svn commit: r456732 - in head/science: . MOOSE-neural-simulator MOOSE-neural-simulator/files
Yuri Victorovich
yuri at FreeBSD.org
Tue Dec 19 16:04:36 UTC 2017
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 at FreeBSD.org>
+# $FreeBSD$
+
+PORTNAME= MOOSE-neural-simulator
+DISTVERSION= 3.1.2
+DISTVERSIONSUFFIX= -382-gc93d23a
+CATEGORIES= science biology
+
+MAINTAINER= yuri at 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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