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Re: [moose-devel] [PATCH 00/19] make moose module Python 3 compatible
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From: Subhasis R. <ray...@gm...> - 2014-04-02 06:25:57
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Hi, Thanks for your contribution to the project. I should point out that (1) the buildQ branch is outdated and it will be better to put your efforts on async13 branch which is the current one. (2) rather than sending patches, create your own branch on sourceforge repo and do the modifications there and once tested ok, merge it to the common branch. Please let me know your sourceforge id and I shall add you to the developer's list. Best, - Subhasis ( ʃʊbʱaːʃɪʃ ) On Wed, Apr 2, 2014 at 2:20 AM, Zbigniew Jędrzejewski-Szmek < zb...@in...> wrote: > Hi, > > Since this is my first post to the list, let me start with an > introduction: I work in the Computational and Experimental > Neuroplasticity Laboratory directed by dr. Avrama Blackwell. > > We are currently using a MOOSE model created in Python to fit model > parameters to experimental data registered in the lab, with promising > results. Following patches allow the MOOSE module to be used from > Python 3. They are based on the buildQ branch. > > Just the module is modified, the GUI parts are still Python 2 only. > > The following approach is taken: code is tweaked to use a common > subset of Python 2 and 3. More specifically, it is made compatible > with Python 2.7 and Python 3.3 or later. In a few unavoidable places, > like the module initialization in the C++ code, separate branches in > #ifdefs are used. In the Python part, some compatiblity imports (in > _compat.py) are used to "wrap" the remaining differences. This (using > the exact same code under both Python 2 and 3) seems to be nicest way > to do the conversion. > > I haven't done very extensive testing, but at least our model seems to > return identical results under Python 2 and 3. > > I hope posting patches to the mailing list the proper way to submit > changes... If no, please let me know. > > Regards, > Zbigniew Jędrzejewski-Szmek > > > Zbigniew Jędrzejewski-Szmek (19): > Add gitignore > Declare that deprecated Numpy API will not be used > Fix warnings about deprecated cast to char* > Use pkg-config for Python compliation flags > Makefile: simplify detection of python flags > Fix compilation under Python 3 > Convert to print() > Apply has_key fixer > Convert to modern raise syntax > Apply except fixer > Remove some unnecessary .keys() and list() calls > Convert to incremental zip, map, filter > Add compatiblity layer for basestr and unicode > Remove unused import > Apply imports fixer > Convert to relative imports > Remove old separate Python 3 code > Make sure classes have __module__ set > Add missing space in output > > .gitignore | 7 + > Makefile | 31 +-- > gui/shell.py | 2 +- > pymoose/ematrix.cpp | 18 +- > pymoose/melement.cpp | 2 + > pymoose/mfield.cpp | 2 + > pymoose/moosemodule.cpp | 38 +++- > pymoose/moosemodule.h | 2 + > python/moose/_compat.py | 5 + > python/moose/alternate.py | 31 +-- > python/moose/graphutil.py | 4 +- > python/moose/hdfutil.py | 45 ++-- > python/moose/moose.py | 38 ++-- > python/moose/moose_py3k.py | 249 > --------------------- > python/moose/mtypes.py | 5 +- > python/moose/multiscale/core/mumbl.py | 14 +- > python/moose/multiscale/core/simulator.py | 6 +- > python/moose/multiscale/core/stimulus.py | 4 +- > python/moose/multiscale/core/types.py | 9 +- > python/moose/multiscale/helper/graph_methods.py | 4 +- > python/moose/multiscale/helper/moose_methods.py | 9 +- > .../neuroml/v1.8/GranuleCell/FvsI_Granule98.py | 5 +- > .../models/neuroml/v1.8/GranuleCell/Granule98.py | 7 +- > .../neuroml/v1.8/GranuleCell/Granule98_hsolve.py | 9 +- > .../moose/multiscale/multi_bhalla/diffusionOnly.py | 21 +- > python/moose/multiscale/multi_bhalla/lm2.py | 7 +- > python/moose/multiscale/multi_bhalla/loadMulti.py | 53 ++--- > python/moose/multiscale/multi_bhalla/minimal.py | 3 +- > python/moose/multiscale/multi_bhalla/runcell18.py | 16 +- > python/moose/multiscale/multi_bhalla/x_compt.py | 3 +- > python/moose/multiscale/parser/ChannelML.py | 12 +- > python/moose/multiscale/parser/MorphML.py | 6 +- > python/moose/multiscale/parser/NetworkML.py | 9 +- > python/moose/multiscale/parser/NeuroML.py | 6 +- > python/moose/multiscale/parser/parser.py | 2 +- > python/moose/multiscale/parser/utils.py | 3 +- > python/moose/neuroml/ChannelML.py | 27 +-- > python/moose/neuroml/MorphML.py | 33 +-- > python/moose/neuroml/NetworkML.py | 23 +- > python/moose/neuroml/NeuroML.py | 13 +- > python/moose/neuroml/utils.py | 13 +- > python/moose/neuroml2/converter.py | 3 +- > python/moose/neuroml2/generated_neuroml.py | 160 ++++++------- > python/moose/neuroml2/hhfit.py | 2 +- > python/moose/neuroml2/reader.py | 26 ++- > python/moose/neuroml2/test_converter.py | 5 +- > python/moose/neuroml2/test_hhfit.py | 19 +- > python/moose/neuroml2/test_reader.py | 3 +- > python/moose/neuroml2/units.py | 5 +- > python/moose/recording.py | 10 +- > python/moose/utils.py | 58 ++--- > python/moose/xmls_to_network/.noweb/main.nw | 6 +- > python/moose/xmls_to_network/core/hhfit.py | 2 +- > python/moose/xmls_to_network/core/load_multi.py | 49 ++-- > python/moose/xmls_to_network/core/multiscale.py | 7 +- > .../moose/xmls_to_network/core/neuroml2_parser.py | 174 +++++++------- > .../moose/xmls_to_network/core/neuroml_to_moose.py | 31 ++- > .../moose/xmls_to_network/helper/graph_methods.py | 4 +- > python/moose/xmls_to_network/parser/nml_parser.py | 170 +++++++------- > .../generatedNEURON/NEURONUtils/NEURONSimUtils.py | 2 +- > .../NeuroMLUtils/NetworkMLHDF5Handler.py | 8 +- > .../generatedNEURON/NeuroMLUtils/NetworkMLNet.py | 5 +- > .../NeuroMLUtils/NetworkMLSaxHandler.py | 91 ++++---- > .../twoNeurons/generatedNEURON/twoNeurons.hoc | 4 +- > .../NeuroMLUtils/NetworkMLHDF5Handler.py | 8 +- > .../generatedPyNN/NeuroMLUtils/NetworkMLNet.py | 5 +- > .../NeuroMLUtils/NetworkMLSaxHandler.py | 85 +++---- > .../twoNeurons/generatedPyNN/PyNNUtils/Pop.py | 13 +- > .../generatedPyNN/PyNNUtils/PyNNUtils.py | 11 +- > 69 files changed, 791 insertions(+), 971 deletions(-) > create mode 100644 .gitignore > create mode 100644 python/moose/_compat.py > delete mode 100644 python/moose/moose_py3k.py > > -- > 1.8.5.3 > > > > ------------------------------------------------------------------------------ > _______________________________________________ > moose-devel mailing list > moo...@li... > https://lists.sourceforge.net/lists/listinfo/moose-devel > |
