choderalab/pymbar: 4.0.1

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.

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.

• 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