Py2neo 3 compatibility

[veleritas]

I'm working on upgrading hetio to be compatible with py2neo 3. Since many parts of the rephetio pipeline use hetio, what do you think the easiest way would be to test them all?

So far I've managed to get hetio to load nodes into Neo4j 3.1.1.

[dhimmel]

I actually think it shouldn't be too hard. hetio/hetio/neo4j.py is the only module in hetio that imports py2neo and it's only used in a few functions:

• export_neo4j which will be the main function that needs to be upgraded
• the Creator class which calls a create method from py2neo
• permute_rel_type which is a cypher implementation of permutation that we've never used (instead we do the permutation in hetio.permute.

Other parts of the rephetio codebase may use py2neo directly, but I think you can just deal with any errors there as they arise. Luckily I think the py2neo upgrade is most likely to cause errors rather than silent bugs.

Happy to review any pull requests!

[dhimmel]

It's ideal if we can upgrade to py2neo 3 and then make a new hetio release. Therefore, you can choose your hetio release based on whether you want to use py2neo 2 or 3.

[veleritas]

I've forked hetio to my account, will install as recommended by cloning and doing a pip install -e .

After it seems that the new hetio plays nice with the pipeline, then I will make a pull request.

[veleritas]

If I want to add additional features to hetio such as having a progress bar (via tqdm) for the node and edge import steps, how would I specify that tqdm is a dependency of hetio?

[dhimmel]

how would I specify that tqdm is a dependency of hetio?

You can add an install_requires in setup.py. See example here.

Currently, I didn't put pandas or py2neo as dependencies although arguable they should be. Or we could put these packages in extras_require.

One option for the progress bar is that you can try to import tqdm. If it fails continue without if that's not too hard to implement. Otherwise, you can just make the progress bar always on.

[veleritas]

I've made some small modifications to hetio and opened up a pull request!