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bbye98 / mdcraft

A Python assistant for performing and analyzing molecular dynamics simulations of soft matter systems
https://mdcraft.readthedocs.io/
GNU General Public License v3.0
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[Functionality/Example usage] Algorithm and analysis modules #8

Closed aazocar closed 3 months ago

aazocar commented 3 months ago

This is part of JOSS review over at https://github.com/openjournals/joss-reviews/issues/7013

algorithm and analysis modules would also greatly benefit from example use cases.

Also, from the paper, most of the mentioned features correspond to the analysis module, it is not clear from the text what is covered in the algorithm module.

pw0908 commented 3 months ago

For each of these:

  1. analysis: We definitely should and will include examples for each of these. We'll probably include them within the API docs rather than standalone examples as these tools themselves are not inherently complicated.
  2. algorithm: This module is intended to be more low-level compared to analysis as it provides functions used within the latter module. I will certainly clarify this distinction in the text. I am less certain how helpful examples will be here as, ideally, only advanced users should be looking at these functions and they are sufficiently commented to be easy to follow. Let us know what you think.
aazocar commented 3 months ago
  1. Including examples in the API docs addressed this point.
  2. For algorithm module, I agree the examples here are not needed. The comment was intended to clarify the differences between both modules and highlighting the distinction within the text should be enough to close this issue.
aazocar commented 3 months ago

looks good to me 👍🏽