Moved from app-sci/pymol to sci-chemistry/pymol.

16 files changed, 397 insertions, 0 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
new file mode 100644
index 000000000000..ae806856ce41
--- /dev/null
+++ b/sci-chemistry/pymol/ChangeLog
@@ -0,0 +1,71 @@
+# ChangeLog for app-sci/pymol
+# Copyright 2002-2004 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.1 2004/12/24 17:00:58 ribosome Exp $
+
+*pymol-0.97 (24 Dec 2004)
+
+  24 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
+  +files/header_order.patch, +files/nosplash-gentoo.patch,
+  +files/pymol-gentoo.diff, +files/setup.py-gentoo.patch,
+  +files/setup2.py-gentoo.patch, +pymol-0.88.ebuild, +pymol-0.90.ebuild,
+  +pymol-0.95.ebuild, +pymol-0.97.ebuild:
+  Moved from app-sci/pymol to sci-chemistry/pymol.
+
+  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/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
new file mode 100644
index 000000000000..6eaa11041f0e
--- /dev/null
+++ b/sci-chemistry/pymol/Manifest
@@ -0,0 +1,15 @@
+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/sci-chemistry/pymol/files/digest-pymol-0.88 b/sci-chemistry/pymol/files/digest-pymol-0.88
new file mode 100644
index 000000000000..bea1a59ed9d6
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.88
@@ -0,0 +1 @@
+MD5 22d56cde503191894cd17a2965981b63 pymol-0_88-src.tgz 2092837
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.90 b/sci-chemistry/pymol/files/digest-pymol-0.90
new file mode 100644
index 000000000000..5d6062d88f16
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.90
@@ -0,0 +1 @@
+MD5 be181d10df622b011725d9541da22070 pymol-0_90-src.tgz 2134293
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.95 b/sci-chemistry/pymol/files/digest-pymol-0.95
new file mode 100644
index 000000000000..99112b99b7c5
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.95
@@ -0,0 +1 @@
+MD5 ca5f7ee698bfec6218f45342bd925e56 pymol-0_95-src.tgz 2676518
diff --git a/sci-chemistry/pymol/files/digest-pymol-0.97 b/sci-chemistry/pymol/files/digest-pymol-0.97
new file mode 100644
index 000000000000..3285748e37b1
--- /dev/null
+++ b/sci-chemistry/pymol/files/digest-pymol-0.97
@@ -0,0 +1 @@
+MD5 e1220898cea37483ddd6f410a6fc02d2 pymol-0_97-src.tgz 2753262
diff --git a/sci-chemistry/pymol/files/header_order.patch b/sci-chemistry/pymol/files/header_order.patch
new file mode 100644
index 000000000000..e11f31b24029
--- /dev/null
+++ b/sci-chemistry/pymol/files/header_order.patch
@@ -0,0 +1,36 @@
+--- 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/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
new file mode 100644
index 000000000000..202a7cf88083
--- /dev/null
+++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch
@@ -0,0 +1,8 @@
+--- 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/sci-chemistry/pymol/files/pymol-gentoo.diff b/sci-chemistry/pymol/files/pymol-gentoo.diff
new file mode 100644
index 000000000000..8b4b2baabd4b
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-gentoo.diff
@@ -0,0 +1,53 @@
+--- 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/sci-chemistry/pymol/files/setup.py-gentoo.patch b/sci-chemistry/pymol/files/setup.py-gentoo.patch
new file mode 100644
index 000000000000..d67559643594
--- /dev/null
+++ b/sci-chemistry/pymol/files/setup.py-gentoo.patch
@@ -0,0 +1,10 @@
+--- 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/sci-chemistry/pymol/files/setup2.py-gentoo.patch b/sci-chemistry/pymol/files/setup2.py-gentoo.patch
new file mode 100644
index 000000000000..1d387eaa0f4c
--- /dev/null
+++ b/sci-chemistry/pymol/files/setup2.py-gentoo.patch
@@ -0,0 +1,17 @@
+--- 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/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
new file mode 100644
index 000000000000..b229aec85b8f
--- /dev/null
+++ b/sci-chemistry/pymol/metadata.xml
@@ -0,0 +1,5 @@
+<?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/sci-chemistry/pymol/pymol-0.88.ebuild b/sci-chemistry/pymol/pymol-0.88.ebuild
new file mode 100644
index 000000000000..491a18c0caf2
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-0.88.ebuild
@@ -0,0 +1,43 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.88.ebuild,v 1.1 2004/12/24 17:00:58 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"
+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/sci-chemistry/pymol/pymol-0.90.ebuild b/sci-chemistry/pymol/pymol-0.90.ebuild
new file mode 100644
index 000000000000..5bf6ec7117e0
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-0.90.ebuild
@@ -0,0 +1,46 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.90.ebuild,v 1.1 2004/12/24 17:00:58 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"
+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/sci-chemistry/pymol/pymol-0.95.ebuild b/sci-chemistry/pymol/pymol-0.95.ebuild
new file mode 100644
index 000000000000..23a56cf3a7d5
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-0.95.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.95.ebuild,v 1.1 2004/12/24 17:00:58 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}
+	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/sci-chemistry/pymol/pymol-0.97.ebuild b/sci-chemistry/pymol/pymol-0.97.ebuild
new file mode 100644
index 000000000000..9b0c8093537e
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-0.97.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2004 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-0.97.ebuild,v 1.1 2004/12/24 17:00:58 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}
+}