Re-added port: science/py-pymol: OpenGL based molecular visualization system (existed 2002/08/13-2014/09/01, deleted in r366862)

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D12902

6 files changed, 1107 insertions, 0 deletions

diff --git a/science/py-pymol/Makefile b/science/py-pymol/Makefile
new file mode 100644
index 000000000000..854b702a15ff
--- /dev/null
+++ b/science/py-pymol/Makefile
@@ -0,0 +1,37 @@
+# Created by: Nakata Maho <chat95@mbox.kyoto-inet.or.jp>
+# $FreeBSD$
+
+PORTNAME=	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 \
+		libmsgpackc.so:devel/msgpack
+
+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 <bsd.port.mk>
diff --git a/science/py-pymol/distinfo b/science/py-pymol/distinfo
new file mode 100644
index 000000000000..e55bbcff39ba
--- /dev/null
+++ b/science/py-pymol/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1509591135
+SHA256 (pymol-v1.8.6.0.tar.bz2) = 7eaaf90ac1e1be0969291cdb1154b3631b5b6403cce1d697133d90cd37a3c565
+SIZE (pymol-v1.8.6.0.tar.bz2) = 8717164
diff --git a/science/py-pymol/files/patch-create__shadertext.py b/science/py-pymol/files/patch-create__shadertext.py
new file mode 100644
index 000000000000..20bf5c027e0e
--- /dev/null
+++ b/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('''
diff --git a/science/py-pymol/files/patch-setup.py b/science/py-pymol/files/patch-setup.py
new file mode 100644
index 000000000000..9c43d171c4cb
--- /dev/null
+++ b/science/py-pymol/files/patch-setup.py
@@ -0,0 +1,22 @@
+--- 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"]
+ 
+ def get_pymol_version():
+     return re.findall(r'_PyMOL_VERSION "(.*)"', open('layer0/Version.h').read())[0]
diff --git a/science/py-pymol/pkg-descr b/science/py-pymol/pkg-descr
new file mode 100644
index 000000000000..1c0af9523b5b
--- /dev/null
+++ b/science/py-pymol/pkg-descr
@@ -0,0 +1,9 @@
+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!
+
+This version represents the community-supported open source distribution
+of the closed source commercial product PyMOL.
+
+WWW: https://www.pymol.org
diff --git a/science/py-pymol/pkg-plist b/science/py-pymol/pkg-plist
new file mode 100644
index 000000000000..22b3ec78cacc
--- /dev/null
+++ b/science/py-pymol/pkg-plist
@@ -0,0 +1,1002 @@
+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%%
+%%PYTHON_SITELIBDIR%%/chempy/brick.py
+%%PYTHON_SITELIBDIR%%/chempy/brick.pyc
+%%PYTHON_SITELIBDIR%%/chempy/brick.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/cc1.py
+%%PYTHON_SITELIBDIR%%/chempy/cc1.pyc
+%%PYTHON_SITELIBDIR%%/chempy/cc1.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/cex.py
+%%PYTHON_SITELIBDIR%%/chempy/cex.pyc
+%%PYTHON_SITELIBDIR%%/chempy/cex.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/champ/__init__.py
+%%PYTHON_SITELIBDIR%%/chempy/champ/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/__init__.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/champ/_champ.so
+%%PYTHON_SITELIBDIR%%/chempy/champ/amber99.py
+%%PYTHON_SITELIBDIR%%/chempy/champ/amber99.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/amber99.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/champ/assign.py
+%%PYTHON_SITELIBDIR%%/chempy/champ/assign.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/assign.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/champ/formal_charges.py
+%%PYTHON_SITELIBDIR%%/chempy/champ/formal_charges.pyc
+%%PYTHON_SITELIBDIR%%/chempy/champ/formal_charges.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/charge.py
+%%PYTHON_SITELIBDIR%%/chempy/charge.pyc
+%%PYTHON_SITELIBDIR%%/chempy/charge.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/cif.py
+%%PYTHON_SITELIBDIR%%/chempy/cif.pyc
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+%%PYTHON_SITELIBDIR%%/chempy/dictdb.py
+%%PYTHON_SITELIBDIR%%/chempy/dictdb.pyc
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+%%PYTHON_SITELIBDIR%%/chempy/fast/__init__.py
+%%PYTHON_SITELIBDIR%%/chempy/fast/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/fast/__init__.%%PYTHON_PYOEXTENSION%%
+%%PYTHON_SITELIBDIR%%/chempy/fragments/__init__.py
+%%PYTHON_SITELIBDIR%%/chempy/fragments/__init__.pyc
+%%PYTHON_SITELIBDIR%%/chempy/fragments/__init__.%%PYTHON_PYOEXTENSION%%
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+%%PYTHON_SITELIBDIR%%/chempy/mass.pyc
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