diff options
| author | Yuri Victorovich <yuri@FreeBSD.org> | 2022-10-20 14:51:06 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2022-10-20 20:31:39 +0000 |
| commit | 2e0d3b8d4533f5472ade919e5c3e71aaefad9da4 (patch) | |
| tree | 3b41e47505930e73ba1fa33f9a4e64ec5f7325c9 /science/smoldyn | |
| parent | 292218a91c013cfe2fdc266d2e174463834754a4 (diff) | |
| download | ports-2e0d3b8d4533f5472ade919e5c3e71aaefad9da4.tar.gz ports-2e0d3b8d4533f5472ade919e5c3e71aaefad9da4.zip | |
science/smoldyn: Update 2.68 -> 2.69; Fix tests
PYTHON options was added but it is disabled because one dependency
is missing. Tests, however, pass with PYTHON=ON
(and only with PYTHON=ON).
Diffstat (limited to 'science/smoldyn')
| -rw-r--r-- | science/smoldyn/Makefile | 31 | ||||
| -rw-r--r-- | science/smoldyn/distinfo | 6 | ||||
| -rw-r--r-- | science/smoldyn/pkg-plist | 28 |
3 files changed, 53 insertions, 12 deletions
diff --git a/science/smoldyn/Makefile b/science/smoldyn/Makefile index a58d63dfaa30..631cc762f026 100644 --- a/science/smoldyn/Makefile +++ b/science/smoldyn/Makefile @@ -1,5 +1,5 @@ PORTNAME= smoldyn -DISTVERSION= 2.68 +DISTVERSION= 2.69 CATEGORIES= science MASTER_SITES= https://www.smoldyn.org/ @@ -11,22 +11,35 @@ LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/License.txt LIB_DEPENDS= libtiff.so:graphics/tiff +TEST_DEPENDS= ${PYTHON_PKGNAMEPREFIX}flaky>0:devel/py-flaky@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \ + ${PYNUMPY} -USES= cmake:testing compiler:c++11-lang gl localbase:ldflags tar:tgz python:test shebangfix xorg +USES= cmake:testing compiler:c++11-lang gl localbase:ldflags python:test tar:tgz shebangfix xorg USE_GL= gl glu glut USE_XORG= xi xmu USE_LDCONFIG= yes SHEBANG_GLOB= *.py.in -CMAKE_OFF= OPTION_PYTHON CMAKE_TESTING_ON= OPTION_EXAMPLES # all tests fail to run, see https://github.com/ssandrews/Smoldyn/issues/127 -PLIST_FILES= bin/${PORTNAME} \ - include/libsmoldyn.h \ - include/smoldyn.h \ - include/smoldynconfigure.h \ - lib/libsmoldyn_shared.so \ - lib/libsmoldyn_static.a +OPTIONS_DEFINE= PYTHON +OPTIONS_DEFAULT= # PYTHON Tests ONLY pass when PYTHON=ON despite biology/py-biosimulators-utils being missing +OPTIONS_SUB= yes + +PYTHON_CMAKE_BOOL= OPTION_PYTHON +PYTHON_USES= python +PYTHON_CMAKE_ON= -DPython3_EXECUTABLE=${PYTHON_CMD} +PYTHON_BUILD_DEPENDS= ${PYTHON_PKGNAMEPREFIX}setuptools>0:devel/py-setuptools@${PY_FLAVOR} +PYTHON_RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}biosimulators-utils>0:biology/py-biosimulators-utils@${PY_FLAVOR} +PYTHON_BROKEN= pending biology/py-biosimulators-utils completion + +post-extract: # see https://github.com/ssandrews/Smoldyn/issues/127 + @${CHMOD} +x ${WRKSRC}/scripts/run_pyscript.py.in + +do-install-PYTHON-on: # workaround for https://github.com/ssandrews/Smoldyn/issues/129 + @cd ${BUILD_WRKSRC}/py && ${COPYTREE_SHARE} ${PORTNAME} ${STAGEDIR}${PYTHON_SITELIBDIR} + @${RM} ${STAGEDIR}${PYTHON_SITELIBDIR}/${PORTNAME}/.DS_Store .include <bsd.port.mk> diff --git a/science/smoldyn/distinfo b/science/smoldyn/distinfo index eaef8f3533d5..dab6130f445b 100644 --- a/science/smoldyn/distinfo +++ b/science/smoldyn/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1659253902 -SHA256 (smoldyn-2.68.tgz) = f84f8bc214110453039ef76b61fd9b8c37bc6a8b584c8bae85171c7e7543df7f -SIZE (smoldyn-2.68.tgz) = 32722229 +TIMESTAMP = 1666163797 +SHA256 (smoldyn-2.69.tgz) = ad0b76cea376419202cd064bad04c2fb47e624ea74db0b96512c54494b44e6ad +SIZE (smoldyn-2.69.tgz) = 32837854 diff --git a/science/smoldyn/pkg-plist b/science/smoldyn/pkg-plist new file mode 100644 index 000000000000..f664bfef6faa --- /dev/null +++ b/science/smoldyn/pkg-plist @@ -0,0 +1,28 @@ +bin/smoldyn +include/libsmoldyn.h +include/smoldyn.h +include/smoldynconfigure.h +lib/libsmoldyn_shared.so +lib/libsmoldyn_static.a +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__main__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/smoldyn%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/types%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/utils%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn.cpython-310-darwin.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_EXT_SUFFIX%%-darwin.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn%%PYTHON_EXT_SUFFIX%%.so +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__init__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__main__.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/__init__%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/_version%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/combine%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/data_model%%PYTHON_EXT_SUFFIX%%.pyc +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/_version.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/combine.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/data_model.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/utils.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/smoldyn.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/types.py +%%PYTHON%%%%PYTHON_SITELIBDIR%%/smoldyn/utils.py |