editorialbot commented 1 year ago

Submitting author: !--author-handle-->@serioushorncat@jmschrei<!--end-editor-- Reviewers: @suragnair, @JDRomano2 Archive: 10.5281/zenodo.8380641

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/8f7091da9fa801c97f60a4af368c7b3a/status.svg)](https://joss.theoj.org/papers/8f7091da9fa801c97f60a4af368c7b3a)

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

@suragnair & @JDRomano2, 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 @suragnair

📝 Checklist for @JDRomano2

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:

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.14 s (1674.9 files/s, 208634.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            31              0              0           8342
JavaScript                      73            973            275           5144
Vuejs Component                 40            491             69           4500
Python                          43           1207            719           3446
Markdown                        10            418              0           1012
SVG                              6              0              2            737
YAML                            12             46              1            495
Bourne Shell                    10            102             54            403
CSS                              3             63             45            295
TeX                              1             13              0            218
Dockerfile                       3              6              6             47
HTML                             1              0              1             18
INI                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                           234           3319           1172          24658
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

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

OK DOIs

- 10.1093/genetics/iyac022 is OK
- 10.1093/bioinformatics/btu613 is OK
- 10.1093/nar/gkx1098 is OK
- 10.1186/s13059-016-0974-4 is OK
- 10.1093/nar/gkaa1043 is OK
- 10.1093/nar/gkl993 is OK
- 10.1093/nar/gkac888 is OK
- 10.1093/nar/gkx1153 is OK
- 10.1093/nar/gku1205 is OK
- 10.1101/gr.176601 is OK
- 10.1038/nmeth0410-248 is OK
- 10.1093/nar/gkv1189 is OK
- 10.1186/s13073-021-00835-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Wordcount for paper.md is 1653

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 @suragnair and @JDRomano2!

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!

jmschrei commented 1 year ago

Hi @suragnair and @JDRomano2

Do you think you'll have a chance to begin your reviews soon?

suragnair commented 1 year ago

Review checklist for @suragnair

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/uab-cgds-worthey/rosalution?
[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 (@serioushorncat) 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?

suragnair commented 1 year ago

@SeriousHorncat would it be possible to include either a link to a demo website (pre-populated with a few examples) or a video covering basic usage in the GitHub README? This would allow potential users to get a quick overview of the functionality and how to use Rosalution.

jmschrei commented 1 year ago

@JDRomano2 can we get an update on your progress?

JDRomano2 commented 1 year ago

@jmschrei I'll have the review completed tomorrow. Thanks for your patience!

JDRomano2 commented 1 year ago

Review checklist for @JDRomano2

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/uab-cgds-worthey/rosalution?
[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 (@serioushorncat) 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?

JDRomano2 commented 1 year ago

@SeriousHorncat I agree with @suragnair - I've been struggling to get the software running on my local computer. I think two things would significantly help:

Provide troubleshooting details for deployment
Stand up a public demo server that will allow users to quickly explore the core functionality of the software.

To provide a bit more information about the issue I'm experiencing, after following all of the deployment instructions I'm seeing a 404 page not found message when I navigate to localhost:80 in my browser.

Nothing in the logs suggests the cause of the issue. E.g., for rosalution-frontend-1:

2023-07-01 09:11:07 yarn run v1.22.5
2023-07-01 09:11:07 $ vite --host 0.0.0.0 --port 80
2023-07-01 09:11:07 
2023-07-01 09:11:07   VITE v4.0.4  ready in 241 ms
2023-07-01 09:11:07 
2023-07-01 09:11:07   ➜  Local:   http://localhost:80/
2023-07-01 09:11:07   ➜  Network: http://172.18.0.2:80/

and for rosalution-backend-1:

2023-07-01 09:11:08 INFO:     Will watch for changes in these directories: ['/app']
2023-07-01 09:11:08 INFO:     Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
2023-07-01 09:11:08 INFO:     Started reloader process [11] using WatchFiles
2023-07-01 09:11:08 INFO:     Started server process [13]
2023-07-01 09:11:08 INFO:     Waiting for application startup.
2023-07-01 09:11:08 INFO:     Application startup complete.

JDRomano2 commented 1 year ago

Please note that I am satisfied with all other aspects of the study. If the authors are able to provide a usable example and improve documentation such that I can get everything running locally I should be able to assess the outstanding items in the checklist.

I do feel that this is within the scope of JOSS and is a valuable contribution to the field.

SeriousHorncat commented 1 year ago

@SeriousHorncat would it be possible to include either a link to a demo website (pre-populated with a few examples) or a video covering basic usage in the GitHub README? This would allow potential users to get a quick overview of the functionality and how to use Rosalution.

@suragnair I meant to follow up on this sooner, we appreciate your patience. We agree a video demonstrating the basic usage of the application would be extremely helpful. @lizworthey-cgds and are reviewing a case that would be a good example to use in a demonstration video. We will follow up once we have a demo video prepared.

@SeriousHorncat I agree with @suragnair - I've been struggling to get the software running on my local computer. I think two things would significantly help:

Provide troubleshooting details for deployment

Stand up a public demo server that will allow users to quickly explore the core functionality of the software.

To provide a bit more information about the issue I'm experiencing, after following all of the deployment instructions I'm seeing a 404 page not found message when I navigate to localhost:80 in my browser.

Nothing in the logs suggests the cause of the issue. E.g., for rosalution-frontend-1:
2023-07-01 09:11:07 yarn run v1.22.5
2023-07-01 09:11:07 $ vite --host 0.0.0.0 --port 80
2023-07-01 09:11:07 
2023-07-01 09:11:07   VITE v4.0.4  ready in 241 ms
2023-07-01 09:11:07 
2023-07-01 09:11:07   ➜  Local:   http://localhost:80/
2023-07-01 09:11:07   ➜  Network: http://172.18.0.2:80/
and for rosalution-backend-1:
2023-07-01 09:11:08 INFO:     Will watch for changes in these directories: ['/app']
2023-07-01 09:11:08 INFO:     Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
2023-07-01 09:11:08 INFO:     Started reloader process [11] using WatchFiles
2023-07-01 09:11:08 INFO:     Started server process [13]
2023-07-01 09:11:08 INFO:     Waiting for application startup.
2023-07-01 09:11:08 INFO:     Application startup complete.

@JDRomano2

Additional and clearer documentation on how to visit the application, along with additional documentation on debugging common deployment issues, would be incredibly helpful. I will create an issue in our repo to track this. https://github.com/uab-cgds-worthey/rosalution/issues/105
We are discussing amongst the maintainers and our PI the potential for a demo site. We would need to remove certain features such as uploading new cases; since that could potentially put a strain on the 3rd party APIs. We try to be careful and limit the potential vectors of misuse of the application.

In the meantime, lets try to help get y'all deploying the application on your machines. We want to help continue to remove barriers for future contributors.

After running the following docker compose command in the code block below, could you visit http://local.rosalution.cgds/rosalution/ and the http://local.rosalution.cgds/rosalution/api/docs instead of visiting localhost:80 ? Do you see a login screen that looks like this picture?

docker compose up --build

If this does not work, could you share the results of the ./setup.sh and the docker ps commands from below?

./setup.sh clean
docker compose down
docker system prune -a --volumes # This will also remove other docker images but it's the fastest way to clear old images
docker compose up
docker ps

note: run the below code block in the project root folder of Rosalution

jmschrei commented 1 year ago

@suragnair I know you've been travelling recently, but can you provide an update when you're back?

@JDRomano2 have you had a chance to try out the above suggestions?

jmschrei commented 1 year ago

@suragnair @JDRomano2 checking in on this again. Have you been able to complete your reviews?

suragnair commented 1 year ago

Sorry for the delay! I was able to successfully install and get Rosalution running. The only items that remain are:

A researcher friendly user guide or video that @SeriousHorncat mentioned they are preparing
a comment on the state of the field in the manuscript

SeriousHorncat commented 1 year ago

Sorry for the delay! I was able to successfully install and get Rosalution running. The only items that remain are:

A researcher friendly user guide or video that @SeriousHorncat mentioned they are preparing

This has been perfect timing. We have finished preparing our first pass for a demonstration video of how Rosalution is being currently used - https://uab.app.box.com/s/r76kbgsmu2w562akfvdcfhutu2jwe6u3 , we have updated our README.md to include a link out to the demonstration video.

a comment on the state of the field in the manuscript

Originally we planed to update the Statement of Need section, but it just kept growing, so we opted to add a whole section dedicated to the State of the field https://github.com/uab-cgds-worthey/rosalution/pull/134 https://github.com/uab-cgds-worthey/rosalution/issues/87. So these changes are included now

Please let us know if there is anything else we can do to help facilitate this review more.

suragnair 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:

suragnair commented 1 year ago

Great, thanks. @jmschrei I have finished my review, all clear!

JDRomano2 commented 1 year ago

I have now completed my review as well and am fully satisfied with the revisions! Thanks for the updates, @SeriousHorncat !

SeriousHorncat commented 1 year ago

@suragnair and @JDRomano2 Thank you so much for investing your time for reviewing Rosalution. We at @uab-cgds-worthey are grateful for the feedback which helps reduce barriers for future contributors of Rosalution. Also, @jmschrei thank you for your time as editor to help this review process proceed smoothly.

Rosalution has a tag and release for version 0.6.0. What are the next steps necessary to help move this submission forward?

jmschrei commented 1 year ago

@JDRomano2 thanks for the review! If you're satisfied would you mind checking all the boxes in your review?

jmschrei 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
[x] Recommend acceptance with @editorialbot recommend-accept

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

- 10.1093/genetics/iyac022 is OK
- 10.1093/bioinformatics/btu613 is OK
- 10.1093/nar/gkx1098 is OK
- 10.1186/s13059-016-0974-4 is OK
- 10.1093/nar/gkaa1043 is OK
- 10.1093/nar/gkl993 is OK
- 10.1093/nar/gkac888 is OK
- 10.1093/nar/gkx1153 is OK
- 10.1093/nar/gku1205 is OK
- 10.1101/gr.176601 is OK
- 10.1038/nmeth0410-248 is OK
- 10.1093/nar/gkv1189 is OK
- 10.1186/s13073-021-00835-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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

@SeriousHorncat can you provide a DOI for the release corresponding to this submission, e.g., on Zenodo?

SeriousHorncat commented 1 year ago

DOI: 10.5281/zenodo.8348761 Is the DOI associated with out tagged 0.6.0 that was released on GitHub. @jmschrei

jmschrei commented 1 year ago

@editorialbot set 0.6.0 as version

editorialbot commented 1 year ago

Done! version is now 0.6.0

jmschrei commented 1 year ago

@editorialbot set 10.5281/zenodo.8348761 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8348761

jmschrei commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1093/genetics/iyac022 is OK
- 10.1093/bioinformatics/btu613 is OK
- 10.1093/nar/gkx1098 is OK
- 10.1186/s13059-016-0974-4 is OK
- 10.1093/nar/gkaa1043 is OK
- 10.1093/nar/gkl993 is OK
- 10.1093/nar/gkac888 is OK
- 10.1093/nar/gkx1153 is OK
- 10.1093/nar/gku1205 is OK
- 10.1101/gr.176601 is OK
- 10.1038/nmeth0410-248 is OK
- 10.1093/nar/gkv1189 is OK
- 10.1186/s13073-021-00835-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4581, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

SeriousHorncat commented 1 year ago

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.
- I fixed the associated license on the Zenodo archive, it was set to "Other" when I thought I had set GNU General Public License v3.0 and later.

Kevin-Mattheus-Moerman commented 1 year ago

@SeriousHorncat I am the AEiC on this track and here to help process final steps. I've checked your repository, the archive link, this review, and the paper. Most seems in order. Can you check the below final points please:

[x] The title for the archive does not match the paper, please edit the archive title to match.
[x] Check spelling of author Alexander Moss in the paper vs Alex Moss for the archive. Can you make these the same?
[x] Check if the word/expression simul is correct in the paper.
[ ] Please add the country to each affiliation. And please spell out the USA as United States of America.

SeriousHorncat commented 1 year ago

@SeriousHorncat I am the AEiC on this track and here to help process final steps. I've checked your repository, the archive link, this review, and the paper. Most seems in order. Can you check the below final points please:

[x] The title for the archive does not match the paper, please edit the archive title to match.
- Have revised the archive to match the title of the paper
[x] Check spelling of author Alexander Moss in the paper vs Alex Moss for the archive. Can you make these the same?
- Resolved the name abbreviation from Alex to Alexander for their author entry
[x] Check if the word/expression simul is correct in the paper.
- I read over the passage and followed up with looking for the definition to be sure. https://www.dictionary.com/browse/simul, several of our contributors use British english, simul can be used to to described as together and also used in place of simultaneous in British english. In the case of the paper is describing that datasets and analyses are being annotated together via a multi-threaded processing pool via different REST APIs. Is it ok if we leave the usage as is?
[x] Please add the country to each affiliation. And please spell out the USA as United States of America.
- Followed up and updated the country to each affiliation in the Zenodo archive and updated the paper in the repository accordingly. I did decide to create a new release so that it may exactly match the archive since we package the paper with the version.

New Version: 0.6.1 Updated Zenodo Archive for 0.6.1: 10.5281/zenodo.8380641

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 0.6.1 as version

editorialbot commented 1 year ago

Done! version is now 0.6.1

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set 10.5281/zenodo.8380641 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8380641

Kevin-Mattheus-Moerman commented 1 year ago

@SeriousHorncat thanks for implementing those changes. I think that addresses everything (and thanks for teaching me about the word simul, a new one for me). We will now proceed to accept this work in JOSS.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

Doing it live! Attempting automated processing of paper acceptance...

openjournals / joss-reviews

[REVIEW]: Rosalution: Supporting data accessibility, integration, curation, interoperability, and reuse for precision animal modeling #5443

Status

Reviewer instructions & questions

Checklists

Review checklist for @suragnair

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @JDRomano2

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

Additional Author Tasks After Review is Complete