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

[editorialbot]

Submitting author: !--author-handle-->@LukeDicks<!--end-author-handle-- (Luke Dicks) Repository: https://github.com/IBM/topography-searcher Branch with paper.md (empty if default branch): Version: v0.0.2 Editor: !--editor-->@crvernon<!--end-editor-- Reviewers: @ml-evs, @lbl59 Managing EiC: Arfon Smith

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)

Author instructions

Thanks for submitting your paper to JOSS @LukeDicks. Currently, there isn't a JOSS editor assigned to your paper.

@LukeDicks if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.15 s (996.6 files/s, 161908.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            40              0              0           9304
Python                          67           1025           1802           8419
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           1448           2860          19250
-------------------------------------------------------------------------------

Commit count by author:

    71  Luke Dicks
     1  IBM Open Source Bot

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1199

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

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

[arfon]

@LukeDicks - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[crvernon]

@editorialbot assign me as editor

[editorialbot]

Assigned! @crvernon is now the editor

[crvernon]

@LukeDicks if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

[crvernon]

👋 @SarthakJariwala - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[crvernon]

👋 @dirmeier - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[LukeDicks]

@LukeDicks if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

@crvernon I think other suitable potential reviewers from the list would be Marjan Albooyeh, Jannis Born, Hengrui Zhang, Matthew Evans, Aakash Ashok Naik and Rocco Meli

[crvernon]

👋 @marjanalbouye - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[crvernon]

👋 @ml-evs - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[ml-evs]

👋 @ml-evs - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

I can review this but realistically not until w/c 13th May, feel free to pass over me if that is not quick enough

[crvernon]

@editorialbot add @ml-evs as reviewer

I think that is fine @ml-evs, much appreciated! I'll go ahead and add you.

[editorialbot]

@ml-evs added to the reviewers list!

[crvernon]

@editorialbot add @lbl59 as reviewer

[editorialbot]

@lbl59 added to the reviewers list!

[crvernon]

👋 - Alright @LukeDicks, @ml-evs, and @lbl59- I am going to close this Pre-Review and kick off the full review which you should receive a notification for. Thanks!

[crvernon]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6711.

[lbl59]

@editorialbot generate my checklist

[editorialbot]

Checklists can only be created once the review has started in the review issue