Implement Connectivity Strategy
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Initial implementation of _propose, using the mean connectivity of the edges' (transformations) nodes as unnormalized weights. The weights have yet to be normalized and the tests are just checking that the means are correct.
In order to preserve unnormalized weights, which might be useful for debugging/have a more intuitive meaning, the StrategyResult now holds onto these values directly and normalization is handled by calling the new `StrategyResult.resolve` method.
* Strategy initialization now checks that the settings provided to the constructor are the correct type specified by the _settings_cls class attribute of any Strategy subclass. This has the effect that a Strategy author must explicitly specify what settings they are will to accept. This deviates slightly from the gufe Protocol class, which doesn't perform such a check. Tests were added to `test_strategy_abstraction.py` showing only specified StrategySettings will be allowed. * Added TypeVar for ProtocolResults in the `Strategy` base class. Any downstream use of the `propose` method will then check that it's being fed a dictionary with subclasses of ProtocolResults. I don't believe there is an easier way to do this since the ProtocolResult is embedded in a dictionary. * gufe doesn't work with pydantic v2, so I now use the pydantic v1 api. * The match statement for capturing the max_runs / cutoff settings was updated and properly catches which of these were set to None
* Provide a variety of parameters to ConnectivityStrategySettings Termination logic within _propose depends on the combination of parameters given to ConnectivityStrategySettings. A preset batch of valid settings are provided through SETTINGS_VALID. * Test ConnectivityStrategySettings validators Add a test for sets of ConnectivityStrategySettings including both valid and invalid settings. If an Exception is expected, check that it is raised, otherwise check that the settings could be instantiated. * Simulate the ConnectivityStrategy Test that the ConnectivityStrategy terminates after a set number of iterations. The max number of iterations is set to 100. * Remove abstract method bodies from coverage reports
Add a test for ConnectivityStrategy demonstrating deterministc proposals. Given random ProtocolResults, show that StrategyResults are the same after multiple runs.
Since features in the planned gufev1.2.0 release are needed by stratocaster, we need to accurately recreate an environment that gufe will provide upon installation. By using a submodule, we can install the base testing environment from the gufe environment.yml file. This will be reverted once gufev1.2.0 is available on conda-forge. This also makes it easier to react to last minute changes to gufe prior to its v1.2.0 release.
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@ianmkenney I'd say go ahead and merge. We'll make changes via other PRs going beyond this. Great work! |
The data structures returned by gufe fixtures have use outside of the package testing (think example systems in docs). I've extracted the network fixture so it is returned by a regular function in the stratocaster.tests.networks module.
gufe v1.2.0 is available on conda-forge, no longer need the submodule for testing. pydantic imports now match the style used in gufe to address version issue.
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