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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