git: 1c0e78eb4b28 - main - biology/py-PySCeS: New port: Python Simulator for Cellular Systems

[Yuri Victorovich]

The branch main has been updated by yuri:

URL: https://cgit.FreeBSD.org/ports/commit/?id=1c0e78eb4b2833ec20fb0addbb001e1e99235982

commit 1c0e78eb4b2833ec20fb0addbb001e1e99235982
Author:     Yuri Victorovich <yuri at FreeBSD.org>
AuthorDate: 2021-08-17 21:29:13 +0000
Commit:     Yuri Victorovich <yuri at FreeBSD.org>
CommitDate: 2021-08-17 21:30:08 +0000

    biology/py-PySCeS: New port: Python Simulator for Cellular Systems
---
 biology/Makefile            |  1 +
 biology/py-PySCeS/Makefile  | 38 ++++++++++++++++++++++++++++++++++++++
 biology/py-PySCeS/distinfo  |  3 +++
 biology/py-PySCeS/pkg-descr |  3 +++
 4 files changed, 45 insertions(+)

diff --git a/biology/Makefile b/biology/Makefile
index d02ab1ac20eb..081fb65708b1 100644
--- a/biology/Makefile
+++ b/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
diff --git a/biology/py-PySCeS/Makefile b/biology/py-PySCeS/Makefile
new file mode 100644
index 000000000000..a399b65938fc
--- /dev/null
+++ b/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 at 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>
diff --git a/biology/py-PySCeS/distinfo b/biology/py-PySCeS/distinfo
new file mode 100644
index 000000000000..5eb6ca09af67
--- /dev/null
+++ b/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
diff --git a/biology/py-PySCeS/pkg-descr b/biology/py-PySCeS/pkg-descr
new file mode 100644
index 000000000000..72ca017a7c61
--- /dev/null
+++ b/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/