Version 0.3.0

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.