science/py-pymol: Update to 2.1.0

Release notes:
https://pymol.org/dokuwiki/?id=media:new21

Port changes:
* Fixed shebang in bin/pymol
* Misc minor changes

Reported by:	portscout

3 files changed, 105 insertions, 35 deletions

diff --git a/science/py-pymol/Makefile b/science/py-pymol/Makefile
index 8b5d05a63f83..bee0da31614f 100644
--- a/science/py-pymol/Makefile
+++ b/science/py-pymol/Makefile
@@ -3,9 +3,9 @@
 
 PORTNAME=	pymol
 DISTVERSIONPREFIX=	v
-DISTVERSION=	1.8.6.0
+DISTVERSION=	2.1.0
 CATEGORIES=	science biology python
-MASTER_SITES=	SF/pymol/pymol/1.8/
+MASTER_SITES=	SF/pymol/pymol/2/
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	yuri@FreeBSD.org
@@ -22,15 +22,16 @@ LIB_DEPENDS=	libfreetype.so:print/freetype2 \
 		libpng.so:graphics/png \
 		libmsgpackc.so:devel/msgpack
 
-WRKSRC=		${WRKDIR}/pymol
-
 USES=		compiler:c++11-lang python:2.7 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
+USE_PYTHON=	distutils concurrent # autoplist is broken: https://sourceforge.net/p/pymol/bugs/189
 SHEBANG_FILES=	test/show test/run test/cyg
 
+WRKSRC=		${WRKDIR}/pymol
+
 post-install:
+	@${REINPLACE_CMD} -i '' -e 's|#!/bin/bash|#!/bin/sh|' ${STAGEDIR}${PREFIX}/bin/pymol
 	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pymol/_cmd.so
 	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/chempy/champ/_champ.so
 
diff --git a/science/py-pymol/distinfo b/science/py-pymol/distinfo
index e55bbcff39ba..81272b0a9e72 100644
--- a/science/py-pymol/distinfo
+++ b/science/py-pymol/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1509591135
-SHA256 (pymol-v1.8.6.0.tar.bz2) = 7eaaf90ac1e1be0969291cdb1154b3631b5b6403cce1d697133d90cd37a3c565
-SIZE (pymol-v1.8.6.0.tar.bz2) = 8717164
+TIMESTAMP = 1521529763
+SHA256 (pymol-v2.1.0.tar.bz2) = 7ae8ebb899533d691a67c1ec731b00518dea456ab3e258aa052a65c24b63eae2
+SIZE (pymol-v2.1.0.tar.bz2) = 8779083
diff --git a/science/py-pymol/pkg-plist b/science/py-pymol/pkg-plist
index d4c9e2d2e9f3..db4e2dd55228 100644
--- a/science/py-pymol/pkg-plist
+++ b/science/py-pymol/pkg-plist
@@ -168,6 +168,72 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/chempy/xyz.py
 %%PYTHON_SITELIBDIR%%/chempy/xyz.pyc
 %%PYTHON_SITELIBDIR%%/chempy/xyz.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/TextEditor.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/TextEditor.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/TextEditor.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/__init__.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/advanced_settings_gui.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/advanced_settings_gui.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/advanced_settings_gui.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/builder.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/builder.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/builder.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/file_dialogs.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/file_dialogs.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/file_dialogs.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/__init__.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/askpartial.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/colors.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/fetch.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/load_mae.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/load_map.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/load_mtz.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/load_traj.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/movieexport.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/pluginitem.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/pluginmanager.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/png.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/props.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/render.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/save_molecule.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/forms/save_object.ui
+%%PYTHON_SITELIBDIR%%/pmg_qt/keymapping.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/keymapping.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/keymapping.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/mimic_pmg_tk.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/mimic_pmg_tk.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/mimic_pmg_tk.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/mimic_tk.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/mimic_tk.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/mimic_tk.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/properties_dialog.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/properties_dialog.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/properties_dialog.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/pymol_gl_widget.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/pymol_gl_widget.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/pymol_gl_widget.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/pymol_qt_gui.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/pymol_qt_gui.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/pymol_qt_gui.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/__init__.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/pml.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/pml.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/pml.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/pmlparser.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/pmlparser.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/pmlparser.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/python.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/python.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/syntax/python.pyo
+%%PYTHON_SITELIBDIR%%/pmg_qt/volume.py
+%%PYTHON_SITELIBDIR%%/pmg_qt/volume.pyc
+%%PYTHON_SITELIBDIR%%/pmg_qt/volume.pyo
 %%PYTHON_SITELIBDIR%%/pmg_tk/ColorEditor.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/ColorEditor.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/ColorEditor.pyo
@@ -219,9 +285,12 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pmg_tk/volume.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/volume.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/volume.pyo
-%%PYTHON_SITELIBDIR%%/pmg_wx/__init__.py
-%%PYTHON_SITELIBDIR%%/pmg_wx/__init__.pyc
-%%PYTHON_SITELIBDIR%%/pmg_wx/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymol/Qt/__init__.py
+%%PYTHON_SITELIBDIR%%/pymol/Qt/__init__.pyc
+%%PYTHON_SITELIBDIR%%/pymol/Qt/__init__.pyo
+%%PYTHON_SITELIBDIR%%/pymol/Qt/utils.py
+%%PYTHON_SITELIBDIR%%/pymol/Qt/utils.pyc
+%%PYTHON_SITELIBDIR%%/pymol/Qt/utils.pyo
 %%PYTHON_SITELIBDIR%%/pymol/__init__.py
 %%PYTHON_SITELIBDIR%%/pymol/__init__.pyc
 %%PYTHON_SITELIBDIR%%/pymol/__init__.pyo
@@ -229,6 +298,9 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/__main__.pyc
 %%PYTHON_SITELIBDIR%%/pymol/__main__.pyo
 %%PYTHON_SITELIBDIR%%/pymol/_cmd.so
+%%PYTHON_SITELIBDIR%%/pymol/_gui.py
+%%PYTHON_SITELIBDIR%%/pymol/_gui.pyc
+%%PYTHON_SITELIBDIR%%/pymol/_gui.pyo
 %%PYTHON_SITELIBDIR%%/pymol/api.py
 %%PYTHON_SITELIBDIR%%/pymol/api.pyc
 %%PYTHON_SITELIBDIR%%/pymol/api.pyo
@@ -244,6 +316,9 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/cmd.py
 %%PYTHON_SITELIBDIR%%/pymol/cmd.pyc
 %%PYTHON_SITELIBDIR%%/pymol/cmd.pyo
+%%PYTHON_SITELIBDIR%%/pymol/colorprinting.py
+%%PYTHON_SITELIBDIR%%/pymol/colorprinting.pyc
+%%PYTHON_SITELIBDIR%%/pymol/colorprinting.pyo
 %%PYTHON_SITELIBDIR%%/pymol/colorramping.py
 %%PYTHON_SITELIBDIR%%/pymol/colorramping.pyc
 %%PYTHON_SITELIBDIR%%/pymol/colorramping.pyo
@@ -271,6 +346,9 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/creating.py
 %%PYTHON_SITELIBDIR%%/pymol/creating.pyc
 %%PYTHON_SITELIBDIR%%/pymol/creating.pyo
+%%PYTHON_SITELIBDIR%%/pymol/diagnosing.py
+%%PYTHON_SITELIBDIR%%/pymol/diagnosing.pyc
+%%PYTHON_SITELIBDIR%%/pymol/diagnosing.pyo
 %%PYTHON_SITELIBDIR%%/pymol/editing.py
 %%PYTHON_SITELIBDIR%%/pymol/editing.pyc
 %%PYTHON_SITELIBDIR%%/pymol/editing.pyo
@@ -325,6 +403,9 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/keywords.py
 %%PYTHON_SITELIBDIR%%/pymol/keywords.pyc
 %%PYTHON_SITELIBDIR%%/pymol/keywords.pyo
+%%PYTHON_SITELIBDIR%%/pymol/lazyio.py
+%%PYTHON_SITELIBDIR%%/pymol/lazyio.pyc
+%%PYTHON_SITELIBDIR%%/pymol/lazyio.pyo
 %%PYTHON_SITELIBDIR%%/pymol/locking.py
 %%PYTHON_SITELIBDIR%%/pymol/locking.pyc
 %%PYTHON_SITELIBDIR%%/pymol/locking.pyo
@@ -376,6 +457,9 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/plugins/managergui.py
 %%PYTHON_SITELIBDIR%%/pymol/plugins/managergui.pyc
 %%PYTHON_SITELIBDIR%%/pymol/plugins/managergui.pyo
+%%PYTHON_SITELIBDIR%%/pymol/plugins/managergui_qt.py
+%%PYTHON_SITELIBDIR%%/pymol/plugins/managergui_qt.pyc
+%%PYTHON_SITELIBDIR%%/pymol/plugins/managergui_qt.pyo
 %%PYTHON_SITELIBDIR%%/pymol/plugins/repository.py
 %%PYTHON_SITELIBDIR%%/pymol/plugins/repository.pyc
 %%PYTHON_SITELIBDIR%%/pymol/plugins/repository.pyo
@@ -523,6 +607,8 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/demo/il2.pdb
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/demo/pept.pdb
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/demo/pept.pkl
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_qt/icons/refresh.svg
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_qt/styles/pymol.sty
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.gif
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro5.xbm
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/pmg_tk/bitmaps/builder/aro6.gif
@@ -545,6 +631,7 @@ bin/pymol
 %%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/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
@@ -582,6 +669,9 @@ bin/pymol
 %%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/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
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/tut/1hpv.pdb
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy/generate_amber.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/chempy/generate_mmff.py
@@ -651,18 +741,6 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/launching/launch_no_tk.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/launching/launch_viewer1.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/launching/launch_viewer2.py
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.93-1.rh62.py152.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.93-1.rh70.py152.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.93-1.rh72.py21.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.93-1.rh73.py22.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.93-1.rh80.py22.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.93-1.rh90.py22.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.96-1.rh62.py152.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.96-1.rh70.py152.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.96-1.rh72.py21.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.96-1.rh73.py22.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.96-1.rh80.py22.spec
-%%PYTHON_SITELIBDIR%%/pymol/pymol_path/examples/package/redhat/pymol-0.96-1.rh90.py22.spec
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/scripts/metaphorics/alignment.pml
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/scripts/metaphorics/annotate.pml
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/scripts/metaphorics/fedora.pml
@@ -871,6 +949,9 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/trim.py
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/vdiff
 %%PYTHON_SITELIBDIR%%/pymol/pymol_path/test/win.py
+%%PYTHON_SITELIBDIR%%/pymol/pymolhttpd.py
+%%PYTHON_SITELIBDIR%%/pymol/pymolhttpd.pyc
+%%PYTHON_SITELIBDIR%%/pymol/pymolhttpd.pyo
 %%PYTHON_SITELIBDIR%%/pymol/querying.py
 %%PYTHON_SITELIBDIR%%/pymol/querying.pyc
 %%PYTHON_SITELIBDIR%%/pymol/querying.pyo
@@ -988,15 +1069,3 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol2/cmd2.py
 %%PYTHON_SITELIBDIR%%/pymol2/cmd2.pyc
 %%PYTHON_SITELIBDIR%%/pymol2/cmd2.pyo
-%%PYTHON_SITELIBDIR%%/web/__init__.py
-%%PYTHON_SITELIBDIR%%/web/__init__.pyc
-%%PYTHON_SITELIBDIR%%/web/__init__.pyo
-%%PYTHON_SITELIBDIR%%/web/examples/__init__.py
-%%PYTHON_SITELIBDIR%%/web/examples/__init__.pyc
-%%PYTHON_SITELIBDIR%%/web/examples/__init__.pyo
-%%PYTHON_SITELIBDIR%%/web/examples/justhttpd.py
-%%PYTHON_SITELIBDIR%%/web/examples/justhttpd.pyc
-%%PYTHON_SITELIBDIR%%/web/examples/justhttpd.pyo
-%%PYTHON_SITELIBDIR%%/web/pymolhttpd.py
-%%PYTHON_SITELIBDIR%%/web/pymolhttpd.pyc
-%%PYTHON_SITELIBDIR%%/web/pymolhttpd.pyo