editorialbot commented 1 year ago

Submitting author: !--author-handle-->@OleBialas@britta-wstnr<!--end-editor-- Reviewers: @Saran-nns, @sappelhoff Archive: 10.5281/zenodo.8321912

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/20004bc0bb3e0918508c3cd45a2909e4"><img src="https://joss.theoj.org/papers/20004bc0bb3e0918508c3cd45a2909e4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/20004bc0bb3e0918508c3cd45a2909e4/status.svg)](https://joss.theoj.org/papers/20004bc0bb3e0918508c3cd45a2909e4)

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

@Saran-nns & @sappelhoff, 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 @britta-wstnr 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 @Saran-nns

📝 Checklist for @sappelhoff

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=0.08 s (313.5 files/s, 32208.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          10            152            497           1040
Markdown                         3             65              0            188
reStructuredText                 5             95             38            164
TeX                              1              8              0             89
YAML                             3              8              9             58
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            24            340            552           1574
-------------------------------------------------------------------------------

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

- 10.1101/2021.08.01.454687 is OK
- 10.48550/arXiv.2304.01799 is OK
- 10.1080/23273798.2018.1499946 is OK
- 10.3389/fnhum.2016.00604 is OK
- 10.1093/cercor/bht355 is OK
- 10.1016/j.neuroimage.2013.10.067 is OK
- 10.1016/j.cub.2015.08.030 is OK
- 10.1016/j.cub.2018.01.080 is OK
- 10.3389/fnins.2013.00267 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Wordcount for paper.md is 943

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:

britta-wstnr commented 1 year ago

Hello again! 👋  @sappelhoff @Saran-nns FYI @OleBialas

This is the review thread for the paper. All of our higher-level communications will happen here from now on, review comments and discussion can happen in the repository of the project (details below).

📓 Please read the "Reviewer instructions & questions" in the comment from our editorialbot (above).

✅ All reviewers get their own checklist with the JOSS requirements - you generate them as per the details in the editorialbot comment. As you go over the submission, please check any items that you feel have been satisfied.

💻 The JOSS review is different from most other journals: The reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention the link to #5657 so that a link is created to this thread. That will also help me to keep track!

❓ Please also feel free to comment and ask questions on this thread if you are unsure about something!

🎯 We aim for the review process to be completed within about 4-6 weeks* but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

*I do appreciate of course that it is summer vacation time 🏖️ - also a heads-up that I will have limited availability myself for the next two weeks.

Saran-nns commented 1 year ago

Review checklist for @Saran-nns

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/powerfulbean/mTRFpy?
[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 (@OleBialas) 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?

sappelhoff commented 1 year ago

Review checklist for @sappelhoff

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/powerfulbean/mTRFpy?
[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 (@OleBialas) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
- [x] https://github.com/powerfulbean/mTRFpy/pull/8
[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] https://github.com/powerfulbean/mTRFpy/issues/11
[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?

sappelhoff commented 1 year ago

I have completed my review of the package. I find it in good order and a helpful addition to the scientific Python ecosystem. I recommend this software and the associated paper for publication in JOSS. I have several minor issues and PRs open for this software that I will continue to work on with the authors, however they may be considered relatively minor and their outcome will not affect my overall judgment of this project.

britta-wstnr commented 1 year ago

Thank you very much for your detailed and thorough review of this, @sappelhoff! I appreciate it 🙏

britta-wstnr commented 1 year ago

Hi @Saran-nns, quickly checking in to see how your reviewing process is going? Don't hesitate to ping me if you have questions!

Saran-nns commented 1 year ago

@britta-wstnr thanks for the alert, i will start this weekend

Saran-nns commented 1 year ago

@britta-wstnr checklist is complete now, i am happy to recommend accept. Good work @OleBialas and team

britta-wstnr commented 1 year ago

Thank you @Saran-nns! Sorry for being slow here - I had a bit of a hectic second half of August.

Let's move this along!

britta-wstnr 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

britta-wstnr 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

- 10.1101/2021.08.01.454687 is OK
- 10.48550/arXiv.2304.01799 is OK
- 10.1080/23273798.2018.1499946 is OK
- 10.3389/fnhum.2016.00604 is OK
- 10.1093/cercor/bht355 is OK
- 10.1016/j.neuroimage.2013.10.067 is OK
- 10.1016/j.cub.2015.08.030 is OK
- 10.1016/j.cub.2018.01.080 is OK
- 10.3389/fnins.2013.00267 is OK

MISSING DOIs

- None

INVALID DOIs

- None

britta-wstnr commented 1 year ago

@editorialbot generate pdf

britta-wstnr commented 1 year ago

@OleBialas my next job is to check the paper - I will get back to you with some to do items once I have done this! 📄

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:

britta-wstnr commented 1 year ago

At this point also already a big thank you to @sappelhoff and @Saran-nns: thanks for your thorough reviews! 🙏 I and the JOSS team appreciate your work and time 💙

OleBialas commented 1 year ago

@britta-wstnr, we completed the checklist, the DOI for the archived package is 10.5281/zenodo.8312219

Also, I would like to repeat the thank you to @sappelhoff and @Saran-nns !

powerfulbean commented 1 year ago

Thank you @britta-wstnr for being the editor! We just updated the DOI and now it is 10.5281/zenodo.8312247. And I also would to thank @sappelhoff and @Saran-nns for being the reviewers and provide valuable modifications and comments!

britta-wstnr 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

- 10.1101/2021.08.01.454687 is OK
- 10.48550/arXiv.2304.01799 is OK
- 10.1080/23273798.2018.1499946 is OK
- 10.3389/fnhum.2016.00604 is OK
- 10.1093/cercor/bht355 is OK
- 10.1016/j.neuroimage.2013.10.067 is OK
- 10.1016/j.cub.2015.08.030 is OK
- 10.1016/j.cub.2018.01.080 is OK
- 10.3389/fnins.2013.00267 is OK

MISSING DOIs

- None

INVALID DOIs

- None

britta-wstnr 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:

britta-wstnr 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:

britta-wstnr commented 1 year ago

Hi @OleBialas,

thanks for starting on the check list. Could you please:

Change the title of the archive to match the title of the paper?
Create a release of the software and post the version number?

Here is the link to the full list: https://github.com/openjournals/joss-reviews/issues/5657#issuecomment-1701244325 (Additional Author Tasks) (You won't be able to tick things off, I will have to do that for you).

Thanks! 🙏

powerfulbean commented 1 year ago

Hi @britta-wstnr,

We just created a latest release and changed the title. Now the latest DOI is: 10.5281/zenodo.8321912.

Thank you!

britta-wstnr commented 1 year ago

@OleBialas the version number is v2.0.2, is that correct?

britta-wstnr commented 1 year ago

@editorialbot set 10.5281/zenodo.8321912 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8321912

powerfulbean commented 1 year ago

@OleBialas the version number is v2.0.2, is that correct?

Hi @britta-wstnr , yes, the version number is v2.0.2. Really sorry that I forgot to post the version number!

britta-wstnr commented 1 year ago

No problem @powerfulbean 🤗

britta-wstnr commented 1 year ago

@editorialbot set v2.0.2 as version

editorialbot commented 1 year ago

Done! version is now v2.0.2

britta-wstnr commented 1 year ago

@powerfulbean @OleBialas only thing to do now is for me to check the paper again. Feel free to also have a look again! (If you make changes, please let me know!)

britta-wstnr 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

- 10.1101/2021.08.01.454687 is OK
- 10.48550/arXiv.2304.01799 is OK
- 10.1080/23273798.2018.1499946 is OK
- 10.3389/fnhum.2016.00604 is OK
- 10.1093/cercor/bht355 is OK
- 10.1016/j.neuroimage.2013.10.067 is OK
- 10.1016/j.cub.2015.08.030 is OK
- 10.1016/j.cub.2018.01.080 is OK
- 10.3389/fnins.2013.00267 is OK

MISSING DOIs

- None

INVALID DOIs

- None

britta-wstnr 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:

britta-wstnr commented 1 year ago

Paper looks good to me - let's move on here! @Saran-nns and @sappelhoff many, many thanks again for your work and time reviewing this paper! 🙏 🌷 Thanks everyone for a smooth process!

I'm handing this off to the EiC team for the next steps.

PS: @OleBialas I could not find you in our reviewer database - we'd be very grateful if you considered signing up to pay it forward ✨ you can do that here: https://reviewers.joss.theoj.org/join

britta-wstnr 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

- 10.1101/2021.08.01.454687 is OK
- 10.48550/arXiv.2304.01799 is OK
- 10.1080/23273798.2018.1499946 is OK
- 10.3389/fnhum.2016.00604 is OK
- 10.1093/cercor/bht355 is OK
- 10.1016/j.neuroimage.2013.10.067 is OK
- 10.1016/j.cub.2015.08.030 is OK
- 10.1016/j.cub.2018.01.080 is OK
- 10.3389/fnins.2013.00267 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/dsais-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/4548, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

gkthiruvathukal commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

openjournals / joss-reviews

[REVIEW]: mTRFpy: A Python package for temporal response function analysis #5657

Status

Reviewer instructions & questions

Checklists

Review checklist for @Saran-nns

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @sappelhoff

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