Skip to content
Permalink

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also or learn more about diff comparisons.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also . Learn more about diff comparisons here.
base repository: choderalab/pymbar
Failed to load repositories. Confirm that selected base ref is valid, then try again.
Loading
base: 3.0.7
Choose a base ref
...
head repository: choderalab/pymbar
Failed to load repositories. Confirm that selected head ref is valid, then try again.
Loading
compare: 3.1
Choose a head ref
  • 10 commits
  • 21 files changed
  • 4 contributors

Commits on Jun 17, 2022

  1. Configuration menu
    Copy the full SHA
    0fac2c2 View commit details
    Browse the repository at this point in the history

Commits on Jun 27, 2022

  1. Merge pull request #441 from choderalab/setlogzero

    Fix for expectations of very small numbers
    mrshirts authored Jun 27, 2022
    Configuration menu
    Copy the full SHA
    07707d9 View commit details
    Browse the repository at this point in the history
  2. 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).
    mrshirts committed Jun 27, 2022
    Configuration menu
    Copy the full SHA
    50b5458 View commit details
    Browse the repository at this point in the history
  3. Fixed documentation.

    mrshirts committed Jun 27, 2022
    Configuration menu
    Copy the full SHA
    aa4378e View commit details
    Browse the repository at this point in the history
  4. Merge pull request #443 from choderalab/setlogzero

    Noticed one bug in setlogzero commit
    mrshirts authored Jun 27, 2022
    Configuration menu
    Copy the full SHA
    2b7fdbc View commit details
    Browse the repository at this point in the history

Commits on Jul 11, 2022

  1. 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
    mikemhenry authored Jul 11, 2022
    Configuration menu
    Copy the full SHA
    e5c82e0 View commit details
    Browse the repository at this point in the history

Commits on Jul 27, 2022

  1. 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]>
    3 people authored Jul 27, 2022
    Configuration menu
    Copy the full SHA
    0024161 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    51a0aed View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    50dfbc9 View commit details
    Browse the repository at this point in the history

Commits on Jul 28, 2022

  1. 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
    mikemhenry authored Jul 28, 2022
    Configuration menu
    Copy the full SHA
    a314f00 View commit details
    Browse the repository at this point in the history
Loading