add avida

BioArchLinux/avida/PKGBUILD

@@ -0,0 +1,52 @@
+# Contributor: Anton Bazhenov <anton.bazhenov at gmail>
+# Contributor: Dmitriy Morozov <archlinux@foxcub.org>
+
+pkgname=avida
+pkgver=2.12.4
+pkgrel=1
+pkgdesc="A software platform to study evolution of digital organisms"
+arch=('i686' 'x86_64')
+url="http://avida.devosoft.org/"
+license=('GPL3' 'custom')
+depends=('gcc-libs' 'ncurses')
+makedepends=('cmake')
+source=("http://downloads.sourceforge.net/$pkgname/$pkgname-$pkgver-src.tar.gz"
+        avida.patch)
+md5sums=('db4a687190f9fcc8b8ae84613d536d0a'
+         'a7ac844269d3f169f53e8e30005755f5')
+
+prepare() {
+  cd "$srcdir/avida-$pkgver-src"
+  patch -p 1 < ../avida.patch
+}
+
+build() {
+  cd "$srcdir/avida-$pkgver-src"
+  cmake .
+  make
+}
+
+package() {
+  cd "$srcdir/avida-$pkgver-src"
+
+  # Install binaries and config files
+  mkdir -p "${pkgdir}/opt/${pkgname}"
+  install -m755 bin/avida* "${pkgdir}/opt/${pkgname}"
+  install -m664 -g users avida-core/support/config/*.{cfg,org} "${pkgdir}/opt/${pkgname}"
+
+  # Install headers and libraries
+  mkdir -p "${pkgdir}/usr/"{include,lib}
+  cp -r libs/apto/include/* "${pkgdir}/usr/include"
+  cp -r lib/* "${pkgdir}/usr/lib"
+
+  # Install launchers
+  mkdir -p "${pkgdir}/usr/bin"
+  echo 'cd /opt/avida && ./avida' > "${pkgdir}/usr/bin/avida"
+  echo 'cd /opt/avida && ./avida-viewer' > "${pkgdir}/usr/bin/avida-viewer"
+  chmod 755 "${pkgdir}/usr/bin/"{avida,avida-viewer}
+
+  # Install documentation and Apto license
+  mkdir -p "${pkgdir}/usr/share/doc/${pkgname}"
+  cp -r avida-core/documentation/* "${pkgdir}/usr/share/doc/${pkgname}"
+  install -Dm644 libs/apto/LICENSE "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE_APTO"
+}

BioArchLinux/avida/avida.patch

@@ -0,0 +1,20 @@
+--- avida-2.12.3-src.orig/avida-core/source/analyze/cAnalyzeTreeStats_Gamma.cc	2012-02-02 22:50:29.000000000 +0600
++++ avida-2.12.3-src/avida-core/source/analyze/cAnalyzeTreeStats_Gamma.cc	2012-05-08 19:32:18.793044457 +0600
+@@ -27,6 +27,7 @@
+ 
+ #include <math.h>
+ #include <iostream>
++#include <cstdlib>
+ 
+ using namespace std;
+ 
+--- avida-2.12.3-src.orig/avida-core/source/tools/tArray.h	2012-02-02 22:50:29.000000000 +0600
++++ avida-2.12.3-src/avida-core/source/tools/tArray.h	2012-05-08 19:33:04.783042892 +0600
+@@ -24,6 +24,7 @@
+ #define tArray_h
+ 
+ #include <cassert>
++#include <cstdlib>
+ 
+ #ifndef NULL
+ #define NULL 0

BioArchLinux/avida/lilac.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+def pre_build():
+    update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+    run_cmd(['updpkgsums'])
+
+def post_build():
+    git_add_files('PKGBUILD')
+    git_commit()

BioArchLinux/avida/lilac.yaml

@@ -0,0 +1,7 @@
+maintainers:
+  - github: starsareintherose
+    email: starsareintherose@outlook.com
+build_prefix: extra-x86_64
+update_on:
+  - source: cmd
+    cmd:  curl -sS "https://sourceforge.net/projects/avida/rss?path=/avida-stable" | grep '<link>' | grep 'src.zip' | sed 's/-/ /g' | awk '{print $3}' | head -n 1