AnalysisBase refactor

[lilyminium]

@ojeda-e could you please start putting your thoughts here on how you want the AnalysisBase refactor to go?

In general, AnalysisBase classes will have four methods defined:

• __init__ this receives arguments. Usually an AtomGroup or Universe is provided here to operate over, and user-arguments such as n_cell.
• _prepare this typically sets up containers for the data to be collected in _single_frame, and maybe performs some pre-emptive computation.
• _single_frame this is the bulk of the class: the functionality that you want to operate over every frame of the trajectory. For example, you could be collecting lipid positions.
• _conclude this does the final computation with the data collected from _single_frame. Sometimes it's very short (e.g. https://github.com/MDAnalysis/mdanalysis/blob/64840d5df32ecb73ceadcc022dc4b71738537404/package/MDAnalysis/analysis/rms.py#L864-L870). Sometimes it's where the bulk of the computation is (e.g. https://github.com/MDAnalysis/mdanalysis/blob/64840d5df32ecb73ceadcc022dc4b71738537404/package/MDAnalysis/analysis/pca.py#L315-L322). For example, the calculation of mean and gaussian curvature could go here.
• (optional) post-run methods. If you don't want to compute the mean and gaussian curvature every time the user calls run() but only when they ask for it, you can add post-run methods instead, e.g. https://github.com/MDAnalysis/mdanalysis/blob/64840d5df32ecb73ceadcc022dc4b71738537404/package/MDAnalysis/analysis/pca.py#L431-L476

[ojeda-e]

Thanks @lilyminium. What's the best way to share the initial AnalysisBase? Should I submit a PR or leave it here as a comment?

[lilyminium]

As a PR would be easier to comment line-by-line, but if you don't have any code yet then you could just comment your ideas here.