JOSS Review Comments - Reviewer 1

[amkrajewski]

trafficstars

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]

https://github.com/openjournals/joss-reviews/issues/6731

[RMeli]

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

[amkrajewski]

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

[amkrajewski]

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 https://github.com/amkrajewski/nimCSO/issues/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]

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.

[RMeli]

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

@Henrium, would you mind looking at your checklist in https://github.com/openjournals/joss-reviews/issues/6731#issuecomment-2099348790 and see if there are still outstanding items to be addressed? Many thanks!

[Henrium]

Thanks for the reminder, all items have been addressed. I've updated the checklist.

On Thu, Sep 12, 2024 at 3:01 AM Rocco Meli @.***> wrote:

Thanks @Henrium https://github.com/Henrium. @amkrajewski https://github.com/amkrajewski, I think we can close the issues then.

@Henrium https://github.com/Henrium, would you mind looking at your checklist in openjournals/joss-reviews#6731 (comment) https://github.com/openjournals/joss-reviews/issues/6731#issuecomment-2099348790 and see if there are still outstanding items to be addressed? Many thanks!

— Reply to this email directly, view it on GitHub https://github.com/amkrajewski/nimCSO/issues/2#issuecomment-2344452689, or unsubscribe https://github.com/notifications/unsubscribe-auth/AITHDEDPJHVU5OFQVMMZTNLZWCHQVAVCNFSM6AAAAABHQ2NN2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBUGQ2TENRYHE . You are receiving this because you were mentioned.Message ID: @.***>

[amkrajewski]

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