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Date:      Tue, 19 Dec 2017 16:04:34 +0000 (UTC)
From:      Yuri Victorovich <yuri@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r456732 - in head/science: . MOOSE-neural-simulator MOOSE-neural-simulator/files
Message-ID:  <201712191604.vBJG4Ysl088850@repo.freebsd.org>

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Author: yuri
Date: Tue Dec 19 16:04:34 2017
New Revision: 456732
URL: https://svnweb.freebsd.org/changeset/ports/456732

Log:
  New port: science/MOOSE-neural-simulator: Multiphysics Object Oriented Simulation Environment
  
  Multiphysics Object Oriented Simulation Environment
  
  MOOSE-neural-simulator allows to simulate
  - chemical and biochemical reactions
  - networks of neurons
  - neural networks
  
  This project is commonly referred to as MOOSE, in the capitalized form.
  There is another science project called MOOSE, completely unrelated to this one, which will also be ported.
  MOOSE-neural-simulator is a candidate for the future 'chemistry' category in case it will be approved.
  
  Approved by:	adamw (mentor)
  Differential Revision:	https://reviews.freebsd.org/D13539

Added:
  head/science/MOOSE-neural-simulator/
  head/science/MOOSE-neural-simulator/Makefile   (contents, props changed)
  head/science/MOOSE-neural-simulator/distinfo   (contents, props changed)
  head/science/MOOSE-neural-simulator/files/
  head/science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py   (contents, props changed)
  head/science/MOOSE-neural-simulator/pkg-descr   (contents, props changed)
  head/science/MOOSE-neural-simulator/pkg-plist   (contents, props changed)
Modified:
  head/science/Makefile

Added: head/science/MOOSE-neural-simulator/Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/MOOSE-neural-simulator/Makefile	Tue Dec 19 16:04:34 2017	(r456732)
@@ -0,0 +1,44 @@
+# Created by: Yuri Victorovich <yuri@FreeBSD.org>
+# $FreeBSD$
+
+PORTNAME=	MOOSE-neural-simulator
+DISTVERSION=	3.1.2
+DISTVERSIONSUFFIX=	-382-gc93d23a
+CATEGORIES=	science biology
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Multiphysics Object Oriented Simulation Environment
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENCE
+
+LIB_DEPENDS=	libgsl.so:math/gsl \
+		libhdf5.so:science/hdf5 \
+		libsbml.so:biology/libsbml \
+		libsz.so:science/szip
+BUILD_DEPENDS=	bash:shells/bash \
+		${PYNUMPY}
+RUN_DEPENDS=	${PYNUMPY} \
+		${PYTHON_PKGNAMEPREFIX}matplotlib>=1.1.0:math/py-matplotlib@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}networkx>=1.0:math/py-networkx@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}pygraphviz>=0:graphics/py-pygraphviz@${PY_FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}suds-jurko>=0.4:net/py-suds-jurko@${PY_FLAVOR}
+
+USES=		cmake:outsource fortran gettext-runtime pyqt:4 python
+USE_GITHUB=	yes
+GH_ACCOUNT=	BhallaLab
+GH_PROJECT=	moose
+USE_PYQT=	core_run gui_run test_run
+
+OPTIONS_DEFINE=	EXAMPLES
+
+PORTEXAMPLES=	*
+
+post-patch:
+	@${REINPLACE_CMD} -e 's|DESTINATION lib/moose/moose-examples|DESTINATION share/examples/${PORTNAME}|' ${WRKSRC}/CMakeLists.txt
+	@${REINPLACE_CMD} -e 's|\.\./moose-examples/|${EXAMPLESDIR}/|' ${WRKSRC}/moose-gui/mgui.py
+
+post-install:
+	@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/moose/_moose.so
+
+.include <bsd.port.mk>

Added: head/science/MOOSE-neural-simulator/distinfo
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/MOOSE-neural-simulator/distinfo	Tue Dec 19 16:04:34 2017	(r456732)
@@ -0,0 +1,3 @@
+TIMESTAMP = 1513628618
+SHA256 (BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz) = d338ba3b01b1569603dd5c6f12d47c576daf04323b845263ea968d2ab3bab47d
+SIZE (BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz) = 20350741

Added: head/science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py	Tue Dec 19 16:04:34 2017	(r456732)
@@ -0,0 +1,10 @@
+--- moose-gui/mgui.py.orig	2017-12-16 19:10:20 UTC
++++ moose-gui/mgui.py
+@@ -44,6 +44,7 @@
+ #
+ 
+ # Code:
++import numpy.core.multiarray # doesn't work without it for some reason
+ import imp
+ import inspect
+ import code

Added: head/science/MOOSE-neural-simulator/pkg-descr
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/MOOSE-neural-simulator/pkg-descr	Tue Dec 19 16:04:34 2017	(r456732)
@@ -0,0 +1,10 @@
+MOOSE is designed to simulate neural systems ranging from biochemical signaling
+to complex models of single neurons, circuits, and large networks. A typical
+use case is to model neural activity-driven synaptic plasticity, in which
+network activity to synapses triggers biochemical reaction-diffusion events,
+which in turn modulate ion channels to give rise to synaptic plasticity.
+MOOSE can operate at many levels of detail, from stochastic chemical
+computations, to multicompartment single-neuron models, to spiking neuron
+network models.
+
+WWW: http://moose.ncbs.res.in

Added: head/science/MOOSE-neural-simulator/pkg-plist
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/science/MOOSE-neural-simulator/pkg-plist	Tue Dec 19 16:04:34 2017	(r456732)
@@ -0,0 +1,204 @@
+bin/moosegui
+lib/moose/gui/.travis.yml
+lib/moose/gui/MdiArea.py
+lib/moose/gui/PlotWidgetContainer.py
+lib/moose/gui/README
+lib/moose/gui/README.md
+lib/moose/gui/RunWidget.py
+lib/moose/gui/SettingsDialog.py
+lib/moose/gui/__init__.py
+lib/moose/gui/about.html
+lib/moose/gui/bioModels/getAllCuratedModelsId.pkl
+lib/moose/gui/bioModels/getModelsIdByChEBI.pkl
+lib/moose/gui/bioModels/getModelsIdByChEBIId.pkl
+lib/moose/gui/biomodelsclient.py
+lib/moose/gui/checkcombobox.py
+lib/moose/gui/colormaps/fire
+lib/moose/gui/colormaps/greenfire
+lib/moose/gui/colormaps/grey
+lib/moose/gui/colormaps/heat
+lib/moose/gui/colormaps/jet
+lib/moose/gui/colormaps/rainbow2.pkl
+lib/moose/gui/colormaps/redhot
+lib/moose/gui/config.py
+lib/moose/gui/configwidget.py
+lib/moose/gui/defaults.py
+lib/moose/gui/global_constants.py
+lib/moose/gui/icons/QMdiBackground.png
+lib/moose/gui/icons/add.png
+lib/moose/gui/icons/add_graph.png
+lib/moose/gui/icons/arrow.png
+lib/moose/gui/icons/arrow_undo.png
+lib/moose/gui/icons/classIcon/BufPool.png
+lib/moose/gui/icons/classIcon/CubeMesh.png
+lib/moose/gui/icons/classIcon/CylMesh.png
+lib/moose/gui/icons/classIcon/Enz.png
+lib/moose/gui/icons/classIcon/FuncPool.png
+lib/moose/gui/icons/classIcon/Function.png
+lib/moose/gui/icons/classIcon/MMenz.png
+lib/moose/gui/icons/classIcon/Pool.png
+lib/moose/gui/icons/classIcon/Reac.png
+lib/moose/gui/icons/classIcon/StimulusTable.png
+lib/moose/gui/icons/classIcon/SumFunc.png
+lib/moose/gui/icons/clone.svg
+lib/moose/gui/icons/connection.png
+lib/moose/gui/icons/continue.png
+lib/moose/gui/icons/delete.svg
+lib/moose/gui/icons/delete_graph.png
+lib/moose/gui/icons/grid.png
+lib/moose/gui/icons/hand.png
+lib/moose/gui/icons/help.png
+lib/moose/gui/icons/hopfield.png
+lib/moose/gui/icons/list.png
+lib/moose/gui/icons/moose_icon.png
+lib/moose/gui/icons/moose_icon_64x64.png
+lib/moose/gui/icons/moose_icon_large.png
+lib/moose/gui/icons/move.svg
+lib/moose/gui/icons/plot.svg
+lib/moose/gui/icons/reset.png
+lib/moose/gui/icons/run.png
+lib/moose/gui/icons/runtime.png
+lib/moose/gui/icons/squid.png
+lib/moose/gui/icons/stop.png
+lib/moose/gui/icons/straight_connector_with_filled_circles.png
+lib/moose/gui/icons/wrench.png
+lib/moose/gui/loaderdialog.py
+lib/moose/gui/mexception.py
+lib/moose/gui/mgui.py
+lib/moose/gui/mload.py
+lib/moose/gui/mplot.py
+lib/moose/gui/mplugin.py
+lib/moose/gui/msearch.py
+lib/moose/gui/mtoolbutton.py
+lib/moose/gui/mtree.py
+lib/moose/gui/mtypes.py
+lib/moose/gui/neuroextractor.py
+lib/moose/gui/newmodeldialog.py
+lib/moose/gui/objectedit.py
+lib/moose/gui/plugins/NeuroKit.py
+lib/moose/gui/plugins/NeuroKitEditor.py
+lib/moose/gui/plugins/NeuroKitRunner.py
+lib/moose/gui/plugins/NeuroKitVisualizer.py
+lib/moose/gui/plugins/PreferencesPresenter.py
+lib/moose/gui/plugins/PreferencesView.py
+lib/moose/gui/plugins/README
+lib/moose/gui/plugins/Runner.py
+lib/moose/gui/plugins/__init__.py
+lib/moose/gui/plugins/buildkkit.py
+lib/moose/gui/plugins/constants.py
+lib/moose/gui/plugins/datastore/preferences.json
+lib/moose/gui/plugins/default.py
+lib/moose/gui/plugins/defines.py
+lib/moose/gui/plugins/kkit.py
+lib/moose/gui/plugins/kkitCalcArrow.py
+lib/moose/gui/plugins/kkitOrdinateUtil.py
+lib/moose/gui/plugins/kkitQGraphics.py
+lib/moose/gui/plugins/kkitUtil.py
+lib/moose/gui/plugins/kkitViewcontrol.py
+lib/moose/gui/plugins/list.txt
+lib/moose/gui/plugins/modelBuild.py
+lib/moose/gui/plugins/setsolver.py
+lib/moose/gui/plugins/test_plotwidget.py
+lib/moose/gui/scishell.py
+lib/moose/gui/shell.py
+lib/moose/gui/sidebar.py
+lib/moose/gui/suds/__init__.py
+lib/moose/gui/suds/argparser.py
+lib/moose/gui/suds/bindings/__init__.py
+lib/moose/gui/suds/bindings/binding.py
+lib/moose/gui/suds/bindings/document.py
+lib/moose/gui/suds/bindings/multiref.py
+lib/moose/gui/suds/bindings/rpc.py
+lib/moose/gui/suds/builder.py
+lib/moose/gui/suds/cache.py
+lib/moose/gui/suds/client.py
+lib/moose/gui/suds/metrics.py
+lib/moose/gui/suds/mx/__init__.py
+lib/moose/gui/suds/mx/appender.py
+lib/moose/gui/suds/mx/basic.py
+lib/moose/gui/suds/mx/core.py
+lib/moose/gui/suds/mx/encoded.py
+lib/moose/gui/suds/mx/literal.py
+lib/moose/gui/suds/mx/typer.py
+lib/moose/gui/suds/options.py
+lib/moose/gui/suds/plugin.py
+lib/moose/gui/suds/properties.py
+lib/moose/gui/suds/reader.py
+lib/moose/gui/suds/resolver.py
+lib/moose/gui/suds/sax/__init__.py
+lib/moose/gui/suds/sax/attribute.py
+lib/moose/gui/suds/sax/date.py
+lib/moose/gui/suds/sax/document.py
+lib/moose/gui/suds/sax/element.py
+lib/moose/gui/suds/sax/enc.py
+lib/moose/gui/suds/sax/parser.py
+lib/moose/gui/suds/sax/text.py
+lib/moose/gui/suds/servicedefinition.py
+lib/moose/gui/suds/serviceproxy.py
+lib/moose/gui/suds/soaparray.py
+lib/moose/gui/suds/store.py
+lib/moose/gui/suds/sudsobject.py
+lib/moose/gui/suds/transport/__init__.py
+lib/moose/gui/suds/transport/http.py
+lib/moose/gui/suds/transport/https.py
+lib/moose/gui/suds/transport/options.py
+lib/moose/gui/suds/umx/__init__.py
+lib/moose/gui/suds/umx/attrlist.py
+lib/moose/gui/suds/umx/basic.py
+lib/moose/gui/suds/umx/core.py
+lib/moose/gui/suds/umx/encoded.py
+lib/moose/gui/suds/umx/typed.py
+lib/moose/gui/suds/version.py
+lib/moose/gui/suds/wsdl.py
+lib/moose/gui/suds/wsse.py
+lib/moose/gui/suds/xsd/__init__.py
+lib/moose/gui/suds/xsd/deplist.py
+lib/moose/gui/suds/xsd/doctor.py
+lib/moose/gui/suds/xsd/query.py
+lib/moose/gui/suds/xsd/schema.py
+lib/moose/gui/suds/xsd/sxbase.py
+lib/moose/gui/suds/xsd/sxbasic.py
+lib/moose/gui/suds/xsd/sxbuiltin.py
+lib/moose/gui/utils.py
+%%PYTHON_SITELIBDIR%%/moose-3.2.git-py%%PYTHON_VER%%.egg-info
+%%PYTHON_SITELIBDIR%%/moose/OrderedDict.py
+%%PYTHON_SITELIBDIR%%/moose/SBML/__init__.py
+%%PYTHON_SITELIBDIR%%/moose/SBML/readSBML.py
+%%PYTHON_SITELIBDIR%%/moose/SBML/validation.py
+%%PYTHON_SITELIBDIR%%/moose/SBML/writeSBML.py
+%%PYTHON_SITELIBDIR%%/moose/__init__.py
+%%PYTHON_SITELIBDIR%%/moose/_moose.so
+%%PYTHON_SITELIBDIR%%/moose/alternate.py
+%%PYTHON_SITELIBDIR%%/moose/chemMerge/__init__.py
+%%PYTHON_SITELIBDIR%%/moose/chemMerge/merge.py
+%%PYTHON_SITELIBDIR%%/moose/chemMerge/mtypes.py
+%%PYTHON_SITELIBDIR%%/moose/chemUtil/__init__.py
+%%PYTHON_SITELIBDIR%%/moose/chemUtil/add_Delete_ChemicalSolver.py
+%%PYTHON_SITELIBDIR%%/moose/chemUtil/chemConnectUtil.py
+%%PYTHON_SITELIBDIR%%/moose/chemUtil/graphUtils.py
+%%PYTHON_SITELIBDIR%%/moose/constants.py
+%%PYTHON_SITELIBDIR%%/moose/genesis/__init__.py
+%%PYTHON_SITELIBDIR%%/moose/genesis/writeKkit.py
+%%PYTHON_SITELIBDIR%%/moose/graph_utils.py
+%%PYTHON_SITELIBDIR%%/moose/graphutil.py
+%%PYTHON_SITELIBDIR%%/moose/hdfutil.py
+%%PYTHON_SITELIBDIR%%/moose/methods_utils.py
+%%PYTHON_SITELIBDIR%%/moose/moose.py
+%%PYTHON_SITELIBDIR%%/moose/moose_config.py
+%%PYTHON_SITELIBDIR%%/moose/moose_constants.py
+%%PYTHON_SITELIBDIR%%/moose/moose_test.py
+%%PYTHON_SITELIBDIR%%/moose/neuroml/ChannelML.py
+%%PYTHON_SITELIBDIR%%/moose/neuroml/MorphML.py
+%%PYTHON_SITELIBDIR%%/moose/neuroml/NetworkML.py
+%%PYTHON_SITELIBDIR%%/moose/neuroml/NeuroML.py
+%%PYTHON_SITELIBDIR%%/moose/neuroml/__init__.py
+%%PYTHON_SITELIBDIR%%/moose/neuroml/utils.py
+%%PYTHON_SITELIBDIR%%/moose/optimizer_interface.py
+%%PYTHON_SITELIBDIR%%/moose/plot_utils.py
+%%PYTHON_SITELIBDIR%%/moose/print_utils.py
+%%PYTHON_SITELIBDIR%%/moose/recording.py
+%%PYTHON_SITELIBDIR%%/moose/utils.py
+%%PYTHON_SITELIBDIR%%/rdesigneur/__init__.py
+%%PYTHON_SITELIBDIR%%/rdesigneur/rdesigneur.py
+%%PYTHON_SITELIBDIR%%/rdesigneur/rdesigneurProtos.py
+%%PYTHON_SITELIBDIR%%/rdesigneur/rmoogli.py

Modified: head/science/Makefile
==============================================================================
--- head/science/Makefile	Tue Dec 19 16:03:32 2017	(r456731)
+++ head/science/Makefile	Tue Dec 19 16:04:34 2017	(r456732)
@@ -6,6 +6,7 @@
     SUBDIR += 2d-rewriter
     SUBDIR += ALPSCore
     SUBDIR += InsightToolkit
+    SUBDIR += MOOSE-neural-simulator
     SUBDIR += PETSc
     SUBDIR += R-cran-AMORE
     SUBDIR += R-cran-DCluster



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