Index: science/MOOSE-neural-simulator/Makefile =================================================================== --- /dev/null +++ science/MOOSE-neural-simulator/Makefile @@ -0,0 +1,44 @@ +# Created by: Yuri Victorovich +# $FreeBSD$ + +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 \ + libsz.so:science/szip \ + libsbml.so:biology/libsbml +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 Index: science/MOOSE-neural-simulator/distinfo =================================================================== --- /dev/null +++ science/MOOSE-neural-simulator/distinfo @@ -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 Index: science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py =================================================================== --- /dev/null +++ science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py @@ -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 Index: science/MOOSE-neural-simulator/pkg-descr =================================================================== --- /dev/null +++ science/MOOSE-neural-simulator/pkg-descr @@ -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 Index: science/MOOSE-neural-simulator/pkg-plist =================================================================== --- /dev/null +++ science/MOOSE-neural-simulator/pkg-plist @@ -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 Index: science/Makefile =================================================================== --- science/Makefile +++ science/Makefile @@ -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