Moving to sci-chemistry/pymol

diff --git a/app-sci/pymol/ChangeLog b/app-sci/pymol/ChangeLog
deleted file mode 100644 (file)
index 24e05e0..0000000
--- a/app-sci/pymol/ChangeLog
+++ /dev/null
@@ -1,62 +0,0 @@
-# ChangeLog for app-sci/pymol
-# Copyright 2002-2004 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/pymol/ChangeLog,v 1.13 2004/11/01 02:43:53 ribosome Exp $
-
-  31 Oct 2004; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild:
-  Added to x86.
-
-*pymol-0.97 (26 Jul 2004)
-
-  26 Jul 2004; Olivier Fisette <ribosome@gentoo.org> pymol-0.97.ebuild:
-  Version bump suggested by Stéphane Gagné <sgagne@rsvs.ulaval.ca> (bug #58097).
-  Removed header order patch since it is no longer needed.
-
-*pymol-0.95 (20 Apr 2004)
-
-  20 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> pymol-0.95.ebuild,
-  files/header_order.patch:
-  Version bump. Needed a little patch and a change to the setup2.py call (if it
-  does not find the modules, it will create no python.com)
-
-  19 Apr 2004; Patrick Kursawe <phosphan@gentoo.org> pymol-0.82.ebuild,
-  pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild:
-  Adding IUSE, cleanup
-
-  03 Mar 2004; Peter Bienstman <pbienst@gentoo.org> pymol-0.90:
-  marked stable on x86
-
-  02 Sep 2003; Alastair Tse <liquidx@gentoo.org> pymol-0.82.ebuild,
-  pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild:
-  moved dev-python/Numeric to dev-python/numeric
-
-*pymol-0.90 (23 Jul 2003)
-
-  23 Jul 2003; George Shapovalov <george@gentoo.org> pymol-0.90, files/setup.py-gentoo.patch :
-  new version + fix for setup.py, (#24967)
-  thanks to Ben Cornett <acornet@emory.edu> for the update
-
-*pymol-0.88 (29 Jun 2003)
-
-  19 Jun 2003; George Shapovalov <george@gentoo.org> pymol-0.88.ebuild, files/{digest-pymol-0.88,nosplash-gentoo.patch,setup2.py-gentoo.patch} :
-  new version (#22235)
-  now uses distutils for python
-  thanks to Todd Geders <geders@purdue.edu> for update notification 
-  and Ben Cornett <acornet@emory.edu>  for "distutilized" ebuild submission
-
-*pymol-0.86 (05 Feb 2003)
-
-  05 Feb 2003; George Shapovalov <george@gentoo.org> pymol-0.86.ebuild, files/digest-pymol-0.86 :
-  new version, (#13531)
-  removed -funroll-loops from CFLAGS
-
-*pymol-0.82 (17 July 2002)
-
-  19 Oct 2002; Daniel Ahlberg <aliz@gentoo.org> pymol-0.82.ebuild :
-  Updated to mirror://sourceforge in SRC_URI.
-
-  17 July 2002; George Shapovalov <george@gentoo.org> pymol-0.82.ebuild, files/digest-pymol-0.82, ChangeLog :
-
-  Inital release,
-  molecular visualization package
-  
-  ebuild submitted by Ben Cornett <acornet@emory.edu>

diff --git a/app-sci/pymol/Manifest b/app-sci/pymol/Manifest
deleted file mode 100644 (file)
index 6eaa110..0000000
--- a/app-sci/pymol/Manifest
+++ /dev/null
@@ -1,15 +0,0 @@
-MD5 e75b67a8a2f68992bd46e30ad133e082 pymol-0.95.ebuild 1137
-MD5 63048c22731a4635d1ecdc59079c0b0c pymol-0.90.ebuild 1127
-MD5 5ac328050fc35ab647dd45d38f1d068a pymol-0.97.ebuild 1097
-MD5 8d66f7e575cf844c9c1c0a0172f4a961 pymol-0.88.ebuild 1027
-MD5 0a316a17e7ddb0116626c55f8d56e0a1 ChangeLog 2368
-MD5 8c623e53daafa025137077c6b65815bd metadata.xml 156
-MD5 34d172ef31b5038e071b634d4e645cf1 files/pymol-gentoo.diff 1566
-MD5 bc61462df500f324f8ba07a1c1f7bdf4 files/digest-pymol-0.88 64
-MD5 6970b70ab3710cde34e422cba7cce5c2 files/digest-pymol-0.90 64
-MD5 b674c205dd6279884c91077eec6e5442 files/digest-pymol-0.95 64
-MD5 cb324029606a6b5048895957143c7a44 files/digest-pymol-0.97 64
-MD5 1a6ba582a7928c370c8dfe44c8867e7c files/header_order.patch 905
-MD5 929741dc2da6577e6e99c5542d68dbd5 files/nosplash-gentoo.patch 332
-MD5 e42746bf581479c61ff1e7cc5b978edd files/setup.py-gentoo.patch 311
-MD5 af2da92225ab57969d18d16ed60324ce files/setup2.py-gentoo.patch 493

diff --git a/app-sci/pymol/files/digest-pymol-0.88 b/app-sci/pymol/files/digest-pymol-0.88
deleted file mode 100644 (file)
index bea1a59..0000000
--- a/app-sci/pymol/files/digest-pymol-0.88
+++ /dev/null
@@ -1 +0,0 @@
-MD5 22d56cde503191894cd17a2965981b63 pymol-0_88-src.tgz 2092837

diff --git a/app-sci/pymol/files/digest-pymol-0.90 b/app-sci/pymol/files/digest-pymol-0.90
deleted file mode 100644 (file)
index 5d6062d..0000000
--- a/app-sci/pymol/files/digest-pymol-0.90
+++ /dev/null
@@ -1 +0,0 @@
-MD5 be181d10df622b011725d9541da22070 pymol-0_90-src.tgz 2134293

diff --git a/app-sci/pymol/files/digest-pymol-0.95 b/app-sci/pymol/files/digest-pymol-0.95
deleted file mode 100644 (file)
index 99112b9..0000000
--- a/app-sci/pymol/files/digest-pymol-0.95
+++ /dev/null
@@ -1 +0,0 @@
-MD5 ca5f7ee698bfec6218f45342bd925e56 pymol-0_95-src.tgz 2676518

diff --git a/app-sci/pymol/files/digest-pymol-0.97 b/app-sci/pymol/files/digest-pymol-0.97
deleted file mode 100644 (file)
index 3285748..0000000
--- a/app-sci/pymol/files/digest-pymol-0.97
+++ /dev/null
@@ -1 +0,0 @@
-MD5 e1220898cea37483ddd6f410a6fc02d2 pymol-0_97-src.tgz 2753262

diff --git a/app-sci/pymol/files/header_order.patch b/app-sci/pymol/files/header_order.patch
deleted file mode 100644 (file)
index e11f31b..0000000
--- a/app-sci/pymol/files/header_order.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- layer0/MyPNG.c     2004-01-30 00:40:33.000000000 +0100
-+++ layer0/MyPNG.c.new 2004-04-20 16:05:35.399498139 +0200
-@@ -14,17 +14,8 @@
- Z* -------------------------------------------------------------------
- */
- 
--#include"os_predef.h"
--#include"os_std.h"
--
--#include"Base.h"
--#include "MyPNG.h"
--#include"MemoryDebug.h"
--#include "Setting.h"
--
- #ifdef _HAVE_LIBPNG
--#include<png.h>
--
-+#include <png.h>
-  /* The png_jmpbuf() macro, used in error handling, became available in
-   * libpng version 1.0.6.  If you want to be able to run your code with older
-   * versions of libpng, you must define the macro yourself (but only if it
-@@ -37,6 +28,14 @@
- 
- #endif
- 
-+#include"os_predef.h"
-+#include"os_std.h"
-+
-+#include"Base.h"
-+#include "MyPNG.h"
-+#include"MemoryDebug.h"
-+#include "Setting.h"
-+
- int MyPNGWrite(char *file_name,unsigned char *p,unsigned int width,unsigned int height)
- {
- #ifdef _HAVE_LIBPNG

diff --git a/app-sci/pymol/files/nosplash-gentoo.patch b/app-sci/pymol/files/nosplash-gentoo.patch
deleted file mode 100644 (file)
index 202a7cf..0000000
--- a/app-sci/pymol/files/nosplash-gentoo.patch
+++ /dev/null
@@ -1,8 +0,0 @@
---- modules/pymol/invocation.py.orig   2003-06-11 13:40:13.000000000 -0400
-+++ modules/pymol/invocation.py        2003-06-11 13:40:29.000000000 -0400
-@@ -179,5 +179,3 @@
- 
-          else:
-             options.deferred.append(a)
--      if options.show_splash and not options.no_gui:
--         options.deferred.insert(0,"_do__ cmd.splash(1)")

diff --git a/app-sci/pymol/files/pymol-gentoo.diff b/app-sci/pymol/files/pymol-gentoo.diff
deleted file mode 100644 (file)
index 8b4b2ba..0000000
--- a/app-sci/pymol/files/pymol-gentoo.diff
+++ /dev/null
@@ -1,53 +0,0 @@
---- Rules.linux        Sun Mar 31 03:06:22 2002
-+++ Rules.make Tue May 21 15:42:31 2002
-@@ -12,14 +12,13 @@
- XLIB_DIR = -L/usr/X11R6/lib
- XINC_DIR = -I/usr/X11R6/include
- #--- Python
--PYTHON_EXE = $(PYMOL_PATH)/ext/bin/python
-+PYTHON_EXE = /usr/bin/python
- PYTHON_LIB =
- PYTHON_LIB_DIR = 
--PYTHON_INC_DIR = -I$(PYMOL_PATH)/ext/include/python2.1 \
--      -I$(PYMOL_PATH)/ext/include/python2.1/Numeric
-+PYTHON_INC_DIR = -I/usr/include/python2.2  -I/usr/include/python2.2/Numeric
- #--- Other external dependencies
--EXT_INC_DIR = -I$(PYMOL_PATH)/ext/include
--EXT_LIB_DIR = -L$(PYMOL_PATH)/ext/lib
-+EXT_INC_DIR = 
-+EXT_LIB_DIR = 
- #---------------------------------------------------------------------
- #
- #- Build for LINUX as an importable module ---------------------------
-@@ -48,7 +47,7 @@
- #
- #- Choose One --------------------------------------------------------
- #--- Workaround for XFree86/DRI linux dll problem for module build
--BUGS = -D_DRI_WORKAROUND
-+DEFS += -D_DRI_WORKAROUND
- #---
- #BUGS =
- #---------------------------------------------------------------------
-@@ -58,7 +57,7 @@
- #PNG = -D_HAVE_LIBPNG 
- #ZLIB = 
- #--- Libpng2 available but needs zlib 
--PNG = -D_HAVE_LIBPNG 
-+DEFS += -D_HAVE_LIBPNG 
- ZLIB = -lz
- #--- Libpng2 not available
- #PNG = 
-@@ -77,12 +76,7 @@
- PYMOL_INC_DIRS = -I../layer0 -I../layer1 -I../layer2 \
-    -I../layer3 -I../layer4 -I../layer5 
- 
--C_FLAGS = $(CCOPT1) $(CCOPT2) $(EXT_INC_DIR) $(PYTHON_INC_DIR) \
--   $(XINC_DIR) $(PNG) $(DEFS) $(BUGS)
--
--CFLAGS = $(C_FLAGS)
--
--
-+C_FLAGS := $(CFLAGS) $(PYTHON_INC_DIR) $(XINC_DIR) $(DEFS)
- 
- 
- 

diff --git a/app-sci/pymol/files/setup.py-gentoo.patch b/app-sci/pymol/files/setup.py-gentoo.patch
deleted file mode 100644 (file)
index d675596..0000000
--- a/app-sci/pymol/files/setup.py-gentoo.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- pymol-0.90/setup.py 2003-04-26 21:22:14.000000000 -0400
-+++ pymol-0.90.new/setup.py     2003-07-21 09:39:51.000000000 -0400
-@@ -71,6 +71,7 @@
-    "layer0/Map.c",
-    "layer0/Match.c",
-    "layer0/Matrix.c",
-+   "layer0/MemoryCache.c",
-    "layer0/MemoryDebug.c",
-    "layer0/MyPNG.c",
-    "layer0/Parse.c",

diff --git a/app-sci/pymol/files/setup2.py-gentoo.patch b/app-sci/pymol/files/setup2.py-gentoo.patch
deleted file mode 100644 (file)
index 1d387ea..0000000
--- a/app-sci/pymol/files/setup2.py-gentoo.patch
+++ /dev/null
@@ -1,17 +0,0 @@
---- setup2.py.orig     2003-06-10 19:12:35.000000000 -0400
-+++ setup2.py  2003-06-10 19:11:46.000000000 -0400
-@@ -12,6 +12,14 @@
- import sys
- from distutils import dir_util,file_util
- 
-+import os.path
-+pmlibs = os.path.join(os.environ['D'],
-+                      sys.prefix[1:],
-+                      'lib/python%s' % sys.version[:3],
-+                      'site-packages')
-+sys.path.insert(0, pmlibs)
-+
-+
- if sys.platform=='win32':
-    launch_script = "pymol.bat"
- elif sys.platform=='cygwin':

diff --git a/app-sci/pymol/metadata.xml b/app-sci/pymol/metadata.xml
deleted file mode 100644 (file)
index b229aec..0000000
--- a/app-sci/pymol/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci</herd>
-</pkgmetadata>

diff --git a/app-sci/pymol/pymol-0.88.ebuild b/app-sci/pymol/pymol-0.88.ebuild
deleted file mode 100644 (file)
index a621b76..0000000
--- a/app-sci/pymol/pymol-0.88.ebuild
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/pymol/pymol-0.88.ebuild,v 1.6 2004/06/24 22:15:39 agriffis Exp $
-
-inherit distutils eutils
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="mirror://sourceforge/pymol/${PN}-${PV/./_}-src.tgz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-IUSE=""
-KEYWORDS="x86 ppc"
-
-DEPEND="dev-lang/python
-       dev-python/pmw
-       dev-python/numeric
-       dev-lang/tk
-       media-libs/libpng
-       sys-libs/zlib
-       media-libs/glut"
-
-src_unpack() {
-       unpack ${A}
-       cd ${S}
-       epatch ${FILESDIR}/setup2.py-gentoo.patch
-       # Turn off splash screen.  Please do make a project contribution
-       # if you are able though.
-       [[ -n "$WANT_NOSPLASH" ]] && epatch ${FILESDIR}/nosplash-gentoo.patch
-}
-
-src_install() {
-       distutils_src_install
-       cd ${S}
-       ${python} setup2.py
-
-       local sedexp="s:${D%/}::g"
-       sed -e ${sedexp} pymol.com > pymol
-       exeinto /usr/bin
-       doexe pymol
-       dodoc DEVELOPERS CHANGES
-}

diff --git a/app-sci/pymol/pymol-0.90.ebuild b/app-sci/pymol/pymol-0.90.ebuild
deleted file mode 100644 (file)
index c99bc6d..0000000
--- a/app-sci/pymol/pymol-0.90.ebuild
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/pymol/pymol-0.90.ebuild,v 1.6 2004/06/24 22:15:39 agriffis Exp $
-
-inherit distutils eutils
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="mirror://sourceforge/pymol/${PN}-${PV/./_}-src.tgz"
-
-LICENSE="PSF-2.2"
-SLOT="0"
-IUSE=""
-KEYWORDS="x86 ~ppc"
-
-DEPEND="dev-lang/python
-       dev-python/pmw
-       dev-python/numeric
-       dev-lang/tk
-       media-libs/libpng
-       sys-libs/zlib
-       media-libs/glut"
-
-src_unpack() {
-       unpack ${A}
-       cd ${S}
-       epatch ${FILESDIR}/setup.py-gentoo.patch
-       epatch ${FILESDIR}/setup2.py-gentoo.patch
-       # Turn off splash screen.  Please do make a project contribution
-       # if you are able though.
-       [[ -n "$WANT_NOSPLASH" ]] && epatch ${FILESDIR}/nosplash-gentoo.patch
-}
-
-src_install() {
-       distutils_src_install
-       cd ${S}
-       ${python} setup2.py
-
-       local sedexp="s:${D%/}::g"
-       sed -e ${sedexp} pymol.com > pymol
-       exeinto /usr/bin
-       doexe pymol
-       dodoc DEVELOPERS CHANGES
-       #install examples
-       mv examples ${D}/usr/share/doc/${PF}
-}

diff --git a/app-sci/pymol/pymol-0.95.ebuild b/app-sci/pymol/pymol-0.95.ebuild
deleted file mode 100644 (file)
index de5180f..0000000
--- a/app-sci/pymol/pymol-0.95.ebuild
+++ /dev/null
@@ -1,45 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/pymol/pymol-0.95.ebuild,v 1.3 2004/06/24 22:15:39 agriffis Exp $
-
-inherit distutils eutils
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="mirror://sourceforge/pymol/${PN}-${PV/./_}-src.tgz"
-
-LICENSE="PSF-2.2"
-IUSE=""
-SLOT="0"
-KEYWORDS="~x86"
-
-DEPEND="dev-lang/python
-       dev-python/pmw
-       dev-python/numeric
-       dev-lang/tk
-       media-libs/libpng
-       sys-libs/zlib
-       media-libs/glut"
-
-src_unpack() {
-       unpack ${A}
-       cd ${S}
-       epatch ${FILESDIR}/header_order.patch
-       # Turn off splash screen.  Please do make a project contribution
-       # if you are able though.
-       [[ -n "$WANT_NOSPLASH" ]] && epatch ${FILESDIR}/nosplash-gentoo.patch
-}
-
-src_install() {
-       distutils_src_install
-       cd ${S}
-       PYTHONPATH=$(find ${D}/usr/lib -type d -name site-packages) ${python} setup2.py
-
-       local sedexp="s:${D%/}::g"
-       sed -e ${sedexp} pymol.com > pymol
-       exeinto /usr/bin
-       doexe pymol
-       dodoc DEVELOPERS CHANGES
-       #install examples
-       mv examples ${D}/usr/share/doc/${PF}
-}

diff --git a/app-sci/pymol/pymol-0.97.ebuild b/app-sci/pymol/pymol-0.97.ebuild
deleted file mode 100644 (file)
index 33b5c56..0000000
--- a/app-sci/pymol/pymol-0.97.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2004 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/app-sci/pymol/pymol-0.97.ebuild,v 1.2 2004/11/01 02:43:53 ribosome Exp $
-
-inherit distutils eutils
-
-DESCRIPTION="A Python-extensible molecular graphics system."
-HOMEPAGE="http://pymol.sourceforge.net/"
-SRC_URI="mirror://sourceforge/pymol/${PN}-${PV/./_}-src.tgz"
-
-LICENSE="PSF-2.2"
-IUSE=""
-SLOT="0"
-KEYWORDS="x86"
-
-DEPEND="dev-lang/python
-       dev-python/pmw
-       dev-python/numeric
-       dev-lang/tk
-       media-libs/libpng
-       sys-libs/zlib
-       media-libs/glut"
-
-src_unpack() {
-       unpack ${A}
-       cd ${S}
-       # Turn off splash screen.  Please do make a project contribution
-       # if you are able though.
-       [[ -n "$WANT_NOSPLASH" ]] && epatch ${FILESDIR}/nosplash-gentoo.patch
-}
-
-src_install() {
-       distutils_src_install
-       cd ${S}
-       PYTHONPATH=$(find ${D}/usr/lib -type d -name site-packages) ${python} setup2.py
-
-       local sedexp="s:${D%/}::g"
-       sed -e ${sedexp} pymol.com > pymol
-       exeinto /usr/bin
-       doexe pymol
-       dodoc DEVELOPERS CHANGES
-       #install examples
-       mv examples ${D}/usr/share/doc/${PF}
-}