diff options
| author | Yuri Victorovich <yuri@FreeBSD.org> | 2022-11-27 12:58:44 -0800 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2022-11-27 13:03:05 -0800 |
| commit | a2b852ee70ee234f4b2360f72ea2d89f48943b37 (patch) | |
| tree | e56e949763f6a05d2c119cdab64ca06d5c064ea6 | |
| parent | x11-wm/gamescope: temporarily disable wayland category (diff) | |
science/py-pymol: Update 2.4.0 -> 2.5.0-97
| -rw-r--r-- | science/py-pymol/Makefile | 24 | ||||
| -rw-r--r-- | science/py-pymol/distinfo | 6 | ||||
| -rw-r--r-- | science/py-pymol/files/patch-layer0_MemoryUsage.cpp | 20 | ||||
| -rw-r--r-- | science/py-pymol/files/patch-modules_pymol_Qt_____init____.py | 20 | ||||
| -rw-r--r-- | science/py-pymol/files/patch-setup.py | 15 | ||||
| -rw-r--r-- | 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 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