4.0.0

[mikemhenry]

Breaking Changes Ahead!

This pymbar release has several API changes and some exciting new features (such as JAX acceleration and support)

See this guide on how to migrate from pymbar 3.x to pymbar 4.x.

pymbar 3.x support

We will still support the pymbar 3.x version line as a long term support release. We encourage new pymbar users to use the 4.x version, but due to the considerable infrastructure build around pymbar 3.x, we will continue to provide maintenance support. Don't expect new features to be backported, but we will fix bugs.

What's Changed

• Fixed return type of multiple values to dict-like object by @mrshirts in Fixed return type of multiple values to dict-like object #325
• Move CI to GHA and start upgrade to Cookiecutter style by @Lnaden in Move CI to GHA and start upgrade to Cookiecutter style #328
• Convert to PyTest by @Lnaden in Convert to PyTest #333
• Reused the gradient calculation in the adaptive algorithm. by @mrshirts in Reused the gradient calculation in the adaptive algorithm. #336
• Add CodeCov by @Lnaden in Add CodeCov #344
• Replace np.matrix calls and other warnings by @Lnaden in Replace np.matrix calls and other warnings #334
• Fix formatting by @mrshirts in Fix formatting #342
• Reduce the cost of check for duplicate states by @mrshirts in Reduce the cost of check for duplicate states #337
• Revamping of PMF by @mrshirts in Revamping of PMF #327
• Start Coverage Improvements (Mbar.py) by @Lnaden in Start Coverage Improvements (Mbar.py) #347
• Bar.py and exp.py tests by @mrshirts in Bar.py and exp.py tests #350
• cleaning up examples by @mrshirts in cleaning up examples  #352
• Remove 2.01 compatible calls for exp and bar. by @mrshirts in Remove 2.01 compatible calls for exp and bar. #354
• Even more coverage! by @Lnaden in Even more coverage! [WIP] #357
• From print to logging by @jaimergp in From print to logging #360
• Add linting to CI by @jaimergp in Add linting to CI #367
• Apply black to the whole package by @jaimergp in Apply black to the whole package #371
• camelCase -> snake_case by @jaimergp in camelCase -> snake_case #372
• Make Pylint less noisy by @Lnaden in Make Pylint less noisy #375
• Modernize examples by @jaimergp in Modernize examples [WIP] #374
• Refactoring pmf code by @mrshirts in Refactoring pmf code #385
• Better dimension checking by @mrshirts in Better dimension checking #386
• Bin edges support by @mrshirts in Bin edges support #387
• Apply Black to examples/ too by @jaimergp in Apply Black to examples/ too #392
• Updated heat capacity example by @mrshirts in Updated heat capacity example #394
• Replace "potential of mean force" with "free energy surface" by @mrshirts in Replace "potential of mean force" with "free energy surface" #397
• Update GHA to use Conda-Incubator by @Lnaden in Update GHA to use Conda-Incubator #410
• Bump conda-incubator in GHA to v2 by @Lnaden in Bump conda-incubator in GHA to v2 #411
• Clean out old Omnia references for Pymbar 4.0 branch by @Lnaden in Clean out old Omnia references for Pymbar 4.0 branch #412
• Modernize setup.py and versioning by @jaimergp in Modernize setup.py and versioning #413
• Fix for expectations of very small numbers by @mrshirts in Fix for expectations of very small numbers #441
• Noticed one bug in setlogzero commit by @mrshirts in Noticed one bug in setlogzero commit #443
• Syncing Pymbar4 with master by @mrshirts in Syncing Pymbar4 with master #444
• Getting CI working on the current default branch by @mikemhenry in Getting CI working on the current default branch #449
• Pymbar 4.0 adaptive logic by @mrshirts in Pymbar 4.0 adaptive logic #446
• Pymbar4 add adaptivity by @mrshirts in Pymbar4 add adaptivity #453
• Convert JAX JIT to Decorators by @Lnaden in Convert JAX JIT to Decorators #451
• Align namespaces to work if JAX is not installed by @Lnaden in Align namespaces to work if JAX is not installed #454
• Pymbar4 bootstrapping by @mrshirts in Pymbar4 bootstrapping #448
• Remove old_mbar.py by @mrshirts in Remove old_mbar.py #457
• Pymbar4 with jax (real try now) by @mrshirts in Pymbar4 with jax (real try now) #447
• Pymbar 4.0 by @mrshirts in Pymbar 4.0 #458
• [WIP] Pymbar4 documentation by @mrshirts in [WIP] Pymbar4 documentation #455
• remove special character for now. by @mrshirts in remove special character for now. #460
• switch to napoleon for better output formatting. by @mrshirts in switch to napoleon for better output formatting. #461
• More working on doc appearance. by @mrshirts in More working on doc appearance. #462

Full Changelog: 3.0.7...4.0.0

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This discussion was created from the release 4.0.0.