diff --git a/dev-python/pmw/Manifest b/dev-python/pmw/Manifest deleted file mode 100644 index be7b3c730..000000000 --- a/dev-python/pmw/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST Pmw.1.3.2.tar.gz 399262 SHA256 0c9ab8f9cbd57f926e22253d73048fdccfb7e033c3482b083a6fb41848074a18 diff --git a/dev-python/pmw/files/1.3.2-python2.5.patch b/dev-python/pmw/files/1.3.2-python2.5.patch deleted file mode 100644 index ff8cce07d..000000000 --- a/dev-python/pmw/files/1.3.2-python2.5.patch +++ /dev/null @@ -1,54 +0,0 @@ -Source: http://github.com/nanotube/pmw_fixes/commit/5e6dcbdaef2bb6c40037b922dd0efa081f1575ab (Daniel Folkinshteyn) - -fix bug in OptionMenu.setitems, introduced with the fixing of this python -bug: -http://bugs.python.org/issue1342811 - -versions of python 2.5.4 and newer now automatically delete commands when -items are deleted -however, that causes error if the command is deleted manually beforehand. -old versions, on the contrary, require manual command deletion to free up -the objects. - -so we put in a python version check to see if we need to manually delete -commands. - -fixes the Pmw bug referred to here: -http://sourceforge.net/forum/forum.php?thread_id=3283195&forum_id=33675 -and here: -http://sourceforge.net/tracker/?func=detail&aid=2795731&group_id=10743&ati -d=110743 - ---- a/src/Pmw/Pmw_1_3/lib/PmwOptionMenu.py -+++ b/src/Pmw/Pmw_1_3/lib/PmwOptionMenu.py -@@ -1,6 +1,7 @@ - import types - import Tkinter - import Pmw -+import sys - - class OptionMenu(Pmw.MegaWidget): - -@@ -59,11 +60,17 @@ class OptionMenu(Pmw.MegaWidget): - - def setitems(self, items, index = None): - -- # Clean up old items and callback commands. -- for oldIndex in range(len(self._itemList)): -- tclCommandName = str(self._menu.entrycget(oldIndex, 'command')) -- if tclCommandName != '': -- self._menu.deletecommand(tclCommandName) -+ # python version check -+ # python versions >= 2.5.4 automatically clean commands -+ # and manually cleaning them causes errors when deleting items -+ -+ if sys.version_info[0] * 100 + sys.version_info[1] * 10 + \ -+ sys.version_info[2] < 254: -+ # Clean up old items and callback commands. -+ for oldIndex in range(len(self._itemList)): -+ tclCommandName = str(self._menu.entrycget(oldIndex, 'command')) -+ if tclCommandName != '': -+ self._menu.deletecommand(tclCommandName) - self._menu.delete(0, 'end') - self._itemList = list(items) - diff --git a/dev-python/pmw/files/pmw-1.3.2-install-no-docs.patch b/dev-python/pmw/files/pmw-1.3.2-install-no-docs.patch deleted file mode 100644 index 325dc4e29..000000000 --- a/dev-python/pmw/files/pmw-1.3.2-install-no-docs.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff -uNr Pmw.1.3.2.orig/src/setup.py Pmw.1.3.2/src/setup.py ---- Pmw.1.3.2.orig/src/setup.py 2008-08-02 15:40:19.000000000 -0430 -+++ Pmw.1.3.2/src/setup.py 2008-08-02 15:40:36.000000000 -0430 -@@ -16,9 +16,7 @@ - 'Pmw.Pmw_1_3.lib',], - - package_data={'Pmw': ['Pmw_1_3/lib/Pmw.def', -- 'Pmw_1_3/doc/*', - 'Pmw_1_3/contrib/*', -- 'Pmw_1_3/demos/*', - 'Pmw_1_3/tests/*', - 'Pmw_1_3/bin/*', - ] diff --git a/dev-python/pmw/pmw-1.3.2-r2.ebuild b/dev-python/pmw/pmw-1.3.2-r2.ebuild deleted file mode 100644 index 12ad500f6..000000000 --- a/dev-python/pmw/pmw-1.3.2-r2.ebuild +++ /dev/null @@ -1,50 +0,0 @@ -# Copyright 1999-2010 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: Exp $ - -EAPI="3" -PYTHON_DEPEND="2" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="3.*" - -inherit distutils eutils - -MY_P="Pmw.${PV}" - -DESCRIPTION="A toolkit for building high-level compound widgets in Python using the Tkinter module." -HOMEPAGE="http://pmw.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${MY_P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="alpha amd64 ia64 ppc sparc x86 ~amd64-linux ~x86-linux" -IUSE="doc examples" - -DEPEND="dev-lang/python[tk]" -RDEPEND="" - -S="${WORKDIR}/${MY_P}/src" - -DOCS="Pmw/README" -PYTHON_MODNAME="Pmw" - -src_prepare() { - distutils_src_prepare - epatch "${FILESDIR}/${P}-install-no-docs.patch" - epatch "${FILESDIR}/${PV}-python2.5.patch" -} - -src_install() { - distutils_src_install - - local DIR="${PYTHON_MODNAME}/Pmw_1_3" - - if use doc; then - dohtml -a html,gif,py "${DIR}"/doc/* || die "Installation of documentation failed" - fi - - if use examples; then - insinto "/usr/share/doc/${PF}/examples" - doins "${DIR}"/demos/* || die "Installation of demos failed" - fi -} diff --git a/sci-chemistry/pymol/Manifest b/sci-chemistry/pymol/Manifest deleted file mode 100644 index 913dfc6d8..000000000 --- a/sci-chemistry/pymol/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST pymol-1.5.0.3.tar.xz 7412080 SHA256 b304c2839bc944bd2619403474d36cb846b372ba281c8f05931d3f155a0aec7a SHA512 a3f1dd3089fa4158840f2cb8c3848ef70284d1f859429cfab6ac9b00f649d7274a3ac7697a7fb4996d7643068a916f9ad7b1952c5ff27003cedcc7c89e795485 WHIRLPOOL 82788bf6fce52d76ff00d1d7243e8f3962027b4512addaf0fc2f881aaf5f0da6582cb3b3b56a178ed36572947273a999be3d67ba49845eb887da6cf242c5b5f3 -DIST pymol-icons.tar.xz 38100 SHA256 03500f28256f67abfbb7d08b798b11aaa208f0ae1473ef2a7205b3c012ddb06a SHA512 5af51014d4fcbc85ef1fecd7667224709c9305b9b72bfdfd89ece2b4420fa8a81bf8c85fcc5903e2a670f44403f12764808f6a16ef42f111bbd0e7ed8e412d54 WHIRLPOOL 6104d378928c56b39f8cbe29184629b73f87da09e81e41ddc08b9b291876f1a30ccaf9ec257f47798c6d03253816f80c14567073c419fa48dd1520fa3fa58ecd diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch deleted file mode 100644 index e865bfd04..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.1-data-path.patch +++ /dev/null @@ -1,147 +0,0 @@ - layer0/ShaderMgr.c | 16 ++++++++-------- - layer1/Setting.c | 2 +- - modules/chempy/__init__.py | 2 +- - modules/chempy/tinker/__init__.py | 2 +- - modules/pymol/commanding.py | 6 +++--- - modules/pymol/importing.py | 2 +- - modules/pymol/wizard/mutagenesis.py | 4 ++-- - 7 files changed, 17 insertions(+), 17 deletions(-) - -diff --git a/layer0/ShaderMgr.c b/layer0/ShaderMgr.c -index cc760ae..364277f 100644 ---- a/layer0/ShaderMgr.c -+++ b/layer0/ShaderMgr.c -@@ -385,7 +385,7 @@ 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; - size_t res; - - PRINTFB(G, FB_ShaderMgr, FB_Debugging) -@@ -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 from disk\n" ENDFB(G); -+ " PyMOLShader_NewFromFile-Warning: PYMOL_DATA not set, cannot read shader config files from disk\n" 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 c2b8bbb..4c6fdb7 100644 ---- a/layer1/Setting.c -+++ b/layer1/Setting.c -@@ -4375,7 +4375,7 @@ 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); -- 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/modules/chempy/__init__.py b/modules/chempy/__init__.py -index 23dbe45..795a223 100644 ---- a/modules/chempy/__init__.py -+++ b/modules/chempy/__init__.py -@@ -235,7 +235,7 @@ if os.environ.has_key('CHEMPY_DATA'): # - elif os.environ.has_key('PYMOL_DATA'): - path = os.environ['PYMOL_DATA'] + '/chempy/' - elif os.environ.has_key('PYMOL_PATH'): -- path = os.environ['PYMOL_PATH'] + '/data/chempy/' -+ path = os.environ['PYMOL_PATH'] + '/chempy/' - elif os.environ.has_key('FREEMOL_MODULES'): - path = os.environ['FREEMOL_MODULES'] + '/chempy/' - else: -diff --git a/modules/chempy/tinker/__init__.py b/modules/chempy/tinker/__init__.py -index a2d8eb1..1e48f81 100644 ---- a/modules/chempy/tinker/__init__.py -+++ b/modules/chempy/tinker/__init__.py -@@ -147,7 +147,7 @@ else: - - if os.environ.has_key('PYMOL_PATH'): - pymol_path = os.environ['PYMOL_PATH'] -- test_path = pymol_path + '/data/chempy/tinker/' -+ test_path = pymol_path + '/chempy/tinker/' - if os.path.exists(test_path): - params_path = test_path - -diff --git a/modules/pymol/commanding.py b/modules/pymol/commanding.py -index 5a202d0..5cb27a6 100644 ---- a/modules/pymol/commanding.py -+++ b/modules/pymol/commanding.py -@@ -219,11 +219,11 @@ USAGE - _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("$PYMOL_DATA/pymol/ipymol.png") - if os.path.exists(png_path): - _self.do("_ cmd.load_png('%s',0,quiet=1)"%png_path) - else: -diff --git a/modules/pymol/importing.py b/modules/pymol/importing.py -index 457ace7..7cc2953 100644 ---- a/modules/pymol/importing.py -+++ b/modules/pymol/importing.py -@@ -191,7 +191,7 @@ SEE ALSO - ''' - r = DEFAULT_ERROR - -- tables = { 'cmyk' : "$PYMOL_PATH/data/pymol/cmyk.png", -+ tables = { 'cmyk' : "$PYMOL_DATA/pymol/cmyk.png", - 'pymol' : 'pymol', - 'rgb' : 'rgb', - 'greyscale': 'greyscale' } -diff --git a/modules/pymol/wizard/mutagenesis.py b/modules/pymol/wizard/mutagenesis.py -index 8a5250d..6c1b26c 100644 ---- a/modules/pymol/wizard/mutagenesis.py -+++ b/modules/pymol/wizard/mutagenesis.py -@@ -53,7 +53,7 @@ class Mutagenesis(Wizard): - self.dep = default_dep - - self.ind_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ -- "/data/chempy/sidechains/sc_bb_ind.pkl") -+ "/chempy/sidechains/sc_bb_ind.pkl") - self.load_library() - self.status = 0 # 0 no selection, 1 mutagenizing - self.bump_check = 1 -@@ -218,7 +218,7 @@ class Mutagenesis(Wizard): - if self.dep == 'dep': - if not hasattr(self,'dep_library'): - self.dep_library = io.pkl.fromFile(os.environ['PYMOL_PATH']+ -- "/data/chempy/sidechains/sc_bb_dep.pkl") -+ "/chempy/sidechains/sc_bb_dep.pkl") - - def set_mode(self,mode): - cmd=self.cmd diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-flags.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-flags.patch deleted file mode 100644 index 9bdba45f3..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.1-flags.patch +++ /dev/null @@ -1,19 +0,0 @@ - setup.py | 5 +---- - 1 files changed, 1 insertions(+), 4 deletions(-) - -diff --git a/setup.py b/setup.py -index 2b6fa35..9c0556d 100755 ---- a/setup.py -+++ b/setup.py -@@ -197,10 +197,7 @@ else: # linux or other unix - ("_PYMOL_GL_CALLLISTS",None), - ("OPENGL_ES_2",None), - ] -- ext_comp_args = [ "-ffast-math", -- "-funroll-loops", -- "-O3", -- "-g" ] -+ ext_comp_args = [] - ext_link_args = [] - - diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch deleted file mode 100644 index 830eb8feb..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.1-prefix.patch +++ /dev/null @@ -1,43 +0,0 @@ - setup.py | 8 ++++---- - 1 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/setup.py b/setup.py -index ce0d271..2b6fa35 100755 ---- a/setup.py -+++ b/setup.py -@@ -104,7 +104,7 @@ elif sys.platform=='darwin': - inc_dirs=["ov/src", - "layer0","layer1","layer2", - "layer3","layer4","layer5", -- "/usr/X11R6/include", -+ "@GENTOO_PORTAGE_EPREFIX@/usr/include", - EXT+"/include", - EXT+"/include/GL", - EXT+"/include/freetype2", -@@ -120,7 +120,7 @@ elif sys.platform=='darwin': - ] - ext_comp_args=[] - ext_link_args=[ -- "-L/usr/X11R6/lib64", "-lGL", "-lXxf86vm", -+ "-L@GENTOO_PORTAGE_EPREFIX@/usr/lib64", "-lGL", "-lXxf86vm", - "-L"+EXT+"/lib", "-lpng", "-lglut", "-lfreetype" - ] - #============================================================================ -@@ -159,7 +159,7 @@ else: # linux or other unix - "layer3", - "layer4", - "layer5", -- "/usr/include/freetype2", -+ "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2", - # VMD plugin support - "contrib/uiuc/plugins/include", - "contrib/uiuc/plugins/molfile_plugin/src", -@@ -180,7 +180,7 @@ else: # linux or other unix - "GLU", - "glut", - "GLEW"] -- lib_dirs = [ "/usr/X11R6/lib64", ] -+ lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/lib64", ] - def_macros = [ ("_PYMOL_MODULE",None), - ("_PYMOL_INLINE",None), - ("_PYMOL_FREETYPE",None), diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch deleted file mode 100644 index 076d6907a..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.1-setup.py.patch +++ /dev/null @@ -1,39 +0,0 @@ - setup.py | 28 ---------------------------- - 1 files changed, 0 insertions(+), 28 deletions(-) - -diff --git a/setup.py b/setup.py -index 18866a2..705b0c5 100755 ---- a/setup.py -+++ b/setup.py -@@ -487,31 +487,3 @@ distribution = setup ( # Distribution meta-data - define_macros = def_macros - ) - ]) -- --# make available for setup2.py --try: -- site_packages = distribution.command_obj['install'].install_libbase --except KeyError: -- print """ -- Error: Please run, 'setup.py install' not 'setup build' or other variant. -- --""" -- sys.exit(2) -- --f = open('setup3.py', 'w') --print >> f, 'site_packages =', repr(site_packages) --f.close() -- --print ''' -- After running: -- -- python setup.py install -- -- Please run, to complete the installation: -- -- python setup2.py install -- -- To uninstall PyMOL, run: -- -- python setup2.py uninstall --''' diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.1-vmd.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-vmd.patch deleted file mode 100644 index cf47082ef..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.1-vmd.patch +++ /dev/null @@ -1,36 +0,0 @@ - setup.py | 8 ++++---- - 1 files changed, 4 insertions(+), 4 deletions(-) - -diff --git a/setup.py b/setup.py -index 366d552..ce0d271 100755 ---- a/setup.py -+++ b/setup.py -@@ -161,8 +161,8 @@ else: # linux or other unix - "layer5", - "/usr/include/freetype2", - # 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", - "generated/include", -@@ -190,7 +190,7 @@ else: # linux or other unix - # Numeric Python support - # ("_PYMOL_NUMPY",None), - # VMD plugin support -- # ("_PYMOL_VMD_PLUGINS",None) -+ ("_PYMOL_VMD_PLUGINS",None), - ("_PYMOL_CGO_DRAWARRAYS",None), - ("_PYMOL_CGO_DRAWBUFFERS",None), - ("_CGO_DRAWARRAYS",None), -@@ -354,7 +354,7 @@ distribution = 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/files/pymol-1.5.0.1-web.patch b/sci-chemistry/pymol/files/pymol-1.5.0.1-web.patch deleted file mode 100644 index fe61f0264..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.1-web.patch +++ /dev/null @@ -1,19 +0,0 @@ - setup.py | 5 +---- - 1 files changed, 1 insertions(+), 4 deletions(-) - -diff --git a/setup.py b/setup.py -index 18866a2..366d552 100755 ---- a/setup.py -+++ b/setup.py -@@ -229,10 +229,7 @@ distribution = setup ( # Distribution meta-data - 'pymol/opengl/gl', - 'pymol/opengl/glu', - 'pymol/opengl/glut', -- 'pymol/wizard', -- 'web', -- 'web/examples', -- 'web/javascript', ], -+ 'pymol/wizard', ], - ext_modules = [ - Extension("pymol._cmd", [ - "modules/cealign/src/ccealignmodule.cpp", diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch b/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch deleted file mode 100644 index 9b0bad342..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.3-prefix.patch +++ /dev/null @@ -1,57 +0,0 @@ -Index: setup.py -=================================================================== ---- setup.py (revision 3983) -+++ setup.py (working copy) -@@ -1,4 +1,4 @@ --#!/usr/bin/env python -+#!@GENTOO_PORTAGE_EPREFIX@/usr/bin/env python - # - # This script only applies if you are performing a Python Distutils-based - # installation of PyMOL. -@@ -35,7 +35,7 @@ - "modules/cealign/src/tnt" ] - libs=["glut32","opengl32","glu32","png"] - pyogl_libs = ["glut32","opengl32","glu32"] -- lib_dirs=["/usr/lib/w32api"] -+ lib_dirs=["@GENTOO_PORTAGE_EPREFIX@/usr/lib/w32api"] - def_macros=[("_PYMOL_MODULE",None), - ("CYGWIN",None), - ("_PYMOL_LIBPNG",None)] -@@ -87,7 +87,7 @@ - "/sw/include/freetype2/freetype", - "/sw/include/freetype2", - "/sw/include", -- "/usr/X11/include", -+ "@GENTOO_PORTAGE_EPREFIX@/usr/X11/include", - "modules/cealign/src", - "modules/cealign/src/tnt", - #"contrib/uiuc/plugins/include/", -@@ -114,8 +114,8 @@ - ext_comp_args=[] - ext_link_args=[ - "-L/sw/lib", "-lpng", -- "/usr/X11/lib/libGL.dylib", -- "/usr/X11/lib/libGLU.dylib", -+ "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGL.dylib", -+ "@GENTOO_PORTAGE_EPREFIX@/usr/X11/lib/libGLU.dylib", - "-lfreeglut", - "-lglew", - "-L/sw/lib/freetype219/lib", "-lfreetype" -@@ -221,7 +221,7 @@ - "layer3", - "layer4", - "layer5", -- "/usr/include/freetype2", -+ "@GENTOO_PORTAGE_EPREFIX@/usr/include/freetype2", - # VMD plugin support - # "contrib/uiuc/plugins/include", - # "contrib/uiuc/plugins/molfile_plugin/src", -@@ -242,7 +242,7 @@ - "GLU", - "glut", - "GLEW"] -- lib_dirs = [ "/usr/X11R6/lib64", ] -+ lib_dirs = [ "@GENTOO_PORTAGE_EPREFIX@/usr/X11R6/lib64", ] - def_macros = [ ("_PYMOL_MODULE",None), - ("_PYMOL_INLINE",None), - ("_PYMOL_FREETYPE",None), diff --git a/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch b/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch deleted file mode 100644 index 4f4814016..000000000 --- a/sci-chemistry/pymol/files/pymol-1.5.0.3-web.patch +++ /dev/null @@ -1,16 +0,0 @@ -Index: setup.py -=================================================================== ---- setup.py (revision 3983) -+++ setup.py (working copy) -@@ -292,10 +292,7 @@ - 'pymol/opengl/glu', - 'pymol/opengl/glut', - 'pymol/wizard', -- 'pymol2', -- 'web', -- 'web/examples', -- 'web/javascript', ], -+ 'pymol2', ], - ext_modules = [ - Extension("pymol._cmd", [ - "modules/cealign/src/ccealignmodule.cpp", diff --git a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild b/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild deleted file mode 100644 index 08026ed1b..000000000 --- a/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild +++ /dev/null @@ -1,129 +0,0 @@ -# Copyright 1999-2012 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.5.0.3-r1.ebuild,v 1.9 2012/10/15 17:22:52 jlec Exp $ - -EAPI=4 - -PYTHON_DEPEND="2:2.7" -SUPPORT_PYTHON_ABIS="1" -RESTRICT_PYTHON_ABIS="2.4 2.5 2.6 3.* *-jython 2.7-pypy-*" -#PYTHON_USE_WITH="tk" -PYTHON_MODNAME="${PN} chempy pmg_tk pmg_wx" - -inherit distutils eutils fdo-mime prefix versionator - -DESCRIPTION="A Python-extensible molecular graphics system" -HOMEPAGE="http://pymol.sourceforge.net/" -SRC_URI=" - http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz - http://dev.gentoo.org/~jlec/distfiles/${PN}-icons.tar.xz" - -LICENSE="PSF-2.2" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="apbs numpy vmd web" - -DEPEND=" - >=dev-lang/python-2.7[tk] setup3.py || die - - sed \ - -e "s:/opt/local:${EPREFIX}/usr:g" \ - -e '/ext_comp_args/s:\[.*\]:[]:g' \ - -i setup.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 "${T}"/20pymol - - cat >> "${T}"/pymol <<- EOF - #!/bin/sh - $(PYTHON -f) -O \${PYMOL_PATH}/__init__.py -q \$* - EOF - - dobin "${T}"/pymol - - insinto /usr/share/pymol - doins -r test data scripts - - insinto /usr/share/pymol/examples - doins -r examples - - dodoc DEVELOPERS README - - doicon "${WORKDIR}"/${PN}.{xpm,png} - make_desktop_entry pymol PyMol ${PN} "Graphics;Education;Science;Chemistry" "MimeType=chemical/x-pdb;" -} - -pkg_postinst() { - elog "\t USE=shaders was removed," - elog "please use pymol config settings (~/.pymolrc)" - elog "\t set use_shaders, 1" - elog "in case of crashes, please deactivate this experimental feature by setting" - elog "\t set use_shaders, 0" - elog "\t set sphere_mode, 0" - distutils_pkg_postinst - fdo-mime_desktop_database_update - fdo-mime_mime_database_update -} - -pkg_postrm() { - fdo-mime_desktop_database_update - fdo-mime_mime_database_update -}