science/py-pymol: Update 2.2.0 -> 2.3.0

Reported by:	portscout

5 files changed, 24 insertions, 28 deletions

diff --git a/science/py-pymol/Makefile b/science/py-pymol/Makefile
index c8b5f0dd948a..6033fb67f85b 100644
--- a/science/py-pymol/Makefile
+++ b/science/py-pymol/Makefile
@@ -3,8 +3,7 @@
 
 PORTNAME=	pymol
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.2.0
-PORTREVISION=	3
+DISTVERSION=	2.3.0
 CATEGORIES=	science biology python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -17,7 +16,8 @@ LICENSE_FILE=	${WRKSRC}/LICENSE
 LICENSE_PERMS=	dist-mirror dist-sell pkg-mirror pkg-sell auto-accept
 
 BUILD_DEPENDS=	${PYNUMPY} \
-		${LOCALBASE}/include/glm/glm.hpp:math/glm
+		${LOCALBASE}/include/glm/glm.hpp:math/glm \
+		${LOCALBASE}/include/mmtf.hpp:science/mmtf
 LIB_DEPENDS=	libfreetype.so:print/freetype2 \
 		libpng.so:graphics/png \
 		libmsgpackc.so:devel/msgpack
@@ -25,7 +25,7 @@ RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}msgpack>0:devel/py-msgpack@${PY_FLAVOR} \
 		${PYTHON_PKGNAMEPREFIX}Pmw>0:x11-toolkits/py-Pmw@${PY_FLAVOR} \
 		${PYNUMPY}
 
-USES=		compiler:c++11-lang python:2.7 shebangfix tar:bz2
+USES=		compiler:c++11-lang gl gnome python:2.7 shebangfix tar:bz2
 USE_GITHUB=	yes
 GH_ACCOUNT=	schrodinger
 GH_PROJECT=	${PORTNAME}-open-source
diff --git a/science/py-pymol/distinfo b/science/py-pymol/distinfo
index a03176e44fcf..bef4d0fbb343 100644
--- a/science/py-pymol/distinfo
+++ b/science/py-pymol/distinfo
@@ -1,3 +1,3 @@
-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
+TIMESTAMP = 1549950556
+SHA256 (schrodinger-pymol-open-source-v2.3.0_GH0.tar.gz) = 62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0
+SIZE (schrodinger-pymol-open-source-v2.3.0_GH0.tar.gz) = 10448674
diff --git a/science/py-pymol/files/patch-modules_pymol_Qt_____init____.py b/science/py-pymol/files/patch-modules_pymol_Qt_____init____.py
index ef91b48ff01e..2075f7ce00ae 100644
--- a/science/py-pymol/files/patch-modules_pymol_Qt_____init____.py
+++ b/science/py-pymol/files/patch-modules_pymol_Qt_____init____.py
@@ -1,15 +1,15 @@
---- modules/pymol/Qt/__init__.py.orig	2018-03-22 05:10:42 UTC
+--- modules/pymol/Qt/__init__.py.orig	2019-02-11 14:08:10 UTC
 +++ modules/pymol/Qt/__init__.py
-@@ -28,7 +28,7 @@ if not PYQT_NAME:
+@@ -29,7 +29,7 @@ if not PYQT_NAME:
          if DEBUG:
              print('import PyQt5 failed')
  
 -if not PYQT_NAME:
 +if False:
      try:
-         __import__("sip").setapi("QString", 2)
-         from PyQt4 import QtGui, QtCore, QtOpenGL
-@@ -37,7 +37,7 @@ if not PYQT_NAME:
+         from PySide2 import QtGui, QtCore, QtOpenGL, QtWidgets
+         PYQT_NAME = 'PySide2'
+@@ -46,7 +46,7 @@ if not PYQT_NAME:
          if DEBUG:
              print('import PyQt4 failed')
  
diff --git a/science/py-pymol/files/patch-setup.py b/science/py-pymol/files/patch-setup.py
index 208c68150b91..062ebccceca4 100644
--- a/science/py-pymol/files/patch-setup.py
+++ b/science/py-pymol/files/patch-setup.py
@@ -1,19 +1,11 @@
---- setup.py.orig	2018-07-24 16:14:37 UTC
+--- setup.py.orig	2019-02-12 06:00:47 UTC
 +++ setup.py
-@@ -54,6 +54,8 @@ try:
-             "keyword support.")
+@@ -52,6 +52,8 @@ try:
+             "shared library; no: disable fast MMTF load 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")
+     parser.add_argument('--testing', action="store_true",
+             help="Build C-level tests")
      options, sys.argv[1:] = parser.parse_known_args(namespace=options)
- except ImportError:
-     print("argparse not available")
-@@ -278,7 +280,6 @@ ext_comp_args = [
-     # optimizations
-     "-ffast-math",
-     "-funroll-loops",
--    "-O3",
-     "-fcommon",
- ]
- ext_link_args = []
diff --git a/science/py-pymol/pkg-plist b/science/py-pymol/pkg-plist
index 06a6a62a8429..254decb9f28f 100644
--- a/science/py-pymol/pkg-plist
+++ b/science/py-pymol/pkg-plist
@@ -189,6 +189,7 @@ bin/pymol
 %%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_aln.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
@@ -279,9 +280,6 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pmg_tk/startup/apbs_tools.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/startup/apbs_tools.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/startup/apbs_tools.pyo
-%%PYTHON_SITELIBDIR%%/pmg_tk/startup/remote_pdb_load.py
-%%PYTHON_SITELIBDIR%%/pmg_tk/startup/remote_pdb_load.pyc
-%%PYTHON_SITELIBDIR%%/pmg_tk/startup/remote_pdb_load.pyo
 %%PYTHON_SITELIBDIR%%/pmg_tk/volume.py
 %%PYTHON_SITELIBDIR%%/pmg_tk/volume.pyc
 %%PYTHON_SITELIBDIR%%/pmg_tk/volume.pyo
@@ -682,6 +680,9 @@ bin/pymol
 %%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/test/double.png
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/test/single-right.png
+%%PYTHON_SITELIBDIR%%/pymol/pymol_path/data/test/single.png
 %%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
@@ -974,6 +975,9 @@ bin/pymol
 %%PYTHON_SITELIBDIR%%/pymol/selector.py
 %%PYTHON_SITELIBDIR%%/pymol/selector.pyc
 %%PYTHON_SITELIBDIR%%/pymol/selector.pyo
+%%PYTHON_SITELIBDIR%%/pymol/seqalign.py
+%%PYTHON_SITELIBDIR%%/pymol/seqalign.pyc
+%%PYTHON_SITELIBDIR%%/pymol/seqalign.pyo
 %%PYTHON_SITELIBDIR%%/pymol/setting.py
 %%PYTHON_SITELIBDIR%%/pymol/setting.pyc
 %%PYTHON_SITELIBDIR%%/pymol/setting.pyo