sci-chemistry/pymol-1.2_beta added. I will maintain all beta versions in sci overlay.

8 files changed, 213 insertions, 0 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
new file mode 100644
index 000000000..d612299b4
--- /dev/null
+++ b/sci-chemistry/pymol/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/pymol
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  06 Feb 2009; justin Lecher (jlec) <jlec@j-schmitz.net>
+  +sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch,
+  +sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch,
+  +sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2,
+  +sci-chemistry/pymol/files/nosplash-gentoo.patch,
+  +sci-chemistry/pymol/metadata.xml:
+  Initial checkin of pymol to sci-overlay
+
diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest
new file mode 100644
index 000000000..45a40a721
--- /dev/null
+++ b/sci-chemistry/pymol/Manifest
@@ -0,0 +1,7 @@
+AUX apbs-070604-r3550.patch.bz2 20283 RMD160 e7fc42934dea043000ba81e4f27b99b6062e4b12 SHA1 1708de792a53ac4819dfe4ec11cc9ee54b3d5fb9 SHA256 ad8ce064ee2ce3310f862b60b8f762ef713f9952fef0ebd329204a2d25b42db5
+AUX nosplash-gentoo.patch 467 RMD160 a6be474aab95e8c8ffd37f509fe3d40cf4db23f7 SHA1 14862bab327fea0cdc8198070f01827d6f832899 SHA256 c4b5384485242165aa517fe2caf83241201c2354d5c964554f6d82c51ba7fba3
+AUX pymol-1.2_beta2-data-path.patch 2584 RMD160 c5fdd7884241a493578be5a2b658ac0cd0bff000 SHA1 1e4cd368ad08b87627ef465fad4ca96dcfbef00b SHA256 39e06459105969e0156bfe71f61bdccd3da4c8d7f2ba6e783aa34e63dc62b0a7
+AUX pymol-1.2_beta2-shaders.patch 524 RMD160 07d83746617fba941bba8ad95d889e22e5310c9a SHA1 2cbbd82a91029d7c540535c83b0f2663e58a891e SHA256 96b1e2b30c7d6699d87a9efb5cab242db66683f71bfd58bbc69f87ce4df397e0
+EBUILD pymol-1.2_beta2.ebuild 2758 RMD160 073aed8dcc3012a1b921ed53f1dd83bfa39f391a SHA1 e206d6f2b7b39b559868c62022914cf5dbcea420 SHA256 276b9ea9c4c4ce9c07f931b46005dddafff6df871e76f761ba411e4cd24f7e44
+MISC ChangeLog 489 RMD160 9a85d57d2087e8ac772d3df0f311487ee1d62f88 SHA1 759c8b8d1bd512fe2a92d4a13896dc3a885498c4 SHA256 c75c41133c6e44ce26865740908f001097e411e38fb57c4cfb16624dde32098f
+MISC metadata.xml 297 RMD160 431061f6875f90a251ae90c5fc5be499da78c9d8 SHA1 b01c71fad62ac24b76a45536f6ddeae3904558dd SHA256 fbe32692a4ff6e595966ca094d9d12912952aaeb639d248fdbd0ed2a9a088d75
diff --git a/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2 b/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2
new file mode 100644
index 000000000..396a4d26d
--- /dev/null
+++ b/sci-chemistry/pymol/files/apbs-070604-r3550.patch.bz2
diff --git a/sci-chemistry/pymol/files/nosplash-gentoo.patch b/sci-chemistry/pymol/files/nosplash-gentoo.patch
new file mode 100644
index 000000000..0ef65b1d8
--- /dev/null
+++ b/sci-chemistry/pymol/files/nosplash-gentoo.patch
@@ -0,0 +1,9 @@
+--- modules/pymol/invocation.py.orig	2008-06-26 20:55:25.000000000 +0200
++++ modules/pymol/invocation.py	2008-06-26 20:56:06.000000000 +0200
+@@ -373,6 +373,4 @@
+         if loaded_something and (options.after_load_script!=""):
+             options.deferred.append(options.after_load_script)
+         options.deferred.extend(final_actions)
+-        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-1.2_beta2-data-path.patch b/sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch
new file mode 100644
index 000000000..329b68292
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.2_beta2-data-path.patch
@@ -0,0 +1,51 @@
+diff -urN pymol-9999.orig/modules/pymol/commanding.py pymol-9999/modules/pymol/commanding.py
+--- pymol-9999.orig/modules/pymol/commanding.py	2008-01-11 13:23:32.000000000 +0100
++++ pymol-9999/modules/pymol/commanding.py	2008-01-11 13:22:57.000000000 +0100
+@@ -198,11 +198,11 @@
+                 _self.unlock(0,_self)
+             r = DEFAULT_SUCCESS
+             if show_splash==1: # generic / open-source
+-                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/splash.png")
++                png_path = _self.exp_path("$PYMOL_DATA/pymol/splash.png")
+             elif show_splash==2: # evaluation builds
+-                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/epymol.png")
++                png_path = _self.exp_path("$PYMOL_DATA/pymol/epymol.png")
+             else: # incentive builds
+-                png_path = _self.exp_path("$PYMOL_PATH/data/pymol/ipymol.png")
++                png_path = _self.exp_path("$PYMOL_DATA/pymol/ipymol.png")
+             if os.path.exists(png_path):
+                 _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path)
+         else:
+#diff -urN pymol-9999.orig/modules/pymol/fitting.py pymol-9999/modules/pymol/fitting.py
+#--- pymol-9999.orig/modules/pymol/fitting.py	2008-01-11 13:23:32.000000000 +0100
+#+++ pymol-9999/modules/pymol/fitting.py	2008-01-11 13:23:00.000000000 +0100
+#@@ -68,7 +68,7 @@
+#         if string.lower(matrix)=='none':
+#             matrix=''
+#         if len(matrix):
+#-            mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
+#+            mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
+#         else:
+#             mfile = ''        
+#         # delete existing alignment object (if asked to reset it)
+#@@ -135,7 +135,7 @@
+#         if string.lower(matrix)=='none':
+#             matrix=''
+#         if len(matrix):
+#-            mfile = cmd.exp_path("$PYMOL_PATH/data/pymol/matrices/"+matrix)
+#+            mfile = cmd.exp_path("$PYMOL_DATA/pymol/matrices/"+matrix)
+#         else:
+#             mfile = ''
+#         if object==None: object=''
+diff -urN pymol-9999.orig/modules/pymol/importing.py pymol-9999/modules/pymol/importing.py
+--- pymol-9999.orig/modules/pymol/importing.py	2008-01-11 13:23:32.000000000 +0100
++++ pymol-9999/modules/pymol/importing.py	2008-01-11 13:23:02.000000000 +0100
+@@ -171,7 +171,7 @@
+         r = DEFAULT_ERROR
+         
+         
+-        tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png",
++        tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png",
+                       'pymol' : 'pymol',
+                       'rgb' : 'rgb' }
+ 
diff --git a/sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch b/sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch
new file mode 100644
index 000000000..7f4a24f48
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol-1.2_beta2-shaders.patch
@@ -0,0 +1,11 @@
+diff -uarN pymol-9999.orig/setup.py pymol-9999/setup.py
+--- pymol-9999.orig/setup.py	2008-06-18 11:47:58.000000000 +0200
++++ pymol-9999/setup.py	2008-06-18 11:48:52.000000000 +0200
+@@ -143,6 +143,7 @@
+     def_macros=[("_PYMOL_MODULE",None),
+                     ("_PYMOL_INLINE",None),
+                     ("_PYMOL_FREETYPE",None),
++                    ("_PYMOL_OPENGL_SHADERS",None),
+ # Numeric Python support                    
+ #                        ("_PYMOL_NUMPY",None),
+ # VMD plugin support                    
diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml
new file mode 100644
index 000000000..1b9609b2a
--- /dev/null
+++ b/sci-chemistry/pymol/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+<maintainer>
+  <email>jlec@j-schmitz.net</email>
+</maintainer>
+<use>
+  <flag name='apbs'>Pymol supprt for sci-chemistry/apbs</flag>
+  <flag name='shaders'>Enable shaders support for Pymol</flag>
+</use>
+</pkgmetadata>
diff --git a/sci-chemistry/pymol/pymol-1.2_beta2.ebuild b/sci-chemistry/pymol/pymol-1.2_beta2.ebuild
new file mode 100644
index 000000000..18ca53e26
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.2_beta2.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+NEED_PYTHON=2.4
+PYTHON_MODNAME="chempy pmg_tk pymol"
+APBS_PATCH="070604-r3550"
+
+inherit distutils subversion
+
+ESVN_REPO_URI="https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol@3580"
+
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+
+LICENSE="PSF-2.2"
+IUSE="apbs shaders"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-python/pmw
+		dev-python/numpy
+		dev-lang/tk
+		media-libs/libpng
+		sys-libs/zlib
+		virtual/glut
+		apbs? ( dev-libs/maloc
+				sci-chemistry/apbs
+				sci-chemistry/pdb2pqr
+		)"
+
+RDEPEND="${DEPEND}"
+
+pkg_setup(){
+	python_tkinter_exists
+	python_version
+}
+
+src_unpack() {
+	subversion_src_unpack
+
+	epatch "${FILESDIR}"/${PF}-data-path.patch || die
+
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though.
+	[[ -z "$WANT_NOSPLASH" ]] && epatch "${FILESDIR}"/nosplash-gentoo.patch ||die
+
+	# Respect CFLAGS
+	sed -i \
+		-e "s:\(ext_comp_args=\).*:\1[]:g" \
+		"${S}"/setup.py
+
+	if use shaders; then
+		epatch "${FILESDIR}"/${PF}-shaders.patch || die
+	fi
+
+	if use apbs; then
+		epatch "${FILESDIR}"/apbs-${APBS_PATCH}.patch.bz2
+		sed "s:LIBANDPYTHON:$(get_libdir)/python${PYVER}:g" \
+			-i modules/pmg_tk/startup/apbs_tools.py || die
+	fi
+}
+
+src_install() {
+	distutils_src_install
+	cd "${S}"
+
+	#The following three lines probably do not do their jobs and should be
+	#changed
+	PYTHONPATH="${D}$(python_get_sitedir)" ${python} setup2.py
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+	PYMOL_PATH=$(python_get_sitedir)/pymol
+	PYMOL_DATA="/usr/share/pymol/data"
+	PYMOL_SCRIPTS="/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol || die "Failed to install env.d file."
+
+	# Make our own wrapper
+	cat >> "${T}"/pymol <<- EOF
+	#!/bin/sh
+	${python} -O \${PYMOL_PATH}/__init__.py \$*
+	EOF
+
+	if ! use apbs; then
+		rm "${D}"$(python_get_sitedir)/pmg_tk/startup/apbs_tools.py
+	fi
+
+	exeinto /usr/bin
+	doexe "${T}"/pymol || die "Failed to install wrapper."
+	dodoc DEVELOPERS || die "Failed to install docs."
+
+	mv examples "${D}"/usr/share/doc/${PF}/ || die "Failed moving docs."
+
+	dodir /usr/share/pymol
+	mv test "${D}"/usr/share/pymol/ || die "Failed moving test files."
+	mv data "${D}"/usr/share/pymol/ || die "Failed moving data files."
+	mv scripts "${D}"/usr/share/pymol/ || die "Failed moving scripts."
+}
+
+pkg_postinst(){
+	distutils_pkg_postinst
+
+	# The apbs ebuild was just corrected and not bumped #213616
+	if use apbs; then
+		[ -e /usr/share/apbs-0.5* ] && \
+		ewarn "You need to reemerge sci-chemistry/apbs!"
+	fi
+}