biology/py-PySCeS: New port: Python Simulator for Cellular Systems

biology/Makefile

@@ -130,6 +130,7 @@
     SUBDIR += protomol
     SUBDIR += psi88
     SUBDIR += py-Genesis-PyAPI
+    SUBDIR += py-PySCeS
     SUBDIR += py-bigwig
     SUBDIR += py-biom-format
     SUBDIR += py-biopython

biology/py-PySCeS/Makefile

@@ -0,0 +1,38 @@
+PORTNAME=	PySCeS
+DISTVERSION=	0.9.8post1
+DISTVERSIONSUFFIX=	-31-g28dd259
+CATEGORIES=	biology python
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Python Simulator for Cellular Systems
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+PY_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}ipython>0:devel/ipython@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}nose>0:devel/py-nose@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}python-libsbml>0:biology/py-python-libsbml@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${PY_FLAVOR}
+BUILD_DEPENDS=	${PY_DEPENDS}
+RUN_DEPENDS=	${PY_DEPENDS}
+
+USES=		fortran python
+USE_PYTHON=	distutils autoplist
+
+USE_GITHUB=	yes
+GH_PROJECT=	${PORTNAME:tl}
+
+LDFLAGS+=	-lpython${PYTHON_VER} -shared # see https://github.com/PySCeS/pysces/issues/29
+
+post-install:
+	@${STRIP_CMD} \
+		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/pitcon/pitcon.cpython-38.so \
+		${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysces/nleq2/nleq2.cpython-38.so
+
+do-test: install # from section 2.1 Loading PySCeS in http://pysces.sourceforge.net/pdf/userguide.pdf
+	@${PYTHON_CMD} -c "import pysces; pysces.test();"
+
+.include <bsd.port.mk>

biology/py-PySCeS/distinfo

@@ -0,0 +1,3 @@
+TIMESTAMP = 1629133609
+SHA256 (PySCeS-pysces-0.9.8post1-31-g28dd259_GH0.tar.gz) = e8634ae766331b57dcc697a4a59c8c2844e744a63e47727a15b4a7f5e32c537d
+SIZE (PySCeS-pysces-0.9.8post1-31-g28dd259_GH0.tar.gz) = 2670650

biology/py-PySCeS/pkg-descr

@@ -0,0 +1,3 @@
+PySCeS provides a variety of tools for the analysis of cellular systems.
+
+WWW: http://pysces.sourceforge.net/