David W.H. Swenson

Thanks -- I thought it might just be that the MDTraj user/dev community is more focused on proteins than nucleic acids, so this hasn't been an itch anyone else wanted...

It's nearly ready. I've been meaning to ask what you think should be included as "nucleic", but got distracted by other things. In short, there are several possibilities to consider...

FWIW, I don't see this problem with MDTraj's docs (it can get close if you expand the correct sidebar items: expand the HDF5 format specification, and Chrome cuts off the...

> Ah! I see what's happening. `deserialize()` actually `pop()`s the `serialized_X` attributes so you don't see them anymore in the `serialized` variable if you print it after calling `deserialize()` on...

Thanks @andrrizzi! > I think you can safely either assign a new `SamplerState` to `MCMCSampler` or even set `MCMCSampler.sampler_state.positions = ...`. Yes, this is even better. Somehow, when I looked...

The test case that is a problem here is actually the one where both are supposed by at 270K already. The problem is a rounding issue in `simtk.unit`: ```python from...

Another one (tested in release 0.10.2 and in current master): ```python In [1]: import toml In [2]: toml.__version__ Out[2]: '0.10.2' In [3]: dct = {'foo': 'bar', 'baz': ['qux', {'quux': 10}]}...

Mainly I keep dragging this "forever PR" along, updating it to master every time it gets marked stale, but not bringing it to conclusion. Sorry about that. I think my...

@sroet : When we do this, can you help ensure that the linked instructions are correct? I got a little confused when doing the openpathsampling-cli change -- the only one...

Hmmm... I haven't received any such emails. Could you forward, if you still have them available? TBH, this isn't super urgent (docs here aren't changing rapidly) but definitely better to...