PTMCMCSampler
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jellis18
Parallel tempering MCMC sampler package written in Python
Because 1. Hot chains must always be loaded for resuming to resume correctly, 2. `writeHotChains=False` by default, and it is not set as a keyword argument in `setup_sampler()` in `enterprise...
specifically with parallel tempering, I am getting failures to start sampling (both resuming and starting a new job) with the following error message: `File "/home/baierj/miniconda3/envs/custom_noise/lib/python3.9/site-packages/PTMCMCSampler/PTMCMCSampler.py", line 303, in initialize raise...
There used to be documentation hosted at http://jellis18.github.io/PTMCMCSampler/, but it no longer exists after the migration of the repository. We should host the documentation somewhere public again.
Should we make a new release , maybe when the current run of changes is finished? It would be nice for people using pip and conda to be able to...
Reading through the body of `sample()`, I realize that statements about the optional `acor` dependency in the README, that I also propagated into log messages in #24, are not correct....
I noticed that I'm getting a new broadcasting error message which I think coincides with the recent version update to PTMCMCSampler. I wrote a very simple toy model problem with...
At the end of `updateChains` is some code which writes to the chain file but only in thread 0 (unless you set `writeHotChains`). Then it writes `cov.npy` and outputs a...
I'm hoping to use `PTMCMCSampler` in a production-quality [scientific application](https://github.com/JBEI/ART), where repeatability is important for error diagnosis and / or for peer review. I see that repeatability hasn't been specifically...
The `acor` [package](https://github.com/dfm/acor) is no longer under active development and has seen recent issues (@svigeland @kdolum) with newer versions of `Numpy`. Currently the import used in PTMCMCSampler is inside a...
It seems that the time.sleep(0.000001) hack has some unwanted consequences on Windows10 in Python 3. A simple %timeit time.sleep(0.000001) reveals that this takes ~15ms on my workstation, which is going...
