[REVIEW]: TopSearch: a Python package for topographical analysis of machine learning models and physical systems

editorialbot commented 2 weeks ago

Submitting author: !--author-handle-->@LukeDicks@crvernon<!--end-editor-- Reviewers: @ml-evs, @lbl59 Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5869f7ba6cf4eaac5d5f9526eb1d2de5"><img src="https://joss.theoj.org/papers/5869f7ba6cf4eaac5d5f9526eb1d2de5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5869f7ba6cf4eaac5d5f9526eb1d2de5/status.svg)](https://joss.theoj.org/papers/5869f7ba6cf4eaac5d5f9526eb1d2de5)

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

@ml-evs & @lbl59, 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 @crvernon 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 @lbl59

📝 Checklist for @ml-evs

editorialbot commented 2 weeks ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 2 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.15 s (986.9 files/s, 162032.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            40              0              0           9304
Python                          67           1040           1836           8618
JavaScript                       1             89             77            458
Markdown                        24            144              0            413
TeX                              1             30              0            253
Jupyter Notebook                 3              0            978            167
CSS                              1            152              3            154
TOML                             1              4              0             30
SparForte                        4              0              0             26
YAML                             1              4              0             19
INI                              1              0              0              6
JSON                             1              0              0              1
-------------------------------------------------------------------------------
SUM:                           145           1463           2894          19449
-------------------------------------------------------------------------------

Commit count by author:

    73  Luke Dicks
     1  IBM Open Source Bot

editorialbot commented 2 weeks ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1017/CBO9780511721724 is OK
- 10.48550/arXiv.2305.10748 is OK
- 10.1088/2632-2153/ac49a9 is OK
- 10.1063/5.0078793 is OK
- 10.1016/j.sbi.2008.01.008 is OK
- 10.1039/D3DD00204G is OK
- 10.48550/arXiv.2306.14346 is OK
- 10.48550/arXiv.2305.17279 is OK
- 10.1039/D3ME00189J is OK
- 10.1021/acs.jctc.5b00743 is OK
- 10.1016/j.cpc.2013.09.018 is OK
- 10.1016/j.cpc.2021.108171 is OK
- 10.1016/j.softx.2015.06.001 is OK
- 10.1109/TETCI.2021.3100641 is OK
- 10.1016/j.cpc.2023.108831 is OK
- 10.1063/5.0004608 is OK
- 10.1016/j.cpc.2018.06.026 is OK
- 10.1002/adts.201800175 is OK
- 10.1063/5.0159367 is OK
- 10.1063/5.0167857 is OK
- 10.1021/acs.jpcc.1c09120 is OK
- 10.1038/s42254-021-00314-5 is OK
- 10.1021/acs.jctc.9b01211 is OK
- 10.1002/widm.1424 is OK
- 10.1016/j.neuron.2017.06.011 is OK

MISSING DOIs

- No DOI given, and none found for title: GMIN: a program for basin-hopping global optimisat...
- No DOI given, and none found for title: OPTIM: a program for geometry optimisation and pat...
- No DOI given, and none found for title: PATHSAMPLE: a program for generating connected sta...
- No DOI given, and none found for title: AMBER 2023
- No DOI given, and none found for title: pylfl
- No DOI given, and none found for title: VTST Tools

INVALID DOIs

- None

editorialbot commented 2 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1199

✅ The paper includes a Statement of need section

editorialbot commented 2 weeks ago

License info:

✅ License found: MIT License (Valid open source OSI approved license)

editorialbot commented 2 weeks ago

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

crvernon commented 2 weeks ago

👋 @LukeDicks, @ml-evs, and @lbl59 - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6711 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

lbl59 commented 2 weeks ago

Review checklist for @lbl59

Conflict of interest

[ ] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[ ] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[ ] Repository: Is the source code for this software available at the https://github.com/IBM/topography-searcher?
[ ] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@LukeDicks) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[ ] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[ ] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

ml-evs commented 6 days ago

Review checklist for @ml-evs

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/IBM/topography-searcher?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@LukeDicks) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[ ] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[ ] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[ ] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

ml-evs commented 6 days ago

I have made my initial comments at https://github.com/IBM/topography-searcher/issues/3 but ran into a few issues and am as of yet am unable to verify the functionality of the package. I have limited availability this week and will be entirely unavailable next week, but happy to test out any fixes when I return.

openjournals / joss-reviews