git: a2b852ee70ee - main - science/py-pymol: Update 2.4.0 -> 2.5.0-97

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From: Yuri Victorovich <yuri_at_FreeBSD.org>
Date: Sun, 27 Nov 2022 21:03:08 UTC
The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=a2b852ee70ee234f4b2360f72ea2d89f48943b37

commit a2b852ee70ee234f4b2360f72ea2d89f48943b37
Author:     Yuri Victorovich <yuri@FreeBSD.org>
AuthorDate: 2022-11-27 20:58:44 +0000
Commit:     Yuri Victorovich <yuri@FreeBSD.org>
CommitDate: 2022-11-27 21:03:05 +0000

    science/py-pymol: Update 2.4.0 -> 2.5.0-97
---
 science/py-pymol/Makefile                          |  24 +-
 science/py-pymol/distinfo                          |   6 +-
 .../py-pymol/files/patch-layer0_MemoryUsage.cpp    |  20 +
 .../files/patch-modules_pymol_Qt_____init____.py   |  20 -
 science/py-pymol/files/patch-setup.py              |  15 +-
 science/py-pymol/pkg-plist                         | 962 +++++++++------------
 6 files changed, 441 insertions(+), 606 deletions(-)

diff --git a/science/py-pymol/Makefile b/science/py-pymol/Makefile
index d65a765b6bd3..a8f87b52626d 100644
--- a/science/py-pymol/Makefile
+++ b/science/py-pymol/Makefile
@@ -1,7 +1,7 @@
 PORTNAME=	pymol
 DISTVERSIONPREFIX=	v
-DISTVERSION=	2.4.0
-PORTREVISION=	7
+DISTVERSION=	2.5.0-97
+DISTVERSIONSUFFIX=	-gd24468af
 CATEGORIES=	science biology python
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -25,23 +25,25 @@ 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 gl gnome python:3.5+ shebangfix tar:bz2
-USE_GITHUB=	yes
-GH_ACCOUNT=	schrodinger
-GH_PROJECT=	${PORTNAME}-open-source
+USES=		compiler:c++11-lang gl gnome python:3.5+ tar:bz2
 USE_GL=		gl glew glu glut
 USE_GNOME=	libxml2
 USE_PYTHON=	distutils concurrent # autoplist is broken: https://github.com/schrodinger/pymol-open-source/issues/99
-SHEBANG_FILES=	test/show test/run test/cyg
 
-CONFLICTS_INSTALL=	${PYTHON_PKGNAMEPREFIX}chempy # https://github.com/schrodinger/pymol-open-source/issues/100
+USE_GITHUB=	yes
+GH_ACCOUNT=	schrodinger
+GH_PROJECT=	${PORTNAME}-open-source
+
+CONFLICTS_INSTALL=	${PYTHON_PKGNAMEPREFIX}chempy # chempy port is unrelated, see https://github.com/schrodinger/pymol-open-source/issues/100
+
+CXXFLAGS+=	-DMSGPACK_NO_BOOST # in line with MSGPACK_USE_BOOST=OFF in devel/msgpack-cxx
 
-OPTIONS_SINGLE=	GUI
+OPTIONS_SINGLE=		GUI
 OPTIONS_SINGLE_GUI=	QT5 TK
 OPTIONS_DEFAULT=	QT5
 
-QT5_USES=	pyqt:5
-QT5_USE=	PYQT=pyqt5:run
+QT5_USES=		pyqt:5
+QT5_USE=		PYQT=pyqt5:run
 
 post-patch-TK-on:
 	@${REINPLACE_CMD} -e ' \
diff --git a/science/py-pymol/distinfo b/science/py-pymol/distinfo
index 869d54d85a75..bb74283b993b 100644
--- a/science/py-pymol/distinfo
+++ b/science/py-pymol/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1590042797
-SHA256 (schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz) = 5ede4ce2e8f53713c5ee64f5905b2d29bf01e4391da7e536ce8909d6b9116581
-SIZE (schrodinger-pymol-open-source-v2.4.0_GH0.tar.gz) = 10552539
+TIMESTAMP = 1669581024
+SHA256 (schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz) = 801e8e71a02c56c07aacd241044e397586a435a4435b74845d779d9846c994af
+SIZE (schrodinger-pymol-open-source-v2.5.0-97-gd24468af_GH0.tar.gz) = 10495556
diff --git a/science/py-pymol/files/patch-layer0_MemoryUsage.cpp b/science/py-pymol/files/patch-layer0_MemoryUsage.cpp
new file mode 100644
index 000000000000..682a34626126
--- /dev/null
+++ b/science/py-pymol/files/patch-layer0_MemoryUsage.cpp
@@ -0,0 +1,20 @@
+--- layer0/MemoryUsage.cpp.orig	2022-11-27 20:14:03 UTC
++++ layer0/MemoryUsage.cpp
+@@ -51,6 +51,8 @@ size_t memory_usage()
+     GetProcessMemoryInfo(hProcess.get(), &pmc, sizeof(pmc));
+   }
+   return pmc.WorkingSetSize;
++#elif defined(__FreeBSD__)
++  return 0; // TODO implement memory_usage()
+ #else
+ #error "platform not handled"
+ #endif
+@@ -92,6 +94,8 @@ size_t memory_available()
+   statex.dwLength = sizeof(statex);
+   GlobalMemoryStatusEx(&statex);
+   return statex.ullAvailPhys;
++#elif defined(__FreeBSD__)
++  return 0; // TODO: implement memory_available()
+ #else
+ #error "platform not handled"
+ #endif
diff --git a/science/py-pymol/files/patch-modules_pymol_Qt_____init____.py b/science/py-pymol/files/patch-modules_pymol_Qt_____init____.py
deleted file mode 100644
index 2075f7ce00ae..000000000000
--- a/science/py-pymol/files/patch-modules_pymol_Qt_____init____.py
+++ /dev/null
@@ -1,20 +0,0 @@
---- modules/pymol/Qt/__init__.py.orig	2019-02-11 14:08:10 UTC
-+++ modules/pymol/Qt/__init__.py
-@@ -29,7 +29,7 @@ if not PYQT_NAME:
-         if DEBUG:
-             print('import PyQt5 failed')
- 
--if not PYQT_NAME:
-+if False:
-     try:
-         from PySide2 import QtGui, QtCore, QtOpenGL, QtWidgets
-         PYQT_NAME = 'PySide2'
-@@ -46,7 +46,7 @@ if not PYQT_NAME:
-         if DEBUG:
-             print('import PyQt4 failed')
- 
--if not PYQT_NAME:
-+if False:
-     try:
-         from PySide import QtGui, QtCore, QtOpenGL
-         PYQT_NAME = 'PySide'
diff --git a/science/py-pymol/files/patch-setup.py b/science/py-pymol/files/patch-setup.py
index 062ebccceca4..fe1059c10949 100644
--- a/science/py-pymol/files/patch-setup.py
+++ b/science/py-pymol/files/patch-setup.py
@@ -1,6 +1,6 @@
---- setup.py.orig	2019-02-12 06:00:47 UTC
+--- setup.py.orig	2021-05-10 18:38:37 UTC
 +++ setup.py
-@@ -52,6 +52,8 @@ try:
+@@ -53,6 +53,8 @@ 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")
@@ -8,4 +8,13 @@
 +            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)
+     parser.add_argument('--openvr', dest='openvr', action='store_true')
+@@ -282,7 +284,7 @@ if DEBUG and not WIN:
+ libs = ["png", "freetype"]
+ lib_dirs = []
+ ext_comp_args = [
+-    "-Werror=return-type",
++    #"-Werror=return-type",
+     "-Wunused-variable",
+     "-Wno-switch",
+     "-Wno-narrowing",
diff --git a/science/py-pymol/pkg-plist b/science/py-pymol/pkg-plist
index 6d85e1f147c4..cac539fae865 100644
--- a/science/py-pymol/pkg-plist
+++ b/science/py-pymol/pkg-plist
@@ -1,91 +1,91 @@
 bin/pymol
 %%PYTHON_SITELIBDIR%%/chempy/__init__.py
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/__init__.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/__init__.cpython-%%PYTHON_SUFFIX%%.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/arc.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/arc.cpython-%%PYTHON_SUFFIX%%.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_amber.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_amber.cpython-%%PYTHON_SUFFIX%%.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_mmff.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bond_mmff.cpython-%%PYTHON_SUFFIX%%.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bonds.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/bonds.cpython-%%PYTHON_SUFFIX%%.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/brick.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/brick.cpython-%%PYTHON_SUFFIX%%.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/cc1.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/cc1.cpython-%%PYTHON_SUFFIX%%.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/charge.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc
-%%PYTHON_SITELIBDIR%%/chempy/__pycache__/charge.cpython-%%PYTHON_SUFFIX%%.pyc
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