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Recent Releases of pymbar

pymbar - 4.0.3 Support for Python 3.12 and Jax 0.3.25+

Updates the builds to work against Python 3.8 through and including Python 3.12. Also fixes some upstream JAX and CI dependency issues.

What's Changed

  • Fixed example bug and updated output. by @mrshirts in https://github.com/choderalab/pymbar/pull/513
  • Update to Python 3.12 by @Lnaden in https://github.com/choderalab/pymbar/pull/526

Full Changelog: https://github.com/choderalab/pymbar/compare/4.0.2...4.0.3

- Python
Published by Lnaden about 2 years ago

pymbar - 4.0.2 Optional JAX build

What's Changed

  • Do not use removed numpy.bool by @mattwthompson in https://github.com/choderalab/pymbar/pull/485
  • switch to using mamba for rtd building by @mikemhenry in https://github.com/choderalab/pymbar/pull/494
  • Minor docstring exp fix by @ijpulidos in https://github.com/choderalab/pymbar/pull/492
  • Make JAX an optional dependency by @Lnaden in https://github.com/choderalab/pymbar/pull/503
  • Warn about JAX bitsize changes by @Lnaden in https://github.com/choderalab/pymbar/pull/504
  • Correctly stagger JIT until first call by @Lnaden in https://github.com/choderalab/pymbar/pull/505
  • Correct docstring default value by @badisa in https://github.com/choderalab/pymbar/pull/507
  • Wrap the preconditioned jit by @Lnaden in https://github.com/choderalab/pymbar/pull/506
  • fixes RTD build by @mikemhenry in https://github.com/choderalab/pymbar/pull/510
  • Fix a small bug in the timeseries test, test against min and max versions by @Lnaden in https://github.com/choderalab/pymbar/pull/512

New Contributors

  • @mattwthompson made their first contribution in https://github.com/choderalab/pymbar/pull/485
  • @ijpulidos made their first contribution in https://github.com/choderalab/pymbar/pull/492
  • @badisa made their first contribution in https://github.com/choderalab/pymbar/pull/507

Full Changelog: https://github.com/choderalab/pymbar/compare/4.0.1...4.0.2

- Python
Published by Lnaden almost 3 years ago

pymbar - 3.1.1

What's Changed

The former is specified using solver_tolerance and the latter is specified using bootstrap_solver_tolerance.

Full Changelog: https://github.com/choderalab/pymbar/compare/3.1...3.1.1

- Python
Published by mikemhenry over 3 years ago

pymbar - pymbar 3.1 LTS Release

What's New

We now support computation of bootstrapped uncertainties for MBAR free energies -- just specify n_bootstraps=n_desired_bootstraps when initializing MBAR(), where n_desired_bootstraps is the number of bootstrap iterations you'd like to run, and uncertainty_method='bootstrap' when calling getFreeEnergyDifferences().

What's Changed

  • 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
  • Getting CI working on the current default branch by @mikemhenry in https://github.com/choderalab/pymbar/pull/449
  • Bootstrap uncertainties first pass by @mrshirts in https://github.com/choderalab/pymbar/pull/302
  • Fix divide by zero warning in pymbar3 by @zhang-ivy in https://github.com/choderalab/pymbar/pull/470
  • sphinx.ext.pngmath is now sphinx.ext.imgmath by @mikemhenry in https://github.com/choderalab/pymbar/pull/471

New Contributors

  • @zhang-ivy made their first contribution in https://github.com/choderalab/pymbar/pull/470

Full Changelog: https://github.com/choderalab/pymbar/compare/3.0.7...3.1

- Python
Published by mikemhenry almost 4 years ago

pymbar - 4.0.1

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

- Python
Published by Lnaden almost 4 years ago

pymbar - 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 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

Full Changelog: https://github.com/choderalab/pymbar/compare/3.0.7...4.0.0

- Python
Published by mikemhenry almost 4 years ago

pymbar - Bugfix Release

What's Changed

  • Fix #427 : Add BAR compute overlap method by @jchodera in https://github.com/choderalab/pymbar/pull/430
  • Add warning about unstable API by @mikemhenry in https://github.com/choderalab/pymbar/pull/432

Full Changelog: https://github.com/choderalab/pymbar/compare/3.0.6...3.0.7

- Python
Published by mikemhenry about 4 years ago

pymbar - Bugfix Release

What's Changed

  • Fixes sanity check for empty bins in computePMF by @tuckerburgin in https://github.com/choderalab/pymbar/pull/324
  • Change anaconda channel from omnia to conda-forge by @chrisjonesBSU in https://github.com/choderalab/pymbar/pull/404
  • Update README installation instructions from -c omnia to -c conda-forge. by @bdice in https://github.com/choderalab/pymbar/pull/418
  • Forward maximum_iterations from MBAR constructor by @maxentile in https://github.com/choderalab/pymbar/pull/425
  • Removed travis CI config file by @mikemhenry in https://github.com/choderalab/pymbar/pull/426

New Contributors

  • @tuckerburgin made their first contribution in https://github.com/choderalab/pymbar/pull/324
  • @chrisjonesBSU made their first contribution in https://github.com/choderalab/pymbar/pull/404
  • @bdice made their first contribution in https://github.com/choderalab/pymbar/pull/418
  • @maxentile made their first contribution in https://github.com/choderalab/pymbar/pull/425
  • @mikemhenry made their first contribution in https://github.com/choderalab/pymbar/pull/426

Full Changelog: https://github.com/choderalab/pymbar/compare/3.0.5...3.0.6

- Python
Published by mikemhenry over 4 years ago

pymbar - Critical bugfix release

In adding support for python 3.8 and scipy 1.0, pymbar 3.0.4 accidentally changed the API for key components to a new experimental API in which dict objects were returned for convenience.

This release restores the previous API behavior in pymbar 3.0.0-3.0.3, but allows the new API to be accessed via the optional keyword argument return_dict=True (via PR https://github.com/choderalab/pymbar/pull/319). Without this keyword, the old API is used.

We will consider making the dict API the default in pymbar 4, but we will plan to add warnings of the API change well in advance of this change.

Apologies to all our users who were affected by this issue!

- Python
Published by jchodera over 6 years ago

pymbar - Python 3.8 and Newer Scipy 1.0 compatibility

This release brings in all the changes from the last months and makes PyMBAR compatible with Python 3.8 and Scipy 1.0.

- Python
Published by Lnaden over 6 years ago

pymbar - Fix PyPi Release

This release fixes a subtle but important issue caused by missing file when PyPi Tarball was compiled from Python 3, but then downloaded in Python 2

Because this changes the setup.py file, this formal release was cut.

- Python
Published by Lnaden over 8 years ago

pymbar - 3.0.2 Updated Numpy Support and Conda Forge Version

- Python
Published by Lnaden almost 9 years ago

pymbar - 3.0.1.beta0 Fixes for Numpy 1.12 and Python 3.6

Cut a release to bring in Numpy 1.12 changes and Python 3.6 support for deployment.

- Python
Published by Lnaden over 9 years ago

pymbar - 3.0.0 beta 2

This release fixes win conda package support.

- Python
Published by jchodera almost 11 years ago

pymbar - 3.0.0 beta 1

- Python
Published by kyleabeauchamp almost 11 years ago

pymbar - Beta release of conda-packageable pymbar distribution

A number of minor improvements (including some API changes) have been made in this version: - Docstrings now conform to the NumPy/SciPy convention - Documentation has been cleaned up - Installation of prerequisites has been automated - Pyflakes was used to remove unused dependencies - Tests have been improved and automated using nose - Automated integration testing implemented with travis-ci - License has been changed to LGPL - Import and init styles have been made more consistent - Source code now more generally follows pep8 - Test systems have been refactored

- Python
Published by jchodera almost 12 years ago