editorialbot commented 1 year ago

Submitting author: !--author-handle-->@ByrumLab@jmschrei<!--end-editor-- Reviewers: @shahmoradi, @MohmedSoudy Archive: 10.5281/zenodo.7962306

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/9cc2593f89f34825b9b3b331d8156a86/status.svg)](https://joss.theoj.org/papers/9cc2593f89f34825b9b3b331d8156a86)

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

@shahmoradi & @MohmedSoudy, 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 @jmschrei 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 @shahmoradi

editorialbot commented 1 year 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:

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

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editorialbot commented 1 year ago

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

OK DOIs

- 10.1021/acsomega.0c02564 is OK
- 10.1021/pr401264n is OK
- 10.12688/f1000research.27893.1 is OK
- 10.1093/bioinformatics/btx094 is OK
- 10.1093/nar/gkv007 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (468.2 files/s, 171424.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                      21           2278           7436           8713
R                               45           1394           2229           4807
Markdown                         7            553              0           3205
CSS                             15            120            176           2551
HTML                             1             35              2            855
Rmd                              4            173            228            252
TeX                              1             13              0             72
YAML                             2              1              4             53
-------------------------------------------------------------------------------
SUM:                            96           4567          10075          20508
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 525

editorialbot commented 1 year ago

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

jmschrei commented 1 year ago

Howdy @shahmoradi and @MohmedSoudy!

Thanks for agreeing to review this submission.

The process for conducting a review is outlined above. Please run the command shown above to have @editorialbot generate your checklist, which will give a step-by-step process for conducting your review. Please check the boxes during your review to keep track, as well as make comments in this thread or open issues in the repository itself to point out issues you encounter. Keep in mind that our aim is to improve the submission to the point where it is of high enough quality to be accepted, rather than to provide a yes/no decision, and so having a conversation with the authors is encouraged rather than providing a single review post at the end of the process.

Here are the review guidelines: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html And here is a checklist, similar to above: https://joss.readthedocs.io/en/latest/review_checklist.html

Please let me know if you encounter any issues or need any help during the review process, and thanks for contributing your time to JOSS and the open source community!

MohmedSoudy commented 1 year ago

Review checklist for @MohmedSoudy

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 proteoDA?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author ByrumLab 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 participant's 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)?
[x] 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?
[ ] 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?
[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?

MohmedSoudy commented 1 year ago

Hi @ByrumLab, Thank you for that great software package. The paper is well-written and the package is well-documented, however, I have some comments that may increase the package's feasibility and usability

State of the field: I believe that this point should be highlighted in the paper to show the significance of the package and the contribution performed by the authors.
write_qc_report function: The names of the samples in the heat map should fit in the graph, and the legend position may be at the right and should be bigger to be more readable
write_limma_plots function: The user should select the p-value adjustment method on the plot and re-plot, and you can plot the box plot for each protein with the point plot for better visualization of the group mean/median and the outliers

ByrumLab commented 1 year ago

HI @MohmedSoudy, Thank you for taking time to review our package.

We have updated the paper.md to include a State of the field section.
write_qc_report has been updated for readability.
write_limma_plots has been updated with a selector to chose the plot type instead of including each as a separate tab. We added a mean line to the point plot to easily see the differences between the groups. The box plot was harder to visualize, especially for projects with only three replicates.

We appreciate your time and helpful suggestions.

jmschrei commented 1 year ago

@shahmoradi, do you think you'll have a chance to look at this submission soon?

shahmoradi commented 1 year ago

Apologies for my delayed response. I can respond as soon as I am back from an ongoing conference by this weekend if that is not too late.

MohmedSoudy commented 1 year ago

Review checklist for @MohmedSoudy

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 proteoDA?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author ByrumLab 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 participant's 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)?
[x] 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?

MohmedSoudy commented 1 year ago

Hi @ByrumLab Thank you for addressing my comments. For me, the paper and the package now are ready and I think it's acceptable for publication.

shahmoradi commented 1 year ago

Review checklist for @shahmoradi

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/ByrumLab/proteoDA?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ByrumLab) 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)?
[x] 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?

shahmoradi commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

shahmoradi commented 1 year ago

I have a few comments for which I'd appreciate the authors' response before I mark the remaining items in the checklist as approved.

I am not entirely familiar with testthat testing framework. Can you clarify how to run the tests? Normally, I'd expect a README file to exist in the appropriate folder that describes the steps to run the tests.
I cannot find any coverage reports in the repository. Unless I missed the report, a test suite without a code coverage report would be of minimal value. An example R package that could help generate coverage reports is covr.
~~I agree with @MohmedSoudy that the "State of the field" can be improved. I see the authors' response, but I cannot find the improvements in the most recent PDF compilation of the paper.~~ I can see the improvements in the most recent version now.
I cannot find "Community guidelines" in the repository. If one is already in the repository, please guide me to its location. See the checklist above for more information on "Community guidelines".

ByrumLab commented 1 year ago

Thank you @shahmoradi, we appreciate the review! We've made some changes to the package in response to your review:

The testthat framework is very commonly used across R packages, but it does have some differences to the way tests are distributed with other software packages and languages. In general, R packages do not have their tests bundled with them, so users cannot re-run testthat locally. See, for example, popular R packages like dplyr and ggplot2, which do not bundle their tests for distribution (that is, the tests are not in the inst/ directory). Instead, testthat runs package tests locally during development and during automated package checking with R CMD check. We have set up some GitHub actions to automatically run R CMD check against the latest R releases for the Mac, Windows, and Unix/Ubuntu operating systems, with the results displayed in a badge on the GitHub README. These tests are also run when packages are submitted to CRAN, which we plan to do upon acceptance.
We have used the R package you suggested to generate a code coverage report: it can be found by clicking on the codecov badge in our README. Currently, we have ~100% test coverage.
We have added community guidelines to our README, and have included a contributor code of conduct (CODE_OF_CONDUCT.md).

We hope these changes address your concerns.

ByrumLab commented 1 year ago

Hi @shahmoradi, I wanted to check if there are anymore concerns you would like us to address for this package?

Thanks!

jmschrei commented 1 year ago

Hi @shahmoradi, do you have any remaining concerns? If not, would you mind ticking the remaining boxes to let us know you're satisfied? Thanks!

jmschrei commented 1 year ago

@shahmoradi can you please provide an update?

shahmoradi commented 1 year ago

Thank you for your response @ByrumLab. I am fine with the latest updates and improvements and have approved all items in the checklist.

jmschrei commented 1 year ago

Great, thanks!

jmschrei commented 1 year ago

@ByrumLab what is the software version you'd like included in this release, and do you have a DOI for the code+paper, e.g. on Zenodo?

ByrumLab commented 1 year ago

@jmschrei This will be version 1.0.0 for the release. We currently do not have a DOI on Zenodo. Thanks.

jmschrei commented 1 year ago

@editorialbot set 1.0.0 as version

editorialbot commented 1 year ago

Done! version is now 1.0.0

jmschrei commented 1 year ago

@ByrumLab would you mind creating a DOI, following the instructions at https://joss.readthedocs.io/en/latest/submitting.html#the-review-process? We need one to accept the paper.

ByrumLab commented 1 year ago

@jmschrei yes, I'll send this as soon as possible. Thanks!

ByrumLab commented 1 year ago

@jmschrei here is the zenodo DOI: [DOI: 10.5281/zenodo.7962306]. url: "https://doi.org/10.5281/zenodo.7962306"

jmschrei commented 1 year ago

Thanks, @ByrumLab. Would you mind making the title and author list match the paper exactly?

ByrumLab commented 1 year ago

@jmschrei The title and author list should now match. Thanks!

jmschrei commented 1 year ago

Great, thank you.

jmschrei commented 1 year ago

@editorialbot set 10.5281/zenodo.7962306 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.7962306

jmschrei commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

jmschrei commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

jmschrei commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1021/acsomega.0c02564 is OK
- 10.1021/pr401264n is OK
- 10.12688/f1000research.27893.1 is OK
- 10.1093/bioinformatics/btx094 is OK
- 10.1093/nar/gkv007 is OK
- 10.1109/ACCESS.2020.3047588 is OK
- 10.1093/nar/gkac1040 is OK
- 10.1093/nar/gkab1038 is OK
- 10.1101/2022.08.17.503867 is OK
- 10.1101/2022.06.07.494524 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1002/bies.201800042 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1002/pmic.202100103 is INVALID because of 'https://doi.org/' prefix

jmschrei commented 1 year ago

@ByrumLab would you mind fixing these two invalid DOIs?

mikerobeson commented 1 year ago

@jmschrei I just committed changes to fix the invalid doi references to the main branch.

mikerobeson commented 1 year ago

@jmschrei @ByrumLab I just noticed that my name is incorrectly formatted in the proof as "II Michael S. Robeson" and it should be "Michael S. Robeson II". I'll see if I can fix ASAP.

mikerobeson commented 1 year ago

Author name has been fixed and committed. :-)

jmschrei commented 1 year ago

Thanks!

jmschrei commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

mikerobeson commented 1 year ago

Fixed affiliation 2 from "Biomedical Imaging" to "Biomedical Informatics". Committed changes.

mikerobeson commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

openjournals / joss-reviews

[REVIEW]: proteoDA: a package for quantitative proteomics #5184

Status

Reviewer instructions & questions

Checklists

Review checklist for @MohmedSoudy

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @MohmedSoudy

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @shahmoradi

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance