Fast and scalable spike sorting in Python"
-HOMEPAGE="http://spyking-circus.rtfd.org;
-SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz;
-
-LICENSE="CeCILL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-
-RDEPEND="
- dev-python/mpi4py[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/cython[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/h5py[${PYTHON_USEDEP}]
- dev-python/colorama[${PYTHON_USEDEP}]
- dev-python/psutil[${PYTHON_USEDEP}]
- dev-python/tqdm[${PYTHON_USEDEP}]
- dev-python/blosc[${PYTHON_USEDEP}]
- dev-python/statsmodels[${PYTHON_USEDEP}]
-"
-DEPEND=""
-
-# Tests do not yet work as per upstream, also a qt5 dependency may need to be
added for them in the future:
-# https://github.com/spyking-circus/spyking-circus/issues/234
-
-RESTRICT="test"
-python_test() {
- nosetests || die "Tests failed under ${EPYTHON}"
-}
diff --git a/sci-libs/spyking-circus/spyking-circus-0.9.9.ebuild
b/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
similarity index 85%
rename from sci-libs/spyking-circus/spyking-circus-0.9.9.ebuild
rename to sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
index ec6f5ee6c..b0881a38a 100644
--- a/sci-libs/spyking-circus/spyking-circus-0.9.9.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.0.6.ebuild
@@ -3,17 +3,20 @@
EAPI=7
-PYTHON_COMPAT=( python3_{6..8} )
+PYTHON_COMPAT=( python3_{7..9} )
inherit distutils-r1
DESCRIPTION="Fast spike sorting by template matching"
HOMEPAGE="https://github.com/spyking-circus/spyking-circus/;
SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz;
-LICENSE="CeCILL-2"
+LICENSE="CeCILL-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: Fix this
+RESTRICT="test"
RDEPEND="
>=dev-python/blosc-1.8[${PYTHON_USEDEP}]
@@ -32,3 +35,6 @@ RDEPEND="
|| ( <=sys-cluster/openmpi-3.0.0 >=sys-cluster/mpich-2.0 )
"
DEPEND="${RDEPEND}"
+
+distutils_enable_sphinx docs_sphinx --no-autodoc
+distutils_enable_tests --install pytest
[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: 44974e46cb4e4d4b2f9625ae2c34839b94c42fab
Author: Thawann Malfatti disroot org>
AuthorDate: Mon Aug 24 19:07:04 2020 +
Commit: Horea Christian gmail com>
CommitDate: Sun Dec 6 04:09:17 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=44974e46
sci-libs/spyking-circus: version bump and fix dependencies
Update PYTHON_COMPAT and change scipy full atom
Change MPI dependency
Add back original MPI constraint
Remove blank line, sort keywords and update dependency name
Signed-off-by: Horea Christian chymera.eu>
Closes: https://github.com/gentoo/sci/pull/965
sci-libs/spyking-circus/metadata.xml | 4 +++
.../spyking-circus/spyking-circus-0.9.9.ebuild | 34 ++
2 files changed, 38 insertions(+)
diff --git a/sci-libs/spyking-circus/metadata.xml
b/sci-libs/spyking-circus/metadata.xml
index aca30bb27..35433c3ae 100644
--- a/sci-libs/spyking-circus/metadata.xml
+++ b/sci-libs/spyking-circus/metadata.xml
@@ -5,6 +5,10 @@
c...@chymera.eu
Horea Christian
+
+ malfa...@disroot.org
+ T Malfatti
+
SpyKING CIRCUS is a Python code to allow fast spike sorting on
multi
channel recordings. A publication on the algorithm can be found
at
diff --git a/sci-libs/spyking-circus/spyking-circus-0.9.9.ebuild
b/sci-libs/spyking-circus/spyking-circus-0.9.9.ebuild
new file mode 100644
index 0..ec6f5ee6c
--- /dev/null
+++ b/sci-libs/spyking-circus/spyking-circus-0.9.9.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..8} )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast spike sorting by template matching"
+HOMEPAGE="https://github.com/spyking-circus/spyking-circus/;
+SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz;
+LICENSE="CeCILL-2"
+
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+ >=dev-python/blosc-1.8[${PYTHON_USEDEP}]
+ >=dev-python/colorama-0.4.1[${PYTHON_USEDEP}]
+ >=dev-python/cython-0.29.14[${PYTHON_USEDEP}]
+ >=dev-python/h5py-2.9.0[${PYTHON_USEDEP}]
+ >=dev-python/matplotlib-2.2.4[${PYTHON_USEDEP}]
+ >=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.17.4[${PYTHON_USEDEP}]
+ >=dev-python/pandas-0.21[${PYTHON_USEDEP}]
+ >=dev-python/psutil-5.6.7[${PYTHON_USEDEP}]
+ >=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}]
+ >=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.3.1[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.21.3
+ || ( <=sys-cluster/openmpi-3.0.0 >=sys-cluster/mpich-2.0 )
+"
+DEPEND="${RDEPEND}"
[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: cf6cfaaf7c4b4ce17950bc3cdd89010c9a072914
Author: Horea Christian chymera eu>
AuthorDate: Tue Mar 24 23:02:42 2020 +
Commit: Horea Christian gmail com>
CommitDate: Tue Mar 24 23:02:42 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=cf6cfaaf
sci-libs/spyking-circus: version bump 0.9.6
and PYTHON_COMPAT update to 3_7
Package-Manager: Portage-2.3.95, Repoman-2.3.21
Signed-off-by: Horea Christian chymera.eu>
...rcus-0.8.3.ebuild => spyking-circus-0.9.6.ebuild} | 20
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/sci-libs/spyking-circus/spyking-circus-0.8.3.ebuild
b/sci-libs/spyking-circus/spyking-circus-0.9.6.ebuild
similarity index 69%
rename from sci-libs/spyking-circus/spyking-circus-0.8.3.ebuild
rename to sci-libs/spyking-circus/spyking-circus-0.9.6.ebuild
index b5eca209c..8d77b3150 100644
--- a/sci-libs/spyking-circus/spyking-circus-0.8.3.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-0.9.6.ebuild
@@ -1,8 +1,8 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
-PYTHON_COMPAT=( python2_7 python3_{5,6} )
+PYTHON_COMPAT=( python3_{6,7} )
inherit distutils-r1
@@ -13,8 +13,7 @@
SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz;
LICENSE="CeCILL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
-RESTRICT="test"
+IUSE="test"
RDEPEND="
dev-python/mpi4py[${PYTHON_USEDEP}]
@@ -28,8 +27,13 @@ RDEPEND="
dev-python/tqdm[${PYTHON_USEDEP}]
dev-python/blosc[${PYTHON_USEDEP}]
dev-python/statsmodels[${PYTHON_USEDEP}]
- sci-libs/scikits_learn[${PYTHON_USEDEP}]
-"
-DEPEND="
- dev-python/setuptools[${PYTHON_USEDEP}]
"
+DEPEND=""
+
+# Tests do not yet work as per upstream, also a qt5 dependency may need to be
added for them in the future:
+# https://github.com/spyking-circus/spyking-circus/issues/234
+
+RESTRICT="test"
+python_test() {
+ nosetests || die "Tests failed under ${EPYTHON}"
+}
[gentoo-commits] proj/sci:master commit in: sci-libs/spyking-circus/
commit: 85c146f1b5cdc1ac126b798e40b73b180a8c57cd
Author: Horea Christian chymera eu>
AuthorDate: Tue Oct 8 14:43:01 2019 +
Commit: Horea Christian gmail com>
CommitDate: Tue Oct 8 14:43:01 2019 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=85c146f1
sci-libs/spyking-circus: new package
Package-Manager: Portage-2.3.76, Repoman-2.3.17
Signed-off-by: Horea Christian chymera.eu>
sci-libs/spyking-circus/metadata.xml | 15 ++
.../spyking-circus/spyking-circus-0.8.3.ebuild | 35 ++
2 files changed, 50 insertions(+)
diff --git a/sci-libs/spyking-circus/metadata.xml
b/sci-libs/spyking-circus/metadata.xml
new file mode 100644
index 0..aca30bb27
--- /dev/null
+++ b/sci-libs/spyking-circus/metadata.xml
@@ -0,0 +1,15 @@
+
+http://www.gentoo.org/dtd/metadata.dtd;>
+
+
+ c...@chymera.eu
+ Horea Christian
+
+
+ SpyKING CIRCUS is a Python code to allow fast spike sorting on
multi
+ channel recordings. A publication on the algorithm can be found
at
+ https://elifesciences.org/articles/34518 . The software has
been tested
+ on datasets coming from in vitro retina with 252 electrodes
MEA, from in
+ vivo hippocampus with tetrodes, and in vivo and in vitro cortex
data.
+
+
diff --git a/sci-libs/spyking-circus/spyking-circus-0.8.3.ebuild
b/sci-libs/spyking-circus/spyking-circus-0.8.3.ebuild
new file mode 100644
index 0..b5eca209c
--- /dev/null
+++ b/sci-libs/spyking-circus/spyking-circus-0.8.3.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
+
+inherit distutils-r1
+
+DESCRIPTION="Fast and scalable spike sorting in Python"
+HOMEPAGE="http://spyking-circus.rtfd.org;
+SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz;
+
+LICENSE="CeCILL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/mpi4py[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/cython[${PYTHON_USEDEP}]
+ sci-libs/scipy[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/colorama[${PYTHON_USEDEP}]
+ dev-python/psutil[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/blosc[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${PYTHON_USEDEP}]
+ sci-libs/scikits_learn[${PYTHON_USEDEP}]
+"
+DEPEND="
+ dev-python/setuptools[${PYTHON_USEDEP}]
+"
