Chore/py3

[vpsx]

Update to python 3 yayayayay!!!

Regarding node level bug (see bug fixes section), see PXP-5067

Breaking Changes

• python 3!

Bug Fixes

• in test, guard case where right_val is list but left_val is None (should not attempt to sort left_val)
• propose fix for bug where node levels of leaf nodes are set to strings, in particular string reprs of edge table names

Improvements

• sort dependencies lexicographically
• use loose pins in setup.py
• rename confusing varname items_equal to items_not_equal
• initialize log level in the parent logger per cdislogging 1.0.0 breaking change
• promote idiomatic python by changing "type(v) is t" to "isinstance(v,t)"

Dependency updates

• require python 3
• bump dictionaryutils, gen3datamodel (fka gdcdatamodel), psqlgraph, psycopg2, pyspark, six
• remove indirect dependencies oauthlib, psutil, python_dateutil, pyyaml

[thanh-nguyen-dang]

I don't understand your comment here. Why do we need to change the logic here? what is the bug?

[vpsx]

@thanh-nguyen-dang, in response to your comments here and elsewhere, here is how you can reproduce the problem at hand:

1. Check out current Tube master branch (0.3.22)
2. Set up test database with tube/tests/metadata_db.sql; set up ES, run ETL
3. Add the following code to tube/etl/indexers/injection/nodes/collecting_node.py, in the __lt__ method of CollectingNode, before the return:

if isinstance(self.level, str) or isinstance(other.level, str):
    import pdb; pdb.set_trace()

4. Run unit tests to see if breakpoint is hit. Behold.
5. Inspect the values: type(self.level), type(other.level), type(self), type(other). You see that both are collecting nodes and that there occur several LT comparisons of int and string.
6. Observe that whereas in python 2 this Just Works, in python 3 this raises a type error.

As I said in the ticket, perhaps this is deliberate, but it is pretty idiosyncratic, and at any rate python 3 won't allow it.