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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
This commit is contained in:
Yuri Victorovich
parent
a4025d28ff
commit
e51eda6b05
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=456732
44
science/MOOSE-neural-simulator/Makefile
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44
science/MOOSE-neural-simulator/Makefile
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# Created by: Yuri Victorovich <yuri@FreeBSD.org>
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# $FreeBSD$
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PORTNAME= MOOSE-neural-simulator
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DISTVERSION= 3.1.2
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DISTVERSIONSUFFIX= -382-gc93d23a
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CATEGORIES= science biology
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MAINTAINER= yuri@FreeBSD.org
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COMMENT= Multiphysics Object Oriented Simulation Environment
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LICENSE= GPLv3
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LICENSE_FILE= ${WRKSRC}/LICENCE
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LIB_DEPENDS= libgsl.so:math/gsl \
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libhdf5.so:science/hdf5 \
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libsbml.so:biology/libsbml \
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libsz.so:science/szip
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BUILD_DEPENDS= bash:shells/bash \
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${PYNUMPY}
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RUN_DEPENDS= ${PYNUMPY} \
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${PYTHON_PKGNAMEPREFIX}matplotlib>=1.1.0:math/py-matplotlib@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}networkx>=1.0:math/py-networkx@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}pygraphviz>=0:graphics/py-pygraphviz@${PY_FLAVOR} \
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${PYTHON_PKGNAMEPREFIX}suds-jurko>=0.4:net/py-suds-jurko@${PY_FLAVOR}
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USES= cmake:outsource fortran gettext-runtime pyqt:4 python
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USE_GITHUB= yes
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GH_ACCOUNT= BhallaLab
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GH_PROJECT= moose
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USE_PYQT= core_run gui_run test_run
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OPTIONS_DEFINE= EXAMPLES
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PORTEXAMPLES= *
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post-patch:
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@${REINPLACE_CMD} -e 's|DESTINATION lib/moose/moose-examples|DESTINATION share/examples/${PORTNAME}|' ${WRKSRC}/CMakeLists.txt
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@${REINPLACE_CMD} -e 's|\.\./moose-examples/|${EXAMPLESDIR}/|' ${WRKSRC}/moose-gui/mgui.py
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post-install:
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@${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/moose/_moose.so
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.include <bsd.port.mk>
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3
science/MOOSE-neural-simulator/distinfo
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science/MOOSE-neural-simulator/distinfo
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TIMESTAMP = 1513628618
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SHA256 (BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz) = d338ba3b01b1569603dd5c6f12d47c576daf04323b845263ea968d2ab3bab47d
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SIZE (BhallaLab-moose-3.1.2-382-gc93d23a_GH0.tar.gz) = 20350741
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10
science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py
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science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py
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--- moose-gui/mgui.py.orig 2017-12-16 19:10:20 UTC
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+++ moose-gui/mgui.py
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@@ -44,6 +44,7 @@
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#
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# Code:
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+import numpy.core.multiarray # doesn't work without it for some reason
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import imp
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import inspect
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import code
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10
science/MOOSE-neural-simulator/pkg-descr
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science/MOOSE-neural-simulator/pkg-descr
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MOOSE is designed to simulate neural systems ranging from biochemical signaling
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to complex models of single neurons, circuits, and large networks. A typical
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use case is to model neural activity-driven synaptic plasticity, in which
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network activity to synapses triggers biochemical reaction-diffusion events,
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which in turn modulate ion channels to give rise to synaptic plasticity.
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MOOSE can operate at many levels of detail, from stochastic chemical
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computations, to multicompartment single-neuron models, to spiking neuron
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network models.
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WWW: http://moose.ncbs.res.in
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204
science/MOOSE-neural-simulator/pkg-plist
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204
science/MOOSE-neural-simulator/pkg-plist
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bin/moosegui
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lib/moose/gui/.travis.yml
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lib/moose/gui/MdiArea.py
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lib/moose/gui/PlotWidgetContainer.py
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lib/moose/gui/README
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lib/moose/gui/README.md
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lib/moose/gui/RunWidget.py
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lib/moose/gui/SettingsDialog.py
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lib/moose/gui/__init__.py
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lib/moose/gui/about.html
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lib/moose/gui/bioModels/getAllCuratedModelsId.pkl
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lib/moose/gui/bioModels/getModelsIdByChEBI.pkl
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lib/moose/gui/bioModels/getModelsIdByChEBIId.pkl
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lib/moose/gui/biomodelsclient.py
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lib/moose/gui/checkcombobox.py
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lib/moose/gui/colormaps/fire
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lib/moose/gui/colormaps/greenfire
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lib/moose/gui/colormaps/grey
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lib/moose/gui/colormaps/heat
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lib/moose/gui/colormaps/jet
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lib/moose/gui/colormaps/rainbow2.pkl
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lib/moose/gui/colormaps/redhot
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lib/moose/gui/config.py
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lib/moose/gui/configwidget.py
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lib/moose/gui/defaults.py
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lib/moose/gui/global_constants.py
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lib/moose/gui/icons/QMdiBackground.png
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lib/moose/gui/icons/add.png
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lib/moose/gui/icons/add_graph.png
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lib/moose/gui/icons/arrow.png
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lib/moose/gui/icons/arrow_undo.png
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lib/moose/gui/icons/classIcon/BufPool.png
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lib/moose/gui/icons/classIcon/CubeMesh.png
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lib/moose/gui/icons/classIcon/CylMesh.png
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lib/moose/gui/icons/classIcon/Enz.png
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lib/moose/gui/icons/classIcon/FuncPool.png
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lib/moose/gui/icons/classIcon/Function.png
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lib/moose/gui/icons/classIcon/MMenz.png
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lib/moose/gui/icons/classIcon/Pool.png
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lib/moose/gui/icons/classIcon/Reac.png
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lib/moose/gui/icons/classIcon/StimulusTable.png
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lib/moose/gui/icons/classIcon/SumFunc.png
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lib/moose/gui/icons/clone.svg
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lib/moose/gui/icons/connection.png
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lib/moose/gui/icons/continue.png
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lib/moose/gui/icons/delete.svg
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lib/moose/gui/icons/delete_graph.png
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lib/moose/gui/icons/grid.png
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lib/moose/gui/icons/hand.png
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lib/moose/gui/icons/help.png
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lib/moose/gui/icons/hopfield.png
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lib/moose/gui/icons/list.png
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lib/moose/gui/icons/moose_icon.png
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lib/moose/gui/icons/moose_icon_64x64.png
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lib/moose/gui/icons/moose_icon_large.png
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lib/moose/gui/icons/move.svg
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lib/moose/gui/icons/plot.svg
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lib/moose/gui/icons/reset.png
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lib/moose/gui/icons/run.png
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lib/moose/gui/icons/runtime.png
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lib/moose/gui/icons/squid.png
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lib/moose/gui/icons/stop.png
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lib/moose/gui/icons/straight_connector_with_filled_circles.png
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lib/moose/gui/icons/wrench.png
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lib/moose/gui/loaderdialog.py
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lib/moose/gui/mexception.py
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lib/moose/gui/mgui.py
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lib/moose/gui/mload.py
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lib/moose/gui/mplot.py
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lib/moose/gui/mplugin.py
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lib/moose/gui/msearch.py
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lib/moose/gui/mtoolbutton.py
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lib/moose/gui/mtree.py
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lib/moose/gui/mtypes.py
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lib/moose/gui/neuroextractor.py
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lib/moose/gui/newmodeldialog.py
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lib/moose/gui/objectedit.py
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lib/moose/gui/plugins/NeuroKit.py
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lib/moose/gui/plugins/NeuroKitEditor.py
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lib/moose/gui/plugins/NeuroKitRunner.py
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lib/moose/gui/plugins/NeuroKitVisualizer.py
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lib/moose/gui/plugins/PreferencesPresenter.py
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lib/moose/gui/plugins/PreferencesView.py
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lib/moose/gui/plugins/README
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lib/moose/gui/plugins/Runner.py
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lib/moose/gui/plugins/__init__.py
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lib/moose/gui/plugins/buildkkit.py
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lib/moose/gui/plugins/constants.py
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lib/moose/gui/plugins/datastore/preferences.json
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lib/moose/gui/plugins/default.py
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lib/moose/gui/plugins/defines.py
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lib/moose/gui/plugins/kkit.py
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lib/moose/gui/plugins/kkitCalcArrow.py
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lib/moose/gui/plugins/kkitOrdinateUtil.py
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lib/moose/gui/plugins/kkitQGraphics.py
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lib/moose/gui/plugins/kkitUtil.py
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lib/moose/gui/plugins/kkitViewcontrol.py
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lib/moose/gui/plugins/list.txt
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lib/moose/gui/plugins/modelBuild.py
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lib/moose/gui/plugins/setsolver.py
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lib/moose/gui/plugins/test_plotwidget.py
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lib/moose/gui/scishell.py
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lib/moose/gui/shell.py
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lib/moose/gui/sidebar.py
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lib/moose/gui/suds/__init__.py
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lib/moose/gui/suds/argparser.py
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lib/moose/gui/suds/bindings/__init__.py
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lib/moose/gui/suds/bindings/binding.py
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lib/moose/gui/suds/bindings/document.py
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lib/moose/gui/suds/bindings/multiref.py
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lib/moose/gui/suds/bindings/rpc.py
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lib/moose/gui/suds/builder.py
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lib/moose/gui/suds/cache.py
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lib/moose/gui/suds/client.py
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lib/moose/gui/suds/metrics.py
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lib/moose/gui/suds/mx/__init__.py
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lib/moose/gui/suds/mx/appender.py
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lib/moose/gui/suds/mx/basic.py
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lib/moose/gui/suds/mx/core.py
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lib/moose/gui/suds/mx/encoded.py
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lib/moose/gui/suds/mx/literal.py
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lib/moose/gui/suds/mx/typer.py
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lib/moose/gui/suds/options.py
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lib/moose/gui/suds/plugin.py
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lib/moose/gui/suds/properties.py
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lib/moose/gui/suds/reader.py
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lib/moose/gui/suds/resolver.py
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lib/moose/gui/suds/sax/__init__.py
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lib/moose/gui/suds/sax/attribute.py
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lib/moose/gui/suds/sax/date.py
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lib/moose/gui/suds/sax/document.py
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lib/moose/gui/suds/sax/element.py
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lib/moose/gui/suds/sax/enc.py
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lib/moose/gui/suds/sax/parser.py
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lib/moose/gui/suds/sax/text.py
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lib/moose/gui/suds/servicedefinition.py
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lib/moose/gui/suds/serviceproxy.py
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lib/moose/gui/suds/soaparray.py
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lib/moose/gui/suds/store.py
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lib/moose/gui/suds/sudsobject.py
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lib/moose/gui/suds/transport/__init__.py
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lib/moose/gui/suds/transport/http.py
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lib/moose/gui/suds/transport/https.py
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lib/moose/gui/suds/transport/options.py
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lib/moose/gui/suds/umx/__init__.py
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lib/moose/gui/suds/umx/attrlist.py
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lib/moose/gui/suds/umx/basic.py
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lib/moose/gui/suds/umx/core.py
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lib/moose/gui/suds/umx/encoded.py
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lib/moose/gui/suds/umx/typed.py
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lib/moose/gui/suds/version.py
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lib/moose/gui/suds/wsdl.py
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lib/moose/gui/suds/wsse.py
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lib/moose/gui/suds/xsd/__init__.py
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lib/moose/gui/suds/xsd/deplist.py
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lib/moose/gui/suds/xsd/doctor.py
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lib/moose/gui/suds/xsd/query.py
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lib/moose/gui/suds/xsd/schema.py
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lib/moose/gui/suds/xsd/sxbase.py
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lib/moose/gui/suds/xsd/sxbasic.py
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lib/moose/gui/suds/xsd/sxbuiltin.py
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lib/moose/gui/utils.py
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%%PYTHON_SITELIBDIR%%/moose-3.2.git-py%%PYTHON_VER%%.egg-info
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%%PYTHON_SITELIBDIR%%/moose/OrderedDict.py
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%%PYTHON_SITELIBDIR%%/moose/SBML/__init__.py
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%%PYTHON_SITELIBDIR%%/moose/SBML/readSBML.py
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%%PYTHON_SITELIBDIR%%/moose/SBML/validation.py
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%%PYTHON_SITELIBDIR%%/moose/SBML/writeSBML.py
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%%PYTHON_SITELIBDIR%%/moose/__init__.py
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%%PYTHON_SITELIBDIR%%/moose/_moose.so
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%%PYTHON_SITELIBDIR%%/moose/alternate.py
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%%PYTHON_SITELIBDIR%%/moose/chemMerge/__init__.py
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%%PYTHON_SITELIBDIR%%/moose/chemMerge/merge.py
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%%PYTHON_SITELIBDIR%%/moose/chemMerge/mtypes.py
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%%PYTHON_SITELIBDIR%%/moose/chemUtil/__init__.py
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%%PYTHON_SITELIBDIR%%/moose/chemUtil/add_Delete_ChemicalSolver.py
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%%PYTHON_SITELIBDIR%%/moose/chemUtil/chemConnectUtil.py
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%%PYTHON_SITELIBDIR%%/moose/chemUtil/graphUtils.py
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%%PYTHON_SITELIBDIR%%/moose/constants.py
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%%PYTHON_SITELIBDIR%%/moose/genesis/__init__.py
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%%PYTHON_SITELIBDIR%%/moose/genesis/writeKkit.py
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%%PYTHON_SITELIBDIR%%/moose/graph_utils.py
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%%PYTHON_SITELIBDIR%%/moose/graphutil.py
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%%PYTHON_SITELIBDIR%%/moose/hdfutil.py
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%%PYTHON_SITELIBDIR%%/moose/methods_utils.py
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%%PYTHON_SITELIBDIR%%/moose/moose.py
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%%PYTHON_SITELIBDIR%%/moose/moose_config.py
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%%PYTHON_SITELIBDIR%%/moose/moose_constants.py
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%%PYTHON_SITELIBDIR%%/moose/moose_test.py
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%%PYTHON_SITELIBDIR%%/moose/neuroml/ChannelML.py
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%%PYTHON_SITELIBDIR%%/moose/neuroml/MorphML.py
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%%PYTHON_SITELIBDIR%%/moose/neuroml/NetworkML.py
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%%PYTHON_SITELIBDIR%%/moose/neuroml/NeuroML.py
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%%PYTHON_SITELIBDIR%%/moose/neuroml/__init__.py
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%%PYTHON_SITELIBDIR%%/moose/neuroml/utils.py
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%%PYTHON_SITELIBDIR%%/moose/optimizer_interface.py
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%%PYTHON_SITELIBDIR%%/moose/plot_utils.py
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%%PYTHON_SITELIBDIR%%/moose/print_utils.py
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%%PYTHON_SITELIBDIR%%/moose/recording.py
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%%PYTHON_SITELIBDIR%%/moose/utils.py
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%%PYTHON_SITELIBDIR%%/rdesigneur/__init__.py
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%%PYTHON_SITELIBDIR%%/rdesigneur/rdesigneur.py
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%%PYTHON_SITELIBDIR%%/rdesigneur/rdesigneurProtos.py
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%%PYTHON_SITELIBDIR%%/rdesigneur/rmoogli.py
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@ -6,6 +6,7 @@
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SUBDIR += 2d-rewriter
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SUBDIR += ALPSCore
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SUBDIR += InsightToolkit
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SUBDIR += MOOSE-neural-simulator
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SUBDIR += PETSc
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SUBDIR += R-cran-AMORE
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SUBDIR += R-cran-DCluster
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