Iván Pulido

Integrate hybrid topology factories into openmmtools

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Current implementation of hybrid topology factories in perses are currently in a state that they could be integrated into openmmtools code base. Maybe an `alchemy` package/module that contains it (for...

Replacing Fire minimization with LocalEnergyMinimizer

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## Description Replaces `FireMinimizer` with `LocalEnergyMinimizer` to do the replica minimization. This should enhance the stability of minimization. Supersedes #557 Resolves #668 ## Todos - [x] Implement feature / fix...

> Not sure exactly what you mean here, but we don't have a way to have no checkpointing at all, as far as I can tell. Tests just make the...

From time to time we get stochastic test failures for the `TestHarmonicOscillatorsMultiStateSampler` with the following traceback: ```python Traceback (most recent call last): File "/home/runner/micromamba-root/envs/openmmtools-test/lib/python3.10/site-packages/nose/case.py", line 197, in runTest self.test(*self.arg) File...

Use `LocalEnergyMinimizer` instead of `FireMinimizer`

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We want to use the `LocalEnergyMinimizer` instead of the `FireMinimizer` in the multistate sampler. Supersedes #557

Change test framework to pytest

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We are currently using `nosetests` for our testing framework and we probably want to use the capabilities of a modern framework such as `pytest`. I can foresee this requiring some...

It should be useful to have a way to store only a subset of the atoms/particles in a simulation. Especially for storage volume usage this might be needed for some...

https://github.com/choderalab/openmmtools/pull/557 We should eliminate the use of the `FireMinimizer` in the multistate sampler.

In order to get the tests passing with OpenMM8, it looks like we need to refactor the `RestorableOpenMMObject` because it is using different default values for the global `_restorable_force__class_hash` and...

@xiki-tempula Thanks for the feedback! This is definitely something that should be improved with the documentation. Even the classes have [docstrings with examples](https://github.com/choderalab/openmmtools/blob/2e64980d86cf087f69e282927eebf2b41b73a3ea/openmmtools/multistate/replicaexchange.py#L113-L206) that may help users figure out how...