Version Bump

(Portage version: 2.2.0_alpha29/cvs/Linux x86_64)

4 files changed, 221 insertions, 2 deletions

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index e07437afcaf9..2b1a95e34f23 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/pymol
-# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.75 2010/11/12 08:20:43 jlec Exp $
+# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.76 2011/04/04 10:13:09 jlec Exp $
+
+*pymol-1.4_beta1 (04 Apr 2011)
+
+  04 Apr 2011; Justin Lecher <jlec@gentoo.org> +files/1.4-shaders.patch,
+  +files/1.4-vmd.patch, +pymol-1.4_beta1.ebuild:
+  Version Bump
 
 *pymol-1.3.1_pre3925-r1 (12 Nov 2010)
 
diff --git a/sci-chemistry/pymol/files/1.4-shaders.patch b/sci-chemistry/pymol/files/1.4-shaders.patch
new file mode 100644
index 000000000000..853ebff9da81
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.4-shaders.patch
@@ -0,0 +1,62 @@
+ layer0/ShaderMgr.c |   16 ++++++++--------
+ layer1/Setting.c   |    2 +-
+ 2 files changed, 9 insertions(+), 9 deletions(-)
+
+diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c
+index 929167f..ecb4130 100644
+--- a/layer0/ShaderMgr.c
++++ b/layer0/ShaderMgr.c
+@@ -386,7 +386,7 @@ int CShaderMgr_ShadersPresent(CShaderMgr * I)
+ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+   FILE* f;
+   long size;
+-  char* buffer = NULL, *p, *pymol_path, *shader_path, *fullFile;
++  char* buffer = NULL, *p, *pymol_data, *shader_path, *fullFile;
+ 
+   PRINTFB(G, FB_ShaderMgr, FB_Debugging)
+     "CShaderMgr_ReadShaderFromDisk: fileName='%s'\n", fileName
+@@ -398,16 +398,16 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+     return NULL;
+   }
+   
+-  pymol_path = getenv("PYMOL_PATH");
+-  if (!pymol_path){
++  pymol_data = getenv("PYMOL_DATA");
++  if (!pymol_data){
+     PRINTFB(G, FB_ShaderMgr, FB_Warnings)
+-      " PyMOLShader_NewFromFile-Warning: PYMOL_PATH not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
++      " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files (%s) from disk\n", fileName ENDFB(G);
+     return NULL;
+   }
+   /* make this a setting */
+-  shader_path = "/data/shaders/";
+-  fullFile = malloc( sizeof(char) * (strlen(pymol_path)+strlen(shader_path)+strlen(fileName)+1));
+-  fullFile = strcpy(fullFile, pymol_path);
++  shader_path = "/shaders/";
++  fullFile = malloc( sizeof(char) * (strlen(pymol_data)+strlen(shader_path)+strlen(fileName)+1));
++  fullFile = strcpy(fullFile, pymol_data);
+   fullFile = strcat(fullFile, shader_path);
+   fullFile = strcat(fullFile, fileName);
+ 
+@@ -416,7 +416,7 @@ char * CShaderMgr_ReadShaderFromDisk(PyMOLGlobals * G, const char * fileName) {
+ 
+   if (!f) {
+     PRINTFB(G, FB_ShaderMgr, FB_Errors)
+-      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_PATH='%s'\n", fullFile, pymol_path ENDFB(G);
++      " PyMOLShader_NewFromFile-Error: Unable to open file '%s' PYMOL_DATA='%s'\n", fullFile, pymol_data ENDFB(G);
+     return NULL;
+   } else {
+     PRINTFB(G, FB_ShaderMgr, FB_Blather)
+diff --git a/layer1/Setting.c b/layer1/Setting.c
+index 3aa0b8d..f9b5789 100644
+--- a/layer1/Setting.c
++++ b/layer1/Setting.c
+@@ -3956,7 +3956,7 @@ void SettingInitGlobal(PyMOLGlobals * G, int alloc, int reset_gui, int use_defau
+     set_b(I, cSetting_line_use_shader, 1);
+     set_b(I, cSetting_sphere_use_shader, 1);
+     set_b(I, cSetting_use_shaders, 0);  /* disable by default until optimized shaders present; doesn't effect vol */
+-    set_s(I, cSetting_shader_path, "data/shaders");
++    set_s(I, cSetting_shader_path, "shaders");
+     set_i(I, cSetting_volume_bit_depth, 8);
+     set_color(I, cSetting_volume_color, "-1");
+     set_f(I, cSetting_volume_layers, 256);
diff --git a/sci-chemistry/pymol/files/1.4-vmd.patch b/sci-chemistry/pymol/files/1.4-vmd.patch
new file mode 100644
index 000000000000..2fd909ffd540
--- /dev/null
+++ b/sci-chemistry/pymol/files/1.4-vmd.patch
@@ -0,0 +1,36 @@
+ setup.py |    8 ++++----
+ 1 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index b0f4dad..4ec5145 100644
+--- a/setup.py
++++ b/setup.py
+@@ -132,8 +132,8 @@ else: # linux or other unix
+               "/usr/include/freetype2",
+ #                 "/users/warren/ext/include",
+ # VMD plugin support
+-#              "contrib/uiuc/plugins/include",
+-#              "contrib/uiuc/plugins/molfile_plugin/src",
++              "contrib/uiuc/plugins/include",
++              "contrib/uiuc/plugins/molfile_plugin/src",
+               "modules/cealign/src",
+ 	      "modules/cealign/src/tnt", ]
+     libs=["GL","GLU","glut","png","z","freetype", "GLEW",
+@@ -153,7 +153,7 @@ else: # linux or other unix
+ # Numeric Python support                    
+ #                ("_PYMOL_NUMPY",None),
+ # VMD plugin support           
+-#               ("_PYMOL_VMD_PLUGINS",None)
++               ("_PYMOL_VMD_PLUGINS",None),
+ 		("NO_MMLIBS",None),
+                 ]
+     ext_comp_args=["-ffast-math","-funroll-loops","-O3"]
+@@ -307,7 +307,7 @@ setup ( # Distribution meta-data
+     "layer5/main.c"
+ # VMD plugin support
+     # switch the 0 to 1 to activate the additional source code
+-    ] + 0 * [
++    ] + 1 * [
+ # (incomplete support -- only TRJ, TRR, XTC, DCD so far...)
+     'contrib/uiuc/plugins/molfile_plugin/src/PlugIOManagerInit.c',
+     'contrib/uiuc/plugins/molfile_plugin/src/avsplugin.cpp',
diff --git a/sci-chemistry/pymol/pymol-1.4_beta1.ebuild b/sci-chemistry/pymol/pymol-1.4_beta1.ebuild
new file mode 100644
index 000000000000..337b9b78e5d7
--- /dev/null
+++ b/sci-chemistry/pymol/pymol-1.4_beta1.ebuild
@@ -0,0 +1,115 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.4_beta1.ebuild,v 1.1 2011/04/04 10:13:09 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2:2.6"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="2.4 2.5 3.*"
+PYTHON_USE_WITH="tk"
+PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx"
+REV="3925"
+
+inherit eutils distutils prefix versionator
+
+DESCRIPTION="A Python-extensible molecular graphics system."
+HOMEPAGE="http://pymol.sourceforge.net/"
+SRC_URI="mirror://sourceforge/project/${PN}/${PN}/$(get_version_component_range 1-2)/${PN}-v${PV/_beta/b}.tar.bz2"
+#SRC_URI="http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/pymol.tar.gz?view=tar&pathrev=${REV} -> ${P}.tar.gz"
+#SRC_URI="mirror://gentoo/${PF}.tar.gz"
+
+LICENSE="PSF-2.2"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="apbs numpy vmd"
+
+DEPEND="
+	dev-python/numpy
+	dev-python/pmw
+	media-libs/freetype:2
+	media-libs/glew
+	media-libs/libpng
+	media-video/mpeg-tools
+	sys-libs/zlib
+	media-libs/freeglut
+	apbs? (
+		dev-libs/maloc
+		sci-chemistry/apbs
+		sci-chemistry/pdb2pqr
+		sci-chemistry/pymol-apbs-plugin
+	)"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/${PN}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/1.2.2-data-path.patch \
+		"${FILESDIR}"/$(get_version_component_range 1-2)-shaders.patch
+
+	epatch "${FILESDIR}"/1.2.2-prefix.patch && \
+		eprefixify setup.py
+
+	# Turn off splash screen.  Please do make a project contribution
+	# if you are able though. #299020
+	epatch "${FILESDIR}"/1.2.1/nosplash-gentoo.patch
+
+	# Respect CFLAGS
+	sed -i \
+		-e "s:\(ext_comp_args=\).*:\1[]:g" \
+		"${S}"/setup.py || die "Failed running sed on setup.py"
+
+	use vmd && epatch "${FILESDIR}"/$(get_version_component_range 1-2)-vmd.patch
+
+	use numpy && \
+		sed \
+			-e '/PYMOL_NUMPY/s:^#::g' \
+			-i setup.py
+
+	rm ./modules/pmg_tk/startup/apbs_tools.py || die
+
+	# python 3.* fix
+	# sed '452,465d' -i setup.py
+	distutils_src_prepare
+}
+
+src_configure() {
+	:
+}
+
+src_install() {
+	distutils_src_install
+
+	# These environment variables should not go in the wrapper script, or else
+	# it will be impossible to use the PyMOL libraries from Python.
+	cat >> "${T}"/20pymol <<- EOF
+		PYMOL_PATH="${EPREFIX}/$(python_get_sitedir -f)/${PN}"
+		PYMOL_DATA="${EPREFIX}/usr/share/pymol/data"
+		PYMOL_SCRIPTS="${EPREFIX}/usr/share/pymol/scripts"
+	EOF
+
+	doenvd "${T}"/20pymol || die "Failed to install env.d file."
+
+	cat >> "${T}"/pymol <<- EOF
+	#!/bin/sh
+	$(PYTHON -f) -O \${PYMOL_PATH}/__init__.py \$*
+	EOF
+
+	dobin "${T}"/pymol || die "Failed to install wrapper."
+
+	insinto /usr/share/pymol
+	doins -r test data scripts || die "no shared data"
+
+	insinto /usr/share/pymol/examples
+	doins -r examples || die "Failed to install docs."
+
+	dodoc DEVELOPERS README || die "Failed to install docs."
+}
+
+pkg_postinst() {
+	elog "\t USE=shaders was removed,"
+	elog "please use pymol config settings"
+	elog "\t set use_shaders, 1"
+	distutils_pkg_postinst
+}