Remove ensmallen & embiggen from requirements

[kevinschaper]

This pulls the specific requirements off, and lets them come in via grape.

I initially started by updating embiggen and ensmallen, so there's some lock file updates that might be unnecessary, but hopefully not a problem.

[caufieldjh]

Should resolve downstream dependency incompatibility, e.g. monarch-initiative/monarch-app#43

[caufieldjh]

Ah, right, that's why ensmallen was explicitly included:

  • Installing ensmallen (0.8.36)

  RuntimeError

  Unable to find installation candidates for ensmallen (0.8.36)

  at ~/.local/venv/lib/python3.9/site-packages/poetry/installation/chooser.py:105 in choose_for
      101│ 
      102│             links.append(link)
      103│ 
      104│         if not links:
    → 105│             raise RuntimeError(f"Unable to find installation candidates for {package}")
      106│ 
      107│         # Get the best link
      108│         chosen = max(links, key=lambda link: self._sort_key(package, link))
      109│ 

[kevinschaper]

👍

[caufieldjh]

Need to rebuild the poetry.lock to make this work - and for some reason that has taken >90 min and counting

[caufieldjh]

Ensmallen 0.8.35 has this issue: AnacletoLAB/ensmallen#192

[caufieldjh]

This works if ensmallen=0.8.36 is installed with pip, but not with poetry.

Even then, one of the tests fails:

_______________________________________________________________________________________ TestGrapeImplementation.test_all_by_all_pairwise_similarity ________________________________________________________________________________________

self = <tests.test_grape_implementation.TestGrapeImplementation testMethod=test_all_by_all_pairwise_similarity>

    def test_all_by_all_pairwise_similarity(self):
        """Verify that all by all pairwise similarity returns expected results."""
        oi = get_implementation_from_shorthand("grape:sqlite:obo:bfo")
        entities = list(oi.entities())
        tps = oi.all_by_all_pairwise_similarity(entities, entities)
>       self.assertEqual(540, len(list(tps)))
E       AssertionError: 540 != 237

tests/test_grape_implementation.py:96: AssertionError

[caufieldjh]

Now there seems to be some kind of dependency parsing issue - I suspect the mixture of installing packages through pip and through poetry is leading to some incongruency