[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

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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

gkthiruvathukal commented 4 months ago

@felixludos Thank you for your patience. Please do the following:

Make a tagged release of your software, and list the version tag of the archived version here as a separate reply.
Archive the reviewed software in Zenodo
Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
List the Zenodo DOI of the archived version here as a separate reply.

danielskatz commented 4 months ago

👋 @felixludos - note that we're just waiting for your actions here, in order to complete your acceptance and publication...

felixludos commented 3 months ago

The release tag is v1.0.5

felixludos commented 3 months ago

I also uploaded the release to Zenodo with DOI 10.5281/zenodo.11424101

Sorry it took so long.

gkthiruvathukal commented 3 months ago

Thanks, @felixludos! No worries. These are busy times for just about everyone. I will work on acceptance shortly.

gkthiruvathukal commented 3 months ago

@editorialbot set v1.0.5 as version

editorialbot commented 3 months ago

Done! version is now v1.0.5

gkthiruvathukal commented 3 months ago

@editorialbot set 10.5281/zenodo.11424101 as archive

editorialbot commented 3 months ago

Done! archive is now 10.5281/zenodo.11424101

gkthiruvathukal commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

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

gkthiruvathukal commented 3 months ago

@editorialbot recomment-accept

editorialbot commented 3 months ago

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

@editorialbot commands

gkthiruvathukal commented 3 months ago

@editorialbot commands

editorialbot commented 3 months ago

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


# List all available commands
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gkthiruvathukal commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

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

OK DOIs

- 10.1109/access.2022.3158675 is OK
- 10.1007/978-3-030-64148-1_10 is OK
- 10.1016/j.knosys.2020.106622 is OK

MISSING DOIs

- No DOI given, and none found for title: Artificial Intelligence for All
- No DOI given, and none found for title: Hydra - A framework for elegantly configuring comp...
- No DOI given, and none found for title: Gin Config - provides a lightweight configuration ...
- No DOI given, and none found for title: pydantic - Data parsing and validation using Pytho...
- No DOI given, and none found for title: OmegaConf - Flexible Python configuration system
- No DOI given, and none found for title: dynaconf - Configuration Management for Python
- No DOI given, and none found for title: configparser - Configuration file parser
- No DOI given, and none found for title: argparse - Parser for command-line options, argume...
- No DOI given, and none found for title: confr–A Configuration System for Machine Learning ...
- No DOI given, and none found for title: Tools and Practices for Responsible AI Engineering
- No DOI given, and none found for title: Measuring reproducibility in computer systems rese...
- No DOI given, and none found for title: DevOps
- 10.1007/978-1-4842-9642-4_1 may be a valid DOI for title: Introducing MLOps
- No DOI given, and none found for title: Improving reproducibility in machine learning rese...
- No DOI given, and none found for title: Pro git
- No DOI given, and none found for title: Machine bias
- No DOI given, and none found for title: Yaml ain’t markup language (yaml™) version 1.1

INVALID DOIs

- None

editorialbot commented 3 months ago

:wave: @openjournals/csism-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/5441, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

gkthiruvathukal commented 3 months ago

@felixludos It looks like there are still some errors in your references. Please fix.

danielskatz commented 3 months ago

Hi - I'm the track editor, and will now proofread this.

danielskatz commented 3 months ago

@felixludos - I've suggested a bunch of small changes in https://github.com/felixludos/omni-fig/pull/6 - please merge this, or let me know what you disagree with, then we can continue.

danielskatz commented 3 months ago

@editorialbot recommend-accept

editorialbot commented 3 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 3 months ago

:wave: @openjournals/csism-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/5444, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz commented 3 months ago

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

felixludos commented 3 months ago

@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 commented 3 months ago

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

I'll proceed to accept at this point.

danielskatz commented 3 months ago

@editorialbot accept

editorialbot commented 3 months ago

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

danielskatz commented 3 months ago

@editorialbot remove @luciorq as reviewer

editorialbot commented 3 months ago

@luciorq removed from the reviewers list!

editorialbot commented 3 months ago

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.

editorialbot commented 3 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 3 months ago

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

Here's what you must now do:

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

Any issues? Notify your editorial technical team...

danielskatz commented 3 months ago

@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.

editorialbot commented 3 months ago

Rebuilding paper!

editorialbot commented 3 months ago

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/5446

danielskatz commented 3 months ago

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

editorialbot commented 3 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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felixludos commented 3 months ago

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

julianpistorius commented 3 months ago

Congratulations @felixludos!

gkthiruvathukal commented 3 months ago

Congratulations, @felixludos!

felixludos commented 2 months ago

@editorialbot generate tex

editorialbot commented 2 months ago

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

@editorialbot commands

felixludos commented 2 months ago

@editorialbot commands

editorialbot commented 2 months ago

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 commented 2 months ago

@editorialbot generate preprint

editorialbot commented 2 months ago

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

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