[REVIEW]: ChainoPy: A Python Library for Discrete Time Markov Chain based stochastic analysis

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@aadya940@mooniean<!--end-editor-- Reviewers: @braniii, @MichalisPanayides Archive: 10.5281/zenodo.13305155

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6"><img src="https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6/status.svg)](https://joss.theoj.org/papers/486cf1a43c0079e0628e044215168ad6)

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

@braniii & @MichalisPanayides, 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 @mooniean 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 @MichalisPanayides

📝 Checklist for @braniii

mooniean commented 1 month ago

@aadya940 that's ok! Just need you to upload to zenodo or figshare and post here the DOI

aadya940 commented 1 month ago

Its done @mooniean

The zenodo DOI for v1.0.3 (latest) is:

10.5281/zenodo.13305155

mooniean commented 1 month ago

Apologies!! The thread hadn't updated when I commented... my bad 🤦‍♀️

aadya940 commented 1 month ago

No worries :)), Let me know if I have anything left to do.

mooniean commented 4 weeks ago

Hi @aadya940! Can you edit the zenodo and make sure the title and the author list match the paper title and author list?

aadya940 commented 4 weeks ago

@mooniean Done :)

mooniean commented 4 weeks ago

@editorialbot set 10.5281/zenodo.13305155 as archive

editorialbot commented 4 weeks ago

Done! archive is now 10.5281/zenodo.13305155

mooniean commented 4 weeks ago

@editorialbot set v1.0.3 as version

editorialbot commented 4 weeks ago

Done! version is now v1.0.3

mooniean commented 4 weeks ago

@editorialbot recommend-accept

editorialbot commented 4 weeks ago

Attempting dry run of processing paper acceptance...

editorialbot commented 4 weeks ago

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

OK DOIs

- 10.1109/CVPRW.2018.00293 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/3620665.3640366 is OK
- 10.1145/2833157.2833162 is OK
- 10.1137/1037083 is OK
- 10.1057/9780230280830_23 is OK

MISSING DOIs

- No DOI given, and none found for title: PyDTMC
- No DOI given, and none found for title: simple-markov
- No DOI given, and none found for title: mchmm

INVALID DOIs

- None

editorialbot commented 4 weeks ago

The paper's PDF and metadata files generation produced some warnings that could prevent the final paper from being published. Please fix them before the end of the review process.

citation paszke2019pytorch not found

editorialbot commented 4 weeks ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

IDREFS attribute rid references an unknown ID "ref-paszke2019pytorch"

mooniean commented 4 weeks ago

@editorialbot generate pdf

editorialbot commented 4 weeks ago

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

mooniean commented 4 weeks ago

@aadya940 in one of the paper iterations after my comments on the references, the pytorch reference was altered and now is not compiling

aadya940 commented 4 weeks ago

@editorialbot generate pdf

editorialbot commented 4 weeks ago

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

aadya940 commented 4 weeks ago

@editorialbot recommend-accept

editorialbot commented 4 weeks ago

I'm sorry @aadya940, I'm afraid I can't do that. That's something only editors are allowed to do.

aadya940 commented 4 weeks ago

@mooniean This should work now, Sorry for missing this bug out :))

mooniean commented 4 weeks ago

@editorialbot recommend-accept

editorialbot commented 4 weeks ago

Attempting dry run of processing paper acceptance...

editorialbot commented 4 weeks ago

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

OK DOIs

- 10.1109/CVPRW.2018.00293 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1145/3620665.3640366 is OK
- 10.1145/2833157.2833162 is OK
- 10.1137/1037083 is OK
- 10.1057/9780230280830_23 is OK

MISSING DOIs

- No DOI given, and none found for title: PyDTMC
- No DOI given, and none found for title: simple-markov
- No DOI given, and none found for title: mchmm

INVALID DOIs

- None

editorialbot commented 4 weeks 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/5771, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon commented 4 weeks ago

@editorialbot generate pdf

🔍 checking out the following:

[x] reviewer checklists are completed or addressed
[x] version set
[x] archive set
[ ] archive names (including order) and title in archive matches those specified in the paper
[x] archive uses the same license as the repo and is OSI approved as open source
[x] archive DOI and version match or redirect to those set by editor in review thread
[ ] paper is error free - grammar and typos
[x] paper is error free - test links in the paper and bib
[x] paper is error free - refs preserve capitalization where necessary
[x] paper is error free - no invalid refs without justification

editorialbot commented 4 weeks ago

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

crvernon commented 4 weeks ago

:wave: @aadya940 - I need to you to fix the following before I move to accept this for publication:

[x] The title of the Zenodo archive should match the title of the paper exactly. No need to conduct another release, you can just edit the metadata in the Zenodo archive.
[x] The license you used in your repository should match the license selected in the Zenodo archive. Please edit the metadata in the Zenodo archive to use the same license as your code.

In the paper:

[x] The title of the paper has mixed case capitalization. Please change to "ChainoPy: A Python Library for Discrete Time Markov Chain Based Stochastic Analysis"
[x] LINE 37: Missing comma after "typing" in "...dynamic typing etc."
[x] LINE 39: "...chain, calculating properties." should be "...chain, and calculating properties."
[x] LINE 50: "numpy" should be written as "NumPy" in this context
[x] LINE 60: "KL" is used here as an acronym before it has been defined as "Kullback–Leibler"
[x] LINES 62 through 112 should be removed. They are not needed in the publication.
[x] LINE 114: the "D" in "Documentation" should not be capitalized here. Not should the "T" or "B" in testing and benchmarking
[x] LINE 123: the "H" in histogram should not be capitalized in this context
[x] Ensure that your references have the proper capitalization where needed. For example in line 131, the "p" in "python" should be capitalized. You can maintain capitalization in your references in the bib file using curly brackets around the characters you wish to maintain for formatting of.
[x] Citations to those GitHub repos should have a date of retrieval or software release data for the version you are citing. A bib format like the following may work:

@misc{yourid,
  title = {title of the package},
  author = {{Package's Development Team}},
  year = {four digit year},
  url = {url to the github repository or docs site},
}

Thanks!

aadya940 commented 4 weeks ago

Hey @crvernon Thanks for the detailed review.

aadya940 commented 4 weeks ago

@editorialbot generate-pdf

editorialbot commented 4 weeks ago

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

@editorialbot commands

aadya940 commented 4 weeks ago

@editorialbot generate pdf

editorialbot commented 4 weeks ago

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

aadya940 commented 4 weeks ago

@crvernon I've fixed the issues now, Does it look fine to you now?

crvernon commented 3 weeks ago

@aadya940 the following is still incorrect:

[x] The title of the Zenodo archive should match the title of the paper exactly. No need to conduct another release, you can just edit the metadata in the Zenodo archive.

And this is a new typo introduced in your last fixes:

[ ] LINE 64 you state "yesting" instead of "testing"

aadya940 commented 3 weeks ago

@crvernon Done, Thank You :+1:

crvernon commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

crvernon commented 3 weeks ago

@editorialbot accept

editorialbot commented 3 weeks ago

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

editorialbot commented 3 weeks 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: Chinubhai given-names: Aadya A. doi: 10.5281/zenodo.13305155 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Chinubhai given-names: Aadya A. date-published: 2024-08-16 doi: 10.21105/joss.06880 issn: 2475-9066 issue: 100 journal: Journal of Open Source Software publisher: name: Open Journals start: 6880 title: "ChainoPy: A Python Library for Discrete Time Markov Chain Based Stochastic Analysis" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06880" volume: 9 title: "ChainoPy: A Python Library for Discrete Time Markov Chain Based Stochastic Analysis" ```

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 weeks ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 3 weeks 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/5777
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06880
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon commented 3 weeks ago

🥳 Congratulations on your new publication @aadya940! Many thanks to @mooniean for editing and @braniii and @MichalisPanayides for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot commented 3 weeks ago

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06880/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06880/status.svg
   :target: https://doi.org/10.21105/joss.06880

This is how it will look in your documentation:

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aadya940 commented 3 weeks ago

@crvernon @mooniean @braniii @MichalisPanayides Thank you so much, really appreciate the effort you've put in :)

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