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Update alchemy gufe import - #102

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kaminow merged 1 commit into
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fix-101
Aug 26, 2025
Merged

Update alchemy gufe import#102
kaminow merged 1 commit into
mainfrom
fix-101

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@kaminow

@kaminow kaminow commented Aug 26, 2025

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A recent update to gufe changed where the JSONCodec class lives, update import to new location. Fixes #101.

@kaminow
kaminow requested a review from mariacm12 August 26, 2025 18:47

@mariacm12 mariacm12 left a comment

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Thanks! The import error is gone.
Non-blocking: Now there's another error:

 def test_plan_from_names(tyk2_ligands, tyk2_small_custom_network):
        """Make sure we can plan a network using the names of the ligands."""
        edges = extract_custom_ligand_network(tyk2_small_custom_network)
        planner = NetworkPlanner(network_planning_method=CustomNetworkPlanner(edges=edges))
        network = planner.generate_network(ligands=tyk2_ligands).to_ligand_network()
        # make sure the edges are as we expect
        for edge in network.edges:
>           assert (edge.componentA.name, edge.componentB.name) in edges
E           AssertionError: assert ('', '') in [('lig_ejm_46', 'lig_jmc_23'), ('lig_jmc_23', 'lig_jmc_28'), ('lig_ejm_31', 'lig_ejm_46')]

drugforge-alchemy/drugforge/alchemy/tests/test_fec_schema.py:117: AssertionError

And another with cinnabar on ubuntu:

E       AttributeError: 'FEMap' object has no attribute 'graph'

drugforge-alchemy/drugforge/alchemy/cli/utils.py:304: AttributeError

Not sure if we want to try and fix it in this PR or make a new one.

@kaminow

kaminow commented Aug 26, 2025

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I feel like those should probably go in a different PR, but I'll leave it up to you

@mariacm12

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I agree, I made a new issue for those two errors in #103. I think you should merge this one for now.

@kaminow
kaminow merged commit ec70f7e into main Aug 26, 2025
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@ijpulidos

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Just for future reference, this needed to update the pins on the gufe requirements, since now we are depending on gufe 1.6.0 after this change. I'll be taking care of that in #106

@chrisiacovella
chrisiacovella deleted the fix-101 branch September 9, 2025 19:27
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asap-alchemy gufe import error

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