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Code Issues Releases Activity

science/py-pymol: Update 2.1.0 -> 2.2.0

Browse Source 
Moved to GitHub.
Also update WWW.
This commit is contained in:
Yuri Victorovich 2018-09-17 20:48:45 +00:00
parent 6fba07757d
commit dde65abe85
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=479957
6 changed files with 52 additions and 39 deletions
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18
science/py-pymol/Makefile
View File

@ -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= ${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \
${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>

6
science/py-pymol/distinfo
View File

@ -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

4
science/py-pymol/files/patch-create__shadertext.py
View File

@ -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='.'):

23
science/py-pymol/files/patch-setup.py
View File

@ -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 = []

2
science/py-pymol/pkg-descr
View File

@ -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/

38
science/py-pymol/pkg-plist
View File

@ -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