[JOSS Review] Reproducibility and functionality

[mbarzegary]

Dear authors,

Generally speaking, the software runs more or less as described in the documentation. However, there are some comments in this regard:

• It's not clear where the user should start using the package after installing it. The way the provided examples are placed is a bit difficult to follow. Except for the electrochemistry and the fracture_mechanics directories, the rest of the examples directories are not clear regarding which functionality they belong to. I suggest that you add a new example directory for getting started with the package, putting some basic examples grouped per feature.
• It's not clear how the distributed computation example is supposed to work.
• Generally speaking, the example directory contains a large number of non-trivial files, most of which are not documented unfortunately. I think this makes it difficult to get started with the package.
• Running the samples_pb_c2d.py and samples_pnp_c2d.py examples results in the following error: ModuleNotFoundError: No module named 'matscipy.electrochemistry.utility'. The error for samples_pnp_by_fenics_fem.py is related to lack of matscipy.electrochemistry.poisson_nernst_planck_solver_fenics module.
• Some examples rely on IPython, which doesn't get installed via the installation procedure of the package.

P.S. This issue is related to https://github.com/openjournals/joss-reviews/issues/5668

[jotelha]

https://github.com/libAtoms/matscipy/pull/192 resolved bullet point 4.

Addressing bullet point 3 for the electrochemistry submodule examples: Within https://github.com/libAtoms/matscipy/pull/210, I have turned the electrochemistry example notebooks into proper documentation and consequently removed them from the not very neatly curated examples/electrochemistry folder. This folder now only contains sample bash scripts for a simple parametric studies with the electrochemistry CLI.