[REVIEW]: pyQCM-BraTaDio: A tool for visualization, data mining, and modelling of Quartz crystal microbalance with dissipation data

editorialbot commented 4 weeks ago

Submitting author: !--author-handle-->@b-pardi@zhubonan<!--end-editor-- Reviewers: @kstenio, @erik-whiting Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/39e8b2bded5c8052e595a80201eedc36/status.svg)](https://joss.theoj.org/papers/39e8b2bded5c8052e595a80201eedc36)

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

@kstenio & @erik-whiting, 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 @zhubonan 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 @erik-whiting

📝 Checklist for @kstenio

editorialbot commented 4 weeks ago

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editorialbot commented 4 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (366.1 files/s, 306097.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              8              0              0          23669
Python                          19            923            970           3335
Markdown                         3            198              0            822
TeX                              2             13              1             99
JSON                             2              0              0             28
YAML                             1              1              4             18
HTML                             1              1              1             15
-------------------------------------------------------------------------------
SUM:                            36           1136            976          27986
-------------------------------------------------------------------------------

Commit count by author:

    94  brandonator24
     5  b-pardi

editorialbot commented 4 weeks ago

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

OK DOIs

- 10.1007/BF01337937 is OK

MISSING DOIs

- No DOI given, and none found for title: Simultaneous AFM and QCM measurements: methodology...
- No DOI given, and none found for title: Integrated QCM-Microtribometry: Friction of Single...
- 10.1021/la0112716 may be a valid DOI for title: Using surface plasmon resonance and the quartz cry...
- 10.1016/j.elecom.2016.03.006 may be a valid DOI for title: Quartz crystal microbalance with dissipation monit...
- 10.1116/1.5142762 may be a valid DOI for title: Investigations of the high-frequency dynamic prope...
- 10.3390/s23031348 may be a valid DOI for title: Effect of Noise on Determining Ultrathin-Film Para...
- 10.1021/la035965l may be a valid DOI for title: Operation of the quartz crystal microbalance in li...
- 10.1063/1.1737049 may be a valid DOI for title: Effects of finite crystal size in the quartz cryst...

INVALID DOIs

- None

editorialbot commented 4 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1699

✅ The paper includes a Statement of need section

editorialbot commented 4 weeks ago

License info:

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

editorialbot commented 4 weeks ago

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

zhubonan commented 4 weeks ago

@kstenio & @erik-whiting, please can each of you generate a separate checklist - you should update when carrying out your review. To create the checklist, simply leave a comment with:

@editorialbot generate my checklist

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

I am hoping to have the review finished in three weeks. Please let me know if you need more time. Thanks in advance.

erik-whiting commented 4 weeks ago

Review checklist for @erik-whiting

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/b-pardi/BraTaDio?
[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 (@b-pardi) 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.
[x] 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?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

kstenio commented 3 weeks ago

Review checklist for @kstenio

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/b-pardi/BraTaDio?
[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 (@b-pardi) 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.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] 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.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

erik-whiting commented 2 weeks ago

Hello @zhubonan, I have completed my initial review and opened an issue for my findings here: https://github.com/b-pardi/BraTaDio/issues/1

zhubonan commented 2 weeks ago

@erik-whiting That's great, thanks for letting me know. 🚀 @b-pardi Please address these comments - you can reply/discuss directly inside the issue opened https://github.com/b-pardi/BraTaDio/issues/1. Please give me a ping when you are done. Thanks.

kstenio commented 2 weeks ago

Hello @zhubonan , I also made my initial review.

Open Issues

b-pardi/BraTaDio#2
b-pardi/BraTaDio#3
b-pardi/BraTaDio#4
b-pardi/BraTaDio#5
b-pardi/BraTaDio#6
b-pardi/BraTaDio#7

b-pardi commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

b-pardi commented 1 week ago

Hey @zhubonan I believe I have remedied all issues outlined in round 1

openjournals / joss-reviews