[REVIEW]: omni-fig: Unleashing Project Configuration and Organization in Python

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@felixludos@gkthiruvathukal<!--end-editor-- Reviewers: @julianpistorius, @jarrah42 Archive: 10.5281/zenodo.11424101

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

@julianpistorius & @luciorq, 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 @gkthiruvathukal 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 @julianpistorius

📝 Checklist for @jarrah42

editorialbot commented 1 year ago

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.17 s (1067.4 files/s, 86334.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          55           3059           2814           4310
Jupyter Notebook                 5              0            819            493
YAML                            70            316             22            469
reStructuredText                32            625            796            295
TeX                              1             23              0            131
Markdown                         3             35              0             84
DOS Batch                        1              8              1             26
CSS                              1             10              6             25
make                             1              4              7              9
SVG                              8              0              0              8
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                           178           4080           4465           5852
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1054

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:

editorialbot commented 1 year ago

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

OK DOIs

- 10.1007/978-3-030-64148-1_10 is OK
- 10.1016/j.knosys.2020.106622 is OK

MISSING DOIs

- 10.1109/access.2022.3158675 may be a valid DOI for title: Reproducibility in Computing Research: An Empirical Study

INVALID DOIs

- None

julianpistorius commented 1 year ago

Review checklist for @julianpistorius

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/felixludos/omni-fig?
[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 (@felixludos) 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?

julianpistorius commented 1 year ago

@gkthiruvathukal I need guidance.

Under the Software Paper heading, the last task is:

[ ] 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?

I noticed that @editorialbot found a missing DOI: https://github.com/openjournals/joss-reviews/issues/5350#issuecomment-1500681422

I created an issue for the author, but have had no response yet: https://github.com/felixludos/omni-fig/issues/2

Does this matter? Shall I consider this task complete even if there is a missing DOI?

gkthiruvathukal commented 1 year ago

The reference should be fixed. Please try to nudge the author again!

On Tue, May 2, 2023 at 3:47 PM Julian Pistorius @.***> wrote:

@gkthiruvathukal https://github.com/gkthiruvathukal I need guidance.

Under the Software Paper heading, the last task is:

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 https://pandoc.org/MANUAL.html#extension-citations?

I noticed that @editorialbot https://github.com/editorialbot found a missing DOI: #5350 (comment) https://github.com/openjournals/joss-reviews/issues/5350#issuecomment-1500681422

I created an issue for the author, but have had no response yet: felixludos/omni-fig#2 https://github.com/felixludos/omni-fig/issues/2

Does this matter? Shall I consider this task complete even if there is a missing DOI?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/5350#issuecomment-1532127829, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAE7B4BR5NVR3ZGMHJ6YAVDXEFXETANCNFSM6AAAAAAWW6XZDI . You are receiving this because you were mentioned.Message ID: @.***>

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julianpistorius commented 1 year ago

Thank you @gkthiruvathukal. I've prodded @felixludos again. In the meantime I'll continue with the other tasks in the review checklist.

felixludos commented 1 year ago

Hi, i just fixed the missing DOI. Sorry for the delay.

Is there anything else you need from me?

julianpistorius commented 1 year ago

Thanks @felixludos! I think that's all for the moment.

julianpistorius commented 1 year ago

I'm done @gkthiruvathukal & @felixludos.

julianpistorius commented 1 year ago

@editorialbot create post-review checklist

editorialbot commented 1 year ago

I'm sorry @julianpistorius, I'm afraid I can't do that. That's something only editors are allowed to do.

danielskatz commented 1 year ago

👋 @gkthiruvathukal - It looks like you have one complete review and one reviewer who hasn't started yet. How do we move this forward?

gkthiruvathukal commented 1 year ago

Ok, I'm sorry for the delay here. And more sorry for not seeing that the other reviewer hasn't started. Let me try an additional nudge.

gkthiruvathukal commented 1 year ago

Hi @luciorq, Can you please update us on when you may be able to complete your review? @julianpistorius's review is complete. We need your input before we can proceed with this JOSS submission.

gkthiruvathukal commented 1 year ago

@felixludos We need to have a second review. Can you please suggest 1-2 other possibilities from the list of reviewers atop the issue thread? Thanks!

felixludos commented 1 year ago

Does someone else from the list I originally suggested work: ChristopherHaydenTodd, urjoshi, jarrah42, erik-whiting, idoby? Thanks!

felixludos commented 1 year ago

@gkthiruvathukal Do any of these work as additional reviewers: ChristopherHaydenTodd, urjoshi, jarrah42, erik-whiting, idoby?

gkthiruvathukal commented 1 year ago

@felixludos I will get on this by the weekend. I am out of office until Friday (18th).

felixludos commented 1 year ago

@gkthiruvathukal Any update?

felixludos commented 1 year ago

@gkthiruvathukal @julianpistorius @luciorq Is there someone I can reach out to to get this moving forward?

gkthiruvathukal commented 1 year ago

Sorry for the delay. I am buried in early semester work. I will try to get things moving again in the next day or two.

gkthiruvathukal commented 1 year ago

@jarrah42 Are you willing to help review this JOSS submission? We need an additional review.

danielskatz commented 11 months ago

@gkthiruvathukal - can you get back to this if you have time?

gkthiruvathukal commented 11 months ago

@ChristopherHaydenTodd Are you willing to help review this JOSS submission? We need an additional review.

jarrah42 commented 11 months ago

@gkthiruvathukal I can review it.

gkthiruvathukal commented 9 months ago

@editorialbot add @jarrah42 as reviewer

editorialbot commented 9 months ago

@jarrah42 added to the reviewers list!

gkthiruvathukal commented 9 months ago

@jarrah42 I need your help to review this submission. Hope you are still willing!

jarrah42 commented 9 months ago

@gkthiruvathukal I'm currently under multiple deadlines so I wouldn't be able to get to this until mid Jan. Let me know if that is ok, otherwise it might be better to get someone else if it is needed sooner.

gkthiruvathukal commented 9 months ago

@jarrah42 I am willing to wait for you. I'm going to assume that you are willing to have me assign you and continue with the review process. Happy holidays!

gkthiruvathukal commented 9 months ago

@editorialbot add @jarrah42 as reviewer

editorialbot commented 9 months ago

@jarrah42 is already included in the reviewers list

arfon commented 7 months ago

:wave: @jarrah42 – how are you getting along with your review?

jarrah42 commented 7 months ago

👋 @jarrah42 – how are you getting along with your review?

Sorry, completely fell off the list. Back on now

jarrah42 commented 7 months ago

Review checklist for @jarrah42

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/felixludos/omni-fig?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@felixludos) 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?

gkthiruvathukal commented 7 months ago

@julianpistorius, @luciorq, @jarrah42: How are things going with the review?

julianpistorius commented 6 months ago

@gkthiruvathukal AFAIK my part is done. Please let me know if you need anything more from me.

jarrah42 commented 6 months ago

@gkthiruvathukal back on it

jarrah42 commented 6 months ago

There are two minor problems.

The community guidelines are very brief. I would be good to provide more information on how to contribute to the project, how to obtain support, etc.
There is a docs:failing badge on the GitHub site.

Other than these I think it is fine.

gkthiruvathukal commented 6 months ago

Thanks @julianpistorius and @jarrah42.

@felixludos Can you let me know when the additional issues from @jarrah42 are resolved?

felixludos commented 6 months ago

@gkthiruvathukal All issues fixed. Thank you for the pull request @jarrah42

gkthiruvathukal commented 6 months ago

@felixludos I'll move toward acceptance. Stay tuned.

jarrah42 commented 6 months ago

@gkthiruvathukal I’m done.

felixludos commented 5 months ago

@gkthiruvathukal Any progress on this? :)

gkthiruvathukal commented 5 months ago

@felixludos I will work on this shortly. Sorry it is not done already. Rest assured, the submission is in good shape and will be accepted, hopefully before the weekend.

gkthiruvathukal commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

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