Initial import

3 files changed, 139 insertions, 0 deletions

diff --git a/.SRCINFO b/.SRCINFO
new file mode 100644
index 000000000000..c1a654db5df0
--- /dev/null
+++ b/.SRCINFO
@@ -0,0 +1,22 @@
+pkgbase = neuron
+	pkgdesc = Empirically-based simulations of neurons and networks of neurons
+	pkgver = 7.3
+	pkgrel = 8
+	url = http://www.neuron.yale.edu
+	arch = i686
+	arch = x86_64
+	license = GPL
+	depends = interviews
+	depends = openmpi
+	depends = python
+	optdepends = python-numpy
+	optdepends = python-scipy
+	optdepends = mpich2
+	options = libtool
+	source = http://www.neuron.yale.edu/ftp/neuron/versions/v7.3/nrn-7.3.tar.gz
+	source = patch.diff
+	md5sums = 993e539cb8bf102ca52e9fefd644ab61
+	md5sums = ba01405ea8ff911a3802459ac2c27b01
+
+pkgname = neuron
+
diff --git a/PKGBUILD b/PKGBUILD
new file mode 100644
index 000000000000..3dd3054b385a
--- /dev/null
+++ b/PKGBUILD
@@ -0,0 +1,53 @@
+# Maintainer: Ali Neishabouri <ali at neishabouri.net>
+# Contributor: David Campbell <davekong@archlinux.us>
+
+pkgname=neuron
+pkgver=7.3
+pkgrel=8
+pkgdesc="Empirically-based simulations of neurons and networks of neurons"
+arch=('i686' 'x86_64')
+url="http://www.neuron.yale.edu"
+license=('GPL')
+depends=('interviews' 'openmpi' 'python')
+optdepends=('python-numpy' 'python-scipy' 'mpich2')
+source=("http://www.neuron.yale.edu/ftp/neuron/versions/v$pkgver/nrn-$pkgver.tar.gz" "patch.diff")
+options=('libtool')
+md5sums=('993e539cb8bf102ca52e9fefd644ab61' 'ba01405ea8ff911a3802459ac2c27b01')
+
+build() {
+  cd "$srcdir/nrn-$pkgver"
+
+  # We do this so the python libraries actually get installed in the package prefix
+  sed -i "s_ac\_pysetup='--home=\$(prefix)'_ac\_pysetup='--home=$pkgdir/usr'_g" "$srcdir/nrn-$pkgver/configure"
+  sed -i 's_exec\_prefix="${prefix}/${host\_cpu}"_exec\_prefix="${prefix}"_g' "$srcdir/nrn-$pkgver/configure"
+
+  # Python 3 complains about a prototype (see http://www.neuron.yale.edu/phpbb/viewtopic.php?f=2&t=3060). 
+  # This part patches some code according to http://www.neuron.yale.edu/hg/neuron/nrn/rev/dce1de58303d.
+  patch -p1 < $srcdir/patch.diff
+	
+  ./configure --prefix=/usr --libdir=/usr/lib --bindir=/usr/bin --with-paranrn --with-nrnpython=`which python`
+  make 
+}
+
+package() {
+  cd "$srcdir/nrn-$pkgver"
+  DESTDIR="$pkgdir"
+  sed -i "s_package\_dir\ =\ {'':instdir+'/share/nrn/lib/python'}\,_package\_dir\ =\ {'':'$pkgdir/usr/share/nrn/lib/python'}\,_g" src/nrnpython/setup.py
+  make DESTDIR="$pkgdir" install
+  #rm -f "$pkgdir/usr/lib/libnrnmpi.la"
+  #rm -f "$pkgdir/usr/lib/libmeschach.la"
+  #rm -f "$pkgdir/usr/lib/libivoc.la"
+  #rm -f "$pkgdir/usr/lib/libscopmath.la"
+  #rm -f "$pkgdir/usr/lib/libneuron_gnu.la"
+  #rm -f "$pkgdir/usr/lib/libmemacs.la"
+  #rm -f "$pkgdir/usr/lib/libnrnoc.la"
+  #rm -f "$pkgdir/usr/lib/libnrnpython.la"
+  #rm -f "$pkgdir/usr/lib/liboc.la"
+  #rm -f "$pkgdir/usr/lib/libnrniv.la"
+  #rm -f "$pkgdir/usr/lib/libsundials.la"
+  #rm -f "$pkgdir/usr/lib/libsparse13.la"
+  #rm -f "$pkgdir/usr/lib/libocxt.la"
+  
+  cd "src/nrnpython/"
+  python setup.py install --root="$pkgdir/"
+}
diff --git a/patch.diff b/patch.diff
new file mode 100644
index 000000000000..f9daec39aed7
--- /dev/null
+++ b/patch.diff
@@ -0,0 +1,64 @@
+
+# HG changeset patch
+# User Michael Hines <michael.hines@yale.edu>
+# Date 1398115465 14400
+# Node ID dce1de58303d5f733ca4fa6701083455ce0d10c8
+# Parent  840b0bd992336e3bc047c829a18a5e609f71de56
+Python 3.4 complained about a prototype.
+
+diff -r 840b0bd99233 -r dce1de58303d src/nrnpython/nrnpython.cpp
+--- a/src/nrnpython/nrnpython.cpp	Mon Apr 21 13:33:19 2014 -0400
++++ b/src/nrnpython/nrnpython.cpp	Mon Apr 21 17:24:25 2014 -0400
+@@ -17,11 +17,11 @@
+ extern int nrnpy_nositeflag;
+ extern char* hoc_ctp;
+ extern FILE* hoc_fin;
+-extern char* hoc_promptstr;
++extern const char* hoc_promptstr;
+ extern char* neuronhome_forward();
+ //extern char*(*PyOS_ReadlineFunctionPointer)(FILE*, FILE*, char*);
+ #if ((PY_MAJOR_VERSION >= 3) || (PY_MAJOR_VERSION == 2 && PY_MINOR_VERSION > 2))
+-static char* nrnpython_getline(FILE*, FILE*, char*);
++static char* nrnpython_getline(FILE*, FILE*, const char*);
+ #else
+ static char* nrnpython_getline(char*);
+ #endif
+@@ -207,7 +207,7 @@
+ }
+ 
+ #if ((PY_MAJOR_VERSION >= 3) || (PY_MAJOR_VERSION == 2 && PY_MINOR_VERSION > 2))
+-static char* nrnpython_getline(FILE*, FILE*, char* prompt) {
++static char* nrnpython_getline(FILE*, FILE*, const char* prompt) {
+ #else
+ static char* nrnpython_getline(char* prompt) {
+ #endif
+diff -r 840b0bd99233 -r dce1de58303d src/oc/hoc.c
+--- a/src/oc/hoc.c	Mon Apr 21 13:33:19 2014 -0400
++++ b/src/oc/hoc.c	Mon Apr 21 17:24:25 2014 -0400
+@@ -122,6 +122,7 @@
+ #endif
+ 
+ #if READLINE
++extern char* readline(const char* prompt);
+ extern void rl_deprep_terminal(void);
+ extern void add_history(const char*);
+ #endif
+@@ -146,7 +147,7 @@
+ #define CBUFSIZE 512
+ HocStr* hoc_tmpbuf;
+ HocStr* hoc_cbufstr;
+-char* hoc_promptstr;
++const char* hoc_promptstr;
+ static CHAR	*cbuf;
+ CHAR	*ctp;
+ int hoc_ictp;
+@@ -1692,7 +1693,7 @@
+ 		}
+ 	}else{
+ #if READLINE
+-		if (nrn_fw_eq(fin, stdin) && nrn_istty_) { char *line, *readline(); int n;
++		if (nrn_fw_eq(fin, stdin) && nrn_istty_) { char *line; int n;
+ #if INTERVIEWS
+ #ifdef MINGW
+ IFGUI
+