Issue when trying to create Python3 bindings when using Python 3.7

[Andreas Tille]

Hi,

I intend to switch the Python bindings of the Debian packaged version of sbml to Python3.  In Debian the default Python3 version is 3.7.  When I try to build libsbml I'm running into

make[4]: Entering directory '/build/libsbml-5.17.0+dfsg/build'
[ 99%] Swig Python source
Traceback (most recent call last):
  File "/usr/lib/python3.7/sre_parse.py", line 1021, in parse_template
    this = chr(ESCAPES[this][1])
KeyError: '\\s'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/build/libsbml-5.17.0+dfsg/src/bindings/python/../swig/swigdoc.py", line 1924, in <module>
    main(sys.argv)
  File "/build/libsbml-5.17.0+dfsg/src/bindings/python/../swig/swigdoc.py", line 1881, in main
    processFile(file, stream, language, preprocessor_defines)
  File "/build/libsbml-5.17.0+dfsg/src/bindings/python/../swig/swigdoc.py", line 1697, in processFile
    processFunctions(ostream, header.functions)
  File "/build/libsbml-5.17.0+dfsg/src/bindings/python/../swig/swigdoc.py", line 1673, in processFunctions
    ostream.write(generateFunctionDocString(f.name, f.docstring, f.args, f.isInternal,f))
  File "/build/libsbml-5.17.0+dfsg/src/bindings/python/../swig/swigdoc.py", line 1617, in generateFunctionDocString
    doc = rewriteDocstringForPython(docstring)
  File "/build/libsbml-5.17.0+dfsg/src/bindings/python/../swig/swigdoc.py", line 1397, in rewriteDocstringForPython
    docstring = translateAllowingBreaks(breakable_translations, docstring)
  File "/build/libsbml-5.17.0+dfsg/src/bindings/python/../swig/swigdoc.py", line 816, in translateAllowingBreaks
    new_pattern = re.sub(' ', r'\s+\*?\s*', pair[0])
  File "/usr/lib/python3.7/re.py", line 192, in sub
    return _compile(pattern, flags).sub(repl, string, count)
  File "/usr/lib/python3.7/re.py", line 309, in _subx
    template = _compile_repl(template, pattern)
  File "/usr/lib/python3.7/re.py", line 300, in _compile_repl
    return sre_parse.parse_template(repl, pattern)
  File "/usr/lib/python3.7/sre_parse.py", line 1024, in parse_template
    raise s.error('bad escape %s' % this, len(this))
re.error: bad escape \s at position 0
make[4]: *** [src/bindings/python/CMakeFiles/binding_python_swig.dir/build.make:618: src/bindings/python/libsbml_wrap.cpp] Error 1

Any idea how to deal with this?

Kind regards, Andreas.

[Michael Hucka]

Hi,

There is indeed a problem with 5.17, and we are right in the process
(this week) of producing a release of 5.18 (experimental) with a fix for
supporting Python 3.7. If you can afford to wait a few days, this will
be available very soon.

MH

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[Andreas Tille]

Hi,

thanks, yes, I can wait.  I'd happily do some test build on Debian in case this might help.

Kind regards, Andreas.

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[Keating, Sarah M.]

Just to note that the release will be 5.17.2-experimental :-)

Sarah

[Michael Hucka]

Whoops, sorry about that! Thanks for catching my error.

MH