Date: Mon, 17 Sep 2018 20:48:45 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r479957 - in head/science/py-pymol: . files Message-ID: <201809172048.w8HKmjwt006569@repo.freebsd.org>
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Author: yuri Date: Mon Sep 17 20:48:45 2018 New Revision: 479957 URL: https://svnweb.freebsd.org/changeset/ports/479957 Log: science/py-pymol: Update 2.1.0 -> 2.2.0 Moved to GitHub. Also update WWW. Modified: head/science/py-pymol/Makefile head/science/py-pymol/distinfo head/science/py-pymol/files/patch-create__shadertext.py head/science/py-pymol/files/patch-setup.py head/science/py-pymol/pkg-descr head/science/py-pymol/pkg-plist Modified: head/science/py-pymol/Makefile ============================================================================== --- head/science/py-pymol/Makefile Mon Sep 17 20:29:11 2018 (r479956) +++ head/science/py-pymol/Makefile Mon Sep 17 20:48:45 2018 (r479957) @@ -3,10 +3,8 @@ PORTNAME= pymol DISTVERSIONPREFIX= v -DISTVERSION= 2.1.0 -PORTREVISION= 3 +DISTVERSION= 2.2.0 CATEGORIES= science biology python -MASTER_SITES= SF/pymol/pymol/2/ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org @@ -17,7 +15,8 @@ LICENSE_NAME= Open-Source PyMOL Copyright LICENSE_FILE= ${WRKSRC}/LICENSE LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept -BUILD_DEPENDS= ${PYNUMPY} +BUILD_DEPENDS= ${PYNUMPY} \ + ${LOCALBASE}/include/glm/glm.hpp:math/glm LIB_DEPENDS= libfreetype.so:print/freetype2 \ libpng.so:graphics/png \ libmsgpackc.so:devel/msgpack @@ -26,13 +25,14 @@ RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py ${PYNUMPY} USES= compiler:c++11-lang python:2.7 shebangfix tar:bz2 +USE_GITHUB= yes +GH_ACCOUNT= schrodinger +GH_PROJECT= ${PORTNAME}-open-source 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 -WRKSRC= ${WRKDIR}/pymol - OPTIONS_SINGLE= GUI OPTIONS_SINGLE_GUI= QT5 TK OPTIONS_DEFAULT= QT5 @@ -44,11 +44,11 @@ post-patch-TK-on: @${REINPLACE_CMD} -e ' \ 23s|if not PYQT_NAME:|if False:| ; \ s|from PyQt5 import|from X import|' \ - ${WRKSRC}/modules/pymol/Qt/__init__.py + ${WRKSRC}/modules/${PORTNAME}/Qt/__init__.py post-install: - @${REINPLACE_CMD} -i '' -e 's|#!/bin/bash|#!/bin/sh|' ${STAGEDIR}${PREFIX}/bin/pymol - @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pymol/_cmd.so + @${REINPLACE_CMD} -i '' -e 's|#!/bin/bash|#!/bin/sh|' ${STAGEDIR}${PREFIX}/bin/${PORTNAME} + @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/${PORTNAME}/_cmd.so @${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/chempy/champ/_champ.so .include <bsd.port.mk> Modified: head/science/py-pymol/distinfo ============================================================================== --- head/science/py-pymol/distinfo Mon Sep 17 20:29:11 2018 (r479956) +++ head/science/py-pymol/distinfo Mon Sep 17 20:48:45 2018 (r479957) @@ -1,3 +1,3 @@ -TIMESTAMP = 1521529763 -SHA256 (pymol-v2.1.0.tar.bz2) = 7ae8ebb899533d691a67c1ec731b00518dea456ab3e258aa052a65c24b63eae2 -SIZE (pymol-v2.1.0.tar.bz2) = 8779083 +TIMESTAMP = 1537213207 +SHA256 (schrodinger-pymol-open-source-v2.2.0_GH0.tar.gz) = 58d910103dc494c49c86bc8fd6cd94b1a030647f9d72f69fbd7d7ad25fb11233 +SIZE (schrodinger-pymol-open-source-v2.2.0_GH0.tar.gz) = 10514753 Modified: head/science/py-pymol/files/patch-create__shadertext.py ============================================================================== --- head/science/py-pymol/files/patch-create__shadertext.py Mon Sep 17 20:29:11 2018 (r479956) +++ head/science/py-pymol/files/patch-create__shadertext.py Mon Sep 17 20:48:45 2018 (r479957) @@ -1,6 +1,6 @@ ---- create_shadertext.py.orig 2017-03-09 18:16:07 UTC +--- create_shadertext.py.orig 2018-07-24 16:14:37 UTC +++ create_shadertext.py -@@ -93,19 +93,20 @@ def create_shadertext(shaderdir, shaderd +@@ -122,19 +122,20 @@ def create_shadertext(shaderdir, shaderd def create_buildinfo(outputdir, pymoldir='.'): Modified: head/science/py-pymol/files/patch-setup.py ============================================================================== --- head/science/py-pymol/files/patch-setup.py Mon Sep 17 20:29:11 2018 (r479956) +++ head/science/py-pymol/files/patch-setup.py Mon Sep 17 20:48:45 2018 (r479957) @@ -1,6 +1,6 @@ ---- setup.py.orig 2017-03-09 18:16:07 UTC +--- setup.py.orig 2018-07-24 16:14:37 UTC +++ setup.py -@@ -52,6 +52,8 @@ try: +@@ -54,6 +54,8 @@ try: "keyword support.") parser.add_argument('--help-distutils', action="store_true", help="show help for distutils options and exit") @@ -9,14 +9,11 @@ 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"] - - def get_pymol_version(): - return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0] +@@ -278,7 +280,6 @@ ext_comp_args = [ + # optimizations + "-ffast-math", + "-funroll-loops", +- "-O3", + "-fcommon", + ] + ext_link_args = [] Modified: head/science/py-pymol/pkg-descr ============================================================================== --- head/science/py-pymol/pkg-descr Mon Sep 17 20:29:11 2018 (r479956) +++ head/science/py-pymol/pkg-descr Mon Sep 17 20:48:45 2018 (r479957) @@ -6,4 +6,4 @@ and movies. Open Source PyMOL is free to everyone! This version represents the community-supported open source distribution of the closed source commercial product PyMOL. -WWW: https://www.pymol.org +WWW: https://pymol.org/2/ Modified: head/science/py-pymol/pkg-plist ============================================================================== --- head/science/py-pymol/pkg-plist Mon Sep 17 20:29:11 2018 (r479956) +++ head/science/py-pymol/pkg-plist Mon Sep 17 20:48:45 2018 (r479957) @@ -479,6 +479,7 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/asn.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/asp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/asph.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/atp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/benzene.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/benzocycloheptane.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/butane.pkl @@ -509,6 +510,7 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ct_trp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ct_tyr.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ct_val.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ctp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/cyanide.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/cyclobutane.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/cycloheptane.pkl @@ -525,6 +527,7 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/glu.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gluh.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gly.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/gtp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/hid.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/hie.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/hip.pkl @@ -578,7 +581,9 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/thr.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/trifluoromethane.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/trp.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/ttp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/tyr.pkl +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/utp.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/fragments/val.pkl %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/sidechains/generate1.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/chempy/sidechains/generate2.py @@ -634,41 +639,46 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/icons/icon2.svg %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/matrices/BLOSUM62 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pymol/splash.png -%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/anaglyph.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/anaglyph_header.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bg.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/bg.vs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/call_compute_color_for_light.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/compute_color_for_light.fs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/compute_fog_color.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/connector.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/connector.gs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/connector.shared +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/connector.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/copy.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/copy.vs %%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/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/defaultscreen.fs -%%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/line.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/line.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/oit.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/oit.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 %%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/surface.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/surface.vs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/trilines.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/trilines.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/shaders/webgl_header.fs +%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/shaders/webgl_header.vs %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/README.txt %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/lightingsettings_gui/__init__.py %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/startup/lightingsettings_gui/main.py @@ -970,6 +980,9 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/shortcut.py %%PYTHON_SITELIBDIR%%/pymol/shortcut.pyc %%PYTHON_SITELIBDIR%%/pymol/shortcut.pyo +%%PYTHON_SITELIBDIR%%/pymol/stereochemistry/__init__.py +%%PYTHON_SITELIBDIR%%/pymol/stereochemistry/__init__.pyc +%%PYTHON_SITELIBDIR%%/pymol/stereochemistry/__init__.pyo %%PYTHON_SITELIBDIR%%/pymol/util.py %%PYTHON_SITELIBDIR%%/pymol/util.pyc %%PYTHON_SITELIBDIR%%/pymol/util.pyo @@ -1033,6 +1046,9 @@ bin/pymol %%PYTHON_SITELIBDIR%%/pymol/wizard/mutagenesis.py %%PYTHON_SITELIBDIR%%/pymol/wizard/mutagenesis.pyc %%PYTHON_SITELIBDIR%%/pymol/wizard/mutagenesis.pyo +%%PYTHON_SITELIBDIR%%/pymol/wizard/nucmutagenesis.py +%%PYTHON_SITELIBDIR%%/pymol/wizard/nucmutagenesis.pyc +%%PYTHON_SITELIBDIR%%/pymol/wizard/nucmutagenesis.pyo %%PYTHON_SITELIBDIR%%/pymol/wizard/pair_fit.py %%PYTHON_SITELIBDIR%%/pymol/wizard/pair_fit.pyc %%PYTHON_SITELIBDIR%%/pymol/wizard/pair_fit.pyo
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