From a8d4c9422e0c626482612403c29247627c316bbb Mon Sep 17 00:00:00 2001 From: Maho Nakata Date: Thu, 16 Feb 2012 02:30:10 +0000 Subject: [PATCH] update to 1.5.0.1. --- biology/pymol/Makefile | 12 +++---- biology/pymol/distinfo | 4 +-- biology/pymol/files/patch-setup.py | 52 ++++++++++++++++++------------ biology/pymol/pkg-plist | 48 ++++++++++++++++++++------- 4 files changed, 76 insertions(+), 40 deletions(-) diff --git a/biology/pymol/Makefile b/biology/pymol/Makefile index dd1f70fa088a..33484a174424 100644 --- a/biology/pymol/Makefile +++ b/biology/pymol/Makefile @@ -18,25 +18,25 @@ RUN_DEPENDS= ${PYNUMERIC} \ LIB_DEPENDS= png.6:${PORTSDIR}/graphics/png \ freetype.9:${PORTSDIR}/print/freetype2 -VERSION= 1.4.1 -SVNREVISION= 3946 +VERSION= 1.5.0.1 +SVNREVISION= 3978 USE_BZIP2= yes WRKSRC= ${WRKDIR}/pymol-${PORTVERSION} USE_GL= glut glew USE_GMAKE= yes USE_PYTHON= yes -PLIST_SUB= PYTHON_VER=${PYTHON_VER} +PLIST_SUB= PYMOL_VER=${VERSION} PYTHON_VER=${PYTHON_VER} pre-build: @${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+" ${WRKSRC}/setup.py +#do build process actually installs some files, so omitted. do-build: - @cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} build do-install: - @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} install \ - ; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup2.py install) + @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} ${PYSETUP} install) + @(cd ${BUILD_WRKSRC}; ${SETENV} ${MAKE_ENV} ${PYTHON_CMD} setup2.py install) @${INSTALL_SCRIPT} ${WRKSRC}/pymol ${PREFIX}/bin/pymol #maintainance diff --git a/biology/pymol/distinfo b/biology/pymol/distinfo index 8472777d7006..509273172d80 100644 --- a/biology/pymol/distinfo +++ b/biology/pymol/distinfo @@ -1,2 +1,2 @@ -SHA256 (pymol-1.4.1.3946.tar.bz2) = 0b505ed6275fa1aeec6036830d28c8ee5feedfd67bcac7def873f0481f2cb558 -SIZE (pymol-1.4.1.3946.tar.bz2) = 9038319 +SHA256 (pymol-1.5.0.1.3978.tar.bz2) = 76ff4a6bc126f3fd4dccb62c2345fea3b2a007ecc687d89f7fe21b8f5a0496fc +SIZE (pymol-1.5.0.1.3978.tar.bz2) = 9730397 diff --git a/biology/pymol/files/patch-setup.py b/biology/pymol/files/patch-setup.py index d81c647b7d31..105d89d8a732 100644 --- a/biology/pymol/files/patch-setup.py +++ b/biology/pymol/files/patch-setup.py @@ -1,21 +1,31 @@ ---- setup.py.bak 2010-09-16 10:45:18.000000000 +0900 -+++ setup.py 2010-09-16 10:51:57.000000000 +0900 -@@ -127,7 +127,8 @@ - inc_dirs=["ov/src", - "layer0","layer1","layer2", - "layer3","layer4","layer5", -- "/usr/include/freetype2", -+ "%%LOCALBASE%%/include", -+ "%%LOCALBASE%%/include/freetype2", - # "/users/warren/ext/include", - # VMD plugin support - # "contrib/uiuc/plugins/include", -@@ -139,7 +140,7 @@ - ] - pyogl_libs = ["GL","GLU","glut"] - lib_dirs=[ -- "/usr/X11R6/lib", -+ "%%LOCALBASE%%/lib", - # "/users/warren/pymol/ext/lib" - ] - def_macros=[("_PYMOL_MODULE",None), +--- setup.py 2012-02-14 04:02:02.000000000 +0900 ++++ setup.py 2012-02-15 13:09:38.000000000 +0900 +@@ -159,7 +159,8 @@ + "layer3", + "layer4", + "layer5", +- "/usr/include/freetype2", ++ "%%LOCALBASE%%/include/freetype2", ++ "%%LOCALBASE%%/include", + # VMD plugin support + # "contrib/uiuc/plugins/include", + # "contrib/uiuc/plugins/molfile_plugin/src", +@@ -181,7 +181,7 @@ + "GLU", + "glut", + "GLEW"] +- lib_dirs = [ "/usr/X11R6/lib64", ] ++ lib_dirs = [ "%%LOCALBASE%%/lib", ] + def_macros = [ ("_PYMOL_MODULE",None), + ("_PYMOL_INLINE",None), + ("_PYMOL_FREETYPE",None), +@@ -201,7 +202,7 @@ + "-funroll-loops", + "-O3", + "-g" ] +- ext_link_args = [] ++ ext_link_args = [ "-L%%LOCALBASE%%/lib" ] + + + distribution = setup ( # Distribution meta-data + diff --git a/biology/pymol/pkg-plist b/biology/pymol/pkg-plist index 4c01bb24eb22..fb7eabf7b538 100644 --- a/biology/pymol/pkg-plist +++ b/biology/pymol/pkg-plist @@ -114,6 +114,8 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pmg_tk/Demo.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/PMGApp.py %%PYTHON_SITELIBDIR%%/pmg_tk/PMGApp.pyc +%%PYTHON_SITELIBDIR%%/pmg_tk/PyMOLMapLoad.py +%%PYTHON_SITELIBDIR%%/pmg_tk/PyMOLMapLoad.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/SetEditor.py %%PYTHON_SITELIBDIR%%/pmg_tk/SetEditor.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/Setting.py @@ -122,21 +124,21 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pmg_tk/__init__.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/skins/__init__.py %%PYTHON_SITELIBDIR%%/pmg_tk/skins/__init__.pyc -%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.py -%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.pyc -%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.py -%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorMap.py %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorMap.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorRampModel.py %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ColorRampModel.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ModalWindow.py %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/ModalWindow.pyc +%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.py +%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/SimpleColorChooser.pyc +%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.py +%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/__init__.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/builder.py %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/builder.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/hist.py -%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/volume.py %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/hist.pyc +%%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/volume.py %%PYTHON_SITELIBDIR%%/pmg_tk/skins/normal/volume.pyc %%PYTHON_SITELIBDIR%%/pmg_tk/startup/__init__.py %%PYTHON_SITELIBDIR%%/pmg_tk/startup/__init__.pyc @@ -146,7 +148,7 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pmg_tk/startup/remote_pdb_load.pyc %%PYTHON_SITELIBDIR%%/pmg_wx/__init__.py %%PYTHON_SITELIBDIR%%/pmg_wx/__init__.pyc -%%PYTHON_SITELIBDIR%%/pymol-1.4.0-py%%PYTHON_VER%%.egg-info +%%PYTHON_SITELIBDIR%%/pymol-%%PYMOL_VER%%-py%%PYTHON_VER%%.egg-info %%PYTHON_SITELIBDIR%%/pymol/__init__.py %%PYTHON_SITELIBDIR%%/pymol/__init__.pyc %%PYTHON_SITELIBDIR%%/pymol/_cmd.so @@ -170,6 +172,8 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/computing.pyc %%PYTHON_SITELIBDIR%%/pymol/constants.py %%PYTHON_SITELIBDIR%%/pymol/constants.pyc +%%PYTHON_SITELIBDIR%%/pymol/constants_palette.py +%%PYTHON_SITELIBDIR%%/pymol/constants_palette.pyc %%PYTHON_SITELIBDIR%%/pymol/contrib/__init__.py %%PYTHON_SITELIBDIR%%/pymol/contrib/__init__.pyc %%PYTHON_SITELIBDIR%%/pymol/controlling.py @@ -192,10 +196,10 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/fitting.pyc %%PYTHON_SITELIBDIR%%/pymol/gui.py %%PYTHON_SITELIBDIR%%/pymol/gui.pyc -%%PYTHON_SITELIBDIR%%/pymol/helping.py -%%PYTHON_SITELIBDIR%%/pymol/helping.pyc %%PYTHON_SITELIBDIR%%/pymol/headering.py %%PYTHON_SITELIBDIR%%/pymol/headering.pyc +%%PYTHON_SITELIBDIR%%/pymol/helping.py +%%PYTHON_SITELIBDIR%%/pymol/helping.pyc %%PYTHON_SITELIBDIR%%/pymol/importing.py %%PYTHON_SITELIBDIR%%/pymol/importing.pyc %%PYTHON_SITELIBDIR%%/pymol/internal.py @@ -405,14 +409,33 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.gif %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder/cyc7.xbm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/cmyk.png +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/hsv.ppm +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/incentive_splash.png %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/matrices/BLOSUM62 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash.old.png -%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/hsv.ppm +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash.png +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash_edu.png +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/cylinder.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/cylinder.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/cylinder_no_ff.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es2.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/default_es2.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/shadertext.txt +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere_arb_fs.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/sphere_arb_vs.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/spheredirect.vs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/volume.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/volume.vs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/tut/1hpv.pdb +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray/atomformfactor2.dat +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray/atomformfactor5.dat +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray/spgbase.dat %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy/generate_amber.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy/generate_mmff.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/cookbook/area_diff.pml @@ -449,6 +472,7 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/chempy_model03.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/click_ordered_list.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/count_molecules.py +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/demo.sdf %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/extend_demo01.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/gl01.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/devel/gl02.py @@ -520,6 +544,7 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/dat/small03.mol2 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/dat/tiny.pdb %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/dat/water.pdb +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/headerTest.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/inp/B01.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/inp/B02.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/inp/B03.py @@ -773,12 +798,12 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/xwin.pyc %%PYTHON_SITELIBDIR%%/web/__init__.py %%PYTHON_SITELIBDIR%%/web/__init__.pyc -%%PYTHON_SITELIBDIR%%/web/pymolhttpd.py -%%PYTHON_SITELIBDIR%%/web/pymolhttpd.pyc %%PYTHON_SITELIBDIR%%/web/examples/__init__.py %%PYTHON_SITELIBDIR%%/web/examples/__init__.pyc %%PYTHON_SITELIBDIR%%/web/examples/justhttpd.py %%PYTHON_SITELIBDIR%%/web/examples/justhttpd.pyc +%%PYTHON_SITELIBDIR%%/web/pymolhttpd.py +%%PYTHON_SITELIBDIR%%/web/pymolhttpd.pyc @dirrm %%PYTHON_SITELIBDIR%%/web/examples @dirrm %%PYTHON_SITELIBDIR%%/web @dirrm %%PYTHON_SITELIBDIR%%/pymol/wizard @@ -795,6 +820,7 @@ bin/pymol @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/cookbook @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples +@dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/xray @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/tut @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders @dirrm %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/matrices