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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).
This commit is contained in:
Yuri Victorovich 2022-10-20 06:51:06 -08:00
parent 292218a91c
commit 2e0d3b8d45
3 changed files with 53 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

31
science/smoldyn/Makefile
View File

@ -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>

6
science/smoldyn/distinfo
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@ -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

28
science/smoldyn/pkg-plist Normal file
View File

@ -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