[moose-devel] [PATCH 00/19] make moose module Python 3 compatible

[Zbigniew Jędrzejewski-S. <zb...@in...>]

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