Find/create Python combine archive tool

[MichaelClerx]

Requirements:

• Reading
• Writing
• Extensible with our own combine format variations

See #23

Step 1: Evaluate https://github.com/FreakyBytes/pyCombineArchive

[jonc125]

Thoughts on https://github.com/FreakyBytes/pyCombineArchive :

• Basically a one-person show from the Rostock group
• Does have tests, using unittest, but no CI
• Uses a custom zipfile module to support deleting files from archives
• Isn't on PyPI
• Is described as very beta, "would not recommend to use this library for anything else than testing"
• BSD 3-clause licence
• Python 2 only
• Conclusion: would need lots of work to adopt and rework to be useful to the community

[jonc125]

Tellurium uses the Python bindings to libCombine, available as tecombine (0.2.2.1) and python-libcombine (0.2.1) from PyPI.

• Uses libSBML's XML parsing & SWIG: quite bulky!
• Bigger community and potential developer pool; Frank is good and responsive
• BSD 2-clause licence
• Slightly confusing packaging with 2 names at different versions! tecombine has wheels but seems to be deprecated? python-libcombine doesn't have wheels and is a lower version!
• There are Python examples used as (manual) tests; no CI
  • There are also Catch tests of the underlying C++ code. But still no CI as far as I can see
• There is API documentation
• Conclusion: not ideal, but probably a better option!

[jonc125]

pysces just has custom write code.

The Physiome Model Repository has an OMEX interface, but it's tightly coupled to the PMR2 codebase.

[jonc125]

Have also asked at https://groups.google.com/forum/?hl=en-GB#!topic/combine-archive/oRQCoZfUblY

[MichaelClerx]

Can't be that hard to build can it? I generate zip files in myokit all the time with no dependencies beyond python's standard library

[jonc125]

There are responses from the main library developers in the thread linked above now. As Michael says, a pure Python library for the functionality we actually need would probably be easy to write, but it might make sense to start with libCombine so we're being 'good citizens'! It did pip install for me, even if there weren't wheels available.

[MichaelClerx]

It does depend on libSBML for XML parsing though, bit overkill?

[jonc125]

Indeed, that is the downside! But if its API isn't too bad we can start there to get something running and switch to a light-weight Python alternative later. If the API is complex, it might be quicker just to write something ourselves...

[jonc125]

Had issues getting libCOMBINE to work in #47, so Helen has written our own thing for just what we need for now. Eventually we'll make this a standalone Python package, with the other features needed for #17 etc.

[jonc125]

Closing for now since we implement features we need as required. Can revisit if we decide to create a standalone library with others (e.g. PMR).