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Version 0.3.0
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@wehs7661 wehs7661 released this 03 Feb 04:13
· 513 commits to master since this release
0.3.0
a0f186d

The following improvements have been made in version 0.3.0:

  • Entry points including run_EEXE and analyze_EEXE were added to allow command-line interfaces.
  • Methods for analyzing EEXE were developed, with all the relevant codes residing in the folder analysis. Relevant codes include analyze_free_energy.py, analyze_matrix.py, analyze_traj.py, and msm_analysis.py.
  • More EEXE parameters are now allowed to be specified in params.yaml to reflect the changes made in the codes.
  • Methods for checkpointing and extending an EEXE simulation has also been implemented.
  • One more weight-combining method is added: g-diff.
  • We have improved the flexibility of parsing parameters from GROMACS MDP files and input YAML files.
  • We have improved the code coverage to 82%. However, CI performed by GitHub Action has been constantly failing (hanging until timeout) whenever test_run_EEXE is run. The reason is unknown but we will change to CircleCI or other similar services in the next release.
  • Documentation was restructured and updated to reflect most changes in the code.

In the next release, we aim to complete at least the following action items.

  • Improve some of the existing unit tests.
  • Fix the issues in building the package documentation, especially the issue that readthedocs was not able to capture the docstrings of classes that used gmxapi.
  • Make sure that the package constantly passes the continuous integration and lining tests.
  • Update the documentation (see issue #2).
  • Deploy the package to PyPI.
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