Py3

[jmrohwer]

Python 3 port

What works

The Python 3 port is complete as far as I can see and test:

• all built-in tests pass, on Windows and Linux, on both Python 2.7 and 3.6
• matplotlib interaction works
• the parallel scanning stuff works (using both multiprocessing and ipcluster)
• SBML export and import works as previously

Distribution and packaging

• The same code, i.e. HEAD of this branch, compiles under Python 2.7 and 3.6 and 3.7 (tested under Linux and Windows, both 32-bit and 64-bit). It can thus serve as unified code base and serve as basis for further development under Python 3. No need to maintain a separate Python 2 branch.
• I have built wheels under Windows and Linux (32 and 64-bit). When installed into a clean virtual environment on the respective OS, everything works and all tests pass. Dependencies (numpy, scipy, matplotlib) are pulled in automatically.

Not tested

• The stuff I never use, e.g. SBW integration, Kraken, Visualise.
• Building under Anaconda (either Win or Linux) - I'll leave this to you Brett, as I don't have it currently set up.

Way forward

• To test the building of wheels, I've bumped the version to 0.9.7 on this branch. However, this version has not been officially released nor uploaded to PyPi.
• This needs more extensive testing. I'll ask my own group to do so. Please do the same - the more the better.
• Once we are satisfied, I suggest releasing a new version that then supports Python 2.7 and 3.6+. This would finally warrant a version bump to 1.0.
• The branch won't automatically merge into master, but
  • the only real changes were to .gitignore which can be merged by hand (or just use the one on this branch);
  • I also converted all source file line endings to UNIX on the master branch (to allow easier code compare between master and Py3.

[jmrohwer]

I see that to properly review this I might have to revert 197e666b on master (Unix line endings) as it seems to have picked up that the whole file has changed by doing this... Should be no issue though.

On second reflection, the issue may also be that the 2to3 script converted all files to Unix endings (a8a3c9a), so that the actual editing changes are not reflected here (only for the files that were in Unix format to start off with). Not sure what the best way is to deal with this, unless we simply make this the new master branch.

[jmrohwer]

Wheels have been uploaded to https://test.pypi.org for easy installation and testing (binary wheels for win32, winx86_64, linux32 and linux64, for Mac OSX the source tarball will be downloaded and compiled). Install with:
pip install -i https://test.pypi.org/simple pysces