paprika - pAPRika v1.3.0

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

Full Changelog: https://github.com/GilsonLabUCSD/pAPRika/compare/v1.2.0...v1.3.0

- Python
Published by jaketanderson over 1 year ago

paprika - pAPRika v1.2.0

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

- Python
Published by jeff231li over 3 years ago

paprika - pAPRika v1.1.0

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

Full Changelog: https://github.com/GilsonLabUCSD/pAPRika/compare/v1.0.4...v1.1.0

- Python
Published by jeff231li over 5 years ago

paprika - pAPRika v1.0.4

• 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

- Python
Published by jeff231li almost 6 years ago

paprika - pAPRika v1.0.3

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

- Python
Published by jeff231li over 6 years ago

paprika - pAPRika v1.0.2

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

- Python
Published by slochower over 6 years ago

paprika - pAPRika v1.0.1

• ~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.

- Python
Published by slochower over 6 years ago

paprika - pAPRika v1.0.0

• 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.

- Python
Published by slochower over 6 years ago

paprika - pAPRika v0.1.1

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

- Python
Published by slochower almost 7 years ago

paprika - pAPRika v0.1.0

This release enables paprika to work with propertyestimator of the Open Force Field Toolkit, and taproom to setup host-guest calculations with either GAFF or SMIRNOFF-based force fields using AMBER or OpenMM as simulation backends.

- Python
Published by slochower almost 7 years ago

paprika - pAPRika v0.0.4

Updates after merging Cookiecutter for Computational Molecular Sciences (CMS) Python Packages and updating tests to pass.

- Python
Published by slochower over 7 years ago

paprika - pAPRika v0.0.3

This code was used to run SAMPLing.

- Python
Published by nhenriksen about 8 years ago