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[REVIEW]: The Argonne Nuclear Data Exploration Software (ANDES) #6546

Open editorialbot opened 3 months ago

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@DeltaSigmaGamma<!--end-author-handle-- (Daniel Santiago-Gonzalez) Repository: https://gitlab.phy.anl.gov/nuclear-data/andes Branch with paper.md (empty if default branch): Version: 0.0 Editor: !--editor-->@kellyrowland<!--end-editor-- Reviewers: @adrien-matta, @fanurs Archive: Pending

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@adrien-matta & @fanurs, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kellyrowland know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @fanurs

📝 Checklist for @adrien-matta

editorialbot commented 3 months ago

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editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (497.4 files/s, 281549.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              3            253            420           4868
TeX                              1             25              0            186
Markdown                         2             45              0            142
C/C++ Header                     2             30             32            130
YAML                             2              6             21             45
make                             1              6              4             14
-------------------------------------------------------------------------------
SUM:                            11            365            477           5385
-------------------------------------------------------------------------------

Commit count by author:

    23  Daniel SG
     8  dasago
     3  DeltaSigmaGamma
     2  Daniel Santiago-Gonzalez
     2  DanielSG
editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 731

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 3 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1103/PhysRev.75.1969 is OK
- 10.1103/PhysRev.75.1766.2 is OK
- 10.1126/science.145.3636.999 is OK
- 10.1088/1674-1137/41/3/030002 is OK
- 10.1088/1674-1137/abddb0 is OK
- 10.1088/1742-6596/219/4/042055 is OK
- 10.1103/PhysRevLett.117.172502 is OK
- 10.1088/1361-6552/aa811a is OK
- 10.1063/1.1945075 is OK
- 10.1088/1674-1137/41/3/030001 is OK
- 10.1088/1674-1137/abddae is OK

MISSING DOIs

- No DOI given, and none found for title: ROOT – An object oriented data analysis framework
- No DOI given, and none found for title: NuDat3.0
- No DOI given, and none found for title: Livechart 3D
- 10.4135/9781446247501.n2125 may be a valid DOI for title: Isotopic enrichment
- No DOI given, and none found for title: Characterization of the shape-staggering effect in...

INVALID DOIs

- None
editorialbot commented 3 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

fanurs commented 3 months ago

Review checklist for @fanurs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

adrien-matta commented 3 months ago

Review checklist for @adrien-matta

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

adrien-matta commented 2 months ago

After careful reading of the article and testing of the software, I can provide the following review:

Concerning the software:

The software meet the scope of minimum scholarly effort set by the journal. The author is commended for the clarity of the documentation and the ease of use of the software. However I found the overall use case of the software limited. The provided visualisation tool is very useful and promising, however it is limited to the provided nuclear databases, for which no clear update mechanism is provided (the included one is 4 years old). Unless I missed it, no mechanism to access online data bases (e.g. IAE NDS or NuDat3 API), are provided. This make the tool effectively usable to discover new phenomena only once new experimental data are included in the data base, and then to the software. The fact no clear mechanism is provided to the user to use its own dataset makes it difficult to use in the scope of new publications and therefore unlikely to be cited (one of the journal criteria). For exemple, it seems practically impossible for a theorist willing to plot prediction of their model on the whole nuclear chart to use this tool, or more generally to adapt it to plot non ground state properties. I believe inclusion of such a features, the ability to use a user provided file plotting arbitrary quantities, would not be a major development, and could be done within the scope of this submission.

Concerning the article:

The article is short but very effective and to the point. The overall speech is clear and well written. There is however a couple of typos (e.g. "patters" line 56). I could not understand the following sentence (I believe there a word is missing) : "The use mass differences and binding energies (which are also based on nuclear masses) in the 3D plots of ANDES is a natural selection given that nuclear masses are one of the more fundamental quantities of atomic nuclei."

The figure is missing a more detailed legend of what is plotted. I feel a more thorough description of the interface would be a plus. Given the length of the article, an example of interface plotting config file would be beneficial to help the reader gauge the level of customisation that can be reach. I would recommend two interface plots side by side with their respective config file, as a way to show the versatility of the tool.

Best regards, Adrien.

kellyrowland commented 2 months ago

hi @fanurs checking in on the review here - please let me know if you need to set this down.

kellyrowland commented 2 months ago

thank you for the review and feedback @adrien-matta ! @DeltaSigmaGamma please see the above notes on the manuscript for proposed edits.

fanurs commented 2 months ago

@kellyrowland Thanks for the reminder. I've been caught up with several matters lately. I can provide first round of review by this Friday.

fanurs commented 2 months ago
  1. After modifying a control file used to start the ANDES GUI, it appears the GUI does not automatically update to reflect these changes. Is there a way to enable automatic updates of the GUI upon control file modifications, or must the GUI be restarted each time?
  2. The purpose of the smaller window titled "Chart" is unclear. Providing a brief documentation in the README or elsewhere would be beneficial.
  3. In line 10, the author cites the work by Huang et al. concerning AME2020. However, upon running the example file ./andes examples/s2.andes_ctrl, the following message occurs: 
    Loading control file: examples/s2.andes_ctrl
*** AME file nucdata/AME2020.txt was not found.

    For consistency and recency, please include the AME2020 file in nucdata/.

  4. The installation process via Makefile is smooth, but it would be better to specify the requirements more explicitly. While ROOT is listed as a requirement, not all versions and installations are compatible with ANDES. For instance, the official Docker Image (6.30.06-ubuntu22.04) and the conda package (6.30.4) failed to locate files like libEve.so in their default configurations. While a comprehensive list of compatible versions and configurations may not be feasible, mentioning at least the ROOT versions and configurations that were used by the author would be a good step forward.
  5. In lines 43-46, the author only mentions about previous works like Livechart 3D and Colourful Nuclide Chart. A comparison highlighting the advantages and limitations of ANDES relative to these works would be valuable.
  6. The sentence in lines 49-51, "The use mass... of atomic nuclei", is unclear and needs revision.
  7. The description in lines 16-19 suggests that ANDES can help visualize deviations from the smooth patterns around the Zr isotopes. Is Figure 1 intended to illustrate this capability? If so, the current figure lacks effectiveness. Given the focus on visualization in this work, including a well-annotated and labeled figure demonstrating how these deviations are visualized is crucial.

Overall, while the work meets the journal's minimum requirements, revisions are necessary for acceptance. The author should address the points raised above and consider feedback from other reviewers.

kellyrowland commented 1 month ago

@DeltaSigmaGamma please see the above - don't hesitate to post back here with any questions.

DeltaSigmaGamma commented 1 month ago

@fanurs @adrien-matta thank you very much for your reviews. I'll address your comments/questions in the next few days.

kellyrowland commented 3 weeks ago

thanks for the work here all 👋 @DeltaSigmaGamma just checking in on things

kellyrowland commented 4 days ago

just a status check @DeltaSigmaGamma 👋