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base repository: choderalab/pymbar
base: 3.0.7
head repository: choderalab/pymbar
compare: 3.1
- 10 commits
- 21 files changed
- 4 contributors
Commits on Jun 17, 2022
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Commits on Jun 27, 2022
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Merge pull request #441 from choderalab/setlogzero
Fix for expectations of very small numbers
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Missed one line in updating to logfactor.
Missed one line when updating min(A)-1 to min(A)-logfactor. Affected the value of min(A) coming out (usually not used).
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Merge pull request #443 from choderalab/setlogzero
Noticed one bug in setlogzero commit
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Commits on Jul 11, 2022
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Getting CI working on the current default branch (#449)
* adding conda env and github workflow * switch to pytest * remove nose from setup.cfg * switch to pytest in recipe * everything is now switched to pytest, need to fix some issues with type errors now * pin statsmodels since version 0.13 has breaking changes * don't worry about linting or testing examples * update badge * change test to check if: absolute(fe_sigma - dfe_t[0,1]) <= (0.01 * absolute(dfe_t[0,1])) * run on pymbar3 branch
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Commits on Jul 27, 2022
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Bootstrap uncertainties first pass (#302)
* Starting bootstrap. * Bootstrap sampling for free energies. * Added test for bootstraps, fixed bug revealed by test. * Boostrap pause. * update with bootstrapping at each K. * fixed float->int typing problem. * fix test * Bootstrap starting from the initial point. * allow solver tolerance specification, skip sc iterations for bootstrapping, fix docs * clean up solver_tolerance * add test * fix call to harmonic oscillators test case in test * Make sure can return uncertainies without dictionaries. Including in case with bootstrap. Co-authored-by: Ivy Zhang <[email protected]> Co-authored-by: Mike Henry <[email protected]>
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backport pymbar4 changes to resolve divide by 0 warning (#470)
Co-authored-by: Mike Henry <[email protected]>
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Commits on Jul 28, 2022
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sphinx.ext.pngmath is now sphinx.ext.imgmath (#471)
* sphinx.ext.pngmath is now sphinx.ext.imgmath * configure bibtex_bibfiles setting * quick pass on the docs, plenty more to fix but will take care of it later * add warning to the docs * add warning to readme
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