svn commit: r469841 - in head/science: . py-MDAnalysis py-MDAnalysis/files

[Yuri Victorovich]

Author: yuri
Date: Mon May 14 00:15:31 2018
New Revision: 469841
URL: https://svnweb.freebsd.org/changeset/ports/469841

Log:
  New port: science/py-MDAnalysis: Python library to analyze molecular dynamics trajectories

Added:
  head/science/py-MDAnalysis/
  head/science/py-MDAnalysis/Makefile   (contents, props changed)
  head/science/py-MDAnalysis/distinfo   (contents, props changed)
  head/science/py-MDAnalysis/files/
  head/science/py-MDAnalysis/files/patch-setup.py   (contents, props changed)
  head/science/py-MDAnalysis/pkg-descr   (contents, props changed)
Modified:
  head/science/Makefile

Modified: head/science/Makefile
==============================================================================
--- head/science/Makefile	Mon May 14 00:08:08 2018	(r469840)
+++ head/science/Makefile	Mon May 14 00:15:31 2018	(r469841)
@@ -165,6 +165,7 @@
     SUBDIR += psychopy
     SUBDIR += pulseview
     SUBDIR += py-DendroPy
+    SUBDIR += py-MDAnalysis
     SUBDIR += py-OpenFermion
     SUBDIR += py-cdo
     SUBDIR += py-coards

Added: head/science/py-MDAnalysis/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/py-MDAnalysis/Makefile	Mon May 14 00:15:31 2018	(r469841)
@@ -0,0 +1,31 @@
+# $FreeBSD$
+
+PORTNAME=	MDAnalysis
+DISTVERSION=	0.18.0
+CATEGORIES=	science python
+MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
+
+MAINTAINER=	yuri at FreeBSD.org
+COMMENT=	Python library to analyze molecular dynamics trajectories
+
+LICENSE=	GPLv2
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	${PYNUMPY}
+RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}biopython>=1.59:biology/py-biopython@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}duecredit>0:textproc/py-duecredit@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}GridDataFormats>=0.4.0:math/py-GridDataFormats@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}gsd>=1.4.0:science/py-gsd@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}joblib>0:devel/py-joblib@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>=1.5.1:math/py-matplotlib@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}mmtf-python>=1.0.0:science/py-mmtf-python@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}networkx>=1.0:math/py-networkx@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>0:science/py-scipy@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}six>=1.4.0:devel/py-six@${FLAVOR}
+
+USES=		python
+USE_PYTHON=	distutils autoplist
+
+.include <bsd.port.mk>

Added: head/science/py-MDAnalysis/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/py-MDAnalysis/distinfo	Mon May 14 00:15:31 2018	(r469841)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1526244200
+SHA256 (MDAnalysis-0.18.0.tar.gz) = a08acea1755112411e7db55e3f282e164b47a59e15794b38744cce6c596f252a
+SIZE (MDAnalysis-0.18.0.tar.gz) = 11085390

Added: head/science/py-MDAnalysis/files/patch-setup.py
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/py-MDAnalysis/files/patch-setup.py	Mon May 14 00:15:31 2018	(r469841)
@@ -0,0 +1,11 @@
+--- setup.py.orig	2018-05-13 20:38:06 UTC
++++ setup.py
+@@ -253,7 +253,7 @@ def extensions(config):
+     use_cython = config.get('use_cython', default=not is_release)
+     use_openmp = config.get('use_openmp', default=True)
+ 
+-    extra_compile_args = ['-std=c99', '-ffast-math', '-O3', '-funroll-loops']
++    extra_compile_args = ['-std=c99', '-ffast-math', '-funroll-loops']
+     define_macros = []
+     if config.get('debug_cflags', default=False):
+         extra_compile_args.extend(['-Wall', '-pedantic'])

Added: head/science/py-MDAnalysis/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/py-MDAnalysis/pkg-descr	Mon May 14 00:15:31 2018	(r469841)
@@ -0,0 +1,6 @@
+MDAnalysis is an object-oriented Python library to analyze trajectories from
+molecular dynamics (MD) simulations in many popular formats. It can write most
+of these formats, too, together with atom selections suitable for visualization
+or native analysis tools.
+
+WWW: https://www.mdanalysis.org