amkrajewski/nimCSO

JOSS Review Comments - Reviewer 1

Closed this issue · 8 comments

amkrajewski commented

Below are initial (itemized) JOSS review comments from @Henrium. I will progressively work on addressing them one-by-one here.

  1. I have tested in both GitHub Codespaces and Linux, the package is easy to install and works as claimed.

  2. Summary: I suggest the following to make it more accessible to "diverse, non-specialist audience": (1) introduce the background first, then what nimCSO is and what it does; (2) elaborate on the purpose and challenges.

  3. State of field: What are some other approaches to compositional space optimization; are there relevant software? References should be added if applicable. It's not necessary to compare with them, but good to make the paper informative.

  4. In quickstart.ipynb: the routine mostCommon is clear at first, but got confusing when it comes to "removing elements". What's the optimization objective of removing elements?

  5. The "Algorithm-Based Search" method relies on an assumption, "elements present in already expanded ...", is it supported by any rationale, experiments, prior studies, etc.?

  6. I didn't find "community guidelines", though it doesn't seem necessary here. Consider adding one?

RMeli commented

@amkrajewski could you please briefly summarise the progress on the items listed here? Thank you.

amkrajewski commented
  • Improvement of the summary to make it more approachable to the general audience.
  • Elaborate on other methods - reference the Python and NumPy implementations presented within the benchmarks directory.
  • Add more references to other scientific domains to broadly present the problem.
  • Clarify "removal of elements" in the quick start guide.
  • Elaborate on the rationale for algorithm assumption.
  • Add "community guidelines" on how to contribute and what.
  • 👍1
amkrajewski commented

Hi @Henrium, thanks again for taking the time and effort to provide valuable feedback. I finished working through all reviewer comments, and I believe the code/paper is ready for you to evaluate my adjustments.

Notes:

  • Above, please find the itemized list of changes I made (some overlapped with #3).
  • In some cases, I wanted to be more verbose, but the paper was already above the recommended length.
  • I am happy to make further adjustments.
Henrium commented

Hi @amkrajewski, thanks for your comprehensive response to my reviews. My concerns are well addressed, and I think the paper is in good shape @RMeli.

  • 👍2
RMeli commented

Thanks @Henrium. @amkrajewski, I think we can close the issues then.

@Henrium, would you mind looking at your checklist in openjournals/joss-reviews#6731 (comment) and see if there are still outstanding items to be addressed? Many thanks!

Henrium commented
  • 👍2
amkrajewski commented

@Henrium Again, thank you for your time and effort in the review. I will close this issue as completed.