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 https://github.com/choderalab/pymbar/pull/325 Move CI to GHA and start upgrade to Cookiecutter style by @Lnaden in https://github.com/choderalab/pymbar/pull/328 Convert to PyTest by @Lnaden in https://github.com/choderalab/pymbar/pull/333 Reused the gradient calculation in the adaptive algorithm. by @mrshirts in https://github.com/choderalab/pymbar/pull/336 Add CodeCov by @Lnaden in https://github.com/choderalab/pymbar/pull/344 Replace np.matrix calls and other warnings by @Lnaden in https://github.com/choderalab/pymbar/pull/334 Fix formatting by @mrshirts in https://github.com/choderalab/pymbar/pull/342 Reduce the cost of check for duplicate states by @mrshirts in https://github.com/choderalab/pymbar/pull/337 Revamping of PMF by @mrshirts in https://github.com/choderalab/pymbar/pull/327 Start Coverage Improvements (Mbar.py) by @Lnaden in https://github.com/choderalab/pymbar/pull/347 Bar.py and exp.py tests by @mrshirts in https://github.com/choderalab/pymbar/pull/350 cleaning up examples by @mrshirts in https://github.com/choderalab/pymbar/pull/352 Remove 2.01 compatible calls for exp and bar. by @mrshirts in https://github.com/choderalab/pymbar/pull/354 Even more coverage! by @Lnaden in https://github.com/choderalab/pymbar/pull/357 From print to logging by @jaimergp in https://github.com/choderalab/pymbar/pull/360 Add linting to CI by @jaimergp in https://github.com/choderalab/pymbar/pull/367 Apply black to the whole package by @jaimergp in https://github.com/choderalab/pymbar/pull/371 camelCase -> snake_case by @jaimergp in https://github.com/choderalab/pymbar/pull/372 Make Pylint less noisy by @Lnaden in https://github.com/choderalab/pymbar/pull/375 Modernize examples by @jaimergp in https://github.com/choderalab/pymbar/pull/374 Refactoring pmf code by @mrshirts in https://github.com/choderalab/pymbar/pull/385 Better dimension checking by @mrshirts in https://github.com/choderalab/pymbar/pull/386 Bin edges support by @mrshirts in https://github.com/choderalab/pymbar/pull/387 Apply Black to examples/ too by @jaimergp in https://github.com/choderalab/pymbar/pull/392 Updated heat capacity example by @mrshirts in https://github.com/choderalab/pymbar/pull/394 Replace "potential of mean force" with "free energy surface" by @mrshirts in https://github.com/choderalab/pymbar/pull/397 Update GHA to use Conda-Incubator by @Lnaden in https://github.com/choderalab/pymbar/pull/410 Bump conda-incubator in GHA to v2 by @Lnaden in https://github.com/choderalab/pymbar/pull/411 Clean out old Omnia references for Pymbar 4.0 branch by @Lnaden in https://github.com/choderalab/pymbar/pull/412 Modernize setup.py and versioning by @jaimergp in https://github.com/choderalab/pymbar/pull/413 Fix for expectations of very small numbers by @mrshirts in https://github.com/choderalab/pymbar/pull/441 Noticed one bug in setlogzero commit by @mrshirts in https://github.com/choderalab/pymbar/pull/443 Syncing Pymbar4 with master by @mrshirts in https://github.com/choderalab/pymbar/pull/444 Getting CI working on the current default branch by @mikemhenry in https://github.com/choderalab/pymbar/pull/449 Pymbar 4.0 adaptive logic by @mrshirts in https://github.com/choderalab/pymbar/pull/446 Pymbar4 add adaptivity by @mrshirts in https://github.com/choderalab/pymbar/pull/453 Convert JAX JIT to Decorators by @Lnaden in https://github.com/choderalab/pymbar/pull/451 Align namespaces to work if JAX is not installed by @Lnaden in https://github.com/choderalab/pymbar/pull/454 Pymbar4 bootstrapping by @mrshirts in https://github.com/choderalab/pymbar/pull/448 Remove old_mbar.py by @mrshirts in https://github.com/choderalab/pymbar/pull/457 Pymbar4 with jax (real try now) by @mrshirts in https://github.com/choderalab/pymbar/pull/447 Pymbar 4.0 by @mrshirts in https://github.com/choderalab/pymbar/pull/458 [WIP] Pymbar4 documentation by @mrshirts in https://github.com/choderalab/pymbar/pull/455 remove special character for now. by @mrshirts in https://github.com/choderalab/pymbar/pull/460 switch to napoleon for better output formatting. by @mrshirts in https://github.com/choderalab/pymbar/pull/461 More working on doc appearance. by @mrshirts in https://github.com/choderalab/pymbar/pull/462 Update classifier to match PyPi expectations. by @Lnaden in https://github.com/choderalab/pymbar/pull/465 Further improve RTD and previous versions. by @mrshirts in https://github.com/choderalab/pymbar/pull/466 Further improve RTD and previous versions. by @mrshirts in https://github.com/choderalab/pymbar/pull/467 Full Changelog: https://github.com/choderalab/pymbar/compare/3.0.7...4.0.1