4.0.0

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

Full Changelog: 3.0.7...4.0.0