editorialbot commented 4 months ago

Submitting author: !--author-handle-->@ialbert@mahfuz05062<!--end-editor-- Reviewers: @sridhar0605, @j-andrews7 Archive: 10.5281/zenodo.11245264

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/95590172072a9d2faec5a82a4920b3cc"><img src="https://joss.theoj.org/papers/95590172072a9d2faec5a82a4920b3cc/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/95590172072a9d2faec5a82a4920b3cc/status.svg)](https://joss.theoj.org/papers/95590172072a9d2faec5a82a4920b3cc)

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

@sridhar0605 & @j-andrews7, 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 @mahfuz05062 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 @j-andrews7

📝 Checklist for @sridhar0605

editorialbot commented 4 months 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 4 months ago

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

OK DOIs

- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (659.0 files/s, 223895.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          13           1226           1167           3746
JSON                             3              0              0           3452
CSS                              2            322             53           1938
CSV                              4              1              0            581
Markdown                         5            164              0            270
TOML                             2             45             12            239
HTML                             2             54             13            143
JavaScript                       3             40             28            118
TeX                              1              9              0             85
make                             2             37             26             78
YAML                             2             11              4             64
DOS Batch                        1              0              0              2
SVG                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            41           1909           1303          10717
-------------------------------------------------------------------------------

Commit count by author:

   211  Istvan Albert
     2  aswathy

editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 844

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago

License info:

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

editorialbot commented 4 months ago

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

mahfuz05062 commented 4 months ago

@sridhar0605 and @j-andrews7 - Thank you for agreeing to review this submission.

This is the review thread for the paper. All of our communications will happen here from now on.

As mentioned above, you can use the command @editorialbot generate my checklist to create your review checklist. 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 (https://joss.readthedocs.io/en/latest/reviewer_guidelines.html)

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6624 so that a link is created to this thread for visibility. 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 reviews to be completed within about 2-4 weeks. Please let me know if you require additional time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period.

Please feel free to ping me (@mahfuz05062) if you have any questions/concerns.

j-andrews7 commented 4 months ago

Review checklist for @j-andrews7

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/ialbert/genescape-central?
[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 (@ialbert) 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?

sridhar0605 commented 4 months ago

Review checklist for @sridhar0605

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/ialbert/genescape-central?
[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 (@ialbert) 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?

j-andrews7 commented 4 months ago

I've done a first pass review detailed more thoroughly in the project's issue tracker. It's generally in pretty good shape, and I expect Istvan will have little trouble addressing most of my points.

ialbert commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

ialbert commented 4 months ago

@j-andrews7 @sridhar0605

Based on reviewer suggestions, the software has been rewritten to be deployed as Shiny app and is now also available at

https://biostar.shinyapps.io/genescape/

A few minor alterations were made to the paper, citing Networkx and Shiny, additional screenshot of the Shiny interface was also added. All other suggestions were addressed. (See PDF above for updated paper).

Additional genomes were also added to the default distribution.

mahfuz05062 commented 4 months ago

I see that the reviews are going well. Please feel free to ask any questions that may arise!

j-andrews7 commented 4 months ago

Istvan has addressed all of my (relatively minor) concerns, and I consider my review complete.

ialbert commented 4 months ago

@sridhar0605 Hey Shridar, would you mind finishing your review? It seems the process is waiting for you to finalize it.

mahfuz05062 commented 4 months ago

@sridhar0605 Please let us know if anything is blocking you or if you need any assistance.

ialbert commented 4 months ago

@sridhar0605 @j-andrews7 all issues brought up by reviewers have been addressed, the interface has been reworked to Shiny app, and the app went through numerous iterations regarding the user interface elements and reporting.

sridhar0605 commented 4 months ago

@sridhar0605 Please let us know if anything is blocking you or if you need any assistance.

@ialbert has addressed all the issues that were raised by me.

mahfuz05062 commented 3 months ago

@sridhar0605 if you are satisfied with it, can you also mark the reproducibility tab? I will then go over the updated submission and take the next steps.

sridhar0605 commented 3 months ago

@mahfuz05062 Done.

mahfuz05062 commented 3 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
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.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
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 pull request)
[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
[ ] Recommend acceptance with @editorialbot recommend-accept

mahfuz05062 commented 3 months ago

@sridhar0605 and @j-andrews7 , thank you for completing your reviews.

@ialbert can you make sure to complete the post-review tasks from above? Thanks!

ialbert commented 3 months ago

@mahfuz05062 ok, I am planning to make a new software release for the paper, so will be doing that in a few days and tag here when done

ialbert commented 3 months ago

@mahfuz05062 Checklist completed.

Software release: 1.0.4

PyPI: https://pypi.org/project/genescape/

Zenodo DOI for the software: 10.5281/zenodo.11245263

Zenodo: https://zenodo.org/doi/10.5281/zenodo.11245263

Thank you reviewers @j-andrews7 @sridhar0605 for the suggestions. The software is now so much more usable.

mahfuz05062 commented 3 months ago

Thanks @ialbert . I will go through my list and take the next steps

mahfuz05062 commented 3 months ago

@editorialbot generate pdf

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:

mahfuz05062 commented 3 months ago

@editorialbot set v1.0.4 as version

editorialbot commented 3 months ago

Done! version is now v1.0.4

mahfuz05062 commented 3 months ago

@editorialbot set 10.5281/zenodo.11245263 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.11245263

mahfuz05062 commented 3 months ago

@editorialbot generate pdf

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:

mahfuz05062 commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

OK DOIs

- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK

MISSING DOIs

- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: shiny: Web Application Framework for R

INVALID DOIs

- None

mahfuz05062 commented 3 months ago

@ialbert - please change the title of your zenodo deposit to match the title of the paper. This is a change of metadata only, which doesn't require a new deposit or new DOI.

ialbert commented 3 months ago

@mahfuz05062 ok, done, zenodo deposit title matches the paper.

mahfuz05062 commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

OK DOIs

- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK

MISSING DOIs

- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: shiny: Web Application Framework for R

INVALID DOIs

- None

editorialbot commented 3 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

mahfuz05062 commented 3 months ago

@editorialbot set 10.5281/zenodo.11245264 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.11245264

mahfuz05062 commented 3 months ago

@editorialbot generate pdf

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:

mahfuz05062 commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

OK DOIs

- 10.1038/75556 is OK
- 10.1093/genetics/iyad031 is OK
- 10.1093/bioinformatics/btn615 is OK
- 10.1038/s41598-018-28948-z is OK
- 10.18129/B9.bioc.topGO is OK
- 10.1093/bioinformatics/btp536 is OK

MISSING DOIs

- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: shiny: Web Application Framework for R

INVALID DOIs

- None

editorialbot commented 3 months ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

Element isbn: [facet 'minLength'] The value has a length of '9'; this underruns the allowed minimum length of '10'.

openjournals / joss-reviews

[REVIEW]: GeneScape: A Python package for gene ontology analysis #6624

Status

Reviewer instructions & questions

Checklists

Review checklist for @j-andrews7

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sridhar0605

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