A list of todos for the next release of `ensemble_md`

Here we list the todos that should be done before the next release of the ensemble_md package. The release number has not been finalized and can be either 0.10.0 or 1.0.0 depending on the status of the paper review. Overall, the todos are to improve the code coverage and the documentation of the package. This issue includes updated components from the plans mentioned in issues #7, #26, and #33, as parts of them have become outdated.

Improving the code coverage

Note that we do not include adding unit tests for analysis/msm_analysis.py since MSM analysis for REXEE is a WIP.

[x] Add unit tests for analysis/analyze_free_energy.py
[x] Add unit tests for analysis/clustering.py
[x] Add unit tests for analysis/synthesize_data.py
[x] Complete test_mpi_func.py, which tests functions that use MPI
[x] Add unit tests for functionalities relevant to MT-REXEE, which are in replica_exchange_EE.py
[x] Re-examine the missed lines to push the code coverage as much as possible.
[x] Check if the warnings are actually harmless.

Potentially, we might want to consider adding regression tests for the CLIs.

Improving the documentation

[x] Update the theory section of the documentation
[x] Describe rules of thumb for REXEE parameters
[x] Proofread the entire documentation
[x] Proofread the docstrings
[x] Adding simple examples in some of the docstrings

Potentially, we might want to add some simple tutorials before the next release.

wehs7661 / ensemble_md

A list of todos for the next release of `ensemble_md` #41

Improving the code coverage

Improving the documentation