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I'd like to get a formal coverage testing suite (like codecov) on this repo, especially as we work towards an overhauld PyMBAR 4.0
Will be easier to do after #330
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Here is an example that came up in a discussion with @mrshirts , where MBAR's uncertainty estimate can revert to a small number when the overlap is brought close to 0.
For comparison, naive impleme…
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Split from #487: Pymbar 4.0 uses jax.numpy and jax is not well configured for newer macs(m1) and I tried using it on an intel i7 cpu but it is not getting initialized.
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Aliases for built-ins were deprecated in February 2021: https://numpy.org/doc/stable/release/1.20.0-notes.html#using-the-aliases-of-builtin-types-like-np-int-is-deprecated
https://github.com/choder…
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**Capture:**
* package
* git-hash
* openmm version
* number of lambda windows
* lambda protocol (i.e. LambdaProtocol in perses)
* transformation (SMIRKS)
* simulation length
* statistical erro…
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Hi All,
I have compiled alchemical_analysis/pymbar with python_2.7.9 and I could not export the overlap matrix within MBAR procedure, though MBAR free energy estimation worked well.
I got this …
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Apologies if this is a duplicate, but I think we want to automatically build and upload the docs to an S3 bucket.
I think @pgrinaway may have set a bucket up already.
I can grab pymbar.org if we thi…
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I've started to build a preliminary Jenkins-based omnia test:
https://jenkins.choderalab.org/job/test-conda-omnia-release-osx/
It creates a fresh `miniconda` installation and cycles through python 2.…
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Doesn't build once we switch to python3, will need to fix it.
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I run into an error while trying to load a JAX NN model, and it took me a while to realize the problem was caused by `import pymbar`. [Here](https://github.com/choderalab/pymbar/blob/master/pymbar/mba…