Matthew Harrigan

Use canonical links for docs

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https://en.wikipedia.org/wiki/Canonical_link_element In addition to `msmbuilder.org/3.5/msm.html` have `msmbuilder.org/latest/msm.html` and use the canonical tag to point to that one

[WIP] Add SymmetryRMSDFeaturizer

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- [x] Implement feature / fix bug - [x] Add tests - [ ] Update changelog For homo-multi-mers, there's rotational or permutational symmetry. This featurizer takes the minimum distance from...

RMSD clustering segfault?

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@jchodera reports on pyemma issue that they want to do rmsd clustering but: > @maxentile can't actually cluster our data with MSMBuilder without it throwing a segfault Can you provide...

GaussianFusionHMM.draw_samples

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`GaussianFusionHMM.draw_samples()` does not return `sample_features` as advertised by the docstring

cc msmbuilder-user mailing list

[XEB] random_quantum_circuit_generation assumes neighboring GridQubits are connected

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The random circuits generated take a list of qubit to implicitly define the device. In particular: it assumes that adjacent GridQubits should be interacted. I don't think this has ever...

Can't use EngineSampler in multiprocessing

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I was trying to call `run` from a function which I am using `multiprocessing.Pool.map` to run a couple in parallel. Multiprocessing requires the function you're mapping over to be pickle-able...

Can't use cirq.Simulator() in a multiprocessing closure (unable to pickle)

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When using python's `multiprocessing`, the function closure must be pickleable so that it can be shipped off to the subprocesses. This means you can't use lambdas or anything. A common...

random_quantum_circuit_generation.random_rotations_between_grid_interaction_layers_circuit should use device_graph instead of qubits

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The arguments for `random_rotations_between_grid_interaction_layers_circuit` combines `qubits` with `pattern: Sequence[GridInteractionLayer]` to figure out what pairs to activate. This assumes that all neighboring GridQubits are able to be activated, which may not...

Consider `--allow-redefinition` for mypy

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See https://github.com/python/mypy/issues/1174 for full context, but there are common idioms where you may want to re-use a variable name ```python items: Set[Item] = set() items.add(...) items = frozenset(items) ``` Mypy...