Release notes from pAPRika

pAPRika v1.3.0

2024-10-14T00:52:42Z

This release adds a few new quality of life features, as well as a new tutorial notebook. Restraints have received a QOL improvement and more extensive unit testing. Automated testing with CI and CodeQL is working again. The development conda environment has been updated, and tests are passing for python versions 3.9, 3.10, 3.11, 3.12. Lastly, some bugs have been fixed.

What's Changed

Update conda and readme by @jeff231li in #182
Update pin on OpenFF-Units by @jeff231li in #184
Update CI.yaml -- include python 3.10 in unit tests by @jeff231li in #186
update readme by @jeff231li in #187
Remove LGTM yaml file by @jeff231li in #188
Update read_yaml module for taproom by @jeff231li in #189
Refactor Analysis Modules by @jeff231li in #190
Fix bugs in restraint modules by @jeff231li in #191
Improve QOL for Restraints Modules by @jeff231li in #192
Fix bug in Analysis module -- saving and loading results by @jeff231li in #193
Fix bug in calculating center of mass with zero masses by @jeff231li in #194
Fixed some imports using old locations in tutorials by @jaketanderson in #196
Avoiding tleap by @jaketanderson in #197
Fixing versioneer issue by @jaketanderson in #201
Fixing GitHub Actions by @jaketanderson in #202

Full Changelog: v1.2.0...v1.3.0

pAPRika v1.2.0

2022-10-26T21:49:38Z

This release adds minor new features and bug fixes to the paprika code.

Integrate OpenFF-units (a wrapper for Pint units) used in DAT_restraints.
Enhances the restraints/openmm module to include centroid-based anchor atom selection.
Updates the analysis module for pymbar v4.0
Minor bug fixes

pAPRika v1.1.0

2022-10-24T23:19:59Z

This release provides a number of enhancements to the paprika code and changes to the API.

Adds support for writing APR restraints to Plumed and Colvars format.
Refactoring of the Amber simulation wrapper code and expanded to include wrappers for GROMACS and NAMD.
Namespace refactoring for the align, dummy, and tleap modules (now under paprika.build).
Namespace refactoring for the OpenFF-Evaluator related modules (now under paprika.evaluator).
Enhancements to the tleap class, which includes a wrapper around InterMol for converting Amber files to other MD formats and support for solvating with the Bind3P water model.
Migrate continuous integration (CI) to Github Actions (GHA).
Minor bug fixes.

What's Changed

Update tutorials by @jeff231li in #131
Fix RTD by removing m2r package by @slochower in #132
Add support for Plumed-based restraints by @jeff231li in #133
Remove codeclimate and use lint by @jeff231li in #136
Update documentation by @jeff231li in #138
Change documentation badge by @slochower in #139
Add new utility functions by @jeff231li in #129
Refactor wrapper and add Gromacs support by @jeff231li in #140
Fixes bug in #140 where additional PDB files were suppressed by filter_template by @slochower in #143
Update README.md by @jeff231li in #144
NAMD+Colvars support and improvement for all simulation classes by @jeff231li in #145
Add a function to rotate a system around an axis by @jeff231li in #147
Fix bug with temperature setter in Analysis class by @jeff231li in #148
Tleap InterMol support by @jeff231li in #146
Set up GitHub Actions CI by @mattwthompson in #151
Fix bug in tleap when solvating a single ion. by @jeff231li in #152
Refactor Evaluator related module by @jeff231li in #153
CI update -> use miniconda v2 by @jeff231li in #154
Refactor build related modules by @jeff231li in #157
Add Bind3P as an option in TLeap module by @jeff231li in #159

Full Changelog: v1.0.4...v1.1.0

pAPRika v1.0.4

2020-08-18T15:37:04Z

Refactor codes for setup.py and analysis.py modules to allow a smoother integration with OpenFF-Evaluator
OpenMM restraints code is now decoupled from setup.py and placed in a separate file restraints/openmm.py
Updated install requirements to Ambertools v20
Added hydrogen mass repartitioning option to TLeap API module
Minor bug fixes

1.0.3: Pymbar fix (#121)

2019-12-04T20:37:49Z

Updated pymbar 3.0.5 API
cosmetic commit
undo cosmetic commit
changed Exception to TypeError

pAPRika v1.0.3

2019-12-04T22:59:44Z

Fixed API compatibility with the new pymbar v3.0.5 and the I/O for ref_structure in the static_DAT_restraint function

pAPRika v1.0.2

2019-11-24T23:20:46Z

Fix parsing of CUDA_VISIBLE_DEVICES class property. This bugfix was intended to go into the v1.0.1 release but was accidentally excluded.

pAPRika v1.0.1

2019-11-24T23:19:51Z

~~Fixes a bug where CUDA_VISIBLE_DEVICES was not being set correctly.~~ This PR was accidentally not merged at this point. Please use the next release.
Provides a more robust method to supply a random number seed to the compute_free_energy method.

Thanks to @jeff231li @wwilla7 @nhenriksen.

pAPRika v1.0.0

2019-11-04T22:23:09Z

The API for paprika.setup and paprika.analyze are now converged.
OpenMM support is proved by PropertyEstimator.
The documentation has (mostly) been updated and expanded.

pAPRika v0.1.1

2019-07-31T03:31:57Z

Minor code cleanup and fix reference values for test cases that were failing in the v0.1.0 release.