Index: MOVED =================================================================== --- MOVED +++ MOVED @@ -6475,7 +6475,6 @@ benchmarks/spec-sfs||2014-09-01|Not staged biology/blast||2014-09-01|Not staged biology/embassy||2014-09-01|Not staged -biology/pymol||2014-09-01|Not staged cad/scv||2014-09-01|Not staged cad/systemc||2014-09-01|Not staged chinese/cmexfonts||2014-09-01|Not staged Index: science/Makefile =================================================================== --- science/Makefile +++ science/Makefile @@ -167,6 +167,7 @@ SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom + SUBDIR += py-pymol SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc Index: science/py-pymol/Makefile =================================================================== --- science/py-pymol/Makefile +++ science/py-pymol/Makefile @@ -2,48 +2,35 @@ # $FreeBSD$ PORTNAME= pymol -PORTVERSION= ${VERSION}.${SVNREVISION} -PORTREVISION= 3 -CATEGORIES= biology python -MASTER_SITES= ${MASTER_SITE_LOCAL:S|%SUBDIR%|maho/pymol|} - -MAINTAINER= ports@FreeBSD.org -COMMENT= Free and Open-Source molecular modeling system - -BUILD_DEPENDS= ${PYNUMERIC} -RUN_DEPENDS= ${PYNUMERIC} \ - ${PYTHON_SITELIBDIR}/Pmw:${PORTSDIR}/x11-toolkits/py-Pmw -LIB_DEPENDS= libpng15.so:${PORTSDIR}/graphics/png \ - libfreetype.so:${PORTSDIR}/print/freetype2 - -VERSION= 1.5.0.1 -SVNREVISION= 3978 - -WRKSRC= ${WRKDIR}/pymol-${PORTVERSION} -USE_GL= glut glew -USES= gmake tar:bzip2 -USE_PYTHON= yes -PLIST_SUB= PYMOL_VER=${VERSION} PYTHON_VER=${PYTHON_VER} - -NO_STAGE= yes -pre-build: - @${REINPLACE_CMD} -e "s+%%LOCALBASE%%+${LOCALBASE}+" ${WRKSRC}/setup.py - -#do build process actually installs some files, so omitted. -do-build: - -do-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 -do-fetch-svn: - #svn ls https://pymol.svn.sourceforge.net/svnroot/pymol/tags - #http://pymol.svn.sourceforge.net/viewvc/pymol/trunk/ - ${RM} -rf pymol-${VERSION}.${SVNREVISION} - svn -r ${SVNREVISION} export http://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-${VERSION}.${SVNREVISION} - tar cvfj pymol-${VERSION}.${SVNREVISION}.tar.bz2 pymol-${VERSION}.${SVNREVISION} - scp pymol-${VERSION}.${SVNREVISION}.tar.bz2 freefall.freebsd.org:public_distfiles/pymol/ +DISTVERSIONPREFIX= v +DISTVERSION= 1.8.6.0 +CATEGORIES= science biology python +MASTER_SITES= SF/pymol/pymol/1.8/ +PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} + +MAINTAINER= yuri@FreeBSD.org +COMMENT= OpenGL-based molecular visualization system + +LICENSE= PyMOL +LICENSE_NAME= Open-Source PyMOL Copyright +LICENSE_FILE= ${WRKSRC}/LICENSE +LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept + +RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}msgpack-python>0:devel/py-msgpack-python@${FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}Pmw>0:x11-toolkits/py-Pmw@${FLAVOR} +LIB_DEPENDS= libfreetype.so:print/freetype2 \ + libpng16.so:graphics/png + +WRKSRC= ${WRKDIR}/pymol + +USES= compiler:c++11-lang python shebangfix tar:bz2 +USE_GL= gl glew glu glut +USE_GNOME= libxml2 +USE_PYTHON= distutils concurrent # autoplist is broken: https://sourceforge.net/p/pymol/bugs/189 +SHEBANG_FILES= test/show test/run test/cyg + +post-install: + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pymol/_cmd.so + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/chempy/champ/_champ.so .include Index: science/py-pymol/distinfo =================================================================== --- science/py-pymol/distinfo +++ science/py-pymol/distinfo @@ -1,2 +1,3 @@ -SHA256 (pymol-1.5.0.1.3978.tar.bz2) = 76ff4a6bc126f3fd4dccb62c2345fea3b2a007ecc687d89f7fe21b8f5a0496fc -SIZE (pymol-1.5.0.1.3978.tar.bz2) = 9730397 +TIMESTAMP = 1509591135 +SHA256 (pymol-v1.8.6.0.tar.bz2) = 7eaaf90ac1e1be0969291cdb1154b3631b5b6403cce1d697133d90cd37a3c565 +SIZE (pymol-v1.8.6.0.tar.bz2) = 8717164 Index: science/py-pymol/files/patch-create__shadertext.py =================================================================== --- /dev/null +++ science/py-pymol/files/patch-create__shadertext.py @@ -0,0 +1,34 @@ +--- create_shadertext.py.orig 2017-03-09 18:16:07 UTC ++++ create_shadertext.py +@@ -93,19 +93,20 @@ def create_shadertext(shaderdir, shaderd + + def create_buildinfo(outputdir, pymoldir='.'): + +- try: +- sha = Popen(['git', 'rev-parse', 'HEAD'], cwd=pymoldir, +- stdout=PIPE).stdout.read().strip().decode() +- except OSError: +- sha = '' ++ #try: ++ # sha = Popen(['git', 'rev-parse', 'HEAD'], cwd=pymoldir, ++ # stdout=PIPE).stdout.read().strip().decode() ++ #except OSError: ++ # sha = '' ++ sha = 'n/a' + + rev = 0 +- try: +- for line in Popen(['svn', 'info'], cwd=pymoldir, stdout=PIPE).stdout: +- if line.startswith(b'Last Changed Rev'): +- rev = int(line.split()[3]) +- except OSError: +- pass ++ #try: ++ # for line in Popen(['svn', 'info'], cwd=pymoldir, stdout=PIPE).stdout: ++ # if line.startswith(b'Last Changed Rev'): ++ # rev = int(line.split()[3]) ++ #except OSError: ++ # pass + + with openw(os.path.join(outputdir, 'PyMOLBuildInfo.h')) as out: + print(''' Index: science/py-pymol/files/patch-setup.py =================================================================== --- science/py-pymol/files/patch-setup.py +++ science/py-pymol/files/patch-setup.py @@ -1,31 +1,22 @@ ---- 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" ] +--- setup.py.orig 2017-03-09 18:16:07 UTC ++++ setup.py +@@ -52,6 +52,8 @@ try: + "keyword support.") + parser.add_argument('--help-distutils', action="store_true", + help="show help for distutils options and exit") ++ parser.add_argument('--single-version-externally-managed', action="store_true", ++ help="single-version-externally-managed") + options, sys.argv[1:] = parser.parse_known_args(namespace=options) + except ImportError: + print("argparse not available") +@@ -318,8 +320,8 @@ else: # unix style (linux, mac, ...) + # optimization currently causes a clang segfault on OS X 10.9 when + # compiling layer2/RepCylBond.cpp +- if sys.platform != 'darwin': +- ext_comp_args += ["-O3"] ++ #if sys.platform != 'darwin': ++ # ext_comp_args += ["-O3"] - distribution = setup ( # Distribution meta-data - + def get_pymol_version(): + return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0] Index: science/py-pymol/pkg-descr =================================================================== --- science/py-pymol/pkg-descr +++ science/py-pymol/pkg-descr @@ -1,9 +1,9 @@ -PyMOL is a molecular graphics system with an embedded Python interpreter -designed for real-time visualization and rapid generation of -high-quality molecular graphics images and animations. It is fully extensible -and available free to everyone via the "Python" license. -PyMOL can be used to create images and animations with unprecedented ease. -It can also perform many other valuable tasks (such as editing PDB files) -to assist you in your research. +PyMOL is a Python-enhanced molecular graphics tool. It excels at +3D visualization of proteins, small molecules, density, surfaces, +and trajectories. It also includes molecular editing, ray tracing, +and movies. Open Source PyMOL is free to everyone! -WWW: http://pymol.sourceforge.net/ +This version represents the community-supported open source distribution +of the closed source commercial product PyMOL. + +WWW: https://www.pymol.org Index: science/py-pymol/pkg-plist =================================================================== --- science/py-pymol/pkg-plist +++ science/py-pymol/pkg-plist @@ -1,257 +1,392 @@ bin/pymol %%PYTHON_SITELIBDIR%%/chempy/__init__.py %%PYTHON_SITELIBDIR%%/chempy/__init__.pyc +%%PYTHON_SITELIBDIR%%/chempy/__init__.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/arc.py %%PYTHON_SITELIBDIR%%/chempy/arc.pyc +%%PYTHON_SITELIBDIR%%/chempy/arc.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.py %%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.pyc +%%PYTHON_SITELIBDIR%%/chempy/bmin/__init__.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bmin/commands.py %%PYTHON_SITELIBDIR%%/chempy/bmin/commands.pyc +%%PYTHON_SITELIBDIR%%/chempy/bmin/commands.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.py %%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.pyc +%%PYTHON_SITELIBDIR%%/chempy/bmin/realtime.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bmin/state.py %%PYTHON_SITELIBDIR%%/chempy/bmin/state.pyc +%%PYTHON_SITELIBDIR%%/chempy/bmin/state.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bmin/util.py %%PYTHON_SITELIBDIR%%/chempy/bmin/util.pyc +%%PYTHON_SITELIBDIR%%/chempy/bmin/util.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bond_amber.py %%PYTHON_SITELIBDIR%%/chempy/bond_amber.pyc +%%PYTHON_SITELIBDIR%%/chempy/bond_amber.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bond_mmff.py %%PYTHON_SITELIBDIR%%/chempy/bond_mmff.pyc +%%PYTHON_SITELIBDIR%%/chempy/bond_mmff.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/chempy/bonds.py %%PYTHON_SITELIBDIR%%/chempy/bonds.pyc +%%PYTHON_SITELIBDIR%%/chempy/bonds.%%PYTHON_PYOEXTENSION%% 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+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/defaultscreen.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/indicator.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/indicator.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/label.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/label.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/labelscreen.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/labelscreen.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/ramp.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/ramp.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/screen.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/screen.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 @@ -433,9 +583,6 @@ %%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 @@ -726,129 +873,130 @@ %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/win.py %%PYTHON_SITELIBDIR%%/pymol/querying.py %%PYTHON_SITELIBDIR%%/pymol/querying.pyc +%%PYTHON_SITELIBDIR%%/pymol/querying.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/pymol/rpc.py %%PYTHON_SITELIBDIR%%/pymol/rpc.pyc +%%PYTHON_SITELIBDIR%%/pymol/rpc.%%PYTHON_PYOEXTENSION%% %%PYTHON_SITELIBDIR%%/pymol/selecting.py %%PYTHON_SITELIBDIR%%/pymol/selecting.pyc 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