[REVIEW]: SigCorr: A Python package for studies of trials factors

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@vindex10@osorensen<!--end-editor-- Reviewers: @BSGalvan, @peifengjing, @gvieralopez Archive: 10.5281/zenodo.8096892

Status

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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

@BSGalvan & @peifengjing 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 @osorensen 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 @BSGalvan

📝 Checklist for @gvieralopez

📝 Checklist for @peifengjing

osorensen commented 1 year ago

Sorry @pibion and @AoifeHughes, I found you through https://reviewers.joss.theoj.org/, but unfortunately didn't notice you're both editors.

And thanks for the suggestion @pibion, I'll contact Dr. Austen.

osorensen commented 1 year ago

:wave: @BSGalvan, could you please check if the authors have solved you're issues satisfactorily, in this link https://gitlab.com/sigcorr/sigcorr/-/issues/2?

If so, please update your checklist higher up in this thread.

osorensen commented 1 year ago

👋 @adavidzh @ankur-gupta @tupi, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

FYI, this review has already been going on for a while, but we try to find some new reviewers as we're not able to get in touch with the ones originally assigned.

osorensen commented 1 year ago

@jdalzatec, could you please update us on how it's going with your review? If you have any questions regarding the process, feel free to ask them here or by contacting me by e-mail.

adavidzh commented 1 year ago

👋 @adavidzh @ankur-gupta @tupi, would any of you be willing to review this submission for JOSS?

While this is a topic I am familiar with, I cannot commit the time to take this through right now.

osorensen commented 1 year ago

Ok, thanks for responind @adavidzh!

osorensen commented 1 year ago

👋 @sajanbhagat @dufourc1 @JohannesBuchner, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

FYI, this review has already been going on for a while, but we try to find some new reviewers as we're not able to get in touch with the ones originally assigned.

vindex10 commented 1 year ago

FYI, the paper that highly relied on this package is out now: https://iopscience.iop.org/article/10.1088/1748-0221/18/05/P05041

JohannesBuchner commented 1 year ago

In August, I should have time again for reviews.

osorensen commented 1 year ago

Thanks for responding @JohannesBuchner. Hopefully we will have the reviews completed before August.

osorensen commented 1 year ago

:wave: @dirmeier @FATelarico would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

FYI, this review has already been going on for a while, but we try to find some new reviewers as we're not able to get in touch with the ones originally assigned.

osorensen commented 1 year ago

@vindex10, I'm really sorry that this review has taken so long. Let me assure you that I'm doing the best I can to find reviewers, but via GitHub and via e-mail. If you have any suggestions for reviewers, you're welcome to state them here.

vindex10 commented 1 year ago

@osorensen thank you for your attention! I really appreciate you keep searching for the reviewers and keep an eye at our submission :)

At the moment i can't come up with the suggestions though. I hope there will be someone available from the list 🤞

osorensen 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:

dirmeier commented 1 year ago

Hello, I don't have much time on my hands right now. Sorry!

osorensen commented 1 year ago

Thanks for responding, @dirmeier!

osorensen commented 1 year ago

👋 @gvieralopez @tbmiller-astro @peifengjing would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

FYI, this review has already been going on for a while, but we try to find some new reviewers as we're not able to get in touch with the ones originally assigned.

gvieralopez commented 1 year ago

Dear Øystein Sørensen:

I could take a look at the paper tomorrow and then give you a definitive answer, but in principle I can do it. I just need to make sure I am qualified to be a reviewer for this work before accepting.

Best regards,

Gustavo

El dom, 11 jun 2023 a las 20:26, Øystein Sørensen @.***>) escribió:

👋 @gvieralopez https://github.com/gvieralopez @tbmiller-astro https://github.com/tbmiller-astro @peifengjing https://github.com/peifengjing would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

FYI, this review has already been going on for a while, but we try to find some new reviewers as we're not able to get in touch with the ones originally assigned.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4989#issuecomment-1586274690, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABPYKYKRO3QAEWAXDCSGTDLXKYEVVANCNFSM6AAAAAASR5ESIU . You are receiving this because you were mentioned.Message ID: @.***>

osorensen commented 1 year ago

Thanks a lot @gvieralopez! Then I look forward to hearing back from you tomorrow.

peifengjing commented 1 year ago

Dear Øystein Sørensen, thank you for reaching out to me regarding the review of this paper. I understand that @gvieralopez has already promptly responded to your request, and if they are available and possess the necessary expertise, they may be better suited to conduct the review. However, if you believe an additional reviewer would be beneficial or if the other reviewer is unable to fulfill the request, I am more than willing to assist.

osorensen commented 1 year ago

Thanks @peifengjing! You are needed, and your review will be highly appreciated.

osorensen commented 1 year ago

@editorialbot add @peifengjing as reviewer

editorialbot commented 1 year ago

@peifengjing added to the reviewers list!

osorensen commented 1 year ago

@peifengjing, please see the instructions on top of this thread to get start with your review. In particular, stating the command @editorialbot generate my checklist in a comment will generate your checklist.

osorensen commented 1 year ago

Note: I removed @jdalzatec and @amorenobr from the list of reviewer because I have not able to get their reviews, despite a large number of attempts be e-mail and GitHub.

gvieralopez commented 1 year ago

Dear @osorensen,

I have reviewed the code from the paper under consideration, but due to limitations in my background and experience, I can only provide a partial assessment of the project.

The software's application is demonstrated through a specific case study related to particle physics, and corroborating the quality of these results is beyond my area of expertise. If you select me as a reviewer, I strongly recommend including another reviewer who is more familiar with that specific field in order to provide a more comprehensive review.

Best regards,

Gustavo

osorensen commented 1 year ago

@editorialbot add @gvieralopez as reviewer

editorialbot commented 1 year ago

@gvieralopez added to the reviewers list!

osorensen commented 1 year ago

Thanks a lot @gvieralopez. Your review will be much appreciated, and we are lucky to have two other reviewers with complementary expertise, so I'm sure this will be fine

osorensen commented 1 year ago

@gvieralopez, you can find the reviewer instructions at the top of this thread. You're also welcome to contact me in case you have questions.

gvieralopez commented 1 year ago

Review checklist for @gvieralopez

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://gitlab.com/sigcorr/sigcorr?
[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 (@vindex10) 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?

peifengjing commented 1 year ago

Review checklist for @peifengjing

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://gitlab.com/sigcorr/sigcorr?
[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 (@vindex10) 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?

sajanbhagat commented 1 year ago

Sure I can review few papers post 15th June.

On Thu, 25 May, 2023, 10:00 am Øystein Sørensen, @.***> wrote:

👋 @sajanbhagat https://github.com/sajanbhagat @dufourc1 https://github.com/dufourc1 @JohannesBuchner https://github.com/JohannesBuchner, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

FYI, this review has already been going on for a while, but we try to find some new reviewers as we're not able to get in touch with the ones originally assigned.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/4989#issuecomment-1562249791, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPELB3YY4Q44GFUS5NCLCTXH3N5PANCNFSM6AAAAAASR5ESIU . You are receiving this because you were mentioned.Message ID: @.***>

osorensen commented 1 year ago

@editorialbot add @sajanbhagat as reviewer

editorialbot commented 1 year ago

@sajanbhagat added to the reviewers list!

osorensen commented 1 year ago

Thanks a lot @sajanbhagat!

Please see the instructions on top of this thread to get start with your review. In particular, stating the command @editorialbot generate my checklist in a comment will generate your checklist.

peifengjing commented 1 year ago

I don't know what is the best way to link GitLab issues to GitHub, so I will put the link here for reproducing the results of the examples in the paper.

https://gitlab.com/sigcorr/sigcorr/-/issues/3

osorensen commented 1 year ago

I don't know what is the best way to link GitLab issues to GitHub, so I will put the link here for reproducing the results of the examples in the paper.

https://gitlab.com/sigcorr/sigcorr/-/issues/3

Thanks @peifengjing, linking here works well.

vindex10 commented 1 year ago

@editorialbot generate pdf

vindex10 commented 1 year ago

@peifengjing I updated the paper and replied in the issue, thank you for your comments!

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:

gvieralopez commented 1 year ago

I just created an issue regarding the manuscript:

https://gitlab.com/sigcorr/sigcorr/-/issues/4

vindex10 commented 1 year ago

@gvieralopez , thank you for your comments! we made the changes to the manuscript: https://gitlab.com/sigcorr/sigcorr/-/merge_requests/1/diffs?commit_id=26d69cdb69180d4cbaa8b2c24dd5dfeb9e05a124

vindex10 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:

peifengjing commented 1 year ago

I have reviewed the article proof and find it to be generally excellent. Here are some suggestions and comments for minor revisions https://gitlab.com/sigcorr/sigcorr/-/issues/5.

gvieralopez commented 1 year ago

@vindex10 I just created an issue with some comments related to the documentation:

https://gitlab.com/sigcorr/sigcorr/-/issues/6

Have a nice day!

vindex10 commented 1 year ago

Hi @peifengjing and @gvieralopez ! Thank you. We implemented the changes based on your comments and suggestions and the manuscript and the docs definitely improved in quality as a result. Please find more details on the changes made in the issues:

https://gitlab.com/sigcorr/sigcorr/-/issues/5 https://gitlab.com/sigcorr/sigcorr/-/issues/6

Cheers, Victor

vindex10 commented 1 year ago

@editorialbot generate pdf

openjournals / joss-reviews