editorialbot commented 1 year ago

Submitting author: !--author-handle-->@jhayer@fboehm<!--end-editor-- Reviewers: @mberacochea, @rcannood Archive: 10.5281/zenodo.8386399

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2"><img src="https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2/status.svg)](https://joss.theoj.org/papers/c60299dd2ffa63c5fb6364ea2d8234d2)

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

@mberacochea & @rcannood, 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 @fboehm 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 @rcannood

📝 Checklist for @mberacochea

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:

@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 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.04 s (340.0 files/s, 50197.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            180            230            797
Markdown                         2            114              0            385
TeX                              1             16              0            292
YAML                             3              5              9             39
-------------------------------------------------------------------------------
SUM:                            14            315            239           1513
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1231

editorialbot commented 1 year ago

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

OK DOIs

- 10.1038/D41586-022-00228-X is OK
- 10.1038/nbt.3820 is OK
- 10.1093/BIOINFORMATICS/BTY560 is OK
- 10.1002/CPBI.102 is OK
- 10.1371/JOURNAL.PCBI.1005595 is OK
- 10.1186/S13059-019-1891-0 is OK
- 10.1038/S41596-022-00738-Y is OK
- 10.1093/BIOINFORMATICS/BTT086 is OK
- 10.1093/MOLBEV/MSAB199 is OK
- 10.1128/AAC.02412-14 is OK
- 10.1099/MGEN.0.000398 is OK
- 10.1093/NAR/GKAC920 is OK
- 10.1038/s41598-021-91456-0 is OK
- 10.1093/BIOINFORMATICS/BTU153 is OK
- 10.1099/MGEN.0.000685 is OK
- 10.1093/BIOINFORMATICS/BTV421 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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:

fboehm commented 1 year ago

@mberacochea @rcannood - please let me know if you have any questions about getting started with the reviews. Thanks again!

fboehm commented 1 year ago

@mberacochea @rcannood - I hope that you're having a good weekend. The first step in the review is to create the checklist. Please try to create it using the instructions above. Let me know if you have any difficulties with it. Thanks again!

rcannood commented 1 year ago

:+1:

rcannood commented 1 year ago

Review checklist for @rcannood

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/jhayer/baargin?
[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 (@jhayer) 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?

fboehm commented 1 year ago

@mberacochea - do you have any questions about starting the review? I suggest that you first create a checklist using the command listed above.

mberacochea commented 1 year ago

@mberacochea - do you have any questions about starting the review? I suggest that you first create a checklist using the command listed above.

No, that is OK, thanks... I just been busy.

mberacochea commented 1 year ago

Review checklist for @mberacochea

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/jhayer/baargin?
[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 (@jhayer) 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?

fboehm commented 1 year ago

@mberacochea - how is the review going? Please feel free to leave comments for the author to improve the submission. If you have any questions, please ask me. Thanks again!

mberacochea commented 1 year ago

@mberacochea - how is the review going? Please feel free to leave comments for the author to improve the submission. If you have any questions, please ask me. Thanks again!

Hey.. apologies this is taking so long. I'll get my review completed before the end of the week.

fboehm commented 1 year ago

@jhayer - how are the revisions going? Please recognize that you'll need to address any issues that are raised by one or both reviewers. So if your team has the capacity to revise the submission to address the open issues, please feel free to do so now.

jhayer commented 1 year ago

@fboehm - Thank you it's ongoing (slowly, also a bit busy ATM). We are making PRs for addressing each comment from @rcannood

mberacochea commented 1 year ago

Hey, my inital review is done -> https://github.com/jhayer/baargin/issues/26

jhayer commented 1 year ago

Hi, We addressed most of your comments by several PRs (linked to issues numbers). We would like to merge all the PRs before proceeding with the remaining issues (tests: issues #47 and #48, and release: #44). Could you please @rcannood and @mberacochea check that all this is ok before we merge? Thank you !

fboehm commented 1 year ago

Thank you, @jhayer! I'll let @rcannood and @mberacochea comment here once they get a chance to look at the revisions.

fboehm commented 1 year ago

@rcannood & @mberacochea - please feel free to update us here as you review the changes. Thanks again!

fboehm commented 1 year ago

@rcannood @mberacochea - how are the reviews going? Please feel free to update us in this thread. Thanks again!

fboehm commented 1 year ago

@rcannood @mberacochea - how are the reviews going? Please examine the revisions from @jhayer and discuss in this thread. Thanks again!

rcannood commented 1 year ago

Thanks for the revisions @jhayer, and thanks @fboehm for reminding me! I'll make some time for it this week still.

mberacochea commented 1 year ago

@rcannood @mberacochea - how are the reviews going? Please examine the revisions from @jhayer and discuss in this thread. Thanks again!

Hi! I haven't been able to go through them, I'll get them done this weekend.

fboehm commented 1 year ago

Thanks for the replies, @rcannood and @mberacochea ! And thanks for agreeing to review the updates. As you proceed, please feel free to discuss things here. Also, feel free to open issues in the baargin repo, like you did with the first iteration of reviews.

Please know that I'm here to help, so if anything is unclear, don't hesitate to ask me about it. Thanks again!

mberacochea commented 1 year ago

Hi @fboehm and @jhayer. I have updated my PR and review checklist, and I've added one minor comment about the installation -> https://github.com/jhayer/baargin/issues/36.

I will go through the installation and functional testing as soon as the PRs are merged

fboehm commented 1 year ago

Thank you for the updates, @mberacochea ! I really appreciate the thorough review!

rcannood commented 1 year ago

Thanks for the updates! It's great that you split up the different items into different PRs, which allowed me to go through them and quickly find out whether the PR addressed the concerns I raised earlier.

With the updated codebase I managed to go through the documentation and execute the pipeline myself. Most of the checkboxes have now been ticked. I updated jhayer/baargin#13 based on some minor issues I encountered.

fboehm commented 1 year ago

@jhayer - how are the revisions going? Do you have any questions on how to proceed?

fboehm commented 1 year ago

@jhayer - how are the revisions going? Please feel free to reply here, even if you haven't completed them yet.

Thanks again!

jhayer commented 1 year ago

Hi, sorry for the late reply. Just 2 things left to do but my colleague is currently on holidays... we complete this ASAP and let you know when the last things are done. Apologies

fboehm commented 1 year ago

Thank you, @jhayer. Please feel free to update us every week, even if no progress is made. Thanks again!

fboehm commented 1 year ago

Hello, @jhayer - how are the updates proceeding? Do you have any questions?

thanks again!

jhayer commented 1 year ago

Hello @fboehm, I am so sorry for the delay (complicated with the summer holidays in the middle...). We should have addressed all the comments from the 2 reviewers now! Please let us know if there is anything else we should do. Thanks!

fboehm commented 1 year ago

Thank you, @jhayer . @mberacochea and @rcannood - please let us know your thoughts on the updates, and please feel free to check the remaining boxes if the criteria are met.

mberacochea commented 1 year ago

I have finished my review. Thank you @jhayer for addressing my comments with such diligence, the review process was very easy to follow. I recommend this manuscript for publication.

fboehm commented 1 year ago

Thank you, @mberacochea, for the thorough review. @rcannood - are there outstanding issues?

rcannood commented 1 year ago

Hi all! Sorry for taking so long to get back to this.

I'm thrilled with the changes that the authors have made! The revised manuscript looks great; I'm very happy that the workflow doesn't generate unnecessary warnings anymore; and the test profile provided by @jhayer works great!

Don't forget to update the manuscript, because the latest build still contains the previously mentioned typos (e.g. "NextFlow" → "Nextflow" and "Hight" → "High"), but I assume @editorialbot will take care of that automatically.

With the completion of jhayer/baargin#13, I can now recommend this manuscript.

fboehm commented 1 year ago

@rcannood - Thank you for the thorough review!

@jhayer - did you have a chance to fix the typos pointed out by @rcannood ? Once you do so, we can proceed. Thanks again!

jhayer commented 1 year ago

@fboehm - It was already fixed so I could not see the typos in my latest build (strange). I have double checked in the paper.md and it is ok there, so it should be fine for the final build. Thanks to all of you !

jhayer commented 1 year ago

Hi @fboehm - how long time should we expect for the article to be accepted and available online?

fboehm commented 1 year ago

Thanks for the question, @jhayer. The next steps require several actions from me and a few tasks from you. In a moment, I'll create the checklists for the remaining tasks. Once they are completed, I'll tell the EiCs that the submission is ready for publication. I expect that we'll need at least a week from now.

fboehm commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @fboehm, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

# Remove from this issue's reviewers list
@editorialbot remove @username from reviewers

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Assign a user as the editor of this submission
@editorialbot assign @username as editor

# Remove the editor assigned to this submission
@editorialbot remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set joss-paper as branch

# Set a value for repository
@editorialbot set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@editorialbot set set 10.5281/zenodo.6861996 as archive

# Mention the EiCs for the correct track
@editorialbot ping track-eic

# Generates the pdf paper
@editorialbot generate pdf

# Recommends the submission for acceptance
@editorialbot recommend-accept

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Flag submission with questionable scope
@editorialbot query scope

# Get a link to the complete list of reviewers
@editorialbot list reviewers

# Creates a post-review checklist with editor and authors tasks
@editorialbot create post-review checklist

# Open the review issue
@editorialbot start review

fboehm commented 1 year 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 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
[ ] Recommend acceptance with @editorialbot recommend-accept

fboehm commented 1 year ago

@jhayer - I'll read the paper and, if needed, suggest minor changes, like typo fixes. I expect to do that in the next few days. I'll notify you here once I've completed that task. In the mean time, please feel free to begin the tasks listed above under "Additional author tasks after review is complete".

jhayer 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. baargin-v1.0.0

[x] Archive the release on Zenodo/figshare/etc and post the DOI here. https://doi.org/10.5281/zenodo.8386399

[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.

fboehm commented 1 year ago

@jhayer - thank you so much for completing those tasks and sharing the information. I expect to review things soon. I'll update you again once I complete my tasks on the checklist.

Thanks again!

fboehm 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]: Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance #5397

Status

Reviewer instructions & questions

Checklists

Review checklist for @rcannood

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @mberacochea

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

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete