Index: head/science/MOOSE-neural-simulator/Makefile =================================================================== --- head/science/MOOSE-neural-simulator/Makefile (nonexistent) +++ head/science/MOOSE-neural-simulator/Makefile (revision 456732) @@ -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 \ + 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 Property changes on: head/science/MOOSE-neural-simulator/Makefile ___________________________________________________________________ Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:keywords ## -0,0 +1 ## +FreeBSD=%H \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/MOOSE-neural-simulator/distinfo =================================================================== --- head/science/MOOSE-neural-simulator/distinfo (nonexistent) +++ head/science/MOOSE-neural-simulator/distinfo (revision 456732) @@ -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 Property changes on: head/science/MOOSE-neural-simulator/distinfo ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py =================================================================== --- head/science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py (nonexistent) +++ head/science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py (revision 456732) @@ -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 Property changes on: head/science/MOOSE-neural-simulator/files/patch-moose-gui_mgui.py ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/MOOSE-neural-simulator/pkg-descr =================================================================== --- head/science/MOOSE-neural-simulator/pkg-descr (nonexistent) +++ head/science/MOOSE-neural-simulator/pkg-descr (revision 456732) @@ -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 Property changes on: head/science/MOOSE-neural-simulator/pkg-descr ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/MOOSE-neural-simulator/pkg-plist =================================================================== --- head/science/MOOSE-neural-simulator/pkg-plist (nonexistent) +++ head/science/MOOSE-neural-simulator/pkg-plist (revision 456732) @@ -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 Property changes on: head/science/MOOSE-neural-simulator/pkg-plist ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/Makefile =================================================================== --- head/science/Makefile (revision 456731) +++ head/science/Makefile (revision 456732) @@ -1,212 +1,213 @@ # $FreeBSD$ # COMMENT = Scientific ports SUBDIR += 2d-rewriter SUBDIR += ALPSCore SUBDIR += InsightToolkit + SUBDIR += MOOSE-neural-simulator SUBDIR += PETSc SUBDIR += R-cran-AMORE SUBDIR += R-cran-DCluster SUBDIR += R-cran-Epi SUBDIR += R-cran-bayesm SUBDIR += R-cran-cmprsk SUBDIR += R-cran-e1071 SUBDIR += R-cran-eco SUBDIR += R-cran-epicalc SUBDIR += R-cran-etm SUBDIR += R-cran-fastICA SUBDIR += R-cran-kernlab SUBDIR += R-cran-snow SUBDIR += R-cran-som SUBDIR += R-cran-udunits2 SUBDIR += afni SUBDIR += aircraft-datcom SUBDIR += avogadro SUBDIR += bddsolve SUBDIR += bft SUBDIR += bodr SUBDIR += brian SUBDIR += buddy SUBDIR += cdcl SUBDIR += cdf SUBDIR += cdo SUBDIR += cgnslib SUBDIR += cgribex SUBDIR += checkmol SUBDIR += chemical-mime-data SUBDIR += chemps2 SUBDIR += chemtool SUBDIR += chemtool-devel SUBDIR += clhep SUBDIR += colt SUBDIR += crf++ SUBDIR += dcl SUBDIR += devisor SUBDIR += dkh SUBDIR += dlpoly-classic SUBDIR += ecs SUBDIR += epte SUBDIR += erd SUBDIR += fastcap SUBDIR += fasthenry SUBDIR += fisicalab SUBDIR += fvcom SUBDIR += fvcom-mpi SUBDIR += fvm SUBDIR += gchemutils SUBDIR += gdma SUBDIR += getdp SUBDIR += ghemical SUBDIR += ghmm SUBDIR += gnudatalanguage SUBDIR += gramps SUBDIR += grib_api SUBDIR += gromacs SUBDIR += gsmc SUBDIR += gtamsanalyzer SUBDIR += gwyddion SUBDIR += h5utils SUBDIR += harminv SUBDIR += hdf SUBDIR += hdf5 SUBDIR += hdf5-18 SUBDIR += hs-bio SUBDIR += hypre SUBDIR += iboview SUBDIR += isaac-cfd SUBDIR += jstrack SUBDIR += kalzium SUBDIR += kst2 SUBDIR += lamprop SUBDIR += libaec SUBDIR += libctl SUBDIR += libefp SUBDIR += libgeodecomp SUBDIR += libghemical SUBDIR += libint SUBDIR += libkml SUBDIR += liblinear SUBDIR += liboglappth SUBDIR += libquantum SUBDIR += libsvm SUBDIR += libsvm-python SUBDIR += libxc SUBDIR += linsmith SUBDIR += massxpert SUBDIR += mbdyn SUBDIR += mcstas SUBDIR += mcstas-comps SUBDIR += mcxtrace SUBDIR += medit SUBDIR += meep SUBDIR += mei SUBDIR += metaf2xml SUBDIR += minc2 SUBDIR += mol2ps SUBDIR += mpb SUBDIR += mpqc SUBDIR += mpqc-mpich SUBDIR += ncs SUBDIR += netcdf SUBDIR += netcdf-cxx SUBDIR += netcdf-fortran SUBDIR += nifticlib SUBDIR += openbabel SUBDIR += openkim SUBDIR += orthanc SUBDIR += orthanc-dicomweb SUBDIR += orthanc-postgresql SUBDIR += orthanc-webviewer SUBDIR += p5-Algorithm-SVMLight SUBDIR += p5-Chemistry-3DBuilder SUBDIR += p5-Chemistry-Bond-Find SUBDIR += p5-Chemistry-Canonicalize SUBDIR += p5-Chemistry-Elements SUBDIR += p5-Chemistry-File-MDLMol SUBDIR += p5-Chemistry-File-Mopac SUBDIR += p5-Chemistry-File-PDB SUBDIR += p5-Chemistry-File-SLN SUBDIR += p5-Chemistry-File-SMARTS SUBDIR += p5-Chemistry-File-SMILES SUBDIR += p5-Chemistry-File-VRML SUBDIR += p5-Chemistry-File-XYZ SUBDIR += p5-Chemistry-FormulaPattern SUBDIR += p5-Chemistry-InternalCoords SUBDIR += p5-Chemistry-Isotope SUBDIR += p5-Chemistry-MacroMol SUBDIR += p5-Chemistry-MidasPattern SUBDIR += p5-Chemistry-Mok SUBDIR += p5-Chemistry-Mol SUBDIR += p5-Chemistry-Pattern SUBDIR += p5-Chemistry-Reaction SUBDIR += p5-Chemistry-Ring SUBDIR += p5-Geo-BUFR SUBDIR += p5-Geo-Coordinates-Converter SUBDIR += p5-Geo-Coordinates-Converter-iArea SUBDIR += p5-Geo-ReadGRIB SUBDIR += p5-Geo-WebService-Elevation-USGS SUBDIR += p5-Mcstas-Tools SUBDIR += p5-PerlMol SUBDIR += p5-Physics-Unit SUBDIR += paje SUBDIR += paraview SUBDIR += pcmsolver SUBDIR += pnetcdf SUBDIR += psychopy SUBDIR += pulseview SUBDIR += py-DendroPy SUBDIR += py-cdo SUBDIR += py-coards SUBDIR += py-h5py SUBDIR += py-hcluster SUBDIR += py-mdp SUBDIR += py-mlpy SUBDIR += py-netCDF4 SUBDIR += py-obspy SUBDIR += py-paida SUBDIR += py-pupynere SUBDIR += py-pyaixi SUBDIR += py-pydicom SUBDIR += py-pysal SUBDIR += py-pyteomics SUBDIR += py-pyteomics.biolccc SUBDIR += py-qspin SUBDIR += py-scikit-fuzzy SUBDIR += py-scikit-learn SUBDIR += py-scikit-sparse SUBDIR += py-scimath SUBDIR += py-scipy SUBDIR += py-scoria SUBDIR += py-tensorflow SUBDIR += py-ws2300 SUBDIR += pybrain SUBDIR += pycdf SUBDIR += pynn SUBDIR += qcl SUBDIR += qtresistors SUBDIR += rubygem-ai4r SUBDIR += rubygem-cdo SUBDIR += rubygem-ruby-dcl SUBDIR += rubygem-ruby-netcdf SUBDIR += sigrok-cli SUBDIR += sigrok-firmware SUBDIR += sigrok-firmware-fx2lafw SUBDIR += sigrok-firmware-utils SUBDIR += silo SUBDIR += simlib SUBDIR += simsmith SUBDIR += step SUBDIR += svmlight SUBDIR += szip SUBDIR += tfel SUBDIR += udunits SUBDIR += v_sim SUBDIR += veusz SUBDIR += vmd SUBDIR += voro++ SUBDIR += xfce4-equake-plugin SUBDIR += xmakemol .include