[REVIEW]: TransitionsInTimeseries.jl: A performant, extensible and reliable software for reproducible detection and prediction of transitions in timeseries

[editorialbot]

Submitting author: @JanJereczek (Jan Swierczek-Jereczek)
Repository: https://github.com/JuliaDynamics/TransitionsInTimeseries.jl
Branch with paper.md (empty if default branch):
Version: 0.1.3
Editor: @lrnv
Reviewers: @felixcremer, @sgeorge91
Archive: 10.5281/zenodo.12731309

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ab051d21d28bdf948541fa15dd077dc7"><img src="https://joss.theoj.org/papers/ab051d21d28bdf948541fa15dd077dc7/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ab051d21d28bdf948541fa15dd077dc7/status.svg)](https://joss.theoj.org/papers/ab051d21d28bdf948541fa15dd077dc7)

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

@felixcremer & @sgeorge91, 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 @lrnv 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 @sgeorge91

📝 Checklist for @felixcremer

[editorialbot]

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]

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

OK DOIs

- 10.1016/j.quascirev.2009.06.013 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1038/nature08227 is OK
- 10.21105/joss.05038 is OK
- 10.1109/ACCESS.2020.3036370 is OK
- 10.21105/joss.04414 is OK
- 10.1016/j.joa.2015.11.003 is OK
- 10.1038/s41467-023-39810-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1804.8 files/s, 126082.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           38            525            909           1642
Markdown                        11            214              0            633
TeX                              2             13              0            228
YAML                             7              9              8            157
TOML                             5              4              0             69
Python                           1             11              4             45
-------------------------------------------------------------------------------
SUM:                            64            776            921           2774
-------------------------------------------------------------------------------

Commit count by author:

    36	Datseris
    18	Jan Swierczek-Jereczek
    17	George Datseris
     5	github-actions[bot]
     2	JanJereczek

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1735

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

[lrnv]

👋🏼 @JanJereczek @felixcremer @sgeorge91 this is the review thread for the paper. All of our communications will happen here from now on.

@felixcremer @sgeorge91, as reviewers, the first step for both of you is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6464 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 6 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@lrnv) if you have any questions/concerns.

[sgeorge91]

Review checklist for @sgeorge91

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/JuliaDynamics/TransitionsInTimeseries.jl?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@JanJereczek) 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?

[felixcremer]

Review checklist for @felixcremer

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/JuliaDynamics/TransitionsInTimeseries.jl?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@JanJereczek) 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?

[Datseris]

Hello @lrnv , thank you for coordinating this review.

We noticed that the title of our paper has a typo. The software is called TransitionsInTimeseries.jl but the title of the paper states TransitionInTimeseries.jl (notice the singular Transition). We hope it is possible to alter the paper title after the review process has started?

[lrnv]

I think you can simply change the title in the paper.md file and that will be enough, since (at the publishing time), this is the fil that will be used everywhere. Let me come back to you with confirmation.

The name of this PR will not match it anymore, and I think I could change it, but it wont matter for the rest of the process.

Also: The title of the pper says TimeSeries and the repo says Timeseries, maybe a second typo ?

[Datseris]

Thank you, yes we will address both typos.

[lrnv]

So confirmed, it is enough. Regenerate the paper after that and I'll edit this issue title accordingly.

[lrnv]

@editorialbot generate pdf

[editorialbot]

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

[lrnv]

@felixcremer @sgeorge91, it has been a while since this review started, did you by chance get an opportunity to review this submission ? If you want, I could setup automatic reminders for you. Note that we usually aim at a 6-8weeks timeframe for the reviews

[felixcremer]

Thanks for the reminder, I haven't gotten to it yet, but I hope to get to it at the beginning of next week.

[sgeorge91]

Hi @lrnv. Sorry! I started and then got caught up with some other things. Automatic reminders would be helpful! I will aim to finish within the time-frame you've mentioned

[lrnv]

@editorialbot remind @sgeorge91 in one week

[editorialbot]

Reminder set for @sgeorge91 in one week

[JanJereczek]

Indeed! It should be corrected now :) Is there any way I can check if the xml metadata file is generated correctly or do you have to run it yourself @lrnv?

[lrnv]

I do not know how you can check it yourself, indeed this is not ideal interface. Let me check it for you

[lrnv]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1016/j.quascirev.2009.06.013 is OK
- 10.1371/journal.pone.0041010 is OK
- 10.1073/pnas.2106140118 is OK
- 10.1038/nature08227 is OK
- 10.21105/joss.05038 is OK
- 10.1109/ACCESS.2020.3036370 is OK
- 10.21105/joss.04414 is OK
- 10.1016/j.joa.2015.11.003 is OK
- 10.1038/s41467-023-39810-w is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-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#5611, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[crvernon]

🔍 checking out the following:

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

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

👋 @JanJereczek - great job on this! We have a few more things to address before moving to accept:

• Please ensure the authors and the author order match between the paper and the Zenodo archive. No need to do another release, just edit the Zenodo archive metadata to fix this.

In the paper:

• LINE 22-23: "...existing softwares Bury (2023) are well suited to apply..." should be written "...existing software detailed in Bury (2023) are well suited to apply..."
• LINE 49: The figure reference is not linking properly due to incorrect formatting. In your paper.md file, you state the following: ...shown in [Fig. 1](@figure1) and display,... which should be ...shown in \autoref{fig:figure1} and display,... Then the figure caption can be referenced as: ![Output of plotting function in usage example.\label{fig:figure1}](figures/figure1.png). This should allow the figure reference in the text to correctly link and format to the figure. Please change the formatting for figure 2 as well.
• LINE 127: "...developed in (Bury et al., 2021), as..." should read "...developed in Bury et al. (2021), as..." You can just remove the brackets around the citation in the text to achieve this.
• LINE 138: missing space between "of" and "bifurcations"

No need to create another release. Just let me know once the changes have been made. Thanks!

[JanJereczek]

@editorialbot generate pdf

[editorialbot]

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

[JanJereczek]

@editorialbot generate pdf

[editorialbot]

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

[JanJereczek]

Hi @crvernon! Thanks for the scrutiny :) I went through your whole checklist and everything should be fine now. Please note that the references at l. 22-23 were badly rendered because of a formatting issue. I did not fix this as you suggested but as it was originally planned to be. Please check if it is ok!

[crvernon]

Thanks @JanJereczek, the paper looks good. I still need you to address the following:

Please ensure the authors and the author order match between the paper and the Zenodo archive. No need to do another release, just edit the Zenodo archive metadata to fix this.

[JanJereczek]

The order matches between both and @felixcremer was added to the author list on zenodo since he made some PRs over the review process. However he is not a co-author of the paper. See the discussion above: #6464 (comment). Sounds good to you?

[crvernon]

Got it. Yes, thank you.

[crvernon]

@editorialbot accept

[editorialbot]

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

[lrnv]

@JanJereczek @Datseris congratulations and happy Juliacon :)

[editorialbot]

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: Swierczek-Jereczek
  given-names: Jan
  orcid: "https://orcid.org/0000-0003-2213-0423"
- family-names: Datseris
  given-names: George
  orcid: "https://orcid.org/0000-0002-6427-2385"
doi: 10.5281/zenodo.12731309
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Swierczek-Jereczek
    given-names: Jan
    orcid: "https://orcid.org/0000-0003-2213-0423"
  - family-names: Datseris
    given-names: George
    orcid: "https://orcid.org/0000-0002-6427-2385"
  date-published: 2024-07-13
  doi: 10.21105/joss.06464
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6464
  title: "TransitionsInTimeseries.jl: A performant, extensible and
    reliable software for reproducible detection and prediction of
    transitions in timeseries"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06464"
  volume: 9
title: "TransitionsInTimeseries.jl: A performant, extensible and
  reliable software for reproducible detection and prediction of
  transitions in timeseries"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06464 joss-papers#5615
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06464
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[crvernon]

🥳 Congratulations on your new publication @JanJereczek! Many thanks to @lrnv for editing and @felixcremer and @sgeorge91 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]

🎉🎉🎉 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.06464/status.svg)](https://doi.org/10.21105/joss.06464)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06464/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06464/status.svg
   :target: https://doi.org/10.21105/joss.06464

This is how it will look in your documentation:

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