Dropped old

Package-Manager: portage-2.2.0_alpha4/cvs/Linux x86_64

6 files changed, 10 insertions, 217 deletions

diff --git a/sci-chemistry/aria/ChangeLog b/sci-chemistry/aria/ChangeLog
index 80357178204e..fb4a32b09d3c 100644
--- a/sci-chemistry/aria/ChangeLog
+++ b/sci-chemistry/aria/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/aria
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/ChangeLog,v 1.6 2010/07/22 07:08:44 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/ChangeLog,v 1.7 2010/11/18 17:10:04 jlec Exp $
+
+  18 Nov 2010; Justin Lecher <jlec@gentoo.org> -files/2.2_p2-numpy.patch,
+  -files/2.2_p2-test.patch, -files/sa_ls_cool2.patch, -aria-2.2_p2.ebuild:
+  Dropped old
 
   22 Jul 2010; Justin Lecher <jlec@gentoo.org> aria-2.3.1.ebuild:
   Added clashscore as DEP
diff --git a/sci-chemistry/aria/Manifest b/sci-chemistry/aria/Manifest
index 9092d4063479..c4432d135608 100644
--- a/sci-chemistry/aria/Manifest
+++ b/sci-chemistry/aria/Manifest
@@ -1,19 +1,14 @@
 -----BEGIN PGP SIGNED MESSAGE-----
 Hash: SHA1
 
-AUX 2.2_p2-numpy.patch 2852 RMD160 eb6ca4b75ffdd4bdc450ecb9a7837197459dfee4 SHA1 59e530aaa11063ea31c59802b01d8c63a6e38386 SHA256 1e8a2008dc273bc6d041b329399f3d1cc3e6b042ca6bbbec11bd674ad419723a
-AUX 2.2_p2-test.patch 338 RMD160 9da69e43a0a5d7c28d7018997d1bb73c7cf734e0 SHA1 565af04fbfac250f37c593a7756f0812a11b30b9 SHA256 0697267252452917da407952b57d6b2a5681d70a504fa7408346552c96b65158
-AUX sa_ls_cool2.patch 388 RMD160 0c375f2b517257d38b446ecc76924cfdaad5bc1b SHA1 1afa3447c1c6594bb9302e4ab33b2df142041a9a SHA256 cfe9e3ffc99d82ca51a3ff2bb50c8ddc8144212b5fde1762a042de6b1b90d47f
-DIST aria2.2.tar.gz 1710084 RMD160 b96a900befd5521649ccce84d4d5b93d30709799 SHA1 faa5ff9e7682026afc334f1c8b3b10259a5e69f9 SHA256 a1695ee11b06a045c4b4bb9f0113d1e48c86e12d4149c0dcb505ca894069d054
 DIST aria2.3.1.tar.gz 1833973 RMD160 f2ee0bfc7e3164b5c34c81abb74256c5d76f53d7 SHA1 b257094bdaf6ba5b64645b8251d9243654e6d0fc SHA256 cc45ed2d66182cf0ee197a7cf3bc7edd8d5043d95cdcd19e1cec9aeb82c2fdbc
-EBUILD aria-2.2_p2.ebuild 2293 RMD160 64bc932be20065eeb3523de378cce48eb3ed97ba SHA1 30fd5e8a3e60cef781d2c1ffc70a71c82f539123 SHA256 82b92ee8d1e4a829e6bcc4a5ed64943976459224ebedeb7c138a291bc3b652b9
 EBUILD aria-2.3.1.ebuild 2037 RMD160 e1490118f42cc833f018a6e7653afd2ea7b057e2 SHA1 999e6749c399601b443cb60c914ae6ae06de7fbe SHA256 81e57e81e06114cca000563c40f4f25430fcd6d4e2ed98589dc1a99681fe326d
-MISC ChangeLog 909 RMD160 33435d8930502f412b2d4c096f7746e24e95c681 SHA1 fcd9911dc5c995b0e4ee5da7a03bdfa4628509ae SHA256 ad278a3b34a859371ffe250e6d0200fe813fb4a83ca75f29533bb83aa2643704
+MISC ChangeLog 1073 RMD160 50d0f1fad7bc86e686924331cfff2709b5ad2295 SHA1 61ee3fddca23c37bfd61e1204b4bce05c6d1360e SHA256 3a93b41575f8b2c235d10b3543559ffbb4e664ba1b415dfd90caa3944219c7e4
 MISC metadata.xml 216 RMD160 04a6fc4e2160b439296b52aa97d5b7d83af75508 SHA1 9561c9e6eada6aac9b503407917900529ce703e9 SHA256 24f5c205c2655ef27138c8aa087701626f5b4c666229c9ef7fe814e63ea2e776
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.15 (GNU/Linux)
+Version: GnuPG v2.0.16 (GNU/Linux)
 
-iEYEARECAAYFAkxH7oMACgkQgAnW8HDreRY1JwCdHr0mFihFPMKTAbNb7hY5xfpM
-J7cAmwRUkfStfWEiA71Q/m0ozqYuFOG4
-=3uot
+iEYEARECAAYFAkzlXfEACgkQgAnW8HDreRaFAwCgk1kctwtZnASz95sN6rUqASWw
+8HEAoMk9JGfUIBKGrXALL6QzYAh4Mwzw
+=pD3y
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/aria/aria-2.2_p2.ebuild b/sci-chemistry/aria/aria-2.2_p2.ebuild
deleted file mode 100644
index abc2582c2f1c..000000000000
--- a/sci-chemistry/aria/aria-2.2_p2.ebuild
+++ /dev/null
@@ -1,99 +0,0 @@
-# Copyright 1999-2010 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/aria/aria-2.2_p2.ebuild,v 1.5 2010/03/09 16:18:54 jlec Exp $
-
-EAPI="3"
-PYTHON_DEPEND="2"
-SUPPORT_PYTHON_ABIS="1"
-PYTHON_USE_WITH="tk"
-
-inherit base python eutils versionator
-
-MY_P="${PN}$(get_version_component_range 1-2 ${PV})"
-
-DESCRIPTION="Software for automated NOE assignment and NMR structure calculation."
-HOMEPAGE="http://aria.pasteur.fr/"
-SRC_URI="http://aria.pasteur.fr/archives/${MY_P}.tar.gz"
-
-SLOT="0"
-LICENSE="cns"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="examples"
-
-RDEPEND="
-	dev-python/numpy
-	dev-python/matplotlib[tk]
-	sci-chemistry/cns[aria,openmp]
-	>=dev-lang/tk-8.3
-	>=dev-python/scientificpython-2.7.3
-	>=sci-chemistry/ccpn-2.0.5
-	>=dev-tcltk/tix-8.1.4"
-DEPEND="${RDEPEND}"
-RESTRICT_PYTHON_ABIS="3.*"
-
-RESTRICT="fetch"
-
-S="${WORKDIR}/${PN}2.2"
-
-src_prepare() {
-	epatch "${FILESDIR}"/sa_ls_cool2.patch
-	epatch "${FILESDIR}"/${PV}-numpy.patch
-	epatch "${FILESDIR}"/${PV}-test.patch
-}
-
-pkg_nofetch(){
-	einfo "Go to ${HOMEPAGE}, download ${A}"
-	einfo "and place it in ${DISTDIR}"
-}
-
-src_test(){
-	test() {
-		export CCPNMR_TOP_DIR="${EPREFIX}"/$(python_get_sitedir)
-		export PYTHONPATH=.:${CCPNMR_TOP_DIR}/ccpn/python
-		$(PYTHON) check.py || die
-	}
-	python_execute_function test
-}
-
-src_install(){
-	installation() {
-		insinto "$(python_get_sitedir)/${PN}"
-		doins -r src aria2.py || die "failed to install ${PN}"
-		insinto "$(python_get_sitedir)/${PN}"/cns
-		doins -r cns/{protocols,toppar,src/helplib} || die "failed to install cns part"
-	}
-	python_execute_function installation
-
-	if use examples; then
-		insinto /usr/share/${P}/
-		doins -r examples
-	fi
-
-	# ENV
-	cat >> "${T}"/20aria <<- EOF
-	ARIA2="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
-	EOF
-
-	doenvd "${T}"/20aria
-
-	# Launch Wrapper
-	cat >> "${T}"/aria <<- EOF
-	#!/bin/sh
-	export CCPNMR_TOP_DIR="${EPREFIX}/$(python_get_sitedir -f)"
-	export PYTHONPATH="${EPREFIX}/$(python_get_sitedir -f)/ccpn/python"
-	exec "$(PYTHON -f)" -O "\${ARIA2}"/aria2.py \$@
-	EOF
-
-	dobin "${T}"/aria || die "failed to install wrapper"
-	dosym aria /usr/bin/aria2
-
-	dodoc README || die
-}
-
-pkg_postinst() {
-	python_mod_optimize ${PN}
-}
-
-pkg_postrm() {
-	python_mod_cleanup ${PN}
-}
diff --git a/sci-chemistry/aria/files/2.2_p2-numpy.patch b/sci-chemistry/aria/files/2.2_p2-numpy.patch
deleted file mode 100644
index 40d81964d9c2..000000000000
--- a/sci-chemistry/aria/files/2.2_p2-numpy.patch
+++ /dev/null
@@ -1,82 +0,0 @@
-diff -arNu aria2.2/aria2.py aria2.2.new/aria2.py
---- aria2.2/aria2.py	2008-02-14 11:02:31.000000000 +0100
-+++ aria2.2.new/aria2.py	2009-07-14 12:01:02.000000000 +0200
-@@ -427,7 +427,7 @@
-         
- def check_numeric_slice():
- 
--    msg = "\nThe version of Numeric (%s) is known to be incompatible with ARIA.\nConsider reverting to a more stable version (like 23.8).\n"
-+    msg = "\nThe version of Numeric (%s) is known to be incompatible with ARIA.\nSo we are using numpy instead.\n"
-     
-     try:
-         from Numeric import ones, __version__ as NUMERIC_VERSION
-diff -arNu aria2.2/check.py aria2.2.new/check.py
---- aria2.2/check.py	2009-07-14 11:50:54.000000000 +0200
-+++ aria2.2.new/check.py	2009-07-14 12:02:56.000000000 +0200
-@@ -55,18 +55,6 @@
-     failed = 0
-     
-     try:
--        import Numeric
--        msg += 'ok (numeric).'
--        
--    except:
--        #msg =  'could not import Numeric module.'
--        failed = 1
--
--    if not failed:
--        print msg
--        return 'numeric'#, None
--
--    try:
-        import numpy.oldnumeric
-        version = LooseVersion(numpy.oldnumeric.__version__)
- 
-@@ -79,14 +67,14 @@
-            msg += 'version > %s required for Numpy' % str(NUMPY_MIN_VERSION)
-            
-     except:        
--        msg += 'could not import Numeric/Numpy module.'
-+        msg += 'could not import Numpy module.'
- 
-     print msg
-     return None
- 
- def check_numeric_slice():
- 
--    msg = "\nWARNING: This version of Numeric (%s) is known to be incompatible with ARIA.\nConsider reverting to a more stable version (like 23.8).\n"
-+    msg = "\nWARNING: This version of Numeric (%s) is known to be incompatible with ARIA.\nSo we use numpy instead.\n"
-     
-     from Numeric import ones, __version__ as NUMERIC_VERSION
-     if not ones(10)[2:]:
-diff -arNu aria2.2/src/py/Merger.py aria2.2.new/src/py/Merger.py
---- aria2.2/src/py/Merger.py	2007-03-05 16:50:12.000000000 +0100
-+++ aria2.2.new/src/py/Merger.py	2009-07-14 12:06:55.000000000 +0200
-@@ -213,12 +213,9 @@
-                 new_long = []
- 
-                 try:
--                    from RandomArray import permutation
-+                    from numpy.oldnumeric.random_array import permutation
-                 except:
--                    try:
--                        from numpy.oldnumeric.random_array import permutation
--                    except:
--                        return n, []
-+                    return n, []
- 
-                 ids = permutation(len(long_range))
-            
-diff -arNu aria2.2/src/py/N.py aria2.2.new/src/py/N.py
---- aria2.2/src/py/N.py	2007-12-04 17:01:46.000000000 +0100
-+++ aria2.2.new/src/py/N.py	2009-07-14 12:07:16.000000000 +0200
-@@ -1,7 +1,4 @@
- try:
--    from Numeric import *
-+    from numpy.oldnumeric import *
- except:
--    try:
--        from numpy.oldnumeric import *
--    except:
--        pass
-+    pass
diff --git a/sci-chemistry/aria/files/2.2_p2-test.patch b/sci-chemistry/aria/files/2.2_p2-test.patch
deleted file mode 100644
index 991a168ab3a5..000000000000
--- a/sci-chemistry/aria/files/2.2_p2-test.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-diff --git a/check.py b/check.py
-index 6592951..47772f5 100644
---- a/check.py
-+++ b/check.py
-@@ -170,8 +170,6 @@ if __name__ == '__main__':
-     print 'Checking Python environment...\n'
- 
-     check_python()
--    numeric = check_numeric()
--    check_numeric_slice()
-     scientific = check_scientific()
-     check_tix()
-     check_ccpn()
diff --git a/sci-chemistry/aria/files/sa_ls_cool2.patch b/sci-chemistry/aria/files/sa_ls_cool2.patch
deleted file mode 100644
index d52666a883f9..000000000000
--- a/sci-chemistry/aria/files/sa_ls_cool2.patch
+++ /dev/null
@@ -1,12 +0,0 @@
---- aria2.2/cns/protocols/sa_ls_cool2.cns.orig	2008-05-07 18:39:59.000000000 +0200
-+++ aria2.2/cns/protocols/sa_ls_cool2.cns	2008-05-07 18:40:29.000000000 +0200
-@@ -33,8 +33,8 @@
-     masym dist &Data.masy_cool2
-     masym hbon &Data.masy_cool2
- 
--    scale ambi &Data.amb_cool2 
-     scale dist &Data.unamb_cool2
-+    scale ambi &Data.amb_cool2 
-     scale hbon &Data.hbond_cool2
- end
-