* [gentoo-commits] proj/sci:master commit in: sci-biology/cnrun/
@ 2015-02-19 18:00 Christoph Junghans
0 siblings, 0 replies; 6+ messages in thread
From: Christoph Junghans @ 2015-02-19 18:00 UTC (permalink / raw
To: gentoo-commits
commit: 925e2d3a5d1026e202d6a1779cd945280e0012b4
Author: Andrei Zavada <johnhommer <AT> gmail <DOT> com>
AuthorDate: Wed Feb 18 21:24:10 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Thu Feb 19 12:47:31 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=925e2d3a
sci-biology/cnrun: initial ebuild, repoman clean
Package-Manager: portage-2.2.17
---
sci-biology/cnrun/ChangeLog | 4 ++--
sci-biology/cnrun/cnrun-2.0.2.ebuild | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/cnrun/ChangeLog b/sci-biology/cnrun/ChangeLog
index 34e6696..e1fc305 100644
--- a/sci-biology/cnrun/ChangeLog
+++ b/sci-biology/cnrun/ChangeLog
@@ -2,5 +2,5 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
- 18 Jan 2015; Andrei Zavada <johnhommer@gmail.com> cnrun-2.0.2.ebuild:
- Initial packaging for gentoo.
+ 19 Feb 2015; Andrei Zavada <johnhommer@gmail.com> cnrun-2.0.2.ebuild:
+ sci-biology/cnrun: initial ebuild, repoman clean
diff --git a/sci-biology/cnrun/cnrun-2.0.2.ebuild b/sci-biology/cnrun/cnrun-2.0.2.ebuild
index dd02af2..b89d325 100644
--- a/sci-biology/cnrun/cnrun-2.0.2.ebuild
+++ b/sci-biology/cnrun/cnrun-2.0.2.ebuild
@@ -13,7 +13,7 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="dev-libs/libxml2
- dev-lang/lua
+ dev-lang/lua:*
sci-libs/gsl"
DEPEND="${RDEPEND}"
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/cnrun/
@ 2015-02-19 18:00 Christoph Junghans
0 siblings, 0 replies; 6+ messages in thread
From: Christoph Junghans @ 2015-02-19 18:00 UTC (permalink / raw
To: gentoo-commits
commit: 793710fde6c3d193a249b5ab6a943a1c596b6abe
Author: Andrei Zavada <johnhommer <AT> gmail <DOT> com>
AuthorDate: Wed Feb 18 01:10:53 2015 +0000
Commit: Christoph Junghans <ottxor <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 01:10:53 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=793710fd
initial ebuild for sci-biology/cnrun
CNrun is a neuronal network simulator, with these features:
* a conductance- and rate-based Hodgkin-Huxley neurons, a Rall and
Alpha-Beta synapses;
* a 6-5 Runge-Kutta integration method: slow but precise, adjustable;
* Poisson, Van der Pol, Colpitts oscillators and interface for
external stimulation sources;
* NeuroML network topology import/export;
* logging state variables, spikes;
* implemented as a Lua module, for scripting model behaviour (e.g.,
to enable plastic processes regulated by model state);
* interaction (topology push/pull, async connections) with other
cnrun models running elsewhere on a network, with interactions
(planned).
---
sci-biology/cnrun/ChangeLog | 6 ++++++
sci-biology/cnrun/cnrun-2.0.2.ebuild | 23 +++++++++++++++++++++++
sci-biology/cnrun/metadata.xml | 29 +++++++++++++++++++++++++++++
3 files changed, 58 insertions(+)
diff --git a/sci-biology/cnrun/ChangeLog b/sci-biology/cnrun/ChangeLog
new file mode 100644
index 0000000..34e6696
--- /dev/null
+++ b/sci-biology/cnrun/ChangeLog
@@ -0,0 +1,6 @@
+# ChangeLog for sci-biology/cnrun
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+ 18 Jan 2015; Andrei Zavada <johnhommer@gmail.com> cnrun-2.0.2.ebuild:
+ Initial packaging for gentoo.
diff --git a/sci-biology/cnrun/cnrun-2.0.2.ebuild b/sci-biology/cnrun/cnrun-2.0.2.ebuild
new file mode 100644
index 0000000..dd02af2
--- /dev/null
+++ b/sci-biology/cnrun/cnrun-2.0.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="5"
+
+DESCRIPTION="A NeuroML-enabled, neuronal network simulator w/ conductance- and rate-based HH neurons"
+HOMEPAGE="http://johnhommer.com/academic/code/cnrun"
+SRC_URI="http://johnhommer.com/academic/code/cnrun/source/${P}.tar.xz"
+
+LICENSE="GPL-2+"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-libs/libxml2
+ dev-lang/lua
+ sci-libs/gsl"
+
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ econf --bindir="${EPREFIX}"/bin
+}
diff --git a/sci-biology/cnrun/metadata.xml b/sci-biology/cnrun/metadata.xml
new file mode 100644
index 0000000..48dcd97
--- /dev/null
+++ b/sci-biology/cnrun/metadata.xml
@@ -0,0 +1,29 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>johnhommer@gmail.com</email>
+ <name>Andrei Zavada</name>
+ </maintainer>
+ <longdescription>
+ CNrun is a neuronal network simulator, with these features:
+
+ * a conductance- and rate-based Hodgkin-Huxley neurons, a Rall and
+ Alpha-Beta synapses;
+ * a 6-5 Runge-Kutta integration method: slow but precise, adjustable;
+ * Poisson, Van der Pol, Colpitts oscillators and interface for
+ external stimulation sources;
+ * NeuroML network topology import/export;
+ * logging state variables, spikes;
+ * implemented as a Lua module, for scripting model behaviour (e.g.,
+ to enable plastic processes regulated by model state);
+ * interaction (topology push/pull, async connections) with other
+ cnrun models running elsewhere on a network, with interactions
+ (planned).
+
+ Note that there is no `cnrun' executable, which existed in cnrun-1.*.
+ Instead, you write a script for your simulation in Lua, and execute
+ it as detailed in /usr/share/lua-cnrun/examples/example1.lua.
+ </longdescription>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/cnrun/
@ 2016-01-20 21:07 Reinis Danne
0 siblings, 0 replies; 6+ messages in thread
From: Reinis Danne @ 2016-01-20 21:07 UTC (permalink / raw
To: gentoo-commits
commit: a9ab3db77039d8a6ca3b0d49db844d33cfa21205
Author: Andrei Zavada <johnhommer <AT> gmail <DOT> com>
AuthorDate: Sun Jan 17 00:50:39 2016 +0000
Commit: Reinis Danne <rei4dan <AT> gmail <DOT> com>
CommitDate: Tue Jan 19 01:20:45 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a9ab3db7
sci-biology/cnrun: bump version, remove old (which was buggy)
also shorten description to make it repoman clean
sci-biology/cnrun/{cnrun-2.0.2.ebuild => cnrun-2.0.3.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/cnrun/cnrun-2.0.2.ebuild b/sci-biology/cnrun/cnrun-2.0.3.ebuild
similarity index 73%
rename from sci-biology/cnrun/cnrun-2.0.2.ebuild
rename to sci-biology/cnrun/cnrun-2.0.3.ebuild
index 50dc815..862ce28 100644
--- a/sci-biology/cnrun/cnrun-2.0.2.ebuild
+++ b/sci-biology/cnrun/cnrun-2.0.3.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
EAPI="5"
-DESCRIPTION="A NeuroML-enabled, neuronal network simulator w/ conductance- and rate-based HH neurons"
+DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
HOMEPAGE="http://johnhommer.com/academic/code/cnrun"
SRC_URI="http://johnhommer.com/academic/code/cnrun/source/${P}.tar.xz"
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/cnrun/
@ 2020-11-27 15:34 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2020-11-27 15:34 UTC (permalink / raw
To: gentoo-commits
commit: 358f70fb4833d2fac7e5c340c66564c06c5dbe48
Author: Andrei Zavada <johnhommer <AT> gmail <DOT> com>
AuthorDate: Sat Nov 21 17:06:37 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Fri Nov 27 15:33:49 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=358f70fb
sci-libs/cnrun: fix source url
Closes: https://bugs.gentoo.org/755293
Signed-off-by: Andrei Zavada <johnhommer <AT> gmail.com>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/cnrun/{cnrun-2.1.0.ebuild => cnrun-2.1.0-r1.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/cnrun/cnrun-2.1.0.ebuild b/sci-biology/cnrun/cnrun-2.1.0-r1.ebuild
similarity index 83%
rename from sci-biology/cnrun/cnrun-2.1.0.ebuild
rename to sci-biology/cnrun/cnrun-2.1.0-r1.ebuild
index d9cf43c76..b4970c70e 100644
--- a/sci-biology/cnrun/cnrun-2.1.0.ebuild
+++ b/sci-biology/cnrun/cnrun-2.1.0-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=6
DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
HOMEPAGE="http://johnhommer.com/academic/code/cnrun"
-SRC_URI="http://alfinston.dlinkddns.com/johnhommer.com/code/cnrun/source/${P}.tar.xz"
+SRC_URI="http://johnhommer.com/code/cnrun/source/${P}.tar.xz"
LICENSE="GPL-2+"
SLOT="0"
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/cnrun/
@ 2021-02-13 9:29 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-13 9:29 UTC (permalink / raw
To: gentoo-commits
commit: 90443541fea7df61872fe5938dcb01895bb30b88
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Feb 13 09:29:28 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Feb 13 09:29:28 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=90443541
sci-biology/cnrun: correctly depend on lua
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../{cnrun-2.1.0-r1.ebuild => cnrun-2.1.0-r2.ebuild} | 20 +++++++++++++++++---
1 file changed, 17 insertions(+), 3 deletions(-)
diff --git a/sci-biology/cnrun/cnrun-2.1.0-r1.ebuild b/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
similarity index 57%
rename from sci-biology/cnrun/cnrun-2.1.0-r1.ebuild
rename to sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
index c4ef17ad8..a70eaa66a 100644
--- a/sci-biology/cnrun/cnrun-2.1.0-r1.ebuild
+++ b/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
@@ -3,6 +3,10 @@
EAPI=7
+LUA_COMPAT=( lua5-{1..4} )
+
+inherit autotools lua
+
DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
HOMEPAGE="http://johnhommer.com/academic/code/cnrun"
SRC_URI="http://johnhommer.com/code/cnrun/source/${P}.tar.xz"
@@ -11,12 +15,22 @@ LICENSE="GPL-2+"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-RDEPEND="dev-libs/libxml2
- dev-lang/lua:*
- sci-libs/gsl"
+REQUIRED_USE="${LUA_REQUIRED_USE}"
+
+RDEPEND="${LUA_DEPS}
+ dev-libs/libxml2
+ sci-libs/gsl"
DEPEND="${RDEPEND}"
+src_prepare() {
+ default
+ # put docs in correct dir
+ sed -i -e "s#docdir=\${datarootdir}/doc/lua-cnrun#docdir=\${datarootdir}/doc/${PF}#g" doc/Makefile.am || die
+ eautoreconf
+
+}
+
src_configure() {
econf --bindir="${EPREFIX}"/bin
}
^ permalink raw reply related [flat|nested] 6+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/cnrun/
@ 2021-02-13 9:35 Andrew Ammerlaan
0 siblings, 0 replies; 6+ messages in thread
From: Andrew Ammerlaan @ 2021-02-13 9:35 UTC (permalink / raw
To: gentoo-commits
commit: 31fc5abffc4b6ff8b33cc1312707ff78d68c1148
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Feb 13 09:35:17 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Feb 13 09:35:17 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=31fc5abf
sci-biology/cnrun: use lua-single instead
Package-Manager: Portage-3.0.14, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/cnrun/cnrun-2.1.0-r2.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild b/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
index a70eaa66a..44eed9cd2 100644
--- a/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
+++ b/sci-biology/cnrun/cnrun-2.1.0-r2.ebuild
@@ -3,9 +3,9 @@
EAPI=7
-LUA_COMPAT=( lua5-{1..4} )
+LUA_COMPAT=( lua5-{1..3} )
-inherit autotools lua
+inherit autotools lua-single
DESCRIPTION="A NeuroML-enabled, precise but slow neuronal network simulator"
HOMEPAGE="http://johnhommer.com/academic/code/cnrun"
^ permalink raw reply related [flat|nested] 6+ messages in thread
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