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[REVIEW]: omni-fig: Unleashing Project Configuration and Organization in Python #5350

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editorialbot opened this issue Apr 7, 2023 · 99 comments
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[REVIEW]: omni-fig: Unleashing Project Configuration and Organization in Python #5350

editorialbot opened this issue Apr 7, 2023 · 99 comments
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@gkthiruvathukal @jarrah42
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accepted Jupyter Notebook published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Apr 7, 2023 •
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Submitting author: @felixludos (Felix Leeb)
Repository: https://github.com/felixludos/omni-fig
Branch with paper.md (empty if default branch):
Version: v1.0.5
Editor: @gkthiruvathukal
Reviewers: @julianpistorius, @jarrah42
Archive: 10.5281/zenodo.11424101

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8eb5d7f02686b32f3102a5a03f92f169"><img src="https://joss.theoj.org/papers/8eb5d7f02686b32f3102a5a03f92f169/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/8eb5d7f02686b32f3102a5a03f92f169/status.svg)](https://joss.theoj.org/papers/8eb5d7f02686b32f3102a5a03f92f169)

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 editorialbot added Jupyter Notebook Python review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Apr 7, 2023
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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 editorialbot mentioned this issue Apr 7, 2023
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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

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Wordcount for paper.md is 1054

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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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

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julianpistorius commented Apr 11, 2023 •
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Review checklist for @julianpistorius

Conflict of interest

  • 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

General checks

  • Repository: Is the source code for this software available at the https://github.com/felixludos/omni-fig?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • 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.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • 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

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • 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?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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 julianpistorius mentioned this issue Apr 20, 2023
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@julianpistorius
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@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: #5350 (comment)

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

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

@gkthiruvathukal
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gkthiruvathukal commented May 2, 2023 via email

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

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

Is there anything else you need from me?

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

@julianpistorius
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I'm done @gkthiruvathukal & @felixludos.

@julianpistorius
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@editorialbot create post-review checklist

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

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

@gkthiruvathukal
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gkthiruvathukal commented Jul 13, 2023 •
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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.

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

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

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

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felixludos commented Sep 14, 2023 •
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@gkthiruvathukal Any update?

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👋 @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5444, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@danielskatz
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@felixludos - please confirm that this proof looks correct to you.

@felixludos
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@danielskatz The proof looks correct to me! Thanks!
@gkthiruvathukal Regarding the missing DOIs, some references don't seem to have any DOI (e.g. other github repos that haven't been archived). Is it ok to leave the references as is (preferable) or is there another workaround? Thanks!

@danielskatz
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The references without DOIs are fine. And the one suggestion from editorialbot is wrong.

I'll proceed to accept at this point.

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@editorialbot accept

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

@danielskatz
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@editorialbot remove @luciorq as reviewer

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@luciorq removed from the reviewers list!

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff 

cff-version: "1.2.0"
authors:
- family-names: Leeb
  given-names: Felix
  orcid: "https://orcid.org/0000-0002-3127-5707"
contact:
- family-names: Leeb
  given-names: Felix
  orcid: "https://orcid.org/0000-0002-3127-5707"
doi: 10.5281/zenodo.11424101
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Leeb
    given-names: Felix
    orcid: "https://orcid.org/0000-0002-3127-5707"
  date-published: 2024-06-04
  doi: 10.21105/joss.05350
  issn: 2475-9066
  issue: 98
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5350
  title: "omni-fig: Unleashing Project Configuration and Organization in
    Python"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05350"
  volume: 9
title: "omni-fig: Unleashing Project Configuration and Organization in
  Python"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.05350 joss-papers#5445
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05350
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jun 4, 2024
@danielskatz
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@editorialbot reaccept

Sorry, I missed the fact that one of the reviewers should have been deleted, and shouldn't appear in the final paper - I changed this after the accept, so now need to re-accept to update the deposited paper.

@gkthiruvathukal - please be sure to remove any reviewers that stop working on a paper via the remove . as reviewer command next time.

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Rebuilding paper!

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🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5446

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Congratulations to @felixludos (Felix Leeb) on your publication!!

And thanks to @julianpistorius and @jarrah42 for reviewing, and to @gkthiruvathukal for editing!
JOSS depends on volunteers and couldn't be successful without your work

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.05350/status.svg)](https://doi.org/10.21105/joss.05350)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05350">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05350/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05350/status.svg
   :target: https://doi.org/10.21105/joss.05350

This is how it will look in your documentation:

DOI

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

@felixludos
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Great thank you to the editors and reviewers for walking me through all the steps and the pull requests to improve things!

@julianpistorius
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Congratulations @felixludos!

@gkthiruvathukal
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Congratulations, @felixludos!

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@editorialbot generate tex

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

@felixludos
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@editorialbot commands

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


# List all available commands
@editorialbot commands

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

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

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

@felixludos
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@editorialbot generate preprint

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📄 Preprint file created: Find it here in the Artifacts list 📄

@editorialbot editorialbot mentioned this issue Jul 30, 2024
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@editorialbot editorialbot mentioned this issue Nov 5, 2024
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@jarrah42 jarrah42

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